{"instruction": "The protein exhibits the following characteristics:\nThe protein should have a WW domain that folds into a stable, triple-stranded beta-sheet and functions as a protein-protein interaction module by recognizing specific proline-rich motifs or phosphoserine- and phosphothreonine-containing sequences. This domain is frequently found in proteins involved in signal transduction, cytoskeletal organization, and transcriptional regulation. It is found in Aphanomyces astaci (Crayfish plague agent).\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 3066, 2162, 43, 6010, 3418, 1988, 16231, 2460, 43, 4700, 16, 10073, 17, 10338, 4666, 17, 11130, 1930, 4088, 1966, 43, 2213, 17, 2213, 2835, 9059, 2007, 15667, 2487, 12958, 17, 5536, 8277, 2014, 8078, 26337, 17, 1930, 8078, 5856, 1021, 12530, 17, 3165, 3709, 18, 2052, 3418, 1977, 5467, 2435, 1922, 2697, 3286, 1922, 2733, 8201, 16, 14787, 5901, 16, 1930, 5224, 3640, 18, 2176, 1977, 2435, 1922, 12274, 9286, 14930, 3707, 5988, 28278, 12, 24422, 1012, 14422, 5606, 11056, 1021, 5899, 13, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MVAEAIAGRPVEFVESSGKPVRGCVLSYCPEDHTNAKVLRIVLFRQLKAAQVVYEIGDMHEWVVEDLVGDLDLKCSLVRFDNGAKEWLDLSQRRVYLLLSSYDPLPYSPRKSPRCTWYKEGNHIELYDATGEFQEGAVICSEYDDPHKLVLHGFSVLKDIPVDHIVEVYSTTKWVDLSSQTFKVVCFPDRIRPLSARERERQLSADATTPPLSEGTQIEVYHREKSLYVKNTVVRSVSNRPYVYTRCKVLWKDAVDLDLTSLVAHVIEVFVKEEKREWVALRARKLKIRLHEAAIVQPLAFTPFVRPLHDNQSQQIQNPPSPHPIRRSFSSSNMMIVRSPVSQLRRMASARTVESLNEGDMIDTPSSSSDWSMQIDPASNQTYYVHGPSVDNHDGRRIRAAPPIGPIQAVRHIRTNTLYNCIVDIGNTISLKIDPKATYRLELELSDGPTATGVLRQHNALASTQAGPPNIPLLAGMLSVANEIRGKFEIAVATQGGFRRGSILKKAESGRLIPILFEHAASMENGVAHKFVRNNPATLNDGATFRFELHAVTSGSRSVVDLAAVDAGRICGCNNKSRMLHVRFQDGRKTASSDDARPKPLQRSHSYVHKSYGDNPPRQQLLRTDSMDSIDAYSIDSGTSQWHPPPNVDIHALQWIATDDWMDKQKHW", "metadata": {"id": "A0A9X8DVJ7", "cluster": 1310154, "interpro_all": ["IPR001202", "IPR036020"], "interpro_used": ["IPR001202"], "interpro_unused": ["IPR036020"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein can be placed in the Integrin alpha, N-terminal superfamily, which constitutes the N-terminal $\\beta$-propeller domain of the alpha subunit in integrin heterodimers. These receptors function as critical metazoan mediators of cell adhesion to extracellular matrix proteins, linking the extracellular environment to the cytoskeleton and activating intracellular signaling pathways. It is produced by Leptospiraceae bacterium.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8920, 4595, 16, 56, 17, 4262, 13975, 16, 2154, 14879, 1920, 56, 17, 4262, 8, 38, 4666, 8, 17, 5062, 13728, 3418, 1927, 1920, 4595, 5903, 1922, 8920, 21523, 18, 2144, 4086, 2347, 1966, 4140, 24207, 1928, 9744, 1927, 2024, 6141, 1942, 5329, 4526, 2697, 16, 9486, 1920, 5329, 3515, 1942, 1920, 11612, 1930, 8019, 4776, 3197, 3873, 18, 2176, 1977, 4152, 2007, 24060, 11979, 1972, 3336, 14061, 18, 3], "output": "MRTTCKNGEFACLCTYNPACNGDTINNHAFFPMDNNGDGFNYQEIGEGNYDNKILVDQKYTIQYNSFLSMGFHSLYVAYSSATSQTGYGFHSPTKTSILTTIGKQWLVDINHDGRMDFVVLSVRLSNGGGFDSEKLLNLDHNDGSDGKLDYVNIKKGTNTISVYKIDLSVIRMAQNPRKKERIICGSPDFTTAKETCLALIQYADRCNKRELFRLVGNSNSEEGIQDVDGKDDFVYTSANEGEESIPKLRIKKSLESQAQKIENPDDKTEDREKKSWAIAKVDGEWEYADEFTQITDMENLTLTNTQHST", "metadata": {"id": "A0A960W1B9", "cluster": 3946834, "interpro_all": ["IPR028994"], "interpro_used": ["IPR028994"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein belongs to the Cullin repeat-like-containing domain superfamily, which constitutes the N-terminal region of cullin proteins and folds into a multi-helical right-handed superhelix. This domain functions as a recruitment platform for specific adaptor proteins, enabling the assembly of Cullin-RING ubiquitin ligase (CRL) complexes that target substrates for ubiquitin-mediated degradation. Also, the protein features a Exocyst complex subunit Exo70, C-terminal domain that mediates the tethering of post-Golgi secretory vesicles to the plasma membrane and promotes SNARE complex assembly for membrane fusion. Composed of \u03b1-helical bundles, it directly binds the small GTPase Rho3 and phosphatidylinositol 4,5-bisphosphate, interactions that are essential for targeting the exocyst complex to specific membrane sites and regulating cell polarity. It has been characterized in Nepenthes gracilis (Slender pitcher plant) and features UniProt keywords Transport. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 22859, 1921, 6865, 17, 3189, 17, 3165, 3418, 13975, 16, 2154, 14879, 1920, 56, 17, 4262, 3031, 1927, 22859, 1921, 2697, 1930, 16231, 2460, 43, 2779, 17, 11514, 3659, 17, 17105, 3356, 23285, 2416, 18, 2052, 3418, 4088, 1966, 43, 6067, 6631, 1958, 2487, 15077, 2697, 16, 12180, 1920, 5957, 1927, 22859, 1921, 17, 6335, 6526, 11905, 12, 21460, 13, 5048, 1988, 2758, 6249, 1958, 6526, 17, 3434, 4877, 18, 2222, 16, 1920, 2213, 4075, 43, 18930, 23159, 1031, 2796, 5903, 18930, 4618, 16, 45, 17, 4262, 3418, 1988, 10412, 1920, 23991, 1927, 2753, 17, 10277, 11518, 8319, 1942, 1920, 3582, 3260, 1930, 7383, 19146, 2796, 5957, 1958, 3260, 5289, 18, 7179, 1927, 160, 17, 11514, 16073, 16, 2176, 4103, 6876, 1920, 2858, 14809, 10585, 1010, 1930, 16927, 24, 16, 25, 17, 29443, 16, 3719, 1988, 2032, 4415, 1958, 5133, 1920, 18930, 23159, 1031, 2796, 1942, 2487, 3260, 3402, 1930, 6773, 2024, 12432, 18, 2176, 2258, 2252, 4378, 1922, 26046, 26624, 1918, 24689, 10401, 1937, 12, 4565, 10249, 1915, 14665, 1915, 4496, 13, 1930, 4075, 20709, 11569, 4860, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MSELRRVEVNGKVHKPTLKERFKNFNQLFDDIHKTQSTGVVNDELTPRSSGSISPVMIPAIDHSRPGLATISPQEDKRRST", "metadata": {"id": "A0AAD3XWS1", "cluster": 4152546, "interpro_all": ["IPR016159", "IPR046364"], "interpro_used": ["IPR016159", "IPR046364"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe protein should have a Bacterial Ig-like domain, group 2 (Big2) domain that functions as a structural module in bacterial surface proteins, phage tails, and eukaryotic nuclear pores. It mediates intimate host-cell adhesion in intimins, supports the assembly of hexameric rings in phage tail tubes, and contributes to the structural integrity of nuclear pore complexes. It originates from Desulfuromonas sp and contains UniProt keyword associations Signal.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 3066, 2162, 43, 4543, 7021, 17, 3189, 3418, 16, 2210, 22, 12, 9769, 1028, 13, 3418, 1988, 4088, 1966, 43, 4346, 9059, 1922, 4543, 3154, 2697, 16, 10503, 18103, 16, 1930, 10825, 4254, 14711, 18, 2176, 10412, 20252, 4423, 17, 2024, 6141, 1922, 11757, 2925, 16, 7825, 1920, 5957, 1927, 25602, 1935, 12750, 1922, 10503, 5281, 9403, 16, 1930, 7624, 1942, 1920, 4346, 7996, 1927, 4254, 8554, 5048, 18, 2176, 22970, 2037, 30311, 18916, 3947, 1934, 2056, 1930, 5461, 20709, 11121, 2538, 5253, 2733, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MFRAILLLLTLLLILAGCGGDSPSHPNDYLAVTSLSTAQLENGQQRDVTDHVDWVSSNPDVAYFGTTDEARNLLNALSSGAVENRAVTAVEIFPKKAVLPSQPSGITLAYRAIASLSDGNTLDVTGNSSIDKGLATVRDVGDATIAATFGIVPVESSSLTVADVDSGGEDQSDDSVVEIFSKARFKTEAWISDAVSQNPEVAVIAPAPNEDGSMEVSALQVGSTTLFADFQVSLRIEPSSVSLAQFTRRQVRLIVTYNNGATRDLASFSVETDRGITLVHGRASGSTVLSVRLEDVTATNSSLIIGTNSRFTATVSIQYAGLNSELSVVVESVDWSVSVTDTENDVATIANGELRGLRIVRVTGTESTEESEDSDFWDVTAQTVWQSTSFRVGLALTVEDNGEVVPLPADSWTIDDPDIA", "metadata": {"id": "A0A2N6ELP9", "cluster": 4903746, "interpro_all": ["IPR003343"], "interpro_used": ["IPR003343"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Function:\nThe protein possesses a Protein kinase ATP binding site that binds ATP to facilitate the transfer of the gamma phosphate to protein substrates during phosphorylation. Located in the N-terminal catalytic domain, this conserved site utilizes a specific lysine residue within a glycine-rich stretch to anchor the nucleotide. This interaction is essential for the activity of serine/threonine, tyrosine, and dual-specificity kinases in regulating processes such as cell division and proliferation. In addition, the protein features a Protein kinase domain that functions as the conserved catalytic core responsible for transferring the gamma phosphate from ATP to serine, threonine, or tyrosine residues on substrate proteins. This phosphorylation event induces conformational changes that regulate diverse cellular processes, such as proliferation, differentiation, and apoptosis. Moreover, the protein has a Tyrosine-protein kinase catalytic domain that catalyzes the transfer of the gamma-phosphate from ATP to tyrosine residues on protein substrates, triggering conformational changes that modulate protein function. This activity drives signal transduction pathways essential for cell proliferation, differentiation, apoptosis, and metabolism in both transmembrane receptor and cytoplasmic non-receptor contexts. It is derived from Rubroshorea leprosula and contains UniProt keyword associations ATP-binding, Transmembrane helix, and Glycoprotein.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 14465, 43, 2213, 4016, 4498, 2743, 3200, 1988, 6876, 4498, 1942, 6628, 1920, 3856, 1927, 1920, 7034, 5413, 1942, 2213, 6249, 2409, 4050, 18, 4810, 1922, 1920, 56, 17, 4262, 6804, 3418, 16, 2052, 5305, 3200, 18127, 43, 2487, 9082, 6181, 2651, 43, 10646, 17, 5536, 9064, 1942, 13333, 1920, 5489, 18, 2052, 2835, 1977, 4415, 1958, 1920, 2455, 1927, 8468, 19, 13143, 16, 6941, 16, 1930, 7064, 17, 4896, 7784, 1922, 6773, 4028, 2427, 1966, 2024, 8451, 1930, 4031, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 2213, 4016, 3418, 1988, 4088, 1966, 1920, 5305, 6804, 4728, 5061, 1958, 21902, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 16, 13143, 16, 2014, 6941, 4248, 1990, 4510, 2697, 18, 2052, 4050, 4817, 6387, 8523, 2840, 1988, 5741, 6445, 3689, 4028, 16, 2427, 1966, 4031, 16, 4155, 16, 1930, 4091, 18, 3950, 16, 1920, 2213, 2258, 43, 6941, 17, 2213, 4016, 6804, 3418, 1988, 17097, 1920, 3856, 1927, 1920, 7034, 17, 5413, 2037, 4498, 1942, 6941, 4248, 1990, 2213, 6249, 16, 14074, 8523, 2840, 1988, 8480, 2213, 2347, 18, 2052, 2455, 15435, 2733, 8201, 3873, 4415, 1958, 2024, 4031, 16, 4155, 16, 4091, 16, 1930, 4714, 1922, 2321, 9117, 3148, 1930, 6823, 2447, 17, 3148, 11144, 18, 2176, 1977, 3595, 2037, 10010, 2263, 10647, 1936, 1019, 24836, 20490, 5148, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 9117, 7864, 16, 1930, 11424, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MILRGLSVSGSLSGDPFWFFCFLFVCVVLCSCTGCFYGCPDLAIAGLDPCRGVLEISCHPLPSRLKGVPLLDLLLLHCVLSLYEILSLWIRPCCRCRMAVLNALLPLRKGNNRSYSTRCIILRQRKAKETIESEDEMIKWQCRQYDFATVQAATNNFSEEAVKRLSGNSRQGDTEFMNEVLLLVKLYHRNLVKFLGFCLEGMERILIYRQYQAQIRGLNAYDRHKKFLNDYVAFYGKDKSQHVKLPVKTDQDTLREGYRFIRSEQYKSGKIGLRWRTEKEVISGKGKNSISSLTDLIKIFSQKFKPGDPRLFPVSGLVPATGCASVFTSLHPLHWVYSATIIISVSGSALIVGVLLLVHNKLGQGGFGTVYKGRLPNIEQDVEFLPNSSLDQFIFGEDDQNPAWEQRLVKRYYDKLFKEYCIADMS", "metadata": {"id": "A0AAV5HMX3", "cluster": 5628315, "interpro_all": ["IPR019129", "IPR011009", "IPR000719", "IPR017441", "IPR001245", "IPR020635"], "interpro_used": ["IPR017441", "IPR000719", "IPR020635"], "interpro_unused": ["IPR019129", "IPR001245", "IPR011009"]}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is categorized in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, the protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It occurs in Leptotrichia sp. oral taxon 847 and has UniProt annotations Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 5110, 1922, 16976, 18935, 19519, 1019, 2056, 18, 4726, 19278, 5686, 1027, 1930, 2258, 20709, 15010, 5239, 1930, 9067, 4587, 18, 3], "output": "MEYHKPVLYDEVIENIITDKDAIYVSKNSKVIAIDQDIEAIEFAKKRLENYNNFTVFQDNDIGVSSNQLDNAKRGFSYRFCAKLDMRMDKSLKLSAYDKIAKNIVEYRKDKKIETTTELADIVIRSIIRIFVNKELEVLTQTLDKAVKLLNDKGKLLVITFHSLEDRIVKEKFREYTKKPIVANDKELTENKRAHSAKLRIFERRENRNEDCTLGGGGHTQGILKNSFKNIDTVVYLAGFEKVDRILMVVNTFSEKEIADIIYKYGEEPKSRGKSMKRHPAKRTFQAENPCTCPKDIPICVCGKKSLGKVI", "metadata": {"id": "A0A0X8JVJ2", "cluster": 7061080, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein I want to design has this role: The protein is grouped in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, the protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Moreover, the protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is derived from Actinobacteria bacterium RBG_13_63_9 and is linked to UniProt keywords rRNA processing. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 1977, 10809, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 3595, 2037, 29130, 14061, 6160, 1029, 41, 2590, 41, 4968, 41, 29, 1930, 1977, 4624, 1942, 20709, 11569, 9067, 4587, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MPNAAASFATEMAMAHVPVLAQELLDLLDVRPDSRVVDCTFGGGGHAAVVAAELGSEGGLVACDQDPIASGYYRDLKRRLPKGSRFCPGNFADVLGELLEEGFKATHIYMDLGVSSMQIDTPERGFSYSYDAPLDMRMDPTLPTTAADIVNTWSERDLARLFGRYGEERYSGRIAHALVVRRATTSYKRTAELVDTVKQAIPTPARFGAGNPARRVFQALRIEVNDELDSLQRALPPAFDLLEPGAVLAVISFHSLEDRIVKEFFAGKARGCTCPPDFPVCACGGRETGE", "metadata": {"id": "A0A1F2X0R2", "cluster": 7847740, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein should include a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. Moreover, the protein incorporates a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. In addition, the protein is assigned to the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. It has been detected in Micromonospora sp. CP22 and is classified with UniProt keywords Hydrolase and Metal-binding.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 3066, 3951, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 3950, 16, 1920, 2213, 19683, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 2176, 2258, 2252, 3330, 1922, 7709, 23557, 3508, 8846, 2056, 18, 4244, 4460, 1930, 1977, 5947, 1956, 20709, 11569, 20748, 1930, 6048, 17, 2743, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MSAPVSTVNDAVMAALATVNDPEIRRPIELLLTVAGCPLKDKLRSDITAAVGAVPGVSGVEIGGATAEPVIPFAQPGSRTRVYAVASGKGGVVVDADIYGHSVPRMLGADGRPTRVEDMIMPVWRGPMLHRALQQFLADVYWGDLDVLLLDLPPGTGDAEVAERAGAIALQTHQRVVGVIENMSWLELPDGSTQAIGAQVPMLGQVPLDTRVRDRLALRRESLLGKPLGLKPAGRTELGMVRSAEVGEDGVVRVEFGVMSTEQRQQLQAKLRGGKSSVTVNLAAALAARGLSVGPQSHGVKVISIGMFTDGNAAVVAISLAQLLPNAEILVVTTPQAAARMEIFGAGGGQTVADSLEAGDEGNPIVLAAPDSPAAKALGQVA", "metadata": {"id": "A0A7K1GWR4", "cluster": 8018576, "interpro_all": ["IPR034904", "IPR002744", "IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR002744", "IPR000808", "IPR033756"], "interpro_unused": ["IPR034904", "IPR044304", "IPR019591", "IPR027417"]}, "task_type": "infilling"} {"instruction": "Target Function: The protein features a fungal rhodopsin domain that functions as a membrane-embedded photoreceptor involved in light-driven proton pumping or sensory signaling. It features seven transmembrane helices that form an internal pocket to covalently bind an all-trans-retinal chromophore to a lysine residue via a protonated Schiff base. This domain is widely distributed across fungi, particularly within plant-associated species. Also, the protein is included in the The Satratoxin biosynthesis SC1 cluster protein 4-like family, which mediates the biosynthesis of diverse secondary metabolites, including satratoxins, wortmanamides, and polyenoic acids, often within gene clusters containing polyketide synthases and acetyltransferases. These proteins, some of which contain rhodopsin domains, contribute to the production of compounds with biological roles ranging from antihypercholesterolemic activity to microbiota manipulation. It is found in Neonectria ditissima and features UniProt keywords Transmembrane helix.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 4075, 43, 8697, 20586, 3418, 1988, 4088, 1966, 43, 3260, 17, 8222, 16383, 3286, 1922, 3696, 17, 6446, 8433, 24430, 2014, 6893, 3197, 18, 2176, 4075, 5260, 9117, 12789, 1988, 2386, 1925, 4495, 10154, 1942, 16590, 4566, 1925, 2136, 17, 2127, 17, 6943, 25801, 1942, 43, 9082, 6181, 3454, 43, 23204, 25214, 5170, 18, 2052, 3418, 1977, 5673, 6533, 3436, 10520, 16, 4443, 2651, 4496, 17, 2458, 3038, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 1920, 5784, 5524, 4575, 10960, 8132, 2160, 1009, 4377, 2213, 24, 17, 3189, 3416, 16, 2154, 10412, 1920, 8132, 1927, 6445, 4067, 6926, 16, 2710, 5784, 5524, 4575, 10960, 1036, 16, 24911, 3862, 20381, 16, 1930, 4286, 19789, 4576, 16, 3868, 2651, 2359, 5859, 3165, 4286, 18540, 2261, 8921, 1036, 1930, 22226, 1036, 18, 2144, 2697, 16, 2673, 1927, 2154, 5531, 20586, 4682, 16, 4672, 1942, 1920, 3372, 1927, 4300, 1956, 3933, 5456, 6485, 2037, 12946, 2085, 3234, 27971, 2156, 6506, 1952, 4913, 2455, 1942, 9825, 10597, 18, 2176, 1977, 2435, 1922, 6621, 2089, 3027, 1019, 2137, 3600, 12924, 3368, 1930, 4075, 20709, 11569, 9117, 7864, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MSTTDVDAPIDPAWAAESNVPRIISVTTVFHVLALTSVGLRLYVRLVGWVIFVIQAFHGLGRHRDTIDPLDYIELQKVGFWQSVISATCAMALLKISIALNLLRLSQSKWYFWSLWISDLLIVRRFRLGIQLHGGHDLLPPLPAHGRALGHSHRREMLLAGAVRAVLAHQLFATFPVPIIWTLQMKLRTRLYLIGILSLGYLCRRRAVIMGILKAVFQIAYSKDVDKTFNQWMIAACAPSLKPLVSKALKLSSYYNSTPYGNRSYGANSRRLTGGRTPAVTTTFYKNRSEDGGTRSGSEEMILGDNPFKAGIVRTTEVTVQRGMVKAAGRDDWTMVASAICALTSIGMRLLGESRHTVSLSPVRDYGGYMFVSSPDKERLLNFLAFNIFTDVIQFWGFLQLNLGNVSNFSRNNDFELGDRRFEGEPSGADTG", "metadata": {"id": "A0A0P7B6G0", "cluster": 9164499, "interpro_all": ["IPR049326", "IPR052337"], "interpro_used": ["IPR049326", "IPR052337"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein is included in the Glycoside hydrolase/deacetylase, beta/alpha-barrel superfamily, which encompasses a structural domain found in enzymes such as alpha-mannosidases, 4-alpha-glucanotransferases, and polysaccharide deacetylases. This domain typically features a seven-stranded beta/alpha barrel fold that supports catalytic activities involved in the hydrolysis or deacetylation of carbohydrate substrates. It occurs in Bdellovibrio sp and corresponds to UniProt keyword Signal. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 1925, 3835, 2687, 3244, 1988, 2469, 16318, 2460, 43, 2213, 22665, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 7533, 2261, 20748, 19, 19489, 16, 4666, 19, 4595, 17, 19560, 13975, 16, 2154, 21569, 43, 4346, 3418, 2435, 1922, 5038, 2427, 1966, 4595, 17, 7338, 12224, 1036, 16, 24, 17, 4595, 17, 18798, 14165, 1036, 16, 1930, 17167, 19489, 1036, 18, 2052, 3418, 5745, 4075, 43, 5260, 17, 10338, 4666, 19, 4595, 19560, 3728, 1988, 7825, 6804, 4209, 3286, 1922, 1920, 9128, 2014, 23764, 1927, 10590, 6249, 18, 2176, 5110, 1922, 5238, 20783, 2165, 2377, 3940, 2056, 1930, 8852, 1942, 20709, 11121, 2538, 2733, 18, 7031, 1920, 3244, 18, 3], "output": "RQALLIVITMALGFSAQAESILPQSCSLFKGRNTAMQAPLAMSDYHVALRSCQVQGHSFVALREFKTSNKTYLLITDPTTLKTDLVDKSCLSCEDITLKQLPESHFRGALKQQSQGSFPLSNDGIRHAQTGSKGYFLTVDLCPSHKEFEKNLFGNQKVSTTSNFPVAVAISGGWIAHHQDEFNQLKNQVLDGQLNVTWVNHSYTHPYQKSLPLDRNFLLTSGTIFADEVLKQEQYMISNGLVPSVYFRFPGLISDRKLILELTSYGLLSLGSDAWLALGQKPTPGSVILVHGNGNEPYGIRLFTAFLQNITDMSVFKPMNDIF", "metadata": {"id": "A0A940R7D5", "cluster": 11541442, "interpro_all": ["IPR011330"], "interpro_used": ["IPR011330"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that will have the following function: The protein possesses a Zinc finger, RING-type domain that mediates protein-protein interactions and typically functions as an E3 ubiquitin-protein ligase. This motif coordinates two zinc ions in a \"cross-brace\" structure to bind E2 ubiquitin-conjugating enzymes, thereby facilitating substrate ubiquitylation. Also, the protein is classified under the Zinc finger, RING/FYVE/PHD-type superfamily, which encompasses RING, PHD, FYVE, and U-box domains that share a common $\\alpha/\\beta$ structural fold, typically stabilized by zinc ions. These versatile motifs act as stable scaffolds to facilitate specific interactions with DNA, RNA, proteins, or lipids, thereby participating in diverse cellular processes ranging from gene transcription and chromatin remodelling to mRNA trafficking. It is present in Entamoeba histolytica KU27 and is annotated with UniProt keywords Metal-binding and Zinc-finger.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 7997, 8497, 16, 6335, 17, 2601, 3418, 1988, 10412, 2213, 17, 2213, 3719, 1930, 5745, 4088, 1966, 1925, 10968, 6526, 17, 2213, 11905, 18, 2052, 5219, 10675, 2288, 7997, 6982, 1922, 43, 6, 3567, 17, 18303, 1972, 6, 3170, 1942, 4566, 6602, 6526, 17, 5225, 2287, 5038, 16, 6113, 12440, 4510, 24320, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 7997, 8497, 16, 6335, 19, 27976, 1961, 19, 13381, 17, 2601, 13975, 16, 2154, 21569, 6335, 16, 13381, 16, 27976, 1961, 16, 1930, 63, 17, 5758, 4682, 1988, 7948, 43, 3059, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3728, 16, 5745, 12017, 2007, 7997, 6982, 18, 2144, 20425, 8277, 4033, 1966, 4700, 10603, 1942, 6628, 2487, 3719, 1956, 2678, 16, 3146, 16, 2697, 16, 2014, 8238, 16, 6113, 9505, 1922, 6445, 3689, 4028, 6485, 2037, 2359, 3213, 1930, 6338, 19935, 1942, 3616, 9604, 18, 2176, 1977, 2481, 1922, 8496, 1976, 6802, 7972, 2968, 26656, 11352, 4282, 1930, 1977, 10633, 1956, 20709, 11569, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 3], "output": "MNKSIESILEGNNTNKIEELKELSNQGEVLSLLYKMKEYEIFRNILNERTKEEIENYQEMIIINICSYPINDNELEKFFKLLINKEIENEIIIRNIQIGSYKNKKGKEQHIQILKIFHRSYNNFLNKSQLFHLHFNELNSIITTPPKPGFSQLQSYPTVTVKGTCLICKNSLFDGQPVTIYPCGHGIHSACSDYINDTSLVCRYCVALSSSPLI", "metadata": {"id": "M2SD37", "cluster": 11694488, "interpro_all": ["IPR001841", "IPR013083"], "interpro_used": ["IPR001841", "IPR013083"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would the protein sequence be if I wanted a protein that could perform the following function: The protein has a Twin-arginine translocation pathway signal sequence conserved site that targets fully folded proteins, such as redox enzymes with complex cofactors, for export across energy-transducing membranes in bacteria, archaea, and chloroplasts. This N-terminal peptide contains a characteristic motif with invariant twin-arginine residues that directs the protein to the Tat translocase machinery, facilitating the secretion of substrates that have already acquired their tertiary structure. Moreover, the protein carries a Beta-lactamase-related domain that functions as a serine-utilizing hydrolase, utilizing a conserved catalytic S-x-x-K motif to cleave amide bonds. This superfamily encompasses beta-lactamases, which mediate antibiotic resistance by hydrolyzing the beta-lactam ring of penicillins and cephalosporins, as well as D-alanyl-D-alanine carboxypeptidases involved in bacterial peptidoglycan synthesis. Also, the protein belongs to the Beta-lactamase AmpC-like family, which encompasses enzymes involved in bacterial cell wall synthesis, modification, and antibiotic resistance. Members function as serine beta-lactamases that hydrolyze cephalosporins, or as peptidases that cleave D-amino acid-containing peptides and Gly-Gly bonds. It is produced by Halobacterium jilantaiense.", "tokenized_instruction": [2, 4663, 2962, 1920, 2213, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 13392, 17, 9732, 7849, 3374, 2733, 3244, 5305, 3200, 1988, 4845, 5437, 16318, 2697, 16, 2427, 1966, 9366, 5038, 1956, 2796, 21362, 16, 1958, 12660, 3436, 3844, 17, 5925, 1941, 5726, 1922, 4802, 16, 21501, 16, 1930, 24627, 18, 2052, 56, 17, 4262, 4207, 5461, 43, 6293, 5219, 1956, 17004, 13392, 17, 9732, 4248, 1988, 28351, 1920, 2213, 1942, 1920, 10687, 12930, 2051, 10853, 16, 12440, 1920, 5512, 1927, 6249, 1988, 2162, 6064, 5815, 2310, 10832, 3170, 18, 3950, 16, 1920, 2213, 16252, 43, 4666, 17, 23023, 17, 2712, 3418, 1988, 4088, 1966, 43, 8468, 17, 10232, 20748, 16, 10232, 43, 5305, 6804, 61, 17, 66, 17, 66, 17, 53, 5219, 1942, 21252, 13601, 9031, 18, 2052, 13975, 21569, 4666, 17, 23023, 1036, 16, 2154, 8265, 7267, 3554, 2007, 7222, 9046, 1920, 4666, 17, 15294, 6335, 1927, 9957, 1036, 1930, 25091, 2925, 16, 1966, 2486, 1966, 46, 17, 10527, 16323, 1024, 17, 46, 17, 10504, 15750, 9626, 2410, 30413, 3286, 1922, 4543, 24183, 4271, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 4666, 17, 23023, 3681, 1030, 17, 3189, 3416, 16, 2154, 21569, 5038, 3286, 1922, 4543, 2024, 4821, 4271, 16, 6295, 16, 1930, 7267, 3554, 18, 4678, 2347, 1966, 8468, 4666, 17, 23023, 1036, 1988, 7222, 6931, 25091, 2925, 16, 2014, 1966, 24050, 1036, 1988, 21252, 46, 17, 3835, 2687, 17, 3165, 5320, 1930, 3376, 17, 3376, 9031, 18, 2176, 1977, 4152, 2007, 23226, 7972, 2341, 18842, 1989, 14280, 17576, 3857, 15960, 1021, 18, 3], "output": "MPRDTPALTPSRRQFLAALGATATATVAGCTDAQTDRPTTESGTTETTATPDYPATGDRVPELAPLDDAVREFAFEHDVPAATLAVAKDDDVVLERGYGYSDPGRSEQTPPDALFRIASLSKSFTSAATRSLFGDGLSPETRVLDVLDVEPADGLGDDRLQSVTVQHLLDHSAGWDHSAAADPMFHPFDVAEKLGLDEPPTTRDFARYVLGQPLQYEPGERHAYSNFGYALLGLVVEAESGQSLPAYVREQFFGGDPPDPLYEGRALPENRRDREVAYESAANCPNAAELDRNEAVPCSDGGFLVSAFGGAGGLVTSARTLVAFAADHRLDGFATAENFEYATAYGSLPGSYGMLQRRRDGVTVAVLFSDRGGSSNALADIQTTVNDAVADVDAWPSSDES", "metadata": {"id": "A0A1I0MFW0", "cluster": 14158180, "interpro_all": ["IPR050491", "IPR001466", "IPR012338", "IPR006311"], "interpro_used": ["IPR006311", "IPR001466", "IPR050491"], "interpro_unused": ["IPR012338"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nIt is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Also, it is part of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, it is part of the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is found in Actinobacteria bacterium BACL4 MAG-121001-bin59 and carries UniProt keyword assignments Cytoplasm and rRNA processing.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 2435, 1922, 29130, 14061, 30491, 1006, 9624, 17, 11844, 18201, 17, 8768, 7308, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MSTDVAHIPVALNRCLDLLSPAITNNEKPFLILHLIGIDRDQSALEIAKNELKKYLNRSTLVNTTYDQIEAVMLGVSSMQLDLAERGFSYSKQAPLDMRMDQSAKQTYGEEKFASKIAENIIKARTQGELKTTKDLAEIVKNSIPAAARREVNQELAILERAIPAALSALSIGGRLVVMSYQSLEDLPNSAAHYRLLVSGSESSAESEQISNPRSQSMRLRAIERVAADATLGLAGHAKLFLEKFDNAQAGVTKVDAVLFDLSAEVILNTYSHGQLAKIITGGNPAKRTFQALRIDRIVKRFFTQVSAAKTPRGLPM", "metadata": {"id": "A0A0R2QN13", "cluster": 19291169, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR023397", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is included in the Diacylglycerol/lipid kinase family, which comprises enzymes that catalyze the phosphorylation of lipids, including the conversion of diacylglycerol (DAG) to phosphatidic acid and phosphatidylglycerol kinase activity. Predominantly found in bacteria where they recycle DAG for lipoteichoic acid synthesis, these kinases show specificity for long-chain DAGs, while eukaryotic members may regulate sphingoid base production and cold stress responses. Moreover, the protein includes a Diacylglycerol kinase, catalytic domain that catalyzes the phosphorylation of diacylglycerol (DAG) to phosphatidic acid, thereby modulating the balance between these signaling lipids. This conserved catalytic region is present in various lipid kinases, including ceramide and sphingosine kinases, across bacteria and mammals. Additionally, the protein has a YegS/DAGK C-terminal domain that forms the C-terminal structural component of lipid kinases, including bacterial diacylglycerol kinase and eukaryotic sphingosine kinase. It adopts a beta-sandwich fold related to NAD kinases and helps form the active site cleft for the phosphorylation of substrates like phosphatidylglycerol. It is present in SAR202 cluster bacterium and has UniProt annotations Lipid metabolism, ATP-binding, and Transferase.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 1977, 3063, 1922, 1920, 29527, 19, 4486, 4016, 3416, 16, 2154, 12936, 5038, 1988, 18170, 1920, 4050, 1927, 8238, 16, 2710, 1920, 7309, 1927, 29527, 12, 18815, 13, 1942, 2766, 8525, 1935, 2687, 1930, 10951, 18207, 4016, 2455, 18, 7700, 2435, 1922, 4802, 2597, 2611, 12381, 1021, 18815, 1958, 3178, 7229, 2108, 8643, 2687, 4271, 16, 2144, 7784, 2146, 4896, 1958, 2815, 17, 4659, 18815, 1036, 16, 2679, 10825, 4678, 2278, 5741, 13502, 2642, 5170, 3372, 1930, 6685, 3071, 3387, 18, 3950, 16, 1920, 2213, 5921, 43, 29527, 4016, 16, 6804, 3418, 1988, 17097, 1920, 4050, 1927, 29527, 12, 18815, 13, 1942, 2766, 8525, 1935, 2687, 16, 6113, 10871, 1920, 6766, 2192, 2144, 3197, 8238, 18, 2052, 5305, 6804, 3031, 1977, 2481, 1922, 3425, 4486, 7784, 16, 2710, 16926, 1930, 26113, 7784, 16, 3436, 4802, 1930, 9902, 18, 4950, 16, 1920, 2213, 2258, 43, 5293, 4874, 19, 18815, 1040, 45, 17, 4262, 3418, 1988, 4952, 1920, 45, 17, 4262, 4346, 4594, 1927, 4486, 7784, 16, 2710, 4543, 29527, 4016, 1930, 10825, 26113, 4016, 18, 2176, 24032, 43, 4666, 17, 18038, 3728, 2712, 1942, 6577, 7784, 1930, 12612, 2386, 1920, 3500, 3200, 14649, 1958, 1920, 4050, 1927, 6249, 3189, 10951, 18207, 18, 2176, 1977, 2481, 1922, 9851, 18406, 4377, 14061, 1930, 2258, 20709, 15010, 4486, 4714, 16, 4498, 17, 2743, 16, 1930, 13763, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MKFVLIVNPHSGKKKGRQILDLVAPIFNLAGIELSILDIYDGLLLVGGDGTFHEVVNGVLNRIDGKVIPIGVIPAGSGNSVLSIDVAQIKMNQVVRYSINLIGWGLVTDVGKRSETLRWLGPRRYTISSIIEIFLRKSRRAKGMKMAPSADLSDGLIDLIVVDGNITRKRLFSVLPKLFDGTHIETKDTLNIDGELVGTTPVDVRVLKHAIKIFAINTEFPGHARELAASLDHDLGLTDPIQAAKAIAAGDTRRLVVDQETIYKQFTFIVACNSVHIGDEPEVTYYQASSFSLHP", "metadata": {"id": "A0A5N9FXZ6", "cluster": 20190383, "interpro_all": ["IPR017438", "IPR005218", "IPR001206", "IPR050187", "IPR016064", "IPR045540"], "interpro_used": ["IPR005218", "IPR001206", "IPR045540"], "interpro_unused": ["IPR017438", "IPR050187", "IPR016064"]}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein is associated with the Fe-S cluster assembly domain superfamily, which facilitates the mobilization, assembly, and transfer of iron-sulfur clusters to recipient apoproteins. Members of this superfamily function within the ISC, SUF, and NIF pathways, often acting as scaffold proteins that transiently bind Fe and S atoms to synthesize [2Fe-2S] or [4Fe-4S] cofactors. These domains are critical for maturing proteins involved in electron transfer, redox catalysis, and nitrogen fixation across bacteria and eukaryotes. Additionally, the protein is grouped in the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. In addition, the protein should feature a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. It is produced by Marisediminicola antarctica and features UniProt keywords ATP-binding, Hydrolase, and Metal-binding.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 1977, 2458, 1956, 1920, 2650, 17, 61, 4377, 5957, 3418, 13975, 16, 2154, 11374, 1920, 14586, 16, 5957, 16, 1930, 3856, 1927, 5680, 17, 12585, 5859, 1942, 10664, 11466, 22163, 1036, 18, 4678, 1927, 2052, 13975, 2347, 2651, 1920, 23924, 16, 2020, 1038, 16, 1930, 17719, 3873, 16, 3868, 8290, 1966, 7281, 2697, 1988, 12145, 4566, 2650, 1930, 61, 9030, 1942, 15541, 37, 13775, 1021, 17, 20759, 39, 2014, 37, 15338, 1021, 17, 26814, 39, 21362, 18, 2144, 4682, 2032, 4140, 1958, 2888, 4729, 2697, 3286, 1922, 4995, 3856, 16, 9366, 15408, 16, 1930, 6634, 7938, 3436, 4802, 1930, 15021, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 2176, 1977, 4152, 2007, 13081, 4127, 7408, 8547, 29902, 25854, 21788, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 20748, 16, 1930, 6048, 17, 2743, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MTDGSVEDGIRAALSRVLDPEIRKPITELTIVGCPAADTIERDVHAAVASAPGVTSATVEITKTIQFGPDSLTRIYTVSSGKGGVGKSTLTANLAVALAALGIAGMKPTQIDGMILPPVAHGVKVISIGMQFLTDVYFGDIDILLVDLPPGTGDVAITIGQLLPHAEVGTVARQTGQKVIGVIENMAGLAQVDGTVIELFGTGGGELVADSGQPIVLSTPDDAAAASIIRVADELARRGRGLAGRKLGFTVRLDMVGGVSVDAAGSATVGIKSIMTREERAALTEKLHGGRKGLAVGVIDADVFGFSIPGIFVDGNAAVSWRGPMLHRTIQLVVTTPQPAAAEVAERSARLSQGQDAPVPVLASIPLSVALRSGG", "metadata": {"id": "A0A7L5AMA5", "cluster": 21260515, "interpro_all": ["IPR034904", "IPR002744", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR034904", "IPR033756", "IPR002744"], "interpro_unused": ["IPR044304", "IPR019591", "IPR027417"]}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein is assigned to the Collagen superfamily family, which serves as the primary structural component of the extracellular matrix, providing mechanical strength and elasticity to tissues such as skin, bone, and cartilage via fibril and network formation. These proteins typically possess characteristic triple-helical domains and interact with partners like laminins and proteoglycans to mediate cell attachment, tissue development, and repair. Beyond structural support, members of this group participate in specialized functions ranging from angiogenesis to host defense mechanisms. It is native to bacterium.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 1977, 6304, 1942, 1920, 5621, 13975, 3416, 16, 2154, 10634, 1966, 1920, 3065, 4346, 4594, 1927, 1920, 5329, 4526, 16, 5453, 5821, 4568, 1930, 19680, 1942, 3878, 2427, 1966, 4407, 16, 3622, 16, 1930, 8642, 3454, 20871, 1930, 3504, 3337, 18, 2144, 2697, 5745, 7150, 6293, 10073, 17, 11514, 4682, 1930, 6310, 1956, 7228, 3189, 15261, 1036, 1930, 25185, 1942, 8265, 2024, 8576, 16, 2960, 2740, 16, 1930, 5059, 18, 6844, 4346, 3373, 16, 4678, 1927, 2052, 2210, 7352, 1922, 11021, 4088, 6485, 2037, 8244, 1942, 4423, 9720, 3531, 18, 2176, 1977, 6196, 1942, 14061, 18, 11586, 5655, 3581, 18, 3], "output": "MPDINIGTGFAYSREQKVIIANALNSTLQLVDYIKGYVISYVGSTLVGATGSSWAISLDGAIGLPGDEGPAGPTGNAGNIGAAGPTGAIGPAGVTGAASIITSTAIPFVDSSVTLILVETNLAYTLGQHIIVAADTDNFRRVNGIDGYTQNSNTFSSWEVNLDGAVGQQGPIGSIPLPGSGGATVNQQLTVGTGLAYTIGQKVIIAHVEVQAYARTYPYDSWNDHQVNLDGAVGKQGQIGPTGSIVPGPEGAVGATGATGAQGTADILYVQIFSKVRSSSLQSEIVGVVAGPQGEPGDLYAGTSLFKAEITSISSNNLTVECSIGATGPIGASGDLYATEIDAAATVAFPDSLNWFSGPVLIYNASTGLMSTQGLLGPTGDLGPTGAD", "metadata": {"id": "A0A2D6E251", "cluster": 25080787, "interpro_all": ["IPR050149"], "interpro_used": ["IPR050149"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, the protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. In addition, the protein is included in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is identified in Chitinophagaceae bacterium and corresponds to UniProt keyword Cytoplasm and rRNA processing.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 2899, 1922, 16588, 4965, 9914, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MEESVYHVPVLLQEVVESLQVREDGVYVDSGKLIVFDQDAAAQQNVPDDDRILFVPHNFRHLQFDEPDRGFSIRFDGDLDMRMDKRQELTAFDLRTNVSMKTIANFKQALHSVVKGNPNRYFAQVFQALPAILKPGGRVAVITFHSLEDRLVKNFFKKGNTISPSLTVITKKPVVPGEAELRKNPRSRSSKLRVAEKIATFGGGGHSKAILAKLGPRMLRLHKVTQVDGILADLGVSSHQVISRYSEQQLHKLFEQYGEVTNSKTLARTIVARIEVNDELGALKELLQQVSFEEEEDTNPFGQ", "metadata": {"id": "A0A936X299", "cluster": 26243890, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein is grouped in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It has been characterized in Planctomycetaceae bacterium and features UniProt keywords Cytoplasm and rRNA processing.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 2258, 2252, 4378, 1922, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 1930, 4075, 20709, 11569, 5239, 1930, 9067, 4587, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MVEEVIRYLNIQPGQTIVDGTLGLDRDPSAIARAEQQLTGLPVLVAQASYCELPEILNEILGDPDRGFSFSSDGPLDLRFDSTSYEFGEERFSRRIARRIVAQRKSQPLHTASTIDAATRTFQALRIFVNDELGRLDKGGTLAIISFHSLEDRKVKRAFREHAQLEIVTKAKLRVARRNVDDNKSVQSRTLGGGHSRALAHLVGNRGRVIGKCQGVDGVLLDLGFSSDQGKPAWQLINQLSENHIADLIRELAELVRSCVPRSKKALRILPQCLLPKPVVPTTAERETNPRSRS", "metadata": {"id": "A0A2E3MT12", "cluster": 26813521, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should have a FMN-dependent alpha-hydroxy acid dehydrogenase active site that catalyzes the oxidation of alpha-hydroxy acids by abstracting a proton from the substrate's $\\alpha$-carbon. This site utilizes a conserved histidine for proton removal and an arginine for substrate binding to facilitate interaction with the FMN cofactor. Also, the protein possesses a FMN hydroxy acid dehydrogenase domain that functions as the catalytic core of FMN-dependent oxidoreductases acting on alpha-hydroxy acids. Adopting a TIM barrel fold, it utilizes a conserved histidine to abstract a proton from substrates such as lactate and glycolate, facilitating their conversion into products like pyruvate and glyoxylate. Also, the protein is grouped in the Aldolase-type TIM barrel superfamily, which forms a TIM \u03b2/\u03b1 barrel fold that typically covers the entire protein structure. This superfamily includes metabolic enzymes such as class I aldolases, class I DAHP synthases, class II fructose-bisphosphate aldolases, and 5-aminolevulinate dehydratase. It is produced by Actinomycetes bacterium and is linked to UniProt keywords Flavoprotein.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 3066, 2162, 43, 29599, 17, 3100, 4595, 17, 8275, 2687, 9294, 3500, 3200, 1988, 17097, 1920, 6638, 1927, 4595, 17, 8275, 4576, 2007, 10929, 1941, 43, 8433, 2037, 1920, 4510, 11, 61, 8, 38, 4595, 8, 17, 5056, 18, 2052, 3200, 18127, 43, 5305, 13873, 1958, 8433, 6025, 1930, 1925, 9732, 1958, 4510, 2743, 1942, 6628, 2835, 1956, 1920, 29599, 15155, 18, 2222, 16, 1920, 2213, 14465, 43, 29599, 8275, 2687, 9294, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 29599, 17, 3100, 27388, 1036, 8290, 1990, 4595, 17, 8275, 4576, 18, 20478, 43, 2267, 19560, 3728, 16, 2176, 18127, 43, 5305, 13873, 1942, 10929, 43, 8433, 2037, 6249, 2427, 1966, 9456, 1930, 14193, 2010, 16, 12440, 2310, 7309, 2460, 4461, 3189, 11867, 1930, 3376, 6644, 2010, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 11174, 21524, 17, 2601, 2267, 19560, 13975, 16, 2154, 4952, 43, 2267, 161, 19, 160, 19560, 3728, 1988, 5745, 10272, 1920, 5346, 2213, 3170, 18, 2052, 13975, 5921, 4487, 5038, 2427, 1966, 2921, 51, 11174, 21524, 1036, 16, 2921, 51, 3692, 15870, 8921, 1036, 16, 2921, 2890, 15102, 17, 29443, 11174, 21524, 1036, 16, 1930, 25, 17, 3835, 1952, 1020, 3392, 2010, 11725, 7234, 18, 2176, 1977, 4152, 2007, 4718, 25148, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 7732, 6657, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MSTATSSPRSGVDVQEPLNVLDFERLAEATLRDNVAAWRRLRLRPRVLVDVSETTAATTVLGTPVSMPLGTIMCLSTLATAGPAEVATAAPGAPRWFQLYVFRDAPRLGRRERDLRTRFRIPENVLVPSIAAATGAWHGAPLPVVVKGIQTAEDAELACEHGASAIVVSNHGGRQLDAVAPTAEEVYVDGGIRRGTDVVVALALGARAVLVGRPVLIELALALCGCPTPDAVTSAHCSRLEPGAHGYFAGGAGDERCLVAPTAFHRMVHADGEPATARATATAERAVTQSLVEQAVEAGFEAIVLTVTPLDALSRIDPTLSWRDLDVLVADSLLPECVDAVGGRIWGLACGGEAGAARVLELLHDE", "metadata": {"id": "A0A7V8YUI1", "cluster": 1090888, "interpro_all": ["IPR013785", "IPR012133", "IPR000262", "IPR037396", "IPR008259"], "interpro_used": ["IPR008259", "IPR037396", "IPR013785"], "interpro_unused": ["IPR000262", "IPR012133"]}, "task_type": "infilling"} {"instruction": "The protein includes a FAD/NAD(P)-binding domain that binds FAD and NAD(P)H cofactors to facilitate electron transfer in class I and class II oxidoreductases. This domain typically adopts a doubly-wound \u03b1/\u03b2 fold and contains a pair of redox-active cysteines involved in transferring reducing equivalents from the FAD cofactor to the substrate. It is characteristic of the pyridine nucleotide-disulphide oxidoreductase family, playing a central role in oxidative metabolism. Furthermore, the protein is associated with the Ferredoxin-NADP reductase-like family, which comprises oxidoreductases that catalyze the transfer of electrons between NADPH and carriers such as ferredoxin or adrenodoxin. This family includes bacterial ferredoxin reductases and the human mitochondrial NADPH:adrenodoxin oxidoreductase. Also, the protein is classified under the Ferredoxin-NADP+ reductase, adrenodoxin-type family, which functions as an NADPH:adrenodoxin oxidoreductase, transferring electrons from NADPH to adrenodoxin or related ferredoxins. This group includes mitochondrial enzymes such as human Fdxr and bacterial homologs like Mycobacterium FprA, playing a vital role in electron transport systems. It is identified in Frankliniella fusca and features UniProt keywords Flavoprotein, Mitochondrion, and Transit peptide.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 5921, 43, 14134, 19, 6577, 12, 58, 13, 17, 2743, 3418, 1988, 6876, 14134, 1930, 6577, 12, 58, 13, 50, 21362, 1942, 6628, 4995, 3856, 1922, 2921, 51, 1930, 2921, 2890, 27388, 1036, 18, 2052, 3418, 5745, 24032, 43, 26783, 17, 6376, 160, 19, 161, 3728, 1930, 5461, 43, 3715, 1927, 9366, 17, 3500, 22446, 3286, 1922, 21902, 5526, 17762, 2037, 1920, 14134, 15155, 1942, 1920, 4510, 18, 2176, 1977, 6293, 1927, 1920, 19604, 5489, 17, 2054, 23138, 2261, 27388, 3416, 16, 14797, 43, 4101, 2770, 1922, 5163, 4714, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 25304, 22389, 10960, 17, 24221, 11386, 17, 3189, 3416, 16, 2154, 12936, 27388, 1036, 1988, 18170, 1920, 3856, 1927, 14354, 2192, 11908, 1930, 8974, 2427, 1966, 25304, 22389, 10960, 2014, 7206, 1986, 9754, 18, 2052, 3416, 5921, 4543, 25304, 22389, 10960, 11386, 1036, 1930, 1920, 2616, 4596, 11908, 30, 7206, 1986, 9754, 27388, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 25304, 22389, 10960, 17, 24221, 15, 11386, 16, 7206, 1986, 9754, 17, 2601, 3416, 16, 2154, 4088, 1966, 1925, 11908, 30, 7206, 1986, 9754, 27388, 16, 21902, 14354, 2037, 11908, 1942, 7206, 1986, 9754, 2014, 2712, 25304, 22389, 10960, 1036, 18, 2052, 2210, 5921, 4596, 5038, 2427, 1966, 2616, 8350, 10024, 1930, 4543, 14279, 3189, 16389, 30276, 1019, 16, 14797, 43, 8970, 2770, 1922, 4995, 4860, 3771, 18, 2176, 1977, 2899, 1922, 24679, 19918, 10630, 3375, 1930, 4075, 20709, 11569, 7732, 6657, 16, 30017, 16, 1930, 16361, 4207, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MIRFCSQSLYKNARFLTGLPNQTKCAKICIVGGGPAGFYAAQHIIKTLLVRFGVAPDHPEVKNVINTFTKTAKSPQVRFVGNVNFGIDINLQDLKESYHAVILTREFVGWYNGLPRDKDLNVDLSNESVVILGQGNVAVDAARMLLSPLDELKKTDITESVYLVGRRGPMQVAFTIKELREMINLKGCSSIFEKEHFRGIPNLIPNLVRPRKRLTRPLFLRSPLAILGDSRVTGVEFGLNTLEGTELENQRAIPTGEREVITKRGRVINTKGRVEHGVYSAGWLSTGPVGVILSTMSNAFETGANVLDDIRQEVINLNEVQTVSFDGWEKIDKEEVTRGKALGKPREKIVDIKEMLQIAETGKKVIDPQCEIDIFERLPVPFGYGAEQDKTFGIPGENLQNVISAHALAKLADSKVKELLVKSALETSPKPSSKEFSGMVLRSIGYKSVCPDPSIPFDNIRPGINAIISKLDAKG", "metadata": {"id": "A0AAE1LHW9", "cluster": 2648047, "interpro_all": ["IPR036188", "IPR023753", "IPR055275", "IPR021163"], "interpro_used": ["IPR023753", "IPR055275", "IPR021163"], "interpro_unused": ["IPR036188"]}, "task_type": "infilling"} {"instruction": "The protein carries a Glutamine amidotransferase domain that catalyzes the removal of ammonia from glutamine and transfers it to a substrate to form a new carbon-nitrogen bond during the biosynthesis of purines, pyrimidines, and amino acids. It operates either as a discrete subunit or as a fused domain within a larger synthase complex, utilizing a conserved catalytic cysteine to facilitate the nitrogen transfer. It has been characterized in Corynebacterium occultum and is associated with UniProt keywords Plasmid. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 16252, 43, 9959, 28813, 14165, 3418, 1988, 17097, 1920, 6025, 1927, 14880, 2037, 9959, 1930, 19180, 2176, 1942, 43, 4510, 1942, 2386, 43, 2814, 5056, 17, 6634, 5403, 2409, 1920, 8132, 1927, 19700, 1036, 16, 21611, 1036, 16, 1930, 3835, 4576, 18, 2176, 22460, 3108, 1966, 43, 10484, 5903, 2014, 1966, 43, 10305, 3418, 2651, 43, 4327, 8921, 2796, 16, 10232, 43, 5305, 6804, 8666, 1942, 6628, 1920, 6634, 3856, 18, 2176, 2258, 2252, 4378, 1922, 2233, 17151, 7972, 2341, 18842, 1989, 23065, 1989, 1930, 1977, 2458, 1956, 20709, 11569, 5609, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MTPTPTKQVTLLITHNPDPDIDQVCQILDNRKKTWRHIQPFAGDKLPNLHEVSQVICFGGPYAAYDQDRFPFLREEAQFLRDAVDADIPVLGICLGSQILAEALGGTSRPGDHGLECGFVDVVPVAGQEDVAHQLTGRYFSFHTDSIDLPPGAELLAVSQRYPQAWRQGSALAIQFHPEMSVTGIRELLRIEKVKIRQHGINVENLMAEAENNRALLQQGAEKVIGGWIDHADARAPVHTGESP", "metadata": {"id": "A0A6B8WR38", "cluster": 3421316, "interpro_all": ["IPR044992", "IPR029062", "IPR017926"], "interpro_used": ["IPR017926"], "interpro_unused": ["IPR029062", "IPR044992"]}, "task_type": "autoregressive"} {"instruction": "The protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, the protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It has been characterized in Candidatus Daviesbacteria bacterium and is annotated with UniProt keywords Cytoplasm and rRNA processing.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 2258, 2252, 4378, 1922, 14550, 1031, 1957, 10022, 2062, 7972, 2341, 18339, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MQGYHSSVLLEEAVDALNIRDVWYLDCTLGDGGHSIEIISRGNLGIGSDKFKLVQGNFRNVENLIQSVFRRNKQMDTLNFEIFSFSKEGPLDMRMDPELEVRALDLVKILSRKELNELFYSLGITTTQDLAGVIVRTVGKNRAAKEQIHPATRVFQALRIAVNDELDVLTEGIRIVKNTFKEWQIRGLGKVLTKKPIMSTTEEVALNPRSRSAKMRVFEKLGKIIGIDVDPQALERVQRRFGAGAIFDLGVSSLQLENPERGEEKYSGRLADALVSTRQIKPNQAVNLIQKNGRIVVISFHSLED", "metadata": {"id": "A0A932EFC5", "cluster": 4066081, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein contains a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. Additionally, the protein is grouped in the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. Additionally, the protein should have a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. It occurs in Paenibacillus nanensis and has UniProt annotations Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 2176, 5110, 1922, 25726, 8635, 7972, 10401, 5277, 1036, 3529, 8134, 1930, 2258, 20709, 15010, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 3], "output": "MTYNNHVDTVSPEGAIYYLFGATGDLAKRKLFPALFSLYKEGKLSDNFAVVGLARRPRTNDQFRSDLYESINEFCRYKPDDAELWNRFTEHFVYMSLDINNVDGFRELNALSTELDKKFNIPGNRLFYLALAPSLFGPVSFNLRDGGMLESKGWHRLVIEKPFGYDLPSAKKLNEQLNQVFKEEEIFRIDHYLGKEMVQNIQVIRFANAFFEPLWNNKHIANVQITLSETVGVEERGGYYDKSGALRDMGQNHMLQMLTMIAMEPPSRLHGEDIRDEKVKVLRSLRGYTSSDDVRKHVVRGQYTEGTVGGKELPGYRQEDSVDPESMTETYFAAKVYVDNFRWAGVPFYIRTGKRLPVKTTEVVVEFKSMPENVLFAQRHDLSPNLLVIRVNPMEGIYIKINAKKPGSDNAVQPVSMEFCQSCQIGINTPEAYERLIHDAARGDSTYFTRWDEVSHAWEFVDRIAQAWREDKSDLAFYPAGSWGPEEVSRLLDEEGFHWWPVNGQEEDNVIWITNNGK", "metadata": {"id": "A0A3A1UX12", "cluster": 8914243, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR019796", "IPR036291", "IPR022674"], "interpro_unused": ["IPR022675", "IPR001282"]}, "task_type": "autoregressive"} {"instruction": "Functionally defined as:\nThe protein is grouped in the Deoxyribonuclease II family, which catalyzes the endonucleolytic cleavage of DNA, preferentially double-stranded DNA, under acidic conditions to yield 3'-phosphomononucleotide and 3'-phosphooligonucleotide products. It may also play a role in apoptosis. It is present in Gonium pectorale (Green alga) and contains UniProt keyword associations Hydrolase and Signal.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 1977, 10809, 1922, 1920, 26405, 13261, 2890, 3416, 16, 2154, 17097, 1920, 16239, 1022, 2626, 6586, 6404, 1927, 2678, 16, 10662, 4825, 17, 10338, 2678, 16, 2441, 9931, 2961, 1942, 4307, 23, 11, 17, 8078, 3947, 5551, 4749, 1930, 23, 11, 17, 8078, 8436, 3827, 1022, 15274, 4461, 18, 2176, 2278, 2222, 3918, 43, 2770, 1922, 4091, 18, 2176, 1977, 2481, 1922, 8239, 2457, 23540, 2603, 12, 4524, 4326, 1019, 13, 1930, 5461, 20709, 11121, 2538, 5253, 20748, 1930, 2733, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MAHPALLALLPILPWALTLSSVVHAPAASASGGVGGAHRPVDWWLLLKYPAGEDAALIDSETEPAAAVAGRGGGVQAPAVAVAAEPACVPNPAGASAAGPGEPITLDSIATGPEQRPQRSPGFASASMPSGINEASSSQPPPRPPPPDADPEGVEHWGFAHAKGVLLFGPERGVWITHSFPRYPANGSSRFGQHALCIELPRSQLLHVAQSLLVARAFVYEYPGAAAGAAAATAINGRRAGLASGGWPEERNVSWHALTSSGGRAWVHVAKEAMAWETWRVGTSYPSECPPEAPFASYNVRRIDMPGVGVEPGNEVQRSVPLGRWGLGGLGVMRSGSETPGRQGQASGWDSLKVPDGRRGGGGDGAPGGEDAAAVSAGTVCVGDLNRQPSQRFRGGGVAELEPCPAAAADANLGTAEGDAVGSASGAASGPQRLLSQQPTPQPLQPPRCISSGGACAWRTGLQVNDPDGPLRATLAAAAQSPVGALPLRRGLTTAARSYRAANSTGYVFYNGRPPRRPAWQQQQQQQRRPAGSAPADAPDELLDEYDAVRQLIEASAAESPNYTVPFHEQVLEPALNACPDGRGVGEGGTGGTGISDHSKWGISAASLLYVCRRDAGLWGAFRAL", "metadata": {"id": "A0A150G9S8", "cluster": 12564937, "interpro_all": ["IPR004947"], "interpro_used": ["IPR004947"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein belongs to the MJ1680-like family, which functions as the toxin component of a type II toxin-antitoxin system found in bacteria and archaea. Members of this family belong to the PIN domain superfamily. Furthermore, the protein includes a PIN domain that functions as a ribonuclease structurally defined by three strictly conserved acidic residues. In eukaryotes, it is involved in nonsense-mediated mRNA decay and 18S rRNA processing, while in prokaryotes, it acts as the toxic VapC component of VapBC toxin-antitoxin systems. It is identified in Cecembia lonarensis (strain CCUG 58316 / KCTC 22772 / LW9).", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 14440, 1942, 1920, 15697, 21580, 1008, 17, 3189, 3416, 16, 2154, 4088, 1966, 1920, 9165, 4594, 1927, 43, 2601, 2890, 9165, 17, 10310, 9754, 2433, 2435, 1922, 4802, 1930, 21501, 18, 4678, 1927, 2052, 3416, 6784, 1942, 1920, 8701, 3418, 13975, 18, 3677, 16, 1920, 2213, 5921, 43, 8701, 3418, 1988, 4088, 1966, 43, 18347, 2051, 12171, 3608, 2007, 2559, 14470, 5305, 9931, 4248, 18, 1922, 15021, 16, 2176, 1977, 3286, 1922, 19605, 17, 3434, 3616, 9310, 1930, 17659, 9067, 4587, 16, 2679, 1922, 28149, 16, 2176, 8016, 1966, 1920, 6161, 16697, 1030, 4594, 1927, 16697, 8284, 9165, 17, 10310, 9754, 3771, 18, 2176, 1977, 2899, 1922, 17967, 4139, 2126, 10969, 2768, 3355, 1937, 12, 3943, 4928, 2215, 4804, 6800, 1016, 19, 14331, 6916, 19797, 10180, 19, 21251, 1026, 13, 18, 3], "output": "MILALLDANVIFPAPIRDHQEWKRNLLQKRPELDSKGLERTITLMNEAFPDASINTDYLVTVNLKDFKTSALKNEKPQVIHPDDFICDVLRTLTKIGLLNTAAKIRGLLALLLSLAEDGHFKPFWTEEIEGYERRIEALSLKDPNDRHVLAAALEALFISENPASVLDCFSRLVSRLKKPPQSKE", "metadata": {"id": "K1KUL3", "cluster": 13283142, "interpro_all": ["IPR029060", "IPR002716", "IPR002850"], "interpro_used": ["IPR002850", "IPR002716"], "interpro_unused": ["IPR029060"]}, "task_type": "infilling"} {"instruction": "Given this biological function:\nIt is part of the The Elongation factor Ts, dimerisation domain superfamily, which adopts a \u03b2(2)-\u03b1(n)-\u03b2 fold and functions as a nucleotide exchange factor for elongation factor 1A (EF1A or EF-Tu). By regenerating the active GTP-bound form of EF1A from its inactive GDP-bound state, this domain enables the recruitment of aminoacyl-tRNA to the ribosome during protein synthesis. In addition, the protein should have a Translation elongation factor Ts conserved site that functions as a guanine nucleotide exchange factor for EF-Tu (EF1A), facilitating the regeneration of the active GTP-bound complex during the elongation cycle. It is primarily found in bacteria, mitochondria, and chloroplasts. Moreover, the protein is assigned to the UBA-like superfamily, which adopts a compact three-helical bundle fold with a conserved hydrophobic surface patch to mediate protein-protein interactions in diverse cellular processes including the ubiquitin/proteasome pathway, DNA excision-repair, and cell signaling. This superfamily encompasses functionally distinct domains such as the TS-N domain of elongation factor Ts, which catalyzes EF-Tu recycling during translation, and the C-terminal domain of TAP/NXF1, which binds FG nucleoporins to facilitate nuclear export. It has been detected in Leptotrichia rugosa and is described by UniProt keywords Cytoplasm and Protein biosynthesis.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 2176, 1977, 3131, 1927, 1920, 1920, 9971, 2991, 4894, 16, 7632, 6284, 3418, 13975, 16, 2154, 24032, 43, 161, 12, 22, 13, 17, 160, 12, 56, 13, 17, 161, 3728, 1930, 4088, 1966, 43, 5489, 6818, 2991, 1958, 9971, 2991, 5123, 12, 8485, 6146, 2014, 8485, 17, 9037, 13, 18, 2007, 23617, 1920, 3500, 9319, 17, 4124, 2386, 1927, 8485, 6146, 2037, 2496, 9078, 15217, 17, 4124, 3360, 16, 2052, 3418, 10217, 1920, 6067, 1927, 3835, 14645, 17, 10089, 1942, 1920, 12794, 2409, 2213, 4271, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 6410, 9971, 2991, 4894, 5305, 3200, 1988, 4088, 1966, 43, 16904, 5489, 6818, 2991, 1958, 8485, 17, 9037, 12, 8485, 6146, 13, 16, 12440, 1920, 8596, 1927, 1920, 3500, 9319, 17, 4124, 2796, 2409, 1920, 9971, 4048, 18, 2176, 1977, 5985, 2435, 1922, 4802, 16, 6489, 16, 1930, 24627, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 4803, 1019, 17, 3189, 13975, 16, 2154, 24032, 43, 13726, 2559, 17, 11514, 14142, 3728, 1956, 43, 5305, 7919, 3154, 7504, 1942, 8265, 2213, 17, 2213, 3719, 1922, 6445, 3689, 4028, 2710, 1920, 6526, 19, 9993, 3374, 16, 2678, 10940, 17, 5059, 16, 1930, 2024, 3197, 18, 2052, 13975, 21569, 9346, 4493, 4682, 2427, 1966, 1920, 4894, 17, 56, 3418, 1927, 9971, 2991, 4894, 16, 2154, 17097, 8485, 17, 9037, 13977, 2409, 6410, 16, 1930, 1920, 45, 17, 4262, 3418, 1927, 10167, 19, 27578, 5739, 16, 2154, 6876, 13320, 2797, 7540, 5572, 1036, 1942, 6628, 4254, 12660, 18, 2176, 2258, 2252, 3330, 1922, 16976, 18935, 19519, 1019, 23148, 5360, 1930, 1977, 2910, 2007, 20709, 11569, 5239, 1930, 2213, 8132, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MAITTALIKELRERDIEKAIDWLREKGIAKAAKKSGRVAAEGLVAKNDEFKSFGEKLVTLTIETHLTELIAKIGENMNIRRLKLVATTGFINVNGEATDENIEKAKGVAMHVAAMDPKYLDKANIIEKILEGKMRKFYEENCLVQQKYVRDRFKVGEGIEKEEVDFAAEVAAQLGQTGAGMLDCKKALGENDGVFAAVSEDRKKGAILEFNSETDFTLEHDLTSEDELKAFEHEGKETYIHLGGKIGVLLSQVTTADLDREKEIARHQLTAEGKPDKVTVEKFIAPSTIISFD", "metadata": {"id": "A0AB39VEU7", "cluster": 13428088, "interpro_all": ["IPR036402", "IPR001816", "IPR014039", "IPR018101", "IPR009060"], "interpro_used": ["IPR036402", "IPR018101", "IPR009060"], "interpro_unused": ["IPR001816", "IPR014039"]}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein falls within the Zinc finger, RING/FYVE/PHD-type superfamily, which encompasses RING, PHD, FYVE, and U-box domains that share a common $\\alpha/\\beta$ structural fold, typically stabilized by zinc ions. These versatile motifs act as stable scaffolds to facilitate specific interactions with DNA, RNA, proteins, or lipids, thereby participating in diverse cellular processes ranging from gene transcription and chromatin remodelling to mRNA trafficking. Furthermore, the protein should contain a Zinc finger, RING-type domain that mediates protein-protein interactions and typically functions as an E3 ubiquitin-protein ligase. This motif coordinates two zinc ions in a \"cross-brace\" structure to bind E2 ubiquitin-conjugating enzymes, thereby facilitating substrate ubiquitylation. It is identified in Pseudocercospora fuligena and carries UniProt keyword assignments Metal-binding and Zinc-finger.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 12182, 2651, 1920, 7997, 8497, 16, 6335, 19, 27976, 1961, 19, 13381, 17, 2601, 13975, 16, 2154, 21569, 6335, 16, 13381, 16, 27976, 1961, 16, 1930, 63, 17, 5758, 4682, 1988, 7948, 43, 3059, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3728, 16, 5745, 12017, 2007, 7997, 6982, 18, 2144, 20425, 8277, 4033, 1966, 4700, 10603, 1942, 6628, 2487, 3719, 1956, 2678, 16, 3146, 16, 2697, 16, 2014, 8238, 16, 6113, 9505, 1922, 6445, 3689, 4028, 6485, 2037, 2359, 3213, 1930, 6338, 19935, 1942, 3616, 9604, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 7997, 8497, 16, 6335, 17, 2601, 3418, 1988, 10412, 2213, 17, 2213, 3719, 1930, 5745, 4088, 1966, 1925, 10968, 6526, 17, 2213, 11905, 18, 2052, 5219, 10675, 2288, 7997, 6982, 1922, 43, 6, 3567, 17, 18303, 1972, 6, 3170, 1942, 4566, 6602, 6526, 17, 5225, 2287, 5038, 16, 6113, 12440, 4510, 24320, 18, 2176, 1977, 2899, 1922, 11520, 2337, 4879, 3508, 8846, 5257, 6419, 1019, 1930, 16252, 20709, 11121, 2538, 18306, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 11586, 5655, 3581, 18, 3], "output": "MDLDIRSPLDATLLPCTIAYPDDCPLCYGQLDSNSDDARDSVWDYPPCGHHYHAGCLHKATDQGSGYNTCLVCRAKWFATLTAIIALARANDGAEVGVLNPDQDPCPEAVVLQHFATEVPNMGFGHYLTGAVVETGGIRHSDFITDCVSQWTALGRGQSQRQDRYIMTTDTTENLQKARNVNYVIQHSHFLTRLSARATGVIFGVYPKS", "metadata": {"id": "A0A8H6VS93", "cluster": 15257151, "interpro_all": ["IPR001841", "IPR013083"], "interpro_used": ["IPR013083", "IPR001841"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein carries a GGDEF domain that catalyzes the synthesis of the secondary messenger cyclic diguanylate (c-diGMP) to regulate prokaryotic signal transduction. This domain adopts an adenylate cyclase-like fold and is frequently associated with upstream sensory or regulatory modules, such as PAS, GAF, or HAMP domains, within multidomain proteins. In addition, the protein possesses a CHASE domain that functions as an extracellular sensory module in transmembrane receptors from bacteria, lower eukaryotes, and plants to mediate signal transduction. It is predicted to bind diverse low molecular weight ligands, such as cytokinin-like adenine derivatives or peptides, and is typically found N-terminal to intracellular enzymatic domains like histidine kinases and nucleotide cyclases. Additionally, the protein contains a EAL domain that functions as a diguanylate phosphodiesterase to catalyze the degradation of the second messenger cyclic di-GMP. It contains conserved acidic residues likely involved in metal binding and often works with GGDEF domains to regulate bacterial cell surface adhesiveness. It has been characterized in Xanthobacteraceae bacterium and exhibits UniProt keyword tags Transmembrane helix. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 16252, 43, 12358, 3695, 1038, 3418, 1988, 17097, 1920, 4271, 1927, 1920, 4067, 16716, 9821, 4325, 13785, 9075, 12, 45, 17, 4325, 6588, 13, 1942, 5741, 21545, 2733, 8201, 18, 2052, 3418, 24032, 1925, 23052, 16526, 17, 3189, 3728, 1930, 1977, 5467, 2458, 1956, 7671, 6893, 2014, 4948, 10803, 16, 2427, 1966, 9233, 16, 4357, 1038, 16, 2014, 8616, 1034, 4682, 16, 2651, 9184, 2954, 1921, 2697, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 22948, 3418, 1988, 4088, 1966, 1925, 5329, 6893, 9059, 1922, 9117, 4086, 2037, 4802, 16, 2826, 15021, 16, 1930, 4793, 1942, 8265, 2733, 8201, 18, 2176, 1977, 4396, 1942, 4566, 6445, 2330, 3272, 3388, 6908, 16, 2427, 1966, 4192, 15020, 17, 3189, 15643, 8383, 2014, 5320, 16, 1930, 1977, 5745, 2435, 56, 17, 4262, 1942, 4776, 8145, 4682, 3189, 13873, 7784, 1930, 5489, 16526, 1036, 18, 4950, 16, 1920, 2213, 5461, 43, 11377, 1024, 3418, 1988, 4088, 1966, 43, 4325, 13785, 9075, 24821, 1942, 18170, 1920, 4877, 1927, 1920, 2812, 16716, 9821, 2137, 17, 18033, 18, 2176, 5461, 5305, 9931, 4248, 3205, 3286, 1922, 6048, 2743, 1930, 3868, 10997, 1956, 12358, 3695, 1038, 4682, 1942, 5741, 4543, 2024, 3154, 13510, 2971, 18, 2176, 2258, 2252, 4378, 1922, 15213, 5883, 9914, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 7864, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MADYLNFIKGQPRFGAARSDPYLNVWFKVMLDRQVMKGRILQHWALLATACVGLVFSCTAWFAASVREDRLAELEFSARADNHLLTLQGGINTYLSRMGALRALYNSDDYVSRSEFQIFSEELLRGQNAILAVSWIPRVTHAQREAHELLAVRDGISGYRIKAAKGDGGLVPAPERAEYFPIFYSSREKPDSHIYGLDLNDGGLRQHTLERARDADQIATSPSFKLSAGEGDRNGFFVTLPVYRVAHPHDTVANRRSNLVGFVQGVFQIGVLIETVLKETASPGGLDLYFYAVDSSRGTSRLYFHPSRIRTDSPQPLPLDTVTAGLHWSGEINVGDAVWKFIAAPIPGGPGTASHAGSLLLLAGCLLITLLVMGYILAAHRHAERIHTKNEQLDAALGNMPQALLMFDSSARLVIGNSHYQEMYGLSPDAAKPGSAFLDMVRQLQQGGMFPADPETYAGDLLSAIAQGNALENVTELPDGRTIAIVHHPIPGGGWVTTHEDITSRVSAEAKMSYMALHDTLTNLPNRLFFHKDLESRLAHLARGQKFAILCLDLDNFKHVNDTLGHPCGDSLLRQAADRLRGCMREGDSLARLGGDEFAILQASATEPAMTTSLMTRIIEVIGAPFDIDGQQVVVGVSIGVALAPSDSTDPDQILKLADMALYRAKADGRGTYRFFEPEMDARMQARRIMELDLRKAITKGEFELHYQPLVNLETEQISGFEALIRWNHPERGMVSPVDFIPLAEETALIVPIGEWALRQACEEAAKWPSHISIAVNLSSIQFRVANVAQAVVKALAHSGLSAGRLELEITESVLLLNGESTLNTLHQLRAMGVRISMDDFGTGYSSLSYLHSFPFDKIKIDRSFVHDLSSSENSMAIIRAVTGLGSSLGMKTTGEGVETREELEYLKREGCTEAQGFLFSKAIPAREVASMLAARPVNAKAVA", "metadata": {"id": "A0A521VVQ8", "cluster": 15953434, "interpro_all": ["IPR052155", "IPR006189", "IPR042240", "IPR001633", "IPR035919", "IPR000160", "IPR029787", "IPR035965", "IPR043128"], "interpro_used": ["IPR000160", "IPR006189", "IPR001633"], "interpro_unused": ["IPR029787", "IPR042240", "IPR043128", "IPR035965", "IPR052155", "IPR035919"]}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein contains a OB-fold nucleic acid binding domain, AA-tRNA synthetase-type domain that forms a five- or six-stranded closed beta-barrel architecture to bind diverse ligands, particularly nucleic acids. It utilizes variable loops and a conserved binding face to interact with substrates ranging from oligonucleotides and oligosaccharides to proteins and metal ions. In addition, the protein incorporates a HD domain that functions as a phosphohydrolase involved in nucleic acid metabolism and signal transduction across bacteria, archaea, and eukaryotes. This catalytic module relies on conserved histidine and aspartate residues to coordinate divalent cations essential for enzymatic activity. Also, the protein possesses a HD/PDEase domain that exhibits predicted or known phosphohydrolase activity within a diverse enzyme superfamily. It encompasses the catalytic region of eukaryotic 3',5'-cGMP phosphodiesterases found in photoreceptor outer segments, where it functions as a light-activated enzyme critical for signal transduction. It is found in Desulfomonile tiedjei.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 5461, 43, 2384, 17, 3728, 11079, 2687, 2743, 3418, 16, 6440, 17, 10089, 18185, 17, 2601, 3418, 1988, 4952, 43, 3628, 17, 2014, 3798, 17, 10338, 8047, 4666, 17, 19560, 9335, 1942, 4566, 6445, 6908, 16, 4443, 11079, 4576, 18, 2176, 18127, 4650, 11109, 1930, 43, 5305, 2743, 6171, 1942, 6310, 1956, 6249, 6485, 2037, 12545, 1930, 22012, 1942, 2697, 1930, 6048, 6982, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 4515, 3418, 1988, 4088, 1966, 43, 8078, 8535, 24605, 1021, 3286, 1922, 11079, 2687, 4714, 1930, 2733, 8201, 3436, 4802, 16, 21501, 16, 1930, 15021, 18, 2052, 6804, 9059, 12850, 1990, 5305, 13873, 1930, 12878, 4248, 1942, 11865, 21610, 16525, 4415, 1958, 8145, 2455, 18, 2222, 16, 1920, 2213, 14465, 43, 4515, 19, 13309, 2051, 3418, 1988, 9826, 4396, 2014, 3171, 8078, 8535, 24605, 1021, 2455, 2651, 43, 6445, 4113, 13975, 18, 2176, 21569, 1920, 6804, 3031, 1927, 10825, 23, 11, 16, 25, 11, 17, 15958, 24821, 1036, 2435, 1922, 16383, 7642, 7492, 16, 2597, 2176, 4088, 1966, 43, 3696, 17, 4128, 4113, 4140, 1958, 2733, 8201, 18, 2176, 1977, 2435, 1922, 30311, 20050, 2383, 24875, 12518, 1033, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MNESSTDLSTWVKDFKPGDNILDVVLSDATGSISGKVWSDVMRKWGHDFTAGDYVKVDTSEIPDADALIKKSKQDPKTLMEELFMQLPAAQMVHHAYQGGLIEHVAAVTRKAMAILPELKPEGAGRSSEGRLIGHVILGLNLLREAAAEVGVHHGETQFGAPVKPFTREAVLVHFVDNLDAKYNKWLEGKAFVGSACLPQEENDVGSQYFRLYSKEIRKTRSGQDYLKVEGRVENYKDKNQIVVEKIRRQIAGTLQPPEMSQLVLELLTRHAEDLEEKINANIAIAGAIRHDIGKVRLDKPWLTELEHIIISLKIMAEALESVEADGFAP", "metadata": {"id": "A0A9D6V141", "cluster": 18491616, "interpro_all": ["IPR003607", "IPR006674", "IPR006675", "IPR012340", "IPR004365", "IPR050798"], "interpro_used": ["IPR004365", "IPR006674", "IPR003607"], "interpro_unused": ["IPR012340", "IPR006675", "IPR050798"]}, "task_type": "infilling"} {"instruction": "Given the following functional description of a protein, generate a complete amino acid sequence that performs the described role. The desired function is: It is part of the RND efflux pump, membrane fusion protein family, which functions as a component of RND transporters to facilitate the export of diverse compounds ranging from drug molecules to large polypeptides. These proteins typically span the periplasm to link the inner and outer membranes, serving as a structural adaptor that connects the pump to an outer membrane channel. It is found in Alicyclobacillus acidocaldarius (strain Tc-4-1) (Bacillus acidocaldarius) and has UniProt annotations Coiled coil and Transmembrane helix.", "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 16, 5655, 43, 4080, 3835, 2687, 3244, 1988, 17436, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 2176, 1977, 3131, 1927, 1920, 6364, 1007, 11247, 8912, 16, 3260, 5289, 2213, 3416, 16, 2154, 4088, 1966, 43, 4594, 1927, 6364, 1007, 10538, 1942, 6628, 1920, 12660, 1927, 6445, 4300, 6485, 2037, 2838, 4206, 1942, 3103, 18633, 18, 2144, 2697, 5745, 7188, 1920, 20171, 1942, 3300, 1920, 6671, 1930, 7642, 5726, 16, 13915, 1966, 43, 4346, 15077, 1988, 26414, 1920, 8912, 1942, 1925, 7642, 3260, 4999, 18, 2176, 1977, 2435, 1922, 15356, 22170, 14357, 8898, 2687, 5000, 3825, 3027, 1957, 12, 3943, 5283, 17, 24, 17, 21, 13, 12, 14587, 2687, 5000, 3825, 3027, 1957, 13, 1930, 2258, 20709, 15010, 17524, 9121, 1930, 9117, 7864, 18, 3], "output": "MAISSEKRTGRRVGAVIGFVLALLALLVGALVVWKSRHALPVVETAPVSLQRIERVTLAAGTVRPVARQIVNLDNLSAPVERVLVHVGQRVQAGQPLIQLSTASAEASVQAAELALSDAESAYQRVLAQYNQAPTALKALFLPQLNAAEASVASARSQLAQAEANEAQLTITATMSGIVLIANPNGVDADGNQTPVVEVASPAKDVVMDLSEVDAAQIKVGMTATMQTDAYPNQTFTGSVTSIAPYAELSSSGAPVVEVTVQPRGSFPVPYGYQLTCRILSRSPSPVPTVPYSAIVQNGTGYAVYEWRNGHVYLVPVKLGMTSDTAVQVLSGVAPGNRVVINPPDNLVNGEAVRTS", "metadata": {"id": "F8IG91", "cluster": 20021752, "interpro_all": ["IPR032317", "IPR006143"], "interpro_used": ["IPR006143"], "interpro_unused": ["IPR032317"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein should contain a Chitin binding domain that mediates binding to chitin, characterized structurally by a six-cysteine motif and conserved aromatic residues. This extracellular domain is typically found in insect peritrophins, animal chitinases, and some baculoviruses. It has been detected in Camponotus floridanus (Florida carpenter ant).", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 16588, 2743, 3418, 1988, 10412, 2743, 1942, 16588, 16, 4378, 12171, 2007, 43, 3798, 17, 8666, 5219, 1930, 5305, 10761, 4248, 18, 2052, 5329, 3418, 1977, 5745, 2435, 1922, 11422, 2953, 1997, 2688, 2925, 16, 4027, 16588, 2319, 16, 1930, 2673, 26647, 1918, 18, 2176, 2258, 2252, 3330, 1922, 6225, 23557, 1031, 1957, 19386, 1022, 1957, 12, 19386, 16549, 9583, 4942, 13, 18, 3], "output": "MWADQVPECRNEEVAGGFTCPAAGEVSGASGLEGVAREYGCPIGTVFKIGDADGSGACEDSELLTGLQNEHKKPHQAPLKPRPLAGGPTRPSSPVQESFSRHAHPEDCRKYYICPEDVPGCEDYYGDLDLKSIRK", "metadata": {"id": "E2A159", "cluster": 21966531, "interpro_all": ["IPR002557", "IPR036508"], "interpro_used": ["IPR002557"], "interpro_unused": ["IPR036508"]}, "task_type": "infilling"} {"instruction": "The protein incorporates a IPT domain that adopts an immunoglobulin-like fold and functions in both cell surface receptors, such as Met and Ron, to control cell dissociation and motility, and in intracellular transcription factors to mediate DNA binding. In addition, the protein is classified under the Immunoglobulin-like fold superfamily, which comprises domains characterized by a beta-sandwich of seven or more strands arranged in a Greek-key topology, facilitating protein-protein interactions often via beta-sheet interfaces. These domains are ubiquitous in animal proteins, playing critical roles in immune recognition, cell adhesion, and structural integrity in muscle proteins such as titin. It is identified in Haptolina brevifila.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 14892, 3418, 1988, 24032, 1925, 11837, 17, 3189, 3728, 1930, 4088, 1922, 2321, 2024, 3154, 4086, 16, 2427, 1966, 2130, 1930, 25851, 16, 1942, 2285, 2024, 9182, 1930, 9254, 16, 1930, 1922, 4776, 3213, 2790, 1942, 8265, 2678, 2743, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 11837, 17, 3189, 3728, 13975, 16, 2154, 12936, 4682, 4378, 2007, 43, 4666, 17, 18038, 1927, 5260, 2014, 2253, 13214, 14940, 1922, 43, 27568, 17, 3834, 13678, 16, 12440, 2213, 17, 2213, 3719, 3868, 3454, 4666, 17, 11130, 14857, 18, 2144, 4682, 2032, 15498, 1922, 4027, 2697, 16, 14797, 4140, 5456, 1922, 3743, 5708, 16, 2024, 6141, 16, 1930, 4346, 7996, 1922, 3760, 2697, 2427, 1966, 7090, 1921, 18, 2176, 1977, 2899, 1922, 29683, 8261, 1019, 3022, 2165, 6870, 1019, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "FGNLSMVNATFLNESALRCVSPPNLYAVGRQHNATLVVSSIYPQAGPKTGGNTITVYGCDAIPSNETASEMLYGPERTEGSLSRGQSKMVGDSRVHGYLLRVDASEPLTPLLDDYVEEDARVGTALICELPAVSVCLEVTLNGNRSQATTDCVEFTFYDTFEDYSVDITLNGEENFLTNSKVPFVYYDSGFRVLGGSLLRACSEPLIDGTNRGLQCLFGNMPAVLPDYVPESYVPGQDQRQLLPGSP", "metadata": {"id": "A0A7S2G4N4", "cluster": 22112657, "interpro_all": ["IPR013783", "IPR002909"], "interpro_used": ["IPR002909", "IPR013783"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to create: The protein belongs to the Uncharacterised conserved protein UCP033563 family, which comprises a group of proteins with no currently defined function or experimental characterization. It has been characterized in Gemmiger sp. An194. Please provide the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 7762, 30, 1920, 2213, 14440, 1942, 1920, 23229, 3495, 5305, 2213, 8577, 1034, 12962, 5798, 7576, 3416, 16, 2154, 12936, 43, 2210, 1927, 2697, 1956, 2239, 5077, 3608, 2347, 2014, 3599, 7285, 18, 2176, 2258, 2252, 4378, 1922, 10607, 7395, 4938, 2056, 18, 1925, 27675, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MSQPCFCPGELLLPGEPVAVERWACPSAGALSRESWQELEARGENAPGVMRLLVPDALLQRVETGEKLAAAKAAMERAGDTLTRAVQGVVYLERTLPDGRVRRGLVGLVDLEQYDFAQGSRTPVRAPQALAARQVLPRLDRWEDAALQSSHILLAADKSEAELFAPLANIQKEAPLYEGELSYGGGSVKGWAVEDTARLNVLTALFDAEKAPEGAALLAPVSGWEDLAAARAFWMLLREELDQAGREHHPARFCLAEVCSIQSPGLHLAPAHRLVMGVQGLPLLAAFRTWCAGQGVRLEDEPAPESLRPLCFVYGAWQRKVWPTGGRWPLAAAVLEAFLQDYLQENPACFTDRISDETELRELAADGNTGILLSETNEDLFRGLCGGEFLPLGLFASLEARQQRYELECRRIR", "metadata": {"id": "A0A1Y4IXX1", "cluster": 23942509, "interpro_all": ["IPR008323"], "interpro_used": ["IPR008323"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein possesses a MacB-like periplasmic core domain that serves as the periplasmic structural component in various ABC transporters. It shares structural similarity with the AcrB multidrug efflux transporter, contributing to the assembly and function of efflux systems within the periplasm. It has been detected in Gemmatirosa kalamazoonensis and exhibits UniProt keyword tags Transmembrane helix, Transmembrane, and Plasmid.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 3433, 1014, 17, 3189, 24334, 4728, 3418, 1988, 10634, 1966, 1920, 24334, 4346, 4594, 1922, 3425, 7219, 10538, 18, 2176, 16495, 4346, 6796, 1956, 1920, 10428, 1014, 16398, 11247, 9054, 16, 8739, 1942, 1920, 5957, 1930, 2347, 1927, 11247, 3771, 2651, 1920, 20171, 18, 2176, 2258, 2252, 3330, 1922, 10607, 3368, 14365, 5360, 17338, 10671, 13642, 2290, 3355, 1937, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 7864, 16, 9117, 16, 1930, 5609, 18, 3], "output": "MNRKLLRDVWRLRGQVLSIAALVSCGASATRAPDALAARIAAIPGVATVPGLALPAGGLLLSVPEQGEPALDGFAEANHLQVGDSLGAVLDGRWRRLRVVGLAIAPSSRGSSPPRWTPRRGCAARSTTWRSHWPRARAVTRVATVVAMYGSMRAIARARDDFYARYRFADVFETRATLRVSLDVVHVVRGRMVRPRSTDEVVLGAGARSRWTRARSACCGCRALP", "metadata": {"id": "W0RNL1", "cluster": 25287857, "interpro_all": ["IPR025857"], "interpro_used": ["IPR025857"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein should feature a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. In addition, the protein belongs to the GHMP kinase, C-terminal domain superfamily, which encompasses the C-terminal structural component of ATP-dependent enzymes involved in amino acid, isoprene, and carbohydrate metabolism. This domain adopts a central alpha-beta plait fold that cooperates with the N-terminal domain to create a nucleotide-binding pocket. While primarily found in homoserine, galacto-, and mevalonate kinases, it is also present in structurally related diphosphomevalonate decarboxylases. Also, the protein belongs to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is found in Roseimicrobium gellanilyticum and carries UniProt keyword assignments Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 21569, 1920, 45, 17, 4262, 4346, 4594, 1927, 4498, 17, 3100, 5038, 3286, 1922, 3835, 2687, 16, 26690, 1021, 16, 1930, 10590, 4714, 18, 2052, 3418, 24032, 43, 4101, 4595, 17, 4666, 5606, 1932, 3728, 1988, 23230, 1036, 1956, 1920, 56, 17, 4262, 3418, 1942, 7762, 43, 5489, 17, 2743, 10154, 18, 2679, 5985, 2435, 1922, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 16, 2176, 1977, 2222, 2481, 1922, 12171, 2712, 11791, 2609, 2225, 4701, 8870, 23922, 1036, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 2435, 1922, 13679, 1980, 1935, 15129, 2457, 4669, 17576, 2869, 2002, 1989, 1930, 16252, 20709, 11121, 2538, 18306, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MSLPPLKLSSPAKVNLSLRVLGKRDEVTVTLKGSGETVLTCSDPTIPTNESNLALKALHAFEQRLGSTSSVLLAANELSGTPFSTSELSAIAAEIGSDVPFFLHRHFPWRLPLVLLKPPFGIPTPWAYKRWKEWGEMVNDLERPVFEKWTMLPTLKTWLLDQPETQAALMAERARTLCGETTHVFVAETLEDGFHTVETRMCPISLAWDIHLEKRVPHGAGLGGGSSNAATKPCDATGRGEVVTPVESKELPGVTYAAQLCASGSGSTVFAVTRSAADAGLL", "metadata": {"id": "A0A366HQ91", "cluster": 26730892, "interpro_all": ["IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR036554", "IPR004424"], "interpro_unused": ["IPR020568", "IPR014721"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: It is part of the RdgB/HAM1 family, which functions as a group of purine NTP pyrophosphatases that sanitize the cellular nucleotide pool by hydrolyzing non-canonical nucleotides, such as dITP, ITP, and XTP, into their corresponding monophosphates. This homodimeric enzyme prevents the incorporation of mutagenic bases into nucleic acids and may also exhibit dihydroneopterin triphosphate diphosphatase activity involved in tetrahydrofolate biosynthesis. Also, the protein falls within the Inosine triphosphate pyrophosphatase-like superfamily, which functions to sanitize the cellular nucleotide pool by hydrolyzing non-canonical purine nucleotides. Members of this family, including Ham1, YjjX, and Maf, exhibit phosphatase or pyrophosphatase activity against substrates such as inosine triphosphate (ITP), xanthosine triphosphate (XTP), and modified derivatives, converting them into their respective mono- or diphosphates. It has been detected in Trichuris trichiura (Whipworm) (Trichocephalus trichiurus) and is linked to UniProt keywords Cytoplasm, Metal-binding, and Hydrolase.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 2176, 1977, 3131, 1927, 1920, 8695, 22297, 19, 8616, 1009, 3416, 16, 2154, 4088, 1966, 43, 2210, 1927, 19700, 29676, 20661, 2609, 18135, 1988, 6867, 2078, 6931, 1920, 3689, 5489, 5562, 2007, 7222, 9046, 2447, 17, 9452, 9519, 16, 2427, 1966, 2137, 17475, 16, 27957, 16, 1930, 23068, 1034, 16, 2460, 2310, 3980, 21363, 1036, 18, 2052, 21189, 1935, 4113, 10299, 1920, 8629, 1927, 21977, 11137, 2460, 11079, 4576, 1930, 2278, 2222, 5987, 11842, 2912, 13798, 1921, 17978, 11791, 2609, 7234, 2455, 3286, 1922, 21196, 27851, 8132, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 10320, 2053, 17978, 20661, 2609, 7234, 17, 3189, 13975, 16, 2154, 4088, 1942, 6867, 2078, 6931, 1920, 3689, 5489, 5562, 2007, 7222, 9046, 2447, 17, 9452, 19700, 9519, 18, 4678, 1927, 2052, 3416, 16, 2710, 8616, 1009, 16, 67, 1013, 1013, 1039, 16, 1930, 16466, 16, 5987, 8167, 2014, 20661, 2609, 7234, 2455, 3316, 6249, 2427, 1966, 10320, 2053, 17978, 12, 27957, 13, 16, 15213, 7506, 17978, 12, 23068, 1034, 13, 16, 1930, 4795, 8383, 16, 15025, 3581, 2460, 2310, 7025, 8914, 17, 2014, 23266, 1036, 18, 2176, 2258, 2252, 3330, 1922, 10477, 18330, 1036, 10477, 1033, 9280, 12, 2003, 2049, 16620, 13, 12, 10477, 1994, 2128, 7289, 1957, 10477, 1033, 19756, 13, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 16, 6048, 17, 2743, 16, 1930, 20748, 18, 3], "output": "MCCYPLATIHHSQINDPFLYEMDVHFVNNIVLQVRRKCVTAAEIVQPVIVEDTCLCFNALGGLPGPYVKSAYALCTYAYKDESSNQVHLIQGKVAGTIVKPRGTSNFGWDACFQPALQKLSEFLRLLYPPDLVKYIDLPEYQGQPEDVAKWFLKAVGPEGLYKMLNAWEDDGHELTYAEMSSEEKRTISHRAQ", "metadata": {"id": "A0A077ZJ27", "cluster": 18345888, "interpro_all": ["IPR027502", "IPR029001", "IPR002637"], "interpro_used": ["IPR002637", "IPR029001"], "interpro_unused": ["IPR027502"]}, "task_type": "infilling"} {"instruction": "The protein incorporates a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein is grouped in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein incorporates a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is expressed in bioreactor metagenome and is connected to UniProt keyword Transferase. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 19683, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 3198, 1922, 25650, 16552, 2225, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 13763, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MEFIKVRTPAKLNLALEVLGLREDGYHEVATVMQTISIYDDIKISRREEGGITLTSSLPFLPLDGRNLAARAASAFFEAAGFSSGIEIEISKRIPVGAGMAGGSANAAGVLTGLNELFGVGFSIDEMTEIGRPLGADVAFCLRRGTYLATGIGDVLTKVTDMPTCTMVVAKPRYSISTPELYRSFDSFSPAPHPDISGLIAALPVGIEQAAPLMVNMLEPVACAQIPQIAEMTQDLKKAGAVTALMTGSGSAVFGIFLRSRQAMICTEAMRKKHSRCFVSPAHPVRE", "metadata": {"id": "A0A645AI18", "cluster": 3801919, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR004424", "IPR013750"], "interpro_unused": ["IPR014721", "IPR036554", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein is assigned to the Serine/Threonine Proteases with Immune and Developmental Roles family, which comprises serine and threonine proteases that function primarily in invertebrate immune defense and developmental morphogenesis. These proteins facilitate the melanization-mediated response by activating the prophenoloxidase cascade or contribute to processes like germ-band retraction, often utilizing a clip domain for regulation or acting as catalytically inactive scaffolds. Moreover, the protein should contain a trypsin-like serine protease domain that functions as the catalytic core for family S1 peptidases, utilizing a conserved Asp-His-Ser triad to hydrolyze peptide bonds. This domain drives diverse physiological processes ranging from digestion and tissue remodeling to blood coagulation and immune response, appearing in enzymes such as thrombin, elastase, and complement factors. Also, the protein is included in the Peptidase S1 (PA clan) chymotrypsin-like fold superfamily, which encompasses a diverse range of serine and cysteine proteases found in viruses, prokaryotes, and eukaryotes. These enzymes are structurally characterized by two six-stranded antiparallel beta-barrels that form a central cleft housing the catalytic machinery responsible for proteolytic activity. It is produced by Biomphalaria glabrata (Bloodfluke planorb) (Freshwater snail) and is classified with UniProt keywords Signal.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 8468, 19, 13143, 12447, 1956, 3743, 1930, 5878, 5456, 3416, 16, 2154, 12936, 8468, 1930, 13143, 12447, 1988, 2347, 5985, 1922, 26381, 3743, 9720, 1930, 5878, 15328, 18, 2144, 2697, 6628, 1920, 5313, 2466, 17, 3434, 2644, 2007, 8019, 1920, 8839, 9356, 19883, 9861, 2014, 4672, 1942, 4028, 3189, 4363, 17, 5472, 20629, 16, 3868, 10232, 43, 18709, 3418, 1958, 3640, 2014, 8290, 1966, 21446, 9078, 10603, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 9527, 17, 3189, 8468, 7154, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 3416, 4062, 24050, 1036, 16, 10232, 43, 5305, 4138, 17, 4167, 17, 2375, 21845, 1942, 7222, 6931, 4207, 9031, 18, 2052, 3418, 15435, 6445, 5005, 4028, 6485, 2037, 9379, 1930, 2960, 8378, 1942, 2877, 12441, 1930, 3743, 2644, 16, 16905, 1922, 5038, 2427, 1966, 12388, 16, 23296, 16, 1930, 5508, 2790, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 24050, 4062, 12, 3838, 6958, 1022, 13, 27799, 17, 3189, 3728, 13975, 16, 2154, 21569, 43, 6445, 3109, 1927, 8468, 1930, 8666, 12447, 2435, 1922, 6241, 16, 28149, 16, 1930, 15021, 18, 2144, 5038, 2032, 12171, 4378, 2007, 2288, 3798, 17, 10338, 28892, 4666, 17, 19560, 1036, 1988, 2386, 43, 4101, 14649, 13178, 1920, 6804, 10853, 5061, 1958, 12712, 2455, 18, 2176, 1977, 4152, 2007, 4071, 6256, 6148, 29866, 12, 2877, 5842, 3324, 4720, 4174, 13, 12, 18762, 15929, 13, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 3], "output": "MNAFISTSFHIFIILGIVNSEQEPDGPLFPSQVEVSVWYSHFNLWYIFCNGVLIALNKVVAPANCLKYHLPKDVRVSLGKVNKTHQQIIYVSRVDKHEDFQWYEWPNDIAIVTLSTPAKLDKNVQVAKLAVNSSIYVETSCMTYGWSGSRVEQVSKTLLSKNECIERSYKDLQYPLSSGLIICVLNRKGDNSAPCMGNLGTPLLCGPNKDTLVGIAKMMGVYCKAGQPSLYTDVTRYRAWILQRM", "metadata": {"id": "A0A9W3AAF4", "cluster": 4481727, "interpro_all": ["IPR009003", "IPR043504", "IPR051487", "IPR001254"], "interpro_used": ["IPR051487", "IPR001254", "IPR043504"], "interpro_unused": ["IPR009003"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein belongs to the HTH-type, TetR-like transcriptional regulator family, which comprises predominantly bacterial DNA-binding proteins that utilize a helix-turn-helix (HTH) motif to repress gene expression. These regulators control diverse physiological processes ranging from antibiotic resistance and lipid metabolism to osmotic stress response and cell division, as exemplified by the nucleoid occlusion factor SlmA. Moreover, the protein should contain a TetR-type DNA-binding HTH domain that functions as a transcriptional regulator in bacteria and archaea, typically acting as a homodimeric repressor to control susceptibility to hydrophobic antibiotics and detergents. It structurally comprises an N-terminal helix-turn-helix motif with an inverse orientation to facilitate DNA binding. In addition, the protein can be placed in the Homeodomain-like superfamily, which comprises transcription factors and DNA-binding proteins that utilize a conserved helix-turn-helix (HTH) motif to interact with the DNA major groove. These proteins are ubiquitous across all domains of life and play critical roles in gene regulation through specific hydrogen bonding and hydrophobic contacts. It is produced by Natranaeroarchaeum sulfidigenes and is associated with UniProt keywords Transcription regulation. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 14440, 1942, 1920, 5334, 1023, 17, 2601, 16, 5575, 17, 3189, 5224, 7888, 3416, 16, 2154, 12936, 7700, 4543, 2678, 17, 2743, 2697, 1988, 12561, 43, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 9055, 2359, 2294, 18, 2144, 9098, 2285, 6445, 5005, 4028, 6485, 2037, 7267, 3554, 1930, 4486, 4714, 1942, 13951, 3071, 2644, 1930, 2024, 8451, 16, 1966, 22236, 2007, 1920, 2797, 2642, 10543, 2991, 2788, 3368, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 5575, 17, 2601, 2678, 17, 2743, 5334, 1023, 3418, 1988, 4088, 1966, 43, 5224, 7888, 1922, 4802, 1930, 21501, 16, 5745, 8290, 1966, 43, 21189, 1935, 14434, 1942, 2285, 6461, 1942, 7919, 7560, 1930, 15814, 1036, 18, 2176, 12171, 12936, 1925, 56, 17, 4262, 7864, 17, 5165, 17, 7864, 5219, 1956, 1925, 9526, 7148, 1942, 6628, 2678, 2743, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4502, 17166, 17, 3189, 13975, 16, 2154, 12936, 3213, 2790, 1930, 2678, 17, 2743, 2697, 1988, 12561, 43, 5305, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 6310, 1956, 1920, 2678, 3044, 15920, 18, 2144, 2697, 2032, 15498, 3436, 2136, 4682, 1927, 3308, 1930, 3918, 4140, 5456, 1922, 2359, 3640, 2596, 2487, 6201, 11463, 1930, 7919, 9070, 18, 2176, 1977, 4152, 2007, 3898, 17182, 29164, 12729, 25588, 3708, 1035, 5141, 13756, 14687, 1036, 1930, 1977, 2458, 1956, 20709, 11569, 3213, 3640, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MGDKTTEEEILEAAGIVLGAEGYNGFTTEKVAERADVSQSLVHYYFETKEDLVRALFEWGGKNVEEAVEDRVDSDDPRERLVEWTDYMIMGGGEFEEVVEVNRVLLELRSLAVRNDWARDIVRGEREGLEAFVADAVADGIERGQFRDVDVESFAAAYASGIEASQDLTAVFADPEAVTAVHDGLINLVDEYLLVNDSA", "metadata": {"id": "A0A897MM04", "cluster": 4587227, "interpro_all": ["IPR009057", "IPR050109", "IPR001647", "IPR036271"], "interpro_used": ["IPR050109", "IPR001647", "IPR009057"], "interpro_unused": ["IPR036271"]}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein is associated with the Nucleotide cyclase superfamily, which encompasses catalytic domains found in adenylyl, guanylyl, and diguanylate cyclases responsible for synthesizing cyclic nucleotide second messengers. These domains share a core ferredoxin-like fold, though the specific nucleotide-binding mode differs between subtypes such as the GGDEF domain and adenylate cyclases. Also, the protein includes a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. In addition, the protein features a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. It is found in Lynx pardinus (Iberian lynx) (Felis pardina) and is classified with UniProt keywords cAMP biosynthesis, Lyase, and Metal-binding.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 1977, 2458, 1956, 1920, 5489, 16526, 13975, 16, 2154, 21569, 6804, 4682, 2435, 1922, 27802, 16, 13504, 25671, 16, 1930, 4325, 13785, 9075, 16526, 1036, 5061, 1958, 25292, 9821, 5489, 2812, 16716, 1036, 18, 2144, 4682, 7948, 43, 4728, 25304, 22389, 10960, 17, 3189, 3728, 16, 4170, 1920, 2487, 5489, 17, 2743, 5754, 11457, 2192, 8160, 2427, 1966, 1920, 12358, 3695, 1038, 3418, 1930, 23052, 16526, 1036, 18, 2222, 16, 1920, 2213, 5921, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 2176, 1977, 2435, 1922, 16722, 1039, 2096, 22816, 1957, 12, 6180, 18339, 1022, 16722, 1039, 13, 12, 19056, 1937, 2096, 22816, 1019, 13, 1930, 1977, 5947, 1956, 20709, 11569, 6225, 8132, 16, 23928, 16, 1930, 6048, 17, 2743, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MSLLPRNVAMEMKEDFLKPPERIFHKITGLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGDCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGAAGLPGKVHITKTTLACLNGDYEVEPGHGHERNSFLKAHNILILSDIKPAKRMKFKTVCYLLVQLMHCRKMFKAEKLRNRSSFSANAVYTTPGTRVNRYIGRLLEARQTELEMADLDFFTSAVVLALVLAALFGLVYLLIIPQNLVLLLLLAFCICFPGCLTIQIRTVLCIFVVVLIYSVAQGCVVGCLPWSWSSTPLPAAPCESAPHALLCGLVGTLPLAVFLRVSGGGVASGRSFEPIMAILLFSCTLALHARQVDVKLRLDYLWLLPAHVAQHFLMSNPRNMDLYYQSYSQVGVMFASIPNFDDFYIELDGNDFYKDLEKIKTIGSTYMAAVGLAPTTGTKCRAVNNVFRLPLKKYIQRHDNVSILFADIVGFYYCVSGLTQPKTDHAHCCLRKWQYDVWSNDVTLANVMEETFFIVPSHRRKIFPGIPFSNVLTCEDDDKRRALRTASEFTLKYKQAERERKYHQLQDEYCFLVACVLYLHVTRVQNGSLVVLTPSGRNAVSLPKMILLFVLTTSYILVLELSGYTRAPAAQAEEERDDMERVKLDNKRILFNNMGVECLRLLNEIIADFDELMDK", "metadata": {"id": "A0A485MTA2", "cluster": 6098206, "interpro_all": ["IPR001054", "IPR018297", "IPR029787"], "interpro_used": ["IPR029787", "IPR001054", "IPR018297"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein incorporates a Alpha crystallin/Hsp20 domain that functions as a molecular chaperone to prevent heat-induced protein denaturation and aggregation. This conserved C-terminal region facilitates the formation of large heterooligomeric complexes and is found in both stress-induced heat-shock proteins and vertebrate eye lens crystallins, where it maintains transparency. In addition, the protein is grouped in the HSP20-like chaperone superfamily, which represents small heat-shock proteins characterized by a $\\beta$-sandwich fold with a Greek-key topology. These proteins typically function as molecular chaperones and tend to form dimers, with mammalian members being particularly abundant in skeletal muscle and heart tissue. It is produced by Deltaproteobacteria bacterium.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 19683, 43, 4595, 24572, 19, 6418, 3520, 3418, 1988, 4088, 1966, 43, 3272, 14044, 1942, 4625, 5631, 17, 2719, 2213, 14299, 1930, 7883, 18, 2052, 5305, 45, 17, 4262, 3031, 11374, 1920, 3337, 1927, 3103, 19732, 8436, 3827, 9213, 1935, 5048, 1930, 1977, 2435, 1922, 2321, 3071, 17, 2719, 5631, 17, 7418, 2697, 1930, 13416, 5723, 8540, 24572, 1036, 16, 2597, 2176, 16566, 20817, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 6418, 3520, 17, 3189, 14044, 13975, 16, 2154, 4972, 2858, 5631, 17, 7418, 2697, 4378, 2007, 43, 8, 38, 4666, 8, 17, 18038, 3728, 1956, 43, 27568, 17, 3834, 13678, 18, 2144, 2697, 5745, 2347, 1966, 3272, 18098, 1930, 5370, 1942, 2386, 13351, 16, 1956, 6492, 4678, 3301, 4443, 7437, 1922, 7345, 3760, 1930, 4003, 2960, 18, 2176, 1977, 4152, 2007, 9649, 9218, 1021, 10296, 14061, 18, 3], "output": "MQPPSVSVSTTFTGRRMGNHSRSAVKCRGTELPGAGGLDSRLVVIIFRAENKRPREGEQWDRQRGVLRPFGEVNAMLRRWFSDDLVQKMEQMQKEMNDFLQTFRPFSERAMPWASFGGVFPAINIYDNGEGYVARAELPGVDPKDVEVTVTGNTLNIKGKREIPDAGEKVAYHRRERAAGQFNRAFRLPDAVDSAKVEARFTNGILEVMLPKAEQAKQRKVQIKTE", "metadata": {"id": "A0A3M1D0L0", "cluster": 9136032, "interpro_all": ["IPR002068", "IPR008978", "IPR031107"], "interpro_used": ["IPR002068", "IPR008978"], "interpro_unused": ["IPR031107"]}, "task_type": "autoregressive"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein features a Archaeal flagellin/pilin N-terminal conserved site that serves as a hydrophobic recognition motif for potential cleavage and methylation. Analogous to bacterial type IV pilin domains, it contains a G^FxxxE-like cleavage pattern followed by a hydrophobic sequence, facilitating the processing and assembly of flagella and pili. It is present in Candidatus Aenigmatarchaeota archaeon.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 22367, 27389, 19, 7547, 1921, 56, 17, 4262, 5305, 3200, 1988, 10634, 1966, 43, 7919, 5708, 5219, 1958, 2889, 6404, 1930, 5547, 18, 12464, 1942, 4543, 2601, 4370, 7547, 1921, 4682, 16, 2176, 5461, 43, 49, 40, 13946, 14710, 1021, 17, 3189, 6404, 3114, 3489, 2007, 43, 7919, 3244, 16, 12440, 1920, 4587, 1930, 5957, 1927, 26538, 1930, 7547, 1033, 18, 2176, 1977, 2481, 1922, 14550, 1031, 1957, 10194, 8635, 22579, 3857, 15618, 20051, 7336, 13470, 1916, 18, 3], "output": "MKGISPIIASVLLIAITMSIAVVLAAYVTSYTREATEAIPSACIGGALFVEGTPDCTGTTLTVVLRAEYVELSSFTADTRDSAGDVIQTGLTMSPSSSILPGQIGTYTATVTDCTSVSDFRITTNCFNIYTGWTAV", "metadata": {"id": "A0A846PRC5", "cluster": 10694854, "interpro_all": ["IPR013373"], "interpro_used": ["IPR013373"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Moreover, it is part of the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It has been characterized in Planctomycetaceae bacterium and has UniProt annotations Cytoplasm and rRNA processing. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 2258, 2252, 4378, 1922, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 1930, 2258, 20709, 15010, 5239, 1930, 9067, 4587, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MSGKPGDQKRPVHLPVLLREVITQLDLSLGLIVVDGTVGAGGHSEHILQKINNEGTLIGLDRDAMMLGFATQKLKPESLPAGRCYLRQSSYAELPAVMEELQIESVDRVLLDLGLSSDQLGDDERGFGFESAGELDLRFDTRTGVPAWQLLESLSESELCEILEVYGEERFSQRIASQIVKQRKAAPVRTAVDLIKVVQQAIPGKALAAARKNPATRVFQALRIAANQELEQLETMLETVLPQVLRSGGRAAIISFHSLEDRMVKQAFKNQKVWKNLTAKPIVATQAEQRVNPRCRTAKLRVAVKT", "metadata": {"id": "A0A954K912", "cluster": 10834465, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein features a ABC transporter-like, ATP-binding domain that utilizes the energy from ATP hydrolysis to power the transmembrane transport of diverse substrates, ranging from ions to macromolecules. It features conserved Walker A and B motifs, a Q-loop, and a signature sequence that form the nucleotide-binding site, typically functioning within a dimer. This module interacts with transmembrane domains to couple ATP-driven conformational changes to the import of nutrients or the export of toxins and membrane components. Moreover, the protein is a member of the The ATP-binding cassette transporter C-like family, which actively extrudes physiological compounds and xenobiotics across cell membranes to facilitate cellular detoxification and multidrug resistance. These transporters handle a broad spectrum of substrates, such as glutathione conjugates, cyclic nucleotides, and drugs, while also regulating epithelial ion and water transport to maintain fluid homeostasis. It is produced by Myxobolus squamalis (Myxosporean) and is described by UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 4075, 43, 7219, 9054, 17, 3189, 16, 4498, 17, 2743, 3418, 1988, 18127, 1920, 3844, 2037, 4498, 9128, 1942, 4215, 1920, 9117, 4860, 1927, 6445, 6249, 16, 6485, 2037, 6982, 1942, 20625, 18, 2176, 4075, 5305, 20138, 43, 1930, 44, 8277, 16, 43, 59, 17, 5881, 16, 1930, 43, 9983, 3244, 1988, 2386, 1920, 5489, 17, 2743, 3200, 16, 5745, 7295, 2651, 43, 7632, 18, 2052, 9059, 9034, 1956, 9117, 4682, 1942, 15116, 4498, 17, 6446, 8523, 2840, 1942, 1920, 2582, 1927, 11312, 2014, 1920, 12660, 1927, 13599, 1930, 3260, 4178, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 1920, 4498, 17, 2743, 12992, 9054, 45, 17, 3189, 3416, 16, 2154, 11182, 2821, 7775, 5005, 4300, 1930, 29821, 1036, 3436, 2024, 5726, 1942, 6628, 3689, 18169, 1930, 16398, 3554, 18, 2144, 10538, 17090, 43, 4949, 5648, 1927, 6249, 16, 2427, 1966, 9153, 14749, 16, 9821, 9519, 16, 1930, 4195, 16, 2679, 2222, 6773, 4944, 4755, 1930, 3224, 4860, 1942, 6698, 5466, 7622, 18, 2176, 1977, 4152, 2007, 21464, 2389, 19574, 4687, 10671, 12191, 1036, 12, 21464, 9890, 5376, 1022, 13, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 7864, 18, 3], "output": "NYIRSAYSMIYVFAAFNTILNVVGFLGLGITYSLTISATLFGFLTSFIELEKNMGDISFNDVKLNYHDSIDVFPKGLNLKIKRGTKIGICGRITIDDIDIKELHGNLSLTNILLNLLDLRCFMQVVLMVSSLLSLYYLKNHSQFVIHAENIIIYLNQLKKDQDRFNPIETSRFFLNTGSGKSSLVKLLFQIVSPTIGT", "metadata": {"id": "A0A6B2FZZ1", "cluster": 15151779, "interpro_all": ["IPR036640", "IPR003439", "IPR050173", "IPR027417"], "interpro_used": ["IPR027417", "IPR003439", "IPR050173"], "interpro_unused": ["IPR036640"]}, "task_type": "infilling"} {"instruction": "Function:\nThe protein incorporates a Adenylate cyclase, N-terminal domain that comprises the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase. It has been characterized in Chiloscyllium punctatum (Brownbanded bambooshark) (Hemiscyllium punctatum) and exhibits UniProt keyword tags Transmembrane helix.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 19683, 43, 23052, 16526, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 56, 17, 4262, 5329, 3031, 1930, 1920, 2561, 9117, 25, 17, 26, 4675, 3031, 1927, 23052, 16526, 18, 2176, 2258, 2252, 4378, 1922, 7368, 6012, 12709, 10196, 2457, 18636, 1031, 1989, 12, 8084, 13879, 1919, 12202, 4627, 13935, 2566, 13, 12, 28881, 12709, 10196, 2457, 18636, 1031, 1989, 13, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 7864, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MSRANSVSPPGAGSAPAGGNEHRAAWTEGEVGTLQSREEDEEDGQRQLPGKSSRLSFRSKSAWQEQLDREGGSASRNSVLRARHQFRLDGSKLADIDSSASDVDISFADCCHRLFRIFQSKKFQSEKLERLYQRYFFRLNQSSLTMLMGVLLVVLAVTIVLVLTLMVVCNRNGFHQDHMWIICYLLILVILAVYIIYTLLPVRMRAAVISGILLSALHLGISWQRNLVDPFLWKQVRLANGISIPSGRARDKRWKGEEVRPKSVEVGLEEGAMVLVCAVLLAFHCVQGSYELPYEIIGLLLVEPRSASEGIWWTIFFI", "metadata": {"id": "A0A401SRY3", "cluster": 18468381, "interpro_all": ["IPR032628"], "interpro_used": ["IPR032628"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein should feature a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Furthermore, the protein carries a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. Also, the protein should feature a Adenylate cyclase, N-terminal domain that comprises the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase. It is produced by Pan troglodytes (Chimpanzee) and carries UniProt keyword assignments Magnesium, ATP-binding, and Lyase.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 3066, 5961, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 3677, 16, 1920, 2213, 16252, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 23052, 16526, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 56, 17, 4262, 5329, 3031, 1930, 1920, 2561, 9117, 25, 17, 26, 4675, 3031, 1927, 23052, 16526, 18, 2176, 1977, 4152, 2007, 3797, 12730, 4365, 2756, 14652, 12, 27534, 13, 1930, 16252, 20709, 11121, 2538, 18306, 13148, 16, 4498, 17, 2743, 16, 1930, 23928, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MYGVFVRILTERSQRKAFLQRLLMSLLPRNVAMEMKEDFLKPPERIFHASQCTAQELVKLLNELFGKFDELATEYYCVSGLTQPKTDHAHCCVEMGLMRVGLHTGRVLCGVLGLRKWQYDVWSNDVTTTLACLNGDYEVEPGYGHERNSFLKTHNIETFFIVPSHRRFKTVCYLLVQLMHCRKMFKAEIPFSNGLDVLLGVWSPTLQRGRLCTARSCIEDRLRLEDENEKQEKIYIQRHDNVSILFADIVGFTGLNHCRRIKILGDCDMIDTITSVAEATEVDLNLANVMEAAGLPGKVHITKKIFPGLILSDIKPAKRMKVMTCEDDDKVQIHPSLS", "metadata": {"id": "A0A6D2WC61", "cluster": 19365977, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR029787"], "interpro_used": ["IPR018297", "IPR001054", "IPR032628"], "interpro_unused": ["IPR029787"]}, "task_type": "infilling"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: It is part of the Ribosomal protein uS5 domain 2-type superfamily, which encompasses proteins sharing a distinctive $\\alpha/\\beta$ fold often utilized for nucleotide binding and processing. This domain is integral to translational machinery, RNA processing complexes, and DNA repair enzymes, while also forming the core structure of GHMP kinases and Hsp90 chaperones. Moreover, the protein features a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Moreover, the protein is categorized in the Small ribosomal subunit protein uS5 domain 2-type fold superfamily, which features a left-handed \u03b2-\u03b1-\u03b2 structure utilized in diverse nucleic acid-binding proteins and GHMP family kinases. This domain serves as a key component in translational machinery and DNA repair enzymes, such as MutL and DNA gyrase B, while also facilitating ATP-dependent phosphoryl transfer in metabolic enzymes like galactokinase and mevalonate kinase. It is derived from Verrucomicrobiaceae bacterium and corresponds to UniProt keyword Transferase. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 1925, 3835, 2687, 3244, 1988, 2469, 16318, 2460, 43, 2213, 22665, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 11196, 2213, 2022, 1015, 3418, 22, 17, 2601, 13975, 16, 2154, 21569, 2697, 10763, 43, 15308, 8, 38, 4595, 19, 38, 4666, 8, 3728, 3868, 7079, 1958, 5489, 2743, 1930, 4587, 18, 2052, 3418, 1977, 12328, 1942, 8414, 10853, 16, 3146, 4587, 5048, 16, 1930, 2678, 5059, 5038, 16, 2679, 2222, 7402, 1920, 4728, 3170, 1927, 6101, 6588, 7784, 1930, 12254, 18098, 18, 3950, 16, 1920, 2213, 4075, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 2858, 11196, 5903, 2213, 2022, 1015, 3418, 22, 17, 2601, 3728, 13975, 16, 2154, 4075, 43, 3506, 17, 17105, 161, 17, 160, 17, 161, 3170, 7079, 1922, 6445, 11079, 2687, 17, 2743, 2697, 1930, 6101, 6588, 3416, 7784, 18, 2052, 3418, 10634, 1966, 43, 3834, 4594, 1922, 8414, 10853, 1930, 2678, 5059, 5038, 16, 2427, 1966, 2446, 1024, 1930, 2678, 9430, 2051, 44, 16, 2679, 2222, 12440, 4498, 17, 3100, 12556, 3856, 1922, 4487, 5038, 3189, 9479, 18655, 1930, 21750, 20807, 5791, 1021, 4016, 18, 2176, 1977, 3595, 2037, 3566, 3176, 13055, 1935, 15129, 19476, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 13763, 18, 7031, 1920, 3244, 18, 3], "output": "MTTYSLNAPAKINLWLRVLGRREDGFHALETRLAPLTLCDRLTLRADAGLAPGNIGFECDDPTVPGNESNLVLKAVRALEKATGPLPGMRFSLTKRIPHGAGLGGGSSDAAAALRLVRAAFCPEAGDAVLFDAAAAVGSDVPFFLLGGMADASGRGEIVMPVPEAELG", "metadata": {"id": "A0A4Q2Y6X3", "cluster": 19543549, "interpro_all": ["IPR006204", "IPR020568", "IPR014721"], "interpro_used": ["IPR020568", "IPR006204", "IPR014721"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein is a member of the Zinc finger, RING/FYVE/PHD-type superfamily, which encompasses RING, PHD, FYVE, and U-box domains that share a common $\\alpha/\\beta$ structural fold, typically stabilized by zinc ions. These versatile motifs act as stable scaffolds to facilitate specific interactions with DNA, RNA, proteins, or lipids, thereby participating in diverse cellular processes ranging from gene transcription and chromatin remodelling to mRNA trafficking. Additionally, the protein includes a Zinc finger, RING-type domain that mediates protein-protein interactions and typically functions as an E3 ubiquitin-protein ligase. This motif coordinates two zinc ions in a \"cross-brace\" structure to bind E2 ubiquitin-conjugating enzymes, thereby facilitating substrate ubiquitylation. It has been detected in Amphimedon queenslandica (Sponge) and is associated with UniProt keywords Metal-binding and Zinc-finger. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 7997, 8497, 16, 6335, 19, 27976, 1961, 19, 13381, 17, 2601, 13975, 16, 2154, 21569, 6335, 16, 13381, 16, 27976, 1961, 16, 1930, 63, 17, 5758, 4682, 1988, 7948, 43, 3059, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3728, 16, 5745, 12017, 2007, 7997, 6982, 18, 2144, 20425, 8277, 4033, 1966, 4700, 10603, 1942, 6628, 2487, 3719, 1956, 2678, 16, 3146, 16, 2697, 16, 2014, 8238, 16, 6113, 9505, 1922, 6445, 3689, 4028, 6485, 2037, 2359, 3213, 1930, 6338, 19935, 1942, 3616, 9604, 18, 4950, 16, 1920, 2213, 5921, 43, 7997, 8497, 16, 6335, 17, 2601, 3418, 1988, 10412, 2213, 17, 2213, 3719, 1930, 5745, 4088, 1966, 1925, 10968, 6526, 17, 2213, 11905, 18, 2052, 5219, 10675, 2288, 7997, 6982, 1922, 43, 6, 3567, 17, 18303, 1972, 6, 3170, 1942, 4566, 6602, 6526, 17, 5225, 2287, 5038, 16, 6113, 12440, 4510, 24320, 18, 2176, 2258, 2252, 3330, 1922, 9141, 28840, 1916, 30144, 6102, 12, 19757, 13, 1930, 1977, 2458, 1956, 20709, 11569, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MEEDHEIEFIEQPPYDCNCPICLETFRDEVCQTTCCGNHICFECADRLKNTDTTCPICRNDNFNAIEDKFFTRMYLSLKVRCFFSKTGCLWTGELRQLQEHVKKSCPKKLETCDQLSKHVPVTNERAITFSNPSIEARFKKECSLNDKPSKGITAVAMNETSVVPLSFKMTDYSRHFETGKPWFSPPFHTHKE", "metadata": {"id": "A0A1X7VU37", "cluster": 22291157, "interpro_all": ["IPR001841", "IPR013083"], "interpro_used": ["IPR013083", "IPR001841"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a polypeptide chain with the following function: The protein possesses a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein should have a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein is a member of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is identified in Cyclobacteriaceae bacterium and contains UniProt keyword associations Isoprene biosynthesis and Transferase. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 2899, 1922, 17009, 7972, 2341, 18339, 1972, 3336, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 26690, 1021, 8132, 1930, 13763, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MVVFPNAKINLGLNIIEKRTDGYHNIESCFYPIPLTDALEVIESDKLSFTSSGIPIPGDPESNLCLKAYHLLKKHYDLPLVEIHLHKNIPIGAGLGGGSSDGAFMLKLLNEKFELGIDNPALEKLAGELGSDCPFFIENKPVFVEGKGNVFSPVEVSLKGKYLVLVMPDVHVSTAQAYAGITPQQPEAGLKEILEQKPMKRWQDLVKNDFEQSVFAKHPELERIKNQLIEEGAIYASMTGSGAAVFGVFEEKPILQLGGNWQIDIVKL", "metadata": {"id": "A0A959A367", "cluster": 23385455, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR014721", "IPR036554", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein has a Alanine racemase C-terminal domain that constitutes the beta-strand-rich structural component of the enzyme alanine racemase. This enzyme isomerizes L-alanine to D-alanine to provide essential precursors for bacterial cell wall biosynthesis. Furthermore, the protein should feature a Alanine racemase, N-terminal domain that forms an eight-stranded alpha/beta barrel structure to covalently bind the pyridoxal 5'-phosphate (PLP) cofactor. This domain facilitates the isomerization of L-alanine to D-alanine for bacterial cell wall biosynthesis and is structurally conserved in the PROSC family of proteins. In addition, the protein should contain a Alanine racemase pyridoxal-phosphate attachment binding site that covalently links the PLP cofactor to a conserved lysine residue via an aldimine bond. This interaction facilitates the catalytic conversion of L-alanine to D-alanine, which is required for bacterial cell wall formation. It is present in Deltaproteobacteria bacterium and is connected to UniProt keyword Isomerase and Pyridoxal phosphate.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 10504, 7442, 3368, 4127, 45, 17, 4262, 3418, 1988, 14879, 1920, 4666, 17, 5984, 17, 5536, 4346, 4594, 1927, 1920, 4113, 10504, 7442, 3368, 4127, 18, 2052, 4113, 15348, 4517, 54, 17, 10504, 1942, 46, 17, 10504, 1942, 3394, 4415, 10416, 1958, 4543, 2024, 4821, 8132, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 10504, 7442, 3368, 4127, 16, 56, 17, 4262, 3418, 1988, 4952, 1925, 5066, 17, 10338, 4595, 19, 4666, 19560, 3170, 1942, 16590, 4566, 1920, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 15155, 18, 2052, 3418, 11374, 1920, 27027, 1927, 54, 17, 10504, 1942, 46, 17, 10504, 1958, 4543, 2024, 4821, 8132, 1930, 1977, 12171, 5305, 1922, 1920, 8181, 1030, 3416, 1927, 2697, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 10504, 7442, 3368, 4127, 24828, 23859, 17, 5413, 8576, 2743, 3200, 1988, 16590, 10069, 1920, 21453, 15155, 1942, 43, 5305, 9082, 6181, 3454, 1925, 11174, 24906, 5403, 18, 2052, 2835, 11374, 1920, 6804, 7309, 1927, 54, 17, 10504, 1942, 46, 17, 10504, 16, 2154, 1977, 3414, 1958, 4543, 2024, 4821, 3337, 18, 2176, 1977, 2481, 1922, 9649, 9218, 1021, 10296, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 25510, 1930, 24828, 23859, 5413, 18, 3], "output": "MKSPDAANSFRPTRARIDLSAKANAYGHGAIHVARICEKEGAAALGVPFTAPGELLAEQGLTPVLYNEEQIRELQASTRLGVLPKMLPRILQTLEQAPRLLPTAEQYRRFAEAEALLKKWRYGANPHPRLQAGAALKPVMNFETKASRPSRIAVLPVGYADGYIRHLVVGRVCMDLTMLDVTDIPEAALGDPVLLSRVPRHYEGEEALRHNFRLAKTLAGPQVGLLAVVATPQEGLELRAAGLRAPILLFGGTTSRLEVQLKIDTGMLTGVLTHLAQADTDSGGPGIKVFQIANSAALLDGKIGACNWARPGILLIVSLKSVPAGTAVSYGGTWVSGVGQVRLRGKLAPWGETLSVETVAAQAGTISYELLCAVS", "metadata": {"id": "A0A3D4Z5I9", "cluster": 24301119, "interpro_all": ["IPR000821", "IPR009006", "IPR011079", "IPR001608", "IPR020622", "IPR029066"], "interpro_used": ["IPR011079", "IPR001608", "IPR020622"], "interpro_unused": ["IPR000821", "IPR029066", "IPR009006"]}, "task_type": "infilling"} {"instruction": "I want to design a protein that can perform the following function: It is part of the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Furthermore, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is derived from Thermotoga petrophila (strain ATCC BAA-488 / DSM 13995 / JCM 10881 / RKU-1) and is linked to UniProt keywords Cytoplasm, rRNA processing, and Transferase..", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 3595, 2037, 7967, 4575, 4223, 16901, 7766, 12, 3943, 11037, 6813, 1019, 17, 11541, 19, 10964, 13316, 8803, 19, 14904, 1035, 9123, 11425, 19, 21179, 1032, 17, 21, 13, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 16, 9067, 4587, 16, 1930, 13763, 18, 18, 3], "output": "MRKYSQRHIPVMVREVIEFLKPEDEKIILDCTVGEGGHSKAILEHCPGCRIIGIDVDSEVLRIAEEKLKEFSDRASLFKISYREADFLLKTLGVEKVDGILMDLGVSTYQLKGENRGFTFEREEPLDMRMDLESEVTAQKVLNELPEEELARIIFEYGEEKKFARRIARKIVENRPLNTTLDLVKAVREALPSYEIRRRKRHFATKTFQAIRIYVNRELENLKEFLRKAEDLLNPGGRIVVISFHSLEDRIVKETFRNSKKLRILTEKPVRPSEEEIRENPRARSGRLRAAERIEKGGD", "metadata": {"id": "A5IIR1", "cluster": 25520595, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein should contain a HD-GYP domain that functions in signal transduction as a specialized member of the HD phosphohydrolase superfamily. It comprises a conserved five-helix core with two additional C-terminal helices and likely serves as a scaffold to facilitate protein-protein interactions with partner GGDEF domains. In addition, the protein has a HD/PDEase domain that exhibits predicted or known phosphohydrolase activity within a diverse enzyme superfamily. It encompasses the catalytic region of eukaryotic 3',5'-cGMP phosphodiesterases found in photoreceptor outer segments, where it functions as a light-activated enzyme critical for signal transduction. Also, the protein should contain a GAF domain that functions as a versatile signaling module structurally related to the PAS domain. It regulates diverse cellular processes by binding small ligands, such as cyclic nucleotides (cAMP and cGMP) to control phosphodiesterases and cyclases, or by acting as a light-sensing chromophore-binding region in phytochromes and transcriptional activators. It originates from Omnitrophica bacterium (Omnitrophota bacterium).\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 3066, 5531, 43, 4515, 17, 8415, 1034, 3418, 1988, 4088, 1922, 2733, 8201, 1966, 43, 11021, 7210, 1927, 1920, 4515, 8078, 8535, 24605, 1021, 13975, 18, 2176, 12936, 43, 5305, 3628, 17, 7864, 4728, 1956, 2288, 3281, 45, 17, 4262, 12789, 1930, 3205, 10634, 1966, 43, 7281, 1942, 6628, 2213, 17, 2213, 3719, 1956, 8240, 12358, 3695, 1038, 4682, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 4515, 19, 13309, 2051, 3418, 1988, 9826, 4396, 2014, 3171, 8078, 8535, 24605, 1021, 2455, 2651, 43, 6445, 4113, 13975, 18, 2176, 21569, 1920, 6804, 3031, 1927, 10825, 23, 11, 16, 25, 11, 17, 15958, 24821, 1036, 2435, 1922, 16383, 7642, 7492, 16, 2597, 2176, 4088, 1966, 43, 3696, 17, 4128, 4113, 4140, 1958, 2733, 8201, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 4357, 1038, 3418, 1988, 4088, 1966, 43, 20425, 3197, 9059, 12171, 2712, 1942, 1920, 9233, 3418, 18, 2176, 7014, 6445, 3689, 4028, 2007, 2743, 2858, 6908, 16, 2427, 1966, 9821, 9519, 12, 6225, 1930, 15958, 13, 1942, 2285, 24821, 1036, 1930, 16526, 1036, 16, 2014, 2007, 8290, 1966, 43, 3696, 17, 9306, 25801, 17, 2743, 3031, 1922, 25512, 2072, 4191, 1036, 1930, 5224, 15497, 18, 2176, 22970, 2037, 18825, 3032, 24888, 3375, 14061, 12, 18825, 3032, 2102, 7336, 14061, 13, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MERILSKFNENWNLKQESSALNKYLSKNVKTESEFRNKLKKIHKVFKKSRRKKTLEQFEYGEKIFSAEFQHVFTSFVDTIIRESRKEIELEELNKTVRLPRVARLSLQVIRANRCSIKLVDKKRKVLKVQIGKYAPGRAVKQGRPIRGRNYLAYPMIDEDEDIMKTLSEQAAIAIKNAQLFKEQTDLTLSSIAEASFLKLISIIGLKFNMNESETKMLQYALTGQEYDIVKTHSMKGASILSKFKPLKPLVPIILYHLAIVSAFEAMITEKPYRKALSVNIAIKEVVDIFCYAVRRKDIERLLKREIGGHYEGKNPVWIIIPILPVRSGELKHMEIAKYISYPLVYDGHIFGMLLVCELKKEISLPRAIALSTVHTVHRLMTSTLDLNELLPRTTIDLRKEKTKLKVVGVITLYDKLDGTKFSEFDKCIAQLLQNRPHGAHRAMLHDAGQISIPEKVLMKKSGHENYDGTGYPRGLKGKEIPLSARIVVRNSGTQFDPD", "metadata": {"id": "A0A9E2IE55", "cluster": 25714786, "interpro_all": ["IPR003018", "IPR029016", "IPR003607", "IPR037522"], "interpro_used": ["IPR037522", "IPR003607", "IPR003018"], "interpro_unused": ["IPR029016"]}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein should feature a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Additionally, the protein belongs to the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. In addition, the protein is a member of the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. It is derived from Massarina eburnea CBS 473.64 and features UniProt keywords Magnesium, Nucleus, and Metal-binding.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 3066, 5961, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 2176, 1977, 3595, 2037, 3411, 6454, 1019, 6560, 3997, 5376, 16341, 24500, 18, 4723, 1930, 4075, 20709, 11569, 13148, 16, 5607, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MEEQPQKQWGTTKPISTTLPTTAELKLTDELVSCQKRKEVLAHVTNVTKEFITRVGRRQKLSEEAISKLSSDIDTCIVAPRNVRREDFFDIWPQLFRDMSDKSQISELVEVLDLIFGSLPSQPSIPEDLDLSNVSILRGLDDVGGRTVNGPRVVKELYALRTIKLWSNQRGIYGAVFGYPGGIAWAIMVARIAQLFPNACSWTFPRPVMLKDVSKTNPLGLPEWNPTQNRNDRAHLMPIMAEFERGVDIVTRIQDGSATWDALFERHTFFTKDHKFYLSVFKGWVQSKISKLAKGIEESDFDLKRKARPVMDYWIRKADLPESGEPSTEDGSTIIYTSTFYIGLTVPEGSRSFMFCRIIHTKDVNLPDDVFVEGEAKPTKPPKDKERKKKKGRTNGDSKNSRPVKALQQSYPRHEASACSHTDSVLILKARDNFETPEGIGGKVVTFGSFALGVYGPPEAHVPIVKMAYRGISLALVPEHKSFRGATIVCKFFNLMKVITPAYPAMCSTHLITKTTKEVVATSLTKDADEKYMKAFDRAHRCANQEQIERVKQGDISHPATTFKEIVESNEVNKAFDREKSRKRHIDETEPEVR", "metadata": {"id": "A0A6A6S668", "cluster": 26419065, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR007012", "IPR043519", "IPR011068"], "interpro_unused": ["IPR014492", "IPR007010", "IPR048840"]}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein is classified under the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Furthermore, the protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Moreover, the protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is expressed in Caldisericota bacterium and is connected to UniProt keyword Cytoplasm and rRNA processing.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 3198, 1922, 2570, 15783, 3383, 7336, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MMKIYHTPVLINEAIDLLDIKKEDIVMDCTIGEGGHSEKILSHLDTAKKRLSSIKTNFTLIHGNFADILNITKEHNVTGVNKIIVDLGISSPLDMRMNREERTTALEIINSFPEYEIADIIYKYGEERFSRKIAKKIVNYRKLYPHKWQKIHPATRTFQALRIKVNKELENLEKFLESFPQILSEELHILNKKVIKPTPEEISRNPRSRSAKLRGAKKLVNKFGHLYGIDRDKETLQIEIEERGFSFKREGKTIKTTTELAEIIKKAAKNGRVAIISYHSLEDRLIKTYFKQ", "metadata": {"id": "A0A661XMM2", "cluster": 27526309, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein incorporates a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Additionally, the protein includes a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. Furthermore, the protein should contain a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It is produced by Branchiostoma floridae (Florida lancelet) (Amphioxus) and is associated with UniProt keywords ATP-binding, Transmembrane helix, and Repeat.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 19683, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 4950, 16, 1920, 2213, 5921, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 1977, 4152, 2007, 6089, 14356, 4575, 3368, 19386, 1021, 12, 19386, 26448, 5484, 13, 12, 9141, 3940, 1039, 1957, 13, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 9117, 7864, 16, 1930, 6865, 18, 3], "output": "MYHKYFVDIAHRRTFLDTRHCIESRIKLEKEREQQERLLLSVHHSTSTCFHSMYIKRHLNVSILYADIVGFTTLASECTPAELVRCYYCVSGLPDPIPDHAKNCVKMGLEICDAIKKVAWATGVDINMHKWQYDVWSHHVTLANHMESGGRPGRVHITKATLDELQGHYKVEPGDGHLRNRVTPHMSQHRKLARDHKQRASVRMTRYLSTWGAHKSPRPTSPTAHPDQVHVNVIRINCVPCSDISGSVQPCALEDQINETLGFKNPEWQEKYREMKVPMFKFNVLCAFMIFVTMAIVHFTVLPPTPILAENIQCYKKHRHPTFSFLASMTSKYWWLRRCLALLVLITISRSFGLHSNGSGTDPTPSMPRCPNSTSASCVQVSPYFLQTGFSVKLGGLTLALVVYSVLIHHTHAWVFNGFDCLYTNMSKDNFYVIDRQVEYTSRMDFLWKTKCKREGEEVGTMESLYSQSYEFVCVMFASIPNFKEFYVETDVNKEGLECLRLLNEHVEKIKTIGSTYMAATGLTSTTGQQGVSYPEKLHLMGNMVDFALALFNDFKLRIGINHGPVIAGVIGARKPQYDIWGNSVNAQFLTELNYHCECRGLIDVKGKGKLKTYLIDTSMATGMQHMANYSHRMSLELPAHLAKEMKEEMMGRVTGTSLTLNELFGKFDQIAEKNNCMRIKILGDRVGVHTGNVLCGVIGLRDDYLKENNVETFFVIDPKAPFQDLPDISRNRNSYLMPERMEQAIEGITTHKQWIKSPDMHRLIWSYLLSTFTLLLVLFLSFLTVAATSILDCGQFLSYLLGMLSCMVFIELHQRGTIYLVLLYITILLNKVLVENVMPVHVADHFLSSSARSSREIIADFDELLSKPKFSVQKLHLINKHSVASRMESTGVMGCIQVTEES", "metadata": {"id": "A0A9J7LBA9", "cluster": 2394125, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR009398", "IPR029787"], "interpro_used": ["IPR018297", "IPR009398", "IPR001054"], "interpro_unused": ["IPR032628", "IPR030672", "IPR029787"]}, "task_type": "infilling"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein falls within the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Furthermore, the protein falls within the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is produced by Pseudomonadota bacterium and is classified with UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 12182, 2651, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 4152, 2007, 11520, 3947, 12595, 3857, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MPAFVIALTGGIASGKTAVSDTFSDLGVAVIDTDVIAREVVLPDSAGLVAIADSFGNQLIQDDGQLNRRALRDIIFADKSKRELLESILHPLIRAESIRQLQQVDTPLAILVIPLLAEGLDSGNTYQWVDRVLVVDVDEAIQIQRLTARDQVSEPLAQAILDNQASRKQRLAIADDVIVNDRDLEYLRVAVGVLYNEYLGMVRS", "metadata": {"id": "A0A929ICE7", "cluster": 2441293, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given the following functional description of a protein, generate a complete amino acid sequence that performs the described role. The desired function is: The protein is assigned to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. In addition, the protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is found in Pseudoclavibacter caeni and corresponds to UniProt keyword ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 16, 5655, 43, 4080, 3835, 2687, 3244, 1988, 17436, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 1977, 6304, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2435, 1922, 11520, 2223, 9188, 7972, 2341, 1915, 21778, 1033, 1930, 8852, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MPTVIALTGGIAAGKSTVARVFARQGARIVDADKVAREVVEPGRPALAEIREAFGDEVIRPDGSLDRKALAERVFGDPEALARLNAITHPRIRDRVAERIAAAPDESIVVYDVPLLVEADLPQPFDAVVTVSAPAEERVSRLVSERGYTAVEAAQRVAAQASDADREAIADYVVDASGDLAGTERHALQVWHQIAAAFL", "metadata": {"id": "A0A7C8FU91", "cluster": 5989695, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is classified under the Protein adenylyltransferase SelO family, which functions as a conserved pseudokinase that catalyzes the AMPylation of serine, threonine, and tyrosine residues on protein substrates. Members of this family feature a protein kinase fold with an inverted ATP binding mode and, in eukaryotes, localize to the mitochondria where they may participate in redox biology. It is native to Comamonadaceae bacterium and features UniProt keywords Nucleotidyltransferase, Metal-binding, and Magnesium.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 1920, 2213, 27802, 9961, 2484, 1037, 3416, 16, 2154, 4088, 1966, 43, 5305, 11520, 25545, 1988, 17097, 1920, 3681, 3017, 1927, 8468, 16, 13143, 16, 1930, 6941, 4248, 1990, 2213, 6249, 18, 4678, 1927, 2052, 3416, 5961, 43, 2213, 4016, 3728, 1956, 1925, 12344, 4498, 2743, 5754, 1930, 16, 1922, 15021, 16, 14380, 1942, 1920, 6489, 2597, 2611, 2278, 7352, 1922, 9366, 7256, 18, 2176, 1977, 6196, 1942, 22337, 3947, 7324, 1972, 3336, 14061, 1930, 4075, 20709, 11569, 2797, 4090, 2199, 9961, 16, 6048, 17, 2743, 16, 1930, 13148, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MNTTPELSFTALMERAHPALLMNLTPDPEQARHPAPRYVIHSHAFFQALGLADEVASDPAFMQFFTGDLDAGVMVNNCPFRTGNGYGDGRAISVLEVLLADGQHWEFQLKGRSSIREFLASEAMAALGVPSARALCLFVSGSETVTRPWYSTGAKPSFLRVGQVELFGRRARHNAHPRALAELEAIFLHALDREYPDLTLADKVVAMAREFGVGLSHLVAHWIRVGYCQGNFNSDNCALGGRTLDYGPMAAMVNFKMFCAAMAPLLGQDTRAIEAMDAVMQALPDSLFAELHTLMAQTPVDYTIFWRELSSLPKQVADLRPSFYASRALMQEGRDPLGVSVAMKQVNPKYIPREWMLVEAYRPYGEQSPELAALYYTKKRDEYFDLGGTSHCSCSSAPNKTARQVKSGHYVEVCPTSLEAANADSLSATLRPKGWATGYALSIYGQEGGTTPYCRGGDGRAVLTEEPDRMVDEPAAITTRAAAAALHGPEVPFGFMEAYDPAFQMWIGGGEHFAFMNQMADTLHAMWAQKMGLIEFRAEGAYGQDPAVMETRWGAWLHKWHTSATDAGDFTLVRRLHALLAN", "metadata": {"id": "A0A4P5U7S4", "cluster": 7680274, "interpro_all": ["IPR003846"], "interpro_used": ["IPR003846"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Moreover, the protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. In addition, the protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is identified in Firmicutes bacterium CAG:124 and contains UniProt keyword associations Cytoplasm and rRNA processing.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3950, 16, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 2899, 1922, 24474, 14061, 13415, 30, 10955, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 1930, 9067, 4587, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MEFAHRSVLLHECIDALAIKPDGIYLDGTLGLIGVDRDLVALEAAKKRLYRHAKKLFDLGVSSPQLDDAERGFSYMAYEIVNNWPREELKSILYEYGEERCAPQIAAAIERVRTDHSFQAIRIAVNDELGAVRQVVITFHSLEDRIVKNVFQNAAKGCTCPPSFPVCVVEENPRSRSAKLRVAEHVGAGHSLEICRSLTTGRVTLVHDNFENVGAILTALGLDRIDGMDAPLDMRMDRDQSLTAPIETTLELVDIIRSAMPPSALREKQHPAKRGMEAAIDHLNPGGRLCGHKPKIKILTKKPIIATREE", "metadata": {"id": "R5INT0", "cluster": 14086994, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a protein with the following function: The protein carries a PAAR motif repeat that is usually found in pairs in a family of bacterial membrane proteins. It occurs in Pseudomonas fluorescens. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 22692, 1005, 5219, 6865, 1988, 1977, 5394, 2435, 1922, 5803, 1922, 43, 3416, 1927, 4543, 3260, 2697, 18, 2176, 5110, 1922, 13461, 17871, 2099, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MGRKVIGIGAPTSTGGAVLEGNAGINIDYAVSTSSIGHMASCPACSAGKGPIVAVGPRTVTLPAGPVALEGDYIACGCPPKSNTLLFGQSSVYGGGEHSAASFSAISSLIPKPKTIQRITFSYGESQTPVDSVSRFYTDLNIHVKTSGYSPGETVTVTISGATEKTLSGTVGAKGIAIIPNAFQGEAFDMEGEI", "metadata": {"id": "A0A7Z3C148", "cluster": 14186458, "interpro_all": ["IPR008727"], "interpro_used": ["IPR008727"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein should have a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein is a member of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is produced by Vibrio scophthalmi LMG 19158 and is classified with UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 4152, 2007, 23280, 25392, 19253, 7289, 7395, 7735, 1029, 18162, 7532, 1930, 1977, 5947, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MISDTTHWPSPAKLNLFLYITGRRANGYHELLSPDIPGVALHDNLIWRAATALQQFTSCQYGAVLVALNHLWQTGCTDDQLAEIGLKLGADVPVFVRGHAAFAEGVTVDIFTHPDLTRDTEKRPLSELLENNYENDCEKIVRMLYPEVDKQLSWLLQQVLEQLPDTVSAFVAKGNNVSPLYQTLANYRLAHNLFIQTLFQFLDHGDELTITANKSGEITDIQLQKILPMGGGIGGGSSNAATGEEIIAVEPEEKYYLVVRPDVSIAYAPSRLTGTGSCVFAEFIRKNDAQ", "metadata": {"id": "F9RN28", "cluster": 14901510, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein is categorized in the RNA methyltransferase RlmH family, which is predicted to function as an S-adenosyl-L-methionine (AdoMet)-dependent methyltransferase based on structural homology. These enzymes likely catalyze the transfer of methyl groups to RNA substrates for regulatory modification. Also, the protein is a member of the tRNA (guanine-N1-)-methyltransferase, N-terminal superfamily, which represents the N-terminal domain of SPOUT superfamily enzymes, including the tRNA:Gm18 methyltransferase TrmH. This domain is characterized by a rare \u03b1/\u03b2 knot structure that poses a significant folding challenge. In addition, the protein is included in the Alpha/beta knot methyltransferases superfamily, which encompasses enzymes containing a deep, rare \u03b1/\u03b2 knot structural domain essential for RNA methylation. This fold is characteristic of S-adenosyl-L-methionine (SAM)-dependent enzymes, including the SPOUT and EMG1/NEP1 families, facilitating the modification of RNA substrates. It is present in Liquorilactobacillus capillatus DSM 19910 and carries UniProt keyword assignments Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 3146, 16478, 11929, 22316, 3416, 16, 2154, 1977, 4396, 1942, 2347, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 12, 2041, 14080, 13, 17, 3100, 16478, 2454, 1990, 4346, 9039, 18, 2144, 5038, 3205, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 3146, 6249, 1958, 4948, 6295, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 10089, 12, 16904, 17, 13007, 17, 13, 17, 16478, 16, 56, 17, 4262, 13975, 16, 2154, 4972, 1920, 56, 17, 4262, 3418, 1927, 18055, 1984, 13975, 5038, 16, 2710, 1920, 10089, 30, 28673, 1025, 16478, 28402, 1023, 18, 2052, 3418, 1977, 4378, 2007, 43, 5844, 160, 19, 161, 26646, 3170, 1988, 17274, 43, 2228, 10328, 6013, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4595, 19, 4666, 26646, 28253, 13975, 16, 2154, 21569, 5038, 3165, 43, 6515, 16, 5844, 160, 19, 161, 26646, 4346, 3418, 4415, 1958, 3146, 5547, 18, 2052, 3728, 1977, 6293, 1927, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5038, 16, 2710, 1920, 18055, 1984, 1930, 13952, 1009, 19, 26046, 1009, 5767, 16, 12440, 1920, 6295, 1927, 3146, 6249, 18, 2176, 1977, 2481, 1922, 5636, 6658, 5148, 2341, 14357, 8898, 16139, 7482, 10964, 8802, 1008, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 3], "output": "MNIKIVVVGKLKEKYLKQGIAEYTKRLSKFCSHAEMEQVKEVEGARILNKIQSKEYVYALAILGKERSSEELADELQKLGTYSFGRFTLPHQLMRLVLTEQVYRSFMINAGSPYHKKFKIIEVADEKAPEKLGHSDITFIIGGSLGLSEAVLKRVEAQV", "metadata": {"id": "A0A0R1MDT5", "cluster": 16316524, "interpro_all": ["IPR029028", "IPR003742", "IPR029026"], "interpro_used": ["IPR003742", "IPR029026", "IPR029028"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein should contain a HNH nuclease domain that functions as a catalytic endonuclease module responsible for DNA cleavage in diverse systems across all domains of life. It is integral to the activity of proteins ranging from CRISPR-associated Cas9 and restriction enzymes to bacteriocins and eukaryotic DNA repair factors. It has been characterized in Cylindrobasidium torrendii FP15055 ss-10. What would its protein sequence look like?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 3066, 5531, 43, 9888, 1023, 16230, 3418, 1988, 4088, 1966, 43, 6804, 18697, 9059, 5061, 1958, 2678, 6404, 1922, 6445, 3771, 3436, 2136, 4682, 1927, 3308, 18, 2176, 1977, 12328, 1942, 1920, 2455, 1927, 2697, 6485, 2037, 12509, 17, 2458, 13474, 1930, 7587, 5038, 1942, 14027, 11778, 1036, 1930, 10825, 2678, 5059, 2790, 18, 2176, 2258, 2252, 4378, 1922, 15460, 15129, 13130, 7408, 1989, 27949, 2200, 3907, 8621, 20091, 7054, 4577, 17, 2119, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "MMSVAWDKITQTSIASSSHSPSINQTAVVVESADRAEQKEFADQLKLRERYQCIVTGYFLPSAPEPWILLPGVGVGELEAAHIIPLALNSDKKPPEPMAPTWDMLKHWTQIDPEDYAGGRITCPENGVLLTKREHHAFGTFKLWFDPVRRQLFLSVLPIDTLRCSLLTLSQSHTPSLACSRAAMNLSRGKYTQS", "metadata": {"id": "A0A0D7BSE7", "cluster": 19434018, "interpro_all": ["IPR003615"], "interpro_used": ["IPR003615"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to make a protein that can have this function: The protein should have a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Furthermore, the protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein belongs to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It has been characterized in uncultured Rubrobacteraceae bacterium and is linked to UniProt keywords Isoprene biosynthesis and Transferase. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 2258, 2252, 4378, 1922, 5269, 21058, 10010, 15129, 2422, 9914, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MREVRLKAYAKVNLALDVVGRRPDGYHELRTVMQSVSLADEVSVRRANEGFELRVEPHRTEVGPREKNTAYRAWRLLCDRLGEELPVRVALRKNVPAGAGLGGGSADAAAVLRGLDALFGLGLSVEEMREVGSGIGADVPFCVSGGTALGEGVGEILSPVPPPPDHRLLVVKPRRGADTAAVYRAFDAVSAVGGAAERVLEALRPGDLAELAGALGNDLAPFTKRMVPEVAQLEERLLEAGAVGASMTGSGTAVYGLFRDEDAVARAGEKVDAHFVGVCAPVPFGSEEF", "metadata": {"id": "A0A6J4S146", "cluster": 21431462, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR006204", "IPR004424"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein incorporates a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein is associated with the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is identified in Treponema sp and is classified with UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 19683, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 2899, 1922, 2171, 21851, 6666, 2056, 1930, 1977, 5947, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MDRRVVVEAPAKINLHLQVLGVRSGGEFRVYGDFDCPERENTIPAGAGLGGGSSDAAAVLKALNIGSDVPFFLGGPCAVVSGRGEILEPGAGRPEYGLRKAAALGEGGVWNRARLLEEYRKEPGSWTKRALEDAGASFAGMTGSGSALFGIYESKGRWIAAAASPLARMPVPRLQKRPDGFHDILSLFQAISLSDTLDVRYRAARVFLAALGRPEGAEIRAAKRILVFREALSEPELARLGAGVVLFPGFPIGTASAYAALDASFRNDFFDALVPDIPELGLAKAAAERAAESLNEREGG", "metadata": {"id": "A0A7X8CY70", "cluster": 23230136, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein possesses a Acyltransferase 3 domain that catalyzes the transfer of acyl groups to various substrates, most notably mediating the O-acetylation of peptidoglycan in bacteria to confer lysozyme resistance. It is also present in rhizobial proteins involved in lipo-chitin oligosaccharide production and in specific eukaryotic regulatory proteins. It has been characterized in metagenome and exhibits UniProt keyword tags Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 14465, 43, 11337, 9961, 23, 3418, 1988, 17097, 1920, 3856, 1927, 11337, 2671, 1942, 3425, 6249, 16, 2501, 7388, 10239, 1920, 57, 17, 10339, 1927, 24183, 1922, 4802, 1942, 7909, 18581, 3554, 18, 2176, 1977, 2222, 2481, 1922, 13458, 18311, 1024, 2697, 3286, 1922, 3178, 1037, 17, 16588, 28215, 3372, 1930, 1922, 2487, 10825, 4948, 2697, 18, 2176, 2258, 2252, 4378, 1922, 16552, 2225, 1930, 9826, 20709, 11121, 2538, 14392, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MQQSLGSALSARRNSLNFVRLVLACAVILGHTTLIGGYRPNALTDVSRMRLSGGRYLWHRVIRIMPAFWVSLVLVALAFSPLAAAISRESIKQRGIGATLQDVPFAGAWNGSLWTLEFEFMAYLLAGLLLASAIVRRHLLEATSYYGFNAAHLFAGFAAGMALWAFRDTLPRNATITGMCGALSVVYFLLSVGGSKRVLLGSVNDISYGAYIYAFPVQQLLVVLGVHRLGYAAFVERPALRLKNLSVARNNSRRRSPFEAPDWSHARSSSIAVDGFFVLSGFLVAGWQPSSALHFLSANWALTKVVVVVLTMITAAGAALAGPLYFQAPTLMYALAPLPLGLFVTALALTLCLAWLSWT", "metadata": {"id": "A0A2P2C1V5", "cluster": 23239756, "interpro_all": ["IPR002656", "IPR050879"], "interpro_used": ["IPR002656"], "interpro_unused": ["IPR050879"]}, "task_type": "infilling"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein features a MORN variant repeat that represents a variation of the Membrane Occupation and Recognition Nexus (MORN) motif, typically involved in facilitating protein-protein or protein-membrane interactions. It is found in Saprospiraceae bacterium.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 2803, 1022, 6031, 6865, 1988, 4972, 43, 4516, 1927, 1920, 3260, 16805, 1930, 5708, 24079, 1957, 12, 2803, 1022, 13, 5219, 16, 5745, 3286, 1922, 12440, 2213, 17, 2213, 2014, 2213, 17, 3260, 3719, 18, 2176, 1977, 2435, 1922, 9235, 5424, 11979, 1972, 3336, 14061, 18, 3], "output": "MKNLLETMKKISISLLIVSLSIYLTIFNSCNQPECSIAKKCHETYFETGDLESKFCTRKDKLSGEVVFFYKSGSLKSKSCDYKEDVMDGERFGFFKDGRPYYYYFYKNGDFVYFKKYLYGDDSTIIDKDTLGTDVKHLKFSAELPIPDSLLNGKELYFAYQMNPISFRDSTQLFYYHVFQKDKKLIMNPTEIIITVLPTSLGSSTVGAGSFDHENGKAEIINCIINESEKYLFYKDDKREGTLINYYENGQIESKEVFKPIVKIEIIDEPAHRFRIAPREKKSVNLPLTESS", "metadata": {"id": "A0A958WVX9", "cluster": 24214412, "interpro_all": ["IPR011652"], "interpro_used": ["IPR011652"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein falls within the Holliday junction branch migration complex subunit RuvB family, which functions as an ATP-dependent 5'-3' helicase that drives the branch migration of Holliday junctions. It assembles into hexameric rings and interacts with the junction-binding protein RuvA to promote the translocation of recombination intermediates along DNA. Also, the protein possesses a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. Furthermore, the protein should include a RuvB, winged helix, C-terminal domain that functions as a putative DNA-binding module facilitating the branch migration of Holliday junctions during genetic recombination and DNA repair. Operating within the RuvABC resolvasome, it supports the ATP-dependent helicase activity of RuvB, which is targeted to DNA junctions by the RuvA protein. It originates from Isosphaeraceae bacterium and contains UniProt keyword associations Cytoplasm, DNA recombination, and Hydrolase.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 14451, 27539, 6910, 6089, 5049, 2796, 5903, 7212, 1020, 1014, 3416, 16, 2154, 4088, 1966, 1925, 4498, 17, 3100, 25, 11, 17, 23, 11, 15318, 1988, 15435, 1920, 6089, 5049, 1927, 14451, 27539, 11245, 18, 2176, 17421, 1036, 2460, 25602, 1935, 12750, 1930, 9034, 1956, 1920, 6910, 17, 2743, 2213, 7212, 7302, 1942, 5527, 1920, 7849, 1927, 7827, 12386, 4231, 2678, 18, 2222, 16, 1920, 2213, 14465, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 7212, 1020, 1014, 16, 12920, 1919, 7864, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 6770, 2678, 17, 2743, 9059, 12440, 1920, 6089, 5049, 1927, 14451, 27539, 11245, 2409, 3299, 7827, 1930, 2678, 5059, 18, 8654, 2651, 1920, 7212, 7302, 8284, 24321, 10916, 2225, 16, 2176, 7825, 1920, 4498, 17, 3100, 15318, 2455, 1927, 7212, 1020, 1014, 16, 2154, 1977, 5154, 1942, 2678, 11245, 2007, 1920, 7212, 7302, 2213, 18, 2176, 22970, 2037, 4911, 3508, 20051, 5524, 1972, 3336, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 16, 2678, 7827, 16, 1930, 20748, 18, 3], "output": "MREPIIKGDTGDAPRRHGEPARPIDPMDEKLRPQRLGEVIGQRKVAERLAIALEAARRRGEPLPHILFDGPPGLGKTTFATVLHNELGVELNMTSGPALDKKMDVMPYLTNAAEGSILFIDEIHRLPKTVEEFIYPVMEDFRVDVVLGEGINARTVNIPLKRFTIIGATTRSGMLSGPLRDRFHMHEHLEFYDVEELAQIVQVNATKLRTTITPEAAYELARRSRGTPRLANARLRWVRDYATARADGHITLAVAQDALAMQEVDTEGLDKQDRRYLETLIQVFRGGPTGVEAIAATMHIAVDTLEDEVEPYLLRRHFIVRTPRGRKVTATAYRHLGMRQPEPDPDFDLLDQPRLFD", "metadata": {"id": "A0A9E3QHG2", "cluster": 24252576, "interpro_all": ["IPR003593", "IPR041445", "IPR004605", "IPR027417", "IPR008824", "IPR008823", "IPR036388", "IPR036390"], "interpro_used": ["IPR004605", "IPR003593", "IPR008823"], "interpro_unused": ["IPR036390", "IPR041445", "IPR027417", "IPR036388", "IPR008824"]}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein can be placed in the Rifampicin monooxygenase-like family, which comprises FAD-dependent monooxygenases and aromatic-ring hydroxylases that catalyze hydroxylation reactions using NAD(P)H as an electron donor. These enzymes are integral to the biosynthesis of polyketide antibiotics, such as anthracyclines and tetracyclines, and mediate antibiotic resistance through the inactivation of compounds like rifampicin. Some members also participate in xenobiotic metabolism, contributing to the degradation of environmental pollutants like pentachlorophenol. Also, the protein features a FAD-binding domain that facilitates the binding of the flavin adenine dinucleotide (FAD) cofactor to support catalytic oxidoreductase activity. This domain functions in diverse enzymes across species, including human kynurenine 3-monooxygenase, archaeal digeranylgeranylglycerophospholipid reductase, and bacterial hydroxylases. Moreover, the protein possesses a Phenol hydroxylase-like, C-terminal dimerisation domain that adopts a thioredoxin-like fold to mediate the formation of the homodimer interface in FAD-dependent monooxygenases. This domain is characteristic of enzymes such as phenol hydroxylase and 3-hydroxybenzoate 4-monooxygenase, which catalyze the hydroxylation of aromatic substrates like phenol to catechol. It is derived from Adineta steineri and exhibits UniProt keyword tags Flavoprotein.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 22648, 8914, 13966, 17, 3189, 3416, 16, 2154, 12936, 14134, 17, 3100, 8914, 13966, 1036, 1930, 10761, 17, 6335, 16324, 1036, 1988, 18170, 21319, 5298, 2193, 6577, 12, 58, 13, 50, 1966, 1925, 4995, 6282, 18, 2144, 5038, 2032, 12328, 1942, 1920, 8132, 1927, 4286, 18540, 2261, 7560, 16, 2427, 1966, 30021, 1036, 1930, 16179, 1036, 16, 1930, 8265, 7267, 3554, 2596, 1920, 8005, 1927, 4300, 3189, 22648, 18, 2673, 4678, 2222, 7352, 1922, 29821, 4714, 16, 8739, 1942, 1920, 4877, 1927, 4813, 16826, 3189, 9412, 22918, 23965, 18, 2222, 16, 1920, 2213, 4075, 43, 14134, 17, 2743, 3418, 1988, 11374, 1920, 2743, 1927, 1920, 26758, 15643, 21302, 12, 14134, 13, 15155, 1942, 3373, 6804, 27388, 2455, 18, 2052, 3418, 4088, 1922, 6445, 5038, 3436, 3038, 16, 2710, 2616, 23523, 24684, 2053, 23, 17, 8914, 13966, 16, 22367, 4325, 7124, 16323, 1024, 4938, 12804, 14966, 8630, 16113, 11386, 16, 1930, 4543, 16324, 1036, 18, 3950, 16, 1920, 2213, 14465, 43, 12658, 16324, 17, 3189, 16, 45, 17, 4262, 7632, 6284, 3418, 1988, 24032, 43, 23684, 17, 3189, 3728, 1942, 8265, 1920, 3337, 1927, 1920, 21189, 6854, 1922, 14134, 17, 3100, 8914, 13966, 1036, 18, 2052, 3418, 1977, 6293, 1927, 5038, 2427, 1966, 12658, 16324, 1930, 23, 17, 8275, 13058, 25120, 24, 17, 8914, 13966, 16, 2154, 18170, 1920, 21319, 1927, 10761, 6249, 3189, 12658, 1942, 14400, 18, 2176, 1977, 3595, 2037, 2041, 2053, 3857, 21557, 18842, 1930, 9826, 20709, 11121, 2538, 14392, 7732, 6657, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MSLQEPELVDVVIVGSGPTGLMLACQLSLGVHARSMEIFQQMGIADEAINHGEVVQGFGSYFNGVKRMRMDMNLIKTQNLTDRQCELISFIELNDKDNLIECVIKDYRSNKEGKLIKIHTKFLCGCDGAHSCHLKFMDTTETGSLLDDAQFNLTKSGLCLLFPLKGHNMDNRWRVIGTVPHQRNIELYDPLWLSIYRTHHRYADRFYIEKKYFLLGDAALAYTIQGKTVDKDKLLQTYNDERIEVAKNLVQSTDRVFSLMTSRFNLAWKLAYTIQGKTVDKDKLLQTYNDERIEVAKNLVQSTDRVFSLMTSRHWSCISSVREAVFKRISMIGIHYRQSQLSMNSNKNSSTDNNVEDDSRRYFHLLVLLTSKSNSKKCFHFVKFIEENYSHRNSNGDAFNLAWKLAYTIQGKTVDKDKLLQTYNDERIEVAKNLRLKILPYILQYIVFPIISCISPIREAVFRRISMIGIHYRQSQSSTDNNVEDDSRRYFHLLVLLTSKSNSKKSFHFVKFIEENYIFLVRPDLHIAYCSTTFDVQHFNTYFSEYFLQKSDLHGVKFRIFDKCINHTTQSRAHFPFILILEQSKTEALLEEFLLKNTRMEVKVRQNLQLSFSGNTYEETLYVLDELLNSSKQLQFEDIAPDFSRRIHIHSPVGGQGMNTGLQDAFNLAWKHWFFSFFRLKILPYILQYXGLQDAFFSFFRLKILPYILQYIVFPIINVQAGDRLPYVYTHPEILLLIKLHEFEYSAATKEIFRVYDVNVQSTDRVFSLMTSRHWFFSFFLSMNSNRNNVQAGDRLPYVYTHPEILLSHLIKLHEFEYSAATKEIFRVYDVNRNSNGG", "metadata": {"id": "A0A814AWF4", "cluster": 25458332, "interpro_all": ["IPR002938", "IPR036188", "IPR012941", "IPR038220", "IPR050641", "IPR036249"], "interpro_used": ["IPR050641", "IPR002938", "IPR012941"], "interpro_unused": ["IPR036249", "IPR036188", "IPR038220"]}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein is included in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Also, the protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is native to Succinivibrio dextrinosolvens and features UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 6196, 1942, 13791, 2068, 3693, 3940, 20256, 5572, 1951, 10131, 3355, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "METAEAESEKRPFVVGLTGGIACGKTSIASLFASLGVPVVDADKVARDVVKVGSPLLKVLAGEFGEDILKEDGSLNRRKLREIVFDPNDKSKLLVLNSLMAPAIHKELKKQIFSYHSDYVIAMIPLLFEHKLEFLVDRILVVDVDDDLQLKRVMARDNISMELARSMIENQVSREYRVKKADDLIESDDSPLDKKLNVVLKLHNEYKHMSSQVKR", "metadata": {"id": "A0A662ZAL5", "cluster": 26108042, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein is associated with the Alpha/Beta hydrolase fold superfamily, which comprises enzymes with diverse catalytic functions sharing a common core structure of a central beta-sheet surrounded by alpha-helices. These proteins typically utilize a catalytic triad hosted on loops, including a conserved nucleophile elbow, to drive hydrolytic activity, though some members lack active sites and function in surface recognition. It is native to Candidatus Melainabacteria bacterium and exhibits UniProt keyword tags Signal.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 4595, 19, 4666, 20748, 3728, 13975, 16, 2154, 12936, 5038, 1956, 6445, 6804, 4088, 10763, 43, 3059, 4728, 3170, 1927, 43, 4101, 4666, 17, 11130, 16006, 2007, 4595, 17, 12789, 18, 2144, 2697, 5745, 12561, 43, 6804, 21845, 4423, 1919, 1990, 11109, 16, 2710, 43, 5305, 2797, 28335, 17621, 16, 1942, 9265, 26702, 2455, 16, 4170, 2673, 4678, 3630, 3500, 3402, 1930, 2347, 1922, 3154, 5708, 18, 2176, 1977, 6196, 1942, 14550, 1031, 1957, 4221, 2005, 20013, 2341, 18339, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 2733, 18, 3], "output": "MICFRVSLIIFFALVASFCLPGVVIAGDGSAAQIAGISTHQILPSDTDSRINTFSGQGFAHWSWFYPSVRDTGQLVVFLPGTGGKGNGSAPFNLTAASLGFHVLCLAYPDDISMSTFNNSDDQGAFAKARTNVITGKVQFGNLNINEFNSMSTGWLWRCVILRVVIRTKTGHNFSIAATM", "metadata": {"id": "A0A431KVG4", "cluster": 27959254, "interpro_all": ["IPR029058"], "interpro_used": ["IPR029058"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein belongs to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, it is part of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is present in Candidatus Curtissbacteria bacterium RIFCSPHIGHO2_01_FULL_40_12 and exhibits UniProt keyword tags Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 2481, 1922, 14550, 1031, 1957, 3580, 3600, 1036, 7972, 2341, 18339, 14061, 12424, 2792, 24888, 2509, 5265, 41, 3287, 41, 4125, 41, 3040, 41, 2369, 1930, 9826, 20709, 11121, 2538, 14392, 5239, 1930, 9067, 4587, 18, 3], "output": "MGKAQGKFRRGAVIHVPVLLQEVVRFLDPKAGKVIIDATAGAGGHTEEFLRRGAQVLAIDRDPEAIKYLKKSYGSQVINHKLVLAQGNFANIGEIAQKKGFSRVDGILFDLGISSDQLADAKRGFAFAKVGPLDMRMDPNLEVTAYDLVNNFDERRLYEIFSTYGQEKFSRAIARAICRARQIAPINSTQRLANIIREVYGKKNIRTKLDCATKSFLALRIVVNSELINLENALPQTIEILKKGGRLAIVSFHSLEDGLVKRFFKQEKQLLVLTKKPVTPGASEILKNPRSRSAKLRVAEKI", "metadata": {"id": "A0A1F5GCT1", "cluster": 28111766, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein is categorized in the G protein-coupled receptor, rhodopsin-like family, which constitutes the extensive Class A group of GPCRs including receptors for hormones, neurotransmitters, and light. These proteins utilize a conserved seven-transmembrane helix architecture to transduce diverse extracellular signals by activating intracellular guanine nucleotide-binding (G) proteins. Furthermore, the protein should include a GPCR, rhodopsin-like, 7TM domain that forms the conserved seven-transmembrane structural core characteristic of Class A G protein-coupled receptors. It transduces diverse extracellular signals, such as hormones, neurotransmitters, and light, into cellular responses by activating intracellular guanine nucleotide-binding (G) proteins. This scaffold supports a wide range of autocrine, paracrine, and endocrine processes by accommodating various ligand structures. It is derived from Pocillopora meandrina and carries UniProt keyword assignments G-protein coupled receptor and Transducer.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 49, 2213, 17, 6416, 3148, 16, 20586, 17, 3189, 3416, 16, 2154, 14879, 1920, 6475, 2921, 43, 2210, 1927, 17723, 2710, 4086, 1958, 10224, 16, 21012, 16, 1930, 3696, 18, 2144, 2697, 12561, 43, 5305, 5260, 17, 9117, 7864, 9335, 1942, 30334, 6445, 5329, 4771, 2007, 8019, 4776, 16904, 5489, 17, 2743, 12, 49, 13, 2697, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 12542, 16, 20586, 17, 3189, 16, 27, 15375, 3418, 1988, 4952, 1920, 5305, 5260, 17, 9117, 4346, 4728, 6293, 1927, 2921, 43, 49, 2213, 17, 6416, 4086, 18, 2176, 30334, 1036, 6445, 5329, 4771, 16, 2427, 1966, 10224, 16, 21012, 16, 1930, 3696, 16, 2460, 3689, 3387, 2007, 8019, 4776, 16904, 5489, 17, 2743, 12, 49, 13, 2697, 18, 2052, 7281, 7825, 43, 4743, 3109, 1927, 19396, 16, 17515, 16, 1930, 10749, 4028, 2007, 11852, 2287, 3425, 5207, 4061, 18, 2176, 1977, 3595, 2037, 18660, 22538, 21086, 2667, 3883, 4058, 1930, 16252, 20709, 11121, 2538, 18306, 49, 17, 2213, 6416, 3148, 1930, 14848, 18, 3], "output": "MNNSTTNLQIGQSECFSAVPSTVFTVALSVITVVAFSGNFLLIAAFLRASNLKTSSNWYIINMAISDVISVLLNWPLYATEGMLKPGGSLITNQAIATFFCKLGIYSRAVLYVVSIESLVLISVDRFIAIVFPLKAIKITARVRKILLLLSWLFPVCGAIPYFYHSKILLEGRQTFCRNFMNTLLFKVYQFASFILFYFAPLVVLLVVHYIGFEHLKRRLVFEISSNEGSTHALRSKENQNILKIFRAVTLGFFMCWTPLYIYLILKSSHPTIVLNDKCLLFIGLLYYVFPLISTAVNPFILISLSSNYRAAVKDVLAKCFAVFKCRSNKIYSTEQVIDLR", "metadata": {"id": "A0AAU9W9F6", "cluster": 28484048, "interpro_all": ["IPR000276", "IPR017452"], "interpro_used": ["IPR000276", "IPR017452"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein possesses a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. Furthermore, the protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein is categorized in the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. It originates from Acidobacteriota bacterium and has UniProt annotations Nucleotide biosynthesis and Transferase.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 14465, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2176, 22970, 2037, 2687, 5883, 3940, 3857, 14061, 1930, 2258, 20709, 15010, 5489, 8132, 1930, 13763, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "RKILLNSETIHLTAASELLLFRGEMVLCDRYYHASMAYQGYGRGIPLDFINKLDIAPEVGLARARARNHGRPEDEGRFEAEDLAERPIDLVHHHILQVLGLEARYASRSQNILEKIKPALELTDLVVAEYRPDMTLLEFYGRIRDGYLEMASEDPRVQLIY", "metadata": {"id": "A0A2V8LYW8", "cluster": 2624676, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR039430", "IPR027417", "IPR018094"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the intended role of my protein: The protein is grouped in the Gas vesicle protein GvpA-like family, which comprises the essential structural components of gas vesicles, hollow organelles that regulate buoyancy in cyanobacteria and archaea. This family includes the highly conserved major core protein GvpA, as well as the related GvpJ and GvpM proteins, which assemble to form the ribbed cylindrical tubes and conical caps of the gas-filled structure. It is produced by candidate division Zixibacteria bacterium 4484_95. Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 30, 1920, 2213, 1977, 10809, 1922, 1920, 4422, 11502, 2213, 12042, 4302, 17, 3189, 3416, 16, 2154, 12936, 1920, 4415, 4346, 4178, 1927, 4422, 8319, 16, 20010, 14487, 1988, 5741, 3168, 3759, 3970, 1922, 21897, 1930, 21501, 18, 2052, 3416, 5921, 1920, 3626, 5305, 3044, 4728, 2213, 12042, 4302, 16, 1966, 2486, 1966, 1920, 2712, 12042, 1034, 1013, 1930, 12042, 17922, 2697, 16, 2154, 17421, 1942, 2386, 1920, 5216, 19011, 18677, 9403, 1930, 26995, 7070, 1927, 1920, 4422, 17, 8924, 3170, 18, 2176, 1977, 4152, 2007, 6610, 8451, 28666, 18068, 7972, 2341, 18339, 14061, 29877, 1006, 41, 3002, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "MTIEQDIGAYGLVELANRIIDKSIATDAWIKASLVGIELLAVEARVVCTGIETFLKYDKTVNLSPVPFAT", "metadata": {"id": "A0A1W9S6Q6", "cluster": 4131258, "interpro_all": ["IPR000638"], "interpro_used": ["IPR000638"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein falls within the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Moreover, it is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is derived from Facklamia sp. 252 and is associated with UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 12182, 2651, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3595, 2037, 3186, 16244, 14981, 1019, 2056, 18, 21979, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 5655, 3581, 18, 3], "output": "MKVIGLTGGIATGKSTVSQYLISKGVQSFGSSILTVDGQLDRKRLGTLIFSDVPKRKREQSNQAILFIDMPLLFEVGYEKQVDEVWLVYVSKDVQLTRLMEPIEQKRQLVTTIIDNSGSVKATYQQVEQALLKLKDYEVIDADLVAREVVEVGQPGLVALQMVNELLHPYIFERIRRRDSLSMDLAKERLSSQW", "metadata": {"id": "A0A6M0L8C7", "cluster": 6190060, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein has a Chromo domain that mediates chromatin organization and gene repression by targeting proteins to specific nuclear sites via interactions with methylated histone tails or RNA. This conserved module, structurally defined by an OB-fold with three $\\beta$-strands packed against an $\\alpha$-helix, is critical for the assembly of heterochromatin complexes and transcriptional silencing. Moreover, the protein falls within the Chromo-like domain superfamily, which functions as a chromatin organization modifier by recognizing nucleic acids and specific lysine-methylated histone tails. These domains adopt an SH3-like $\\beta$-barrel fold capped by a C-terminal helix and are integral to heterochromatin formation and gene silencing in nuclear proteins like HP1 and Polycomb. It originates from Dictyostelium purpureum (Slime mold).", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 2258, 43, 3233, 1037, 3418, 1988, 10412, 6338, 5901, 1930, 2359, 10084, 2007, 5133, 2697, 1942, 2487, 4254, 3402, 3454, 3719, 1956, 11882, 6632, 18103, 2014, 3146, 18, 2052, 5305, 9059, 16, 12171, 3608, 2007, 1925, 2384, 17, 3728, 1956, 2559, 8, 38, 4666, 8, 17, 13214, 15827, 3316, 1925, 8, 38, 4595, 8, 17, 7864, 16, 1977, 4140, 1958, 1920, 5957, 1927, 18933, 5048, 1930, 5224, 8343, 18, 3950, 16, 1920, 2213, 12182, 2651, 1920, 3233, 1037, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 6338, 5901, 22883, 2007, 15667, 11079, 4576, 1930, 2487, 9082, 17, 11882, 6632, 18103, 18, 2144, 4682, 14103, 1925, 18824, 17, 3189, 8, 38, 4666, 8, 17, 19560, 3728, 22069, 2007, 43, 45, 17, 4262, 7864, 1930, 2032, 12328, 1942, 18933, 3337, 1930, 2359, 8343, 1922, 4254, 2697, 3189, 27575, 1930, 28962, 18, 2176, 22970, 2037, 29060, 18092, 12191, 1989, 25945, 2027, 1989, 12, 2788, 11593, 20459, 13, 18, 3], "output": "MNRKELEIEENSLVLVKRCFLNTIKNIVAQDQFKLLPKYSGPFKVIKRKENTNNYKPLVDEIEKIIKRRIRKYGKGERIEYLIRYKNSNEDNDTWVPNFFLEDECEDMVNSFEADYRDVGKSIQV", "metadata": {"id": "F0ZQP6", "cluster": 7397310, "interpro_all": ["IPR016197", "IPR000953", "IPR023780"], "interpro_used": ["IPR023780", "IPR016197"], "interpro_unused": ["IPR000953"]}, "task_type": "autoregressive"} {"instruction": "Functionally defined as:\nThe protein has a GPI inositol-deacylase PGAP1-like alpha/beta domain that functions as an endoplasmic reticulum-localized lipase responsible for the deacylation of GPI-anchored proteins. It adopts a typical \u03b1/\u03b2/\u03b1 hydrolase architecture with a conserved catalytic serine to facilitate the efficient transport of GPI-anchored proteins to the Golgi body and the degradation of misfolded substrates. Additionally, the protein can be placed in the Alpha/Beta hydrolase fold superfamily, which comprises enzymes with diverse catalytic functions sharing a common core structure of a central beta-sheet surrounded by alpha-helices. These proteins typically utilize a catalytic triad hosted on loops, including a conserved nucleophile elbow, to drive hydrolytic activity, though some members lack active sites and function in surface recognition. Additionally, the protein is associated with the GPI inositol-deacylase family, which functions to deacylate the inositol moiety of glycosylphosphatidylinositol (GPI) anchors, a critical step for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body. Mutations in the encoding gene PGAP1 are associated with autosomal recessive mental retardation 42. It originates from Trichoplax sp. H2 and contains UniProt keyword associations Transmembrane helix, Membrane, and Transmembrane.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 2258, 43, 17497, 16246, 17, 30097, 13796, 24605, 1021, 25546, 5113, 17, 3189, 4595, 19, 4666, 3418, 1988, 4088, 1966, 1925, 13355, 12279, 17, 6579, 16653, 5061, 1958, 1920, 30097, 13796, 6055, 1927, 17497, 17, 17199, 2697, 18, 2176, 24032, 43, 5939, 160, 19, 161, 19, 160, 20748, 9335, 1956, 43, 5305, 6804, 8468, 1942, 6628, 1920, 5807, 4860, 1927, 17497, 17, 17199, 2697, 1942, 1920, 10277, 3362, 1930, 1920, 4877, 1927, 20303, 6249, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4595, 19, 4666, 20748, 3728, 13975, 16, 2154, 12936, 5038, 1956, 6445, 6804, 4088, 10763, 43, 3059, 4728, 3170, 1927, 43, 4101, 4666, 17, 11130, 16006, 2007, 4595, 17, 12789, 18, 2144, 2697, 5745, 12561, 43, 6804, 21845, 4423, 1919, 1990, 11109, 16, 2710, 43, 5305, 2797, 28335, 17621, 16, 1942, 9265, 26702, 2455, 16, 4170, 2673, 4678, 3630, 3500, 3402, 1930, 2347, 1922, 3154, 5708, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 17497, 16246, 17, 30097, 13796, 24605, 1021, 3416, 16, 2154, 4088, 1942, 30097, 13796, 5148, 2057, 1920, 16246, 11804, 1927, 20067, 7824, 10244, 15651, 12, 17497, 13, 27127, 16, 43, 4140, 3537, 1958, 1920, 5807, 4860, 1927, 17497, 17, 17199, 2697, 2037, 1920, 13355, 12279, 1942, 1920, 10277, 3362, 18, 3527, 1922, 1920, 5797, 2359, 25546, 5113, 2032, 2458, 1956, 13027, 13992, 5018, 16342, 3858, 18, 2176, 22970, 2037, 10477, 3513, 3013, 2056, 18, 4881, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 16, 3260, 16, 1930, 9117, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MGLYESYGSNLLSYTTLRVNTKTLRNDHIFGIPILFIPGNAGSYKQVRSLAGTLRDQAEYVNYCIKRILAGYRNLPSPPRSVVVIGHSIGGMTTVITIATPHRSPVFYADKYVADFYDTVNTFWQEQSSSGQILDQSLASVANYNRSINAITTAVPRTWLTIDHRCIVWCKELVLAHHLIKHNGMRNYPYKLGKKFLKIDQERPVNICISRIWSNGLHRKLMTTSNANAWIISCNGIDYHKCDSPSDLLNHVQIIPHATMVSTATHDSVFAEFYRDAVKTKHIRLPSIVGFTAVDSDDNYVQINSSDRCLRHTTIQFHAPWFHEDVFRYVRPESIRLTIWSTNAKCRYKIIVTTDYTRLLGQMVNETYQSKSTDSQDGKERLNTSPGVALALKQQTSKFAASLVSFSYLFSSTFSKFAWPFPIFPQPDIFNVFSISGLHFQFCIMDWLVYGVASVLRFTSRWLSMARLTGNIFTAICFNMCGALGLYCTILYCYVKLVAIINSRQNKEREYCGSSYGFNVMPDPFMHESLLASCGLLVLFQKSSFYEDMSISYQKSMNRKEHFNYYTIDLNEEISGLYGIARALFTLPNFDNSTVVIIASVGGGLRDVIVRSDLTAIVRALYDMIEAHGQISSSTSKRRNVLQSSKRCLMAFPLKPQRIAKDRLLGTLKLLDVNINSELSQATHVDQYILNYNLPDMRQIWEAYDNGKLNFSIYMQTPRPNDNKYQNMVRYYAIFLPGWTMAIIILLAFNLVKYDHFSIKTLLNQELDRRWMKSGEWSTYLLSVIHMLYFNIIFGLLVITICLTDLCFLLLNSSLLSSFLTIPSAIMWFKNLR", "metadata": {"id": "A0A369SAK0", "cluster": 8617941, "interpro_all": ["IPR029058", "IPR012908", "IPR039529"], "interpro_used": ["IPR012908", "IPR029058", "IPR039529"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe protein belongs to the Membrane bound O-acyl transferase (MBOAT) family, which comprises membrane-embedded enzymes that catalyze the transfer of acyl groups to various substrates, typically utilizing a conserved histidine active site. Members of this family are integral to lipid metabolism and homeostasis, facilitating processes such as the synthesis of triacylglycerols from diacylglycerol and fatty acyl-CoA and the remodeling of phosphatidylinositol acyl-chains. Also, it is part of the Membrane-bound O-acyltransferase family, which comprises enzymes that catalyze the transfer of acyl groups to various lipid and protein substrates, regulating their function and localization. Members of this family mediate diverse processes ranging from the remodeling of glycosylphosphatidylinositol (GPI) anchors and the palmitoylation of Hedgehog signaling proteins to the modification of bacterial cell wall components like alginate and teichoic acids. Collectively, these activities are essential for cell signaling, structural integrity, and host-pathogen interactions. Additionally, the protein is included in the Alginate O-acetyltransferase AlgI/D-alanyl transfer protein DltB family, which functions as membrane-embedded O-acyl transferases responsible for modifying bacterial surface polymers by transferring organic acids onto hydroxyl groups. Specific members include DltB, which esterifies teichoic acids with D-alanine in Gram-positive bacteria, and AlgI, which mediates the O-acetylation of alginate or cellulose in Gram-negative organisms. These modifications to the cell envelope are critical for bacterial survival and environmental adaptation. It is found in Myxococcales bacterium and is classified with UniProt keywords Cell membrane and Transmembrane helix.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 14440, 1942, 1920, 3260, 4124, 57, 17, 11337, 13763, 12, 5667, 6952, 1031, 13, 3416, 16, 2154, 12936, 3260, 17, 8222, 5038, 1988, 18170, 1920, 3856, 1927, 11337, 2671, 1942, 3425, 6249, 16, 5745, 10232, 43, 5305, 13873, 3500, 3200, 18, 4678, 1927, 2052, 3416, 2032, 12328, 1942, 4486, 4714, 1930, 7622, 16, 12440, 4028, 2427, 1966, 1920, 4271, 1927, 5083, 21295, 1036, 2037, 29527, 1930, 5934, 11337, 17, 10027, 1930, 1920, 8378, 1927, 16927, 11337, 17, 7835, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 3260, 17, 4124, 57, 17, 11337, 9961, 3416, 16, 2154, 12936, 5038, 1988, 18170, 1920, 3856, 1927, 11337, 2671, 1942, 3425, 4486, 1930, 2213, 6249, 16, 6773, 2310, 2347, 1930, 5363, 18, 4678, 1927, 2052, 3416, 8265, 6445, 4028, 6485, 2037, 1920, 8378, 1927, 20067, 7824, 10244, 15651, 12, 17497, 13, 27127, 1930, 1920, 28167, 1927, 20931, 3197, 2697, 1942, 1920, 6295, 1927, 4543, 2024, 4821, 4178, 3189, 17987, 1930, 3602, 2108, 8643, 4576, 18, 10182, 16, 2144, 4209, 2032, 4415, 1958, 2024, 3197, 16, 4346, 7996, 16, 1930, 4423, 17, 7055, 3719, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 17987, 57, 17, 22226, 4326, 1033, 19, 46, 17, 10527, 16323, 1024, 3856, 2213, 5268, 27414, 3416, 16, 2154, 4088, 1966, 3260, 17, 8222, 57, 17, 11337, 13763, 1036, 5061, 1958, 12691, 4543, 3154, 11039, 2007, 21902, 6805, 4576, 6131, 9420, 2671, 18, 2487, 4678, 3951, 5268, 27414, 16, 2154, 9603, 13208, 3602, 2108, 8643, 4576, 1956, 46, 17, 10504, 1922, 8604, 17, 2843, 4802, 16, 1930, 4326, 1033, 16, 2154, 10412, 1920, 57, 17, 10339, 1927, 17987, 2014, 12343, 1922, 8604, 17, 3136, 7373, 18, 2144, 6920, 1942, 1920, 2024, 11262, 2032, 4140, 1958, 4543, 3298, 1930, 4813, 7810, 18, 2176, 1977, 2435, 1922, 21464, 11748, 1918, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MIFTSAQFVLFFIAFFTVYPALKGQNRKHFLLYQIAGWISRSDDARRRRLLITGSVVANLGVLAFFKYCNFFVHIVLPVGISFYTFQSMSYTIDVYRRRMSKARTFEDFALYVAFFPQLVAGAPDFTGFLLIAMGVFKKVVIADHMAVLVDATYAHPENTPGMGLGRLLGFDLMQNFRAPYSAESPSDFWRRWHISLSTWLRDYLYGGLWHGAAWNYVLWGAFHGTLLLVWRFLPNGGEARPRPSLSDCGSIFSGLFGLRDWDLAAWLKVVKASGEGPYLAFMAVELANRAMKAPLAVRVFGVCIVLYVSMLLASEKPPPFIYFQFLSSWVFYGCFSLPFLLLLIATTVLDDSAVRLSETLGLSFAAPALPIERGHQLVAQVQRVGTSDEPPALWLGTYAFAMQIYFDFSGYSDIAIPLGGNRGTGLFTSRNLFLTMLLGALGLFLTGLRRVLFFHLICLGWALFRASASMVALVLVQQVFREGT", "metadata": {"id": "A0A964JRM8", "cluster": 13451318, "interpro_all": ["IPR024194", "IPR028362", "IPR051085", "IPR004299"], "interpro_used": ["IPR004299", "IPR051085", "IPR024194"], "interpro_unused": ["IPR028362"]}, "task_type": "infilling"} {"instruction": "Generate a protein sequence for a protein with the following function: It is part of the p53-like transcription factor, DNA-binding domain superfamily, which functions as the DNA-binding module in transcription factors regulating diverse cellular processes such as the cell cycle, apoptosis, and immune responses. This domain adopts a nine-stranded \u03b2-sandwich structure with a Greek-key topology that clamps or encircles the DNA target to stabilize the protein-DNA complex. In addition, the protein is assigned to the Fungal transcription regulator family, which functions as a positive regulator of acid phosphatase activity and mediates responses to nitrogen and carbon starvation. Members are crucial for vegetative incompatibility, meiosis, and sporulation, recognizing specific DNA sequences to activate gene transcription. Furthermore, they modulate virulence, hyphal growth, and drug sensitivity by regulating ergosterol biosynthesis and cell wall components. Furthermore, the protein possesses a NDT80 DNA-binding domain that functions as a transcriptional activator involved in sensing nutritional status and regulating developmental checkpoints like meiotic progression and heterokaryon incompatibility. It structurally resembles an s-type immunoglobulin fold, consisting of a central $\\beta$-sandwich with an N-terminal extension containing a $\\beta$-hairpin and loop. It originates from Basidiobolus meristosporus CBS 931.73.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1958, 43, 2213, 1956, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 5105, 17, 3189, 3213, 2991, 16, 2678, 17, 2743, 3418, 13975, 16, 2154, 4088, 1966, 1920, 2678, 17, 2743, 9059, 1922, 3213, 2790, 6773, 6445, 3689, 4028, 2427, 1966, 1920, 2024, 4048, 16, 4091, 16, 1930, 3743, 3387, 18, 2052, 3418, 24032, 43, 6360, 17, 10338, 161, 17, 18038, 3170, 1956, 43, 27568, 17, 3834, 13678, 1988, 10209, 1036, 2014, 3350, 13220, 2612, 1920, 2678, 2758, 1942, 13448, 1920, 2213, 17, 2678, 2796, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 8697, 3213, 7888, 3416, 16, 2154, 4088, 1966, 43, 2843, 7888, 1927, 2687, 8167, 2455, 1930, 10412, 3387, 1942, 6634, 1930, 5056, 12767, 18, 4678, 2032, 6608, 1958, 18823, 15819, 11516, 16, 17979, 16, 1930, 23647, 16, 15667, 2487, 2678, 3709, 1942, 6980, 2359, 3213, 18, 3677, 16, 2611, 8480, 9304, 16, 27125, 2905, 16, 1930, 2838, 3802, 2007, 6773, 11949, 23030, 8132, 1930, 2024, 4821, 4178, 18, 3677, 16, 1920, 2213, 14465, 43, 8026, 1031, 4476, 2678, 17, 2743, 3418, 1988, 4088, 1966, 43, 5224, 9518, 3286, 1922, 9306, 9369, 3642, 1930, 6773, 5878, 28799, 3189, 16205, 4380, 1930, 19732, 15292, 1916, 15819, 11516, 18, 2176, 12171, 17602, 1925, 61, 17, 2601, 11837, 3728, 16, 7600, 1927, 43, 4101, 8, 38, 4666, 8, 17, 18038, 1956, 1925, 56, 17, 4262, 7140, 3165, 43, 8, 38, 4666, 8, 17, 14565, 1930, 5881, 18, 2176, 22970, 2037, 2726, 13756, 2389, 19574, 24108, 9890, 1957, 16341, 6156, 1009, 18, 5356, 18, 3], "output": "MTVMMQENKWPVQPQHLQPISLPHQPIQHNMTPMHSQNESFVDSYPYSDQTQHMPSNNVSHQADQNGAPMFLAPLPQKPDIDPVRSAYQSANYMSMNGSIPRPLDMSKPRLAVPPQFDRKYSLDSSLASMSYGAPSFHPTLRKRRSDSLGFPNEAGPYFTQTKQHHNLYSMDKLNNYSIRIDSKFDRGFFLADNDWTCYRRNYFQVSSAFSLIGSNHPPTDPECPCIVEVDGVQHTVVQFFLGAAARVSNSDKKIDLIQHTPKRDKGPQTTPMARPIKAGGNVNLSSVGSNQTIVTFERIQFKTATANNGKRRAAQQYYVLVVELLAECDNGEQYKVASTQSAPLVVRGRSPGHYADSHERFNPLASGPATDSRYFAQHRMSADLGSPYSNFTPYAPFPTHSPSQMMMTPPTPNTGNTFQNPSPYMMSGISESSNATPEIFSNGMNSGLNSPTANDIGSQGQSHASLPRMNQLPVGLNIHNVQPEADDAWSRSRNNSTTSVGSYHSGNAYNTEDTSGYQHPANMAGSAFNSYDTENKSQLGGPISQDRFNGHESMNNANLNASYHQQDYSSNLQWQGHHSNGYNPDSERHIPPHHMQPQHYQFNIAHQAK", "metadata": {"id": "A0A1Y1Y274", "cluster": 13801869, "interpro_all": ["IPR052605", "IPR024061", "IPR037141", "IPR008967"], "interpro_used": ["IPR008967", "IPR052605", "IPR024061"], "interpro_unused": ["IPR037141"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein is classified under the WD repeat-containing GAD-1 family, which facilitates the assembly of multi-protein complexes through conserved WD repeat domains. Members contribute to a variety of cellular processes, with specific roles identified in the initiation of gastrulation during embryonic development. It is expressed in Lygus hesperus (Western plant bug).", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 17907, 6865, 17, 3165, 10279, 17, 21, 3416, 16, 2154, 11374, 1920, 5957, 1927, 2779, 17, 2213, 5048, 2596, 5305, 17907, 6865, 4682, 18, 4678, 4672, 1942, 43, 5386, 1927, 3689, 4028, 16, 1956, 2487, 5456, 2899, 1922, 1920, 6035, 1927, 14860, 2281, 2409, 7231, 2740, 18, 2176, 1977, 3198, 1922, 7518, 13057, 10688, 2116, 1957, 12, 4540, 4496, 25761, 13, 18, 3], "output": "MYPGDVVRNYWNTQTCESVQGNLQRAKSVLGRSQPGSDDDPISKNHQHKHKSLHYYLRDKVQKNQFNVAQDPREALLNAADSDDDSPVKQREKQPKIFTSFSDGTIIGIFNRSGDGGTSRNAINFVDEVQAFEHSFVKHTVKRPPAYREAEYSQTSHKYTQDKDSTYYLAAYNKTQPNPIFT", "metadata": {"id": "A0A0A9YI48", "cluster": 14274179, "interpro_all": ["IPR051858"], "interpro_used": ["IPR051858"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein is a member of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is native to Lactiplantibacillus paraplantarum and contains UniProt keyword associations ATP-binding, Cytoplasm, and Transferase.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 6196, 1942, 5641, 13229, 10402, 7972, 10401, 5277, 1036, 22224, 17576, 3857, 24277, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MTNLIGLTGGIATGKSTVSKLLAAKLPIVDADKIAWQVEGPGQPTTQKIALGQLVFNDPQALQALTAITRLPIQYAMFEAIVAANQHQPAAIILDIPLLFESGWQHICLSQQAAQARIDSQMPLAQKVAQADVVIDNGANIDKTKAAVLKWLKTITNAYFGQQAVLADGQLNRPWDQVLVVTAPPTVVLQRLMARNH", "metadata": {"id": "A0A4Q9Y3K7", "cluster": 16068416, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein incorporates a Rad50/SbcC-type AAA domain that functions as a central ATPase module in DNA repair and structural maintenance proteins, such as Rad50, SbcC, and Smc5-Smc6. It contains a P-loop NTPase subdomain with conserved Walker A and B motifs that facilitate ATP binding and hydrolysis to drive DNA replication, recombination, and repair. Additionally, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is present in Salinicoccus sediminis and exhibits UniProt keyword tags Coiled coil. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 4226, 3382, 19, 7760, 2437, 17, 2601, 13835, 3418, 1988, 4088, 1966, 43, 4101, 9444, 9059, 1922, 2678, 5059, 1930, 4346, 6291, 2697, 16, 2427, 1966, 4226, 3382, 16, 7760, 2437, 16, 1930, 16312, 1015, 17, 16312, 1016, 18, 2176, 5461, 43, 58, 17, 5881, 29676, 2051, 27517, 1956, 5305, 20138, 43, 1930, 44, 8277, 1988, 6628, 4498, 2743, 1930, 9128, 1942, 9265, 2678, 5158, 16, 7827, 16, 1930, 5059, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2481, 1922, 30128, 5670, 2437, 1957, 6276, 1980, 15472, 1930, 9826, 20709, 11121, 2538, 14392, 17524, 9121, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MKPIRLDMKYFGPFEDESIDFSSIKDSMFLISGRTGSGKTMIFDAITYALYGTLSTSDRMEGSVRSQFATDSDISRVKLTFEIRGSQYTVERTLSYQKEGRKTPVPPKAAIYDQEGEVLEGSINGVKEKVLGIIGLDADQFRQILILPQGEFKRLLVSSSESKQEILRTLFRTERFVHFEMRLNELKKEKLKSIELVESRVEELFSTLSANGDAELQKLIDAEYPTAAKRIEVIEEIGTTLGNRYRMLEEALQKLKQEATSLRETISRRERHNEQALKLASTKQELKDHEENAASIERLETAVRQYRKVKTVEYELRSEQDLIKQKEELETRLNTIDTGLKELETSGEALRQTLDKISRYREGYTKLVKWINSTERFVEDPRFRDMDGVLQSKMKERQNLASDIKAQEAKLAEVRQEDDSIHWEHAESEILRNELSASVAECRKMREWIERENKSAGYDGKKQTLEKEITELRKKMEDTETAIKKIQEDTGSMYSPEDKVHIEHLAGHLKKDGECPVCRQTVSVLPVARDYMSEEDEAELRALETKKQECGNALETAEKNLGIVDGILGSMERYDTEKLEKELEAEERHQNEVRKKIDDNHKRYDRKKQLDEEMRRLESSISDNRIRMNNAENAVEQQKSLKKEFSEQTQFETCEEFQREFQARQQKVSRYEKQQEEAEQERQRYREEKSRLEENRAAARRQLSEMSGQLEENTRVIDDFLKDNEFAGRNVLFSILKNTDVNEDEERIRAYHTQKDILKSRINDLESVLESTEEIPVEEDREKLSVLDKEIETKTNDNARLYARMQHNGNIKEKISDFAEKHEAELGEVDELVELVNAVSGKNEQKVSLERFVLTYYLDRILHIANIRLLEMTSHRYELRRSTGKSNRKTGLDIEVFDFYNNRARHISSLSGGETFQASLTLALALNEALQQESGGISLDTMLIDEGFGTLDPETLDMAISTLIELQTSGKMVGIISHVEELKERMENILEVKAVNERSTANFK", "metadata": {"id": "A0A0M2SQW9", "cluster": 16864445, "interpro_all": ["IPR027417", "IPR038729"], "interpro_used": ["IPR038729", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The desired role of my protein is: The protein carries a Histidine kinase domain that functions as the catalytic core of two-component signal transduction systems, orchestrating cellular responses to environmental stimuli. It undergoes ATP-dependent autophosphorylation on a conserved histidine residue within a homodimer before transferring the high-energy phosphoryl group to an aspartate residue on a partner response regulator protein. This domain contains a dimerization interface and a structurally distinct ATP-binding cleft defined by conserved nucleotide-binding motifs. Also, the protein incorporates a PAS fold-3 domain that functions as a versatile sensory module involved in signal transduction and protein-protein interactions across all domains of life. It typically contains a central S-box region capable of binding diverse prosthetic groups, such as haem, FAD, or chromophores, to sense stimuli including oxygen levels, redox potential, and light. Frequently found in tandem repeats, this domain facilitates signal transfer to downstream effector regions like histidine kinase or response regulator domains. In addition, the protein contains a GAF domain that functions as a versatile signaling module structurally related to the PAS domain. It regulates diverse cellular processes by binding small ligands, such as cyclic nucleotides (cAMP and cGMP) to control phosphodiesterases and cyclases, or by acting as a light-sensing chromophore-binding region in phytochromes and transcriptional activators. It is native to Halobacteriales archaeon QH_3_68_24 and has UniProt annotations Transferase. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 16252, 43, 13873, 4016, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 2288, 17, 4594, 2733, 8201, 3771, 16, 21991, 2287, 3689, 3387, 1942, 4813, 5458, 18, 2176, 14928, 4498, 17, 3100, 22009, 1990, 43, 5305, 13873, 6181, 2651, 43, 21189, 3119, 21902, 1920, 2149, 17, 3844, 12556, 2210, 1942, 1925, 12878, 6181, 1990, 43, 8240, 2644, 7888, 2213, 18, 2052, 3418, 5461, 43, 13640, 6854, 1930, 43, 12171, 4493, 4498, 17, 2743, 14649, 3608, 2007, 5305, 5489, 17, 2743, 8277, 18, 2222, 16, 1920, 2213, 19683, 43, 9233, 3728, 17, 23, 3418, 1988, 4088, 1966, 43, 20425, 6893, 9059, 3286, 1922, 2733, 8201, 1930, 2213, 17, 2213, 3719, 3436, 2136, 4682, 1927, 3308, 18, 2176, 5745, 5461, 43, 4101, 61, 17, 5758, 3031, 7131, 1927, 2743, 6445, 19019, 2671, 16, 2427, 1966, 7105, 16, 14134, 16, 2014, 25801, 1036, 16, 1942, 7534, 5458, 2710, 4612, 2428, 16, 9366, 2889, 16, 1930, 3696, 18, 5467, 2435, 1922, 10361, 9569, 16, 2052, 3418, 11374, 2733, 3856, 1942, 5863, 7917, 3451, 3189, 13873, 4016, 2014, 2644, 7888, 4682, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 4357, 1038, 3418, 1988, 4088, 1966, 43, 20425, 3197, 9059, 12171, 2712, 1942, 1920, 9233, 3418, 18, 2176, 7014, 6445, 3689, 4028, 2007, 2743, 2858, 6908, 16, 2427, 1966, 9821, 9519, 12, 6225, 1930, 15958, 13, 1942, 2285, 24821, 1036, 1930, 16526, 1036, 16, 2014, 2007, 8290, 1966, 43, 3696, 17, 9306, 25801, 17, 2743, 3031, 1922, 25512, 2072, 4191, 1036, 1930, 5224, 15497, 18, 2176, 1977, 6196, 1942, 23226, 7972, 2341, 18339, 2612, 13470, 1916, 59, 1023, 41, 23, 41, 5117, 41, 2686, 1930, 2258, 20709, 15010, 13763, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MAGGRTVNGDRPASSTYVRPLERCDPAPTVLCVAADEALLSSLVSGLERADPDIRLLEARTLAQAFQVLDAENAGCVVSALSLADVDGVQFLRQIRAKYDDLPFVLVADRGSESVAADAINEGVDGYVPYEDELGDEAFETLVDRIETVVRDYRSSRRFEDATDLLFRLTEYTTDVLWMFTDDWEETVVINEAYEDIWDRRKADVIEDPADFLEGIYPDDRPGVLEKMEVISGGDPADLEYRIRTDDGVAWVSAHAEPVLSDGEVEHVAGFTREITERRESTKQLEALVENLPVIVFTFDADGVCTTSVGAGLEMLGLEPGELEGLSIYEAYAEHDDLVDAVNRALDGEELRVTLEVEGFVFETWYRPVFDEAGNVVEVVGVSHDVTRLKEREDLIERVNEATRELQNARTGAEVGRVVVEIIESVIGCPVTAYWRYDDENDRLEPTAASEPALDIGDDDDVSDLPHIEAGHAEMEVFRTGESRWVRDYADLTDPAHEAADLGRLLLVPLGDHGMVNIGHAEPGEFDDFDRYLVEILGQTATSALNRVERERALESRTAELERSNESLQQFAYVASHDLQEPLRMVSSYVSLLEAEYGDMFDEEATEYMHYAVDGATRMQDMIDALLRYSRIRTEGDDFVEVDLEAVLDETRRSLKLLVDEEEATVRAGDLPRVTADRSQVGQLLQNLVKNAVEHGGPEPTVEVDAVVEGDRVHLTVADDGPGVDGSQHERIFDIFKSNSDSTGIGLAVCERIAYRHDGDIWVESDPGAGATFHVTLPAVDADPDPGLDPQSAAVDGGHE", "metadata": {"id": "A0A2R6E4D4", "cluster": 17249546, "interpro_all": ["IPR011006", "IPR003018", "IPR029016", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR001610", "IPR000014", "IPR000700", "IPR035965", "IPR013656", "IPR013655", "IPR052162", "IPR004358", "IPR001789"], "interpro_used": ["IPR005467", "IPR013655", "IPR003018"], "interpro_unused": ["IPR004358", "IPR011006", "IPR000014", "IPR052162", "IPR013656", "IPR000700", "IPR001610", "IPR036097", "IPR001789", "IPR003661", "IPR029016", "IPR036890", "IPR035965"]}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence of a protein with the following function look like? Here is the function: The protein carries a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. Also, the protein contains a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. Also, the protein should have a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. It is present in Scleropages formosus (Asian bonytongue) (Osteoglossum formosum) and is connected to UniProt keyword Glycoprotein, Coated pit, and ATP-binding.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 1920, 2213, 16252, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2222, 16, 1920, 2213, 5461, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 2176, 1977, 2481, 1922, 8266, 8228, 2286, 2386, 13650, 12, 9686, 18525, 5405, 11056, 1021, 13, 12, 4416, 5581, 3117, 1989, 2386, 14740, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 11424, 16, 7242, 10795, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MELSEVRCSSASEELYTINRTPTTTTTSTSGTSSSNSSSRPKRLLWQNAVRHITEQRFISEQKSIITAEEPCVQSLRKHSSGRTSVGDRHNNGGTKVFPERASSDLGFLQIDCAPSNSDFFLNWGYTYRGVIFPTLRNSFKSRDLERLYQRYFLGQRRKSVVVMNILDVVTKLTLLVLHLTLASAPMDPIKGMLLGFFTGIEVVICALVVVRKDTTSHSYLQYSGVVTWVAMATQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAIIAGFVTSALHIVVQLVIPQNAQISTNQLVAQAVLFTCMNTAGVFISYLSDRAQRQAFLETRRCIEARLRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQHQFHKIYIHRYENVSILFADVKGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRPDHAHCCVEMGLSMIKTIRYVRSRTKHDIDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKLESGGIPGRIHISKAALDCLNGDYEVEEGHGKERNDFLRRHNIETYLIKQPEESLLSLPEDIAKESASVTGRRSSSATFTEGSWSPELPFDNIVGKQNTLAALTRNSINLLPNHLAQALHVQSGPEEINKRIENAIDLRSGDKLRREHIKPFSLMFKDSSLEEKYSQMRDEVFKSNLVCAFIVLIFITAIQSLLPSARMVTMVVQFSVLIMLHSALVLVTTAEDYKCLPLVLRQACCWINETYVARNVIIFVSILINFLAAMINIYFVFTGVLAMVTCAVFLRLNSILKLAVLLVMIAIYSLLTEAFYASLFVRYDTVHHNGDKNFLGTKETSLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVARHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDELLGEDRFQDIEKIKTIGSTYMAVSGLSPEKQQCEDKWGHLCALADFAIALNESIQEINKHSFNNFELRIGIAHGSVVAGVIGAKKPQYDIWGKTVNLASRMDSTGVSGKIQVPEETFGILKERGFAFEYRGEIYVKGISEQEGKIRTHFLLGRVQPNPLILQPRRLTGQYSLAAVVLGLVQSLNRQKQKQILNENNNSGIMKGHYNRRTLLTPGGPEAGPHAESSDKAELP", "metadata": {"id": "A0A8C9SXZ5", "cluster": 18987598, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR009398", "IPR029787"], "interpro_used": ["IPR001054", "IPR009398", "IPR018297"], "interpro_unused": ["IPR032628", "IPR030672", "IPR029787"]}, "task_type": "autoregressive"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein is grouped in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is identified in Paenibacillus chitinolyticus and is annotated with UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2899, 1922, 25726, 8635, 7972, 10401, 5277, 1036, 16588, 29370, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MNIGLTGGIACGKSTVSAMLVRRGAILIDADRIAREVVEPGSPVLAQVAAHFGQDMLLPDGSLHRKKLGKTVFGNEEARKALEDLLHPSIRALMKERMAAAEREFPDKLVVVDVPLLYESGLQSMFSSVMVVYVPREVQLRRLMERDGLNAEQAESRLAAQWPIERKKELADSCIDNSGTLEQTEQFVERFWLQRGL", "metadata": {"id": "A0A410WTS0", "cluster": 19241652, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nIt is part of the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Moreover, the protein is grouped in the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. Moreover, the protein carries a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. It is native to Malassezia caprae and has UniProt annotations mRNA processing, Nucleus, and Manganese.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 2176, 1977, 3131, 1927, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 3950, 16, 1920, 2213, 16252, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 2176, 1977, 6196, 1942, 3054, 2331, 11788, 2126, 2853, 5524, 1021, 1930, 2258, 20709, 15010, 3616, 4587, 16, 5607, 16, 1930, 19516, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MSTYLGVTPPISLNNVFESKEEAKLRYVRLTHNIEHGLPESAARAAGGKIFTFGSYRLGVHGPGFFRIFERLLKERDDVTEVAAVLPRIDDSLDLRDDNLLKNLDEREVRSLGRLALRCIKLWASRRAIYSNVMGFLGGVNEVAGAIISRFFIILLQWKWPQPVLLKNIETDRLHRMPIITPAYPSMCATHNVAQWSELFEMHDFFHKYKYYLQVIRQLVMKLELVPTLLCAHPFVKVATGDVPPEVAGRSKLKKLPETEDRRTVYTTTFYIGLKIEPRQAHDGPTRRGIVVRHIKGLRLGPTERDIEMTKTLEEELRAHSEVVLGHVDALVKQFVYQASSDIDTLCVAPKHVQREDPEAFVPLITSNFMGIPIDFLFARIAGSRVTDEILSLVPNVKVFAWAMLVARICQLYPEGPLPIRVWNPRLYPNQSTQMIMTQEFQRGAEIVDRIFLGKASSGSADLQLKWEGTVESRLSFEHENICHSDEEVRRAAKEKDEAVQQSDAESGLDISYPTMDFTQKVKQWDQFDEAAM", "metadata": {"id": "A0AAF0IU44", "cluster": 21244284, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR043519", "IPR011068", "IPR007012"], "interpro_unused": ["IPR048840", "IPR007010", "IPR014492"]}, "task_type": "infilling"} {"instruction": "Function:\nThe protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, it is part of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is expressed in Lentilactobacillus kefiri (Lactobacillus kefiri) and is connected to UniProt keyword ATP-binding, Cytoplasm, and Transferase.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 3198, 1922, 10226, 5148, 2341, 14357, 8898, 3364, 30480, 1033, 12, 18134, 3364, 30480, 1033, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MTKLVGLTGGIATGKSLVSGYLQKKGIEALVKAFGPQIILSDGALNRSELRIIDPFIRSEIFKQLAAYQSVPVYTDPVTQLHRLMKRNKLSIVNASGTAEQTLLQVDNWLANEMKPVIDADLVTHKVEAKGTPGLGKIVFNNPSDLKQLVLTVLDAPTLFENGYAHLVDELVVNKRIQNQWPLQTKCNLADTIIYN", "metadata": {"id": "A0A511DSY0", "cluster": 24584331, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein includes a Peptidase M16, middle/third domain that serves as a structural component of M16 zinc metallopeptidases, such as eukaryotic insulin-degrading enzymes and bacterial protease 3. It constitutes the third unit of a four-domain clamshell architecture, helping to enclose a central chamber for the metabolism of bioactive peptides like insulin and amyloid-\u03b2. This non-catalytic domain facilitates hinge-like conformational changes for substrate access and provides a docking interface for triphosphates. Furthermore, the protein is associated with the Metalloenzyme, LuxS/M16 peptidase-like superfamily, which comprises proteins characterized by a two-layer $\\alpha/\\beta$ fold and a conserved HxxEH active site motif responsible for metal coordination. This diverse group includes the bacterial quorum-sensing enzyme LuxS (S-ribosylhomocysteinase) as well as M16 family metallopeptidases, such as insulin-degrading enzyme and mitochondrial processing peptidase, that perform specific proteolytic cleavage functions. It is derived from Alexandrium andersonii.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 24050, 8510, 1016, 16, 5576, 19, 4563, 3418, 1988, 10634, 1966, 43, 4346, 4594, 1927, 8510, 1016, 7997, 8969, 24897, 1036, 16, 2427, 1966, 10825, 4122, 17, 18192, 5038, 1930, 4543, 7154, 23, 18, 2176, 14879, 1920, 4563, 5344, 1927, 43, 3006, 17, 3418, 6958, 2800, 23285, 1024, 9335, 16, 16235, 1942, 17439, 2217, 43, 4101, 7329, 1958, 1920, 4714, 1927, 13570, 5320, 3189, 4122, 1930, 8186, 17, 161, 18, 2052, 2447, 17, 6804, 3418, 11374, 20484, 17, 3189, 8523, 2840, 1958, 4510, 4065, 1930, 4558, 43, 10909, 6854, 1958, 17978, 1036, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 8969, 6802, 1022, 9318, 16, 17851, 1036, 19, 8510, 1016, 24050, 17, 3189, 13975, 16, 2154, 12936, 2697, 4378, 2007, 43, 2288, 17, 4757, 8, 38, 4595, 19, 38, 4666, 8, 3728, 1930, 43, 5305, 22721, 1039, 29586, 3500, 3200, 5219, 5061, 1958, 6048, 9478, 18, 2052, 6445, 2210, 5921, 1920, 4543, 28481, 17, 9306, 4113, 17851, 1036, 12, 61, 17, 29117, 2199, 25808, 16330, 14818, 2051, 13, 1966, 2486, 1966, 8510, 1016, 3416, 8969, 24897, 1036, 16, 2427, 1966, 4122, 17, 18192, 4113, 1930, 4596, 4587, 24050, 16, 1988, 2385, 2487, 12712, 6404, 4088, 18, 2176, 1977, 3595, 2037, 10460, 10249, 3027, 1989, 16163, 3907, 18, 3], "output": "PKLPVALDVSVPPISRIFHRQDDVFEQPKAHVIFHIFSPYAVQDAETWMKVEVWSQCVQEALNEYAYDATVAGVSYALGMRSGFISLAVAGFNDKLGVLLAAVTEKMCELKEVPENIFSIVSDAYGDDIRNQAFHSPPYQQCTMRFNELTTRGMTFPSYIRYERFQSLKREDLSNLAEKIFSACHVE", "metadata": {"id": "A0A7S2DM35", "cluster": 24767683, "interpro_all": ["IPR011249", "IPR050626", "IPR032632"], "interpro_used": ["IPR032632", "IPR011249"], "interpro_unused": ["IPR050626"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein features a Rare lipoprotein A domain that functions as a lytic transglycosylase localized to the outer membrane septal ring, specifically targeting naked glycan strands to support efficient daughter cell separation and bacterial rod shape maintenance. Moreover, the protein features a Sporulation-like (SPOR) domain that mediates localization to the cell division septum by binding preferentially to septal peptidoglycan. Found in bacterial proteins involved in cytokinesis and sporulation, this domain adopts an RNP-like fold to facilitate specific interaction with the cell wall. Moreover, the protein should feature a RlpA-like double-psi beta-barrel domain that functions as a lytic transglycosylase involved in bacterial septal ring formation, rod shape maintenance, and daughter cell separation. This structural element adopts a six-stranded fold often associated with enzymatic activity and specifically targets peptidoglycan lacking stem peptides. It is found in Henriciella mobilis and is annotated with UniProt keywords Cell wall biogenesis/degradation, Lyase, and Signal.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 5844, 9694, 43, 3418, 1988, 4088, 1966, 43, 17033, 2127, 17038, 4879, 18801, 24605, 1021, 6579, 1942, 1920, 7642, 3260, 16458, 6335, 16, 4475, 5133, 24197, 15060, 13214, 1942, 3373, 5807, 16229, 2024, 7106, 1930, 4543, 6275, 5989, 6291, 18, 3950, 16, 1920, 2213, 4075, 43, 23647, 17, 3189, 12, 9130, 13, 3418, 1988, 10412, 5363, 1942, 1920, 2024, 8451, 17026, 2007, 2743, 10662, 1942, 16458, 24183, 18, 2435, 1922, 4543, 2697, 3286, 1922, 20825, 1930, 23647, 16, 2052, 3418, 24032, 1925, 24767, 17, 3189, 3728, 1942, 6628, 2487, 2835, 1956, 1920, 2024, 4821, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 11929, 4302, 17, 3189, 4825, 17, 14748, 4666, 17, 19560, 3418, 1988, 4088, 1966, 43, 17033, 2127, 17038, 4879, 18801, 24605, 1021, 3286, 1922, 4543, 16458, 6335, 3337, 16, 6275, 5989, 6291, 16, 1930, 16229, 2024, 7106, 18, 2052, 4346, 6149, 24032, 43, 3798, 17, 10338, 3728, 3868, 2458, 1956, 8145, 2455, 1930, 4475, 4845, 24183, 7046, 4402, 5320, 18, 2176, 1977, 2435, 1922, 14618, 3133, 19918, 20407, 1937, 1930, 1977, 10633, 1956, 20709, 11569, 2024, 4821, 13008, 19, 4877, 16, 23928, 16, 1930, 2733, 18, 3], "output": "MARRFKSGFSPIAIAALAVTMAPAATADRKHPAPIEYVVPKPNSGATYDEWRGPVTQTRAVQLPESREKVRFSSVDSSPLASQPQIPTRLWPAEASASPLEASKSPSVSTLKASGVPHEEHGLASWYGEDFHGQPTANGEIFDMYAMTAAHRTLPLPSLVEDGRIIDLSKRAADALGFAEQQDAPLIVRYLGPAPALGSTQFANAETSDMLLGAYEPSLGVPDPGNSIATPARLASPSQTRTDIVPVRTVSASPRTMNVRQTTFSPEIYVQIGAFADIGNAQGRHAQVGGMFPVFPTRDAAERARVQLRTRGINDSFVALRSVGQGGARIQADQTRQTSSYPGSGSQSVAQQRQYATLGEGAVSSSQPAVSQTVTPQVVNERNGKEIVVRVNDRGPFLPDVRNTEMANEASSRMSRPDLYEADINEESLPPLQPYSAPAPAKVEDVQMHGADYFRVMVGP", "metadata": {"id": "A0A399RC33", "cluster": 2196114, "interpro_all": ["IPR034718", "IPR009009", "IPR036908", "IPR012997", "IPR007730", "IPR036680"], "interpro_used": ["IPR012997", "IPR007730", "IPR009009"], "interpro_unused": ["IPR036680", "IPR034718", "IPR036908"]}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein has a Furin-like repeat that is a cysteine-rich region involved in the aggregation of receptor tyrosine kinases during signal transduction in eukaryotes. Also, the protein should feature a Myxococcus cysteine-rich repeat that spans approximately 40 amino acids and contains conserved cysteine residues presumed to form stabilizing disulfide bonds. This region appears in multiple copies in *Myxococcus xanthus* and is shared with eukaryotic proteins such as human pappalysin-1. In addition, the protein belongs to the Growth factor receptor cysteine-rich domain superfamily, which forms a structural motif within eukaryotic receptor tyrosine kinases and binding proteins that is critical for signal transduction. Characterized by a disulfide-bound fold containing a \u03b2-hairpin, this domain contributes to ligand specificity and hormone binding in proteins such as the epidermal growth factor (EGF) receptor family and insulin-like growth factor-binding proteins (IGFBPs). It originates from Stylonychia lemnae (Ciliate) and exhibits UniProt keyword tags Membrane, Transmembrane, and Transmembrane helix.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 2258, 43, 30470, 17, 3189, 6865, 1988, 1977, 43, 8666, 17, 5536, 3031, 3286, 1922, 1920, 7883, 1927, 3148, 6941, 7784, 2409, 2733, 8201, 1922, 15021, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 21464, 8256, 8666, 17, 5536, 6865, 1988, 23658, 3993, 3040, 3835, 4576, 1930, 5461, 5305, 8666, 4248, 15326, 1942, 2386, 14384, 11830, 9031, 18, 2052, 3031, 5107, 1922, 3137, 9425, 1922, 14, 21464, 8256, 15213, 1957, 14, 1930, 1977, 7115, 1956, 10825, 2697, 2427, 1966, 2616, 3860, 13797, 2012, 1921, 17, 21, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 2905, 2991, 3148, 8666, 17, 5536, 3418, 13975, 16, 2154, 4952, 43, 4346, 5219, 2651, 10825, 3148, 6941, 7784, 1930, 2743, 2697, 1988, 1977, 4140, 1958, 2733, 8201, 18, 4378, 2007, 43, 11830, 17, 4124, 3728, 3165, 43, 161, 17, 14565, 16, 2052, 3418, 7624, 1942, 5207, 4896, 1930, 6365, 2743, 1922, 2697, 2427, 1966, 1920, 9844, 2905, 2991, 12, 4451, 13, 3148, 3416, 1930, 4122, 17, 3189, 2905, 2991, 17, 2743, 2697, 12, 16568, 1036, 13, 18, 2176, 22970, 2037, 26435, 14186, 19519, 1019, 15551, 26243, 12, 15714, 2057, 13, 1930, 9826, 20709, 11121, 2538, 14392, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MVGIDTGYISGIAYRFSFFIINTKQNSFPLKFPGFKYDTWDLQYSNSYADTSQDRFQVYVDPNFGMQYAGQRSFHDCSTDSFVLFTIQERDGPSDVTDSDFNFLSIGVQGDGYIYIEMRLVDNEVVVALKEKTTTLQHIYEFSYVNMYHRSEYTTASPYYSKYYTFFRGFYSGCKDYITYDTAIPDESVYGLCMRGWIQYAELWTSSSSVWTSSTARETDNTFAITATQMLIFDSSTATLASNIVKSPASSYYTCNIDLSTFKCTLSRVTATSWISFFPAMFTMEAWFRLDPIDLRPDGYISQVFALYDNTAKDHDLHYLFNETTDYWHYVAVSYTRLFERETRIQVFLDNISVLTTRIFDMNARPYCLNDKSLWINVDSTKCVKKGATGCTFCDTDETGVTAGTYNGCRYCKSAATSSDCYLCNQTSLFHKDYTKTATTDVATIKNADRITCICSLRCAVCTDILNLNCDMCADGAYKVYKGKCEYKCPELPQDPQGCIDGYYWDWAKMNCTQCYSLCRTCEFKSPLCTSCPIGRYVGTNGMCVETCGDGYRFSLTGCDDGNTKDGDGCSSQCIPEDGYQCYVNEFNDVILNFSRPINLTSGTLTIKDLRLFIRDSLYLYTIFKDDVIGGAYYDQIMRIEYQNTKTIIDINKKEVKKSTYARVLGFVFSAIAFWMTIAEFTKKSVLPAVFVLLAFQQIFYIGCQDLYLDQKTIQNNWIEVSYYFKRIFNNNFYFLGEVEMLGFLLFIFTQCISQKRLLWFNKYIAKQYFFSGPLLMTFIFCYPMQMYSLVVSFFIAFMLFLVWLCSWLVVVLHYKYRGHSLLIDKYSFLASSIILAVLVKYTLGPLVIQAFLCAAVNTYKFIYLQVIVYLLVFRELLIGILNFECLLFSDYGSDKSMIGEINTLNFFTTYDGTNNRIVNSNSIGHTGTQFINHPDFFYHMWFYTVRAGWNYIAIDVSESEDDEVSKDVVVVFAITGYIDCTGTHRFCNNRFGTVKYLDTKTYKPFYQPSIGRITTNETNYYRLGFGISNTFLRIYIDDTIWYIFQPDQTHEIHIANNFPGIVRKTKCFYNCYDFGYYISGTSCTECHDGTITMGGGDLCMKCDENYEKDDENRICNYDKTKLLKPELTTEQNCEKCESFWNNAMMFGGDPNKKDTCLYIPTELVGATGNFKDIDYKVKLFNLPSNYWLYTYKFFPEIERSDAELYGKLSSYFFSFFRIFRLEHTKLQNYFNNSIKIYSLYIYFFFMPLVLIIDSVTTFLEIRTMTTKNEYYKNVKNYSFLLQICIPFLITRRLSFKQTITNAIVIGT", "metadata": {"id": "A0A078B7H0", "cluster": 2245783, "interpro_all": ["IPR013320", "IPR006212", "IPR009030", "IPR011936"], "interpro_used": ["IPR006212", "IPR011936", "IPR009030"], "interpro_unused": ["IPR013320"]}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein belongs to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It originates from Rhodanobacter sp. SCN 68-63 and exhibits UniProt keyword tags Cytoplasm and rRNA processing.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 14440, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 22970, 2037, 11490, 9286, 7972, 2341, 1915, 2056, 18, 14870, 5117, 17, 4968, 1930, 9826, 20709, 11121, 2538, 14392, 5239, 1930, 9067, 4587, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MAQSRNTNSGSAPLQHIPVMLGVLSRLGPDGRLLLMDRDPQAIAAEWDETAAGLDGILLDLGVSSPQLDEAARGFSFMALARADEREIADVLWQFGEERHARRIARALIERVVGRREPGKHPAGLDAALERLKVGGRLSIISFHSLEDRAVKPVGKAQFPSDAEQAANPRSRSAVLRVAEKLAEAVEGLAVKAGGRYLDGTFGRGGHARAAAKAAFADDPRVSIRHANFSSLDAPLDMRMDTTQGESAAEFAIVADRDATPFTRTGQLATRSFQALRIRVNGELESLQRLFIRDHSGRTQGSRRGPPVAAAPARLA", "metadata": {"id": "A0A1E4Q4U4", "cluster": 5286398, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein can be placed in the Protein kinase-like domain superfamily, which modifies other proteins by chemically adding phosphate groups. This enzymatic activity is fundamental to most signaling and regulatory processes in the eukaryotic cell. Moreover, the protein contains a Serine/threonine-protein kinase active site that catalyzes the transfer of the gamma phosphate from ATP to serine or threonine residues on protein substrates, utilizing a conserved aspartic acid residue essential for enzymatic activity. This reversible phosphorylation regulates diverse cellular processes, including division, proliferation, and apoptosis. It is expressed in Pseudocercospora eumusae and features UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2213, 4016, 17, 3189, 3418, 13975, 16, 2154, 25436, 2303, 2697, 2007, 13944, 8013, 5413, 2671, 18, 2052, 8145, 2455, 1977, 8829, 1942, 2501, 3197, 1930, 4948, 4028, 1922, 1920, 10825, 2024, 18, 3950, 16, 1920, 2213, 5461, 43, 8468, 19, 13143, 17, 2213, 4016, 3500, 3200, 1988, 17097, 1920, 3856, 1927, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 2014, 13143, 4248, 1990, 2213, 6249, 16, 10232, 43, 5305, 23047, 2687, 6181, 4415, 1958, 8145, 2455, 18, 2052, 10743, 4050, 7014, 6445, 3689, 4028, 16, 2710, 8451, 16, 4031, 16, 1930, 4091, 18, 2176, 1977, 3198, 1922, 11520, 2337, 4879, 3508, 8846, 4791, 23084, 3336, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MSSQPPGTFLPNTKVTVGNKHELAVLKRVAVPDKEHLANMRTEVETMKKLKGHTVFLLMEYCSGGGLIDFMNTRLQHRLTEPEILKIFLKPPLLHRDLKVENVLISKTANGTEGRLIEEDVQKHTTMQYRSPEMILCYYTTPFEAVGQMAILNATFKYPSYPPFSDRLKKLIGWMVCSMRGSEIPIKDIYANRTHSEVRRNEQQIPDITPMRRGRLPAPPQQGAAPAKAPPYDVRAGAVDELSKRFPSVDEFAIAHSTKTNDPNDLNQRVTNALADEVFSTSGRVAQMIETVQGSPEKSEFAITSTGKEHRPGFNYKSTAVGSSPPPGSIKKLPNVSDRPIWRVPAVASSLKPSLRSTQRPALLDVHRSKSQIGTLAVDHALADAGIHRAKSLNARSRPTSMYVSSNMDYLRSHEAAIEDDMEFLRDGEVSSDHRKMIGKKFGNAFKRFENNDGKRTQGFATPETHDTEDLPPDVKRELERQKLAAEENRVAAAAEEYRTRIANQGRVQSLLDEGRQSPQPRRTAEGYGRRPPIIAPKPAINPNSTGNPYMKTRLLPSRVVSRPSAPPKPTVLRTGTGPRAPLKLEGVPDYPAASGLSQSQAQNNLMEVETEIGGERRTMRVKEIHKVYIEKYLSEGGFAHVYVVRIPRENNKIVTYYDSHASQLKGGGYEGDCAEGVATMHYPVYKICDFGSAAQPRPAAKTAEDVWRKQPINEKADIWALGVLLYKLKEDPRNRPTIYQVIKESLPSSDAVSTAPVGLQKTAPQVQVSPARGDPFAALDSKNDGGKFSFPPTSPPVASPKVSGSPAPTASSKTSRVPTTSSQPVAQQVQQFNQIEQPFPIPDSSRPSSQPHASEEASSSSRPSLEGGRPSAHEDQEQQRKRPSMEMRRHSRHASQSRDPTLKGSHHRKRSSLGETGDGTQMLSPITGSEATPSRHSDMNSEIDEPGIAIPSRASTIQQYTEPSDGEQRQAPQQQLPVTSGTDPPPASTPPPPTTSATESASLQPPYDPVKAVQPEQTGRLAALLAKDFSPTSPEDLESFSKRYPSLNMEM", "metadata": {"id": "A0A139HY18", "cluster": 7635739, "interpro_all": ["IPR011009", "IPR000719", "IPR008271"], "interpro_used": ["IPR011009", "IPR008271"], "interpro_unused": ["IPR000719"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein features a Glycosyltransferase 2-like domain that catalyzes the transfer of sugar moieties from activated nucleotide donors, such as UDP-glucose or GDP-mannose, to specific acceptor molecules to form glycosidic bonds. This domain participates in the biosynthesis of diverse structures, including cellulose, dolichol phosphate, and teichoic acids. It is expressed in Rhizobium sp. BK619.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 4075, 43, 20067, 9961, 22, 17, 3189, 3418, 1988, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 5489, 8276, 16, 2427, 1966, 18500, 17, 3817, 2014, 15217, 17, 17936, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2052, 3418, 17241, 1922, 1920, 8132, 1927, 6445, 4061, 16, 2710, 12343, 16, 17837, 2108, 1945, 5413, 16, 1930, 3602, 2108, 8643, 4576, 18, 2176, 1977, 3198, 1922, 13458, 23156, 2056, 18, 13702, 9171, 1026, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MLSILICTTGGGDLQEVVDTFRLNALAATDKRLKIHVNPSNLGLIPTEQRLAKIYAHFQATSADFVYSFAEGKSVASTVAYRRSRVVDIGGYCEPFRYAQDYELYLRSITVAKRKRQALFSFAARLMDISEAGNFFRRLRRSIGLGKRETDVPLEIVIVVDDPSADVAKTKSLNVGLRIASGDVIVRNDDDDEGNSSTWAIKGPIEGHEIVAALRKRNFISARQGLTFSCIPEQLIQRRYSAESLSDAARTILKYSFILLTP", "metadata": {"id": "A0A7W5XAK0", "cluster": 7747650, "interpro_all": ["IPR001173", "IPR050834", "IPR029044"], "interpro_used": ["IPR001173"], "interpro_unused": ["IPR029044", "IPR050834"]}, "task_type": "infilling"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein contains a Serine/threonine-protein kinase active site that catalyzes the transfer of the gamma phosphate from ATP to serine or threonine residues on protein substrates, utilizing a conserved aspartic acid residue essential for enzymatic activity. This reversible phosphorylation regulates diverse cellular processes, including division, proliferation, and apoptosis. Moreover, the protein is assigned to the Protein kinase-like domain superfamily, which modifies other proteins by chemically adding phosphate groups. This enzymatic activity is fundamental to most signaling and regulatory processes in the eukaryotic cell. Also, the protein belongs to the Serine/threonine-protein kinase Atg1-like family, which comprises enzymes such as Atg1, Unc-51, and Ulk1-3 that function as central regulators of autophagy and vesicle formation, particularly in response to starvation. These kinases often associate with Atg13 to drive autophagosome formation and the cytoplasm-to-vacuole targeting pathway. Additionally, they play essential structural roles in neuronal development, facilitating axonal elongation, guidance, and filopodia extension. It occurs in Entamoeba histolytica HM-1:IMSS-B and is linked to UniProt keywords Transferase.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 5461, 43, 8468, 19, 13143, 17, 2213, 4016, 3500, 3200, 1988, 17097, 1920, 3856, 1927, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 2014, 13143, 4248, 1990, 2213, 6249, 16, 10232, 43, 5305, 23047, 2687, 6181, 4415, 1958, 8145, 2455, 18, 2052, 10743, 4050, 7014, 6445, 3689, 4028, 16, 2710, 8451, 16, 4031, 16, 1930, 4091, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2213, 4016, 17, 3189, 3418, 13975, 16, 2154, 25436, 2303, 2697, 2007, 13944, 8013, 5413, 2671, 18, 2052, 8145, 2455, 1977, 8829, 1942, 2501, 3197, 1930, 4948, 4028, 1922, 1920, 10825, 2024, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 8468, 19, 13143, 17, 2213, 4016, 9353, 1009, 17, 3189, 3416, 16, 2154, 12936, 5038, 2427, 1966, 9353, 1009, 16, 5269, 17, 4892, 16, 1930, 3570, 4835, 17, 23, 1988, 2347, 1966, 4101, 9098, 1927, 6661, 1930, 11502, 3337, 16, 4443, 1922, 2644, 1942, 12767, 18, 2144, 7784, 3868, 11774, 1956, 9353, 3633, 1942, 9265, 21631, 3337, 1930, 1920, 5239, 17, 1942, 17, 20309, 5133, 3374, 18, 4950, 16, 2611, 3918, 4415, 4346, 5456, 1922, 5121, 2740, 16, 12440, 10623, 9971, 16, 9765, 16, 1930, 24137, 7140, 18, 2176, 5110, 1922, 8496, 1976, 6802, 7972, 2968, 26656, 5833, 17, 21, 30, 23828, 1036, 17, 44, 1930, 1977, 4624, 1942, 20709, 11569, 13763, 18, 3], "output": "MENYTLAPLSQVTKFTIQDELYKDSKIEIHKATERSGLRHRQVRIVAIKMIKVDENKIEENKRREVYSKYMETIDNPHVLQYFNSFYTTIRGSLEYWIIMEYCSFKSIDEYWKSNAIIQQDQNLFFISDIAIGLEYIYETLNHQHLHLYPCNILLSRDPASIFPKVKLSNFGLCDQFEQTIPNELELCDVDYAAPEYLNWYSHSKSDVWSFGMLIFKLLVGRLPFELMQMDSFSAIPAQVFIDVSSFIQNEMACDLLSKMLQYDPDERISMQEVLTHPFIQMCKNYKYGTQGKRENYKPLKQLDHGQFGQVFLAENTDHTQFAIKEISQRIDSLIREASCMRLCKHPNLVEYKDFFEWNHSMIAEIRGEQSPEGKYVYLVMEYCNAGNLEIYIKNKPTPLSNEEISYFLGEICSGLWYLHFNKRLIHRDLKPANLLLKSSSSKYPLLKIADYGFSRGIDGMMKSMVGTPLYEAPEIRKNQPYTAKADLYSLGVILYYMATKEFPFTDIPDVFQNAMTNELPAEFRDDIIINDQLKHLILHLITHHEKDRLSWKEVYKHPYVIQSLNLSKRIRSANDEVNSF", "metadata": {"id": "M3SDW4", "cluster": 8100790, "interpro_all": ["IPR045269", "IPR011009", "IPR000719", "IPR008271"], "interpro_used": ["IPR008271", "IPR011009", "IPR045269"], "interpro_unused": ["IPR000719"]}, "task_type": "autoregressive"} {"instruction": "The desired role of my protein is: The protein is assigned to the Hemingway/CFA97 family, which is required for motile cilia function and sperm flagella assembly, as characterized in *Drosophila*. Members of this family, including the human orthologue CFAP97, typically localize to ciliary structures such as the primary cilium. It has been detected in Clytia hemisphaerica. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 1977, 6304, 1942, 1920, 28881, 2029, 5234, 19, 18456, 8528, 3416, 16, 2154, 1977, 3414, 1958, 21150, 15714, 2347, 1930, 6283, 26538, 5957, 16, 1966, 4378, 1922, 14, 8273, 14, 18, 4678, 1927, 2052, 3416, 16, 2710, 1920, 2616, 11382, 2182, 18456, 1034, 8528, 16, 5745, 14380, 1942, 17542, 4061, 2427, 1966, 1920, 3065, 28997, 18, 2176, 2258, 2252, 3330, 1922, 2111, 2355, 2126, 9459, 29164, 6102, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MSFQSEGIRHIEINKKSNYDSDNFESDDNDDVDETNSYSSSQQSSSNSDEDSDKSESEDEVSISSKSDIEEKGNTVNEESDKDIEDEKEEEYIKPKKSVNFDSLLKAVIEINDKIEDKERQLKALGDTKNKHFKKGSKSNPGKKTRPRTAVLEYRDESEYSSFDGNESDSESHVSMNSRASSSIRKRPQSSVPSLHGSSSTSRMNMSFSNEKVKSIDKENQRLLKQLLHTKLSAKKPAIVRKKAPQARVQSASSINRNKRQLEIERENLRLLGKLQNVKPSSGITRTTLLSDHSKHEQFSGRIGRSSRPVSAISASHGRRPFSGRSSSSKYFDDSASMMSASSTSSKKSNKDRLTKGNLERQRNWNDRW", "metadata": {"id": "A0A7M5TY83", "cluster": 9311685, "interpro_all": ["IPR038791", "IPR029488"], "interpro_used": ["IPR029488"], "interpro_unused": ["IPR038791"]}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein contains a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is identified in Ignavibacteriota bacterium.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 5461, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 2899, 1922, 12046, 9188, 7972, 2341, 18842, 7336, 14061, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "YFSTNDSIDFTLIKDIMIESKCLFSLMSHISNLNFLQNEIRNDFEKYVFKYYPEIKGTGSTVYGIFDNLESAESAAVKLPISYFK", "metadata": {"id": "A0A959P0X5", "cluster": 11054834, "interpro_all": ["IPR013750", "IPR036554"], "interpro_used": ["IPR013750"], "interpro_unused": ["IPR036554"]}, "task_type": "infilling"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein is assigned to the Immunoglobulin-like fold superfamily, which comprises domains characterized by a beta-sandwich of seven or more strands arranged in a Greek-key topology, facilitating protein-protein interactions often via beta-sheet interfaces. These domains are ubiquitous in animal proteins, playing critical roles in immune recognition, cell adhesion, and structural integrity in muscle proteins such as titin. It is derived from Planctomycetales bacterium and exhibits UniProt keyword tags Signal. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 6304, 1942, 1920, 11837, 17, 3189, 3728, 13975, 16, 2154, 12936, 4682, 4378, 2007, 43, 4666, 17, 18038, 1927, 5260, 2014, 2253, 13214, 14940, 1922, 43, 27568, 17, 3834, 13678, 16, 12440, 2213, 17, 2213, 3719, 3868, 3454, 4666, 17, 11130, 14857, 18, 2144, 4682, 2032, 15498, 1922, 4027, 2697, 16, 14797, 4140, 5456, 1922, 3743, 5708, 16, 2024, 6141, 16, 1930, 4346, 7996, 1922, 3760, 2697, 2427, 1966, 7090, 1921, 18, 2176, 1977, 3595, 2037, 4720, 2341, 13386, 3949, 1918, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 2733, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MKNSSKWSNRILASGILLGALAVSSCGGGGGAAGQPDPGNGVAPGTTNVSGQLVQGSDVKVSATVGSGLPGILVSLLNGSGQSFGTDVTDSTGHYEFKGVPSGNGYMVKVEFQSSQDLDGDGNPDHVELNFPVNLADQSVTQLLQRIGVSDSDDDGEFDAVEVEFHYSDDHGHMEDHHSEHRHRSGETLIDDDGDGQFEDSFDDSDADGISDDDDDHDSSDDNGGDDIGDDNGGDDNGGDDVGDDNGGDDNGGDDVGDDSGDDSGDDVGDDSGDDSGDDSGDDSGDDSGDDSGDDSGDDSGDDI", "metadata": {"id": "A0A9E6ZLT4", "cluster": 11761945, "interpro_all": ["IPR013783"], "interpro_used": ["IPR013783"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein is classified under the prokaryotic S-adenosylmethionine decarboxylase family, which regulates polyamine biosynthesis by generating the n-propylamine group necessary for spermidine and spermine production. These enzymes rely on a covalently bound pyruvate cofactor, generated through the autocatalytic cleavage of a precursor protein into active alpha and beta subunits, rather than pyridoxal 5'-phosphate. This group encompasses S-adenosylmethionine and arginine decarboxylases found in bacteria and archaea. Furthermore, the protein is a member of the S-adenosylmethionine decarboxylase proenzyme family, which consists of the single-chain precursors that mature into the active S-adenosylmethionine decarboxylase enzyme found in a wide range of species. This enzyme catalyzes the decarboxylation of S-adenosylmethionine to provide the aminopropyl moiety required for the biosynthesis of spermidine from putrescine. In addition, the protein is categorized in the S-adenosylmethionine decarboxylase, core superfamily, which catalyzes the decarboxylation of S-adenosylmethionine to generate S-adenosyl-5'-3-methylpropylamine, an essential n-propylamine donor for the synthesis of spermidine and spermine. This activity relies on a covalently bound pyruvoyl cofactor, which is generated post-translationally via a self-catalyzed intramolecular cleavage that processes the enzyme into alpha and beta chains. It has been detected in Synechococcus sp. A18-25c and is connected to UniProt keyword Zymogen, Lyase, and S-adenosyl-L-methionine.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 1977, 5947, 2441, 1920, 21545, 61, 17, 29283, 23568, 11215, 23922, 3416, 16, 2154, 7014, 27883, 8132, 2007, 9155, 1920, 56, 17, 20299, 3812, 2210, 4680, 1958, 6283, 5802, 1930, 6283, 2053, 3372, 18, 2144, 5038, 11396, 1990, 43, 16590, 4124, 11867, 15155, 16, 3999, 2596, 1920, 22658, 18914, 6404, 1927, 43, 7897, 2213, 2460, 3500, 4595, 1930, 4666, 6991, 16, 4356, 2254, 24828, 23859, 25, 11, 17, 5413, 18, 2052, 2210, 21569, 61, 17, 29283, 23568, 11215, 1930, 9732, 23922, 1036, 2435, 1922, 4802, 1930, 21501, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 23568, 11215, 23922, 1965, 14896, 3416, 16, 2154, 7543, 1927, 1920, 2957, 17, 4659, 10416, 1988, 6665, 2460, 1920, 3500, 61, 17, 29283, 23568, 11215, 23922, 4113, 2435, 1922, 43, 4743, 3109, 1927, 3038, 18, 2052, 4113, 17097, 1920, 22429, 1943, 1927, 61, 17, 29283, 23568, 11215, 1942, 3394, 1920, 3835, 20194, 2199, 11804, 3414, 1958, 1920, 8132, 1927, 6283, 5802, 2037, 5366, 2808, 11388, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 23568, 11215, 23922, 16, 4728, 13975, 16, 2154, 17097, 1920, 22429, 1943, 1927, 61, 17, 29283, 23568, 11215, 1942, 5655, 61, 17, 29283, 17, 25, 11, 17, 23, 17, 4963, 20194, 2199, 3812, 16, 1925, 4415, 56, 17, 20299, 3812, 6282, 1958, 1920, 4271, 1927, 6283, 5802, 1930, 6283, 2053, 18, 2052, 2455, 12850, 1990, 43, 16590, 4124, 6487, 12631, 10921, 15155, 16, 2154, 1977, 3999, 2753, 17, 8414, 1954, 3454, 43, 3543, 17, 12139, 18083, 6404, 1988, 4028, 1920, 4113, 2460, 4595, 1930, 4666, 7835, 18, 2176, 2258, 2252, 3330, 1922, 26734, 8256, 2056, 18, 8080, 1025, 17, 2637, 1030, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 15856, 2404, 16, 23928, 16, 1930, 61, 17, 29283, 17, 54, 17, 12417, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MEQSLPCLHPNPGWGDAQINPVSSSSPANTSATDMVGKHCIAGATLLNLITHRFEPQGVTGLALLAESHISIHTMPESACEHLRIELGARKHALRSFLRETPAAIAEAERTPCPERGLELYECDHSKLDDEAFLRTTITTAAKRWPENGYAAVDVFTCGDHT", "metadata": {"id": "A0A7G8IKE6", "cluster": 11782988, "interpro_all": ["IPR042286", "IPR003826", "IPR042284", "IPR016067", "IPR017716"], "interpro_used": ["IPR003826", "IPR017716", "IPR016067"], "interpro_unused": ["IPR042284", "IPR042286"]}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein incorporates a Leucine-rich repeat that folds into a characteristic horseshoe shape to provide a versatile structural framework for protein-protein interactions. Found in organisms ranging from viruses to eukaryotes, this motif typically utilizes its concave beta-sheet face to bind ligands, such as alpha-helices, and is involved in diverse processes including signal transduction, cell adhesion, and immune response. Furthermore, the protein is assigned to the Arabidopsis Inactive Receptor-like Kinases family, which functions in signal transduction and cellular communication, often acting as scaffolds or recognition receptors despite predominantly lacking catalytic kinase activity. These proteins regulate diverse plant processes including early zygote development, secondary cell wall formation, and immunity against pathogens like *Pseudomonas syringae* via interactions involving leucine-rich repeats and calmodulin binding. Also, the protein belongs to the Six-hairpin glycosidase superfamily, which encompasses glycosyltransferases that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptors to form glycosidic bonds. Characterized by an \u03b1/\u03b1 toroid fold with six \u03b1-hairpins arranged in a circular array, these enzymes are essential for the biosynthesis of disaccharides, oligosaccharides, and polysaccharides. It is native to Levilactobacillus hammesii DSM 16381.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 19683, 43, 12624, 17, 5536, 6865, 1988, 16231, 2460, 43, 6293, 15638, 10647, 1021, 5989, 1942, 3394, 43, 20425, 4346, 6465, 1958, 2213, 17, 2213, 3719, 18, 2435, 1922, 7373, 6485, 2037, 6241, 1942, 15021, 16, 2052, 5219, 5745, 18127, 2496, 26019, 4666, 17, 11130, 6171, 1942, 4566, 6908, 16, 2427, 1966, 4595, 17, 12789, 16, 1930, 1977, 3286, 1922, 6445, 4028, 2710, 2733, 8201, 16, 2024, 6141, 16, 1930, 3743, 2644, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 8900, 9078, 3148, 17, 3189, 7784, 3416, 16, 2154, 4088, 1922, 2733, 8201, 1930, 3689, 6396, 16, 3868, 8290, 1966, 10603, 2014, 5708, 4086, 4281, 7700, 7046, 6804, 4016, 2455, 18, 2144, 2697, 5741, 6445, 4496, 4028, 2710, 3120, 16160, 7229, 2740, 16, 4067, 2024, 4821, 3337, 16, 1930, 7611, 3316, 7741, 3189, 14, 13461, 19468, 3336, 14, 3454, 3719, 5884, 12624, 17, 5536, 9569, 1930, 17537, 2743, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 3798, 17, 14565, 7533, 9200, 13975, 16, 2154, 21569, 20067, 18580, 1988, 18170, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 6282, 4206, 1942, 2487, 27916, 1942, 2386, 7533, 12546, 9031, 18, 4378, 2007, 1925, 160, 19, 160, 8184, 2642, 3728, 1956, 3798, 160, 17, 14565, 1036, 14940, 1922, 43, 10262, 6472, 16, 2144, 5038, 2032, 4415, 1958, 1920, 8132, 1927, 2054, 11926, 16, 22012, 16, 1930, 18686, 18, 2176, 1977, 6196, 1942, 10157, 19167, 2341, 14357, 8898, 20355, 18522, 1033, 10964, 15199, 11425, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MANLFLQFSVLNLSNNDISGDLSQFPVTKWSKLKQLQLKENQLTGSIPENWAGLTNLDKDGFTGNIPAACFTSNLTHFEANGNQLSGSLPATLSKATNLKWLDVAANQLTGITSGRAAAGSSGTYQDWRISAPDWQTSHDGKTMTLDLSKYYGGEQGQSGYSNKTDPDHPLLTIDTASTNVTNGDFSFYLFDQAGSQAVFKQSMNYMAQTDDKIDFASKVGAGDKIGFVSPKVGAGVVPATNFKLGVSSTNAVGDSYQNGQHSTLLTDVAQSIYDYQPTLADDTTTVGDSSDATKGNLSTEVGSTAYKGTYKTSDAGQISPTTVSQMSPTLSGLPLEQEATRAKLQADMTKFVPKLAPYQELTESSGLWLLSLAMAGDESDFDTALSGIKARFYDSDTHTFNWQSASIDDLRIIQALLVMNRKSPNNDRTALISELIDGFTKYDMNAYYQMIIRLDYLDLATLKTIYEAKGLGTTTGTAGGTAYQQQLKLIKDSYISDQLPMFNTYYNYSTGSYQVTMLNLAKVGELPQTSLDWITAHTTADEKIYNDYNLDGSPASPTKLNAMTSTDTTSPLYGSAEAGGESYAFNDLNMLLAYNSVIAGSLNILELSSNQLSGTLDNISQLADLTEIYNLPDLSNNQQLTTLAYSNNQLGIEPAGGQTGVTLDVAVPITLAIPKTYAIDTGLTAQTTGLTSAGHTLPIYYSTGDVTYTLASAPADDPTTAADTDGVLYSGYLASQGKTDSAKGQDHTVTQGDGYSTKDGQEKRSDDNVSGQINVTDGLLYDAASNYAYVAQIAVALGDTKLYGQAL", "metadata": {"id": "A0A0R1UQR9", "cluster": 12197285, "interpro_all": ["IPR008928", "IPR012341", "IPR050994", "IPR001611", "IPR032675"], "interpro_used": ["IPR001611", "IPR050994", "IPR008928"], "interpro_unused": ["IPR012341", "IPR032675"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to create: The protein features a Sporulation-like (SPOR) domain that mediates localization to the cell division septum by binding preferentially to septal peptidoglycan. Found in bacterial proteins involved in cytokinesis and sporulation, this domain adopts an RNP-like fold to facilitate specific interaction with the cell wall. It is found in Novosphingopyxis sp. YJ-S2-01 and is annotated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix. Please provide the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 7762, 30, 1920, 2213, 4075, 43, 23647, 17, 3189, 12, 9130, 13, 3418, 1988, 10412, 5363, 1942, 1920, 2024, 8451, 17026, 2007, 2743, 10662, 1942, 16458, 24183, 18, 2435, 1922, 4543, 2697, 3286, 1922, 20825, 1930, 23647, 16, 2052, 3418, 24032, 1925, 24767, 17, 3189, 3728, 1942, 6628, 2487, 2835, 1956, 1920, 2024, 4821, 18, 2176, 1977, 2435, 1922, 9441, 3508, 7969, 2029, 14864, 18068, 1036, 2056, 18, 67, 1013, 17, 5159, 17, 3287, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MTDDVRRDLDLGEDDSLPWLETADDYDKPDGPSTGKVVLLVIAGLALIAVIFGGIFAFHNNSQEQSGNGELIAAQEGDYKVAPEDPQGKQFEGEGDAAFAASEGKSRESNAMPAKPAPPEPKATPAAAASSAAAGANAPASGGVMVQLAALNSEAAAEQQWSKLSGQYEYLKDMRHRVVKAEVEGRTVYRLSAVSSDRANANSLCNRIKSDGGSCLIAG", "metadata": {"id": "A0A8J7IAE5", "cluster": 12332951, "interpro_all": ["IPR007730", "IPR036680"], "interpro_used": ["IPR007730"], "interpro_unused": ["IPR036680"]}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein can be placed in the Zinc finger, RING/FYVE/PHD-type superfamily, which encompasses RING, PHD, FYVE, and U-box domains that share a common $\\alpha/\\beta$ structural fold, typically stabilized by zinc ions. These versatile motifs act as stable scaffolds to facilitate specific interactions with DNA, RNA, proteins, or lipids, thereby participating in diverse cellular processes ranging from gene transcription and chromatin remodelling to mRNA trafficking. Additionally, the protein possesses a Zinc finger, RING-type domain that mediates protein-protein interactions and typically functions as an E3 ubiquitin-protein ligase. This motif coordinates two zinc ions in a \"cross-brace\" structure to bind E2 ubiquitin-conjugating enzymes, thereby facilitating substrate ubiquitylation. It is identified in Stentor coeruleus and is annotated with UniProt keywords Transmembrane helix, Transmembrane, and Membrane. Generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1988, 2258, 1920, 2894, 3879, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 7997, 8497, 16, 6335, 19, 27976, 1961, 19, 13381, 17, 2601, 13975, 16, 2154, 21569, 6335, 16, 13381, 16, 27976, 1961, 16, 1930, 63, 17, 5758, 4682, 1988, 7948, 43, 3059, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3728, 16, 5745, 12017, 2007, 7997, 6982, 18, 2144, 20425, 8277, 4033, 1966, 4700, 10603, 1942, 6628, 2487, 3719, 1956, 2678, 16, 3146, 16, 2697, 16, 2014, 8238, 16, 6113, 9505, 1922, 6445, 3689, 4028, 6485, 2037, 2359, 3213, 1930, 6338, 19935, 1942, 3616, 9604, 18, 4950, 16, 1920, 2213, 14465, 43, 7997, 8497, 16, 6335, 17, 2601, 3418, 1988, 10412, 2213, 17, 2213, 3719, 1930, 5745, 4088, 1966, 1925, 10968, 6526, 17, 2213, 11905, 18, 2052, 5219, 10675, 2288, 7997, 6982, 1922, 43, 6, 3567, 17, 18303, 1972, 6, 3170, 1942, 4566, 6602, 6526, 17, 5225, 2287, 5038, 16, 6113, 12440, 4510, 24320, 18, 2176, 1977, 2899, 1922, 10772, 1924, 4815, 3176, 1952, 1957, 1930, 1977, 10633, 1956, 20709, 11569, 9117, 7864, 16, 9117, 16, 1930, 3260, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MVRLDTFMILLSIAWGKCNLCSTSGNLWWNNYTTNFICPYSSTCDSGCYKCINDNIEASCIDSSVVINCITNIVNIIQRTCSSSYYSKSSGGFRIKTPLEVLCYWQLDLRLFNKYSDQVEISLSNNTTLNDMVFILVYNIPYTDGIPFLRNYIGSLYTLKKSYIKVQGNYIVISFWRTSQNNVDFSLKWTTGDSNDSNSKLYLILSVFLPCVGICCCALCIYSFYRKKISRRIRPNVPYQVMNCTEHIDDSYIEEQIPAKYFLTKEKIICPICFDKYYIYSLTLGDQIRETFCKHVFHSKCIEEWIESKPLQYVCPVCKTCLFDIGRIGK", "metadata": {"id": "A0A1R2B9M9", "cluster": 14921057, "interpro_all": ["IPR001841", "IPR013083"], "interpro_used": ["IPR013083", "IPR001841"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein includes a Methyltransferase FkbM domain that functions as a methyltransferase involved in the biosynthesis of diverse secondary metabolites, including the immunosuppressant FK506. It catalyzes specific methylation steps required for the production of glycoside antibiotics and toxic antimetabolites like AMB across various bacterial and fungal species. Also, the protein falls within the S-adenosyl-L-methionine-dependent methyltransferase family, which catalyzes the transfer of methyl groups to various substrates involved in the biosynthesis of complex secondary metabolites. These enzymes modify compounds such as glycoside and macrolide antibiotics or iron-chelating agents, playing a crucial role in the production of molecules with antibiotic and immunosuppressant activities. It is present in Saprospiraceae bacterium and is connected to UniProt keyword Membrane, Transmembrane, and Transmembrane helix. What would its protein sequence look like?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 5921, 43, 16478, 13134, 20891, 3418, 1988, 4088, 1966, 43, 16478, 3286, 1922, 1920, 8132, 1927, 6445, 4067, 6926, 16, 2710, 1920, 27996, 2031, 30269, 18, 2176, 17097, 2487, 5547, 5983, 3414, 1958, 1920, 3372, 1927, 7533, 2261, 7560, 1930, 6161, 20330, 9215, 4627, 12191, 14652, 3189, 6168, 3436, 3425, 4543, 1930, 8697, 3038, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 3416, 16, 2154, 17097, 1920, 3856, 1927, 4963, 2671, 1942, 3425, 6249, 3286, 1922, 1920, 8132, 1927, 2796, 4067, 6926, 18, 2144, 5038, 11675, 4300, 2427, 1966, 7533, 2261, 1930, 23929, 2261, 7560, 2014, 5680, 17, 25814, 4820, 16, 14797, 43, 6608, 2770, 1922, 1920, 3372, 1927, 4206, 1956, 7267, 1930, 27996, 2031, 4209, 18, 2176, 1977, 2481, 1922, 9235, 5424, 11979, 1972, 3336, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "MSYLKQYILHKTGLLTFYNYWLFSGLHLFLMKWKNRSQWEEIKNEDLFYSGLLSPLKKSDALIFDIGANYGWTTLTFLKFSSQVIAYEPDINNLKILRYRFGDTNRLVIEAKAISNNIDGAVFYQNRNNSALNTLSLKWVDALTNGVYREKKIFTSEKYKVETSTLDIEMRKYGKPVFLKVDVEGHEYSVFEGLHSSIPLVVFEANLPEFVDETLSILEYIKNLDQNCSFNFAYNYNLQLKEYVNTDVLALKLKECNFSSIDIICRMSSYSNHFNDV", "metadata": {"id": "A0A935RZ57", "cluster": 18486428, "interpro_all": ["IPR006342", "IPR052514", "IPR029063"], "interpro_used": ["IPR006342", "IPR052514"], "interpro_unused": ["IPR029063"]}, "task_type": "autoregressive"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein is a member of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. In addition, it is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is expressed in Bacilli bacterium and is connected to UniProt keyword ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3198, 1922, 25332, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MIVGLTGGIASGKSTICHHLVDFGCYVMDADIVAREVVDVGTPGLEEVIRFFGEAYRQEDGSLNRAMLGQTIFHDEEKRQQLNAIVHPLVRERLWKEARAFSKAHTKAVVVLDIPLLFESGIASLADLTVLIYAPKNVQVERLMMRNQFDREEALARIEAQMSIEAKRALADWVVYNTGAQEDTMRLAHDLAEQLHQLAGQGSLEDGRVMRNLITKRAFQ", "metadata": {"id": "A0A7Y3KD16", "cluster": 18623262, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that will have the following function: The protein contains a PilZ domain that functions as a receptor for the bacterial second messenger cyclic-di-GMP (c-di-GMP) to regulate diverse behaviors including biofilm formation and motility. Upon binding c-di-GMP via conserved motifs, this domain undergoes a conformational switch that creates a new allosteric interaction surface to initiate signal transduction. Structurally characterized by a six-stranded beta-barrel and C-terminal alpha-helix, it is frequently found in effector proteins such as cellulose synthases and flagellar brake proteins. It is present in hydrothermal vent metagenome.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 7547, 1011, 3418, 1988, 4088, 1966, 43, 3148, 1958, 1920, 4543, 2812, 16716, 9821, 17, 2137, 17, 18033, 12, 45, 17, 2137, 17, 18033, 13, 1942, 5741, 6445, 5888, 2710, 9638, 3337, 1930, 9254, 18, 4073, 2743, 45, 17, 2137, 17, 18033, 3454, 5305, 8277, 16, 2052, 3418, 14928, 43, 8523, 6195, 1988, 15628, 43, 2814, 14772, 2835, 3154, 1942, 11051, 2733, 8201, 18, 12171, 4378, 2007, 43, 3798, 17, 10338, 4666, 17, 19560, 1930, 45, 17, 4262, 4595, 17, 7864, 16, 2176, 1977, 5467, 2435, 1922, 7917, 2697, 2427, 1966, 12343, 8921, 1036, 1930, 24154, 18303, 3324, 2697, 18, 2176, 1977, 2481, 1922, 26959, 14654, 16552, 2225, 18, 3], "output": "MAAGGAPRQGILSLTIKDKAALYAAYMPFVGNGGLFIPTSKSYNLGEEVFMLLTLMDDSERLPVAGKIIWITPAGAQGNKAAGIGVQFGPQDNGQTRAKIETYLA", "metadata": {"id": "A0A3B0XDN1", "cluster": 18992747, "interpro_all": ["IPR009875"], "interpro_used": ["IPR009875"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should feature a FecR protein domain that serves as a transmembrane signal transducer regulating ferric citrate transport. It senses periplasmic iron dicitrate and modulates the activity of the sigma factor FecI, activating transcription of the *fecABCDE* operon when citrate is present and inactivating FecI in its absence. Furthermore, it is part of the Fe(2+)-dicitrate sensor, transmembrane component family, which functions as a distinct group of transmembrane anti-sigma factors involved in signal transduction for iron sensing. These proteins, typified by *Escherichia coli* FecR, transmit signals from the outer membrane receptor FecA to the cytoplasmic sigma factor FecI in response to ferric citrate binding. It is native to Planctomycetaceae bacterium and is classified with UniProt keywords Transmembrane helix. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 16688, 1005, 2213, 3418, 1988, 10634, 1966, 43, 9117, 2733, 14848, 6773, 20247, 11599, 4860, 18, 2176, 7534, 1036, 24334, 5680, 9192, 26813, 1930, 13112, 1920, 2455, 1927, 1920, 5139, 2991, 16688, 1033, 16, 8019, 3213, 1927, 1920, 14, 16688, 20973, 3695, 14, 15675, 2469, 11599, 1977, 2481, 1930, 20862, 16688, 1033, 1922, 2496, 3905, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 2650, 12, 22, 15, 13, 17, 9192, 26813, 6443, 16, 9117, 4594, 3416, 16, 2154, 4088, 1966, 43, 4493, 2210, 1927, 9117, 2246, 17, 5139, 2790, 3286, 1922, 2733, 8201, 1958, 5680, 9306, 18, 2144, 2697, 16, 2357, 2828, 2007, 14, 10210, 5178, 14, 16688, 1005, 16, 17404, 4771, 2037, 1920, 7642, 3260, 3148, 16688, 1019, 1942, 1920, 6823, 5139, 2991, 16688, 1033, 1922, 2644, 1942, 20247, 11599, 2743, 18, 2176, 1977, 6196, 1942, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 7864, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MNEPDNTHPAGDLGDQEFLEWVMRYQDGTLTFAEVRQFSEMLQNDPAKKTQFRRIQLRTATLHDLFRMDAFSRSGMLLDDQRDSDPAKRTPRRTLLRDAFRPAILGWTGVISLSLLLVCGLSFWNRIHSPKPGASVVAPLMAESSVLLVEENRATFFGSKVLVAGQNVPLHQDYLLNTGMIKLRFPSGATAIVEAPSIFRVNSEDSLVLNTGGCSVHAPPGAEGFEVLTPMTKVVDRGTRFYVNVQDTSETEVHVIEGAADLYAINRVEEGTDKSSTAQPPLGDSAALRLVDGEAVQLGGFVADSGERTVFNPARYRGQLPDRLISYEATSTVDGMADELTSLTVQRRGHIQTYAVEDLVPIEVLAFGGSSEPEANGYLCGSRKRPSRPENWLEDRTLSTGLINFGGQESPLEQLPLREDGTLDVALCPPGLGIRFRTPVVNHPGPDVVLFEIQSFVNLAEGDPFHVYPVSPREDLRPFTVRKYDLTLNSSGIRQVAPLWSHRFPEPMWSLDELRDRDAPVIVDVGRMHFHVIAAGIDLSDLGYAQGEAVSELFIQHASPDLKVKVDPVFIAGLPPLNREDFPEPNPADSH", "metadata": {"id": "A0A954E962", "cluster": 21937190, "interpro_all": ["IPR006860", "IPR012373"], "interpro_used": ["IPR006860", "IPR012373"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein should include a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. Additionally, the protein is grouped in the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. In addition, the protein should include a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. It is native to Arachnia propionica and corresponds to UniProt keyword Hydrolase and Metal-binding.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 2176, 1977, 6196, 1942, 15243, 10306, 5062, 14207, 1019, 1930, 8852, 1942, 20709, 11121, 2538, 20748, 1930, 6048, 17, 2743, 18, 3], "output": "MTNENPLLPLVRAALHTVEDPEIRRPITELGMVDELTADDEGQLFIRVLLTVPGCPMRAEITKRVTEAVETVEGVKGVHVELGVMDDEQRSAMRQVLRGGQPEREIPFAKPGNLTKVIAVASGKGGVGKSSVTVNLALALAKAGRDVAILDADIYGHSIPDMLGLGDSRPTVVDDMILPVPAAEGLKVISVGMLKPSRDQVVAWRGPILDRALTQLLADVFWGDVDFLLLDLPPGTGDVAMSLGQKIPNSEVLVVTTPQLAASEVSERAGTMAHILKQRVLGVVENMSWLEFTAPDTGKSYRIELFGSGGGTLVAEALSERLGYDVPLLAQVPFDEALLAGGDRGEPLVLSAPDHPAAQALLNLGEDLANRSRNLLGRMLPVSPV", "metadata": {"id": "A0AB37I0P6", "cluster": 26011681, "interpro_all": ["IPR034904", "IPR002744", "IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR000808", "IPR033756", "IPR002744"], "interpro_unused": ["IPR044304", "IPR034904", "IPR019591", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: It is part of the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. In addition, the protein is included in the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It is found in Betaproteobacteria bacterium and is classified with UniProt keywords Transferase, Cell membrane, and Phospholipid metabolism.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 2176, 1977, 3131, 1927, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 1977, 2435, 1922, 4666, 9218, 1021, 10296, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 13763, 16, 2024, 3260, 16, 1930, 14608, 4714, 18, 3], "output": "MSDSDLPESPHKGQRESAFRQEVALAVVLIPLAGSVLLVLLVELLNSSTHRLSKRAKDLGSAAVGQAFALLPRGLQRLLNALFYSLSGLRLAFHHCIVDVSAAERVLLFVEAAVDRIGFDLTALVLLATTWGLIALPALIRL", "metadata": {"id": "A0A536ZG59", "cluster": 26620611, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR033718", "IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: It is part of the Alpha/beta knot methyltransferases superfamily, which encompasses enzymes containing a deep, rare \u03b1/\u03b2 knot structural domain essential for RNA methylation. This fold is characteristic of S-adenosyl-L-methionine (SAM)-dependent enzymes, including the SPOUT and EMG1/NEP1 families, facilitating the modification of RNA substrates. Furthermore, the protein is a member of the RNA methyltransferase RlmH family, which is predicted to function as an S-adenosyl-L-methionine (AdoMet)-dependent methyltransferase based on structural homology. These enzymes likely catalyze the transfer of methyl groups to RNA substrates for regulatory modification. Also, the protein can be placed in the tRNA (guanine-N1-)-methyltransferase, N-terminal superfamily, which represents the N-terminal domain of SPOUT superfamily enzymes, including the tRNA:Gm18 methyltransferase TrmH. This domain is characterized by a rare \u03b1/\u03b2 knot structure that poses a significant folding challenge. It is native to Methanocalculus chunghsingensis and exhibits UniProt keyword tags Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 2176, 1977, 3131, 1927, 1920, 4595, 19, 4666, 26646, 28253, 13975, 16, 2154, 21569, 5038, 3165, 43, 6515, 16, 5844, 160, 19, 161, 26646, 4346, 3418, 4415, 1958, 3146, 5547, 18, 2052, 3728, 1977, 6293, 1927, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5038, 16, 2710, 1920, 18055, 1984, 1930, 13952, 1009, 19, 26046, 1009, 5767, 16, 12440, 1920, 6295, 1927, 3146, 6249, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 3146, 16478, 11929, 22316, 3416, 16, 2154, 1977, 4396, 1942, 2347, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 12, 2041, 14080, 13, 17, 3100, 16478, 2454, 1990, 4346, 9039, 18, 2144, 5038, 3205, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 3146, 6249, 1958, 4948, 6295, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 10089, 12, 16904, 17, 13007, 17, 13, 17, 16478, 16, 56, 17, 4262, 13975, 16, 2154, 4972, 1920, 56, 17, 4262, 3418, 1927, 18055, 1984, 13975, 5038, 16, 2710, 1920, 10089, 30, 28673, 1025, 16478, 28402, 1023, 18, 2052, 3418, 1977, 4378, 2007, 43, 5844, 160, 19, 161, 26646, 3170, 1988, 17274, 43, 2228, 10328, 6013, 18, 2176, 1977, 6196, 1942, 17348, 5000, 18021, 5277, 1036, 29052, 8092, 19017, 8362, 1930, 9826, 20709, 11121, 2538, 14392, 5239, 1930, 9067, 4587, 18, 3], "output": "MHIRIIAIGKVKDSWMKEGIRDEEKYSSEGEKRRAMEREGATLLAAFADLVREREIAGTGDLVFLIGGPDGLSDELLLEQIYRAFRIIRGEPYHRLHSRLRPYTRLSITEFPASKDPALLIALDPAGKEMPSEVKKRSDLLLSLSEMTFPHTLARL", "metadata": {"id": "A0A8J7W6I1", "cluster": 27643178, "interpro_all": ["IPR029028", "IPR003742", "IPR029026"], "interpro_used": ["IPR029028", "IPR003742", "IPR029026"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein is included in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Furthermore, the protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It originates from Wenzhouxiangella sp and has UniProt annotations ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 22970, 2037, 2038, 1022, 19902, 18068, 5285, 11560, 1019, 2056, 1930, 2258, 20709, 15010, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MSAPAAANSDRQRPLLVALTGGIASGKTAVSDRLAALGAQVIDTDLIARKVVEPGQPGLAAILEAFGKEVIRDDGRLDRAELRARIFEDAASRQRLENLLHPLIKARVEQDIATSTDSPYIVLVVPLLVETGLFTDADRIVVVDVPEATQLERLTRRDGGDERQARAILAAQASRRQRLDKATDVIDNSGSLAELQAQVDSLHERLTGLAE", "metadata": {"id": "A0A8B5WGZ6", "cluster": 28945305, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Moreover, the protein contains a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein is a member of the Small ribosomal subunit protein uS5 domain 2-type fold superfamily, which features a left-handed \u03b2-\u03b1-\u03b2 structure utilized in diverse nucleic acid-binding proteins and GHMP family kinases. This domain serves as a key component in translational machinery and DNA repair enzymes, such as MutL and DNA gyrase B, while also facilitating ATP-dependent phosphoryl transfer in metabolic enzymes like galactokinase and mevalonate kinase. It is found in marine metagenome and is annotated with UniProt keywords Transferase.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3950, 16, 1920, 2213, 5461, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2858, 11196, 5903, 2213, 2022, 1015, 3418, 22, 17, 2601, 3728, 13975, 16, 2154, 4075, 43, 3506, 17, 17105, 161, 17, 160, 17, 161, 3170, 7079, 1922, 6445, 11079, 2687, 17, 2743, 2697, 1930, 6101, 6588, 3416, 7784, 18, 2052, 3418, 10634, 1966, 43, 3834, 4594, 1922, 8414, 10853, 1930, 2678, 5059, 5038, 16, 2427, 1966, 2446, 1024, 1930, 2678, 9430, 2051, 44, 16, 2679, 2222, 12440, 4498, 17, 3100, 12556, 3856, 1922, 4487, 5038, 3189, 9479, 18655, 1930, 21750, 20807, 5791, 1021, 4016, 18, 2176, 1977, 2435, 1922, 10789, 16552, 2225, 1930, 1977, 10633, 1956, 20709, 11569, 13763, 18, 3], "output": "GVDIKLEKRIPSGAGLGGGSSNASGVIKGLNSIYKLNLTEAQMKSIASSLGADISFFIHGGTQKGEGIGDRLYILPHPVKGAILLVIPDVNIDTSWAYGLIKNKLEYVGKSPNFASFFQENIFPEEIFKNDFEEVVFPAYPEIGKIKTALIKLGAVYASLSGSGSTVYGIFNDESVAVSAESHFNSSYHTIVTFSANSKISY", "metadata": {"id": "A0A382DSJ2", "cluster": 909947, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR014721"], "interpro_unused": ["IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence be if I wanted a protein that could perform the following function: The protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein has a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is present in Deltaproteobacteria bacterium and is associated with UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 2481, 1922, 9649, 9218, 1021, 10296, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MKIRAPAKINLRLRVVGKRKDGYHLIDTIVVPVSLYDEIEITKKRTHGAGEMNSKHLEVTCDHPLVPGGEKNLAYQAASTLLKHKEIRESVHIHISKRIPVGAGLGGGSSDAAAVLVGLNRLLGLDYSLKKLEKIALSLGADVPFFIKGVPARARGIGERLTPISGFSPLWLVIAYPGFPVSTAWVYGNLRLKLTKSRVNTSIISLLRSPDKIKRLLVNDLETVATGRYPEIGLLKEKLIRTGAAGALMSGSGSSVFGVFDSRRRAEQALRRLRKQEGVETFLVQALTQRNVKEAH", "metadata": {"id": "A0A535B4S8", "cluster": 3415430, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR013750", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein should include a HPr kinase/phosphorylase, C-terminal domain that functions as the catalytic core of the bifunctional enzyme HprK/P, regulating carbon source utilization in Gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 on the phosphocarrier protein HPr and its dephosphorylation via phosphorolysis, typically within a hexameric assembly. Furthermore, the protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is native to Elusimicrobia bacterium CG11_big_fil_rev_8_21_14_0_20_64_6.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 3066, 3951, 43, 18542, 4016, 19, 12556, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 1920, 29491, 4113, 18542, 1040, 19, 58, 16, 6773, 5056, 4585, 8422, 1922, 8604, 17, 2843, 4802, 18, 2176, 17097, 2321, 1920, 4498, 17, 3100, 4050, 1927, 2375, 17, 4182, 1990, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 2496, 16881, 3454, 3421, 6892, 16, 5745, 2651, 43, 25602, 1935, 5957, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 6196, 1942, 2349, 24327, 4913, 15129, 2126, 14061, 7294, 3242, 41, 9769, 41, 3313, 41, 5197, 41, 28, 41, 2900, 41, 2607, 41, 20, 41, 2036, 41, 4723, 41, 26, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MEIRGLGVIDLESWTAGTMYDRTRIPVSPGRNLAVLIEVAALNTKERGVKLLFGIGAIRDRTRIELAIKGLDAKKLTILDVEIPLIQRLRSQGYFSAENFNKRLIERMK", "metadata": {"id": "A0A2H0P033", "cluster": 4494541, "interpro_all": ["IPR011104", "IPR027417"], "interpro_used": ["IPR011104", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein should include a TRAP C4-dicarboxylate transport system permease DctM subunit domain that serves as the large integral membrane component of tripartite ATP-independent periplasmic (TRAP) transporters. It utilizes an electrochemical ion gradient to mediate the uptake of specific substrates, including C4-dicarboxylates like succinate and malate, sialic acid, or 2,3-diketo-L-gulonate. It is native to Cupriavidus necator (Alcaligenes eutrophus) (Ralstonia eutropha) and contains UniProt keyword associations Cell inner membrane, Cell membrane, and Transmembrane helix. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 10947, 10872, 17, 9192, 15441, 2010, 4860, 2433, 6191, 2051, 22936, 1035, 5903, 3418, 1988, 10634, 1966, 1920, 3103, 12328, 3260, 4594, 1927, 8027, 24707, 4498, 17, 3484, 24334, 12, 10947, 13, 10538, 18, 2176, 18127, 1925, 13197, 4755, 6494, 1942, 8265, 1920, 5047, 1927, 2487, 6249, 16, 2710, 10872, 17, 9192, 15441, 2209, 3189, 19234, 1930, 24260, 16, 20436, 2687, 16, 2014, 22, 16, 23, 17, 2137, 18540, 1037, 17, 54, 17, 3194, 6012, 5791, 1021, 18, 2176, 1977, 6196, 1942, 14967, 3027, 9188, 10015, 1036, 3296, 3061, 12, 4143, 12498, 14687, 1036, 24048, 2789, 1957, 13, 12, 15906, 20476, 2126, 24048, 2789, 1019, 13, 1930, 5461, 20709, 11121, 2538, 5253, 2024, 6671, 3260, 16, 2024, 3260, 16, 1930, 9117, 7864, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MEHTAETFAAAPQEPGAALAFWGRAMRWVVEIPAALIVLAEIAILGGGAFARYVLHAPIPWTDELASILFLWLAMLGAIIALQRSAHMQLTTFIKNLAPSRRAWLDAFGMWLVVAFLLMLVWPAYEHLSEHIDVSSPTLEISEGYRSAAVLAGALLMLATAAIRLVAQADWKRVLVSGVAVGVLGAILWALSPVLAELGNINLVIFFLLMLVVCVAIGVPIAFAFGLATMCYLAFTTTTPLSIVPNRMQEGMSHLILLAVPLFVFLGALIEMTGLARAMISFLANLIGHVRGGLQYVLLGAMYIVSGISGAKAADMAAVAPALFPEMKQRGAKDGDLIGLLSASGAMSETIPPSIVLITVGSVTGVSITSLFIGGLMPAAVGLVMMACVVWFQTRKEDMSTAVRPTRAVIVKSLLVALPALALPVIIRTAVVEGVATATEVSTIGIFYAVLAGIIVYRRFHWRSIYPMLVDTAALSGAILLIVGCATTMAWALTQSGFADDLVKIMSAVPGGKTGFLLVSALAFVLLGSLLEGIPAIVLFGPLLFPIAKIVGVHEVHYAMVVIFAMGLGLFAPPFGVGFYAACAIGRVSPDVAMPRVWPHMAALLVALLLLTLVPWFSIGFL", "metadata": {"id": "A0A1K0JIT7", "cluster": 4657650, "interpro_all": ["IPR010656", "IPR055348", "IPR004681"], "interpro_used": ["IPR010656"], "interpro_unused": ["IPR055348", "IPR004681"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Furthermore, the protein is associated with the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It originates from Dehalococcoidia bacterium and carries UniProt keyword assignments Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 22970, 2037, 2028, 7289, 26941, 2642, 2126, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 3], "output": "MTKVNEPAISPIHVPVMSTEAIEGLGLTPGGAYIDCNVGEGGHADAIFRAGDDVSVLGIDLDDTALNFARLRLADYTDRLELAQSNFSELAHIAGGGLFEGVLFDLGVSSLQLDTPERGFSFRNEAALDMRFNPQTELTAYDIVNHYQERELAAVIREYGEEPRARSIARAIISRRRITTTTELADVVKRAVNWSTRSRVHPATRTFQALRIAVNGELDNLEKGLMAAIQALRPNGRLVVLSYHSLEDRVVKNVMRREASECICPPGLPICVCEHTPRLSLINRRVITPSDEEIRSNPRARSAKLRIAQRI", "metadata": {"id": "A0A354P0E8", "cluster": 5014795, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein is associated with the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. In addition, the protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Also, it is part of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It occurs in Deltaproteobacteria bacterium CG_4_9_14_3_um_filter_63_12 and is linked to UniProt keywords Cytoplasm and rRNA processing.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 1977, 2458, 1956, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 5110, 1922, 9649, 9218, 1021, 10296, 14061, 7294, 41, 24, 41, 29, 41, 2607, 41, 23, 41, 8736, 41, 6199, 41, 4968, 41, 2369, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 1930, 9067, 4587, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MSDLEYHVPVLRDAVLGALRPAPGERAIDLTLGGGGHARAMGERAGLECKVLVVRCNFAQFDGGLRSLGIASPAEEPGGGVDVMLADLGVSSHQLDTSSRELARILREGGEVPNAMRIALALKTEAAAGRLQRTSQLAALCERLMPPAVNQELEVLDTLLERAKQWMRPGGRLGIISFHSLEDRRVKQAFKKWTSFGESASKRPIVASDKELEENPRARSAKLRVFRFLLGPQGTLIGLDQDPDAIEQAARTLGFSFSQDGPLDMRMSKEGPDALALILDTTPHRHKGKGKKIHPATTVFQALRIMEGYCICPPKLPICCCG", "metadata": {"id": "A0A2M8B655", "cluster": 5107799, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein should have a CBS domain that functions as a regulatory sensor for adenosyl-containing ligands such as AMP, ATP, and S-AdoMet. These domains typically pair to form intramolecular structures known as Bateman domains, making the protein sensitive to cellular energy status or metabolite levels. It occurs in Gammaproteobacteria bacterium.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 3066, 2162, 43, 16341, 3418, 1988, 4088, 1966, 43, 4948, 6443, 1958, 29283, 17, 3165, 6908, 2427, 1966, 3681, 16, 4498, 16, 1930, 61, 17, 2041, 14080, 18, 2144, 4682, 5745, 3715, 1942, 2386, 18083, 4061, 3171, 1966, 11579, 17119, 4682, 16, 5399, 1920, 2213, 4532, 1942, 3689, 3844, 3642, 2014, 9483, 2428, 18, 2176, 5110, 1922, 7034, 9218, 1021, 10296, 14061, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MSRLHVFQTTEEDQLACPTQLVDQSMFASISALEVKQIMARSHLKMMFVVDEKSQCIGVVVTEMMIPKHALHAFDFHELETAEIGDVLAAMKELKTTQVFHNRPALYHLMTASLTPALRFLTDFEKVQPHVVDTSRQLSDRKFVKLISQGFDRHEVSSGERYALVLERESHQIRGIFCADELERG", "metadata": {"id": "A0A2E6M0W6", "cluster": 6287843, "interpro_all": ["IPR000644", "IPR046342"], "interpro_used": ["IPR000644"], "interpro_unused": ["IPR046342"]}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein is grouped in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Additionally, the protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It occurs in Thermoanaerobacter italicus (strain DSM 9252 / Ab9) and is described by UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 5110, 1922, 7967, 7241, 6506, 7972, 2341, 1915, 25200, 24375, 12, 3943, 10964, 6224, 8982, 19, 2186, 1026, 13, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MQVIGLTGGIASGKSTVSKLLIVEYFGKEILKEDGEIDRKKLGNIVFADRKKLKKLQQKAIVLDAALLIEMKLYKMVDEVWLVVVDSKTQIKRVMERDEKMKYADFIINNSKDFKAMEKQVTLFWERFATKKMGAVVIDADIVSREIMVKGTEAYNRNEITHPIIIERIKEKIEEERKKNDKLSYKDAINRIKSQMPL", "metadata": {"id": "D3T808", "cluster": 7474034, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein carries a 3-dehydroquinate synthase, N-terminal domain that adopts a Rossmann-fold structure to bind NAD+ in an inverted orientation and contributes to the formation of the enzyme's active site cleft. It facilitates the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate to 3-dehydroquinate and orthophosphate, a critical step in the shikimate pathway for aromatic amino acid biosynthesis. Moreover, the protein should feature a 3-dehydroquinate synthase C-terminal domain that contains the key catalytic and Zn2+-binding residues required to convert 3-deoxy-D-arabino heptulosonic 7 phosphate into dehydroquinate. This alpha-helical module functions within the shikimate pathway for aromatic amino acid biosynthesis, existing either in isolation or as part of the pentafunctional AROM polypeptide. Additionally, the protein belongs to the Dehydroquinate Synthase family, which catalyzes the cyclization of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ), a pivotal step in the shikimate pathway. This enzymatic activity is essential for the biosynthesis of aromatic amino acids in bacteria, fungi, and plants. It has been characterized in Bacillus cereus VD196 and is described by UniProt keywords Metal-binding, Membrane, and Amino-acid biosynthesis.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 16252, 43, 23, 17, 28936, 11072, 2010, 8921, 16, 56, 17, 4262, 3418, 1988, 24032, 43, 18215, 8890, 17, 3728, 3170, 1942, 4566, 6577, 15, 1922, 1925, 12344, 7148, 1930, 7624, 1942, 1920, 3337, 1927, 1920, 4113, 11, 61, 3500, 3200, 14649, 18, 2176, 11374, 1920, 7309, 1927, 23, 17, 16333, 17, 46, 17, 20790, 1037, 17, 20662, 11677, 8870, 27, 17, 5413, 1942, 23, 17, 28936, 11072, 2010, 1930, 17266, 10647, 3508, 2722, 2057, 16, 43, 4140, 3537, 1922, 1920, 20837, 7369, 23874, 3374, 1958, 10761, 3835, 2687, 8132, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 23, 17, 28936, 11072, 2010, 8921, 45, 17, 4262, 3418, 1988, 5461, 1920, 3834, 6804, 1930, 21061, 15, 17, 2743, 4248, 3414, 1942, 14450, 23, 17, 16333, 17, 46, 17, 20790, 1037, 20662, 11677, 3490, 27, 5413, 2460, 28936, 11072, 2010, 18, 2052, 4595, 17, 11514, 9059, 4088, 2651, 1920, 20837, 7369, 23874, 3374, 1958, 10761, 3835, 2687, 8132, 16, 6124, 3108, 1922, 7152, 2014, 1966, 3131, 1927, 1920, 9412, 2624, 20839, 8981, 13022, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 28936, 11072, 2010, 8921, 3416, 16, 2154, 17097, 1920, 25267, 1927, 23, 17, 16333, 17, 46, 17, 20790, 1037, 17, 20662, 11677, 8870, 27, 17, 5413, 12, 3692, 15870, 13, 1942, 28936, 11072, 2010, 12, 6781, 1055, 13, 16, 43, 13637, 3537, 1922, 1920, 20837, 7369, 23874, 3374, 18, 2052, 8145, 2455, 1977, 4415, 1958, 1920, 8132, 1927, 10761, 3835, 4576, 1922, 4802, 16, 10520, 16, 1930, 4793, 18, 2176, 2258, 2252, 4378, 1922, 14587, 29533, 13411, 27608, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 16, 3260, 16, 1930, 3835, 17, 2687, 8132, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MGNIHIQTKSKEYDVHVGKAVASLHLQTVIDALQVEQHVFSFVVPSGEKEKSLILALGGGMIGDLAGFVAASFMRGIRFVSAVGGKVAINHPLGKNMPFLQSLPEKEWRSGYAEVIKHALIGDVELYHWLKEEVPVKANVVSQDETEKGVRAHLNFGHTLGHALEKELGYGVYKVDLAYEDMKQWFLKYGYPKMPIHMVLMQEYGVVNVVSISDETVHIALEAFQKDMVEVLSNLTTIVQNMQPAVSNVMIISDESFENFYAAHTSALENKLDRNQVPTTLLAHDIGAFHQPEAVVYHTQTLADLHDEKLIHILTKAINITHGDGVAVGMLFAIFLSEQGDLNVERLVQLMKQDKKANAGA", "metadata": {"id": "A0A9W5VB26", "cluster": 8394970, "interpro_all": ["IPR050071", "IPR016037", "IPR030963", "IPR030960", "IPR056179"], "interpro_used": ["IPR030960", "IPR056179", "IPR050071"], "interpro_unused": ["IPR030963", "IPR016037"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein is categorized in the Protein of unknown function DUF2271 family, which comprises functionally uncharacterised bacterial proteins containing a conserved [S/T]GA[S/T] motif. These proteins serve as substrates for ApbE, suggesting a potential involvement in extracytosolic redox activities. It originates from Coprococcus comes.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 6680, 4282, 1009, 3416, 16, 2154, 12936, 9346, 23229, 3495, 4543, 2697, 3165, 43, 5305, 37, 61, 19, 62, 39, 4357, 37, 61, 19, 62, 39, 5219, 18, 2144, 2697, 7120, 1966, 6249, 1958, 2100, 5873, 16, 3783, 43, 2889, 5668, 1922, 3439, 2355, 1951, 4485, 9366, 4209, 18, 2176, 22970, 2037, 3725, 4104, 15648, 1957, 12458, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MDFVHSNTQASNQSNGGYTMREDSIPTWVSHAKPSEMTKTQIYSYIWDGTDNNGNEVANGTYTFHIELLDVEAVYTEETNQNKNMLSNVTAEYIIEEYAVWIENMDGDVVKTLFVTNFTDAITGATPSNGTGTLYWSSIVHYQGNVDMGASENS", "metadata": {"id": "A0A412QGJ4", "cluster": 9901174, "interpro_all": ["IPR014469"], "interpro_used": ["IPR014469"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein has a CHAD domain that functions as a specific binding module for inorganic polyphosphates (polyPs), utilizing a structure composed of two four-helix bundles with a central pore and basic surface patches to interact with the substrate. This domain enhances the activity of associated polyP-metabolizing enzymes and facilitates subcellular localization, such as targeting proteins to the nucleus. Moreover, the protein is a member of the CYTH-like domain superfamily, which encompasses enzymes such as adenylyl cyclases and thiamine triphosphatases that catalyze reactions involving triphosphorylated substrates. These proteins, often characterized as Triphosphate Tunnel Metalloenzymes (TTMs), typically employ a divalent metal cation-dependent mechanism within a predicted \u03b1/\u03b2 scaffold or \u03b2-barrel tunnel to bind nucleotides and facilitate phosphatase or cyclase activity. In addition, the protein should feature a CYTH domain that functions as the catalytic core for enzymes including CyaB-like adenylyl cyclases and thiamine triphosphatases. This domain utilizes a conserved $\\alpha+\\beta$ scaffold to coordinate divalent metal cations, facilitating the processing of triphosphorylated substrates. It is native to Corynebacterium pseudotuberculosis 258. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 13297, 1007, 3418, 1988, 4088, 1966, 43, 2487, 2743, 9059, 1958, 13849, 11769, 11787, 1036, 12, 17410, 13, 16, 10232, 43, 3170, 7179, 1927, 2288, 3006, 17, 7864, 16073, 1956, 43, 4101, 8554, 1930, 5937, 3154, 12667, 1942, 6310, 1956, 1920, 4510, 18, 2052, 3418, 9515, 1920, 2455, 1927, 2458, 6240, 17, 27044, 5038, 1930, 11374, 11309, 5363, 16, 2427, 1966, 5133, 2697, 1942, 1920, 5607, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2702, 1023, 17, 3189, 3418, 13975, 16, 2154, 21569, 5038, 2427, 1966, 27802, 16526, 1036, 1930, 26901, 14051, 2609, 18135, 1988, 18170, 5298, 5884, 14051, 2609, 2247, 15793, 6249, 18, 2144, 2697, 16, 3868, 4378, 1966, 17978, 16403, 8969, 6802, 1022, 16367, 12, 7382, 2800, 13, 16, 5745, 4417, 43, 21610, 6048, 9976, 17, 3100, 2856, 2651, 43, 4396, 160, 19, 161, 7281, 2014, 161, 17, 19560, 16403, 1942, 4566, 9519, 1930, 6628, 8167, 2014, 16526, 2455, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 2702, 1023, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 5038, 2710, 6002, 1993, 17, 3189, 27802, 16526, 1036, 1930, 26901, 14051, 2609, 18135, 18, 2052, 3418, 18127, 43, 5305, 8, 38, 4595, 15, 38, 4666, 8, 7281, 1942, 11865, 21610, 6048, 16525, 16, 12440, 1920, 4587, 1927, 14051, 2609, 2247, 15793, 6249, 18, 2176, 1977, 6196, 1942, 2233, 17151, 7972, 2341, 18842, 1989, 11520, 1031, 29603, 8071, 22187, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MGITQQLEVERKFSVADDQPVPQLVDITYVSHVAETTVHSLSALYFDTPDLRLSRSKIALRRRTGGKDAGWHLKISTPEGRVETHVPLGDDSVEAPCIPEDLLAFVRSITRSQPLAPIARIDNERHESLLTDDKGEYLAEFCDDHVHAWSYLPGGSESRWREWEIEITAYAQDQGLGTELIDSAETVLVEQGAHTARSSSKIAQALGDSVNNVPSPPQMAELDPKSPEYALVAALKRNRDRLVALDPLVRQDAPDSIHQMRVATRELRSHMKTFDGLLGGKEYKQMEKDLKIFGRILGSARDAEVIAARFEKLLSLNSDRLVDSTTSEFLLKDIQRDYLLAHRRVVSTLNHQRYLDFLDSLDSLLAEPPVLREDTTFGQETPDESHSEAILFHHLEKTMQRLYAQDRKARQEQHDPAIPLERREANFHNVRKAAKKLRYSAEAVGDSTSLNTDKLYAACKHLQTVLGDFQDAVTSRDRLYEKALRAERKGNPTFGYGVLHQQEHQNALSALDDYSEAFYKVTKAYRKFSKNVENFHKKAQKKAAKKSRKRN", "metadata": {"id": "A0AAU8PNM7", "cluster": 12721509, "interpro_all": ["IPR007899", "IPR038186", "IPR033469", "IPR023577"], "interpro_used": ["IPR007899", "IPR033469", "IPR023577"], "interpro_unused": ["IPR038186"]}, "task_type": "autoregressive"} {"instruction": "Here is the protein function: The protein features a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Furthermore, the protein falls within the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein has a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is expressed in beta proteobacterium KB13 and is classified with UniProt keywords Isoprene biosynthesis and Transferase. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 4075, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 3198, 1922, 4666, 2174, 12022, 6633, 3633, 1930, 1977, 5947, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MTSKILYSPAKINLFLKVINQREDGYHNLQSLFTYIDLYDEIKVSLHKDNKNQIIVNNPSIDCPADEDLIFMACKKILPKNFSIEIDVNKNIPDGAGLGGGSSNAATILIAINDLCSLNLSKKELANIGANLGADVPFFIYNNSAIVEGIGDKITPIDLAPIKFLLCCPSVKISTKDIFTSYKLTNKSKELKITALSNYEDLIDGLGNDLEAFVRQKNSTIDDLLSYLQKFGVAKLTGTGSSCFLILNETINLDEVKQNLPKNVRIYEVSSVNYNIAYDAQH", "metadata": {"id": "B6BWP5", "cluster": 14943318, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "The protein should contain a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein includes a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is produced by Aureibacillus halotolerans and contains UniProt keyword associations Isoprene biosynthesis and Transferase. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 4152, 2007, 8689, 26073, 10401, 5277, 1036, 23226, 4575, 3823, 2075, 1930, 5461, 20709, 11121, 2538, 5253, 26690, 1021, 8132, 1930, 13763, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MKIFIKAPAKINLSLDVLHKRQDGFHEVKMIMTTIDLSDRIELTDLPSNRIQLVSQHRFVPNDHRNLAYRAAALLQETYNVNRGVKIALQKRIPVAAGLAGGSSDAAAVLRGLNRLWDLRLSLPELAKLGAQIGSDVSFCVHGGTALATGRGEVITPLPPPPSCWVVLAKPTVGVSTADVYGQFNVNQTIHPDVEGMVDALYRQDYHQICALLGNALEPITMKLHPEVAQIKEQMHRFGADAVLMSGSGPTVFALVHHESRMQRIYNGLRGFCDQVYTVRMDGEPNMS", "metadata": {"id": "A0A4R6TXK3", "cluster": 17027506, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR006204", "IPR004424"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to this functional description: The protein possesses a SGNH hydrolase-type esterase domain that functions as a hydrolase with esterase or lipase activity, utilizing a Ser/Acid/His catalytic triad stabilized by a unique hydrogen bond network. This domain adopts a three-layer $\\alpha/\\beta/\\alpha$ fold and is found in diverse proteins, ranging from viral haemagglutinin-esterase surface glycoproteins to mammalian acetyl hydrolases and bacterial thioesterases. Also, the protein can be placed in the Diverse Ester Hydrolysis Enzymes family, which encompasses proteins with broad esterase capabilities involved in the degradation of substrates ranging from plant biomass components like cellulose and xylan to synthetic esters and triglycerides. Members often exhibit multifunctional activities, including thioesterase, arylesterase, and protease functions, with specificities for short-chain fatty acyl esters, aromatic esters, or acetyl groups. These enzymes play roles in processes such as spore germination and intracellular survival, potentially functioning within multienzyme complexes. It originates from Gammaproteobacteria bacterium.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 14465, 43, 10075, 21677, 20748, 17, 2601, 26389, 3418, 1988, 4088, 1966, 43, 20748, 1956, 26389, 2014, 16653, 2455, 16, 10232, 43, 2375, 19, 2687, 19, 4167, 6804, 21845, 12017, 2007, 43, 5008, 6201, 5403, 3504, 18, 2052, 3418, 24032, 43, 2559, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 1930, 1977, 2435, 1922, 6445, 2697, 16, 6485, 2037, 4324, 7105, 17003, 1921, 17, 26389, 3154, 16268, 1942, 6492, 6894, 30337, 1930, 4543, 30215, 2319, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 6445, 9603, 9128, 5038, 3416, 16, 2154, 21569, 2697, 1956, 4949, 26389, 13693, 3286, 1922, 1920, 4877, 1927, 6249, 6485, 2037, 4496, 9397, 4178, 3189, 12343, 1930, 23665, 1942, 6830, 16785, 1930, 13631, 18, 4678, 3868, 5987, 20136, 4209, 16, 2710, 30215, 2051, 16, 15578, 8342, 2051, 16, 1930, 7154, 4088, 16, 1956, 18764, 1958, 3662, 17, 4659, 5934, 11337, 16785, 16, 10761, 16785, 16, 2014, 6894, 2671, 18, 2144, 5038, 3918, 5456, 1922, 4028, 2427, 1966, 18445, 14609, 1930, 4776, 3298, 16, 5063, 7295, 2651, 2779, 14896, 5048, 18, 2176, 22970, 2037, 7034, 9218, 1021, 10296, 14061, 18, 3], "output": "MSVIFSLFAVKFALRFAGYEPLKAMAAGKDLVLRRSEHPDTGYELIQGAEGRAFKTDVKVNSLGFRSLEPDRSGDARRVLFLGDSITFGSELLAGTAWPELMATRLESRDPRFDVQNLALSGYDDVQELAVLEHRGLTLSPGLVVIGFCLNDVGVVSANFEYHERAYAWAQSSLAGSRVGQLLLTIADRLLGRRFEAEANEPDVFAARHAGHISAIGEDEMRLRGLVREVTDRPPSAWYGDADRIGRLRYVLERLTALRDQYAFRLQIVVFPLHETAADGTYPHWVAYAIVGLEAERMRIPVLDLAGPFQREGLVELRNDPDDPVHPSPRGHEIAAEKVWESWLNLRVI", "metadata": {"id": "A0A938PP57", "cluster": 17728878, "interpro_all": ["IPR051532", "IPR013830", "IPR036514"], "interpro_used": ["IPR013830", "IPR051532"], "interpro_unused": ["IPR036514"]}, "task_type": "autoregressive"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein should contain a Lcl, C-terminal domain that exhibits structural similarity to C-type lectins and mediates glycan recognition. Found in Legionella collagen-like proteins, it binds sulphated glycosaminoglycans (GAGs) on eukaryotic cell surfaces and stimulates bacterial aggregation in the presence of divalent cations. It is derived from Sulfuricella sp and exhibits UniProt keyword tags Signal.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 3066, 5531, 43, 5236, 1024, 16, 45, 17, 4262, 3418, 1988, 9826, 4346, 6796, 1942, 45, 17, 2601, 25607, 1930, 10412, 15060, 5708, 18, 2435, 1922, 27836, 5870, 5621, 17, 3189, 2697, 16, 2176, 6876, 20415, 1007, 25982, 19900, 12, 9819, 1036, 13, 1990, 10825, 2024, 7553, 1930, 11803, 4543, 7883, 1922, 1920, 2990, 1927, 21610, 16525, 18, 2176, 1977, 3595, 2037, 12585, 2927, 11560, 1019, 2056, 1930, 9826, 20709, 11121, 2538, 14392, 2733, 18, 3], "output": "MKCAFSSFHAMVGTGQTSCYISYYGTGQTVACNDAANVGNGGLTKTGGGVAGFDFTRICWNGAAEGAANCTGTLAANTTGTADSASPLQTLGAMNWTAAQSATANDNELLNIVNNGGGSPAIDGNYFPATRTTGYWSTDVVGFGDGGVDLPAQTDSNFVRLVRVLTAIGGGSVAHAQTGLLNDYSPHQDGRYGRDVAAAAGQATDWACTRDNVTGLVWSTNRRCGYSDWRLPIRRSRSYSNIAMGFVDYAWI", "metadata": {"id": "A0A942Q075", "cluster": 18760036, "interpro_all": ["IPR011460"], "interpro_used": ["IPR011460"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein incorporates a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. It is present in Qipengyuania flava and is associated with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 19683, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2176, 1977, 2481, 1922, 8165, 17125, 26983, 13785, 2126, 7732, 1019, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MTRGRFIAFEGGEGMGKSTQARMLAESLRESGLTVTLTREPGGTPGAEAIRELLLAPPGSGWTMEAEALLFAAARADHVAHSIRPALDSGGWVICDRFIDSSRAYQGVAGEMGDDAIMGLHAFGSDGLMPDLTIMIEAPQDIVSARLAERDGDNSDAIGGRTSAYHAAVNEAFRDLASREPARFAIVDGAGSIEDVHRRVLSEVARRLGASE", "metadata": {"id": "A0A5P6NCB7", "cluster": 19100781, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR027417", "IPR018095"], "interpro_unused": ["IPR018094", "IPR039430"]}, "task_type": "autoregressive"} {"instruction": "The protein incorporates a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. In addition, the protein contains a Rho termination factor, RNA-binding domain that binds single-stranded RNA to facilitate the disengagement of newly transcribed RNA from its DNA template. It features an N-terminal OB-type fold with an indented face that serves as the primary binding site and supports the formation of a functional hexameric complex. Furthermore, the protein includes a ATPase alpha/beta subunit nucleotide-binding domain that forms the central structural component of the catalytic or regulatory subunits in F-, V-, and A-type ATPases, as well as flagellar ATPases and termination factor Rho. It binds nucleotides to drive ATP synthesis or hydrolysis through conformational changes linked to the complex's rotary motor mechanism, coupling chemical energy with proton translocation. It occurs in Peptidiphaga gingivicola and is classified with UniProt keywords Transcription termination, Transcription, and Transcription regulation. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 10585, 12462, 2991, 16, 3146, 17, 2743, 3418, 1988, 6876, 2957, 17, 10338, 3146, 1942, 6628, 1920, 28347, 8909, 1927, 7471, 10078, 3146, 2037, 2496, 2678, 7662, 18, 2176, 4075, 1925, 56, 17, 4262, 2384, 17, 2601, 3728, 1956, 1925, 2063, 12871, 6171, 1988, 10634, 1966, 1920, 3065, 2743, 3200, 1930, 7825, 1920, 3337, 1927, 43, 3183, 25602, 1935, 2796, 18, 3677, 16, 1920, 2213, 5921, 43, 9444, 4595, 19, 4666, 5903, 5489, 17, 2743, 3418, 1988, 4952, 1920, 4101, 4346, 4594, 1927, 1920, 6804, 2014, 4948, 6991, 1922, 48, 17, 16, 64, 17, 16, 1930, 43, 17, 2601, 28132, 16, 1966, 2486, 1966, 24154, 28132, 1930, 12462, 2991, 10585, 18, 2176, 6876, 9519, 1942, 9265, 4498, 4271, 2014, 9128, 2596, 8523, 2840, 4624, 1942, 1920, 2796, 11, 61, 23548, 4842, 2856, 16, 7590, 4399, 3844, 1956, 8433, 7849, 18, 2176, 5110, 1922, 3431, 6285, 10349, 12485, 2068, 29902, 1930, 1977, 5947, 1956, 20709, 11569, 3213, 12462, 16, 3213, 16, 1930, 3213, 3640, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MRLPELREAAKALGLEVDPKAKKADLVAAIRSVTGPARRGRPPKNRTEIKVRYEAPKIKADAAKSASGEANPLAGRVNAAPASAGANAAKGGDAGASAGAKPAKEKEKVETNTPFEWPAARDAHNPSGSGDNSNGRDNSNGGDNSSDNAQDRNGAKAAGQDGFKPENRSDDRGSQGSDRGSQGSDRSAQGPRVRRRGPRDGEIDIVLPESKGSEDKPEHLSRRQRRERNERVARERAERNNERNGRGKNRDDRGRDGGMTESDKRAALDAIGDAAERRAGGDDTASDRRSRNRNRNRNRDRSEFQEATQRDDEDLLQVAGILDFEGNNAFLRTGGYLPGGNDAAVSQQIVKQHGLRRGDAIVGAVRPRTEADQHYNNRNRNRNRNHYNQLNQLVQIDTINSLDVERSLTRPEFNKLTPLYPQDMLRLETTPKAMTPRAIDLVAPIGKGQRGLIVAPPKAGKTMVMQQIAMAIASNNPRVHLMVVLVDERPEEVTDMKRLVKGEVIASTFDRPASDHTIVAELAIERAKRLVELGQDVVVLLDSLTRLSRAYNLAAPASGRILSGGVDAAALYPPKKFFGAARNIENGGSLTIIASALVETGSKMDEVIFEEFKGTGNMELRLSRQLADRRIFPAIDVNASGTRREELLFSQEELKVIWQLRRALGTLDVAEASDFMLGRLRKTESNAEFLVQIMKSMQAN", "metadata": {"id": "A0A179B3N6", "cluster": 19718931, "interpro_all": ["IPR003593", "IPR000194", "IPR012340", "IPR027417", "IPR041703", "IPR011113", "IPR004665"], "interpro_used": ["IPR003593", "IPR011113", "IPR000194"], "interpro_unused": ["IPR012340", "IPR004665", "IPR041703", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein should contain a Phospholipase D, N-terminal domain that constitutes the N-terminal region of phospholipase D (PLD) enzymes, which catalyze the hydrolysis of the ester bond between phosphatidic acid and alcohol moieties in phospholipids. Also, the protein should include a PhoD-like metallophosphatase domain that functions as an alkaline phosphatase or phosphodiesterase to catalyze the hydrolysis of phosphate monoesters. It shares structural similarity with Ca2+-dependent phospholipase D and is often targeted for secretion via the Twin-arginine translocation (Tat) pathway. Also, the protein should contain a Twin-arginine translocation pathway signal sequence conserved site that targets fully folded proteins, such as redox enzymes with complex cofactors, for export across energy-transducing membranes in bacteria, archaea, and chloroplasts. This N-terminal peptide contains a characteristic motif with invariant twin-arginine residues that directs the protein to the Tat translocase machinery, facilitating the secretion of substrates that have already acquired their tertiary structure. It originates from Actinomycetota bacterium.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 17570, 46, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 3031, 1927, 17570, 46, 12, 22985, 13, 5038, 16, 2154, 18170, 1920, 9128, 1927, 1920, 9603, 5403, 2192, 2766, 8525, 1935, 2687, 1930, 4284, 16706, 1922, 15619, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 20175, 1007, 17, 3189, 8969, 8630, 7234, 3418, 1988, 4088, 1966, 1925, 10746, 8167, 2014, 24821, 1942, 18170, 1920, 9128, 1927, 5413, 8914, 26934, 18, 2176, 16495, 4346, 6796, 1956, 5497, 15, 17, 3100, 17570, 46, 1930, 1977, 3868, 5154, 1958, 5512, 3454, 1920, 13392, 17, 9732, 7849, 12, 10687, 13, 3374, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 13392, 17, 9732, 7849, 3374, 2733, 3244, 5305, 3200, 1988, 4845, 5437, 16318, 2697, 16, 2427, 1966, 9366, 5038, 1956, 2796, 21362, 16, 1958, 12660, 3436, 3844, 17, 5925, 1941, 5726, 1922, 4802, 16, 21501, 16, 1930, 24627, 18, 2052, 56, 17, 4262, 4207, 5461, 43, 6293, 5219, 1956, 17004, 13392, 17, 9732, 4248, 1988, 28351, 1920, 2213, 1942, 1920, 10687, 12930, 2051, 10853, 16, 12440, 1920, 5512, 1927, 6249, 1988, 2162, 6064, 5815, 2310, 10832, 3170, 18, 2176, 22970, 2037, 4718, 13386, 19446, 3857, 14061, 18, 3], "output": "MAGPRSSCHTLVQIEAAEELMGTRQPNGLVVTSGSGLSRRDLLMALGFGAGAAVAVGGCVVPAPGPTPPSPPPGTPETGLFPDGVAAGDPLPGASTIWTRVLADGSGAPVALLWSVAEDEAFSELVAGGIVVADAARGHTVTVGVDGLENDRWYFYRFETTGPSAQTSRTGRLRTAPASGSAPDHLRFAFGSCQQITGTWFNAHRAITAEPGLDFFMHLGDYVYVSDTSTLSVEDYRNVYRRWRREPLLRDLHAHLPVVGMWDDGEFYNGIDAFGPPDRLAAGKQAWFENFPQIDPGDQRLYRALHWGSLADIPVIDVRAYRDPAIDNPVHVSPGGMDDPTRTTLGATQLAWLKDQLAGSSANWRLIGNPYNINPWRLVNLEFLRFFRPDLPRNPGVYAPNEAWDDYMAERRDLLQFLADEAVGPTAFCSAHTHIYLAAELKPDVD", "metadata": {"id": "A0A938J2H6", "cluster": 21360949, "interpro_all": ["IPR029052", "IPR018946", "IPR038607", "IPR032093", "IPR052900", "IPR006311"], "interpro_used": ["IPR032093", "IPR018946", "IPR006311"], "interpro_unused": ["IPR052900", "IPR029052", "IPR038607"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein should contain a RIO-type domain that functions as an atypical serine/threonine kinase primarily involved in the cytoplasmic maturation of pre-40S ribosomal subunits. Found in conserved RIO family proteins and the KEOPS complex subunit BUD32, it facilitates late 18S rRNA processing and is required for cell cycle progression and chromosome maintenance. It originates from Parascaris equorum (Equine roundworm) and is annotated with UniProt keywords Nucleotide-binding, Serine/threonine-protein kinase, and ATP-binding.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 3066, 5531, 43, 23017, 17, 2601, 3418, 1988, 4088, 1966, 1925, 10834, 8468, 19, 13143, 4016, 5985, 3286, 1922, 1920, 6823, 7655, 1927, 2097, 17, 29805, 11196, 6991, 18, 2435, 1922, 5305, 23017, 3416, 2697, 1930, 1920, 3364, 4001, 2796, 5903, 8344, 6763, 16, 2176, 11374, 5058, 17659, 9067, 4587, 1930, 1977, 3414, 1958, 2024, 4048, 4380, 1930, 5597, 6291, 18, 2176, 22970, 2037, 5336, 15339, 1937, 3009, 17279, 12, 22279, 7464, 16620, 13, 1930, 1977, 10633, 1956, 20709, 11569, 5489, 17, 2743, 16, 8468, 19, 13143, 17, 2213, 4016, 16, 1930, 4498, 17, 2743, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MIFHFLQTLFAYHKHYKDDQIYIIDVSQSVEHDHPHSLEPSINRVEFYDVAEFTEFKRLVLMQKVMNEIV", "metadata": {"id": "A0A914S6X0", "cluster": 22949935, "interpro_all": ["IPR018934"], "interpro_used": ["IPR018934"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein is categorized in the Lambda repressor-like, DNA-binding domain superfamily, which functions as a transcriptional regulator controlling critical genetic switches such as bacteriophage lysogeny and bacterial sporulation. This domain typically adopts a four-helix closed folded leaf topology, a variation of the helix-turn-helix motif, to mediate specific DNA binding and interactions with RNA polymerase. Structural analogs of this fold are also conserved in eukaryotic POU transcription factors and the N-terminal domain of the metabolic enzyme cyanase. Additionally, the protein includes a LacI-type HTH domain that functions as the N-terminal DNA-binding module in the LacI/GalR family of prokaryotic transcriptional regulators. It utilizes a helix-turn-helix motif to bind the major groove and a hinge helix to contact the minor groove of specific operator DNA. This domain is essential for coordinating catabolic and metabolic operons, often in response to sugar inducers. Moreover, the protein includes a Periplasmic binding protein/LacI sugar binding domain that functions as a primary receptor for the chemotaxis and transport of sugar-based solutes or as the ligand-binding sensor in LacI-family transcriptional regulators. In regulatory contexts, sugar binding typically induces conformational changes that modulate the DNA-binding activity of the repressor. It occurs in Paraphotobacterium marinum and features UniProt keywords Transcription regulation. Can you generate the amino acid sequence corresponding to this polypeptide chain?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 13022, 4659, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 18279, 14434, 17, 3189, 16, 2678, 17, 2743, 3418, 13975, 16, 2154, 4088, 1966, 43, 5224, 7888, 7138, 4140, 3299, 21529, 2427, 1966, 24613, 3629, 27791, 1930, 4543, 23647, 18, 2052, 3418, 5745, 24032, 43, 3006, 17, 7864, 8047, 16318, 6998, 13678, 16, 43, 4516, 1927, 1920, 7864, 17, 5165, 17, 7864, 5219, 16, 1942, 8265, 2487, 2678, 2743, 1930, 3719, 1956, 3146, 6479, 18, 4346, 13204, 1927, 2052, 3728, 2032, 2222, 5305, 1922, 10825, 28398, 3213, 2790, 1930, 1920, 56, 17, 4262, 3418, 1927, 1920, 4487, 4113, 10208, 2051, 18, 4950, 16, 1920, 2213, 5921, 43, 7511, 1033, 17, 2601, 5334, 1023, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 2678, 17, 2743, 9059, 1922, 1920, 7511, 1033, 19, 5179, 1005, 3416, 1927, 21545, 5224, 9098, 18, 2176, 18127, 43, 7864, 17, 5165, 17, 7864, 5219, 1942, 4566, 1920, 3044, 15920, 1930, 43, 20484, 7864, 1942, 5217, 1920, 5857, 15920, 1927, 2487, 14012, 2678, 18, 2052, 3418, 1977, 4415, 1958, 19355, 22112, 1930, 4487, 28748, 16, 3868, 1922, 2644, 1942, 9523, 23329, 18, 3950, 16, 1920, 2213, 5921, 43, 24334, 2743, 2213, 19, 7511, 1033, 9523, 2743, 3418, 1988, 4088, 1966, 43, 3065, 3148, 1958, 1920, 16884, 1930, 4860, 1927, 9523, 17, 2454, 27993, 2014, 1966, 1920, 5207, 17, 2743, 6443, 1922, 7511, 1033, 17, 3416, 5224, 9098, 18, 1922, 4948, 11144, 16, 9523, 2743, 5745, 6387, 8523, 2840, 1988, 8480, 1920, 2678, 17, 2743, 2455, 1927, 1920, 14434, 18, 2176, 5110, 1922, 22224, 10647, 4575, 7972, 2341, 18842, 1989, 13081, 1022, 1989, 1930, 4075, 20709, 11569, 3213, 3640, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MATIKDIAKKAGVSISTVSHVLNKTRFVSESLSNKVKKIAIELNYSPSAIARSLKKNETKTIGVIFDRNTNPYFAELLSAVDKRAYENGYSIIISNFESEHKRFEFNLNTLMQKKVDGLLLFGSEINSYPLSCLEQYSKTPMVFMDIDISVKNHLVDQILSNSVYGAYKATDYLIACGHKQIGCISGNMSSKVNRDRFKGYQKALEKAGLMVNKNYIFEGNFDCRSGQDCFEKYMRLPRNKRPTALFIFNDLMAMGFMNKAYSNGFTIPDDISIIGYDNIEYSEFLNPALTTIHQPKYELGIQSVDLLMQRIKDPKLETQVFQLKPDLIKRNSVSLLDQKGR", "metadata": {"id": "A0A220VH05", "cluster": 25501535, "interpro_all": ["IPR000843", "IPR010982", "IPR001761", "IPR028082"], "interpro_used": ["IPR010982", "IPR000843", "IPR001761"], "interpro_unused": ["IPR028082"]}, "task_type": "autoregressive"} {"instruction": "The protein falls within the Phosphoribosyltransferase-like superfamily, which encompasses enzymes such as phosphoribosyltransferases (PRTases) and phosphoribosylpyrophosphate synthetase-like proteins. These domains typically catalyze the transfer of phosphoribosyl groups to specific substrates, playing a central role in nucleotide biosynthesis and salvage pathways. Additionally, the protein should feature a Phosphoribosyltransferase domain that catalyzes the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP) by a nitrogen-containing nucleophile to yield an alpha-1 substituted ribose-5'-phosphate and free pyrophosphate. This domain is essential for nucleotide synthesis and salvage pathways and features a conserved PRPP binding motif. In addition, the protein falls within the Uracil phosphoribosyltransferase/Adenine phosphoribosyltransferase family, which catalyzes the conversion of uracil or adenine and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP or AMP and diphosphate within nucleotide salvage pathways. These enzymes facilitate energy-efficient nucleotide pool maintenance and are typically allosterically activated by GTP. It is identified in Kitasatospora sp. NA04385 and is connected to UniProt keyword Magnesium, Glycosyltransferase, and Allosteric enzyme.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 3421, 2023, 25566, 17, 3189, 13975, 16, 2154, 21569, 5038, 2427, 1966, 3421, 2023, 25566, 1036, 12, 2033, 3857, 4127, 1036, 13, 1930, 3421, 2023, 11731, 18425, 15707, 18185, 17, 3189, 2697, 18, 2144, 4682, 5745, 18170, 1920, 3856, 1927, 3421, 2023, 11731, 2671, 1942, 2487, 6249, 16, 14797, 43, 4101, 2770, 1922, 5489, 8132, 1930, 17577, 3873, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 3421, 2023, 25566, 3418, 1988, 17097, 1920, 9514, 1927, 1920, 4595, 17, 21, 11, 17, 24937, 1927, 25, 17, 3421, 2023, 11731, 17, 4595, 17, 21, 17, 24937, 12, 11533, 1034, 13, 2007, 43, 6634, 17, 3165, 2797, 28335, 1942, 4307, 1925, 4595, 17, 21, 11798, 17870, 17, 25, 11, 17, 5413, 1930, 3294, 24937, 18, 2052, 3418, 1977, 4415, 1958, 5489, 4271, 1930, 17577, 3873, 1930, 4075, 43, 5305, 11533, 1034, 2743, 5219, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 22761, 3421, 2023, 25566, 19, 15643, 3421, 2023, 25566, 3416, 16, 2154, 17097, 1920, 7309, 1927, 22761, 2014, 15643, 1930, 25, 17, 8078, 17, 4595, 17, 46, 17, 17870, 21, 17, 23266, 12, 11533, 1034, 13, 1942, 8736, 1034, 2014, 3681, 1930, 23266, 2651, 5489, 17577, 3873, 18, 2144, 5038, 6628, 3844, 17, 5807, 5489, 5562, 6291, 1930, 2032, 5745, 14772, 2169, 4128, 2007, 9319, 18, 2176, 1977, 2899, 1922, 4712, 23738, 4575, 3508, 8846, 2056, 18, 4049, 14743, 4745, 1015, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 13148, 16, 20067, 9961, 16, 1930, 14772, 4113, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MRLHVVDHPLVAHKLSTLRDDVRTDTVEITTPVAVTRGTRLSYPRPLVVPILRMVRNEETLEASTYATRMPDDLSGRQIDVTAVVLLAAPEGVEVMERELAGRPVTVIVPGLGDAGDRLYGTAGERTDSPTFRRLTDELVTLLAYEATRAGLGMLDGMTRLLPTAEVGFLGYVLDPMLATGGTLVAAIRMLLERGATVTAAVDERLNEHGY", "metadata": {"id": "A0A7H8KU75", "cluster": 20426086, "interpro_all": ["IPR000836", "IPR029057", "IPR034332", "IPR050054", "IPR005765"], "interpro_used": ["IPR029057", "IPR000836", "IPR050054"], "interpro_unused": ["IPR005765", "IPR034332"]}, "task_type": "infilling"} {"instruction": "Give me the sequence of a polypeptide chain with the following function. The function of the polypeptide chain is The protein is associated with the TerB-like superfamily, which constitutes a multihelical domain found in the tellurium resistance protein TerB and the co-chaperone DjlA. This domain is typically associated with stress response mechanisms, including tellurium resistance and chaperone activity. Furthermore, the protein should contain a Co-chaperone DjlA, N-terminal domain that constitutes the N-terminal region of the DjlA protein. This structural module is also conserved in the tellurium resistance protein TerB. It has been characterized in Spirochaetota bacterium (Spirochaetes).", "tokenized_instruction": [2, 7031, 2142, 1920, 3244, 1927, 43, 13022, 4659, 1956, 1920, 2894, 2347, 18, 1920, 2347, 1927, 1920, 13022, 4659, 1977, 1920, 2213, 1977, 2458, 1956, 1920, 6005, 1014, 17, 3189, 13975, 16, 2154, 14879, 43, 2779, 23285, 2046, 3418, 2435, 1922, 1920, 17812, 15709, 3554, 2213, 6005, 1014, 1930, 1920, 2081, 17, 14044, 17224, 5148, 18, 2052, 3418, 1977, 5745, 2458, 1956, 3071, 2644, 3531, 16, 2710, 17812, 15709, 3554, 1930, 14044, 2455, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 2081, 17, 14044, 17224, 5148, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 3031, 1927, 1920, 17224, 5148, 2213, 18, 2052, 4346, 9059, 1977, 2222, 5305, 1922, 1920, 17812, 15709, 3554, 2213, 6005, 1014, 18, 2176, 2258, 2252, 4378, 1922, 22075, 25588, 19446, 3857, 14061, 12, 22075, 25588, 3764, 13, 18, 3], "output": "MVIYRRACMKKLDLTPVEAGIALSTLVAFSDDNPSEEEGVIMRKYYRSADADSFQKKLEEAGYSYPSDLKTLFPVVIDTLKSVPVDFRLRTIAVGYLLARADGNVDQNEMQILSKAAAGLEVSLYDAKVFAEERLKEIDEVTGYEDYRAASFSGPVLELTLEEAGAALSILVGFSDDDPSDAEAAVMREYFPAESITSLFEKLKAAGVEYPDSLPETKESIKKTFSMASRDDQLRMLAIAWKVAAADGTIDELETGLIKEFCEELVIGLAEVKDYFKAVPE", "metadata": {"id": "A0A496RBR1", "cluster": 564467, "interpro_all": ["IPR007791", "IPR029024"], "interpro_used": ["IPR029024", "IPR007791"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein should contain a ABC transporter-like conserved site that functions as the ATP-hydrolyzing motor of the ATP-Binding Cassette (ABC) superfamily to energize transmembrane transport. This region contains the nucleotide-binding pocket formed by the conserved Walker A and Walker B motifs, the Q-loop, and the switch region. It facilitates the translocation of a diverse array of substrates, ranging from ions to macromolecules, by coupling ATP hydrolysis to conformational changes in the associated transmembrane domains. Additionally, the protein features a ABC transporter type 1 transmembrane domain that serves as the integral membrane component responsible for substrate recognition and translocation. Functioning within the ATP-binding cassette (ABC) superfamily, it couples with nucleotide-binding domains to utilize ATP hydrolysis for the import of nutrients or the export of diverse molecules ranging from ions to macromolecules. Moreover, the protein should have a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. It originates from Dadabacteria bacterium and contains UniProt keyword associations Transmembrane helix.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 3066, 5531, 43, 7219, 9054, 17, 3189, 5305, 3200, 1988, 4088, 1966, 1920, 4498, 17, 7222, 9046, 4842, 1927, 1920, 4498, 17, 2743, 12992, 12, 7219, 13, 13975, 1942, 2066, 2693, 2606, 9117, 4860, 18, 2052, 3031, 5461, 1920, 5489, 17, 2743, 10154, 5333, 2007, 1920, 5305, 20138, 43, 1930, 20138, 44, 8277, 16, 1920, 59, 17, 5881, 16, 1930, 1920, 6195, 3031, 18, 2176, 11374, 1920, 7849, 1927, 43, 6445, 6472, 1927, 6249, 16, 6485, 2037, 6982, 1942, 20625, 16, 2007, 7590, 4498, 9128, 1942, 8523, 2840, 1922, 1920, 2458, 9117, 4682, 18, 4950, 16, 1920, 2213, 4075, 43, 7219, 9054, 2601, 21, 9117, 3418, 1988, 10634, 1966, 1920, 12328, 3260, 4594, 5061, 1958, 4510, 5708, 1930, 7849, 18, 7295, 2651, 1920, 4498, 17, 2743, 12992, 12, 7219, 13, 13975, 16, 2176, 14002, 1956, 5489, 17, 2743, 4682, 1942, 12561, 4498, 9128, 1958, 1920, 2582, 1927, 11312, 2014, 1920, 12660, 1927, 6445, 4206, 6485, 2037, 6982, 1942, 20625, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 2176, 22970, 2037, 23053, 20013, 2341, 18339, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 18, 3], "output": "MVFSVALQLAGPQVLRRGVDALAGGEGDVLDLALVLGGLAAGQALFRFASRRLTLGAARAVEHDLRMAYVGHVLRLPLETLDRARRGDLVSRALHDLQDLRLFLGAGWLNLCQTLLVGSGTAVLLWRIHPGLTAVALAPFPAIAWVVRRMSPRLHRRFLAADRAAGAVADRVHETLTAIRLLRALRRERWQEERFRGENEALCRARERVVWAWAAVFPAVGVLAGLGHVAVLGLGGYWVATGALSLGGFVAFSAYLAMLIWPMVALGWTLSLVQRGAAALGRLEEVRRWPAEPEPGAPLPPPAGVCLRAEGVTYAYPDAAGPAVAGVGWELPEGGMWALVGPTASGKSTLVSLVARLRRPQRGAIEIHGEALERIADPELRRHLAVVPQEDFFFSDSVAANVLLGRPRDDGRIWEVLALAGLEADVRSLPDGLDTRVGEGGITLSGGQRQRLGIARALYGDPDVLVLDGSLSNLDARTAREVLGRVRQRLRGRTLVVVSHRAFEVEEADGVWFLERGRIVASGTHGELWRRLPGYRRLYREEELRRELEEAP", "metadata": {"id": "A0A3M2A1K9", "cluster": 2017516, "interpro_all": ["IPR003593", "IPR011527", "IPR036640", "IPR003439", "IPR017871", "IPR027417", "IPR039421"], "interpro_used": ["IPR017871", "IPR011527", "IPR003593"], "interpro_unused": ["IPR036640", "IPR039421", "IPR003439", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Here is the polypeptide chain function: The protein is a member of the Poly(ADP-ribose) glycohydrolase family, which functions as an exo- and endoglycohydrolase that hydrolyzes O-glycosidic linkages to reverse the effects of poly(ADP-ribose). By degrading ADP-ribose polymers without cleaving the terminal protein-ribose bond, these enzymes generate mono-ADP-ribosylated proteins. They also play roles in nuclear ATP synthesis for chromatin remodeling, DNA repair, and responses to oxidative or abiotic stress. Also, the protein carries a Poly (ADP-ribose) glycohydrolase, helical domain domain that structurally precedes the catalytic core in Poly(ADP-ribose) glycohydrolase (PARG) enzymes found in animals, plants, and fungi. This region is part of the enzyme responsible for hydrolyzing O-glycosidic linkages in ADP-ribose polymers, acting as an exo- and endoglycohydrolase to reverse the effects of poly(ADP-ribosylation). It originates from Anaeromyces robustus. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 4286, 12, 9828, 17, 17870, 13, 4235, 8601, 21524, 3416, 16, 2154, 4088, 1966, 1925, 18930, 17, 1930, 16239, 17038, 4879, 8535, 24605, 1021, 1988, 7222, 20887, 57, 17, 7533, 12546, 19949, 1942, 5267, 1920, 2564, 1927, 4286, 12, 9828, 17, 17870, 13, 18, 2007, 18192, 9828, 17, 17870, 11039, 2979, 28634, 1920, 4262, 2213, 17, 17870, 5403, 16, 2144, 5038, 5655, 8914, 17, 9828, 17, 29117, 4336, 2697, 18, 2611, 2222, 3918, 5456, 1922, 4254, 4498, 4271, 1958, 6338, 8378, 16, 2678, 5059, 16, 1930, 3387, 1942, 5163, 2014, 16596, 3071, 18, 2222, 16, 1920, 2213, 16252, 43, 4286, 12, 9828, 17, 17870, 13, 4235, 8601, 21524, 16, 11514, 3418, 3418, 1988, 12171, 24373, 1920, 6804, 4728, 1922, 4286, 12, 9828, 17, 17870, 13, 4235, 8601, 21524, 12, 2096, 1029, 13, 5038, 2435, 1922, 3555, 16, 4793, 16, 1930, 10520, 18, 2052, 3031, 1977, 3131, 1927, 1920, 4113, 5061, 1958, 7222, 9046, 57, 17, 7533, 12546, 19949, 1922, 9828, 17, 17870, 11039, 16, 8290, 1966, 1925, 18930, 17, 1930, 16239, 17038, 4879, 8535, 24605, 1021, 1942, 5267, 1920, 2564, 1927, 4286, 12, 9828, 17, 29117, 3017, 13, 18, 2176, 22970, 2037, 11381, 29249, 5786, 1957, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MYNQIYNNNYNPNRNKNRPNGKKYVQTKLNFGQKPLDNYEDDPTLLDYNFGNIMLSQNELNVSDELKTHLHYIRIPYYENNNPEKLNEKKYNIIKEALTKFPIRNCNAFQYALLKYHTELSENDNSLLNNLRLYEKRYSDEAKYFFIEILPFIIEQALKLPEYLTKPIPLLGKYMNIAITFNKLQVISLLANQFLCIFTEENNKLYHTPECSFLGIFSTPKSTVDSSVEKIRSVVHYFDKMRKRSIDSLKSELLTFQRVSLKEKSLPDWINSSMNICNVIIDKGRNIEECENMLQVDFANSYLGGGVLRTGCVQEEIRFVITPELFVSMIFTQKLDNLETAFIIGAERVSKFKGYGRSFKFNGDHNDCYIKYDKWNRKSTEIVALDATHYSPSLKKYIQFSTKETIREMNKLYVGFKNNELSNLSEGSYIATGNWGCGAYNGDLELKAMLQVLVASITEKNICYCPFDKVEFADRLGVVVHSLKTHNVTTDLLYKLIRSYNTEVIFKHVNHNSPPKISLFDYILGTLQYN", "metadata": {"id": "A0A1Y1XCH6", "cluster": 5002132, "interpro_all": ["IPR046372", "IPR048362", "IPR007724"], "interpro_used": ["IPR007724", "IPR048362"], "interpro_unused": ["IPR046372"]}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein carries a Tetratricopeptide repeat that mediates protein-protein interactions and the assembly of multiprotein complexes. This motif consists of tandem 34-amino acid residues adopting a helix-turn-helix arrangement, which stacks to form a right-handed superhelical structure involved in diverse processes such as cell cycle regulation and protein folding. Additionally, the protein should feature a Protein kinase ATP binding site that binds ATP to facilitate the transfer of the gamma phosphate to protein substrates during phosphorylation. Located in the N-terminal catalytic domain, this conserved site utilizes a specific lysine residue within a glycine-rich stretch to anchor the nucleotide. This interaction is essential for the activity of serine/threonine, tyrosine, and dual-specificity kinases in regulating processes such as cell division and proliferation. Furthermore, the protein should have a Protein kinase domain that functions as the conserved catalytic core responsible for transferring the gamma phosphate from ATP to serine, threonine, or tyrosine residues on substrate proteins. This phosphorylation event induces conformational changes that regulate diverse cellular processes, such as proliferation, differentiation, and apoptosis. It occurs in Ignavibacteriota bacterium and has UniProt annotations Coiled coil, Transmembrane, and Membrane. Generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1988, 2258, 1920, 2894, 3879, 30, 1920, 2213, 16252, 43, 12470, 3319, 21305, 6865, 1988, 10412, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 18, 2052, 5219, 7543, 1927, 10361, 3540, 17, 3835, 2687, 4248, 20478, 43, 7864, 17, 5165, 17, 7864, 13002, 16, 2154, 20836, 1942, 2386, 43, 3659, 17, 17105, 3356, 23285, 2046, 3170, 3286, 1922, 6445, 4028, 2427, 1966, 2024, 4048, 3640, 1930, 2213, 10328, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 2213, 4016, 4498, 2743, 3200, 1988, 6876, 4498, 1942, 6628, 1920, 3856, 1927, 1920, 7034, 5413, 1942, 2213, 6249, 2409, 4050, 18, 4810, 1922, 1920, 56, 17, 4262, 6804, 3418, 16, 2052, 5305, 3200, 18127, 43, 2487, 9082, 6181, 2651, 43, 10646, 17, 5536, 9064, 1942, 13333, 1920, 5489, 18, 2052, 2835, 1977, 4415, 1958, 1920, 2455, 1927, 8468, 19, 13143, 16, 6941, 16, 1930, 7064, 17, 4896, 7784, 1922, 6773, 4028, 2427, 1966, 2024, 8451, 1930, 4031, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 2213, 4016, 3418, 1988, 4088, 1966, 1920, 5305, 6804, 4728, 5061, 1958, 21902, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 16, 13143, 16, 2014, 6941, 4248, 1990, 4510, 2697, 18, 2052, 4050, 4817, 6387, 8523, 2840, 1988, 5741, 6445, 3689, 4028, 16, 2427, 1966, 4031, 16, 4155, 16, 1930, 4091, 18, 2176, 5110, 1922, 12046, 9188, 7972, 2341, 18842, 7336, 14061, 1930, 2258, 20709, 15010, 17524, 9121, 16, 9117, 16, 1930, 3260, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MIGETISHYKIVEKLGEGGMGVVYKAQDTKLDRLVALKFLPQHLLSDATEKERFIHEAKAASALSHQNITTIHEIDEFNGKMFIAMEYCEGRTLRELIGREELSVTHVVEIAIQICEGLTLAHEKGIIHRDIKSDNIMLNHRNQVKIMDFGIAKLKGASKLTKTGSTLGTTAYMSPEQARGEEVDHRSDIFSFGVVLYELLTCKLPFRGEHQAAIMYSIVNEEPAPIARFNEKVSTELVRIVTKALAKDREERYQHIDDLLADLRREKKNLEYAKMTHVSTISGTAEVQRVHSRIAFKYGIFVAVVMLTTFLVYFLFLRQEEGIDSVAVLPLVNASADPNTEYLTDGITENIINSLSQLPNLRVVPRSTVFRYKGEKVDPEEVGKKLNVRSILTGRVLQRDDYINLQMELIDVVRQSQLWGKQYNRRSTDVLSLQEEIVREISTTLQPRLGGEEKKQLAKTQTADDEAFRLYLRGRYHWNKRSPEHLRKSIQYLEEALSKDPGYAKAYAGLADSYIILGDFNVLPPKETYPKAREAAMKALDLDTEIPEAHTSLAYALMHYDWDWSAVEREFHRAIELSPNSAQAHSWYALYLSLMGRFDEAVTESQQACLLDPFSAVIRTDAGLTLYFARKYDLAINQCREALELDPTFVVANIPLGGAYVQKQMYPEAIKAFQDLILASSLATSKAHPVPIAALAHVYALSGRSEDAMNMIELLQEKSKEEYVAPYWMSIAYAGLGNSAEVFRWLQQAYEEKDGSIIFLKAESIFDKWHSNPRFTALLNKLGFER", "metadata": {"id": "A0A933D4U0", "cluster": 6167052, "interpro_all": ["IPR011009", "IPR000719", "IPR017441", "IPR008271", "IPR011990", "IPR019734"], "interpro_used": ["IPR019734", "IPR017441", "IPR000719"], "interpro_unused": ["IPR011009", "IPR011990", "IPR008271"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to this functional description: The protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It occurs in marine sediment metagenome.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 5110, 1922, 10789, 10363, 16552, 2225, 18, 3], "output": "GYLKMSAEEPDRWLVVDATLPKKKISEIIWEKVNHLLAEKGYL", "metadata": {"id": "X1K197", "cluster": 7700718, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is assigned to the Golgi phosphoprotein 3-like family, which comprises proteins that localize to the cytosolic face of the Golgi complex to facilitate membrane trafficking. These proteins bind phosphatidylinositol-4-phosphate to link Golgi membranes to the cytoskeleton, thereby participating in the tensile force required for vesicle budding. It is identified in Streptomyces sp. NL15-2K and is associated with UniProt keywords Golgi apparatus and Lipid-binding. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 1977, 6304, 1942, 1920, 10277, 8078, 22163, 23, 17, 3189, 3416, 16, 2154, 12936, 2697, 1988, 14380, 1942, 1920, 9410, 6171, 1927, 1920, 10277, 2796, 1942, 6628, 3260, 9604, 18, 2144, 2697, 4566, 16927, 17, 24, 17, 5413, 1942, 3300, 10277, 5726, 1942, 1920, 11612, 16, 6113, 9505, 1922, 1920, 15984, 5495, 3414, 1958, 11502, 15909, 18, 2176, 1977, 2899, 1922, 22874, 2056, 18, 9092, 3962, 17, 25307, 1930, 1977, 2458, 1956, 20709, 11569, 10277, 11161, 1930, 4486, 17, 2743, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MNTSLADQVMLHIADSTGGRTAAWHTELAIALTGAVLIDLALADHIAIRRNQILINHPGPLDDPVQDEILRRLASRRRPGSVQEWIERLAPLMPDQVQENLLARGLLIPSIGRCTLRLHPRHNSEPPDPPPSEALSRLLHASHQNWTPSQTPSRTPSRTAQPDEPDAVTIVCSAVASCIGSAVQQLMCSF", "metadata": {"id": "A0A401MVR5", "cluster": 12259941, "interpro_all": ["IPR008628", "IPR038261"], "interpro_used": ["IPR008628"], "interpro_unused": ["IPR038261"]}, "task_type": "autoregressive"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein should contain a Glucose-6-phosphate dehydrogenase, C-terminal domain that forms the C-terminal region of the enzyme catalyzing the first step of the pentose phosphate pathway. This component contributes to the conversion of glucose-6-phosphate to gluconolactone 6-phosphate, generating NADPH crucial for reductive biosynthetic processes and maintaining cellular redox homeostasis. It has been characterized in Bacillus wiedmannii. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 3066, 5531, 43, 3817, 17, 26, 17, 5413, 9294, 16, 45, 17, 4262, 3418, 1988, 4952, 1920, 45, 17, 4262, 3031, 1927, 1920, 4113, 29601, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 4594, 7624, 1942, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 9155, 11908, 6608, 1958, 23335, 14041, 4028, 1930, 8231, 3689, 9366, 7622, 18, 2176, 2258, 2252, 4378, 1922, 14587, 11980, 1919, 8890, 3907, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "KNPLNNGELEPIRIHFTCEQTGVGIPEAYERLIYDAVCGDSTFFAHWREVELSWEWVQPILEAFEENLLPLHEYKSGSYGPDAANALLQESEFKWWLDEELKK", "metadata": {"id": "A0A4U3B274", "cluster": 15340917, "interpro_all": ["IPR001282", "IPR022675"], "interpro_used": ["IPR022675"], "interpro_unused": ["IPR001282"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein falls within the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Moreover, the protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is identified in Desulfosarcina alkanivorans and is associated with UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2899, 1922, 30311, 5360, 15618, 4058, 5638, 8150, 15525, 17182, 1036, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MIIAGLTGGIASGKSTVCGFLRDAGARIVDADKIARAVVRQGTPAYDEICSYFGGTILQPDGGIDRERLGDIIFNDPEKKARLDAIVHPRVFEQSAHMIDRIAVQAPDAVIILDVPLLLEAGMEKDLAEVIVVYVPETLQLKRLMKRDGIGEKAAMARIRSQMPIEEKRRRATIVIDNSGAMETTQRSALAVFKRLQKKAAPPFAGDPTTA", "metadata": {"id": "A0A5K7YFB1", "cluster": 17763450, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein possesses a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein includes a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Moreover, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is native to Ignavibacteria bacterium and exhibits UniProt keyword tags Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 14465, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 6196, 1942, 12046, 9188, 7972, 2341, 18339, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MTLRAYAKINLGLHVVGKRPDGYHNIETVFHQIDLFDEIEIVQSDEGPQFVSDVDLTGCHSGVEITLRKRIPIGAGLGGGSTDAAAVLRGLVKLWNSDITDDELKTMSTAYATGRGEVLEPCDLSVPYWILVVTPPLHVSTSWAYAKLSLAEGTRRLHIPTLLRRRIKQTLLDRGAALALMSGTGSSVFGFFEDEVAVRTLSDEFSLSCHVSVTKPLFNPEPNPGLPSDSSNLCIRAMNVLRATLGSDVPYFLIGGASLKNPAKLREGLRNEFEPVVFDAYPEV", "metadata": {"id": "A0A938NYC1", "cluster": 18486699, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR020568", "IPR014721", "IPR036554"]}, "task_type": "infilling"} {"instruction": "I want to design a protein that has the following function: The protein is a member of the Nodulation factor ABC transporter family, which functions as part of an ABC transporter complex to facilitate the export of lipooligosaccharide signal molecules across the bacterial membrane. These nodulation factors are modified beta-1,4-linked N-acetylglucosamine oligosaccharides that are essential for establishing symbiosis with host plants and triggering nodule formation. Additionally, the protein should feature a ABC-2 type transporter transmembrane domain that constitutes the integral membrane component of ATP-binding cassette (ABC) transport systems, typically comprising six transmembrane helices. It assembles into homo- or hetero-oligomeric channels that interact with cytosolic ATPase subunits to facilitate the ATP-dependent translocation of diverse substrates, including toxins and macromolecules, across the membrane. It originates from Gemmatimonadales bacterium and carries UniProt keyword assignments Cell membrane and Transmembrane helix. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 3889, 2281, 2991, 7219, 9054, 3416, 16, 2154, 4088, 1966, 3131, 1927, 1925, 7219, 9054, 2796, 1942, 6628, 1920, 12660, 1927, 3178, 4545, 21592, 5735, 2437, 28476, 2261, 2733, 4206, 3436, 1920, 4543, 3260, 18, 2144, 3889, 2281, 2790, 2032, 4795, 4666, 17, 21, 16, 24, 17, 4624, 56, 17, 6894, 22988, 17454, 22012, 1988, 2032, 4415, 1958, 11810, 17246, 2475, 1956, 4423, 4793, 1930, 14074, 17149, 3337, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 7219, 17, 22, 2601, 9054, 9117, 3418, 1988, 14879, 1920, 12328, 3260, 4594, 1927, 4498, 17, 2743, 12992, 12, 7219, 13, 4860, 3771, 16, 5745, 10351, 3798, 9117, 12789, 18, 2176, 17421, 1036, 2460, 16350, 17, 2014, 19732, 17, 19206, 5628, 1988, 6310, 1956, 9410, 9444, 6991, 1942, 6628, 1920, 4498, 17, 3100, 7849, 1927, 6445, 6249, 16, 2710, 13599, 1930, 20625, 16, 3436, 1920, 3260, 18, 2176, 22970, 2037, 10607, 3368, 2265, 12502, 3825, 2612, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 2024, 3260, 1930, 9117, 7864, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MRSVLALMRVSWLTHTSYRLNVIMSVLGLGALFIPIYFVADALQPVVADSIADEGEVYFGFLITGMVILQFLSVGMNAVPNAVSGGINSGVLEALFATPTRLERLLAGMIGYETLWAAFKGLLLLVAFVAVGGEVALSGIPLALGILVLLFVAHLPLGLLAAAMILVFRTSGPLIPGLMAAFSLLGGVYYSTTVIPEVVRPLAEAIPLTYGLRAFRRSFLSGEPLAAVVGDVLILAGMAAALMLVGVLAFRWALNYARRAGSLAQY", "metadata": {"id": "A0A651HW69", "cluster": 21024448, "interpro_all": ["IPR013525", "IPR047817", "IPR051784"], "interpro_used": ["IPR051784", "IPR013525"], "interpro_unused": ["IPR047817"]}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: The protein incorporates a Cupin 2 domain that forms the conserved beta-barrel structure characteristic of the cupin superfamily. This versatile fold serves as a scaffold for diverse biological activities, ranging from enzymatic functions like dioxygenases and isomerases to non-enzymatic roles such as seed storage. Moreover, the protein can be placed in the Quercetin 2,3-dioxygenase-like family, which mediates the metabolic breakdown of flavonoids by catalyzing the dioxygenolytic cleavage of the O-heteroaromatic ring in quercetin. This enzymatic activity produces 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide, playing a key role in the microbial degradation of plant-derived compounds for use as a carbon source. In addition, the protein is categorized in the RmlC-like cupin domain superfamily, which is characterized by a conserved beta-sandwich fold that often accommodates metal-binding sites to facilitate diverse enzymatic and binding activities. Members include the bacterial virulence factor RmlC (a dTDP-sugar isomerase), various dioxygenases and oxidases, as well as non-catalytic seed storage globulins and auxin-binding proteins. It is derived from Pedobacter sp. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 19683, 43, 14967, 1921, 22, 3418, 1988, 4952, 1920, 5305, 4666, 17, 19560, 3170, 6293, 1927, 1920, 14967, 1921, 13975, 18, 2052, 20425, 3728, 10634, 1966, 43, 7281, 1958, 6445, 3933, 4209, 16, 6485, 2037, 8145, 4088, 3189, 23652, 10465, 2432, 2319, 1930, 25510, 1036, 1942, 2447, 17, 8145, 5456, 2427, 1966, 4861, 7451, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 16766, 22, 16, 23, 17, 23652, 10465, 2432, 2051, 17, 3189, 3416, 16, 2154, 10412, 1920, 4487, 13630, 1927, 16192, 2007, 29601, 1920, 23652, 10465, 2432, 6586, 6404, 1927, 1920, 57, 17, 19732, 14128, 2479, 6335, 1922, 16766, 18, 2052, 8145, 2455, 9300, 22, 17, 3899, 20884, 22914, 2199, 17, 29554, 30232, 22988, 21092, 18708, 2687, 1930, 5056, 26662, 16, 14797, 43, 3834, 2770, 1922, 1920, 7293, 4877, 1927, 4496, 17, 3595, 4300, 1958, 2485, 1966, 43, 5056, 4585, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 10625, 8293, 17, 3189, 14967, 1921, 3418, 13975, 16, 2154, 1977, 4378, 2007, 43, 5305, 4666, 17, 18038, 3728, 1988, 3868, 16848, 1036, 6048, 17, 2743, 3402, 1942, 6628, 6445, 8145, 1930, 2743, 4209, 18, 4678, 3951, 1920, 4543, 9304, 2991, 10625, 8293, 12, 43, 7711, 10274, 17, 9523, 25510, 13, 16, 3425, 23652, 10465, 2432, 2319, 1930, 10488, 1036, 16, 1966, 2486, 1966, 2447, 17, 6804, 4861, 7451, 24366, 1036, 1930, 16243, 17, 2743, 2697, 18, 2176, 1977, 3595, 2037, 5296, 5883, 2056, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MNMKRRNFLVTSILAAPLMTLSDWIIKPLTTNPKKAFVVKNGESRFFGKNTSASPNYGRCILSSVDTQNQLYIAGGSINSSTKKGGPALHIHYQDDEIFYVVSGEFLFQLENEIVLGKAGDTIFVPRGIAHTFANPIDNNPGELLTIHQPISSSLEKFYEVFSTIGYMNEKMLQENFEPEILNDLMKNNAFVGPPIDIDAALKKLKQK", "metadata": {"id": "A0A520CIN5", "cluster": 22086947, "interpro_all": ["IPR013096", "IPR053146", "IPR014710", "IPR011051"], "interpro_used": ["IPR013096", "IPR053146", "IPR011051"], "interpro_unused": ["IPR014710"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe protein incorporates a Thioredoxin domain that functions as a ubiquitous protein disulphide oxidoreductase, utilizing a conserved active site with two cysteines to facilitate reversible redox reactions. It mediates electron transfer in NADPH-dependent pathways and serves as a core component of enzymes like protein disulphide isomerases (PDI) and bacterial Dsb proteins, where it catalyzes the formation and rearrangement of disulphide bonds during protein folding. In addition, the protein should include a Alkyl hydroperoxide reductase subunit C/Thiol specific antioxidant domain that functions as a peroxiredoxin to reduce organic hydroperoxides and protect the cell against oxidative stress. It utilizes an active-site cysteine to neutralize sulfur-containing radicals, thereby serving as a defense mechanism against protein misfolding and aggregation. In addition, the protein is a member of the Thioredoxin family ResA/DsbE subfamily, which comprises thiol-disulfide oxidoreductases essential for the synthesis of c-type cytochromes. These proteins catalyze dithiol-disulfide exchange reactions, primarily reducing disulfide bonds in apocytochrome c to allow for covalent heme attachment. Some members also participate in sporulation or the oxidative folding of periplasmic proteins. It originates from Deltaproteobacteria bacterium and is linked to UniProt keywords Signal.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 19683, 43, 23684, 3418, 1988, 4088, 1966, 43, 15498, 2213, 2054, 23138, 2261, 27388, 16, 10232, 43, 5305, 3500, 3200, 1956, 2288, 22446, 1942, 6628, 10743, 9366, 5298, 18, 2176, 10412, 4995, 3856, 1922, 11908, 17, 3100, 3873, 1930, 10634, 1966, 43, 4728, 4594, 1927, 5038, 3189, 2213, 2054, 23138, 2261, 25510, 1036, 12, 20506, 13, 1930, 4543, 15136, 2697, 16, 2597, 2176, 17097, 1920, 3337, 1930, 14154, 1927, 2054, 23138, 2261, 9031, 2409, 2213, 10328, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 13345, 25461, 6211, 11386, 5903, 45, 19, 13914, 2487, 7335, 3418, 1988, 4088, 1966, 43, 11456, 3030, 9754, 1942, 4412, 6805, 25461, 29508, 1930, 9145, 1920, 2024, 3316, 5163, 3071, 18, 2176, 18127, 1925, 3500, 17, 3200, 8666, 1942, 25885, 12585, 17, 3165, 12467, 16, 6113, 13915, 1966, 43, 9720, 2856, 3316, 2213, 28200, 1930, 7883, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 23684, 3416, 1995, 1019, 19, 15136, 1021, 16227, 16, 2154, 12936, 13914, 17, 11830, 27388, 1036, 4415, 1958, 1920, 4271, 1927, 45, 17, 2601, 9387, 1036, 18, 2144, 2697, 18170, 18061, 1945, 17, 11830, 6818, 5298, 16, 5985, 5526, 11830, 9031, 1922, 26970, 2355, 8719, 45, 1942, 3235, 1958, 13577, 10954, 8576, 18, 2673, 4678, 2222, 7352, 1922, 23647, 2014, 1920, 5163, 10328, 1927, 24334, 2697, 18, 2176, 22970, 2037, 9649, 9218, 1021, 10296, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 2733, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MRRVALIVSLLVVCWPWAGARADDGQGPARGHADAAKRSPSMKESPPKNRSSAAKGLRTSQAATTLQRLVVGQRAPIFSLRDHVGDQAPPNGQGVLLSFAASFCEPCRQELAALRDLAPRTDPEGLAIMEQLTVHELKLPFPVLSDRFGVVGRRYGVSALGYQKEALDALKDALGLVDSELQGSALRSKEQRIPSVETTLSANGSPSASGSPSEATLNAKLSGRSVFALRLAAAGISVAVVVTDPMTVVIDRKGAVRWQSI", "metadata": {"id": "A0A935WYW1", "cluster": 24024671, "interpro_all": ["IPR000866", "IPR036249", "IPR013766", "IPR050553"], "interpro_used": ["IPR013766", "IPR000866", "IPR050553"], "interpro_unused": ["IPR036249"]}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein is a member of the C-type lectin and matrix domain-containing protein family, which functions primarily through cell surface receptors that bind specific carbohydrate structures to mediate immune recognition, lymphocyte proliferation, and antigen presentation. Members also contribute to bone homeostasis by inhibiting osteoclast formation and include developmental matrix proteins involved in biomineralization as well as viral proteins that down-regulate MHC-I expression. Additionally, the protein has a C-type lectin-like domain that typically functions as a calcium-dependent carbohydrate-recognition module to mediate immune responses, cell trafficking, and pathogen defense. Stabilized by conserved disulfide bonds, this versatile fold is also utilized in non-sugar binding contexts to facilitate protein-protein interactions, such as those seen in snake venom phospholipase A2 inhibitors. Moreover, the protein is associated with the C-type lectin fold superfamily, which encompasses a versatile structural domain originally characterized by calcium-dependent carbohydrate binding but capable of mediating diverse protein-protein, protein-lipid, and protein-nucleic acid interactions. This fold appears in a wide array of functional contexts, ranging from immune system receptors and cell adhesion molecules to bacterial toxins and extracellular matrix components like collagen. It has been detected in Mugilogobius chulae (yellowstripe goby).", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 45, 17, 2601, 13468, 1930, 4526, 3418, 17, 3165, 2213, 3416, 16, 2154, 4088, 5985, 2596, 2024, 3154, 4086, 1988, 4566, 2487, 10590, 4061, 1942, 8265, 3743, 5708, 16, 10009, 4031, 16, 1930, 4730, 6544, 18, 4678, 2222, 4672, 1942, 3622, 7622, 2007, 7918, 14731, 3337, 1930, 3951, 5878, 4526, 2697, 3286, 1922, 4071, 29384, 1966, 2486, 1966, 4324, 2697, 1988, 3292, 17, 5741, 8709, 17, 51, 2294, 18, 4950, 16, 1920, 2213, 2258, 43, 45, 17, 2601, 13468, 17, 3189, 3418, 1988, 5745, 4088, 1966, 43, 5016, 17, 3100, 10590, 17, 5708, 9059, 1942, 8265, 3743, 3387, 16, 2024, 9604, 16, 1930, 7055, 9720, 18, 12017, 2007, 5305, 11830, 9031, 16, 2052, 20425, 3728, 1977, 2222, 7079, 1922, 2447, 17, 9523, 2743, 11144, 1942, 6628, 2213, 17, 2213, 3719, 16, 2427, 1966, 2690, 3945, 1922, 24044, 15540, 17570, 8595, 4472, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 45, 17, 2601, 13468, 3728, 13975, 16, 2154, 21569, 43, 20425, 4346, 3418, 10398, 4378, 2007, 5016, 17, 3100, 10590, 2743, 2308, 7131, 1927, 10239, 6445, 2213, 17, 2213, 16, 2213, 17, 4486, 16, 1930, 2213, 17, 11079, 2687, 3719, 18, 2052, 3728, 5107, 1922, 43, 4743, 6472, 1927, 3183, 11144, 16, 6485, 2037, 3743, 2433, 4086, 1930, 2024, 6141, 4206, 1942, 4543, 13599, 1930, 5329, 4526, 4178, 3189, 5621, 18, 2176, 2258, 2252, 3330, 1922, 28991, 1970, 2021, 17428, 1957, 27772, 5148, 1021, 12, 7463, 2156, 3027, 9626, 3611, 4864, 13, 18, 3], "output": "MVIVAVVLIVALIVAYVFKGVVLFLHNKECSNRLQTTANLTTMAPVATTCPPPPPSCPPPRTCPFPPPPPSCPPPHICPPPRTCPRPPPPPSCPPPRNCPPLLLPPLPPPPPLCPFPAPSCPIKLQCDNGWELHGATCYYFSTVKNTWSQSRYRCRLAGGDLVKIDTAEKQWFLYWKVMSLMSDNEDKFWIGLTDAETEGWWKWTDSSFLNQK", "metadata": {"id": "A0AAW0NLH3", "cluster": 26802832, "interpro_all": ["IPR001304", "IPR016186", "IPR050828", "IPR016187"], "interpro_used": ["IPR050828", "IPR001304", "IPR016187"], "interpro_unused": ["IPR016186"]}, "task_type": "autoregressive"} {"instruction": "Here is the protein function: The protein contains a ATPase alpha/beta subunit nucleotide-binding domain that forms the central structural component of the catalytic or regulatory subunits in F-, V-, and A-type ATPases, as well as flagellar ATPases and termination factor Rho. It binds nucleotides to drive ATP synthesis or hydrolysis through conformational changes linked to the complex's rotary motor mechanism, coupling chemical energy with proton translocation. In addition, the protein should have a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. Also, the protein has a Rho termination factor, RNA-binding domain that binds single-stranded RNA to facilitate the disengagement of newly transcribed RNA from its DNA template. It features an N-terminal OB-type fold with an indented face that serves as the primary binding site and supports the formation of a functional hexameric complex. It occurs in Actinotalea ferrariae CF5-4 and contains UniProt keyword associations Hydrolase, Helicase, and Transcription regulation. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 5461, 43, 9444, 4595, 19, 4666, 5903, 5489, 17, 2743, 3418, 1988, 4952, 1920, 4101, 4346, 4594, 1927, 1920, 6804, 2014, 4948, 6991, 1922, 48, 17, 16, 64, 17, 16, 1930, 43, 17, 2601, 28132, 16, 1966, 2486, 1966, 24154, 28132, 1930, 12462, 2991, 10585, 18, 2176, 6876, 9519, 1942, 9265, 4498, 4271, 2014, 9128, 2596, 8523, 2840, 4624, 1942, 1920, 2796, 11, 61, 23548, 4842, 2856, 16, 7590, 4399, 3844, 1956, 8433, 7849, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 2222, 16, 1920, 2213, 2258, 43, 10585, 12462, 2991, 16, 3146, 17, 2743, 3418, 1988, 6876, 2957, 17, 10338, 3146, 1942, 6628, 1920, 28347, 8909, 1927, 7471, 10078, 3146, 2037, 2496, 2678, 7662, 18, 2176, 4075, 1925, 56, 17, 4262, 2384, 17, 2601, 3728, 1956, 1925, 2063, 12871, 6171, 1988, 10634, 1966, 1920, 3065, 2743, 3200, 1930, 7825, 1920, 3337, 1927, 43, 3183, 25602, 1935, 2796, 18, 2176, 5110, 1922, 4718, 10868, 5376, 12210, 6148, 1021, 4920, 1015, 17, 24, 1930, 5461, 20709, 11121, 2538, 5253, 20748, 16, 15318, 16, 1930, 3213, 3640, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "EADAPQRDVAQRETAPREGNRREGAQRTPQRDGRQAEQLQQQRDPRLAEAGRDELDEEGGGRRRRGRYRDRDRNKRRGRGPELGGFEEQPEVSDDDVLLPVAGILDIKDNYAFVRTSGYLPGDNDVYVSMNQVKKHGLRKGDAVVGAVRQPRDGEQLPPQGRNSKVNALVRLDSVNGMAPEQARTRPEFGKLTPLYPQERLRLETGPTVMTTRIIDLVAPIGKGQRGLIVSPPKAGKTLVLQAIANAITTNNPEVHLMVVLVDERPEEVTDMQRTVKGEVIASTFDRPADDHTTVAELAIERAKRLVELGQDVVVLLDSITRLGRAYNIAAPASGRILSGGVDSSALYPPKRFFGAARNIEHGGSLTILATALVETGSKADEVIFEEFKGTGNMELKLSRQLADKRIFPAVDVDASGTRREEILIPADELKINWKLRRVMSALDQQQAIELLLSKLRETSSNVEFLLQVQKTTPSAPGHHHD", "metadata": {"id": "A0A021VU40", "cluster": 27537400, "interpro_all": ["IPR003593", "IPR000194", "IPR011129", "IPR012340", "IPR027417", "IPR041703", "IPR011113", "IPR004665"], "interpro_used": ["IPR000194", "IPR003593", "IPR011113"], "interpro_unused": ["IPR011129", "IPR041703", "IPR027417", "IPR004665", "IPR012340"]}, "task_type": "autoregressive"} {"instruction": "I want to make a protein that can have this function: The protein is associated with the Glycosyltransferase family 87, which comprises enzymes involved in the biosynthesis of mycobacterial cell wall glycolipids. This family includes PimE, a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose during phosphatidylinositol mannoside (PIM) synthesis, as well as alpha(1-->3) arabinofuranosyltransferases involved in arabinogalactan formation. It is derived from Lachnospiraceae bacterium and carries UniProt keyword assignments Membrane, Transmembrane, and Transmembrane helix. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 20067, 9961, 3416, 5783, 16, 2154, 12936, 5038, 3286, 1922, 1920, 8132, 1927, 21424, 2024, 4821, 14193, 2049, 3753, 18, 2052, 3416, 5921, 17019, 1021, 16, 43, 6240, 2825, 1945, 17, 5413, 17, 17936, 17, 3100, 7338, 25566, 1988, 19180, 1920, 12052, 17936, 2409, 16927, 7338, 8028, 12, 17019, 13, 4271, 16, 1966, 2486, 1966, 4595, 12, 21, 17, 17, 34, 23, 13, 20790, 4199, 20028, 25566, 1036, 3286, 1922, 20790, 27395, 1928, 3337, 18, 2176, 1977, 3595, 2037, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MVLQDKRRFAFFHKKSHVFFAVSILSTVLFFVVCSLLKTGSIGILDYLVLGNKDEWEFADFYRHIGYGSDLSRVYETSPDACFPPLSYLFFHFLYLLNPVQAAAVDWRAFRDAPYGRLSYLFCMMLLVLLFSYVAHRVAGMTEKTGLILSILLLTSAPFFTAIERGNPVFLTMILLLYALWWKESDNRYLREAALVFIAIAAGFKILPALYGLLYVREKRWKEAGRLLLYGILLFFVPFLLTGGREGFSSYIRLLLDSHYHADFM", "metadata": {"id": "A0A929UR57", "cluster": 27708012, "interpro_all": ["IPR018584"], "interpro_used": ["IPR018584"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is derived from Luoshenia tenuis and has UniProt annotations Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 3595, 2037, 28327, 6150, 8572, 5656, 8694, 1930, 2258, 20709, 15010, 5239, 1930, 9067, 4587, 18, 3], "output": "MGEFTHVTVLLQEAVEALQVKPGGVYLDGTLGGGGHTEAILRQSGPDGVVERLKPLHGNFHDAKALLAAQGVAQLDGAVLDLGVSSFQFDEGERGFSFQEDARLDNTLSGEELTRIIRDYGEERWAARIAAFILQAREKKHPARRTFQALRIAVNDELEPLAKALEELVSLLAPGGRLAVITFHSLEDRIVAPVCTCGKLPVAQVVTRKPILPSPAEVEQNPRSRSAKLRVVQKLYGIDRDRDALRAAGERLAAFGMRMDQSCGRTAADLCPVETTGELVSIIKAAIPKGARRDGPKQTFKRLQNPCICPPK", "metadata": {"id": "A0A926D1N2", "cluster": 28716093, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein is included in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Moreover, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is native to Deltaproteobacteria bacterium and contains UniProt keyword associations ATP-binding, Cytoplasm, and Transferase.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 6196, 1942, 9649, 9218, 1021, 10296, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MGENVLVLGITGNIASGKSTVSKELARRSALKKVVKLFGTEILQKDGDLVRAMLNGIIHPEIAKKSIEQLQQLRETTVKIDPEEQIRRLMARDRLSEAGARSGTLAETQKQVDALWGELVDSTSKCTTGAVVLDADQLAREVVASGSDRDRLGQMVFADVKAAPLIIYEAPLLFEVGAENRVDKVLVQRMNSQMQQEKKIIRADFVIDN", "metadata": {"id": "A0A661PX16", "cluster": 135320, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein contains a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. Moreover, the protein features a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. Additionally, the protein should contain a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. It is present in Terrapene triunguis (Three-toed box turtle) and features UniProt keywords ATP-binding, Metal-binding, and Manganese.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 3950, 16, 1920, 2213, 4075, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 2176, 1977, 2481, 1922, 11420, 4608, 2912, 5083, 3317, 8694, 12, 2559, 17, 22820, 1007, 5758, 7431, 4131, 13, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 6048, 17, 2743, 16, 1930, 19516, 18, 3], "output": "MWQEAMMRRRRYLLERAEQAADGGCGVSSEQPRSRDWLYESYYCMSQQHPLLVFLLLIVMGACLALLAVFFASGLEIDDHVAFLITVPTALAIFFAIFILVCIESVFKKLLRIFSLVVWVCLVAMGYLFMCFGGIMCPWDQVSFFLFIIFVVYTMLPFNMRDAIIASVLTSSSHTIVLSICLSTTAIIKEHLVWQILANAIIFICGNLAGAYHKHLMELALQQTYQDTCNCIKSRIKLEFEKRQQERLLLSLLPAHIAMEMKAEIIQRLQGPKAGQLENTNNFHNLYVKRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPISLQNHAKNCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITSVTLAHLNGAYKVEEGDGDVRDPYLKEHNVKTYFVINPKGERRSPQHHFRPRHTLDGAKMRASVRMTRYLESWGAAKPFAHLHHRDSMTTENGKISTTDVPMGQYHFQRCRERTKSQKKRFEEELNERMIQAIDGINAQKQWLKSEDIQRISLLFYNKTLEKEYRTTTLPAFKYYVTCACLIFFCIFIVQILVLPKTSILGISFGVAFLLLSFILFICFAGQLLQCSNKASASLLWILKSSGIIANRPWPRITLTLTTTTITLTMAIFNMFFLDDPVISFIPILNSSNASFPESSAQTLWYIQNNYFYLPYFIYSCILGLISCSVFLRINYELKMVIMLIALVGYNVILLHTHGSTLDDYSKFLMLLGEGQLIILLNEYYCRLDFLWKNKFKKEREEIETMENLNRVLLENVLPAHVAEHFLARNLKNEELYHQSYDCVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDDLLSKPKFSGVEKIKTIGSTYMAATGLSATPSQEHSQEPERQYMHIGTMVEFAFALVAKLDVINKHSFNDFKLRIGINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLDKIQVTEETNNVLQTLGYMCTCRGIINVKGKGELKTYFVHTEMTRSLSQGNVAS", "metadata": {"id": "A0A674I7U8", "cluster": 961435, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR009398", "IPR029787"], "interpro_used": ["IPR009398", "IPR001054", "IPR018297"], "interpro_unused": ["IPR029787", "IPR030672", "IPR032628"]}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein should have a DNA polymerase III, delta prime subunit domain that constitutes the N-terminal half of the delta' subunit within the bacterial DNA polymerase III holoenzyme. It functions as a component of the gamma complex to facilitate the assembly of the replicative machinery and shares structural homology with the gamma and tau subunits. Additionally, the protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein belongs to the DNA Replication and Repair Clamp Loader Complex family, which functions as a key component of DNA replication and repair machinery by utilizing ATPase activity to load sliding clamps, such as PCNA, onto DNA. These proteins ensure the processivity of DNA polymerases delta and epsilon during template elongation and contribute to chromatin assembly and sister chromatid cohesion. Additionally, specific members regulate developmental processes such as plant trichome branching. It occurs in Deltaproteobacteria bacterium GWB2_55_19 and has UniProt annotations Nucleotidyltransferase and Transferase.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 3066, 2162, 43, 2678, 6479, 4337, 16, 9649, 13476, 5903, 3418, 1988, 14879, 1920, 56, 17, 4262, 4768, 1927, 1920, 9649, 11, 5903, 2651, 1920, 4543, 2678, 6479, 4337, 20403, 14896, 18, 2176, 4088, 1966, 43, 4594, 1927, 1920, 7034, 2796, 1942, 6628, 1920, 5957, 1927, 1920, 20604, 10853, 1930, 16495, 4346, 9039, 1956, 1920, 7034, 1930, 7462, 6991, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 2678, 5158, 1930, 5059, 10209, 4019, 1915, 2796, 3416, 16, 2154, 4088, 1966, 43, 3834, 4594, 1927, 2678, 5158, 1930, 5059, 10853, 2007, 10232, 9444, 2455, 1942, 4019, 17324, 10209, 1036, 16, 2427, 1966, 14381, 16, 6131, 2678, 18, 2144, 2697, 6486, 1920, 2585, 10794, 1927, 2678, 20910, 9649, 1930, 22206, 2409, 7662, 9971, 1930, 4672, 1942, 6338, 5957, 1930, 14611, 28829, 21275, 18, 4950, 16, 2487, 4678, 5741, 5878, 4028, 2427, 1966, 4496, 10477, 2225, 13898, 18, 2176, 5110, 1922, 9649, 9218, 1021, 10296, 14061, 8997, 8520, 41, 4288, 41, 2282, 1930, 2258, 20709, 15010, 2797, 4090, 2199, 9961, 1930, 13763, 18, 3], "output": "MPFKDILGHEREIRVLREALNTGRLAHSYLFAGPEGIGKRKTAFELARALNTNIVEVAPTVKDRDELVPDPSGLIRIEQIRDILSLLKYKADGGRKAVIVDGLKTLEEPPAGSIIMLVTSRPADLLPTIISRCQRVSFRPLPEEALIVALVEGEGRGDKGRELIKRLQSITDVSEALKFAEELSKKDDILEALETLKGWYREGRRREGLAEDFFSIEETRRMIAPPRYANKLLAMEALILKLVDCASATDDACGECASCLRAASGTHAERLMPQAANAFKTGATEEEAMTAARMTGRSLSLALKYIDRAIAASGAENLLVNRDVYGYSDGSF", "metadata": {"id": "A0A1F8XXU1", "cluster": 3055097, "interpro_all": ["IPR004622", "IPR050238", "IPR027417"], "interpro_used": ["IPR004622", "IPR027417", "IPR050238"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein belongs to the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Also, the protein is a member of the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. Moreover, the protein carries a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. It is native to Catenaria anguillulae PL171 and is associated with UniProt keywords mRNA processing, Nucleus, and Magnesium.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 14440, 1942, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 3950, 16, 1920, 2213, 16252, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 2176, 1977, 6196, 1942, 3115, 11496, 3027, 1019, 3409, 15444, 11560, 16842, 2123, 27077, 1930, 1977, 2458, 1956, 20709, 11569, 3616, 4587, 16, 5607, 16, 1930, 13148, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MLALDPHSHKQCLGVTAPVSHASPTPQDVQLNANLISTLRSMDLFPQLYALVKSFVRRVAMNQGLPEELAEETGGTIYSFGSFRLGVHGPGADIDTLCVAPKHVSRDDVTELAAVPDAFVPVITFEMRGVPIDLLFCRLDMTQVPENLSLSGIDILSKLDERDIEFRTALRAIKRWAKVRGIYSNVMGFLGGVAWAMLVARVCQLYPILLKPIEEAPLPFRIWNPRLYPADRQHRMPIITPAYPSMCATHNVTKSTFDVLKGELAWSALFTPHSYFSKYKYYLQLVVSSTAKETHLKFSGHPYFKGVERVFTYETDEQRVALAGGAWADRLPALSGEAVAQAESAAAAAAAAEAQVLYTTSFYLGLVLKDAATQQPGQRRRLDIGWLLPQIVATAKAFVGFDEKDIDPKQQQAQAGQGANKRKVEEEAVQGAGEESIKRQKQAHEAASAMSMSTSAEDSQLREQVLGNRDDFFSVMYEMLKRSLNGSRVTDEILRLVPDINPNANSGTIVIKFFAIMQAWPWPEHEFHLGTQLTQRIQRYMESRLRRQVLDLEDHGELDLITAAAGSEGGPAQVAAPKGLANMSVTMQTLRKATLP", "metadata": {"id": "A0A1Y2HEZ9", "cluster": 4635115, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR043519", "IPR011068", "IPR007012"], "interpro_unused": ["IPR014492", "IPR048840", "IPR007010"]}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein belongs to the DNA/RNA polymerase superfamily, which encompasses enzymes such as DNA polymerase I, reverse transcriptase, and viral RNA polymerases that catalyze the template-directed synthesis of nucleic acids. Members of this superfamily share a conserved active site fold resembling the palm subdomain of right-hand-shaped polymerases. Also, the protein should include a Reverse transcriptase domain that functions as an RNA-directed DNA polymerase (EC 2.7.7.49) to synthesize DNA from an RNA template. This domain is central to the replication of retroid elements, such as retroviruses and retrotransposons, and is often expressed as part of the POL polyprotein to facilitate integration into the host genome. In addition, the protein falls within the Reverse transcriptase/Diguanylate cyclase domain superfamily, which encompasses diverse enzymatic domains found in reverse transcriptases, DNA polymerase IV, and nucleotide cyclases such as the GGDEF domain. These members exhibit DNA-directed DNA polymerase, RNA-directed RNA polymerase, or diguanylate cyclase activities, facilitating processes ranging from viral replication to signal transduction and nucleotide binding. It occurs in Solanum verrucosum.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14440, 1942, 1920, 2678, 19, 3146, 6479, 13975, 16, 2154, 21569, 5038, 2427, 1966, 2678, 6479, 51, 16, 5267, 13335, 16, 1930, 4324, 3146, 20910, 1988, 18170, 1920, 7662, 17, 6554, 4271, 1927, 11079, 4576, 18, 4678, 1927, 2052, 13975, 7948, 43, 5305, 3500, 3200, 3728, 18994, 1920, 15516, 27517, 1927, 3659, 17, 3897, 17, 9132, 20910, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 5267, 13335, 3418, 1988, 4088, 1966, 1925, 3146, 17, 6554, 2678, 6479, 12, 3270, 22, 18, 27, 18, 27, 18, 4343, 13, 1942, 15541, 2678, 2037, 1925, 3146, 7662, 18, 2052, 3418, 1977, 4101, 1942, 1920, 5158, 1927, 7332, 1960, 5362, 16, 2427, 1966, 26371, 1930, 27181, 2101, 16, 1930, 1977, 3868, 3198, 1966, 3131, 1927, 1920, 2492, 6240, 5684, 1942, 6628, 7122, 2460, 1920, 4423, 3843, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 5267, 13335, 19, 4325, 13785, 9075, 16526, 3418, 13975, 16, 2154, 21569, 6445, 8145, 4682, 2435, 1922, 5267, 13335, 1036, 16, 2678, 6479, 4370, 16, 1930, 5489, 16526, 1036, 2427, 1966, 1920, 12358, 3695, 1038, 3418, 18, 2144, 4678, 5987, 2678, 17, 6554, 2678, 6479, 16, 3146, 17, 6554, 3146, 6479, 16, 2014, 4325, 13785, 9075, 16526, 4209, 16, 12440, 4028, 6485, 2037, 4324, 5158, 1942, 2733, 8201, 1930, 5489, 2743, 18, 2176, 5110, 1922, 2638, 24961, 3566, 3176, 4879, 20490, 1035, 18, 3], "output": "MTTRRDFTRSNEEHNVNQGAPLEAPQALVDPLVENVTHMEFRIDLVNPNVNSAASRVRDFARMNPPKFLSSKVEEDPERFPIASWAAFAPFAFQVAFGNRTRYGHYEFLVMSFGLTNINDILIYSRSENEYVNHLRIVLSHPARRNADPQDQGVPNAPWMLFQVVANQVGQQRGDQHDVADISRVLEFLRMNPPDVTGRKTLWKSYKRDEGAPVVSWAAFAPIASHVAFGNRDAGSISLVSNLSGMAFCSNLYPITAISILISPTTTTINVTTLVPARPRIAQTRTPTWFDKNATIQVLAKVVTAQANRGVIDEVDKGVARVWYDQWKKSRAEGSAPAAFMNLMNEVFRQYLDIFVIVFDVQLQVEVINAEFIDAISRVSRILILTVQEEAHNDLYNDPYLS", "metadata": {"id": "A0AAF0UIW0", "cluster": 4701891, "interpro_all": ["IPR043502", "IPR043128", "IPR053134", "IPR000477"], "interpro_used": ["IPR043502", "IPR000477", "IPR043128"], "interpro_unused": ["IPR053134"]}, "task_type": "infilling"} {"instruction": "The protein is categorized in the HIT-like superfamily, which functions as a group of nucleotide hydrolases and transferases acting on the alpha-phosphate of ribonucleotides via a conserved histidine triad motif. These proteins are involved in diverse pathways ranging from galactose metabolism and phospholipid regulation to DNA repair and mRNA decapping, often hydrolyzing substrates like dinucleotide polyphosphates and phosphoramidates. It is found in Candidatus Pacearchaeota archaeon. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 11314, 17, 3189, 13975, 16, 2154, 4088, 1966, 43, 2210, 1927, 5489, 30337, 1930, 13763, 1036, 8290, 1990, 1920, 4595, 17, 5413, 1927, 18347, 7314, 3454, 43, 5305, 13873, 21845, 5219, 18, 2144, 2697, 2032, 3286, 1922, 6445, 3873, 6485, 2037, 15996, 4714, 1930, 14608, 3640, 1942, 2678, 5059, 1930, 3616, 2344, 5041, 16, 3868, 7222, 9046, 6249, 3189, 21302, 11769, 11787, 1036, 1930, 3421, 25238, 2209, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 19589, 3983, 3336, 7336, 13470, 1916, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MKRRTNINDLVELVTRTISHAQEKFTDSKTTLSPDFMLGFSLSNQGIDRATYTPILNHWGFGTIDYLMTGEGSSCLPWLHEDTWRYLTDSSEDSPAEKPLVLDSERGWSAVTEGIRAGQIMFTQSPESIHLYTPSIAGGTRTGGKILVSKMQRPWQVEGPIHKLEDCPLCKRSEREKQGVGEPGYKDLNVIHNRFTPYNFHQLIVPTSSFYKNTGDDNSFIYQQEGLAQVLDLAFDTFFNSKKQTLMLGVHKGYLAGQNLGHLHFHLHSHD", "metadata": {"id": "A0A8T4MKP9", "cluster": 6994849, "interpro_all": ["IPR036265"], "interpro_used": ["IPR036265"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence be if I wanted a protein that could perform the following function: The protein can be placed in the Polysaccharide Synthase-Related Protein family, which mediates the biosynthesis and modification of polysaccharides through enzymatic activities such as the epimerization of UDP-galactose and the production of pseudaminic acid via C6 dehydratase and C5 epimerase functions. These proteins play critical roles in flagellin modification, biofilm formation, and the synthesis of capsular polysaccharides associated with bacterial virulence. In addition, the protein is grouped in the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. It has been characterized in Patescibacteria bacterium.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 17167, 8921, 17, 2712, 2213, 3416, 16, 2154, 10412, 1920, 8132, 1930, 6295, 1927, 18686, 2596, 8145, 4209, 2427, 1966, 1920, 13872, 9213, 2466, 1927, 18500, 17, 15996, 1930, 1920, 3372, 1927, 6050, 3717, 1935, 2687, 3454, 12822, 11725, 7234, 1930, 13441, 13872, 9213, 2051, 4088, 18, 2144, 2697, 3918, 4140, 5456, 1922, 27389, 6295, 16, 9638, 3337, 16, 1930, 1920, 4271, 1927, 22590, 18686, 2458, 1956, 4543, 9304, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 2176, 2258, 2252, 4378, 1922, 2917, 1918, 3349, 7972, 2341, 18339, 14061, 18, 3], "output": "MGDAGEQIIQQLLKENSQYLPVGLVDDDLAFQDISIHGVRVLGKREDIPRLVKEYQTDNLLIAMPSATSRSVREIIEVGDILCLVTHSVSTYE", "metadata": {"id": "A0A9E5YBT9", "cluster": 7528486, "interpro_all": ["IPR036291", "IPR051203"], "interpro_used": ["IPR051203", "IPR036291"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein contains a Putative T7SS secretion signal domain that likely mediates secretion via the type VII secretion system. This $\\alpha$-helical domain is primarily found in Actinomycetes. It is produced by Actinomycetales bacterium SN12.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 5461, 43, 6770, 13359, 5590, 5512, 2733, 3418, 1988, 3205, 10412, 5512, 3454, 1920, 2601, 16852, 5512, 2433, 18, 2052, 8, 38, 4595, 8, 17, 11514, 3418, 1977, 5985, 2435, 1922, 4718, 25148, 18, 2176, 1977, 4152, 2007, 4718, 13386, 3949, 1918, 14061, 3437, 3112, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MELGQTQSPTDLVPGSLRTLDDAGTWKGDAYDAYLAGALFTWADALQWAQDEADRAITLWNEAEQQVGQGLRHPEVDVPFVDPSGPAHDEARELDTAADQARMPLTESEAGRAANNAIAETLSIAAQTLWEHPDIILELLGGAATFLGGAAPGLVVAGVGVAGTGAGLMGDAAGRWYAGTFANGQANKPWVDKEKLGLDEYAEEQRVYDGLERNNDGTYTAIEIKSGPSARSEYNSAGSGDSIEITHVEVRYVPVSDVRSTAESWKAPGRAATEVRDAERFERQLLHWQNAGESLDAGAAQALAAHRDYLRELRVLFNARATLEVYARDCAIRAVFTIAVVQPFQATMQMAVGGGGLTVTGVGALAGALTESHGVGDRVRGVDRGDGRDGADVIRIKIKVDYDGSPQNGTQRQFDDSVNAGTPARGKLD", "metadata": {"id": "A0A2N1JKJ9", "cluster": 7764032, "interpro_all": ["IPR049082"], "interpro_used": ["IPR049082"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein possesses a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein contains a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Furthermore, the protein is assigned to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is native to candidate division Zixibacteria bacterium RBG_16_48_11 and has UniProt annotations Transferase. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 5461, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 6196, 1942, 6610, 8451, 28666, 18068, 7972, 2341, 18339, 14061, 6160, 1029, 41, 2641, 41, 3427, 41, 2513, 1930, 2258, 20709, 15010, 13763, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "LFLKVLRQRKDGFHQIFSWMQAVDLQDELEIKRIEKGIKISCDDPCVPADKTNLAYRAAELFLRRTKIKAGVKIKIMKRIPVAGGLGGGSSNAATVILGLQKSFKVKLTKTQMLSIAEKIGSDVPFFFTSGSAVASGRGEKLKNIKLPLNYWLVLINPGFEVSTKWAYSKVKPKPLKRKLLPSRSRVTLNLMLKEIKVWGNDLQGVVCKRYPEIKTVIGKLNQSGALYSAMSGSGPTVFGIFSDRNEAKKAAEKLTRRKIWKTWVVRPIKLWPQGLP", "metadata": {"id": "A0A1F4Y5J3", "cluster": 8248907, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "I want a protein that has the function: The protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein belongs to the GHMP kinase, C-terminal domain superfamily, which encompasses the C-terminal structural component of ATP-dependent enzymes involved in amino acid, isoprene, and carbohydrate metabolism. This domain adopts a central alpha-beta plait fold that cooperates with the N-terminal domain to create a nucleotide-binding pocket. While primarily found in homoserine, galacto-, and mevalonate kinases, it is also present in structurally related diphosphomevalonate decarboxylases. Additionally, the protein falls within the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is found in Elusimicrobia bacterium CG08_land_8_20_14_0_20_59_10 and contains UniProt keyword associations Isoprene biosynthesis and Transferase. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 21569, 1920, 45, 17, 4262, 4346, 4594, 1927, 4498, 17, 3100, 5038, 3286, 1922, 3835, 2687, 16, 26690, 1021, 16, 1930, 10590, 4714, 18, 2052, 3418, 24032, 43, 4101, 4595, 17, 4666, 5606, 1932, 3728, 1988, 23230, 1036, 1956, 1920, 56, 17, 4262, 3418, 1942, 7762, 43, 5489, 17, 2743, 10154, 18, 2679, 5985, 2435, 1922, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 16, 2176, 1977, 2222, 2481, 1922, 12171, 2712, 11791, 2609, 2225, 4701, 8870, 23922, 1036, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 2435, 1922, 2349, 24327, 4913, 15129, 2126, 14061, 7294, 13895, 41, 7559, 41, 28, 41, 2036, 41, 2607, 41, 20, 41, 2036, 41, 4777, 41, 2119, 1930, 5461, 20709, 11121, 2538, 5253, 26690, 1021, 8132, 1930, 13763, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MKTILNCRIQVKAPAKINLFLEVTGRRRDGYHNLATIFARLALCDTLTFKKGRVPGISLKVTGLRIPGLKEPEDNIVYKAAAAFLRAFGIKPAVEIRLFKALPSGAGLGGGSSDAAAALLGLCRLYGIPRAVNMRKLLRLASALGSDVPFFLLDSPMAAGTGRGVRLKPVKFRGRAPRVVLAYPGAPVSTGKVYSRLKLAPAREIKTRLAEFRGFVKSLESGVFDASRVFNRLEDAVLPVNPRVRGAKRGLAGLLRLTIASQDHVPSKPWRRRTGPGAEAVLMSGSGAAVFALVRGLKKARALAAAASRNRSYRVFLTEFC", "metadata": {"id": "A0A2M6XYC9", "cluster": 8550840, "interpro_all": ["IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR036554", "IPR004424"], "interpro_unused": ["IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to create: The protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Furthermore, the protein is categorized in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is identified in Bacillota bacterium (Firmicutes bacterium) and exhibits UniProt keyword tags Cytoplasm and rRNA processing. Please provide the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 7762, 30, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 2899, 1922, 8175, 22538, 3857, 14061, 12, 24474, 14061, 13, 1930, 9826, 20709, 11121, 2538, 14392, 5239, 1930, 9067, 4587, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MEPYHIPVMFDECMEALQVKDDGIYFDGTLGGGSHTAGILSRGGRVIAVDRDDDAIEYCRQRFADSPFADHLTIVKSNFKDFSHIIAKLGVKKIDGALLDLGISSHQISSVERGFTFQQDAPLDMRMDREQKLSAKDIVNSWPQEKIADVIFDYGEEKFAKRIAANICAFRQKKEIETTFELVDIIKHSVDSAAMKNGHPAKRTFQALRIAVNDELSGLGELIEDIVNKLNVGGRIAIISFHSLEDRIVKRKFAFMATDCICDKTLPVCVCGHKADIKIIGKYRPSEKELDKNPRSSSATLRVAEKLAKK", "metadata": {"id": "A0A9D1Q4N5", "cluster": 10183027, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR002903", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should have a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. Also, the protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein can be placed in the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. It is produced by Burkholderiaceae bacterium and is annotated with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 3066, 2162, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2176, 1977, 4152, 2007, 18359, 18681, 19476, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MTFAQSKNRPGFFISFEGIDGAGKSTHIERSAELLTALGESLREMLLHHKMHLETEALLMFAARREHLATVIEGGGRGLDLAKLYELEVWVQMRLKEGQRYLVQPDMTFLFDLPSEVAQGVRQEYRRRAIEDTDRFVLIDANQSVESIAKTLEEYILNIQSRYPERQVVLTREPGGPALAAGHIVISDRFTDATFAYQRRSLARNPDKFESLDDVFFDR", "metadata": {"id": "A0A965JRS7", "cluster": 11876031, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR039430", "IPR027417", "IPR018094"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein carries a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. Also, the protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is present in Alphaproteobacteria bacterium CG11_big_fil_rev_8_21_14_0_20_44_7 and carries UniProt keyword assignments ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 16252, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2481, 1922, 4595, 9218, 1021, 10296, 14061, 7294, 3242, 41, 9769, 41, 3313, 41, 5197, 41, 28, 41, 2900, 41, 2607, 41, 20, 41, 2036, 41, 4044, 41, 27, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSKFITFEGGEGCGKSTQVELLAEHLRRIGHRVITTREPGGTEGAEEIRELLIHGDKEKWDGKQEVLLNFAARMDHVNNLIKPALERGEWVICDRFFDSTYVYQGIAQGVGSEYIDIIREASMGGFAPDKTFILDMEVKESLDRVNSRGEQNRYDEMDVEFHQKIRAGFLKIAQDNPERCVVINALQDIKKVHEEIVEKL", "metadata": {"id": "A0A2H0QEY8", "cluster": 13320762, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "autoregressive"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein is classified under the Ferredoxin-NADP reductase-like family, which comprises oxidoreductases that catalyze the transfer of electrons between NADPH and carriers such as ferredoxin or adrenodoxin. This family includes bacterial ferredoxin reductases and the human mitochondrial NADPH:adrenodoxin oxidoreductase. Furthermore, the protein is classified under the Ferredoxin-NADP+ reductase, adrenodoxin-type family, which functions as an NADPH:adrenodoxin oxidoreductase, transferring electrons from NADPH to adrenodoxin or related ferredoxins. This group includes mitochondrial enzymes such as human Fdxr and bacterial homologs like Mycobacterium FprA, playing a vital role in electron transport systems. In addition, the protein incorporates a FAD/NAD(P)-binding domain that binds FAD and NAD(P)H cofactors to facilitate electron transfer in class I and class II oxidoreductases. This domain typically adopts a doubly-wound \u03b1/\u03b2 fold and contains a pair of redox-active cysteines involved in transferring reducing equivalents from the FAD cofactor to the substrate. It is characteristic of the pyridine nucleotide-disulphide oxidoreductase family, playing a central role in oxidative metabolism. It is derived from Corynebacterium glutamicum (Brevibacterium saccharolyticum) and has UniProt annotations Flavoprotein.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 25304, 22389, 10960, 17, 24221, 11386, 17, 3189, 3416, 16, 2154, 12936, 27388, 1036, 1988, 18170, 1920, 3856, 1927, 14354, 2192, 11908, 1930, 8974, 2427, 1966, 25304, 22389, 10960, 2014, 7206, 1986, 9754, 18, 2052, 3416, 5921, 4543, 25304, 22389, 10960, 11386, 1036, 1930, 1920, 2616, 4596, 11908, 30, 7206, 1986, 9754, 27388, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 25304, 22389, 10960, 17, 24221, 15, 11386, 16, 7206, 1986, 9754, 17, 2601, 3416, 16, 2154, 4088, 1966, 1925, 11908, 30, 7206, 1986, 9754, 27388, 16, 21902, 14354, 2037, 11908, 1942, 7206, 1986, 9754, 2014, 2712, 25304, 22389, 10960, 1036, 18, 2052, 2210, 5921, 4596, 5038, 2427, 1966, 2616, 8350, 10024, 1930, 4543, 14279, 3189, 16389, 30276, 1019, 16, 14797, 43, 8970, 2770, 1922, 4995, 4860, 3771, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 14134, 19, 6577, 12, 58, 13, 17, 2743, 3418, 1988, 6876, 14134, 1930, 6577, 12, 58, 13, 50, 21362, 1942, 6628, 4995, 3856, 1922, 2921, 51, 1930, 2921, 2890, 27388, 1036, 18, 2052, 3418, 5745, 24032, 43, 26783, 17, 6376, 160, 19, 161, 3728, 1930, 5461, 43, 3715, 1927, 9366, 17, 3500, 22446, 3286, 1922, 21902, 5526, 17762, 2037, 1920, 14134, 15155, 1942, 1920, 4510, 18, 2176, 1977, 6293, 1927, 1920, 19604, 5489, 17, 2054, 23138, 2261, 27388, 3416, 16, 14797, 43, 4101, 2770, 1922, 5163, 4714, 18, 2176, 1977, 3595, 2037, 2233, 17151, 7972, 2341, 18842, 1989, 18626, 1989, 12, 3022, 2165, 7972, 2341, 18842, 1989, 14175, 15742, 1954, 2002, 1989, 13, 1930, 2258, 20709, 15010, 7732, 6657, 18, 3], "output": "MSRPLRVAVVGAGPAGIYARMPAPFGLIRYGVAPDHPRIKGIVKSLHNVMDKEQLRFGATGDQDLRVPGSDLEGSWGAGEFVGFYDGNAVVGVGNVALDVARILAKTGDELLVTEIPDNVYESLAKFTPLELKELDHSDTIEVIVNPEDDSKSQDLVCQTLESYAMRDPKGAPHKLFIHERTQLDGNGGVTGTGEFKTWDVQSERAVVPNDGGHIIDPEVGSPITGLYATGWIKRGPIDHAAGSLPAPAKPELESIIEFLDERKVAFTTRKKIVEWNDMVRHARPEYDISDLLMKSDTDVQIDLFELGNIEVGKDITVEELREFYDAIVFSTPNFERNWDLSAEKVKNQAKEVHVFGRRGPAQAIDYDAASEQARRFFESPVEILGEDGKVVGLKTVYRAVGYRSDAIEGVPFDDGLIGNTKSDAKETTEMLLAWDGWHLLDAAERALGEPEGRE", "metadata": {"id": "A0AAE6LT63", "cluster": 14121076, "interpro_all": ["IPR036188", "IPR023753", "IPR055275", "IPR021163"], "interpro_used": ["IPR055275", "IPR021163", "IPR023753"], "interpro_unused": ["IPR036188"]}, "task_type": "infilling"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein should include a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein is grouped in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein includes a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It originates from Fibrobacter sp. UWT3 and is annotated with UniProt keywords Isoprene biosynthesis and Transferase. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 1925, 3835, 2687, 3244, 1988, 2469, 16318, 2460, 43, 2213, 22665, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 22970, 2037, 5094, 7972, 2341, 1915, 2056, 18, 25933, 8034, 1930, 1977, 10633, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 7031, 1920, 3244, 18, 3], "output": "MTIKEFAPAKINLFLDVIRKREDGYHDLGTVFQTVDVGDTLEFSARDDGEIHLEYSNPQEYPVESDLVYKAAVALRSHVGNNDLGADIFLDKIMPLGAGLGGGSADAAAALRALNRLWELRLPPAELERIGAKLGADVPFLVRGGTAFAEGIGERLSFISPLDLPAGEVLLIATPHDSVPTKDAYAGVPKSGPDRWEGYKLAWETASDAERSFGGPLLDSGAFFNAFEVSVFPKHPLVGAMKDKFLDLGARVALMSGSGASVFGIFADRTTAETAAETLKPYSRYIALTKFWHT", "metadata": {"id": "A0A2C8Z0V3", "cluster": 14650288, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR004424", "IPR013750"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein should have a GUN4-like domain that binds porphyrins, including protoporphyrin IX and Mg-protoporphyrin IX, to regulate chlorophyll biosynthesis and facilitate chloroplast-to-nucleus retrograde signaling in aerobic photosynthetic organisms. It additionally contributes to cellular protection against reactive oxygen species-mediated damage. It is produced by Leptolyngbyaceae cyanobacterium RM1_1_2.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 3066, 2162, 43, 20992, 1006, 17, 3189, 3418, 1988, 6876, 24944, 1036, 16, 2710, 23583, 2074, 25818, 5572, 13848, 1930, 2786, 17, 23583, 2074, 25818, 5572, 13848, 16, 1942, 5741, 16553, 8132, 1930, 6628, 17471, 17, 1942, 17, 5607, 14492, 3197, 1922, 11251, 16068, 7373, 18, 2176, 4950, 7624, 1942, 3689, 6202, 3316, 6079, 4612, 3038, 17, 3434, 4293, 18, 2176, 1977, 4152, 2007, 16976, 26558, 2029, 4864, 9914, 26898, 7972, 2341, 18842, 1989, 10625, 1009, 41, 21, 41, 22, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MGQEAERRGYLELEEIRNFPCGDLLLIDQLWKQIWLDVGGKLDFGEDYQSAKQAYEKMSDRNGWIAHLPLVCIGLGGWVCCGVGGGFGFSRIETCKLVKFSGGKFGFSVQRKSAQYISYKDAIFSTSAP", "metadata": {"id": "A0A968ZWZ8", "cluster": 15347367, "interpro_all": ["IPR008629", "IPR037215"], "interpro_used": ["IPR008629"], "interpro_unused": ["IPR037215"]}, "task_type": "infilling"} {"instruction": "The protein I want to design has this role: The protein should feature a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Furthermore, the protein has a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Furthermore, the protein features a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. It has been characterized in Acinetobacter nectaris CIP 110549 and is linked to UniProt keywords DNA repair, Excision nuclease, and Cytoplasm. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 3066, 5961, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 3677, 16, 1920, 2213, 2258, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 3677, 16, 1920, 2213, 4075, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2176, 2258, 2252, 4378, 1922, 27182, 28339, 17295, 12998, 8139, 10883, 1930, 1977, 4624, 1942, 20709, 11569, 2678, 5059, 16, 10940, 16230, 16, 1930, 5239, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MSDHQPFELVTSYEPAGDQPQAIQKLVSGIKKGMKNQLLLGVTGSGKTYTMANVIANLQRPTIIMAHNKTLAAQLYGEFKSFFPNNAVEYFVSYYDYYQPEAYVPSSDTFIEKDAAINDHIDQMRLSATRALLERKDAIIIASVSAIYGLGDPEAYMQMLLHIVENDRISRDDIIRRLVEMQYTRNDLEFLRATYRIRGEIIDIFPAESEQYAIRVELFDDEVDSIRWFDPITGKMIRKVPRVTIYPKSHYVTPKDNLQRAIGTIKEELKERIEFLKANDKLLEAQRIEQRTRYDLEMMQQLGYTNGIENYSRHLSGREEGAAPPTLFDYIPEDALLILDESHVTIPQIGAMYKGDRSRKENLVNYGFRLPSALDNRPMKFEEWERITPTTLYVSATPALYELEHAEQVVEQVVRPTGLIDPEIEVRPVLTQVDDILSEINLRREQDERVLITTLTKRMAEDLTSYLKEYGIKVAYLHSDIDTVERVKIIHDLRSGIYDVLVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVKGKAILYADRITDSMRKAIDETDRRREKQLAFNAEHGITPRSTVRQVVKEIDTGEVFDDETSTNIPIDTKLTADEQHIVSDPKLLTKHLAKLEKEMLKASKELQFEQAAKIRDEMVHLKSYLLQ", "metadata": {"id": "V2TQ01", "cluster": 19821339, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001943", "IPR001650", "IPR014001"], "interpro_unused": ["IPR024759", "IPR041471", "IPR036876", "IPR006935", "IPR004807", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "The protein is associated with the Quinoprotein alcohol dehydrogenase-like superfamily, which comprises bacterial enzymes that utilize a pyrroloquinoline quinone (PQQ) prosthetic group to catalyze the oxidation of alcohols such as methanol and ethanol. These proteins typically adopt an 8-bladed beta-propeller structure and may include C-terminal heme or cytochrome c domains to facilitate electron transfer in methylotrophic or autotrophic pathways. In addition, the protein is classified under the WD40/YVTN repeat-like-containing domain superfamily, which features repeating motifs of approximately 40 residues that fold into a seven- or eight-bladed beta-propeller structure composed of four-stranded beta-sheets. This architecture typically serves as a rigid scaffold for mediating diverse protein-protein interactions and facilitating the assembly of multi-protein complexes. It is present in Spirochaetales bacterium.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 9012, 6657, 4284, 9294, 17, 3189, 13975, 16, 2154, 12936, 4543, 5038, 1988, 12561, 43, 23878, 1037, 11072, 8419, 25093, 12, 15564, 1055, 13, 19019, 2210, 1942, 18170, 1920, 6638, 1927, 21773, 2427, 1966, 8570, 1930, 5757, 18, 2144, 2697, 5745, 14103, 1925, 28, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 1930, 2278, 3951, 45, 17, 4262, 10954, 2014, 9387, 45, 4682, 1942, 6628, 4995, 3856, 1922, 4963, 13653, 2014, 5728, 1997, 2688, 1935, 3873, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 17907, 4241, 19, 67, 25641, 1022, 6865, 17, 3189, 17, 3165, 3418, 13975, 16, 2154, 4075, 21763, 8277, 1927, 3993, 3040, 4248, 1988, 3728, 2460, 43, 5260, 17, 2014, 5066, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 7179, 1927, 3006, 17, 10338, 4666, 17, 14685, 18, 2052, 9335, 5745, 10634, 1966, 43, 12383, 7281, 1958, 10239, 6445, 2213, 17, 2213, 3719, 1930, 12440, 1920, 5957, 1927, 2779, 17, 2213, 5048, 18, 2176, 1977, 2481, 1922, 22075, 25588, 3949, 1918, 14061, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MRYLLIGIIAGALMGLTPVWQAEPAIELYPEWHGPIAAPESIERSLLAADGRLISRRAFGETLFAPSGSGGYYAAYQKLGTSVEFFAADQSRARALDFHGNQAGEPVSGRFLTVIAFSKGTDIAALGFLDGSYHVIDSTGRRLHYGNEKGDYIALIDTADGSARASALSRVHVARTALTVLDDGTAAVLDYNAARTGMASLDRDGGVYVAGYTRSEGGAQALAFLPDGTMLFARNFPMESYLSPNTALSARVVPPVISADTLGSPFWKIDSREYPYLSYNGKLVLLVNSDLRARTGGGTLVKSIAVSPSGTYVALRILIVNRKARPTAAIKIP", "metadata": {"id": "A0A3N5T3I4", "cluster": 20698057, "interpro_all": ["IPR011047", "IPR015943"], "interpro_used": ["IPR011047", "IPR015943"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein should include a Thioredoxin domain that functions as a ubiquitous protein disulphide oxidoreductase, utilizing a conserved active site with two cysteines to facilitate reversible redox reactions. It mediates electron transfer in NADPH-dependent pathways and serves as a core component of enzymes like protein disulphide isomerases (PDI) and bacterial Dsb proteins, where it catalyzes the formation and rearrangement of disulphide bonds during protein folding. Additionally, the protein is grouped in the Thioredoxin-like superfamily, which encompasses a diverse group of redox-active proteins characterized by a conserved $\\alpha$/$\\beta$/$\\alpha$ structural fold and a CXXC active site motif. These enzymes primarily facilitate electron transfer via thiol-disulfide exchange reactions to maintain cellular redox homeostasis, assist in protein folding through disulfide bond formation or isomerization, and participate in signaling pathways like the glutathione/glutaredoxin system. It is present in Calditrichota bacterium. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 3066, 3951, 43, 23684, 3418, 1988, 4088, 1966, 43, 15498, 2213, 2054, 23138, 2261, 27388, 16, 10232, 43, 5305, 3500, 3200, 1956, 2288, 22446, 1942, 6628, 10743, 9366, 5298, 18, 2176, 10412, 4995, 3856, 1922, 11908, 17, 3100, 3873, 1930, 10634, 1966, 43, 4728, 4594, 1927, 5038, 3189, 2213, 2054, 23138, 2261, 25510, 1036, 12, 20506, 13, 1930, 4543, 15136, 2697, 16, 2597, 2176, 17097, 1920, 3337, 1930, 14154, 1927, 2054, 23138, 2261, 9031, 2409, 2213, 10328, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 23684, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 9366, 17, 3500, 2697, 4378, 2007, 43, 5305, 8, 38, 4595, 8, 19, 8, 38, 4666, 8, 19, 8, 38, 4595, 8, 4346, 3728, 1930, 43, 5639, 21487, 3500, 3200, 5219, 18, 2144, 5038, 5985, 6628, 4995, 3856, 3454, 13914, 17, 11830, 6818, 5298, 1942, 6698, 3689, 9366, 7622, 16, 6589, 1922, 2213, 10328, 2596, 11830, 5403, 3337, 2014, 27027, 16, 1930, 7352, 1922, 3197, 3873, 3189, 1920, 9153, 19, 19406, 1919, 9754, 2433, 18, 2176, 1977, 2481, 1922, 2570, 7408, 3319, 10647, 3857, 14061, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MVQKSIFRSLFGLVLLGFLATGFAQEKETVEPGWFTNMDKAMESAGKDGKLVLAYFSGSDWCKPCIMLKKKILTSDTFKKYASEKLVIVQLDFPAKKKNQLPEDEKKHNEAMAERYNAGGAFPLVALIDKDGEKIGELSGYDRQTPDEYVNQLKEITKNAGKTGN", "metadata": {"id": "A0A958IZK4", "cluster": 21151675, "interpro_all": ["IPR036249", "IPR013766"], "interpro_used": ["IPR013766", "IPR036249"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein can be placed in the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. Also, the protein includes a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. Additionally, the protein is grouped in the Fe-S cluster assembly domain superfamily, which facilitates the mobilization, assembly, and transfer of iron-sulfur clusters to recipient apoproteins. Members of this superfamily function within the ISC, SUF, and NIF pathways, often acting as scaffold proteins that transiently bind Fe and S atoms to synthesize [2Fe-2S] or [4Fe-4S] cofactors. These domains are critical for maturing proteins involved in electron transfer, redox catalysis, and nitrogen fixation across bacteria and eukaryotes. It is identified in Chlorobium phaeovibrioides and is linked to UniProt keywords ATP-binding, Hydrolase, and Metal-binding.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 2222, 16, 1920, 2213, 5921, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2650, 17, 61, 4377, 5957, 3418, 13975, 16, 2154, 11374, 1920, 14586, 16, 5957, 16, 1930, 3856, 1927, 5680, 17, 12585, 5859, 1942, 10664, 11466, 22163, 1036, 18, 4678, 1927, 2052, 13975, 2347, 2651, 1920, 23924, 16, 2020, 1038, 16, 1930, 17719, 3873, 16, 3868, 8290, 1966, 7281, 2697, 1988, 12145, 4566, 2650, 1930, 61, 9030, 1942, 15541, 37, 13775, 1021, 17, 20759, 39, 2014, 37, 15338, 1021, 17, 26814, 39, 21362, 18, 2144, 4682, 2032, 4140, 1958, 2888, 4729, 2697, 3286, 1922, 4995, 3856, 16, 9366, 15408, 16, 1930, 6634, 7938, 3436, 4802, 1930, 15021, 18, 2176, 1977, 2899, 1922, 10107, 3821, 1989, 18421, 1021, 25210, 2377, 3940, 3726, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 16, 20748, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MATIDEHQILKALSTVLDPDLKKDLVSLGMIRGISVTEPLKDEIRQSCIDAIRAELPAAERIDVEMTAEVTSSCSHGHDDHHHEDGHQCSGGQCGKGGVGKSTVAVNLAVSLAATGASVGLVDADLYGPSIPTMFGLHSEQPKVVEKMLQPLAIKQFITEVAWGELDYLIFDLPPGTGDIQLTLAQTIPLTGAVIVTTPQDVIENMSWYELPDGSRDYLFGQKGGERFAKARGLAFLGIGTPDSSAAEAFKSASKEVARQISIANASPSSSCCCSGGDISFQVVLTTPACGQEERPLKEVKNIIAVASGEKYGVKLMSIGFLVETDTALIWRGPMASSALADVSKAVNMFAKVNVPILGVSVPINRSVGEGGDSGTPAV", "metadata": {"id": "A0A3S0NYW9", "cluster": 22185150, "interpro_all": ["IPR034904", "IPR002744", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR033756", "IPR002744", "IPR034904"], "interpro_unused": ["IPR019591", "IPR044304", "IPR027417"]}, "task_type": "infilling"} {"instruction": "The protein can be placed in the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. Moreover, the protein is categorized in the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. It is derived from Paraburkholderia sp. SOS3 and carries UniProt keyword assignments Phospholipid metabolism, Metal-binding, and Magnesium.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 2176, 1977, 3595, 2037, 8202, 13789, 20045, 2643, 18339, 2056, 18, 17668, 1010, 1930, 16252, 20709, 11121, 2538, 18306, 14608, 4714, 16, 6048, 17, 2743, 16, 1930, 13148, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MRARHPHLLRASQRAQHDDEAHSAGDDPFADNGTATHAFDERARIERTAAADPASMRYAGHPTTPRKPAPFNPYKGNRGLTRAWHAMKNSLAGFRVPVSRVLLLGSVLLVLIVELLNSSVEAAIDRVALFMCVMTWALIVGPLIARWIGVLFHIHEHEHGRDERAAHREPAQMHSEPSPRRESDAHEPLGPDDPLAPLAIREESAFRQELTLAAILVPCGLAVPVDISLERHELSRRAKDLGSAAVM", "metadata": {"id": "A0A1L6HY80", "cluster": 23031929, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR000829", "IPR033718"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: It is part of the Protein CONTINUOUS VASCULAR RING 1-like family, which consists of integral membrane proteins including Arabidopsis COV1 and homologs in bacteria and archaea. The plant member COV1 is involved in the regulation of vascular patterning in the stem, probably by negatively regulating the differentiation of vascular tissue. It is native to Micavibrio aeruginosavorus (strain ARL-13) and contains UniProt keyword associations Transmembrane helix.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 2176, 1977, 3131, 1927, 1920, 2213, 4798, 4541, 6335, 21, 17, 3189, 3416, 16, 2154, 7543, 1927, 12328, 3260, 2697, 2710, 8900, 6083, 1009, 1930, 14279, 1922, 4802, 1930, 21501, 18, 1920, 4496, 7210, 6083, 1009, 1977, 3286, 1922, 1920, 3640, 1927, 4541, 16060, 1922, 1920, 4402, 16, 6226, 2007, 7191, 6773, 1920, 4155, 1927, 4541, 2960, 18, 2176, 1977, 6196, 1942, 26288, 2165, 2377, 3940, 10830, 15525, 3176, 1036, 12, 3943, 2245, 1024, 17, 2590, 13, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 18, 3], "output": "MTTEQPQTPPDQPQEREPFHLSVFAKIRGYFLAGIKFIDSKVSAIIPAHYYPETAVPGLGLIIAVAFFITIGIVDRMPVIRTLYGATKQVFETVMGAQSQAFREAVMFQYPRPGEVVNVFLPTTPNPTSGFLLFIPRKDLIFLEMTPSDPTLNPPQPKNGNGKKKLVTAPISITLYLTWVFLWFARNFMGRVVINISEYIWAMGFVTGTTKGEVQRLTDDNVEDAIKMIVSGGII", "metadata": {"id": "G2KQK6", "cluster": 24532004, "interpro_all": ["IPR007462"], "interpro_used": ["IPR007462"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein should include a Regulator of chromosome condensation (RCC1) repeat that functions as a guanine-nucleotide dissociation stimulator (GDS) for the nuclear GTP-binding protein Ran, promoting the exchange of GDP for GTP. Structurally, these repeats form a seven-bladed beta-propeller domain that facilitates binding to chromatin. In addition, the protein contains a S-layer homology (SLH) domain that anchors surface proteins to the bacterial cell wall by binding to pyruvylated secondary cell wall polymers (SCWPs). This motif is characteristic of S-layer assemblies and mediates the attachment of the protein coat to structures such as teichoic or teichuronic acids. Additionally, the protein can be placed in the Ran GTPase-activating family, which acts as a guanine-nucleotide releasing factor to facilitate the exchange of GDP for GTP on the Ran GTPase, a process critical for nucleocytoplasmic transport, mitotic spindle assembly, and chromosome condensation. Members may also bind chromatin to influence transcriptional dynamics or serve as components of the SCF E3 ubiquitin-protein ligase complex for targeted protein degradation. It has been detected in Acidimicrobiaceae bacterium and is classified with UniProt keywords Signal.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 3066, 3951, 43, 7888, 1927, 5597, 16112, 12, 13253, 1009, 13, 6865, 1988, 4088, 1966, 43, 16904, 17, 5489, 9182, 24052, 12, 29650, 13, 1958, 1920, 4254, 9319, 17, 2743, 2213, 2845, 16, 7356, 1920, 6818, 1927, 15217, 1958, 9319, 18, 12171, 16, 2144, 9569, 2386, 43, 5260, 17, 22707, 1007, 4666, 17, 5062, 13728, 3418, 1988, 11374, 2743, 1942, 6338, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 61, 17, 4757, 9039, 12, 2788, 1023, 13, 3418, 1988, 27127, 3154, 2697, 1942, 1920, 4543, 2024, 4821, 2007, 2743, 1942, 6487, 12631, 4336, 4067, 2024, 4821, 11039, 12, 2160, 1018, 2523, 13, 18, 2052, 5219, 1977, 6293, 1927, 61, 17, 4757, 16137, 1930, 10412, 1920, 8576, 1927, 1920, 2213, 15642, 1942, 4061, 2427, 1966, 3602, 2108, 8643, 2014, 3602, 2108, 21280, 4576, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2845, 14809, 17, 8019, 3416, 16, 2154, 8016, 1966, 43, 16904, 17, 5489, 13182, 2991, 1942, 6628, 1920, 6818, 1927, 15217, 1958, 9319, 1990, 1920, 2845, 14809, 16, 43, 2585, 4140, 1958, 2797, 3107, 11302, 4860, 16, 9566, 10716, 5957, 16, 1930, 5597, 16112, 18, 4678, 2278, 2222, 4566, 6338, 1942, 4039, 5224, 5565, 2014, 7120, 1966, 4178, 1927, 1920, 12437, 10968, 6526, 17, 2213, 11905, 2796, 1958, 5154, 2213, 4877, 18, 2176, 2258, 2252, 3330, 1922, 2687, 1980, 1935, 15129, 19476, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MWMARPAGAARRLGRRRLVSVVATAAGAQPGEFGDVDDDAYYAEAVASLASRIVRVLDGEDPEPRAGSSFDDVDAAGFHAPFVEDRSTTRAQMAAFLARAYHFADGPDPDFDDASGITQGCGDGAGFCPDRSTTRAQMAAFLHRAETRRYDREERAVRLDGGVTCWGSGRLRDRYALALHSDGTISCWGDASNGELGQGDTDTHYLPVRVPGITDGGVSCWGANTVGRADDGPRMAGHSPRRVPGLSEVVVSCWGSPYTHADPAPKRISTRSMISVGAGWGRVCAATVITELTEVVEVSVGNETLCALHRDGGISCLGVNDVGQVGSDAVAVSVGVGRLLDSDPVGPHACLVGQLGDGTTAKSLVPTRVRQPLPIPADQVQEREAEYPWMRVAWDHIRDSTEAGRLGGGNVSEGIAVHELLHVYDLHTGLAPRAAWGAVQADTVTRIMVPSEFLAYYNLPGCPTLPGAGKVPDWYRENITNGAELWEAWRRGPSLPALANLSDITPLLDSDRFHEAGSNPFRDGGCAVAFGPLAGLASTPGVFAGTECDDGFCPAAPVDRKTMAVWRMADLGITRGCRDGGGFCPIAAGAWYAADVARLATAFSIEERPGNGPLISASRGSTCGLQNVVAVSTGNPDQGAHTCAAAAVSAGPNHTCAAHRDALASGTDNTCAVHRDGSAGSVYCWRPSSGNPRLNHDGTTTRRSKPVRLDGVLHADGSASCWGANETPATATDLLRAWIEALLTSCHTTAGEFGCRAEDMLITRMLYFATTYPDCFADNGYHGAEILGGEPTAEAERVASQGLEFGGLCSTDW", "metadata": {"id": "A0A7K2E1Z9", "cluster": 25731068, "interpro_all": ["IPR051553", "IPR009091", "IPR000408", "IPR001119"], "interpro_used": ["IPR000408", "IPR001119", "IPR051553"], "interpro_unused": ["IPR009091"]}, "task_type": "infilling"} {"instruction": "I want to generate an amino acid sequence for a protein. The protein should have the function The protein falls within the DUF5688 family, which consists of proteins of unknown function found in bacteria. It is native to Lachnospiraceae bacterium KHCPX20.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 12182, 2651, 1920, 4855, 17968, 6735, 1025, 3416, 16, 2154, 7543, 1927, 2697, 1927, 5435, 2347, 2435, 1922, 4802, 18, 2176, 1977, 6196, 1942, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 8855, 10020, 8014, 1008, 18, 3], "output": "MIETYEEFVSRLMNRIAEESSEEISFSRRSILKNNNKRLDAITVCRAGYDLCPTIYPEFYYQQYQKGEDFETLLMRIMEGIRHEITAERIELKNVSDFHRMKDKVVFRLINASRNQELLSDLAHVLYLDLAIVFACVVSVKEEETASFLIHKEHLMMWNTTVEELFELAKDNTPRLFPACCQDLSDVIEKEYPKELPPMGNLKHECMYVLSNQHRIHGASCILYRHILKEIGEKMGCDLYIIPSSVHETLIIPSRLDLDVSQFRKVIMEVNATAVSEEEYLSDHAYLYKRKSNKLQSIA", "metadata": {"id": "A0A1H2WIK6", "cluster": 26875342, "interpro_all": ["IPR043743"], "interpro_used": ["IPR043743"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein is associated with the Protein of unknown function DUF937 family, which comprises hypothetical bacterial proteins of unknown function. It is derived from Dermacoccus sp. 147Ba.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 2213, 1927, 5435, 2347, 4855, 1038, 22366, 3416, 16, 2154, 12936, 15148, 4543, 2697, 1927, 5435, 2347, 18, 2176, 1977, 3595, 2037, 8960, 20682, 2437, 1957, 2056, 18, 13625, 7972, 18, 3], "output": "MSATSEILSELPIDQLAEQVNIQHPGGQSALLEALGGHVDSSPTLDEVNTDDGAKIAQHVFNDLVRRLIPIIAPIVISYLAKRVLGGGADTNASAGAGSQQAQPQQQAGPNWGDILGNVLGGGTRIGASPEETEAAVRSVVPALLGGMEAGDQQDAVVNQLGGLPGTSSADILTQILSGVLGGSVPGAQSAGQGS", "metadata": {"id": "A0A4Q4C0K4", "cluster": 27463338, "interpro_all": ["IPR009282"], "interpro_used": ["IPR009282"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein belongs to the K homology domain-like, alpha/beta superfamily, which comprises RNA-binding modules that adopt a characteristic two-layer \u03b1/\u03b2 fold found in diverse prokaryotic and eukaryotic regulatory proteins. These domains can function independently or cooperatively to bind RNA substrates and are integral to complexes such as the ribosome, Era GTPases, and the NusA transcription factor. Also, the protein includes a Transcription factor NusA, first KH domain that functions as an RNA-binding module to facilitate RNA recognition. It contributes to the regulation of transcriptional pausing, termination, and anti-termination by interacting with nascent RNA transcripts. Moreover, the protein has a K Homology (KH) domain that binds RNA and mediates specific RNA recognition. This evolutionarily conserved domain of approximately 70 amino acids adopts a characteristic \u03b2-\u03b1-\u03b1-\u03b2-\u03b2-\u03b1 fold and is found in diverse nucleic acid-binding proteins, including ribosomal subunits and exosome components. It frequently appears in multiple copies within a protein, allowing for cooperative or independent interactions with specific RNA targets. It is native to Armatimonadetes bacterium CG_4_8_14_3_um_filter_66_20 and contains UniProt keyword associations Transcription termination, Cytoplasm, and Transcription regulation.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 14440, 1942, 1920, 53, 9039, 3418, 17, 3189, 16, 4595, 19, 4666, 13975, 16, 2154, 12936, 3146, 17, 2743, 10803, 1988, 14103, 43, 6293, 2288, 17, 4757, 160, 19, 161, 3728, 2435, 1922, 6445, 21545, 1930, 10825, 4948, 2697, 18, 2144, 4682, 2112, 2347, 6407, 2014, 13350, 1954, 1942, 4566, 3146, 6249, 1930, 2032, 12328, 1942, 5048, 2427, 1966, 1920, 12794, 16, 14821, 18390, 16, 1930, 1920, 13232, 5735, 3213, 2991, 18, 2222, 16, 1920, 2213, 5921, 43, 3213, 2991, 13232, 5735, 16, 2561, 8855, 3418, 1988, 4088, 1966, 1925, 3146, 17, 2743, 9059, 1942, 6628, 3146, 5708, 18, 2176, 7624, 1942, 1920, 3640, 1927, 5224, 3838, 16435, 16, 12462, 16, 1930, 2246, 17, 12462, 2007, 8615, 1956, 16861, 3146, 6247, 18, 3950, 16, 1920, 2213, 2258, 43, 53, 9039, 12, 8855, 13, 3418, 1988, 6876, 3146, 1930, 10412, 2487, 3146, 5708, 18, 2052, 18584, 5305, 3418, 1927, 3993, 3895, 3835, 4576, 24032, 43, 6293, 161, 17, 160, 17, 160, 17, 161, 17, 161, 17, 160, 3728, 1930, 1977, 2435, 1922, 6445, 11079, 2687, 17, 2743, 2697, 16, 2710, 11196, 6991, 1930, 20235, 4178, 18, 2176, 5467, 5107, 1922, 3137, 9425, 2651, 43, 2213, 16, 7201, 1958, 13350, 2014, 3484, 3719, 1956, 2487, 3146, 4845, 18, 2176, 1977, 6196, 1942, 6011, 1968, 3947, 2873, 14652, 14061, 7294, 41, 24, 41, 28, 41, 2607, 41, 23, 41, 8736, 41, 6199, 41, 4970, 41, 2036, 1930, 5461, 20709, 11121, 2538, 5253, 3213, 12462, 16, 5239, 16, 1930, 3213, 3640, 18, 3], "output": "QAVVEELGGEKIDIIRWSAVLEEYIAAALSPAKVPTAGQNVRLAAKLTGLRIDIKSQQQHADEQATVAAAGRAAAEQSAAETAAESGPESPVVEPAAVEAAEAVAESPVAAEITEVVEPEPVEPAIAATEAAPPAAEPELDPTLLEEAEAAVPVVERALEPAPPGTPTELPDVVASPEEPPAPAAVEEIAQAASVLLSTTNSACTVVVPEDQLSLAIGKAAVEAARVATEAAEAVALAAEASAEVVGESPAAGGPTAEPAPPAEAASVPPAAIVEPASQVIVLAPEAAGVEGPAES", "metadata": {"id": "A0A2M7KHS8", "cluster": 27548177, "interpro_all": ["IPR004087", "IPR015946", "IPR025249", "IPR004088", "IPR009019", "IPR030842"], "interpro_used": ["IPR015946", "IPR025249", "IPR004087"], "interpro_unused": ["IPR009019", "IPR004088", "IPR030842"]}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein carries a HAMP domain that serves as an $\\alpha$-helical linker in signal transduction proteins, transmitting conformational changes from periplasmic ligand-binding domains to cytoplasmic signaling domains. It is widely distributed in bacterial two-component sensors, chemotaxis receptors, and eukaryotic histidine kinases, where it regulates phosphorylation or methylation by coupling sensory input to catalytic output. Moreover, the protein possesses a Histidine kinase domain that functions as the catalytic core of two-component signal transduction systems, orchestrating cellular responses to environmental stimuli. It undergoes ATP-dependent autophosphorylation on a conserved histidine residue within a homodimer before transferring the high-energy phosphoryl group to an aspartate residue on a partner response regulator protein. This domain contains a dimerization interface and a structurally distinct ATP-binding cleft defined by conserved nucleotide-binding motifs. Furthermore, the protein should include a Signal transduction histidine kinase dimerisation and phosphoacceptor domain that facilitates homodimerisation and histidine autophosphorylation within two-component signal transduction systems. This domain forms a four-helical bundle structure that catalyzes the transfer of a phosphate from ATP to a conserved histidine, and subsequently to an aspartate residue on a response regulator. It is found in Caballeronia insecticola and features UniProt keywords Transmembrane helix, Transferase, and Transmembrane.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 16252, 43, 8616, 1034, 3418, 1988, 10634, 1966, 1925, 8, 38, 4595, 8, 17, 11514, 11040, 1922, 2733, 8201, 2697, 16, 27622, 8523, 2840, 2037, 24334, 5207, 17, 2743, 4682, 1942, 6823, 3197, 4682, 18, 2176, 1977, 5673, 6533, 1922, 4543, 2288, 17, 4594, 9189, 16, 16884, 4086, 16, 1930, 10825, 13873, 7784, 16, 2597, 2176, 7014, 4050, 2014, 5547, 2007, 7590, 6893, 5877, 1942, 6804, 6647, 18, 3950, 16, 1920, 2213, 14465, 43, 13873, 4016, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 2288, 17, 4594, 2733, 8201, 3771, 16, 21991, 2287, 3689, 3387, 1942, 4813, 5458, 18, 2176, 14928, 4498, 17, 3100, 22009, 1990, 43, 5305, 13873, 6181, 2651, 43, 21189, 3119, 21902, 1920, 2149, 17, 3844, 12556, 2210, 1942, 1925, 12878, 6181, 1990, 43, 8240, 2644, 7888, 2213, 18, 2052, 3418, 5461, 43, 13640, 6854, 1930, 43, 12171, 4493, 4498, 17, 2743, 14649, 3608, 2007, 5305, 5489, 17, 2743, 8277, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 2733, 8201, 13873, 4016, 7632, 6284, 1930, 8078, 22790, 1924, 3418, 1988, 11374, 21189, 6284, 1930, 13873, 22009, 2651, 2288, 17, 4594, 2733, 8201, 3771, 18, 2052, 3418, 4952, 43, 3006, 17, 11514, 14142, 3170, 1988, 17097, 1920, 3856, 1927, 43, 5413, 2037, 4498, 1942, 43, 5305, 13873, 16, 1930, 5326, 1942, 1925, 12878, 6181, 1990, 43, 2644, 7888, 18, 2176, 1977, 2435, 1922, 11026, 2214, 6506, 10306, 15350, 10173, 1930, 4075, 20709, 11569, 9117, 7864, 16, 13763, 16, 1930, 9117, 18, 3], "output": "MTSVRRFAHIKPRSLFARNILLLVALVAVSQVCAIAVLLHFIQTPRIERAAATFASYIVAASTAVAHLDVRAALPEGAASSAPESRLRFYQTYQRRTFIESLRRHLPAEMLVRWQGADTSGDGQQRDDGLTTALLLSLGLGALAIATAYVIQRHLNRPLAHLADAARLVSAGGEPGALKEADATRALMLAGISHDIRTPMTKLRLAMAMSSVPSTDASFAQSAEGYLDTIDTILQQFMDADFAGLGHEFTLDLGRIEPFAFRPIGMMRMLMNVMQNAVLYGVTGLEVRTWTDERTKRACIVIPFKRGGGEGQPKGTGLGLAIVERIARLHGGTLELRAREGGGAQACIELPLNAPDASGRLIPEPRATATLDTLLRATPTALWIRAHLSSEPRWIALPVPEAAHVLPTDGPTEIAQVSNAFNRMTAYAGSGAKETPVVGDLNALIANLAADRGKGLGGQDPEALKQ", "metadata": {"id": "R4WW70", "cluster": 27643498, "interpro_all": ["IPR050980", "IPR003660", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR004358"], "interpro_used": ["IPR003660", "IPR005467", "IPR003661"], "interpro_unused": ["IPR004358", "IPR036890", "IPR036097", "IPR050980"]}, "task_type": "infilling"} {"instruction": "The protein features a GTP binding domain that contains five conserved structural motifs to bind guanosine triphosphate (GTP). It is present in a diverse array of proteins, such as the developmentally regulated DRG, the essential bacterial OBG, and ferrous iron transport protein B, indicating a broad role in cellular regulation and transport. Additionally, the protein incorporates a TrmE-type guanine nucleotide-binding domain that functions as a P-loop GTPase molecular switch to facilitate tRNA modification. It adopts a canonical Ras-like fold that dimerizes in a potassium-dependent manner and utilizes conformational changes driven by GTP hydrolysis to modify uridine bases at the tRNA wobble position. Moreover, the protein includes a Small GTP-binding domain that functions as a molecular switch by binding and hydrolyzing GTP to regulate diverse cellular processes, including signal transduction, vesicle transport, and protein biosynthesis. It is found in the Ras superfamily of small GTPases as well as within larger proteins such as translation elongation factors. It is identified in Fidelibacterota bacterium and has UniProt annotations Magnesium, Cytoplasm, and tRNA processing.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 4075, 43, 9319, 2743, 3418, 1988, 5461, 3628, 5305, 4346, 8277, 1942, 4566, 24870, 17978, 12, 9319, 13, 18, 2176, 1977, 2481, 1922, 43, 6445, 6472, 1927, 2697, 16, 2427, 1966, 1920, 23130, 4335, 14801, 16, 1920, 4415, 4543, 2384, 1029, 16, 1930, 26739, 5680, 4860, 2213, 44, 16, 4168, 43, 4949, 2770, 1922, 3689, 3640, 1930, 4860, 18, 4950, 16, 1920, 2213, 19683, 43, 28402, 1021, 17, 2601, 16904, 5489, 17, 2743, 3418, 1988, 4088, 1966, 43, 58, 17, 5881, 14809, 3272, 6195, 1942, 6628, 10089, 6295, 18, 2176, 24032, 43, 9452, 6520, 17, 3189, 3728, 1988, 7632, 4517, 1922, 43, 9057, 17, 3100, 5222, 1930, 18127, 8523, 2840, 6446, 2007, 9319, 9128, 1942, 11675, 26104, 11137, 2019, 1920, 10089, 26334, 6936, 1952, 3507, 18, 3950, 16, 1920, 2213, 5921, 43, 2858, 9319, 17, 2743, 3418, 1988, 4088, 1966, 43, 3272, 6195, 2007, 2743, 1930, 7222, 9046, 9319, 1942, 5741, 6445, 3689, 4028, 16, 2710, 2733, 8201, 16, 11502, 4860, 16, 1930, 2213, 8132, 18, 2176, 1977, 2435, 1922, 1920, 6520, 13975, 1927, 2858, 18390, 1966, 2486, 1966, 2651, 4327, 2697, 2427, 1966, 6410, 9971, 2790, 18, 2176, 1977, 2899, 1922, 26209, 30466, 2422, 7336, 14061, 1930, 2258, 20709, 15010, 13148, 16, 5239, 16, 1930, 10089, 4587, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MYKTNDTIVALATVPGKAALNVVREFPKANFAHLCNVYNKAKISFTSEHMLEISTHGGKVIVQQIIGLAFINQKIDLSQAEAINAAISSSNQISSFYHINEALTIIEHELDFNEEEIDFLGEQKITNIRVAIVGVPNSGKSSLFNLIVGDNRAIVSFTLVDTAGIRKTKDSLELLGIEKTIEEIKKASILLVLNKTDLFSSVPKTKGLGISCKTGSGKRGKKYSLFLNKRQFLILKELLRGVEKALRGLLSLFDDLLKPVDNQKIINNIFKGFCVGKRLSGNEFVLKLYKTITKKIDQAVCVFYKSPKLLDLGARQASPGEFTYRSIRGGLSKKIKKTQKTIIEILQSVYNNVDKVLDSSFFQEKDTKIKGTTRDTIEGIITYKNTDVICVDDKDPKKIQTKIKKHLKNKECLLTLLSTSVQKNTNEYFLKEYKNNKDVVVLASN", "metadata": {"id": "A0A2E5U2E8", "cluster": 9440365, "interpro_all": ["IPR031168", "IPR006073", "IPR018948", "IPR004520", "IPR027368", "IPR025867", "IPR027417", "IPR005225", "IPR027266"], "interpro_used": ["IPR006073", "IPR031168", "IPR005225"], "interpro_unused": ["IPR025867", "IPR027266", "IPR027368", "IPR018948", "IPR004520", "IPR027417"]}, "task_type": "infilling"} {"instruction": "Here is the intended role of my protein: The protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. In addition, the protein is classified under the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. In addition, it is part of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is produced by Acidobacteria bacterium 13_1_40CM_56_16 and has UniProt annotations Cytoplasm and rRNA processing. Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 4152, 2007, 2687, 10296, 14061, 2590, 41, 21, 41, 3040, 12819, 41, 4489, 41, 2641, 1930, 2258, 20709, 15010, 5239, 1930, 9067, 4587, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "MFRHTPVLAEEVIQFLNPRPGGFFIDVTVGAGGHSRVILELTAPDGKLLAIDQDESALTQAGQELAVFGPRVVFVHANFREVAQVAAAHGFSGCDGVLADIGISSMMVDDPSRGFSFMREGPLDMRMDRTQPLTAAEVVNTFSEKDIADILFHYGEERRSRAIARSIVRGRPLRSTADLVRAIERVAGRPRYGRIHPATRTFQALRIFVNDELKNLEIFLDSSMAIVGSRGRIVVITFHSLEDRIVKQKFRAPAVAGSVLTKKVVAANQKELQRNPRSRSAKLRAWERS", "metadata": {"id": "A0A1Q7FPJ6", "cluster": 2801654, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR002903", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "\"The protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, the protein is grouped in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Furthermore, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is found in Fidelibacterota bacterium and features UniProt keywords Cytoplasm and rRNA processing.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 2435, 1922, 26209, 30466, 2422, 7336, 14061, 1930, 4075, 20709, 11569, 5239, 1930, 9067, 4587, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MIESTLQEKHVNHIPVMLSEVLEYLNLQKHGVYIDGTIKVIGLDRDAKALEICKNQFGASAHLLTTHRTSYHLDLGLSSMQLNSNSRGFAFESNGILDMRFNKSSGQTASDLIIAYNIKTMKKMTAVADLKEAIRRSTPPHKRKKSLARVFQLFLNSFIDYLTINGRVVIISYHSIEDLIPSKKEQEINSRSRSAKLRAAERIIGAGGHAKNILGSPSFSRKFPEIMHELGISLVNGILRESTEEELANIIYNFGEERRSRKALRIAVNSELDKLERMVKHAFRTLKNDQRLNQLTKKP", "metadata": {"id": "A0A9E1LC04", "cluster": 3766166, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein carries a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein features a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Moreover, the protein is assigned to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It occurs in Elusimicrobia bacterium RIFOXYA2_FULL_40_6 and is associated with UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 4075, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 5110, 1922, 2349, 24327, 4913, 15129, 2126, 14061, 12424, 7221, 8398, 41, 4125, 41, 3040, 41, 26, 1930, 1977, 2458, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MKILAPAKINLFLEITGKTKTGYHTLNTVFQAVSLYDEITITDERHHEIDFTCNWSGVGVSYSSPVEENLCYRAASALKAYLKEKRGAKIKLIKKIPVGAGLGGGSSDAAAVLRGLLKFWNREIDNNSLNRIAVELGADVPFFLYGGCCFAEGIGERLFPLRTEWDEKPLNLLLVKPDISKSSGDIYRAYDKRAANKPATINDTSKIKREKSVSLDNLEFVNNLEGVVFEKYPILETIKTNLKGLEAFVSLMSGGGTAIFGIFKAESIAKKAFLEIKKSGFNAWLVHTL", "metadata": {"id": "A0A1F9WZV4", "cluster": 11508494, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: The protein is a member of the Phosphoribosyltransferase-like superfamily, which encompasses enzymes such as phosphoribosyltransferases (PRTases) and phosphoribosylpyrophosphate synthetase-like proteins. These domains typically catalyze the transfer of phosphoribosyl groups to specific substrates, playing a central role in nucleotide biosynthesis and salvage pathways. Moreover, the protein is classified under the Uracil phosphoribosyltransferase/Adenine phosphoribosyltransferase family, which catalyzes the conversion of uracil or adenine and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP or AMP and diphosphate within nucleotide salvage pathways. These enzymes facilitate energy-efficient nucleotide pool maintenance and are typically allosterically activated by GTP. Furthermore, the protein features a Phosphoribosyltransferase domain that catalyzes the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP) by a nitrogen-containing nucleophile to yield an alpha-1 substituted ribose-5'-phosphate and free pyrophosphate. This domain is essential for nucleotide synthesis and salvage pathways and features a conserved PRPP binding motif. It occurs in Colocasia esculenta (Wild taro) (Arum esculentum) and is annotated with UniProt keywords Allosteric enzyme, Glycosyltransferase, and GTP-binding. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 3421, 2023, 25566, 17, 3189, 13975, 16, 2154, 21569, 5038, 2427, 1966, 3421, 2023, 25566, 1036, 12, 2033, 3857, 4127, 1036, 13, 1930, 3421, 2023, 11731, 18425, 15707, 18185, 17, 3189, 2697, 18, 2144, 4682, 5745, 18170, 1920, 3856, 1927, 3421, 2023, 11731, 2671, 1942, 2487, 6249, 16, 14797, 43, 4101, 2770, 1922, 5489, 8132, 1930, 17577, 3873, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 22761, 3421, 2023, 25566, 19, 15643, 3421, 2023, 25566, 3416, 16, 2154, 17097, 1920, 7309, 1927, 22761, 2014, 15643, 1930, 25, 17, 8078, 17, 4595, 17, 46, 17, 17870, 21, 17, 23266, 12, 11533, 1034, 13, 1942, 8736, 1034, 2014, 3681, 1930, 23266, 2651, 5489, 17577, 3873, 18, 2144, 5038, 6628, 3844, 17, 5807, 5489, 5562, 6291, 1930, 2032, 5745, 14772, 2169, 4128, 2007, 9319, 18, 3677, 16, 1920, 2213, 4075, 43, 3421, 2023, 25566, 3418, 1988, 17097, 1920, 9514, 1927, 1920, 4595, 17, 21, 11, 17, 24937, 1927, 25, 17, 3421, 2023, 11731, 17, 4595, 17, 21, 17, 24937, 12, 11533, 1034, 13, 2007, 43, 6634, 17, 3165, 2797, 28335, 1942, 4307, 1925, 4595, 17, 21, 11798, 17870, 17, 25, 11, 17, 5413, 1930, 3294, 24937, 18, 2052, 3418, 1977, 4415, 1958, 5489, 4271, 1930, 17577, 3873, 1930, 4075, 43, 5305, 11533, 1034, 2743, 5219, 18, 2176, 5110, 1922, 2503, 21259, 12924, 1019, 14382, 19072, 1019, 12, 3576, 14517, 1037, 13, 12, 2245, 1989, 14382, 19072, 1989, 13, 1930, 1977, 10633, 1956, 20709, 11569, 14772, 4113, 16, 20067, 9961, 16, 1930, 9319, 17, 2743, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MGGAVCHVTRSLAARECDNVGFCRIPDCELRRIPDFEHRADLLLPPRSGTLLHRPLLPSPMATWSVKISPHSSATPRPPSSRRFFPIPPRAAFILLPPRPKCVATSGRRRRVLSCAAAASMALDNKAVSKDRMLVFVPPHPLIKHWVSVLRNEETPCAIFKSAMAELGRLLIYEASRDWLPTISGEIQTPMDVASVEFIDPREPVLLVPILRAGLALVEHASSILPATKTYHLGLRRDESTLHPSIYLNNLPDKFPEGCRVFVVDPMLATGVHFHFFSPIALLINVSLQQLCYC", "metadata": {"id": "A0A843V8F6", "cluster": 12061091, "interpro_all": ["IPR000836", "IPR029057", "IPR050054"], "interpro_used": ["IPR029057", "IPR050054", "IPR000836"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: It is part of the Short-chain dehydrogenase/reductase (SDR) family, which comprises a large and diverse group of NAD- or NADP-dependent oxidoreductases. These enzymes typically possess a conserved coenzyme-binding domain and a variable substrate-binding domain that determines catalytic specificity. Additionally, it is part of the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. It is derived from Aplanochytrium stocchinoi.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 2176, 1977, 3131, 1927, 1920, 3662, 17, 4659, 9294, 19, 11386, 12, 4035, 1005, 13, 3416, 16, 2154, 12936, 43, 3103, 1930, 6445, 2210, 1927, 6577, 17, 2014, 24221, 17, 3100, 27388, 1036, 18, 2144, 5038, 5745, 7150, 43, 5305, 22051, 17, 2743, 3418, 1930, 43, 4650, 4510, 17, 2743, 3418, 1988, 13554, 6804, 4896, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 2176, 1977, 3595, 2037, 18373, 9286, 2072, 2355, 3027, 1989, 13046, 2437, 7969, 11873, 1033, 18, 3], "output": "MGSCRCGKCLGVLVVATAILIGFLHGMVPALHYGSPWGFTHNELSKLDLSEHIAVGAEVVLACRSKQKCDHSVQRLQNTVGKNCAREFEGKYGSRGLDILILNAGILAPPFSLTKLLLPQLLKVADENAKGIATVVAVSSAGNFESNYNRKKTYGMSKLANILFAQELSDRYKDRNILRTVFRAAYEGLVQKLLWTAEDAALTQLFAIARPTHPDPHAFNYTLQKKLWVLSEQVTAMSDSSARLLKYIDELENDRGKRYMITGANSGLGYWTAYHLANRKVSGMGLDLASFSSIRKFDDGIESTMGVNHFGHFLLTDTPPGGVFTTIEQINNVNAVHPGAVVTDIARNIIDMVPTEYGAVSPVLKKSKTTGKYFHP", "metadata": {"id": "A0A7S3UY29", "cluster": 12461339, "interpro_all": ["IPR036291", "IPR002347"], "interpro_used": ["IPR002347", "IPR036291"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is included in the Immunoglobulin-like fold superfamily, which comprises domains characterized by a beta-sandwich of seven or more strands arranged in a Greek-key topology, facilitating protein-protein interactions often via beta-sheet interfaces. These domains are ubiquitous in animal proteins, playing critical roles in immune recognition, cell adhesion, and structural integrity in muscle proteins such as titin. Moreover, the protein belongs to the Immunoglobulin-like domain superfamily, which utilizes a conserved Greek-key $\\beta$-sandwich fold to mediate protein-protein interactions and structural stability. These modular domains are critical for diverse biological processes, including immune system recognition, cell-surface receptor signaling, cell-cell adhesion, and muscle organization. Furthermore, the protein is included in the Immunoglobulin Heavy Variable family, which comprises the antigen-binding variable region of heavy chains found in B cell receptors and antibodies essential for adaptive immunity. These proteins undergo V-(D)-J rearrangement and somatic hypermutation to generate vast diversity and high affinity, pairing with light chains to specifically recognize and neutralize antigens. It is expressed in Cirrhinus molitorella (mud carp).\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 1977, 3063, 1922, 1920, 11837, 17, 3189, 3728, 13975, 16, 2154, 12936, 4682, 4378, 2007, 43, 4666, 17, 18038, 1927, 5260, 2014, 2253, 13214, 14940, 1922, 43, 27568, 17, 3834, 13678, 16, 12440, 2213, 17, 2213, 3719, 3868, 3454, 4666, 17, 11130, 14857, 18, 2144, 4682, 2032, 15498, 1922, 4027, 2697, 16, 14797, 4140, 5456, 1922, 3743, 5708, 16, 2024, 6141, 16, 1930, 4346, 7996, 1922, 3760, 2697, 2427, 1966, 7090, 1921, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 11837, 17, 3189, 3418, 13975, 16, 2154, 18127, 43, 5305, 27568, 17, 3834, 8, 38, 4666, 8, 17, 18038, 3728, 1942, 8265, 2213, 17, 2213, 3719, 1930, 4346, 5057, 18, 2144, 16078, 4682, 2032, 4140, 1958, 6445, 3933, 4028, 16, 2710, 3743, 2433, 5708, 16, 2024, 17, 3154, 3148, 3197, 16, 2024, 17, 2024, 6141, 16, 1930, 3760, 5901, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 11837, 7881, 4650, 3416, 16, 2154, 12936, 1920, 4730, 17, 2743, 4650, 3031, 1927, 7881, 7835, 2435, 1922, 44, 2024, 4086, 1930, 3788, 4415, 1958, 7617, 7611, 18, 2144, 2697, 4978, 64, 17, 12, 46, 13, 17, 52, 14154, 1930, 8548, 13317, 9897, 1942, 5655, 10983, 5935, 1930, 2149, 5173, 16, 15438, 1956, 3696, 7835, 1942, 4475, 9967, 1930, 25885, 7769, 18, 2176, 1977, 3198, 1922, 10094, 22214, 2629, 6733, 5870, 12, 23910, 16549, 13, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MEMIWFGVLLMIISTVSGESLTSSDPVVKKPGESVTLSCTASLTLGSAGSLGCGDDSTGISRDGILLDQSPAVIGIPMTEYYMHWIRQKKNKESSGVDWESGFSVLILLGQQESSPGRRPGETVRISCNTS", "metadata": {"id": "A0AA88Q614", "cluster": 13786390, "interpro_all": ["IPR036179", "IPR013783", "IPR050199"], "interpro_used": ["IPR013783", "IPR036179", "IPR050199"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me the sequence of a polypeptide chain with the following function. The function of the polypeptide chain is The protein is grouped in the Protein kinase-like domain superfamily, which modifies other proteins by chemically adding phosphate groups. This enzymatic activity is fundamental to most signaling and regulatory processes in the eukaryotic cell. In addition, the protein carries a Serine/threonine-protein kinase active site that catalyzes the transfer of the gamma phosphate from ATP to serine or threonine residues on protein substrates, utilizing a conserved aspartic acid residue essential for enzymatic activity. This reversible phosphorylation regulates diverse cellular processes, including division, proliferation, and apoptosis. It has been characterized in Albula glossodonta (roundjaw bonefish) and is described by UniProt keywords ATP-binding and Transferase.", "tokenized_instruction": [2, 7031, 2142, 1920, 3244, 1927, 43, 13022, 4659, 1956, 1920, 2894, 2347, 18, 1920, 2347, 1927, 1920, 13022, 4659, 1977, 1920, 2213, 1977, 10809, 1922, 1920, 2213, 4016, 17, 3189, 3418, 13975, 16, 2154, 25436, 2303, 2697, 2007, 13944, 8013, 5413, 2671, 18, 2052, 8145, 2455, 1977, 8829, 1942, 2501, 3197, 1930, 4948, 4028, 1922, 1920, 10825, 2024, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 8468, 19, 13143, 17, 2213, 4016, 3500, 3200, 1988, 17097, 1920, 3856, 1927, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 2014, 13143, 4248, 1990, 2213, 6249, 16, 10232, 43, 5305, 23047, 2687, 6181, 4415, 1958, 8145, 2455, 18, 2052, 10743, 4050, 7014, 6445, 3689, 4028, 16, 2710, 8451, 16, 4031, 16, 1930, 4091, 18, 2176, 2258, 2252, 4378, 1922, 5311, 5617, 30402, 12268, 3857, 12, 7464, 14174, 1018, 3622, 14422, 13, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 1930, 13763, 18, 3], "output": "MINCFTRPGNKVRILTGSRQKNMYLNKRQTTRSWLAFTLVSKLRVGTGSHMSVPDLITCRKAGLQGGGGGGGGGGIRLPCERLFLVIEYVNGGDLMFHMQRQRKLPEEHARFYAAEICIALNFLHEKGIIYRDLKLDNVLLDHEGHIKLTDYGMCKEGIRPGDTTSTFCGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPFDIITDNPDMNTEEYLFQARDAEVSAAAPLALGSWIPPQSVEQTLLAGAAQPYAAAPNPPVPDQPPCPRSSTVAPSPLRAGWGPAGRCCRSHQLQLGWLPSSVGQNQKSRQTAPDNQERQIHLIILEKPIRIPRSLSVKAASVLKGFLNKDPKERLGCQVQTGFTDIKSHTFFRSIDWDQVSYGVNIIVYLTG", "metadata": {"id": "A0A8T2MXF9", "cluster": 13895909, "interpro_all": ["IPR011009", "IPR000719", "IPR008271"], "interpro_used": ["IPR011009", "IPR008271"], "interpro_unused": ["IPR000719"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to this functional description: The protein is grouped in the GPI-anchor maturation lipid remodeler family, which mediates lipid remodeling during the maturation of glycosylphosphatidylinositol (GPI) anchors. Members of this family specifically replace the diacylglycerol moiety with ceramides, a modification essential for maintaining cell wall integrity in fungi. Also, the protein should have a Endonuclease/exonuclease/phosphatase domain that functions as a magnesium-dependent catalytic module involved in nucleic acid cleavage and intracellular signaling. It confers enzymatic activity to a diverse group of proteins, including AP endonucleases, DNase I, sphingomyelinases, and inositol-1,4,5-trisphosphate phosphatases like synaptojanin. It is present in Bacteroidota bacterium.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 1977, 10809, 1922, 1920, 17497, 17, 13333, 7655, 4486, 7456, 12015, 1005, 3416, 16, 2154, 10412, 4486, 8378, 2409, 1920, 7655, 1927, 20067, 7824, 10244, 15651, 12, 17497, 13, 27127, 18, 4678, 1927, 2052, 3416, 4475, 14732, 1920, 29527, 11804, 1956, 16926, 1036, 16, 43, 6295, 4415, 1958, 8231, 2024, 4821, 7996, 1922, 10520, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 18697, 19, 24966, 19, 8167, 3418, 1988, 4088, 1966, 43, 13148, 17, 3100, 6804, 9059, 3286, 1922, 11079, 2687, 6404, 1930, 4776, 3197, 18, 2176, 16556, 8145, 2455, 1942, 43, 6445, 2210, 1927, 2697, 16, 2710, 2100, 18697, 1036, 16, 12861, 51, 16, 28057, 2319, 16, 1930, 16246, 17, 21, 16, 24, 16, 25, 17, 6349, 25324, 19131, 3189, 14009, 1037, 23236, 1921, 18, 2176, 1977, 2481, 1922, 24323, 7336, 14061, 18, 3], "output": "METSRKSHTNRRLAARTAMVVVFAILLAGCGSSRPGSTRTTIRVMTWNIHHGEGTDGIIDIDRIAKLIVDEKIDVVALQEIDRGVPRSKKIDIITALADKTDRTYAFGKTIDYQGGDYGNGFLTRFPILEERNILYKETYGREQRAVLLLVLDYKGQEFVVANTHLDSRSDDSARITAVRELKPLLARFASRPMLLFGDMNDQPDSKVVGEISEMMNDSWTEVGKGNGLTYPSASPRKRIDYIFNLKKQTTDSISTLVRLLPVSARVVQSTASDHLPTIVEFTLATGN", "metadata": {"id": "A0A3D0QDH7", "cluster": 14775834, "interpro_all": ["IPR036691", "IPR005135", "IPR051916"], "interpro_used": ["IPR051916", "IPR005135"], "interpro_unused": ["IPR036691"]}, "task_type": "autoregressive"} {"instruction": "The protein is grouped in the Terpene cyclase-like 2 family, which comprises monomeric enzymes, such as sesquiterpene cyclases and 2-methylisoborneol synthase, that catalyze the complex cyclization of isoprenoid substrates. These proteins utilize a terpenoid synthase fold with an $\\alpha$-barrel active site and conserved metal-binding motifs to coordinate Mg2+ and stabilize reactive carbocation intermediates during catalysis. They are predominantly found in fungi, bacteria, and some plant species. Additionally, the protein is associated with the Isoprenoid synthase domain superfamily, which functions in the biosynthesis of diverse terpene compounds by catalyzing the cyclization and rearrangement of isoprenoid diphosphate precursors. This domain adopts a characteristic structural fold composed mostly of \u03b1-helices arranged in a core anti-parallel bundle. It has been detected in Streptacidiphilus fuscans and is annotated with UniProt keywords Lyase and Magnesium.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 6005, 17125, 1021, 16526, 17, 3189, 22, 3416, 16, 2154, 12936, 14457, 5038, 16, 2427, 1966, 9924, 2048, 23582, 2880, 16526, 1036, 1930, 22, 17, 4963, 23854, 17545, 1945, 8921, 16, 1988, 18170, 1920, 2796, 25267, 1927, 26690, 2642, 6249, 18, 2144, 2697, 12561, 43, 6005, 17125, 2642, 8921, 3728, 1956, 1925, 8, 38, 4595, 8, 17, 19560, 3500, 3200, 1930, 5305, 6048, 17, 2743, 8277, 1942, 11865, 14756, 15, 1930, 13448, 6079, 3697, 5980, 12386, 2409, 15408, 18, 2611, 2032, 7700, 2435, 1922, 10520, 16, 4802, 16, 1930, 2673, 4496, 3038, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 26690, 2642, 8921, 3418, 13975, 16, 2154, 4088, 1922, 1920, 8132, 1927, 6445, 6005, 17125, 1021, 4300, 2007, 29601, 1920, 25267, 1930, 14154, 1927, 26690, 2642, 23266, 10416, 18, 2052, 3418, 24032, 43, 6293, 4346, 3728, 7179, 6969, 1927, 160, 17, 12789, 14940, 1922, 43, 4728, 2246, 17, 6110, 14142, 18, 2176, 2258, 2252, 3330, 1922, 8987, 29272, 6285, 1970, 1957, 10630, 8337, 1036, 1930, 1977, 10633, 1956, 20709, 11569, 23928, 1930, 13148, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MDTSTGEITIPGQVRVNPLRDAAAAHNLDWLRAHLADLCLAVDQCAFYFLFDDQFDADLGALPAEKPSPVESAFADLWRRESQGMSPRWRSRAAYHWEGYFSRAAYMVLRRGASGVDTVLDMVERILGEIPPTIFHRGDVYNLAVILQHERQCGLDEAFALVHGDATRMVEEFYRLRYREGLADWMRGYFTWEASTIRYRPEGALPLDQPNYLEELLGMLRDDEAEQHYNRWNIPQLAAVSFPDAGVARVCAPLISTLHTGRAPESAHPSEALGRRTLHADHFPNPTVTLMRQLAGDAPAVNNDVYSYPKEAPLNALVPELCVELGLTPSETEAT", "metadata": {"id": "A0A931B3J5", "cluster": 15640085, "interpro_all": ["IPR008949", "IPR034686"], "interpro_used": ["IPR034686", "IPR008949"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a polypeptide chain that performs the following role: The protein carries a C2 domain that functions as a calcium-dependent membrane-targeting module involved in signal transduction and membrane trafficking. It adopts an eight-stranded beta-sandwich structure that binds phospholipids, such as phosphatidylserine and phosphatidylcholine, often coordinating calcium ions within apical loops to trigger subcellular localization. Additionally, the protein possesses a Synaptotagmin domain that functions as a calcium sensor to mediate the docking and fusion of synaptic vesicles with the plasma membrane during neurotransmitter release. This region typically folds into an 8-stranded beta-sandwich containing C2 domains, which facilitate interactions with phospholipids and inositol polyphosphates in both calcium-dependent and independent manners. It is produced by Oikopleura dioica (Tunicate) and has UniProt annotations Repeat. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 16252, 43, 8453, 3418, 1988, 4088, 1966, 43, 5016, 17, 3100, 3260, 17, 5133, 9059, 3286, 1922, 2733, 8201, 1930, 3260, 9604, 18, 2176, 24032, 1925, 5066, 17, 10338, 4666, 17, 18038, 3170, 1988, 6876, 15619, 16, 2427, 1966, 28563, 1930, 23842, 16, 3868, 19355, 5016, 6982, 2651, 8913, 11109, 1942, 6086, 11309, 5363, 18, 4950, 16, 1920, 2213, 14465, 43, 14009, 7336, 18266, 1921, 3418, 1988, 4088, 1966, 43, 5016, 6443, 1942, 8265, 1920, 10909, 1930, 5289, 1927, 6251, 8319, 1956, 1920, 3582, 3260, 2409, 15223, 4012, 18, 2052, 3031, 5745, 16231, 2460, 1925, 28, 17, 10338, 4666, 17, 18038, 3165, 8453, 4682, 16, 2154, 6628, 3719, 1956, 15619, 1930, 16246, 11769, 11787, 1036, 1922, 2321, 5016, 17, 3100, 1930, 3484, 5222, 1036, 18, 2176, 1977, 4152, 2007, 25166, 8323, 2202, 9280, 23652, 6102, 12, 29171, 2010, 13, 1930, 2258, 20709, 15010, 6865, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MKICSDYSFEANLLKVHLNKATDLPAMDIGGTSDPYVKLFFLPDKKRRLTTKVHRKTLNPVFDERFDLPLLYKDIAQKTLVFGIYDYDRFGKHDSIGSVEIPLSTIDLGAPFLGSKPIKSLTQKTLGDICFSLRYVPTSGKMTVGILEAKNLKKMDAYGLSDPYVKIYLNRNGKRLKKKKTSIKKNTLTPYYNESFAFEVSQEIIQSVELVIKVVDHDQVGSNDPIGKVVLSKNAEGQALKHWTGMINVPRRPVVLWHTLEVCRC", "metadata": {"id": "E4X4A9", "cluster": 19388903, "interpro_all": ["IPR000008", "IPR035892", "IPR001565"], "interpro_used": ["IPR000008", "IPR001565"], "interpro_unused": ["IPR035892"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is associated with the ROK family, which encompasses bacterial proteins functioning as transcriptional repressors, sugar kinases, or uncharacterized open reading frames. The repressor members, such as XylR and NagC, are distinguished by an N-terminal helix-turn-helix DNA-binding motif used to regulate operons involved in sugar metabolism. Moreover, the protein is categorized in the ATPase, nucleotide binding domain superfamily, which encompasses the nucleotide-binding domain (NBD) found in diverse proteins including actin, Hsp70, and sugar kinases. This domain constitutes the first lobe of a bilobed structure and contains a conserved ATP-binding site located in a deep cleft that facilitates ATP hydrolysis. It has been detected in Trueperaceae bacterium.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 3039, 1040, 3416, 16, 2154, 21569, 4543, 2697, 7295, 1966, 5224, 26446, 16, 9523, 7784, 16, 2014, 24528, 4437, 7461, 12249, 18, 1920, 14434, 4678, 16, 2427, 1966, 9639, 1005, 1930, 14466, 1030, 16, 2032, 12080, 2007, 1925, 56, 17, 4262, 7864, 17, 5165, 17, 7864, 2678, 17, 2743, 5219, 2251, 1942, 5741, 28748, 3286, 1922, 9523, 4714, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 9444, 16, 5489, 2743, 3418, 13975, 16, 2154, 21569, 1920, 5489, 17, 2743, 3418, 12, 23889, 13, 2435, 1922, 6445, 2697, 2710, 4718, 16, 12886, 16, 1930, 9523, 7784, 18, 2052, 3418, 14879, 1920, 2561, 9581, 1927, 43, 5088, 16248, 1007, 3170, 1930, 5461, 43, 5305, 4498, 17, 2743, 3200, 4810, 1922, 43, 6515, 14649, 1988, 11374, 4498, 9128, 18, 2176, 2258, 2252, 3330, 1922, 6228, 2116, 9914, 14061, 18, 3], "output": "MARSLRDHATGSQEREPRSARTRDGRGADSADGGVLARVRRKTPVGGNAALAAAVAELVGELLEPGFIDSRSGVIVDASNLGVRDLPLTGGLADRFGLPVRGAGVANFAYVNIGTGVAAGFIFGHRLYTGTASGAALDKLAAEATEAHPGSLLARSLATRRQERGHVLSQATSHLGLVVAGLVDTLALERVVIGGGLMSALGADVGAIGAALAARRGMEPVLEEVTAVVGIDVGGTKILGIVRQAAATDRTVTGIGVAALVHDVRAATVAEATFGASGKAGELGHVVVDPSGPACTCGKRGCLEAFAALAKAASEGDALAAKIGRLRAEIFEPLRGVALGAVLEANRAPRLIT", "metadata": {"id": "A0A952UQG2", "cluster": 22557907, "interpro_all": ["IPR043129", "IPR000600"], "interpro_used": ["IPR000600", "IPR043129"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a protein that has the following properties: The protein belongs to the Glycosaminoglycan & Ulvan Degrading Sulfatases family, which comprises enzymes that hydrolyze sulfate groups to facilitate the degradation of complex polysaccharides such as glycosaminoglycans and ulvan. These activities enable the breakdown of chondroitin and dermatan sulfates by gut symbionts for persistence in the gastrointestinal tract, as well as the utilization of green seaweed cell walls in marine ecosystems. Moreover, the protein should contain a Tetratricopeptide repeat that mediates protein-protein interactions and the assembly of multiprotein complexes. This motif consists of tandem 34-amino acid residues adopting a helix-turn-helix arrangement, which stacks to form a right-handed superhelical structure involved in diverse processes such as cell cycle regulation and protein folding. In addition, the protein possesses a Sulfatase, N-terminal domain that comprises the N-terminal region of sulfatase enzymes, responsible for catalyzing the hydrolysis of sulfate ester bonds from diverse substrates including glycosaminoglycans and sulfolipids. It has been characterized in Acidobacteria bacterium 37-71-11 and is connected to UniProt keyword TPR repeat. Generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1988, 2258, 1920, 2894, 3879, 30, 1920, 2213, 14440, 1942, 1920, 25982, 15391, 10, 3570, 25777, 18192, 5141, 18135, 3416, 16, 2154, 12936, 5038, 1988, 7222, 6931, 8767, 2671, 1942, 6628, 1920, 4877, 1927, 2796, 18686, 2427, 1966, 25982, 19900, 1930, 3570, 25777, 18, 2144, 4209, 8675, 1920, 13630, 1927, 26437, 1930, 13467, 1928, 8767, 1036, 2007, 7660, 22282, 1973, 1958, 10804, 1922, 1920, 8375, 6482, 16, 1966, 2486, 1966, 1920, 8422, 1927, 4524, 19636, 3831, 2024, 12430, 1922, 10789, 16828, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 12470, 3319, 21305, 6865, 1988, 10412, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 18, 2052, 5219, 7543, 1927, 10361, 3540, 17, 3835, 2687, 4248, 20478, 43, 7864, 17, 5165, 17, 7864, 13002, 16, 2154, 20836, 1942, 2386, 43, 3659, 17, 17105, 3356, 23285, 2046, 3170, 3286, 1922, 6445, 4028, 2427, 1966, 2024, 4048, 3640, 1930, 2213, 10328, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 5141, 7234, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 56, 17, 4262, 3031, 1927, 5141, 7234, 5038, 16, 5061, 1958, 29601, 1920, 9128, 1927, 8767, 9603, 9031, 2037, 6445, 6249, 2710, 25982, 19900, 1930, 5141, 18954, 18, 2176, 2258, 2252, 4378, 1922, 2687, 10296, 14061, 3191, 17, 5858, 17, 2513, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 22288, 6865, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MAKIQQNRGLSARRWKADGALACGRRRNAAATLAVGLSAALGLFAVSCGRGHGVPTSPNAPVVLISIDTLRADHLPAYGYTKIRTPFIDALAKDSWLFENAYTPCPMTLPAHTTMLTGELPPEHGVRNNVGFVFDGRAHPSLPLLLKAHGYATGAAVSSYVLRSDTGLGPLFDYYEDSTEAAPGMAPVHYRRTGDKTEAVAKEWIAKHAGQPFFFFFHIYEPHLPYNPPEPFLSLYGKTYDGAIASADAIIGTFLDDLKRLGVYDRAMVVLVGDHGEGLGDHGEEQHSILLYREAIHVPMIIKLPGEFGAGRRIAWPAQLSDIVPTVTSVLGIKTPKEVSGSSLVTMDPKVGAQRVLYSETLYPRLQLGWSDLHSTLDARYQYIQSPRPELYDMVADPAEKHDLIGSRAADAARLAADLQKFPQGSDKPAAVDEETLRRLAALGYIGGLRDTAASASLPNPVDNLQYLQRMQDGWRLADEKQFPQAIAALRAILKDNPGMVDVWLKLGEVLTNAGLDEQAVAAYRDAMQRSPIFLPDVSVSLGYVELNLKRLPEAEAAARRALKDVPTKAHELLARVALARGDFAAATEEARAAAAERNPQPPALLVMAEVQLGEGKPADALGTIERAAQRANELRFPEVYNLEYLRGDALARLNRVAEAEAAFRREIAAFPSHSRAYANLAVIRFIQGDRAGVAQLMDEMARANPTGQTYLLAATTFASLGETGEAAAWRRRAESADAGAGLR", "metadata": {"id": "A0A257V4K3", "cluster": 22578170, "interpro_all": ["IPR017850", "IPR052701", "IPR000917", "IPR011990", "IPR019734"], "interpro_used": ["IPR052701", "IPR019734", "IPR000917"], "interpro_unused": ["IPR011990", "IPR017850"]}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein is categorized in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Also, the protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is present in Hymenobacter sp. CCM 8763 and carries UniProt keyword assignments Cytoplasm and rRNA processing.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 1977, 10234, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 2481, 1922, 28034, 19824, 7972, 2341, 1915, 2056, 18, 25993, 5783, 7576, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MNDYANDTAYHRPVMLRECLEALGGGHSARMLERLQSPGHLYSFDQDADAEAEARHLFQELNQRGVLPVDGLLADLGVSSHQFDTPERGPDGPDASAADLINEYSEAELHRIFGMYGEVTSALKKAIAPCTPRGKENKYLAQVFQALRIRLVVMSYHSLEDRLVKNFLAKVVTRKPMEATAEEIALNSRARSAKLRIAIKKDLQPGGRYVDVTFGAQLARPEFTFIRANFFSTRFDGPLDMRMDNARTLAATVVSARRGQSITTIEANDEMAALREMLEQTTQVLRPGGGKFFGEADKDLFGRTDLPFE", "metadata": {"id": "A0A372E2V7", "cluster": 22927696, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein can be placed in the The PhoD-like superfamily, which functions as alkaline phosphatase D to catalyze the hydrolysis of phosphate monoesters into an alcohol and inorganic phosphate. These enzymes share structural and functional similarity with Ca(2+)-dependent phospholipase D, indicating a conserved mechanism for hydrolyzing ester bonds within phospholipid substrates. It originates from Ignavibacteriota bacterium. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 1920, 20175, 1007, 17, 3189, 13975, 16, 2154, 4088, 1966, 10746, 8167, 46, 1942, 18170, 1920, 9128, 1927, 5413, 8914, 26934, 2460, 1925, 4284, 1930, 13849, 5413, 18, 2144, 5038, 7948, 4346, 1930, 3183, 6796, 1956, 2332, 12, 22, 15, 13, 17, 3100, 17570, 46, 16, 4168, 43, 5305, 2856, 1958, 7222, 9046, 9603, 9031, 2651, 14608, 6249, 18, 2176, 22970, 2037, 12046, 9188, 7972, 2341, 18842, 7336, 14061, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MPTYPWDNISALPLVLCGPILRRVEKDSVTVWVALKEEKSLFLEIFETTGSKEVVANGFTDTIKFGKNLHIACVTAIPLSGNLTQGKIYAYDITFSGSEKLAGKDIVCSDSGKFKSEFCYGSYDLPSFCLPSEYVDNTKLEHLKIAHGSCRKPHGGKRDAFRLLDGKLSDYHKVIDPKERIQMLFLTGDQIYADDVDPYLFEMLEKVTDSIVNIPEILPIENDSSIYNDGFSQSELEKNNRYQLIKKIGFTADENESQNHVIKLGEFYSMYLFAWSDVLWPDLDAEAHENSIEIQNYWRALPKVRKVLANIPTYMIFDDHEITDDWFRTFEWSEKTLSDPTARRVLANGLSAYAVFQGWGNIPEKFDNTLLPYIDILENLKINSSPKPNFSTLESLLLP", "metadata": {"id": "A0A959N8Y8", "cluster": 23037525, "interpro_all": ["IPR038607"], "interpro_used": ["IPR038607"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein is grouped in the CBM2, carbohydrate-binding domain superfamily, which functions as an ancillary module in microbial cellulases and xylanases to target these enzymes to cellulose or xylan substrates. This $\\beta$-sheet domain utilizes a planar hydrophobic face of conserved tryptophan residues to facilitate specific binding, thereby enhancing the degradation of plant cell wall polysaccharides. Moreover, the protein possesses a Carbohydrate-binding type-2 domain that mediates the specific attachment of microbial enzymes, such as cellulases and xylanases, to cellulose or xylan substrates. It utilizes a beta-sheet structure with a planar hydrophobic face of aromatic residues, typically tryptophans, to interact with the carbohydrate ligand. This domain includes both the cellulose-binding CBM2a and xylan-binding CBM2b subfamilies, serving to anchor the catalytic domain to the target polysaccharide. Moreover, the protein is included in the CBM2/CBM3 carbohydrate-binding domain superfamily, which mediates substrate recognition and binding in various carbohydrate-active enzymes. It is frequently associated with bacterial glycoside hydrolases, such as cellulases, xylanases, and chitobiases, as well as scaffoldin and cohesin proteins. Structurally, the domain adopts an immunoglobulin-like \u03b2-sandwich fold formed by nine strands with a Greek-key topology. It is identified in Actinomadura rubteroloni and is linked to UniProt keywords Signal, Transmembrane, and Glycosidase.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 28230, 1028, 16, 10590, 17, 2743, 3418, 13975, 16, 2154, 4088, 1966, 1925, 27952, 9059, 1922, 7293, 18485, 2319, 1930, 23665, 2319, 1942, 2758, 2144, 5038, 1942, 12343, 2014, 23665, 6249, 18, 2052, 8, 38, 4666, 8, 17, 11130, 3418, 18127, 43, 14334, 7919, 6171, 1927, 5305, 13489, 4248, 1942, 6628, 2487, 2743, 16, 6113, 9221, 1920, 4877, 1927, 4496, 2024, 4821, 18686, 18, 3950, 16, 1920, 2213, 14465, 43, 10590, 17, 2743, 2601, 17, 22, 3418, 1988, 10412, 1920, 2487, 8576, 1927, 7293, 5038, 16, 2427, 1966, 18485, 2319, 1930, 23665, 2319, 16, 1942, 12343, 2014, 23665, 6249, 18, 2176, 18127, 43, 4666, 17, 11130, 3170, 1956, 43, 14334, 7919, 6171, 1927, 10761, 4248, 16, 5745, 13489, 1036, 16, 1942, 6310, 1956, 1920, 10590, 5207, 18, 2052, 3418, 5921, 2321, 1920, 12343, 17, 2743, 28230, 5896, 1930, 23665, 17, 2743, 28230, 9385, 24167, 16, 13915, 1942, 13333, 1920, 6804, 3418, 1942, 1920, 2758, 17167, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 28230, 1028, 19, 28230, 1010, 10590, 17, 2743, 3418, 13975, 16, 2154, 10412, 4510, 5708, 1930, 2743, 1922, 3425, 10590, 17, 3500, 5038, 18, 2176, 1977, 5467, 2458, 1956, 4543, 7533, 2261, 30337, 16, 2427, 1966, 18485, 2319, 16, 23665, 2319, 16, 1930, 12972, 18311, 4127, 1036, 16, 1966, 2486, 1966, 7281, 1921, 1930, 22822, 2697, 18, 12171, 16, 1920, 3418, 24032, 1925, 11837, 17, 3189, 161, 17, 18038, 3728, 5333, 2007, 6360, 13214, 1956, 43, 27568, 17, 3834, 13678, 18, 2176, 1977, 2899, 1922, 4718, 2954, 10015, 5524, 10010, 4947, 13339, 1930, 1977, 4624, 1942, 20709, 11569, 2733, 16, 9117, 16, 1930, 7533, 9200, 18, 3], "output": "MTEVTGRGRRRAPGGRRPVLFMAVAGVAVVGATAFNGCALPPVPVSPTGTKEHPQAQPSRTSAPGAGKKRKHTTSDRWDSGFVGQITVVNTSEATVWAWGTGADHDVTRLLGTGGPLAPGATPSACVLNGAPCRRRERPDERRGLHAAAEDGSAPRPGGAPGDCRTVSPSPSASPSVSPTTSAPLGRPDRQGPPGRTRTTGLEATYNGWNLTASFPGARITVQLGFQAEGRPPGS", "metadata": {"id": "A0A2P4UR62", "cluster": 23410373, "interpro_all": ["IPR001919", "IPR008965", "IPR012291"], "interpro_used": ["IPR012291", "IPR001919", "IPR008965"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is found in Pedobacter yonginense.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 2435, 1922, 5296, 5883, 7419, 2029, 2053, 3355, 1021, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MVPYCNLCQSNHVQLHLKLNDSHSIYTCKEDFHEQFGFTTIADLPKQWRNSVLKQLEIGCGQGLFLTQLEKEGYQVYGIEPAQNFDGVKFDLIIMAQVLEHVEAPLELLQQISSNWYAWVPDQHFTHFTAKGIRFLTQTINWLSKCASILPGTGDQIHAMIKLFNCGNGFTDPPPQTIAYTEIKFIKKYIHPNANIPSVKASAVARSKGLNVKTGYYLNKNAYLLLVQTNFKGLVPQKQKQLKTIEIEYSTLEHNNY", "metadata": {"id": "A0A317EIL7", "cluster": 24003457, "interpro_all": ["IPR029063"], "interpro_used": ["IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein is included in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, the protein is assigned to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is expressed in Myxococcales bacterium and contains UniProt keyword associations Cytoplasm and rRNA processing.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 3198, 1922, 21464, 11748, 1918, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 1930, 9067, 4587, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MTEPRQFSHQPVLLNEVLEALAPVAGGVYCDATIIDRDPAAVAAARQRLAHFGDRVQIIHGRFSELERLLAQVSSHQLDVAARGFSFMNSGPLDMRMNPTEGETASELLARVARSIKRMANDGTMASTADLAVAVRRVVGKTPKGKSDPATRALPAPLAVGGTVAIIAFHSIEDRMVKQRFAQLVQPCVCPPSMEEADNRRSRSARVRAIRRILGGGGHAESVLEASAPDGRLIGGVPAVDGLLVDLGVVSEDELADIIYRFGEERLSRRTFQAIRIAVNNELGELESLLDPVCPCPPPVAELRTRRSVRVTHR", "metadata": {"id": "A0A970M6W0", "cluster": 26727321, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein is a member of the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Moreover, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, the protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It originates from Terriglobus albidus and is connected to UniProt keyword Cytoplasm and rRNA processing.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 22970, 2037, 11420, 17780, 2389, 1957, 5311, 22291, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MIASLHVPVLFEEVLNFLNVRLAGHTSGIARRLGPHGTLHCFDAAELKATMPKVEFHARAFSEADQVHDGPLDMRMNPKVGVSAEQVVNQIDENRAIVRARPITTTGELARVVAAAAPAMSAPSLLKPGGRLAVISFHSLEDRLVKDDFEMERNPRARSAKLRVAEKKRGGNYADATLGRDPDAMKLAKERLEHLIAPGTLDGILADFGVSSLQLDTPHRGFSFRELADLIYEFGEERSSRRIAKGEKIHPATKTFQALRIYVNDELGEIRSLLGRERSRTGEYEVLTKKPVTATED", "metadata": {"id": "A0A5B9EBM5", "cluster": 28392172, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein is categorized in the Protein of unknown function DUF3833 family, which consists of uncharacterised proteins found in Proteobacteria. It originates from Pseudoalteromonas aliena and has UniProt annotations Signal. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 10892, 11368, 1010, 3416, 16, 2154, 7543, 1927, 23229, 3495, 2697, 2435, 1922, 22266, 18, 2176, 22970, 2037, 11520, 1923, 1967, 10480, 15356, 11496, 1930, 2258, 20709, 15010, 2733, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MNVSNMLKLVAVSLLALLLVSCSAPNVEHYKNTSPNFDFKTFFSGNLKAYGVVQDFKGELTRKLVVDMKATWNGNEGVIEEDFIYDDGQTQKRIWKITLNDDNSLTGTADDVLGIAKGKSQGSVFHWNYNVELPYDGSTLEVNFDDWMYLVTQTRLINRTSIVKFGVEVGEVTLVIEKI", "metadata": {"id": "A0A1Q2GTS7", "cluster": 242950, "interpro_all": ["IPR024409"], "interpro_used": ["IPR024409"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein includes a Replicative helicase inhibitor G39P, N-terminal domain that constitutes the folded structural component of the G39P inhibitor, functioning to prevent the initiation of DNA replication by blocking the G40P replicative helicase. It is identified in Agathobacter rectalis CAG:36.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 5921, 43, 20604, 15318, 4106, 15991, 1026, 1034, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 16318, 4346, 4594, 1927, 1920, 15991, 1026, 1034, 4106, 16, 7295, 1942, 4625, 1920, 6035, 1927, 2678, 5158, 2007, 7472, 1920, 14036, 1008, 1034, 20604, 15318, 18, 2176, 1977, 2899, 1922, 8770, 1963, 5883, 11635, 1937, 13415, 30, 3480, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MTKKDAAQLVAIVVTAYPNYDMMFEDVDAPLVALAVKKHIATSKWPAPDQAWLAVSDLLYSEGEFNHGDLKQQLGHWGGSKPGMDRVAFMQQYTPMYEASLPDKGQKKLADRESDRRKREQYYAALSGWNRREPGHIRAHTSPHSRRNSRGRAYKFRDADSVKATVSLWAPSVAELREILLEIAHPDLIPPLVARAVESIGWSNLWEMHRREKARDMTPGELTTQIDAVAALAAADPLALEAGKETAEVFGQSP", "metadata": {"id": "R6TS44", "cluster": 2887399, "interpro_all": ["IPR024424"], "interpro_used": ["IPR024424"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein is included in the PH-like domain superfamily, which comprises a diverse group of modular domains, including Pleckstrin homology (PH), PTB, EVH1, and FERM domains, that share a conserved structural fold consisting of a partly opened \u03b2-barrel capped by an \u03b1-helix. These domains primarily function in cellular signaling and subcellular targeting by mediating specific interactions with membrane phospholipids, phosphotyrosines, or peptide motifs. It is expressed in Ceratobasidium theobromae.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2087, 17, 3189, 3418, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 16078, 4682, 16, 2710, 6483, 12940, 2156, 5572, 9039, 12, 2087, 13, 16, 19562, 16, 2180, 8600, 16, 1930, 20620, 4682, 16, 1988, 7948, 43, 5305, 4346, 3728, 7600, 1927, 43, 10028, 16645, 161, 17, 19560, 22069, 2007, 1925, 160, 17, 7864, 18, 2144, 4682, 5985, 2347, 1922, 3689, 3197, 1930, 11309, 5133, 2007, 10239, 2487, 3719, 1956, 3260, 15619, 16, 29552, 1036, 16, 2014, 4207, 8277, 18, 2176, 1977, 3198, 1922, 6580, 8286, 7972, 12924, 7408, 1989, 1920, 2389, 2018, 3336, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MQRFPSRESRKPKSVSPIDIIRPVLSLKGSGLFVDTTWHALCDKPADSTRLRCNTSRKTLSAPAPNNRESPRRSVDRTPRPSVSLSGRPLTLGGMSMRLSPSVPRPVMPTDTIAKRCAQASTVHCDPNGESPQVVLSKLDVIRSPLCPLPAPKLLMYSCGIHIEGMVPRKMEFNALGVLAKDRRGKVKERSTNDLLQRVKLTRSLSALQPSHASLVVKKPTGPAWPKDITTPTLDQPEPSKGSPERNSGYASVAGALPTVPIPILNLPPLPPATPRATPNPPLTPTLYHQVSQSMMNLSSPPPALGLVRHNSMPTMVPREEEGKEGEKKQYIALHGTTLSVYKNDVRKFPI", "metadata": {"id": "A0A5N5QA16", "cluster": 3443909, "interpro_all": ["IPR011993"], "interpro_used": ["IPR011993"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein is assigned to the Uncharacterised nucleotidyltransferase family, which represents a group of proteins predicted to function as nucleotidyltransferases, enzymes that catalyze the transfer of nucleotide residues. It originates from Thomasclavelia spiroformis. Please provide the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 7762, 30, 1920, 2213, 1977, 6304, 1942, 1920, 23229, 3495, 2797, 4090, 2199, 9961, 3416, 16, 2154, 4972, 43, 2210, 1927, 2697, 4396, 1942, 2347, 1966, 2797, 4090, 2199, 18580, 16, 5038, 1988, 18170, 1920, 3856, 1927, 5489, 4248, 18, 2176, 22970, 2037, 17737, 2223, 7921, 12191, 1019, 22075, 2231, 1937, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MGYINEQYYILSLAKAIVLQDEIPIDKSVNWKVIYNLCKYHKIDNLIAYGIDYLKQEIDIPKQIIEAFDYARKQGIMRQTIQDHELKEIEEKFEQLKVSNVALKGSFLKQYYPSKDMRLLTDLDILFKSEEKEKMHQGLKELGYYLKYPGSHHDVYVKQPLTVVEMHYSCYSNSYLNQHFNNLFSRVVNKSSKKYCFEMSLEDYYLFMIGHMAKHFVYGGIGVRSIIDLIVFNVNFKDECDWKFVDEQLNYAGLLCFRNLLQKLIDGYRDDELLNCIFKSGAFGTSVNSLNLAIVKDGESEIKILKNRLYLMLSMSYHLAFPKIDFMKEKYPYLRKYTFLLPFAYFQRGFSKLVNNRQEFFNIIKKPFIPKKKGIKEIAKIYKRAGLKRENFHG", "metadata": {"id": "A0A943ELB5", "cluster": 4431984, "interpro_all": ["IPR039498"], "interpro_used": ["IPR039498"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein is assigned to the Immunoglobulin-like fold superfamily, which comprises domains characterized by a beta-sandwich of seven or more strands arranged in a Greek-key topology, facilitating protein-protein interactions often via beta-sheet interfaces. These domains are ubiquitous in animal proteins, playing critical roles in immune recognition, cell adhesion, and structural integrity in muscle proteins such as titin. Moreover, the protein should contain a Immunoglobulin subtype 2 domain that adopts a conserved Greek-key $\\beta$-sandwich structure and serves as a modular building block in diverse proteins, including growth factor receptors and neural cell adhesion molecules. It mediates critical protein-protein interactions essential for cell-cell recognition, receptor signaling, and immune system function. Furthermore, the protein contains a Immunoglobulin I-set domain that adopts a Greek-key $\\beta$-sandwich fold intermediate between variable and constant types to mediate protein-protein interactions and structural stability. This motif is widely distributed, facilitating cell-cell recognition in adhesion molecules (such as VCAM and ICAM), supporting axonal guidance, and contributing to the elasticity of muscle proteins like titin. It is produced by Tropilaelaps mercedesae and is connected to UniProt keyword Immunoglobulin domain, Transmembrane helix, and Repeat.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 11837, 17, 3189, 3728, 13975, 16, 2154, 12936, 4682, 4378, 2007, 43, 4666, 17, 18038, 1927, 5260, 2014, 2253, 13214, 14940, 1922, 43, 27568, 17, 3834, 13678, 16, 12440, 2213, 17, 2213, 3719, 3868, 3454, 4666, 17, 11130, 14857, 18, 2144, 4682, 2032, 15498, 1922, 4027, 2697, 16, 14797, 4140, 5456, 1922, 3743, 5708, 16, 2024, 6141, 16, 1930, 4346, 7996, 1922, 3760, 2697, 2427, 1966, 7090, 1921, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 11837, 8856, 22, 3418, 1988, 24032, 43, 5305, 27568, 17, 3834, 8, 38, 4666, 8, 17, 18038, 3170, 1930, 10634, 1966, 43, 16078, 9086, 3367, 1922, 6445, 2697, 16, 2710, 2905, 2991, 4086, 1930, 5181, 2024, 6141, 4206, 18, 2176, 10412, 4140, 2213, 17, 2213, 3719, 4415, 1958, 2024, 17, 2024, 5708, 16, 3148, 3197, 16, 1930, 3743, 2433, 2347, 18, 3677, 16, 1920, 2213, 5461, 43, 11837, 51, 17, 2735, 3418, 1988, 24032, 43, 27568, 17, 3834, 8, 38, 4666, 8, 17, 18038, 3728, 6129, 2192, 4650, 1930, 5168, 3584, 1942, 8265, 2213, 17, 2213, 3719, 1930, 4346, 5057, 18, 2052, 5219, 1977, 5673, 6533, 16, 12440, 2024, 17, 2024, 5708, 1922, 6141, 4206, 12, 2427, 1966, 19942, 1930, 14085, 13, 16, 6184, 10623, 9765, 16, 1930, 8739, 1942, 1920, 19680, 1927, 3760, 2697, 3189, 7090, 1921, 18, 2176, 1977, 4152, 2007, 8465, 19167, 15208, 2523, 8687, 1919, 1918, 3336, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 11837, 3418, 16, 9117, 7864, 16, 1930, 6865, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MVLEVIVLDRMGSNVMFSWEKDGSSMQESRARDAGKYTCTAMNAVSSHRGFIPSFEVLKEIADTTELSSERPIGSRFQIFCSALEIRNEDATSILSIQKVARTSSVSAKLIVRVMYEW", "metadata": {"id": "A0A1V9XVL3", "cluster": 6429013, "interpro_all": ["IPR007110", "IPR036179", "IPR013783", "IPR013098", "IPR003599", "IPR003598"], "interpro_used": ["IPR013783", "IPR003598", "IPR013098"], "interpro_unused": ["IPR003599", "IPR036179", "IPR007110"]}, "task_type": "infilling"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein has a MotA/TolQ/ExbB proton channel domain that functions as an integral membrane proton-conducting unit essential for energy transduction. It harnesses the proton motive force to drive diverse cellular processes, such as generating rotational motion in the bacterial flagellar motor or energizing the transport of large molecules via the TonB complex. Furthermore, the protein is classified under the The ExbB/TolQ Biopolymer Transport family, which mediates energy-dependent transport across the bacterial outer membrane and maintains cell envelope integrity. Members function as integral components of the TonB system to facilitate nutrient uptake by stabilizing TonB and ExbD, or the Tol-Pal system to support cell division and outer membrane invagination. These proteins also serve as entry points for colicins and bacteriophage DNA, playing a critical role in bacterial survival. It is derived from Pararobbsia silviterrae and contains UniProt keyword associations Cell membrane, Protein transport, and Transmembrane helix. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 1925, 3835, 2687, 3244, 1988, 2469, 16318, 2460, 43, 2213, 22665, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 12798, 1019, 19, 21930, 1055, 19, 1975, 6936, 8433, 4999, 3418, 1988, 4088, 1966, 1925, 12328, 3260, 8433, 17, 12335, 5344, 4415, 1958, 3844, 8201, 18, 2176, 25852, 1918, 1920, 8433, 7038, 1021, 5495, 1942, 9265, 6445, 3689, 4028, 16, 2427, 1966, 9155, 16577, 6269, 1922, 1920, 4543, 24154, 4842, 2014, 2066, 2693, 3903, 1920, 4860, 1927, 3103, 4206, 3454, 1920, 16501, 1014, 2796, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 1920, 1975, 6936, 19, 21930, 1055, 20864, 14083, 4860, 3416, 16, 2154, 10412, 3844, 17, 3100, 4860, 3436, 1920, 4543, 7642, 3260, 1930, 16566, 2024, 11262, 7996, 18, 4678, 2347, 1966, 12328, 4178, 1927, 1920, 16501, 1014, 2433, 1942, 6628, 8708, 5047, 2007, 14384, 16501, 1014, 1930, 1975, 13602, 16, 2014, 1920, 21930, 17, 5755, 2433, 1942, 3373, 2024, 8451, 1930, 7642, 3260, 27134, 2636, 18, 2144, 2697, 2222, 7120, 1966, 6904, 4273, 1958, 5178, 3665, 1036, 1930, 24613, 2678, 16, 14797, 43, 4140, 2770, 1922, 4543, 3298, 18, 2176, 1977, 3595, 2037, 8202, 15129, 2083, 2126, 4059, 2165, 1967, 5524, 1021, 1930, 5461, 20709, 11121, 2538, 5253, 2024, 3260, 16, 2213, 4860, 16, 1930, 9117, 7864, 18, 7031, 1920, 3244, 18, 3], "output": "MLSPQSLIVAAGTVGWILVPLALLGGVAFALIAERIVALRLMASPIAQFEPLHSGDASTQASDAFRHRLTSALAAMPRRHVIHRWMAPVVAHDVLDHAPLWWIEAQLEARAPRIEKSLNRGLWLLDTIVTTAPLVGLFGTVTGMMDAFHLIGAQGLVNPSGVSGGVAQALIATAIGLVIAVVSLIAFNALTQRVDATLDDLQAFGTQWLATLRYMRDTRTVDAGAAGAGAGAGAGAGAGAGAGAGAGAGAATTRAASAHAQIHAPATAASTAAHTSARHTS", "metadata": {"id": "A0A494X785", "cluster": 6787300, "interpro_all": ["IPR050790", "IPR002898"], "interpro_used": ["IPR002898", "IPR050790"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given the following functional description of a protein, generate a complete amino acid sequence that performs the described role. The desired function is: The protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein carries a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. Additionally, the protein is included in the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. It is native to Methylomonas koyamae and is classified with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 16, 5655, 43, 4080, 3835, 2687, 3244, 1988, 17436, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 16252, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2176, 1977, 6196, 1942, 4963, 10480, 6235, 28477, 1021, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MKPGRFITLEGGEGVGKSTNLQFIRHCLAERGIPLLITREPGGTPIAEKIRGILLERSDEALSEQAELLLVFAARAQHIRHVIEPALLRGEWVVCDRFTDATYAYQGAGRNMDLATIAWLERTVQGGLRPDLTFVLDAPVATGLQRAKRRGELDRFETEQLDFFERIRQSYLHRAADDPARYKVIDAALPLPQVQARLLAELETLWAN", "metadata": {"id": "A0A177NP53", "cluster": 9227695, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR027417", "IPR039430", "IPR018094"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein belongs to the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. Also, the protein is associated with the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It is native to Paraburkholderia sp. WP4_3_2 and is linked to UniProt keywords Cell membrane, ATP-binding, and Transmembrane helix.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 14440, 1942, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 1977, 6196, 1942, 8202, 13789, 20045, 2643, 18339, 2056, 18, 21459, 1006, 41, 23, 41, 22, 1930, 1977, 4624, 1942, 20709, 11569, 2024, 3260, 16, 4498, 17, 2743, 16, 1930, 9117, 7864, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MSGAANAPQNPPALHRPAQAEPPEPPHLHEPYKGNRGVTRAWKALQYSIKGFRTAIHNESAFFVPVEPVERVLLLGSVMLVLIVELLNSSIENAVDRVTCVMTWGLILVPRFGPTLMHWIGARGLGPDDPLAPLPFNPRQELTLAAIMVPIGVIGLERNELSGRAKDLGSAAVTVAL", "metadata": {"id": "A0A7W5NIF2", "cluster": 9326194, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR033718", "IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe protein is classified under the U6 snRNA phosphodiesterase 1 family, which functions as a nuclear phosphodiesterase responsible for trimming the 3' poly(U) tract of pre-U6 snRNA to facilitate its maturation. These enzymes adopt a globular $\\alpha$-$\\beta$ architecture and catalyze the formation of a terminal 2',3'-cyclic phosphate by degrading oligo(U) and oligo(A) tails. Mutations in this family are associated with the genetic disorder poikiloderma with neutropenia. It originates from Haematococcus lacustris (Green alga) (Haematococcus pluvialis) and exhibits UniProt keyword tags Hydrolase, Lyase, and Nuclease.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 22275, 11970, 2175, 24821, 21, 3416, 16, 2154, 4088, 1966, 43, 4254, 24821, 5061, 1958, 30241, 1920, 23, 11, 4286, 12, 63, 13, 6482, 1927, 2097, 17, 22275, 11970, 2175, 1942, 6628, 2496, 7655, 18, 2144, 5038, 14103, 43, 20975, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 9335, 1930, 18170, 1920, 3337, 1927, 43, 4262, 22, 11, 16, 23, 11, 17, 9821, 5413, 2007, 18192, 15039, 12, 63, 13, 1930, 15039, 12, 43, 13, 18103, 18, 3527, 1922, 2052, 3416, 2032, 2458, 1956, 1920, 3299, 4770, 2510, 26144, 6012, 2179, 3368, 1956, 18005, 18, 2176, 22970, 2037, 13080, 8256, 7511, 3894, 1937, 12, 4524, 4326, 1019, 13, 12, 13080, 8256, 2123, 12631, 2086, 1937, 13, 1930, 9826, 20709, 11121, 2538, 14392, 20748, 16, 23928, 16, 1930, 16230, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "VSDAVRSICQGPFRLLDELEGQLRDALAGTAVNDEGTRSFLALPLTQGQLPTYYQVRTPTLVTRALPLVTVKARSDLTHASSTTSLHLSLSRVLPVGAELMAQGLTSLRAEVCALIRHVDQALALHPRQHQAPXLGDGVTV", "metadata": {"id": "A0A699Z8M8", "cluster": 11093139, "interpro_all": ["IPR027521"], "interpro_used": ["IPR027521"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein incorporates a TetR-type DNA-binding HTH domain that functions as a transcriptional regulator in bacteria and archaea, typically acting as a homodimeric repressor to control susceptibility to hydrophobic antibiotics and detergents. It structurally comprises an N-terminal helix-turn-helix motif with an inverse orientation to facilitate DNA binding. In addition, the protein is grouped in the Homeodomain-like superfamily, which comprises transcription factors and DNA-binding proteins that utilize a conserved helix-turn-helix (HTH) motif to interact with the DNA major groove. These proteins are ubiquitous across all domains of life and play critical roles in gene regulation through specific hydrogen bonding and hydrophobic contacts. Additionally, the protein is a member of the HTH-type, TetR-like transcriptional regulator family, which comprises predominantly bacterial DNA-binding proteins that utilize a helix-turn-helix (HTH) motif to repress gene expression. These regulators control diverse physiological processes ranging from antibiotic resistance and lipid metabolism to osmotic stress response and cell division, as exemplified by the nucleoid occlusion factor SlmA. It originates from Aquifex aeolicus and is annotated with UniProt keywords Transcription regulation.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 5575, 17, 2601, 2678, 17, 2743, 5334, 1023, 3418, 1988, 4088, 1966, 43, 5224, 7888, 1922, 4802, 1930, 21501, 16, 5745, 8290, 1966, 43, 21189, 1935, 14434, 1942, 2285, 6461, 1942, 7919, 7560, 1930, 15814, 1036, 18, 2176, 12171, 12936, 1925, 56, 17, 4262, 7864, 17, 5165, 17, 7864, 5219, 1956, 1925, 9526, 7148, 1942, 6628, 2678, 2743, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 4502, 17166, 17, 3189, 13975, 16, 2154, 12936, 3213, 2790, 1930, 2678, 17, 2743, 2697, 1988, 12561, 43, 5305, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 6310, 1956, 1920, 2678, 3044, 15920, 18, 2144, 2697, 2032, 15498, 3436, 2136, 4682, 1927, 3308, 1930, 3918, 4140, 5456, 1922, 2359, 3640, 2596, 2487, 6201, 11463, 1930, 7919, 9070, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 5334, 1023, 17, 2601, 16, 5575, 17, 3189, 5224, 7888, 3416, 16, 2154, 12936, 7700, 4543, 2678, 17, 2743, 2697, 1988, 12561, 43, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 9055, 2359, 2294, 18, 2144, 9098, 2285, 6445, 5005, 4028, 6485, 2037, 7267, 3554, 1930, 4486, 4714, 1942, 13951, 3071, 2644, 1930, 2024, 8451, 16, 1966, 22236, 2007, 1920, 2797, 2642, 10543, 2991, 2788, 3368, 18, 2176, 22970, 2037, 10059, 10528, 1039, 10194, 4485, 1957, 1930, 1977, 10633, 1956, 20709, 11569, 3213, 3640, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MRQRALKEHLREEMPDIAQALGMSVGNLYNYFRRVRIIRTACRLFAEKGYHSAT", "metadata": {"id": "A0A7C5QDY7", "cluster": 12383217, "interpro_all": ["IPR009057", "IPR050109", "IPR001647"], "interpro_used": ["IPR001647", "IPR009057", "IPR050109"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein contains a Carbohydrate kinase PfkB domain that functions as the catalytic component in a diverse family of carbohydrate and pyrimidine kinases. It participates in essential metabolic processes, including thiamine pyrophosphate (TPP) synthesis via phosphomethylpyrimidine kinase and the Entner-Doudoroff pathway in hyperthermophilic archaea through 2-keto-3-deoxygluconate kinase activity. Also, the protein incorporates a RfaE bifunctional protein, domain I domain that acts in the biosynthesis of D-glycero-D-manno-heptose 1-phosphate. This N-terminal module contributes to the production of ADP-L-glycero-D-manno-heptose, a key precursor for the assembly of the lipopolysaccharide inner core. Additionally, the protein is grouped in the Ribokinase-like superfamily, which comprises phosphotransferases that transfer a phosphate group from ATP to an acceptor containing an alcohol group. These enzymes are structurally characterized by a central eight-stranded sheet flanked by conserved helices, forming a shallow active site groove where the substrate and ATP bind to facilitate phosphoryl transfer. It is produced by Gemmataceae bacterium.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 5461, 43, 10590, 4016, 5099, 11228, 3418, 1988, 4088, 1966, 1920, 6804, 4594, 1922, 43, 6445, 3416, 1927, 10590, 1930, 21611, 7784, 18, 2176, 17241, 1922, 4415, 4487, 4028, 16, 2710, 26901, 24937, 12, 25282, 13, 4271, 3454, 8078, 21312, 18425, 29899, 4016, 1930, 1920, 8496, 3239, 17, 2608, 2009, 30232, 2040, 3374, 1922, 19144, 12492, 24888, 3742, 21501, 2596, 22, 17, 21471, 17, 23, 17, 16333, 22988, 8870, 4016, 2455, 18, 2222, 16, 1920, 2213, 19683, 43, 22465, 1021, 29491, 2213, 16, 3418, 51, 3418, 1988, 8016, 1922, 1920, 8132, 1927, 46, 17, 7757, 1037, 17, 46, 17, 7338, 1037, 17, 20662, 2217, 21, 17, 5413, 18, 2052, 56, 17, 4262, 9059, 7624, 1942, 1920, 3372, 1927, 9828, 17, 54, 17, 7757, 1037, 17, 46, 17, 7338, 1037, 17, 20662, 2217, 16, 43, 3834, 7897, 1958, 1920, 5957, 1927, 1920, 15614, 6671, 4728, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 21857, 25545, 17, 3189, 13975, 16, 2154, 12936, 8078, 18580, 1988, 3856, 43, 5413, 2210, 2037, 4498, 1942, 1925, 12641, 3165, 1925, 4284, 2210, 18, 2144, 5038, 2032, 12171, 4378, 2007, 43, 4101, 5066, 17, 10338, 11130, 20185, 2007, 5305, 12789, 16, 7402, 43, 17272, 3500, 3200, 15920, 2597, 1920, 4510, 1930, 4498, 4566, 1942, 6628, 12556, 3856, 18, 2176, 1977, 4152, 2007, 10607, 3368, 3857, 1972, 3336, 14061, 18, 3], "output": "MVSQPPDWNAAVAALAGCVCPEAPVPVVEVATRWVVPGEHLAWAVRAAGVEPDGLVADPGRPTTVKLRVGAAAEQLAGWAERIAACADAVLLSDYFAGRPVVVDPKGTDATRYRGATVLKPNGPGDVLDAGRALAEQLPGTAILVTLGAEGAGDTVAATLALALGAGLSVEAAARLTPDELRAALADSVPAFAPLGRLLVVGDVMLDEYLAGDARRGAANAAGNAAALGSRPVLGGVTGADAAALARGQQVIRADTESTAPLSGKGVLADGLAARVIAAARLGELGDLVGRRVRGMALFRAGAAPLGLPAAHAQRVFDVTANAAGSVAVSKVGTAVV", "metadata": {"id": "A0A4V0IC05", "cluster": 13634539, "interpro_all": ["IPR011611", "IPR011913", "IPR029056"], "interpro_used": ["IPR011611", "IPR011913", "IPR029056"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein belongs to the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Moreover, the protein should feature a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. It is native to Rhodocyclaceae bacterium and has UniProt annotations ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 2176, 1977, 6196, 1942, 11490, 20446, 9914, 14061, 1930, 2258, 20709, 15010, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSKGRFITLEGVDGAGKSTHLSWLIDHLRARGHVLETEALLMFAARREHLERVIKPAIERGEWVVCDRFTDASFAYQGDLQPDLTLLFDLPIDIAAQRMAGAERQLDRFEQERIRIIDARQTLEHIQKQLEQILASGVVQTREPGGTPLGEKLRALLLNEPMHGGGRGLSVEKLGQLETWVQKTEFHERVRAAYLARAAETPG", "metadata": {"id": "A0A838M041", "cluster": 15521113, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR027417", "IPR018094", "IPR039430"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein can be placed in the RNA-directed RNA polymerase beta-chain family, which constitutes the catalytic core of the RNA replicase found in *Leviviridae* bacteriophages. This enzyme catalyzes the synthesis of complementary RNA strands from an RNA template through a primer-independent mechanism that initiates de novo and proceeds via the sequential addition of nucleotide triphosphates. Also, the protein possesses a Bacteriophage RNA-directed RNA polymerase (RdRp) catalytic domain that synthesizes a complementary RNA strand from a given RNA template. It functions through a two-step mechanism involving primer-independent de novo initiation followed by elongation via nucleotidyl transfer. This region corresponds to the catalytic palm structure essential for viral genome replication. Additionally, the protein is a member of the DNA/RNA polymerase superfamily, which encompasses enzymes such as DNA polymerase I, reverse transcriptase, and viral RNA polymerases that catalyze the template-directed synthesis of nucleic acids. Members of this superfamily share a conserved active site fold resembling the palm subdomain of right-hand-shaped polymerases. It is expressed in ssRNA phage Gephyllon.2_7 and is associated with UniProt keywords Magnesium, Metal-binding, and Viral RNA replication.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 3146, 17, 6554, 3146, 6479, 4666, 17, 4659, 3416, 16, 2154, 14879, 1920, 6804, 4728, 1927, 1920, 3146, 5825, 2051, 2435, 1922, 14, 10157, 20614, 10828, 14, 24613, 1036, 18, 2052, 4113, 17097, 1920, 4271, 1927, 8862, 3146, 13214, 2037, 1925, 3146, 7662, 2596, 43, 6194, 17, 3484, 2856, 1988, 18637, 2028, 9441, 1930, 20737, 3454, 1920, 9454, 2459, 1927, 5489, 17978, 1036, 18, 2222, 16, 1920, 2213, 14465, 43, 24613, 3146, 17, 6554, 3146, 6479, 12, 24468, 1034, 13, 6804, 3418, 1988, 15541, 1036, 43, 8862, 3146, 5984, 2037, 43, 3258, 3146, 7662, 18, 2176, 4088, 2596, 43, 2288, 17, 3537, 2856, 5884, 6194, 17, 3484, 2028, 9441, 6035, 3489, 2007, 9971, 3454, 2797, 4090, 2199, 3856, 18, 2052, 3031, 8852, 1942, 1920, 6804, 15516, 3170, 4415, 1958, 4324, 3843, 5158, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2678, 19, 3146, 6479, 13975, 16, 2154, 21569, 5038, 2427, 1966, 2678, 6479, 51, 16, 5267, 13335, 16, 1930, 4324, 3146, 20910, 1988, 18170, 1920, 7662, 17, 6554, 4271, 1927, 11079, 4576, 18, 4678, 1927, 2052, 13975, 7948, 43, 5305, 3500, 3200, 3728, 18994, 1920, 15516, 27517, 1927, 3659, 17, 3897, 17, 9132, 20910, 18, 2176, 1977, 3198, 1922, 19314, 2175, 10503, 3929, 25818, 11560, 1916, 18, 22, 41, 27, 1930, 1977, 2458, 1956, 20709, 11569, 13148, 16, 6048, 17, 2743, 16, 1930, 4324, 3146, 5158, 18, 3], "output": "MKSNGNDFYLEVMRDVYIDACMKCSADVFNLRDLETIRSRVEKEGISFLTITLPQFSKAFERSLELGVIGPACFSGFHHLKHEAIPVFLQGMLSQIFDRKTGKVITYEPPTDNKSAEGLAPCDISTIVEAVRQVCRVFSKVELECTPKRVKQALRSFYEIEQDLQTFSVSSEKEAKFLAVSRMLWDSMFRDFNPNSILPKHGPGATADRISGNQKYVWRRWHGRLESYFPLIDNGYPLGIPLDSEELEIVSIVPEEDEQPVRVITVPKTLKSPRVIAIEPACMQYVQQGIRDYLYDRIESHWLTCNRINFRRQDINQRLALKSSRTGRLATIDLSEASDRVPLSLAMKMFEANRDLHDSILACRSTRARLPDGQIIDPLRKFASMGSALCFPVEAMYFYTCCIVALLDCFNLSCTQRNIKFVSRRVHVYGDDIIVPSTYADVVLDYLHEYNCKVNTNKTFYRGSFRESCGTDAYAGYEVTPTYIRQPHPENKQQHDRIISWCATANLFYLKGYWRTATLLFRKLEKIIGPLPYVRESSGVLGRYSYLGYESVHRWAKPKPFTPFNKEDWDRRTLEKDYSKIENPTEPFYQRSEIRGWMPRPVYRSDELDGWSALAKCFIKMDGASRTGIRNMRDQELNSPKPRPIDRRLDSQADLTSDLVKAFSAMASLEDVQSIDQLHLSRSALHGAVTLKRRWAPPH", "metadata": {"id": "A0A8S5L040", "cluster": 17244395, "interpro_all": ["IPR043502", "IPR007096", "IPR005093"], "interpro_used": ["IPR005093", "IPR007096", "IPR043502"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Functionally defined as:\nIt is part of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein features a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is produced by Pseudomonadota bacterium and is classified with UniProt keywords Isoprene biosynthesis and Transferase.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 2176, 1977, 3131, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 4075, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 4152, 2007, 11520, 3947, 12595, 3857, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MKKISLPAPAKINLFLHIVGRREDGYHLLQSLFHYLDYGDSLHEQDNLIYKAARALQQSAQCNQGVNIHWEKRLPLGSGLGGGSSNAATCLLGVTLGADVPFFLFGHTALGEGIGEKLTALTIAPTWFLVITPDCNVAVEGGINYALSECRNDFEPVVRQHYAEVNDAFKWLSNYSQAQAQEVAQQLPAHLKGFIAKGMNSSPLMQSALSKGIINNDWGVAKRFELRADNKICLHPQEHLGINALNALWDLNWSQDNLINLTPKMYALSELTRNTPRLRIGTLRMSGSGASVFASFSTKA", "metadata": {"id": "A0A941NR29", "cluster": 20190378, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR013750", "IPR006204"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nIt is part of the RNA polymerase sigma factor, region 3/4-like superfamily, which constitutes conserved domains within bacterial and plastid sigma factors that are essential for transcription initiation. These regions feature a nucleotide-binding 3-helical core topology, with region 4 specifically employing a helix-turn-helix motif to bind the -35 promoter element and facilitate the formation of the RNA polymerase holoenzyme. It originates from Paraglaciecola Antarctic JLT virus 2.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 2176, 1977, 3131, 1927, 1920, 3146, 6479, 5139, 2991, 16, 3031, 23, 19, 24, 17, 3189, 13975, 16, 2154, 14879, 5305, 4682, 2651, 4543, 1930, 19754, 5139, 2790, 1988, 2032, 4415, 1958, 3213, 6035, 18, 2144, 3451, 5961, 43, 5489, 17, 2743, 23, 17, 11514, 4728, 13678, 16, 1956, 3031, 24, 4475, 12003, 43, 7864, 17, 5165, 17, 7864, 5219, 1942, 4566, 1920, 17, 3259, 4465, 6149, 1930, 6628, 1920, 3337, 1927, 1920, 3146, 6479, 20403, 14896, 18, 2176, 22970, 2037, 8202, 4365, 28278, 1940, 10173, 25854, 2002, 27061, 1031, 3413, 22, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MKTFNQRSVFFDCNKKREAEHVRRMLVAQGQLLAIRLYAMEDKSLAEIALVFKCP", "metadata": {"id": "A0A9E7E4L6", "cluster": 1404520, "interpro_all": ["IPR013324"], "interpro_used": ["IPR013324"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is grouped in the U11/U12 small nuclear ribonucleoprotein 25kDa protein family, which serves as a component of the U11/U12 di-snRNP complex found in animals, plants, and fungi. This complex binds U12-type pre-mRNAs to simultaneously recognize the 5' splice site and branchpoint sequence during splicing. Furthermore, the protein is a member of the Ubiquitin-like domain superfamily, which is typified by a \u03b2-grasp fold and includes modifiers like ubiquitin, Nedd8, and SUMO that covalently link to target polypeptides. This fold also serves as a protein interaction module in ubiquitin-related domains such as the UBX and Ras-binding domains. Moreover, the protein should contain a SNRNP25, ubiquitin-like domain that adopts a conserved \u03b2-grasp fold to facilitate protein-protein interactions. This domain is characteristically found in RNP25, a component of the U11/U12 small nuclear ribonucleoproteins (snRNPs) essential for the function of the U12-type spliceosome. It is found in Varroa destructor (Honeybee mite). What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 22978, 1009, 19, 22978, 1028, 2858, 4254, 18347, 6657, 2637, 30493, 2213, 3416, 16, 2154, 10634, 1966, 43, 4594, 1927, 1920, 22978, 1009, 19, 22978, 1028, 2137, 17, 11970, 6708, 2796, 2435, 1922, 3555, 16, 4793, 16, 1930, 10520, 18, 2052, 2796, 6876, 22978, 1028, 17, 2601, 2097, 17, 8806, 1942, 7159, 9967, 1920, 25, 11, 10708, 3200, 1930, 6089, 6881, 3244, 2409, 8490, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 6526, 17, 3189, 3418, 13975, 16, 2154, 1977, 2357, 2828, 2007, 43, 161, 17, 22815, 3728, 1930, 5921, 22688, 3189, 6526, 16, 20210, 1025, 16, 1930, 12009, 1988, 16590, 3300, 1942, 2758, 18633, 18, 2052, 3728, 2222, 10634, 1966, 43, 2213, 2835, 9059, 1922, 6526, 17, 2712, 4682, 2427, 1966, 1920, 4803, 1039, 1930, 6520, 17, 2743, 4682, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 11970, 6708, 4198, 16, 6526, 17, 3189, 3418, 1988, 24032, 43, 5305, 161, 17, 22815, 3728, 1942, 6628, 2213, 17, 2213, 3719, 18, 2052, 3418, 1977, 6293, 2169, 2435, 1922, 24767, 4198, 16, 43, 4594, 1927, 1920, 22978, 1009, 19, 22978, 1028, 2858, 4254, 18347, 14070, 12, 11970, 13983, 13, 4415, 1958, 1920, 2347, 1927, 1920, 22978, 1028, 17, 2601, 10708, 4283, 18, 2176, 1977, 2435, 1922, 4953, 1931, 1019, 10455, 2434, 1924, 12, 16400, 5873, 1021, 24688, 13, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MNRDKIMAELKQLDKKMFNLVKSDNLLSGLETSSLERIQQLIDAETGQKIRIFIVRDDGKRLDVVVSPDASILELRRAVELATEDYYLRSTCPDNPCFPKPRISWKQFWGHHTLVAHDVRIDEVDCSIREYNITSGTVLKFAKRLRIRAAATVNQTRDFLTDQPSTSSSQGRRFHAYEAYRASKK", "metadata": {"id": "A0A7M7K199", "cluster": 1478498, "interpro_all": ["IPR039690", "IPR040610", "IPR029071"], "interpro_used": ["IPR039690", "IPR029071", "IPR040610"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should feature a L,D-transpeptidase catalytic domain domain that functions as a bacterial enzyme, likely utilizing peptidoglycan or its precursors as substrates. It features a conserved active site containing histidine and cysteine residues required for catalytic activity. Furthermore, the protein is categorized in the Bacterial Cell Wall Dynamics Protein family, which includes enzymes that hydrolyze peptidoglycan to regulate cell wall integrity during bacterial growth, sporulation, and germination. Some members contribute to pathogenicity by facilitating toxin release, while others may function as ionophores to transport ions across lipid membranes. Furthermore, the protein should have a bacterial-type SH3-like domain that mediates protein-protein interactions by binding proline-rich sequences containing a PXXP motif within a hydrophobic pocket composed of anti-parallel $\\beta$-strands. This prokaryotic homologue may facilitate pathogen invasion or survival by modulating host signaling pathways or binding eukaryotic receptors. It has been characterized in Clostridium sp. CAG:226 and is linked to UniProt keywords Transferase, Peptidoglycan synthesis, and Cell shape.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 54, 16, 46, 17, 22796, 18877, 6804, 3418, 3418, 1988, 4088, 1966, 43, 4543, 4113, 16, 3205, 10232, 24183, 2014, 2496, 10416, 1966, 6249, 18, 2176, 4075, 43, 5305, 3500, 3200, 3165, 13873, 1930, 8666, 4248, 3414, 1958, 6804, 2455, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 4543, 2024, 4821, 5565, 2213, 3416, 16, 2154, 5921, 5038, 1988, 7222, 6931, 24183, 1942, 5741, 2024, 4821, 7996, 2409, 4543, 2905, 16, 23647, 16, 1930, 14609, 18, 2673, 4678, 4672, 1942, 15903, 2007, 12440, 9165, 4012, 16, 2679, 4991, 2278, 2347, 1966, 4755, 14820, 1942, 4860, 6982, 3436, 4486, 5726, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 4543, 17, 2601, 18824, 17, 3189, 3418, 1988, 10412, 2213, 17, 2213, 3719, 2007, 2743, 12958, 17, 5536, 3709, 3165, 43, 15194, 1039, 1034, 5219, 2651, 43, 7919, 10154, 7179, 1927, 2246, 17, 6110, 8, 38, 4666, 8, 17, 13214, 18, 2052, 21545, 17986, 2278, 6628, 7055, 6254, 2014, 3298, 2007, 10871, 4423, 3197, 3873, 2014, 2743, 10825, 4086, 18, 2176, 2258, 2252, 4378, 1922, 21156, 2056, 18, 13415, 30, 19637, 1930, 1977, 4624, 1942, 20709, 11569, 13763, 16, 24183, 4271, 16, 1930, 2024, 5989, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MLKRTVALMLCMLSVFTLLPAFSSAQTLEIDLVNQIITVYEGQIGGRIVLQSLCTTGDAEHQTGAFGYFVAFGQYAQYWTQVVRGIYIHSVMYNSKKLTSMSRPHVAQFIYYNCPPGTTCVINRKKAADPELVKRPPEIPAVIKYDGTPLRTGFSRTKDTTVATLSRGDKVMLPVKTEYILAYPDNANAVKTAYTAKSKTYVYKSMYGSYNGVYGYMRTRYVIKSETVEYPVLEDVAQPSTNGSFPSATPTPTPAPAQSGANASIAAGIIANMRSGVIRLDGTWYYCQVNGQYGYIYSGCIVMKSGWTSKVDYDNTDPNKYSIGTFKLGDMKERGAYRKLGQAVSHGCVRVLLKKEIPAYADYKQPEDNRAYQLAADWCKVRTADGKLGYSTDSAKLATIPGGAQANVEANPKKGWWGANNSGASNGWSTGGGMFNAGKDFPVIGSFSQGTDVT", "metadata": {"id": "R5B1Y4", "cluster": 2517369, "interpro_all": ["IPR052354", "IPR005490", "IPR003646", "IPR038063"], "interpro_used": ["IPR005490", "IPR052354", "IPR003646"], "interpro_unused": ["IPR038063"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein should contain a DUF5723 domain that is found in bacteria and currently lacks a characterized biological function. It is identified in Bacteroidetes bacterium RIFOXYA12_FULL_38_20. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 3066, 5531, 43, 4855, 17968, 10180, 1010, 3418, 1988, 1977, 2435, 1922, 4802, 1930, 5077, 13012, 43, 4378, 3933, 2347, 18, 2176, 1977, 2899, 1922, 26808, 14061, 12424, 7221, 4904, 1028, 41, 4125, 41, 3738, 41, 2036, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MSGLNAQRNNTLYFMESIPQSNLLNPAIQHECKWNIGGLITPILPPVELDFGLNGFAIKELVPIDKSLDSIIHPEHPLFDYDKYYKRLRKMNYITADVNINLLSAGYKWKDDWYFTFNLSEKIFSRTGISKNLLTFIDEGNGKSLMNKDVELAGVLVDVVHYREYAIGASKKLDDKLIVGGKVKFLFGKANIYTRHNDLLMKTFDDPTSNFETVFTTDIEYNMSQPFFSIDTIRYDNENDSVILVDTTYEIEPMDYVMNNKNFGLALDLGATYKLNAKTTLYASILDIGWITFKDNVSTIRSKGQFMFDGVDVVPYLEETDSAYVADLTDSVVDIFFPTLDKGKYKYYLAPKIYLGGNYEINDKFSVQGLYRVELYRSTPMMGLTLSGQANLKKWVSLSLSYAVTNNTFKNLGLGIMLKAWRMQFYFVGDNLLGTWQIIRQDGEFSGVMPYTMRYVSFRFGMNLIFGCPKASQSMFGS", "metadata": {"id": "A0A1F3PLJ8", "cluster": 5411629, "interpro_all": ["IPR043781"], "interpro_used": ["IPR043781"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein is assigned to the Small ribosomal subunit protein mS23 family, which consists of fungal proteins (previously known as S25) that serve as a component of the 37S mitochondrial small ribosomal subunit. It is present in Tulasnella sp. JGI-2019a and is connected to UniProt keyword Mitochondrion, Ribonucleoprotein, and Ribosomal protein.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 2858, 11196, 5903, 2213, 24140, 1010, 3416, 16, 2154, 7543, 1927, 8697, 2697, 12, 3024, 3171, 1966, 5159, 1015, 13, 1988, 7120, 1966, 43, 4594, 1927, 1920, 3191, 1036, 4596, 2858, 11196, 5903, 18, 2176, 1977, 2481, 1922, 29592, 1934, 28690, 1019, 2056, 18, 52, 6121, 17, 14064, 1019, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 30017, 16, 18347, 6657, 16, 1930, 11196, 2213, 18, 3], "output": "MPRRFASQVHLTVSRLLQSNFLAQKPAWYDPVLQYPPIPTTFDTISPNAPRLRLKRQLNVENDAWDRPKAEAIVYLEDRETAAEHEMTGEKWTRLIQRGRNPTPEDAIKYAINLHEHHAVPLSLLRAEHDFSNAFAAQEAEAYGAEFGPTELEKGHELERKSLESKLPWTPVWKLPGNPRPEETWSRGIEYQERAEKGVRPDYHPDFDARRGKTSRPGSSRPESRGMQSRAMGAASRIAASRPPRTPSTSRSVRRQFFKDHPFEAFRARSLVENDLAYKGAVREFRSFLPQSQFSEQYTGSTPLAVAEPPRQPRTLQQPISASRSE", "metadata": {"id": "A0A9P8BG44", "cluster": 5511208, "interpro_all": ["IPR016939"], "interpro_used": ["IPR016939"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein is assigned to the Prefoldin superfamily, which functions as a hexameric molecular chaperone in eukaryotes and archaea to stabilize nascent polypeptide chains. This complex promotes correct protein folding by capturing unfolded substrates and transferring them to the central cavity of chaperonins. In addition, the protein is categorized in the Prefoldin alpha-like family, which comprises the alpha-type subunits of the hexameric prefoldin (PFD) chaperone complex found in archaea and eukaryotes. This complex stabilizes nascent polypeptides, including actin and tubulin, and delivers them to type II chaperonins (CCT) for folding through interactions mediated by a distinctive jellyfish-like coiled-coil structure. It occurs in Entamoeba histolytica HM-1:IMSS-B and has UniProt annotations Coiled coil.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 9328, 2643, 1921, 13975, 16, 2154, 4088, 1966, 43, 25602, 1935, 3272, 14044, 1922, 15021, 1930, 21501, 1942, 13448, 16861, 13022, 7835, 18, 2052, 2796, 7383, 5550, 2213, 10328, 2007, 19249, 17416, 6249, 1930, 21902, 3581, 1942, 1920, 4101, 8568, 1927, 10686, 28756, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 9328, 2643, 1921, 4595, 17, 3189, 3416, 16, 2154, 12936, 1920, 4595, 17, 2601, 6991, 1927, 1920, 25602, 1935, 9328, 2643, 1921, 12, 5099, 1007, 13, 14044, 2796, 2435, 1922, 21501, 1930, 15021, 18, 2052, 2796, 19658, 16861, 18633, 16, 2710, 4718, 1930, 9332, 16, 1930, 30070, 3581, 1942, 2601, 2890, 10686, 28756, 12, 15117, 13, 1958, 10328, 2596, 3719, 3434, 2007, 43, 15308, 8988, 11560, 1012, 14422, 17, 3189, 17524, 17, 9121, 3170, 18, 2176, 5110, 1922, 8496, 1976, 6802, 7972, 2968, 26656, 5833, 17, 21, 30, 23828, 1036, 17, 44, 1930, 2258, 20709, 15010, 17524, 9121, 18, 3], "output": "MTETLTQLHKTRIEMGSLRQVLEIISLRTETAPIPMQVPLAVDSSNEPVALFPVTVDPMKLNTFVVQLSDEYYLEMTAKEVERRLNEKIKNLEAKEKTLLDKIKNTTNEAKHNIEGDVRNITEFITEEEYQQMQQKKRPVQKTKEVDYQKEREYINELASLERELERSGKLEYVEKVGTTEEIEEIPESEFSEMPGVKATIVERKKDKKQPTHEEKPNIPLTKSNDIVERKKEKKNLSQDNNPPKRVSLFKQRMGK", "metadata": {"id": "M3TBU6", "cluster": 6083543, "interpro_all": ["IPR009053", "IPR004127"], "interpro_used": ["IPR009053", "IPR004127"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein should have a Cytochrome c assembly protein domain that facilitates the biogenesis of c-type cytochromes in bacteria, mitochondria, and chloroplasts by mediating heme handling and attachment. This domain interacts directly with heme to execute critical steps such as heme transfer or ligation to the apoprotein, with some members serving as putative cytochrome c synthetases. Furthermore, the protein includes a Cytochrome c-type biogenesis protein CcmF, C-terminal domain that constitutes the C-terminal region of CcmF and facilitates cytochrome c maturation, possibly by delivering reductant to heme bound to the chaperone CcmE. Furthermore, the protein is classified under the Cytochrome c-type biogenesis protein family, which mediates the assembly of periplasmic c-type cytochromes in mitochondria and bacteria. These integral membrane proteins likely guide apocytochromes and haem groups to facilitate their covalent linkage by cytochrome-c-haem lyase. It is identified in Phototrophicales bacterium and is associated with UniProt keywords Cell inner membrane, Cell membrane, and Transmembrane helix.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 9387, 45, 5957, 2213, 3418, 1988, 11374, 1920, 13008, 1927, 45, 17, 2601, 9387, 1036, 1922, 4802, 16, 6489, 16, 1930, 24627, 2007, 10239, 10954, 12361, 1930, 8576, 18, 2052, 3418, 9034, 4103, 1956, 10954, 1942, 29583, 4140, 5983, 2427, 1966, 10954, 3856, 2014, 11102, 1942, 1920, 11466, 22163, 16, 1956, 2673, 4678, 13915, 1966, 6770, 9387, 45, 18185, 1036, 18, 3677, 16, 1920, 2213, 5921, 43, 9387, 45, 17, 2601, 13008, 2213, 25993, 1038, 16, 45, 17, 4262, 3418, 1988, 14879, 1920, 45, 17, 4262, 3031, 1927, 25993, 1038, 1930, 11374, 9387, 45, 7655, 16, 6553, 2007, 16310, 28403, 2031, 1942, 10954, 4124, 1942, 1920, 14044, 25993, 1021, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 9387, 45, 17, 2601, 13008, 2213, 3416, 16, 2154, 10412, 1920, 5957, 1927, 24334, 45, 17, 2601, 9387, 1036, 1922, 6489, 1930, 4802, 18, 2144, 12328, 3260, 2697, 3205, 7857, 26970, 2355, 28726, 1930, 7105, 2671, 1942, 6628, 2310, 13577, 8611, 2007, 9387, 17, 45, 17, 7105, 23928, 18, 2176, 1977, 2899, 1922, 10066, 1997, 2688, 2046, 1918, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 2024, 6671, 3260, 16, 2024, 3260, 16, 1930, 9117, 7864, 18, 3], "output": "MLAEIGVVALGLAFIASMYAIVAAIYGGRTHQERWVISARNAAIATFPLMLIACLVLVIALMNGEYQINYVRATTDPSTPDFYRFTALWGSQEGSLLFWSSIMSLFAMLAMLINWHNERRLMPYVIAYSMATLAFFLFLSLFLENPFERVWLTLGEDGQTRVVDSLFIPPNAFPPTLESLAADARGLNPLLRHFGMIIHPPMLYLGFVGFTIPFAFAMAALASGDLSTNWIKATRRWTLVAWLFLSLGLILGGRWAYDVLGWGGYWGWDPVENAAFLPWLIGTAFLHSVMIQEKRGMLKVWNMFLIIGTFSAVMFGTFATRSGLIESVHSFARSEIGLPMFIFWAGITLVSVSMIIWRWNRGELQDEHHFAGWFSRETMFVLNNIVFIVLAVAIFWGSFGAPIISELFAGEEITLGTDYFMRVTPPLFALMYILMGVAPISAWGATSINRMGRAMVIPLMLTFLTLVLIVLLGTRHLVALVAYGVVSLAGWVAVYETYRGMMARVRTRHENPLVALIALFTRNRRRYGGYIVHLGIVVIGIGIIGSTLFQIERQGLILRGETLQINDEYALRFDDFTVAQANDGRIMDIATVTVIRNNKEIAQLQPRIDQFPSMPMSIAGAHSTLENDFYVLLVPWENISAESAIFKVYINPLVNLVWWGGLILILGTIISVYPNDKIPVRVRSTVQPQLATGAAWGD", "metadata": {"id": "A0A2M8NCI6", "cluster": 9095321, "interpro_all": ["IPR032523", "IPR002541", "IPR003567", "IPR003568"], "interpro_used": ["IPR002541", "IPR032523", "IPR003567"], "interpro_unused": ["IPR003568"]}, "task_type": "autoregressive"} {"instruction": "Generate a complete amino acid sequence given the following functional description of a protein that will be able to perform the described role. The desired function is: The protein is classified under the GDP-fucose protein O-fucosyltransferase family, which functions as a manganese-activated enzyme responsible for adding O-fucose to epidermal growth factor-like (EGF) repeats. These membrane-bound proteins are characterized by six conserved cysteines and a DXD-like motif, and are released via proteolysis. Moreover, the protein is included in the Putative O-fucosyltransferase, plant family, which consists of plant-specific, GDP-fucose dependent enzymes that function as soluble endoplasmic reticulum proteins similar to family 1 glycosyltransferases. These enzymes mediate the O-fucosylation of protein substrates, including the core fucosylation of growth factor receptors. It is present in Oryza sativa subsp. japonica (Rice) and has UniProt annotations Fucose metabolism, Transmembrane helix, and Carbohydrate metabolism.", "tokenized_instruction": [2, 5655, 43, 4080, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 1977, 5947, 2441, 1920, 15217, 17, 15423, 2217, 2213, 57, 17, 15423, 25566, 3416, 16, 2154, 4088, 1966, 43, 19516, 17, 4128, 4113, 5061, 1958, 8013, 57, 17, 15423, 2217, 1942, 9844, 2905, 2991, 17, 3189, 12, 4451, 13, 9569, 18, 2144, 3260, 17, 4124, 2697, 2032, 4378, 2007, 3798, 5305, 22446, 1930, 43, 14852, 1007, 17, 3189, 5219, 16, 1930, 2032, 6988, 3454, 15439, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 6770, 57, 17, 15423, 25566, 16, 4496, 3416, 16, 2154, 7543, 1927, 4496, 17, 2487, 16, 15217, 17, 15423, 2217, 3100, 5038, 1988, 2347, 1966, 6622, 13355, 12279, 2697, 2551, 1942, 3416, 21, 20067, 18580, 18, 2144, 5038, 8265, 1920, 57, 17, 15423, 21385, 1927, 2213, 6249, 16, 2710, 1920, 4728, 15423, 21385, 1927, 2905, 2991, 4086, 18, 2176, 1977, 2481, 1922, 19745, 1019, 22939, 19615, 18, 27096, 12, 8674, 13, 1930, 2258, 20709, 15010, 15423, 2217, 4714, 16, 9117, 7864, 16, 1930, 10590, 4714, 18, 3], "output": "GGGAMARSRPRVWLLAGCSAVLLWAFVGQLVAVGRLLALFGLAGDAEPSPPPTALPPRRVYKSNGYLKVSCNGGLNQMRSEICDMVAVARLLNLTMVVPELDKRSFWADQSNFEDIFDVKHFIDTLRDEVHIVKQLPKRFGPEDSNNILNMPPVSWSDEKYYLHQILPLFSKYSVIHFNKTDARLANNGISTQLQLLRCRVNFHALKFTPQIEALGNKLVQKLQAKGSFAALHLRYEMDMLAFSGCNHGLSQEEAEELKRMRYAYPWWREKEIDSQAKRLQGLCPLTPEETSFILKALGFQKDTLIYIAAGEIYGGEKRLEPLQAAFPKLVRKETLLDLEALRQFQNHSSQMAALDFIVSTASDIFIPTYDGNMAKLVEGHRRFLGFRRSVLLDRQKLVGFIDLYNNKTISWNNFASSVQETHRNRVVQPSCRQKLENKPKEEDYFYANPHECLANSRFCSRTKDAISVR", "metadata": {"id": "Q0DUS7", "cluster": 11318734, "interpro_all": ["IPR024709", "IPR019378"], "interpro_used": ["IPR019378", "IPR024709"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Function:\nThe protein is classified under the Rossmann-like alpha/beta/alpha sandwich fold superfamily, which adopts a characteristic three-layer architecture serving as a scaffold for diverse enzymatic activities, particularly nucleotide binding and transfer. This group includes the catalytic domains of Class I aminoacyl-tRNA synthetases and nucleotidylyl transferases, alongside ATP pyrophosphatases, electron transfer flavoproteins, and DNA photolyases. In addition, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein is associated with the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is present in Alona affinis and exhibits UniProt keyword tags ATP-binding.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 18215, 8890, 17, 3189, 4595, 19, 4666, 19, 4595, 18038, 3728, 13975, 16, 2154, 24032, 43, 6293, 2559, 17, 4757, 9335, 13915, 1966, 43, 7281, 1958, 6445, 8145, 4209, 16, 4443, 5489, 2743, 1930, 3856, 18, 2052, 2210, 5921, 1920, 6804, 4682, 1927, 2921, 51, 3835, 14645, 17, 10089, 18185, 1036, 1930, 2797, 4090, 25671, 13763, 1036, 16, 17764, 4498, 20661, 2609, 18135, 16, 4995, 3856, 7732, 14070, 16, 1930, 2678, 10066, 1954, 2319, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2481, 1922, 1969, 12502, 14819, 1937, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MANSTGFLFLQLSSIRIILSDFRDSLLGLSAKRRDPIKTSQKVDMVKSQVLVIDGLEENSSDFEQTEAIPDRFKSHVVLGGTFDRLHTGHKILLSAATDGSMIQTKKLWELIEPCQSPFPXXIEDTQATSGEESKVSSSSLRKNKPFVIGLSGGIASGKTTICNRLQKGTKCYEEMVQYFGDSILNEGQEIDRKSMVWPEIRRLYTEEIDRMKRDEGFEGVIILDACDDVWVSIVPPSEAIKRITERFSSIWEPDVTAAQVQKAWQYVQNFIAKSTNILSKIVASAVQKVGKTLLDAILTLNNQEHILPNSLANTDAAVPNLAGDGKMYQVLRCTERLTIGVXXXXXXXXXLRQEKSLSTLDIHPISLRLLGSHLKPPKGKKGLGARIISCDHLGHAAYKLGPIVFSDKVHLNKLNAILLEAGWDADDHLSAEQAENRVKSQLSNSQRVSKANVV", "metadata": {"id": "A0A9N6WWI6", "cluster": 17350093, "interpro_all": ["IPR001977", "IPR027417", "IPR014729"], "interpro_used": ["IPR014729", "IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein incorporates a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. In addition, the protein possesses a FtsK domain that functions as an ATP-dependent DNA translocase to facilitate chromosome segregation and intercellular DNA transfer. It utilizes a conserved ATP-binding P-loop motif to couple ATP hydrolysis to movement along the DNA axis. This domain is widely distributed in bacteria and archaea, appearing in cell division proteins like SpoIIIE and conjugative Tra proteins. Furthermore, the protein should include a Sigma-54 interaction domain ATP-binding site 1 binding site that functions as an atypical P-loop motif to facilitate ATPase activity. This site drives the conformational changes required for bacterial regulatory proteins to interact with the alternative sigma-54 factor during transcriptional activation. It originates from Candidatus Saccharibacteria bacterium. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 19683, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 17022, 1040, 3418, 1988, 4088, 1966, 1925, 4498, 17, 3100, 2678, 12930, 2051, 1942, 6628, 5597, 12707, 1930, 15685, 2678, 3856, 18, 2176, 18127, 43, 5305, 4498, 17, 2743, 58, 17, 5881, 5219, 1942, 15116, 4498, 9128, 1942, 5829, 4231, 1920, 2678, 5432, 18, 2052, 3418, 1977, 5673, 6533, 1922, 4802, 1930, 21501, 16, 16905, 1922, 2024, 8451, 2697, 3189, 18055, 10831, 1021, 1930, 5225, 2178, 3390, 2697, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 5139, 17, 4584, 2835, 3418, 4498, 17, 2743, 3200, 21, 2743, 3200, 1988, 4088, 1966, 1925, 10834, 58, 17, 5881, 5219, 1942, 6628, 9444, 2455, 18, 2052, 3200, 15435, 1920, 8523, 2840, 3414, 1958, 4543, 4948, 2697, 1942, 6310, 1956, 1920, 5012, 5139, 17, 4584, 2991, 2409, 5224, 2936, 18, 2176, 22970, 2037, 14550, 1031, 1957, 14175, 26845, 2422, 2126, 14061, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MERITLSYSAIMCFLNNQIQFKKRYIAKVYDEPSSPALVVGKAMHKMIEERLKGQSFEIAIQSGLQEIENVADYEIDYGKTGSREKIIDQYQKLSTIVINELPTYDDILAIEDRVECELLIRNKKIPMKGYIDVVRDFGDTLEIIDWKSATSYSDEDTENWAYLIQSWIYVQLIEFKYKKPVSRMVFKEVKKTINRDGMPQIKDYVLDRHSIEEANDVIGRVVKAVSDYVDNPDATYFPNPRDMMNGAQSMHIVAQMEGISVRTVHTTERHKKFAPVNTVVAEDIASDDGSEIDLIKGKLVEFGIGVRIEKVIKSNTVDTYMFRPNRGVKMSKIATMGDDLSLALGSDAVRVIAPIYGTKTIGIEVPHEQSFPTFDGKASSHQIPIGVDTMNNVIYDDIAKMPHMLIGGQTGSGKSVFIRNIIQSLNNCEVDIIDMKGLDFDDLGKNIISEVGESLELIRHLVELMDNRYKNKRANAKRRVLIIDEYADLIMQTGKEIRTRIDGYKKDGEPKIKQYTYDTRNELETNLARILQKGRSANINVIIATQRPSADIVAPIIKANCPVKACLRVATAKNSEIILDEAGGERLLGKGDMLYLGSGMVKPVRVQCFSPIEKGGSK", "metadata": {"id": "A0A7W4HT60", "cluster": 17432578, "interpro_all": ["IPR003593", "IPR050206", "IPR041027", "IPR002543", "IPR027417", "IPR011604", "IPR038726", "IPR011335", "IPR025662"], "interpro_used": ["IPR003593", "IPR002543", "IPR025662"], "interpro_unused": ["IPR038726", "IPR011335", "IPR027417", "IPR050206", "IPR041027", "IPR011604"]}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein is classified under the Phytanoyl-CoA dioxygenase-like family, which encompasses eukaryotic peroxisomal enzymes that catalyze the alpha-oxidation of phytanic acid to prevent toxic accumulation associated with Refsum's disease. Additionally, this family includes bacterial dioxygenases involved in phosphonate degradation and the biosynthesis of the osmoprotectant 5-hydroxyectoine. It occurs in Chlamydiales bacterium SCGC AB-751-O23.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 1977, 5947, 2441, 1920, 9321, 28271, 17, 10027, 23652, 10465, 2432, 2051, 17, 3189, 3416, 16, 2154, 21569, 10825, 28765, 5038, 1988, 18170, 1920, 4595, 17, 6638, 1927, 9321, 19510, 2687, 1942, 4625, 6161, 4858, 2458, 1956, 17558, 1989, 11, 61, 2573, 18, 4950, 16, 2052, 3416, 5921, 4543, 23652, 10465, 2432, 2319, 3286, 1922, 8078, 5791, 1021, 4877, 1930, 1920, 8132, 1927, 1920, 9405, 18018, 2341, 2031, 25, 17, 8275, 2089, 9024, 1021, 18, 2176, 5110, 1922, 21079, 2612, 14061, 2160, 5813, 2186, 17, 4089, 1009, 17, 8259, 1010, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MSSILNIPQSFTGSIEGGICLESGYLILRGVFESKSDDLLKSCKRMYLRGSQVVFRKEEGISPSILRIVGCGSYNAFSALLSSRELEHIICQFHPKSPGDKVFFPRHVVALDEMTDQNGPLVIEPLSHLGPSQSSYHYSKANQSDSSRMTLLTGYCPNGSFQTQPAPWKKEFPDSSSSSTDRLLVNAEAKKAFFFEEVIDEISKEAYSCKEDEQIIDDDLLQFSRSKEIVKDISNRRLFDPDWQEVGQDCSFIIGPVTLNMKAGDILFMHPELVSGANHANYPGNCSNELISVN", "metadata": {"id": "A0A212KQT4", "cluster": 18719230, "interpro_all": ["IPR008775"], "interpro_used": ["IPR008775"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a polypeptide chain that performs the following role: The protein can be placed in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is identified in Omnitrophica WOR_2 bacterium SM23_72 and is annotated with UniProt keywords Cytoplasm and rRNA processing. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 2899, 1922, 18825, 3032, 24888, 3375, 4315, 41, 22, 14061, 2426, 4553, 41, 4395, 1930, 1977, 10633, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MFNSEIQDLEFLVDTRYHTPVMLSEVLNYLNLGPGKIVVDATIGTGGHSEAMLKRILPGGRLIGIDRDQESLTVARERLADYSQFCDFVHANFIDMDKVLTDLNIKKADAILFDLGVSSFQLEDPKRGFSFQHEGPLDMRMDRDSYISAYDLLNNLNEEEISTLLWNFGQERWHSRIARLLIKERRLHPIVTTSQLSNIVVRSIPHRYSHRHFRIHPATRTFQAVRIAVNRELETLESAIQKAITVLSKKARIAVISFHSLEDRVVKLSFRQAYAQGLIHIKTPKPLTANRLEVNTNPSSRSSKLRVAERV", "metadata": {"id": "A0A0S8IKU1", "cluster": 20327421, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein can be placed in the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. It has been detected in Formosa sediminum.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2176, 2258, 2252, 3330, 1922, 2386, 5360, 6276, 1980, 28658, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MRKILQIINTNLGSENVIKQNFSGSVPLLDKFNNALKLSGGIITPSDDFLVIFKLDSGLMALCREENTASNVFKDSATSFSWDTIFHVKNNSGHHDVNINRFGTSNIEAAKFNEEDYESGVNALDEFSKYYNINDLDLDDSSFYTINNYINLYKERGEIESYTYELKGELLFKQKVKTKKEEVYTKLKKKFLKIPYQERKLVFVSEDIYATTSNDIVVLNEVYICHPFKQDLYLPLRSYTEILFLERVEEFIKIQNQQYDFNPTQAPILPNSLVWYHSDVNWSQMSSDDLKKLNEELKLVLPKAGEKFNKKSEALDKLPSSKEKLENPTPINSNLKDNDYKINLEIDVSERKILNRKIKKLGITKADALAIEDEVLLSNYSENEILNRYALKFKVSTKRQKEIDSKYLDYIQSDNGLGLDENEFIHELSEIKDEKTVKVEHNYYRSTIIDRVELLENTTEDSFYFFRSILKMLSEIIVYKNAYIDKHAELQSTIERLYFNKTFGLRSMGRLDDALDKYIPAINCFAISEENYENQGYKKGKKNSLPISINFLEGHPRNIYLVQGLGATQLELTTGPNDDGTQKLVDLRMYTGIISHSELISSIATSFNKTSFKTIEWIFKIHFKYKEEVLFMIEDDGIKLYIEELKDIVEDGKISDKERK", "metadata": {"id": "A0A516GUH3", "cluster": 22878828, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should include a Zinc finger, CCCH-type domain that mediates RNA-binding and protein-protein interactions, playing a critical role in post-transcriptional regulation processes such as mRNA decay and splicing. Often interacting with the 3'-untranslated regions of mRNA, this motif is characterized by a C-x8-C-x5-C-x3-H sequence that stabilizes the fold for specific target recognition. It is native to Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (Thermochaetoides thermophila) and is classified with UniProt keywords Metal-binding, Signal, and Zinc-finger. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 3066, 3951, 43, 7997, 8497, 16, 15526, 1023, 17, 2601, 3418, 1988, 10412, 3146, 17, 2743, 1930, 2213, 17, 2213, 3719, 16, 14797, 43, 4140, 2770, 1922, 2753, 17, 5224, 3640, 4028, 2427, 1966, 3616, 9310, 1930, 8490, 18, 3868, 8615, 1956, 1920, 23, 11, 17, 19522, 3451, 1927, 3616, 16, 2052, 5219, 1977, 4378, 2007, 43, 45, 17, 66, 1025, 17, 45, 17, 66, 1015, 17, 45, 17, 66, 1010, 17, 50, 3244, 1988, 19658, 1920, 3728, 1958, 2487, 2758, 5708, 18, 2176, 1977, 6196, 1942, 13297, 23345, 2457, 7967, 24888, 5277, 1035, 12, 3943, 10964, 14094, 1015, 19, 16341, 12851, 18, 2761, 19, 2042, 1033, 24302, 9948, 1026, 13, 12, 7967, 25588, 19446, 3726, 7967, 24888, 5148, 13, 1930, 1977, 5947, 1956, 20709, 11569, 6048, 17, 2743, 16, 2733, 16, 1930, 7997, 17, 8497, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MKFFTALLALAITALAAPHNPNNNADISARNGGGETCTFGTYRCTTPNTGIEICNVTNKWELVGDCPQGTECTNLAQNGYELPFCTTKPKTIDSRDPGHHGGSGSSGGWWPGSWCPTPGRYDCLGWGAIQVCDVTHISRFVGTCPAGSHCAYLHGIPYCVAN", "metadata": {"id": "G0S2U2", "cluster": 23471463, "interpro_all": ["IPR000571"], "interpro_used": ["IPR000571"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein should have a PfaD-like, TIM-barrel domain that participates in the biosynthesis of omega-3 polyunsaturated fatty acids and polyketides. It constitutes the C-terminal region of polyunsaturated fatty acid synthase subunits and related biosynthesis proteins, often within high-pressure or cold-adapted bacteria. Moreover, the protein incorporates a Acyl transferase domain that functions as a catalytic unit within polyketide synthase (PKS) and fatty acid synthase complexes to facilitate the transfer of acyl groups. It plays a critical role in the biosynthesis of fatty acids and secondary metabolites, such as patulin and conidial pigments, in both bacteria and eukaryotes. In addition, the protein features a [Acyl-carrier-protein] S-malonyltransferase-like, inserted helical domain that functions as the substrate-binding component of the enoyl reductase (ER) region in bacterial polyunsaturated fatty acid (PUFA) synthases. This $\\alpha$-helical insertion is typically found in proteins such as *Bacillus velezensis* FabD, where it contributes to the biosynthesis of antibiotics like difficidin A. It is identified in Ruminococcus flavefaciens and exhibits UniProt keyword tags Acyltransferase.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 3066, 2162, 43, 17340, 1007, 17, 3189, 16, 2267, 17, 19560, 3418, 1988, 17241, 1922, 1920, 8132, 1927, 15142, 17, 23, 22736, 5934, 4576, 1930, 4286, 18540, 3726, 18, 2176, 14879, 1920, 45, 17, 4262, 3031, 1927, 22736, 5934, 2687, 8921, 6991, 1930, 2712, 8132, 2697, 16, 3868, 2651, 2149, 17, 3772, 2014, 6685, 17, 8461, 4802, 18, 3950, 16, 1920, 2213, 19683, 43, 11337, 13763, 3418, 1988, 4088, 1966, 43, 6804, 5344, 2651, 4286, 18540, 2261, 8921, 12, 26137, 13, 1930, 5934, 2687, 8921, 5048, 1942, 6628, 1920, 3856, 1927, 11337, 2671, 18, 2176, 5705, 43, 4140, 2770, 1922, 1920, 8132, 1927, 5934, 4576, 1930, 4067, 6926, 16, 2427, 1966, 2917, 3392, 1930, 20071, 1024, 23756, 16, 1922, 2321, 4802, 1930, 15021, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 37, 11337, 17, 9685, 17, 2213, 39, 61, 17, 3054, 12831, 9961, 17, 3189, 16, 9103, 11514, 3418, 1988, 4088, 1966, 1920, 4510, 17, 2743, 4594, 1927, 1920, 2066, 10921, 11386, 12, 2668, 13, 3031, 1922, 4543, 22736, 5934, 2687, 12, 18282, 13, 8921, 1036, 18, 2052, 8, 38, 4595, 8, 17, 11514, 7413, 1977, 5745, 2435, 1922, 2697, 2427, 1966, 14, 14587, 6217, 11788, 8134, 14, 6914, 1007, 16, 2597, 2176, 7624, 1942, 1920, 8132, 1927, 7560, 3189, 4130, 7650, 43, 18, 2176, 1977, 2899, 1922, 22631, 8256, 7732, 7726, 25018, 1930, 9826, 20709, 11121, 2538, 14392, 11337, 9961, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MYKSIVFMFAGQGTHYYHMGADLFSKDLVFRQNMDDLTDLGTTHPAIFMTEYSLAQVMRSKGVEPDYVMGCSLGEIVKHAQTVQQTVEYGRMISVFADKSFYYENNELKLNCELAGVNYFLKQKGVIFQELQVSYPFHSSMCMRSRDAMKQLNGTISVGVPKIPVIPVKTMQVKKAFEAAEKTGPKQYVDLCFTGTMANFIRYNERRDTASFKNNYEKIKLNMVEKENYTERNRKMSDTLIYAFPGQGSQKSIRDLCLNDSEGNLNKTNYTQPALYVVNALSYLKKIKETGRKPDFVLGHRGQLMSEIKGGAMAAVIGLDEETISNILTENGLTDLQAAEQLYMDAGARKYVVLNVSGAFHHGKYMKAAQDKFAEYLLRLKETLREQMSHGVRWVESIRYLLAENEPVFEQIGPGDTVYSLMMMIDVPVEAVNVQGPETGTKKGLTASELGNMAFKQELGLKYAYLQMVIRLANAGMLGFLGTGGQSFDKIREGIKLIRSSVTDGAFGVNFLFDPDDMRKQLSITMPLVYYKAKGLSVDQTGNIVRKNKIFAKISRPEVAVEMGKITKLQADIAASLPIADAITVEADSGGHTDQGVADRIYIGAAGGIGTPEAMLAMFMLGADYVLTGSLNQCTVEADTSDAVGAKVQVVKKGGFFHARANKLYSLYCNNESLEELDETTRKNLVYNKVKQHYDQDIIRKADNNPKYRMSLIFRWYFHNATVSAISGDMDNKLESWKNRHVDSIGIFLMEGTAMLLEKMIGSYSKLRLDDIVRKECGFSVIDRLYDEEHRKTALAVAGAVSAEDALRFVISGNFIVSAAQDKTADVTASCLTGEITNSIDFEHMLDITDIVAMASIMRDFSEKGMGEELFDEFPEYVRRADEVLGYSLGEYDALFAAGAFSFEDGLRLVKIIANINSPVQVILSGKRDDIIDKMTFNKLQIPVISNYTARPYDDKRKCEPLSEEERKANILDGGGMYKGIASPELVELFIREDVRIIEAAAFMEAFMSPAPQKLLNELLALFPAIKKICGNCMKKYNYAKDILQSIGVQDTGYAPAGDMFEYESKYFKCSFDEVNFQIHCGPALGAFNECVRGTE", "metadata": {"id": "A0A315Y185", "cluster": 23574514, "interpro_all": ["IPR001227", "IPR014043", "IPR016035", "IPR013785", "IPR049489", "IPR050858", "IPR004410", "IPR016036", "IPR014179"], "interpro_used": ["IPR014179", "IPR014043", "IPR049489"], "interpro_unused": ["IPR050858", "IPR016035", "IPR004410", "IPR016036", "IPR013785", "IPR001227"]}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein contains a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Moreover, the protein should include a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein falls within the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is native to Candidatus Lambdaproteobacteria bacterium and is classified with UniProt keywords Isoprene biosynthesis and Transferase. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 6196, 1942, 14550, 1031, 1957, 18279, 9218, 1021, 10296, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MKIRTPAKINPQLYILSQCDDGFHELYMHMVPVSLFDTLSFSQNNKQELKFRMNGASFSATPEENLVVRAIRSFEKAGGITASLDVVLEKTIPSGAGLGGGSGNTAGTLKVLNHIYRESSSAEGLLPPETLAELALELGSDVPFFLEPTPSEIRGRGEKINPLQEYPKFYVVIIKPPLSIPTQEAYNNCQPEVHTTFPEVKSFDDIKNHLYNQFETSLLAQYPVLSELKSLLLQNGAFGALVSGSGSAVFGVFNNKKQQYHAFINLSCLHIGKIFSCETLATHRYY", "metadata": {"id": "A0A7Z9I4G5", "cluster": 26356113, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR014721", "IPR036554", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein should feature a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Also, the protein possesses a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Furthermore, the protein carries a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. It is expressed in Pseudomonadota bacterium and is annotated with UniProt keywords DNA repair, DNA excision, and SOS response.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 3066, 5961, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2222, 16, 1920, 2213, 14465, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 3677, 16, 1920, 2213, 16252, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2176, 1977, 3198, 1922, 11520, 3947, 12595, 3857, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 2678, 5059, 16, 2678, 10940, 16, 1930, 17668, 2644, 18, 3], "output": "MPFTLRSEFSPKGDQPAAIESLVRGFAEGAPMQTLLGITGSGKTFTIANLIQRLQKPTYAEMRDLFPENAVAFFVSYYDYYQPEAYIPNTDTYIEKDAIINDQIDRMRHHATRIGSAETYSGLLIEINKGEELRRDELLRRLVDIQYERNDTDFHRGTFRVRGDVEAISEVDPLRGKILSSLDRYAVYPGSHYVTPRQQLQRAIAAIRDELRERLDYFDKNGRFVEKQFVQGIENYSRHLSGRAPGEPPPTLIDYFPNDFLLIIDESHQTIPQLGAMYRGDRSRKETLVEYYMKRVVFVSATPGDYELAHSNGRVVEQLIRPTGLLDPDVSVRPVAGQVDDLYAEIRKRVAANERVLVLHSDIDTLERVEILRDLRAGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSPRSLIQTIGRAARRTLQIEYNTKHGITPETVKRAIFDINPASGQSDYYAIPRSPVRAGEAASGAVLPAAEQFETAARLRDEIRRLQGLTGGAEAEPPRSSTGARAPARPARRGAAAGRRRRLIIAPNKTLSAQLSLLSREDVIIVASVSCIYGVEIFPAYEESIAIRVEFFGDEVRLAQRTLYDLEMLEQMGGFRLPSALDNRPLKFEEFEKTTLTKRMAEELTEYYAELGIRVRYNANGHVIMYADRITDAMKVAIDETRRRTVDLAERIQALRQEMFSAAENL", "metadata": {"id": "A0A2W4M0N8", "cluster": 26800543, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001943", "IPR014001", "IPR001650"], "interpro_unused": ["IPR024759", "IPR036876", "IPR041471", "IPR004807", "IPR006935", "IPR027417"]}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein possesses a Amino acid adenylation domain that functions as the specific recognition and activation module within non-ribosomal peptide synthetases (NRPS) by catalyzing the ATP-dependent conversion of a selected amino acid into an aminoacyl-adenylate intermediate. This activated substrate is subsequently transferred as a thioester to the phosphopantetheine cofactor of a downstream thiolation domain to facilitate peptide chain elongation. Moreover, the protein carries a Phosphopantetheine binding ACP domain that serves as a central carrier for acyl intermediates during the synthesis of fatty acids, polyketides, and non-ribosomal peptides. It forms a four-helical bundle and covalently attaches a phosphopantetheine prosthetic group to a conserved serine residue, utilizing it as a 'swinging arm' to shuttle activated substrates between enzymatic active sites. Furthermore, the protein incorporates a AMP-binding conserved site that catalyzes the ATP-dependent activation of substrates via the formation of an acyl-AMP intermediate. This glycine-rich motif is essential for the function of luciferases, acyl-CoA ligases, and non-ribosomal peptide synthetases involved in the biosynthesis of secondary metabolites like antibiotics and siderophores. It has been characterized in Planctomycetales bacterium. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 3835, 2687, 4670, 3017, 3418, 1988, 4088, 1966, 1920, 2487, 5708, 1930, 2936, 9059, 2651, 2447, 17, 11196, 4207, 18185, 1036, 12, 5214, 2523, 13, 2007, 29601, 1920, 4498, 17, 3100, 7309, 1927, 43, 3790, 3835, 2687, 2460, 1925, 3835, 14645, 17, 23052, 6129, 18, 2052, 4128, 4510, 1977, 5326, 6311, 1966, 43, 30215, 1942, 1920, 8078, 6528, 2057, 20536, 2053, 15155, 1927, 43, 5863, 13914, 1943, 3418, 1942, 6628, 4207, 4659, 9971, 18, 3950, 16, 1920, 2213, 16252, 43, 8078, 6528, 2057, 20536, 2053, 2743, 18543, 3418, 1988, 10634, 1966, 43, 4101, 9685, 1958, 11337, 12386, 2409, 1920, 4271, 1927, 5934, 4576, 16, 4286, 18540, 3726, 16, 1930, 2447, 17, 11196, 5320, 18, 2176, 4952, 43, 3006, 17, 11514, 14142, 1930, 16590, 5823, 1918, 43, 8078, 6528, 2057, 20536, 2053, 19019, 2210, 1942, 43, 5305, 8468, 6181, 16, 10232, 2176, 1966, 43, 11, 24775, 1941, 6011, 11, 1942, 23814, 4128, 6249, 2192, 8145, 3500, 3402, 18, 3677, 16, 1920, 2213, 19683, 43, 3681, 17, 2743, 5305, 3200, 1988, 17097, 1920, 4498, 17, 3100, 2936, 1927, 6249, 3454, 1920, 3337, 1927, 1925, 11337, 17, 3681, 6129, 18, 2052, 10646, 17, 5536, 5219, 1977, 4415, 1958, 1920, 2347, 1927, 7362, 1036, 16, 11337, 17, 10027, 22423, 16, 1930, 2447, 17, 11196, 4207, 18185, 1036, 3286, 1922, 1920, 8132, 1927, 4067, 6926, 3189, 7560, 1930, 22940, 14820, 18, 2176, 2258, 2252, 4378, 1922, 4720, 2341, 13386, 3949, 1918, 14061, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MTRRQSHSNSVESTANLATNQRLIWLGQQLHPDTPLYEVPYLYTFHASIDPTRFVDAMKQLVSEHPVLRIVATDDSWTAPRIRPTRLTECAVVDFSNQNKPHDAADDFVNRRLRSRFRPTESLFEATLIRISEGHWKLLLVIHHALTDASAGRAILGRLSQIYLSELNHSGEIIHDPYAAYLESESALLQNNADEKQRVWFQSRSIPAERFKFYSSIDTALSCHQTREIVNLDDDENRAISVLTARQPFRQITDLLSHFNIFSSALIAWLSRLETRSIARIGATTHGRTNQAFRNTPGLFMQVLPFQVAIDADETFESLSRKVAVESMGFLANGRPGMMSAATQRAFDVAINVIDLQVDDVGDIPTSLEWLHNGYGDPERILTVSAHQNRSGKWQLLFDFSDDAFSATDRIRSIEHFRKTLAAMHAHPQAPLAGYDLLTETDQAFLSNHSGSTSFPAKTNLWSRFEAICSEYEDRIAVQGPRLQISYGALRNLALQLAGEIETWNCDDVVPVICRRDEKAIIAILGVLASGRCYLVVDAANPRDRRDQMLRQSGVHIALDATSDSITRHEIEPYEERASRDDHCDLVKGACYVLFTSGSTGQPNGVVVGHEAIWNLVKEFESLCPLTSEARCSWWTNIGFDVAMYEIWSALLFGRTLCLASEECRIDAESMLEWLQKERIESAYLPPFFLEMADRKLSRGEQLDLQRLLVGVEPIPQKILASIARKIPSLNLVNGYGPTEATVCATLHRIDRTHDADGLASIGAPIAGNQIRIADSNGRQVPPGVAGELWIGGAGLARGYLGNPELTARRFITVDSVCGPQRWYRTGDVVRQIHDGSLLFVGRVDEQIKIAGMRVEPAEIASAIRQCVGVTDCFVLPNNRPGEPTELIAFVESNSALDFSHVRTQLRQRLPGAMVPKRFVLQNRLPRNTNGKVDRAALRLMTADQLSDLDDSPQLSPEDLPQTPVQYTLLELARGILGVPVLGVNHDLFESGASSLDAMSLVSKANEVGVPIQVHDVLTQRTVGNLAAKANRSETNSSNERVRPETPSFTWGQRAIWLFCQQHPKSPAYHFQTVWSCNGRLDFERIADCFYRISMRHPALRTSVEVINGAPVPVVHDSLPPFVQRFDRAVTNDELVTEGRRTFDLSADSPIRIHVVQPPDGRDQIAITFHHIAVDQQSVSQIMREFAAFYRADGYETAAATELPRNPRHTNRSNIDNSDRWWQDRLIGHDQSVELPFDFDSVNESHDGELVEFQLPDELCQSLRDTAAKCGVTLGTLLLGSYACLISRYSGSERFTIGVPVSMRDSSRQDPPVGYAIESLPFTVCVDGDQPLERWLVALHDDFSAMLKHRWTSWDQLKQNLGPLFNTMFAFRDEPNQISLVDDLTLSPKTTNLGIAKFDLTWFVAESKSQILCAVEYRDSRFRRETIDLMIEHWISMLKSIARSPGQQIRELDFRTELDHFAGDALRGNRESGPRRTQWRCITELIGAKAKELPDQEAVRFDGRSLTYRQLIEKTDQLSASLAQLGVKQNVPVAVCMPRSMEMLIGILAILKSGGAYVPFDPDQPLARLAKSARSIGVEIALGWDDEISSIFPHMIDPRMIDPRIQLGSQINAPPSKEVDSASLAYILQTSGSTGEPKYVEVSRQSLLDSTMDRHMYYDLRPTRFLMVSPIWFDSSIAGVFWTLSCGGTLVIPTDDQLQDIQSIENLINGSEVTTTLMLPTYYQILLAHANPAKLQSLQCVIVAGEACARSVVKSHFRIVPRSQLFNEYGPTEASVWATVTELHGHEQFIPIGRSVSGTPVHLRGRKGEKIPVGGVGEIVIGGSRLANGYRNDLQQTSLRFVSNDDTKHPGRCYRTGDLARLLRDGSLVHVGRIDDQLKVNGMRVDPAEIEAALLEIDGILDAGVALVDRPHDIEKASTEEVIASLRAMPSQDVERLLESAERIGQHRNETVSTGNGHARVSIELIDPGYLKTPRSRQRKWLLDRALQETISDLEALNMVASRMVPGSDSPHLPRDISIDQLTPQEIMEDWQTPLMKSMADWVCQSGGDVLEIGFGRGVAAT", "metadata": {"id": "A0A954Q1E3", "cluster": 27646550, "interpro_all": ["IPR010071", "IPR036736", "IPR045851", "IPR020845", "IPR000873", "IPR042099", "IPR023213", "IPR001242", "IPR009081", "IPR029063"], "interpro_used": ["IPR010071", "IPR009081", "IPR020845"], "interpro_unused": ["IPR001242", "IPR000873", "IPR036736", "IPR029063", "IPR023213", "IPR045851", "IPR042099"]}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein can be placed in the Serine/Threonine Kinases and Pseudokinases family, which comprises both active enzymes regulating signal transduction and stress responses, and catalytically inactive pseudokinases essential for necroptosis. These proteins are often activated by phosphorylation or inositol phosphate binding, leading to diverse outcomes ranging from potassium homeostasis and gene expression modulation to membrane permeabilization during programmed cell death. Additionally, some members participate in defense mechanisms and the maintenance of nuclear envelope integrity in response to viral infection. Furthermore, the protein features a Protein kinase ATP binding site that binds ATP to facilitate the transfer of the gamma phosphate to protein substrates during phosphorylation. Located in the N-terminal catalytic domain, this conserved site utilizes a specific lysine residue within a glycine-rich stretch to anchor the nucleotide. This interaction is essential for the activity of serine/threonine, tyrosine, and dual-specificity kinases in regulating processes such as cell division and proliferation. Additionally, the protein possesses a Protein kinase domain that functions as the conserved catalytic core responsible for transferring the gamma phosphate from ATP to serine, threonine, or tyrosine residues on substrate proteins. This phosphorylation event induces conformational changes that regulate diverse cellular processes, such as proliferation, differentiation, and apoptosis. It is found in Ursus americanus (American black bear) (Euarctos americanus) and is connected to UniProt keyword Cytoplasm, Transferase, and Necrosis.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8468, 19, 13143, 7784, 1930, 11520, 25545, 1036, 3416, 16, 2154, 12936, 2321, 3500, 5038, 6773, 2733, 8201, 1930, 3071, 3387, 16, 1930, 21446, 9078, 11520, 25545, 1036, 4415, 1958, 29570, 18, 2144, 2697, 2032, 3868, 4128, 2007, 4050, 2014, 16246, 5413, 2743, 16, 4523, 1942, 6445, 3685, 6485, 2037, 9057, 7622, 1930, 2359, 2294, 7145, 1942, 3260, 22271, 2409, 13839, 2024, 3539, 18, 4950, 16, 2673, 4678, 7352, 1922, 9720, 3531, 1930, 1920, 6291, 1927, 4254, 11262, 7996, 1922, 2644, 1942, 4324, 2909, 18, 3677, 16, 1920, 2213, 4075, 43, 2213, 4016, 4498, 2743, 3200, 1988, 6876, 4498, 1942, 6628, 1920, 3856, 1927, 1920, 7034, 5413, 1942, 2213, 6249, 2409, 4050, 18, 4810, 1922, 1920, 56, 17, 4262, 6804, 3418, 16, 2052, 5305, 3200, 18127, 43, 2487, 9082, 6181, 2651, 43, 10646, 17, 5536, 9064, 1942, 13333, 1920, 5489, 18, 2052, 2835, 1977, 4415, 1958, 1920, 2455, 1927, 8468, 19, 13143, 16, 6941, 16, 1930, 7064, 17, 4896, 7784, 1922, 6773, 4028, 2427, 1966, 2024, 8451, 1930, 4031, 18, 4950, 16, 1920, 2213, 14465, 43, 2213, 4016, 3418, 1988, 4088, 1966, 1920, 5305, 6804, 4728, 5061, 1958, 21902, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 16, 13143, 16, 2014, 6941, 4248, 1990, 4510, 2697, 18, 2052, 4050, 4817, 6387, 8523, 2840, 1988, 5741, 6445, 3689, 4028, 16, 2427, 1966, 4031, 16, 4155, 16, 1930, 4091, 18, 2176, 1977, 2435, 1922, 29321, 1957, 5339, 1957, 12, 5339, 5010, 16969, 13, 12, 4791, 5332, 4575, 1036, 5339, 1957, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5239, 16, 13763, 16, 1930, 7476, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MSGSKLWSVEASLVSVEELENWGLDVAVKILKGEAISREVKAMASLHNQHALVTQFMENGSLAGLLQPHCPRPWPLLCRSNVLLDSDLHAKLTDFGLATFHRGSLLADVNRKASMASDVYRNLCQQLGQEAETPGLEGLKELMQHCWNQDPRDRPSFQECRPNTEEAMSSAPKPGPGGTEMEGPRGTTGSHDIIATEMKKCTNLPERIRAQGDKVQPARRAGIPSDFRNQMPGPNLAWTPGPRPEGSQGAKRRGTNWPFLCSVLPMASSSRLSIDSGYTGPKFIGAGRFGVVFQARHRTILLLLGVTQKLRWESTCGPLLQELVLGMCYLHSQNPVLLHRDLKPRSGAGSGESAPAYLAPEGCEGQIRPPLTKLPQPSPLNLVNKEMDAAVSTVKKFLCENQGSNRLNKLSLKESPNSVPSTAPSPQTPETSPSPRAPRANPIPGTYSSLL", "metadata": {"id": "A0A452SHL9", "cluster": 28931508, "interpro_all": ["IPR011009", "IPR000719", "IPR017441", "IPR008271", "IPR051681"], "interpro_used": ["IPR051681", "IPR017441", "IPR000719"], "interpro_unused": ["IPR011009", "IPR008271"]}, "task_type": "infilling"} {"instruction": "Given the following functional description of a protein, generate a complete amino acid sequence that performs the described role. The desired function is: The protein is a member of the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Furthermore, the protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It occurs in Parachlamydiaceae bacterium and carries UniProt keyword assignments Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 16, 5655, 43, 4080, 3835, 2687, 3244, 1988, 17436, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 5110, 1922, 13344, 7806, 26984, 7408, 9914, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 3], "output": "MTTPHLSVLRNEIVESFSSCSLSYFVDGTLGAGGHSEAILETHPELKTLIGIDQDEQALEIARHRLMPWNSKVHFASGNFSQLSQILQSIRLPQVNGILLDIGVSSMQLDQAEKGFSFMRNGPLDMRMNIKDPLTAAEIVNTWPEKELGRIFREYGEEKQWRSAAQAIVKARAINPILTTHALADILRPHFFWKKKGVNPLTLIFQALRICVNRELEVLEAVIPQAIEKLAPQGRLAIISFHSLEDRIVKNAFRFAASDKESTSGIGGIFLTKIPTVKLLHNRPIIPTDEEIAQNPRSRSAKLRVLEKL", "metadata": {"id": "A0A7W1U1E2", "cluster": 2431643, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein can be placed in the Protein of unknown function DUF6164 family, which comprises functionally uncharacterised proteins found primarily in Proteobacteria. It is identified in Oleispira antarctica RB-8 and contains UniProt keyword associations Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 17136, 22934, 3416, 16, 2154, 12936, 9346, 23229, 3495, 2697, 2435, 5985, 1922, 22266, 18, 2176, 1977, 2899, 1922, 12188, 1937, 10984, 5524, 25854, 21788, 6160, 17, 28, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTKLLFNLHGVPDDEIQEVRELCEAWLSDDSQLPAAKTLLHEYQQARYENAQEDRMLTLIGMTVVLGLTLYPFLSLHEFAVYETEVGRWGIGLAAIAKLQGLSISEGLYVKFKQDPNQF", "metadata": {"id": "R4YML2", "cluster": 3467800, "interpro_all": ["IPR046162"], "interpro_used": ["IPR046162"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein belongs to the RuvA domain 2-like superfamily, which mediates structure-specific DNA binding in prokaryotic repair and recombination proteins such as RuvA, UvrC, and NAD+-dependent DNA ligases. Characterized by a SAM-like alpha-bundle fold with helix-hairpin-helix (HhH) motifs, this domain facilitates the recognition and processing of DNA intermediates, including Holliday junctions and single-stranded-double-stranded junctions. It is expressed in marine sediment metagenome. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 7212, 7302, 3418, 22, 17, 3189, 13975, 16, 2154, 10412, 3170, 17, 2487, 2678, 2743, 1922, 21545, 5059, 1930, 7827, 2697, 2427, 1966, 7212, 7302, 16, 5819, 15618, 16, 1930, 6577, 15, 17, 3100, 2678, 22423, 18, 4378, 2007, 43, 2235, 17, 3189, 4595, 17, 14142, 3728, 1956, 7864, 17, 14565, 17, 7864, 12, 9645, 1023, 13, 8277, 16, 2052, 3418, 11374, 1920, 5708, 1930, 4587, 1927, 2678, 12386, 16, 2710, 14451, 27539, 11245, 1930, 2957, 17, 10338, 17, 4825, 17, 10338, 11245, 18, 2176, 1977, 3198, 1922, 10789, 10363, 16552, 2225, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "IAQGVLTERENLGKFRELQEVTVVRGIGPKRFNVIVNALGH", "metadata": {"id": "X1VVA2", "cluster": 4604037, "interpro_all": ["IPR010994"], "interpro_used": ["IPR010994"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein has a Phosphoglycerate/bisphosphoglycerate mutase active site that catalyzes the transfer of phospho groups between carbon atoms of phosphoglycerate via a phosphohistidine intermediate. This site facilitates the isomerization of 2-phosphoglycerate to 3-phosphoglycerate as well as the synthesis and degradation of 2,3-diphosphoglycerate, playing critical roles in glycolysis and the regulation of hemoglobin oxygen affinity. Additionally, the protein is grouped in the Phosphoglycerate mutase/phosphatase family, which primarily catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in glycolysis and gluconeogenesis. Members of this family may also exhibit phosphatase activity involved in serine biosynthesis, vitamin B12 intermediate hydrolysis, or the regulation of carbohydrate metabolism. Collectively, these enzymes are central to metabolic flux and can participate in stress responses and immune modulation. In addition, it is part of the Histidine phosphatase superfamily, clade-1 family, which catalyzes reactions via a conserved histidine residue that is transiently phosphorylated within a phosphate pocket during the catalytic cycle. This diverse group encompasses various enzymatic functions, including fructose 2,6-bisphosphatase activity, cofactor-dependent phosphoglycerate mutase activity, and bacterial regulatory protein phosphatase activity. While some members like SixA retain a minimal structure, others feature large domain insertions that facilitate the binding of small molecules. It is produced by Pseudohongiella nitratireducens.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 2258, 43, 8078, 14966, 2010, 19, 16982, 13572, 13108, 2446, 2051, 3500, 3200, 1988, 17097, 1920, 3856, 1927, 8078, 2671, 2192, 5056, 9030, 1927, 8078, 14966, 2010, 3454, 43, 8078, 17210, 10873, 6129, 18, 2052, 3200, 11374, 1920, 27027, 1927, 22, 17, 8078, 14966, 2010, 1942, 23, 17, 8078, 14966, 2010, 1966, 2486, 1966, 1920, 4271, 1930, 4877, 1927, 22, 16, 23, 17, 11791, 2609, 13572, 13108, 16, 14797, 4140, 5456, 1922, 13393, 1930, 1920, 3640, 1927, 9652, 4612, 5173, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 8078, 14966, 2010, 2446, 2051, 19, 8167, 3416, 16, 2154, 5985, 17097, 1920, 8590, 12766, 2045, 2001, 1927, 22, 17, 8078, 14966, 2010, 1930, 23, 17, 8078, 14966, 2010, 1922, 13393, 1930, 25680, 18, 4678, 1927, 2052, 3416, 2278, 2222, 5987, 8167, 2455, 3286, 1922, 8468, 8132, 16, 6111, 17492, 6129, 9128, 16, 2014, 1920, 3640, 1927, 10590, 4714, 18, 10182, 16, 2144, 5038, 2032, 4101, 1942, 4487, 8220, 1930, 2112, 7352, 1922, 3071, 3387, 1930, 3743, 7145, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 13873, 8167, 13975, 16, 11315, 17, 21, 3416, 16, 2154, 17097, 5298, 3454, 43, 5305, 13873, 6181, 1988, 1977, 12145, 7199, 2651, 43, 5413, 10154, 2409, 1920, 6804, 4048, 18, 2052, 6445, 2210, 21569, 3425, 8145, 4088, 16, 2710, 15102, 22, 16, 26, 17, 16982, 7234, 2455, 16, 15155, 17, 3100, 8078, 14966, 2010, 2446, 2051, 2455, 16, 1930, 4543, 4948, 2213, 8167, 2455, 18, 2679, 2673, 4678, 3189, 3798, 1019, 13562, 43, 6343, 3170, 16, 4991, 5961, 3103, 3418, 15135, 1988, 6628, 1920, 2743, 1927, 2858, 4206, 18, 2176, 1977, 4152, 2007, 11520, 10647, 2029, 19918, 8214, 1968, 3510, 3005, 3355, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MAEDLKQPMTATTRYIYESRLTEQGRQQAQELGLRMAEQHLDSINMAITYCDRLREIRMGTWEGRLSPDQFQVDGAETFKELQQRAITRLQKSVLCAIEQRPLNQKRTILTYADQPYTHLISQEDNALLRHGETDWNRERRAQGQQYCSSSLRTRETADLAFGARYDDIRRDNQAQFDAFWHEILDDNGHQHIAIVSHGAWILWHPPRMHNCSLSKIRINELG", "metadata": {"id": "A0A916QLL3", "cluster": 8112597, "interpro_all": ["IPR013078", "IPR029033", "IPR001345", "IPR050275"], "interpro_used": ["IPR001345", "IPR050275", "IPR013078"], "interpro_unused": ["IPR029033"]}, "task_type": "infilling"} {"instruction": "Here is the protein function: The protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein is grouped in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is identified in Bacillus sp. DNRA2 and is linked to UniProt keywords ATP-binding, Cytoplasm, and Transferase. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2899, 1922, 14587, 2056, 18, 5956, 5524, 1028, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MAVIIGLTGGIASGKSTVSNMLKELGIPVIDADEEARLAVEKGEKAYDEIVAYFGKEILLEDGSIDRPKLGSIIFPNEEKREVLNHIVHPAVRQNMLRKKEQYVAGGNELVVLDIPLLFESKLTYLVDKIILVFVDEQTQLNRLMARNNFTESEAKSRIASQLPLRDKLQWADEVINNNGSIVDTKQQLLKILSQWGYTNHELV", "metadata": {"id": "A0A7X9QSR9", "cluster": 8631423, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to create: The protein should include a SseB protein N-terminal domain that constitutes the N-terminal region of the SseB protein, a component of the Salmonella pathogenicity island 2 (SPI-2) translocon found in Enterobacteria. The SseB protein is known to enhance serine sensitivity in *Escherichia coli* and plays a role in type III secretion. It is native to Leptotrichia wadei. Please provide the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 7762, 30, 1920, 2213, 3066, 3951, 43, 24773, 1014, 2213, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 3031, 1927, 1920, 24773, 1014, 2213, 16, 43, 4594, 1927, 1920, 11681, 15903, 10269, 22, 12, 15776, 17, 22, 13, 12930, 1916, 2435, 1922, 20351, 2126, 18, 1920, 24773, 1014, 2213, 1977, 3171, 1942, 4826, 8468, 3802, 1922, 14, 10210, 5178, 14, 1930, 5705, 43, 2770, 1922, 2601, 4337, 5512, 18, 2176, 1977, 6196, 1942, 16976, 18935, 19519, 1019, 4114, 3695, 1033, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MIDVNKPLENPVLKELFSRIGKNQKSDLELQNKILDEIIMRAYFLSYVFFDKPIETDETGKGTVKEDLNVSFYMISSSDGKQFYPAFTDWEELNKWNIGIDKIQTLILSFDDYAEMVLLNPDIEGFVINPFTTSFTFTREQLKILKKEKEERLKVVETKVEKDTPVMIGEAKEYPEDMLEALKSACKLDKNIKRTWLMLMYKEGQESYLLVVDSMGNEKESIEFIGRKITPYLNGKYIDMLSYKDSFGKDVVKDKKPFYEKKNSI", "metadata": {"id": "A0A510KSI6", "cluster": 9203061, "interpro_all": ["IPR027945", "IPR009839"], "interpro_used": ["IPR009839"], "interpro_unused": ["IPR027945"]}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein has a Helicase Helix-turn-helix domain that is typically found at the C-terminus of multifunctional helicases, such as the human WRN enzyme, which performs magnesium and ATP-dependent 3'-5' DNA unwinding and exonuclease activity. This domain contributes to the processing of partially duplex DNA substrates, playing a critical role in maintaining genome stability and preventing chromosomal breaks. It is produced by Staphylococcus condimenti.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 15318, 7864, 17, 5165, 17, 7864, 3418, 1988, 1977, 5745, 2435, 2019, 1920, 45, 17, 7822, 1927, 20136, 29919, 16, 2427, 1966, 1920, 2616, 28612, 4113, 16, 2154, 17436, 13148, 1930, 4498, 17, 3100, 23, 11, 17, 25, 11, 2678, 26801, 1930, 24966, 2455, 18, 2052, 3418, 7624, 1942, 1920, 4587, 1927, 6426, 12450, 2678, 6249, 16, 14797, 43, 4140, 2770, 1922, 8231, 3843, 5057, 1930, 8444, 9220, 13065, 18, 2176, 1977, 4152, 2007, 13452, 8646, 8721, 1033, 18, 3], "output": "TYRHLKNDKNMQEIAVIESVKENTVEDHVLENNKEERLKEFKLKFPDHSYFEIKLAIVRFSREELFIKGYLSNYDLYINQTFYSAFKSFYQ", "metadata": {"id": "A0A4Q7CJ49", "cluster": 10401294, "interpro_all": ["IPR029491"], "interpro_used": ["IPR029491"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein should feature a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. In addition, the protein should include a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Moreover, the protein should include a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. It is derived from Pseudomonas sp. CFII64 and contains UniProt keyword associations Cytoplasm, DNA excision, and DNA repair.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2176, 1977, 3595, 2037, 13461, 2056, 18, 23908, 1033, 8760, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 16, 2678, 10940, 16, 1930, 2678, 5059, 18, 3], "output": "MSEFQLVTRFEPAGDQPEAIRLMVEGIEAGLAHQTLLGVTGSGKTFSIANVIAQVQRPTLVLAPNKTLAAQLYGEFKAFFPNNAVEYFVSYYDYYQPEAYVPSSDTFIEKDASINDHIEQMRLSATKALLERKDAIIVTTVSCIYGLGSPETYLRMVLHVDRGDKLDQRALLRRLADLQYTRNDMDFARATFRVRGDVIDIYPAESDLEAIRIELFDDEVESLSAFDPLTGEVIRKLPRFTFYPKSHYVTPRETLVDAMEGIKVELQERLEYLRNNNKLVEAQRLEQRTRFDLEMILELGYCNGIENYSRYLSGRPSGAPPPTLYDYLPADALLVIDESHVSVPQVGAMYKGDRSRKETLVEYGFRLPSALDNRPMRFDEWEAVSPQTIFVSATPGNYEAEHAGRVIEQLVRPTGLVDPQIEIRPALTQVDDLLSEIGKRVALEERVLVTTLTKRMSEDLTDYLADHGVRVRYLHSDIDTVERVEIIRDLRLGTFDVLVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGRAILYADRITGSMERAIGETERRRDKQIAYNLEHGITPKGVFKDVADIMEGATVPGSRSKKRKGMAKAAEENAKYENELRSPSEITKRIRQLEEKMYQLARDLEFEAAAQMRDEIGKLRERLLTV", "metadata": {"id": "S6GRI0", "cluster": 10564045, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR014001", "IPR001650", "IPR001943"], "interpro_unused": ["IPR006935", "IPR004807", "IPR036876", "IPR027417", "IPR024759", "IPR041471"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein is categorized in the RNA Processing and Spliceosome Component family, which functions in pre-mRNA splicing and spliceosome assembly. Members participate in the removal of introns, including U12-type introns, and may regulate nuclear pre-mRNA retention. Additionally, specific members play a role in male sexual differentiation by modulating the splicing of sex determination genes. Furthermore, the protein should have a RNA recognition motif domain that specifically binds single-stranded RNA (ssRNA) using a conserved $\\beta$-$\\alpha$-$\\beta$-$\\beta$-$\\alpha$-$\\beta$ fold where amino acid side chains stack with RNA bases. This module is integral to post-transcriptional regulation, mediating processes such as alternative splicing, mRNA stability, and translation in diverse protein families including hnRNPs and snRNPs. Also, the protein is a member of the Nucleotide-binding alpha-beta plait domain superfamily, which facilitates nucleic acid recognition through a characteristic ferredoxin-like \u03b1-\u03b2 plait topology. This structural motif is prominent in the RNA-binding domains of various ribonucleoproteins, ribosomal protein L23, and viral DNA-binding proteins. It occurs in Hermanssonia centrifuga.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 10234, 1922, 1920, 3146, 4587, 1930, 10708, 4283, 4594, 3416, 16, 2154, 4088, 1922, 2097, 17, 3616, 8490, 1930, 10708, 4283, 5957, 18, 4678, 7352, 1922, 1920, 6025, 1927, 15778, 16, 2710, 22978, 1028, 17, 2601, 15778, 16, 1930, 2278, 5741, 4254, 2097, 17, 3616, 7521, 18, 4950, 16, 2487, 4678, 3918, 43, 2770, 1922, 4005, 5702, 4155, 2007, 10871, 1920, 8490, 1927, 3486, 7063, 2628, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 3146, 5708, 5219, 3418, 1988, 4475, 6876, 2957, 17, 10338, 3146, 12, 19314, 2175, 13, 2193, 43, 5305, 8, 38, 4666, 8, 17, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 17, 8, 38, 4666, 8, 17, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 3728, 2597, 3835, 2687, 4159, 7835, 10496, 1956, 3146, 11137, 18, 2052, 9059, 1977, 12328, 1942, 2753, 17, 5224, 3640, 16, 10239, 4028, 2427, 1966, 5012, 8490, 16, 3616, 5057, 16, 1930, 6410, 1922, 6445, 2213, 5767, 2710, 20015, 1036, 1930, 11970, 13983, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 5489, 17, 2743, 4595, 17, 4666, 5606, 1932, 3418, 13975, 16, 2154, 11374, 11079, 2687, 5708, 2596, 43, 6293, 25304, 22389, 10960, 17, 3189, 160, 17, 161, 5606, 1932, 13678, 18, 2052, 4346, 5219, 1977, 8753, 1922, 1920, 3146, 17, 2743, 4682, 1927, 3425, 18347, 14070, 16, 11196, 2213, 12051, 1010, 16, 1930, 4324, 2678, 17, 2743, 2697, 18, 2176, 5110, 1922, 19432, 2075, 5810, 2126, 5814, 1019, 18, 3], "output": "MNVVREINKINERELDLGISGSWHDDYKDSAYIFIGGLNTELTEGDVITIFSQYGEIMDVNLPRDKNTGKTKGFGFLMYEDQRSTILAVDNLNGATVLERTLRVDHVKNYKQPRAKGEDGEWQDREEQSLNAKPQLLTIDEDAASESSESDGPDIDPEDPMRDYLIARRKEEKALKKAKSKVDNHFRIPPTRYLVKVGYRTMTKLAVIVELPSGINGHEHIDVPFA", "metadata": {"id": "A0A4S4K7P4", "cluster": 12774898, "interpro_all": ["IPR012677", "IPR035979", "IPR051847", "IPR000504", "IPR045844"], "interpro_used": ["IPR051847", "IPR000504", "IPR012677"], "interpro_unused": ["IPR035979", "IPR045844"]}, "task_type": "autoregressive"} {"instruction": "\"The protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, the protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. In addition, the protein is a member of the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is identified in Ignavibacteria bacterium and is linked to UniProt keywords Cytoplasm and rRNA processing.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 2899, 1922, 12046, 9188, 7972, 2341, 18339, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 1930, 9067, 4587, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MREEVLSLLITAAGGVYVDATLGGGGHAESILQRLTEKLSRYRDRFVTVHDNFRNLSSALSQRGFNQASGILFDLGFSFRSDDRLDMRMDRTQALDAHEVVNRYTERKRAIVHRRSASPIDTTGELAAIVRGVVGDRFSLRRGLEQAITVLTSGGRLVVISYHSLEDRIVKEAFRNAAASVKKPMQTSEEEVQENPRARGAKLRAAEKLDPTGKLVGIDADLDAIHVAGVSSYQLDERSKLADLFWRYGEEKKSRAVAPVKSLARVFQAIRIEVNDELERSGSRLLPDAQVQPRIKLLMK", "metadata": {"id": "A0A938P0T5", "cluster": 13293657, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein is grouped in the Plasmodium vivax Vir family, which comprises immunovariant proteins specific to the genus *Plasmodium*, particularly *P. vivax*. These proteins likely facilitate the establishment of chronic infections by utilizing antigenic variation to evade host immune surveillance. It is expressed in Plasmodium coatneyi. Please provide the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 7762, 30, 1920, 2213, 1977, 10809, 1922, 1920, 15663, 20236, 2787, 3416, 16, 2154, 12936, 6595, 19313, 19196, 2697, 2487, 1942, 1920, 9487, 14, 15663, 14, 16, 4443, 14, 58, 18, 20236, 14, 18, 2144, 2697, 3205, 6628, 1920, 11108, 1927, 3724, 5024, 2007, 10232, 14606, 4516, 1942, 28917, 4423, 3743, 7889, 18, 2176, 1977, 3198, 1922, 15663, 15642, 4578, 1033, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MKEQTKLSCIYDQNYCNVNTLPSRKVYAAFEQKNGKHHQCDNISTWIQGIEEILGDNLRMGAYSTVSLELIAGAWCLLSKVSTENPPCKVGVLCDFFYFWLGDQLHGKLSGWNTSLPTIMQQIYTKLGGNNGPCSYGTIDNTNDGGFLQRRKKVFDYYYDYRTIWKQLMENDAPCSTAYGEYLKDAQDAYGRVQANCPTNNDDFCKEFWNKKFQNGTIPKPEDLKSKAASEQDLPPSDDEGDEKNLLSCLEVLSSKVATVPKETSSHLSPASPEVEGAAESSRSIAPIVSSTLAALGLPAAVFLLYKYTNLFSGIDGTFPKERNKRKRGSPVERHFNKSSVDDDDTLTTTEETSSTVDSSTITDSITEYSAPPSNRRRTNNRKGHQQQRQRKTNISYHNM", "metadata": {"id": "A0A1B1E6C4", "cluster": 13542410, "interpro_all": ["IPR008780"], "interpro_used": ["IPR008780"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is classified under the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. In addition, the protein has a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein should include a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is derived from Bacteroidetes bacterium RBG_13_43_22 and is described by UniProt keywords Isoprene biosynthesis and Transferase. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 3595, 2037, 26808, 14061, 6160, 1029, 41, 2590, 41, 3941, 41, 2950, 1930, 1977, 2910, 2007, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MISFPRAKINLGLRVLEKRPDGFHEIETIFYPIALSDALEFVVSSGKAAGDELVITGINIKTRPEKNLVTRAVKRLRTGYPVPPLKIHLHKAIPAGAGLGGGSSDAACMIRSMTKCFRFSITDDELKAIALELGSDCPFFLNPVPSIGTGRGEILKPINPALEGFYIMLLNPGFLISTKEAYHNCIPARREADLEELVAHPLSAWKKLIVNDFEDFVFKVYPMVGDLKRALYKAGAVYCSMTGSGSTVYGIFAEKPEISGKLKDYLIYEGIL", "metadata": {"id": "A0A1F3NFM6", "cluster": 15218476, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR013750", "IPR006204"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein is grouped in the HAD-like hydrolase superfamily family, which encompasses a diverse range of enzymes, including phosphonoacetaldehyde hydrolases and pyrophosphatases, involved in cellular metabolism and stress responses. Members play critical roles in the degradation of phosphonates, the regulation of intracellular pyrophosphate pools, and the dephosphorylation of 2-phosphoglycolate during DNA repair. Additionally, this family supports bacterial physiology through cell wall recycling and can contribute to pathogenicity via kinase activity. Additionally, the protein is classified under the HAD hydrolase, subfamily IA family, which comprises enzymes within the Haloacid Dehalogenase (HAD) superfamily that utilize three conserved catalytic motifs for hydrolytic activity. This subfamily is structurally distinguished by an $\\alpha$-helical bundle capping domain inserted between the first and second motifs, differentiating it from other HAD lineages. Additionally, the protein is grouped in the HAD superfamily, which encompasses enzymes such as phosphatases, P-type ATPases, and dehalogenases involved in diverse cellular processes ranging from amino acid biosynthesis to detoxification. These proteins share a conserved \u03b1/\u03b2-hydrolase fold similar to the Rossmann fold, featuring a core domain and a variable cap domain that allows for structural and functional variation. It has been characterized in Tepidimonas thermarum and is linked to UniProt keywords Calvin cycle and Carbohydrate metabolism.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2430, 17, 3189, 20748, 13975, 3416, 16, 2154, 21569, 43, 6445, 3109, 1927, 5038, 16, 2710, 8078, 11873, 7681, 8790, 30337, 1930, 20661, 2609, 18135, 16, 3286, 1922, 3689, 4714, 1930, 3071, 3387, 18, 4678, 3918, 4140, 5456, 1922, 1920, 4877, 1927, 8078, 5791, 1918, 16, 1920, 3640, 1927, 4776, 24937, 12808, 16, 1930, 1920, 16881, 1927, 22, 17, 8078, 17038, 4879, 5148, 2057, 2409, 2678, 5059, 18, 4950, 16, 2052, 3416, 7825, 4543, 10498, 2596, 2024, 4821, 13977, 1930, 2112, 4672, 1942, 15903, 3454, 4016, 2455, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2430, 20748, 16, 16227, 11640, 3416, 16, 2154, 12936, 5038, 2651, 1920, 23226, 29272, 2028, 7289, 2404, 2051, 12, 2430, 13, 13975, 1988, 12561, 2559, 5305, 6804, 8277, 1958, 26702, 2455, 18, 2052, 16227, 1977, 12171, 12080, 2007, 1925, 8, 38, 4595, 8, 17, 11514, 14142, 23565, 3418, 9103, 2192, 1920, 2561, 1930, 2812, 8277, 16, 14252, 2176, 2037, 2303, 2430, 10439, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2430, 13975, 16, 2154, 21569, 5038, 2427, 1966, 19131, 16, 58, 17, 2601, 28132, 16, 1930, 2028, 7289, 2404, 2319, 3286, 1922, 6445, 3689, 4028, 6485, 2037, 3835, 2687, 8132, 1942, 18169, 18, 2144, 2697, 7948, 43, 5305, 160, 19, 161, 17, 20748, 3728, 2551, 1942, 1920, 18215, 8890, 3728, 16, 29931, 43, 4728, 3418, 1930, 43, 4650, 2853, 3418, 1988, 5731, 1958, 4346, 1930, 3183, 4516, 18, 2176, 2258, 2252, 4378, 1922, 27120, 13756, 3947, 1934, 4311, 10599, 1930, 1977, 4624, 1942, 20709, 11569, 27489, 1921, 4048, 1930, 10590, 4714, 18, 3], "output": "MTRRQAFQAVLFDLDGTLLDTAPDLGHAANLMRERRGLPPLDEAYYRPRASSGARGMIEAAFGLTPQHPDYEAFRLEYLDTYGAVLTRRTQPFDGVADVIAALERAGLPWGVVTNKVERFALPLTAAIPLFTHAATVVGGDTTPHAKPHPAPLLEAARRLDVVPDACLYVGDDERDIVAGRAAGMGTVAARYGYLGVDADVEAWAADAVIDAPPELLNFLGLA", "metadata": {"id": "A0A554WTR4", "cluster": 16265568, "interpro_all": ["IPR050155", "IPR036412", "IPR006439", "IPR041492", "IPR023214", "IPR023198"], "interpro_used": ["IPR050155", "IPR006439", "IPR023214"], "interpro_unused": ["IPR036412", "IPR023198", "IPR041492"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to create: The protein contains a HPr(Ser) kinase/phosphorylase, N-terminal domain that constitutes the structural blades of the hexameric HPr serine/threonine kinase PtsK, a sensor protein controlling bacterial carbon catabolite repression. This domain facilitates the assembly of the enzyme's three-bladed propeller structure, allowing it to function within a multicomponent phosphorelay system. Furthermore, the protein contains a HPr kinase/phosphorylase, C-terminal domain that functions as the catalytic core of the bifunctional enzyme HprK/P, regulating carbon source utilization in Gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 on the phosphocarrier protein HPr and its dephosphorylation via phosphorolysis, typically within a hexameric assembly. Furthermore, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It originates from Pajaroellobacter abortibovis and is connected to UniProt keyword Serine/threonine-protein kinase, Magnesium, and Metal-binding. Please provide the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 7762, 30, 1920, 2213, 5461, 43, 18542, 12, 2375, 13, 4016, 19, 12556, 2051, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 4346, 22707, 1036, 1927, 1920, 25602, 1935, 18542, 8468, 19, 13143, 4016, 8618, 1040, 16, 43, 6443, 2213, 7138, 4543, 5056, 3115, 3016, 2394, 10084, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 4113, 11, 61, 2559, 17, 22707, 1007, 5062, 13728, 3170, 16, 7201, 2176, 1942, 2347, 2651, 43, 8844, 28155, 1939, 3421, 15208, 1012, 2433, 18, 3677, 16, 1920, 2213, 5461, 43, 18542, 4016, 19, 12556, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 1920, 29491, 4113, 18542, 1040, 19, 58, 16, 6773, 5056, 4585, 8422, 1922, 8604, 17, 2843, 4802, 18, 2176, 17097, 2321, 1920, 4498, 17, 3100, 4050, 1927, 2375, 17, 4182, 1990, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 2496, 16881, 3454, 3421, 6892, 16, 5745, 2651, 43, 25602, 1935, 5957, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 22970, 2037, 3838, 14174, 1931, 20783, 7972, 2341, 1915, 11380, 4397, 25210, 1036, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 8468, 19, 13143, 17, 2213, 4016, 16, 13148, 16, 1930, 6048, 17, 2743, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MHLSEESRQFIPEVCVEALVRSPHLTVSLEQVAGAKGISRLLRHPRIQKSGLALTGHFFGVVPTRVQILGETELSYLHALDHTQRQTASRGFFSLKLSCVIITHNQKPLASLVENAEETNTPLFVSDSRSSRTINSIHEVLDELLAPRSMLHGVLMDVFGIGLLILGKSGIGKSECALELILRGHRLVADDVVQCEWHPPGTLFGSPSHTLRHHIEIRGLGVLNIKALFGVTSICKRKRIDLVVRLEEWNDRQEYERIGLEKKCFMFLGTKVPELTVPVRPGRDMGSILEMAARNELLRQAGTDSARDFFAKVNSHLGNYPIESEEEENVNFLHYHFSKQAQTSPPPSKKKSRENNVFSVTTESASWIPTAEPSVEGEDS", "metadata": {"id": "A0A1L6MX96", "cluster": 17647700, "interpro_all": ["IPR003755", "IPR011104", "IPR011126", "IPR027417", "IPR028979"], "interpro_used": ["IPR011126", "IPR011104", "IPR027417"], "interpro_unused": ["IPR028979", "IPR003755"]}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein is grouped in the Pre-ATP-grasp domain superfamily, which constitutes an N-terminal structural unit that precedes the core ATP-grasp fold in enzymes such as peptide synthetases, biotin carboxylase, and glutathione synthetase. While distinct from the ATP-binding site, this domain is thought to mediate substrate recognition and binding, thereby facilitating the ATP-dependent ligation of carboxylate-containing molecules to amino or thiol groups during macromolecular synthesis. Moreover, the protein contains a D-alanine--D-alanine ligase C-terminal domain that functions as the catalytic core for the ATP-dependent ligation of two D-alanine molecules. This enzymatic activity generates the D-alanyl-D-alanine dipeptide precursor essential for the cross-linking step of bacterial peptidoglycan assembly. It is found in Verrucomicrobiia bacterium.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2097, 17, 4498, 17, 22815, 3418, 13975, 16, 2154, 14879, 1925, 56, 17, 4262, 4346, 5344, 1988, 24373, 1920, 4728, 4498, 17, 22815, 3728, 1922, 5038, 2427, 1966, 4207, 18185, 1036, 16, 8622, 29073, 16, 1930, 9153, 18185, 18, 2679, 4493, 2037, 1920, 4498, 17, 2743, 3200, 16, 2052, 3418, 1977, 6212, 1942, 8265, 4510, 5708, 1930, 2743, 16, 6113, 12440, 1920, 4498, 17, 3100, 11102, 1927, 20877, 17, 3165, 4206, 1942, 3835, 2014, 13914, 2671, 2409, 21815, 4271, 18, 3950, 16, 1920, 2213, 5461, 43, 46, 17, 10504, 17, 17, 46, 17, 10504, 11905, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 1920, 4498, 17, 3100, 11102, 1927, 2288, 46, 17, 10504, 4206, 18, 2052, 8145, 2455, 12399, 1920, 46, 17, 10527, 16323, 1024, 17, 46, 17, 10504, 9137, 8253, 7897, 4415, 1958, 1920, 3567, 17, 9486, 3537, 1927, 4543, 24183, 5957, 18, 2176, 1977, 2435, 1922, 3566, 3176, 13055, 1935, 15129, 3907, 1019, 14061, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MSEFRIALLFGGPSAERGISLNSARSAADIGRECLYSNTPSDFDFKINDLGDFGEGGELQALLEKHGIPFIGSSSRAAFTLPCLLLEGKDQEANLARVESFFQNNQLERCLRAYEQMVEEGIDNRFVLEPFAKGKEFHEQTLFDYRMKYLPTRQVAHLEGVEIVPIYFNLKKEAFLGKALNETELIVELKSVQLAFPAIHAKAFDKFDASWFLERAGFAILKPARSGSSIGVTEVRDPEHTVIVLQNWQGKAVALLPTEIEITD", "metadata": {"id": "A0A960SH84", "cluster": 18235358, "interpro_all": ["IPR013815", "IPR011095", "IPR011127", "IPR016185"], "interpro_used": ["IPR016185", "IPR011095"], "interpro_unused": ["IPR013815", "IPR011127"]}, "task_type": "infilling"} {"instruction": "We aim to build a protein that does the following:\nThe protein is assigned to the Protein arginine methyltransferase NDUFAF7 family, which functions as an assembly factor essential for the activity of the mitochondrial NADH:ubiquinone oxidoreductase (Complex I). Also known as MidA, this protein acts as an arginine methyltransferase to support mitochondrial respiratory function. Additionally, the protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is produced by Nitrospirota bacterium.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 1977, 6304, 1942, 1920, 2213, 9732, 16478, 8026, 25824, 2624, 1027, 3416, 16, 2154, 4088, 1966, 1925, 5957, 2991, 4415, 1958, 1920, 2455, 1927, 1920, 4596, 14261, 30, 5582, 22123, 27388, 12, 2796, 51, 13, 18, 2222, 3171, 1966, 3953, 1019, 16, 2052, 2213, 8016, 1966, 1925, 9732, 16478, 1942, 3373, 4596, 5481, 2347, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 4152, 2007, 16665, 10984, 6843, 1019, 14061, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MELGHPGLVQKLVARLEREGPLSFYMTAGPRIGPEGDYYTSLDVHPIFAELVGEMGAGKGLLAKHLLTAYRRDNPDFLACLRYLLVLNAIPADSITGVFLSNELVDAFPVHRVVKRPFIEIEAPPCSSALEAYFARLGISLEVGQRRGLVVTIDYGHAAADLFALARKTGTLLGYYRHQDLTAHVDFTSLALAGQDVGLEVTIESTFAGLDQESPQVAAMRELLRPDGMGTTYKILPYFLDALGVPERRPGRSLENVVPAAFMEAALYDPEFGYRQVVQAAEAIAPSGEFTIVERSPAMVETQKQRLRELTDAGLSVAWVPDLGLREIFVGWDGSRQAEVNLEALEWMRQAGTRLTVADSPYVRIGQGFTNQLHFLINLGVQHKGMLAPQLDGLRSR", "metadata": {"id": "A0A533YYP7", "cluster": 19051780, "interpro_all": ["IPR003788", "IPR038375", "IPR029063"], "interpro_used": ["IPR003788", "IPR029063"], "interpro_unused": ["IPR038375"]}, "task_type": "infilling"} {"instruction": "I want to design a protein that has the following function: The protein should include a Release factor glutamine methyltransferase, N-terminal domain that forms the $\\alpha$-helical N-terminal region of the PrmC/HemK protein. This enzyme functions as a methyltransferase that specifically modifies the N5 nitrogen of the glutamine residue within the conserved GGQ motif of class-1 translation release factors. Also, the protein is included in the Methyltransferase HemK-like family, which functions as an S-adenosyl-L-methionine-dependent enzyme that modifies class 1 translation termination release factors, such as bacterial RF1/RF2 and yeast MRF1. These proteins specifically methylate the glutamine residue of the universally conserved GGQ motif. The family is broadly conserved across nearly all genomes, typically occurring as a single copy. Additionally, the protein incorporates a Methyltransferase small domain that is found in ribosomal RNA small subunit methyltransferase C and related enzymes. It contributes to the methylation of ribosomal RNA, thereby participating in the maturation of the small ribosomal subunit. It originates from Clostridiaceae bacterium. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 4012, 2991, 9959, 16478, 16, 56, 17, 4262, 3418, 1988, 4952, 1920, 8, 38, 4595, 8, 17, 11514, 56, 17, 4262, 3031, 1927, 1920, 23043, 1030, 19, 3243, 1040, 2213, 18, 2052, 4113, 4088, 1966, 43, 16478, 1988, 4475, 25436, 1920, 56, 1015, 6634, 1927, 1920, 9959, 6181, 2651, 1920, 5305, 12358, 1055, 5219, 1927, 2921, 17, 21, 6410, 4012, 2790, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 16478, 3243, 1040, 17, 3189, 3416, 16, 2154, 4088, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 4113, 1988, 25436, 2921, 21, 6410, 12462, 4012, 2790, 16, 2427, 1966, 4543, 7751, 1009, 19, 7751, 1028, 1930, 5688, 2852, 5739, 18, 2144, 2697, 4475, 4963, 2010, 1920, 9959, 6181, 1927, 1920, 22809, 5305, 12358, 1055, 5219, 18, 1920, 3416, 1977, 11984, 5305, 3436, 6737, 2136, 7313, 16, 5745, 6966, 1966, 43, 2957, 6983, 18, 4950, 16, 1920, 2213, 19683, 43, 16478, 2858, 3418, 1988, 1977, 2435, 1922, 11196, 3146, 2858, 5903, 16478, 45, 1930, 2712, 5038, 18, 2176, 7624, 1942, 1920, 5547, 1927, 11196, 3146, 16, 6113, 9505, 1922, 1920, 7655, 1927, 1920, 2858, 11196, 5903, 18, 2176, 22970, 2037, 17938, 14773, 1972, 3336, 14061, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MVIANHVSVSRRTFLDQATDRLRKAGIEEARKEARLLIEDVADISIAHQLAFPDILLSDKQLAALDEALAMREARIPLSQIVGKASFYGQTFATTKDTLTPRPESELLVDAVIEYTRGLESVSLLDAFTGTGAVGISAARCLHEAGIEVILTMTDNSWHALEIAGKNACRLIPAVNWHLEHVDIWPSTYRLYDVITSNPPYVATDEIMTLMPEVSRSEPFSALDGGQDGLDFYRRLSRETGRYLSDNGVLLIEIGASQEEEVVRLFLDRGAWREVDRKKDLAGHTRVLAFCKVA", "metadata": {"id": "A0A7X9CXN9", "cluster": 19109494, "interpro_all": ["IPR004556", "IPR050320", "IPR040758", "IPR019874", "IPR029063", "IPR007848"], "interpro_used": ["IPR040758", "IPR004556", "IPR007848"], "interpro_unused": ["IPR050320", "IPR019874", "IPR029063"]}, "task_type": "autoregressive"} {"instruction": "I want to make a protein that can have this function: The protein is a member of the Peptidase S1A, chymotrypsin family, which comprises serine peptidases and homologues belonging to MEROPS subfamily S1A that typically utilize a conserved histidine, aspartate, and serine catalytic triad. These enzymes primarily function extracellularly in physiological processes such as food digestion, fibrinolysis, and complement activation, although some perform intracellular roles. The essential catalytic unit is approximately 220 amino acids in length and is frequently extended at the N-terminus with modular sequences. In addition, the protein is assigned to the Peptidase S1, PA clan superfamily, which represents a domain found in serine and cysteine proteases characterized by a chymotrypsin-like two \u03b2-barrel structure. The active site is located at the interface between the barrels, allowing these enzymes to catalyze the hydrolysis of peptide bonds in organisms ranging from bacteria to animals. Furthermore, the protein should include a trypsin-family serine protease serine active site that acts as the catalytic nucleophile within a conserved Asp-His-Ser triad to mediate peptide bond hydrolysis. It occurs in Petromyzon marinus (Sea lamprey) and contains UniProt keyword associations Disulfide bond and Hydrolase. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24050, 17727, 16, 27799, 3416, 16, 2154, 12936, 8468, 24050, 1036, 1930, 18541, 10588, 1942, 6902, 4001, 16227, 17727, 1988, 5745, 12561, 43, 5305, 13873, 16, 12878, 16, 1930, 8468, 6804, 21845, 18, 2144, 5038, 5985, 2347, 5329, 1954, 1922, 5005, 4028, 2427, 1966, 3959, 9379, 16, 9450, 6892, 16, 1930, 5508, 2936, 16, 2876, 2673, 2385, 4776, 5456, 18, 1920, 4415, 6804, 5344, 1977, 3993, 12391, 3835, 4576, 1922, 3471, 1930, 1977, 5467, 6091, 2019, 1920, 56, 17, 7822, 1956, 16078, 3709, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 24050, 4062, 16, 3838, 6958, 1022, 13975, 16, 2154, 4972, 43, 3418, 2435, 1922, 8468, 1930, 8666, 12447, 4378, 2007, 43, 27799, 17, 3189, 2288, 161, 17, 19560, 3170, 18, 1920, 3500, 3200, 1977, 4810, 2019, 1920, 6854, 2192, 1920, 19560, 1036, 16, 7201, 2144, 5038, 1942, 18170, 1920, 9128, 1927, 4207, 9031, 1922, 7373, 6485, 2037, 4802, 1942, 3555, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 9527, 17, 3416, 8468, 7154, 8468, 3500, 3200, 1988, 8016, 1966, 1920, 6804, 2797, 28335, 2651, 43, 5305, 4138, 17, 4167, 17, 2375, 21845, 1942, 8265, 4207, 5403, 9128, 18, 2176, 5110, 1922, 16901, 3542, 13642, 1022, 13081, 1022, 1957, 12, 9309, 12503, 19916, 13, 1930, 5461, 20709, 11121, 2538, 5253, 11830, 5403, 1930, 20748, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MEFSHYYYSDPRRWTVLAGTVRQKPSATPSAYVASITRHPQYDADTSDYDLALMKLSSTLSVDGDSIRPVCLPEYSQSFPDGQTCWITGWGVTSESSSVVPESLQEAKVSLISTSVCNRATVYHNSVTARMVCAGFLAGKIDACQGDSGGPLVCSEGDGGTTFRLVGATSWGEGCARKNQPGVYSRVSSMMEWVYSTMDA", "metadata": {"id": "A0AAJ7UD67", "cluster": 20795772, "interpro_all": ["IPR009003", "IPR043504", "IPR001314", "IPR001254", "IPR033116"], "interpro_used": ["IPR001314", "IPR009003", "IPR033116"], "interpro_unused": ["IPR001254", "IPR043504"]}, "task_type": "autoregressive"} {"instruction": "The protein features a Carbohydrate-binding module family 96 domain that adopts a nucleoplasmin-like beta-sandwich fold and is found in functionally diverse multi-domain proteins, including tRNA nuclease WapA, alginate lyases, and chondroitinases. In addition, the protein includes a Domain of unknown function DUF6531 domain that is a putative component found in a range of Rearrangement Hotspot (RHS) proteins. Additionally, the protein includes a Rhs repeat-associated core domain that forms a conserved structural element often found in large proteins containing FG-GAP or Rhs repeats, such as secreted bacterial insecticidal toxins and eukaryotic teneurins. It is also present in the N-terminal region of shorter, uncharacterized proteins across bacteria and eukaryotes. It is expressed in Egicoccus halophilus and is associated with UniProt keywords Transmembrane, Transmembrane helix, and Membrane.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 4075, 43, 10590, 17, 2743, 9059, 3416, 4746, 3418, 1988, 24032, 43, 2797, 4318, 1921, 17, 3189, 4666, 17, 18038, 3728, 1930, 1977, 2435, 1922, 9346, 6445, 2779, 17, 3418, 2697, 16, 2710, 10089, 16230, 4114, 4302, 16, 17987, 23928, 1036, 16, 1930, 26437, 2319, 18, 1922, 2459, 16, 1920, 2213, 5921, 43, 3418, 1927, 5435, 2347, 4855, 17136, 3786, 1009, 3418, 1988, 1977, 43, 6770, 4594, 2435, 1922, 43, 3109, 1927, 14154, 24225, 12, 3617, 1036, 13, 2697, 18, 4950, 16, 1920, 2213, 5921, 43, 3617, 1036, 6865, 17, 2458, 4728, 3418, 1988, 4952, 43, 5305, 4346, 6149, 3868, 2435, 1922, 3103, 2697, 3165, 13320, 17, 5750, 2014, 3617, 1036, 9569, 16, 2427, 1966, 8366, 4543, 15350, 7161, 13599, 1930, 10825, 5656, 3708, 5572, 1036, 18, 2176, 1977, 2222, 2481, 1922, 1920, 56, 17, 4262, 3031, 1927, 7310, 16, 24528, 2697, 3436, 4802, 1930, 15021, 18, 2176, 1977, 3198, 1922, 7282, 5670, 2437, 1957, 23226, 24888, 5277, 1036, 1930, 1977, 2458, 1956, 20709, 11569, 9117, 16, 9117, 7864, 16, 1930, 3260, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MCEHSLRYVAGVAASGVEGFQVLVVRVRGPLVVLLDAEMEVSESVAAEPESPVASGAVVPVREDALAASLSAVGSGQRVLVESATSETSQTFANEAGDAGAWREIDTRLQRSEGAVVPRVTAAEVSFSAGGVGPMVGLSLPSPELDGNVARYRQVQPGLDLELEALPAGYAKRLVLHERPAAPVTWRFGLELVDADDEAVIVVDGLYMWGAERNEQADEPARVAEVEHRLVRRGGRTVLEITPDFGFLSDPQNLASTPQASATELRVGTYDGGTSRARTLIQFDSWSCTARQVNVRRLSAPFNSSTTWSNQPASPSTVYASASFARGHSSNGLMLLAADETDNAGWKKFYSSEHATGSQRPKLTVTYNTYPNLVAGRRGTFCDGDAGTSGRVVFEVFDATKSTRVATVNGNSGVSCHSSTGRVPAGVLREYSSWIHLVPDVTRPITPRISSTTHEVATESDVTSVAFDWTVSTTTPSGPLQTATSFAKANVEGGIWWLHVRARDRVGNWSTIRRFQVNISAGSLVAATFQWRRSDSDAWTTVPAARLALASSPSVPLTSSVQPLSEQMAGEAAGRYRTSRELVWSASKVAKVTLDQLGAGKDYGTVPLGPGQANLLTGNFSMTDADVSVTGWTSGVPVLDAGAGFRLLETPEHASASTPAPFVVVEDHRYQAVEAGFEDLTLTHRGSQYVLSDLDGMQVTFRSHEAELRPTTLRAPGPAGAACGQPGPGCRALHLVYDPPNASTSRLQSVQLETWDAANGTTRSTQLATTFGYAGSTARLTTLTPPGVEPWTLVYAASSGPEAGRLQAVEYDVPRTGSGAPHPMGDTELDRWGQAGRNLPTDVTAVFPPEQVPSSTGRSVNVASPGGRISVTEHDVYGNVVRELTPANRAQALTEPDTQAAAGLLATVRELQLARRHTRHHYPQIPTADGSDTETATLPTSSWVGALLTSGQVVDEQLDPDGLGLVTVTRYDDEGREIERRQPSEADGGGPGTLRTVRYTAPANPAAQPAMASGLPGLATIHTAGYNRLLQPTQVAESVPRAGGGTTVRTTTTSYDTETTTVYDPATGAVSETRSDGRTLVRSYDRLGRLTSYTDSVGTHGQGLGTRSFTYDDTTGYTTAVTDSQVGSFTASVSDYDGDGTLRRWTTPAGWRHQQITQTRNCGPGGCLSFDEHVTVDIHGRWVAHVRAGMARSYRYDYAFDGAAGANANRSSKAVTRAGADGNCDLDTRTTTDYAYDQADRLLSGTVYDGLGRSLTQNGQRRTYTLDPAMRFASETRQDGTTDRWRYADDTDAPAWIDHPGLGATTTITEQLTDLFGSVIANVGNDPQAAIPGTTVLATSITDEYGAPLAILMGVRAYLPQLGRFLQIDPVIGGSASAYDYCYADPINCTDLDGKRARWSRLVGRWNTPFTAGAYLWGRAWGGTCTRQRGLMITCTGMRGGHARGGTQVGNVFLTRDHATQWAVMGFAFPLAYLAGGTNPCRNWAERQAGLKAGNYDWCIWALVAAVAPVAAVAQPVPDGTFTDEVHFGPQRVFDVELGDGEGQGVTFDWSEVSAERLEVVEPAEGVQLPITIDPTASLAIAQDTFVQSPAPLAGKDVESASLQLYNFHACAAGWASFDVTDRVRQWVNGETNASDDSQFSTGTVAYVPTLTPMLSDGQSYYWRARGFDGKLYSDGNNGSGVAGYAVEFDQDRWPETGDRTQRRMVLQAMGPVRLSTDLAATVGSVDGPVQVRALFDDGTTTDLTVTRSYNSRADLTQIDPLFGAGVEGAEFWFDTPEAHDGGSFVPEVVKHTPDAAATSITYSRIGGMTRAVRDVLVSYEYDAARRLVGVVDPRTRAEPGSGVNRWTLVSAASLTAAGYARAEVHYLDRNLFDASGLRLERELGPQHQVQLSNGTQTEYDWKLRLATRQTLPTYPQCGGRPDWHGQVCLITAGRVTRVAVTAGAGSTIGTAVATRYDRFGRVASVGDQTTLDPAGNPVGGAGRLITATDAGAACQIRETTRVPAGLLEGHGQLDATYYANDLVHGWTRHVTGITGDLAATITSPDDTTTITGRYHWLGGKQRAAVLASGYRGIRRTGHVVRAARRSVSPSLLRHESR", "metadata": {"id": "A0A8J3ADF4", "cluster": 21233574, "interpro_all": ["IPR055372", "IPR045351", "IPR022385", "IPR050708"], "interpro_used": ["IPR055372", "IPR045351", "IPR022385"], "interpro_unused": ["IPR050708"]}, "task_type": "infilling"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein contains a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Moreover, the protein includes a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Furthermore, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It occurs in Denitromonas halophila and is connected to UniProt keyword Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 5461, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3950, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 5110, 1922, 26319, 10480, 23226, 24888, 5148, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MSDTLSALAPAKLNLFLHVVGRRPDGYHLLQTAFRTDVPGVPAEQDLVVRAARRLQAAAGVSAATTLLALNRLWRLDWSRARLQALGLELGADVPTPMCLPPSWYVVIAPGASVPTAEIFCAKELTHTTRNDLQPVVCHRYPQVADAIDWLNHHAAARMTGVAQCPERWQAWAVSSLQRHPLYDWAVLLDWGDQLQFRCRDDGQILRMAGVEIHVDKVLPMGGGLGGGSSDFFIFGRDAFAEGVGETLRSTEIIKMPDFAISGACVFASMETEAQARQV", "metadata": {"id": "A0A557QIH4", "cluster": 22272238, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "infilling"} {"instruction": "The protein falls within the Mobilization protein NikA-like family, which facilitates the mobilization and replication of plasmids. These proteins likely adopt a homodimeric structure consisting of an N-terminal DNA-binding ribbon-helix-helix (RHH) domain and a C-terminal stalk domain. It is found in Ferrovum sp. JA12. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 14586, 2213, 12833, 1019, 17, 3189, 3416, 16, 2154, 11374, 1920, 14586, 1930, 5158, 1927, 8069, 18, 2144, 2697, 3205, 14103, 43, 21189, 1935, 3170, 7600, 1927, 1925, 56, 17, 4262, 2678, 17, 2743, 25149, 17, 7864, 17, 7864, 12, 3617, 1023, 13, 3418, 1930, 43, 45, 17, 4262, 19447, 3418, 18, 2176, 1977, 2435, 1922, 20976, 1020, 1989, 2056, 18, 13149, 3112, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MARPEKLDAEKFTKSVAFRMTEGTFKMYERKFMAAGLKQSEFFRLHVVNNTTLVVAKSPTASRAVLLLSKASNNLNQLAHRANAANLSRTISDDTFKVISTQLQLLNDFMLSQVQEASQ", "metadata": {"id": "A0A0R0LTA8", "cluster": 25051885, "interpro_all": ["IPR053842"], "interpro_used": ["IPR053842"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein belongs to the Immunoglobulin-like fold superfamily, which comprises domains characterized by a beta-sandwich of seven or more strands arranged in a Greek-key topology, facilitating protein-protein interactions often via beta-sheet interfaces. These domains are ubiquitous in animal proteins, playing critical roles in immune recognition, cell adhesion, and structural integrity in muscle proteins such as titin. Furthermore, the protein belongs to the WD40/YVTN repeat-like-containing domain superfamily, which features repeating motifs of approximately 40 residues that fold into a seven- or eight-bladed beta-propeller structure composed of four-stranded beta-sheets. This architecture typically serves as a rigid scaffold for mediating diverse protein-protein interactions and facilitating the assembly of multi-protein complexes. Also, the protein is a member of the Quinoprotein alcohol dehydrogenase-like superfamily, which comprises bacterial enzymes that utilize a pyrroloquinoline quinone (PQQ) prosthetic group to catalyze the oxidation of alcohols such as methanol and ethanol. These proteins typically adopt an 8-bladed beta-propeller structure and may include C-terminal heme or cytochrome c domains to facilitate electron transfer in methylotrophic or autotrophic pathways. It is found in Candidatus Bathyarchaeota archaeon and features UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14440, 1942, 1920, 11837, 17, 3189, 3728, 13975, 16, 2154, 12936, 4682, 4378, 2007, 43, 4666, 17, 18038, 1927, 5260, 2014, 2253, 13214, 14940, 1922, 43, 27568, 17, 3834, 13678, 16, 12440, 2213, 17, 2213, 3719, 3868, 3454, 4666, 17, 11130, 14857, 18, 2144, 4682, 2032, 15498, 1922, 4027, 2697, 16, 14797, 4140, 5456, 1922, 3743, 5708, 16, 2024, 6141, 16, 1930, 4346, 7996, 1922, 3760, 2697, 2427, 1966, 7090, 1921, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 17907, 4241, 19, 67, 25641, 1022, 6865, 17, 3189, 17, 3165, 3418, 13975, 16, 2154, 4075, 21763, 8277, 1927, 3993, 3040, 4248, 1988, 3728, 2460, 43, 5260, 17, 2014, 5066, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 7179, 1927, 3006, 17, 10338, 4666, 17, 14685, 18, 2052, 9335, 5745, 10634, 1966, 43, 12383, 7281, 1958, 10239, 6445, 2213, 17, 2213, 3719, 1930, 12440, 1920, 5957, 1927, 2779, 17, 2213, 5048, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 9012, 6657, 4284, 9294, 17, 3189, 13975, 16, 2154, 12936, 4543, 5038, 1988, 12561, 43, 23878, 1037, 11072, 8419, 25093, 12, 15564, 1055, 13, 19019, 2210, 1942, 18170, 1920, 6638, 1927, 21773, 2427, 1966, 8570, 1930, 5757, 18, 2144, 2697, 5745, 14103, 1925, 28, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 1930, 2278, 3951, 45, 17, 4262, 10954, 2014, 9387, 45, 4682, 1942, 6628, 4995, 3856, 1922, 4963, 13653, 2014, 5728, 1997, 2688, 1935, 3873, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 10481, 9771, 15618, 20051, 7336, 13470, 1916, 1930, 4075, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MAEEGMAYYWAKTYGSLLDDLPLDMAITEDGDIVLAGGQTGDVLWAKTYDIMDIQTAYGLAITPDGDILLRLDSDDGSVMWQKHYGEGRFSDIIIGQDGYAYVLKLDTDDGAIVWQMTYGGADSDVGAGIVGTLSFGAGWLDVLVLKLDRADGHVIKAVSLGGPDVIIAGSTASFGSGEHDGWLIRLDGDDLSLKWAKAYGGANLDSFGTGEWDLWLMKLDAYGNIAWQRAYGGAFSEWGDTIAGGYYDIWLLKTDTEGSIKDCLLCTETEAISTPTDITAFVMSISPSVSTQCWAEVDVAPPEVAITSPSEGSAIGGTITVQDLAYTDDTAPYEYEWDTTSVADGSHTIRAVAYDAEGNSGEDEVNPVEGESVTITVQASDATSGIAHVILYAGVWTATIPGQSAGTMVEYYVEVVDEAGNSAQLGMELWQLVLIVCAIAIVIILAIIAVKKTFFYQEGSSSLFVFKVDLVAGFCWDADAGAYYALVIGLTNVYGAGDNDVWMLPDGSLIAMGDMDGVERMAVTPDGGLYGLTLAPDGSIVVTGSTAINSNGDVFVVGITNSFGVGPILILGLTGTPSAAAPHDVSVDASDNVGVERVEFYIDGVVVDNVAPVIISVSRSPEEYHIGGGSWTSVEMSPVSVIEHYTVASKPAPPPTGI", "metadata": {"id": "A0A7J2JXM5", "cluster": 26284376, "interpro_all": ["IPR013783", "IPR011047", "IPR015943"], "interpro_used": ["IPR013783", "IPR015943", "IPR011047"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein carries a 2EXR domain that contains two conserved ExR motifs of potential functional significance and is predominantly found in fungi. It originates from Phialemonium atrogriseum.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 16252, 43, 11416, 10024, 3418, 1988, 5461, 2288, 5305, 1975, 1005, 8277, 1927, 2889, 3183, 4550, 1930, 1977, 7700, 2435, 1922, 10520, 18, 2176, 22970, 2037, 17971, 2603, 3947, 2457, 6204, 2685, 2870, 1989, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MTAPVATLDSFPLFSRLPPEIRIKIWEDTWPESSDALFDRVSLRLTCGVARWLQTNFDSRICHESRAHTIRHFTPIQHSKLDTWPFYFNPRSDILWLNNYYGRQLDQIERVFVLQSEWEFLEGYAPDVRGKSTSKLQTGFEPRTYLSLVNGTGRFSIEPRVIELAYAEEPVYNAEEGDDSSMGYQPLEKCLDPIALQVDVTDELTTLDGLRDLDVFGGLRLVQIFLDDLIFL", "metadata": {"id": "A0AAJ0FLD6", "cluster": 26594184, "interpro_all": ["IPR045518"], "interpro_used": ["IPR045518"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein includes a Signal transduction response regulator, receiver domain that functions as a phosphorylation-activated switch within two-component systems to couple environmental sensing with cellular adaptation. It accepts a phosphoryl group from a cognate sensor histidine kinase, inducing a conformational change that activates an associated effector domain to regulate gene expression. In addition, the protein is included in the The CheY-like superfamily, which functions primarily as the receiver module in two-component signaling systems, mediates signal transduction through the phosphorylation of a conserved aspartate residue by a partner histidine kinase. Adopting a compact flavodoxin-like $\\alpha/\\beta/\\alpha$ fold, these domains often serve as N-terminal regulators coupled to DNA-binding effectors to control gene expression in response to environmental stimuli, though divergent members may bind RNA or lack the active phosphorylation site. Moreover, the protein belongs to the Bacterial response regulator family, which functions as the effector component of two-component signal transduction systems to regulate adaptive responses to environmental stimuli. Upon phosphorylation of their receiver domain by a sensor kinase, these proteins modulate critical cellular processes ranging from transcriptional regulation to chemotaxis and sporulation. It is expressed in Deltaproteobacteria bacterium.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 2733, 8201, 2644, 7888, 16, 12608, 3418, 1988, 4088, 1966, 43, 4050, 17, 4128, 6195, 2651, 2288, 17, 4594, 3771, 1942, 15116, 4813, 9306, 1956, 3689, 7810, 18, 2176, 5861, 1036, 43, 12556, 2210, 2037, 43, 15786, 6443, 13873, 4016, 16, 7834, 43, 8523, 3185, 1988, 9094, 1925, 2458, 7917, 3418, 1942, 5741, 2359, 2294, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 1920, 10003, 1012, 17, 3189, 13975, 16, 2154, 4088, 5985, 1966, 1920, 12608, 9059, 1922, 2288, 17, 4594, 3197, 3771, 16, 10412, 2733, 8201, 2596, 1920, 4050, 1927, 43, 5305, 12878, 6181, 2007, 43, 8240, 13873, 4016, 18, 20478, 43, 13726, 7732, 1986, 9754, 17, 3189, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 16, 2144, 4682, 3868, 7120, 1966, 56, 17, 4262, 9098, 6416, 1942, 2678, 17, 2743, 13066, 1942, 2285, 2359, 2294, 1922, 2644, 1942, 4813, 5458, 16, 4170, 13609, 4678, 2278, 4566, 3146, 2014, 3630, 1920, 3500, 4050, 3200, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 4543, 2644, 7888, 3416, 16, 2154, 4088, 1966, 1920, 7917, 4594, 1927, 2288, 17, 4594, 2733, 8201, 3771, 1942, 5741, 7617, 3387, 1942, 4813, 5458, 18, 4073, 4050, 1927, 2310, 12608, 3418, 2007, 43, 6443, 4016, 16, 2144, 2697, 8480, 4140, 3689, 4028, 6485, 2037, 5224, 3640, 1942, 16884, 1930, 23647, 18, 2176, 1977, 3198, 1922, 9649, 9218, 1021, 10296, 14061, 18, 3], "output": "PEPSARTRRVLVIEDNVDAAESLKDLLQLDGHEVRIAFDGPSGLAVARDFRPEVVLCDIGLPGMSGYEVAQRLRSDDDLRDAVLVALTGYSLPEDRQRAAEAGFAHHIAKPPSIEAIERVLASSCSLAPRPG", "metadata": {"id": "A0A933ZR49", "cluster": 27661511, "interpro_all": ["IPR050595", "IPR011006", "IPR001789"], "interpro_used": ["IPR001789", "IPR011006", "IPR050595"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Moreover, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein should include a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is native to Kandleria vitulina DSM 20405 and exhibits UniProt keyword tags Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 6196, 1942, 12916, 5395, 3027, 1019, 5208, 3392, 1019, 10964, 16368, 15264, 1930, 9826, 20709, 11121, 2538, 14392, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MKVRAYAKVNLALDVVRKIALHDLIIIDRIESGIELTANDKYHIDGGVRMHVYKHIPSQAGLAGGSADGAALAALGKEVGADIPFCIHNKINHFQAHLLLVKPKKGVSTKRCFESLNIPESSHEKVVASLGNTLETPSLKMVKDIEKIKDRAIPFFRARYPFVRKTKILERREDGYHDLEMIMAPTYRVPTDERNIMYKVAKLMIVMRAINKLYKLHLSNEEALVKGIGEDLTFINDPDIDKMKQGIQENDYEMRSMGFDGALMSGSGSCVFGITQDEELIE", "metadata": {"id": "A0A0R2HBT5", "cluster": 28484332, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR004424", "IPR013750"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "infilling"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein is included in the Phosphatidylinositol-4-phosphate 4/5-kinase, C-terminal domain superfamily, which adopts a 2-layer sandwich fold and functions as the catalytic core of PIP4K and PIP5K enzymes. This domain mediates the phosphorylation of phosphatidylinositol-4-phosphate to generate phosphoinositol-4,5-bisphosphate, a key intermediate in the phosphoinositide signaling pathway. Furthermore, the protein features a Phosphatidylinositol-4-phosphate 4/5-kinase, core domain that functions as the conserved catalytic region responsible for phosphorylating phosphoinositides at the fifth hydroxyl position of the myo-inositol ring. It typically catalyzes the conversion of phosphatidylinositol-4-phosphate to the signaling precursor phosphoinositol-4,5-bisphosphate, but is also utilized by enzymes such as FAB1 to generate phosphatidylinositol-3,5-bisphosphate from a phosphatidylinositol-3-phosphate substrate. Moreover, the protein falls within the Phosphatidylinositol-4/5-phosphate 5/4-kinase family, which comprises type I and type II enzymes responsible for catalyzing the formation of phosphoinositol-4,5-bisphosphate. These kinases phosphorylate phosphatidylinositol-4-phosphate and phosphatidylinositol-5-phosphate, respectively, playing a central role in the phosphoinositide signaling pathway. It is native to Heterosigma akashiwo (Chromophytic alga) (Heterosigma carterae) and is classified with UniProt keywords ATP-binding, Nucleotide-binding, and Transferase.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 1977, 3063, 1922, 1920, 16927, 17, 24, 17, 5413, 24, 19, 25, 17, 4016, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 24032, 43, 22, 17, 4757, 18038, 3728, 1930, 4088, 1966, 1920, 6804, 4728, 1927, 6556, 1006, 1040, 1930, 6556, 1015, 1040, 5038, 18, 2052, 3418, 10412, 1920, 4050, 1927, 16927, 17, 24, 17, 5413, 1942, 5655, 8078, 15651, 17, 24, 16, 25, 17, 29443, 16, 43, 3834, 6129, 1922, 1920, 23546, 3197, 3374, 18, 3677, 16, 1920, 2213, 4075, 43, 16927, 17, 24, 17, 5413, 24, 19, 25, 17, 4016, 16, 4728, 3418, 1988, 4088, 1966, 1920, 5305, 6804, 3031, 5061, 1958, 12556, 2287, 23546, 1036, 2019, 1920, 12052, 9420, 3507, 1927, 1920, 15924, 17, 16246, 6335, 18, 2176, 5745, 17097, 1920, 7309, 1927, 16927, 17, 24, 17, 5413, 1942, 1920, 3197, 7897, 8078, 15651, 17, 24, 16, 25, 17, 29443, 16, 2308, 1977, 2222, 7079, 2007, 5038, 2427, 1966, 6914, 1009, 1942, 5655, 16927, 17, 23, 16, 25, 17, 29443, 2037, 43, 16927, 17, 23, 17, 5413, 4510, 18, 3950, 16, 1920, 2213, 12182, 2651, 1920, 16927, 17, 24, 19, 25, 17, 5413, 25, 19, 24, 17, 4016, 3416, 16, 2154, 12936, 2601, 51, 1930, 2601, 2890, 5038, 5061, 1958, 29601, 1920, 3337, 1927, 8078, 15651, 17, 24, 16, 25, 17, 29443, 18, 2144, 7784, 18730, 16927, 17, 24, 17, 5413, 1930, 16927, 17, 25, 17, 5413, 16, 2763, 16, 14797, 43, 4101, 2770, 1922, 1920, 23546, 3197, 3374, 18, 2176, 1977, 6196, 1942, 27814, 29043, 1019, 4464, 16569, 1018, 1037, 12, 3233, 2688, 4274, 4326, 1019, 13, 12, 27814, 29043, 1019, 17302, 20938, 13, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 17, 2743, 16, 1930, 13763, 18, 3], "output": "MDYSLLVGVTAPTMPLDHHQADEVNFFSPIHGQGADEHYFIGHWGRREKIAAVDPEAYAKRFQNFMSTVLVAAEEAKEEAPDKRVSKIREIIDILTPYNAAKKGETMFKSMM", "metadata": {"id": "A0A7S4D6X0", "cluster": 1444357, "interpro_all": ["IPR027483", "IPR002498", "IPR023610"], "interpro_used": ["IPR027483", "IPR002498", "IPR023610"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that has this function description: The protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein is categorized in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is expressed in Plectonema cf. radiosum LEGE 06105 and is classified with UniProt keywords ATP-binding, Cytoplasm, and Transferase. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 2052, 2347, 8418, 30, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 3198, 1922, 6483, 2341, 2290, 3368, 4920, 18, 17544, 1989, 6703, 1021, 6604, 14234, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MKRIIGLTGGIATGKTTVANYLADAYNLPILDADIYAREAVAVNSLLLQQIVKRYGEKILLADGSLNRQKLAEIIFNNQQERLWIDNLIHPYVGDRLSVAIKETAVETLILVVPLLFEAGMTDLVTEIWVVSCSEQQQLERLLERNQLTLEQAQARISSQMSLKQKIQKADIVLDNSSNVEKLLQQVDIAIFR", "metadata": {"id": "A0A8J7F6J3", "cluster": 3109370, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein carries a Putative metal-binding motif repeat that likely serves as a binding site for metal ions, such as zinc or calcium. This region is characterized by conserved cysteine residues and a notable lack of hydrophobic residues. Also, the protein should feature a PKD/Chitinase domain that adopts an immunoglobulin-like $\\beta$-sandwich fold with a Greek key topology. Originally identified in polycystin-1, it is commonly associated with cell-surface proteins involved in adhesive protein-protein and protein-carbohydrate interactions. In addition, the protein includes a PKD domain that likely mediates protein-protein and protein-carbohydrate interactions in extracellular environments. This module adopts an immunoglobulin-like fold consisting of two face-to-face $\\beta$-sheets and is commonly found in diverse proteins ranging from human polycystin-1 to bacterial collagenases. It is produced by Desulfobacteraceae bacterium IS3.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 16252, 43, 6770, 6048, 17, 2743, 5219, 6865, 1988, 3205, 10634, 1966, 43, 2743, 3200, 1958, 6048, 6982, 16, 2427, 1966, 7997, 2014, 5016, 18, 2052, 3031, 1977, 4378, 2007, 5305, 8666, 4248, 1930, 43, 11892, 3630, 1927, 7919, 4248, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 26643, 19, 16588, 2051, 3418, 1988, 24032, 1925, 11837, 17, 3189, 8, 38, 4666, 8, 17, 18038, 3728, 1956, 43, 27568, 3834, 13678, 18, 10398, 2899, 1922, 12043, 29764, 17, 21, 16, 2176, 1977, 5384, 2458, 1956, 2024, 17, 3154, 2697, 3286, 1922, 13510, 2213, 17, 2213, 1930, 2213, 17, 10590, 3719, 18, 1922, 2459, 16, 1920, 2213, 5921, 43, 26643, 3418, 1988, 3205, 10412, 2213, 17, 2213, 1930, 2213, 17, 10590, 3719, 1922, 5329, 8114, 18, 2052, 9059, 24032, 1925, 11837, 17, 3189, 3728, 7600, 1927, 2288, 6171, 17, 1942, 17, 6171, 8, 38, 4666, 8, 17, 14685, 1930, 1977, 5384, 2435, 1922, 6445, 2697, 6485, 2037, 2616, 12043, 29764, 17, 21, 1942, 4543, 18174, 1036, 18, 2176, 1977, 4152, 2007, 30311, 5883, 9914, 14061, 1977, 1010, 18, 3], "output": "MYFYKLESNTLSKYGYLPKYVVVEGWVFGFSYNFITKKADILSKSPDGLINSYFDVPIDTARLAEINPNGFYSMTQVSAQGGMGNALTAVGDIIQILSCAIAEIAGNISSVQEGCSGTLISGSVPVGSFETVACEGGVSECANIDLYDLYPLVTASQEKINVYLSDFKDNDGDGRTERDGDCNDYDRDIYPGATELCDDGIDNNCDGRTDESECRDLGIPVASFTAEPSSGKAPLVVNFDGTGSYCLKGSIISYSWSCSDGQSAARSTVVMAFNEPGTYTVRLTVTTQDGKTDTAEQKIVVESGK", "metadata": {"id": "A0A1W9LMT3", "cluster": 12396349, "interpro_all": ["IPR013783", "IPR022409", "IPR000601", "IPR035986", "IPR021655"], "interpro_used": ["IPR021655", "IPR022409", "IPR000601"], "interpro_unused": ["IPR013783", "IPR035986"]}, "task_type": "autoregressive"} {"instruction": "Here is the intended role of my protein: The protein carries a Hotdog acyl-CoA thioesterase (ACOT)-type domain that catalyzes the hydrolysis of acyl-CoA thioesters to yield free fatty acids and coenzyme A, acting on substrates ranging from acetyl-CoA to long-chain acyl-CoAs. Structurally defined by an antiparallel beta-sheet wrapping around a central alpha-helix, this domain plays key roles in fatty acid metabolism, phenylacetic acid degradation, and transcriptional regulation across prokaryotes and eukaryotes. In addition, the protein should feature a Thioesterase domain that catalyzes the hydrolysis of thioester bonds in substrates such as long-chain fatty acyl-CoAs and 4-hydroxybenzoyl-CoA. This activity facilitates diverse metabolic processes, including the conversion of palmitoyl-CoA to palmitate and the biosynthesis of 4-hydroxybenzoate. Also, the protein is included in the Cytosolic acyl coenzyme A thioester hydrolase family, which comprises bacterial and eukaryotic enzymes that catalyze the hydrolysis of fatty acyl-CoAs into free fatty acids and coenzyme A (CoA-SH). These cytosolic proteins regulate intracellular lipid metabolism and are expressed in diverse tissues such as the liver, brain, and brown fat. It is expressed in Halostagnicola sp. A56. Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 30, 1920, 2213, 16252, 43, 9529, 22389, 1029, 11337, 17, 10027, 30215, 2051, 12, 2000, 1991, 13, 17, 2601, 3418, 1988, 17097, 1920, 9128, 1927, 11337, 17, 10027, 30215, 1036, 1942, 4307, 3294, 5934, 4576, 1930, 22051, 43, 16, 8290, 1990, 6249, 6485, 2037, 6894, 17, 10027, 1942, 2815, 17, 4659, 11337, 17, 10027, 1036, 18, 12171, 3608, 2007, 1925, 28892, 4666, 17, 11130, 4573, 5041, 4760, 43, 4101, 4595, 17, 7864, 16, 2052, 3418, 5705, 3834, 5456, 1922, 5934, 2687, 4714, 16, 7971, 13722, 2687, 4877, 16, 1930, 5224, 3640, 3436, 28149, 1930, 15021, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 30215, 2051, 3418, 1988, 17097, 1920, 9128, 1927, 30215, 9031, 1922, 6249, 2427, 1966, 2815, 17, 4659, 5934, 11337, 17, 10027, 1036, 1930, 24, 17, 8275, 13058, 10921, 17, 10027, 18, 2052, 2455, 11374, 6445, 4487, 4028, 16, 2710, 1920, 7309, 1927, 25997, 17, 10027, 1942, 22047, 1930, 1920, 8132, 1927, 24, 17, 8275, 13058, 25120, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 9410, 11337, 22051, 43, 30215, 20748, 3416, 16, 2154, 12936, 4543, 1930, 10825, 5038, 1988, 18170, 1920, 9128, 1927, 5934, 11337, 17, 10027, 1036, 2460, 3294, 5934, 4576, 1930, 22051, 43, 12, 10027, 17, 2044, 13, 18, 2144, 9410, 2697, 5741, 4776, 4486, 4714, 1930, 2032, 3198, 1922, 6445, 3878, 2427, 1966, 1920, 3568, 16, 3068, 16, 1930, 8084, 3777, 18, 2176, 1977, 3198, 1922, 23226, 2156, 2531, 29902, 2056, 18, 22915, 1016, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "MTDLLETVVENREMVQPHHANALDVTHGGNVMKWMDEVGAMAAMRFAGEACVTARVDQMNFERPIPVGDTAFITAYVYDVGDSSVKVRIVTEREDLRTHERERTTESYFVYVAIDEDERPTSVPGLTVSTEEGERLRREARTGENSR", "metadata": {"id": "A0A063ZUC6", "cluster": 13547724, "interpro_all": ["IPR040170", "IPR033120", "IPR029069", "IPR006683"], "interpro_used": ["IPR033120", "IPR006683", "IPR040170"], "interpro_unused": ["IPR029069"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein is categorized in the Flavin transferase ApbE family, which acts as a Mg2+-dependent enzyme that catalyzes the covalent attachment of flavin mononucleotide (FMN) to threonine residues in bacterial flavoproteins. Also, the protein is a member of the ApbE-like superfamily, which encompasses Mg2+-dependent flavin-trafficking proteins (Ftp) that function as FAD pyrophosphatases and flavin transferases. These enzymes catalyze the hydrolysis of FAD to generate FMN, often facilitating the covalent attachment of the FMN moiety to specific threonine residues in target bacterial flavoproteins such as the Nqr redox pump. Members of this family share a conserved FAD-binding fold and are found in bacteria as well as lower eukaryotes, where they may be fused to fumarate reductases. It has been characterized in Acholeplasmataceae bacterium and is linked to UniProt keywords Magnesium, Lipoprotein, and Cell membrane.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 26758, 13763, 2100, 5873, 3416, 16, 2154, 8016, 1966, 43, 14756, 15, 17, 3100, 4113, 1988, 17097, 1920, 13577, 8576, 1927, 26758, 29932, 4749, 12, 29599, 13, 1942, 13143, 4248, 1922, 4543, 7732, 14070, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2100, 5873, 17, 3189, 13975, 16, 2154, 21569, 14756, 15, 17, 3100, 26758, 17, 9604, 2697, 12, 8916, 1034, 13, 1988, 2347, 1966, 14134, 20661, 2609, 18135, 1930, 26758, 13763, 1036, 18, 2144, 5038, 18170, 1920, 9128, 1927, 14134, 1942, 5655, 29599, 16, 3868, 12440, 1920, 13577, 8576, 1927, 1920, 29599, 11804, 1942, 2487, 13143, 4248, 1922, 2758, 4543, 7732, 14070, 2427, 1966, 1920, 20579, 1005, 9366, 8912, 18, 4678, 1927, 2052, 3416, 7948, 43, 5305, 14134, 17, 2743, 3728, 1930, 2032, 2435, 1922, 4802, 1966, 2486, 1966, 2826, 15021, 16, 2597, 2611, 2278, 1998, 10305, 1942, 28343, 11386, 1036, 18, 2176, 2258, 2252, 4378, 1922, 3546, 2456, 15403, 26317, 5376, 1021, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 13148, 16, 9694, 16, 1930, 2024, 3260, 18, 3], "output": "MKSLTKKIFAVLLFLAIFLITGCKQGIVYNEITLTGAFRNASNTVKIFTEKAQSEEKLAALKKDMDSILINLDMLFDIQGTYKDSELMQIKNQAGIAPVEVSSEVIYVIQEALKMSERSIVDGVALFDPTIAPVWNEWDFPNNVYDECFVDLGMELSLEEIDEIKAAIQATIEAGLVDYRNIEINLEESTVFLKKAGMEIDLGAIVKGYAADKIKTYLIEQGYTSAVIDIGGNIQILGNLADQPFKVGIRTPYKKWCNIDYNENYEPLDETYGTIMVI", "metadata": {"id": "A0A7X7C6X9", "cluster": 14110881, "interpro_all": ["IPR024932", "IPR003374"], "interpro_used": ["IPR024932", "IPR003374"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein is categorized in the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It is native to Gammaproteobacteria bacterium and is connected to UniProt keyword Cell membrane, Magnesium, and ATP-binding.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 1977, 10234, 1922, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 1977, 6196, 1942, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2024, 3260, 16, 13148, 16, 1930, 4498, 17, 2743, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MKIPEAITSEAAFIQEVIIFLVAMVASVLVVELLNSRRTGLSRIWAAFFYSLDGLKHLVFMPLPLMWKALLVFVTA", "metadata": {"id": "A0A967LDG5", "cluster": 14540323, "interpro_all": ["IPR000829", "IPR036945"], "interpro_used": ["IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein should include a Signal transduction response regulator, receiver domain that functions as a phosphorylation-activated switch within two-component systems to couple environmental sensing with cellular adaptation. It accepts a phosphoryl group from a cognate sensor histidine kinase, inducing a conformational change that activates an associated effector domain to regulate gene expression. In addition, the protein should include a Histidine kinase domain that functions as the catalytic core of two-component signal transduction systems, orchestrating cellular responses to environmental stimuli. It undergoes ATP-dependent autophosphorylation on a conserved histidine residue within a homodimer before transferring the high-energy phosphoryl group to an aspartate residue on a partner response regulator protein. This domain contains a dimerization interface and a structurally distinct ATP-binding cleft defined by conserved nucleotide-binding motifs. Moreover, the protein should contain a GAF domain that functions as a versatile signaling module structurally related to the PAS domain. It regulates diverse cellular processes by binding small ligands, such as cyclic nucleotides (cAMP and cGMP) to control phosphodiesterases and cyclases, or by acting as a light-sensing chromophore-binding region in phytochromes and transcriptional activators. It has been detected in Desulfoluna spongiiphila and is described by UniProt keywords Coiled coil, Transmembrane helix, and Transferase.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 2733, 8201, 2644, 7888, 16, 12608, 3418, 1988, 4088, 1966, 43, 4050, 17, 4128, 6195, 2651, 2288, 17, 4594, 3771, 1942, 15116, 4813, 9306, 1956, 3689, 7810, 18, 2176, 5861, 1036, 43, 12556, 2210, 2037, 43, 15786, 6443, 13873, 4016, 16, 7834, 43, 8523, 3185, 1988, 9094, 1925, 2458, 7917, 3418, 1942, 5741, 2359, 2294, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 13873, 4016, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 2288, 17, 4594, 2733, 8201, 3771, 16, 21991, 2287, 3689, 3387, 1942, 4813, 5458, 18, 2176, 14928, 4498, 17, 3100, 22009, 1990, 43, 5305, 13873, 6181, 2651, 43, 21189, 3119, 21902, 1920, 2149, 17, 3844, 12556, 2210, 1942, 1925, 12878, 6181, 1990, 43, 8240, 2644, 7888, 2213, 18, 2052, 3418, 5461, 43, 13640, 6854, 1930, 43, 12171, 4493, 4498, 17, 2743, 14649, 3608, 2007, 5305, 5489, 17, 2743, 8277, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 4357, 1038, 3418, 1988, 4088, 1966, 43, 20425, 3197, 9059, 12171, 2712, 1942, 1920, 9233, 3418, 18, 2176, 7014, 6445, 3689, 4028, 2007, 2743, 2858, 6908, 16, 2427, 1966, 9821, 9519, 12, 6225, 1930, 15958, 13, 1942, 2285, 24821, 1036, 1930, 16526, 1036, 16, 2014, 2007, 8290, 1966, 43, 3696, 17, 9306, 25801, 17, 2743, 3031, 1922, 25512, 2072, 4191, 1036, 1930, 5224, 15497, 18, 2176, 2258, 2252, 3330, 1922, 30311, 1945, 17864, 19513, 3907, 24888, 5148, 1930, 1977, 2910, 2007, 20709, 11569, 17524, 9121, 16, 9117, 7864, 16, 1930, 13763, 18, 3], "output": "MAFHMRLQTKLLVVVSVLVLGVVLVTSGLVTYSQKKRATESTYRLMERDARYLSRRISHNIYNSNWRTIQITLDMALQSNGDMLYYAIHDKDDRILFSSDTKSVGTWQPGCIAEAPQSEESVRYRSNEFTVRELPLSEPVAYKGAPRGAKGEVVFDTCMKVSYIGRPIGCLRVGYSTRELSAHIQKSATDVLAGGAAILLTVIPGLLILIRISIAPLGRLNRNLLLLRKRAETESIGKVLGSVDIDEISDGSTTTEIRELSLSFGALSGMLVENWQQLEAQQYNLEMNVTRRTGALRKANRALLREIAEKKEAEEKLRVKNSLMEALHDTTLDLMRHLEFNELLELLLRRAGGLMSMESGYYFEYRESTRQLYPIVTSGRFEEVPKLPTRIGEGLVGRVWETDRPLYVEDYKTWSGRVKGHPGLESLGASVAVPIRLEGNVGGVMGLAQFGDEFEMEETAMGVLARFAELASIALNNAMMHSKLQGELDERRRVEKEKDRLFQHLLQAQKLEAIGTLAGGIAHDINNLLMAVQGNISLIMSLTSPGDIVHKRGGKIEELVASGSALTSQLLGFARGGRYHVRPESVNTVVKSSLSMFGRTRKGIMISESLAEWLPNVEIDRTQMEQVLLNLYLNASHAMPDGGRIRIETGMTDLDDKLAAAFNLKSGAYVTVAVSDTGVGMDKSTQSKIFDPFFTTREMGRGTGLGLASAYGIVKNHKGAITVTSEKGRGACFTIHLPATAKPCWEDEASPLAIHSGEGTVLVVDDEPEIREVVKTMLKGLGYLCLEAENSSQCVSVYREKARDIDLVLLDVVMPDAGGDIAYQAMKKINPEVRVILCSGYSLEGRAEKMIEAGCNGFIQKPFTMEVLSTEIHRVMEG", "metadata": {"id": "A0A1G5CKL5", "cluster": 16928301, "interpro_all": ["IPR011006", "IPR003018", "IPR029016", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR004358", "IPR001789"], "interpro_used": ["IPR001789", "IPR005467", "IPR003018"], "interpro_unused": ["IPR004358", "IPR011006", "IPR036097", "IPR003661", "IPR036890", "IPR029016"]}, "task_type": "autoregressive"} {"instruction": "I want a protein that has the function: The protein should have a Hydantoinase A/oxoprolinase domain that is found in enzymes such as hydantoinase A and oxoprolinase, where it catalyzes the hydrolysis of internal imide bonds in 5-membered rings. It also functions in methanofuran biosynthesis by facilitating condensation reactions between furan-diphosphate precursors and gamma-glutamyltyramine. Additionally, the protein can be placed in the ATPase, nucleotide binding domain superfamily, which encompasses the nucleotide-binding domain (NBD) found in diverse proteins including actin, Hsp70, and sugar kinases. This domain constitutes the first lobe of a bilobed structure and contains a conserved ATP-binding site located in a deep cleft that facilitates ATP hydrolysis. Also, it is part of the 4-[[4-(2-aminoethyl)phenoxy]-methyl]-2-furanmethanamine-glutamate synthase (MfnF) family, which functions in the methanofuran biosynthetic pathway to catalyze the coupling of F1-PP with gamma-glutamyltyramine to form the methanofuran core structure, APMF-Glu. Members of this family exhibit a distinctive \u03b1/\u03b2 two-layer sandwich structure. It is present in miscellaneous Crenarchaeota group-6 archaeon AD8-1. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 3066, 2162, 43, 2993, 26182, 11413, 43, 19, 18588, 15743, 11413, 3418, 1988, 1977, 2435, 1922, 5038, 2427, 1966, 2993, 26182, 11413, 43, 1930, 18588, 15743, 11413, 16, 2597, 2176, 17097, 1920, 9128, 1927, 4495, 20697, 1021, 9031, 1922, 25, 17, 30261, 12750, 18, 2176, 2222, 4088, 1922, 17348, 4199, 20028, 8132, 2007, 12440, 16112, 5298, 2192, 28028, 1022, 17, 23266, 10416, 1930, 7034, 17, 25345, 3145, 29085, 2053, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 9444, 16, 5489, 2743, 3418, 13975, 16, 2154, 21569, 1920, 5489, 17, 2743, 3418, 12, 23889, 13, 2435, 1922, 6445, 2697, 2710, 4718, 16, 12886, 16, 1930, 9523, 7784, 18, 2052, 3418, 14879, 1920, 2561, 9581, 1927, 43, 5088, 16248, 1007, 3170, 1930, 5461, 43, 5305, 4498, 17, 2743, 3200, 4810, 1922, 43, 6515, 14649, 1988, 11374, 4498, 9128, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 24, 17, 37, 37, 24, 17, 12, 22, 17, 3835, 5188, 13, 3037, 7221, 39, 17, 4963, 39, 17, 22, 17, 28028, 11664, 3184, 7241, 25157, 17, 7627, 8921, 12, 8168, 3938, 13, 3416, 16, 2154, 4088, 1922, 1920, 17348, 4199, 20028, 14041, 3374, 1942, 18170, 1920, 7590, 1927, 9154, 17, 4108, 1956, 7034, 17, 25345, 3145, 29085, 2053, 1942, 2386, 1920, 17348, 4199, 20028, 4728, 3170, 16, 2100, 1035, 1038, 17, 9258, 18, 4678, 1927, 2052, 3416, 5987, 43, 15308, 160, 19, 161, 2288, 17, 4757, 18038, 3170, 18, 2176, 1977, 2481, 1922, 5682, 9631, 3646, 3478, 20164, 25588, 1021, 7336, 2210, 17, 26, 13470, 1916, 2041, 1025, 17, 21, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MIGWDIGGANIKVSAIKLKGNEIDSIRIIIEHFPIWKKPEKLPKILCEIKNRIYSKKPESMSLTMTGELSDVFRNKKEGVNYILDSASQAFNNYDYSVLNIRSKLISVDEAKANPIEVAGANWVATGWLISKKIRNCVVIDIGSTSTSIIPIMKGKIAALGKTDFEKLIVGELVYTGVLRTNVAAIVNEVPIKGAKVGISSEFFSQSGDIHLILGNISYEDYLTETPDNRGKNLINATKRLARVICADLEDLKKSEIIRIARYIYEKQIDQIMTGLEKVYSRLDPNNKREIPVITTGIGKKFLAKKAAKQLNIKKIVDINKIIDNFTFMATPAVGVAIMQAHKLLGRNVIWKH", "metadata": {"id": "A0A0M0BZL8", "cluster": 21996151, "interpro_all": ["IPR043129", "IPR002821", "IPR002756"], "interpro_used": ["IPR002821", "IPR043129", "IPR002756"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein should have a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. Moreover, the protein contains a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Furthermore, the protein should have a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. It has been detected in Pocillopora meandrina and is linked to UniProt keywords Transmembrane helix, Manganese, and Magnesium.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 3066, 2162, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 3950, 16, 1920, 2213, 5461, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 2176, 2258, 2252, 3330, 1922, 18660, 22538, 21086, 2667, 3883, 4058, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 7864, 16, 19516, 16, 1930, 13148, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MSAHTDSATFNRRSSTPSRRAWEETGEKPNKSVRQERTGSEGQKTMTSMESNGSTEVRLRSVEVGVEENANIKKNGKKNGAKDPEALKGDHVCEDSCCGDWTLFTRVFKSKRFESEKLEGILTFILIGLQFGMENEMPPETNAEGITLCIFAVAYILQSNLNWVSYILLAISCGFVLASVVCPPSEDVEPSHLPVRMRIAVFGGCLLPAIHLISSAAMNNKDPNLSRLLVGNLFIFVCANRRCIESRLTIMKENQNQERLLLSVLPRFVAMEMKADIENVSILFADIEGFTMLSSQCTAQKLVQYLNELFASFDMLAVENHCLRIKARPDHAHCCIEMGLEMIDAIASVREATGVNLNMRVGVHMGKVHSGVLGLVGRVHITDSVLNCLSGDYEVEEGRGQERDPYLKQYNIESYLIVAEHMQARLGITASNQQDPEDEVNEFLGSSIDARSIDKLRKYSQEKDRMFKSYTACILLLFVLIVMVQITTLPRTYVTMAVFISTFLVVGALFLLVVTSCRVVATVLVLTLYIAAIGNFFGCDLGRELMEGKSRCNESHLFSVMLVMIGCAVFLQLSTVHKFSMLAAMSTIFIVLIRVVFTDLFNNHWIDLSIVIVVMLTIALTAHGYLHEEISRLDFLWKLQATEEREEMEKLREYNKLAQQAKKNDELYYQSCDKVIVMFSSICNFSDFYTELDFQCIEKIKTIGETYMAAAGIKPESQEKLATLSHINLHSFNDFKMKIGLNFGPVVAGVIGAHKPQYDIWGILSTRGYTFECRGLVAVKGKGKMVTYWMTGKEGDQSNEPAGDSQNDLNKNVADGTSKGEIAQKDNTTNGFPDVNVLYQRYVFRLNQKFMSWLIGLLLLALIVNRSGSSPKSLYSPSDGVWLTTFFVYMTYTMITGVFTKYPTEISQRRAFLETESGASETMQFHKIYIQRHILGDCYYCVSGLPEKWQYDVWSDDVTTANHMESGGLPPRRKNTALKETKQDDQDKKDYVRPVLLTFKDPDKEELAEKCQNIPSGLRSISAKLAQSQSYVGLHPDTEFCDYPQYFTDKIHYCWLLPEEPISTGGYIKKLLYNILPDHVAQHFANGEGVECLRLLNEILVDFDELLSEQRVTMADFAMAMKKKLADIDTVNVASRMYSTGKPKHIQVTQSVYN", "metadata": {"id": "A0AAU9WRN2", "cluster": 22208343, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR009398", "IPR029787"], "interpro_used": ["IPR001054", "IPR018297", "IPR009398"], "interpro_unused": ["IPR029787", "IPR032628", "IPR030672"]}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein is classified under the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein includes a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. In addition, the protein contains a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is produced by Desulfobacterales bacterium and exhibits UniProt keyword tags Isoprene biosynthesis and Transferase. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 4152, 2007, 30311, 5883, 3955, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 26690, 1021, 8132, 1930, 13763, 18, 7031, 1920, 3244, 18, 3], "output": "MSAQSETLIVRAPAKVNLNLHILGKRSDGYHDLDTVMQKLDLADILTLRRLEHPGIQLACPDSDLPEDDSNLIWQAAAAYLEKTGLEKECGVSVILEKRIPIAAGLGGGSSDAGAVLTGLNQLFKKRLEENELLSIGAVLGADVPFFIVPYAAVHATGIGDRMTPHDALDKCSLLLVNPGFSVSTAWVYKNFTLTRPDKDSNLSDSRENESLSGGARPLYNDLETVTIVHYPELRDIKRFMNDCGASGTLMSGSGPTVFGVFPDQESNNNSGLQECAEKLTEKYGRGVFITRPVC", "metadata": {"id": "A0A7Z9YWN2", "cluster": 22291396, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR020568", "IPR014721", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is grouped in the Type II secretion system protein GspN, Leptospira-type family, which constitutes the GspN component of the type II secretion system (T2SS) distinct to genera such as *Leptospira*, *Geobacter*, and *Myxococcus*. This system spans the bacterial membranes to facilitate the secretion of folded proteins, including toxins and hydrolytic enzymes, into the extracellular space. It has been detected in Deltaproteobacteria bacterium and contains UniProt keyword associations Transmembrane helix.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2601, 2890, 5512, 2433, 2213, 5022, 27257, 16, 24060, 11979, 17, 2601, 3416, 16, 2154, 14879, 1920, 5022, 27257, 4594, 1927, 1920, 2601, 2890, 5512, 2433, 12, 5787, 5590, 13, 4493, 1942, 12774, 2427, 1966, 14, 24060, 11979, 14, 16, 14, 14136, 7972, 2341, 1915, 14, 16, 1930, 14, 21464, 8256, 14, 18, 2052, 2433, 23658, 1920, 4543, 5726, 1942, 6628, 1920, 5512, 1927, 16318, 2697, 16, 2710, 13599, 1930, 26702, 5038, 16, 2460, 1920, 5329, 5230, 18, 2176, 2258, 2252, 3330, 1922, 9649, 9218, 1021, 10296, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MRFKSILIYIGYSLAFVVSLYLFTLISLPEEEIAKYVIQRYIKPNDEMGVGDVVKKVSLERLKIGVSVFSYLFGKMPLSIRALFIDVDTDDVDLSQVDYLKEKSGLNLKGILSLSFRLNYNKKESQKNNGAIKLKGEIEIKEGKFKVINFKSKGKDVEIRITGDGQFTSPPGFIDRQEKIKTLLFGIGNTLDREGFYNFAIKGSISNPTFTPEKKGINITYKSASISPDLSLVLKDVKGFGGDISISLGTKKDEISIADVAIKGGKIMGFEAPPVDIGDSKGSLNLTLRFKPSQ", "metadata": {"id": "A0A7V5P343", "cluster": 23973654, "interpro_all": ["IPR030925"], "interpro_used": ["IPR030925"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein is classified under the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is produced by Elusimicrobiota bacterium and is associated with UniProt keywords ATP-binding, Cytoplasm, and Transferase. Can you generate the amino acid sequence corresponding to this polypeptide chain?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 13022, 4659, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 4152, 2007, 2349, 24327, 4913, 15129, 3940, 3857, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MIFGLTGGIASGKSTVLNQFAHLGAKIIESDRIAHDIYAKGKPVYKKIIKQFGREVLNAEKNIDRRKLGKIVFSNQSQRKKLEKITHPEIIAEIKNQINRFKRSNKVIMVDAPLLFEAKLQKMFDKIIVVWIPEKVQIQRLIKRDKITKAEAQKRLSAQISLDKKKKIGDYVIDNSGSPAATAAKIKCFWQVFGQGPVKPSKKVTLVGACRAI", "metadata": {"id": "A0A947VSK7", "cluster": 28220014, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein has a BTB/POZ domain that functions as an N-terminal homodimerization module, typically mediating transcriptional regulation and chromatin remodeling in proteins containing C2H2 zinc fingers or Kelch repeats. It forms a tightly intertwined dimer with an extensive hydrophobic interface and a surface-exposed groove that serves as a specific peptide-binding site. Furthermore, the protein is a member of the SKP1/BTB/POZ domain superfamily, which functions as a versatile protein-protein interaction motif involved in diverse cellular processes including transcriptional regulation, cytoskeleton dynamics, ion channel assembly, and targeting proteins for ubiquitination. Characterized by a conserved 2-layer $\\alpha/\\beta$ fold, this domain often mediates transcriptional repression by interacting with histone deacetylase co-repressor complexes such as N-CoR and SMRT. It is derived from Sistotremastrum niveocremeum HHB9708. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 2258, 43, 29034, 19, 2510, 1011, 3418, 1988, 4088, 1966, 1925, 56, 17, 4262, 21189, 2466, 9059, 16, 5745, 10239, 5224, 3640, 1930, 6338, 8378, 1922, 2697, 3165, 8453, 6951, 7997, 18233, 2014, 16080, 2072, 9569, 18, 2176, 4952, 43, 12129, 27332, 17860, 1919, 7632, 1956, 1925, 6475, 7919, 6854, 1930, 43, 3154, 17, 4616, 15920, 1988, 10634, 1966, 43, 2487, 4207, 17, 2743, 3200, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 3097, 5113, 19, 29034, 19, 2510, 1011, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 2213, 17, 2213, 2835, 5219, 3286, 1922, 6445, 3689, 4028, 2710, 5224, 3640, 16, 11612, 5565, 16, 4755, 4999, 5957, 16, 1930, 5133, 2697, 1958, 11758, 18, 4378, 2007, 43, 5305, 22, 17, 4757, 8, 38, 4595, 19, 38, 4666, 8, 3728, 16, 2052, 3418, 3868, 10412, 5224, 10084, 2007, 8615, 1956, 6632, 19489, 2081, 17, 14434, 5048, 2427, 1966, 56, 17, 2233, 1930, 28018, 1031, 18, 2176, 1977, 3595, 2037, 19149, 4575, 4265, 3368, 2156, 24277, 18054, 1021, 10981, 17800, 1989, 9645, 1014, 8528, 13895, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MSGFSMENHIGCWDAFFCFPDGDLIIRTEGRLGFKVHKSVMGMISNVFRDMFSLEEINLFPVHPPPPLLSYIDPETKKTLALVDVPEDNSVIRYALGMIYHAPRAERSFVPMSIDFIQKIVDVIDRYDMPRLREPLQDLILTDFHSLTPIRFYAVAKLNDLDRVAKATLPYVVGRNIHRLPPHEIPDEMGSLPFREYHKLHFFSERRAALIIKALDAVTPPPCLCKHEGNNISPDTRIKCDTWAIYLKMAKKEVAVVPTHSITSNDFRSKAAQKSACPFAHRWLFDERGAVFIKLENKVKTLLWAFDSEYSS", "metadata": {"id": "A0A164Y5Q3", "cluster": 28839240, "interpro_all": ["IPR000210", "IPR011333"], "interpro_used": ["IPR000210", "IPR011333"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a polypeptide chain that performs the following role: The protein is classified under the Immunoglobulin-like fold superfamily, which comprises domains characterized by a beta-sandwich of seven or more strands arranged in a Greek-key topology, facilitating protein-protein interactions often via beta-sheet interfaces. These domains are ubiquitous in animal proteins, playing critical roles in immune recognition, cell adhesion, and structural integrity in muscle proteins such as titin. It is produced by Hyalangium minutum and carries UniProt keyword assignments Hydrolase and Protease. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 11837, 17, 3189, 3728, 13975, 16, 2154, 12936, 4682, 4378, 2007, 43, 4666, 17, 18038, 1927, 5260, 2014, 2253, 13214, 14940, 1922, 43, 27568, 17, 3834, 13678, 16, 12440, 2213, 17, 2213, 3719, 3868, 3454, 4666, 17, 11130, 14857, 18, 2144, 4682, 2032, 15498, 1922, 4027, 2697, 16, 14797, 4140, 5456, 1922, 3743, 5708, 16, 2024, 6141, 16, 1930, 4346, 7996, 1922, 3760, 2697, 2427, 1966, 7090, 1921, 18, 2176, 1977, 4152, 2007, 14871, 9506, 1989, 2360, 30454, 1930, 16252, 20709, 11121, 2538, 18306, 20748, 1930, 7154, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MSRVEFFLDGNYMTSVTSATYSTFWFTDDFPNGPHVLTAKAYDGDGHVTTSAPVSIIVDNDYVPPAVSIISPAQGASLAGMVSVEASASDDRSVSSVYFYADGTFVKAVYSAPFVLTWDSHAVPNGTHTLTAEARDEQGNRTLSVPVTVTVAQPGSAEYDLGRGVPTCPEGSSICDTAALVQGRGFYGPEPHAPNTIGGSCADGTDNSYRDEQIHWLRVSRSDGLPFAAGRRVRVDVAVEADLFPGYVVELFSATDASAPVWTHLATHRLDWNMRDLQVFSSEYVLPEGRVQAVRANYHYGEMFPTPCSNGPIDDRDDLVFGVGEAVDVAAPTAVITAPVANQQITGTFTVKVAAEDDFNVTRVEVYDGQTLIGTDTTAPFAVAWGTQTAADGTHTLTAKAYDAVGHVGTSAPLSMIVDRNRPGVALTAPARASVVRGVVQLTASASDDRGVTRVEFYEYGYYASALIGTDTTAPYSVPWDTLAFSNVQHGMFARAFDIAGNYQDSEIIGITVDNASPTVVITSPANGAKVSLSTTIQANASDTNGVAQVAFYDGSKLIGTDTTAPYSVTWGLLLVSRGQHTLTARATDLVGNVTTSALVVVTVQ", "metadata": {"id": "A0A085W3C7", "cluster": 270454, "interpro_all": ["IPR013783"], "interpro_used": ["IPR013783"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein features a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Also, the protein is a member of the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Additionally, the protein is grouped in the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. It is found in Vairimorpha ceranae and features UniProt keywords ATP-binding, Magnesium, and Nucleus.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 4075, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 2176, 1977, 2435, 1922, 9315, 23576, 12492, 11119, 2722, 6580, 7241, 1021, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 13148, 16, 1930, 5607, 18, 3], "output": "MEKNSRYGITGPLSLQESTLKEKQCSEEMDKFIQDCGFFEDESEGQTRERVLGKLNSFGSYRLGVHSKGADIDVLCVVPKHITRKDFFTDFFELLSQDSDVKEITKIEEAYVPLIKLTYLKNMDDKCVLSINGSRVTDEILNLIPNVKTFHSALRCIKYWAKRRCIPNASSYTIVSKFFELYSFWKWPSPVLLKPVIDLSYNMKVWDPKLICSTHNIIASTQQLIINEFTRGHEIFCNEKGTTKDILKKLCSLSDFFYKESKIRILALKIESLDDVLYAVPFPRSFNITKEKLSFFTFKTKHIKICTSDHPIKEFIEFINNYDKKDENMKLEINSMKKRDVHAFFSVIYKLLKQFVQKTSENKNIYLNDKNNNNGKIFTIIQGIPIDLTFARLNIGIVNDNVNLLNNYGNSYGYYGGVAFSISVGRICQLFYPADKYHKMPVITPAYPSYKSYIQINAISQDETNHKLWLGFVFFIGLECPSTKAKKVFI", "metadata": {"id": "A0A0F9ZDX1", "cluster": 2667672, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR007012", "IPR043519", "IPR011068"], "interpro_unused": ["IPR007010", "IPR048840", "IPR014492"]}, "task_type": "infilling"} {"instruction": "The protein is included in the Large ribosomal subunit protein uL22 family, which constitutes a core component of the large ribosomal subunit that directs the proper folding and stabilization of the 23S rRNA by interacting with all six of its domains. This protein serves as the largest contributor to the surface of the polypeptide exit channel and is situated at the putative translocon binding site on the ribosome's exterior. It is identified in Blattabacterium sp. (Carbrunneria paramaxi) and is associated with UniProt keywords Ribonucleoprotein, Ribosomal protein, and rRNA-binding. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 3103, 11196, 5903, 2213, 3570, 4460, 3416, 16, 2154, 14879, 43, 4728, 4594, 1927, 1920, 3103, 11196, 5903, 1988, 28351, 1920, 3405, 10328, 1930, 10281, 1927, 1920, 3020, 1036, 9067, 2007, 8615, 1956, 2136, 3798, 1927, 2496, 4682, 18, 2052, 2213, 10634, 1966, 1920, 7585, 17679, 1942, 1920, 3154, 1927, 1920, 13022, 14185, 4999, 1930, 1977, 18287, 2019, 1920, 6770, 12930, 1916, 2743, 3200, 1990, 1920, 12794, 11, 61, 2897, 18842, 1924, 18, 2176, 1977, 2899, 1922, 18208, 3519, 20013, 2341, 18842, 1989, 2056, 18, 12, 3697, 3176, 16443, 18339, 3167, 3013, 1033, 13, 1930, 1977, 2458, 1956, 20709, 11569, 18347, 6657, 16, 11196, 2213, 16, 1930, 9067, 17, 2743, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "ASASLNGVRSSPRKIRLIVDLIRNREIQKALDILTYSNKKRISFFLKKLLLSLLSNWKKKYNDFHELYIKEIRVNQGKTLKRLRPVPQGRGHRIRKKSSNVIVLLEKR", "metadata": {"id": "A0A6G6BNU9", "cluster": 7146610, "interpro_all": ["IPR001063", "IPR005727", "IPR047867", "IPR036394"], "interpro_used": ["IPR001063"], "interpro_unused": ["IPR047867", "IPR036394", "IPR005727"]}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein carries a HPr kinase/phosphorylase, C-terminal domain that functions as the catalytic core of the bifunctional enzyme HprK/P, regulating carbon source utilization in Gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 on the phosphocarrier protein HPr and its dephosphorylation via phosphorolysis, typically within a hexameric assembly. Moreover, the protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein incorporates a HPr(Ser) kinase/phosphorylase, N-terminal domain that constitutes the structural blades of the hexameric HPr serine/threonine kinase PtsK, a sensor protein controlling bacterial carbon catabolite repression. This domain facilitates the assembly of the enzyme's three-bladed propeller structure, allowing it to function within a multicomponent phosphorelay system. It has been detected in Lentibacillus sp. CBA3610 and is classified with UniProt keywords ATP-binding, Carbohydrate metabolism, and Transferase.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 16252, 43, 18542, 4016, 19, 12556, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 1920, 29491, 4113, 18542, 1040, 19, 58, 16, 6773, 5056, 4585, 8422, 1922, 8604, 17, 2843, 4802, 18, 2176, 17097, 2321, 1920, 4498, 17, 3100, 4050, 1927, 2375, 17, 4182, 1990, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 2496, 16881, 3454, 3421, 6892, 16, 5745, 2651, 43, 25602, 1935, 5957, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 19683, 43, 18542, 12, 2375, 13, 4016, 19, 12556, 2051, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 4346, 22707, 1036, 1927, 1920, 25602, 1935, 18542, 8468, 19, 13143, 4016, 8618, 1040, 16, 43, 6443, 2213, 7138, 4543, 5056, 3115, 3016, 2394, 10084, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 4113, 11, 61, 2559, 17, 22707, 1007, 5062, 13728, 3170, 16, 7201, 2176, 1942, 2347, 2651, 43, 8844, 28155, 1939, 3421, 15208, 1012, 2433, 18, 2176, 2258, 2252, 3330, 1922, 10226, 7972, 10401, 5277, 1036, 2056, 18, 26853, 5677, 2930, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 10590, 4714, 16, 1930, 13763, 18, 3], "output": "MMAKVRTQDLLDNFNLTLVATGYFDYYPRERLQLIGKTEMAYITPVIVISRGMDIPDVMLETADKAGVPIKFAPFTAIHGVLVDIYGVGVLLTGQSGVGKSRQEDYDRLIGNSPPLIEHLLEIRGLGIIWDEKKQYDRLGLDEETMKVMDVNLPKATILKRMGVNAAEEFSERLTDMIDQGNETDGADGVHREITSSDVHRPGIEMFLDLSDEAKRSRMEQLCTDLHSPRQTTRVISRLTNYLEAESALELVKRGHRLIADDSVEINVMTLFGAGAVRSHKKISLIINLELPVRPGRNLAVIIEVAAMNFR", "metadata": {"id": "A0A7H8S7D8", "cluster": 7834385, "interpro_all": ["IPR003755", "IPR011104", "IPR011126", "IPR027417", "IPR028979"], "interpro_used": ["IPR011104", "IPR027417", "IPR011126"], "interpro_unused": ["IPR003755", "IPR028979"]}, "task_type": "infilling"} {"instruction": "Here is the intended role of my protein: The protein is categorized in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein should feature a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Furthermore, the protein should feature a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is produced by Clostridium uliginosum and is connected to UniProt keyword Isoprene biosynthesis and Transferase. Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 30, 1920, 2213, 1977, 10234, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 4152, 2007, 21156, 3570, 1950, 11096, 1989, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 26690, 1021, 8132, 1930, 13763, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "MKVKAYAKINIALDVIGKREDGYHLLRMIMQCIDLYDVVEIEKISSGIQLKCNKSYVPTDERNLAYKAAKLFKETYKIECGVCINLEKNIPVSAGLAGGSTDAAAVLKVMNKLFNINVSENELMELGLKLGADVPYCIVGGTALCEGIGEKLTKLKPFKDKILVLVKPPFGVSTKEVYKAFDLSKVVFHPKTEELISNIEKDNFQFVANNMKNLLENVTLGRHRVISVIKEDINDSGAIGSIMSGSGPTVFGFFDDMLKAQRCYENMKKKYVDVFITRTI", "metadata": {"id": "A0A1I1ID95", "cluster": 8248548, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR013750", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein includes a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. In addition, the protein should include a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Also, the protein carries a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It is native to Acanthoscelides obtectus (Bean weevil) (Bruchus obtectus) and exhibits UniProt keyword tags Magnesium, Metal-binding, and Transmembrane helix.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 5921, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 2222, 16, 1920, 2213, 16252, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 1977, 6196, 1942, 25645, 21624, 11085, 7980, 25683, 2089, 1957, 12, 21266, 2038, 9488, 1970, 13, 12, 20788, 24315, 1036, 25683, 2089, 1957, 13, 1930, 9826, 20709, 11121, 2538, 14392, 13148, 16, 6048, 17, 2743, 16, 1930, 9117, 7864, 18, 3], "output": "MSFSNNISIQSDTGSIKNGKIEEHLDDYPCSTNPEKMYKGIYWPSLTNSFHCKHLELAYLRYSHRQRQKALIIVNIVDLLLKIALILVVIIWSVCCMSINIAVCVLGWWRCFANNYLHWAAVCTWFDLVWYVLFTIFVQYAMLPLPLRWCMLAGGLSSIGHIVTISVECKIRMIVANTLLYICVNFAGMYTKYLTDRSQKQEKLLLSVLPDFVAREMIKDIEREEKGGAFQVHQFHKIYIHRYENVSILFADIKGFTAQENYCLRIKLLGDCYYCVSGLPTPRSDHAHCCVEMGLHMIIGIHSGSVLCGVLGLRKWQFDIWSSDVRLANHMESGGKPGQVHNGQERDAYLKEHRVVTYLIKQVEPMRSRRRLASRPSIFSNKLWPPEERSDSGIQQSGIDDENTTDWTPEIPFENLHRTLSNELEEETTFIPTVEQVDDIIDHSIEIESNKRMRNANVNPWTLRFKDKDMELKFSQLFIVICQAIIVNLAQYFVVICIILTTLILTSISVLVMAEEFEQLPVSLLINISENPNLNITEYNSNPLVGARVLNVNVQATVHNNFTINVENKPENITKLANKTNTVLQSLNLKLSNLSRSLRFNRRRRKRSLVVGGSINMLRPNCKHPEYIVFTWVLCMVALATALKLYYLIKLFLAILMVVIYTMSSQMLILLNVFFLMVAYHARLVEVTSRLDFLWKQQAERELNDMEETRHNNTSSERNSEELYAQYREEIGVLFASIPNFTDFYSEDINKGVECIRLLNEKIKTISATATYMAASGLNPSHKDLRNSDSPEHLCALVDFAMSCGPLVCGVIGARKPVFDVWGDTVNLASRMDSTGVMGTIQVPKLMETYYVTGRQVKRPPSFQRQPSHPSSLAAVVYALAQTRRKHTVNRIINYSSMRLSQRPGGYPIRRNTTRAHQKQMHARSQPNMRQLNNHHKMAVSQSAPHTPVSATSHEGSIFKSVPRLLSEPIVNRSKSCSPGSKGSPKKKDSKFSLRSPLIKRETKVQVDRDRLNKVHSLDGTHVIMCVLDEDTYSAVHKADFATVFKSGLWTVFNNYQIDPRKYADLLTVQSLGGRAVGFSDKEYMFIFDSKRHDHMRKAFLETHRSMEMRYRTQNENDLASKCTAQELVKILNELFARFDRLAKAIKDTRQRTQVENLDMRISESTYQSLNGAYEVEPGDDDLKSGNTTPKSPSTPVSIPMQSETVSYKQKYDTVEKYKKRNSREDMFKSNMMCCFVIWLQKISSTFMHNRRRRTLLICGVIILMSIMSSITNCTDNCLKKLIGNIDIDGILKDAHNITSIEPDSESETNDTFSLILRPTDNIFRFFTSNPKADIPQLLKNILPDHVAQHFLEIIADFDELLDEERFSTIEMRVKLDEINKDSFNDFGLRVGIETAQMLGMRGYELKKRGIVDVKGKGTPGSAVLGRARTQQRADGRSGSGTYLENMKSMRSIDHDPIPHRDRKLDSYANDLNDSFKIKNTNVVAAQ", "metadata": {"id": "A0A9P0L3A4", "cluster": 8516702, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR009398", "IPR029787"], "interpro_used": ["IPR009398", "IPR018297", "IPR001054"], "interpro_unused": ["IPR032628", "IPR029787"]}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein is classified under the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. In addition, the protein is classified under the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It originates from Pseudomonadota bacterium and is classified with UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 22970, 2037, 11520, 3947, 12595, 3857, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MRVVGLTGGIASGKSTVSVVEPDRRAWKRIVGRFGPEIAQERRFLNRVTHPPIYWEILKSLARHLLFETPLRLFLRPVVVVYADPGTQLEAMRKIRAQMPLEEKKKRADYVIDNLWRRLAPGRGPVSPHSDLLRQLGAVVIDADRIARRLLPDRTLDRKRLAERVFRSWWMKTPLVVVDAAERLVRRDGIDRESGSLERTAQQVQD", "metadata": {"id": "A0A7C4SUR2", "cluster": 12097546, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein incorporates a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Also, the protein includes a SNF2, N-terminal domain that functions as the catalytic ATPase component of the SNF2/SWI complex to disrupt histone-DNA interactions and remodel chromatin. By utilizing energy derived from ATP hydrolysis, it increases DNA accessibility for critical processes such as transcription regulation, DNA repair, and recombination. Additionally, the protein possesses a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. It is present in Chaetothyriales sp. CBS 134916 and has UniProt annotations Hydrolase and Nucleus.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 19683, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2222, 16, 1920, 2213, 5921, 43, 22280, 1028, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 9444, 4594, 1927, 1920, 22280, 1028, 19, 19532, 2796, 1942, 12512, 6632, 17, 2678, 3719, 1930, 7456, 1938, 6338, 18, 2007, 10232, 3844, 3595, 2037, 4498, 9128, 16, 2176, 4041, 2678, 12995, 1958, 4140, 4028, 2427, 1966, 3213, 3640, 16, 2678, 5059, 16, 1930, 7827, 18, 4950, 16, 1920, 2213, 14465, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2176, 1977, 2481, 1922, 13297, 19446, 28935, 3027, 3955, 2056, 18, 16341, 12724, 12118, 1016, 1930, 2258, 20709, 15010, 20748, 1930, 5607, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MRPFKPLTLRKPGLITRASSTESTEPTEPTTKRRKVLPTYIPPGDEALMPISNPPSTEVLNITPIASHYTVLWRNPTLKKNKTWTGDGVLSLSGGIATLYDSSGKTTIGGKEVEIDSVICREQFLTTVLPKAKTGPQTFVSSGPKNISTRITTSAAKEIKTAYRVPVKTSIDHRQSLIDMPMPRYDPEARGALLFRRPKEPPAGKQECVSGLRDPNHQGCILADDMGLGKTVQTIALLWTLIKQNPIYKQPPVVKKALVVLSHTNVGVLVFEDPKSTKLKMFDGRVYNVMIIGYERLRTVADELANSHDIDAIQSLNTARRIILSGTPIQNDLTEFYCMVNFVNDGCLGSAKAFVRDFEQAAAEELARTTSSFILRRTADILSNILPKKTEFVLFCKPTAEQAKLYRSIVSSPMFTSAVGLFNMDGAKSTADAGVSKSLTALNEVLDPSLLRLYRNDLSAKIRLLDILLQEIRQTTDEKVVLISTGLRYLQLDGSTSSGKRQALVDQFNQSPPSKAFAFLLSAKAGGVGINLVGASRVVLFDADKRPTIIYRFIAKGTIEERIWQRQMVKRGLADSILENGDHSDTSISKRSKTLGLRTHDLIGCKCTRGMTTDAASKSERHQSPELPGLGDIVPASQLNMDESGSFSPGKDSAHIIAELEKLQLNIDDSCLTHLLLQDEDEVASSVEFVFKRVWGTSVTITHNAAKPLSHLGLCAYSRPLLPGLTLCYNSQQFSEHKHANPLVLQGATVIASSSIVDVVLDPSLGKSLHAHQKEGVQFMYCPVSVIQNWKREFRKWIVVCDEGHRLKTEKNKSAKNPIMRSRQPHAATDAIEKGLQLITILKKLCNSPALLKASYTSTLNLLANLLNNWNPATEDQAIARVHRQGQGAAFSTEELRDLFRYDDKRELDYEELMKYSHIDTSRVSSYADGT", "metadata": {"id": "A0A3M7NUT9", "cluster": 13599025, "interpro_all": ["IPR014001", "IPR001650", "IPR027417", "IPR038718", "IPR049730", "IPR000330", "IPR050496"], "interpro_used": ["IPR001650", "IPR000330", "IPR014001"], "interpro_unused": ["IPR050496", "IPR027417", "IPR049730", "IPR038718"]}, "task_type": "infilling"} {"instruction": "The protein should feature a Zinc finger, SWIM-type domain that functions as a zinc-binding module involved in diverse signaling and regulatory pathways, including homologous recombination and the ubiquitin-proteasome system. It is found in prokaryotic and eukaryotic proteins, such as MEKK1 and the E3 ubiquitin ligase MEX, where it is essential for mediating protein interactions and ubiquitination activity. Also, the protein has a Zinc finger, PMZ-type domain that functions as a specialized DNA-binding motif specifically associated with plant mutator transposases. It facilitates the recognition and interaction with genetic elements to support the transposition process within the plant genome. It is produced by Lactuca sativa (Garden lettuce).\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 7997, 8497, 16, 12283, 17, 2601, 3418, 1988, 4088, 1966, 43, 7997, 17, 2743, 9059, 3286, 1922, 6445, 3197, 1930, 4948, 3873, 16, 2710, 8725, 7827, 1930, 1920, 6526, 17, 9993, 2433, 18, 2176, 1977, 2435, 1922, 21545, 1930, 10825, 2697, 16, 2427, 1966, 12551, 4835, 1930, 1920, 10968, 6526, 11905, 10114, 16, 2597, 2176, 1977, 4415, 1958, 10239, 2213, 3719, 1930, 11758, 2455, 18, 2222, 16, 1920, 2213, 2258, 43, 7997, 8497, 16, 4394, 1011, 17, 2601, 3418, 1988, 4088, 1966, 43, 11021, 2678, 17, 2743, 5219, 4475, 2458, 1956, 4496, 2446, 3061, 12935, 2319, 18, 2176, 11374, 1920, 5708, 1930, 2835, 1956, 3299, 5362, 1942, 3373, 1920, 22596, 2585, 2651, 1920, 4496, 3843, 18, 2176, 1977, 4152, 2007, 5641, 29394, 22939, 12, 26981, 23121, 3005, 13, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MFFNGNVQTGRAVSDVLISNMCEIREYLMKRICNVMKEMKKAKGPLTPTWNGGDKYQVTGALGDQHVVDVMNKLNKMSKDLEAELDIYKWVHNGRVGRLRKKEDKVRVKGVFKGKIEKGRDKPVIGCFEYTTDILAARKTVVSQYIARTCTCRKWELIGIPFIHAIVTSMWPKSECPTKLIPPPHRTQ", "metadata": {"id": "A0A9R1XC42", "cluster": 15327820, "interpro_all": ["IPR006564", "IPR007527"], "interpro_used": ["IPR007527", "IPR006564"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: It is part of the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Furthermore, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is native to Elusimicrobia bacterium CG1_02_37_114 and has UniProt annotations Cytoplasm and rRNA processing. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 2176, 1977, 3131, 1927, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 6196, 1942, 2349, 24327, 4913, 15129, 2126, 14061, 7294, 1009, 41, 5725, 41, 3191, 41, 11296, 1930, 2258, 20709, 15010, 5239, 1930, 9067, 4587, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MVIHTPVLVKEVIKYLRIRPEGVYVDATVGTGGHAKFILEKLKTGLFVGIDRDKYQLDITRNYLKAYKKKARFFQSNYTSLKELLKKLQIKFIDGILFDFGISSIQLETPSRGFSFQSDGPLDMRMGTTGKNTITAGDIINTYSRENLAEIFYKYGEEKYSRRIASGIVDYRSSKKIESTEELNRIIISAIPNNFYSVNISARIFQSLRIAVNDELDNISAGLNKAVGVLSKGGRIVAISFHSLEDRIVKNFFRNKKPELKILTAKPIVPAEEEIEKNPRSRSAKLRSAERL", "metadata": {"id": "A0A1J4YMQ9", "cluster": 16092389, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein should feature a UvrD-like DNA helicase C-terminal domain that constitutes the C-terminal half of the RecA-like core in Superfamily 1 helicases, undergoing significant conformational swiveling to facilitate ATP-dependent DNA unwinding. Typically exhibiting 3'-5' polarity, it is essential for genomic maintenance processes such as nucleotide excision repair, mismatch repair, and replication. Also, the protein belongs to the DNA helicase, UvrD/REP type family, which catalyzes the ATP-dependent unwinding of double-stranded DNA into single-stranded DNA. This family includes both UvrD and Rep helicases, with Rep proteins functioning as dimers composed of four structural domains. It is identified in Crocinitomicaceae bacterium and carries UniProt keyword assignments ATP-binding and Isomerase. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 5819, 8544, 17, 3189, 2678, 15318, 45, 17, 4262, 3418, 1988, 14879, 1920, 45, 17, 4262, 4768, 1927, 1920, 21534, 17, 3189, 4728, 1922, 13975, 21, 29919, 16, 7258, 2228, 8523, 19532, 2035, 1941, 1942, 6628, 4498, 17, 3100, 2678, 26801, 18, 5745, 12196, 23, 11, 17, 25, 11, 12432, 16, 2176, 1977, 4415, 1958, 4935, 6291, 4028, 2427, 1966, 5489, 10940, 5059, 16, 10265, 5059, 16, 1930, 5158, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 2678, 15318, 16, 5819, 8544, 19, 3073, 2601, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 26801, 1927, 4825, 17, 10338, 2678, 2460, 2957, 17, 10338, 2678, 18, 2052, 3416, 5921, 2321, 5819, 8544, 1930, 3073, 29919, 16, 1956, 3073, 2697, 7295, 1966, 13351, 7179, 1927, 3006, 4346, 4682, 18, 2176, 1977, 2899, 1922, 9442, 3665, 8752, 4913, 9914, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 1930, 25510, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MQLSVYKSSAGSGKTFTLVKDFLTLALISDKPELVRNILALTFTNKAAQEMKDRILDSLHAFANGPISGKNLALLESLCASKKLKLSEDEIKKRSEKLLKYILHNYSSFSVSTIDKFNYRLIQTFAQDLGVSSSAEVELDELELLEEAINNLLEESATNDLLAEWLTDFLISQLNEDKSWNIKRHFIDFSKITLNENDQYLIDQLSELELSDFKNILKNTRKRISIIETEAKAIAKTGYDVLRNHDIDSDNYFGGKNSVTIFLRILQESTLEKFPNPAILTMLDKEDWSKGGAPTDQKNKIEASKEEFIHIINKGLEFGDREVEKWILLKALLKNIHGVGLLSEVRKKFKLLTEELNVIPISTFNKNIANVVRNEPSPYIYERLGNRYRNFLLDEFQDTSKMQWHNLLPLVENGLSTLGNSLIVGDAKQAIYRWRGGDADQFVYLPKITDPNADELTLERSKLLEQYINNQTLTSNWRSSAEIVKFNNNFFSKLVKIKGGLIADVYQSVEQEPQLKDVSGYINYELIPVEGKEPELEESVTQEERLLNAVFARIQDLLNKCYQKGDIAILCRSNKQISALSQYLAPKIDIVTSEGLLLFSHPSSLLLHTAFKHAQLSRNLTKDEQTTKTNLSVQIILLLSKLGKITQEDLHEFLSSVAEDKSDINLNLMLSSLGIDYKTEEIEGLTIYQQIMGLARMFGLSNHPSPYIILLLEKTLEYSKKYPAKTASQFIKWIELKGEKTSLALPENMGAVKIMTIHKAKGLEFPAVIFPFANTVVKSDTKLWVNSNYLDVGLPFGLINSSSTLERTKFSEIYNSEKSKTWLDTINTYYVAFTRAENALFIIAHEYKRSKTDMRSVYQPILEEYSEFNKEKNSLELGVLAPPERRKEVDSPLKQSVFLEKIYCENWLENIAFAPVFRNDSSSLSPSAYGDLVHELLRSIVNSSQYAEQLEPRLSLMNIEANTKLKIESEFKALFEHKTFRKLFDSPGKRYLERDMIASNGKIIRPDCVILGSEKNILFDYKTGTPELAHEKQILEYKNNLEVMVNKPVEAYLVYTENAQLKKVN", "metadata": {"id": "A0A2E2TCK0", "cluster": 18125004, "interpro_all": ["IPR014017", "IPR000212", "IPR027417", "IPR014016"], "interpro_used": ["IPR027417", "IPR014017", "IPR000212"], "interpro_unused": ["IPR014016"]}, "task_type": "autoregressive"} {"instruction": "The protein has a DTW domain that is predicted to function as an S-adenosyl-L-methionine (SAM)-dependent acp transferase. Characterized by the presence of a conserved DTXW motif, this domain is found in proteins such as human DTWD1/DTWD2 and Escherichia coli YfiP. It is derived from Deltaproteobacteria bacterium and is classified with UniProt keywords tRNA processing.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 7711, 1018, 3418, 1988, 1977, 4396, 1942, 2347, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 18543, 13763, 18, 4378, 2007, 1920, 2990, 1927, 43, 5305, 7711, 1039, 1018, 5219, 16, 2052, 3418, 1977, 2435, 1922, 2697, 2427, 1966, 2616, 7711, 29322, 1009, 19, 7711, 29322, 1028, 1930, 10210, 5178, 29962, 2049, 18, 2176, 1977, 3595, 2037, 9649, 9218, 1021, 10296, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 10089, 4587, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MLVGLCLCAEIPQVATRHRFLLIRHRLCQLCQYGTRTEPPTPPPQWGAPSLRYLFYPRQVVLDGTWSQTRKMARTIPQLAEVPTETFGGGLATLDAISWLVEAVEGPEGTPLDPASPLHRPEAVREDAPEQWKTTNTGRLAAAALSNGGPAPRPPSELRDLEQPATIVALPAGAEPRFSLREVADPLNELYSAFVHRVLESR", "metadata": {"id": "A0A2E7M787", "cluster": 18231352, "interpro_all": ["IPR005636", "IPR039262"], "interpro_used": ["IPR005636"], "interpro_unused": ["IPR039262"]}, "task_type": "infilling"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein is assigned to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is found in Caloramator australicus RC3 and is described by UniProt keywords ATP-binding, Cytoplasm, and Transferase. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 1925, 3835, 2687, 3244, 1988, 2469, 16318, 2460, 43, 2213, 22665, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2435, 1922, 11816, 10671, 2684, 9417, 24375, 7399, 1010, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 7031, 1920, 3244, 18, 3], "output": "MIVLGLTGGIASGKSTVSQMLKEKGFPIIDADMIAREILKIGEVAFNRVIESFGIQILNPEGEIDRKRLREIVFNDNEKLKTLNEITHPEILKRINEKIKIYDTKGYRLCVVDAALLIETGFYKNVDFVLLVYCDRETQLNRLMNRDGLTYEQAIRMINSQMDFEEKKKYADYIIDNSKDLENTKKQLDYIINSILSMEEMNE", "metadata": {"id": "G0V407", "cluster": 20333791, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence be if I wanted a polypeptide chain capable of the following function: The protein possesses a Hedgehog/Intein (Hint) domain that functions as an autoprocessing module, structurally resembling the $\\beta$-strand core of intein splicing domains. It mediates the intramolecular cleavage of precursor proteins, including Hedgehog signaling molecules, to release their active N-terminal components. In addition, the protein includes a RTX calcium-binding nonapeptide repeat that binds calcium ions to form a parallel beta-roll structure. These Asp-rich repeats are found in Gram-negative bacterial proteins, such as toxins and metallopeptidases, where they facilitate Type I secretion by folding in the extracellular environment to prevent backsliding and accelerate transport. Additionally, the protein should include a Hemolysin-type calcium-binding conserved site that binds calcium ions within a parallel beta-roll structure formed by tandem nonapeptide repeats. Found in Gram-negative bacterial secreted proteins like hemolysins and metallopeptidases, this domain facilitates calcium-mediated interactions with host cells such as erythrocytes. It has been characterized in Paracoccaceae bacterium.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 20931, 19, 21318, 1921, 12, 24892, 13, 3418, 1988, 4088, 1966, 1925, 5728, 15883, 1941, 9059, 16, 12171, 18994, 1920, 8, 38, 4666, 8, 17, 5984, 4728, 1927, 21318, 1921, 8490, 4682, 18, 2176, 10412, 1920, 18083, 6404, 1927, 7897, 2697, 16, 2710, 20931, 3197, 4206, 16, 1942, 4012, 2310, 3500, 56, 17, 4262, 4178, 18, 1922, 2459, 16, 1920, 2213, 5921, 43, 29839, 5016, 17, 2743, 2447, 24010, 6865, 1988, 6876, 5016, 6982, 1942, 2386, 43, 6110, 4666, 17, 12970, 3170, 18, 2144, 4138, 17, 5536, 9569, 2032, 2435, 1922, 8604, 17, 3136, 4543, 2697, 16, 2427, 1966, 13599, 1930, 8969, 24897, 1036, 16, 2597, 2611, 6628, 2601, 51, 5512, 2007, 10328, 1922, 1920, 5329, 3515, 1942, 4625, 3231, 1036, 12191, 2117, 1930, 15947, 4860, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 3243, 23872, 17, 2601, 5016, 17, 2743, 5305, 3200, 1988, 6876, 5016, 6982, 2651, 43, 6110, 4666, 17, 12970, 3170, 5333, 2007, 10361, 2447, 24010, 9569, 18, 2435, 1922, 8604, 17, 3136, 4543, 8366, 2697, 3189, 3243, 23872, 1036, 1930, 8969, 24897, 1036, 16, 2052, 3418, 11374, 5016, 17, 3434, 3719, 1956, 4423, 2094, 2427, 1966, 14161, 18, 2176, 2258, 2252, 4378, 1922, 13344, 15648, 9914, 14061, 18, 3], "output": "MATSTGSSGNDTLTGTSNADSISGLGGDDSLYGAGGNDTIYGGDGNDYLFGGSGSDSLYGDAGNDTLQGGTGNDLINGGTGINTADFSDAGGAETVNLTTGRATGGAGADGSDTLANIQNVIGSGYNDSITGDTGDNALYGGIGNDTIYAGGGGNDSLYGGAGNDRLYGSTGNDLLQGGAGSDSIVGGGGNDTADFSDSATGITLTLNNGAGTAYGDGTDTLSGIENVIGGTGNDNITGDSLSNWISGDLYGNDSLYGGLGDDTLVDGFGNDVIQGGTGMDYLDISNSTVGVSVNLTTEMAYGMGTDTMSGMDGVIGSSHDDTLIGFDGQGLVGSGDVYTNVLYGAGGNDQIYGLGGADSLYGGDGADTIYGGSGNDSMYGDAGNDVLYADSGNNQVYGGDGNDTLYGGTGADTLSGGAGDDVLYGQGAGASLDGGDGNDTLYGAPNEVLTGGAGSDVFYAAVGDTINGGLGDQDTLNLAGNYHFVAVPGNPLLENVVDSLGNVVGHVDFAPGDVQSGVVSFTDSSGNTTSTITFSNIEKIVPCFTPGTLIATRDGLVAVEALVPGDEILTRDHGYRPLCWIGRQTIAAARLAAEPALQPILIRARALGPDAPARDMMVSRQHRMLIQDIRAELLFGEAEVLVRAAHLVGQPGIEAVVLDEVTYVHLLFAAHEVILADGAWSESFQPGDRTLAGFDDAQRHELYAIFPELALPAATESYAAARLTLKAHEARVLLRDRRPEPRRAARAMPSSILLDNPRALPLPPIARPLGEGSLTAVA", "metadata": {"id": "A0A9D6C7D1", "cluster": 21400260, "interpro_all": ["IPR028992", "IPR018511", "IPR001343", "IPR036844", "IPR050557", "IPR011049"], "interpro_used": ["IPR028992", "IPR001343", "IPR018511"], "interpro_unused": ["IPR050557", "IPR011049", "IPR036844"]}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein is associated with the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Additionally, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It originates from Legionellales bacterium and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 1977, 2458, 1956, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 22970, 2037, 27836, 5870, 2612, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MKKILSVALTGGIGAGKSTITSKFHALGTPIIDSDIISRSIVAPGKPCLDAIISEFGKKILDLRGEIHRQKLRNIIFNDSEAKKRLESIVHPVIYKEIADEISNINYPYCLIVVPLLIETRATERFDRILLIDVTEKTQLIRAAKRDKASIKHILETIKNQTSRKQRLHYADDIIDNNTEIEKLDYIVEMLHEKYLRLSELSKY", "metadata": {"id": "A0A2E0PVA8", "cluster": 21597010, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein is grouped in the BTG family, which regulates cell proliferation via a conserved N-terminal APRO domain. These proteins interact with the CAF1 subunit of the CCR4-NOT complex to exert their antiproliferative effects. Moreover, the protein carries a Anti-proliferative protein domain that regulates cell cycle progression and constitutes the conserved N-terminal region of BTG family members, such as BTG1 and Tob. This structural module typically contains three conserved cysteine residues and is essential for the family's function in modulating cellular proliferation across various cell types. Moreover, the protein belongs to the BTG-like domain superfamily, which functions as a conserved N-terminal module in anti-proliferative proteins to regulate cell cycle progression. This domain is characterized by high sequence similarity and the presence of three conserved cysteine residues. It has been detected in Hucho hucho (huchen) and carries UniProt keyword assignments Signal.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 1977, 10809, 1922, 1920, 8626, 1029, 3416, 16, 2154, 7014, 2024, 4031, 3454, 43, 5305, 56, 17, 4262, 24309, 3418, 18, 2144, 2697, 6310, 1956, 1920, 20250, 1009, 5903, 1927, 1920, 8519, 1006, 17, 2084, 2796, 1942, 10788, 2310, 21447, 2564, 18, 3950, 16, 1920, 2213, 16252, 43, 2246, 17, 9842, 2213, 3418, 1988, 7014, 2024, 4048, 4380, 1930, 14879, 1920, 5305, 56, 17, 4262, 3031, 1927, 8626, 1029, 3416, 4678, 16, 2427, 1966, 8626, 9114, 1930, 7551, 18, 2052, 4346, 9059, 5745, 5461, 2559, 5305, 8666, 4248, 1930, 1977, 4415, 1958, 1920, 3416, 11, 61, 2347, 1922, 10871, 3689, 4031, 3436, 3425, 2024, 3584, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 8626, 1029, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 5305, 56, 17, 4262, 9059, 1922, 2246, 17, 9842, 2697, 1942, 5741, 2024, 4048, 4380, 18, 2052, 3418, 1977, 4378, 2007, 2149, 3244, 6796, 1930, 1920, 2990, 1927, 2559, 5305, 8666, 4248, 18, 2176, 2258, 2252, 3330, 1922, 25558, 10647, 25558, 10647, 12, 25558, 22467, 13, 1930, 16252, 20709, 11121, 2538, 18306, 2733, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MKTEVSTAASFVARLLRLITSAQGLMLCSHCPLTEHYQHHWFPQAEDGSICVLYESTPPVPTNANTSDMVSCKEELRFGRSSPSKWFMMTVSINSFRPCEGSGYRCLRINHKMDPLIGQAVSYRIG", "metadata": {"id": "A0A4W5K3K8", "cluster": 23378897, "interpro_all": ["IPR002087", "IPR033332", "IPR036054"], "interpro_used": ["IPR033332", "IPR002087", "IPR036054"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein is categorized in the The TB2/DP1/HVA22 family, which encompasses Receptor expression-enhancing proteins (REEPs) and fungal Yop1, regulates the organization and shaping of the endoplasmic reticulum and sarcoplasmic reticulum membranes. This eukaryotic family includes members crucial for cardiac development as well as the abscisic acid-induced HVA22 regulatory proteins found in plants. It is found in Cucumis melo (Muskmelon) and is linked to UniProt keywords Transmembrane helix.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 1977, 10234, 1922, 1920, 1920, 5152, 1028, 19, 5679, 1009, 19, 12948, 8398, 1028, 3416, 16, 2154, 21569, 3148, 2294, 17, 9221, 2697, 12, 21747, 2523, 13, 1930, 8697, 7419, 5113, 16, 7014, 1920, 5901, 1930, 19515, 1927, 1920, 13355, 12279, 1930, 30060, 29327, 12279, 5726, 18, 2052, 10825, 3416, 5921, 4678, 6608, 1958, 4435, 2740, 1966, 2486, 1966, 1920, 23006, 1937, 1935, 2687, 17, 2719, 12948, 8398, 1028, 4948, 2697, 2435, 1922, 4793, 18, 2176, 1977, 2435, 1922, 18242, 28851, 1036, 4221, 1037, 12, 3177, 16386, 1938, 1916, 13, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 7864, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MLGDFLVRFLLMIFGYCYPAFQCYKVVVKSPIQVQELLYWCQFWIIVAILTVVERIADVFVGWFLVDSNDKDIEKMLLDLRVKAWDLAIFYWNNCTELSQSAFVRVVNYIAAQSNNLGSTSSPPSKKEMPMYGELKLALFIYLWYPKTMGSGYVFDQLLRP", "metadata": {"id": "A0A1S3B7K3", "cluster": 24466640, "interpro_all": ["IPR004345"], "interpro_used": ["IPR004345"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein is grouped in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, the protein falls within the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. In addition, the protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is found in Clostridium ljungdahlii and corresponds to UniProt keyword Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 2435, 1922, 21156, 25348, 3317, 3825, 7806, 3907, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 3], "output": "MKFKHVPVLLNETINSLNIKEDGILSDKGRLIGIDEDTYAINATRERLNEFKNITYVHNLGVSSYQLDESERGFSYMKDAPLDMRMENLHNVIRDYGEENFSKRIAKFIVAEIPARFQKEGHPAKRTFQAIRIEVNGELKITFHSLEDRIIKTKFKKLENPCTCPPDFPLCTEEEKEKNSRSKSSKLRTAEKIYVDCTLGGGGHSFEILKRNFYYIDEILEELKIDKVDGILMDNRDSSLSAYEVINNYSEREKAPINTTLQLVDIIRNALNKAVEDSVKRLNTGGRISIIVCGKKPIVKIINKKPIIP", "metadata": {"id": "A0A170NBX1", "cluster": 28090077, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein possesses a Domain of unknown function DUF6532 domain that is found in a group of uncharacterised fungal proteins. It is present in Paxillus rubicundulus Ve08.2h10.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 14465, 43, 3418, 1927, 5435, 2347, 4855, 17136, 3786, 1028, 3418, 1988, 1977, 2435, 1922, 43, 2210, 1927, 23229, 3495, 8697, 2697, 18, 2176, 1977, 2481, 1922, 10532, 8898, 10010, 1935, 2652, 9605, 3428, 13895, 18, 7478, 2930, 18, 11586, 5655, 3581, 18, 3], "output": "MLIPSLFQACTFDKQQPFRHVKYPEAFKGIPLPLLALVECALRSYISGVKDHLRKNSLTWCKGMTKELYRAVWLIIKDLIISQWFGGKGEGASWTINFSGSEFSIRYIFYAQKL", "metadata": {"id": "A0A0D0DD36", "cluster": 542457, "interpro_all": ["IPR045341"], "interpro_used": ["IPR045341"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein is associated with the The ExbB/TolQ Biopolymer Transport family, which mediates energy-dependent transport across the bacterial outer membrane and maintains cell envelope integrity. Members function as integral components of the TonB system to facilitate nutrient uptake by stabilizing TonB and ExbD, or the Tol-Pal system to support cell division and outer membrane invagination. These proteins also serve as entry points for colicins and bacteriophage DNA, playing a critical role in bacterial survival. Additionally, the protein should have a MotA/TolQ/ExbB proton channel domain that functions as an integral membrane proton-conducting unit essential for energy transduction. It harnesses the proton motive force to drive diverse cellular processes, such as generating rotational motion in the bacterial flagellar motor or energizing the transport of large molecules via the TonB complex. It originates from Campylobacter blaseri and contains UniProt keyword associations Signal, Protein transport, and Transmembrane helix.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 1920, 1975, 6936, 19, 21930, 1055, 20864, 14083, 4860, 3416, 16, 2154, 10412, 3844, 17, 3100, 4860, 3436, 1920, 4543, 7642, 3260, 1930, 16566, 2024, 11262, 7996, 18, 4678, 2347, 1966, 12328, 4178, 1927, 1920, 16501, 1014, 2433, 1942, 6628, 8708, 5047, 2007, 14384, 16501, 1014, 1930, 1975, 13602, 16, 2014, 1920, 21930, 17, 5755, 2433, 1942, 3373, 2024, 8451, 1930, 7642, 3260, 27134, 2636, 18, 2144, 2697, 2222, 7120, 1966, 6904, 4273, 1958, 5178, 3665, 1036, 1930, 24613, 2678, 16, 14797, 43, 4140, 2770, 1922, 4543, 3298, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 12798, 1019, 19, 21930, 1055, 19, 1975, 6936, 8433, 4999, 3418, 1988, 4088, 1966, 1925, 12328, 3260, 8433, 17, 12335, 5344, 4415, 1958, 3844, 8201, 18, 2176, 25852, 1918, 1920, 8433, 7038, 1021, 5495, 1942, 9265, 6445, 3689, 4028, 16, 2427, 1966, 9155, 16577, 6269, 1922, 1920, 4543, 24154, 4842, 2014, 2066, 2693, 3903, 1920, 4860, 1927, 3103, 4206, 3454, 1920, 16501, 1014, 2796, 18, 2176, 22970, 2037, 22657, 18208, 13545, 1033, 1930, 5461, 20709, 11121, 2538, 5253, 2733, 16, 2213, 4860, 16, 1930, 9117, 7864, 18, 3], "output": "MKTLLSLILFFNVSFALVVEGDSTTNLSYSNFTEQNFTANEKDIQVNSDKKLELSIYSFYKQSDFVTKIIIYILVIFSILTWSVLIGKTIHYYVVFHILNKDREIVSKIVNLNKNINFHKNSFVKILIEEIKDETNKSKNYSKDTIDRIRYRIESNNLSFLANCKSYTPILATIGSSATFLGLFGTVWGIMNSFIAIASISNPNLSVVAPGIAQALFTTALGLGVAIPAVLFYNYLSRRSVKFANELSKISTTLFVIAHRNLNKENYDKS", "metadata": {"id": "A0A2P8R434", "cluster": 944054, "interpro_all": ["IPR050790", "IPR002898"], "interpro_used": ["IPR050790", "IPR002898"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein features a Bacterial Ig-like domain, group 2 (Big2) domain that functions as a structural module in bacterial surface proteins, phage tails, and eukaryotic nuclear pores. It mediates intimate host-cell adhesion in intimins, supports the assembly of hexameric rings in phage tail tubes, and contributes to the structural integrity of nuclear pore complexes. Also, the protein is assigned to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It has been characterized in Dethiobacter sp and features UniProt keywords ATP-binding, Cytoplasm, and Transferase. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 4075, 43, 4543, 7021, 17, 3189, 3418, 16, 2210, 22, 12, 9769, 1028, 13, 3418, 1988, 4088, 1966, 43, 4346, 9059, 1922, 4543, 3154, 2697, 16, 10503, 18103, 16, 1930, 10825, 4254, 14711, 18, 2176, 10412, 20252, 4423, 17, 2024, 6141, 1922, 11757, 2925, 16, 7825, 1920, 5957, 1927, 25602, 1935, 12750, 1922, 10503, 5281, 9403, 16, 1930, 7624, 1942, 1920, 4346, 7996, 1927, 4254, 8554, 5048, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 2258, 2252, 4378, 1922, 2212, 7969, 5883, 2056, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MLILGLTGGIATGKSTAAAIFEKMGAYRIDADRLAREVVQPGKPAWQAIVSHFGPGVLYFDRQLNRHALASVIFNDPNERHVLEAITHPQIRKLIDQQIIKARQSGAKVALLEVPLLYEVGLDRVADKVLVVVTDEATQLKRMMKRDNLTENEARLRVKAQMSLAEKAKQADFVIYNTGTPAELDEQAKRLWLELTAVVIIPETLKDNSVVWKSDNEEVAVVSDSGIVSPVGPGTATISVTAANGAGSAHCSVTVQEPPQVSVYIIDCTAGGESTVAESNEGGPLTLKIRPKEIRDFGYGRAKLNVAVTDKPPGSTVRLMTKDKKGLAYDAAALGCIAPDEGFAMTKDYSEDIELSTWFDKPGAYTISFILVDLENNAEIAAAASTSMQVRPQQKVSSYKVTCDTAGLKFVAGTAIPLPVTVRAAEVNDFGYERVRFNVRVLKNPAGAEVRLQTQDSRGYPQDAAILGYFDRANGFPLSKDHNKTIEFESCFDKTGEYSLSFTLVNLDNEAELIAEHSVNFSVQKLPEASKYELSADTSALKFLAGSETGTVIPLVIMTKEVKDIGYNSVKLTTDIIDRPHDGRAQLLAADSHGGVYDAAATNDVQEYFSLGTEYNHAIDFNAKFNKPGYYTIRFSLTDSGNGFQIACLTKVIRVFAIPQASEYEFVCNTKGLKFVADPEKTTSLPVTLRTREVKDFGYDNVRLNVAVTGRPVDAKAQLFARSSRGRVYDAAVLGYWGAVTGFAVSRDFNTTMEINVKFDTVGSYTITFTLADLNDESNIITSGIVLITVEAQPEVSTYEIAADTEGLVFVAGSETGTVLNITLSSKKVKDLGYESATLYTVITRRPARSKAQLLAADSKGQLYDTLLQGFWGPAEGFQLDREFALNLEFHAKFDTPGIYTVTFTLADKKAGGAVIAKSKVQARVKLEAAESGATQLVLNRHSLKLIAGGTPAVLVATPAKESKEDSKPKA", "metadata": {"id": "A0A942MPJ6", "cluster": 2675980, "interpro_all": ["IPR003343", "IPR001977", "IPR008964", "IPR027417"], "interpro_used": ["IPR027417", "IPR003343", "IPR001977"], "interpro_unused": ["IPR008964"]}, "task_type": "autoregressive"} {"instruction": "The protein is included in the Membrane Fusion Protein Cation Efflux System family, which mediates the active transport of heavy metal cations across cellular membranes to confer resistance against toxicity. These proteins typically function as components of proton/cation antiporter efflux complexes, coupling the expulsion of ions such as copper, silver, zinc, and cadmium with proton influx. It originates from Bryobacteraceae bacterium. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 3260, 5289, 2213, 9976, 11247, 2433, 3416, 16, 2154, 10412, 1920, 3500, 4860, 1927, 7881, 6048, 16525, 3436, 3689, 5726, 1942, 7909, 3554, 3316, 5532, 18, 2144, 2697, 5745, 2347, 1966, 4178, 1927, 8433, 19, 9976, 2246, 24095, 11247, 5048, 16, 7590, 1920, 2887, 12138, 1927, 6982, 2427, 1966, 9541, 16, 11078, 16, 7997, 16, 1930, 17203, 1956, 8433, 12403, 18, 2176, 22970, 2037, 26949, 5883, 9914, 14061, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "TRQVGEVITVAENPNHDLPPGANINAAIRSEAVENALTIPKAALRREAGRFGVYLLAGDRIEWKPVELGVSSATLAEVRSGLKDGDAVALPSDAALAAGMRVRPVLKP", "metadata": {"id": "A0A7Y8LGR2", "cluster": 2851082, "interpro_all": ["IPR051909"], "interpro_used": ["IPR051909"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein should feature a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. Also, the protein should have a MgsA AAA+ ATPase, C-terminal domain that possesses DNA-dependent ATPase and ssDNA annealing activities essential for the recovery of stalled replication forks and chromosomal segregation. It contributes to genomic stability by co-localising with the replisome and is also found in WRNIP1, where it aids in modulating DNA polymerase delta-mediated synthesis. Moreover, the protein should include a AAA-type ATPase core domain that functions as a molecular motor, coupling ATP binding and hydrolysis to conformational changes that remodel or translocate target substrates. It typically assembles into oligomeric ring structures, often hexamers, containing conserved Walker A and B motifs essential for enzymatic activity. This module drives diverse cellular processes, such as protein unfolding and DNA processing, by mechanically manipulating macromolecules. It is derived from bacterium and features UniProt keywords ATP-binding.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 2786, 5735, 13835, 15, 9444, 16, 45, 17, 4262, 3418, 1988, 14465, 2678, 17, 3100, 9444, 1930, 15063, 12932, 4209, 4415, 1958, 1920, 5241, 1927, 27084, 5158, 24487, 1930, 9220, 12707, 18, 2176, 7624, 1942, 4935, 5057, 2007, 2081, 17, 3076, 4007, 1956, 1920, 4856, 23854, 3870, 1930, 1977, 2222, 2435, 1922, 28612, 11692, 16, 2597, 2176, 8494, 1922, 10871, 2678, 6479, 9649, 17, 3434, 4271, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 13835, 17, 2601, 9444, 4728, 3418, 1988, 4088, 1966, 43, 3272, 4842, 16, 7590, 4498, 2743, 1930, 9128, 1942, 8523, 2840, 1988, 7456, 1938, 2014, 26377, 2758, 6249, 18, 2176, 5745, 17421, 1036, 2460, 19206, 6335, 4061, 16, 3868, 25602, 1036, 16, 3165, 5305, 20138, 43, 1930, 44, 8277, 4415, 1958, 8145, 2455, 18, 2052, 9059, 15435, 6445, 3689, 4028, 16, 2427, 1966, 2213, 17490, 1930, 2678, 4587, 16, 2007, 17841, 23107, 20625, 18, 2176, 1977, 3595, 2037, 14061, 1930, 4075, 20709, 11569, 4498, 17, 2743, 18, 3], "output": "MKKPLSIILRPKNFYEFVGHKEILTESFKEKIRKGDIPHIIMWGPPGSGKTTLSEVIAKKEKEFFQKETILFIDEIHRLDRKEQDFLLSFVENRDIILIGATTENPYFTIVSPLLSRCFLIILKPYDKKFLIEISYGDARFILNVLDSLKDEVGDREVQISYEDINRFLSTKKIKFDKREEHYNLIGGEDLRFITRRLIILASEDIGLSDPMALVITNSGAEAVERVGLPEAKLILSEVVLYLSKAPKDNLVEQFGELPVPLHLRNPVLKGLENLGWGKGYKYPHNHKDEKIEYLPDEIKDIKIFEDRKNESNLNFVRVSGAESGIKELRVIIDNYNEMNEILERSLKYLKNLKIDEDTSALIKSIRGSNADAALYYLFRLVERVLRSMENAIK", "metadata": {"id": "A0A7X8ARV8", "cluster": 4139623, "interpro_all": ["IPR003593", "IPR032423", "IPR051314", "IPR003959", "IPR008921", "IPR021886", "IPR027417"], "interpro_used": ["IPR003593", "IPR021886", "IPR003959"], "interpro_unused": ["IPR027417", "IPR032423", "IPR008921", "IPR051314"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is a member of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Additionally, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is derived from Sorangium cellulosum (Polyangium cellulosum) and carries UniProt keyword assignments ATP-binding, Cytoplasm, and Transferase.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3595, 2037, 6548, 9506, 1989, 18485, 14740, 12, 4286, 9506, 1989, 18485, 14740, 13, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MGLVLFGLTGGLGSGKSTVAARFRAQGLVAKGTEGLEEVVRAFGPEVLSPDGSLDRARALTLERAAALEAQGEPLACYEAALLVENMERDGATEDEVRARLAAQLPLSSKVAVADHVIELAAIRARFGVPPAPPAPDPARAPDVASPDHPVIDADALAREVVAAIVFADPDRRRQLNAIVHPRITRVADAFRPLVVVAVPEAVQIARANSGDRAATERQADEV", "metadata": {"id": "A0A150PZC9", "cluster": 4705803, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein is classified under the The Tic22-like family, which functions as a core component of the Tic complex to facilitate the import of nuclear-encoded proteins into chloroplasts. These soluble intermembrane space proteins interact with preproteins to prevent misfolding and potentially serve as a bridge between the outer membrane Toc and inner membrane Tic complexes. It has been characterized in Striga asiatica (Asiatic witchweed) (Buchnera asiatica) and is annotated with UniProt keywords Plastid.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 1920, 18298, 4460, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 4728, 4594, 1927, 1920, 18298, 2796, 1942, 6628, 1920, 2582, 1927, 4254, 17, 7905, 2697, 2460, 24627, 18, 2144, 6622, 15177, 8591, 5230, 2697, 6310, 1956, 10719, 10355, 1942, 4625, 28200, 1930, 5063, 7120, 1966, 43, 11925, 2192, 1920, 7642, 3260, 21682, 1930, 6671, 3260, 18298, 5048, 18, 2176, 2258, 2252, 4378, 1922, 2114, 1950, 1019, 11624, 21788, 12, 11624, 2002, 16086, 2072, 29775, 13, 12, 25485, 3239, 1019, 11624, 21788, 13, 1930, 1977, 10633, 1956, 20709, 11569, 19754, 18, 3], "output": "MGSLKKKDDLLPNASNTLKTQFSNFINHINPKLLLTPFCSLFPKNNCNHALPTAEIKKRLAGIRAYKITDRCDTHVGLIGKNRGIHLLYLGEQDAHSFLNSVESLGDKVDMHVDDLRVYDTPITEILDVGVDDPPMKLVPELLQVKYAIEEIKKNSNENTADGSFSGVPVFQSDGLAVDDGKGKRYRPCYLRKEDLEYARSAVLTKSDLMIDNIKVTSLEKIIQEMKDSSISKSNNILIAGPGMSWRWFDEQNQKKR", "metadata": {"id": "A0A5A7QN71", "cluster": 6040701, "interpro_all": ["IPR007378"], "interpro_used": ["IPR007378"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein is grouped in the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Also, it is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein should feature a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. It has been detected in Pseudomonadota bacterium and is connected to UniProt keyword ATP-binding, Nucleotide biosynthesis, and Transferase.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 1977, 10809, 1922, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 2176, 2258, 2252, 3330, 1922, 11520, 3947, 12595, 3857, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MDDRPGVPLRRDLVRRVRRRPITRPHAGTFVALEGKPVELTREPGGTPFAEAVRELLLAPRDEAAHLQDRIIPAIGAGKWVVCDRFTDATYAYQGATILLDAPVDIGLERAKGRSGKPDRFEREDIAFFHIVDAAQPLGAVNRGVEAVLEKLLEKHGGEGAGKSTQLAGIRDFLLRAGPVTPDAELLLMFAARGGRGISPARIAVLEQFVQDTFRPHTRVRNAYLERARAEPERF", "metadata": {"id": "A0A951JLV2", "cluster": 7344312, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR018094", "IPR027417", "IPR039430"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The desired role of my protein is: The protein belongs to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Furthermore, it is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is found in Eubacterium aggregans and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 14440, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2435, 1922, 4791, 7972, 2341, 18842, 1989, 5206, 2075, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MKVIGLTGGIASGKSTVSRILREEFGIPIVDADQISRDVVAPGGAALERIAESFGSEYLMPEGGLDRKRMGALICEDPKAKNRLEGILHPIIEHHVENIIADYRARGMDLIVYDCPLLIEARQERFVDSVALVVTDIALRVQRLMERDGIAEDEARKKIAIQMSDDDKERYADFLISNDGDEEALREALSRLVMRWKNC", "metadata": {"id": "A0A1H3YAQ5", "cluster": 7665805, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to create: The protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Moreover, the protein is included in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It has been characterized in Deltaproteobacteria bacterium and has UniProt annotations rRNA processing. Please provide the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 7762, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 2258, 2252, 4378, 1922, 9649, 9218, 1021, 10296, 14061, 1930, 2258, 20709, 15010, 9067, 4587, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MALFHTPVMVREVIASLHCHAGAMYVDGTVGGGGHAEAILLDMAPDGLLIGIDADGDALREAEKRLAPFGKRKLLVKGNFADMETILVERNIGKVDGILLDLGVSSHQLDTAERGFSFSMDAPLDMRMDRSRGTSAYDLIHTLSGG", "metadata": {"id": "A0A3N5W3Y7", "cluster": 7717401, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein should include a Glycosyl transferase, family 1 domain that catalyzes the transfer of sugar moieties from activated UDP-, ADP-, GDP-, or CMP-linked donors to specific acceptor molecules, forming glycosidic bonds. This enzymatic activity is essential for diverse biosynthetic processes, including the synthesis of glycogen, bacterial lipopolysaccharides, and human GPI anchors. It is identified in Candidatus Dojkabacteria bacterium.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 3066, 3951, 43, 20067, 13763, 16, 3416, 21, 3418, 1988, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 18500, 17, 16, 9828, 17, 16, 15217, 17, 16, 2014, 28738, 17, 4624, 8276, 1942, 2487, 12641, 4206, 16, 7402, 7533, 12546, 9031, 18, 2052, 8145, 2455, 1977, 4415, 1958, 6445, 14041, 4028, 16, 2710, 1920, 4271, 1927, 13302, 16, 4543, 15614, 1036, 16, 1930, 2616, 17497, 27127, 18, 2176, 1977, 2899, 1922, 14550, 1031, 1957, 2608, 29431, 20013, 2341, 18339, 14061, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MDKKQIQIIGPYATEYSLARVNRALDLKKYPWLTGLEDSDQNPDVYIFNNFPELAKFKGNNKIAYLAWEETIMPKRWIDEMNENLHGVMVTSDHVNLGIDQDLPNKAELYKLNTSKKYKFLHISSDDVVLVLKLFPNPNSKVDEIIANLRNENSPEVLYSQCDAVVLPSRAEGFGIPMACNAENAFLLDYQLINSDSQLGTPGAKVAEPSIDDIVKSKVANAKKRVSELTWEKNANETLQFINEINGPRNSTDGIAEYIKNFYTNIESSFADILYLANIKRTWEMGEKTFAETQNAISEFQPDINLISELTNKNIKVYLTPHAVQVDYIDFAANSEALNVELFKFGILEFNKEDRYRLRKRLGITSQHVVAILLKDKYPDILLISATALNTDNITSSATYEQMQQAIRNDDADIVMFAYPDLKEGASGAVRKSFAALRPVVITNSHIFRDLDVGYKEYQSIVDKVKNESWGIISEKYLLGLGTNGEALNKYQDEYQVRFWRSEEFTDRLPNNNKSINSPYVRHVFRNSGLKIPIRTAHYRKGVDVLIKGYFETFTKDEIINNPDLTDGEIISEAMLMEKPLITTGYSGHMDFDLKKHMKFLAENPDSKLAMYKNKKLVVLDASGRVFEDDKNVVHIQYHPAYFSLPDMANKCEKIYVHADFDKEFLNSKSLTHGLIHNQKGMVEAIKAVSLEDNVIAITDFIDTAEVIKLLQIRIENNQPEVIASAVTKLFEDQDLYN", "metadata": {"id": "A0A955RIH8", "cluster": 11586393, "interpro_all": ["IPR001296"], "interpro_used": ["IPR001296"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to create: The protein belongs to the LexA/Signal peptidase-like superfamily, which encompasses serine peptidases and homologues sharing a structural fold characterized by an SH3-like barrel. This group includes signal peptidases that cleave signal peptides from translocated proteins, as well as bacterial transcriptional repressors and DNA polymerases that undergo RecA-activated self-cleavage during the SOS response. Furthermore, the protein features a Peptidase S26A, signal peptidase I conserved site that is located in the C-terminal section of S26 serine peptidases, including prokaryotic SPase I and mitochondrial IMP subunits, which are responsible for removing signal peptides from secretory proteins. These integral membrane enzymes utilize a catalytic serine-lysine dyad to process exported pre-proteins across the cytoplasmic, mitochondrial, or endoplasmic reticulum membranes. In addition, the protein possesses a Peptidase S26 domain that functions as a signal peptidase responsible for removing N-terminal signal peptides during protein translocation across membranes. This serine endopeptidase utilizes a distinctive serine/lysine catalytic dyad mechanism to process secretory proteins or elements of conjugative transfer systems. It is identified in Acidovorax sp. 62 and is described by UniProt keywords Hydrolase and Protease. Please provide the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 7762, 30, 1920, 2213, 14440, 1942, 1920, 14596, 1019, 19, 2733, 24050, 17, 3189, 13975, 16, 2154, 21569, 8468, 24050, 1036, 1930, 18541, 10763, 43, 4346, 3728, 4378, 2007, 1925, 18824, 17, 3189, 19560, 18, 2052, 2210, 5921, 2733, 24050, 1036, 1988, 21252, 2733, 5320, 2037, 22198, 2697, 16, 1966, 2486, 1966, 4543, 5224, 26446, 1930, 2678, 20910, 1988, 4978, 21534, 17, 4128, 3543, 17, 6404, 2409, 1920, 17668, 2644, 18, 3677, 16, 1920, 2213, 4075, 43, 24050, 5159, 11084, 16, 2733, 24050, 51, 5305, 3200, 1988, 1977, 4810, 1922, 1920, 45, 17, 4262, 3314, 1927, 5159, 1016, 8468, 24050, 1036, 16, 2710, 21545, 19361, 4127, 51, 1930, 4596, 2754, 6991, 16, 2154, 2032, 5061, 1958, 11340, 2733, 5320, 2037, 11518, 2697, 18, 2144, 12328, 3260, 5038, 12561, 43, 6804, 8468, 17, 9082, 28679, 1942, 2585, 20721, 2097, 17, 2697, 3436, 1920, 6823, 16, 4596, 16, 2014, 13355, 12279, 5726, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 24050, 5159, 1016, 3418, 1988, 4088, 1966, 43, 2733, 24050, 5061, 1958, 11340, 56, 17, 4262, 2733, 5320, 2409, 2213, 7849, 3436, 5726, 18, 2052, 8468, 16239, 9626, 2410, 9200, 18127, 43, 15308, 8468, 19, 9082, 6804, 28679, 2856, 1942, 2585, 11518, 2697, 2014, 5362, 1927, 5225, 2178, 3856, 3771, 18, 2176, 1977, 2899, 1922, 2687, 2579, 18897, 2056, 18, 5374, 1930, 1977, 2910, 2007, 20709, 11569, 20748, 1930, 7154, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MLRNWIKSNRGFLVLLLCFGIFRTAVADWNPIPSGSMRPTLLEGDVVFVNRLAYDVKLPLTDVVLLPLGEPQRGDVVTFTSPQDGTRLIKRIAAVPGDRVEMRNEVLYINGQAAQYDAPEVVQEAVGVGAMVQATRWTERLGGHERRVQWLHGVPARSTFDAIEVPAGQYLMLGDNRDDSVDSRYIGLVPRHLLIGQARRVLVSADILGHWAPRLQRIGLPL", "metadata": {"id": "A0A2G6YEZ0", "cluster": 11812993, "interpro_all": ["IPR036286", "IPR000223", "IPR019758", "IPR019757", "IPR019533"], "interpro_used": ["IPR036286", "IPR019758", "IPR019533"], "interpro_unused": ["IPR000223", "IPR019757"]}, "task_type": "autoregressive"} {"instruction": "The protein is classified under the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. Additionally, the protein is categorized in the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. It has been detected in Aliarcobacter butzleri (strain RM4018) (Arcobacter butzleri) and contains UniProt keyword associations Transmembrane helix, Magnesium, and Cell membrane.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 2176, 2258, 2252, 3330, 1922, 15356, 5332, 5883, 2308, 26262, 18842, 12, 3943, 10625, 4241, 3928, 13, 12, 9952, 5883, 2308, 26262, 18842, 13, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 16, 13148, 16, 1930, 2024, 3260, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MNNKPKYHIFKNELLCAIFIVAGIFYIDTSIELVNSAIENVVDLVILLHCSCWIVIILFTKYAVEGLFHALRTESSFRLTNKLILLVTGILVLIITKEIHPLAKNAKDIGSTAVMFS", "metadata": {"id": "A8EVT6", "cluster": 15764439, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR000829", "IPR033718"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein should have a ATP-grasp fold, PylC-type domain that catalyzes the ATP-dependent formation of amide bonds by ligating a carboxylate-containing molecule to an amino or thiol group-containing molecule. This structural feature utilizes ATP hydrolysis to activate substrates and is central to enzymes involved in macromolecular synthesis, such as peptide synthetases. It is present in Planctopirus hydrillae and is connected to UniProt keyword ATP-binding.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 3066, 2162, 43, 4498, 17, 22815, 3728, 16, 9796, 1030, 17, 2601, 3418, 1988, 17097, 1920, 4498, 17, 3100, 3337, 1927, 13601, 9031, 2007, 3650, 2287, 43, 20877, 17, 3165, 5388, 1942, 1925, 3835, 2014, 13914, 2210, 17, 3165, 5388, 18, 2052, 4346, 5961, 18127, 4498, 9128, 1942, 6980, 6249, 1930, 1977, 4101, 1942, 5038, 3286, 1922, 21815, 4271, 16, 2427, 1966, 4207, 18185, 1036, 18, 2176, 1977, 2481, 1922, 4720, 2341, 2011, 5811, 9698, 10888, 1021, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MNPPCLVCEYLCAFEGDNLSATDSASTAEIGLVHAGWKESWTGHPGVRWIWTEDDDHSRSLIHSAISGGWKVVIVAARVHNSTSAAIQLTSDKLQLAEHLEKHRIPTIPTRLVQHAEELGTYSRYVVKPIDGAGSETCQIVQPYLRGRSASVAVIMPALVVGEDRDSPGDSSMAPASLKYQGGALPSDEFTSEERARLEALALKACESIEGLRGYTGVDLVWPSYLGYRKIFGSQAALVVAGYGEAHAKTESFADKAGWKTSRAEWRREGMAMLQALTEDLAASQIQVAPEIDGTLAAIIQLCEFLGLDVFVVNDWREAPESPIVWPVASQRIIESKGEGHLEESTEPLVVEINPRLCT", "metadata": {"id": "A0A1C3ENR5", "cluster": 16668295, "interpro_all": ["IPR011761", "IPR003806"], "interpro_used": ["IPR003806"], "interpro_unused": ["IPR011761"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: It is part of the YefM-like superfamily, which functions as the antitoxin component in type II toxin-antitoxin systems. These proteins form a compact dimer with a \u03b2-\u03b1(2)-\u03b2(2)-\u03b1 fold that neutralizes cognate toxins and represses operon transcription by binding DNA via the N-terminus. Moreover, the protein is a member of the Type II toxin-antitoxin system, antitoxin Phd/YefM family, which acts as the antitoxin component in type II toxin-antitoxin systems. Upon binding to their toxin partners, members of this family bind DNA via their N-terminus to repress the expression of the operon encoding the toxin and antitoxin genes. It has been detected in Gemmatimonadota bacterium.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 5293, 19934, 17, 3189, 13975, 16, 2154, 4088, 1966, 1920, 10310, 9754, 4594, 1922, 2601, 2890, 9165, 17, 10310, 9754, 3771, 18, 2144, 2697, 2386, 43, 13726, 7632, 1956, 43, 161, 17, 160, 12, 22, 13, 17, 161, 12, 22, 13, 17, 160, 3728, 1988, 25885, 1036, 15786, 13599, 1930, 21688, 15675, 3213, 2007, 2743, 2678, 3454, 1920, 56, 17, 7822, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2601, 2890, 9165, 17, 10310, 9754, 2433, 16, 10310, 9754, 13381, 19, 5293, 19934, 3416, 16, 2154, 8016, 1966, 1920, 10310, 9754, 4594, 1922, 2601, 2890, 9165, 17, 10310, 9754, 3771, 18, 4073, 2743, 1942, 2310, 9165, 7228, 16, 4678, 1927, 2052, 3416, 4566, 2678, 3454, 2310, 56, 17, 7822, 1942, 9055, 1920, 2294, 1927, 1920, 15675, 5797, 1920, 9165, 1930, 10310, 9754, 2628, 18, 2176, 2258, 2252, 3330, 1922, 10607, 3368, 2265, 12502, 22389, 3857, 14061, 18, 3], "output": "MSKKSSIVGARELKTRLRGNPIAELRPVGASEDATEQALRRMEAEGLITRELILRERDEGFGKYLARVRAGETILVTDATRRGGLTPFKPIELPPGVSAS", "metadata": {"id": "A0A964QBB2", "cluster": 16846259, "interpro_all": ["IPR006442", "IPR051416", "IPR036165"], "interpro_used": ["IPR036165", "IPR006442"], "interpro_unused": ["IPR051416"]}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein features a Peptidase S26A, signal peptidase I conserved site that is located in the C-terminal section of S26 serine peptidases, including prokaryotic SPase I and mitochondrial IMP subunits, which are responsible for removing signal peptides from secretory proteins. These integral membrane enzymes utilize a catalytic serine-lysine dyad to process exported pre-proteins across the cytoplasmic, mitochondrial, or endoplasmic reticulum membranes. Additionally, the protein possesses a Peptidase S26 domain that functions as a signal peptidase responsible for removing N-terminal signal peptides during protein translocation across membranes. This serine endopeptidase utilizes a distinctive serine/lysine catalytic dyad mechanism to process secretory proteins or elements of conjugative transfer systems. In addition, the protein is included in the LexA/Signal peptidase-like superfamily, which encompasses serine peptidases and homologues sharing a structural fold characterized by an SH3-like barrel. This group includes signal peptidases that cleave signal peptides from translocated proteins, as well as bacterial transcriptional repressors and DNA polymerases that undergo RecA-activated self-cleavage during the SOS response. It occurs in Bifidobacterium biavatii DSM 23969 and is classified with UniProt keywords Hydrolase, Protease, and Transmembrane helix.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 4075, 43, 24050, 5159, 11084, 16, 2733, 24050, 51, 5305, 3200, 1988, 1977, 4810, 1922, 1920, 45, 17, 4262, 3314, 1927, 5159, 1016, 8468, 24050, 1036, 16, 2710, 21545, 19361, 4127, 51, 1930, 4596, 2754, 6991, 16, 2154, 2032, 5061, 1958, 11340, 2733, 5320, 2037, 11518, 2697, 18, 2144, 12328, 3260, 5038, 12561, 43, 6804, 8468, 17, 9082, 28679, 1942, 2585, 20721, 2097, 17, 2697, 3436, 1920, 6823, 16, 4596, 16, 2014, 13355, 12279, 5726, 18, 4950, 16, 1920, 2213, 14465, 43, 24050, 5159, 1016, 3418, 1988, 4088, 1966, 43, 2733, 24050, 5061, 1958, 11340, 56, 17, 4262, 2733, 5320, 2409, 2213, 7849, 3436, 5726, 18, 2052, 8468, 16239, 9626, 2410, 9200, 18127, 43, 15308, 8468, 19, 9082, 6804, 28679, 2856, 1942, 2585, 11518, 2697, 2014, 5362, 1927, 5225, 2178, 3856, 3771, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 14596, 1019, 19, 2733, 24050, 17, 3189, 13975, 16, 2154, 21569, 8468, 24050, 1036, 1930, 18541, 10763, 43, 4346, 3728, 4378, 2007, 1925, 18824, 17, 3189, 19560, 18, 2052, 2210, 5921, 2733, 24050, 1036, 1988, 21252, 2733, 5320, 2037, 22198, 2697, 16, 1966, 2486, 1966, 4543, 5224, 26446, 1930, 2678, 20910, 1988, 4978, 21534, 17, 4128, 3543, 17, 6404, 2409, 1920, 17668, 2644, 18, 2176, 5110, 1922, 21724, 12022, 2273, 15777, 16373, 10964, 19919, 7093, 1930, 1977, 5947, 1956, 20709, 11569, 20748, 16, 7154, 16, 1930, 9117, 7864, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MAETGLRDMTHAENVANDGGKESLLELIPWIVVPIIQLKDRVAAVKVIKPQRGDIVVFRDPVIGLPGDTVSCAGNGAPVEVNGKAIDDGMMWVMGDNRSGSADSRAHRMHVLDSHHEVFANVPDAGTSNNGERKPDADRKGRNDKNDRVVFALIRVFLIGLYVIPSGSMLDTDHWLASGEGNDLIKRESAYLRSGVNPSDEAFSVTVQQSDAHGGQVPLSDVQGVAVFTFWPVG", "metadata": {"id": "A0A087A0H1", "cluster": 16851502, "interpro_all": ["IPR036286", "IPR000223", "IPR019758", "IPR019533"], "interpro_used": ["IPR019758", "IPR019533", "IPR036286"], "interpro_unused": ["IPR000223"]}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence be if I wanted a polypeptide chain capable of the following function: The protein is classified under the FAD/NAD(P)-binding domain superfamily, which comprises flavoprotein oxidoreductases, such as glutathione reductase and thioredoxin reductase, that utilize FAD and NAD(P)H cofactors to catalyze electron transfer reactions. These enzymes typically adopt a doubly-wound $\\alpha/\\beta$ fold with nested binding domains to facilitate oxidative metabolism. Additionally, the protein carries a FAD-binding domain that facilitates the binding of the flavin adenine dinucleotide (FAD) cofactor to support catalytic oxidoreductase activity. This domain functions in diverse enzymes across species, including human kynurenine 3-monooxygenase, archaeal digeranylgeranylglycerophospholipid reductase, and bacterial hydroxylases. It occurs in Halobacteriovoraceae bacterium and contains UniProt keyword associations NADP.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 14134, 19, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 12936, 7732, 6657, 27388, 1036, 16, 2427, 1966, 9153, 11386, 1930, 23684, 11386, 16, 1988, 12561, 14134, 1930, 6577, 12, 58, 13, 50, 21362, 1942, 18170, 4995, 3856, 5298, 18, 2144, 5038, 5745, 14103, 43, 26783, 17, 6376, 8, 38, 4595, 19, 38, 4666, 8, 3728, 1956, 13735, 2743, 4682, 1942, 6628, 5163, 4714, 18, 4950, 16, 1920, 2213, 16252, 43, 14134, 17, 2743, 3418, 1988, 11374, 1920, 2743, 1927, 1920, 26758, 15643, 21302, 12, 14134, 13, 15155, 1942, 3373, 6804, 27388, 2455, 18, 2052, 3418, 4088, 1922, 6445, 5038, 3436, 3038, 16, 2710, 2616, 23523, 24684, 2053, 23, 17, 8914, 13966, 16, 22367, 4325, 7124, 16323, 1024, 4938, 12804, 14966, 8630, 16113, 11386, 16, 1930, 4543, 16324, 1036, 18, 2176, 5110, 1922, 23226, 7972, 2341, 18842, 2579, 8846, 1972, 3336, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 24221, 18, 3], "output": "MPKKVLIAGAGLVGPMLAIAMSKEGHQVTLFEARSDRRKISQDAGKSINLIITAKGLKTVEEAGILKEVKAITTPVYGRMMHSKTGELTFQAYGKDESEFNYSISRAKLNMLLMTLAEREGVQIYFDEPLEAIDFENRQASFCTHKNCQYDLFFGTDGAGSVTRKELVRIHAGAMENRVEPLGIDYKELFMPAGEQDSYQIDQKSLHIWPRGNHMLMALPNSDGSFTMTLYMPSVEFEKLDSSEKLKNYFETEYPDALPLMPDYQLDFEKNPQGFLGTVRCNPWVYQDSVALVGDAAHAVVPFFGQGMNCGFEDITYLTKMMKCHSDWATILEEYNQHQKLSDDAIADMAIENWNVMSSSVADKNYLLRKSVEKILENEFPKKYKSRYGMVVYTLIPYHFAQRVGLLQKEILETLCSNLLNAEEVDLKQASVLIDQKLVPYYREHNLSLDNFMP", "metadata": {"id": "A0A944Y5M8", "cluster": 17094523, "interpro_all": ["IPR002938", "IPR036188"], "interpro_used": ["IPR036188", "IPR002938"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Function:\nThe protein is assigned to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein includes a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein possesses a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is produced by Candidatus Aminicenantes bacterium and is linked to UniProt keywords Isoprene biosynthesis and Transferase.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 4152, 2007, 14550, 1031, 1957, 8584, 2927, 24254, 14652, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MFVRKNNQEIINGISLKAPAKINLFLEVLGEFEEIDEGIKLECENSSIPLNENNLVYKAAELVLRECGIGGGSSDAAATLKALNSLWGIGLNDVELCRGRGEKVYPVEVKSKLNYLVVFPHVEISTKSIYGNLKAVENSDVAEIGKLLFNRLEETIFSLYPDLLQTKNLLAEMIRNQIELRGMGKVFVAANTIIPQTTRKRNDGYHELETVMQEIDLVDSLKKGVAIRLEKRIPVGAGLMELAAKIGSDVAFFIKGKTSLIDLTKNRKDVSVFAKERFGFCGLLVSGSGSAIYGLCSNRNQ", "metadata": {"id": "A0A7V1MP27", "cluster": 19742710, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "infilling"} {"instruction": "The protein is categorized in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Furthermore, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It originates from Thermosulfurimonas dismutans and carries UniProt keyword assignments Cytoplasm and rRNA processing.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 22970, 2037, 7967, 19028, 18330, 3947, 1934, 16208, 2075, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MKVGHEPVLVREVLEWLAVRPGGWYADGTVGLGGHSEAILRASSPDGFLFFRLFRANFAEMPQILAREGVQVEGILLDLGLSSFLLKGSGRGFSFLREEPLDMRMDTRLRITARYGEEPRAAKIARAIVEARRKKRIETSLELARIVEKAVRPRKRGEHPATLTFQALRIAVNRELENLEFHSLEDRMVKRAFREDPRLRVLTRKPVRPSEDEVRRNPRARSARLRVAERCRSGFEWDEESLHQAEKRLSPFAGRDLVNRLSYPQLVELLRNHFLSRAPEILKPGGRLAIIS", "metadata": {"id": "A0A7C3CPI1", "cluster": 20147079, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein is included in the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Also, the protein is included in the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. In addition, the protein carries a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. It is identified in Pseudogymnoascus sp. VKM F-4513 (FW-928) and features UniProt keywords Magnesium, Metal-binding, and Nucleus.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 2176, 1977, 2899, 1922, 11520, 26983, 18044, 6952, 12709, 1957, 2056, 18, 26855, 1035, 48, 17, 26401, 1010, 12, 16451, 17, 6224, 1025, 13, 1930, 4075, 20709, 11569, 13148, 16, 6048, 17, 2743, 16, 1930, 5607, 18, 3], "output": "MASTGEKPLGITAPLSTALPTDSENQASSEALKALQAITEEFIKQVSKAQGLPDSVANSAGPKHVTRDDFFKYFPDLLVKMSVPIIKFEYEGISIDLIFSRIAVLNQIPQSLTLQDSRVTDAILDLVPQKTIFRTALRGIKLWAQRRAIYANATSSTVVLKFFRIMEKWQWPTPVIYKHDSFHLMPIITPAYPSMDQIMSGKLQWKDLFGKHTFFTEGYKYYLSVILVLSLEGHDSISLAHPFNKGSERVPTASEKPDDKPKEENAEDVKAENGEDEKKEEPKTTMVYTTTYYIGLELKEGARSLSWDKHDDSLNALNIVHTRNCDLPDDVFAEESNGSAPPPKRQQTSVAAQGALIEELKRQNNYESVVDTQKRTGGKIFTYGSFRLGVFGPGSDIDTLVVPPGAITDLTPVVDSFNLLRGLDEADLRSLNGTIIGFPGGVAWAMLVARVCQLYPKLLTHIASGPLQVKVWNPRCATHNITRSTKEIIQRELKRGGNITSASTTREAQNIWGGLVESKIRLHECHSEEEVEKAKSGSLQFLVKGEGVKTENGEDVKKEDEDLSYQVDDFKYRCTSPGEVKPTRPVKKKTVVKKRTV", "metadata": {"id": "A0A094BSG3", "cluster": 22319964, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR043519", "IPR011068", "IPR007012"], "interpro_unused": ["IPR007010", "IPR048840", "IPR014492"]}, "task_type": "infilling"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein belongs to the Acyl-CoA N-acyltransferase superfamily, which encompasses enzymes featuring a 3-layer $\\alpha/\\beta/\\alpha$ domain that catalyze the transfer of an acyl group, typically from acyl-CoA, to a nitrogen atom on diverse substrates. This versatile fold is utilized by histone acetyltransferases for chromatin regulation, aminoglycoside N-acetyltransferases for antibiotic resistance, and autoinducer synthetases for bacterial quorum sensing. Structural variations, including domain duplications and swapping, allow members like N-myristoyl transferases and non-ribosomal peptidyl transferases to perform specialized modifications such as protein lipidation and cell wall synthesis. It has been detected in Clostridium beijerinckii (Clostridium MP). Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 1925, 3835, 2687, 3244, 1988, 2469, 16318, 2460, 43, 2213, 22665, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 11337, 17, 10027, 56, 17, 11337, 9961, 13975, 16, 2154, 21569, 5038, 29931, 43, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3418, 1988, 18170, 1920, 3856, 1927, 1925, 11337, 2210, 16, 5745, 2037, 11337, 17, 10027, 16, 1942, 43, 6634, 6761, 1990, 6445, 6249, 18, 2052, 20425, 3728, 1977, 7079, 2007, 6632, 22226, 1036, 1958, 6338, 3640, 16, 23029, 8028, 56, 17, 22226, 1036, 1958, 7267, 3554, 16, 1930, 27485, 4600, 1005, 18185, 1036, 1958, 4543, 28481, 9306, 18, 4346, 6740, 16, 2710, 3418, 20559, 1930, 3476, 5041, 16, 3235, 4678, 3189, 56, 17, 20234, 10921, 13763, 1036, 1930, 2447, 17, 11196, 3431, 2199, 13763, 1036, 1942, 2385, 11021, 6920, 2427, 1966, 2213, 4486, 1943, 1930, 2024, 4821, 4271, 18, 2176, 2258, 2252, 3330, 1922, 21156, 13643, 16654, 12940, 3907, 12, 21156, 5438, 13, 18, 7031, 1920, 3244, 18, 3], "output": "MKIKNLIKSYKSNGIQEVLHKIISKIYLKEYLYKVEITNGYSYTNNKFRLSELNLQILNEMMSNYPGEIDECKYNILKERLKKPDENTYVVFENEEICGYFNIAYKDTKESCANVIINISKDSIYLYDDYTFIKHRGKGVHKFSILSRINMGINKKKKYAYVAIVFENIISEKSYEKFSFKKVKKYHCFKIGKIKKTFEKGDKNEHFYL", "metadata": {"id": "A0A0B5QLZ3", "cluster": 24003292, "interpro_all": ["IPR016181"], "interpro_used": ["IPR016181"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is classified under the Ankyrin Repeat and Cyclin-Dependent Kinase Inhibitor family, which plays critical roles in cell cycle regulation and protein ubiquitination. Members function as inhibitors that interact with CDK4 and CDK6 to check cell proliferation, or act as substrate-recognition components of E3 ubiquitin-protein ligase complexes to mediate the proteasomal degradation of target proteins. Also, the protein is categorized in the Ankyrin repeat-containing domain superfamily, which functions as a versatile protein-protein interaction module defined by tandem repeats of a \u03b22-\u03b12 structural motif. Predominantly found in eukaryotes, these domains mediate molecular recognition in diverse biological processes, including transcriptional regulation, cell-cycle control, cytoskeletal organization, and signal transduction. In addition, the protein incorporates a Ankyrin repeat that mediates protein-protein interactions through tandemly repeated helix-loop-helix modules which stack to form an L-shaped structure. This versatile motif is found in diverse eukaryotic proteins, including transcriptional initiators, cell-cycle regulators, cytoskeletal components, and signal transducers. It has been characterized in Ferrimonas marina and carries UniProt keyword assignments ANK repeat.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 1920, 28336, 6865, 1930, 8180, 17, 3100, 4016, 4106, 3416, 16, 2154, 5705, 4140, 5456, 1922, 2024, 4048, 3640, 1930, 2213, 11758, 18, 4678, 2347, 1966, 4472, 1988, 6310, 1956, 19646, 1930, 9727, 1016, 1942, 5588, 2024, 4031, 16, 2014, 4033, 1966, 4510, 17, 5708, 4178, 1927, 10968, 6526, 17, 2213, 11905, 5048, 1942, 8265, 1920, 19308, 4877, 1927, 2758, 2697, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 28336, 6865, 17, 3165, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 2213, 17, 2213, 2835, 9059, 3608, 2007, 10361, 9569, 1927, 43, 11157, 17, 13213, 4346, 5219, 18, 7700, 2435, 1922, 15021, 16, 2144, 4682, 8265, 3272, 5708, 1922, 6445, 3933, 4028, 16, 2710, 5224, 3640, 16, 2024, 17, 4048, 2285, 16, 14787, 5901, 16, 1930, 2733, 8201, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 28336, 6865, 1988, 10412, 2213, 17, 2213, 3719, 2596, 10361, 1954, 5116, 7864, 17, 5881, 17, 7864, 10803, 2154, 10496, 1942, 2386, 1925, 54, 17, 9132, 3170, 18, 2052, 20425, 5219, 1977, 2435, 1922, 6445, 10825, 2697, 16, 2710, 5224, 23467, 1036, 16, 2024, 17, 4048, 9098, 16, 14787, 4178, 16, 1930, 2733, 26307, 18, 2176, 2258, 2252, 4378, 1922, 12210, 1980, 9259, 13081, 2175, 1930, 16252, 20709, 11121, 2538, 18306, 9808, 6865, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MGSVITSHLFNRWRRMQELRLKVLVLISTLLMQACSAIFTSADFLSAKPSPLQVFSAVRERDFLLLNELVAQGSDINFKVGDGSPLLLCALDDVEMFRELLRLGADPSELIIFSGNIEIEDDFRATPIFSTIDPFNEEVPSAMIFLVDAGANIEHVNRGCVLYENGASVEVTSCAGLSFKELMSTYNERIVHGSEKHIKYLRAMEIMGLDNNVSYFVSYSCKFDEVSENNNVKFNGTTLLHLTAENEFVSLLTVMYMAAQVGRFDAVVY", "metadata": {"id": "A0A1M5R3G0", "cluster": 24175103, "interpro_all": ["IPR050776", "IPR002110", "IPR036770"], "interpro_used": ["IPR050776", "IPR036770", "IPR002110"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein is grouped in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is identified in Micromonospora sp. HUAS YX12 and features UniProt keywords Cytoplasm and rRNA processing.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 2899, 1922, 7709, 23557, 3508, 8846, 2056, 18, 5897, 1934, 67, 7653, 1028, 1930, 4075, 20709, 11569, 5239, 1930, 9067, 4587, 18, 11586, 5655, 3581, 18, 3], "output": "MGELRGTHVPVLLERCLELLAPALGRPGRTVHVDATLGLAGHAEAVLTAHPDTVLIGLDFADRIHLEHAVYDELPEVLDRLGYPAIDGVLFDLGVSSLQLDAPDRGFAYAQDAPLDMRMDQTRGVTRVYGEEKFAGKIASAIIRERERARITSSARLAELVRDAIPAPARRTGGHPAKRTFQALRIEVNRLSYHSLEDRLTKHALADRVRSKGPVDLPVELPGSGPTFRLLSRGAELPGEAEVARQGSTDRERYRRRVKAMHQPGTGSPGSGKDPRSAPGDANGTDEEGEGTRDTEALAHARVRLARAEEVVNTYSHPDLARLLELAALETALPAALDKLTVGGRMVVANPRAASVRLRAAERLDPEAA", "metadata": {"id": "A0AAU7QTL8", "cluster": 25190994, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein is included in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, the protein is associated with the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Moreover, the protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It occurs in Actinomycetota bacterium and is associated with UniProt keywords Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 5110, 1922, 4718, 13386, 19446, 3857, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 3], "output": "MGEGQVREFTHEPVLLERCILERFPQVRLVGLDRDPVALEMSRKDLGIAHVNGILFDLGVSSMQLDDADRGFAAEVVNTYSARDLAHVLRSYGDERFAKRIADRIVGSIPAAARRTGGHPAKRSFQALRIEVNGELDALEAAYQSLEDHIVKISMAERAKSTSPRGLPVELPGHASDDELARNPRSAPARLRAAQRIRVAALALLAPALEADDAVAVDATLGLGGHSEARLAPFAQRTTLVHAVYDQLPSVLSAYSQDAPLDMRMDNTQSLTEREREPFNSTARLAEVVREIPAAIDSLALNGRIVVMSGPELEILTRKVET", "metadata": {"id": "A0A6I3DZQ5", "cluster": 27081403, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Target Function: The protein carries a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. Furthermore, the protein is categorized in the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. Furthermore, the protein contains a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. It is present in Deltaproteobacteria bacterium and exhibits UniProt keyword tags Hydrolase and Metal-binding.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 16252, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 3677, 16, 1920, 2213, 5461, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 2176, 1977, 2481, 1922, 9649, 9218, 1021, 10296, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 20748, 1930, 6048, 17, 2743, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MGVSAEQVLSTLKDLKDPSSGRPMSELGYFKHPEMLDGGGVRVRVELPTLPRVEVAFGANVRPSPAKQHNPNDLVPSVKNVVLVGSGKGGVGKVRLLDADIYGPSLPLMMGLFGARPTSEDGKSVVPLTAFGVKVISIGFFLRDVRWGDLDYLILDLPPGTGDIQLTIAQQVSVSGAVVVTTPQDVALGFVENMSGFVCPHCHHETDIFSKGGAEQAAAKLGVPFLGRVPINPAIRPGLPEAQALTRIAQNVADRVALANMTAVPRGQKPLVQLGKKAPASPHKARIEEAVRAMLSPLQKSTVSANVAVALANLGCVDPDQAMIWRGPMLHGALVQLADAIKAKTMFDKVNIPVLVGSDDGRPVVAAD", "metadata": {"id": "A0A534TIX4", "cluster": 27520525, "interpro_all": ["IPR034904", "IPR002744", "IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR000808", "IPR033756", "IPR002744"], "interpro_unused": ["IPR027417", "IPR019591", "IPR034904", "IPR044304"]}, "task_type": "infilling"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein should feature a Cell envelope-related transcriptional attenuator domain that functions in the extracellular region of membrane-anchored proteins to regulate cell wall and exocellular polysaccharide biosynthesis. Also known as the LCP domain, it contains conserved aspartate and arginine residues essential for cell envelope maintenance and bacterial growth. Furthermore, the protein falls within the LytR/CpsA/Psr (LCP) family, which facilitates the transfer of anionic cell wall polymers, such as teichoic acids, from lipid-linked precursors to peptidoglycan, a critical step in maintaining cell wall integrity. These proteins are essential for cell envelope biosynthesis and are implicated in biofilm formation, virulence regulation, and resistance to antibiotics like oxacillin. Specific members function as polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferases or act as regulators in stress response pathways. It is found in Clostridium frigidicarnis.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 3066, 5961, 43, 2024, 11262, 17, 2712, 5224, 5693, 3061, 3418, 1988, 4088, 1922, 1920, 5329, 3031, 1927, 3260, 17, 17199, 2697, 1942, 5741, 2024, 4821, 1930, 18930, 9631, 2168, 17167, 8132, 18, 2222, 3171, 1966, 1920, 5236, 1034, 3418, 16, 2176, 5461, 5305, 12878, 1930, 9732, 4248, 4415, 1958, 2024, 11262, 6291, 1930, 4543, 2905, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 7518, 1997, 19, 15158, 1019, 19, 2742, 1005, 12, 5236, 1034, 13, 3416, 16, 2154, 11374, 1920, 3856, 1927, 19696, 2024, 4821, 11039, 16, 2427, 1966, 3602, 2108, 8643, 4576, 16, 2037, 4486, 17, 4624, 10416, 1942, 24183, 16, 43, 4140, 3537, 1922, 8231, 2024, 4821, 7996, 18, 2144, 2697, 2032, 4415, 1958, 2024, 11262, 8132, 1930, 2032, 6835, 1922, 9638, 3337, 16, 9304, 3640, 16, 1930, 3554, 1942, 7560, 3189, 28905, 10401, 7782, 18, 2487, 4678, 2347, 1966, 4286, 23854, 20367, 2199, 17, 3602, 2108, 8643, 2687, 17, 17, 24183, 3602, 2108, 8643, 2687, 13763, 1036, 2014, 4033, 1966, 9098, 1922, 3071, 2644, 3873, 18, 2176, 1977, 2435, 1922, 21156, 9081, 6121, 7408, 15339, 11110, 18, 3], "output": "MSTRMDKYHSTDKKPTNRNTKPYSNDSRKPNPKKRRRKKKNPTVRIILLSIALLFLLGIGWGAYYAVNLLGKVNTEKLDKSNLGVDEDLNARLKSLGKDNIINIALFGLDKTNEEELGRSDATMILSIDADNKKIKLVSLMRDCYVNINGHGKDKLNHAHSFGGPELAIRTINKNFNLNVTDFVSVDFAHMQKIIDALGGVEIDVKSTELETANKYVVELALLGRTDPDYIDKAGKQTLSGMQALSYSRIRNVGNGDFERTDRQRTVLEALFNKIKHAGSTEFPKIVSDLLPMVTTSLSSTDIIKLGSDLLLKGITNLEQERFPIDGDYVDGGKMINGVWYLPFDEKSTQGKIHKYIFEDIKPS", "metadata": {"id": "A0A1I0W0H6", "cluster": 28073365, "interpro_all": ["IPR050922", "IPR004474"], "interpro_used": ["IPR004474", "IPR050922"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein incorporates a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Furthermore, the protein features a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Also, the protein should include a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. It is found in Mucilaginibacter straminoryzae and corresponds to UniProt keyword Coiled coil, Hydrolase, and DNA damage.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 19683, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 3677, 16, 1920, 2213, 4075, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2176, 1977, 2435, 1922, 3422, 19167, 26296, 26073, 2341, 1915, 9402, 8547, 2247, 12813, 1021, 1930, 8852, 1942, 20709, 11121, 2538, 17524, 9121, 16, 20748, 16, 1930, 2678, 4293, 18, 3], "output": "MEFKLNSHYKPTGDQPGAIKQLVEGVESGEQYQTLLGVTGSGKTFTVQLYGEFKQFFPENAVNYFVSYYDYYQPEAFIPTTNTRLRTTSSLMAGRRDVIVVSSISCIYGMGNPEDFSNSVFRFAVGTRISRNAGTFRVKGDTVDIYPAYLDYAYRISFYGDDIEELSSFDVDRFTKSIWAIQEELEMRKQQFLDEKRFLEAKRLEERVNYRFFDGRRPGARPFCLLDYFPDDYLMVIDESHVTVPQIRAMYGGEFEGLAPQTIYVSATPGDYELEKSGGVVVEQVIRPTGLLDPEIEIRPVINTKRMSEELAKYMDRLGIKCRYIHSEVKTLERVEILRGLRLGEFDVLDADKEGFLRSERSLIQTIGRAARNDRGRVIMYADTITDSMQITEEHGIVPKTVGKSKEAIIEQTSVVDFKGGVQRAYVEEIDSATSIAADPIVEMVAAAKDMDFLQAAKLRDEMFALEKMLSEKANVIAETQRPTLVLSHNKTLAAYIEKDLQINDEIEKLFLHRLVEILYSRTTADFKRKTGKTLEKMENMVLFPANLYVAPRDLEMIRELGYCSGIENYSDRSRKISLVEYGFRLPAALDNRPLNFQQVDDLLDEVDKTVKLGDRVLVTTLIGINLLREGLDLPEVSLVAILIDETTRRREKQIAYNQYMTKADLKKAIENTRK", "metadata": {"id": "A0A9X1X5Z0", "cluster": 28363854, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001650", "IPR014001", "IPR001943"], "interpro_unused": ["IPR004807", "IPR006935", "IPR027417", "IPR041471", "IPR036876", "IPR024759"]}, "task_type": "infilling"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein is grouped in the Acyl-CoA N-acyltransferase superfamily, which encompasses enzymes featuring a 3-layer $\\alpha/\\beta/\\alpha$ domain that catalyze the transfer of an acyl group, typically from acyl-CoA, to a nitrogen atom on diverse substrates. This versatile fold is utilized by histone acetyltransferases for chromatin regulation, aminoglycoside N-acetyltransferases for antibiotic resistance, and autoinducer synthetases for bacterial quorum sensing. Structural variations, including domain duplications and swapping, allow members like N-myristoyl transferases and non-ribosomal peptidyl transferases to perform specialized modifications such as protein lipidation and cell wall synthesis. Also, the protein should feature a GNAT domain that functions as a Gcn5-related N-acetyltransferase, utilizing a conserved structural fold to catalyze the transfer of an acetyl group from acetyl-CoA to primary amines on a diverse array of substrates. This enzymatic activity drives critical biological processes, including chromatin remodeling via histone acetylation, antibiotic resistance through aminoglycoside modification, and the regulation of circadian rhythms. It is found in Chloroflexota bacterium.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 1977, 10809, 1922, 1920, 11337, 17, 10027, 56, 17, 11337, 9961, 13975, 16, 2154, 21569, 5038, 29931, 43, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3418, 1988, 18170, 1920, 3856, 1927, 1925, 11337, 2210, 16, 5745, 2037, 11337, 17, 10027, 16, 1942, 43, 6634, 6761, 1990, 6445, 6249, 18, 2052, 20425, 3728, 1977, 7079, 2007, 6632, 22226, 1036, 1958, 6338, 3640, 16, 23029, 8028, 56, 17, 22226, 1036, 1958, 7267, 3554, 16, 1930, 27485, 4600, 1005, 18185, 1036, 1958, 4543, 28481, 9306, 18, 4346, 6740, 16, 2710, 3418, 20559, 1930, 3476, 5041, 16, 3235, 4678, 3189, 56, 17, 20234, 10921, 13763, 1036, 1930, 2447, 17, 11196, 3431, 2199, 13763, 1036, 1942, 2385, 11021, 6920, 2427, 1966, 2213, 4486, 1943, 1930, 2024, 4821, 4271, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 9005, 1926, 3418, 1988, 4088, 1966, 43, 5469, 19870, 17, 2712, 56, 17, 22226, 16, 10232, 43, 5305, 4346, 3728, 1942, 18170, 1920, 3856, 1927, 1925, 6894, 2210, 2037, 6894, 17, 10027, 1942, 3065, 20739, 1990, 43, 6445, 6472, 1927, 6249, 18, 2052, 8145, 2455, 15435, 4140, 3933, 4028, 16, 2710, 6338, 8378, 3454, 6632, 10339, 16, 7267, 3554, 2596, 23029, 8028, 6295, 16, 1930, 1920, 3640, 1927, 10507, 16622, 18, 2176, 1977, 2435, 1922, 10107, 18222, 7336, 14061, 18, 3], "output": "MTSISNADTNLTFRDMTTDDAQALCNCVETCYGDTYFVDDFYDPDRLACLIDQGLINSRIAVTSAGEVIGHLGLTLERSCDITADTLAAMVAPEYRGHRILVDLGMQLVETYEKLNLVGLQLYAIAIHPIVQDHSTEAGGVETGILLGHFPTDLEIEGFPNIYDGRRIAAVMLYFPLHPAPSQTIYVPEHYRDVVDSVYEQLKQDRTTSIETEHPSVATTMVTIDEKPRQGTARMRIDQPGHDLLQMVTAFKQRASSSFPVLYVDLPLADPASARFIDDLRSLGFFYGGIVLERSGSDILRMQCLNRKDVNPEAIVLARPHAKDMLKFILSDWQEKV", "metadata": {"id": "A0A972TPT4", "cluster": 28503913, "interpro_all": ["IPR016181", "IPR000182"], "interpro_used": ["IPR016181", "IPR000182"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a polypeptide chain with the following function: The protein is categorized in the Chlorophyll A-B binding protein family, which functions as a core component of the light-harvesting complex (LHC) to capture and deliver excitation energy to photosystems I and II. These proteins bind chlorophylls A and B and utilize an N-terminal stromal extension to mediate granal membrane adhesion and regulate energy distribution through reversible phosphorylation. The family also includes members like PsbS that facilitate the thermal dissipation of excess light energy through energy-dependent quenching. Furthermore, the protein belongs to the Aspartic peptidase domain superfamily, which comprises widely distributed endopeptidases that utilize a catalytic dyad of two aspartic acid residues to activate a water molecule for peptide bond hydrolysis. Members of this superfamily, including pepsin and retroviral proteases, typically adopt a retropepsin-like fold and function as bilobed monomers or homodimers to perform roles ranging from general protein degradation to specific signal peptide processing. It occurs in Tanacetum cinerariifolium (Dalmatian daisy) (Chrysanthemum cinerariifolium) and is connected to UniProt keyword Chloroplast, Photosystem II, and Photosynthesis. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 16553, 43, 17, 44, 2743, 2213, 3416, 16, 2154, 4088, 1966, 43, 4728, 4594, 1927, 1920, 3696, 17, 17318, 2796, 12, 9107, 1030, 13, 1942, 7573, 1930, 3971, 8392, 3844, 1942, 8811, 8130, 51, 1930, 2890, 18, 2144, 2697, 4566, 16553, 1036, 43, 1930, 44, 1930, 12561, 1925, 56, 17, 4262, 9709, 7140, 1942, 8265, 5559, 1923, 3260, 6141, 1930, 5741, 3844, 3282, 2596, 10743, 4050, 18, 1920, 3416, 2222, 5921, 4678, 3189, 2742, 2083, 1988, 6628, 1920, 7111, 25303, 1927, 5799, 3696, 3844, 2596, 3844, 17, 3100, 16721, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 23047, 24050, 3418, 13975, 16, 2154, 12936, 5673, 6533, 16239, 9626, 2410, 30413, 1988, 12561, 43, 6804, 28679, 1927, 2288, 23047, 2687, 4248, 1942, 6980, 43, 3224, 5388, 1958, 4207, 5403, 9128, 18, 4678, 1927, 2052, 13975, 16, 2710, 27979, 1930, 16599, 12447, 16, 5745, 14103, 43, 7332, 9626, 2523, 1921, 17, 3189, 3728, 1930, 2347, 1966, 5088, 16248, 1007, 13256, 2014, 29227, 1942, 2385, 5456, 6485, 2037, 3335, 2213, 4877, 1942, 2487, 2733, 4207, 4587, 18, 2176, 5110, 1922, 10434, 7681, 1989, 29245, 5524, 21094, 25203, 1989, 12, 15880, 3368, 17322, 23708, 18801, 13, 12, 21367, 7744, 1987, 1989, 29245, 5524, 21094, 25203, 1989, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 17471, 16, 8811, 2405, 2890, 16, 1930, 18133, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MLFTINLRPHNPTNDNANVKSFSSFQIPNQESKPCQEEIDVVSETNDVLPPSDDDSDDEVDVVGSLLVDNVIQDSKHEYSESEDSDLDNPLLPLTPPEPPDKEFDFEIDFEKEISVMRSLIVKFECIDARMKFDIFNAENDVFKFIMFSLLSAESEDMIFDLANILRFANPLMKELKNTTSASLQEKVLVITALKETISNLKGKKVVTEAVSLNPIGPELLKIDVAPIALKLRKNRTAHTDYIRHTQEEAATLREIVESERLLNLLNTSLDYALKRKVWQPIENASKTIRHIWKATGWTFTLVGKVCPLTRIATTTIVPPREPIPVVNSTDKLVVTLVYSRKTKAANKKVPVSNSTITKSLVANKMEPNNSWGSSSSNVPSPLIDCSNNMQTQTSNTLHNAIMEAGSKDRPPMLAPGTDTLSLVSKYLNGMEDILDDGDSMEARKLTIEKSKEELELFEALNHKSVIANEETKVRGMPTLILRIHSITLWKKVIVYANKGEPLVLFGRDFLVTSKSGADFGIGEMRSDLTMLEDMKEIDVMLDALVENLEKVGSSNGDLVNMGKASRNKNHKVNKLTPPPQINIKEIPPISNIAPQSPIYHPLTQTKRESERSVGSARLNSDDYGDEVKMRIVEHGLPKKMCDPGNFVLLLKVNGTIKMNALVDTRVSVSVLPYFLYMNLGLGVPKPYNSNLTMADNTQAKAINIPVDKELPLLLGRPFLRTCGAVIDMGRGTLCIDDGVIRHTYFPKPRAKAYLDNFAQEEDDDWLSCFEVGRDEDGNPKYGPVAPLFLDIEDDKERALAMEAYFNTFKNITFFKKLIDFLVTQGSSPNLLITIVCSGYSRWIATLIFSSATLVMEEGCAYGPETIVHSSRIILLRRTFNELGVGDFVHECEDSHALRGSLDMPTLSLESLHEIFYRFPLSLLDVLSMNSGGRSSNHTLADPPGLFWEVEVADAGCERLSDCADTLFSLPHSLLNTPSSLLSLPTGMCLGNSDLSRLILEKTLVRLGLSDMLRERLDLRPLRAASDAGMFGFLRLAHSHCVLHGGRGWAISSAGSLMAVNPVPSTPSLFGEGRVTMRKTAAKPKKVTSDSPWYGEFPGDYGWDTAGLSADPETFAKNHELEVIHSRWAMLGALGCVFPELLARNGVNFGEAVWFKDGSQIFSEGGLDYLGNPNLVHAQSILAIWATQVILMGAIEGYRIAGGPLGEVVDYLYPGAIVTGKGPLENLADHLADPISNNAWAFATNFVPGK", "metadata": {"id": "A0A6L2LJY7", "cluster": 20808315, "interpro_all": ["IPR001344", "IPR022796", "IPR021109"], "interpro_used": ["IPR022796", "IPR021109"], "interpro_unused": ["IPR001344"]}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein should feature a Small GTP-binding domain that functions as a molecular switch by binding and hydrolyzing GTP to regulate diverse cellular processes, including signal transduction, vesicle transport, and protein biosynthesis. It is found in the Ras superfamily of small GTPases as well as within larger proteins such as translation elongation factors. Moreover, the protein carries a TrmE-type guanine nucleotide-binding domain that functions as a P-loop GTPase molecular switch to facilitate tRNA modification. It adopts a canonical Ras-like fold that dimerizes in a potassium-dependent manner and utilizes conformational changes driven by GTP hydrolysis to modify uridine bases at the tRNA wobble position. Furthermore, the protein should have a GTP binding domain that contains five conserved structural motifs to bind guanosine triphosphate (GTP). It is present in a diverse array of proteins, such as the developmentally regulated DRG, the essential bacterial OBG, and ferrous iron transport protein B, indicating a broad role in cellular regulation and transport. It is present in Gammaproteobacteria bacterium and is described by UniProt keywords Magnesium, Metal-binding, and Cytoplasm.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 3066, 5961, 43, 2858, 9319, 17, 2743, 3418, 1988, 4088, 1966, 43, 3272, 6195, 2007, 2743, 1930, 7222, 9046, 9319, 1942, 5741, 6445, 3689, 4028, 16, 2710, 2733, 8201, 16, 11502, 4860, 16, 1930, 2213, 8132, 18, 2176, 1977, 2435, 1922, 1920, 6520, 13975, 1927, 2858, 18390, 1966, 2486, 1966, 2651, 4327, 2697, 2427, 1966, 6410, 9971, 2790, 18, 3950, 16, 1920, 2213, 16252, 43, 28402, 1021, 17, 2601, 16904, 5489, 17, 2743, 3418, 1988, 4088, 1966, 43, 58, 17, 5881, 14809, 3272, 6195, 1942, 6628, 10089, 6295, 18, 2176, 24032, 43, 9452, 6520, 17, 3189, 3728, 1988, 7632, 4517, 1922, 43, 9057, 17, 3100, 5222, 1930, 18127, 8523, 2840, 6446, 2007, 9319, 9128, 1942, 11675, 26104, 11137, 2019, 1920, 10089, 26334, 6936, 1952, 3507, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 9319, 2743, 3418, 1988, 5461, 3628, 5305, 4346, 8277, 1942, 4566, 24870, 17978, 12, 9319, 13, 18, 2176, 1977, 2481, 1922, 43, 6445, 6472, 1927, 2697, 16, 2427, 1966, 1920, 23130, 4335, 14801, 16, 1920, 4415, 4543, 2384, 1029, 16, 1930, 26739, 5680, 4860, 2213, 44, 16, 4168, 43, 4949, 2770, 1922, 3689, 3640, 1930, 4860, 18, 2176, 1977, 2481, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 13148, 16, 6048, 17, 2743, 16, 1930, 5239, 18, 3], "output": "MYSLNDNIVALATAPGSSALSVVRCSGPQVLFFLKKIIFKKKLTSPKTVSLCSIFNPVNKKQIDQCLVVFFKGPNSFTGDDVVEFSLHGGSVISSKIIQVLIDLGCREASPGEFTYRAFINGKIDLIQAEAINSLIKTSKDVNAFYASKNVEGFLSKSLVECQKKLKELITYIEHELDFTEEEIGHVSVENYLLQTTKIIKEAKKIERSSFVGSEQNTDLEVCIAGXPNAGKSSLFNRLVGKNRSIVTSASGTTRDFISASFVVDGFLVDLVDTAGLRVSSDXVEKQGIDRALSKIKQSDIILFVSEEXPLKXFKSFNFSXXPXQKTLFIQNKTDXNKKXKNTSVFNVSCKTKKGLRKLQTELSTLIKAQKESFYIKNKYLISSRAQKGLSSFIKSLKTAHKNLKNNRDLVVFVSSLYVAQESIQGTINPTNKSEIINNIFKGFCVGK", "metadata": {"id": "A0A2D8QTQ1", "cluster": 25647526, "interpro_all": ["IPR031168", "IPR006073", "IPR018948", "IPR004520", "IPR027368", "IPR025867", "IPR027417", "IPR005225", "IPR027266"], "interpro_used": ["IPR005225", "IPR031168", "IPR006073"], "interpro_unused": ["IPR004520", "IPR027417", "IPR027368", "IPR018948", "IPR025867", "IPR027266"]}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein includes a JmjC domain that adopts a cupin fold to coordinate Fe(II) and alpha-ketoglutarate, functioning as a metalloenzyme involved in chromatin remodeling. This catalytic domain primarily acts as a histone demethylase conserved from yeast to humans, although some variants display hydroxylase activity involved in processes such as tRNA modification. In addition, the protein is assigned to the JMJD6 family, which functions as a bifunctional arginine demethylase and lysyl-hydroxylase involved in RNA splicing and gene expression regulation. These dioxygenases modify histones and interact with transcriptional machinery to modulate RNA polymerase II pause release, playing critical roles in embryonic development, hematopoietic differentiation, and angiogenesis. Moreover, the protein includes a Cupin-like domain 8 domain that shares structural similarity to the JmjC domain, suggesting a potential role in histone demethylation or oxidative catalysis. It likely adopts the conserved beta-barrel fold characteristic of the cupin superfamily. It is identified in Chloropicon laureae.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 5921, 43, 16097, 30271, 3418, 1988, 24032, 43, 14967, 1921, 3728, 1942, 11865, 2650, 12, 2890, 13, 1930, 4595, 17, 21471, 16542, 17488, 16, 7295, 1966, 43, 8969, 6802, 1022, 9318, 3286, 1922, 6338, 8378, 18, 2052, 6804, 3418, 5985, 8016, 1966, 43, 6632, 21732, 2051, 5305, 2037, 5688, 1942, 5209, 16, 2876, 2673, 4936, 4434, 16324, 2455, 3286, 1922, 4028, 2427, 1966, 10089, 6295, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 16097, 24628, 1016, 3416, 16, 2154, 4088, 1966, 43, 29491, 9732, 21732, 2051, 1930, 3629, 2199, 17, 16324, 3286, 1922, 3146, 8490, 1930, 2359, 2294, 3640, 18, 2144, 23652, 10465, 2432, 2319, 11675, 15808, 1930, 6310, 1956, 5224, 10853, 1942, 8480, 3146, 6479, 2890, 25863, 4012, 16, 14797, 4140, 5456, 1922, 7231, 2740, 16, 9960, 4155, 16, 1930, 8244, 18, 3950, 16, 1920, 2213, 5921, 43, 14967, 1921, 17, 3189, 3418, 28, 3418, 1988, 16495, 4346, 6796, 1942, 1920, 16097, 30271, 3418, 16, 3783, 43, 2889, 2770, 1922, 6632, 20254, 2014, 5163, 15408, 18, 2176, 3205, 24032, 1920, 5305, 4666, 17, 19560, 3728, 6293, 1927, 1920, 14967, 1921, 13975, 18, 2176, 1977, 2899, 1922, 10107, 19232, 1916, 27940, 5376, 1021, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "GVVASDDGLHVATSVSIIEWFLVEAGEVIFVPRGWWHLVVNLEESVAITQNYVSRANLTLHARFRSALGDRKPALLESVEGGGNFYEAAREEGECQPRECVKQVLEYIEKPELVSGCPVEQRG", "metadata": {"id": "A0A7S3E4V0", "cluster": 476015, "interpro_all": ["IPR041667", "IPR003347", "IPR050910"], "interpro_used": ["IPR003347", "IPR050910", "IPR041667"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein features a Flagellin hook, IN motif conserved site that is present in various flagellar hook proteins, including FliD homologues. Defined by centrally conserved Ile-Asn (IN) residues, this region occurs as a single copy or in repeats within the flagellar apparatus, though its precise function is not yet clear. In addition, the protein should have a Flagellar hook-associated protein 2 C-terminal domain that forms the distal end of the flagellum, acting as the filament cap (also known as HAP2 or FliD). This region is essential for structural integrity and facilitates bacterial attachment to host tissues through mucin-specific adhesion. It is present in Dissulfuribacter thermophilus and is linked to UniProt keywords Secreted, Cell projection, and Cilium.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 27389, 17185, 16, 1922, 5219, 5305, 3200, 1988, 1977, 2481, 1922, 3425, 24154, 17185, 2697, 16, 2710, 2300, 1960, 18541, 18, 3608, 2007, 20424, 5305, 9940, 17, 15118, 12, 1922, 13, 4248, 16, 2052, 3031, 5110, 1966, 43, 2957, 6983, 2014, 1922, 9569, 2651, 1920, 24154, 11161, 16, 4170, 2496, 8162, 2347, 1977, 2084, 4898, 4021, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 24154, 17185, 17, 2458, 2213, 22, 45, 17, 4262, 3418, 1988, 4952, 1920, 6583, 2482, 1927, 1920, 7030, 10757, 16, 8290, 1966, 1920, 10797, 2853, 12, 2222, 3171, 1966, 13466, 1028, 2014, 2300, 1960, 13, 18, 2052, 3031, 1977, 4415, 1958, 4346, 7996, 1930, 11374, 4543, 8576, 1942, 4423, 3878, 2596, 14455, 17, 2487, 6141, 18, 2176, 1977, 2481, 1922, 3904, 4042, 18330, 7972, 2341, 1915, 7967, 24888, 5277, 1036, 1930, 1977, 4624, 1942, 20709, 11569, 8366, 16, 2024, 11244, 16, 1930, 28997, 18, 3], "output": "MAGTISILGMGSGLQLQDILDQLKAADRAPITRLKAKQLQAKDRVAELDTLKKLLSVSLSDSSPVSVSVSSGASTGSYNIEVIRLAQYSAWRSTSGFASEVNGKSTSLSVASGTTLQQLAALINDDPNNPGVTASVVKDGTGATPYKLLIQSNTLGESGRGTGGSSLDAEIKIDGVSYTKGSNEITDILTGVTFTLQATGQTTLSILNEYFQEVNTNSSYDTDTGVGGSLYGVTSIQLFKSQVIESVSDKVDDTLNQALSEHFNDVKSFFLGDTDNNITGWADRVNTILRTATKANTGLIDAEKKKYEILARQFLELDRYMNNMQSISSYLSQQFEAFNNALKNKLDLKDKALTLGLSSTYLGREDSVINGTGSTETFTYISITKQLTDITLAEETTTDTSGIAALVKDFVTGVSGAITSIFDLGFEFARDGTISINESAANSQINNLDEQITSAEARLE", "metadata": {"id": "A0A1B9F329", "cluster": 1832134, "interpro_all": ["IPR010810", "IPR040026", "IPR010809", "IPR003481"], "interpro_used": ["IPR010810", "IPR010809"], "interpro_unused": ["IPR040026", "IPR003481"]}, "task_type": "infilling"} {"instruction": "We aim to build a protein that does the following:\nIt is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein is grouped in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is identified in Streptococcus sp. GMD4S and is classified with UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2899, 1922, 15746, 2056, 18, 5711, 15005, 1036, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MGKIIGITGGIASGKSTVTNFLREQGFLLVQHFGQEIILENGELNRPLLASLIFSNPEEREWSKQTQGKIIREELAALRDYSAWFDETWLVYVDRDVQVERFMKRDHLSKEVAESRLNNGSRDQLVAQVVKLLEGGDSCARDQVVDADAVVHQLQKPGGRLYQDQLTQTETVFFMDIPLLFEQAAQWSLEEKKKLASHILD", "metadata": {"id": "K0ZXV9", "cluster": 2934685, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that has the following function: The protein includes a Protein-glutamine gamma-glutamyltransferase-like, C-terminal domain that contributes to essential cell wall functions and bacterial viability in prokaryotes, often in concert with a transglutaminase core. It contains a conserved TXXE motif and is required for the survival of organisms such as *Pseudomonas aeruginosa*. It is expressed in Cyclobacteriaceae bacterium and has UniProt annotations Transmembrane helix, Signal, and Membrane. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 2213, 17, 9959, 7034, 17, 25345, 9961, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 7624, 1942, 4415, 2024, 4821, 4088, 1930, 4543, 6432, 1922, 28149, 16, 3868, 1922, 21799, 1956, 43, 2127, 16542, 15848, 4728, 18, 2176, 5461, 43, 5305, 10117, 1039, 1021, 5219, 1930, 1977, 3414, 1958, 1920, 3298, 1927, 7373, 2427, 1966, 14, 13461, 10830, 14, 18, 2176, 1977, 3198, 1922, 17009, 7972, 2341, 18339, 1972, 3336, 14061, 1930, 2258, 20709, 15010, 9117, 7864, 16, 2733, 16, 1930, 3260, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MKRISFLTFFFFISLWCFAQSDSLSDSVPADTASIELPKFKISKDTIAFAKRGFSKTVIENFKADEDFRYGRPKQGLTAWQRFMIWLVSLIAAILDVLTNTTLGQIVFYGTCLLLLLWVILKLLKIDAKDLFYNRAGKNSLILTGADNIHEVDFENELQLAAAQKKYREAVRLMFLFALKKLADAHLIKWIPGKTNDEYLVELRQHPSHTHLQNLRHYFEYSWYGHFEVTEQTYQHIQGVFLEFKNKLS", "metadata": {"id": "A0A5C7Z3V7", "cluster": 3632044, "interpro_all": ["IPR025403"], "interpro_used": ["IPR025403"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein incorporates a Protein kinase domain that functions as the conserved catalytic core responsible for transferring the gamma phosphate from ATP to serine, threonine, or tyrosine residues on substrate proteins. This phosphorylation event induces conformational changes that regulate diverse cellular processes, such as proliferation, differentiation, and apoptosis. Additionally, the protein can be placed in the Serine/Arginine-Rich Protein Kinase (SRPK) family, which comprises serine/threonine kinases that specifically phosphorylate serine residues within the arginine/serine-rich (RS) domains of splicing factors to regulate pre-mRNA splicing and mRNA maturation. These enzymes control the intranuclear distribution of splicing factors and nuclear speckle reorganization, while also contributing to chromatin remodeling, cell cycle progression, and muscle development. Moreover, the protein possesses a Protein kinase ATP binding site that binds ATP to facilitate the transfer of the gamma phosphate to protein substrates during phosphorylation. Located in the N-terminal catalytic domain, this conserved site utilizes a specific lysine residue within a glycine-rich stretch to anchor the nucleotide. This interaction is essential for the activity of serine/threonine, tyrosine, and dual-specificity kinases in regulating processes such as cell division and proliferation. It is expressed in Gymnopus androsaceus JB14 and exhibits UniProt keyword tags ATP-binding, Serine/threonine-protein kinase, and Transferase.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 2213, 4016, 3418, 1988, 4088, 1966, 1920, 5305, 6804, 4728, 5061, 1958, 21902, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 16, 13143, 16, 2014, 6941, 4248, 1990, 4510, 2697, 18, 2052, 4050, 4817, 6387, 8523, 2840, 1988, 5741, 6445, 3689, 4028, 16, 2427, 1966, 4031, 16, 4155, 16, 1930, 4091, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8468, 19, 9732, 17, 5536, 2213, 4016, 12, 19939, 1040, 13, 3416, 16, 2154, 12936, 8468, 19, 13143, 7784, 1988, 4475, 18730, 8468, 4248, 2651, 1920, 9732, 19, 8468, 17, 5536, 12, 4366, 13, 4682, 1927, 8490, 2790, 1942, 5741, 2097, 17, 3616, 8490, 1930, 3616, 7655, 18, 2144, 5038, 2285, 1920, 16091, 13821, 3282, 1927, 8490, 2790, 1930, 4254, 29564, 18062, 16, 2679, 2222, 8739, 1942, 6338, 8378, 16, 2024, 4048, 4380, 16, 1930, 3760, 2740, 18, 3950, 16, 1920, 2213, 14465, 43, 2213, 4016, 4498, 2743, 3200, 1988, 6876, 4498, 1942, 6628, 1920, 3856, 1927, 1920, 7034, 5413, 1942, 2213, 6249, 2409, 4050, 18, 4810, 1922, 1920, 56, 17, 4262, 6804, 3418, 16, 2052, 5305, 3200, 18127, 43, 2487, 9082, 6181, 2651, 43, 10646, 17, 5536, 9064, 1942, 13333, 1920, 5489, 18, 2052, 2835, 1977, 4415, 1958, 1920, 2455, 1927, 8468, 19, 13143, 16, 6941, 16, 1930, 7064, 17, 4896, 7784, 1922, 6773, 4028, 2427, 1966, 2024, 8451, 1930, 4031, 18, 2176, 1977, 3198, 1922, 26024, 11873, 1034, 1957, 1930, 2263, 8565, 1036, 29316, 3745, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 8468, 19, 13143, 17, 2213, 4016, 16, 1930, 13763, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MNIESAYRYCPGGYHPVHLDDKFYDSQIGRYAALKICVANLERSISRVFDEITVVKEGNNHVVQIFDVFTHKGPNGTHLCIVTEILGPGIAKRLGAQVAYGLRYLHKHGIVHGDLHVRYIPHAWKADAPTSDLSLNPAPDPASLHVKICDFGESFLAVPGSGFENLLSPASDIWALAHLINYLFLRRFLFSMWSGSANGSDTSSASSDMSDSSTASSGERWDWGKWLMLPRQFPFEGEAEEDRAMVERILRKMTFYDRPGEEGIDWPVMPDDDPHNGRYTVVNKLGHGTYAVVWLVYLQHVRAQSSQSPDDDNLADALFYMYREDPAPTRNVLLYAPTIISSSQEHTEKMIRKPRPHIPQYLVLPCLEDSFIEICFADSRIRPSHCPEVFASPEVFEPAPFSRAVMVLKLGKFPEKWWAFDEDENWCSRKRKPGKGSDVEKRATAAEVVELIPDRWMR", "metadata": {"id": "A0A6A4IK14", "cluster": 4398828, "interpro_all": ["IPR011009", "IPR000719", "IPR017441", "IPR051334"], "interpro_used": ["IPR000719", "IPR051334", "IPR017441"], "interpro_unused": ["IPR011009"]}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein is categorized in the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. Moreover, the protein should have a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. In addition, the protein contains a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. It is produced by Planosporangium flavigriseum and is annotated with UniProt keywords Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 2176, 1977, 4152, 2007, 4720, 9890, 9506, 1989, 7732, 3770, 2870, 1989, 1930, 1977, 10633, 1956, 20709, 11569, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 7031, 1920, 3244, 18, 3], "output": "MSFTQVVPCDFVVFGGTGDLAMRKLLPALYLRDVDGQLPPAFRIVGVSRAGLDNDGYRGKVEAELGTHVPAAALSATAVASFLRRLHFVSADAAAGSGDWQKLVDLLAEAPDRTRVFYLSCAPRLYGPISRTLANSGLVSEQSRVVLEKPIGVDLQSARDINDQVGEVFAESQVFRIDHYLGKEAVQNLLVLRFANMLLEPLWNASAIDHVQITVAESLGAGQRAGYYDGSGALRDMVQNHLLQLLCLVAMEPPASVTDDGVRYEKLKVLRALQPVTGQLAATHTVRAQYEAGALDGRPVPGYRDELDGAESDTETFVALKAEVHNLRWRGVPFYLRTGKRLDARRSEIVVAFKPVPHSIWPGLEPTMTPNRLVIRLQPDEGVRLHMLAKQPGPGGIQLRPVNLGLNFADQIPDRIPDAYERLLMDVVRGNPTLFMRRDEVEAAWVWTESILHAWRDGHAPVHRYPAGSDGPTAAHTLIESDGRHWNEDNA", "metadata": {"id": "A0A8J3LLY2", "cluster": 5879194, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR036291", "IPR022674", "IPR019796"], "interpro_unused": ["IPR022675", "IPR001282"]}, "task_type": "autoregressive"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: It is part of the Sperm-activating peptide family, which stimulates respiration and motility in sea urchin spermatozoa. Derived from the egg jelly, these peptides induce intracellular alkalinization and transiently elevate cAMP, cGMP, and Ca2+ levels in the target cells. It is identified in Hemicentrotus pulcherrimus (Sea urchin) (Strongylocentrotus pulcherrimus) and is classified with UniProt keywords Direct protein sequencing.. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 1925, 3835, 2687, 3244, 1988, 2469, 16318, 2460, 43, 2213, 22665, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 6283, 17, 8019, 4207, 3416, 16, 2154, 11803, 11695, 1930, 9254, 1922, 9309, 3674, 28964, 18211, 18, 3595, 2037, 1920, 7094, 8988, 11560, 1012, 16, 2144, 5320, 4769, 4776, 25178, 8635, 7659, 1930, 12145, 27565, 6225, 16, 15958, 16, 1930, 5497, 15, 2428, 1922, 1920, 2758, 2094, 18, 2176, 1977, 2899, 1922, 25482, 2334, 1991, 1957, 3784, 8172, 3027, 23084, 12, 9309, 3674, 28964, 13, 12, 3206, 2199, 26907, 6843, 1957, 3784, 8172, 3027, 23084, 13, 1930, 1977, 5947, 1956, 20709, 11569, 3083, 2213, 4754, 18, 18, 7031, 1920, 3244, 18, 3], "output": "SFALGGGGVG", "metadata": {"id": "Q7M4D1", "cluster": 7618121, "interpro_all": ["IPR013254"], "interpro_used": ["IPR013254"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I'm looking for a protein that can perform the following function: The protein should have a Cytochrome P450 conserved site that centers on a highly conserved cysteine residue responsible for binding the haem iron cofactor essential for mono-oxygenase activity. This site facilitates the oxidation of diverse substrates, including steroids, fatty acids, and xenobiotics, playing critical roles in detoxification and biosynthetic pathways across all kingdoms of life. The catalytic process utilizes electrons from redox partners to split molecular oxygen and insert a single atom into the substrate. It is identified in Stutzerimonas kirkiae. Give the amino acid chain.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 9387, 12088, 5305, 3200, 1988, 7365, 1990, 43, 3626, 5305, 8666, 6181, 5061, 1958, 2743, 1920, 7105, 5680, 15155, 4415, 1958, 8914, 17, 25298, 2455, 18, 2052, 3200, 11374, 1920, 6638, 1927, 6445, 6249, 16, 2710, 13039, 16, 5934, 4576, 16, 1930, 29821, 1036, 16, 14797, 4140, 5456, 1922, 18169, 1930, 14041, 3873, 3436, 2136, 13543, 1036, 1927, 3308, 18, 1920, 6804, 2585, 18127, 14354, 2037, 9366, 7228, 1942, 10030, 3272, 4612, 1930, 12844, 43, 2957, 6761, 2460, 1920, 4510, 18, 2176, 1977, 2899, 1922, 1955, 24793, 18842, 3947, 1934, 10717, 7369, 3336, 18, 7031, 1920, 3835, 2687, 4659, 18, 3], "output": "MKGKFDGNARVHIVEDYEAALPFLSDPRFIVPDLGGFLERLEQHGQAGSFRYLRLFVEHSPFFLEGAQHKTLRGIASQYFSHRALKRWEPFILDELQGIVDALDVPEFEVVSAVGARIFTRVAKPILGLAFIEDERFDVLVMGLQRLVEPMQSLSRLRRMNEELGWLLDKVASGVGSGHACADGVLPRLLADAQSPLSLEGRMALAVTLYAAMAPLAQTVANVILRLCERPTPSPFDADRFIEDIASHIHGAVAPHYVHRVALEDCRMGDLSIGRGDTVMIDIEQAVLLPAADSGTALRSFSFGHGAHYCLGAVMSKFIIAALIPRLLGRFGHLTLVRKELDINNHIANALGTLVVRGRA", "metadata": {"id": "A0A4Q9RBP0", "cluster": 9448913, "interpro_all": ["IPR017972", "IPR036396"], "interpro_used": ["IPR017972"], "interpro_unused": ["IPR036396"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein has a Oxysterol-binding protein conserved site that identifies eukaryotic proteins involved in sterol synthesis and regulation. This sequence region contains a conserved pentapeptide and is present in mammalian oxysterol-binding proteins (OSBPs), which bind oxygenated cholesterol derivatives, as well as in fungal and plant homologs essential for ergosterol and enfumafungin biosynthesis. It is derived from Torulaspora delbrueckii (Yeast) (Candida colliculosa) and is linked to UniProt keywords Lipid transport, Lipid-binding, and Transport.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 2258, 43, 20004, 2156, 6506, 1024, 17, 2743, 2213, 5305, 3200, 1988, 14133, 10825, 2697, 3286, 1922, 20408, 4271, 1930, 3640, 18, 2052, 3244, 3031, 5461, 43, 5305, 9412, 24010, 1930, 1977, 2481, 1922, 6492, 20004, 2156, 6506, 1024, 17, 2743, 2697, 12, 3125, 3846, 1036, 13, 16, 2154, 4566, 25241, 5463, 8383, 16, 1966, 2486, 1966, 1922, 8697, 1930, 4496, 14279, 4415, 1958, 11949, 23030, 1930, 2066, 19073, 3368, 19073, 2029, 1921, 8132, 18, 2176, 1977, 3595, 2037, 8184, 16811, 21086, 2723, 2377, 2182, 12940, 3907, 12, 5688, 13, 12, 14550, 2674, 16058, 5360, 13, 1930, 1977, 4624, 1942, 20709, 11569, 4486, 4860, 16, 4486, 17, 2743, 16, 1930, 4860, 18, 3], "output": "MPLNKLRPKSLNDSSVSSISESTYADDPVDTDDLDENDESGQNILLNIISQLKPGCDLSRITLPTFILEKKSMLERITNQLQFPDLVLDAHQEKDELQRFVKVVKWYLAGWHIAPKAVKKPLNPVLGEHFTCYWDLPNKQQAYYISEQTSHHPPESAYFYMIPESSIRVDGVCIPKSKFLGNSTAAMMAGLTVLQFLDMMNSNGKPEKYTLSQPNMYARGILFGKMRLELGDHMIIKGPKYKIDIEFKTKGFISGTYDAIAGVVKDLNGKEYYEITGKWNDIMYIKDLRDKHSKKIVLFDAHKSKVSKPSVRPLEEQGEFESRRLWKKVTDALAARDHEVATDEKFKIENYQRELAKKRVQDGVEFYPKLFRRAKPGEDLDYYIYKHIPEGNDYEEQIKSILEIAPILPGQHFTEKFAIPAFKKSEIQEKELSQTP", "metadata": {"id": "G8ZLX7", "cluster": 9921805, "interpro_all": ["IPR037239", "IPR000648", "IPR018494"], "interpro_used": ["IPR018494"], "interpro_unused": ["IPR037239", "IPR000648"]}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that can perform the following function: The protein incorporates a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. Furthermore, the protein falls within the ABC transporter ATP-binding component family, which functions as the ATP-hydrolyzing subunit of ABC transporter complexes to drive the active transport of diverse molecules across cellular membranes. These proteins utilize energy from ATP hydrolysis to export substrates such as nodulation factors involved in bacterial symbiosis and antibiotics, often contributing to multidrug resistance. Furthermore, the protein incorporates a ABC transporter-like, ATP-binding domain that utilizes the energy from ATP hydrolysis to power the transmembrane transport of diverse substrates, ranging from ions to macromolecules. It features conserved Walker A and B motifs, a Q-loop, and a signature sequence that form the nucleotide-binding site, typically functioning within a dimer. This module interacts with transmembrane domains to couple ATP-driven conformational changes to the import of nutrients or the export of toxins and membrane components. It is produced by Chloroflexota bacterium.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 19683, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 7219, 9054, 4498, 17, 2743, 4594, 3416, 16, 2154, 4088, 1966, 1920, 4498, 17, 7222, 9046, 5903, 1927, 7219, 9054, 5048, 1942, 9265, 1920, 3500, 4860, 1927, 6445, 4206, 3436, 3689, 5726, 18, 2144, 2697, 12561, 3844, 2037, 4498, 9128, 1942, 12660, 6249, 2427, 1966, 3889, 2281, 2790, 3286, 1922, 4543, 17246, 2475, 1930, 7560, 16, 3868, 8739, 1942, 16398, 3554, 18, 3677, 16, 1920, 2213, 19683, 43, 7219, 9054, 17, 3189, 16, 4498, 17, 2743, 3418, 1988, 18127, 1920, 3844, 2037, 4498, 9128, 1942, 4215, 1920, 9117, 4860, 1927, 6445, 6249, 16, 6485, 2037, 6982, 1942, 20625, 18, 2176, 4075, 5305, 20138, 43, 1930, 44, 8277, 16, 43, 59, 17, 5881, 16, 1930, 43, 9983, 3244, 1988, 2386, 1920, 5489, 17, 2743, 3200, 16, 5745, 7295, 2651, 43, 7632, 18, 2052, 9059, 9034, 1956, 9117, 4682, 1942, 15116, 4498, 17, 6446, 8523, 2840, 1942, 1920, 2582, 1927, 11312, 2014, 1920, 12660, 1927, 13599, 1930, 3260, 4178, 18, 2176, 1977, 4152, 2007, 10107, 18222, 7336, 14061, 18, 3], "output": "MTERPSSCIIQPPLLVATGIVRRFGRTLALRGVSLNIMPCECVALLGPNGAGKTTLVRVLATALQPSAGALTIGGVDALRDAARARPLVGAVGHETHLYQDLTARENLRFYGRLYGVRGLEDRVSTVLKESDIAAVADRPVRTLSRGMQQRVALGRAILHEPMLLLLDEPETGLDDTAQRRLARMLEDWTDRGRAVVLTSHRLEWTRRLADRAIVLREGQIVAHIDRSDLEPDIVAAAYSGALSSAG", "metadata": {"id": "A0A6A7LTK5", "cluster": 10478313, "interpro_all": ["IPR003593", "IPR003439", "IPR050763", "IPR027417"], "interpro_used": ["IPR003593", "IPR050763", "IPR003439"], "interpro_unused": ["IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein possesses a Domain of unknown function DUF7619 domain that is typically found in proteins containing cell wall anchoring or secretion system sorting motifs. It is predicted to contain an intramolecular isopeptide bond, suggesting a role in structural stability. Furthermore, the protein carries a DUF11 repeat that acts as a conserved structural element in cell wall-anchored and outer membrane proteins, potentially stabilizing surface cell wall structures. This ~53 amino acid motif is found in bacteria and archaea and, while often present in adhesion proteins, is likely distinct from the aggregation functions of the full-length molecules. Furthermore, the protein carries a Secretion system, C-terminal sorting domain that targets proteins to the type IX secretion system (T9SS) for outer membrane sorting and covalent modification. Adopting an Ig-like fold, this domain is secreted and subsequently cleaved by a C-terminal signal peptidase. It is identified in Flavobacterium sp.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 14465, 43, 3418, 1927, 5435, 2347, 4855, 1038, 10308, 4136, 3418, 1988, 1977, 5745, 2435, 1922, 2697, 3165, 2024, 4821, 20816, 2014, 5512, 2433, 11404, 8277, 18, 2176, 1977, 4396, 1942, 5531, 1925, 18083, 10301, 8253, 5403, 16, 3783, 43, 2770, 1922, 4346, 5057, 18, 3677, 16, 1920, 2213, 16252, 43, 4855, 5739, 1009, 6865, 1988, 8016, 1966, 43, 5305, 4346, 6149, 1922, 2024, 4821, 17, 17199, 1930, 7642, 3260, 2697, 16, 5063, 14384, 3154, 2024, 4821, 4061, 18, 2052, 72, 4522, 3835, 2687, 5219, 1977, 2435, 1922, 4802, 1930, 21501, 1930, 16, 2679, 3868, 2481, 1922, 6141, 2697, 16, 1977, 3205, 4493, 2037, 1920, 7883, 4088, 1927, 1920, 4125, 17, 3471, 4206, 18, 3677, 16, 1920, 2213, 16252, 43, 5512, 2433, 16, 45, 17, 4262, 11404, 3418, 1988, 4845, 2697, 1942, 1920, 2601, 13848, 5512, 2433, 12, 62, 1026, 5590, 13, 1958, 7642, 3260, 11404, 1930, 13577, 6295, 18, 20478, 1925, 7021, 17, 3189, 3728, 16, 2052, 3418, 1977, 8366, 1930, 5326, 10246, 2007, 43, 45, 17, 4262, 2733, 24050, 18, 2176, 1977, 2899, 1922, 7732, 12022, 2056, 18, 3], "output": "MINIDPSSGNFTYSIDNNAPITITSTNFIILANSISPGNHMLYVNDNISTCYVGHPFTIGTAQQTSITLSMTGTYNDYNNDGFTNVGDVVNYQFTVNNPNNVAIDNVVVSNQQLIMNGSPITSLAAMSSDSTTFTGTYVLTQQDINLGTVFGSAVVTGSVNGLQLLNDAGLRTNLNISRGFKLNAFIDTNGNGIQDGAEVNFSSGNFAYQLNGAVAQNAYSYNGVFYLYESNPNNSYNFSIVLPNYNNLCGNGYVVTTSTYTNVTLSGTGITTYNFAITQGTCTDLSVYLQNFGGPRPGFVDSNYVYYSNNGNTTIPSGTITFTRDNALSIISTSPATTAIANGFNYNFTNLLPYETRYIYVNMQVPTIPTVSLGQLVANAVSISIPAGDINTANNSSTLTQDIRGAYDPNDKQESHGPQIVKSTFTANDYLTYKIQFENTGNENAINIKVNDVLSNLLDPTSIKMVDASHPYILDRVGNNLEWKFSGINLPPSVANTQIGHGYVVFQIKPMAGYAVGTTIPNTANIYFDFNPAIVTNTCTTEFVTTLSTNNFDFNDLKIYPNPINNILNIDNNEPIDQLEITNLLGQTIMTKSPNSLSYNLDLWNVATGVYFVKVFVGDNSQTVKVIKE", "metadata": {"id": "A0A924LRQ4", "cluster": 11068689, "interpro_all": ["IPR047589", "IPR055354", "IPR055353", "IPR026444"], "interpro_used": ["IPR055353", "IPR047589", "IPR026444"], "interpro_unused": ["IPR055354"]}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein can be placed in the RNA polymerase sigma factor, region 2 superfamily, which comprises the conserved sigma2 domain found in bacterial sigma factors essential for transcription initiation. This domain, characterized by a four-helical core, mediates the association of the RNA polymerase holoenzyme with specific promoter elements to regulate gene expression. It originates from Planctomycetaceae bacterium. Can you generate the amino acid sequence corresponding to this protein?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 3146, 6479, 5139, 2991, 16, 3031, 22, 13975, 16, 2154, 12936, 1920, 5305, 5139, 1028, 3418, 2435, 1922, 4543, 5139, 2790, 4415, 1958, 3213, 6035, 18, 2052, 3418, 16, 4378, 2007, 43, 3006, 17, 11514, 4728, 16, 10412, 1920, 3279, 1927, 1920, 3146, 6479, 20403, 14896, 1956, 2487, 4465, 5362, 1942, 5741, 2359, 2294, 18, 2176, 22970, 2037, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "MSIDQTLIEQLRRGDRAAFAAVIERHQRAIYGYL", "metadata": {"id": "A0A926AP05", "cluster": 13629824, "interpro_all": ["IPR013325"], "interpro_used": ["IPR013325"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to generate an amino acid sequence for a protein. The protein should have the function The protein has a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. Moreover, the protein contains a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Moreover, the protein should feature a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It has been characterized in Sinocyclocheilus anshuiensis and is connected to UniProt keyword Magnesium, Lyase, and Manganese.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 2258, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 3950, 16, 1920, 2213, 5461, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 2258, 2252, 4378, 1922, 3132, 20446, 2694, 14209, 5277, 1036, 18229, 24315, 24222, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 13148, 16, 23928, 16, 1930, 19516, 18, 3], "output": "MLRTTVEDILPVYRPRTTARASVLHLKDLCEQEHDPHKPQPPPNREEHNASSMWREAMRKRSYLLERGSRTGGDVIGGGGVRGRRQRSLDWLYDSYYRMSQQHPLIVFLLLIVMGACLALLAVFFASGLDIEDHIAFVITVPTALAIFLTIFVLVCIESIFKKLLRVFSLVIWACLVAMGYLFMFFGGIICPWDQVSFFLFIIFVAYTMLPFSMRDAIIASVLTASSHTVVLSVCLSSTVDHVEPLVWQILANIIIFICGNLAGAYHKHLMELALKQTYQDTCNCIKSPIKLEFEKRQQERLLLSLLPAHIARVMKAEIIQRLQGPKFGQVENTNNFHNLYVQRHTNVSILYADIVGFTRLASDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPESLPNHAKNCVKMGLDMCEAIKKVRDATVVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHITSVTLEHLNGAYKVEDGDGQERDPYLKEHGAVTYLVINPKAERKSPQHHYRPRHTMDGAKMRASVRMTRYLESWGAAKPFANLHHRDSMTNENGKINTADVPMGQYHFQRRSERIKSQKKRFEEELNERMIRTFDGISSQKQWLKSEDIQRISLFFHNKTLEKEYRATTLPAFKYYVTCACLIFICIFIVQILVLPKTAILGISFGMSFLILSVVLLICFIGHFLHCDKTASTSWLWILRSSEFIANKPWPRITITMATTVLILIMAIFNMFFVEDNLTSTDAVYNASNETLLQPDGHPISYLDNNTFYLPYFIYSCILGLISCSVFLRINYELKMLIMLTAVVLYSVIILQTHAFLLDEYSKFLYKTEILDRPGVLKDLKTMGSVSLFIFFITLLVLARQNEYYCRLDFLWKNKFKKECEEIETMENLNRVLLENVLPAHVAEHFLARNWKNEDLYHQSYDLVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATPGPEYIQVSEILHPNYLFIYLTLCTFINLKSFSFNSCINHGPVIAGVIGAQKPQYDIWGNTVNVASRMDSTGVLGKIQVTEETSRILQTLGYMCTCRGIINVKGKGELKTYFVHTEMSRSLSQGNLNKPNK", "metadata": {"id": "A0A671SQL8", "cluster": 17241200, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR009398", "IPR029787"], "interpro_used": ["IPR009398", "IPR018297", "IPR001054"], "interpro_unused": ["IPR029787", "IPR032628", "IPR030672"]}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein should have a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. Moreover, the protein falls within the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. Additionally, the protein has a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. It has been detected in Actinomycetota bacterium and is linked to UniProt keywords Hydrolase and Metal-binding.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 3066, 2162, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 3950, 16, 1920, 2213, 12182, 2651, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 4950, 16, 1920, 2213, 2258, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 2176, 2258, 2252, 3330, 1922, 4718, 13386, 19446, 3857, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 20748, 1930, 6048, 17, 2743, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MAIDRDAILKALERVIDPELQKPVTRVTIALTVAGCPLRNSFQEQVAEHVGTLTALSTRLRGGRPEKSISLDPRTRVIALDAQGKTVGLIDADIYGHSIPHLLPVRGRLKFISIGNFLDENGPVMWRGPMLVIDMPPGTGDMAISLGQLLPRAEVLLVTTPQPVENMAGETFGAGGGELLARQLETPFLGSVPLAQAIVAIAELVVVPRPGAIQKPLTLLTELEMVREIEIDGPDVAGVRRVELRFDVMSPEEKVASGKGGVGKSSLTVNLAAAGINQRPIVVDKMIVPHRALEQFLSDVHWGELDVILAQEVASRAAVMAQRTGQRLVGVDVELREAGDRGEPVVESRPDSAS", "metadata": {"id": "A0A7W0GB30", "cluster": 20897174, "interpro_all": ["IPR034904", "IPR002744", "IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR000808", "IPR033756", "IPR002744"], "interpro_unused": ["IPR027417", "IPR019591", "IPR034904", "IPR044304"]}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein should feature a Glycosyltransferase 2-like domain that catalyzes the transfer of sugar moieties from activated nucleotide donors, such as UDP-glucose or GDP-mannose, to specific acceptor molecules to form glycosidic bonds. This domain participates in the biosynthesis of diverse structures, including cellulose, dolichol phosphate, and teichoic acids. It has been detected in filamentous cyanobacterium CCT1.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 3066, 5961, 43, 20067, 9961, 22, 17, 3189, 3418, 1988, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 5489, 8276, 16, 2427, 1966, 18500, 17, 3817, 2014, 15217, 17, 17936, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2052, 3418, 17241, 1922, 1920, 8132, 1927, 6445, 4061, 16, 2710, 12343, 16, 17837, 2108, 1945, 5413, 16, 1930, 3602, 2108, 8643, 4576, 18, 2176, 2258, 2252, 3330, 1922, 18706, 26898, 7972, 2341, 18842, 1989, 15117, 1009, 18, 3], "output": "MAPIVSVVIPSYNSMMFLPTTLNSVLVKDWFTTISDSRVKLFSQENKGYAGACNTGILNTKLEKQFRCLEDNPEVGLVDTLVFFVDSEGEKLFTAGSIYRLCFDTVGVFDESIKGPSDWHMWVRIASQYNFQTDIMLRGGLQAINSMFDDAPPHLQYKKKESYGVNRNYKQAVYLCLRVLQIYPNKCFSRDFIYLFSKNRVVSQLKNLSRALVSRPPQGFQQTFSDFEVLIIDDGSQDNAQGKYIAFLDADDVWVPKPGNVYETMLVKNLVPCGSTPMVRVIEEPLVHYRQHSSSVSRNNLYYVLALKAYTIILYFTLSEQGYNQV", "metadata": {"id": "A0A2P8W9D7", "cluster": 23784085, "interpro_all": ["IPR001173", "IPR050834", "IPR029044"], "interpro_used": ["IPR001173"], "interpro_unused": ["IPR050834", "IPR029044"]}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein is a member of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is identified in Bacillus cereus HuA2-1 and is classified with UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2899, 1922, 14587, 29533, 5897, 8398, 17, 21, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MTVVIGLTGGIASGKSTVSEMFCEMGTEVLQKDGELDRPKLGSVVFYNEEKRLQLNEIVHPVLDIPLLFESKLINLVDRVLVIAVTPNTQKVKKADEVIYNDGTITGTKTQLASILKEWNIIDSIPVIDADIIAREVVERGKPAYNKIVEVFAVREEMNAQKEMYIKEGMQAVLERLMKRNNFSEEEATARIQSQMPLEE", "metadata": {"id": "J9C1C2", "cluster": 25241551, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want a protein that has the function: The protein possesses a Competence protein ComEA, helix-hairpin-helix domain that functions as an essential component of the DNA uptake machinery in naturally competent bacteria. Comprising two tandem copies of a helix-hairpin-helix motif, this domain likely mediates DNA binding to facilitate the transport of exogenous genetic material into the cytoplasm during transformation. In addition, the protein possesses a Helix-hairpin-helix DNA-binding motif, class 1 domain that mediates non-sequence-specific DNA binding in prokaryotic and eukaryotic proteins, typically those involved in enzymatic activities. It interacts with the DNA phosphate backbone via a conserved loop and the N-terminus of the second helix, rather than engaging the major groove like helix-turn-helix motifs. Moreover, the protein has a Soluble ligand binding domain that adopts a \u03b2-grasp fold to facilitate diverse processes ranging from vitamin transport to polysaccharide export. It mediates vitamin B12 uptake in animal proteins such as transcobalamin and intrinsic factor, while functioning in colanic acid export or electron transport in bacteria. It occurs in Atribacter laminatus and exhibits UniProt keyword tags Membrane, Transmembrane, and Transmembrane helix. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 14465, 43, 12939, 2213, 10449, 1019, 16, 7864, 17, 14565, 17, 7864, 3418, 1988, 4088, 1966, 1925, 4415, 4594, 1927, 1920, 2678, 5047, 10853, 1922, 10414, 13527, 4802, 18, 10351, 2288, 10361, 9425, 1927, 43, 7864, 17, 14565, 17, 7864, 5219, 16, 2052, 3418, 3205, 10412, 2678, 2743, 1942, 6628, 1920, 4860, 1927, 8278, 3299, 3485, 2460, 1920, 5239, 2409, 7002, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 7864, 17, 14565, 17, 7864, 2678, 17, 2743, 5219, 16, 2921, 21, 3418, 1988, 10412, 2447, 17, 3244, 17, 2487, 2678, 2743, 1922, 21545, 1930, 10825, 2697, 16, 5745, 2690, 3286, 1922, 8145, 4209, 18, 2176, 9034, 1956, 1920, 2678, 5413, 10787, 3454, 43, 5305, 5881, 1930, 1920, 56, 17, 7822, 1927, 1920, 2812, 7864, 16, 4356, 2254, 15888, 1920, 3044, 15920, 3189, 7864, 17, 5165, 17, 7864, 8277, 18, 3950, 16, 1920, 2213, 2258, 43, 6622, 5207, 2743, 3418, 1988, 24032, 43, 161, 17, 22815, 3728, 1942, 6628, 6445, 4028, 6485, 2037, 6111, 4860, 1942, 17167, 12660, 18, 2176, 10412, 6111, 17492, 5047, 1922, 4027, 2697, 2427, 1966, 14613, 26205, 10082, 1921, 1930, 7598, 2991, 16, 2679, 7295, 1922, 2503, 19510, 2687, 12660, 2014, 4995, 4860, 1922, 4802, 18, 2176, 5110, 1922, 26500, 7972, 2341, 1915, 14310, 1031, 1957, 1930, 9826, 20709, 11121, 2538, 14392, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MLFSRQERIVFVVLSLILVFSISFLFYKTRVVSATGADSSDKRPESYIVQIAGEVLKPGVYQVEEGTRLYQLIELSGGVTPQADISSLNLAAPVHDGLRINIPAQNSIQGDLDRFQFSFSEQIPLSEETDSDLVVQINTASLEELKRLPGIGDVIAQRIIEYRKTYGPFRSVDDLINVKGIGAKKLQDIKNSIRN", "metadata": {"id": "A0A7T1ALZ9", "cluster": 28016291, "interpro_all": ["IPR004509", "IPR051675", "IPR003583", "IPR010994", "IPR019554"], "interpro_used": ["IPR004509", "IPR003583", "IPR019554"], "interpro_unused": ["IPR051675", "IPR010994"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein has a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein should feature a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Moreover, the protein is associated with the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It originates from Clostridiales bacterium and carries UniProt keyword assignments Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 22970, 2037, 17938, 26890, 1918, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MAMLRLNSYAKINLFLDIKGKLQNGYHIIKTVMQSIDIYDEITLIPLNDNKIIIECSDKSIPINEKNTCYKAVLLLKKAYGINSGIQIYINKMIPAGAGMAGGSSNAAAVIKGLNKMWKLNLSEQEMIDIGAQIGADVPFCLVGGTCLAEGIGDKVTDLNDFQWDNILLVKPEFSISTAFVYKNLDTNYYNSNCEEYILKYITSYDYEKAAKCAANTLEKVVEKYHPEINYIKKLMIDNGAISSIMTGSGSAVFALFKDNDSLNKAYEIAKKIYPSTFKSKTYKYGVKFID", "metadata": {"id": "A0A349HNU6", "cluster": 1852331, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "The protein is a member of the Metallo-dependent phosphatase-like superfamily, which encompasses a diverse group of enzymes, including purple acid phosphatases and DNA repair nucleases, that catalyze the hydrolysis of phosphate esters. These proteins utilize a conserved binuclear metal center, typically composed of manganese, iron, or zinc ions coordinated by histidine, aspartate, and asparagine residues, to facilitate functions ranging from nucleotide metabolism to signal transduction. Furthermore, the protein should include a Calcineurin-like, phosphoesterase domain that functions as the catalytic center in diverse enzymes, ranging from nucleotidases and sphingomyelin phosphodiesterases to nucleases like Mre11. This domain adopts a fold comprising two sandwiched $\\beta$-sheets flanked by $\\alpha$-helices, which coordinate a binuclear metal center essential for hydrolyzing phosphoester bonds. It is identified in Actinomycetota bacterium.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 1920, 8969, 1037, 17, 3100, 8167, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 5038, 16, 2710, 14308, 2687, 19131, 1930, 2678, 5059, 29305, 16, 1988, 18170, 1920, 9128, 1927, 5413, 16785, 18, 2144, 2697, 12561, 43, 5305, 8768, 13821, 6048, 4102, 16, 5745, 7179, 1927, 19516, 16, 5680, 16, 2014, 7997, 6982, 11651, 2007, 13873, 16, 12878, 16, 1930, 23677, 4248, 16, 1942, 6628, 4088, 6485, 2037, 5489, 4714, 1942, 2733, 8201, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 19555, 17, 3189, 16, 8078, 8342, 2051, 3418, 1988, 4088, 1966, 1920, 6804, 4102, 1922, 6445, 5038, 16, 6485, 2037, 2797, 4090, 2319, 1930, 28057, 24821, 1036, 1942, 29305, 3189, 26460, 18, 2052, 3418, 24032, 43, 3728, 10351, 2288, 18038, 1919, 8, 38, 4666, 8, 17, 14685, 20185, 2007, 8, 38, 4595, 8, 17, 12789, 16, 2154, 11865, 43, 8768, 13821, 6048, 4102, 4415, 1958, 7222, 9046, 8078, 8342, 9031, 18, 2176, 1977, 2899, 1922, 4718, 13386, 19446, 3857, 14061, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MYQLPKSGTLVIFSDVHVDAAVFLNGDLIENAIISGKAPGEMILEQAKRGRIVGVTRGNHESRSRREYVRLKHGAQVYTGGIQHGKSGAQHALAAREVFQLRIGPDGTEQVSRRWAVGSPVFQFDPKTHHMTVDVRTLAWLGAEHHDERRFDEALAFCKEATLTPTEQVRQFCSKLKPLAMLDLCELIALHLQVPYLRIGGNIWLELDKLMRIYPEADFVASGHNQVRTGTYLGYADYAREAALAPG", "metadata": {"id": "A0A965CFJ6", "cluster": 2964031, "interpro_all": ["IPR004843", "IPR029052"], "interpro_used": ["IPR029052", "IPR004843"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is categorized in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein should have a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is present in Acidobacteriota bacterium and is associated with UniProt keywords Isoprene biosynthesis and Transferase. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 2481, 1922, 2687, 5883, 3940, 3857, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MTLRRLSVPSFAKINWTLKILGQRSDGYQQIKTLYQTVDLSEELVFETTSNRGIEIEVEGRKVAPGEDNLLYQTAELLRQTTGSQAGIRIKLQKKIPVGAGLGGGSSNAALALLALNQLWDCKIGEKELVELAGQLGSDVPFFLVGGTALGWGRGAEVVPLPDLPQEKSLLLLYPHLEISTREAYALGKWGTYGGTGQLTREWAETTMRDLLRAVGPKGVGWSFLENDFEDVLFAHYPVLVEAREALKKAGCERVMLCGSGSTLLGFGSDQQVKEAAAFMTREGIGETFFCRTLSREHYRQVLMNSGLLLL", "metadata": {"id": "A0A523D6T7", "cluster": 3914128, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein belongs to the The Transcription factor GRAS family, which plays a critical role in regulating plant growth and development, including gibberellin signaling and root radial patterning. Although implicated in transcriptional regulation, these proteins share structural homology with Rossmann-fold SAM-dependent methyltransferases, indicating they likely function mechanistically by binding or methylating small molecules. It is expressed in Dillenia turbinata and is classified with UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 14440, 1942, 1920, 1920, 3213, 2991, 22217, 3416, 16, 2154, 5705, 43, 4140, 2770, 1922, 6773, 4496, 2905, 1930, 2740, 16, 2710, 10122, 2361, 20912, 3197, 1930, 5904, 10575, 16060, 18, 2876, 6835, 1922, 5224, 3640, 16, 2144, 2697, 7948, 4346, 9039, 1956, 18215, 8890, 17, 3728, 2235, 17, 3100, 28253, 16, 4168, 2611, 3205, 2347, 21173, 2007, 2743, 2014, 4963, 2287, 2858, 4206, 18, 2176, 1977, 3198, 1922, 4333, 15253, 2126, 13840, 4058, 3857, 1930, 1977, 5947, 1956, 20709, 11569, 3213, 3640, 18, 3], "output": "MADRCPFCVSNPVQRVVFYFAEALRERIGATIICHSDIPLIQVLVFTGVQAILDSVASAGKVHIIDLAIRRGAHWEILSSEQKIGDTGKNLKSFSASLNLPFSFQQICLSDMSELREEHFSKPKCLDSLMWLLRKLNPSIMVVGEIDANHNSTSFGNRFIKALSLILKEGIRNVVATEGIDRTIWNVKIYVWRAFFARFGMGKNGKSLIFGWKGTPLFSFSAWKFICERKKNCRRPREARRITAKGFKQKARSEIIESALNHDPMQALAERRDNSIQLLKITAIAINREADETIILKTMIFFYSAYFDCLEACITRDNNSRLAIEEVELSESSFYQASLVVEKNFGTID", "metadata": {"id": "A0AAN8VNG2", "cluster": 4098003, "interpro_all": ["IPR005202"], "interpro_used": ["IPR005202"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want a protein that has the function: The protein should include a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. Furthermore, the protein should have a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. In addition, the protein features a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. It occurs in Diabrotica virgifera virgifera (western corn rootworm) and features UniProt keywords Lyase, Manganese, and Transmembrane helix. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 3066, 3951, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 2176, 5110, 1922, 3517, 18147, 1019, 16374, 19582, 16374, 19582, 12, 4540, 12856, 5904, 16620, 13, 1930, 4075, 20709, 11569, 23928, 16, 19516, 16, 1930, 9117, 7864, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MKKVCSTHQFRNEQVEMLYQRYFLKMNQSNMTNLITLLLMICVVMLVISLTDFAMPRKLATNSTEVHATQYDKLLVLVCTSACCIAIYGILLNVVSRPAMNEVYLIIISYFILVTFVILEICISYYFDDKRPLLGSSFTLATTYLTYALMPNRLKDALLSGFILAVADLLLLVYVGTMSGIADVTSCFIILLCGNIAGVCTHYPREVAQRKAFLETRQCIEARLKIQRENQQQERLLLSVLPRHVAMEMKADIAGQPKQEQFHKIYIQKHENVSILFADICGFTTLSDQCTAEELVRILNELFARFDRLAAEHHCLRIKLLGDCYYCVSGLPEARPDHAHCTVEMGLDMIDAIALVREVMNVNVNMRVGIHTGRVHCGVLGLRKWQFDVWSNDVTLANYMESGGIPGRVHITKETLSCLGNDYVVEPGNGGERNSYLKDHNIDTYLIVAPSYRGDTSIPYHNHPMNGNIAKEMRIMGHGSQHGHSSKLGFGESTEREKNPEDEVNEYLMKAIDARSIDRLRIEHCRTLLLNFRDPVKEAKYLLEKDRMLTMYFYCSTFCFITVLLVQLVIFNRHDPALFYSTPIIFLLVLIPLLVYMNNIKKRRGFSTLFFVSRTIHKNRNVAQIFCFVMAACIYGLVMFRAFSLSIEVQCLNSTFEGHNNCTNENKGCRQYYLIDYLMLLVMVSMIACAVYQILISLLKAIILLGGMAGFLAAYFIYIKNVDSIICLYRSSEHTFTHQYMNIVVLGGFVTALIIHGQQTEATYRLDFVWKLQATEEKEDMEHLEAYNRKLLANILPVHVAEHFLNSDKNNDELYHEQCDCVCIMFATIPNFSEFYVELESNNEGVECLRLLNEIIADFDELLSEEQFKYIEKIKSTGSTYMAASGLTQNTCDMHDYKHVTAMADYALRLKELLEEVNEHSFNHFRIRIGINVGPVVAGVIGARKPQYDIWGNAVNVASRMDSTGIPDKIQITKEVNQILHAKGYPTKCRGTINVKGKGSMETFFLEGPVKNRPNITLNPLASSFDDKSEEPMRTTLGTISEKN", "metadata": {"id": "A0A6P7FQZ3", "cluster": 5352188, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR009398", "IPR029787"], "interpro_used": ["IPR001054", "IPR009398", "IPR018297"], "interpro_unused": ["IPR030672", "IPR032628", "IPR029787"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is assigned to the Cation Transport ATPase Type IB family, which couples ATP hydrolysis to the efflux of heavy metals such as cadmium, zinc, cobalt, and lead across cellular membranes. These transporters play a critical role in metal detoxification and homeostasis by reducing the bioavailability of toxic ions through export or vacuolar sequestration. Additionally, the protein includes a P-type ATPase phosphorylation site, which contains a conserved aspartate residue that forms an essential aspartyl phosphate intermediate during ATP hydrolysis to drive the active transport of various cations. In addition, the protein is classified under the HAD superfamily, which encompasses enzymes such as phosphatases, P-type ATPases, and dehalogenases involved in diverse cellular processes ranging from amino acid biosynthesis to detoxification. These proteins share a conserved \u03b1/\u03b2-hydrolase fold similar to the Rossmann fold, featuring a core domain and a variable cap domain that allows for structural and functional variation. It is native to Acholeplasmataceae bacterium and is classified with UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 9976, 4860, 9444, 2601, 6180, 3416, 16, 2154, 14002, 4498, 9128, 1942, 1920, 11247, 1927, 7881, 11570, 2427, 1966, 17203, 16, 7997, 16, 20773, 16, 1930, 2949, 3436, 3689, 5726, 18, 2144, 10538, 3918, 43, 4140, 2770, 1922, 6048, 18169, 1930, 7622, 2007, 5526, 1920, 13574, 1927, 6161, 6982, 2596, 12660, 2014, 21582, 19001, 18, 4950, 16, 1920, 2213, 5921, 43, 58, 17, 2601, 9444, 4050, 3200, 16, 2154, 5461, 43, 5305, 12878, 6181, 1988, 4952, 1925, 4415, 12053, 2199, 5413, 6129, 2409, 4498, 9128, 1942, 9265, 1920, 3500, 4860, 1927, 3425, 16525, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2430, 13975, 16, 2154, 21569, 5038, 2427, 1966, 19131, 16, 58, 17, 2601, 28132, 16, 1930, 2028, 7289, 2404, 2319, 3286, 1922, 6445, 3689, 4028, 6485, 2037, 3835, 2687, 8132, 1942, 18169, 18, 2144, 2697, 7948, 43, 5305, 160, 19, 161, 17, 20748, 3728, 2551, 1942, 1920, 18215, 8890, 3728, 16, 29931, 43, 4728, 3418, 1930, 43, 4650, 2853, 3418, 1988, 5731, 1958, 4346, 1930, 3183, 4516, 18, 2176, 1977, 6196, 1942, 3546, 2456, 15403, 26317, 5376, 1021, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 7864, 18, 3], "output": "MEVSIKKEIFLANLPCQICRENIINATKLQYDDQTDYVFLAKEIRNILKDHKHQIRIKLSIEAGIKELSGVKDVSIINHKLHIVSNVSNQKPIIRQRFDIITLIISFLLFLSALLFNLSTAWEFALFFLAYLILQGRFFEETFLMSIATVGAFIIGEYPRSISKLMDLRPDYANLLIDGKTTRVDPENVPTSALDVSALTGEAEFQTIEPGSRVLSKTYHDSTASKILELVETSASRKAPTEKMITKFSFTDHNFSAWIYRALILLVISCPCALVISIPLGFFGLKTIVFDKTGTLTKGSFSIKEIIPASDYTKEEVLSYTADDLEIPEISSYQEHPGLGIQVQRQKGIHSEFDSEQQILNQESESLFVREYRLENNHWDIRKLFKGLKISETEEETVSLAGYKVIIASIRAEGVAVMLFYCVGEIIQEAALDKSRIGAMVLVQPGERIPLDGIVLEGGSINTSQVFTIQVDRYYTPVVVIGALILAFVVPLGIGNASRNGILVKGSNYLDALNSAILAESHSHHPLARSF", "metadata": {"id": "A0A7X7HB47", "cluster": 5943474, "interpro_all": ["IPR023299", "IPR018303", "IPR023298", "IPR008250", "IPR051014", "IPR023214", "IPR027256", "IPR001757"], "interpro_used": ["IPR051014", "IPR018303", "IPR023214"], "interpro_unused": ["IPR008250", "IPR027256", "IPR023299", "IPR001757", "IPR023298"]}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein is grouped in the FAD/NAD(P)-binding domain superfamily, which comprises flavoprotein oxidoreductases, such as glutathione reductase and thioredoxin reductase, that utilize FAD and NAD(P)H cofactors to catalyze electron transfer reactions. These enzymes typically adopt a doubly-wound $\\alpha/\\beta$ fold with nested binding domains to facilitate oxidative metabolism. Additionally, the protein carries a FAD-binding domain that facilitates the binding of the flavin adenine dinucleotide (FAD) cofactor to support catalytic oxidoreductase activity. This domain functions in diverse enzymes across species, including human kynurenine 3-monooxygenase, archaeal digeranylgeranylglycerophospholipid reductase, and bacterial hydroxylases. Furthermore, the protein is categorized in the Geranylgeranyl reductase family, which catalyzes the hydrogenation of unsaturated isoprenoid chains essential for the biosynthesis of archaeal membrane lipids and chlorophylls. These enzymes reduce substrates such as unsaturated archaeols to saturated forms or convert geranylgeranyl diphosphate to phytyl diphosphate, providing precursors for tocopherols and bacteriochlorophylls. It has been detected in Planctomycetales bacterium.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 1977, 10809, 1922, 1920, 14134, 19, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 12936, 7732, 6657, 27388, 1036, 16, 2427, 1966, 9153, 11386, 1930, 23684, 11386, 16, 1988, 12561, 14134, 1930, 6577, 12, 58, 13, 50, 21362, 1942, 18170, 4995, 3856, 5298, 18, 2144, 5038, 5745, 14103, 43, 26783, 17, 6376, 8, 38, 4595, 19, 38, 4666, 8, 3728, 1956, 13735, 2743, 4682, 1942, 6628, 5163, 4714, 18, 4950, 16, 1920, 2213, 16252, 43, 14134, 17, 2743, 3418, 1988, 11374, 1920, 2743, 1927, 1920, 26758, 15643, 21302, 12, 14134, 13, 15155, 1942, 3373, 6804, 27388, 2455, 18, 2052, 3418, 4088, 1922, 6445, 5038, 3436, 3038, 16, 2710, 2616, 23523, 24684, 2053, 23, 17, 8914, 13966, 16, 22367, 4325, 7124, 16323, 1024, 4938, 12804, 14966, 8630, 16113, 11386, 16, 1930, 4543, 16324, 1036, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 9559, 12804, 4938, 12804, 11386, 3416, 16, 2154, 17097, 1920, 6201, 1943, 1927, 19172, 26690, 2642, 7835, 4415, 1958, 1920, 8132, 1927, 22367, 3260, 8238, 1930, 16553, 1036, 18, 2144, 5038, 4412, 6249, 2427, 1966, 19172, 13470, 3706, 1942, 11709, 4952, 2014, 14450, 9559, 12804, 4938, 12804, 23266, 1942, 9321, 2199, 23266, 16, 5453, 10416, 1958, 21432, 1036, 1930, 14027, 20845, 13384, 1036, 18, 2176, 2258, 2252, 3330, 1922, 4720, 2341, 13386, 3949, 1918, 14061, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MIDAADRLRELDSRPEPWDVAIIGAGPAGATLAALMATGCLNRRGQLQLAACGLDRALRQAQPVELQRLHLVSLAVEHGAQFLSGVRVRVVPDPQRHVLRTVELLTTHDQPSVAACGLTHHGTFADSELSQVVRATSRIGLGARIRTTDAVVGAVRLTDGSLNLAAAATPTALRTYGAEMWVRGTLRSVGLDAIGDAAGYVEPFTGEGMGWAIDSAIIAADWVDRGLQAAKRQQACRLIAHLLSRPWAVRLSLATLAACPPLTRSLVRHFSSSAARGRRVILLDRQTFPRDKVCGLRHALHHVDVCLEDMCAIARDVFDAQGQPSPLPVAIESRIVCTEMSSRFAPHALTMAIGRDGYMPEAAELAWRGTAPLTRHCEHPVGHRLIWTPALEQRCCEQLKLTL", "metadata": {"id": "A0A954QEW5", "cluster": 6077019, "interpro_all": ["IPR002938", "IPR036188", "IPR050407"], "interpro_used": ["IPR036188", "IPR002938", "IPR050407"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein falls within the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein has a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein contains a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is native to Clostridiales bacterium and is classified with UniProt keywords Transferase.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 12182, 2651, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 5461, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 6196, 1942, 17938, 26890, 1918, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 13763, 18, 3], "output": "MNATAYAKLNLTLDILRRREDGYHDLQMVMQTISLTDTLTITPAQGEGKMTSNLSFLPTDGTNLAQKAAAAFRRATGLGEEVDISIDKHIPVCAGMAGGSADAAAVLRAMNQLTAAGLSPLALAQIGQSVGSDVPYCVLGGTALAEGRGERLTPLPALPPCHIVVCKPSFPVSTPQLFSRVDVRKILRRPDTQGMLEALEQGDLSGIARRMYNVFEDVLEPWKRAEVHAIQNALLDAGALGAIMTGSGPTVFGLF", "metadata": {"id": "A0A3D3TCG5", "cluster": 8308328, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "The protein falls within the Bacterial response regulator family, which functions as the effector component of two-component signal transduction systems to regulate adaptive responses to environmental stimuli. Upon phosphorylation of their receiver domain by a sensor kinase, these proteins modulate critical cellular processes ranging from transcriptional regulation to chemotaxis and sporulation. Additionally, the protein incorporates a Signal transduction response regulator, receiver domain that functions as a phosphorylation-activated switch within two-component systems to couple environmental sensing with cellular adaptation. It accepts a phosphoryl group from a cognate sensor histidine kinase, inducing a conformational change that activates an associated effector domain to regulate gene expression. In addition, the protein belongs to the The CheY-like superfamily, which functions primarily as the receiver module in two-component signaling systems, mediates signal transduction through the phosphorylation of a conserved aspartate residue by a partner histidine kinase. Adopting a compact flavodoxin-like $\\alpha/\\beta/\\alpha$ fold, these domains often serve as N-terminal regulators coupled to DNA-binding effectors to control gene expression in response to environmental stimuli, though divergent members may bind RNA or lack the active phosphorylation site. It has been detected in Lachnospiraceae bacterium MD335. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 4543, 2644, 7888, 3416, 16, 2154, 4088, 1966, 1920, 7917, 4594, 1927, 2288, 17, 4594, 2733, 8201, 3771, 1942, 5741, 7617, 3387, 1942, 4813, 5458, 18, 4073, 4050, 1927, 2310, 12608, 3418, 2007, 43, 6443, 4016, 16, 2144, 2697, 8480, 4140, 3689, 4028, 6485, 2037, 5224, 3640, 1942, 16884, 1930, 23647, 18, 4950, 16, 1920, 2213, 19683, 43, 2733, 8201, 2644, 7888, 16, 12608, 3418, 1988, 4088, 1966, 43, 4050, 17, 4128, 6195, 2651, 2288, 17, 4594, 3771, 1942, 15116, 4813, 9306, 1956, 3689, 7810, 18, 2176, 5861, 1036, 43, 12556, 2210, 2037, 43, 15786, 6443, 13873, 4016, 16, 7834, 43, 8523, 3185, 1988, 9094, 1925, 2458, 7917, 3418, 1942, 5741, 2359, 2294, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 1920, 10003, 1012, 17, 3189, 13975, 16, 2154, 4088, 5985, 1966, 1920, 12608, 9059, 1922, 2288, 17, 4594, 3197, 3771, 16, 10412, 2733, 8201, 2596, 1920, 4050, 1927, 43, 5305, 12878, 6181, 2007, 43, 8240, 13873, 4016, 18, 20478, 43, 13726, 7732, 1986, 9754, 17, 3189, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 16, 2144, 4682, 3868, 7120, 1966, 56, 17, 4262, 9098, 6416, 1942, 2678, 17, 2743, 13066, 1942, 2285, 2359, 2294, 1922, 2644, 1942, 4813, 5458, 16, 4170, 13609, 4678, 2278, 4566, 3146, 2014, 3630, 1920, 3500, 4050, 3200, 18, 2176, 2258, 2252, 3330, 1922, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 4445, 6498, 1015, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MKKKLLIMGNNKRLITDFFMQLDFYFDCASTSLIAPDLRIHYQFFQPDAIVYCMHAESRDNINSVIRFADGAPKDDKVPFIVVADGSDYEFLCKMPGGRADLRIGASASVSELQSEISSVIARHKNNKIEGKLQTAPKLDDALDTLSQLDEELKKLESGDLNVNLPTSLLSALGRPRILVVDDSTIIHKAIKGYIEKDYDISTAINGAAALRFLKTKEVNLILLDYEMPEMNGAEVLKALRENPLTASIPVVFLTGVNDTAKIQKVLRLKPDGYLLKPIDKNVLLSKIKEILG", "metadata": {"id": "R9L325", "cluster": 9958964, "interpro_all": ["IPR050595", "IPR011006", "IPR001789"], "interpro_used": ["IPR050595", "IPR001789", "IPR011006"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: The protein should feature a Alpha-ketoglutarate-HExxH-type peptide beta-hydroxylase domain that functions as an alpha-ketoglutarate (aKG)-dependent non-heme iron beta-hydroxylase. It utilizes a characteristic HEXXH motif and is typically associated with the FxsB family of radical SAM proteins, where it performs post-translational modifications on FxSxx-COOH family RiPP precursor peptides. It is produced by Mycolicibacterium fluoranthenivorans. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 5961, 43, 4595, 17, 21471, 16542, 17488, 17, 7142, 1039, 1023, 17, 2601, 4207, 4666, 17, 16324, 3418, 1988, 4088, 1966, 1925, 4595, 17, 21471, 16542, 17488, 12, 4464, 1029, 13, 17, 3100, 2447, 17, 10954, 5680, 4666, 17, 16324, 18, 2176, 18127, 43, 6293, 7142, 1039, 1023, 5219, 1930, 1977, 5745, 2458, 1956, 1920, 29028, 1014, 3416, 1927, 6917, 2235, 2697, 16, 2597, 2176, 17436, 2753, 17, 8414, 6920, 1990, 29028, 14710, 17, 20729, 3416, 8936, 1034, 7897, 5320, 18, 2176, 1977, 4152, 2007, 5078, 4485, 26073, 2341, 18842, 1989, 5533, 7744, 28131, 15525, 17182, 1036, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MQPDLETRLRGTVADDSMLTEYRRELTRWFKIAGMTAISRQLVSHGDGQAIRSMLTEIHTHHGQLTNPMFEYASQVMRDAVTEERSVPDGFGNMIAAAAHPVPAGIVRIAPPEHHGTYKMILDQVIARQDDIETASIPSTLMSDTRAEENIRRCTEIINRHVPRDLVDLPSFANTIVAFDHPEVSGTSVSGATGLVFVRPEPRIVDTIDHIIHEWSHNKFELILHSYQLWTDDTRLHRSPIRDAPRPLYGVFHAIYVLLVVSDAMVHLMELDELRDGATHKVDSFLAECDASLRSLETEPSLTDDGRLFIDICLDWITTIAKDHAAS", "metadata": {"id": "A0A1G4VU34", "cluster": 11887432, "interpro_all": ["IPR026337"], "interpro_used": ["IPR026337"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein can be placed in the Cysteine synthase/cystathionine beta-synthase family, which plays a pivotal role in sulfur amino acid metabolism by catalyzing the synthesis of cysteine from O-acetylserine or converting L-serine and L-homocysteine to L-cystathionine. Members may display bifunctional activity involved in cyanide detoxification or siderophore precursor synthesis and often contain heme groups that influence redox sensitivity. Additionally, these enzymes are frequently regulated allosterically by S-adenosyl-methionine to maintain cellular sulfur homeostasis. In addition, the protein incorporates a Tryptophan synthase beta chain-like, PALP domain that functions as a catalytic module within the pyridoxal phosphate (PLP)-dependent enzyme superfamily. Represented by the beta subunit of tryptophan synthase, this domain supports diverse enzymatic activities found in proteins such as threonine dehydratase, cysteine synthase, and threonine synthase. It is expressed in Dokdonella fugitiva.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8666, 8921, 19, 9446, 2183, 11215, 4666, 17, 8921, 3416, 16, 2154, 5705, 43, 13637, 2770, 1922, 12585, 3835, 2687, 4714, 2007, 29601, 1920, 4271, 1927, 8666, 2037, 57, 17, 6894, 26337, 2014, 15025, 54, 17, 8468, 1930, 54, 17, 19211, 1942, 54, 17, 9446, 2183, 11215, 18, 4678, 2278, 4434, 29491, 2455, 3286, 1922, 26164, 18169, 2014, 22940, 11082, 7897, 4271, 1930, 3868, 5531, 10954, 2671, 1988, 4039, 9366, 3802, 18, 4950, 16, 2144, 5038, 2032, 5467, 4335, 14772, 2169, 2007, 61, 17, 29283, 17, 12417, 1942, 6698, 3689, 12585, 7622, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 13489, 8921, 4666, 4659, 17, 3189, 16, 15771, 3418, 1988, 4088, 1966, 43, 6804, 9059, 2651, 1920, 24828, 23859, 5413, 12, 21453, 13, 17, 3100, 4113, 13975, 18, 5960, 2007, 1920, 4666, 5903, 1927, 13489, 8921, 16, 2052, 3418, 7825, 6445, 8145, 4209, 2435, 1922, 2697, 2427, 1966, 13143, 11725, 7234, 16, 8666, 8921, 16, 1930, 13143, 8921, 18, 2176, 1977, 3198, 1922, 2608, 16200, 2290, 11560, 1019, 26399, 2078, 7302, 18, 3], "output": "MNGATSDAGRDWVHGAIDALEREAARSADTHLLKIDLPGFPGIDVYFKDEAAHPTGSLKHRLARSLYLYALCNGRLREGQAVVDASSGSTAIAEAWFARLLGLCFTAVMPACTAPAKIRAVEALGATCDLVDDPATVRTRARAHAVAGACDLDQFGLAERATDWRGNNNIAESILGQLAREPHPRPAWIVCGAGTGGTSATIGRYLRYRRLPTRLCVAEPLGGAFARGWRAHDADACATRSTVIEGIGRPRVEPGFLFDIVDRVVEVPDAASIAAMHLLEALLGRRYGGSSGTNFVACLRLAAAMRARGECGSIVSLLCDRGERYAETLFDPGWLAARALDAAPWRAALLACIDDGGWREP", "metadata": {"id": "A0A4R2I3T8", "cluster": 12162963, "interpro_all": ["IPR050214", "IPR001926", "IPR036052"], "interpro_used": ["IPR050214", "IPR001926"], "interpro_unused": ["IPR036052"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein falls within the Calmodulin/Myosin light chain/Troponin C-like family, which comprises calcium-binding proteins essential for regulating muscle contraction and intracellular signaling. Members such as troponin C and myosin light chains modulate actomyosin ATPase activity and actin interaction, while calmodulins mediate the control of various enzymes and ion channels through calcium-dependent mechanisms. Also, the protein carries a EF-Hand 1 calcium binding site that coordinates calcium ions in a pentagonal bipyramidal configuration using a conserved twelve-residue loop. This binding event triggers a conformational shift that activates or inactivates the target protein. Moreover, the protein incorporates a EF-hand domain that functions as a calcium-binding motif characterized by a twelve-residue loop flanked by two alpha-helices. Upon coordinating calcium ions, it undergoes a conformational change that triggers the activation or inactivation of target proteins, often occurring in pairs or higher copy numbers. It is found in [Myrmecia] bisecta and has UniProt annotations Repeat.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 12182, 2651, 1920, 17537, 19, 10863, 3696, 4659, 19, 18714, 45, 17, 3189, 3416, 16, 2154, 12936, 5016, 17, 2743, 2697, 4415, 1958, 6773, 3760, 8332, 1930, 4776, 3197, 18, 4678, 2427, 1966, 18714, 45, 1930, 10863, 3696, 7835, 8480, 4033, 22125, 9444, 2455, 1930, 4718, 2835, 16, 2679, 17537, 1036, 8265, 1920, 2285, 1927, 3425, 5038, 1930, 4755, 5628, 2596, 5016, 17, 3100, 3531, 18, 2222, 16, 1920, 2213, 16252, 43, 8485, 17, 3897, 21, 5016, 2743, 3200, 1988, 10675, 5016, 6982, 1922, 43, 9412, 13481, 8446, 3553, 25238, 1923, 9674, 2193, 43, 5305, 12367, 17, 6181, 5881, 18, 2052, 2743, 4817, 11847, 43, 8523, 5950, 1988, 9094, 2014, 22331, 1036, 1920, 2758, 2213, 18, 3950, 16, 1920, 2213, 19683, 43, 8485, 17, 3897, 3418, 1988, 4088, 1966, 43, 5016, 17, 2743, 5219, 4378, 2007, 43, 12367, 17, 6181, 5881, 20185, 2007, 2288, 4595, 17, 12789, 18, 4073, 19355, 5016, 6982, 16, 2176, 14928, 43, 8523, 3185, 1988, 11847, 1920, 2936, 2014, 8005, 1927, 2758, 2697, 16, 3868, 6966, 1922, 5803, 2014, 2580, 6983, 4630, 18, 2176, 1977, 2435, 1922, 37, 14227, 28882, 2126, 39, 7266, 2089, 1019, 1930, 2258, 20709, 15010, 6865, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MASAAARERFARKNEAADLKRAFDKLDTKKSEIEDMIWEVDEDCDQCLTWAEFQAMYHGTGHVSLEEAMQIMYLRYGRSLLDAQLEQSLHISQVKQLRNRITAKTYKPPPVTQKKRMSQSAKTDGKIDTEELNELFLKLGHKRCRNDMTGYEPRRLFNVVQFVMNDREEIFGTSDLNSGKTLTLTEFL", "metadata": {"id": "A0AAW1PEY8", "cluster": 14054553, "interpro_all": ["IPR050230", "IPR011992", "IPR018247", "IPR002048"], "interpro_used": ["IPR050230", "IPR018247", "IPR002048"], "interpro_unused": ["IPR011992"]}, "task_type": "infilling"} {"instruction": "The protein is included in the Leucine-rich repeat domain superfamily, which forms a right-handed beta-alpha superhelix that typically adopts an arc or horseshoe shape to provide a structural framework for protein-protein interactions. Found in diverse proteins from viruses to eukaryotes, including tyrosine kinase receptors and virulence factors, this domain facilitates processes such as signal transduction, immune responses, and cell adhesion. In addition, the protein should feature a F-box domain that functions as a protein-protein interaction motif linking the protein to Skp1 and the core of SCF (Skp1-cullin-F-box) E3 ubiquitin ligase complexes. This association facilitates the ubiquitination and degradation of specific substrates, such as G1 cyclins and Cdk inhibitors, which are typically recognized by variable secondary motifs within the F-box protein. It is expressed in Rhizopogon vesiculosus. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 12624, 17, 5536, 6865, 3418, 13975, 16, 2154, 4952, 43, 3659, 17, 17105, 4666, 17, 4595, 3356, 23285, 2416, 1988, 5745, 24032, 1925, 9952, 2014, 15638, 10647, 1021, 5989, 1942, 3394, 43, 4346, 6465, 1958, 2213, 17, 2213, 3719, 18, 2435, 1922, 6445, 2697, 2037, 6241, 1942, 15021, 16, 2710, 6941, 4016, 4086, 1930, 9304, 2790, 16, 2052, 3418, 11374, 4028, 2427, 1966, 2733, 8201, 16, 3743, 3387, 16, 1930, 2024, 6141, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 48, 17, 5758, 3418, 1988, 4088, 1966, 43, 2213, 17, 2213, 2835, 5219, 9486, 1920, 2213, 1942, 3097, 5113, 1930, 1920, 4728, 1927, 12437, 12, 3097, 5113, 17, 22859, 1921, 17, 48, 17, 5758, 13, 10968, 6526, 11905, 5048, 18, 2052, 3279, 11374, 1920, 11758, 1930, 4877, 1927, 2487, 6249, 16, 2427, 1966, 8533, 29201, 1930, 9727, 4472, 16, 2154, 2032, 5745, 6783, 2007, 4650, 4067, 8277, 2651, 1920, 48, 17, 5758, 2213, 18, 2176, 1977, 3198, 1922, 13458, 7540, 3827, 1022, 5634, 16058, 13650, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MRHVHVCLLPTEILLGIFTIIREEPGTRDSLKRETIAALARTCKTFKEPALDVLWENISGIKPLISFLPEGVVSRTRNQKLKTSLRGEWKIFAQYARRIHSLAIDKCNLDEISEQVVEALVSTPSLALLSNLRKLQWLDDRGCFFPLLRTLLVPTITSIKLGIDSSELWLSSFSKSALLTFLGARCPSIRELDCVYDGHSDEFSDAISEAVCCCHELVHLKAGVLNAQALVHLASLPLLKSLHLWLSFDVVDKPPTNSIPMFISKLDELSITARSHTSLTQCFRNVRFLSCRSVVLSIDLDWMDPDEPYDPLDIPDLIVAFSECFSPVLEELWVHSDFGHHNERILDHRFAFGFDVIAPFLQFSHLTMLDLDWLCTSDIGDEAFRNMVQSWPLLKDFRFESGDRWVVPPSLTFTGLVHLIQHCRHLRRIDIHFSACSIDANSEPFSTTLPNEMITCLFVGFSPIVDPKAVARQLHVLLPNLTHVVRYEWGGDDDREVPFVKGWNTVDEYLELLTEGAVLREKIGELWEES", "metadata": {"id": "A0A1J8QE62", "cluster": 15707105, "interpro_all": ["IPR001810", "IPR032675"], "interpro_used": ["IPR032675", "IPR001810"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Give me a peptide sequence capable of: The protein is included in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Furthermore, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is found in Jeongeupia sp. USM3 and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2435, 1922, 8988, 18771, 3481, 2126, 2056, 18, 2022, 17796, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MRVVGLTGGIASGKSTVGALFEQYGVPLIDTDAIAHRLSQAPSPLLDEVRAQFGPSSIDANGALARDWMRQHVFEDTGARRRLEAIMHPRILAELERELAALPVDTPYALVAVPLLFEARGFRERVDRALVVDCDTAMQRQRLLGRPGMTEALADAIIASQLDRTRRRAQADDVIDNVGSLEQLAETVAHQHQQYLRWSTTTKK", "metadata": {"id": "A0A1D9BGT1", "cluster": 20159915, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein should have a T-box DNA-binding domain that functions as a sequence-specific transcriptional regulator, acting as either an activator or repressor by binding to the consensus sequence TCACACCT. This highly conserved region is essential for early cell-fate decisions, tissue differentiation, and organogenesis during embryonic development. Also, it is part of the p53-like transcription factor, DNA-binding domain superfamily, which functions as the DNA-binding module in transcription factors regulating diverse cellular processes such as the cell cycle, apoptosis, and immune responses. This domain adopts a nine-stranded \u03b2-sandwich structure with a Greek-key topology that clamps or encircles the DNA target to stabilize the protein-DNA complex. It is found in Caenorhabditis nigoni and is linked to UniProt keywords Nucleus and Transcription regulation.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 3066, 2162, 43, 62, 17, 5758, 2678, 17, 2743, 3418, 1988, 4088, 1966, 43, 3244, 17, 2487, 5224, 7888, 16, 8290, 1966, 3108, 1925, 9518, 2014, 14434, 2007, 2743, 1942, 1920, 7076, 3244, 13828, 3375, 2437, 1031, 18, 2052, 3626, 5305, 3031, 1977, 4415, 1958, 3120, 2024, 17, 11211, 8693, 16, 2960, 4155, 16, 1930, 3090, 3761, 2409, 7231, 2740, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 5105, 17, 3189, 3213, 2991, 16, 2678, 17, 2743, 3418, 13975, 16, 2154, 4088, 1966, 1920, 2678, 17, 2743, 9059, 1922, 3213, 2790, 6773, 6445, 3689, 4028, 2427, 1966, 1920, 2024, 4048, 16, 4091, 16, 1930, 3743, 3387, 18, 2052, 3418, 24032, 43, 6360, 17, 10338, 161, 17, 18038, 3170, 1956, 43, 27568, 17, 3834, 13678, 1988, 10209, 1036, 2014, 3350, 13220, 2612, 1920, 2678, 2758, 1942, 13448, 1920, 2213, 17, 2678, 2796, 18, 2176, 1977, 2435, 1922, 22418, 19000, 13339, 1930, 1977, 4624, 1942, 20709, 11569, 5607, 1930, 3213, 3640, 18, 3], "output": "MHDWYEFLGATEQRRSKPKLKRCRYSAKAHYHHGASEWMESQISFDVTMQKYVPLLSCYYYVDEKEIRARIFGSLPRISRKQMELVGDSRYKYFNEQWVVHFKITTELGTTDATMIPL", "metadata": {"id": "A0A2G5VB28", "cluster": 25542441, "interpro_all": ["IPR008967", "IPR046360", "IPR036960"], "interpro_used": ["IPR046360", "IPR008967"], "interpro_unused": ["IPR036960"]}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: The protein is a member of the UROD/MetE-like superfamily, which encompasses enzymes containing a ($\\beta/\\alpha$)$_8$-barrel fold, including uroporphyrinogen decarboxylase (URO-D) and cobalamin-independent methionine synthase (MetE). These proteins catalyze essential steps in metabolic pathways, with URO-D mediating the decarboxylation of uroporphyrinogen in heme biosynthesis and the zinc-dependent MetE transferring a methyl group to L-homocysteine during methionine synthesis. Moreover, the protein should contain a Uroporphyrinogen decarboxylase (URO-D) domain that catalyzes the sequential decarboxylation of uroporphyrinogen to yield coproporphyrinogen as the fifth enzyme of the heme biosynthetic pathway. This domain adopts a conserved (\u03b2/\u03b1)8-barrel fold with a deep active site cleft and typically forms a dimer that juxtaposes the catalytic centers of the monomers. Also, the protein is associated with the Methylcobamide/Methylated-thiol:CoM methyltransferase family, which catalyzes the transfer of methyl groups from methylated corrinoid proteins or free cob(I)alamin to coenzyme M during archaeal methanogenesis. These enzymes facilitate methane production via the methanol, methylamine, and methylated-thiol pathways by generating the substrate for coenzyme-B sulfoethylthiotransferase. It is found in Candidatus Bathyarchaeota archaeon.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 14984, 1007, 19, 22031, 17, 3189, 13975, 16, 2154, 21569, 5038, 3165, 43, 12, 8, 38, 4666, 19, 38, 4595, 8, 13, 8, 41, 28, 8, 17, 19560, 3728, 16, 2710, 14984, 2074, 25818, 5572, 2404, 23922, 12, 14984, 17, 46, 13, 1930, 18477, 3717, 17, 3484, 12417, 8921, 12, 22031, 13, 18, 2144, 2697, 18170, 4415, 5983, 1922, 4487, 3873, 16, 1956, 14984, 17, 46, 10239, 1920, 22429, 1943, 1927, 14984, 2074, 25818, 5572, 2404, 1922, 10954, 8132, 1930, 1920, 7997, 17, 3100, 22031, 21902, 43, 4963, 2210, 1942, 54, 17, 19211, 2409, 12417, 4271, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 14984, 2074, 25818, 5572, 2404, 23922, 12, 14984, 17, 46, 13, 3418, 1988, 17097, 1920, 9454, 22429, 1943, 1927, 14984, 2074, 25818, 5572, 2404, 1942, 4307, 3725, 17351, 11119, 30338, 5572, 2404, 1966, 1920, 12052, 4113, 1927, 1920, 10954, 14041, 3374, 18, 2052, 3418, 24032, 43, 5305, 12, 161, 19, 160, 13, 28, 17, 19560, 3728, 1956, 43, 6515, 3500, 3200, 14649, 1930, 5745, 4952, 43, 7632, 1988, 21887, 2026, 12278, 1920, 6804, 7365, 1927, 1920, 13256, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 4963, 4879, 7972, 16408, 1021, 19, 11882, 17, 13914, 30, 2008, 16478, 3416, 16, 2154, 17097, 1920, 3856, 1927, 4963, 2671, 2037, 11882, 2233, 5572, 2642, 2697, 2014, 3294, 22528, 12, 51, 13, 10527, 8547, 1942, 22051, 55, 2409, 22367, 17348, 3761, 18, 2144, 5038, 6628, 18863, 3372, 3454, 1920, 8570, 16, 4963, 3812, 16, 1930, 11882, 17, 13914, 3873, 2007, 9155, 1920, 4510, 1958, 22051, 17, 44, 5141, 6802, 28935, 19174, 7969, 14165, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 10481, 9771, 15618, 20051, 7336, 13470, 1916, 18, 3], "output": "MPVSLYEVNTQFKNWDTFVMIPIGDPNFTYFLRENKDKHEPFYIKGVGDLGVFFSVIYRENIETPKGTVTATFRVDDRVATTWQVKVDLEPLKDAQKKLGDKGIIVLSVGDPLGLVVPLDYFYERLLKLYRQVSEQVTEVIFRFWGPIDTVKCHGNYACIHCHGRIRSVLEMIRSLLKRSVGDEICLMGYVEYEDIISVTPSAIKSITRRVNDNFIAFLRWGRKLGKYPFLKNRVLEPSYSELMRVAEDLQSSNEARKKVIRKREGNSVEPYIKSIEDIEKILSIPYDPLFKYERFLFFSLYKKEKVKELEYITPPSMSPKYFDEMVVEYDYKLRPDIIEPIEPPPYGDITLKEGIVRKAIEEGAPGGGYIMIPSSMPIKT", "metadata": {"id": "A0A419KNL9", "cluster": 26063212, "interpro_all": ["IPR052024", "IPR038071", "IPR000257"], "interpro_used": ["IPR038071", "IPR000257", "IPR052024"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein incorporates a von Willebrand factor, type A domain that mediates the formation of multiprotein complexes and interacts with a wide array of ligands to facilitate cell adhesion, migration, and signal transduction. Commonly found in extracellular proteins like integrins and collagens, this versatile module also functions intracellularly in processes such as transcription and DNA repair. It is identified in Planctomycetaceae bacterium.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 19683, 43, 14147, 30067, 2991, 16, 2601, 43, 3418, 1988, 10412, 1920, 3337, 1927, 20677, 5684, 5048, 1930, 9034, 1956, 43, 4743, 6472, 1927, 6908, 1942, 6628, 2024, 6141, 16, 5049, 16, 1930, 2733, 8201, 18, 5384, 2435, 1922, 5329, 2697, 3189, 15563, 1930, 5621, 1036, 16, 2052, 20425, 9059, 2222, 4088, 26511, 1922, 4028, 2427, 1966, 3213, 1930, 2678, 5059, 18, 2176, 1977, 2899, 1922, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 18, 3], "output": "MFAPSAPKGLGVGAETTREVSIVVARDQRYFLPPSTEETPLLPEMELPSINFPKHAGLLADAEARRAARAAQGNSVNMSLFGGPNAQGRSFVFVIDRVELETALSHLEPVHRFTVIAYHHQPYYLDGRKLLPMGLKAALFLNPDVVYLMTDGGLPALDKPKRDLIRRRPRPQDGHFMMLLAKENAGGYSYVRKQEAVRSPSSEAAAAQSKQAASVGAPSTLSARGSPQATTTFDYSNVSKSMGTSGLDALSDVAATEENKKRIAKFFRNLAAFGQTEHEEARRSGSTIHCIHFGT", "metadata": {"id": "A0A7C7X2W9", "cluster": 27568640, "interpro_all": ["IPR002035", "IPR036465"], "interpro_used": ["IPR002035"], "interpro_unused": ["IPR036465"]}, "task_type": "infilling"} {"instruction": "The protein belongs to the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. Moreover, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein includes a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. It occurs in Chryseobacterium sp. legu1 and is described by UniProt keywords Metal-binding. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 5921, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 2176, 5110, 1922, 21367, 1021, 12022, 2056, 18, 6703, 24396, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MLTKVKVQEFLKEIEVDDLVNNFQVVGNDVYIDMTAHSPAMHEKKKLEAAMKQAFASEFGEEVVLKLKIASPEPSQVQQNQIKGKQIPGIQNIIAIASGKGGVGKSTVAANLAVTLAKMGFKVGILDADIYGPSVPTMFDTEGAKPISVEKDGKNLMKPIENYGVKMLSIGYFSGANQAVVWRGPMASKALNQMIRDADWGELDFLLIDLPPGTGDIHLSIIQEVPVTGAVIVSTPQHIALADVRKGIAMFQMESINIPVLGLIENMSYFTPEELPENKYYIFGNQGAQYMAEDLGIPVLGEIPLIQSIREAGDVGRPAALQEGSKIEEIYKTTAQNMIESLVERNKSLPATEAVKITTMAGCSPKK", "metadata": {"id": "A0A5C7EWD6", "cluster": 3676389, "interpro_all": ["IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR033756", "IPR027417", "IPR000808"], "interpro_unused": ["IPR019591", "IPR044304"]}, "task_type": "autoregressive"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein incorporates a Glycerophosphodiester phosphodiesterase domain that catalyzes the hydrolysis of glycerophosphodiesters, such as glycerophosphocholine and glycerophosphoethanolamine, to produce alcohols and sn-glycerol-3-phosphate. This domain adopts a TIM barrel \u03b1/\u03b2 fold and plays diverse roles ranging from bacterial nutrient acquisition and host-membrane degradation to mammalian skeletal muscle development. Additionally, the protein is grouped in the PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily, which contains a structural domain found in enzymes such as phospholipase C and glycerophosphodiester phosphodiesterases. These proteins play a critical role in signal transduction by hydrolyzing phosphatidylinositol 4,5-bisphosphate to generate the second messengers diacylglycerol and inositol 1,4,5-trisphosphate, often under the regulation of G proteins and Ras-like GTPases. Also, the protein includes a Phosphatidic acid phosphatase type 2/haloperoxidase domain that functions as a type 2 phosphatidic acid phosphatase (PAP2) to dephosphorylate phosphatidate into diacylglycerol for lipid synthesis and signaling, or acts as a vanadium-dependent haloperoxidase to catalyze halide oxidation. This domain features a core 5-helical bundle structure with conserved residues for binding phosphate or vanadate cofactors. It originates from Alicyclobacillus sp. SO9 and corresponds to UniProt keyword Transmembrane helix.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 19683, 43, 7757, 8630, 3462, 1967, 24821, 3418, 1988, 17097, 1920, 9128, 1927, 7757, 8630, 3462, 3341, 16, 2427, 1966, 7757, 8630, 29999, 1930, 7757, 8630, 6802, 1963, 4296, 3812, 16, 1942, 5074, 21773, 1930, 3437, 17, 9244, 17, 23, 17, 5413, 18, 2052, 3418, 24032, 43, 2267, 19560, 160, 19, 161, 3728, 1930, 5705, 6445, 5456, 6485, 2037, 4543, 8708, 6165, 1930, 4423, 17, 3260, 4877, 1942, 6492, 7345, 3760, 2740, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 12897, 17, 3189, 24821, 16, 2267, 4666, 19, 4595, 17, 19560, 3418, 13975, 16, 2154, 5461, 43, 4346, 3418, 2435, 1922, 5038, 2427, 1966, 17570, 45, 1930, 7757, 8630, 3462, 1967, 24821, 1036, 18, 2144, 2697, 3918, 43, 4140, 2770, 1922, 2733, 8201, 2007, 7222, 9046, 16927, 24, 16, 25, 17, 29443, 1942, 5655, 1920, 2812, 16716, 1036, 29527, 1930, 16246, 21, 16, 24, 16, 25, 17, 6349, 25324, 16, 3868, 2441, 1920, 3640, 1927, 49, 2697, 1930, 6520, 17, 3189, 18390, 18, 2222, 16, 1920, 2213, 5921, 43, 2766, 8525, 1935, 2687, 8167, 2601, 22, 19, 24980, 19883, 3418, 1988, 4088, 1966, 43, 2601, 22, 2766, 8525, 1935, 2687, 8167, 12, 3860, 1028, 13, 1942, 13517, 9075, 2766, 8525, 2010, 2460, 29527, 1958, 4486, 4271, 1930, 3197, 16, 2014, 8016, 1966, 43, 7409, 21913, 17, 3100, 24980, 19883, 1942, 18170, 4217, 2261, 6638, 18, 2052, 3418, 4075, 43, 4728, 25, 17, 11514, 14142, 3170, 1956, 5305, 4248, 1958, 2743, 5413, 2014, 7409, 24675, 21362, 18, 2176, 22970, 2037, 15356, 22170, 14357, 8898, 2056, 18, 2577, 1026, 1930, 8852, 1942, 20709, 11121, 2538, 9117, 7864, 18, 3], "output": "MYSTPLLITLQHALSWIGVPVLRAISTLGGFGLFLIVIPLIYWTVNRSKAHHLTLTLLVSIWLNAFLKDMVAISRPVATSTLHVFVQPLTNGFPSAIAQNGTVFWGTLMAFIKSVWFRIFGLVVIISIGISRIAVGADYPTDVLGGFILGLMLLIGFSFRRKHRDPEKGTIQKEVQQKQPAVGRKLLLFALISLLLMFLDTASTEYASLGLLFGWLASNTYALQHFPYREKAPIGVQALKVLVGYAGMAFLLLVNVRFVPVGLPEFLGFALVSVWVTLGAPYLFQRMGLAPIPGTATGAKHDNGRPKQLRAVAIAAGIDVAVVTLLTLTAVANIGGTHETVPAFADADSAVAQSSPITEQDGLDVKHTSLIGRPFAVLGHRGDAAKLPQETLPGFRQAVKLGVDLLDLDVRLTKDHHFVLLHNPTVDATTNGHGPVSDMTLKQVQSLDAGYWMTTDGGKTYPFRGKGIHLMSLTGFFKAFPHQQVNIEIKNDSYTAGSDLARVIAASHAANRVIVGSFYQSPLDSFRKHLPTARTMLSKHEMIQAYVWAHLGLEAYYTPPGNFAEVPETEGPLRVVTPGFVDFLHQHGVIVYVWTVDDTASMKRLMKMGVDGIISDNPGLLLQTDTKGV", "metadata": {"id": "A0A7T5EUB4", "cluster": 4931444, "interpro_all": ["IPR030395", "IPR036938", "IPR000326", "IPR017946"], "interpro_used": ["IPR030395", "IPR017946", "IPR000326"], "interpro_unused": ["IPR036938"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein belongs to the Nucleotide cyclase superfamily, which encompasses catalytic domains found in adenylyl, guanylyl, and diguanylate cyclases responsible for synthesizing cyclic nucleotide second messengers. These domains share a core ferredoxin-like fold, though the specific nucleotide-binding mode differs between subtypes such as the GGDEF domain and adenylate cyclases. Moreover, the protein features a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It is derived from Photinus pyralis (Common eastern firefly) (Lampyris pyralis) and is connected to UniProt keyword Lyase, ATP-binding, and Magnesium.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 5489, 16526, 13975, 16, 2154, 21569, 6804, 4682, 2435, 1922, 27802, 16, 13504, 25671, 16, 1930, 4325, 13785, 9075, 16526, 1036, 5061, 1958, 25292, 9821, 5489, 2812, 16716, 1036, 18, 2144, 4682, 7948, 43, 4728, 25304, 22389, 10960, 17, 3189, 3728, 16, 4170, 1920, 2487, 5489, 17, 2743, 5754, 11457, 2192, 8160, 2427, 1966, 1920, 12358, 3695, 1038, 3418, 1930, 23052, 16526, 1036, 18, 3950, 16, 1920, 2213, 4075, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 1977, 3595, 2037, 3822, 22214, 6487, 19337, 12, 3059, 11562, 21235, 13, 12, 12503, 3553, 1937, 6487, 19337, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 23928, 16, 4498, 17, 2743, 16, 1930, 13148, 18, 3], "output": "ENLEAYNKKLLANILPVHVAEHFLNSDNNDELYHEQCDFVCIMFASIPNFSEFYVELEGNNEGVECLRLLNEIIADFDELLSEEQFRYIEKIKSTGATYMAASGLTQNTCDMKQFQHVTAMADYALRIREQLAVVNEHSFNNFRIRIG", "metadata": {"id": "A0A1Y1NFD5", "cluster": 13965856, "interpro_all": ["IPR001054", "IPR029787"], "interpro_used": ["IPR029787", "IPR001054"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein is categorized in the Protein of unknown function DUF192 family, which consists of proteins that currently lack a defined biological role or characterized enzymatic activity. In addition, the protein is included in the Saro_0823-like superfamily, which includes bacterial proteins such as Saro_0823 and SMc00288 defined by a shared structural fold featuring a \u03b2-sheet decorated with helices. It is present in Patescibacteria bacterium. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 5739, 11884, 3416, 16, 2154, 7543, 1927, 2697, 1988, 5077, 3630, 43, 3608, 3933, 2770, 2014, 4378, 8145, 2455, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 9851, 1037, 41, 6709, 4553, 17, 3189, 13975, 16, 2154, 5921, 4543, 2697, 2427, 1966, 9851, 1037, 41, 6709, 4553, 1930, 16312, 22536, 7331, 3608, 2007, 43, 7115, 4346, 3728, 29931, 43, 161, 17, 11130, 30425, 1956, 12789, 18, 2176, 1977, 2481, 1922, 2917, 1918, 3349, 7972, 2341, 18339, 14061, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MLMKKVILIIAILFLIGALAFLTVRNQSGRPTVAINGQTYFIEIADTAASQQHGLSDRLSLPQDHGMLFIFPEKQVRSFWMQDMQFPLDIIWIDGDTIVDISENIPPPAVDEQPAIVYPKAPVDKVLEVNAGEVKRLSVSVDQKIITDL", "metadata": {"id": "A0A3D4R8C5", "cluster": 14002594, "interpro_all": ["IPR003795", "IPR038695"], "interpro_used": ["IPR003795", "IPR038695"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that has the following function: The protein is a member of the Protein adenylyltransferase SelO family, which functions as a conserved pseudokinase that catalyzes the AMPylation of serine, threonine, and tyrosine residues on protein substrates. Members of this family feature a protein kinase fold with an inverted ATP binding mode and, in eukaryotes, localize to the mitochondria where they may participate in redox biology. It is native to Variovorax sp. EL159 and contains UniProt keyword associations Magnesium, Metal-binding, and ATP-binding. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2213, 27802, 9961, 2484, 1037, 3416, 16, 2154, 4088, 1966, 43, 5305, 11520, 25545, 1988, 17097, 1920, 3681, 3017, 1927, 8468, 16, 13143, 16, 1930, 6941, 4248, 1990, 2213, 6249, 18, 4678, 1927, 2052, 3416, 5961, 43, 2213, 4016, 3728, 1956, 1925, 12344, 4498, 2743, 5754, 1930, 16, 1922, 15021, 16, 14380, 1942, 1920, 6489, 2597, 2611, 2278, 7352, 1922, 9366, 7256, 18, 2176, 1977, 6196, 1942, 2309, 2579, 18897, 2056, 18, 2349, 20982, 1930, 5461, 20709, 11121, 2538, 5253, 13148, 16, 6048, 17, 2743, 16, 1930, 4498, 17, 2743, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MSLLAEDTDVADLGLRWKPGFSTLGPAFFTALQPTPLPDPYWVCRSEAVARELGLPADWPSDSTLSALTGSMQIAGTQPFATVYSGHQFGVWAGQLGDGRAIMIGETEAGLEVQLKGAGRTPYSRGGDGRAVLRSSIREFLCSEAMHGLGIPTTRALCVTGSDARVRREELESAAVVTRVAPSFIRFGHFEHFAANQREDELRALADYVIDRYYPACRTTERFDGNAYAAFLEAVSERTAALLAQWQAVGFCHGVMNTDNMSILGLTIDYGPFQFLDGFDPRHICNHSDTGGRYAFNQQPNVAYWNLFCLAQALLPLIGDQEVAVAALESYKTVFPTEFEARMRAKLGLTDSAEGDRALIEGVLKLLAAGKVDYTIFWRRLSHFMADGQVEPVRDLFLDREGFDAWLLLFSERHVKGQRSQAADLMLKSNPKFVLRNHLGQQAIEASQQKDNSGVAVLLALLETPFEEHPGADAYAGFPPDWASTIEISCSS", "metadata": {"id": "A0A1G4ZMS9", "cluster": 14364891, "interpro_all": ["IPR003846"], "interpro_used": ["IPR003846"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is assigned to the Tetraspanin/Peripherin family, which comprises integral membrane proteins containing four transmembrane domains that organize other proteins into multimolecular membrane microdomains known as the 'tetraspanin web'. This group includes retinal-specific peripherins located at photoreceptor disk rims, where they are involved in disk morphogenesis. Furthermore, the protein can be placed in the Tetraspanin, EC2 domain superfamily, which represents the large extracellular loop consisting of a five-helix, disulfide-linked array that mediates homodimerization. This domain is critical for organizing the \"tetraspanin web\" of membrane microdomains through specific lateral associations with other tetraspanins, integrins, and signaling enzymes. It originates from Oncorhynchus tshawytscha (Chinook salmon) (Salmo tshawytscha) and is annotated with UniProt keywords Transmembrane helix. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 1977, 6304, 1942, 1920, 27346, 6528, 1921, 19, 4709, 1921, 3416, 16, 2154, 12936, 12328, 3260, 2697, 3165, 3006, 9117, 4682, 1988, 25681, 2303, 2697, 2460, 11129, 9525, 3260, 27628, 2617, 3171, 1966, 1920, 11, 27346, 6528, 1921, 8391, 11, 18, 2052, 2210, 5921, 6943, 17, 2487, 4709, 2925, 4810, 2019, 16383, 15598, 14764, 1036, 16, 2597, 2611, 2032, 3286, 1922, 15598, 15328, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 27346, 6528, 1921, 16, 3270, 1028, 3418, 13975, 16, 2154, 4972, 1920, 3103, 5329, 5881, 7600, 1927, 43, 3628, 17, 7864, 16, 11830, 17, 4624, 6472, 1988, 10412, 21189, 2466, 18, 2052, 3418, 1977, 4140, 1958, 22308, 1920, 6, 27346, 6528, 1921, 8391, 6, 1927, 3260, 27628, 2617, 2596, 2487, 5347, 5253, 1956, 2303, 27346, 6528, 2925, 16, 15563, 16, 1930, 3197, 5038, 18, 2176, 22970, 2037, 5595, 14514, 2304, 2072, 1957, 14459, 3160, 2355, 14920, 1019, 12, 6790, 17276, 1040, 9590, 13, 12, 3370, 12492, 14459, 3160, 2355, 14920, 1019, 13, 1930, 1977, 10633, 1956, 20709, 11569, 9117, 7864, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MGRMNIWVKRAFICVCVLIGIISTLLLAITLFGHGHFHQSEEIDKMLPGIAVLYVLEAATLALSIFGVYGARKEKKWAVILFSVGMSLASLYLFVECVKIYQAKHEMEELSRKEDLAMMPLSGAKQNDIEQMYYFQANFKCCGLVQGYQDWGTDIPLSCLCSDEDSTDFTCVARGNNTRFVIHYPNSDMSEDDDHKGLMDEHMLVYKEPCLPILISFMGYAISLMIGTLVALNALWVCISYLCLYYLTTSGLGSIQFFQSNQLKFNSPKIVRSGFFNSGNEMKLTTRIENFSSICLL", "metadata": {"id": "A0AAZ3PL53", "cluster": 17215411, "interpro_all": ["IPR018499", "IPR008952"], "interpro_used": ["IPR018499", "IPR008952"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has this function description: The protein should have a Amino acid transporter, transmembrane domain that serves as the integral membrane component for various carriers, including vesicular GABA transporters and system N amino acid transporters. It facilitates the translocation of substrates such as proline and GABA across cellular membranes. It has been characterized in Mytilus edulis (Blue mussel) and is described by UniProt keywords Transmembrane helix. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 2052, 2347, 8418, 30, 1920, 2213, 3066, 2162, 43, 3835, 2687, 9054, 16, 9117, 3418, 1988, 10634, 1966, 1920, 12328, 3260, 4594, 1958, 3425, 8974, 16, 2710, 16168, 7992, 10538, 1930, 2433, 56, 3835, 2687, 10538, 18, 2176, 11374, 1920, 7849, 1927, 6249, 2427, 1966, 12958, 1930, 7992, 3436, 3689, 5726, 18, 2176, 2258, 2252, 4378, 1922, 3057, 2583, 1957, 11941, 12191, 1036, 12, 4735, 26874, 1938, 13, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 7864, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MSNEQASHHGLTIWTTAVFIIGEIAGGGVLALPKAVEDTGWIGIPLLVVFTLTSSYTGTIIAKSWIIIQDRFPEYRNHVPDPYPVIGEKAYGKHGRHLVTFSINFTLFGASTVYLILASENIEDLMSDVTKDISFCYWLLILGAILTPITCLGTPADFWPIGVGATMSTGIACILILIQVLHDNKSAPPVTHSSTDFMKFSAAFGTLVFSVSGHPVFPTFIADMKKKTDFKWAILIGYIIVMLMYIPTTTSGYFVYGRNLNPNIVKNMTSGPITYIIDILMTLHLIFGYLILINPVCQGLEAKVGVPKAFTWKRCIARSTIVMVVIFVAESVPHFGAILSLIGGSTTTLLSYILPCVFYLKLAKGSNNQTSHKKYGISYQNAESTDEGDLSEQNYTEKQKKTPLIKDLNTTKHDIKEVNGAPPHSYEESDRELIEEISDQVSVQLTWTKTKAKEPEASSSKSKPALKSKPPSTRRRDAKRFDQWKATKTAVIPAEQVQQTTNTQTEARDSVVGHVLTPTKYKGEPVGVVVNRDIVTSPYNPNKACHRLVFYTSTNDRGKRSRIDYEDGFDIDHPDLLRTPPHTSPVYNEQSKEAIQSAIQAARPDTPYQQDQRSRSKMKAKRPTDSSL", "metadata": {"id": "A0A8S3UZR8", "cluster": 18385430, "interpro_all": ["IPR013057"], "interpro_used": ["IPR013057"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein features a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Also, the protein should feature a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Also, the protein should contain a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. It is expressed in Lactobacillus crispatus and carries UniProt keyword assignments DNA damage, Excision nuclease, and DNA repair.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 4075, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2176, 1977, 3198, 1922, 18134, 9635, 4302, 1031, 1957, 1930, 16252, 20709, 11121, 2538, 18306, 2678, 4293, 16, 10940, 16230, 16, 1930, 2678, 5059, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MIKRQKNRKFELVSKFKPAGDQEQAIDKLTKTFTMANIIAKLNKPTLVITHNKTLVGQLYPQSDTYIEKDSAINDEIDQLRHATTSALMIYGLGDPKEYARSVLMIHEGEEYDRNTLLFRVRGDVVEVFPAGNSNHAYRIEFFGDEIDRIVFMTNDEQLRRALGAISKEMKLQVKKFETNGIENYSRHMEGRKAGEPPYTLLDFFPDDRNRKQTLIDYGFRLPSALDNRPLKLSEFEKHVNQILYVGLLDPKIEVRPIEGQIDDLVGEINKRIDRHERVFVTVRYLHSDIKTLERMQILRDLRLGKFDVDKEGFLRAYRPLVQTMGRAARNANGEVIMKRRRKIQMEFNKEHGITPKTIIKSFADLNFDELTAKQKKTMISNLQEQMQEAAKKSSRKPKTRKGKNFNGKVGFKKGYKEQILEGATGTGGEFKSFFPNNAVEYFVSYYDYYQPEAYVERNDVVVVASVSCRDLVNIQYDRNDIDFQRGREVDSLTGEVIGERESISLFPATHGEGKLLEAERIKQRTTYDMEMMGEVGYDFLILIDESHATMPEIRAMYNGSATPGDYELERTDHKVEQIIRPTTLTKKMAEDLTDYLKDLGIKLIGINLLREGIDVPEVSLVAILDAYADTITDSMRAAIKATPIQDVISITKPSSEKEEKSDKLDFEEAANLRDAIMELQ", "metadata": {"id": "A0AAW4DNK6", "cluster": 22044192, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001650", "IPR001943", "IPR014001"], "interpro_unused": ["IPR006935", "IPR027417", "IPR036876", "IPR004807", "IPR024759", "IPR041471"]}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein is classified under the Zinc finger C2H2 superfamily, which comprises stable, zinc-coordinated $\\beta/\\beta/\\alpha$ motifs that primarily function as DNA-binding domains in eukaryotic transcription factors. These versatile scaffolds typically interact with the DNA major groove in tandem clusters, but can also be adapted to bind RNA, proteins, or lipids to regulate diverse cellular processes. Furthermore, the protein features a Zinc finger C2H2-type domain that functions as a classical DNA-binding motif, typically found in eukaryotic transcription factors where it interacts with the DNA major groove using a conserved $\\beta/\\beta/\\alpha$ fold coordinated by a zinc ion. These domains frequently appear in tandem arrays to facilitate specific recognition of nucleic acids, proteins, or lipids, acting as stable scaffolds for diverse biological activities ranging from gene transcription to chromatin remodeling. It occurs in Pediculus humanus subsp. corporis (Body louse) and carries UniProt keyword assignments Nucleus, Repeat, and Transcription regulation.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 7997, 8497, 8453, 6951, 13975, 16, 2154, 12936, 4700, 16, 7997, 17, 11651, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 8277, 1988, 5985, 2347, 1966, 2678, 17, 2743, 4682, 1922, 10825, 3213, 2790, 18, 2144, 20425, 10603, 5745, 6310, 1956, 1920, 2678, 3044, 15920, 1922, 10361, 5859, 16, 2308, 2112, 2222, 1998, 8461, 1942, 4566, 3146, 16, 2697, 16, 2014, 8238, 1942, 5741, 6445, 3689, 4028, 18, 3677, 16, 1920, 2213, 4075, 43, 7997, 8497, 8453, 6951, 17, 2601, 3418, 1988, 4088, 1966, 43, 8445, 2678, 17, 2743, 5219, 16, 5745, 2435, 1922, 10825, 3213, 2790, 2597, 2176, 9034, 1956, 1920, 2678, 3044, 15920, 2193, 43, 5305, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 3728, 11651, 2007, 43, 7997, 4755, 18, 2144, 4682, 5467, 3267, 1922, 10361, 10517, 1942, 6628, 2487, 5708, 1927, 11079, 4576, 16, 2697, 16, 2014, 8238, 16, 8290, 1966, 4700, 10603, 1958, 6445, 3933, 4209, 6485, 2037, 2359, 3213, 1942, 6338, 8378, 18, 2176, 5110, 1922, 5296, 21206, 2616, 1957, 19615, 18, 27357, 1937, 12, 3362, 3004, 2517, 13, 1930, 16252, 20709, 11121, 2538, 18306, 5607, 16, 6865, 16, 1930, 3213, 3640, 18, 3], "output": "MSSSDSNTGDVKIKTEVLLPNSTPQDTQPSPLALLAATCSKIGGVNQAQQNEQQSDGHSNQSNTVAQAIQAGQIRVVSAAVLQQLQEQQNRSQAQGQTQPQVITLSQLQNFLPPLQQQTSTASDTQQDVKVFTSASGNSNQLPGVVSVQGLPTQLFQASNTGNPNAGFNVVHPVQTINIDGQEALFIPTAMTNLGGQFIPGGQVVRPNVLQTIQLPNGQSLSVRPQIMQMSAVQQTVPVQVPISSANGQTIYQTVHFPLHAFGSNVPGLFQTAGQPVQMLPALTSMSAVPQPQVAQIITPSGQIQQIQLTQLGGGLAGSNVLPQTNHANIITQSSQSNLMPTSQPNVIASQGNQGSMIAQTSQNNMISQANILGPANHSNLITQSQQIISSSNASHAATTTSWCTTATPTPSVTVQTISAPTILNSAESQQQQQQQQQQQQQQQQQQQQNLLHSLGLTQQFTLAVPGSQNQQPVTVIPASNIANLAQARPNIGLIQTFLVQNVPGLGPVQVIPASAFQSQQTQPSQTIQGLPLGTQIIQTGQQVQEVVDPPKWQIVTVPSIPVANNNNQNNISQSINDISFNDEDGPKQKIRRVACSCPNCVENDRNMRAGGERVLKRQHICHIAGCNKVYGKTSHLRAHLRWHSGDRPFICTWMYCGKRFTRSDELQRHRRTHTGEKRFQCPDCQKKFMRSDHLSKHIKTHQKQKLMEAATSTISLLTEDSSSEENKMMIHDLNGEGDHDLVSHSENT", "metadata": {"id": "E0VPS6", "cluster": 22731684, "interpro_all": ["IPR036236", "IPR013087"], "interpro_used": ["IPR036236", "IPR013087"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Functionally defined as:\nThe protein possesses a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. Also, the protein is grouped in the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Also, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It occurs in Leifsonia sp and is linked to UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 14465, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 5110, 1922, 20014, 3544, 6114, 2056, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MRGLFLTFEGGDGSGKSTQAALLEEHLVGIGREVVRTREPGGTDYAADRAHHIATLVRPALERGAIVLQDRYLDSSVAYQGAGRVLDATEIRDLSLWATGGLLPDVTLEAEASDFHARVRSAYLELAAAEPERFLVLDGSRPVDELAAAIRDRVSDLLDLGVELREIVLHRRGEMEPRAEALIVLLDLDETVGRERLDGARTRYDR", "metadata": {"id": "A0A2E0SR32", "cluster": 23203959, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR039430", "IPR018094", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein contains a Putative glycogen debranching enzyme, N-terminal domain that is located at the N-terminus of enzymes involved in glycogen metabolism. While its precise function is unknown, it is analogous to the GDE_N domain and is usually followed by the C-terminal GDE_C domain. It is identified in Chloroflexota bacterium.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 5461, 43, 6770, 13302, 12929, 5584, 1941, 4113, 16, 56, 17, 4262, 3418, 1988, 1977, 4810, 2019, 1920, 56, 17, 7822, 1927, 5038, 3286, 1922, 13302, 4714, 18, 2679, 2496, 8162, 2347, 1977, 5435, 16, 2176, 1977, 12464, 1942, 1920, 7113, 1021, 41, 56, 3418, 1930, 1977, 5394, 3489, 2007, 1920, 45, 17, 4262, 7113, 1021, 41, 45, 3418, 18, 2176, 1977, 2899, 1922, 10107, 18222, 7336, 14061, 18, 3], "output": "MIDAVQVGAANVTINRNDHVLVTQPDGRVKRGSDGGFYARDTRFVSSYELTLAGKRPQLLNAPGAHPVAHDPGRRP", "metadata": {"id": "A0A535XKM9", "cluster": 24902399, "interpro_all": ["IPR032856"], "interpro_used": ["IPR032856"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has this function description: The protein is assigned to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Moreover, the protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is expressed in Gammaproteobacteria bacterium and is linked to UniProt keywords ATP-binding, Cytoplasm, and Transferase. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 2052, 2347, 8418, 30, 1920, 2213, 1977, 6304, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3198, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MKDTLKIGLTGGIASGKSTVCDLFSQLSVEIIDADTISHYLTKSDGLAFQEILDHFGDRILGSDGELDRQQLRSIIFNDVAEKQALENIIHPKVLDKINKNISDSTAPYLIIAVPLMIETGMNLLMDRVLLIDCSIETQIKRLIERDKCTKQQAESIIENQASLESKRAICDDVILNEEDTSFDQLKTEVIRLHSFYSDLEIKRLHKLP", "metadata": {"id": "A0A7C7WN52", "cluster": 25495731, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the protein function: The protein should include a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is derived from Burkholderiaceae bacterium. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 3595, 2037, 18359, 18681, 19476, 14061, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MPFFLHGCNAYAEGIGERLSTIEVPPTWFAIIWPRVHVSTREIFNDTGLTRNSKATKMRALSVAADFVAAENSARGLPANTFEISSLGVNDLELVARRRYPVIDQALSWLERFGVARMTGSGSAVFLAAESRAQAELAVADLPQEWRGWVVEGATEHPLAAW", "metadata": {"id": "A0A926AUM2", "cluster": 26754216, "interpro_all": ["IPR013750", "IPR036554"], "interpro_used": ["IPR013750"], "interpro_unused": ["IPR036554"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein incorporates a Phosphatidylinositol-specific phospholipase C, X domain domain that functions as the conserved \"X-box\" catalytic region essential for phospholipase C activity. It mediates the hydrolysis of 1-phosphatidyl-D-myo-inositol-3,4,5-triphosphate into the second messengers diacylglycerol and inositol-1,4,5-triphosphate, playing a central role in intracellular signal transduction. This region is structurally conserved across eukaryotes and some prokaryotes. It is present in Campylobacterota bacterium.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 19683, 43, 16927, 17, 2487, 17570, 45, 16, 66, 3418, 3418, 1988, 4088, 1966, 1920, 5305, 6, 66, 17, 5758, 6, 6804, 3031, 4415, 1958, 17570, 45, 2455, 18, 2176, 10412, 1920, 9128, 1927, 21, 17, 10951, 17, 46, 17, 15924, 17, 16246, 17, 23, 16, 24, 16, 25, 17, 17978, 2460, 1920, 2812, 16716, 1036, 29527, 1930, 16246, 17, 21, 16, 24, 16, 25, 17, 17978, 16, 14797, 43, 4101, 2770, 1922, 4776, 2733, 8201, 18, 2052, 3031, 1977, 12171, 5305, 3436, 15021, 1930, 2673, 28149, 18, 2176, 1977, 2481, 1922, 22657, 7336, 14061, 18, 3], "output": "MKNKIIVLTIALCTNMKITTQHVTKQYKSSDTTQINTGEQCSWTVTNPNQFILGLQLIQSIPTPFLDFPINQNGCCIGQYGKYQQQTQFHNKSVLHALCLKEPITFTNLIGDGATPAMLALKNNRLSDDQTLKILKLFTILPKTIAFLSEQNSHNSSSDDTITQRYKIHNPYSKETTPQNRKLSFSDMRCFNVFKNTEPLNSHSLVNSNQSVLFTAWLKKGARCTALTSLIEQVASKNPNLIAAAQHPHALHTQQSKSLLDWIEKKDRK", "metadata": {"id": "A0A2E6XWT1", "cluster": 27016776, "interpro_all": ["IPR000909"], "interpro_used": ["IPR000909"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein is a member of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein possesses a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Moreover, the protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is derived from Gilliamella sp. Lep-s5 and features UniProt keywords Isoprene biosynthesis and Transferase.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 3595, 2037, 18859, 2126, 22629, 5148, 2056, 18, 8530, 17, 8357, 1930, 4075, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MKQWLSPAKLNLFLYITGRRADNYHNLQTLFQFVDYYDILTFTVRQDDKLIMIAAERLKNYTNKKNLGVDITIDKKIPMGGGLGGASSNAATVLVALNQLWQLNLIHGHTAFAEGIGDQFQSVDVPEYWYLVACPNIEISTVEIFNDPELTRNTPAQSITDLLSLKFNELKNNLTGTGACVFTQCESKQQALAIQGKLNAALSVNSFVAKSLNNSPLYTNIKLLTPFANIPDDKNSTDELIKIGRIIGADVPIFCEEVVRKRYPTIDNIITYLSQYGTTR", "metadata": {"id": "A0A844X4E1", "cluster": 2436468, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR013750", "IPR006204"], "interpro_unused": ["IPR020568", "IPR036554", "IPR014721"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein can be placed in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It originates from Jeotgalicoccus coquinae and is linked to UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 22970, 2037, 8988, 1991, 5411, 5670, 2437, 1957, 25147, 18402, 3336, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MYKIIGLTGGIASGKTTVSDTAKNGPAIPAIIEAFGKDIIDNNGELDRKKHPLIREMMNADEQKFIKEGHVFLDIPDTQVKRLIKRNDLTAGEAEARINSQLYEQLDRFTEELESLYLKERGYTVLDADAYSRKTLGSIIFNDAGKRRELNEIVLLFENGLDERCDLVVTVFVDRMPLTEKVQKSDCHLDNNGTVEE", "metadata": {"id": "A0A6V7R9C1", "cluster": 4503003, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein incorporates a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein has a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein is assigned to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is derived from Verrucomicrobiales bacterium and corresponds to UniProt keyword Isoprene biosynthesis and Transferase.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 19683, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 3595, 2037, 3566, 3176, 13055, 1935, 7839, 1918, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 26690, 1021, 8132, 1930, 13763, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MRHLEFAPAKLNLWLKIHKKREDGFHEIETLMVPIATECNDFSLESDRHNLVLQALRALQCEAGNGFHGSDAAATLRAVNKILECPLSSRSLHSLAAKIGSDVPFFLDGSPAICSGRGEKIQVLKDSSAWAYSKWATAEPLPEVSYVPQSTAWGAFYNDLELPVFQKYIGLANMKSGSTLYALCQHPDEADQLLNKIRVEFGPSVWTAVSSIGEVKDELHFDLNLGSGKLIFKIRLVKKIPVGAGLGGGSSVPAYSVVLVKPEFGVMWLLEQGESEIALMSG", "metadata": {"id": "A0A800MD89", "cluster": 4938777, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR020568", "IPR036554", "IPR014721"]}, "task_type": "infilling"} {"instruction": "The protein should include a SpoVT-AbrB domain that functions as a DNA-binding module involved in diverse regulatory processes such as sporulation, cell division, and plasmid maintenance. Structurally characterized by a pair of beta hairpins linked by an alpha helix, it is a key component of bacterial transition-state regulators and antitoxins within toxin-antitoxin systems. Moreover, the protein incorporates a MraZ domain that functions as a bacterial transcriptional regulator structurally similar to the AbrB transition state regulator. It comprises a 70 amino acid region that is typically found duplicated within the protein. Also, the protein carries a MraZ, C-terminal domain that constitutes the C-terminal subdomain of the highly conserved bacterial transcriptional regulator MraZ. It contains a conserved DXXXR sequence motif suggested to form the functional site and is structurally related to the N-terminal subdomain by a pseudo two-fold axis. It has been detected in Gracilibacillus dipsosauri and corresponds to UniProt keyword Cell cycle, Repeat, and Transcription regulation.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 3066, 3951, 43, 18055, 25641, 17, 16746, 1014, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 9059, 3286, 1922, 6445, 4948, 4028, 2427, 1966, 23647, 16, 2024, 8451, 16, 1930, 5609, 6291, 18, 12171, 4378, 2007, 43, 3715, 1927, 4666, 14565, 1036, 4624, 2007, 1925, 4595, 7864, 16, 2176, 1977, 43, 3834, 4594, 1927, 4543, 4832, 17, 3360, 9098, 1930, 10310, 21269, 2651, 9165, 17, 10310, 9754, 3771, 18, 3950, 16, 1920, 2213, 19683, 43, 24564, 1011, 3418, 1988, 4088, 1966, 43, 4543, 5224, 7888, 12171, 2551, 1942, 1920, 16746, 1014, 4832, 3360, 7888, 18, 2176, 12936, 43, 3895, 3835, 2687, 3031, 1988, 1977, 5745, 2435, 19479, 2651, 1920, 2213, 18, 2222, 16, 1920, 2213, 16252, 43, 24564, 1011, 16, 45, 17, 4262, 3418, 1988, 14879, 1920, 45, 17, 4262, 27517, 1927, 1920, 3626, 5305, 4543, 5224, 7888, 24564, 1011, 18, 2176, 5461, 43, 5305, 14852, 14710, 1005, 3244, 5219, 3978, 1942, 2386, 1920, 3183, 3200, 1930, 1977, 12171, 2712, 1942, 1920, 56, 17, 4262, 27517, 2007, 43, 11520, 2288, 17, 3728, 5432, 18, 2176, 2258, 2252, 3330, 1922, 24689, 10401, 26073, 10401, 5277, 1036, 9137, 2204, 5735, 18330, 1930, 8852, 1942, 20709, 11121, 2538, 2024, 4048, 16, 6865, 16, 1930, 3213, 3640, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MFMGEYQHNIDNKGRIIVPSKFRDNLGEQFVITRGLDLPLTKKDARAFTRFFFSGAVECEIDKQGRINIPAPLRSASKWNEFVDESEESFAEIAENMLDFEMQCLFAYPMDEWRLLEEKLKKKYAQIEKECSVIGVSNRVEFW", "metadata": {"id": "A0A317KZJ4", "cluster": 4979440, "interpro_all": ["IPR003444", "IPR035644", "IPR020603", "IPR035642", "IPR038619", "IPR007159", "IPR037914"], "interpro_used": ["IPR007159", "IPR020603", "IPR035644"], "interpro_unused": ["IPR037914", "IPR038619", "IPR003444", "IPR035642"]}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein possesses a JmjC domain that adopts a cupin fold to coordinate Fe(II) and alpha-ketoglutarate, functioning as a metalloenzyme involved in chromatin remodeling. This catalytic domain primarily acts as a histone demethylase conserved from yeast to humans, although some variants display hydroxylase activity involved in processes such as tRNA modification. It has been detected in Thrips palmi (Melon thrips). Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 16097, 30271, 3418, 1988, 24032, 43, 14967, 1921, 3728, 1942, 11865, 2650, 12, 2890, 13, 1930, 4595, 17, 21471, 16542, 17488, 16, 7295, 1966, 43, 8969, 6802, 1022, 9318, 3286, 1922, 6338, 8378, 18, 2052, 6804, 3418, 5985, 8016, 1966, 43, 6632, 21732, 2051, 5305, 2037, 5688, 1942, 5209, 16, 2876, 2673, 4936, 4434, 16324, 2455, 3286, 1922, 4028, 2427, 1966, 10089, 6295, 18, 2176, 2258, 2252, 3330, 1922, 8481, 5689, 29686, 12, 4221, 1916, 8481, 5689, 13, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MPKKLQRRFGVQTFEISEDEFLNPGDLFDLMVKDPNVRKTGCFVGRLKGGPTLTENYIAEVKDLVDGDNGFQFFKPLLIRRKAVWRELGFFYVTTEEEGATPSQVRTLATKRNVFKETFLNMNFEETPKSHLQEVLESRGVGPCIDAFYEHLSRNNTPILYAANVDSVELGKAQKKAVNLQITQNVSMGKMESLIKYLVGGKHPGIVTPTLYIGNEASSFQCHHEDVSFEAVNMHVAGAPKIWFVVPPRYRRAFCVQLSAMGLERVDLACANFLQHKFYFCDPRVILSQKIPVYTIVQMPGDTVFLLPNAIHWGFNVGWNINEAVNCCSKSYAYPGMLASQRCQCDVDAHLKYFFDITKILKHAGVPRDTISLYRERKVFHILTEFQILYPDLDPESGRPGDSEVDFENLLGLSIDESQIGKFWQRCRQAPTCDDHFLGGFLEIDLEQEEKEEEEEEEEEEEEEEEEVNLNSKGTRKCPRCEHDSRKYGVKARLNIERHANKCHSSDFEDVMAEYDKKYERTTNFKTDSVSCHRCHKTFHGHTGTLNRHLAKCTVQDSEAPATKRMKR", "metadata": {"id": "A0A6P9ABK1", "cluster": 5517859, "interpro_all": ["IPR003347"], "interpro_used": ["IPR003347"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: It is part of the Dynein light chain, type 1/2 family, which functions as a non-catalytic accessory component of the cytoplasmic dynein 1 complex to link the motor to cargos and adapter proteins. These highly conserved small subunits possess a two-layer \u03b1-\u03b2 core structure and regulate dynein function, while also contributing to nuclear pore complex stability in organisms such as yeast. It is present in Durio zibethinus (Durian) and is connected to UniProt keyword Microtubule, Cytoskeleton, and Coiled coil.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 2176, 1977, 3131, 1927, 1920, 18188, 3696, 4659, 16, 2601, 21, 19, 22, 3416, 16, 2154, 4088, 1966, 43, 2447, 17, 6804, 15954, 4594, 1927, 1920, 6823, 18188, 21, 2796, 1942, 3300, 1920, 4842, 1942, 14713, 1036, 1930, 21054, 2697, 18, 2144, 3626, 5305, 2858, 6991, 7150, 43, 2288, 17, 4757, 160, 17, 161, 4728, 3170, 1930, 5741, 18188, 2347, 16, 2679, 2222, 8739, 1942, 4254, 8554, 2796, 5057, 1922, 7373, 2427, 1966, 5688, 18, 2176, 1977, 2481, 1922, 2335, 3940, 28666, 5873, 22523, 1022, 1957, 12, 2335, 3122, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 10544, 16, 11612, 16, 1930, 17524, 9121, 18, 3], "output": "MLRGSIGVYFVVTKISIKLEELEQHESDIRTLREQKDQKEALASASRALDLYEVFDCIAFAVDSVVGTNFSCFFNIFKGISSNSTSSTGETSAFKQGEENMAGVEQIILQDVVQMQEGKAVIEDTDMPLKILAQAYIKKDFDKMHGPGWQCHFKGTFIYFALETLNFL", "metadata": {"id": "A0A6P5XQB3", "cluster": 6660203, "interpro_all": ["IPR037177", "IPR001372"], "interpro_used": ["IPR001372"], "interpro_unused": ["IPR037177"]}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence of a protein with the following function look like? Here is the function: The protein has a CAP domain that adopts a conserved three-layer \u03b1-\u03b2-\u03b1 fold and mediates diverse extracellular functions such as cell adhesion, matrix regulation, and ion channel modulation. Found in secreted proteins across various organisms, it likely operates via a calcium-chelating histidine-glutamate pocket or protease-inhibitor activity. In addition, the protein contains a Allergen V5/Tpx-1-related conserved site that characterizes the cysteine-rich secretory protein (CRISP) superfamily, encompassing mammalian sperm proteins involved in ion channel regulation and capacitation, potent insect venom allergens, and plant pathogenesis-related defense proteins. Additionally, the protein is categorized in the Cysteine-rich secretory protein-related family, which encompasses a diverse group of proteins involved in mammalian reproduction, plant defense responses, and venom toxicity. Members function in varied capacities, ranging from regulating ion channels and calcium fluxes during sperm capacitation to acting as potent allergens in insect and reptile venoms. It has been detected in Cocleimonas flava.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 1920, 2213, 2258, 43, 2853, 3418, 1988, 24032, 43, 5305, 2559, 17, 4757, 160, 17, 161, 17, 160, 3728, 1930, 10412, 6445, 5329, 4088, 2427, 1966, 2024, 6141, 16, 4526, 3640, 16, 1930, 4755, 4999, 7145, 18, 2435, 1922, 8366, 2697, 3436, 3425, 7373, 16, 2176, 3205, 22460, 3454, 43, 5016, 17, 25814, 13873, 17, 7627, 10154, 2014, 7154, 17, 4106, 2455, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 15468, 16382, 19, 6213, 1039, 17, 21, 17, 2712, 5305, 3200, 1988, 26735, 1920, 8666, 17, 5536, 11518, 2213, 12, 9635, 1034, 13, 13975, 16, 17527, 6492, 6283, 2697, 3286, 1922, 4755, 4999, 3640, 1930, 4477, 3644, 16, 6828, 11422, 15540, 19226, 16, 1930, 4496, 6559, 17, 2712, 9720, 2697, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 8666, 17, 5536, 11518, 2213, 17, 2712, 3416, 16, 2154, 21569, 43, 6445, 2210, 1927, 2697, 3286, 1922, 6492, 12426, 16, 4496, 9720, 3387, 16, 1930, 15540, 5532, 18, 4678, 2347, 1922, 6760, 16817, 16, 6485, 2037, 6773, 4755, 5628, 1930, 5016, 18181, 2409, 6283, 4477, 3644, 1942, 8290, 1966, 6828, 19226, 1922, 11422, 1930, 3073, 5425, 15540, 1036, 18, 2176, 2258, 2252, 3330, 1922, 6880, 28875, 3947, 1934, 7732, 1019, 18, 3], "output": "MHTRIKPIQRSMLFFISSLLLISCSVEQKESPPLEIIEPTEELVEGFTHDPKNIELPPEDPIEQQIIEVRPPAKPPLSKSQLFSGVLKSHNRVRAKHRLKPLKWSNKLARYSKEWANHLGSGSSCTMRHRSGQPPYGENLYWSSAVVWSDGFRETNRVTIKDVVKAWTDEERWYDYQSNSCKPGQKCGHYTQVVWKNTTEVGCAVKVCNDKSQTWVCSYNPPGNYTGMRPY", "metadata": {"id": "A0A4R1F8C6", "cluster": 7536997, "interpro_all": ["IPR018244", "IPR014044", "IPR035940", "IPR001283", "IPR002413"], "interpro_used": ["IPR014044", "IPR018244", "IPR001283"], "interpro_unused": ["IPR002413", "IPR035940"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein should include a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. Also, the protein possesses a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Furthermore, the protein should have a Adenylate cyclase, N-terminal domain that comprises the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase. It is found in Caloenas nicobarica (Nicobar pigeon) and exhibits UniProt keyword tags Glycoprotein, Transmembrane helix, and Metal-binding.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2222, 16, 1920, 2213, 14465, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 23052, 16526, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 56, 17, 4262, 5329, 3031, 1930, 1920, 2561, 9117, 25, 17, 26, 4675, 3031, 1927, 23052, 16526, 18, 2176, 1977, 2435, 1922, 2570, 6802, 3676, 7718, 8751, 6102, 12, 7718, 8751, 27188, 1916, 13, 1930, 9826, 20709, 11121, 2538, 14392, 11424, 16, 9117, 7864, 16, 1930, 6048, 17, 2743, 18, 3], "output": "ACEDEFDCKELEALFQSYNLKLEQTSTLKALAVLIVLTASLALVELLSGPSLTISKGSHPVHCIIFLSLFSFTFSFLCCPFSLGAYGMEPPSAPEQGMWQLMLVTFVSYSLLPVRTLLSANRQRLWRTLVANAILFVSVNLYGVFVRILTERAQRKAFLQARNCIEDRLRLEDENEKQERLLMSLLPIYIQRHDNVSILFADIVGFTSLASQCTAQELVKLLNELFGKFDELATENHCRRIKILGKTDHAHCCVEMGLDMIDTITSVAEATEVDLNMRVGLHTGRVLCGVLGLRKWQYDVWSITKTTLECLNGDYEVEPGHGHERNSFLKKHNIETYFIVPSHRRKIFPGLILSDIKPAKRMKFKTVCYLLVQLMVMTCEDDDKRRALRTASEKLRNRSSFSTNVVYNTPGTRVNRYISRLIEARQTESEMADLNFITLTSAVVLSLILAALFGLVYLLIIPQSTVVLVLLVFCICFLVACIMYLHVTQVQCFPGCLTIQILIYSVAQGCVVGCMPWVWNINSSSSIVIISSGGTNRTMNELPCDTAHYAFLSCVVGTLTLAIFLRVSSLPKMILVILELSGYRKAVGGGSFYMRGYEPILAILLFSCALALHSRQVDLKLRLDYLWAVQAAQHFLMSNPRNMDLYYQSYSQVGVMFASIPNFNDFYIELDGNNMGVECLRLLNEEKIKTIGSTYMAAVGLVPTSGTKAKKSIYSHLSTLADFAIEMFDVLDEINYQSYNDFVLRVGITVNVASRMDSTGVQGKIQVTEEVQRILKRCSYEFMCRGKVSVKGKGEMLTYFLERANIQTKLGTSCPSVSSVASFNVKAGLGAGQVPATQTNQTLHYLPSVPAVKEALFIVTNVKYLQVTQLQQIVKLTLAIVFGLVVSVSHLIVTATSVRNVAMEMKEDFLKPPERIFHKDCYYCVSGLTQPNDVTLANVMEAGGLPGKVHHCRKMFKAEIPFSNKYKQIERENKYHQLQDEYFRTILCIFIVILLFVTILYIEEERDDMERVKLDNKRILFNLLPAHVIIADFDELMDKEYYKDINVGPVVAGVIGARRPQYDIWGNGKADGNNSQTRSLNLERKTYPYG", "metadata": {"id": "A0A7K6T2Q4", "cluster": 8958787, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR029787"], "interpro_used": ["IPR001054", "IPR018297", "IPR032628"], "interpro_unused": ["IPR030672", "IPR029787"]}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein includes a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein belongs to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It occurs in Ferruginibacter sp and carries UniProt keyword assignments Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 5110, 1922, 12210, 10189, 26073, 2341, 1915, 2056, 1930, 16252, 20709, 11121, 2538, 18306, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MIAFPNAKINLGLHVLSRRADGYHNLETVFYPVNLKDAVEIVENYNTPAPEVLWSASGIRVPGDLENNLCLKAFHLIKNDFSPIPPIKLHLHKNIPLGAGLGGGSANAAFTLQLLNEKFNLQIPKNKLQQYALKLGSDCPFFLVNNPSLAHGRGEELLPIEINLDSYKILMVNPGIIVNTAWAFSKIELQPQQRETIASIIKMPVTEWKNRLENDFEKPVFAAHPQIKNIKEALFEQGAVYAAMSGSGSSVFGIFHEQKEIKFPETYFYKWV", "metadata": {"id": "A0A9D9VZF6", "cluster": 10847524, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR020568", "IPR036554", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein includes a Type I restriction modification DNA specificity domain that functions as the target recognition component within a heteromeric bacterial restriction-modification complex. It determines the specific DNA sequence to be bound, thereby directing the associated modification and restriction subunits to either protect the host genome via methylation or destroy foreign DNA via endonucleolytic cleavage. It occurs in Streptococcus azizii and is linked to UniProt keywords Restriction system.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 2601, 51, 7587, 6295, 2678, 4896, 3418, 1988, 4088, 1966, 1920, 2758, 5708, 4594, 2651, 43, 19732, 9213, 1935, 4543, 7587, 17, 6295, 2796, 18, 2176, 13554, 1920, 2487, 2678, 3244, 1942, 1998, 4124, 16, 6113, 23258, 1920, 2458, 6295, 1930, 7587, 6991, 1942, 3108, 9145, 1920, 4423, 3843, 3454, 5547, 2014, 19259, 12400, 2678, 3454, 16239, 1022, 2626, 6586, 6404, 18, 2176, 5110, 1922, 15746, 6352, 2061, 3907, 1930, 1977, 4624, 1942, 20709, 11569, 7587, 2433, 18, 3], "output": "MWLQYLGFTESSYIELSLDSSIIKQLIDSTSGTTVGTLTIEKTKKLPLAVPPLAEQKRISLFIENIFNVLKMVC", "metadata": {"id": "A0AB36JRQ5", "cluster": 12595436, "interpro_all": ["IPR000055", "IPR044946"], "interpro_used": ["IPR000055"], "interpro_unused": ["IPR044946"]}, "task_type": "autoregressive"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein includes a Ankyrin repeat that mediates protein-protein interactions through tandemly repeated helix-loop-helix modules which stack to form an L-shaped structure. This versatile motif is found in diverse eukaryotic proteins, including transcriptional initiators, cell-cycle regulators, cytoskeletal components, and signal transducers. Additionally, the protein should have a NFkappaB IPT domain that adopts an immunoglobulin-like fold within NF-kappa-B and related transcription factors to regulate responses to physical, oxidative, and chemical stress. This domain contributes to cell proliferation and differentiation processes by functioning as a central regulator that blocks apoptosis in various cell types. Furthermore, the protein includes a Rel homology N-terminal DNA-binding domain that mediates specific DNA recognition in eukaryotic transcription factors such as NF-kappaB and NFAT. Structurally resembling the p53 core domain, it employs a recognition loop to interact with DNA bases in the major groove to regulate gene expression. It has been characterized in Nasonia vitripennis (Parasitic wasp) and is connected to UniProt keyword ANK repeat. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 5921, 43, 28336, 6865, 1988, 10412, 2213, 17, 2213, 3719, 2596, 10361, 1954, 5116, 7864, 17, 5881, 17, 7864, 10803, 2154, 10496, 1942, 2386, 1925, 54, 17, 9132, 3170, 18, 2052, 20425, 5219, 1977, 2435, 1922, 6445, 10825, 2697, 16, 2710, 5224, 23467, 1036, 16, 2024, 17, 4048, 9098, 16, 14787, 4178, 16, 1930, 2733, 26307, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 4651, 7640, 9434, 1993, 14892, 3418, 1988, 24032, 1925, 11837, 17, 3189, 3728, 2651, 4651, 17, 12093, 17, 44, 1930, 2712, 3213, 2790, 1942, 5741, 3387, 1942, 3841, 16, 5163, 16, 1930, 4399, 3071, 18, 2052, 3418, 7624, 1942, 2024, 4031, 1930, 4155, 4028, 2007, 7295, 1966, 43, 4101, 7888, 1988, 7644, 4091, 1922, 3425, 2024, 3584, 18, 3677, 16, 1920, 2213, 5921, 43, 2139, 9039, 56, 17, 4262, 2678, 17, 2743, 3418, 1988, 10412, 2487, 2678, 5708, 1922, 10825, 3213, 2790, 2427, 1966, 4651, 17, 19901, 1930, 16537, 18, 12171, 18994, 1920, 5105, 4728, 3418, 16, 2176, 22620, 43, 5708, 5881, 1942, 6310, 1956, 2678, 11137, 1922, 1920, 3044, 15920, 1942, 5741, 2359, 2294, 18, 2176, 2258, 2252, 4378, 1922, 7312, 6114, 27877, 25535, 16443, 1937, 12, 16445, 21830, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9808, 6865, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MSTAGSFSPSSVESPLMDTCENLNLSTEQVITIIGNPIDQNAIYAIPNNSTELKIVVQPVDKFRFRYKSEMMGTHGSLLGEREETSHKKEVPTAQLINCHLPEAVIRCTLVTADEDRRFPHAHHLVKKDGNSDKDDPHDINVSRENNYTAMFCNMGIIHTAKKNIKEEIMRKRKIEVMEEKKRKNFENPVISTREDLEMKMEAEKAQKWMNLNSVALCFQGFAPGANDVLIPITEKVYSRPINNLKSALTGELKICRIDKHTSSCEGNEEVWLLVEKVGKKNIKVIFYEVDEKDNTIWSAEGRFSELDVHHQYAIVFKTPSYKDVNITQPVEVLLKLERPSDGETSNSITFVYKPSDKVLNRKRPRLSTSGSMEFAHSPVPAPQLDICMPMAETCINLGEENISNLSGEIKKLLNDGQHCNSADLDEFLKDNSSLEKFYNLLPSNFVDGVDTDGGGPTEFERSQQDFANDSLRKVTNVLKEADGTPGSKRMTIDKIQDLLQESTIFGDTPLHFSLRHEQFDTAKYLLLILGSDPSFKAIVNMQNSAQKTPLHMAVLQNQADIVRALLRLGADPNLCDEEDASSLHNAVIVNANACIDELLKSNVKLNLEAHTEAGWSALHLAAKVGSLHAVKALIEAGADVNSTDMSYGRTALHIAVDSNHKHIVEYLLTKTNIHVNTKNFGGNTALHSAVVKGGKCAEELIKILKKHGADPQIRNNNINRDEEDEDNSLLPPIHTPIDSSATPTIKSESSDSEDDAPRPGESSFDLAKGDPKLMQLLSEGKPDDPIQEELDLKEESEDEMMLQDRAILQASRTFSQGRRISTQERPAVQPTVTKTSPTTKPQLQPARPGDEKLSDAHVNRILHILDRTGGWERLAQHTNHGSLVRLYKKMKSPSKALFVKIRLQNPDITVRQVKKLLIEVQAFEAATALETGR", "metadata": {"id": "A0A7M7GL58", "cluster": 16069471, "interpro_all": ["IPR002110", "IPR036770", "IPR011029", "IPR013783", "IPR014756", "IPR002909", "IPR033926", "IPR000451", "IPR008967", "IPR032397", "IPR011539", "IPR037059"], "interpro_used": ["IPR002110", "IPR033926", "IPR011539"], "interpro_unused": ["IPR013783", "IPR036770", "IPR037059", "IPR002909", "IPR032397", "IPR008967", "IPR011029", "IPR000451", "IPR014756"]}, "task_type": "autoregressive"} {"instruction": "The protein incorporates a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. Moreover, the protein contains a Adenylate cyclase, N-terminal domain that comprises the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase. Additionally, the protein should include a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. It is native to Harpegnathos saltator (Jerdon's jumping ant) and features UniProt keywords Repeat, ATP-binding, and Metal-binding.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 3950, 16, 1920, 2213, 5461, 43, 23052, 16526, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 56, 17, 4262, 5329, 3031, 1930, 1920, 2561, 9117, 25, 17, 26, 4675, 3031, 1927, 23052, 16526, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 2176, 1977, 6196, 1942, 4303, 9626, 3223, 2183, 1951, 7012, 3061, 12, 26482, 28615, 11, 61, 16870, 1941, 4942, 13, 1930, 4075, 20709, 11569, 6865, 16, 4498, 17, 2743, 16, 1930, 6048, 17, 2743, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MADPARTIFFHFIFQGISLIPDLIHASTLTTMTQLPSVMSSRRSRILIGAASSVVFGLGILILKSVLPVLVHISRRYVFDNLLDYYDVIQIVVEIVFLLAAVLAGLYLECEREQQEQLLLSVIPAYIAAEVKRSIMLKMVQRHNNVSILYADIVNFTPLSEQLSASDLVKTLNELFVSGLPVSRPNHAYNCVNMGLQMIDAIRFVREATGFNVDMRIGIHTGLANHMESGGLPGRVHITKATLLQLGDRFEVEPGDGGSRESYKSREESEMENGGNRIHGPGPVPSRSRPSSEATLAKNIGLTSIAMIESNLLSNNASCFDTQHWCGQYREQRDEQYSWYVIASNVVYTLMFCIQLIYLPRSIVVIIFAVISWFNGKVDSSGSEESTNQIALSRGIRITVYLIDQTVGYIVPLYVYSTVMALVVGWTHLRVDFLLKLSVMFLSVVVGIHYLMQVGYLLTLVSVILHILDRQVEYTSREQDEVETMRGINKILLENILPAHVADHFLATRDTASIPNYKEFYDETDINKQGLECLRLLNEIIGSTYMLASGLSPGKEDGDGKDPLKQQDHNVIVLVEFRFKLRMGLNHGPVIAGVVGAQKPQYDIWGNTVNDAGYELVCRGPTYVKGKGTLTTYFVKTPFDDKEDNYLIASLILLLVLFVCVLSIIAILPKMRFEAPFVIACTLYRLLTASALRKTFSGTKTVIESRIKADACQEANKHKQTTFQEMYGRFDQIAQDNQCMRIKILGDCYYCNVLCGVLGLRKWQFDVWSDDVTLAQHKVETFLIMPPKKMTKYVECWGADKPFANIAGNEGISPFTYWFKDKNQEQYGCFAAGLASLTALLAVASSVISLIDVILAVFSQAPVIQLYYENPGSKFYTDILWKSKLRVQELYHERYSSIAVMFCDFDKLLLKPKFSGIEKIKTIAIALMTILDQINRDSFQVASRMDSCGEMGKLQVTEDTAKILI", "metadata": {"id": "E2BM54", "cluster": 16271934, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR029787"], "interpro_used": ["IPR001054", "IPR032628", "IPR018297"], "interpro_unused": ["IPR030672", "IPR029787"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein is a member of the GHMP kinase, C-terminal domain superfamily, which encompasses the C-terminal structural component of ATP-dependent enzymes involved in amino acid, isoprene, and carbohydrate metabolism. This domain adopts a central alpha-beta plait fold that cooperates with the N-terminal domain to create a nucleotide-binding pocket. While primarily found in homoserine, galacto-, and mevalonate kinases, it is also present in structurally related diphosphomevalonate decarboxylases. Moreover, the protein is grouped in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein should feature a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It originates from Anaeroplasma bactoclasticum and is linked to UniProt keywords Isoprene biosynthesis and Transferase. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 21569, 1920, 45, 17, 4262, 4346, 4594, 1927, 4498, 17, 3100, 5038, 3286, 1922, 3835, 2687, 16, 26690, 1021, 16, 1930, 10590, 4714, 18, 2052, 3418, 24032, 43, 4101, 4595, 17, 4666, 5606, 1932, 3728, 1988, 23230, 1036, 1956, 1920, 56, 17, 4262, 3418, 1942, 7762, 43, 5489, 17, 2743, 10154, 18, 2679, 5985, 2435, 1922, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 16, 2176, 1977, 2222, 2481, 1922, 12171, 2712, 11791, 2609, 2225, 4701, 8870, 23922, 1036, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 22970, 2037, 11381, 15851, 17170, 5406, 4054, 1989, 1930, 1977, 4624, 1942, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MIKIKAYAKINLALEVMEKECGYHRVNNLMIPIDLYDEITLEKDDKIIILNDPFPGENIMEKAAKLFFLKTKIDGGVFITIKKNIPSAAGLAGGSSDAAAILKGLNELYSTNLKKEELIEMSAELGSDVGFFIETKIALCTGRGEIIHPLDIDTPKLNVLIIKQDIGLSTAMIYKNYSYDGNRKEDKINNIIQALSTRNIPMLDLNIFNDLEPVALKVSKVLNDGFNAIKNMGISVHVSGSGPTMFVLNPTMEEILKIKGAAKKDTIILLTNTF", "metadata": {"id": "A0A397RMK8", "cluster": 16997390, "interpro_all": ["IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR036554", "IPR004424", "IPR006204"], "interpro_unused": ["IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "I want to generate an amino acid sequence for a protein. The protein should have the function The protein should include a Thiamine phosphate synthase/TenI domain that functions in thiamine biosynthesis by catalyzing the coupling of pyrimidine pyrophosphate and thiazole phosphate to yield thiamine phosphate. In TenI homologs, this domain acts as a thiazole tautomerase that regulates extracellular enzyme production. Additionally, the protein is categorized in the Thiamin phosphate synthase superfamily, which primarily catalyzes the condensation of pyrimidine and thiazole precursors to yield thiamine phosphate in the thiamine biosynthesis pathway. While most members function as synthases, structurally homologous variants such as the bacterial regulator TenI lack this activity and instead act as thiazole tautomerases involved in controlling extracellular enzyme production. Moreover, the protein is categorized in the Aldolase-type TIM barrel superfamily, which forms a TIM \u03b2/\u03b1 barrel fold that typically covers the entire protein structure. This superfamily includes metabolic enzymes such as class I aldolases, class I DAHP synthases, class II fructose-bisphosphate aldolases, and 5-aminolevulinate dehydratase. It is derived from Methylobacterium sp. Leaf399.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 3066, 3951, 43, 26901, 5413, 8921, 19, 5656, 1033, 3418, 1988, 4088, 1922, 26901, 8132, 2007, 29601, 1920, 7590, 1927, 21611, 24937, 1930, 27225, 2456, 5413, 1942, 4307, 26901, 5413, 18, 1922, 5656, 1033, 14279, 16, 2052, 3418, 8016, 1966, 43, 27225, 2456, 7462, 4575, 9213, 2051, 1988, 7014, 5329, 4113, 3372, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 7566, 3717, 5413, 8921, 13975, 16, 2154, 5985, 17097, 1920, 16112, 1927, 21611, 1930, 27225, 2456, 10416, 1942, 4307, 26901, 5413, 1922, 1920, 26901, 8132, 3374, 18, 2679, 2501, 4678, 2347, 1966, 8921, 1036, 16, 12171, 8725, 4936, 2427, 1966, 1920, 4543, 7888, 5656, 1033, 3630, 2052, 2455, 1930, 5974, 4033, 1966, 27225, 2456, 7462, 4575, 9213, 2319, 3286, 1922, 7138, 5329, 4113, 3372, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 11174, 21524, 17, 2601, 2267, 19560, 13975, 16, 2154, 4952, 43, 2267, 161, 19, 160, 19560, 3728, 1988, 5745, 10272, 1920, 5346, 2213, 3170, 18, 2052, 13975, 5921, 4487, 5038, 2427, 1966, 2921, 51, 11174, 21524, 1036, 16, 2921, 51, 3692, 15870, 8921, 1036, 16, 2921, 2890, 15102, 17, 29443, 11174, 21524, 1036, 16, 1930, 25, 17, 3835, 1952, 1020, 3392, 2010, 11725, 7234, 18, 2176, 1977, 3595, 2037, 4963, 12022, 2056, 18, 6998, 6021, 1026, 18, 3], "output": "MKPLPSPLLVVTDRGPIRSPSDLAPAGARLLATVEAALEGGARWLWFREKDMASGERRRLAVAVMTRVRAFGGTFTLGGEAAAAVEIGADGVHLPGDATQDAIAAARRAMPDGLVGVSGHGVSDIGRAADAGADYATLSPIFLTASKPGYGPALGVDAIRAASGSGLPVIALGGIAPAHVAGCRGAGAAGIAVMGGIMAADDPGSATARYLGAYKG", "metadata": {"id": "A0A0Q5Z1A7", "cluster": 17496029, "interpro_all": ["IPR013785", "IPR036206", "IPR022998"], "interpro_used": ["IPR022998", "IPR036206", "IPR013785"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is included in the FAD-dependent monooxygenase family, which catalyzes hydroxylation, epoxidation, and oxidative decarboxylation reactions essential for the biosynthesis of diverse secondary metabolites and the degradation of environmental toxins. These enzymes modify substrates such as polyketides, indole alkaloids, and flavonoids to produce bioactive compounds ranging from pigments and quorum sensing molecules to antimicrobials. In addition, the protein is assigned to the FAD/NAD(P)-binding domain superfamily, which comprises flavoprotein oxidoreductases, such as glutathione reductase and thioredoxin reductase, that utilize FAD and NAD(P)H cofactors to catalyze electron transfer reactions. These enzymes typically adopt a doubly-wound $\\alpha/\\beta$ fold with nested binding domains to facilitate oxidative metabolism. Moreover, the protein possesses a FAD-binding domain that facilitates the binding of the flavin adenine dinucleotide (FAD) cofactor to support catalytic oxidoreductase activity. This domain functions in diverse enzymes across species, including human kynurenine 3-monooxygenase, archaeal digeranylgeranylglycerophospholipid reductase, and bacterial hydroxylases. It has been characterized in Phialophora macrospora.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 1977, 3063, 1922, 1920, 14134, 17, 3100, 8914, 13966, 3416, 16, 2154, 17097, 21319, 16, 15751, 18068, 3825, 1929, 16, 1930, 5163, 22429, 1943, 5298, 4415, 1958, 1920, 8132, 1927, 6445, 4067, 6926, 1930, 1920, 4877, 1927, 4813, 13599, 18, 2144, 5038, 11675, 6249, 2427, 1966, 4286, 18540, 3726, 16, 18050, 22390, 16, 1930, 16192, 1942, 5074, 13570, 4300, 6485, 2037, 23756, 1930, 28481, 9306, 4206, 1942, 23044, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 14134, 19, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 12936, 7732, 6657, 27388, 1036, 16, 2427, 1966, 9153, 11386, 1930, 23684, 11386, 16, 1988, 12561, 14134, 1930, 6577, 12, 58, 13, 50, 21362, 1942, 18170, 4995, 3856, 5298, 18, 2144, 5038, 5745, 14103, 43, 26783, 17, 6376, 8, 38, 4595, 19, 38, 4666, 8, 3728, 1956, 13735, 2743, 4682, 1942, 6628, 5163, 4714, 18, 3950, 16, 1920, 2213, 14465, 43, 14134, 17, 2743, 3418, 1988, 11374, 1920, 2743, 1927, 1920, 26758, 15643, 21302, 12, 14134, 13, 15155, 1942, 3373, 6804, 27388, 2455, 18, 2052, 3418, 4088, 1922, 6445, 5038, 3436, 3038, 16, 2710, 2616, 23523, 24684, 2053, 23, 17, 8914, 13966, 16, 22367, 4325, 7124, 16323, 1024, 4938, 12804, 14966, 8630, 16113, 11386, 16, 1930, 4543, 16324, 1036, 18, 2176, 2258, 2252, 4378, 1922, 17971, 20807, 2102, 8846, 26967, 21086, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MATSDDRLKVIIAGAGIAGLATAVALSPNGLRTLERLGVKNALDDEVAFRGPSGIPMIYRHWKFHRAHLHQALLEHVPRELIHLGKKVSGAQVNDRFDGINSKVRQAFNPNFELSYTNRTALRATFDVARLGRNQFAVVGMYNPTSLPEAYRDHQNNAINTWNDEGSVEALTEATPNVRRFPNYAGQHIPTWVFGSRVTLVGDAAHAHLFLALQHTIPDWQKSKPSIAQLQTALSLYEETRRPHTDKRQRMLHRASTLWLTEHDVVGTFWGVVAAHAGREGNAVAKSRLALRQLPNVDVELYERSAELREIGASITNEIVSEDHFRNVPNLLHQTARVSLSFEDGTAAVGDLLIGALVEGIPDLPIDSTHWWGLDKTFFASLLRELYKDWNPIVKGGAHATGGSLALDDSYALLYSVLASKDVKPALDDEEL", "metadata": {"id": "A0A0D2FMI9", "cluster": 18676961, "interpro_all": ["IPR002938", "IPR050493", "IPR036188"], "interpro_used": ["IPR050493", "IPR036188", "IPR002938"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence be if I wanted a polypeptide chain capable of the following function: It is part of the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. Moreover, the protein is a member of the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It is present in Opitutia bacterium and is associated with UniProt keywords Transmembrane helix, Magnesium, and ATP-binding.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 1977, 2481, 1922, 7976, 1031, 1984, 2126, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 9117, 7864, 16, 13148, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MQNPEPYGEAMKSKGGLSRIVNALRYTWDGLKAAAKHEEAFKQELILVVPLSVAAWFIPVTLSERALLFSVLQLILIVELINSAIEANTDHISLERHPLAKRAKDMGSAAVFLTIVIALAVWGTILWQKFGA", "metadata": {"id": "A0A388PQM4", "cluster": 20264816, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR033718", "IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "autoregressive"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein is associated with the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Furthermore, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It has been characterized in Geosporobacter subterraneus DSM 17957 and is described by UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 1977, 2458, 1956, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 2258, 2252, 4378, 1922, 14136, 3508, 30232, 7972, 2341, 1915, 13329, 5385, 2516, 1957, 10964, 16182, 5071, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MKIIGLTGGIASGKSTVSNYLEALGFPVIDADLIAREIVEIGQPALEEIALTFGKQVLNEDGGLNRKALGEIVFSSEYLLKKLNRITHPRIINEITNRIELYRIKGKNSILFLDAALLIEMNMRKLVDEVWLVKVDQETQIRRLMNRDGFSVTEAKKRINAQMSMNEKEKYADVILDNNKGMDELYMQIQMQLARVTGNFSEG", "metadata": {"id": "A0A1M6HH83", "cluster": 23231587, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein has a eCIS core domain that functions as a toxic effector within prokaryotic extracellular Contractile Injection Systems (eCIS), which are cell-free delivery structures evolved from bacteriophage tails. This domain contains a conserved HEXXH metallopeptidase motif with a putative zinc-binding site and is responsible for periplasmic toxicity. It is typically associated with a downstream immunity partner that prevents self-intoxication in the producing cell. It has been characterized in Acidobacteriota bacterium.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 2258, 43, 3270, 1937, 4728, 3418, 1988, 4088, 1966, 43, 6161, 7917, 2651, 21545, 5329, 13750, 4107, 3771, 12, 3270, 1937, 13, 16, 2154, 2032, 2024, 17, 3294, 4868, 4061, 10764, 2037, 24613, 18103, 18, 2052, 3418, 5461, 43, 5305, 7142, 1039, 1023, 8969, 24897, 5219, 1956, 43, 6770, 7997, 17, 2743, 3200, 1930, 1977, 5061, 1958, 24334, 5532, 18, 2176, 1977, 5745, 2458, 1956, 43, 5863, 7611, 8240, 1988, 10299, 3543, 17, 20965, 1922, 1920, 7144, 2024, 18, 2176, 2258, 2252, 4378, 1922, 2687, 5883, 3940, 3857, 14061, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MPSPDRTSERSGAEPSRAPPARAAPKAKERGEASRAPAMPPALQSGFGNRYTQDVLAARARSRVPGRPPPAAAPAPGVQRAVAIGSAVPQASISAIAAAPEKKSQQVHRLAADEKAAEQDEARMEQTAARAIDAKDTGEPLPPATRATLEAQGAAAGRSARDLHARAFTHGRDIWLGEGESPTDLGLMAHEATHVVQQNGGVQLAELLDREKGEGAARPPAEVAADDDRLEREAEQVASRVATGQALGTDLGDVRVHR", "metadata": {"id": "A0A2V8IHQ8", "cluster": 23728562, "interpro_all": ["IPR025295"], "interpro_used": ["IPR025295"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence of a protein with the following function look like? Here is the function: The protein is categorized in the Acyl-CoA N-acyltransferase superfamily, which encompasses enzymes featuring a 3-layer $\\alpha/\\beta/\\alpha$ domain that catalyze the transfer of an acyl group, typically from acyl-CoA, to a nitrogen atom on diverse substrates. This versatile fold is utilized by histone acetyltransferases for chromatin regulation, aminoglycoside N-acetyltransferases for antibiotic resistance, and autoinducer synthetases for bacterial quorum sensing. Structural variations, including domain duplications and swapping, allow members like N-myristoyl transferases and non-ribosomal peptidyl transferases to perform specialized modifications such as protein lipidation and cell wall synthesis. Furthermore, the protein should include a GNAT domain that functions as a Gcn5-related N-acetyltransferase, utilizing a conserved structural fold to catalyze the transfer of an acetyl group from acetyl-CoA to primary amines on a diverse array of substrates. This enzymatic activity drives critical biological processes, including chromatin remodeling via histone acetylation, antibiotic resistance through aminoglycoside modification, and the regulation of circadian rhythms. It originates from Streptococcus zalophi and exhibits UniProt keyword tags Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 11337, 17, 10027, 56, 17, 11337, 9961, 13975, 16, 2154, 21569, 5038, 29931, 43, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3418, 1988, 18170, 1920, 3856, 1927, 1925, 11337, 2210, 16, 5745, 2037, 11337, 17, 10027, 16, 1942, 43, 6634, 6761, 1990, 6445, 6249, 18, 2052, 20425, 3728, 1977, 7079, 2007, 6632, 22226, 1036, 1958, 6338, 3640, 16, 23029, 8028, 56, 17, 22226, 1036, 1958, 7267, 3554, 16, 1930, 27485, 4600, 1005, 18185, 1036, 1958, 4543, 28481, 9306, 18, 4346, 6740, 16, 2710, 3418, 20559, 1930, 3476, 5041, 16, 3235, 4678, 3189, 56, 17, 20234, 10921, 13763, 1036, 1930, 2447, 17, 11196, 3431, 2199, 13763, 1036, 1942, 2385, 11021, 6920, 2427, 1966, 2213, 4486, 1943, 1930, 2024, 4821, 4271, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 9005, 1926, 3418, 1988, 4088, 1966, 43, 5469, 19870, 17, 2712, 56, 17, 22226, 16, 10232, 43, 5305, 4346, 3728, 1942, 18170, 1920, 3856, 1927, 1925, 6894, 2210, 2037, 6894, 17, 10027, 1942, 3065, 20739, 1990, 43, 6445, 6472, 1927, 6249, 18, 2052, 8145, 2455, 15435, 4140, 3933, 4028, 16, 2710, 6338, 8378, 3454, 6632, 10339, 16, 7267, 3554, 2596, 23029, 8028, 6295, 16, 1930, 1920, 3640, 1927, 10507, 16622, 18, 2176, 22970, 2037, 15746, 26112, 6012, 24888, 1930, 9826, 20709, 11121, 2538, 14392, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MAEQLIQKKVTLFSKVSKDVKELYLSAFPEVERFPYLPLLLNAYRRDIEFIAYYDDDKFVGLSYIIFSKHFVFLLFLAVNPLHRNQSYGSRLLNTIRSSSKGRPVVLAIEEMDEEADNYQERLNRLAFYEKNGYHLMPHFYYEMGEKYQLLSTSSEIDMGEFKKMLRKISYGIIPIDID", "metadata": {"id": "A0A934P9E2", "cluster": 23775088, "interpro_all": ["IPR016181", "IPR000182"], "interpro_used": ["IPR016181", "IPR000182"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein possesses a Aminopeptidase N-like, N-terminal domain that constitutes the N-terminal $\\beta$-structural component of broad specificity zinc exopeptidases belonging to family M1. It serves as an integral part of the four-domain architecture found in enzymes such as *Escherichia coli* aminopeptidase N. Moreover, the protein contains a Peptidase M1, membrane alanine aminopeptidase domain that functions as a zinc-dependent metallopeptidase responsible for removing single amino acids from the amino terminus of small peptides. This activity facilitates physiological processes including final peptide digestion, antigen trimming for MHC class II molecules, and chemokine processing. Additionally, the domain can exhibit leukotriene-A4 hydrolase activity and serves as a cellular receptor for coronaviruses. Additionally, the protein falls within the Aminopeptidase N-type family, which comprises zinc-dependent M1 metallopeptidases that catalyze the removal of N-terminal amino acids from oligopeptides, often with a preference for neutral residues. These enzymes, including APN and ERAP1, are critical for diverse physiological processes such as antigen presentation, peptide hormone regulation, and the final stages of protein degradation. Additionally, specific members function as cellular receptors for pathogens, including coronaviruses, and binding targets for insect Cry toxins. It is identified in Ignelater luminosus (Cucubano) (Pyrophorus luminosus) and exhibits UniProt keyword tags Glycoprotein, Metalloprotease, and GPI-anchor.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 14465, 43, 3835, 9626, 2410, 9200, 56, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 8, 38, 4666, 8, 17, 4346, 4594, 1927, 4949, 4896, 7997, 18930, 9626, 2410, 30413, 10588, 1942, 3416, 8510, 18, 2176, 10634, 1966, 1925, 12328, 3131, 1927, 1920, 3006, 17, 3418, 9335, 2435, 1922, 5038, 2427, 1966, 14, 10210, 5178, 14, 3835, 9626, 2410, 9200, 56, 18, 3950, 16, 1920, 2213, 5461, 43, 24050, 8510, 16, 3260, 10504, 3835, 9626, 2410, 9200, 3418, 1988, 4088, 1966, 43, 7997, 17, 3100, 8969, 24897, 5061, 1958, 11340, 2957, 3835, 4576, 2037, 1920, 3835, 7822, 1927, 2858, 5320, 18, 2052, 2455, 11374, 5005, 4028, 2710, 3948, 4207, 9379, 16, 4730, 30241, 1958, 8709, 2921, 2890, 4206, 16, 1930, 11673, 4587, 18, 4950, 16, 1920, 3418, 2112, 5987, 26045, 2880, 17, 16440, 20748, 2455, 1930, 10634, 1966, 43, 3689, 3148, 1958, 5548, 26979, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 3835, 9626, 2410, 9200, 56, 17, 2601, 3416, 16, 2154, 12936, 7997, 17, 3100, 8510, 8969, 24897, 1036, 1988, 18170, 1920, 6025, 1927, 56, 17, 4262, 3835, 4576, 2037, 15039, 9626, 2410, 3726, 16, 3868, 1956, 43, 8308, 1958, 5459, 4248, 18, 2144, 5038, 16, 2710, 2100, 1022, 1930, 14821, 5113, 16, 2032, 4140, 1958, 6445, 5005, 4028, 2427, 1966, 4730, 6544, 16, 4207, 6365, 3640, 16, 1930, 1920, 3948, 5143, 1927, 2213, 4877, 18, 4950, 16, 2487, 4678, 2347, 1966, 3689, 4086, 1958, 7741, 16, 2710, 5548, 26979, 16, 1930, 2743, 4845, 1958, 11422, 7443, 13599, 18, 2176, 1977, 2899, 1922, 12046, 15208, 1967, 16410, 13650, 12, 18242, 26605, 11873, 13, 12, 20661, 1924, 1957, 16410, 13650, 13, 1930, 9826, 20709, 11121, 2538, 14392, 11424, 16, 28629, 2051, 16, 1930, 17497, 17, 13333, 18, 3], "output": "MIPRSILLVLVSVVALNMVSSEVYRLPNNIKPIRYYLTFEPQLNLTKPYKYIPYYGSVTMELKILENTRNITFNKKRLEIDESSIKVLNKAGKELKVIATSSNAVEEMYTVQMKRELIKNKTYTLEINNFHNNLSHDGLGFFRAYYRLHNEETGEAESRLLAATHFQPAGARIAFPCFDEPAIKAKFIVSLIRKKGFNSVSNEALESTKDLGDGRFKDTFKETPLMSTYILAFAVSDYEFKSLGKFRILAKSSAIKNNETDFALDTSIKTLKALEEYTGVNFVIDKMDQFAVPDSYFRYYAMENWGLVIYGESHLLRSKTHDSADDYQRTTLMISHEFGHQWFGNLVTPAWWDYMWMSESFAAYFQYHTADVVRFEFTVLTLK", "metadata": {"id": "A0A8K0D2R1", "cluster": 24236616, "interpro_all": ["IPR045357", "IPR042097", "IPR034016", "IPR001930", "IPR050344", "IPR014782", "IPR027268"], "interpro_used": ["IPR045357", "IPR014782", "IPR034016"], "interpro_unused": ["IPR001930", "IPR042097", "IPR027268", "IPR050344"]}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein falls within the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is derived from Sporomusaceae bacterium and has UniProt annotations ATP-binding, Cytoplasm, and Transferase. Can you generate the amino acid sequence corresponding to this protein?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 12182, 2651, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 3595, 2037, 9130, 1947, 28553, 1972, 3336, 14061, 1930, 2258, 20709, 15010, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "MYTIGLTGGISSGKSTVSAMLEQLGAAIIDTDIIARKIVEPGQPAWQEIVAAFGKSCLFPDGHINRKLLGEIIFTDDHKRRVLDKITHPHIQNTARQALQAAAQQGIKTAVLDAPLLIEVGWQHMVQAVWVVYVDEETQIERLMRRDRLDRSQALARIHSQMSLREKLLFATVVIDNSGNLETTQKQVFAAWQCLAANQ", "metadata": {"id": "A0A3C0UGL6", "cluster": 627610, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein has a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. It is found in Verrucomicrobiota bacterium and is associated with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 2258, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2176, 1977, 2435, 1922, 3566, 3176, 13055, 1935, 15129, 3940, 3857, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MINRRLISFEGPEGSGKSEMGEQVISVREPGGTHLGESIRQSLVNEIILPALHEGKWVLCDRFIDSSVAYYATQGLFPSLTVLLELNIRGEKDRIESESLDFHQRVIDGYRMDNIFQWIIKLGSTQIKYLSDKLILQAKDPAGLSNTAELLLFMSSRAQQGYGRGGDIDLIERLNCTCFERLTRRYSEINLSTTENRFKSMDGSQDPDVIA", "metadata": {"id": "A0A356I7W3", "cluster": 1712004, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR027417", "IPR018095"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that has the following function: The protein is included in the DUF4831 family, which comprises uncharacterised proteins of approximately 350 residues primarily found in various *Bacteroides* species. It is derived from Breznakibacter xylanolyticus and is classified with UniProt keywords Signal. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 4855, 10432, 11368, 1009, 3416, 16, 2154, 12936, 23229, 3495, 2697, 1927, 3993, 11936, 4248, 5985, 2435, 1922, 3425, 14, 27978, 14, 3038, 18, 2176, 1977, 3595, 2037, 3022, 29798, 12588, 7972, 2341, 1915, 23665, 29370, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MKHILLPAAVASLMTISCSTARQAAVKVSVTPTSSMSNATDNVVVYHLPQTVLRVEVEMDKVIRKAGPYFRYTERLLNISNVILEDSESWRIRSIKVVPVGRADDNQAYAIAMDGPGVAQNVTLNNQGVLCGINLSTPCMDVPAASYVYTHEMQKTDVTFDAVPRLEKLLKQTSTAAMAEEAANYIYKIRKRRSKIFSANFPILPPDGLSLELTKAELDTLETQFMELFTGKETVQTIKRVIEYIPTRTNPDNMVLFRFSANAGMVDPMDLSGAPVYLEVKHKNIPELPHAEAKKETKSNGLYHIKPGKATVRIVDRSTLMLEEEMDIAQFGQVMSMPAAVLEQPNVSIELSPVTGALKRVNTSK", "metadata": {"id": "A0A2W7MUH9", "cluster": 4490506, "interpro_all": ["IPR032265"], "interpro_used": ["IPR032265"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the protein function: The protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, it is part of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is found in Lujinxingia litoralis and corresponds to UniProt keyword ATP-binding, Cytoplasm, and Transferase. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2435, 1922, 10908, 28298, 10960, 11966, 4471, 6277, 1937, 1930, 8852, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MSTNSPGVVLGLTGGIASGKSTVSHYFRALGVTVIDADLIARKIVEPGQPALSEIVETFGEDVLHRDGTLNRTSLGERIFQDADARARLGTITHPRIAQEMARQSAAAFERGEPWVLYDAALIVENGLYRAFDALIVVACSPQTQLQRLMSRDDLSRTDAQRRIDAQMPLADKLKVADFVIDNDQSLDHTQAQVEELFSTINERVRTGGSARTPA", "metadata": {"id": "A0A328CCP9", "cluster": 4705539, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is associated with the Isonitrile Hydratase and Quaternary Amine Regulator family, which encompasses enzymes that hydrate isonitriles to formamides for detoxification and transcriptional regulators that control quaternary amine metabolism. The regulatory members activate genes for the transport and catabolism of substrates like choline and carnitine, playing a key role in bacterial interactions with eukaryotes. Also, the protein is grouped in the Class I glutamine amidotransferase-like superfamily, which catalyzes the removal of ammonia from glutamine and its subsequent transfer to a substrate to form a new carbon-nitrogen bond. This domain typically employs a conserved Cys-His-Glu catalytic triad with the active site cysteine located at the tip of a nucleophile elbow, and can exist as a standalone subunit or fused to a synthase domain. In addition, the protein carries a DJ-1/PfpI domain that functions as a versatile catalytic or regulatory module within the DJ-1/ThiJ/PfpI superfamily. It exhibits diverse enzymatic activities, including cysteine peptidase, aminopeptidase, and glyoxalase functions, depending on the specific protein context. Additionally, this domain can act as a transcriptional regulator when associated with DNA-binding motifs such as the helix-turn-helix domain. It originates from Cadophora sp. MPI-SDFR-AT-0126.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 4911, 8635, 1997, 2383, 22420, 3857, 4127, 1930, 21920, 13610, 7888, 3416, 16, 2154, 21569, 5038, 1988, 27864, 4911, 8635, 1997, 14464, 1942, 2386, 20381, 1958, 18169, 1930, 5224, 9098, 1988, 2285, 21920, 13610, 4714, 18, 1920, 4948, 4678, 6980, 2628, 1958, 1920, 4860, 1930, 19480, 1927, 6249, 3189, 15440, 1930, 21118, 16, 14797, 43, 3834, 2770, 1922, 4543, 3719, 1956, 15021, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2921, 51, 9959, 28813, 14165, 17, 3189, 13975, 16, 2154, 17097, 1920, 6025, 1927, 14880, 2037, 9959, 1930, 2496, 4521, 3856, 1942, 43, 4510, 1942, 2386, 43, 2814, 5056, 17, 6634, 5403, 18, 2052, 3418, 5745, 22620, 43, 5305, 4998, 17, 4167, 17, 9258, 6804, 21845, 1956, 1920, 3500, 3200, 8666, 4810, 2019, 1920, 7933, 1927, 43, 2797, 28335, 17621, 16, 1930, 2112, 5516, 1966, 43, 2924, 20807, 2912, 5903, 2014, 10305, 1942, 43, 8921, 3418, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 17224, 17, 21, 19, 5099, 10984, 3418, 1988, 4088, 1966, 43, 20425, 6804, 2014, 4948, 9059, 2651, 1920, 17224, 17, 21, 19, 7566, 1013, 19, 5099, 10984, 13975, 18, 2176, 9826, 6445, 8145, 4209, 16, 2710, 8666, 24050, 16, 3835, 9626, 2410, 9200, 16, 1930, 3376, 23859, 2051, 4088, 16, 6362, 1990, 1920, 2487, 2213, 4491, 18, 4950, 16, 2052, 3418, 2112, 4033, 1966, 43, 5224, 7888, 2469, 2458, 1956, 2678, 17, 2743, 8277, 2427, 1966, 1920, 7864, 17, 5165, 17, 7864, 3418, 18, 2176, 22970, 2037, 5643, 22575, 1019, 2056, 18, 26586, 17, 18876, 1005, 17, 2019, 17, 14632, 1016, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MAFSPRALSKSHPHPLKEVLSQANRNNPDPSNPSNTSPIFTLTLAADRPLVEEWDIVLLPGGVRDVILGVIEGHEKGKCTGSLFLAAVGGLDGRTVWVDSKEERLPRLISAGGVACGIMDYQRRGEELQEDYVIPEGKVLIPLFPSFNTFDANGPITRSIEGVSIERDISLIDALARERSVLMELLEGYKAVRDGLMLTVTSHWAALGTVKNLCERNGSKTKVVRARDATFYLVELIAGAELAEKAATV", "metadata": {"id": "A0A9P9QET9", "cluster": 5334185, "interpro_all": ["IPR029062", "IPR002818", "IPR052158"], "interpro_used": ["IPR052158", "IPR029062", "IPR002818"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein can be placed in the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Furthermore, the protein falls within the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein possesses a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. It is derived from Marinobacter nauticus (Marinobacter hydrocarbonoclasticus) (Marinobacter aquaeolei) and corresponds to UniProt keyword ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 14465, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 2176, 1977, 3595, 2037, 13081, 11873, 7972, 2341, 1915, 4049, 1984, 24375, 12, 13081, 11873, 7972, 2341, 1915, 21638, 5406, 4054, 1957, 13, 12, 13081, 11873, 7972, 2341, 1915, 10059, 3336, 2456, 1033, 13, 1930, 8852, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MILARGRFITFEGTEGVGKSTTPMAESIRELLLAPREESVHETTELLGKWVLCDRFTDATFAYQGGGRGVARMARARKRGELDRFEREAQAFFQRIRETYSVSALLTALAKLPVSDQLDNAAKTLERLGIDYIVTREPGGLMFAARAQHLHNRILPALSAERIALLEALVQGEVRPDHVILLDAPVETGLERATEMPGRYHVVNAALPLEQVSE", "metadata": {"id": "A0A833JQ71", "cluster": 6910163, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR018094", "IPR027417", "IPR039430"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is classified under the NagB/RpiA transferase-like superfamily, which comprises enzymes sharing a common $\\alpha/\\beta$ structural core, including ribose-5-phosphate isomerase A (RpiA), glucosamine-6-phosphate deaminase (NagB), and 6-phosphogluconolactonase (6PGL). These proteins facilitate critical steps in metabolic processes such as the pentose phosphate pathway and N-acetylneuraminate degradation. Additionally, the protein is included in the Coenzyme A transferase family I family, which catalyzes the reversible transfer of coenzyme A from donors such as succinyl-CoA or acetyl-CoA to substrates including 3-oxoacids, short-chain fatty acids, and glutaconate. These enzymes are conserved across all kingdoms, functioning as heterodimers in prokaryotes and single-chain proteins in eukaryotes. It originates from Chthoniobacterales bacterium.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 1920, 14466, 1014, 19, 4822, 2126, 13763, 17, 3189, 13975, 16, 2154, 12936, 5038, 10763, 43, 3059, 8, 38, 4595, 19, 38, 4666, 8, 4346, 4728, 16, 2710, 17870, 17, 25, 17, 5413, 25510, 43, 12, 4822, 2126, 13, 16, 28627, 17, 26, 17, 5413, 27955, 12, 14466, 1014, 13, 16, 1930, 26, 17, 8078, 22988, 23557, 5148, 2341, 9259, 1021, 12, 26, 15209, 1024, 13, 18, 2144, 2697, 6628, 4140, 5983, 1922, 4487, 4028, 2427, 1966, 1920, 9412, 2217, 5413, 3374, 1930, 56, 17, 6894, 2912, 9280, 8547, 2010, 4877, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 22051, 43, 13763, 3416, 51, 3416, 16, 2154, 17097, 1920, 10743, 3856, 1927, 22051, 43, 2037, 8276, 2427, 1966, 13791, 2199, 17, 10027, 2014, 6894, 17, 10027, 1942, 6249, 2710, 23, 17, 18588, 29272, 1036, 16, 3662, 17, 4659, 5934, 4576, 16, 1930, 4354, 26704, 2010, 18, 2144, 5038, 2032, 5305, 3436, 2136, 13543, 1036, 16, 7295, 1966, 21523, 1922, 28149, 1930, 2957, 17, 4659, 2697, 1922, 15021, 18, 2176, 22970, 2037, 2016, 1963, 13339, 5883, 3955, 14061, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MTKVYSDAGFGLCGIPELQREPTAALDSLLHDNMTIVANLLAALRDSGVKGLTV", "metadata": {"id": "A0A7W1SAA5", "cluster": 7970447, "interpro_all": ["IPR004165", "IPR037171"], "interpro_used": ["IPR037171", "IPR004165"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is associated with the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein possesses a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein should feature a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It originates from Ignavibacteria bacterium and exhibits UniProt keyword tags Isoprene biosynthesis and Transferase. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 22970, 2037, 12046, 9188, 7972, 2341, 18339, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 26690, 1021, 8132, 1930, 13763, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MKAKSVAKINIGLQVLKRREDGFHNINSVFFPLENLFDEMEFEKSSETSIKIEPNNISIDLHNNLIYKAVAELKDFTKRDDIFVKVQLKKRIPIGAGLGGGSSNAASTLLSLNELFNLDLSKQQLKEIALKIGSDVPFFLEGKTALASGRGEQLQFFEYKPSYSIRLYDTKINISTKWAYEQLKRDSIAIEKVDFKSILLESENNRAILKEKLFNDFEEIVFNKQPELAEIKENAYKEGAIYAQMTGSGSSIFAFFDDGKKEFSLIG", "metadata": {"id": "A0A970PUP7", "cluster": 13296634, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "The protein is a member of the Type III secretion system substrate exporter family, which mediates the translocation of virulence factors or flagellar components across the inner and outer membranes of proteobacteria such as *Salmonella*. This system functions as part of a needle-like apparatus to inject effector proteins directly into host cells upon contact. It originates from Marinomonas arctica and exhibits UniProt keyword tags Bacterial flagellum protein export, Protein transport, and Transport. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2601, 4337, 5512, 2433, 4510, 12660, 1915, 3416, 16, 2154, 10412, 1920, 7849, 1927, 9304, 2790, 2014, 24154, 4178, 3436, 1920, 6671, 1930, 7642, 5726, 1927, 22266, 2427, 1966, 14, 11681, 14, 18, 2052, 2433, 4088, 1966, 3131, 1927, 43, 9351, 17, 3189, 11161, 1942, 27270, 7917, 2697, 4103, 2460, 4423, 2094, 4073, 5217, 18, 2176, 22970, 2037, 13081, 11873, 3947, 1934, 23937, 1019, 1930, 9826, 20709, 11121, 2538, 14392, 4543, 7030, 10757, 2213, 12660, 16, 2213, 4860, 16, 1930, 4860, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MQKAVALKYDFSAAPTVVAKGNGLLAEKIMAVAKENDVLLHQSPELVELLSTLELGEEIPESLYLAVAEVIAFAHKIRDHQW", "metadata": {"id": "A0A7H1J3A7", "cluster": 19873659, "interpro_all": ["IPR006135", "IPR029025"], "interpro_used": ["IPR006135"], "interpro_unused": ["IPR029025"]}, "task_type": "autoregressive"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein incorporates a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. It originates from Alteriqipengyuania halimionae and is described by UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2176, 22970, 2037, 4238, 22570, 25535, 2029, 1012, 13785, 2126, 4217, 1980, 2001, 3336, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSGRFITFEGGEGVGKSTQAKLLVAALQEQGISCTLTREPGGTEGAEAIRNLLLDGDGFGARAEALLFAAARADHVDRLIRPALERGEWVVCDRFLDSSRAYQGGAGDLGDEAVLRLHEIGSAGLLPDRTLLFTLPSAEAEARLDARDGGISDAIGSRGRDYHAAVASNFARLADEDSTRFATIDASGTPGEVHARVLAALKDLIEADGVC", "metadata": {"id": "A0A6I4U5F9", "cluster": 21645095, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR027417", "IPR018095"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "autoregressive"} {"instruction": "The protein incorporates a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is expressed in Verrucomicrobiota bacterium and has UniProt annotations Transferase. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 3198, 1922, 3566, 3176, 13055, 1935, 15129, 3940, 3857, 14061, 1930, 2258, 20709, 15010, 13763, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "QLKMWQLEQPEVGAALISGSGSTVFAMMRESADARQLAKRAKAALDPELWTCACETL", "metadata": {"id": "A0A2V6J8A6", "cluster": 22519620, "interpro_all": ["IPR013750", "IPR036554"], "interpro_used": ["IPR013750"], "interpro_unused": ["IPR036554"]}, "task_type": "autoregressive"} {"instruction": "I'm looking for a protein that can perform the following function: The protein includes a SGNH hydrolase-type esterase domain that functions as a hydrolase with esterase or lipase activity, utilizing a Ser/Acid/His catalytic triad stabilized by a unique hydrogen bond network. This domain adopts a three-layer $\\alpha/\\beta/\\alpha$ fold and is found in diverse proteins, ranging from viral haemagglutinin-esterase surface glycoproteins to mammalian acetyl hydrolases and bacterial thioesterases. It is produced by Cytophaga sp. Give the amino acid chain.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 10075, 21677, 20748, 17, 2601, 26389, 3418, 1988, 4088, 1966, 43, 20748, 1956, 26389, 2014, 16653, 2455, 16, 10232, 43, 2375, 19, 2687, 19, 4167, 6804, 21845, 12017, 2007, 43, 5008, 6201, 5403, 3504, 18, 2052, 3418, 24032, 43, 2559, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 1930, 1977, 2435, 1922, 6445, 2697, 16, 6485, 2037, 4324, 7105, 17003, 1921, 17, 26389, 3154, 16268, 1942, 6492, 6894, 30337, 1930, 4543, 30215, 2319, 18, 2176, 1977, 4152, 2007, 22953, 4151, 4223, 2056, 18, 7031, 1920, 3835, 2687, 4659, 18, 3], "output": "SLGTNEAFSIGFDKVLFTRNIDTLITKIKLASPNASILLTTPADSFRKTRKGRVKNPDMQQARIAIINYCMQNNLPYWDLYEIMGGYGSMGKWFVAQLSSKDRVHFNGKGYKIQGDLFYQALMNGFGKYTMLK", "metadata": {"id": "A0A923WNC6", "cluster": 22939432, "interpro_all": ["IPR013830", "IPR036514"], "interpro_used": ["IPR013830"], "interpro_unused": ["IPR036514"]}, "task_type": "autoregressive"} {"instruction": "Target Function: The protein is associated with the Putative membrane protein FidL-like family, which comprises bacterial proteins predicted to function as integral membrane components. It occurs in Jejubacter calystegiae.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 6770, 3260, 2213, 22394, 1024, 17, 3189, 3416, 16, 2154, 12936, 4543, 2697, 4396, 1942, 2347, 1966, 12328, 3260, 4178, 18, 2176, 5110, 1922, 8988, 13267, 7972, 2341, 1915, 2570, 2298, 6541, 7955, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MKRTIALLLILMALAASCEVNLNYSDSTEGDPYHFYGNLVYIFSRYVNFSYLNENNNRYRMAINKGVYVYMERHRDGYILLGNMVSPVMTCVILSFAWLSLNHGRGYYQSSFDFETNRTGQLYLSGSARSADQDVNKIGHDSAPDEVAQKIYRVIGLVG", "metadata": {"id": "A0A4P8YKW1", "cluster": 24302951, "interpro_all": ["IPR031854"], "interpro_used": ["IPR031854"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein contains a Zinc finger C2H2-type domain that functions as a classical DNA-binding motif, typically found in eukaryotic transcription factors where it interacts with the DNA major groove using a conserved $\\beta/\\beta/\\alpha$ fold coordinated by a zinc ion. These domains frequently appear in tandem arrays to facilitate specific recognition of nucleic acids, proteins, or lipids, acting as stable scaffolds for diverse biological activities ranging from gene transcription to chromatin remodeling. Furthermore, the protein is categorized in the Zinc finger C2H2 superfamily, which comprises stable, zinc-coordinated $\\beta/\\beta/\\alpha$ motifs that primarily function as DNA-binding domains in eukaryotic transcription factors. These versatile scaffolds typically interact with the DNA major groove in tandem clusters, but can also be adapted to bind RNA, proteins, or lipids to regulate diverse cellular processes. It is native to Synchytrium microbalum and features UniProt keywords Metal-binding, Repeat, and Zinc-finger.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 5461, 43, 7997, 8497, 8453, 6951, 17, 2601, 3418, 1988, 4088, 1966, 43, 8445, 2678, 17, 2743, 5219, 16, 5745, 2435, 1922, 10825, 3213, 2790, 2597, 2176, 9034, 1956, 1920, 2678, 3044, 15920, 2193, 43, 5305, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 3728, 11651, 2007, 43, 7997, 4755, 18, 2144, 4682, 5467, 3267, 1922, 10361, 10517, 1942, 6628, 2487, 5708, 1927, 11079, 4576, 16, 2697, 16, 2014, 8238, 16, 8290, 1966, 4700, 10603, 1958, 6445, 3933, 4209, 6485, 2037, 2359, 3213, 1942, 6338, 8378, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 7997, 8497, 8453, 6951, 13975, 16, 2154, 12936, 4700, 16, 7997, 17, 11651, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 8277, 1988, 5985, 2347, 1966, 2678, 17, 2743, 4682, 1922, 10825, 3213, 2790, 18, 2144, 20425, 10603, 5745, 6310, 1956, 1920, 2678, 3044, 15920, 1922, 10361, 5859, 16, 2308, 2112, 2222, 1998, 8461, 1942, 4566, 3146, 16, 2697, 16, 2014, 8238, 1942, 5741, 6445, 3689, 4028, 18, 2176, 1977, 6196, 1942, 25054, 2355, 3027, 1989, 11565, 2700, 1035, 1930, 4075, 20709, 11569, 6048, 17, 2743, 16, 6865, 16, 1930, 7997, 17, 8497, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MTSSIEDSLNPRRRMITSSSNIDLLQSRWYADQMHYTLPPLYNLIGHRQHNIYTEEFKSSLSDAIPGMLTALNEEDAYPGWPMQAQPACYHNLPPHMDMYYHHSHMPTTMQHDTPPYTASSAPTTVVNNYNTDVYDGQEYVYEIYGNETSNDTVKPSESILLAAIMAKNPAPPSPPTIDTQLLTVKVEYGNNEQVTAKNKDVESADEVLSDVLSDSDTDDAAEQDTEYAEDNEDGDASEYDPSGNGRVEIESDSDDYLENYKHRNYSRKSSTDKKRLYPCQLPGCTKTFTRRYNLASHIRCHSSVHARARTHSCPYCPLSFTRSDALKRHLDIEFKRRNKVEKMEKEQVAFEHYPAAEYTPPRPRPTQTPWNLLDAAIEAGEDVQQVSKPALKTPAPTKPVDEDPESDYDASPPPSRRRGRGGRPFCCKDCPATFSRTHDLRRHIK", "metadata": {"id": "A0A507BKN2", "cluster": 27957206, "interpro_all": ["IPR036236", "IPR013087"], "interpro_used": ["IPR013087", "IPR036236"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein possesses a Zinc finger, PARP-type domain that functions as a zinc-dependent DNA nick sensor by specifically recognizing single-stranded DNA breaks. It is primarily found in the N-terminus of poly(ADP-ribose) polymerases (PARPs) and DNA ligase III, where it plays a critical role in detecting DNA damage and initiating repair pathways. It is found in Neodrepanis coruscans (wattled asity) and features UniProt keywords Metal-binding, Nucleus, and Zinc-finger.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 7997, 8497, 16, 12007, 17, 2601, 3418, 1988, 4088, 1966, 43, 7997, 17, 3100, 2678, 12657, 6443, 2007, 4475, 15667, 2957, 17, 10338, 2678, 13065, 18, 2176, 1977, 5985, 2435, 1922, 1920, 56, 17, 7822, 1927, 4286, 12, 9828, 17, 17870, 13, 20910, 12, 12007, 1036, 13, 1930, 2678, 11905, 4337, 16, 2597, 2176, 5705, 43, 4140, 2770, 1922, 9227, 2678, 4293, 1930, 12410, 5059, 3873, 18, 2176, 1977, 2435, 1922, 11724, 3883, 2128, 8150, 1036, 2233, 7801, 2075, 12, 9071, 4131, 1007, 25872, 3145, 13, 1930, 4075, 20709, 11569, 6048, 17, 2743, 16, 5607, 16, 1930, 7997, 17, 8497, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "SPMFDGKVPHWHHYSCFWKRARIVSHTDIDGFPELRWEDQKSLNDFAAEYAKSNRSTCKGCEQKIEKEKIKKAIETGGPGGGGEQEGGGKAE", "metadata": {"id": "A0A7L2RLE0", "cluster": 28403986, "interpro_all": ["IPR001510", "IPR036957"], "interpro_used": ["IPR001510"], "interpro_unused": ["IPR036957"]}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein features a GTP binding domain that contains five conserved structural motifs to bind guanosine triphosphate (GTP). It is present in a diverse array of proteins, such as the developmentally regulated DRG, the essential bacterial OBG, and ferrous iron transport protein B, indicating a broad role in cellular regulation and transport. Furthermore, the protein should have a TrmE-type guanine nucleotide-binding domain that functions as a P-loop GTPase molecular switch to facilitate tRNA modification. It adopts a canonical Ras-like fold that dimerizes in a potassium-dependent manner and utilizes conformational changes driven by GTP hydrolysis to modify uridine bases at the tRNA wobble position. In addition, the protein should contain a Small GTP-binding domain that functions as a molecular switch by binding and hydrolyzing GTP to regulate diverse cellular processes, including signal transduction, vesicle transport, and protein biosynthesis. It is found in the Ras superfamily of small GTPases as well as within larger proteins such as translation elongation factors. It is produced by Candidatus Calescamantes bacterium and is linked to UniProt keywords Cytoplasm, Metal-binding, and tRNA processing.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 4075, 43, 9319, 2743, 3418, 1988, 5461, 3628, 5305, 4346, 8277, 1942, 4566, 24870, 17978, 12, 9319, 13, 18, 2176, 1977, 2481, 1922, 43, 6445, 6472, 1927, 2697, 16, 2427, 1966, 1920, 23130, 4335, 14801, 16, 1920, 4415, 4543, 2384, 1029, 16, 1930, 26739, 5680, 4860, 2213, 44, 16, 4168, 43, 4949, 2770, 1922, 3689, 3640, 1930, 4860, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 28402, 1021, 17, 2601, 16904, 5489, 17, 2743, 3418, 1988, 4088, 1966, 43, 58, 17, 5881, 14809, 3272, 6195, 1942, 6628, 10089, 6295, 18, 2176, 24032, 43, 9452, 6520, 17, 3189, 3728, 1988, 7632, 4517, 1922, 43, 9057, 17, 3100, 5222, 1930, 18127, 8523, 2840, 6446, 2007, 9319, 9128, 1942, 11675, 26104, 11137, 2019, 1920, 10089, 26334, 6936, 1952, 3507, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 2858, 9319, 17, 2743, 3418, 1988, 4088, 1966, 43, 3272, 6195, 2007, 2743, 1930, 7222, 9046, 9319, 1942, 5741, 6445, 3689, 4028, 16, 2710, 2733, 8201, 16, 11502, 4860, 16, 1930, 2213, 8132, 18, 2176, 1977, 2435, 1922, 1920, 6520, 13975, 1927, 2858, 18390, 1966, 2486, 1966, 2651, 4327, 2697, 2427, 1966, 6410, 9971, 2790, 18, 2176, 1977, 4152, 2007, 14550, 1031, 1957, 2570, 1918, 15024, 21861, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 16, 6048, 17, 2743, 16, 1930, 10089, 4587, 18, 3], "output": "MNDTIVSHATPLFPSAIGVVRLSGPRVKEIITKLTRKNNFRRRYAHLVEIYDDDGKNIDECILIFYEKPSSYTGEDMAEIFLHGNPVIINHVVSLCIKNGARMAREGEFTKRAFLNGKITLERAESILSIVNSSTIDGVKASIRILKGEFQDVVERIRLKIVDILSDLEASLDFPEDVDMEITKEKIQQNIYEALEEIQKIYLSWKNSRMMVDGAMCTIIGKPNAGKSSLFNLLVGESRSIISPFPGTTRDYIDTRIDVGGGVLIRLIDTAGVRQTPDPIEQEGIKRAIEISSESDIILCVFDSSSEFDEDDKKSVEVSLSSKAQLVIFIINKSDKGDVSRYERIIENFKTEDKETKTLSVSCLKNENIDKVREEIKDFVVKGKDHDFFALSARQIGLLSLIIDKLKNALEFISNSDYLGSVLCIREALTSIDDLLGRGSSPEVIENIFKKFCIGK", "metadata": {"id": "A0A7C5RX73", "cluster": 27159107, "interpro_all": ["IPR031168", "IPR006073", "IPR018948", "IPR004520", "IPR027368", "IPR025867", "IPR027417", "IPR005225", "IPR027266"], "interpro_used": ["IPR006073", "IPR031168", "IPR005225"], "interpro_unused": ["IPR027368", "IPR004520", "IPR027417", "IPR018948", "IPR027266", "IPR025867"]}, "task_type": "autoregressive"} {"instruction": "I am designing a protein with the following function: The protein should contain a MgtE intracellular domain that forms the $\\alpha$-helical N-terminal region of eubacterial magnesium transporters. This domain acts as a regulatory sensor by binding magnesium ions at the interface with downstream CBS domains, undergoing a significant conformational shift in the absence of magnesium to modulate transport activity. Additionally, the protein should include a CBS domain that functions as a regulatory sensor for adenosyl-containing ligands such as AMP, ATP, and S-AdoMet. These domains typically pair to form intramolecular structures known as Bateman domains, making the protein sensitive to cellular energy status or metabolite levels. Furthermore, the protein has a PRC-barrel domain that adopts an all $\\beta$-barrel fold and serves as a versatile regulatory module in processes ranging from photosynthesis to RNA metabolism. It is essential for RimM-mediated 16S rRNA processing and ribosomal maturation in bacteria, while stand-alone forms facilitate FtsZ-based cell division in archaea. It occurs in Pseudoclavibacter sp. 8L. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 2786, 2057, 4776, 3418, 1988, 4952, 1920, 8, 38, 4595, 8, 17, 11514, 56, 17, 4262, 3031, 1927, 4791, 7972, 2341, 18339, 1024, 13148, 10538, 18, 2052, 3418, 8016, 1966, 43, 4948, 6443, 2007, 2743, 13148, 6982, 2019, 1920, 6854, 1956, 5863, 16341, 4682, 16, 7258, 43, 2228, 8523, 5950, 1922, 1920, 3905, 1927, 13148, 1942, 8480, 4860, 2455, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 16341, 3418, 1988, 4088, 1966, 43, 4948, 6443, 1958, 29283, 17, 3165, 6908, 2427, 1966, 3681, 16, 4498, 16, 1930, 61, 17, 2041, 14080, 18, 2144, 4682, 5745, 3715, 1942, 2386, 18083, 4061, 3171, 1966, 11579, 17119, 4682, 16, 5399, 1920, 2213, 4532, 1942, 3689, 3844, 3642, 2014, 9483, 2428, 18, 3677, 16, 1920, 2213, 2258, 43, 29134, 17, 19560, 3418, 1988, 24032, 1925, 2136, 8, 38, 4666, 8, 17, 19560, 3728, 1930, 10634, 1966, 43, 20425, 4948, 9059, 1922, 4028, 6485, 2037, 18133, 1942, 3146, 4714, 18, 2176, 1977, 4415, 1958, 14764, 1035, 17, 3434, 11209, 9067, 4587, 1930, 11196, 7655, 1922, 4802, 16, 2679, 2924, 17, 4298, 4952, 6628, 27497, 17, 2454, 2024, 8451, 1922, 21501, 18, 2176, 5110, 1922, 11520, 2223, 9188, 7972, 2341, 1915, 2056, 18, 28, 1024, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MFAVGWRVARGDYHWPVSVSKVFTARLSACPVFDEDGDRIGKVRDVIVEYRAAHSPRVNGLVVETKSKRLIFIPIRQVESIGSGQIVVSGEIDSRPFVQHGQEVRVLADLADRAVTFNDGTASGTIEDVQIEEDAQGNWSVGQLFVRLPRKSKQLFGTGPTRFAPWGEVTPELTIGEQQAATQFLTAHSDMKPSDFATALLDLPDARLKEVVSMLPDERLADVLEEMRESDQVTIIEWLDEEHAADVLDRMQPDDAADLVAKLDAVKSEALLQRMDPEEAEEVRMLLEFAPDTAGGLMTTDPVILPGDATVAEALVLIRRKDLPAALATSVFVTLSPYEPPTGRYLGLVHFQRLLRYPPHERLDTILDREMEPAPTTMRDAEVARVLASYDLVALPVIDDAHRLVGVVTIDDVLDHLLPEDWRQVDAEGEVVPSRVSQRVGTKRVVTAPANSPAARRTHGTS", "metadata": {"id": "A0A653QQ17", "cluster": 236539, "interpro_all": ["IPR000644", "IPR046342", "IPR006668", "IPR038076", "IPR006669", "IPR027275", "IPR011033"], "interpro_used": ["IPR006668", "IPR000644", "IPR027275"], "interpro_unused": ["IPR046342", "IPR006669", "IPR038076", "IPR011033"]}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein includes a PAN/Apple domain that functions as a protein-protein interaction module, mediating binding to partners such as high molecular weight kininogen, Factor XIIa, platelets, and heparin. This cysteine-rich domain typically adopts a characteristic fold stabilized by disulfide bonds and is often found in the N-terminal region of plasma serine proteases. It has been detected in Phytophthora fragariae and is classified with UniProt keywords Signal.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 3797, 19, 19663, 3418, 1988, 4088, 1966, 43, 2213, 17, 2213, 2835, 9059, 16, 10239, 2743, 1942, 7228, 2427, 1966, 2149, 3272, 3388, 3498, 3522, 2432, 16, 2991, 11551, 2126, 16, 10097, 16, 1930, 9962, 18, 2052, 8666, 17, 5536, 3418, 5745, 24032, 43, 6293, 3728, 12017, 2007, 11830, 9031, 1930, 1977, 3868, 2435, 1922, 1920, 56, 17, 4262, 3031, 1927, 3582, 8468, 12447, 18, 2176, 2258, 2252, 3330, 1922, 25512, 2102, 1963, 8846, 4145, 6148, 1021, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 3], "output": "MLSAKLLFVCVGLLGAAEYSGAAVGRVPSSSANGCCSIKSGEGSSKENLGAISGVLKAVSEAATCSTLQQDVCAKVNGCNAFTWTNDNRGTCWL", "metadata": {"id": "A0A6A3IVN6", "cluster": 4018880, "interpro_all": ["IPR000177", "IPR003609"], "interpro_used": ["IPR003609"], "interpro_unused": ["IPR000177"]}, "task_type": "infilling"} {"instruction": "I want to make a protein that can have this function: The protein is classified under the 5-bromo-4-chloroindolyl phosphate hydrolysis protein family, which consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds. It is produced by Clostridiales bacterium and is associated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 25, 17, 21392, 17, 24, 17, 10107, 2762, 26558, 1024, 5413, 9128, 2213, 3416, 16, 2154, 7543, 1927, 21545, 2697, 1988, 8265, 1920, 9128, 1927, 25, 17, 21392, 17, 24, 17, 10107, 2762, 26558, 1024, 5413, 9031, 18, 2176, 1977, 4152, 2007, 17938, 26890, 1918, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MATNNSGNTNPKNTTYNYTPPSGSRSSKKNDQKGDIPWWLIIVLLFSWTPAGFMLLFAKLFLMLKNGQLNSVSAKAKTASSHTGTKHAFGTNAADKTAKVKTPGKALGIFLKVFGGILIGSGIIALFTAIDSLLYWGWDSYVASEFLDAALVGLGGIVSFIAGQNNTRRANKFRKYTAVIGDRDSMLIRNIAAAIPTSYKKACKDLQRLIDQGAFGPDAYLDMYTHNFMRSASAVPEEDPIVAKRKAAGYAPQPSAAAAAGAAPAVSLSESDAVIAEIRRLNDEIDDEDVSRRIDRIEKISADIFRLVEKDPAKRSQAKSFLDYYLPTTLKLLGAYSQFEDQAASGENIRAAKENIENILDTLVKGFEQQLDRLFEADAMDISGDIRVLEQMMARDGLTEQKHTIRVPANQPAANQKAAAATAATYAAAGAAAAVQEKQE", "metadata": {"id": "A0A927ZIF4", "cluster": 5133174, "interpro_all": ["IPR018770"], "interpro_used": ["IPR018770"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is included in the Plastid division protein CDP1-like family, which serves as a core component of the plastid division machinery essential for chloroplast replication. Members such as ARC6 and PARC6 are integral to the inner envelope membrane, where they coordinate the assembly of the stromal FtsZ ring and interact with outer envelope proteins to facilitate organelle constriction. It is expressed in Lactuca virosa.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 19754, 8451, 2213, 26707, 1009, 17, 3189, 3416, 16, 2154, 10634, 1966, 43, 4728, 4594, 1927, 1920, 19754, 8451, 10853, 4415, 1958, 17471, 5158, 18, 4678, 2427, 1966, 9952, 1016, 1930, 2096, 24304, 2032, 12328, 1942, 1920, 6671, 11262, 3260, 16, 2597, 2611, 11865, 1920, 5957, 1927, 1920, 9709, 27497, 6335, 1930, 6310, 1956, 7642, 11262, 2697, 1942, 6628, 19309, 19837, 18, 2176, 1977, 3198, 1922, 5641, 29394, 2787, 5360, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MERTATPCCIHLPLSIVNWGQTNNADPNDLTATTLSCSPPARSLTSSETELEYVMKLVVLAMAQEEGTSSLAPDLQAQIDEALEEINFRNVIIYGQLEEVVSLAVLHMKISGMHLSFYVTTFGKIVRKSIALRPLTATYVFPSTSTKCSSYVEISRDTMTLCPPYYIKGCELMETVLKLLQKLLALPLDGEHRTRRTEGLQGVHN", "metadata": {"id": "A0AAU9P1P7", "cluster": 6420573, "interpro_all": ["IPR044685"], "interpro_used": ["IPR044685"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein is categorized in the Lambda repressor-like, DNA-binding domain superfamily, which functions as a transcriptional regulator controlling critical genetic switches such as bacteriophage lysogeny and bacterial sporulation. This domain typically adopts a four-helix closed folded leaf topology, a variation of the helix-turn-helix motif, to mediate specific DNA binding and interactions with RNA polymerase. Structural analogs of this fold are also conserved in eukaryotic POU transcription factors and the N-terminal domain of the metabolic enzyme cyanase. Furthermore, the protein should include a Cro/C1-type, helix-turn-helix domain that functions as a DNA-binding module within transcriptional regulators found in bacteriophages, prokaryotes, and eukaryotes. This motif typically employs a specific recognition helix to bind the DNA major groove, often operating within a dimer to control gene expression, such as the regulation of phage lysogeny and lytic growth. It is native to Singulisphaera sp. GP187.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10234, 1922, 1920, 18279, 14434, 17, 3189, 16, 2678, 17, 2743, 3418, 13975, 16, 2154, 4088, 1966, 43, 5224, 7888, 7138, 4140, 3299, 21529, 2427, 1966, 24613, 3629, 27791, 1930, 4543, 23647, 18, 2052, 3418, 5745, 24032, 43, 3006, 17, 7864, 8047, 16318, 6998, 13678, 16, 43, 4516, 1927, 1920, 7864, 17, 5165, 17, 7864, 5219, 16, 1942, 8265, 2487, 2678, 2743, 1930, 3719, 1956, 3146, 6479, 18, 4346, 13204, 1927, 2052, 3728, 2032, 2222, 5305, 1922, 10825, 28398, 3213, 2790, 1930, 1920, 56, 17, 4262, 3418, 1927, 1920, 4487, 4113, 10208, 2051, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 9442, 19, 8817, 17, 2601, 16, 7864, 17, 5165, 17, 7864, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 9059, 2651, 5224, 9098, 2435, 1922, 24613, 1036, 16, 28149, 16, 1930, 15021, 18, 2052, 5219, 5745, 22620, 43, 2487, 5708, 7864, 1942, 4566, 1920, 2678, 3044, 15920, 16, 3868, 8654, 2651, 43, 7632, 1942, 2285, 2359, 2294, 16, 2427, 1966, 1920, 3640, 1927, 10503, 3629, 27791, 1930, 17033, 2905, 18, 2176, 1977, 6196, 1942, 2896, 13004, 3508, 20051, 5524, 2056, 18, 4882, 19544, 18, 3], "output": "MGVMNVEQKNTSFDELVAACRTFADCLAAFPDVDELERESLFATIAQALFPMSEVVSSASRDFGSPLSQEEAAAMNEKKMTQSALATAIGVGQPAVSMASDLWPNFHVGKTETHSPVLTNSVIVWTDLSSGYWTKLEELDALSRSTLKGATLKGAAQACDAETRADIEELIAYARDAACAELDAEEATFASRLSMLSRGCRPQRRTVKKIAEALSIPPSAKNAALVWESPKTATGH", "metadata": {"id": "A0A1N6DFI0", "cluster": 6634492, "interpro_all": ["IPR001387", "IPR010982"], "interpro_used": ["IPR010982", "IPR001387"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein is categorized in the Protein of unknown function DUF4407 family, which comprises uncharacterized proteins distinguished by a single completely conserved arginine residue that may be functionally important. It originates from Lysobacteraceae bacterium NML95-0200 and exhibits UniProt keyword tags Transmembrane, Membrane, and Coiled coil.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 30138, 3416, 16, 2154, 12936, 24528, 2697, 12080, 2007, 43, 2957, 5796, 5305, 9732, 6181, 1988, 2278, 1998, 9346, 2715, 18, 2176, 22970, 2037, 3629, 5883, 9914, 14061, 2943, 1024, 8803, 17, 18773, 1008, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 16, 3260, 16, 1930, 17524, 9121, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MRISPEISSRIQSQSAKLYPKELQHQGQFHNHLLEQYEIFISAPQATQDLVQRGIAILISCMAFQYGVYQFSINLLLKPWHSAFAFTREIIRERQMTRRARYFRITIIAIMSMCAFLAVMGPLKDDIDAMLLEARQGLQRALNDWQQREAEVLRLSNEIATLKAEHQKSLSNGPKYGGHIQKAKQHQADFEAKESQLAHYASLISRDELDKASGAVERFGVLVILMFATSFAMTATSCFIVLFYMLLALLPEGLDLESLRRQERARSIRALMREESYRRFFEKKEGAIPEKADSSENGGRQPVDGESIMEWLQRFIVQTIFRYTDSAACAFIMFLLEVGNRVNATRASLENDARYKDRLIQAEVEAEGYEMDGIKAVDGKKEEVASIDREIKAEAVKMHAWRSQSAPGDNLFSLVQQID", "metadata": {"id": "A0A2M9EIX5", "cluster": 7333725, "interpro_all": ["IPR025519"], "interpro_used": ["IPR025519"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence be if I wanted a polypeptide chain capable of the following function: The protein includes a tRNA/rRNA methyltransferase (SpoU type) domain that functions as a 2'-O-methyltransferase acting on tRNA and rRNA substrates. It specifically catalyzes the methylation of conserved nucleotides in the peptidyl transferase center of the large ribosomal RNA, a modification required for the formation of functional large ribosomal subunits. Additionally, the protein belongs to the Ribosomal protein eL30-like superfamily, which comprises RNA-binding domains found in ribosomal proteins eL30 and eL8, RNA 2'-O ribose methyltransferases, and the translation release factor eRF1. These domains typically serve as structural modules involved in ribosome assembly, RNA modification, and the recognition of stop codons during translation termination. Additionally, the protein is grouped in the Ribosomal RNA Methyltransferase family, which catalyzes the S-adenosyl-L-methionine (SAM)-dependent methylation of ribose in ribosomal RNA (rRNA) molecules. These Class IV-like enzymes are essential for post-transcriptional modifications that fine-tune ribosome structure and function. Members include mitochondrial and bacterial 23S rRNA methyltransferases, the latter of which are frequently associated with antibiotic resistance mechanisms. It occurs in Chlamydiales bacterium SCGC AG-110-M15.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 10089, 19, 9067, 16478, 12, 18055, 1032, 2601, 13, 3418, 1988, 4088, 1966, 43, 22, 11, 17, 57, 17, 16478, 8290, 1990, 10089, 1930, 9067, 6249, 18, 2176, 4475, 17097, 1920, 5547, 1927, 5305, 9519, 1922, 1920, 3431, 2199, 13763, 4102, 1927, 1920, 3103, 11196, 3146, 16, 43, 6295, 3414, 1958, 1920, 3337, 1927, 3183, 3103, 11196, 6991, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 11196, 2213, 2349, 4294, 17, 3189, 13975, 16, 2154, 12936, 3146, 17, 2743, 4682, 2435, 1922, 11196, 2697, 2349, 4294, 1930, 2349, 1025, 16, 3146, 22, 11, 17, 57, 17870, 28253, 16, 1930, 1920, 6410, 4012, 2991, 2668, 5739, 18, 2144, 4682, 5745, 7120, 1966, 4346, 10803, 3286, 1922, 12794, 5957, 16, 3146, 6295, 16, 1930, 1920, 5708, 1927, 6875, 14500, 2409, 6410, 12462, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 11196, 3146, 16478, 3416, 16, 2154, 17097, 1920, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5547, 1927, 17870, 1922, 11196, 3146, 12, 9067, 13, 4206, 18, 2144, 2921, 4370, 17, 3189, 5038, 2032, 4415, 1958, 2753, 17, 5224, 6920, 1988, 8882, 17, 23703, 12794, 3170, 1930, 2347, 18, 4678, 3951, 4596, 1930, 4543, 3020, 1036, 9067, 28253, 16, 1920, 6296, 1927, 2154, 2032, 5467, 2458, 1956, 7267, 3554, 3531, 18, 2176, 5110, 1922, 21079, 2612, 14061, 2160, 5813, 2260, 17, 8139, 17, 8510, 1015, 18, 3], "output": "MQVITSTQNPYIKHLVKLRSNSSYRRSQRSLVLPGKIVLSELPSNYPIKKLMLLDGYDFNEICNAEEIIYASAPVLKKASGLENPDPVLIELDLPPEGLPETINRLLICDAVSDPGNMGTLIRTALAFDWDAIYFLNSCVDPFNDKAIRASKGALFHLPFAQGNWDDLSQIIQQHKLHPWVADLKGESPDTIPQSNPIALVVCSESQGPSNETVNHCKPLSIPMPGKMESLNVAVAGGILMHTLSKQPQVIPND", "metadata": {"id": "A0A212KSM5", "cluster": 10020334, "interpro_all": ["IPR029028", "IPR029064", "IPR051259", "IPR001537", "IPR029026"], "interpro_used": ["IPR001537", "IPR029064", "IPR051259"], "interpro_unused": ["IPR029028", "IPR029026"]}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein is included in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Additionally, the protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is derived from Gloeothece citriformis (strain PCC 7424) (Cyanothece sp. (strain PCC 7424)) and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3595, 2037, 25632, 1021, 26943, 1021, 9230, 27511, 12, 3943, 16003, 5446, 4561, 13, 12, 26898, 20536, 1972, 2056, 18, 12, 3943, 16003, 5446, 4561, 13, 13, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MSPTQKRLIGLTGGIATGKSTVSRYLAERYGLPIFSRYGNQVQFPDGTLNRKELGEIIFNNSEQSKNDTLVLVIPLLFEAKLTHLVTEIWVVYCSDDAQIKRKVAAADLVLDNSSDLNSVFRQIDQAIKINDELDADVYAREAVKLGSPILEQIEKVWLENQIHPYVRACFKKEIDLKERDNLTDEQAKARIKNQLPIEQ", "metadata": {"id": "B7KCM3", "cluster": 10590467, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nIt is part of the Aldolase-type TIM barrel superfamily, which forms a TIM \u03b2/\u03b1 barrel fold that typically covers the entire protein structure. This superfamily includes metabolic enzymes such as class I aldolases, class I DAHP synthases, class II fructose-bisphosphate aldolases, and 5-aminolevulinate dehydratase. Additionally, the protein should contain a Triosephosphate isomerase active site that catalyzes the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. This highly conserved feature is essential for efficient energy production via glycolysis and utilizes a catalytic glutamic acid residue within a characteristic TIM barrel structure. It is found in Litorivicinus lipolyticus and exhibits UniProt keyword tags Cytoplasm and Gluconeogenesis.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 2176, 1977, 3131, 1927, 1920, 11174, 21524, 17, 2601, 2267, 19560, 13975, 16, 2154, 4952, 43, 2267, 161, 19, 160, 19560, 3728, 1988, 5745, 10272, 1920, 5346, 2213, 3170, 18, 2052, 13975, 5921, 4487, 5038, 2427, 1966, 2921, 51, 11174, 21524, 1036, 16, 2921, 51, 3692, 15870, 8921, 1036, 16, 2921, 2890, 15102, 17, 29443, 11174, 21524, 1036, 16, 1930, 25, 17, 3835, 1952, 1020, 3392, 2010, 11725, 7234, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 30224, 4127, 25324, 25510, 3500, 3200, 1988, 17097, 1920, 10743, 8590, 12766, 2045, 2001, 1927, 22447, 23, 17, 5413, 1930, 20684, 7681, 2290, 5413, 18, 2052, 3626, 5305, 5961, 1977, 4415, 1958, 5807, 3844, 3372, 3454, 13393, 1930, 18127, 43, 6804, 18626, 2687, 6181, 2651, 43, 6293, 2267, 19560, 3170, 18, 2176, 1977, 2435, 1922, 4471, 6658, 9833, 22214, 3178, 29370, 1930, 9826, 20709, 11121, 2538, 14392, 5239, 1930, 25680, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MNTLIAGNWKTNLLADSAQALAQAVRDHCNQTNVCVIPVALGLQDISDQGMGATTGDICAQQAVDVGAKYVLVGHSERRVRQFETSDVCVGESLDDREAGRHEQVVGEQLAPVIQALGTVMDCVVAYEPVWAIGTGKTASAEQGGSVNAANAAELAACPDVNGALVGGAALTIESFAVIVKAFTEQNPALYAGKVAELLATSDLVARKALAAASAGLVPIAQAMHAVIRRMLVDAGKGQTKILY", "metadata": {"id": "A0A5Q2Q987", "cluster": 11401848, "interpro_all": ["IPR013785", "IPR035990", "IPR022896", "IPR000652", "IPR020861"], "interpro_used": ["IPR013785", "IPR020861"], "interpro_unused": ["IPR035990", "IPR000652", "IPR022896"]}, "task_type": "infilling"} {"instruction": "The protein incorporates a PatA-like, N-terminal domain that regulates heterocyst pattern formation in bacteria such as *Nostoc* sp. It is specifically required for the differentiation of intercalary heterocysts, playing a critical role in spatial developmental patterning distinct from terminal heterocyst formation. It is found in Planctomycetota bacterium. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 2917, 1019, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 7014, 27804, 2298, 3114, 3337, 1922, 4802, 2427, 1966, 14, 9291, 4575, 1030, 14, 2056, 18, 2176, 1977, 4475, 3414, 1958, 1920, 4155, 1927, 19014, 2141, 27804, 29664, 16, 14797, 43, 4140, 2770, 1922, 5067, 5878, 16060, 4493, 2037, 4262, 27804, 2298, 3337, 18, 2176, 1977, 2435, 1922, 4720, 2341, 13386, 19446, 3857, 14061, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MALGKNFRKNLLKEKTTILDGIGRISSVLSSTEEINQQVAALERENRKLAEKVEILEEKLKASEKHRQHASEAKNEKKAFEKEKKSLKLHLESEKRSRKYIEENYMKLLSESEQAAAKLEKEEKKTRKQLRAIKDLKREKKALLSERDFLEGERAELERVKKELEDSVAATEVEYENARKRVTSLDTELVEMRSEKEIAEKNLAASEHSKKKLSKTLSDKNEKIAEMETKVSQAGREKEKLASLNAEMEKEKEKASTLRIEVRELEKKYHERIKEIGALRKDVQLKKSLLDRAEVNISEREEQLKVVSEKLDIVELENEALTKNVSALEEEISEMEEATQEATMVLDRFAVLKDELKLKSGEVDALQQEKEGLEKKLQRSASDMEQLSTRIAAKEKEIGEDEKKTDQLKERLEQVESAKEKAEKALEKTDGFLARALEKMESVEGELKVRKEKADKYAEETTNLKKRIEELSEELSEKENEITATLEKSQYKQEHFRKEIQDVMSELDNASEKTEMLQREVFEKAGRVGELEEANEQSQKMLEEIVAERNKALKQLAEETEEKAREINRTTILMDQARRRLEKQTMVPNAATVQTSEPGESFAVTEQMSGDRPASDFVTEENSSGAKLQNQKPDFEKILLNNPQIDPEIDVALSRYLASKHPDAKMLGKGDDGDTLSGSLDVLDLPNLIQAINLRQKTGIIELPEIDAKIEISDGQIIAVFNPECPSGGYSGEEAFFLLVEKKPRVFRFLVKPLSGTRNVSFNTTQLLFECMRRLDEKGNT", "metadata": {"id": "A0A523TRN5", "cluster": 11516817, "interpro_all": ["IPR025497"], "interpro_used": ["IPR025497"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Moreover, the protein is included in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is found in Bacteroides uniformis and carries UniProt keyword assignments Cytoplasm and rRNA processing.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 2435, 1922, 27978, 7565, 1937, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MKEETTYHIPVLLMPSVDAMNIREILSRLEDGGRLLSFDQDEDAERNIVNNPHFTDLGVSSHHFDDSERGFSFRFDGALDMRMNKRAGLTAADIVNGELKNSRKLASVIVKARATQRIATIGEFLEIVKPLFGRALRIEVNQEMEALKEMLYAATEALKPGGRLVVITYHFGNVLTPFRLVNNKVIVPDEKEIERNPRSRSAKLRIAERIMNDRPDGTYVDVTFGGGGHSFVRSNFRYLHNFLRYHGIEKVDAILATYEEEKLADIFYLYEREKKELAKVFQSLEDRMVKNIMKTGNVEGKAEKDF", "metadata": {"id": "A0A7J5HR66", "cluster": 12090791, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein features a Serine/threonine-protein kinase N, first HR1 domain that forms an anti-parallel coiled-coil structure to specifically bind Rho family small GTPases. This interaction mediates the activation of Protein-kinase C-related kinases (PKN), facilitating downstream signaling in cytoskeletal regulation, cell adhesion, and vesicle transport. Furthermore, the protein carries a HR1 rho-binding domain that functions as a specific effector for GTP-bound Rho family small G proteins, facilitating downstream signaling events such as kinase activation. It adopts a left-handed antiparallel coiled-coil (ACC) finger fold, utilizing two long \u03b1-helices with basic and leucine-repeat regions to form the binding interface. This module is integral to proteins like PRK1 and TOCA, linking Rho GTPases to cytoskeletal actin assembly. It is present in Daphnia galeata and is connected to UniProt keyword Coiled coil.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 4075, 43, 8468, 19, 13143, 17, 2213, 4016, 56, 16, 2561, 3668, 1009, 3418, 1988, 4952, 1925, 2246, 17, 6110, 17524, 17, 9121, 3170, 1942, 4475, 4566, 10585, 3416, 2858, 18390, 18, 2052, 2835, 10412, 1920, 2936, 1927, 2213, 17, 4016, 45, 17, 2712, 7784, 12, 4652, 1022, 13, 16, 12440, 5863, 3197, 1922, 14787, 3640, 16, 2024, 6141, 16, 1930, 11502, 4860, 18, 3677, 16, 1920, 2213, 16252, 43, 3668, 1009, 10585, 17, 2743, 3418, 1988, 4088, 1966, 43, 2487, 7917, 1958, 9319, 17, 4124, 10585, 3416, 2858, 49, 2697, 16, 12440, 5863, 3197, 3916, 2427, 1966, 4016, 2936, 18, 2176, 24032, 43, 3506, 17, 17105, 28892, 17524, 17, 9121, 12, 2280, 13, 8497, 3728, 16, 10232, 2288, 2815, 160, 17, 12789, 1956, 5937, 1930, 12624, 17, 6865, 3451, 1942, 2386, 1920, 2743, 6854, 18, 2052, 9059, 1977, 12328, 1942, 2697, 3189, 22615, 1009, 1930, 21682, 1019, 16, 9486, 10585, 18390, 1942, 14787, 4718, 5957, 18, 2176, 1977, 2481, 1922, 8243, 11619, 2126, 5179, 5376, 3857, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 17524, 9121, 18, 3], "output": "MDYVSSIAALNRVVRHLSQSLLELSSKYGLQTDVSDASLGQQLEDLREQIRREIRVTAMVKKANNKLQELQAELQELDSQILLAPMSPPVYHNQQSSSVSNSHGGSVSSGGLGSSNGYETPMSPSDVAVPRPDEGSLQQYCNGPTRDKKLLAEAQQMLADSKAGKGLGDGSRARGDRNCDFGLMTPLEVRIEELRHLQSARSTDKKALQEAFEGRFKFMKSCAASLGGQMVQSTNNGNVQTNGIRFEYSWSNSVPDLSPTCNHRKNSSSGYGSGETAAPLMAATLTVSHPAGLTQPYERRCRSTCSITLQTNQEENPVDHFRRCSEGETWNSHTQMPQLSVPPPPVQSPCPIQSGKKKGRERPRTVHIDVYCTASESETDTCLQTVLRADQTGTRVRHIRKKTSLPPVLSYRISTKELAEAVERKRMSSKTTDASDLLDDADSEPESSDTRFSEDSYLDAKESDAAKSAEKCEESARLASRAMPIRPPSSPDGGSDRVSRCNSQRCPIVDQIYPSRAQDSSASIQSSRPNSSIDVPVAQLVVPTKFEMPWQWRIQQPTSKFGRHVGPARNPDCSCAHCLDHFARLRSISKSGGMIRSMVDKRMALKGDYIRYPALKELKIKEGAENFKKVATDKRSLADTQGQGSCGQGGTMMLMNMNTPPNNSSSTGGGGGNVHHSSTLSSQPSSSEQRISSLEKQLNIEQKVKQGAENMIKIEYIKMRIMKVKQVQSEEMDHLRIESAVVEGAKNVIRLPATLAMTDRHCSVSINAYMTLPRTPNRRSTSTARVSRPSMDTDPNVFRTCSSMSGDSGRRANRTLQGAATGGYPLHPHPLPVSPVATASPADKVKRRKDEESDESNESNTSTGNGLTTKNGCAPGLKELFRDLTLTDSSVVSLLKTWRSPEKERKRKMLEQRKQQWRNTLLSATYDLREKFKQQLLGRVGSESTQISSPSYCSSVLGSSSVTDSPVKSPVSGTPSNWTLK", "metadata": {"id": "A0A8J2RI78", "cluster": 16959292, "interpro_all": ["IPR011072", "IPR036274", "IPR037313"], "interpro_used": ["IPR037313", "IPR011072"], "interpro_unused": ["IPR036274"]}, "task_type": "infilling"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, the protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It occurs in Desulfobacteraceae bacterium and features UniProt keywords Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 5110, 1922, 30311, 5883, 9914, 14061, 1930, 4075, 20709, 11569, 5239, 1930, 9067, 4587, 18, 3], "output": "MADYHISCMPVEAAHYLNLRPGGTYVDGTVGGAGHSRMICTRIQPGGLLVGIDQDLDAIRHAQDVLAPFFPRVSLHHDTFSHLDRIIGNLGLAGVDGILLDLGLSLHQLEGSGRGFSFKREEPLDMRMNTKATITAADIVNSWDVDDLIRIFREYGEEHRARSIAKAIVKARARKPLESSKALADLIYRSMPPAAARKQKIHPATRVFQALRITVNRELDRLQRTLPMAVACLNPGGRLCVLSFHSLEDRIVKQTFREMARTCTCPPRAPVCTCGGEAQVTLLTRKVVRPTAEEIAANPMARSTRLRAVEKR", "metadata": {"id": "A0A7X1GXI9", "cluster": 18174385, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence of a protein with the following function look like? Here is the function: It is part of the Metal-dependent hydrolase superfamily, which comprises a diverse group of hydrolytic enzymes characterized by a (\u03b2/\u03b1)8-barrel (TIM barrel) fold coordinating mono- or binuclear transition metal ions within the active site. These enzymes utilize these metal centers to catalyze the hydrolysis of a broad spectrum of substrates involved in fundamental metabolic processes. Moreover, the protein should include a Amidohydrolase-related domain that functions as the metal-dependent catalytic core for a diverse superfamily of hydrolases, including adenine deaminase, dihydroorotase, and the urease alpha subunit. These enzymes catalyze the hydrolysis of carbon-nitrogen bonds, contributing to critical processes such as purine metabolism and nitrogen source utilization. It is derived from Uncultured archaeon and is connected to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 2176, 1977, 3131, 1927, 1920, 6048, 17, 3100, 20748, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 26702, 5038, 4378, 2007, 43, 12, 161, 19, 160, 13, 28, 17, 19560, 12, 2267, 19560, 13, 3728, 19355, 8914, 17, 2014, 8768, 13821, 4832, 6048, 6982, 2651, 1920, 3500, 3200, 18, 2144, 5038, 12561, 2144, 6048, 7365, 1942, 18170, 1920, 9128, 1927, 43, 4949, 5648, 1927, 6249, 3286, 1922, 8829, 4487, 4028, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 28813, 8601, 21524, 17, 2712, 3418, 1988, 4088, 1966, 1920, 6048, 17, 3100, 6804, 4728, 1958, 43, 6445, 13975, 1927, 30337, 16, 2710, 15643, 27955, 16, 11842, 30232, 3857, 4127, 16, 1930, 1920, 10505, 4127, 4595, 5903, 18, 2144, 5038, 18170, 1920, 9128, 1927, 5056, 17, 6634, 9031, 16, 8739, 1942, 4140, 4028, 2427, 1966, 19700, 4714, 1930, 6634, 4585, 8422, 18, 2176, 1977, 3595, 2037, 5269, 21058, 13470, 1916, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MAKNGIGIVCFLFLFSILIHISAAAGDICAPSSTDASPDKMKIFDAHVHMTQDYTSDFVISEMDQAGVSMALLYPNGKNDDQTSLDYIAKYPGRFSAFVAFTNTNDQHLVEYTRTQLGTGRFTGIGEINLRYYSGQSYTPPPTAYIQPDTPLILQLVDLSAAYHVPLSFHFVPDDPSANAALERMFSHNKDAIFLWCHLGFNNMPLDADALDDYLLRYPNLYFDTAGIQNMMNDPGELNSNWRGVLVNQSDGHLNARWEQFFETWNARILWASDAGGGNDKNRWLNYASDTVQNAPPNAVGRWRSALADLDSNSFRNIFIANAKAVIMKEARPDYDYSVASDGQCFPLSIRSNSSVSALAFDQTAGTITFKTADSNGTTDSAVVSMPAGLLNGTFTVQVNGQGAQFGETSNSTHTGISVGYGGGINTIAITATPSVNQTPSVNQTQSVNQASQNQSSTQQPAVATESDARSVLSAARTAISDADKAGKNVSAAKDKLADANAAFVAGDYDLAKELANETETLALGAPNVVAANQTATAEPAANQTTNITPANTSPETNVFDWVPAIGAVAAIIVIAAAYLVTRKPPKR", "metadata": {"id": "A0A5E4J9Q3", "cluster": 18193492, "interpro_all": ["IPR006680", "IPR032466"], "interpro_used": ["IPR032466", "IPR006680"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein should feature a NADP-dependent oxidoreductase domain that functions as a monomeric aldo-keto reductase, utilizing a parallel \u03b28/\u03b18 barrel fold to catalyze NADPH-dependent reductions. Its deep, hydrophobic active site preferentially binds aromatic and apolar substrates, while a novel NADP-binding motif undergoes a significant conformational change to lock the coenzyme in place. Also, the protein belongs to the Aldo-keto reductase 2 subfamily oxidoreductase family, which utilizes NADPH or NADH to reduce aldehydes and ketones into their corresponding alcohols. These enzymes participate in diverse metabolic processes, including aldehyde detoxification and the metabolism of sugars and steroids. In addition, the protein is assigned to the Aldo-keto reductase family, which consists of NAD(P)H-dependent oxidoreductases that primarily reduce carbonyl substrates such as sugar aldehydes, keto-steroids, and lipid peroxidation by-products. Characterized by a conserved (\u03b1/\u03b2)8-barrel motif, these enzymes utilize a deep hydrophobic pocket to bind aromatic or apolar substrates and operate via an ordered bi-bi kinetic mechanism that involves a significant conformational change upon cofactor binding. It is identified in Chloroflexota bacterium.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 3066, 5961, 43, 24221, 17, 3100, 27388, 3418, 1988, 4088, 1966, 43, 14457, 11174, 1037, 17, 21471, 11386, 16, 10232, 43, 6110, 161, 1025, 19, 160, 1025, 19560, 3728, 1942, 18170, 11908, 17, 3100, 9350, 18, 2496, 6515, 16, 7919, 3500, 3200, 10662, 6876, 10761, 1930, 11466, 5148, 1005, 6249, 16, 2679, 43, 4008, 24221, 17, 2743, 5219, 14928, 43, 2228, 8523, 3185, 1942, 12756, 1920, 22051, 1922, 4368, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 11174, 1037, 17, 21471, 11386, 22, 16227, 27388, 3416, 16, 2154, 18127, 11908, 2014, 14261, 1942, 4412, 25075, 1930, 21876, 1036, 2460, 2310, 3980, 21773, 18, 2144, 5038, 7352, 1922, 6445, 4487, 4028, 16, 2710, 18727, 18169, 1930, 1920, 4714, 1927, 15592, 1930, 13039, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 11174, 1037, 17, 21471, 11386, 3416, 16, 2154, 7543, 1927, 6577, 12, 58, 13, 50, 17, 3100, 27388, 1036, 1988, 5985, 4412, 14201, 6249, 2427, 1966, 9523, 25075, 16, 21471, 17, 13039, 16, 1930, 4486, 14214, 2007, 17, 4461, 18, 4378, 2007, 43, 5305, 12, 160, 19, 161, 13, 28, 17, 19560, 5219, 16, 2144, 5038, 12561, 43, 6515, 7919, 10154, 1942, 4566, 10761, 2014, 11466, 5148, 1005, 6249, 1930, 15336, 3454, 1925, 12011, 2273, 17, 2273, 9010, 2856, 1988, 7077, 43, 2228, 8523, 3185, 4073, 15155, 2743, 18, 2176, 1977, 2899, 1922, 10107, 18222, 7336, 14061, 18, 3], "output": "MSAIHIELGSISMETRRLGGTDMDVSWLGFGAARIATDTGSPAAAERLLNTLLDSGVNYIDTAECYGESEETLGKYISHRRDEYWLTTKCGHVAGDITAPEWTAAAVTQSVDQSLRRMQTDYIDLIHIHTCEADVLRQGDVLRALQDAQQAGKTRYIGFSGDNEVALEAIGMGKFATLLTSFNVLDQRGLDEVLPAAEAAGMGIIAKRPIANAAFNRPASPYDYADAYWQRAQHFTVPEGAPADGVALALRFCHSFDYIDTAIVGIDSLEQLQSNTEQVAAGPLPPDVLASLRTQFQEHGRDWPQLS", "metadata": {"id": "A0A8T6G0E1", "cluster": 18242791, "interpro_all": ["IPR020471", "IPR053135", "IPR023210", "IPR036812"], "interpro_used": ["IPR023210", "IPR053135", "IPR020471"], "interpro_unused": ["IPR036812"]}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein is classified under the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Additionally, the protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is derived from Anaerovibrio lipolyticus DSM 3074 and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3595, 2037, 11381, 25210, 2377, 3940, 3178, 29370, 10964, 23863, 1006, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MKIIGLTGGIASGKSTVTKYLRQQGYTVVDCDKGSKVINPDRSLNRQAVADIVFRDEMMSQVKAAGDEGEKVIFLDVPLLFETSYDKLVDEKWLVYVSRDTQLRKKLSDVIINNNADRKRLRRQLDEKLEHLRIEGEIAWELAEPDCSIWQVYFARYKKELDAINSLVHPLIKDRLMSRNDFNHDEAVRRIDSQMSLEEK", "metadata": {"id": "A0A1M6CWG2", "cluster": 21473884, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein according to the following functional description: It is part of the DASH complex subunit Spc19 family, which functions as a component of the DASH complex, a microtubule-binding subcomplex of the outer kinetochore essential for proper chromosome segregation. As part of this complex, it mediates the formation and maintenance of bipolar kinetochore-microtubule attachments by forming closed rings around spindle microtubules and establishing interactions with central kinetochore proteins. It is identified in Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) and exhibits UniProt keyword tags Chromosome partition, Cell division, and Nucleus.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 2176, 1977, 3131, 1927, 1920, 9490, 2796, 5903, 20692, 4136, 3416, 16, 2154, 4088, 1966, 43, 4594, 1927, 1920, 9490, 2796, 16, 43, 10544, 17, 2743, 5736, 19667, 1927, 1920, 7642, 21563, 4415, 1958, 3405, 5597, 12707, 18, 1966, 3131, 1927, 2052, 2796, 16, 2176, 10412, 1920, 3337, 1930, 6291, 1927, 10275, 21563, 17, 10544, 29993, 2007, 7402, 8047, 12750, 4760, 10716, 12444, 1930, 11810, 3719, 1956, 4101, 21563, 2697, 18, 2176, 1977, 2899, 1922, 7071, 5360, 2437, 28476, 29249, 22168, 12, 3943, 5749, 1028, 19, 11037, 21103, 7514, 13, 12, 16150, 5688, 13, 1930, 9826, 20709, 11121, 2538, 14392, 5597, 11334, 16, 2024, 8451, 16, 1930, 5607, 18, 3], "output": "MSYLDGLQQCVDSLQISIGTLSSSIDTLESGIHDFPRIKHILKVQRHFNLISEDELSARQAKFEEIVKPILSKAFQRLEDSISSLQRQEDSLKTKYELQEARLDMLKNRPATSAFSVTTESSEQLKAIIAKRQKLVYTLERYTLQLQQKRGH", "metadata": {"id": "Q50HP3", "cluster": 23580533, "interpro_all": ["IPR013251"], "interpro_used": ["IPR013251"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: It is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein belongs to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It has been characterized in Anaerobranca californiensis DSM 14826 and is annotated with UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 2258, 2252, 4378, 1922, 29163, 17182, 3375, 9939, 24222, 10964, 13623, 4684, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MKKIGLTGGIASGKSTISKILRRLGAAIIDADLEAKATLKPETKCWELLVKEFGRGILKPDNTIDRKKLGNIVFGKPEKLKKLNEIVHPFVKERIKNKMAEIETKGKHKAIVLDAPLLIETGFHNLVDEVWVVDVDRETQVQRVMKRDSLSREQAIARINSQLPREERIKYATAIIDNMGTRKNTREQIIHLWKTKVEREIN", "metadata": {"id": "A0A1M6PQU3", "cluster": 24455146, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that can perform the following function: The protein possesses a Aminotransferase class V domain that functions as a pyridoxal-phosphate (PLP)-dependent catalytic module found in aminotransferases and related enzymes such as cysteine desulfurase. This domain facilitates enzymatic transformations by covalently binding the PLP cofactor to a conserved lysine residue. In addition, the protein is classified under the Pyridoxal phosphate-dependent transferase, major domain superfamily, which forms the large catalytic component with a 3-layer \u03b1/\u03b2/\u03b1 sandwich topology in enzymes that utilize pyridoxal 5'-phosphate (PLP) as a cofactor. Through a Schiff base linkage with an active site lysine, members of this superfamily facilitate diverse chemical transformations, including transamination, decarboxylation, and deamination, which are essential for the biosynthesis and catabolism of amino acids and neurotransmitters. Moreover, the protein is grouped in the Kynureninase family, which functions as a pyridoxal-5'-phosphate (PLP)-dependent enzyme catalyzing the hydrolytic cleavage of L-kynurenine or 3-hydroxykynurenine to yield L-alanine and anthranilic or 3-hydroxyanthranilic acid. This reaction constitutes a key step in the L-tryptophan catabolic pathway involved in NAD biosynthesis across bacteria, fungi, and vertebrates. Structurally, the enzyme belongs to subgroup IVa of the aminotransferase superfamily. It is derived from Angomonas deanei and is annotated with UniProt keywords Cytoplasm, Hydrolase, and Pyridine nucleotide biosynthesis.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 15817, 2921, 64, 3418, 1988, 4088, 1966, 43, 24828, 23859, 17, 5413, 12, 21453, 13, 17, 3100, 6804, 9059, 2435, 1922, 15817, 1036, 1930, 2712, 5038, 2427, 1966, 8666, 30311, 9280, 4127, 18, 2052, 3418, 11374, 8145, 18510, 2007, 16590, 2743, 1920, 21453, 15155, 1942, 43, 5305, 9082, 6181, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 3044, 3418, 13975, 16, 2154, 4952, 1920, 3103, 6804, 4594, 1956, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 18038, 13678, 1922, 5038, 1988, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 18, 2596, 43, 25214, 5170, 8611, 1956, 1925, 3500, 3200, 9082, 16, 4678, 1927, 2052, 13975, 6628, 6445, 4399, 18510, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 2154, 2032, 4415, 1958, 1920, 8132, 1930, 19480, 1927, 3835, 4576, 1930, 21012, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 23523, 24684, 11413, 3416, 16, 2154, 4088, 1966, 43, 24828, 23859, 17, 25, 11, 17, 5413, 12, 21453, 13, 17, 3100, 4113, 29601, 1920, 26702, 6404, 1927, 54, 17, 23523, 24684, 2053, 2014, 23, 17, 8275, 6716, 1022, 24684, 2053, 1942, 4307, 54, 17, 10504, 1930, 14228, 16692, 1935, 2014, 23, 17, 8275, 7744, 17182, 10029, 2687, 18, 2052, 3227, 14879, 43, 3834, 3537, 1922, 1920, 54, 17, 13489, 22112, 3374, 3286, 1922, 6577, 8132, 3436, 4802, 16, 10520, 16, 1930, 14976, 18, 12171, 16, 1920, 4113, 14440, 1942, 6200, 4370, 1019, 1927, 1920, 15817, 13975, 18, 2176, 1977, 3595, 2037, 3409, 10480, 30097, 2912, 1033, 1930, 1977, 10633, 1956, 20709, 11569, 5239, 16, 20748, 16, 1930, 19604, 5489, 8132, 18, 3], "output": "MASSVGLSLTDDAFAEHRDEIDVLNEHRQSYHFPKQPSGAPFIYLVGNSLGLQHVGVRTAVDEFLQKWQDQAVEGHFMQPNPWFEIDEILRADMAKIVGADRREVVLMNTLTVNIHFMMAAFYRPEGKRKKILMENQGFPSDTHALISQLQLHGYGPEDLITVSAPGHEEVTAPVSPVTTEAFIAAIEQHADEIAIVMITAIHFLTGQLFDIPAIVKAAHAHNIVVGVDCAHAVGNVPLQLHDWDVDFACWCTYKYLNSGPGNVGGAFVHSKHTDGHSNLTYLKGWWGHDRKSRFSLHREFEPADGAACFQCSTAPTSSLTILQPSLQLMASIGMPKLREKSLHLTAYMELLLHELVPAGCIESVTPADPEQRGAQLSIRILPGKLKTTASSTAGYECGVAGEGSCDADIAQRQLLDCGVMVDNRPPDIIRLAPAPLYNSYMDVLQAVRVFASLFE", "metadata": {"id": "A0A7G2CS61", "cluster": 25005880, "interpro_all": ["IPR000192", "IPR010111", "IPR015424", "IPR015421", "IPR015422"], "interpro_used": ["IPR000192", "IPR015421", "IPR010111"], "interpro_unused": ["IPR015422", "IPR015424"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein is associated with the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It originates from Halobacteriovoraceae bacterium and has UniProt annotations ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 22970, 2037, 23226, 7972, 2341, 18842, 2579, 8846, 1972, 3336, 14061, 1930, 2258, 20709, 15010, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MHILNNIHIRLSPEQRLHRCNVPIIGLTGGIATGKSTVAQYLRSRGLNLIDADALIKNIYQLPSTLKFLSQRVPEVIEQQVVNFKLLREKFFTDKDLQKDLETLLYNELPAMFQRELSRQDWKRADFLIYDIPLLFEKNLAHQFDLSVLVYAPQNIQIERVIARDQCSPEVAQKVISHQLPINQKKEMSDYVISNESSKQDLYSSIDKFIKYLCE", "metadata": {"id": "A0A2E4D5X5", "cluster": 26879217, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein carries a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein is grouped in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein includes a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It has been detected in Rhodoferax sp and is annotated with UniProt keywords Isoprene biosynthesis and Transferase.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 16252, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 2258, 2252, 3330, 1922, 11490, 28079, 3013, 2056, 1930, 1977, 10633, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MQALYDVAAPAKLNLFLHITGRRATLHFELRSDGQLSREDLSTPLPPDPAQAGMGGGSSDAASTLLALNRLWNLNLPLAPFFLCCSNAWVEGIGEHLTPISLPPARFAVVKGFAAQPYCFGTNDLQPVAQNLCPAVSQALEWLGGKSLNSDVDLSDVPGSPGTWQVRKCSNMDVHPLKGWASSDGDGYHLLQSVFMLIDWCDDLVLRAARALQTATGTIRGAHIGVLKSIQLQTIGLQLGADVPPEGLDTKLIFSSPNLKRNSPGAILVARMTGSGSAVFAQML", "metadata": {"id": "A0A924NTB3", "cluster": 28644320, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR004424", "IPR013750"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "infilling"} {"instruction": "We aim to build a protein that does the following:\nThe protein is a member of the Protein of unknown function DUF2125 family, which comprises conserved hypothetical proteins with currently uncharacterized biological functions. It is present in Maritimibacter sp and is described by UniProt keywords Membrane, Transmembrane, and Transmembrane helix.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2213, 1927, 5435, 2347, 4855, 6680, 15174, 3416, 16, 2154, 12936, 5305, 15148, 2697, 1956, 5077, 24528, 3933, 4088, 18, 2176, 1977, 2481, 1922, 13081, 2265, 26073, 2341, 1915, 2056, 1930, 1977, 2910, 2007, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MRKAPQIIIALILLIFIRVLAGWFEDRRAEGWTAQYDSLNTAGFPSRPIFQNLSLSYSPTEVIAVLPGEASFAPAVELPIRRSVIEIDGATIATTMRETPDRQGHVYDFDVNATGIRPDPALLSGARNAGADRFAIERARPQPREIELTRLSVDWGALTLDATMIAVAQAAGAVPEMLVGTITRAGLRFENGRAFLGPVPLGPAPVIRLPGWGGYWVVGSQATEFDTTITDLNIADPETGIAWSAQVFATRDASHRITSETFRASARGETRETGLEHAQISIPEVIDRARLTATVRFDNPWGVLVVGQNGVTEGEVDVKAENWRDEMLARLSGDPETLDAT", "metadata": {"id": "A0A2D8PC51", "cluster": 2781695, "interpro_all": ["IPR018666"], "interpro_used": ["IPR018666"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein should have a Beta-lactamase class A catalytic domain that functions as a serine-utilizing hydrolase to cleave the beta-lactam ring of antibiotics, including penicillins and cephalosporins. Utilizing an active site serine within a conserved S-x-x-K motif, this domain confers bacterial resistance to these drugs and is typically susceptible to inhibition by clavulanic acid. Moreover, it is part of the Beta-lactamase/transpeptidase-like superfamily, which comprises enzymes sharing a core \u03b1/\u03b2 sandwich structure involved in cell wall biosynthesis and antibiotic resistance. Members include DD-transpeptidases and penicillin-binding proteins that cross-link peptidoglycan, as well as beta-lactamases that confer resistance by hydrolyzing beta-lactam antibiotics. It is expressed in Bacillus cereus VD118. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 2162, 43, 4666, 17, 23023, 2921, 43, 6804, 3418, 1988, 4088, 1966, 43, 8468, 17, 10232, 20748, 1942, 21252, 1920, 4666, 17, 15294, 6335, 1927, 7560, 16, 2710, 9957, 1036, 1930, 25091, 2925, 18, 10232, 1925, 3500, 3200, 8468, 2651, 43, 5305, 61, 17, 66, 17, 66, 17, 53, 5219, 16, 2052, 3418, 16556, 4543, 3554, 1942, 2144, 4195, 1930, 1977, 5745, 7819, 1942, 3523, 2007, 19887, 5617, 19730, 2687, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 4666, 17, 23023, 19, 22796, 18877, 17, 3189, 13975, 16, 2154, 12936, 5038, 10763, 43, 4728, 160, 19, 161, 18038, 3170, 3286, 1922, 2024, 4821, 8132, 1930, 7267, 3554, 18, 4678, 3951, 6758, 17, 22796, 18877, 1036, 1930, 9957, 17, 2743, 2697, 1988, 3567, 17, 3300, 24183, 16, 1966, 2486, 1966, 4666, 17, 23023, 1036, 1988, 7909, 3554, 2007, 7222, 9046, 4666, 17, 15294, 7560, 18, 2176, 1977, 3198, 1922, 14587, 29533, 13411, 19475, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "METVIRKIKEIQSGQVGVSVYSTKYENIVASYNNNLYIPLASAAKVAIGFAVARMVKDKQINWNDTLHHIKFNPNEDSVQLYPHLQGRTTLTLSKAVEVMIACHDSYIAHSVVMHYGGWETVRENVLTYFSKIHIQENPRDEQNVGELNQVLSLLVHIFQGYKAEPELWEPIISGMVRQQGNYEGIPYYHLAHVTGGLSTATINIGIIGMFHEFPFLYVIGGRDLPNRFDNKEVDETILEALKCLYKEYKMTSQTNVVTDN", "metadata": {"id": "R8QG08", "cluster": 4210538, "interpro_all": ["IPR012338", "IPR045155"], "interpro_used": ["IPR045155", "IPR012338"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has the following function: The protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein is classified under the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is expressed in Limosilactobacillus mucosae DSM 13345 and is linked to UniProt keywords ATP-binding, Cytoplasm, and Transferase. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 3198, 1922, 2784, 27545, 5148, 2341, 14357, 8898, 9680, 1021, 10964, 12147, 6803, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MTKVIGLTGGIASGKSTISNIFKEVGWPVIDADQTARQVVMPGSLGLAQIVSRFGSQVLQPDGTLDRAALGSMVFDDPQNLSDLDQIEHPLIMAAIDKQLAGLKKQGLPVVVLDVPLLFETGMDQECDLTVLAVVDRKTQLERLMKRDHCSKAAALKRINAQMPLEEKMRRADVTIDNNGSLAQTRLQVAKLVERVSQQK", "metadata": {"id": "A0A0R1P8L9", "cluster": 4762787, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein is grouped in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Also, the protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is present in Lacisediminihabitans changchengi and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2481, 1922, 7511, 3495, 1980, 11566, 2722, 5443, 2075, 17583, 22132, 6121, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MHLIGLTGGIASGKSAVAQRLASHVADRFGAGVITADGMLDRPALGAIIFTDDRARLDLNAITHPLVQQPDAVVVYDVPLLLEASSQSGYHRFEKIIVVEAEPATRIRRLVELRGMIADIVIDSNGTLDDTLAQADDVWTQLRELGAIVIDADRLAREVVEPGTPGLAARARDLIAAAEAHDSDHDAARRIASQATDAERRA", "metadata": {"id": "A0A934W3U3", "cluster": 5753988, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein possesses a LysR substrate-binding domain that constitutes the C-terminal effector-binding region of prokaryotic LysR-type transcriptional regulators (LTTRs), facilitating oligomerization and ligand sensing. Upon binding diverse effectors ranging from amino acids to reactive oxygen species, this domain undergoes conformational changes that modulate the regulator's interaction with DNA and RNA polymerase to control gene expression. Additionally, the protein is included in the Winged helix-like DNA-binding domain superfamily, which encompasses diverse DNA-binding proteins including transcriptional regulators, helicases, and endonucleases that utilize a winged helix-turn-helix motif for sequence-specific recognition. This domain engages the DNA major groove via a recognition helix while loop structures known as wings contact the minor groove or backbone, often serving as a scaffold for protein-protein interactions. Moreover, the protein contains a LysR, HTH, N-terminal domain that serves as the DNA-binding module of bacterial LysR-type transcriptional regulators (LTTRs), utilizing a helix-turn-helix fold to recognize specific promoter sequences. It typically functions within a homotetrameric complex to repress or activate genes involved in diverse metabolic and physiological processes, often in response to conformational changes triggered by small-molecule effectors. It has been detected in Pseudoalteromonas luteoviolacea and has UniProt annotations Transcription regulation.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 14465, 43, 3629, 1005, 4510, 17, 2743, 3418, 1988, 14879, 1920, 45, 17, 4262, 7917, 17, 2743, 3031, 1927, 21545, 3629, 1005, 17, 2601, 5224, 9098, 12, 3457, 1997, 1036, 13, 16, 12440, 17371, 1930, 5207, 9306, 18, 4073, 2743, 6445, 13066, 6485, 2037, 3835, 4576, 1942, 6079, 4612, 3038, 16, 2052, 3418, 14928, 8523, 2840, 1988, 8480, 1920, 7888, 11, 61, 2835, 1956, 2678, 1930, 3146, 6479, 1942, 2285, 2359, 2294, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 12920, 1919, 7864, 17, 3189, 2678, 17, 2743, 3418, 13975, 16, 2154, 21569, 6445, 2678, 17, 2743, 2697, 2710, 5224, 9098, 16, 29919, 16, 1930, 18697, 1036, 1988, 12561, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 1958, 3244, 17, 2487, 5708, 18, 2052, 3418, 11580, 1036, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 2679, 5881, 4061, 3171, 1966, 28297, 5217, 1920, 5857, 15920, 2014, 10787, 16, 3868, 13915, 1966, 43, 7281, 1958, 2213, 17, 2213, 3719, 18, 3950, 16, 1920, 2213, 5461, 43, 3629, 1005, 16, 5334, 1023, 16, 56, 17, 4262, 3418, 1988, 10634, 1966, 1920, 2678, 17, 2743, 9059, 1927, 4543, 3629, 1005, 17, 2601, 5224, 9098, 12, 3457, 1997, 1036, 13, 16, 10232, 43, 7864, 17, 5165, 17, 7864, 3728, 1942, 9967, 2487, 4465, 3709, 18, 2176, 5745, 4088, 2651, 43, 16350, 28959, 17118, 2796, 1942, 9055, 2014, 6980, 2628, 3286, 1922, 6445, 4487, 1930, 5005, 4028, 16, 3868, 1922, 2644, 1942, 8523, 2840, 9436, 2007, 2858, 17, 5388, 13066, 18, 2176, 2258, 2252, 3330, 1922, 11520, 1923, 1967, 10480, 12867, 25210, 10173, 1972, 1019, 1930, 2258, 20709, 15010, 3213, 3640, 18, 3], "output": "MNEYHCSKNLLNMIDELKSIAIFSTVVEQGLETKLDTALLYRSTRKLSLTEQGQQLFKMSTNMLKTVEQLPTVLIRSHYTRVLADFCQQHSRLEVNFHFSDVYENLSELKSKKLGNIKRKLTCSPAFLTNNPLPKTPEDLEQDIHFDYQVTANSVEGMTQLCMEGLGIATPADFAIWPNNITKKSATMAMVAHLAKAITSFRGAARALNLSPSVISYHITLGLSDISAQQEALSGRITVSIEKGIDIAIRLGDLPNNLPWIKLSSLPNKRTITHPELGKLVEQALREKKLIELLPNWQVTPIPAY", "metadata": {"id": "A0A0C1QA43", "cluster": 6581966, "interpro_all": ["IPR005119", "IPR000847", "IPR036388", "IPR036390"], "interpro_used": ["IPR005119", "IPR036388", "IPR000847"], "interpro_unused": ["IPR036390"]}, "task_type": "infilling"} {"instruction": "I need a polypeptide chain that performs the following role: The protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, it is part of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is expressed in Phascolarctobacterium faecium and is classified with UniProt keywords ATP-binding, Cytoplasm, and Transferase. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 3198, 1922, 18421, 12709, 4362, 2341, 12022, 5685, 27372, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MKIIGLTGGIASGKSTVASILQKLGAHIFDADIASRQAVARGSQGLQQVIDVFGRDYLTIDGELDRQKIAQLVFENKAALGQLESIVHTYVRSEAKKFLEQCRRQNFSAAVLDVPLLIECGWYKEVDLVWLVAVDEQTQIERAIARSGMSQQEVAVRIAAQMTLAAKCQYADLIIDNSGSLKQTELTVKKEWEKVLQMED", "metadata": {"id": "R6IBP4", "cluster": 7853086, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein is a member of the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Moreover, the protein has a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. In addition, the protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It has been detected in Cryobacterium sp. Hh11 and contains UniProt keyword associations ATP-binding, Nucleotide biosynthesis, and Transferase.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 3950, 16, 1920, 2213, 2258, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 2258, 2252, 3330, 1922, 15822, 7972, 2341, 18842, 1989, 2056, 18, 9645, 3242, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MTGLFITLEGGDGSGKTTQALGTDVGVAIREIVLHHRGEVDPRAEGDVIVQDRYLDSSVAYQGAGRVLGATEVRDLSLRAARARLEADDKVFDRLEAEKNDFHARPAAEVAAIIRARVSTLLLLTNWLEERGRTVVRTREPGALLYAADRAQHVGTKLRPALARWAAEGLLPDLTVLLDLDSVRAAFLELAAAEPARFLVVDAAA", "metadata": {"id": "A0A4R8ZVV0", "cluster": 8220220, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR018094", "IPR039430", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that has the following function: The protein is grouped in the Pyridoxal phosphate-dependent transferase, small domain superfamily, which comprises the complex $\\alpha/\\beta$ structural domain found in enzymes such as aspartate aminotransferase and DOPA decarboxylase. These proteins utilize pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze diverse reactions, including transamination, decarboxylation, and deamination, playing a vital role in amino acid biosynthesis and neurotransmitter metabolism. It has been characterized in Flavobacteriales bacterium. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 2858, 3418, 13975, 16, 2154, 12936, 1920, 2796, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3418, 2435, 1922, 5038, 2427, 1966, 12878, 15817, 1930, 19428, 23922, 18, 2144, 2697, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 1942, 18170, 6445, 5298, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 14797, 43, 8970, 2770, 1922, 3835, 2687, 8132, 1930, 15223, 4714, 18, 2176, 2258, 2252, 4378, 1922, 7732, 15229, 1918, 14061, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "GGSACSSGSNTGSHVLGALYGDRPGANIRFSFSRYNTMAEVDRTVDVLLQVLGIREGIPVRNV", "metadata": {"id": "A0A959TQU8", "cluster": 11601774, "interpro_all": ["IPR015424", "IPR015422"], "interpro_used": ["IPR015422"], "interpro_unused": ["IPR015424"]}, "task_type": "autoregressive"} {"instruction": "The protein possesses a DUF4131 domain that is a functionally uncharacterised feature frequently located in the N-terminal section of bacterial proteins involved in competence. It is found in Sphingomonadaceae bacterium. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 4855, 10432, 22977, 3418, 1988, 1977, 43, 9346, 23229, 3495, 5961, 5467, 4810, 1922, 1920, 56, 17, 4262, 3314, 1927, 4543, 2697, 3286, 1922, 12939, 18, 2176, 1977, 2435, 1922, 13502, 20050, 7324, 1972, 3336, 14061, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MALVAGIVGAIGCGAIWTRADRLAAPVLTRTAITTFTGRIEQIEIQAAKATVRLTLATEGAPALPPRVRVTVDVDKMPDGIVAGERVSLRARLVAPQGASVRGGFDFARVACSSALARPARRSGR", "metadata": {"id": "A0A838VIA1", "cluster": 13249550, "interpro_all": ["IPR025405"], "interpro_used": ["IPR025405"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that will have the following function: The protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein carries a HPr kinase/phosphorylase, C-terminal domain that functions as the catalytic core of the bifunctional enzyme HprK/P, regulating carbon source utilization in Gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 on the phosphocarrier protein HPr and its dephosphorylation via phosphorolysis, typically within a hexameric assembly. Furthermore, the protein should include a HPr(Ser) kinase/phosphorylase, N-terminal domain that constitutes the structural blades of the hexameric HPr serine/threonine kinase PtsK, a sensor protein controlling bacterial carbon catabolite repression. This domain facilitates the assembly of the enzyme's three-bladed propeller structure, allowing it to function within a multicomponent phosphorelay system. It has been detected in Zetaproteobacteria bacterium CG12_big_fil_rev_8_21_14_0_65_55_1124 and is described by UniProt keywords Multifunctional enzyme, ATP-binding, and Magnesium.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 16252, 43, 18542, 4016, 19, 12556, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 1920, 29491, 4113, 18542, 1040, 19, 58, 16, 6773, 5056, 4585, 8422, 1922, 8604, 17, 2843, 4802, 18, 2176, 17097, 2321, 1920, 4498, 17, 3100, 4050, 1927, 2375, 17, 4182, 1990, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 2496, 16881, 3454, 3421, 6892, 16, 5745, 2651, 43, 25602, 1935, 5957, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 18542, 12, 2375, 13, 4016, 19, 12556, 2051, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 4346, 22707, 1036, 1927, 1920, 25602, 1935, 18542, 8468, 19, 13143, 4016, 8618, 1040, 16, 43, 6443, 2213, 7138, 4543, 5056, 3115, 3016, 2394, 10084, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 4113, 11, 61, 2559, 17, 22707, 1007, 5062, 13728, 3170, 16, 7201, 2176, 1942, 2347, 2651, 43, 8844, 28155, 1939, 3421, 15208, 1012, 2433, 18, 2176, 2258, 2252, 3330, 1922, 18943, 9218, 1021, 10296, 14061, 7294, 3112, 41, 9769, 41, 3313, 41, 5197, 41, 28, 41, 2900, 41, 2607, 41, 20, 41, 4459, 41, 4288, 41, 11147, 1006, 1930, 1977, 2910, 2007, 20709, 11569, 20136, 4113, 16, 4498, 17, 2743, 16, 1930, 13148, 18, 3], "output": "MHEDYSRVSVTDVLKEQGEALGMTVLTGEAGLGRYIDHPRVEKPSLAFAGYLEKLNDYRLQVVGKSELGYLATRPEAERKKAVDAVFDLRLAAVVITYGMHVPDIVLEAAKRTDTPLISTPLDSQTFMTNMMLYLSRRLAPRTFQHGVYMDIFGLGVLLTGGSGIGKSEIALELVSRGHRLIADDMVELSRVGTDVLVGRSPEALKYHMEIRGIGILNIRDLFGAAAITDAKRVGLVLEIVHWDDMSEQIRLLGEDASIVLHDVKIPKALLPVRPGRSLAVLVEVAARNQLLKQRGIESGKAFMLELENRIQQGQG", "metadata": {"id": "A0A2M7H9Y7", "cluster": 15433181, "interpro_all": ["IPR003755", "IPR011104", "IPR011126", "IPR027417", "IPR028979"], "interpro_used": ["IPR027417", "IPR011104", "IPR011126"], "interpro_unused": ["IPR003755", "IPR028979"]}, "task_type": "autoregressive"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein can be placed in the Protein of unknown function DUF169 family, which comprises uncharacterized proteins found in prokaryotes, including the representative member MJ0308. Furthermore, it is part of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Furthermore, the protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It originates from Desulfobacteraceae bacterium and is classified with UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 5739, 7093, 3416, 16, 2154, 12936, 24528, 2697, 2435, 1922, 28149, 16, 2710, 1920, 5051, 7210, 15697, 12962, 13895, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 22970, 2037, 30311, 5883, 9914, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 5655, 3581, 18, 3], "output": "MDFLKDVKGWDKKVQKLDTLLRLRSFPVAFRRIDKRLTLCQMINLVRNFDWTVGAEGKDFIFPTCSSIIGLGKLKKEDARRFEESIPRLPLGKYEAVALAPLRYNPFHPDIVLIYGNPAQMIGESSCADVIVRSIQERKAYLTIPCYGERRYGHAQDDELVMAIPAEMISYAGVESDLLEVFPPAYRDLDIVEKVRSKGRRLVVGLSGGIASGKSTVDILAREVVKPGRPAWKDIVEYFGRQILAEDNTIDRKRLSEIVFQMEEITQKEDTPIIVVDIPLLFELNLQYRFLKNILVFVPKDIQIERLIQKLGYADYIIYNDKEVTHTERQVDRLWSELKRLRDEIKIQKKECMLENREWLNHIPYLRPEIYTDGTFRSIVWVKLLINAIQLESYQVMQFFCVIDMVIRGLEGLYRRGVRYPSGMLRERGAHIIDFKDMEKRKKLESFTHPRIMDEFLIRDGIDEAEAEARLRAQLPMEE", "metadata": {"id": "A0A7C0V974", "cluster": 16304684, "interpro_all": ["IPR001977", "IPR003748", "IPR027417"], "interpro_used": ["IPR003748", "IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein can be placed in the Nickel/cobalt homeostasis protein RcnB family, which maintains nickel and cobalt homeostasis in Proteobacteria. It functions in conjunction with the RcnA efflux pump to regulate intracellular metal ion levels. It is produced by Sphingomonas sp. 32-62-10.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 16541, 19, 20773, 7622, 2213, 7399, 17046, 3416, 16, 2154, 16566, 16541, 1930, 20773, 7622, 1922, 22266, 18, 2176, 4088, 1922, 11799, 1956, 1920, 7399, 2175, 11247, 8912, 1942, 5741, 4776, 6048, 4755, 2428, 18, 2176, 1977, 4152, 2007, 13502, 10480, 2056, 18, 3323, 17, 5374, 17, 2119, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MAGPADAQRLGGGRMVAPQIAVPPAGPQGQPRMSGQRMAGQRFQGQQFQGQRWGGRVGGRWIGGLPSYWIAPSFFIGNFASYGLAPPPYGYHWSRYYDDAVDDASEDGYGDDQPGYGAPYAAPTTGYQGSYEVQGGAVVQPLYPHGYTQSWSAGSGYYYPGGVTTTITVQETVYRAPVRRSYRKPVRKWQPKAKAPCACQCACRGPPVAITPQPAPQMGMPAPRVGVQAPGGWNAYRRPGRGFALIDDRGRVHDSVQGIGWGTYEVGGQRGYQRGQQSGSYLPQVQQAPIVTTTVTEYIE", "metadata": {"id": "A0A258G0B8", "cluster": 16338977, "interpro_all": ["IPR024572"], "interpro_used": ["IPR024572"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein should include a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein contains a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Furthermore, the protein belongs to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is found in candidate division KSB3 bacterium and exhibits UniProt keyword tags Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 5461, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 2435, 1922, 6610, 8451, 11626, 13965, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MQHNYDLALPSYAKINLGLKVLAQRPDGYHAIETIFQEIEFHDMLYFRKQPGALTLDSDHPALPLDKDNLVYKAIQLLRDHCRCPDRVHVYIQKNIPLGAGLGGGSSNAAKTLEAMNQLFDLRLSVSELAELSAKLGSDISFFHYGGTALGTGRGEEIYPLPGVPRFWILLVNPRIHVSSAWAYKNINLKLTNSHGLINVFRILKAGHITDFPFRALSNDLEGPVMERYPIVRSIKKQLCEAGAEWAMMSGSGSTVFGIFYKKEFAENALQQLQNPDWMTCLTRMRSGNP", "metadata": {"id": "A0A2G6E4P0", "cluster": 16545173, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "The protein carries a MvdD-like, pre-ATP grasp domain that functions as part of the ATP-grasp machinery, such as MvdD, involved in the biosynthesis of microviridin K. This pathway produces ribosomally synthesized and post-translationally modified peptides (RiPPs) that act as peptidase inhibitors. It is present in Candidatus Berkiella cookevillensis.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 16252, 43, 29007, 1007, 17, 3189, 16, 2097, 17, 4498, 22815, 3418, 1988, 4088, 1966, 3131, 1927, 1920, 4498, 17, 22815, 10853, 16, 2427, 1966, 29007, 1007, 16, 3286, 1922, 1920, 8132, 1927, 14264, 23576, 22816, 53, 18, 2052, 3374, 9300, 11196, 1954, 6653, 1930, 2753, 17, 8414, 1954, 4795, 5320, 12, 8936, 2523, 13, 1988, 4033, 1966, 24050, 4472, 18, 2176, 1977, 2481, 1922, 14550, 1031, 1957, 8310, 7369, 5870, 14943, 9488, 10760, 3355, 1937, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MVKILILTNVEDAHSRIVFDCLKKKGASPIRWYPEEYIINQDSKITISKEATVNIKISSQDSIDIEENRAHMDSLLLLLEEKATWVNPLSSYRISNSKLVQLREAARLKMEIPKTLITNHKKKTFLPPYWEESKNYYNLYTSVINKEILPNESIMRITPGIYQQNIDKQYEIRVTFFGQEYIKINLTILPHEIEKKCIQLMQKLGIIFGCFDFIVTPKDEYVFLEVNEMGQFSAQSQLNQEKTKFSLHEITTSETYKHLLQNDKIHHAIIETTSASNMKNIDVVWNRRFQYPNLSKLVHPDDYDFVNRDIIDFIDENNALGIRTIYAIKIDNSDEQDWRILSGTSQFSWIEEMLPNVKIVDRFCDFLID", "metadata": {"id": "A0A0Q9YEB1", "cluster": 17168936, "interpro_all": ["IPR048936"], "interpro_used": ["IPR048936"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein is grouped in the C2 domain superfamily, which functions as a calcium-dependent membrane-targeting module involved in signal transduction and membrane trafficking. This domain facilitates subcellular localization by binding to phospholipids, such as phosphatidylserine and phosphatidylcholine, often in a calcium-regulated manner. Structurally, it adopts an eight-stranded antiparallel beta-sandwich fold featuring a calcium-binding pocket formed by apical loops. It has been detected in Vitis vinifera (Grape).", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10809, 1922, 1920, 8453, 3418, 13975, 16, 2154, 4088, 1966, 43, 5016, 17, 3100, 3260, 17, 5133, 9059, 3286, 1922, 2733, 8201, 1930, 3260, 9604, 18, 2052, 3418, 11374, 11309, 5363, 2007, 2743, 1942, 15619, 16, 2427, 1966, 28563, 1930, 23842, 16, 3868, 1922, 43, 5016, 17, 4335, 5222, 18, 12171, 16, 2176, 24032, 1925, 5066, 17, 10338, 28892, 4666, 17, 18038, 3728, 29931, 43, 5016, 17, 2743, 10154, 5333, 2007, 8913, 11109, 18, 2176, 2258, 2252, 3330, 1922, 29677, 1036, 11132, 19582, 12, 18673, 13, 18, 3], "output": "MSEGDELGQAPKGYKYKRTQTSALYQVSTMERIFRIKVYALVSISGDPFIYCERSLGDEIVGEFSIPVKSLFDKVGNRNVSEQGAVKFTFEFGQPLARVVTPPRSQLPPRPQGYTAACDDDNELACDDCCDEEDDYDDFLCRSLVIRNISAEDLQDVRPAGKWNSTTRLNFQFSSGCYPVTSSSGGQVHVQPTVDVQLNLNISGDCLQ", "metadata": {"id": "A0A438F4K2", "cluster": 17874929, "interpro_all": ["IPR035892"], "interpro_used": ["IPR035892"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, the protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is native to Desulfobotulus alkaliphilus and corresponds to UniProt keyword Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 6196, 1942, 30311, 2389, 1991, 9605, 25178, 24888, 5277, 1036, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 3], "output": "MDFHHISCMPDEVLAFLQGKEKGIYVDATLGGCGHSRRILTEVPESHLIGIDQDPHGNFSGIGSILNDLGISAVDGILADLGLSLYQLEASGRGFSFKGDEPLDMRMDPASPRSAADIVNQHAREENPIEKTGQLAEIVRMCIPAKHRAKQKIHPATRVFMALRIAVNEELEKLDFFLKEAPLRLLAFPCTCPPDFPLCNCGGRADFRLLTSKAVKPGEKEILANPMARSTRLRALQRLPYAIAHAKEALAPYGNRVTLVEKEQTLKTLFRDLGEERFAGPIARRIVPGGKMVVLSFHSLEDRRVKQAFRKL", "metadata": {"id": "A0A562RIF4", "cluster": 18748438, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to generate an amino acid sequence for a protein. The protein should have the function The protein falls within the Plant secondary wall-associated transcription factors family, which regulates secondary wall biosynthesis in fibers and vessels by binding to specific DNA consensus sequences to activate genes involved in cellulose, xylan, and lignin synthesis. These proteins function as key components of transcriptional networks controlling plant structure and xylem differentiation, while also participating in diverse developmental processes such as stomatal closure, lateral root formation, and metal ion homeostasis. Furthermore, the protein should feature a Myb domain that functions as a DNA-binding module in eukaryotic transcription factors, typically occurring in tandem repeats. It adopts a helix-turn-helix (HTH) structure where the third helix acts as a recognition motif to bind the DNA major groove, often targeting specific sequences such as YAAC(G/T)G. Furthermore, the protein should include a SANT/Myb domain that adopts a helix-turn-helix fold and functions as either a DNA-binding module or a protein-protein interaction interface. This domain, structurally related to the DNA-binding region of Myb transcription factors and the chromatin-associated SANT domain, typically consists of three alpha-helices arranged in tandem repeats. It originates from Rhizophora mucronata (Asiatic mangrove) and is annotated with UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 12182, 2651, 1920, 4496, 4067, 4821, 17, 2458, 3213, 2790, 3416, 16, 2154, 7014, 4067, 4821, 8132, 1922, 6989, 1930, 7208, 2007, 2743, 1942, 2487, 2678, 7076, 3709, 1942, 6980, 2628, 3286, 1922, 12343, 16, 23665, 16, 1930, 16965, 4271, 18, 2144, 2697, 2347, 1966, 3834, 4178, 1927, 5224, 5849, 7138, 4496, 3170, 1930, 27253, 4155, 16, 2679, 2222, 9505, 1922, 6445, 5878, 4028, 2427, 1966, 23075, 10408, 16, 5347, 5904, 3337, 16, 1930, 6048, 4755, 7622, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 16851, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 9059, 1922, 10825, 3213, 2790, 16, 5745, 6966, 1922, 10361, 9569, 18, 2176, 24032, 43, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 3170, 2597, 1920, 4563, 7864, 8016, 1966, 43, 5708, 5219, 1942, 4566, 1920, 2678, 3044, 15920, 16, 3868, 5133, 2487, 3709, 2427, 1966, 26169, 1948, 12, 49, 19, 62, 13, 49, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 7628, 19, 16851, 3418, 1988, 24032, 43, 7864, 17, 5165, 17, 7864, 3728, 1930, 4088, 1966, 3108, 43, 2678, 17, 2743, 9059, 2014, 43, 2213, 17, 2213, 2835, 6854, 18, 2052, 3418, 16, 12171, 2712, 1942, 1920, 2678, 17, 2743, 3031, 1927, 16851, 3213, 2790, 1930, 1920, 6338, 17, 2458, 7628, 3418, 16, 5745, 7543, 1927, 2559, 4595, 17, 12789, 14940, 1922, 10361, 9569, 18, 2176, 22970, 2037, 13458, 22575, 1019, 3422, 2830, 5499, 12, 11624, 2002, 22383, 1931, 1961, 13, 1930, 1977, 10633, 1956, 20709, 11569, 3213, 3640, 18, 3], "output": "MLGNRWSAIAAKLPGRTDNEIKNVWHTHLKKRVLKQKQDSRPQLYVTKSESESANSIDQTLPRLVEIKGCARMSSRPSSSEQSSVSTDISVTTAQTSNIGMVNGGESTDSSEIIPLIDENFWSEPELVEKSSVPSSFLDELHFQSPYTNVFDNTSVVGDGMDFWYELFVKTGGLQELL", "metadata": {"id": "A0A2P2Q669", "cluster": 19485850, "interpro_all": ["IPR009057", "IPR017930", "IPR051953", "IPR001005"], "interpro_used": ["IPR051953", "IPR017930", "IPR001005"], "interpro_unused": ["IPR009057"]}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that can perform the following function: The protein is associated with the Nitrogen regulatory protein PII/ATP phosphoribosyltransferase C-terminal superfamily, which comprises a ferredoxin-like $\\alpha/\\beta$ sandwich domain that typically forms trimers to regulate metabolic pathways. Specific members include the nitrogen regulatory protein PII, which controls glutamine synthetase activity in response to nitrogen availability, and the C-terminal domain of ATP phosphoribosyltransferase, which binds the allosteric inhibitor histidine to control histidine biosynthesis. Additionally, the protein is classified under the Cyclic-di-AMP receptor family, which binds the bacterial secondary messenger cyclic-di-AMP (c-di-AMP) to regulate processes such as DNA integrity sensing, cell wall metabolism, and potassium transport. These proteins adopt a ferredoxin-like fold and are structurally related to Pii-signal transduction proteins. Also, the protein is classified under the Nitrogen regulatory PII-like, alpha/beta superfamily, which forms a ferredoxin-like \u03b1/\u03b2 sandwich structure that typically assembles into trimers with orthogonally packed \u03b2-sheets. This domain is integral to diverse proteins, including nitrogen regulatory protein PII, the C-terminus of ATP phosphoribosyltransferases, and the divalent ion tolerance protein CutA1. It is found in Candidatus Segetimicrobium genomatis.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 6634, 4948, 2213, 4269, 1033, 19, 4498, 3421, 2023, 25566, 45, 17, 4262, 13975, 16, 2154, 12936, 43, 25304, 22389, 10960, 17, 3189, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3418, 1988, 5745, 4952, 28220, 1942, 5741, 4487, 3873, 18, 2487, 4678, 3951, 1920, 6634, 4948, 2213, 4269, 1033, 16, 2154, 3562, 9959, 18185, 2455, 1922, 2644, 1942, 6634, 6855, 16, 1930, 1920, 45, 17, 4262, 3418, 1927, 4498, 3421, 2023, 25566, 16, 2154, 6876, 1920, 14772, 4106, 13873, 1942, 2285, 13873, 8132, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 9821, 17, 2137, 17, 3681, 3148, 3416, 16, 2154, 6876, 1920, 4543, 4067, 16716, 9821, 17, 2137, 17, 3681, 12, 45, 17, 2137, 17, 3681, 13, 1942, 5741, 4028, 2427, 1966, 2678, 7996, 9306, 16, 2024, 4821, 4714, 16, 1930, 9057, 4860, 18, 2144, 2697, 14103, 43, 25304, 22389, 10960, 17, 3189, 3728, 1930, 2032, 12171, 2712, 1942, 4269, 1033, 17, 2733, 8201, 2697, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 6634, 4948, 4269, 1033, 17, 3189, 16, 4595, 19, 4666, 13975, 16, 2154, 4952, 43, 25304, 22389, 10960, 17, 3189, 160, 19, 161, 18038, 3170, 1988, 5745, 17421, 1036, 2460, 28220, 1956, 15581, 1954, 15827, 161, 17, 14685, 18, 2052, 3418, 1977, 12328, 1942, 6445, 2697, 16, 2710, 6634, 4948, 2213, 4269, 1033, 16, 1920, 45, 17, 7822, 1927, 4498, 3421, 2023, 25566, 1036, 16, 1930, 1920, 21610, 4755, 6555, 2213, 4665, 4904, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 4133, 4988, 4913, 15129, 2457, 2065, 24200, 18, 3], "output": "MRLVLAIVQEKDVGRLIDALTEDGFNATMLASTGGFLREGNSTILIGVDDQQIQQVLAIIQRSAHRREQFVSPMPPAVEPVDSYVTYPVKVEVGGAIVFVLQVERMERF", "metadata": {"id": "A0A537LND4", "cluster": 20565769, "interpro_all": ["IPR010375", "IPR011322", "IPR015867"], "interpro_used": ["IPR015867", "IPR010375", "IPR011322"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is grouped in the Nucleotide cyclase superfamily, which encompasses catalytic domains found in adenylyl, guanylyl, and diguanylate cyclases responsible for synthesizing cyclic nucleotide second messengers. These domains share a core ferredoxin-like fold, though the specific nucleotide-binding mode differs between subtypes such as the GGDEF domain and adenylate cyclases. Furthermore, the protein carries a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. In addition, the protein includes a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It is identified in Brenthis ino (lesser marbled fritillary) and is associated with UniProt keywords Lyase, Repeat, and ATP-binding. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 5489, 16526, 13975, 16, 2154, 21569, 6804, 4682, 2435, 1922, 27802, 16, 13504, 25671, 16, 1930, 4325, 13785, 9075, 16526, 1036, 5061, 1958, 25292, 9821, 5489, 2812, 16716, 1036, 18, 2144, 4682, 7948, 43, 4728, 25304, 22389, 10960, 17, 3189, 3728, 16, 4170, 1920, 2487, 5489, 17, 2743, 5754, 11457, 2192, 8160, 2427, 1966, 1920, 12358, 3695, 1038, 3418, 1930, 23052, 16526, 1036, 18, 3677, 16, 1920, 2213, 16252, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 1922, 2459, 16, 1920, 2213, 5921, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 1977, 2899, 1922, 3022, 4905, 17210, 26848, 12, 11318, 3684, 7272, 1007, 9081, 3839, 2141, 13, 1930, 1977, 2458, 1956, 20709, 11569, 23928, 16, 6865, 16, 1930, 4498, 17, 2743, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MLKMASACADSSKQTRFHEMHVQRHNNVSILYADIVNFTPLSERLSASDLVKTLNELFGRFDQIAQENQCMRIKILGDCYYCVSGLPVSRPNHAYNCVNMGLQMIDAIRFVREATGFNVDMRIGIHTGNVLCGVLGLRKWQFDVWSDDVTLANHMESGGIAGRVHITKATMLQLGGKFEVEPGEGASREGYLADHKVETYLIVPPKKPGISENGRLSVCTVDRKASIVSSICQEVSPTKPKDISPAPSQHSFVEQENTKVMRAESLRNPDLNRRASVKVDGLKTVAFEHNSSASNSGDTVVNGAVTKPKSRSGSIIGAISPIMGTATPGVPTRSRPSSKMTKYVECWGADKPFANITDSTLAKNIGISSLAMIEQHLLPQRTCCDCSNNSEGLIPLTLGFQNRNQERQYRNQPDAQFKYYIACSTALFMLLAFIQILTVPKGIVIYASFGPTLVTLLVFLYLSWSDGREGLLLSDVPDDLYVDNCSKPGQVVANNCYIRLTMFVISVVLISSCAVINLFQGYIIQDFPEDLNNSSSWNATSAPRIPIYLDVDSAPSYLYSSVLTLASISVFLRLGFVLKLFLMIGTLIGHITLFSSAELFSQYQNKDPDTEFSMLPYAAKAGLVLVFLAALLHILDRQIEFTSRTDFLWKDKLKFEQEEVETMRGINKILLENILPAHVAQHFLTSVASKEELYHERYSSIAVMFASIPNYKEFYDETDVNKQGLECLRLLNEIICDFDKLLLKPKFSCIEKIKTIGSTYMIASGLRPGKEEQIDGNSKEEHTVAILVEFAIALMTILDQINRESFQRFKLRIGLNHGPVIAGVVGAQKPQYDIWGNAVNVASRMDSTGLMGKIHVTEDTAKVLMNAGYTCECRGPTFVKGKGTLVTYFVKTPNIGV", "metadata": {"id": "A0A8J9VMM4", "cluster": 21986462, "interpro_all": ["IPR001054", "IPR018297", "IPR029787"], "interpro_used": ["IPR029787", "IPR018297", "IPR001054"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein possesses a Cyanovirin-N domain that displays virucidal activity against viruses such as HIV and influenza by binding with high affinity to viral surface glycoproteins and high-mannose oligosaccharides. Originally identified in the cyanobacterium *Nostoc ellipsosporum*, this evolutionarily conserved module features a complex fold composed of tandem repeats of beta-sheets and beta-hairpins. It is found in Diaporthe ampelina.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 26898, 3026, 1921, 17, 56, 3418, 1988, 10750, 2787, 6817, 1923, 2455, 3316, 6241, 2427, 1966, 3525, 1930, 7108, 2007, 2743, 1956, 2149, 5173, 1942, 4324, 3154, 16268, 1930, 2149, 17, 17936, 22012, 18, 10398, 2899, 1922, 1920, 26898, 7972, 2341, 18842, 1989, 14, 9291, 4575, 1030, 25467, 3508, 17279, 14, 16, 2052, 18584, 5305, 9059, 4075, 43, 2796, 3728, 7179, 1927, 10361, 9569, 1927, 4666, 17, 14685, 1930, 4666, 17, 14565, 1036, 18, 2176, 1977, 2435, 1922, 27314, 10148, 1021, 3681, 11136, 1019, 18, 3], "output": "MTNFPIRMNGFLDFCSAYSLARNMGAALFTSHININECLSNNGFTLCETCNGTSLQCVCKQFLGIGLDGEGRIVLYCDGVDQKNNVLQVSGECSPEPNGDGKLVPKKHGGALGSCECDVDRPGTGKKTNMMDMN", "metadata": {"id": "A0A0G2FMR1", "cluster": 23813989, "interpro_all": ["IPR011058", "IPR036673"], "interpro_used": ["IPR011058"], "interpro_unused": ["IPR036673"]}, "task_type": "infilling"} {"instruction": "Given the following functional description of a protein, generate a complete amino acid sequence that performs the described role. The desired function is: The protein is assigned to the Trimeric LpxA-like superfamily, which encompasses trimeric enzymes characterized by a single-stranded left-handed \u03b2-helix fold composed of tandem hexapeptide repeats. Members of this group primarily act as bacterial transferases involved in lipid A, lysine, and UDP-N-acetylglucosamine biosynthesis, or as zinc-dependent carbonic anhydrases that catalyze the reversible hydration of carbon dioxide. Moreover, the protein should have a Hexapeptide transferase conserved site that forms a left-handed parallel $\\beta$-helix structure composed of tandem repeats of a [LIV]-G-X(4) motif. This structural feature is characteristic of diverse bacterial enzymes, including UDP N-acetylglucosamine acyltransferases, galactoside acetyltransferases, and gamma-class carbonic anhydrases. It is expressed in Paenibacillus sp. FSL R7-0331.", "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 16, 5655, 43, 4080, 3835, 2687, 3244, 1988, 17436, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 1977, 6304, 1942, 1920, 29177, 8182, 11414, 17, 3189, 13975, 16, 2154, 21569, 29177, 5038, 4378, 2007, 43, 2957, 17, 10338, 3506, 17, 17105, 161, 17, 7864, 3728, 7179, 1927, 10361, 7142, 24010, 9569, 18, 4678, 1927, 2052, 2210, 5985, 4033, 1966, 4543, 13763, 1036, 3286, 1922, 4486, 43, 16, 9082, 16, 1930, 18500, 17, 56, 17, 6894, 22988, 17454, 8132, 16, 2014, 1966, 7997, 17, 3100, 5056, 1935, 22018, 2319, 1988, 18170, 1920, 10743, 16561, 1927, 5056, 15422, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 7142, 24010, 13763, 5305, 3200, 1988, 4952, 43, 3506, 17, 17105, 6110, 8, 38, 4666, 8, 17, 7864, 3170, 7179, 1927, 10361, 9569, 1927, 43, 37, 15260, 39, 17, 49, 17, 66, 12, 24, 13, 5219, 18, 2052, 4346, 5961, 1977, 6293, 1927, 6445, 4543, 5038, 16, 2710, 18500, 56, 17, 6894, 22988, 17454, 11337, 18580, 16, 9479, 8028, 22226, 1036, 16, 1930, 7034, 17, 2921, 5056, 1935, 22018, 2319, 18, 2176, 1977, 3198, 1922, 25726, 8635, 7972, 10401, 5277, 1036, 2056, 18, 28782, 29396, 17, 23343, 1009, 18, 3], "output": "MLVTGAGAYTAGVGVAGGAGVAVGVDVAVGVGVAVGAVGAGVAVGAGVAVGAGVAFGVGIAVGFGVTVGSGVTVGFGVIVGPGVAVGSGVAVGVGVAVGSGVAVGAGVAVGSGVGSTAGLPITTSRNGLA", "metadata": {"id": "A0A089L615", "cluster": 24155042, "interpro_all": ["IPR018357", "IPR011004"], "interpro_used": ["IPR011004", "IPR018357"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein is categorized in the Light-independent protochlorophyllide reductase family, which comprises the BchN/ChlN subunits of the dark-operative protochlorophyllide reductase (DPOR) complex. These proteins associate with BchB/ChlB to form a catalytic core that utilizes Mg-ATP and reduced ferredoxin to reduce protochlorophyllide to chlorophyllide a during light-independent chlorophyll and bacteriochlorophyll biosynthesis. Additionally, the protein features a Nitrogenase/oxidoreductase, component 1 domain that functions as a catalytic subunit in cofactor-dependent oxidoreductases, specifically within the nitrogenase complex or as protochlorophyllide reductase. In nitrogen fixation, it serves as the molybdenum-iron, vanadium-iron, or iron-iron component to catalyze nitrogen reduction, while in chlorophyll biosynthesis, it mediates the light-dependent reduction of protochlorophyllide to chlorophyllide. It is found in Synechococcus sp. (strain RCC307) and has UniProt annotations Photosynthesis, Metal-binding, and Iron-sulfur.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 3696, 17, 3484, 3899, 7806, 30232, 25818, 11560, 2261, 11386, 3416, 16, 2154, 12936, 1920, 6452, 11619, 19, 17906, 1022, 6991, 1927, 1920, 6190, 17, 8116, 3899, 7806, 30232, 25818, 11560, 2261, 11386, 12, 5679, 1924, 13, 2796, 18, 2144, 2697, 11774, 1956, 6452, 18549, 19, 17906, 1014, 1942, 2386, 43, 6804, 4728, 1988, 18127, 2786, 17, 4498, 1930, 3028, 25304, 22389, 10960, 1942, 4412, 3899, 7806, 30232, 25818, 11560, 2261, 1942, 16553, 2261, 43, 2409, 3696, 17, 3484, 16553, 1930, 14027, 20845, 13384, 8132, 18, 4950, 16, 1920, 2213, 4075, 43, 6634, 2051, 19, 27388, 16, 4594, 21, 3418, 1988, 4088, 1966, 43, 6804, 5903, 1922, 15155, 17, 3100, 27388, 1036, 16, 4475, 2651, 1920, 6634, 2051, 2796, 2014, 1966, 3899, 7806, 30232, 25818, 11560, 2261, 11386, 18, 1922, 6634, 7938, 16, 2176, 10634, 1966, 1920, 2629, 16924, 5233, 1989, 17, 5680, 16, 7409, 21913, 17, 5680, 16, 2014, 5680, 17, 5680, 4594, 1942, 18170, 6634, 3378, 16, 2679, 1922, 16553, 8132, 16, 2176, 10412, 1920, 3696, 17, 3100, 3378, 1927, 3899, 7806, 30232, 25818, 11560, 2261, 1942, 16553, 2261, 18, 2176, 1977, 2435, 1922, 26734, 8256, 2056, 18, 12, 3943, 13253, 28569, 13, 1930, 2258, 20709, 15010, 18133, 16, 6048, 17, 2743, 16, 1930, 5680, 17, 12585, 18, 3], "output": "MQLQLLKESGQREVFCGLTSIQSAAGVMIFAEPRFGTVADLLQRRPEIRTLFLVGSCPSEVIKLDLSIETTFTQGEDQALTALVPLMPQSTTPQLLVASLPPRRSTELPAVGPGTKLLLTQPFLGQTARALQAKGRAAARAFGISDEHTTSVLEPLVTRGRAALEPHRKALEGKRLGRFLQRECGMELVEVGTPEQLQRVRQSHPDLVVCGMGLANPLEAEPIHGCDQAGDLAELFARPLRRRGALTFAIVWLHRRMPDAFFLVVGSRTCAHLAILGERDLAGLADANEELDRVKAAERLNQQHRGRVQVVNYSGSGLVGTLADGVEERFLTLFERLGIGPAELISSPYPLGVEGSELWFLFLLPDSQMELAYLDRALQQEELDLLPADVQLSEGQNVEGITTKWSIELVFS", "metadata": {"id": "A5GUA8", "cluster": 24501650, "interpro_all": ["IPR050293", "IPR000510", "IPR005970"], "interpro_used": ["IPR050293", "IPR000510"], "interpro_unused": ["IPR005970"]}, "task_type": "infilling"} {"instruction": "I am designing a protein with the following function: The protein includes a Double Cache 1 domain that functions as an extracellular sensor predicted to recognize small molecules. This domain is found in diverse proteins, including animal dihydropyridine-sensitive voltage-gated calcium channel alpha-2delta subunits and bacterial chemotaxis receptors. Additionally, the protein falls within the Periplasmic sensor-like domain superfamily, which serves as a sensory module typically found in the periplasmic region of two-component sensor kinases and proteins such as LuxQ. This domain adopts an \u03b1(2)-\u03b2(2)-\u03b1(2)-\u03b2(3) fold potentially related to the PAS domain, playing a key role in signal transduction by detecting environmental stimuli. It is expressed in Clostridia bacterium and features UniProt keywords Cell membrane, Transmembrane helix, and Transmembrane. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 4825, 23630, 1021, 21, 3418, 1988, 4088, 1966, 1925, 5329, 6443, 4396, 1942, 9967, 2858, 4206, 18, 2052, 3418, 1977, 2435, 1922, 6445, 2697, 16, 2710, 4027, 11842, 18425, 5802, 17, 4532, 6889, 17, 12336, 5016, 4999, 4595, 17, 5941, 9551, 1019, 6991, 1930, 4543, 16884, 4086, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 24334, 6443, 17, 3189, 3418, 13975, 16, 2154, 10634, 1966, 43, 6893, 9059, 5745, 2435, 1922, 1920, 24334, 3031, 1927, 2288, 17, 4594, 6443, 7784, 1930, 2697, 2427, 1966, 17851, 1055, 18, 2052, 3418, 24032, 1925, 160, 12, 22, 13, 17, 161, 12, 22, 13, 17, 160, 12, 22, 13, 17, 161, 12, 23, 13, 3728, 5063, 2712, 1942, 1920, 9233, 3418, 16, 14797, 43, 3834, 2770, 1922, 2733, 8201, 2007, 9227, 4813, 5458, 18, 2176, 1977, 3198, 1922, 17938, 14773, 14061, 1930, 4075, 20709, 11569, 2024, 3260, 16, 9117, 7864, 16, 1930, 9117, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MINMGNDHIASNKLLRRVAGISAETDRCARAVCRNHHHKTEVLRMTKMEATAEVKKEKVKKLKQKRDQRKSSLKSKIISSVVALVLVTILLFGVASCVLCYQSTIEGLEQSMAATANATAKSIANGIRSFTNVMQELGRDPAIGDQNISVRVKEAEANAKVTSYGMTAAYVLDTSGNMSSGGDNYAQADFFVAAMQGKTFITTPSTSKATGELVVALSAPIWEDGKVNSEITGVILAIAPGTLLYEAVEGINVSPSGYTYVIDKNGYTIADPDTQLVIDRENIEELAKENTALKSLADIHTKARAGEAGFDRYTYK", "metadata": {"id": "A0A965U4X7", "cluster": 25768335, "interpro_all": ["IPR033479", "IPR029151"], "interpro_used": ["IPR033479", "IPR029151"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein is grouped in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is produced by Catenibacterium sp. BIOML-A1 and features UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 4152, 2007, 3115, 28131, 7972, 2341, 18842, 1989, 2056, 18, 4071, 1024, 17, 8080, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MQVIGLTGGIASGKSTVALEPATEAFKQVIEHFPVLDNGIINRLEGILHPYIRSVIVQKIKQSKNNIVFIDVPLLFEAGWDDHCTRTQALDRIRNQMYYDLEKEILKVLKEVESYYLITHGYEVIDADDISRHQKLADIIFNNQNEKNYLCDSTIVVSCDKETQIQRVLSRDSLEDKEQRADYIIRNNTN", "metadata": {"id": "A0A6N9L5E9", "cluster": 28532016, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein possesses a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. Moreover, the protein is categorized in the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. Moreover, the protein should include a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. It is expressed in Bacteroidota bacterium and is classified with UniProt keywords Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 2176, 1977, 3198, 1922, 24323, 7336, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "NKVAEFTGKLHYFPMDFKNAEGYEKLSKEIHSLSGTCGSECNYIYYLATIPALFPEITVNLGKAGLNKSAGGFCRIIVEKPFGYDLDSAIELNKVMHGVFEEDQIYRIDHYLGKETVQNIMVTRFANGIFEPIWNRNYIHHIEVTSSENIGIENRGGYYETAGALRDMVQSHLLRLVTLIAMEPPSSFDSDAVRNEQLKVLQSLRKLKPEEVDSNVIRGQYISSLINGNIVKAYREEKGVDPESRVETYAAIKFYIDNWRWGSVPFYIRTGKHLPTRVTEAVIHFRKTPHYLFKESQNNSDNQLILRIQPDEGILLKFGMKEPGAGFKVHNVSMDFHYKDITNVYIPEAYERLIYDCMIGDSTLFLRADAVEEAWKFVEPIQKAWADNGSVKIYGYPAGTWGPDVADKLIDGGDNTSWRYPCKNLADYGIYCEL", "metadata": {"id": "A0A350V253", "cluster": 1907906, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR019796", "IPR036291", "IPR022674"], "interpro_unused": ["IPR001282", "IPR022675"]}, "task_type": "autoregressive"} {"instruction": "I want a protein that has the function: The protein includes a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Furthermore, the protein features a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Furthermore, the protein carries a SNF2, N-terminal domain that functions as the catalytic ATPase component of the SNF2/SWI complex to disrupt histone-DNA interactions and remodel chromatin. By utilizing energy derived from ATP hydrolysis, it increases DNA accessibility for critical processes such as transcription regulation, DNA repair, and recombination. It is derived from Striga hermonthica (Purple witchweed) (Buchnera hermonthica) and is described by UniProt keywords Hydrolase. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 5921, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 3677, 16, 1920, 2213, 4075, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 3677, 16, 1920, 2213, 16252, 43, 22280, 1028, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 9444, 4594, 1927, 1920, 22280, 1028, 19, 19532, 2796, 1942, 12512, 6632, 17, 2678, 3719, 1930, 7456, 1938, 6338, 18, 2007, 10232, 3844, 3595, 2037, 4498, 9128, 16, 2176, 4041, 2678, 12995, 1958, 4140, 4028, 2427, 1966, 3213, 3640, 16, 2678, 5059, 16, 1930, 7827, 18, 2176, 1977, 3595, 2037, 2114, 1950, 1019, 19432, 4202, 23733, 1019, 12, 14308, 16086, 2072, 29775, 13, 12, 25485, 3239, 1019, 19432, 4202, 23733, 1019, 13, 1930, 1977, 2910, 2007, 20709, 11569, 20748, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MRPRTRNQWDHHYRNLFSANVKKKKKTKTPNDYGGEKHGLVILGKKNIAHAGPSVKRGRGRPRKIENVNSIKCDDDSIDLEVDRITGKRCRGVPPAPPLDDSLVDLTETTSEEEDFSDEDYSESSTDSDPDERAGENAKIIIIKKGNVEKVNIEEESDDRGSPSPIRPFNLNTKSQNFVPHINDNQEFIDVRGNIRKGGKIECGAEQERDLEIVDADGEKFSGINKSARHKPLAGLPRDNRSHLSSYGCVLKDRRDGGNSVSSRAKRHKLGSDESFKNKPLVDAGGGHLEDAVERNPRFTLSKKKNSRATNQDLIEILVDSINSNSANEYDQCYGKKNEFTVPGLPLRFRFEDEVEPPRDKPDWEKEIDSLFCALDIGLLESEIDRASSCVNDDNLTEIDESRAGCCARGQHVPILDEQIGIICKYCLIVVLEIKHVLPPFYTRPPGRHKWKDPDDPARYCVDEIHLHRSGFNKPPRGSISRNRGTVWDLIPGVENEMYPHQREGFEFMWNNIAGGIVIEKMKQPLSGGRGCIISHAPGTGKTRLAIVFLQSFLKLYPSCKPVIIAPKGMLLTWESEFLKWKVDIPFHNLNRKDLSENEQAFAAHVLVRAGKGSGPMSIDCIRLTKLASWVSETSILGISYHVFKNLARGNGGGVAGQIQKVLLEYPGLLVLDEGHTPRNDDSQIWKALSKVATERRIILSGTPFQNNLAELYNTLCIVNPRFANGIDSPNARVRGRKRRLVEKKKWVEFAGGSIGLRKLREMLGPFVHVHKGSILEESLPGLRDTLVFLRPTEEQRVLLEDSARIKNIFNKIHQVSLVSVHPSGSGVKTTFVMKLIQLADALGERVLIFSQYLKPLMFIKKQIKSRFSWQEEREILYMDGQLDEKHRQNSISSFNDERSKAKVLLASERACSEGINLVGASRVVLLDTVWNPSVEKQAVSRAYRLGQKRIVHVYRLFTSGTEVTQYAHQIHKDRISHLLFSSTERGENLGCELGPYEDRILQAMLHQEGFAHIFDKVIYQPKESDLINIFGPELGVCSV", "metadata": {"id": "A0A9N7NEL0", "cluster": 4829949, "interpro_all": ["IPR044567", "IPR014001", "IPR001650", "IPR027417", "IPR038718", "IPR049730", "IPR000330"], "interpro_used": ["IPR014001", "IPR001650", "IPR000330"], "interpro_unused": ["IPR038718", "IPR044567", "IPR049730", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "The protein possesses a transcriptional regulator LacI/GalR-like sensor domain that functions as a C-terminal ligand-binding module in bacterial transcription factors to regulate gene expression in response to metabolic cues. Structurally related to periplasmic binding proteins, it binds effectors such as sugars, sugar phosphates, and purines to modulate the affinity of the associated N-terminal DNA-binding domain. This activity allows bacteria to fine-tune metabolic pathways, particularly those involved in carbohydrate utilization. Furthermore, the protein should contain a LacI-type HTH domain that functions as the N-terminal DNA-binding module in the LacI/GalR family of prokaryotic transcriptional regulators. It utilizes a helix-turn-helix motif to bind the major groove and a hinge helix to contact the minor groove of specific operator DNA. This domain is essential for coordinating catabolic and metabolic operons, often in response to sugar inducers. In addition, the protein carries a MerR-type HTH domain that functions as a winged helix-turn-helix DNA-binding module in bacterial transcriptional regulators responsive to environmental stimuli such as heavy metals, oxidative stress, or antibiotics. Acting typically as a dimer, it binds promoter regions between the -35 and -10 elements and distorts the DNA structure to modulate RNA polymerase initiation. It is found in Lactococcus hircilactis and corresponds to UniProt keyword Transcription regulation. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 5224, 7888, 7511, 1033, 19, 5179, 1005, 17, 3189, 6443, 3418, 1988, 4088, 1966, 43, 45, 17, 4262, 5207, 17, 2743, 9059, 1922, 4543, 3213, 2790, 1942, 5741, 2359, 2294, 1922, 2644, 1942, 4487, 8972, 18, 12171, 2712, 1942, 24334, 2743, 2697, 16, 2176, 6876, 13066, 2427, 1966, 15592, 16, 9523, 26473, 16, 1930, 19700, 1036, 1942, 8480, 1920, 5173, 1927, 1920, 2458, 56, 17, 4262, 2678, 17, 2743, 3418, 18, 2052, 2455, 5731, 4802, 1942, 8882, 17, 23703, 4487, 3873, 16, 4443, 2690, 3286, 1922, 10590, 8422, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 7511, 1033, 17, 2601, 5334, 1023, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 2678, 17, 2743, 9059, 1922, 1920, 7511, 1033, 19, 5179, 1005, 3416, 1927, 21545, 5224, 9098, 18, 2176, 18127, 43, 7864, 17, 5165, 17, 7864, 5219, 1942, 4566, 1920, 3044, 15920, 1930, 43, 20484, 7864, 1942, 5217, 1920, 5857, 15920, 1927, 2487, 14012, 2678, 18, 2052, 3418, 1977, 4415, 1958, 19355, 22112, 1930, 4487, 28748, 16, 3868, 1922, 2644, 1942, 9523, 23329, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 6902, 1005, 17, 2601, 5334, 1023, 3418, 1988, 4088, 1966, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 2678, 17, 2743, 9059, 1922, 4543, 5224, 9098, 8487, 1942, 4813, 5458, 2427, 1966, 7881, 11570, 16, 5163, 3071, 16, 2014, 7560, 18, 8290, 5745, 1966, 43, 7632, 16, 2176, 6876, 4465, 3451, 2192, 1920, 17, 3259, 1930, 17, 2119, 5362, 1930, 11606, 1973, 1920, 2678, 3170, 1942, 8480, 3146, 6479, 6035, 18, 2176, 1977, 2435, 1922, 5641, 8256, 15086, 10401, 2131, 1937, 1930, 8852, 1942, 20709, 11121, 2538, 3213, 3640, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MITIKEIAKKAGVSPTTVSNVLHNRTTEIRPEKLAHVKQIISENGYVPNMAGKALAGHKSQLIGVILSTEYRESKSILDDGYHGCLVGSIEQTLKAAGYYMLLSSAKTPIETLTTAKAWKVDGLIILESKAADVAPILQEIKTPTLFIDGEKPTHAENFYNISTDDFDGGFQMANYLKLIEKRKILFISDAPKPFGVDLARYKGVKQVFPNVMYHAFSSDFEIRTTQIRQWIIQKQWQAYDALFFSSDKIASETMQEMQDCGINVPNDIIIVGYDDSLYARTSRPQLTTIRQNIALKGQKAVETLVKLINHENAAFEIQLQSELIIRDSSTIKKK", "metadata": {"id": "A0A7X1ZB36", "cluster": 6721648, "interpro_all": ["IPR000843", "IPR046335", "IPR010982", "IPR000551", "IPR028082"], "interpro_used": ["IPR046335", "IPR000843", "IPR000551"], "interpro_unused": ["IPR010982", "IPR028082"]}, "task_type": "autoregressive"} {"instruction": "Here is the protein function: The protein is classified under the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Moreover, the protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is identified in Paenibacillus ihbetae and contains UniProt keyword associations ATP-binding, Cytoplasm, and Transferase. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2899, 1922, 25726, 8635, 7972, 10401, 5277, 1036, 13379, 20440, 1021, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MNIGLTGGIATGKSTVSSMLTKKGALLVDADVIAREVMLPGHPVLAEVTAHFGQHILLEDGTLNRKKLGEIIFRDPEQREALNRMTHPAIRQEIRDRTAAYERDYPDRLVVADIPLLLESREQYSFLEQIVVVYVPRELQIRRLMQRDALTEGQAAARLGSQMDIEVKKRLADIVIDNSGTPDETRQQVDKLWNRMVRV", "metadata": {"id": "A0A1B2E4H8", "cluster": 7577253, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein possesses a SIS domain that functions as a phosphosugar-binding module involved in sugar isomerization and metabolic regulation. It adopts an $\\alpha$-$\\beta$-$\\alpha$ sandwich fold and serves either as a catalytic domain in isomerases or as a sensor for phosphorylated sugar substrates in transcriptional regulators. Furthermore, the protein should include a GlmS/AgaS, SIS domain 1 domain that functions as a sugar isomerase module involved in hexosamine metabolism. In glucosamine-6-phosphate synthase (GlmS), this domain contributes to the conversion of fructose 6-phosphate into glucosamine 6-phosphate using glutamine as a nitrogen source, and it is also conserved in the putative isomerase AgaS. It is expressed in actinobacterium acAMD-5 and is annotated with UniProt keywords Repeat.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 19149, 3418, 1988, 4088, 1966, 43, 8078, 20490, 13279, 17, 2743, 9059, 3286, 1922, 9523, 27027, 1930, 4487, 3640, 18, 2176, 24032, 1925, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 17, 8, 38, 4595, 8, 18038, 3728, 1930, 10634, 3108, 1966, 43, 6804, 3418, 1922, 25510, 1036, 2014, 1966, 43, 6443, 1958, 7199, 9523, 6249, 1922, 5224, 9098, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 20458, 1036, 19, 8770, 1036, 16, 19149, 3418, 21, 3418, 1988, 4088, 1966, 43, 9523, 25510, 9059, 3286, 1922, 7142, 17454, 4714, 18, 1922, 28627, 17, 26, 17, 5413, 8921, 12, 20458, 1036, 13, 16, 2052, 3418, 7624, 1942, 1920, 7309, 1927, 15102, 26, 17, 5413, 2460, 28627, 26, 17, 5413, 2193, 9959, 1966, 43, 6634, 4585, 16, 1930, 2176, 1977, 2222, 5305, 1922, 1920, 6770, 25510, 8770, 1036, 18, 2176, 1977, 3198, 1922, 4718, 12022, 18699, 13620, 17, 25, 1930, 1977, 10633, 1956, 20709, 11569, 6865, 18, 3], "output": "MTQNIVTDLNEQPALMNDLISALTEFSTGTPWWDENYKRVLVIARGSSARVGELLVRSVAKSHPGLVTSFSPTDITADQDLRNVLVIAISQSGSTDEVVRAAALAQQNHAYVMAITNDPQSQLAKHCDYLVNLNLGPERAVPATKTVTATALVLLMIANVINGQKIESKQWLLLPDLIQKVLKSKSNGLAQIPAFVLSRGVGTPMAMEAALKFTEITKVPVVALSANDFLHGTTAALQPSDEVLLISLADDDLPGGLDLVKKHLEAKAINWHVIDSSMFCNSDFPSSLQAIISLVQVQVCVLETCINLGIDPDQDVGLTKITKT", "metadata": {"id": "A0A094RU35", "cluster": 8640430, "interpro_all": ["IPR035466", "IPR001347", "IPR046348"], "interpro_used": ["IPR001347", "IPR035466"], "interpro_unused": ["IPR046348"]}, "task_type": "autoregressive"} {"instruction": "Give me the sequence of a polypeptide chain with the following function. The function of the polypeptide chain is The protein features a AP180 N-terminal homology (ANTH) domain that functions as a membrane-binding module in endocytotic accessory proteins. It specifically recognizes phosphatidylinositol 4,5-bisphosphate (PIP2) and plays a universal role in the nucleation of clathrin-coated pits. In addition, the protein has a ENTH domain that functions as a membrane-interacting module primarily involved in clathrin-mediated endocytosis. It binds specific phosphoinositides, such as PtdIns(4,5)P2, and inserts an N-terminal helix into the lipid bilayer to induce the membrane curvature and tubulation necessary for vesicle budding. Furthermore, it serves as an accessory clathrin adaptor, linking membrane invagination with clathrin polymerization. In addition, the protein includes a Plant AP180-like N-terminal domain that facilitates clathrin-mediated endocytosis and cell wall assembly by contributing to the nucleation and formation of clathrin coats on membranes. This module binds phosphoinositide PtdIns(4,5)P2 and proteins such as alphaC-adaptin via a structure containing an alpha-helical superhelix and a spectrin-like coiled-coil. It has been detected in Ceratopteris richardii (Triangle waterfern) and exhibits UniProt keyword tags Cytoplasmic vesicle and Golgi apparatus.", "tokenized_instruction": [2, 7031, 2142, 1920, 3244, 1927, 43, 13022, 4659, 1956, 1920, 2894, 2347, 18, 1920, 2347, 1927, 1920, 13022, 4659, 1977, 1920, 2213, 4075, 43, 30102, 4476, 56, 17, 4262, 9039, 12, 8795, 13, 3418, 1988, 4088, 1966, 43, 3260, 17, 2743, 9059, 1922, 13573, 2355, 3153, 15954, 2697, 18, 2176, 4475, 16197, 16927, 24, 16, 25, 17, 29443, 12, 21753, 13, 1930, 5705, 43, 10321, 2770, 1922, 1920, 17254, 1927, 17053, 17, 7242, 27928, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 22696, 3418, 1988, 4088, 1966, 43, 3260, 17, 8615, 9059, 5985, 3286, 1922, 17053, 17, 3434, 11914, 18, 2176, 6876, 2487, 23546, 1036, 16, 2427, 1966, 21915, 12, 24, 16, 25, 13, 7535, 16, 1930, 17520, 1925, 56, 17, 4262, 7864, 2460, 1920, 4486, 14269, 1942, 4769, 1920, 3260, 13996, 1930, 25860, 1943, 4680, 1958, 11502, 15909, 18, 3677, 16, 2176, 10634, 1966, 1925, 15954, 17053, 15077, 16, 9486, 3260, 27134, 2636, 1956, 17053, 11486, 18, 1922, 2459, 16, 1920, 2213, 5921, 43, 4496, 30102, 4476, 17, 3189, 56, 17, 4262, 3418, 1988, 11374, 17053, 17, 3434, 11914, 1930, 2024, 4821, 5957, 2007, 8739, 1942, 1920, 17254, 1930, 3337, 1927, 17053, 15642, 1036, 1990, 5726, 18, 2052, 9059, 6876, 23546, 21915, 12, 24, 16, 25, 13, 7535, 1930, 2697, 2427, 1966, 4595, 1030, 17, 10044, 1921, 3454, 43, 3170, 3165, 1925, 4595, 17, 11514, 3356, 23285, 2416, 1930, 43, 27478, 17, 3189, 17524, 17, 9121, 18, 2176, 2258, 2252, 3330, 1922, 6580, 8286, 2410, 18842, 1036, 21097, 3907, 12, 18566, 3224, 2070, 1022, 13, 1930, 9826, 20709, 11121, 2538, 14392, 6823, 11502, 1930, 10277, 11161, 18, 3], "output": "MDSMQGKLKKALGAVKDQTSISIAKVGSTGSPEVEIALVKATSHDESALEEKYVQELLLLTSSRQHVEACITIMGRRLRKTHNWIVAVKVLMVAHRLLRDGDAAIQHALASTRKKGMCVFSTYAFRDESHSNGWEFSAFVRAYGMYLDERSEYSSPSLSLPNSHQSSKDGSLYDQDHPYNSSSASPSGNDDDRSRGKQRRRRPVKKMRTSELLQKFPLFLRLLERILACRPVGAAKTNRLVLFALHPIVRESFLVYSDIRDGMSILLDAFFDLEELECLGAFDIYSKAAKQLEELTSFYGFCKSLGVCKTTEYPAVEKVSNEMLQTMSASLRLRLDSDRGNNRKAKAHEVKEELSCDSDHASKEAGSSRPPSSTRTRIMTSDPVCPRLEQEETPEVSSALINQSKDYPDLLDLDENPTQMTHKRGENPTSTIFPGTGTRIDTTWQTFSHGSTGNSSLNLCDFEKSGKQTADWELALESNSSLSRWTSADLASGFDLLHLDSLYDLGSNNQIRQAHEFGSRRSVSVMASDQPLQPDLLTFPASNAGSLNEQLHVVRDPFALSTNVPLIPCVLMSHPRQDQQPGIEEQQRWHEWQQHSQNFSYSVSPIDIVTNPFATPFQSPACTVPDSRMQSNYT", "metadata": {"id": "A0A8T2UVU7", "cluster": 8804165, "interpro_all": ["IPR011417", "IPR014712", "IPR048050", "IPR045192", "IPR013809", "IPR008942"], "interpro_used": ["IPR011417", "IPR013809", "IPR048050"], "interpro_unused": ["IPR045192", "IPR008942", "IPR014712"]}, "task_type": "autoregressive"} {"instruction": "Functionally defined as:\nThe protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Also, the protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein is classified under the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is native to Weissella halotolerans DSM 20190 and contains UniProt keyword associations Cytoplasm and rRNA processing.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 6196, 1942, 24634, 5870, 23226, 4575, 3823, 2075, 10964, 14064, 1008, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 1930, 9067, 4587, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MTAFEHVTVLLNEAIEQLAVQPAGQYVDATLRQGHLWSFDQDITAIHYNEEHLAAEIAADKVTLINDNFRNLDGVLYDLGVSSPQFDDGKRGFSYNYEAPLDMRMDQSQALDRYGEERFAKQIARGIERERAKAPIETTFDLVNIIRIAVNDELGAVETSLEQALDMLAIHGRIAVITFQSLEDRLVKSMFRHKPILPNEQELSQNHRAHSAKLRVIERIKLGGGGHSKLLASQTQDLAQVGVTRVAYQVVNTWSFHDLMRILSKDAIPAAARRTGGHPAKKSFQAIERASLPELPAGLPVIPAELEPDFKLIT", "metadata": {"id": "A0A0R2FTI9", "cluster": 9952641, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR023397", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein includes a IstB-like ATP-binding domain that contains an ATP/GTP-binding P-loop motif and is found in proteins such as the DNA replication factor DnaC and the transposase regulator IstB. This domain facilitates nucleotide binding and protein complex formation, specifically enabling DnaC to interact with DnaB to assemble the primosome for DNA replication. Moreover, the protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is found in Candidatus Goldiibacteriota bacterium HGW-Goldbacteria-1.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 5921, 43, 1977, 27414, 17, 3189, 4498, 17, 2743, 3418, 1988, 5461, 1925, 4498, 19, 9319, 17, 2743, 58, 17, 5881, 5219, 1930, 1977, 2435, 1922, 2697, 2427, 1966, 1920, 2678, 5158, 2991, 2678, 1030, 1930, 1920, 12935, 2051, 7888, 1977, 27414, 18, 2052, 3418, 11374, 5489, 2743, 1930, 2213, 2796, 3337, 16, 4475, 12180, 2678, 1030, 1942, 6310, 1956, 2678, 1014, 1942, 17421, 1920, 2610, 4283, 1958, 2678, 5158, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 6557, 3907, 7972, 2341, 18842, 7336, 14061, 7175, 1018, 17, 6557, 7972, 2341, 18339, 17, 21, 18, 3], "output": "MACAFGNLFCRNGFTVSHFRKLSKTNLLLIDDFGISALFDYDRKYFLWNKFMGKPTIADAVMDRLLHISYKFETLNKALDCGIFWPRLFGDIMASKDASNYLKHLKEIISNRYMAGSTIITIQFPIKELRGGSMRKPQK", "metadata": {"id": "A0A2N1W845", "cluster": 11451390, "interpro_all": ["IPR002611", "IPR027417"], "interpro_used": ["IPR002611", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein incorporates a HPr kinase/phosphorylase, C-terminal domain that functions as the catalytic core of the bifunctional enzyme HprK/P, regulating carbon source utilization in Gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 on the phosphocarrier protein HPr and its dephosphorylation via phosphorolysis, typically within a hexameric assembly. Also, the protein includes a HPr(Ser) kinase/phosphorylase, N-terminal domain that constitutes the structural blades of the hexameric HPr serine/threonine kinase PtsK, a sensor protein controlling bacterial carbon catabolite repression. This domain facilitates the assembly of the enzyme's three-bladed propeller structure, allowing it to function within a multicomponent phosphorelay system. It is native to Gammaproteobacteria bacterium and is linked to UniProt keywords Metal-binding, Multifunctional enzyme, and Serine/threonine-protein kinase. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 19683, 43, 18542, 4016, 19, 12556, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 1920, 29491, 4113, 18542, 1040, 19, 58, 16, 6773, 5056, 4585, 8422, 1922, 8604, 17, 2843, 4802, 18, 2176, 17097, 2321, 1920, 4498, 17, 3100, 4050, 1927, 2375, 17, 4182, 1990, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 2496, 16881, 3454, 3421, 6892, 16, 5745, 2651, 43, 25602, 1935, 5957, 18, 2222, 16, 1920, 2213, 5921, 43, 18542, 12, 2375, 13, 4016, 19, 12556, 2051, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 4346, 22707, 1036, 1927, 1920, 25602, 1935, 18542, 8468, 19, 13143, 4016, 8618, 1040, 16, 43, 6443, 2213, 7138, 4543, 5056, 3115, 3016, 2394, 10084, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 4113, 11, 61, 2559, 17, 22707, 1007, 5062, 13728, 3170, 16, 7201, 2176, 1942, 2347, 2651, 43, 8844, 28155, 1939, 3421, 15208, 1012, 2433, 18, 2176, 1977, 6196, 1942, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 6048, 17, 2743, 16, 20136, 4113, 16, 1930, 8468, 19, 13143, 17, 2213, 4016, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MSARLSVGGQGARTGPLMSDALTAGQLFDSHHERLKLTWLAGREGADTAISFPPRDAPDQKLVDYLNPGRPHPIQLIGRSEHRYLSSLDATMRKSWLTSIFHTRPAMLILTDGLEAGTELVEMAEATMTPLLATPLEELRVMEYLQYQLEGLAADSEILHGVFLEVLGIGVLLTGLSGAGKSELALELINRGHRLIADDAAQFSCRSPGVIIGNCPQLLRDFLEVRGLGILNIRAMFGDNALLSSKRLRLIISLDVSSEKFSDESTRLDGGHQLRNIQGVEIPQLTVPVAPGRNLAVIIEAAVRNHLLTRSGYNAADDFIERQKRFMAGQKP", "metadata": {"id": "A0A7C1TJJ2", "cluster": 11571194, "interpro_all": ["IPR003755", "IPR011104", "IPR011126", "IPR027417", "IPR028979"], "interpro_used": ["IPR027417", "IPR011104", "IPR011126"], "interpro_unused": ["IPR028979", "IPR003755"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to create: The protein is assigned to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Moreover, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Furthermore, the protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is found in Austwickia chelonae NBRC 105200 and is linked to UniProt keywords Cytoplasm and rRNA processing. Please provide the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 7762, 30, 1920, 2213, 1977, 6304, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 2435, 1922, 18238, 1031, 17045, 12940, 2126, 11749, 12502, 1021, 8789, 15618, 7991, 11943, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 1930, 9067, 4587, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MSLSASERHVPVMCARITELLAPALNAPGSVYVDGTLGMGGHTEAVLSACPGARAIGIDRDEQALEQARERLAPFGERFVGVHARYDQIDEVLSDLTVGPVQAILLDLGVSSLQLDEAGRGFAYRMDAPLDMRMDRGLPRTAADVLNSYAVDELTRILRDYGEERFASRIARAVVTEREHEPFESSGRLVELLYRVIPAGSRKTGGHPAKRTFQALRIEVNEELESLSRVLPRAVESCAVDGRFAVLSYHSLEDRMVKKTFAAGLADTSPPDMPVQLPQHAPFLAPLTRGAETADDDEVARNPRSASAKLRVVRRIAPTPPGRLSDDSYADLSPRSRHQNRRKGQPR", "metadata": {"id": "K6UKL8", "cluster": 11886090, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, it is part of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is identified in Sorangium cellulosum (strain So ce56) (Polyangium cellulosum (strain So ce56)) and is associated with UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2899, 1922, 6548, 9506, 1989, 18485, 14740, 12, 3943, 2577, 5827, 6369, 13, 12, 4286, 9506, 1989, 18485, 14740, 12, 3943, 2577, 5827, 6369, 13, 13, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MGIVLFGLTGGLGVIDADALAREVVAKGTEGLDEVVRALGPEVADPDKRRQLNAIVHPRITALTLQGEPLACYEAALLVENGVADAFRPLVLAAQLPLASKVAVADYVIENSGIRAKLGVGPSAARKGAGQDPSGKSTVAAHFRARGLPVSPDGSLDRARVAAVVFERAAELEAVVAVPEAVQIARAMARDGATEHHVRARDRAATERQADEVLAA", "metadata": {"id": "A9GW10", "cluster": 13415817, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Target Function: The protein is associated with the Transcriptional regulatory protein WalR-like family, which functions as a response regulator within bacterial two-component systems to modulate gene expression via an N-terminal receiver domain and a C-terminal OmpR/PhoB-type DNA-binding domain. These proteins regulate diverse physiological processes, ranging from cell wall metabolism and heme homeostasis to envelope stress responses and virulence factor production. Also, the protein is included in the The CheY-like superfamily, which functions primarily as the receiver module in two-component signaling systems, mediates signal transduction through the phosphorylation of a conserved aspartate residue by a partner histidine kinase. Adopting a compact flavodoxin-like $\\alpha/\\beta/\\alpha$ fold, these domains often serve as N-terminal regulators coupled to DNA-binding effectors to control gene expression in response to environmental stimuli, though divergent members may bind RNA or lack the active phosphorylation site. Also, the protein carries a Signal transduction response regulator, receiver domain that functions as a phosphorylation-activated switch within two-component systems to couple environmental sensing with cellular adaptation. It accepts a phosphoryl group from a cognate sensor histidine kinase, inducing a conformational change that activates an associated effector domain to regulate gene expression. It is produced by Planctomycetota bacterium and corresponds to UniProt keyword Transcription regulation and Two-component regulatory system.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 5224, 4948, 2213, 16567, 1005, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 2644, 7888, 2651, 4543, 2288, 17, 4594, 3771, 1942, 8480, 2359, 2294, 3454, 1925, 56, 17, 4262, 12608, 3418, 1930, 43, 45, 17, 4262, 21921, 1005, 19, 20175, 1014, 17, 2601, 2678, 17, 2743, 3418, 18, 2144, 2697, 5741, 6445, 5005, 4028, 16, 6485, 2037, 2024, 4821, 4714, 1930, 10954, 7622, 1942, 11262, 3071, 3387, 1930, 9304, 2991, 3372, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 1920, 10003, 1012, 17, 3189, 13975, 16, 2154, 4088, 5985, 1966, 1920, 12608, 9059, 1922, 2288, 17, 4594, 3197, 3771, 16, 10412, 2733, 8201, 2596, 1920, 4050, 1927, 43, 5305, 12878, 6181, 2007, 43, 8240, 13873, 4016, 18, 20478, 43, 13726, 7732, 1986, 9754, 17, 3189, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 16, 2144, 4682, 3868, 7120, 1966, 56, 17, 4262, 9098, 6416, 1942, 2678, 17, 2743, 13066, 1942, 2285, 2359, 2294, 1922, 2644, 1942, 4813, 5458, 16, 4170, 13609, 4678, 2278, 4566, 3146, 2014, 3630, 1920, 3500, 4050, 3200, 18, 2222, 16, 1920, 2213, 16252, 43, 2733, 8201, 2644, 7888, 16, 12608, 3418, 1988, 4088, 1966, 43, 4050, 17, 4128, 6195, 2651, 2288, 17, 4594, 3771, 1942, 15116, 4813, 9306, 1956, 3689, 7810, 18, 2176, 5861, 1036, 43, 12556, 2210, 2037, 43, 15786, 6443, 13873, 4016, 16, 7834, 43, 8523, 3185, 1988, 9094, 1925, 2458, 7917, 3418, 1942, 5741, 2359, 2294, 18, 2176, 1977, 4152, 2007, 4720, 2341, 13386, 19446, 3857, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 3213, 3640, 1930, 2288, 17, 4594, 4948, 2433, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MKILLAEDDLVSRRMLEAFLKRRLAILDWMMPGMDGLQVCREVRNLKDRPLTKPFDAYELKARLNAGNDYEVVVVGDGTQASRLLQEEQGPYVYLILLTAKDRKEDIIEGLEAGADDY", "metadata": {"id": "A0A950RQY3", "cluster": 13540681, "interpro_all": ["IPR011006", "IPR001789", "IPR039420"], "interpro_used": ["IPR039420", "IPR011006", "IPR001789"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Moreover, the protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is present in Clostridiales bacterium and is connected to UniProt keyword Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 2481, 1922, 17938, 26890, 1918, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 3], "output": "MEFKHIPVLLNECIEGLNIKSCEKLNKIGTLIGIDQDEDAISTASKNLEGVKNRLYVVRDNYSHGVSSYQLDSAERGFSYMKDAPLDMRMDRGNDLTAEKVVNEIVSEREKSRVETTLQLVDIIDRAIPSKKGSKGHPAKRQNSIEKMVDRLNYGGRLCIITFHSLEDRIVKHIFKGLENPCICITNKPIISSNEEIKVNKRATSAKLRIVEKIDGVYVDCTLGSGGHSMKIIEKILNGLNFGTVDGFLLDIYSEHKLFEIIKEYGEERYAKRIANLTFQAIRIEVNGELEVLPPRLPICGCGRKQKAKI", "metadata": {"id": "A0A3D0YAL3", "cluster": 13836907, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein has a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Moreover, the protein incorporates a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is produced by Desulfurellaceae bacterium and is linked to UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3950, 16, 1920, 2213, 19683, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 4152, 2007, 30311, 2027, 11560, 9914, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MRVFAPAKVNLFLRILGRREDGYHLLDSLMLPVSLCDEIRIRLDGAVSAERPASSAQIRLSCDDSRIPSDETNLASRAASLVCREAGLAARVSLRLVKRIPAGAGLGGGSSDAAAVLKGLNSLLKLGWGEPRLCELGLRLGADVPFFIPCRPARATGIGEELRPAGLVGRRWLVLVVPSFGVSTPWAYRRFDQLVGMTAPSPTITVPADGWPPPAACLNDLERAVLPAHPLLQQLKNMLLSAQAEVALMSGSGSAVFGLFGRKEAAQRAADGIRQTVAQHSRVFVVESLAEAPCSNPPEVRSV", "metadata": {"id": "A0A9E4GIL2", "cluster": 14645629, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein includes a CHAP domain that functions as a cysteine- and histidine-dependent amidohydrolase or peptidase, primarily implicated in peptidoglycan hydrolysis. This domain utilizes invariant cysteine and histidine residues for catalytic nucleophilic attack, adopts an $\\alpha+\\beta$ structural fold, and is frequently associated with bacterial SH3 domains to facilitate cell wall degradation or remodeling. Moreover, the protein is classified under the Immunoglobulin-like fold superfamily, which comprises domains characterized by a beta-sandwich of seven or more strands arranged in a Greek-key topology, facilitating protein-protein interactions often via beta-sheet interfaces. These domains are ubiquitous in animal proteins, playing critical roles in immune recognition, cell adhesion, and structural integrity in muscle proteins such as titin. Additionally, the protein features a Secretion system, C-terminal sorting domain that targets proteins to the type IX secretion system (T9SS) for outer membrane sorting and covalent modification. Adopting an Ig-like fold, this domain is secreted and subsequently cleaved by a C-terminal signal peptidase. It is identified in Bacteroidetes bacterium GWA2_31_9.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 5921, 43, 14950, 3418, 1988, 4088, 1966, 43, 8666, 17, 1930, 13873, 17, 3100, 28813, 8601, 21524, 2014, 24050, 16, 5985, 6835, 1922, 24183, 9128, 18, 2052, 3418, 18127, 17004, 8666, 1930, 13873, 4248, 1958, 6804, 24456, 8926, 16, 24032, 1925, 8, 38, 4595, 15, 38, 4666, 8, 4346, 3728, 16, 1930, 1977, 5467, 2458, 1956, 4543, 18824, 4682, 1942, 6628, 2024, 4821, 4877, 2014, 8378, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 11837, 17, 3189, 3728, 13975, 16, 2154, 12936, 4682, 4378, 2007, 43, 4666, 17, 18038, 1927, 5260, 2014, 2253, 13214, 14940, 1922, 43, 27568, 17, 3834, 13678, 16, 12440, 2213, 17, 2213, 3719, 3868, 3454, 4666, 17, 11130, 14857, 18, 2144, 4682, 2032, 15498, 1922, 4027, 2697, 16, 14797, 4140, 5456, 1922, 3743, 5708, 16, 2024, 6141, 16, 1930, 4346, 7996, 1922, 3760, 2697, 2427, 1966, 7090, 1921, 18, 4950, 16, 1920, 2213, 4075, 43, 5512, 2433, 16, 45, 17, 4262, 11404, 3418, 1988, 4845, 2697, 1942, 1920, 2601, 13848, 5512, 2433, 12, 62, 1026, 5590, 13, 1958, 7642, 3260, 11404, 1930, 13577, 6295, 18, 20478, 1925, 7021, 17, 3189, 3728, 16, 2052, 3418, 1977, 8366, 1930, 5326, 10246, 2007, 43, 45, 17, 4262, 2733, 24050, 18, 2176, 1977, 2899, 1922, 26808, 14061, 8997, 8398, 41, 3470, 41, 29, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MTDVSNNVVFSSNSITDTYYQFSGGTLFYDQTYQWKVSALGHFNDAVIYKGNSNYPLNSEDYEQCVAFVKRYYGNVQISFGKFPNGGSYAPQIGDIVCLSGGYGQQNVGSIISNHISQQVSLTYSNGTYTIANFAGKTVEGWRPMVIWLPHTSPQSYRVDASKQNPVTGCYEPISGYNGATIYTQLAGYVQTEPIYFEIAPNANSVAQIAGQYFINTQVQNSMNLEKGYSDENGNAFIEVAPELNIGDTLIASGTGVISQEIIANPSVYILNNTSMFIENVVELKVTAQNHTSYMPDDSLVTYSLSQVGINFIQVRFLGADTVDVIKTVFINGSYAGNITDYEGVVTLPHGYHQFSFTKDNYGSIFADNSSYISILPNPSNGLYRVECNKSAENVIIIVYDLIELDLSNFASGSYLVKIQIDEQHIVKSVIKKRALLNGSPVSDWSNNRSFTIKPQSPDSPAEGQNVVYGLNMPSIGHAFQYHVAIIRDVQFANDGVNNDFVYVARALPTVSHPYDNEVFSTTTAGSTYYTFPSGILEAGGKYRLRVGVINKNIQSTSIAANILITQKINGITQEMLLSNNISILLVPDVTNFIYRILDFANSNDTLTAYTEYYNPSPTGNDVYAVTIIADNSSLNSQMSTIVADTIYLSMNELSPTIVGKKQGNQIINKRFQNLSKSWS", "metadata": {"id": "A0A1F3BI40", "cluster": 14855692, "interpro_all": ["IPR007921", "IPR013783", "IPR038765", "IPR026444"], "interpro_used": ["IPR007921", "IPR013783", "IPR026444"], "interpro_unused": ["IPR038765"]}, "task_type": "infilling"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein contains a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. In addition, it is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein belongs to the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. It has been detected in Ramlibacter cellulosilyticus and is connected to UniProt keyword ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 5461, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2176, 2258, 2252, 3330, 1922, 8221, 30466, 2422, 18485, 27545, 1954, 2002, 1957, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSGLFLSFEGIDGAGKSTHIEALAQALRARGRTVVLTREPGGTPLAEKLRALALNDPMDPLTEALLMFAARRDHLQQVIEPALARGDVVLCDRFTDATFAYQGGGRGFDLDVLATLERWVQSVPATPLRQPDVTVWFDLPAAVAAQRLAGARVPDRFESQPQAFFERVAGGYAARAKADPGRFLRVAADQPRDQVWQDVEEGLRKRGVL", "metadata": {"id": "A0A923SDP5", "cluster": 15118627, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR039430", "IPR027417", "IPR018094"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is grouped in the Acyl-CoA N-acyltransferase superfamily, which encompasses enzymes featuring a 3-layer $\\alpha/\\beta/\\alpha$ domain that catalyze the transfer of an acyl group, typically from acyl-CoA, to a nitrogen atom on diverse substrates. This versatile fold is utilized by histone acetyltransferases for chromatin regulation, aminoglycoside N-acetyltransferases for antibiotic resistance, and autoinducer synthetases for bacterial quorum sensing. Structural variations, including domain duplications and swapping, allow members like N-myristoyl transferases and non-ribosomal peptidyl transferases to perform specialized modifications such as protein lipidation and cell wall synthesis. It originates from Petrimonas sp.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 11337, 17, 10027, 56, 17, 11337, 9961, 13975, 16, 2154, 21569, 5038, 29931, 43, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3418, 1988, 18170, 1920, 3856, 1927, 1925, 11337, 2210, 16, 5745, 2037, 11337, 17, 10027, 16, 1942, 43, 6634, 6761, 1990, 6445, 6249, 18, 2052, 20425, 3728, 1977, 7079, 2007, 6632, 22226, 1036, 1958, 6338, 3640, 16, 23029, 8028, 56, 17, 22226, 1036, 1958, 7267, 3554, 16, 1930, 27485, 4600, 1005, 18185, 1036, 1958, 4543, 28481, 9306, 18, 4346, 6740, 16, 2710, 3418, 20559, 1930, 3476, 5041, 16, 3235, 4678, 3189, 56, 17, 20234, 10921, 13763, 1036, 1930, 2447, 17, 11196, 3431, 2199, 13763, 1036, 1942, 2385, 11021, 6920, 2427, 1966, 2213, 4486, 1943, 1930, 2024, 4821, 4271, 18, 2176, 22970, 2037, 19802, 3947, 1934, 2056, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MEGEIMTDETLKQYILDYKPKNRRDVLDMTCEPHLYVLEEYRGYGYGSRLIQITQMDGYDFTFLIQDGKAIGV", "metadata": {"id": "A0A7C6JMY8", "cluster": 15498657, "interpro_all": ["IPR016181"], "interpro_used": ["IPR016181"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein is grouped in the Small ribosomal subunit protein uS5 domain 2-type fold superfamily, which features a left-handed \u03b2-\u03b1-\u03b2 structure utilized in diverse nucleic acid-binding proteins and GHMP family kinases. This domain serves as a key component in translational machinery and DNA repair enzymes, such as MutL and DNA gyrase B, while also facilitating ATP-dependent phosphoryl transfer in metabolic enzymes like galactokinase and mevalonate kinase. Also, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein possesses a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is native to bacterium and has UniProt annotations Transferase.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2858, 11196, 5903, 2213, 2022, 1015, 3418, 22, 17, 2601, 3728, 13975, 16, 2154, 4075, 43, 3506, 17, 17105, 161, 17, 160, 17, 161, 3170, 7079, 1922, 6445, 11079, 2687, 17, 2743, 2697, 1930, 6101, 6588, 3416, 7784, 18, 2052, 3418, 10634, 1966, 43, 3834, 4594, 1922, 8414, 10853, 1930, 2678, 5059, 5038, 16, 2427, 1966, 2446, 1024, 1930, 2678, 9430, 2051, 44, 16, 2679, 2222, 12440, 4498, 17, 3100, 12556, 3856, 1922, 4487, 5038, 3189, 9479, 18655, 1930, 21750, 20807, 5791, 1021, 4016, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 6196, 1942, 14061, 1930, 2258, 20709, 15010, 13763, 18, 3], "output": "MSDASRLPERVEAFAPAKLNLLFQTVDWGDRLVFTRRPDKADLELRITGQPLADGGVRVDLDKRIPVGAGLGGGSSDGAAALLALNRLFFLAGGTAIGRGRGERLEALPPLHRGAFLLLTGHPYRISVEQVKVYLSRFPVGLEVLRRRPDGYHDIETETHNTARRAYALLRETRPGRLFGLDLDAATLGRLALELGSDVPVHPGFSVSTAWAYEHLRLG", "metadata": {"id": "A0A960UF61", "cluster": 18656504, "interpro_all": ["IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR014721", "IPR004424", "IPR006204"], "interpro_unused": ["IPR020568"]}, "task_type": "infilling"} {"instruction": "The protein is a member of the Type 1 protein exporter family, which comprises ATP-binding cassette (ABC) transporters that utilize energy from ATP hydrolysis to translocate a diverse array of substrates across cellular membranes. These proteins typically contain a transmembrane pore-forming domain and a nucleoside triphosphate hydrolase domain to facilitate the export of molecules such as lipids, toxins, xenobiotics, peptides, and iron-sulfur clusters. Found across bacteria and eukaryotes, members play critical roles in processes ranging from multidrug resistance and toxin secretion to mitochondrial function and antigen presentation. Moreover, the protein incorporates a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. In addition, the protein should contain a ABC transporter-like, ATP-binding domain that utilizes the energy from ATP hydrolysis to power the transmembrane transport of diverse substrates, ranging from ions to macromolecules. It features conserved Walker A and B motifs, a Q-loop, and a signature sequence that form the nucleotide-binding site, typically functioning within a dimer. This module interacts with transmembrane domains to couple ATP-driven conformational changes to the import of nutrients or the export of toxins and membrane components. It is expressed in Acidilutibacter cellobiosedens and is classified with UniProt keywords Transmembrane helix. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2601, 21, 2213, 12660, 1915, 3416, 16, 2154, 12936, 4498, 17, 2743, 12992, 12, 7219, 13, 10538, 1988, 12561, 3844, 2037, 4498, 9128, 1942, 26377, 43, 6445, 6472, 1927, 6249, 3436, 3689, 5726, 18, 2144, 2697, 5745, 5531, 43, 9117, 8554, 17, 7402, 3418, 1930, 43, 18015, 17978, 20748, 3418, 1942, 6628, 1920, 12660, 1927, 4206, 2427, 1966, 8238, 16, 13599, 16, 29821, 1036, 16, 5320, 16, 1930, 5680, 17, 12585, 5859, 18, 2435, 3436, 4802, 1930, 15021, 16, 4678, 3918, 4140, 5456, 1922, 4028, 6485, 2037, 16398, 3554, 1930, 9165, 5512, 1942, 4596, 2347, 1930, 4730, 6544, 18, 3950, 16, 1920, 2213, 19683, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 7219, 9054, 17, 3189, 16, 4498, 17, 2743, 3418, 1988, 18127, 1920, 3844, 2037, 4498, 9128, 1942, 4215, 1920, 9117, 4860, 1927, 6445, 6249, 16, 6485, 2037, 6982, 1942, 20625, 18, 2176, 4075, 5305, 20138, 43, 1930, 44, 8277, 16, 43, 59, 17, 5881, 16, 1930, 43, 9983, 3244, 1988, 2386, 1920, 5489, 17, 2743, 3200, 16, 5745, 7295, 2651, 43, 7632, 18, 2052, 9059, 9034, 1956, 9117, 4682, 1942, 15116, 4498, 17, 6446, 8523, 2840, 1942, 1920, 2582, 1927, 11312, 2014, 1920, 12660, 1927, 13599, 1930, 3260, 4178, 18, 2176, 1977, 3198, 1922, 2687, 1970, 1984, 26073, 2341, 1915, 2024, 17428, 10350, 2099, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 7864, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MRDILFGDKKGIIKFFIGIVFSAVTTILLQLIFTVVLYAVSPASQLSLKAVLFILITISILNPILYLISRIFRIGFIRDALSEIRKKIFESVLHKSYKEYFEHLTSEYLSRLTNDISQFESNFFPVLLENISAILVYIFSFGIIFINNRKIALGLFSASMLFLVFTFFLRKYTKELQLGVNKTNSKLMKIFSDFLGGLQELKMNLVEKAYADRINWNVELNEKVKFNQQFLYSILRIGKEFFSIVTPIIIFYIGIMYFDLEISSKLLSIVLPFSISMFSSISEIGFSYNRMKAAYDILDGYISEKTADDYDIGRDFRFEKEIEIKDFSFAYDSRKILQSSDFEIERGKKYLLLGKSGSGKSTFLKCISGMNKSFSGEIKYDGCDIRKISLKKYFENVSFLTQDVFLFNDTVENNIKLYKAESEELYQKIIRLMGIEKITSDNNPYLTLSGGEKEKVSLARELIKEPKLILLDEMTKGLDEENSRRIEDIILSGDFTVINATHKLIKDIHIKYDYVIQIVDGKIRLMDSASYWRNRDEK", "metadata": {"id": "A0A410QDS2", "cluster": 20248182, "interpro_all": ["IPR003593", "IPR011527", "IPR036640", "IPR003439", "IPR027417", "IPR039421"], "interpro_used": ["IPR039421", "IPR003593", "IPR003439"], "interpro_unused": ["IPR011527", "IPR036640", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Generate a complete amino acid sequence given the following functional description of a protein that will be able to perform the described role. The desired function is: The protein features a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. Moreover, the protein should contain a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. In addition, the protein features a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. It is found in Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri) and is classified with UniProt keywords Transmembrane helix, Glycoprotein, and Repeat.", "tokenized_instruction": [2, 5655, 43, 4080, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 4075, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 2176, 1977, 2435, 1922, 5595, 14514, 2304, 2072, 1957, 3057, 7369, 5590, 12, 28945, 23071, 13, 12, 3370, 12492, 4357, 1996, 21018, 18842, 13, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 7864, 16, 11424, 16, 1930, 6865, 18, 3], "output": "RVYRLLSRFSLLFLNSLPPSPPLLPFSLTSPLSLQNMEDHLAFLITVPTTLFLFLSIFILVCIESVFNRMLRLFSLLIWACLVAMGYLFMFSGGILCPWDQVSFFLFIVFVVYTMLPFSMRGAVLASIITCLSHTITLSVCLAFTAEALEPLVWQILANIIIFTCGNLAGAYHKHLMNLALRQTYQDTCNCIKSPIKLEFEKHQQERLLLSLLPAHIARVMKAEIIQRLQGPRDRDFGRAEGTNNFHNLYVQRHTNVSILYADIVGFTKLAGDCSPGELVHMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPESLPHHARNCVKMGLDMCEAIKKVRDATGVDINMRVGVHSGNVLCGVIGLQKWQYDVWSHDVTLANHMEAGGVPGRVHISSVTLEHLKGSYKVEPGEGQSRDFYLKEHGVITYLVINPKRRSPHLCARSRSSLEGGKMRASVRMTRYLESWGAAKPFANLHHRDSMTTDNGKINTTVSSHINTHTHTHTHTHTHTHTHSETQTGNEYYCRLDFLWRDKFKRECEEIETMENLNRVLLENVLPAHVAEHFLGRNWKNEDLYHQSYESVCVMFASIPDFKEFYTESDVNKEGLECLRLLNEIIADFDELLSKPKFSGVEKIKTIGSTYMAATGLNATPGPEYTQEHDRQYMHIGTMMEFAFALVGKLDVINKHSFNDFRLRVGINHGPVIAGVIGAQKPQYDIWGNSVNVASRMESTGVLGKIQVTEETSRILLTLGYMCSCRGIINVKGKGELKTFFVHTEMTRSLSQGTVMP", "metadata": {"id": "A0A8K9UVS8", "cluster": 23688315, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR009398", "IPR029787"], "interpro_used": ["IPR001054", "IPR018297", "IPR009398"], "interpro_unused": ["IPR032628", "IPR029787"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein includes a Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead domain that functions as a conserved structural component in molybdoenzymes catalyzing the oxidation of aldehydes to acids and xanthine to urate. These enzymes typically operate as homodimers requiring FAD, molybdenum, and iron-sulfur clusters as cofactors, and include variants involved in nicotine degradation. It originates from Dehalococcoidia bacterium.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 18727, 10488, 19, 26059, 9294, 16, 43, 19, 44, 20355, 1915, 10611, 3418, 1988, 4088, 1966, 43, 5305, 4346, 4594, 1922, 2629, 16924, 22389, 26897, 29601, 1920, 6638, 1927, 25075, 1942, 4576, 1930, 26059, 1942, 3674, 2010, 18, 2144, 5038, 5745, 15336, 1966, 29227, 8887, 14134, 16, 2629, 16924, 5233, 1989, 16, 1930, 5680, 17, 12585, 5859, 1966, 21362, 16, 1930, 3951, 4936, 3286, 1922, 9303, 4877, 18, 2176, 22970, 2037, 2028, 7289, 26941, 2642, 2126, 14061, 18, 3], "output": "MAAEKALYKGHAVAAVAAINNEIAEQAAALIDVDYEVLPAVTDVLGNYERRRPCSARKTCQLHQRRYTSRWP", "metadata": {"id": "A0A920PS71", "cluster": 23896936, "interpro_all": ["IPR000674", "IPR036856"], "interpro_used": ["IPR000674"], "interpro_unused": ["IPR036856"]}, "task_type": "autoregressive"} {"instruction": "Give me a peptide sequence capable of: The protein can be placed in the ANL N-terminal domain superfamily, which comprises the large structural domain found in Acyl-CoA synthetases, NRPS adenylation domains, and luciferase enzymes. This domain houses the majority of active site residues and catalyzes the initial adenylation of a carboxylate to form an acyl-AMP intermediate, typically followed by a second reaction such as thioester formation. It cooperates with a smaller C-terminal domain that undergoes a significant rotation to alternate between catalytic conformations. Additionally, the protein should include a AMP-binding conserved site that catalyzes the ATP-dependent activation of substrates via the formation of an acyl-AMP intermediate. This glycine-rich motif is essential for the function of luciferases, acyl-CoA ligases, and non-ribosomal peptide synthetases involved in the biosynthesis of secondary metabolites like antibiotics and siderophores. Also, the protein carries a AMP-dependent synthetase/ligase domain that catalyzes the ATP-dependent covalent binding of AMP to a substrate to form a reactive intermediate. This domain is conserved in enzymes such as luciferases, acetyl-CoA synthetases, and long-chain fatty acid CoA ligases, where it facilitates substrate activation. It is produced by Gammaproteobacteria bacterium.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 1925, 1024, 56, 17, 4262, 3418, 13975, 16, 2154, 12936, 1920, 3103, 4346, 3418, 2435, 1922, 11337, 17, 10027, 18185, 1036, 16, 5214, 2523, 4670, 3017, 4682, 16, 1930, 7362, 5038, 18, 2052, 3418, 23407, 1920, 4827, 1927, 3500, 3200, 4248, 1930, 17097, 1920, 3754, 4670, 3017, 1927, 43, 20877, 1942, 2386, 1925, 11337, 17, 3681, 6129, 16, 5745, 3489, 2007, 43, 2812, 3227, 2427, 1966, 30215, 3337, 18, 2176, 23230, 1036, 1956, 43, 5322, 45, 17, 4262, 3418, 1988, 14928, 43, 2228, 8891, 1942, 14263, 2192, 6804, 12526, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 3681, 17, 2743, 5305, 3200, 1988, 17097, 1920, 4498, 17, 3100, 2936, 1927, 6249, 3454, 1920, 3337, 1927, 1925, 11337, 17, 3681, 6129, 18, 2052, 10646, 17, 5536, 5219, 1977, 4415, 1958, 1920, 2347, 1927, 7362, 1036, 16, 11337, 17, 10027, 22423, 16, 1930, 2447, 17, 11196, 4207, 18185, 1036, 3286, 1922, 1920, 8132, 1927, 4067, 6926, 3189, 7560, 1930, 22940, 14820, 18, 2222, 16, 1920, 2213, 16252, 43, 3681, 17, 3100, 18185, 19, 11905, 3418, 1988, 17097, 1920, 4498, 17, 3100, 13577, 2743, 1927, 3681, 1942, 43, 4510, 1942, 2386, 43, 6079, 6129, 18, 2052, 3418, 1977, 5305, 1922, 5038, 2427, 1966, 7362, 1036, 16, 6894, 17, 10027, 18185, 1036, 16, 1930, 2815, 17, 4659, 5934, 2687, 10027, 22423, 16, 2597, 2176, 11374, 4510, 2936, 18, 2176, 1977, 4152, 2007, 7034, 9218, 1021, 10296, 14061, 18, 3], "output": "MTLSGLFLERVRRSPQQIAYRSFDKVHRAWHELSWQQIENRVQQWVAALVGESLATGERVALQCRNGVNWVVFEQAALRLGLVVVPIYVEDRPQNILYVLRDSGARLLLVESLFQYKRLPEDVLQCTALQRVVVMNPLPQQQPGLVSSREWLTAADLRQSVSCTQDSQAMATLVYTSGTTGKPKGVMLTHQNVLSNATACLQASAVYRGDLFLSFLPLSHMLERTVGYYVPMMAGATVVYARSIRDLAADLLTVKPTCLVAVPRIFERAERRIQEHLQGSPAYQRWLFGLAVHVGWNRFQRLQGRAMWTPLEWVCNPLYKRVVRKVLNRFGGRLRLVITGGAALPPAVAKTLIAMGLPLVQGYGMTECSPVATSNRLDKNRPESIGRSLEGVEVRVGEGGELQIRGASVMRGYWNNETATQEAFTDDGWLRSGDCTRQDEDGFWYITGRIKEIMVLTTGEKIPPMDIENAILEDPLFQQVMIVGEGRSYLALLAVVDGQRWQECLSEAGLASPVGREQINALLLPRVRARMSSFPGYAKIHQVCVDTVPWDTENGLLTPTLKLKRKAVAERYASEISAMYEGH", "metadata": {"id": "A0A9C9G085", "cluster": 28793681, "interpro_all": ["IPR020845", "IPR000873", "IPR042099"], "interpro_used": ["IPR042099", "IPR020845", "IPR000873"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein falls within the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Also, the protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, the protein is categorized in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is expressed in Spiroplasma alleghenense and carries UniProt keyword assignments Cytoplasm and rRNA processing.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 12182, 2651, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 3198, 1922, 22075, 15403, 1019, 11169, 2509, 2880, 3355, 1021, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MTELHVPVLLKETLQILNIQEILKRLTVGQLFGLDQDTTAIEYSQFSEIATLLALNDVFKVDGILFDLGVRMNQKSNELTAWKIVNEWSLKDLIQARELKQINTTLELVDVIKTALPQKCVNNEIEVLKMALKSSLKLLKVVKEVFKSVTIDEQDKFIAKLPIPMTNRAHSAKLWAIKKIKESGVYVDATLGRAGHSSVLKNVGKNFRILQGNSSPQFDNADRGFSYRLEGKLDMIFREYGEENYAVRIANRIIEVLKEKKHPAKKVFQALRVKDGILAVITFQSLEEKSKKDFELAVKKPIKPSEEEIMIN", "metadata": {"id": "A0A345Z3W7", "cluster": 606656, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR023397", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to generate an amino acid sequence for a protein. The protein should have the function The protein is grouped in the NADH-quinone oxidoreductase subunit E-like family, which functions as a subunit of the respiratory-chain NADH dehydrogenase (Complex I), an oligomeric enzyme essential for cellular bioenergetics. Located within the enzyme's iron-sulfur fragment, this protein binds a 2Fe-2S cluster to facilitate electron transfer in mitochondria, chloroplasts, and bacteria. Also, the protein belongs to the Thioredoxin-like superfamily, which encompasses a diverse group of redox-active proteins characterized by a conserved $\\alpha$/$\\beta$/$\\alpha$ structural fold and a CXXC active site motif. These enzymes primarily facilitate electron transfer via thiol-disulfide exchange reactions to maintain cellular redox homeostasis, assist in protein folding through disulfide bond formation or isomerization, and participate in signaling pathways like the glutathione/glutaredoxin system. Also, the protein features a NuoE domain that forms the C-terminal region of the 24kDa subunit of NADH:ubiquinone oxidoreductase (Complex I), housing a [2Fe-2S] cluster essential for electron transfer. It facilitates the relay of electrons from NADH to quinone, contributing to the generation of the proton motive force in bacteria and mitochondria. This structural module is also conserved in functionally related enzymes, such as formate dehydrogenases and NiFe hydrogenases. It has been characterized in Mycolicibacterium wolinskyi and carries UniProt keyword assignments Metal-binding.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 1977, 10809, 1922, 1920, 14261, 17, 25093, 27388, 5903, 47, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 5903, 1927, 1920, 5481, 17, 4659, 14261, 9294, 12, 2796, 51, 13, 16, 1925, 19206, 4113, 4415, 1958, 3689, 28584, 2837, 18, 4810, 2651, 1920, 4113, 11, 61, 5680, 17, 12585, 5302, 16, 2052, 2213, 6876, 43, 13775, 1021, 17, 20759, 4377, 1942, 6628, 4995, 3856, 1922, 6489, 16, 24627, 16, 1930, 4802, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 23684, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 9366, 17, 3500, 2697, 4378, 2007, 43, 5305, 8, 38, 4595, 8, 19, 8, 38, 4666, 8, 19, 8, 38, 4595, 8, 4346, 3728, 1930, 43, 5639, 21487, 3500, 3200, 5219, 18, 2144, 5038, 5985, 6628, 4995, 3856, 3454, 13914, 17, 11830, 6818, 5298, 1942, 6698, 3689, 9366, 7622, 16, 6589, 1922, 2213, 10328, 2596, 11830, 5403, 3337, 2014, 27027, 16, 1930, 7352, 1922, 3197, 3873, 3189, 1920, 9153, 19, 19406, 1919, 9754, 2433, 18, 2222, 16, 1920, 2213, 4075, 43, 13232, 6802, 3418, 1988, 4952, 1920, 45, 17, 4262, 3031, 1927, 1920, 2686, 30493, 5903, 1927, 14261, 30, 5582, 22123, 27388, 12, 2796, 51, 13, 16, 13178, 43, 37, 13775, 1021, 17, 20759, 39, 4377, 4415, 1958, 4995, 3856, 18, 2176, 11374, 1920, 22092, 1927, 14354, 2037, 14261, 1942, 25093, 16, 8739, 1942, 1920, 4841, 1927, 1920, 8433, 7038, 1021, 5495, 1922, 4802, 1930, 6489, 18, 2052, 4346, 9059, 1977, 2222, 5305, 1922, 9346, 2712, 5038, 16, 2427, 1966, 25741, 9294, 1036, 1930, 17719, 1021, 6201, 2319, 18, 2176, 2258, 2252, 4378, 1922, 5078, 4485, 26073, 2341, 18842, 1989, 12697, 2925, 6716, 1033, 1930, 16252, 20709, 11121, 2538, 18306, 6048, 17, 2743, 18, 3], "output": "MTEVFLELGQRPDEAGPPINGPVAYPDDVTTRLRADAEQITARYPDARSALLPLLHLVQAEDGYLTPAGIAFCADQLSLTEAEVTAVATFYSMYRRTPTGDYLVGVCTNTLCAIMGGDAILDALQDHLDIHAGQTTADGRVTLEHIECNAACDYAPVVMVNWEFYDNQTPSSARDLVDGLRSGDAPAPSRGAPLCNFRETARTLAGLGDPRVPGGAPGDATLAGLRVARERGMTAPDSNASASSEETVDDEQVAAEATQDAPAPGPSATVPPEPNTTETDPDATDSRS", "metadata": {"id": "A0A132PEG8", "cluster": 1445434, "interpro_all": ["IPR002023", "IPR042128", "IPR041921", "IPR036249"], "interpro_used": ["IPR002023", "IPR036249", "IPR042128"], "interpro_unused": ["IPR041921"]}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein incorporates a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein is associated with the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein incorporates a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It has been characterized in Tannerella sp. oral taxon 808 and features UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 19683, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 19683, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 2258, 2252, 4378, 1922, 22669, 1959, 11560, 1019, 2056, 18, 4726, 19278, 3729, 1025, 1930, 4075, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MIGFPNAKINLGLHVVSRRPDGYHGIETVFYPVPLCGPADDNLVMRALAAMRRQADIPPAAIHLKKAIPFGAGLGGGSLTDDALERMAARLGADCAFFVRNRPVMATGIGDVFSPADISVSTRAAYAAIRPAKPAVPLSEIIRRPIAEWRGLLRNDFEAPLFALHMSGSGSAVFGLFRSAPSLPPLADCFVWQGRLDALEIVPAEAFSFHTYGLAIDSADAAFMLKLLRDYARLSLAGYHIAIVKPSVPTISAIKAQLYDAGAVYAS", "metadata": {"id": "A0A2N8NC83", "cluster": 6753216, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "infilling"} {"instruction": "Target Function: The protein is classified under the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. Additionally, the protein is assigned to the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. It is derived from Halieaceae bacterium and is described by UniProt keywords Metal-binding, ATP-binding, and Transferase.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 2176, 1977, 3595, 2037, 4217, 2621, 9914, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 16, 4498, 17, 2743, 16, 1930, 13763, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MTADQDRDTGEVVRREEAFQLEALLACVLIPVAVFTVLIVEVLNTSIEVLTDAIVWGVIVPNYWPFAMTGLRRLLFTLVNSGKGLRFLLRKAILLPVSPVERLLLIGRVSLDRHQLSGLAKDLGSLAVTLSLLLW", "metadata": {"id": "A0A520SE26", "cluster": 6766658, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR000829", "IPR033718"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "Here is the intended role of my protein: The protein is a member of the Type IV secretion system-coupling protein family, which mediates the conjugative transfer of plasmid DNA between bacterial cells, playing a central role in the propagation of antibiotic resistance and virulence factors. These proteins interact with relaxase enzymes and likely form a pore-like structure to facilitate single-stranded DNA transport through the type IV secretion system. Additionally, some members subvert human endothelial cell function, inducing cytoskeletal rearrangements, pro-inflammatory activation, and apoptosis inhibition. Furthermore, the protein is included in the Type IV secretion system protein TraG/VirD4 family, which functions as an essential coupling factor with NTPase activity to drive DNA transfer in bacterial conjugation and type IV secretion systems. These proteins bridge the DNA-processing and mating pair formation machineries, serving as critical virulence factors in pathogens like *Agrobacterium tumefaciens*. Moreover, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is identified in Thermoplasmata archaeon. Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2601, 4370, 5512, 2433, 17, 7590, 2213, 3416, 16, 2154, 10412, 1920, 5225, 2178, 3856, 1927, 5609, 2678, 2192, 4543, 2094, 16, 14797, 43, 4101, 2770, 1922, 1920, 11728, 1927, 7267, 3554, 1930, 9304, 2790, 18, 2144, 2697, 6310, 1956, 7327, 2051, 5038, 1930, 3205, 2386, 43, 8554, 17, 3189, 3170, 1942, 6628, 2957, 17, 10338, 2678, 4860, 2596, 1920, 2601, 4370, 5512, 2433, 18, 4950, 16, 2673, 4678, 2316, 22212, 2616, 5003, 2024, 2347, 16, 7834, 14787, 13955, 16, 1965, 17, 3769, 2936, 16, 1930, 4091, 3523, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2601, 4370, 5512, 2433, 2213, 3390, 1029, 19, 2787, 15005, 3416, 16, 2154, 4088, 1966, 1925, 4415, 7590, 2991, 1956, 29676, 2051, 2455, 1942, 9265, 2678, 3856, 1922, 4543, 14122, 1930, 2601, 4370, 5512, 3771, 18, 2144, 2697, 11925, 1920, 2678, 17, 4587, 1930, 11786, 3715, 3337, 10112, 25921, 16, 13915, 1966, 4140, 9304, 2790, 1922, 7741, 3189, 14, 26896, 30258, 25018, 14, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2899, 1922, 7967, 15403, 5499, 13470, 1916, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "MDAVRKRNSAWLCGMTPEAMAARSRRSAPAVRGLASEADLEAVLTPSPTGSPEGRGGMPLLLRDGRAYLEERDKHMLVIGPSGVGKSLRALGPMIPNAGGSILVTDPKGEMYRMYHSCLRDRMRVRVIDFREPWKSDCWNPMAEMYDDCRSGDPSKVDRARAQCRDLSYMLVPYNPDNKDPSWDNTARAFLEVLAWAVVTRSKGRDECSLASMAGAWVDLSEEKDGFERFLDSLDDSLDRLAVDPLVHNAEGTLKCHRSLIDQYIRGTMGSDSLMQMTASDGIDFRMMGTDRTAVFLIFPEEKDTHKELMSMIIQQAYAQLVDLAQESGGKLPVPVDMILDEFANVGRIRGFETMISAGRSRGIRFTLAVQSRGQLFDVYGRDSGAEIMDCCTDWIYFRSKDSAFVRDISDMVGRDRDGNPLLTPEDLCSFTDGKVLAMLDGVRPALVTLPTIFDHGLGLEPSDTRGFRPRVEIGRVDLIRRPRTKAPSDEYASIQACKAKYMGAVARVALMRRNGEDVAAEHEDFEALADFVTEVDDLLFWHWPGARQVRAKVLVDMLGMFIDNVAETDEAVSASARELLHAFERFEDDERVCLSRLMMAMDAAVAMRAVESEE", "metadata": {"id": "A0AA43ULI4", "cluster": 6883810, "interpro_all": ["IPR027417", "IPR051539", "IPR003688"], "interpro_used": ["IPR051539", "IPR003688", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein is classified under the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein is categorized in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is present in Pediococcus pentosaceus (strain ATCC 25745 / CCUG 21536 / LMG 10740 / 183-1w) and is classified with UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2481, 1922, 5296, 3940, 4879, 2437, 1957, 9412, 5360, 1972, 1957, 12, 3943, 11037, 21579, 6803, 19, 4928, 2215, 17639, 5677, 19, 7735, 1029, 9176, 4241, 19, 16228, 17, 21, 1018, 13, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MTVIVGLTGGIAMGKTTISQFLKSTVDEVKVKLMDTFGESILDKNQNIDRRKLGPLDTFSASKVVVLDAPVLFEQGSLNEIDAQKRIQAQMPIEETRSQVVKWLVDKNLFKAIPVVDADQIAHEILIVFNDQRQLEKLNIIVQPYIRTEIVRQYEKMVDYLMVIKTSAQIQVERLMQRDIEEKVKKADIVIDTSGT", "metadata": {"id": "Q03GC1", "cluster": 8324941, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein is included in the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. It is identified in Bacteroidota bacterium and is associated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2176, 1977, 2899, 1922, 24323, 7336, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MAPELFIRIEDYLDNTLSPAERLAFESEMRADPELAQTVALVREARDRLVRQWASEPADAALMETLREIGKEHFKGEALATTTPPKSHRVVFFQRVVWAAAAVLVLLTAAWLFFLRPPYHERLYAQYKHLPEASFTVRSVDNGSAAAEAAEAFNNKNYDKALALLEQHLHQAPDDAEARYFTGLCLLEMRRFEEARAAFAQIENTPAWMEEARWYIALTYLRENRLDDCRLQLERIPSESPHYERAQQLLKAVAP", "metadata": {"id": "A0A7C4JW54", "cluster": 9163923, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein belongs to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. In addition, the protein should have a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Moreover, the protein should feature a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It occurs in Bacteroidota bacterium and is connected to UniProt keyword Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 14440, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 5110, 1922, 24323, 7336, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MKEYSAKACAKINIGLKVLGRRDLCDEISISTAEKGIQIAQLLQAFSGEKRGCNIHIAKRINLGLDDEVLFKIALKLGADVPFFLNFGVVVYPNIRISTAWAYGNLKLNLTNKKNYIKSNDFESLVLEFYPELNEIKALILKSGAALTLFDSHPYQKFFVRPYREVPDADGYHDIETIFQSIISGHRDVPADETNLCWRAPVGAGLGGGSSDAAVTLRLLNRLWPGSAVAYGVGEELRRFENKCVFLETYFVEKLLLQEYPLFFADFAGLSGSGSAFFGLFQQEEKAK", "metadata": {"id": "A0A7V1F8S2", "cluster": 9982859, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR013750", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "infilling"} {"instruction": "Generate a protein according to these design specifications: The protein should feature a Calcineurin-like, phosphoesterase domain that functions as the catalytic center in diverse enzymes, ranging from nucleotidases and sphingomyelin phosphodiesterases to nucleases like Mre11. This domain adopts a fold comprising two sandwiched $\\beta$-sheets flanked by $\\alpha$-helices, which coordinate a binuclear metal center essential for hydrolyzing phosphoester bonds. Moreover, the protein should have a FlgD/Vpr, Ig-like domain that features an immunoglobulin-like \u03b2-sandwich fold inserted within a Tudor-like \u03b2-barrel structure. It is present in the flagellar hook-capping protein FlgD and the *Bacillus subtilis* minor extracellular serine protease Vpr, where it supports flagellar assembly and the production of the competence and sporulation stimulating factor. Furthermore, the protein carries a Purple acid phosphatase, N-terminal domain that adopts an immunoglobulin-like $\\beta$-sandwich fold and constitutes the N-terminal region of binuclear metallohydrolases involved in hydrolyzing phosphate esters and anhydrides. These enzymes function in acidic conditions using variable metal cofactors (such as Fe, Zn, or Mn) to mediate processes including bone resorption, microbial killing through radical production, and phosphate scavenging. It is found in hydrothermal vent metagenome and is connected to UniProt keyword Signal.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 3066, 5961, 43, 19555, 17, 3189, 16, 8078, 8342, 2051, 3418, 1988, 4088, 1966, 1920, 6804, 4102, 1922, 6445, 5038, 16, 6485, 2037, 2797, 4090, 2319, 1930, 28057, 24821, 1036, 1942, 29305, 3189, 26460, 18, 2052, 3418, 24032, 43, 3728, 10351, 2288, 18038, 1919, 8, 38, 4666, 8, 17, 14685, 20185, 2007, 8, 38, 4595, 8, 17, 12789, 16, 2154, 11865, 43, 8768, 13821, 6048, 4102, 4415, 1958, 7222, 9046, 8078, 8342, 9031, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 2300, 11526, 19, 23925, 16, 7021, 17, 3189, 3418, 1988, 4075, 1925, 11837, 17, 3189, 161, 17, 18038, 3728, 9103, 2651, 43, 9037, 22389, 1005, 17, 3189, 161, 17, 19560, 3170, 18, 2176, 1977, 2481, 1922, 1920, 24154, 17185, 17, 23565, 2213, 2300, 11526, 1930, 1920, 14, 14587, 14745, 14, 5857, 5329, 8468, 7154, 23925, 16, 2597, 2176, 7825, 24154, 5957, 1930, 1920, 3372, 1927, 1920, 12939, 1930, 23647, 9868, 2991, 18, 3677, 16, 1920, 2213, 16252, 43, 14308, 2687, 8167, 16, 56, 17, 4262, 3418, 1988, 24032, 1925, 11837, 17, 3189, 8, 38, 4666, 8, 17, 18038, 3728, 1930, 14879, 1920, 56, 17, 4262, 3031, 1927, 8768, 13821, 8969, 8601, 21524, 1036, 3286, 1922, 7222, 9046, 5413, 16785, 1930, 22018, 3726, 18, 2144, 5038, 2347, 1922, 9931, 2961, 2193, 4650, 6048, 21362, 12, 2427, 1966, 2650, 16, 7230, 16, 2014, 5890, 13, 1942, 8265, 4028, 2710, 3622, 14843, 16, 7293, 11879, 2596, 6917, 3372, 16, 1930, 5413, 15561, 18, 2176, 1977, 2435, 1922, 26959, 14654, 16552, 2225, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 18, 3], "output": "MYKRTIIVFFTIIAGLADVTAATHLDDDFNGYATTAGLQNKWGLSWKRAGVTTFSRTLDPSNGEGGSNAALWVDDITYIGGLPPLVRSPYLQNITQSSVKVMWGSNEPAGKVFWGSTVGNYPNSTPSVTFKDNNGVYVHTATISGLTAGETVYYYVEDGANGNIGENDDTYHATSAPASGTPFRLIVYSDSQASWKKITHHGQVISAMIPHNPDVILNCGDLAYDGLLSYFNDNFFSNAAPIQKNTAIYPAPGNHDVRVLAANRTNWDADIKNWRDLFDLPKNTKNNTEDYYYFDYADVRFIALNSVTTNYNNGNVYYNTTRNQLMKDWLRETLAATTQTWKIVYFHHQAFTDFVSDQGWDALFEQYGVQMVFFGHGHTYYPTHKNGVMYTMNGGGGGPLHEVPWWGFYDYYVPGAFREHHFVQVDISSEKLAVNVYNENGVLRHSYMLDTGGNLTNNVATPPQEAVDNFELYVDGNDFSEDWEWYGGVNGGTLNRYFDIGGASGNSHVIRTEFSFSSGDSNPYGYAGLGGLWRWEDYTGLKLWVKGSQSGAGHNFEIRILEGSGEDKFKYSIPISGLDTNGQYIYPQFSDFVWYGDGGRPAANGKLDLDRIVAFFVGAGFTGTATSSGASTIFVDDITAVINPPSRTGLDFALPGKFTLHQNYPNPFNSTTAIQYDLPKSANVQLIVYDIFGREIISLVNSRSDAGYHNVQWDGRNMIGGKVPPGIYVYQIKTEGGTSSRKLLKCYK", "metadata": {"id": "A0A3B0UH09", "cluster": 10026940, "interpro_all": ["IPR004843", "IPR025965", "IPR008979", "IPR029052", "IPR039331", "IPR008963", "IPR015914", "IPR026444"], "interpro_used": ["IPR004843", "IPR025965", "IPR015914"], "interpro_unused": ["IPR008963", "IPR039331", "IPR029052", "IPR008979", "IPR026444"]}, "task_type": "autoregressive"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein carries a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Furthermore, the protein should include a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Moreover, the protein should have a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. It is produced by Streptococcus sp. SS6 and is linked to UniProt keywords Cytoplasm, DNA damage, and SOS response.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 16252, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2176, 1977, 4152, 2007, 15746, 2056, 18, 4577, 1016, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 16, 2678, 4293, 16, 1930, 17668, 2644, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MIDRKEDNQFHLVSKYEPSGDQPQAIEALVDNIEGGRVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFSSDTYIEKDSSVNDEIDKLRHSATSALLERNDVIYADSAVSLRPGQEISRDKLLNDLVDIQFERNDISRDEHAFRVEFFGDEIDRICEIESLTGRNLGEVHMEEAIKNIMEEMEAQVKQFEAEGKLIEAQRIRQRTEYDVENYSRHMDGRKEGEPPFTLLDFFPEDFLIMIDNGDQARKKMLVDYGFRLPSALDNRPLRREEFESHVHQGLLDPEVEVRPTMGQMDDLLGEINARTEKGEAEDLTDYLKEMGVKVKYMHSDIKTLERTEIIRDLRREGIDVPEVSLVAILDADKEGFLRNERGLIQTIGRAARNSEGHVIMYREIQMAYNKEHGIVPQTIKKEIRDLISITKANEAEVAEQMHEAAELLDFELAAQIRDMVLELKSMDEKAQILKGATGTGKTYTMSQVIQVSYYDFYQPEAYVPVVASVSCIYGLGSPKEDFQRGKFRVRGDVVEIFPAEHLVLFPATHFMTNEEMLREMGYTNGVEESHMTMGQIKGMYIVYVSATPGDYEMEQTETVVEQIIRPTRVFVTTLTKKMLGVFDVLIGINLLADKITESMQKAMDETARRDTVDYSAMNKKERQEAIKKLQK", "metadata": {"id": "A0AAW7PM66", "cluster": 13511203, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR014001", "IPR001650", "IPR001943"], "interpro_unused": ["IPR041471", "IPR006935", "IPR036876", "IPR027417", "IPR024759", "IPR004807"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein falls within the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. In addition, it is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein includes a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. It originates from bioreactor metagenome and exhibits UniProt keyword tags Metal-binding. Please provide the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 7762, 30, 1920, 2213, 12182, 2651, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 5921, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 2176, 22970, 2037, 25650, 16552, 2225, 1930, 9826, 20709, 11121, 2538, 14392, 6048, 17, 2743, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MSDCSTCPSKNKCSSKDTVGSQGCGKLLPKYGTIKNVIGIISGKGGVGKSTVTGILASTLRKKGYKVGVLDADITGPSMPRFFGINDKRAVIEPIDENNFKYNPVESKGGTKVLSMNLLIPKEDDPVVWRGPIVTSVLTQLFTDTVWGELDYLLIDMPPGTSDITLTVMQSFPITELIIVSTPQDMVSMIVKKVITMAKKMPLQIRGVVENMSYIVCPGCDTKMRVFSKKSAEEHAEYLGIPLLGELPINVDLTEALEQGIAEQYVMDNDLYSLIFEGLY", "metadata": {"id": "A0A644ZZ92", "cluster": 14343322, "interpro_all": ["IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR033756", "IPR027417", "IPR000808"], "interpro_unused": ["IPR019591", "IPR044304"]}, "task_type": "autoregressive"} {"instruction": "What would the protein sequence be if I wanted a protein that could perform the following function: The protein possesses a DUF112 domain that functions as the integral membrane TctA subunit of the tripartite tricarboxylate transport (TTT) system found in prokaryotes. Typically covering the full length of the protein, this domain facilitates tricarboxylate uptake and has been identified as essential for natural transformation in species such as *Methanococcus maripaludis*. It is found in endosymbiont of Tevnia jerichonana (vent Tica) and features UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 4663, 2962, 1920, 2213, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 4855, 5739, 3112, 3418, 1988, 4088, 1966, 1920, 12328, 3260, 21939, 1019, 5903, 1927, 1920, 8027, 24707, 12258, 15441, 2010, 4860, 12, 22817, 13, 2433, 2435, 1922, 28149, 18, 5745, 12275, 1920, 4125, 3471, 1927, 1920, 2213, 16, 2052, 3418, 11374, 12258, 15441, 2010, 5047, 1930, 2258, 2252, 2899, 1966, 4415, 1958, 4613, 7002, 1922, 3038, 2427, 1966, 14, 17348, 8256, 13081, 13797, 16698, 1036, 14, 18, 2176, 1977, 2435, 1922, 22868, 19077, 2001, 1031, 1927, 25321, 10306, 26482, 2108, 12502, 2175, 12, 14654, 18298, 1019, 13, 1930, 4075, 20709, 11569, 9117, 7864, 18, 3], "output": "MVWSGWCWESSPASASLRPPYGLAAAEAGNSGVCGATLIPLMELGIPGDVITAVILGTFTLHGLPPGPLLFTQHQSELAPLFWGLILSTPLLFGLVAIRGFSRLSLLPEWALYPAIVTTALFGVYSLQASIFDIQLALITGLAGLTMRQIDLPTTPLLIAFILGPLIEENLRRALLLSQGTLEIFIHSPFVWGCVAATLLLCFWLAIQHHPWLGKRPAMHSGDRPGSAAEKNKLCRKRKGTKEKPIPLIAPASGSPPAAVTCPTSTWACWSTAKSRTINTSTAMRGDESSYDGSALPNRWTSLFGVNQTNFQPGDQAQLQHHPL", "metadata": {"id": "G2FEY5", "cluster": 14427906, "interpro_all": ["IPR002823"], "interpro_used": ["IPR002823"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein incorporates a Transcription regulator IclR, C-terminal domain that functions as a ligand-binding regulatory module with a GAF-like fold in bacterial transcription factors. It binds diverse small-molecule effectors, including glyoxylate, pyruvate, and glycerol-3-phosphate, to modulate the activity of the associated N-terminal DNA-binding domain. Furthermore, the protein possesses a Transcription regulator IclR, N-terminal domain that mediates DNA binding in bacterial transcription factors via a helix-turn-helix motif. It facilitates the regulation of metabolic pathways, functioning as a repressor for the acetate operon or an activator for the glycerol operon. Moreover, the protein is grouped in the HTH-type Transcriptional Regulators in Metabolic Pathways family, which functions as bacterial transcriptional activators or repressors that modulate gene expression in response to specific metabolic cues. These proteins bind to promoter regions to control operons involved in the catabolism and utilization of diverse compounds, such as allantoin, glyoxylate, glycerol, and aromatic substances, facilitating adaptation to environmental changes. It is present in Antricoccus suffuscus and is associated with UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 19683, 43, 3213, 7888, 25175, 1005, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 5207, 17, 2743, 4948, 9059, 1956, 43, 4357, 1038, 17, 3189, 3728, 1922, 4543, 3213, 2790, 18, 2176, 6876, 6445, 2858, 17, 5388, 13066, 16, 2710, 3376, 6644, 2010, 16, 11867, 16, 1930, 9244, 17, 23, 17, 5413, 16, 1942, 8480, 1920, 2455, 1927, 1920, 2458, 56, 17, 4262, 2678, 17, 2743, 3418, 18, 3677, 16, 1920, 2213, 14465, 43, 3213, 7888, 25175, 1005, 16, 56, 17, 4262, 3418, 1988, 10412, 2678, 2743, 1922, 4543, 3213, 2790, 3454, 43, 7864, 17, 5165, 17, 7864, 5219, 18, 2176, 11374, 1920, 3640, 1927, 4487, 3873, 16, 7295, 1966, 43, 14434, 1958, 1920, 7959, 15675, 2014, 1925, 9518, 1958, 1920, 9244, 15675, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 5334, 1023, 17, 2601, 5224, 9098, 1922, 4487, 3873, 3416, 16, 2154, 4088, 1966, 4543, 5224, 15497, 2014, 26446, 1988, 8480, 2359, 2294, 1922, 2644, 1942, 2487, 4487, 8972, 18, 2144, 2697, 4566, 1942, 4465, 3451, 1942, 2285, 28748, 3286, 1922, 1920, 19480, 1930, 8422, 1927, 6445, 4300, 16, 2427, 1966, 2136, 26182, 1921, 16, 3376, 6644, 2010, 16, 9244, 16, 1930, 10761, 10054, 16, 12440, 7810, 1942, 4813, 2840, 18, 2176, 1977, 2481, 1922, 4942, 3133, 15648, 1957, 18064, 7801, 1957, 1930, 1977, 2458, 1956, 20709, 11569, 3213, 3640, 18, 3], "output": "MTTTPVQERNSSTVKSFAVLELLGQAGVPMALADIARATDLNKTTARRFLATLCDLGYVERLPDGTHKLTARVLDLSSMYFRTTVLPTHAMPHLERFCRDTHTSTSLAILDRTETVYTAHVSEREALSVGVQIGTRLPAHATAVGKVLLSQLAAPEVERLYAGHPLTAHTSRTITTLPDLVGALGEIRRQGFAVSEEEYEPGVRGAACAMTAADGSVIGAINVSVRTENVARIDFYSDILPRLLRTAYDIAADAGRTGTA", "metadata": {"id": "A0A2T0ZRU0", "cluster": 15448632, "interpro_all": ["IPR029016", "IPR050707", "IPR014757", "IPR005471", "IPR036388", "IPR036390"], "interpro_used": ["IPR014757", "IPR005471", "IPR050707"], "interpro_unused": ["IPR036388", "IPR036390", "IPR029016"]}, "task_type": "autoregressive"} {"instruction": "The protein is categorized in the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. Also, the protein incorporates a Tetratricopeptide repeat that mediates protein-protein interactions and the assembly of multiprotein complexes. This motif consists of tandem 34-amino acid residues adopting a helix-turn-helix arrangement, which stacks to form a right-handed superhelical structure involved in diverse processes such as cell cycle regulation and protein folding. Moreover, the protein incorporates a F-box domain that functions as a protein-protein interaction motif linking the protein to Skp1 and the core of SCF (Skp1-cullin-F-box) E3 ubiquitin ligase complexes. This association facilitates the ubiquitination and degradation of specific substrates, such as G1 cyclins and Cdk inhibitors, which are typically recognized by variable secondary motifs within the F-box protein. It is identified in Bimuria novae-zelandiae CBS 107.79 and carries UniProt keyword assignments TPR repeat.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2222, 16, 1920, 2213, 19683, 43, 12470, 3319, 21305, 6865, 1988, 10412, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 18, 2052, 5219, 7543, 1927, 10361, 3540, 17, 3835, 2687, 4248, 20478, 43, 7864, 17, 5165, 17, 7864, 13002, 16, 2154, 20836, 1942, 2386, 43, 3659, 17, 17105, 3356, 23285, 2046, 3170, 3286, 1922, 6445, 4028, 2427, 1966, 2024, 4048, 3640, 1930, 2213, 10328, 18, 3950, 16, 1920, 2213, 19683, 43, 48, 17, 5758, 3418, 1988, 4088, 1966, 43, 2213, 17, 2213, 2835, 5219, 9486, 1920, 2213, 1942, 3097, 5113, 1930, 1920, 4728, 1927, 12437, 12, 3097, 5113, 17, 22859, 1921, 17, 48, 17, 5758, 13, 10968, 6526, 11905, 5048, 18, 2052, 3279, 11374, 1920, 11758, 1930, 4877, 1927, 2487, 6249, 16, 2427, 1966, 8533, 29201, 1930, 9727, 4472, 16, 2154, 2032, 5745, 6783, 2007, 4650, 4067, 8277, 2651, 1920, 48, 17, 5758, 2213, 18, 2176, 1977, 2899, 1922, 11753, 8754, 6862, 3336, 17, 6116, 4702, 7955, 16341, 9176, 18, 5637, 1930, 16252, 20709, 11121, 2538, 18306, 22288, 6865, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MTRTLSREDYQELGKSYYKLKQYDKLYDYRAASYEKLADFNSAIKDGRETIRTHKLDTALNIFKYGMKNVPVGNKDFQLLQRSHDKLTRQLSPPKSRGWKNYLTKRHKLWAEIDFSEATRPVSRASLHTLIAHRVQHVDMLRNIATACQSLRSLTIMEFPYLVSGSLIETMDTIGQILRRRPELERIDFKDISTDSQTGVTWEGKPGRRPCGYQVIDLVQQAPQLQWLYYIDGRRDTTTLEHLVFDPPSGFAHDLVLAIGLSAMSRTSSLVSLTLGASMTLDDDGTLETLQDGAPLRSLSISGEVYVAKVAAAPRRLLVSTYLATSPRILTRSLTSLEVPGLPLTDDTGFGIKQLADQAPTLRHIESKGVYVSYTMAESGGKGRKVRYGAIEAFTNGIEASAVPSATKQDVRGYLRTANALIKLNAIDPFTILPVELAEMVLGYVSFKTIVKCLRVLRNAVQYSQNTIAQRARNLKVLTVHSEVGPFTKLEYISLRGSREAVAKFHQTSLRGLVLKNVNLLLPRLPPYPSFLTTLLDHVKHAEDGQASVTIDHQADIRVITESTSLTYIDVSKTEIKADHCRNLSSRDAIEYA", "metadata": {"id": "A0A6A5VCL7", "cluster": 17325611, "interpro_all": ["IPR036047", "IPR001810", "IPR032675", "IPR011990", "IPR019734"], "interpro_used": ["IPR011990", "IPR019734", "IPR001810"], "interpro_unused": ["IPR036047", "IPR032675"]}, "task_type": "infilling"} {"instruction": "The protein features a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Moreover, the protein should have a Adenylate cyclase, N-terminal domain that comprises the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase. Moreover, the protein incorporates a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It occurs in Aedes aegypti (Yellowfever mosquito) (Culex aegypti) and is connected to UniProt keyword Lyase, Metal-binding, and Transmembrane helix. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 4075, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 23052, 16526, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 56, 17, 4262, 5329, 3031, 1930, 1920, 2561, 9117, 25, 17, 26, 4675, 3031, 1927, 23052, 16526, 18, 3950, 16, 1920, 2213, 19683, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 5110, 1922, 26098, 21308, 12, 7463, 10140, 2004, 9719, 13, 12, 6710, 2783, 21308, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 23928, 16, 6048, 17, 2743, 16, 1930, 9117, 7864, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MESVTFRKARSNAQRIQDDIDSENSHLDDLYTRYRQRLRKSLFISGLGISILACLISIIMCKLQEEIVADLTMLTGASVVLCVISVALHFPMVMNSPLAALSFAMLTTGTIGAVAIAVGAELAPLPLFALILGVHTMLPISWPVSVVLAVILCLVHIGCRLWSGVQDLPAYFFPQLVAEMIFLASASISGLYYRIMSDAAHIDAVDGTRIGIEQRVRLECEREQQEQLLLSVIPAYIAAEVKRSIMLKMADACQTAGGQSQTRFHEMHVQRHNNVSILYADIVNFTPLSEQLTASDLVKTLNELFGRFDQIAQENQCLRIKILGDCYYCVSGLPVSRPQHAANCVNMGLQMIEAIRFVREATGFNVDMRIGIHTGNVLCGVLGLRKWQFDVWSDDVTLANHMESGGVAGRVHITKATLDYLGDRFEVEPGGGAGRESYLADHKIETYLIVPPKKQSINDPPKRSPSSNAHTPSPTATIQITEPDLLDSTSLGEPPKTPKTPRTPKTPEDLRRSHASIASSVIPEEQERLLPRQSSVPLSPLPPPPSPLPLIKQTSITITTETINEETTENGDDGEQDQCKKACLTLPVEPITTNGHLPERVGSRKLSVQGLMAFAERRKSSSSIFGDMRKMSINNIDCLRSPMVATPGPLMRNRPSSKMTKYVECWGADKPFANITDSKMAKNIGLASIAMIESNLLPEDGHCGECKCWGPPKELQPVTMWYRNDSREAMYRTQPDSSFRYDLICTFILFLSIGLIQIVVFKSNVVVIGSLSATTVALGLFLYLSNRQMSDLSSPASNGPGQVIAANRSLRIAIFVISTALIAACAIFSVINFDDLVIANVLLVNNGTESVTYDVQFAPLAPVYLYMCAISLAAVSAFLQSGFIIKLLLMLLFIGVQCSLLWQSSLFETYQILNNSWPLAFQGGLFLLLIASVLHTLDRQGEYVSRTDFLWKAKLKVEQEEVETMRGINKILLENILPAHVAQHFLKKERAVQELYHESYSSVAVMFASIPNYKEFYDETDVNKQGLECLRLLNEIICDFDKLLLKPKFSGIEKIKTIGSTYMVASGLRPGKEEGATKNNELDEKRTEEHNVVVLVDFAIALMTALDQINRESFQRFRLRIGLNHGPVIAGVIGAQKPQYDIWSNTVNVASRMDSCGVMGRIQVSENTAKVLMAAGYSCECRGPIPVKGKGILTTYYVKTPFDEKI", "metadata": {"id": "A0A6I8TW35", "cluster": 22421419, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR029787"], "interpro_used": ["IPR018297", "IPR032628", "IPR001054"], "interpro_unused": ["IPR030672", "IPR029787"]}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein is classified under the Phosphatidylinositol Transfer CRAL-TRIO Domain-Containing Protein family, which facilitates the transfer of phosphatidylinositol between membrane compartments to regulate the phospholipid composition of plasma and endomembranes. These proteins modulate lipid metabolism by regulating phospholipase activity, participating in sterol biosynthesis, and controlling fatty acid release from lipid droplets. Additionally, they maintain organelle lipid homeostasis through interactions with enzymes like phosphatidylserine decarboxylase and may contribute to multidrug resistance mechanisms. Moreover, the protein should include a CRAL-TRIO lipid binding domain that binds small lipophilic molecules, including retinaldehyde and alpha-tocopherol, within a hydrophobic pocket composed of alpha helices and a six-stranded beta-sheet. This structural motif is commonly found in GTPase-activating proteins (GAPs), guanine nucleotide exchange factors (GEFs), and lipid-transfer proteins like Sec14. It originates from Scenedesmus sp. NREL 46B-D3.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 16927, 3856, 24422, 1024, 17, 30224, 3418, 17, 3165, 2213, 3416, 16, 2154, 11374, 1920, 3856, 1927, 16927, 2192, 3260, 10436, 1942, 5741, 1920, 14608, 5128, 1927, 3582, 1930, 16239, 3870, 17010, 10513, 1036, 18, 2144, 2697, 8480, 4486, 4714, 2007, 6773, 17570, 2455, 16, 9505, 1922, 20408, 8132, 16, 1930, 7138, 5934, 2687, 4012, 2037, 4486, 14215, 18, 4950, 16, 2611, 6698, 19309, 4486, 7622, 2596, 3719, 1956, 5038, 3189, 28563, 23922, 1930, 2278, 4672, 1942, 16398, 3554, 3531, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 24422, 1024, 17, 30224, 4486, 2743, 3418, 1988, 6876, 2858, 21140, 4206, 16, 2710, 6943, 6542, 1930, 4595, 17, 21432, 16, 2651, 43, 7919, 10154, 7179, 1927, 4595, 12789, 1930, 43, 3798, 17, 10338, 4666, 17, 11130, 18, 2052, 4346, 5219, 1977, 5384, 2435, 1922, 14809, 17, 8019, 2697, 12, 11349, 13, 16, 16904, 5489, 6818, 2790, 12, 15022, 1036, 13, 16, 1930, 4486, 17, 3856, 2697, 3189, 2532, 3745, 18, 2176, 22970, 2037, 17235, 7980, 23084, 2056, 18, 5214, 1938, 4182, 1014, 17, 11319, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MTWLLDFVGYSMRNAPAIRTSLAVLHTLQNHYPERLGDAVTKNKITFVEKGPQEEPEMSARFHMEHIEACMGGRNSIRMLEVHAGSPSMASDLSDASSATQYARSPSLRRRARSCRPGSPSRAGGRVWCLLAASMAVCVVWAVVPACASCRSLLRLCQVLMWQLSPCAALQGAMQAVCYYAPTLFSMTWKAVCPFIHQGLLFQLDDYRQRMQVEDAAVAPLAMAAERAGGARQQQAWWARPCHVLGAAHRLLHS", "metadata": {"id": "A0A7J7PQQ7", "cluster": 22626193, "interpro_all": ["IPR001251", "IPR036865", "IPR052578"], "interpro_used": ["IPR052578", "IPR001251"], "interpro_unused": ["IPR036865"]}, "task_type": "infilling"} {"instruction": "The protein should contain a SANT/Myb domain that adopts a helix-turn-helix fold and functions as either a DNA-binding module or a protein-protein interaction interface. This domain, structurally related to the DNA-binding region of Myb transcription factors and the chromatin-associated SANT domain, typically consists of three alpha-helices arranged in tandem repeats. Also, the protein is grouped in the Homeodomain-like superfamily, which comprises transcription factors and DNA-binding proteins that utilize a conserved helix-turn-helix (HTH) motif to interact with the DNA major groove. These proteins are ubiquitous across all domains of life and play critical roles in gene regulation through specific hydrogen bonding and hydrophobic contacts. It is present in Piromyces finnis and corresponds to UniProt keyword Coiled coil. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 3066, 5531, 43, 7628, 19, 16851, 3418, 1988, 24032, 43, 7864, 17, 5165, 17, 7864, 3728, 1930, 4088, 1966, 3108, 43, 2678, 17, 2743, 9059, 2014, 43, 2213, 17, 2213, 2835, 6854, 18, 2052, 3418, 16, 12171, 2712, 1942, 1920, 2678, 17, 2743, 3031, 1927, 16851, 3213, 2790, 1930, 1920, 6338, 17, 2458, 7628, 3418, 16, 5745, 7543, 1927, 2559, 4595, 17, 12789, 14940, 1922, 10361, 9569, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 4502, 17166, 17, 3189, 13975, 16, 2154, 12936, 3213, 2790, 1930, 2678, 17, 2743, 2697, 1988, 12561, 43, 5305, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 6310, 1956, 1920, 2678, 3044, 15920, 18, 2144, 2697, 2032, 15498, 3436, 2136, 4682, 1927, 3308, 1930, 3918, 4140, 5456, 1922, 2359, 3640, 2596, 2487, 6201, 11463, 1930, 7919, 9070, 18, 2176, 1977, 2481, 1922, 13774, 29249, 3502, 11110, 1930, 8852, 1942, 20709, 11121, 2538, 17524, 9121, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MMTNSTSSTNEYKWSTYECIVLVQAFLKFGEDHWKDISKILTKNLSPENGKDIFSQKNCQQKFNSLLEEYIKSEEKLAIIPKVKQLTNKLLQKRSRQLQYELELNKKNFIKLKKEIHEIKEGKWDNRLIKELNEINISKLKISDDKVKEESNKANSNKQVIENKDHDKDIDISKHKIEESNNNSNELIEDSSKNNNIKNELNTEISNKLIGNSEIIIKEQKKENNESELLTSIKSKDLEDLLTNDNKKINENDKHQSSTIKDIKIPEENILNIKDEEKSDKALLNTKENKKILESHDNNEKEIVTTISAIETENSIKFHINIKSDNKKLLFNEVGVENNLKLSKKEASNEKDNQDEDKALSLGLKINNNANKEKYSSLLNNDEKLDNNKEDKKNNNIENNKGPIKEEERDIVKSEDNENITQQEYKIKFETNKKENEDNMKEENNIIKSNDNEDDNIDIEEKVNEIELKNENDDDEDIIIDIENTEKSSLSETEKEDDVNEIKDNKESYPIIKSLDGIEKELKNEDKLSKKEKENNEEIITDEKMELKEKINNEITKTDNKNIENDKLVSENLNIDEGINDNKNEIIIEKENEIDDEKNEKKIQEVSKNLNINLNKKELNVEKIENISDIELTKNKKDNDLEKTEDKEETLLLKENEVFSNDETLINDDVDNNVNKDAASNNNKNKSFSLSLSKKNKKELNNNEKECNQVLEKIDKETKNTGNIEVVFAKDNNEKLENEQDELVNKTINETFDKNKNIIENEKENINLIIKDNINSDEEENKDKEIIGSKVNYSDGVIEKNIGQKEVDENEDIDITNNIDKEVIEKKKNINDNMEIDDESKQVIIETKNIGKSDESDETKTTIESNINDDKNNDKINDKEFRVEDNNNNKKEDEKSIIKNDDKIENSEFKESNKNDNKIEQISKDENIIEKVVKEKIKNEELEEVKSEKENNVINDVNSKDLCDSSKDQNNKDNNISNIEKKSEIKESRNLEDIPTNEGNIIEGKEIKNEIISLDERNENEKMEKGEEKLENKSEEKEEEKKEKGNKNNDKEYKKRFNKYEITTRRKDKISYEKHEKDVMKEKIKYNDKVENEEKENDDITKGEKKEKKEEYKNEEEVKEKEKS", "metadata": {"id": "A0A1Y1UZA9", "cluster": 23151760, "interpro_all": ["IPR009057", "IPR001005"], "interpro_used": ["IPR001005", "IPR009057"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "It is part of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein has a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein includes a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It has been characterized in Prochlorococcus marinus str. MIT 9302 and contains UniProt keyword associations Isoprene biosynthesis and Transferase. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 2176, 1977, 3131, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 2258, 2252, 4378, 1922, 9823, 7806, 30232, 4879, 2437, 1957, 13081, 1022, 1957, 2114, 18, 3263, 6156, 11636, 1930, 5461, 20709, 11121, 2538, 5253, 26690, 1021, 8132, 1930, 13763, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MQDLAKTKIIIKSPAKINLHLEVIGKREDGFHELAMIMQNIDLSDYLEFQINNEGLIKLESDCNNLSLASDNLIVKSANLLRKKLNIDLGANIFLRKNIPIGAGLAGGSSNAAATLIGLNKLWDLNLDQKTLCSLASMLGSDIPFFINGGIQLCFGRGEILEKLDSNFEYGVLLLKNPKVSVSTAETYKKYSNKFCDQYLTNREKIENIRKNLRDNGLKNLSFDNKHLTIKNDLQLVVENDNDSVKQSLYLLSKLKNCLTSSMSGSGPTCFALFKDIETAKKELSANYKLFKDKGYDAWVCTFLEMGIAFM", "metadata": {"id": "A0A0A2ADK0", "cluster": 23626706, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Furthermore, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Also, it is part of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is found in Candidatus Cloacimonetes bacterium HGW-Cloacimonetes-1 and has UniProt annotations Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 12596, 28278, 3947, 3764, 14061, 7175, 1018, 17, 12596, 28278, 3947, 3764, 17, 21, 1930, 2258, 20709, 15010, 5239, 1930, 9067, 4587, 18, 3], "output": "MKPYHVPVMVTECIEFLHLKNGGIYVDATLGGGGHSKAMLEANPTISLFGLDQDIEAIEQATIVLEPWADQVCIIQNNFTALRTELAMRKIKGIDGILFDLGVSSHQIDQVSRGFSFEGDAELDMRMDQESELNAFKIVNEMEMYDLAKIIKDFGEELYAKRIAKAIVEARATAEIKSTKQLAAIVESCVKFGKESVKSKARVFQAIRIHVNSELDVLQSALADSINILNPGGRIVVMSYHSLEDRIVKQAFKTASTGCDCPPQAPMCFCNKVPILKSLTRRPILASDSEIENNSRSRSAKLRAAEKIPVEEK", "metadata": {"id": "A0A2N2LBE4", "cluster": 24036610, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein should contain a Transposase IS4-like domain that catalyzes the excision and insertion of autonomous mobile genetic elements, including transposons and insertion sequences (IS). It functions as the essential enzymatic component of the IS4 family, facilitating the transposition of these elements within the genome. It has been detected in Ignavibacteria bacterium.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 3066, 5531, 43, 12935, 2051, 1977, 1006, 17, 3189, 3418, 1988, 17097, 1920, 10940, 1930, 7413, 1927, 15452, 8785, 3299, 5362, 16, 2710, 18808, 1036, 1930, 7413, 3709, 12, 1977, 13, 18, 2176, 4088, 1966, 1920, 4415, 8145, 4594, 1927, 1920, 1977, 1006, 3416, 16, 12440, 1920, 22596, 1927, 2144, 5362, 2651, 1920, 3843, 18, 2176, 2258, 2252, 3330, 1922, 12046, 9188, 7972, 2341, 18339, 14061, 18, 3], "output": "MTKHPNQQFRKLVVDTRNKNFKYPEQEHRKTHWHDYNLSKINDIKSILIFIRNSVDSIFINEDFDKVGRPPVNPRHLTKAILFCEAVGIPERQAQGWLGIMSPFLGIYEKLDDRVIGKAYENPEVVRILKKVFEKTKSSDGLLNGDGTGLERSRKDNYESTKKKKAGQYMTSVVDSREIVQAFDISGTQECQIMHKLIKNVDGKVLTLDAGFNDRKLVSEISRLGMKPYIFPKKNNNINGDVYWQKMYLDFYYDTINWLRNYHQRSHTESFHSSFKRTFGIITKLKFCSKFTQVCARIIIHNFRRINYFESPNK", "metadata": {"id": "A0A7V1PW99", "cluster": 24069702, "interpro_all": ["IPR002559"], "interpro_used": ["IPR002559"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should contain a Rho termination factor, RNA-binding domain that binds single-stranded RNA to facilitate the disengagement of newly transcribed RNA from its DNA template. It features an N-terminal OB-type fold with an indented face that serves as the primary binding site and supports the formation of a functional hexameric complex. Additionally, the protein should feature a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. Also, the protein should feature a ATPase alpha/beta subunit nucleotide-binding domain that forms the central structural component of the catalytic or regulatory subunits in F-, V-, and A-type ATPases, as well as flagellar ATPases and termination factor Rho. It binds nucleotides to drive ATP synthesis or hydrolysis through conformational changes linked to the complex's rotary motor mechanism, coupling chemical energy with proton translocation. It originates from Mycolicibacter engbaekii and is described by UniProt keywords Hydrolase, Transcription regulation, and Transcription termination.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 3066, 5531, 43, 10585, 12462, 2991, 16, 3146, 17, 2743, 3418, 1988, 6876, 2957, 17, 10338, 3146, 1942, 6628, 1920, 28347, 8909, 1927, 7471, 10078, 3146, 2037, 2496, 2678, 7662, 18, 2176, 4075, 1925, 56, 17, 4262, 2384, 17, 2601, 3728, 1956, 1925, 2063, 12871, 6171, 1988, 10634, 1966, 1920, 3065, 2743, 3200, 1930, 7825, 1920, 3337, 1927, 43, 3183, 25602, 1935, 2796, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 9444, 4595, 19, 4666, 5903, 5489, 17, 2743, 3418, 1988, 4952, 1920, 4101, 4346, 4594, 1927, 1920, 6804, 2014, 4948, 6991, 1922, 48, 17, 16, 64, 17, 16, 1930, 43, 17, 2601, 28132, 16, 1966, 2486, 1966, 24154, 28132, 1930, 12462, 2991, 10585, 18, 2176, 6876, 9519, 1942, 9265, 4498, 4271, 2014, 9128, 2596, 8523, 2840, 4624, 1942, 1920, 2796, 11, 61, 23548, 4842, 2856, 16, 7590, 4399, 3844, 1956, 8433, 7849, 18, 2176, 22970, 2037, 5078, 4485, 26073, 2341, 1915, 3814, 7972, 2819, 3907, 1930, 1977, 2910, 2007, 20709, 11569, 20748, 16, 3213, 3640, 16, 1930, 3213, 12462, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MTETDLFAAEGSTDQESLPTPPITSATSPDAAADGGEAAPSAPAESASAPESGAAATSGMRKSELIAAIREAGANGGQASEPSAEQSANGVANGTEPAEAAQVEAPDAAADKPAEQDNAAAADKPAEQDNAAAADKPAEQDKPAEQGKPAEQDKAGDGDAPGGSRRQRRTEGAKAEDGAQAKNDDQGDGANRGDDDEGRGGRRGRRFRDRRRRGERGGEGGAGGETAELRDDTSGYLAGPNDVYVSMNMVRKNGLRRGDAVTGAVRIPRDGDQLNQRQKFNPLVRLDSVSKLTPLYPNQRLRLETSPEKLTTRVIDLIMPIGKGQRALIVSPPKAGKTTIMQDIANAITTDMQRSVKGEVIASTFDRPPSDHTQAAELAIERAKRLVEQGKDVVVLLDSITRLGRAYNNASPAARNIEDGGSLTIIATAMVETGSTGDTVIFEEFKGTGNAELKLDRKIAERRVFPAVFAIVHKLRRLLSGLDSHQAIDLLMSQLRKTKNNYEFLVQVSKTTPGMDNDVADGALSSMVLPELRALANRVGVKGSAAPPRRERRGASRATGAPAGNDRAEKSDKPEQSGERRERDDVVQPVAGILDVLDNYAFVRNGGPVEDARKRPEFRNNPECHLMVVLVDERPEEVSGRILSGGVDSTALYPPKRFLGADVNPSGTRKDELLLSPDE", "metadata": {"id": "A0A1X1TRZ1", "cluster": 26380317, "interpro_all": ["IPR003593", "IPR000194", "IPR011129", "IPR012340", "IPR027417", "IPR011112", "IPR041703", "IPR036269", "IPR011113", "IPR004665"], "interpro_used": ["IPR011113", "IPR003593", "IPR000194"], "interpro_unused": ["IPR012340", "IPR011129", "IPR011112", "IPR004665", "IPR036269", "IPR027417", "IPR041703"]}, "task_type": "infilling"} {"instruction": "The protein is included in the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. In addition, the protein is classified under the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Moreover, the protein features a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. It is found in Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (Yeast) (Candida guilliermondii) and is classified with UniProt keywords Magnesium, Metal-binding, and mRNA processing. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 3950, 16, 1920, 2213, 4075, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 2176, 1977, 2435, 1922, 22319, 4490, 2229, 1019, 22833, 12191, 2166, 2315, 3907, 12, 3943, 11037, 5374, 5127, 19, 16341, 4489, 1016, 19, 10964, 4968, 11425, 19, 14904, 1035, 13751, 1026, 19, 8789, 15618, 10049, 9364, 19, 5214, 1005, 1024, 67, 17, 24067, 13, 12, 5688, 13, 12, 14550, 22833, 12191, 2166, 2315, 3907, 13, 1930, 1977, 5947, 1956, 20709, 11569, 13148, 16, 6048, 17, 2743, 16, 1930, 3616, 4587, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MSYQTYGVTPPISTAEPTSKEKSLNDSLIKELRKRGSFENEAATKKRVEVLNTLQKITEEFVYRVSLNKNMSEGMARDAGGKIFTYGSYRLGVYGPGSDIDTLVVVPKHVNRTDFFTVFESLLRERPELEEIASVPDAFVPIIKIEFGGISIDLICAKLDIGKVPRDLTLGDKNLLRNLDEKDLRSLNGTRVTDEILTLVPKPTVFKHALRCIKMWAQQRAIYANIFGFPGGVAWAMLTARICQLYPNAVSAVIVEKFFHIYSQWSWPQPVLLKQIEDGPLQVRVWNPRLYPHDRSHRMPVITPAYPSMCATHNITSSTQAIIVSEFKRGAEIMNDISIGKKEWGDLFARHEFFFRYKFYLCVVASTKGSAEEHLKWSGMVESKLRILVQKLELTEGITIAHPYVKTFEDGYVCKTADEASTIISSYGTLKGEKATEGARKIENPKETYTNDEIALHLTKLYIGLDIDIKGAKSLDIQVPCSEFFNLCKGWPTYNEDMHAIQIKNVKLHDLPNDVYVEGEERPMKIPKRKRLDSNGDTNKRLKNIGTVATAANN", "metadata": {"id": "A5DJF1", "cluster": 27374107, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR011068", "IPR043519", "IPR007012"], "interpro_unused": ["IPR048840", "IPR014492", "IPR007010"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein is associated with the Dockerin domain superfamily, which functions as an enzyme-integrating module within the bacterial cellulosome complex by binding tenaciously to complementary cohesin domains on scaffolding subunits. This domain adopts a structure of three $\\alpha$-helices containing duplicated EF-hand-like motifs that coordinate calcium ions to stabilize the protein-protein interface. Also, the protein should have a Ice-binding protein, C-terminal domain domain that is found in prokaryotes and exhibits ice-structuring activity in vitro. This 25-residue C-terminal feature contains an invariant Pro-Glu-Pro (PEP) sequence, a hydrophobic region likely to span the membrane, and a basic arginine-rich cluster. It is present in Phycisphaerae bacterium SM23_33. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 2458, 1956, 1920, 9170, 16654, 3418, 13975, 16, 2154, 4088, 1966, 1925, 4113, 17, 14042, 9059, 2651, 1920, 4543, 18485, 4283, 2796, 2007, 2743, 5656, 28278, 8232, 1942, 8862, 22822, 4682, 1990, 22582, 6991, 18, 2052, 3418, 24032, 43, 3170, 1927, 2559, 8, 38, 4595, 8, 17, 12789, 3165, 19479, 8485, 17, 3897, 17, 3189, 8277, 1988, 11865, 5016, 6982, 1942, 13448, 1920, 2213, 17, 2213, 6854, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 7133, 17, 2743, 2213, 16, 45, 17, 4262, 3418, 3418, 1988, 1977, 2435, 1922, 28149, 1930, 9826, 7133, 17, 2581, 4729, 2455, 1922, 3596, 18, 2052, 2637, 17, 6181, 45, 17, 4262, 5961, 5461, 1925, 17004, 1965, 17, 9258, 17, 1965, 12, 9110, 13, 3244, 16, 43, 7919, 3031, 3205, 1942, 7188, 1920, 3260, 16, 1930, 43, 5937, 9732, 17, 5536, 4377, 18, 2176, 1977, 2481, 1922, 25511, 9119, 29164, 3336, 14061, 2426, 4553, 41, 3401, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "LVDLSRIYFVKLKDVLGDGSQPDRFGNPIYDPTGNMDPPYDDETSADVDAVTVIHGLAAPPAGDANLDQVVDGLDYNTWSLHYRMSAMTWTEGDFNGDTIVDGLDYNIWSGNYAHGGQGSAVPEPAALVLSLAGAVLLGRGRRRPWQRTGPPAGQGAGPEGYPRPRPGLPMA", "metadata": {"id": "A0A0S8H152", "cluster": 28522582, "interpro_all": ["IPR036439", "IPR013424"], "interpro_used": ["IPR036439", "IPR013424"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is associated with the Beta-carotene 15,15'-dioxygenase, Brp/Blh family, which comprises prokaryotic integral membrane proteins, such as Brp and Blh, that catalyze the cleavage of beta-carotene to produce all-trans retinal. This enzymatic activity supplies the essential chromophore for bacteriorhodopsin and related light-driven proton pumps. It has been detected in Methylobacterium gregans and corresponds to UniProt keyword Oxidoreductase, Cell membrane, and Iron.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 4666, 17, 21498, 2461, 16, 2461, 11, 17, 23652, 10465, 2432, 2051, 16, 2387, 1034, 19, 2266, 1023, 3416, 16, 2154, 12936, 21545, 12328, 3260, 2697, 16, 2427, 1966, 2387, 1034, 1930, 2266, 1023, 16, 1988, 18170, 1920, 6404, 1927, 4666, 17, 21498, 1942, 5074, 2136, 17, 2127, 6943, 18, 2052, 8145, 2455, 21451, 1920, 4415, 25801, 1958, 14027, 14514, 1986, 16729, 1930, 2712, 3696, 17, 6446, 8433, 19263, 18, 2176, 2258, 2252, 3330, 1922, 4963, 12022, 29721, 2075, 1930, 8852, 1942, 20709, 11121, 2538, 27388, 16, 2024, 3260, 16, 1930, 5680, 18, 3], "output": "MAARASGPTLGVSSEASRRRSVLVGAATLPREASWLAALAAVIVLGVPHGALDGAVAAPLLRPLGLSALVLLAWQAAPMTTLVGFLALSLLVRGGAPIALPALLRPEETAEVFALVARWEVLAEVLILVAAFRLLPPLTAFALYFIGLHLGRAVVAALPVFALTLLLGAALWPLYQGLSALTVPHVLLDRLATRHNEHRTGAGLHGTKRLPVAGALVALALVASRYGRAWFGVFAVPYILHFGEEDAGPGRPFERVPMPLLPAWWTVAAWLWLALAVVWLLGHLRAPRHMRALIRDPVRAPGINTAAGSPNKAGALLTLTL", "metadata": {"id": "A0AA37MAN0", "cluster": 28531701, "interpro_all": ["IPR022270"], "interpro_used": ["IPR022270"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein has a Phosphoribosyltransferase domain that catalyzes the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP) by a nitrogen-containing nucleophile to yield an alpha-1 substituted ribose-5'-phosphate and free pyrophosphate. This domain is essential for nucleotide synthesis and salvage pathways and features a conserved PRPP binding motif. Also, the protein is a member of the Uracil phosphoribosyl transferase family, which catalyzes the conversion of uracil and 5'-phosphoribosyl-1-pyrophosphate (PRPP) to yield uridine 5'-monophosphate (UMP) and diphosphate. This enzymatic activity plays a key role in the pyrimidine salvage pathway by recycling free uracil into nucleotide monophosphates. Also, the protein is assigned to the Phosphoribosyltransferase-like superfamily, which encompasses enzymes such as phosphoribosyltransferases (PRTases) and phosphoribosylpyrophosphate synthetase-like proteins. These domains typically catalyze the transfer of phosphoribosyl groups to specific substrates, playing a central role in nucleotide biosynthesis and salvage pathways. It is identified in Bacteroidota bacterium and carries UniProt keyword assignments Glycosyltransferase, Allosteric enzyme, and Nucleotide-binding.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 2258, 43, 3421, 2023, 25566, 3418, 1988, 17097, 1920, 9514, 1927, 1920, 4595, 17, 21, 11, 17, 24937, 1927, 25, 17, 3421, 2023, 11731, 17, 4595, 17, 21, 17, 24937, 12, 11533, 1034, 13, 2007, 43, 6634, 17, 3165, 2797, 28335, 1942, 4307, 1925, 4595, 17, 21, 11798, 17870, 17, 25, 11, 17, 5413, 1930, 3294, 24937, 18, 2052, 3418, 1977, 4415, 1958, 5489, 4271, 1930, 17577, 3873, 1930, 4075, 43, 5305, 11533, 1034, 2743, 5219, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 22761, 3421, 2023, 11731, 13763, 3416, 16, 2154, 17097, 1920, 7309, 1927, 22761, 1930, 25, 11, 17, 3421, 2023, 11731, 17, 21, 17, 24937, 12, 11533, 1034, 13, 1942, 4307, 26104, 25, 11, 17, 21363, 12, 8736, 1034, 13, 1930, 23266, 18, 2052, 8145, 2455, 5705, 43, 3834, 2770, 1922, 1920, 21611, 17577, 3374, 2007, 13977, 3294, 22761, 2460, 5489, 21363, 1036, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 3421, 2023, 25566, 17, 3189, 13975, 16, 2154, 21569, 5038, 2427, 1966, 3421, 2023, 25566, 1036, 12, 2033, 3857, 4127, 1036, 13, 1930, 3421, 2023, 11731, 18425, 15707, 18185, 17, 3189, 2697, 18, 2144, 4682, 5745, 18170, 1920, 3856, 1927, 3421, 2023, 11731, 2671, 1942, 2487, 6249, 16, 14797, 43, 4101, 2770, 1922, 5489, 8132, 1930, 17577, 3873, 18, 2176, 1977, 2899, 1922, 24323, 7336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 20067, 9961, 16, 14772, 4113, 16, 1930, 5489, 17, 2743, 18, 3], "output": "MSLQAPVTVLQHPVVARDLTSTILAYTALMDLPLRSRPIETPVRETEGFDILNFVPEAKVGHLGMYRDEKTHQPVDYDAITFLKEKGAHQIRFISLISAPEGLEFIVPGLGDAGDRYFGTLILRDRETGISQFRAAMHRIINTEIIVVPILRAGLSLVDAYSKLPSEIQDGLVLLVDPMLATGGSADRIRKHHPEVSLITASIDEKLNDNA", "metadata": {"id": "A0A2T4XHB8", "cluster": 17650497, "interpro_all": ["IPR000836", "IPR029057", "IPR034332", "IPR050054", "IPR005765"], "interpro_used": ["IPR000836", "IPR005765", "IPR029057"], "interpro_unused": ["IPR034332", "IPR050054"]}, "task_type": "infilling"} {"instruction": "We aim to build a protein that does the following:\nThe protein is grouped in the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Moreover, the protein contains a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Additionally, the protein can be placed in the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. It is produced by Bombardia bombarda and is described by UniProt keywords mRNA processing, Magnesium, and Nucleus.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 3950, 16, 1920, 2213, 5461, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 2176, 1977, 4152, 2007, 23152, 13047, 23152, 2211, 1019, 1930, 1977, 2910, 2007, 20709, 11569, 3616, 4587, 16, 13148, 16, 1930, 5607, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MSDRDLGVTPPISTALPTEDEKRLSYESPAETNKREVVLKSLERITDEFVKRAAMERLGVYGPGSDIDTLVVAPRYVTVQQYFDIFPKLLLEYSGISIDLIFCSIQGKKQLDDDPHWNLQDNSLATFRVALRAIKLWAQRKAIYANIMGYPGGVALVVNKFFNIMLKWPWPLPVLLKIYPSDRNHKMPIITPAYPSMCSTHNIGQSSMTVHTFFTSDFKYYLTVVSSGRTRESQNSWAGFVESKVRILVGKLNQTEIEEVQAGSLAYQVKPGAGPLNAKVEAKVKSDPIDTEPNLQNIAVAENGQVVIFTTNHYIGLQLVQKAKSLDLSREVNPDDVFEPGEEKPKKAVKRKRPENGSVAATNRDELLLRELRAQGTKEPKNTVLIRDARGRVFTYGSYMAPPGSITDLTTVPEAFVPIIKFELRGLSENEVRSLNGTRVTDEIINLVPEVAWAMLVARVCQLYPKAASDIEYGHSVTRVPVWNPKIQQELANGVKITEEIMVGKRPWKDLFTKELHPSIALARPFNKGYERVHRCKPEVKSETTTTENGAGPHRAEPPPPAEEEQEVEIDFKAMLTANESAYDRHMNFLTVQHVKSWEL", "metadata": {"id": "A0AA39XBE3", "cluster": 3443261, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR043519", "IPR007012", "IPR011068"], "interpro_unused": ["IPR014492", "IPR007010", "IPR048840"]}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein has a 4Fe-4S ferredoxin, iron-sulphur binding conserved site that mediates electron transfer in a range of metabolic reactions. It typically coordinates a 4Fe-4S cluster using four conserved cysteine residues, a structural arrangement characteristic of bacterial-type ferredoxins. In addition, the protein should include a Cysteine-rich domain that functions as a conserved module in oxidoreductase enzymes such as heterodisulphide reductase subunit B and anaerobic glycerol-3-phosphate dehydrogenase subunit C. Typically found in two copies per protein, it contains up to four conserved cysteine residues that likely coordinate iron-sulfur clusters to facilitate electron transfer. It has been characterized in Planctomycetota bacterium and is annotated with UniProt keywords Metal-binding.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 2258, 43, 15338, 1021, 17, 26814, 25304, 22389, 10960, 16, 5680, 17, 13528, 1949, 2743, 5305, 3200, 1988, 10412, 4995, 3856, 1922, 43, 3109, 1927, 4487, 5298, 18, 2176, 5745, 10675, 43, 15338, 1021, 17, 26814, 4377, 2193, 3006, 5305, 8666, 4248, 16, 43, 4346, 13002, 6293, 1927, 4543, 17, 2601, 25304, 22389, 10960, 1036, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 8666, 17, 5536, 3418, 1988, 4088, 1966, 43, 5305, 9059, 1922, 27388, 5038, 2427, 1966, 11330, 1937, 23138, 2261, 11386, 5903, 44, 1930, 12554, 9244, 17, 23, 17, 5413, 9294, 5903, 45, 18, 5745, 2435, 1922, 2288, 9425, 2079, 2213, 16, 2176, 5461, 2353, 1942, 3006, 5305, 8666, 4248, 1988, 3205, 11865, 5680, 17, 12585, 5859, 1942, 6628, 4995, 3856, 18, 2176, 2258, 2252, 4378, 1922, 4720, 2341, 13386, 19446, 3857, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 6048, 17, 2743, 18, 3], "output": "LLGALEACNGAGFCRRRRGGVMCPSFRATLDERHSTRGRANALRLALTAGPASGVDVARLKSEYLAQSRARGALRATRAERWALRMRTGARAASLAPWLAGALLRIAPSRRLPAPGRRLPLRDPPRRAGRMRVALFLDCFTGFGEREIALDAVAALEAAGCDVVVRDVGCCQRRLGTLADEVDAIAALEPSCWSALRDDLPALALDERTRTRLQRVGEKALLFEQHLHCHQRALGAGGATQRLLGRLGVAEAVETLETTCCGMAGLFGMLADPETLQTLDLCLSCKACKGECPAPGAERAVKKALGPALSMGFLDRAARAARRLARVLVDALEKSGRKVEPPPDQRRGLL", "metadata": {"id": "A0A3M0XT95", "cluster": 3868914, "interpro_all": ["IPR017896", "IPR017900", "IPR004017"], "interpro_used": ["IPR017900", "IPR004017"], "interpro_unused": ["IPR017896"]}, "task_type": "infilling"} {"instruction": "\"The protein features a YGX type MBG domain that is found in a variety of bacterial extracellular proteins. This domain represents a structural variant of the standard MBG domain, distinguished by the replacement of the characteristic N-terminal YDG motif with a YGX sequence. In addition, the protein is a member of the Cell Envelope Structural Component family, which maintains the structural integrity and organization of the bacterial cell envelope. These proteins typically display a tripartite architecture comprising a C-terminal outer membrane beta-barrel, a central trimeric coiled coil, and an N-terminal domain that interacts with the peptidoglycan layer. Members may function as cellulosome anchors or form protective S-layer assemblies that facilitate substance exchange with the environment. Moreover, the protein incorporates a S-layer homology (SLH) domain that anchors surface proteins to the bacterial cell wall by binding to pyruvylated secondary cell wall polymers (SCWPs). This motif is characteristic of S-layer assemblies and mediates the attachment of the protein coat to structures such as teichoic or teichuronic acids. It is expressed in Anaerolineales bacterium.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 4075, 43, 67, 1029, 1039, 2601, 5667, 1029, 3418, 1988, 1977, 2435, 1922, 43, 5386, 1927, 4543, 5329, 2697, 18, 2052, 3418, 4972, 43, 4346, 6031, 1927, 1920, 2970, 5667, 1029, 3418, 16, 12080, 2007, 1920, 7619, 1927, 1920, 6293, 56, 17, 4262, 67, 18641, 5219, 1956, 43, 67, 1029, 1039, 3244, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2024, 11262, 4346, 4594, 3416, 16, 2154, 16566, 1920, 4346, 7996, 1930, 5901, 1927, 1920, 4543, 2024, 11262, 18, 2144, 2697, 5745, 4434, 43, 8027, 24707, 9335, 10351, 43, 45, 17, 4262, 7642, 3260, 4666, 17, 19560, 16, 43, 4101, 29177, 17524, 9121, 16, 1930, 1925, 56, 17, 4262, 3418, 1988, 9034, 1956, 1920, 24183, 4757, 18, 4678, 2278, 2347, 1966, 18485, 4283, 27127, 2014, 2386, 6337, 61, 17, 4757, 16137, 1988, 6628, 7311, 6818, 1956, 1920, 3515, 18, 3950, 16, 1920, 2213, 19683, 43, 61, 17, 4757, 9039, 12, 2788, 1023, 13, 3418, 1988, 27127, 3154, 2697, 1942, 1920, 4543, 2024, 4821, 2007, 2743, 1942, 6487, 12631, 4336, 4067, 2024, 4821, 11039, 12, 2160, 1018, 2523, 13, 18, 2052, 5219, 1977, 6293, 1927, 61, 17, 4757, 16137, 1930, 10412, 1920, 8576, 1927, 1920, 2213, 15642, 1942, 4061, 2427, 1966, 3602, 2108, 8643, 2014, 3602, 2108, 21280, 4576, 18, 2176, 1977, 3198, 1922, 11381, 8419, 3955, 14061, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MYPRSLIRHLFVFSRAIVFIVILLALVGMTTSVAGKSWTNVSYSMASDNLYATSKKTNKQLKLSNFTIPGQANVALSYNGGTNYTTAFSTALTGTESINSLGGPTNTWTGTGDPIYVDQIQVRVYYSPPPTTLTLSPVTGPYGGTASMSATLGNGLDVSGNCTGTYAGSAATNGSGVATLASADLSGINAGSYPYGAPTAGTYGGTVTLSATLTSEGSPVNGEWITFYLFGNPDIGASFEGNSNLDPANANALLTIDPRPITVTALKDKITSGSLVTGDTASFTQAFASKDVGTGKIITPVGVVADDNSGLNYITVTADNKLKFVGQPDPAFTYRYTGLVGSDTGADIDGGADNNYNLSYINGTLTVSNPTFSDVPTAYWLNYCPDSTVTRAQMAVFLLKGVHGSNYTPPAVGGSTGFADVPTGGNFCPDTPVTRAQMAVFLLKSKHGVSYTPPAAVGVFTGGCGGGNYCPDTPVTRAQMAVFLVKTFNLPFASDTGFSSPGVVSTPIPGGATIDGIEVRVEGFTGGLGRSWGPSDFTNANFIVRLTTTLTAAGTPISLKNIDFYLGCARYAGDLSYQGTSISGNLIVVGTSTELVAAVGNSKTNNSGVASLPNVSLVGYNAETSNTKVYDGTTSSSGVPVSFAPVTNGAINKAPLTKPVCTVSVAHNTVGTYPIVCSAWNFIERLYAAGITGGCSTTPTYWAAPWIKQLAAEGITGGCGNDVPVGYWADKWIEQLAAEGI", "metadata": {"id": "A0A363U7C4", "cluster": 4876112, "interpro_all": ["IPR051465", "IPR013783", "IPR041286", "IPR001119", "IPR041248"], "interpro_used": ["IPR041286", "IPR051465", "IPR001119"], "interpro_unused": ["IPR041248", "IPR013783"]}, "task_type": "infilling"} {"instruction": "The protein should contain a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Furthermore, the protein features a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Also, the protein carries a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. It is native to Sphingomonas sp and carries UniProt keyword assignments Excision nuclease, DNA repair, and Cytoplasm.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 3066, 5531, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 3677, 16, 1920, 2213, 4075, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2222, 16, 1920, 2213, 16252, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2176, 1977, 6196, 1942, 13502, 10480, 2056, 1930, 16252, 20709, 11121, 2538, 18306, 10940, 16230, 16, 2678, 5059, 16, 1930, 5239, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "SAIGDGEKDQVLLGVTGSGKTFTMASVINRVQRPALILAPNKILAAQLYGEMKSFIEKESSTNESIDRMRHSATRALLERDDVIIVASVSCLYGIGSVETYSLVALQYKRNDAAFQRGNFRVKGDTLEIFPSHYEDSAWRISFFGASLNSVRVYANSHYVTPGPTLKQAGEAIKHELAERLKELVLEGKLLEAQRLEQRTNFDLPTLFEYLPDNALLFVDESHVTIGQINGMSRGDHRRKLTLAEYGFRLPSAIDNRPLRATPGSWEMEQTGGVFAEQVIRPTGLIDPPVEIKPVEEQVQDLIVEVGKTTATEYMHEAGIKVRYMHSDVETLERIELIRDLRLGVYDVLIGINLLREGLDIPECGLVQTIGRAARNVDGRVILYADRVTGSMERAMNETSRRREKQVAYNGDIIAHVASQDQVTIPIDEDRPHMVGHNLRAYIEDLEKQMRKNEELGLPVDQQKAPVIGRSNEGKPGTRKTRYGKSQKMRMGGSRSRFPDNAVEYFVSYYDYYQPEAYVARSDTYAMIFDLKKGTTVDQREIVRKDDIEEIIEFDPLTGKKVEMIAATGSCAGIENYSRFLTGRMPGEPPFNEWDAMRPPTTYVSLGYRTLVTTLTKRMAEDLAILDADKEGFLRSETSLITEHGITPTTIRRNIAASDLEFETAGRLRDEIRQLE", "metadata": {"id": "A0A520JH88", "cluster": 5199884, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001650", "IPR001943", "IPR014001"], "interpro_unused": ["IPR004807", "IPR006935", "IPR041471", "IPR024759", "IPR036876", "IPR027417"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein can be placed in the Cyclin PHO80-like family, which functions as a regulatory subunit for cyclin-dependent kinases (CDKs), preferentially interacting with partners such as PHO85 and CDKA1. These complexes modulate kinase activity to control diverse cellular processes, including both standard cell-cycle progression and alternative regulatory pathways distinct from cell division. It originates from Ascosphaera apis ARSEF 7405.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8180, 20175, 4476, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 4948, 5903, 1958, 8180, 17, 3100, 7784, 12, 9727, 1036, 13, 16, 10662, 8615, 1956, 7228, 2427, 1966, 20175, 10025, 1930, 9727, 4904, 18, 2144, 5048, 8480, 4016, 2455, 1942, 2285, 6445, 3689, 4028, 16, 2710, 2321, 2970, 2024, 17, 4048, 4380, 1930, 5012, 4948, 3873, 4493, 2037, 2024, 8451, 18, 2176, 22970, 2037, 7249, 2609, 29164, 1019, 20655, 1036, 9896, 7726, 5446, 15264, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MSSIPTHTTAPDPRNLDNHNQNHIHQNYDQSYNHIQSALPTSTATTVVIPSGVKSQQAEEEAKPAHSCYYQAQGKGKENENENQNSNHLQQQQQQQQQQQQQHTTHRHHILHSQYAHHYSAPTHPRSGNVNNSSNSHTSNSNNHHNPLLHHHHHTPPASASSTVNANAHATRTAPLPPPSGAPAGAQQQQHHHHSSTKSPASPILAPAHPSMASLSFASEEMLGAAASASYASVDAALAGGTAMNTAGGGPRSRQRASSGLFGVEFQRSGAGSLPPAMGVIEMVAGILTKITTNNDAQHEPLHKYLTPQENGVDPTSPSQQPFVQPPLDPQSSSVLAFHGRNVPLSLLVYFDRMSAKVNGPLMQRILKREKEQERARRRQGQGQGQGSPQRVRGYSNAQAGGNTAHGSTASHLQPGPVHDPSSPFSARQDGSFAGTDSDPVFENFGFPPMLSSSFDSITESDLESSSSDEDEFWDSTFVIDSYNVHRLIIAGVTCASKFFSDVFYTNSRYAKVGGFRLSVTIEELEAYGTMLVEFYASEVLSQQRARESPANQGGGDNHSPTNYRAGTGHNGMPSVRSAAADRERERERERERERAAASRYQQGHQPRQTPSSSSASASDSSSLQQTAAVAAKNEKKQDELQRQNQNQNSDSRLTSTSTITAATAATSHIANTGASISIRHYNQYPASTSASTPPPSASSSSSSRMSSNRAPPHAADAADLSSPSRIKVRNLSHIHSFGGGAGGGGRRGSSMSSSAGLAGSAGAGRQYEISDMPVTDGSRDSSSPSSSSSAAQTNGGGSISILSYLSRIHRYCPTTYEVFEEKLAAKGGGGSRRQSEQGQARAQGSDSAQPPLMSSRYMSNPSSVNRDGREFTRSLTEDSAEYTETVFDGLDDGIALSRTLPLSELNHLELQFLFLNNQKQRESLMRAQAQFSRSPSYEDERRASAGSASSGSEVCM", "metadata": {"id": "A0A162I2R6", "cluster": 5528414, "interpro_all": ["IPR013922"], "interpro_used": ["IPR013922"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein carries a Zinc knuckle CX2CX3GHX4C domain that functions as a zinc-binding motif characterized by the conserved sequence CxxCxxxGHxxxxC. It is notably present in the MPE1 protein, where it acts as a component of the cleavage and polyadenylation factor (CPF) complex to facilitate polyadenylation-dependent pre-mRNA 3'-end formation. Also, the protein should include a Zinc finger, CCHC-type domain that functions as a zinc-binding motif primarily involved in recognizing single-stranded nucleic acids. It plays a critical role in retroviral genome packaging within nucleocapsid proteins and facilitates RNA or single-stranded DNA binding in eukaryotic cellular processes. It is produced by Amylocarpus encephaloides and is described by UniProt keywords Metal-binding and Zinc-finger. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 7997, 2547, 9764, 1952, 5639, 10866, 12001, 2509, 16277, 1030, 3418, 1988, 4088, 1966, 43, 7997, 17, 2743, 5219, 4378, 2007, 1920, 5305, 3244, 5639, 21487, 14710, 1039, 2509, 14710, 14710, 1030, 18, 2176, 1977, 7388, 2481, 1922, 1920, 5438, 12474, 2213, 16, 2597, 2176, 8016, 1966, 43, 4594, 1927, 1920, 6404, 1930, 24544, 2991, 12, 4244, 1038, 13, 2796, 1942, 6628, 24544, 17, 3100, 2097, 17, 3616, 23, 11, 17, 2482, 3337, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 7997, 8497, 16, 21846, 1030, 17, 2601, 3418, 1988, 4088, 1966, 43, 7997, 17, 2743, 5219, 5985, 3286, 1922, 15667, 2957, 17, 10338, 11079, 4576, 18, 2176, 5705, 43, 4140, 2770, 1922, 16599, 3843, 15627, 2651, 2797, 28712, 1960, 2697, 1930, 11374, 3146, 2014, 2957, 17, 10338, 2678, 2743, 1922, 10825, 3689, 4028, 18, 2176, 1977, 4152, 2007, 7061, 7095, 1034, 1957, 11591, 12363, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MTVYLRWLEVHRKSPSDFSNHWGNTVYQWGQSLRSRGFKEYEVIREVELWKEGKGPFSKIEGRPPPVSSDLYKSFNEPLNGGKPGERKPDPSGGLSWRRDGPLLDVRPNQPSHAYYQEKTSKSEPFCEPPKKKTLDMFLGAPPGNYVCNRCGKKGHHLQACPTNMDPTYDKPPSNEYICAVCDARGLHYKSLCPTNPDPYSIIQRRKAQGFRT", "metadata": {"id": "A0A9P7YEI0", "cluster": 7585761, "interpro_all": ["IPR025829", "IPR001878", "IPR036875"], "interpro_used": ["IPR025829", "IPR001878"], "interpro_unused": ["IPR036875"]}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein falls within the eukaryotic histidine acid phosphatase family, which catalyzes the hydrolysis of phosphate monoesters, particularly phytic acid and inositol polyphosphates, to liberate inorganic phosphate. Members of this family regulate intracellular inositol pools and metal availability, playing roles in processes such as neuronal development and homeostasis. Furthermore, the protein is included in the Histidine phosphatase superfamily, clade-2 family, which functions primarily as a group of acid phosphatases and phytases that hydrolyze phosphate esters, optimally at low pH. Catalysis centers on a conserved histidine residue that is transiently phosphorylated during the reaction cycle to facilitate substrate transfer. Members of this clade exhibit diverse activities, including glucose-1-phosphatase function and the hydrolysis of phytate to myo-inositol and inorganic phosphate. It is present in Geotrichum candidum (Oospora lactis) (Dipodascus geotrichum) and is annotated with UniProt keywords Disulfide bond, Signal, and Glycoprotein.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 12182, 2651, 1920, 10825, 13873, 2687, 8167, 3416, 16, 2154, 17097, 1920, 9128, 1927, 5413, 8914, 26934, 16, 4443, 9321, 1935, 2687, 1930, 16246, 11769, 11787, 1036, 16, 1942, 9954, 13108, 13849, 5413, 18, 4678, 1927, 2052, 3416, 5741, 4776, 16246, 12808, 1930, 6048, 6855, 16, 14797, 5456, 1922, 4028, 2427, 1966, 5121, 2740, 1930, 7622, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 13873, 8167, 13975, 16, 11315, 17, 22, 3416, 16, 2154, 4088, 5985, 1966, 43, 2210, 1927, 2687, 19131, 1930, 9321, 2319, 1988, 7222, 6931, 5413, 16785, 16, 22364, 2019, 2330, 2087, 18, 15408, 7365, 1990, 43, 5305, 13873, 6181, 1988, 1977, 12145, 7199, 2409, 1920, 3227, 4048, 1942, 6628, 4510, 3856, 18, 4678, 1927, 2052, 11315, 5987, 6445, 4209, 16, 2710, 3817, 17, 21, 17, 8167, 2347, 1930, 1920, 9128, 1927, 9321, 2010, 1942, 15924, 17, 16246, 1930, 13849, 5413, 18, 2176, 1977, 2481, 1922, 14136, 3319, 24315, 1035, 5033, 1989, 12, 57, 9890, 1019, 25300, 13, 12, 9137, 25033, 12709, 1957, 14136, 3319, 24315, 1035, 13, 1930, 1977, 10633, 1956, 20709, 11569, 11830, 5403, 16, 2733, 16, 1930, 11424, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MKLFSKISVLALNAVSLVLADKPYSQEARDQVNILKHQGGHGPYSDHSGFGIDNRTPENCVVDQVQFLRHGERYDKNLAKNKLEFLNTYESPALDENNYEQQSLMGPYGGYSSMFLCGSELRSRYNHLWSINVARGFLGSNWKKHSKFIVLNETEEVGLNSLTPVLGCPMFNPNYKGDYTVKYGQVGLQNLCMYDLNVVGHSPLCDYFEPNDWKAFEYKRDLDYYYYSGKGNPIVPAVGGIVANASLIILMYLTTVGLFNPDTDLDWRTIEFNNRWTTSQIVPMGTRVALERMSCKNKDDTFSKYVRFLVNEYIKIQRSRIPDIHNTCGIDENYKLPNALTFYWDWKKSPEKYRNWVVDLEDFPTFDLGFALSKFLYQFKRENDDAVLPLFTASQERIVVTLLKRFKEDVGNSVNVTTEDLANLMALNQDESDNDKIYISFAHETNINAVIPHDSCKSGPGFSCPLE", "metadata": {"id": "A0A0J9X8Z1", "cluster": 7855336, "interpro_all": ["IPR000560", "IPR029033", "IPR016274"], "interpro_used": ["IPR016274", "IPR000560"], "interpro_unused": ["IPR029033"]}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that can perform the following function: The protein falls within the Isoprenylcysteine carboxyl methyltransferase family, which catalyzes the carboxyl methylation of cleaved proteins terminating in a CaaX motif. These integral endoplasmic reticulum membrane proteins comprise a core of five transmembrane $\\alpha$-helices and a conserved C-terminal catalytic subdomain that encloses a cofactor-binding pocket. Additionally, the protein is classified under the Heavy metal cation-efflux system component family, which comprises bacterial proteins involved in cation-efflux systems that confer resistance to heavy metals such as cobalt, zinc, cadmium, and nickel. These members contribute to detoxification mechanisms by mediating the specificity and transport of these cations out of the cell. It is present in Deltaproteobacteria bacterium and corresponds to UniProt keyword Transmembrane helix. Give the amino acid chain.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 26690, 2199, 23159, 7595, 9943, 16478, 3416, 16, 2154, 17097, 1920, 9943, 5547, 1927, 10246, 2697, 5475, 2287, 1922, 43, 20951, 1039, 5219, 18, 2144, 12328, 13355, 12279, 3260, 2697, 13817, 43, 4728, 1927, 3628, 9117, 8, 38, 4595, 8, 17, 12789, 1930, 43, 5305, 45, 17, 4262, 6804, 27517, 1988, 17439, 12278, 43, 15155, 17, 2743, 10154, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 7881, 6048, 9976, 17, 11247, 2433, 4594, 3416, 16, 2154, 12936, 4543, 2697, 3286, 1922, 9976, 17, 11247, 3771, 1988, 7909, 3554, 1942, 7881, 11570, 2427, 1966, 20773, 16, 7997, 16, 17203, 16, 1930, 16541, 18, 2144, 4678, 4672, 1942, 18169, 3531, 2007, 10239, 1920, 4896, 1930, 4860, 1927, 2144, 16525, 2397, 1927, 1920, 2024, 18, 2176, 1977, 2481, 1922, 9649, 9218, 1021, 10296, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 9117, 7864, 18, 7031, 1920, 3835, 2687, 4659, 18, 3], "output": "MSDERVTTSMRCVVVWMIDLCRDTVRSWAVCFLRPSGRLELVMEQTEHTQEKPHQVANFWPKIIFGVPFTIAFFWGYMWLGGGVRWWQGWLMLGVMFVGETLRAVYVSRKQPEMFKRRGEFGEGTQSWDKAWLTVFGLVLTVMFVIGPLDGGRYLWAPLPVWTIPIGIVLYILYLVFFGWAMSVNPHFEKTVRLQEDRGHKVITTGPYAYIRHPGYIGSILGFGIAPPLMMCSAWALVPGLLLIPCFMVRTAWEDAFLQRELDGYAAYAQKVKYKLFPGLW", "metadata": {"id": "A0A2E9R161", "cluster": 8324620, "interpro_all": ["IPR007269", "IPR052527"], "interpro_used": ["IPR007269", "IPR052527"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein is a member of the Plavaka transposase family, which functions as a transposase containing an RNaseH catalytic domain. Members of this family often feature a C-terminal histone-binding BAM/BAH domain and are sometimes associated with TET/JBP family dioxygenases in fungi. It has been characterized in Amanita muscaria (strain Koide BX008).", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 5606, 7302, 7640, 12935, 2051, 3416, 16, 2154, 4088, 1966, 43, 12935, 2051, 3165, 1925, 9843, 1023, 6804, 3418, 18, 4678, 1927, 2052, 3416, 3868, 5961, 43, 45, 17, 4262, 6632, 17, 2743, 12202, 19, 24891, 3418, 1930, 2032, 8929, 2458, 1956, 9717, 19, 29316, 1034, 3416, 23652, 10465, 2432, 2319, 1922, 10520, 18, 2176, 2258, 2252, 4378, 1922, 2150, 8150, 3857, 7841, 6148, 12, 3943, 6235, 2261, 16720, 23789, 13, 18, 3], "output": "MDAALALAAEGIEVKRPSPPPADDTDSSEPAHTLVGTRRGPATRLRGGAEPQLEKRPYIVTYPSAAAGAVYRASERTENSRYGELVGDASQTNPYAPFTSPLEWEMAMWAKLRGPSSTAFTELMAIEGVQEQLKLSYKNTRELNKLIDEHLPGRPPFERHDILVGKEVCEVYFRDIIACIRSLFGDPDFAPYLVFKPEKHYTDETRQERMYHDMHTGEWWWATQAKIETDKPGATIVPIIVSTDKTQLTLFRNKNAYPIYMTIGNIPKEIRRRPSSRAYILLGYLPTSRLEHVTNKSAKRRMITNLYHACLARILEPLVSAGEDGVYMSTASGQVHRNHLILASFIGDYPEQVLTTCTLTGDCPQCEQPRNSLGDFDANQPPPLRNLRSILRAIDSFDSQPDRFLQTCSANRLKPVPRPFWNDLPYMNIYRSITPDVLHQLYQGIVKHLIAWVTTACGAAEIDARCRCMPQNHNIRLFTKGISSLSRVTGQEHDQMCRFLLGLIIDIRLPNRLSNVRLLRSVRALLDFVYFSQYPIHTV", "metadata": {"id": "A0A0C2TA91", "cluster": 8367872, "interpro_all": ["IPR041078"], "interpro_used": ["IPR041078"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should feature a TOPRIM domain that functions as a catalytic center for DNA strand breakage and rejoining in enzymes such as topoisomerases, primases, and nucleases. It adopts a compact $\\alpha/\\beta$ fold containing a conserved glutamate residue and a DxD motif responsible for coordinating the magnesium ions essential for enzymatic activity. Moreover, the protein should have a DNA primase, DnaG domain that synthesizes RNA primers for Okazaki fragments during bacterial lagging strand DNA synthesis. It interacts with the replicative DnaB helicase, single-stranded DNA binding protein (SSB), and DNA polymerase III holoenzyme to coordinate replication and restrict primer length within the replisome. Moreover, the protein includes a Bacterial DnaG primase, TOPRIM domain that houses the nucleotidyl transferase active site responsible for synthesizing RNA primers to initiate DNA replication. It utilizes conserved glutamate and DxD motifs to coordinate Mg2+ cofactors required for catalysis. This domain often associates with DNA helicases as part of primosome assemblies. It has been characterized in Savagea serpentis and is described by UniProt keywords Nucleotidyltransferase, Transcription, and Zinc. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 3700, 3027, 1035, 3418, 1988, 4088, 1966, 43, 6804, 4102, 1958, 2678, 5984, 25816, 1930, 12677, 9024, 1941, 1922, 5038, 2427, 1966, 20294, 1036, 16, 2610, 2319, 16, 1930, 29305, 18, 2176, 24032, 43, 13726, 8, 38, 4595, 19, 38, 4666, 8, 3728, 3165, 43, 5305, 7627, 6181, 1930, 43, 14852, 1007, 5219, 5061, 1958, 19355, 1920, 13148, 6982, 4415, 1958, 8145, 2455, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 2678, 2610, 2051, 16, 2678, 1029, 3418, 1988, 15541, 1036, 3146, 5696, 1958, 12167, 3408, 12588, 6535, 2409, 4543, 9333, 6066, 5984, 2678, 4271, 18, 2176, 9034, 1956, 1920, 20604, 2678, 1014, 15318, 16, 2957, 17, 10338, 2678, 2743, 2213, 12, 22228, 13, 16, 1930, 2678, 6479, 4337, 20403, 14896, 1942, 11865, 5158, 1930, 18240, 6194, 3471, 2651, 1920, 4856, 23854, 3870, 18, 3950, 16, 1920, 2213, 5921, 43, 4543, 2678, 1029, 2610, 2051, 16, 3700, 3027, 1035, 3418, 1988, 23407, 1920, 2797, 4090, 2199, 13763, 3500, 3200, 5061, 1958, 25292, 3146, 5696, 1942, 11051, 2678, 5158, 18, 2176, 18127, 5305, 7627, 1930, 14852, 1007, 8277, 1942, 11865, 14756, 15, 21362, 3414, 1958, 15408, 18, 2052, 3418, 3868, 14162, 1956, 2678, 29919, 1966, 3131, 1927, 2610, 4283, 16137, 18, 2176, 2258, 2252, 4378, 1922, 13243, 2170, 1019, 27453, 10442, 1930, 1977, 2910, 2007, 20709, 11569, 2797, 4090, 2199, 9961, 16, 3213, 16, 1930, 7997, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MSKIDEVVIERIRKETDIIDLIGEHVQLTKRGKNWFGLCPFHDEQSPSFSVSEDKQLYHCFGCGASGNAISFLMELEHRTFVDAVATLAGRLGMELDIEEGQRSARHQEDSQSEKLLKAAHAQATQFYHHLLMNTVEGERALHYLYERGFTEEQLIEHQIGWTLNQSDSLLHVLQDDYPLPLLAEGGLLTYYEDHDQYYDRFRERIMFPLRNERGEVVGFSGRVIEKKEGAPKYLNSPETPIFKKNQLLYNLDRAKSSIRKANEVVLFEGFMDTLAAERASIDETVAVMGTALSEQHIIQMRRLTNRLIICCDGDDAGWEASYRFAKFATEHKMEATIAILPQNMDPDDYIKTYGGKQFRERILEMSHSFMSFMIQYARRGKNLSLDYEVEQYIHEVLVELAERRSIIERDLIIQQLAELTTVHETTLREKLAQLTTHQAPQRQPTETARIVPETKRKKRRSEVLLFSHLLHERSLFNLAIQEGIEIFIDDDFTTLFVRLAAHYETYEGEGDSFAQSFAEQIEERELRELAMFCIAYERADDDTDQEVKDCIQHLKKLKIAEQIDDKIQQSKQLEQQQDYEGALALIQEVIELKKSITP", "metadata": {"id": "A0A8J7GB16", "cluster": 8679886, "interpro_all": ["IPR016136", "IPR037068", "IPR019475", "IPR006295", "IPR036977", "IPR030846", "IPR013264", "IPR050219", "IPR034151", "IPR006171", "IPR002694"], "interpro_used": ["IPR006171", "IPR006295", "IPR034151"], "interpro_unused": ["IPR030846", "IPR050219", "IPR013264", "IPR002694", "IPR016136", "IPR036977", "IPR019475", "IPR037068"]}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein carries a Pentatricopeptide repeat that mediates sequence-specific binding to single-stranded RNA to regulate post-transcriptional processes within mitochondria and plastids. These degenerate 35-amino acid motifs assemble into a right-handed superhelical spiral structure to specifically recognize nucleotide sequences, a mechanism notably expanded in plant genomes. In addition, the protein is included in the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. It is identified in Symbiodinium microadriaticum (Dinoflagellate) (Zooxanthella microadriatica). What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 16252, 43, 9412, 16036, 21305, 6865, 1988, 10412, 3244, 17, 2487, 2743, 1942, 2957, 17, 10338, 3146, 1942, 5741, 2753, 17, 5224, 4028, 2651, 6489, 1930, 19754, 1036, 18, 2144, 23336, 3259, 17, 3835, 2687, 8277, 17421, 2460, 43, 3659, 17, 17105, 3356, 23285, 2046, 17366, 3170, 1942, 4475, 9967, 5489, 3709, 16, 43, 2856, 7388, 8899, 1922, 4496, 7313, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2176, 1977, 2899, 1922, 17246, 25435, 2457, 2703, 2015, 3027, 2479, 1989, 12, 11687, 4199, 5148, 20178, 5148, 2057, 13, 12, 11906, 25821, 20536, 11560, 1019, 2703, 2015, 3027, 2479, 1019, 13, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MTLLGQVAKTVVTYGAIISACERNGRWQLALDFLVSMESERIS", "metadata": {"id": "A0A1Q9BRF2", "cluster": 11639651, "interpro_all": ["IPR002885", "IPR011990"], "interpro_used": ["IPR002885", "IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein is assigned to the Homeodomain-like superfamily, which comprises transcription factors and DNA-binding proteins that utilize a conserved helix-turn-helix (HTH) motif to interact with the DNA major groove. These proteins are ubiquitous across all domains of life and play critical roles in gene regulation through specific hydrogen bonding and hydrophobic contacts. Furthermore, the protein includes a HTH domain AraC-type conserved site that functions as a DNA-binding motif in bacterial transcriptional regulators, most of which act as positive factors. This region comprises two helix-turn-helix subdomains that bind the major groove of DNA, structurally inducing a bend in the double helix. Additionally, the protein incorporates a Transcription regulator HTH, AraC- type, HTH domain that binds DNA via a helix-turn-helix motif to regulate transcription in bacteria. Typically situated towards the C-terminus, this domain is found in a diverse family of proteins, including SoxS and VirF, where it facilitates specific genomic interactions to control gene expression. It is found in Clostridiaceae bacterium and contains UniProt keyword associations Transcription regulation.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 4502, 17166, 17, 3189, 13975, 16, 2154, 12936, 3213, 2790, 1930, 2678, 17, 2743, 2697, 1988, 12561, 43, 5305, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 6310, 1956, 1920, 2678, 3044, 15920, 18, 2144, 2697, 2032, 15498, 3436, 2136, 4682, 1927, 3308, 1930, 3918, 4140, 5456, 1922, 2359, 3640, 2596, 2487, 6201, 11463, 1930, 7919, 9070, 18, 3677, 16, 1920, 2213, 5921, 43, 5334, 1023, 3418, 20289, 1030, 17, 2601, 5305, 3200, 1988, 4088, 1966, 43, 2678, 17, 2743, 5219, 1922, 4543, 5224, 9098, 16, 2501, 1927, 2154, 4033, 1966, 2843, 2790, 18, 2052, 3031, 12936, 2288, 7864, 17, 5165, 17, 7864, 30103, 1988, 4566, 1920, 3044, 15920, 1927, 2678, 16, 12171, 7834, 43, 20672, 1922, 1920, 4825, 7864, 18, 4950, 16, 1920, 2213, 19683, 43, 3213, 7888, 5334, 1023, 16, 20289, 1030, 17, 2601, 16, 5334, 1023, 3418, 1988, 6876, 2678, 3454, 43, 7864, 17, 5165, 17, 7864, 5219, 1942, 5741, 3213, 1922, 4802, 18, 5745, 18287, 5681, 1920, 45, 17, 7822, 16, 2052, 3418, 1977, 2435, 1922, 43, 6445, 3416, 1927, 2697, 16, 2710, 9149, 1036, 1930, 2787, 1038, 16, 2597, 2176, 11374, 2487, 4935, 3719, 1942, 2285, 2359, 2294, 18, 2176, 1977, 2435, 1922, 17938, 14773, 1972, 3336, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 3213, 3640, 18, 3], "output": "MIRDISLRKKASYIIPEIDFFDKRHSVRQLDRIIQDSFKMSFKNKIIEKRMEISRVGYNTESNFYKVFKQKNGHTPAEYRKKYKTSLIIENFFEANYNTNKTIHDLAKMLNVKNLLRNTKLPVKTIAE", "metadata": {"id": "A0A7X7B5V7", "cluster": 12611751, "interpro_all": ["IPR009057", "IPR018060", "IPR018062", "IPR020449"], "interpro_used": ["IPR009057", "IPR018062", "IPR020449"], "interpro_unused": ["IPR018060"]}, "task_type": "infilling"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein is included in the Glycerol-3-phosphate acyltransferase, PlsY family, which catalyzes the transfer of an acyl group to glycerol-3-phosphate to form lysophosphatidic acid using acyl-phosphate as a donor. This enzyme plays a critical role in the initial stage of glycerolipid synthesis in bacteria, often functioning within the PlsX/Y system. It is expressed in Ignavibacteria bacterium and exhibits UniProt keyword tags Cell membrane, Transmembrane, and Lipid metabolism.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 9244, 17, 23, 17, 5413, 11337, 9961, 16, 17859, 1012, 3416, 16, 2154, 17097, 1920, 3856, 1927, 1925, 11337, 2210, 1942, 9244, 17, 23, 17, 5413, 1942, 2386, 29712, 8525, 1935, 2687, 2193, 11337, 17, 5413, 1966, 43, 6282, 18, 2052, 4113, 5705, 43, 4140, 2770, 1922, 1920, 3754, 3587, 1927, 9244, 2049, 1960, 4271, 1922, 4802, 16, 3868, 7295, 2651, 1920, 17859, 1039, 19, 67, 2433, 18, 2176, 1977, 3198, 1922, 12046, 9188, 7972, 2341, 18339, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 2024, 3260, 16, 9117, 16, 1930, 4486, 4714, 18, 3], "output": "MSKYLIIFALSYIVGSIPFAYIIVRLSYEVTGRKWVGFLVFLFDFLKGISVVLISRHLIPDDDFAILAASFSVVLGLLLWVILWLLIYNFVKKDMDIANPATSVISPFLRIVLYITIGLLALLILSKYFIVLKLKLSKKFFRKDISKEGSGNVGAMNHNFSLFLRFKGGKGLATSAGVLLLIQPIIFFVLPEDFVLKANIIPFQS", "metadata": {"id": "A0A7V5LGU5", "cluster": 14568737, "interpro_all": ["IPR003811"], "interpro_used": ["IPR003811"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nIt is part of the Protein of unknown function DUF6062 family, which comprises functionally uncharacterised proteins found in bacteria and archaea. Members of this family contain two repeated domains featuring conserved CXXC and GXCXXH motifs, suggesting a potential metal-binding capability. It has been characterized in Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12).\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 2176, 1977, 3131, 1927, 1920, 2213, 1927, 5435, 2347, 4855, 17136, 14265, 1028, 3416, 16, 2154, 12936, 9346, 23229, 3495, 2697, 2435, 1922, 4802, 1930, 21501, 18, 4678, 1927, 2052, 3416, 5531, 2288, 5116, 4682, 29931, 5305, 5639, 21487, 1930, 26615, 1030, 14710, 1023, 8277, 16, 3783, 43, 2889, 6048, 17, 2743, 10956, 18, 2176, 2258, 2252, 4378, 1922, 29060, 5581, 1947, 1957, 7967, 24888, 5277, 1035, 12, 3943, 11037, 27204, 6106, 19, 10964, 29050, 1008, 19, 50, 17, 26, 17, 2369, 13, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MNRKSLINKDWEEAFYWEGLYENVNDVSLRKEIREKGGFCENHHLQLLTFRDLLGIIPSLKKGEVPKIKSCIFCEQESLNLWKEIAYDFCNPHKEKIKILSPYPEYFYKSFPWDKDYSEIFLKKLRILESKKGKCPLCYLTQKALRNYMENFVSIVYEDIIKNYKEEEYEKLYIQGLSEVLKNETYRKIEPYLSEKRRK", "metadata": {"id": "B5YB33", "cluster": 14603329, "interpro_all": ["IPR045706"], "interpro_used": ["IPR045706"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to generate an amino acid sequence for a protein. The protein should have the function The protein features a Strawberry notch, helicase C domain that promotes the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes. This domain is typically found in proteins containing DExD/H-box motifs. Furthermore, it is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It originates from Chlorogloea sp. CCALA 695.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 4075, 43, 19379, 18642, 8091, 16, 15318, 45, 3418, 1988, 7383, 1920, 2294, 1927, 6445, 4845, 16, 5063, 2596, 3719, 1956, 5224, 9518, 2014, 14434, 5048, 18, 2052, 3418, 1977, 5745, 2435, 1922, 2697, 3165, 7473, 1007, 19, 50, 17, 5758, 8277, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 22970, 2037, 10107, 4365, 6802, 1019, 2056, 18, 13980, 5148, 5349, 1015, 18, 3], "output": "MWAESGGCIRCEKSYEGVEFGVAKYPVDLQTAETNSKILNLIWQFDYIKEKVVKEISGDYADAGEAARKNNPALGGAGASSTIFTSVLHNLTAVTALGLKAEETANAAIADIEQGRKPILMLFNTMESTVRDFVDSHNQLPAIHNAEFPDSPMQPIRVGDDITINAGQLFTRYLEKARSIKITELYLDELTGKQVTRTHRLTDTEIGIEGVAAFNKAESAIATADWSKLPISPIDYIKQKIEDAGHSIGEITGRTHVLKYGSAEDLASGVVTYQTRERGTAQKKQVMDDFQNGRVDAVITNSTTGYSLHASRTVADQRQRVMYIVQPHLDVNQVEQSIGRSHRSGQVNPALHPPDKLDEGGQPMWGQYSGTFGLPAFKLVVGQDLPTEERAVAILMKKMSHLKANTTGNSSSSFGLADMPDFINDYGNEVAQNLMEQNPDLHEDLDFSLSGVDGFKNPQAIVGSAGVAV", "metadata": {"id": "A0A2T1E4Q6", "cluster": 14679393, "interpro_all": ["IPR027417", "IPR026937"], "interpro_used": ["IPR026937", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to create: The protein has a Prepilin peptidase A24, N-terminal domain that likely provides the N-methylation activity within bifunctional prepilin peptidases. This intracellular module is flanked by transmembrane segments and coordinates a zinc ion via four conserved cysteine residues that are essential for enzymatic function. Also, the protein should include a Prepilin type IV endopeptidase, peptidase domain that functions as a membrane-bound aspartic endopeptidase responsible for cleaving charged leader peptides from type IV pilin precursors and general secretion pathway components. This activity is essential for type IV pilus biogenesis and extracellular protein secretion in Gram-negative bacteria and archaea, often occurring within bifunctional enzymes that subsequently methylate the mature N-terminal phenylalanine. In addition, the protein is classified under the The Peptidase A24A, prepilin type IV, bacterial family, which functions as a leader peptidase that mediates the post-translational cleavage and N-terminal methylation of type IV prepilin precursors. This processing is essential for the maturation and assembly of pili on the surface of Gram-negative pathogens, such as *Pseudomonas aeruginosa* and *Neisseria gonorrhoeae*, facilitating host cell attachment. It has been detected in Pseudomonas aeruginosa and features UniProt keywords Transmembrane helix, Hydrolase, and Cell inner membrane. Please provide the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 7762, 30, 1920, 2213, 2258, 43, 10719, 16207, 24050, 8595, 1006, 16, 56, 17, 4262, 3418, 1988, 3205, 4558, 1920, 56, 17, 5547, 2455, 2651, 29491, 10719, 16207, 24050, 1036, 18, 2052, 4776, 9059, 1977, 20185, 2007, 9117, 7492, 1930, 10675, 43, 7997, 4755, 3454, 3006, 5305, 8666, 4248, 1988, 2032, 4415, 1958, 8145, 2347, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 10719, 16207, 2601, 4370, 16239, 9626, 2410, 9200, 16, 24050, 3418, 1988, 4088, 1966, 43, 3260, 17, 4124, 23047, 16239, 9626, 2410, 9200, 5061, 1958, 28634, 9516, 17442, 5320, 2037, 2601, 4370, 7547, 1921, 10416, 1930, 3335, 5512, 3374, 4178, 18, 2052, 2455, 1977, 4415, 1958, 2601, 4370, 7547, 1957, 13008, 1930, 5329, 2213, 5512, 1922, 8604, 17, 3136, 4802, 1930, 21501, 16, 3868, 6966, 2651, 29491, 5038, 1988, 5326, 4963, 2010, 1920, 6665, 56, 17, 4262, 17388, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 1920, 24050, 8595, 9458, 16, 10719, 16207, 2601, 4370, 16, 4543, 3416, 16, 2154, 4088, 1966, 43, 17442, 24050, 1988, 10412, 1920, 2753, 17, 8414, 6404, 1930, 56, 17, 4262, 5547, 1927, 2601, 4370, 10719, 16207, 10416, 18, 2052, 4587, 1977, 4415, 1958, 1920, 7655, 1930, 5957, 1927, 7547, 1033, 1990, 1920, 3154, 1927, 8604, 17, 3136, 7741, 16, 2427, 1966, 14, 13461, 10830, 14, 1930, 14, 28356, 18339, 27702, 6802, 3336, 14, 16, 12440, 4423, 2024, 8576, 18, 2176, 2258, 2252, 3330, 1922, 13461, 10830, 1930, 4075, 20709, 11569, 9117, 7864, 16, 20748, 16, 1930, 2024, 6671, 3260, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MTLLDYLASHPLAFVLCAILLGLLVGSFLNVVVHRLPKMMERNWKAEAREALGLEPEPKQATYNLVLPNSACPRCGHEIRPWENIPLVSYLALGGKCSSCKAAIGKRYPLVELATALLSGYVAWHFGFTWQAGAMLLLTWGLLAMSLIDADHQLLPDVLVLPLLWLGLVANHFGLFASLDDALFGAVFGYLSLWSVFWLFKLVTGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVGAILGVIMLRLRNAESGTPIPFGPYLAIAGWIALLWGDQITRTYLQFAGFK", "metadata": {"id": "A0A6A9K2W7", "cluster": 17823538, "interpro_all": ["IPR014032", "IPR000045", "IPR010627", "IPR050882"], "interpro_used": ["IPR010627", "IPR000045", "IPR014032"], "interpro_unused": ["IPR050882"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein is classified under the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein contains a HPr(Ser) kinase/phosphorylase, N-terminal domain that constitutes the structural blades of the hexameric HPr serine/threonine kinase PtsK, a sensor protein controlling bacterial carbon catabolite repression. This domain facilitates the assembly of the enzyme's three-bladed propeller structure, allowing it to function within a multicomponent phosphorelay system. Also, the protein should include a HPr kinase/phosphorylase, C-terminal domain that functions as the catalytic core of the bifunctional enzyme HprK/P, regulating carbon source utilization in Gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 on the phosphocarrier protein HPr and its dephosphorylation via phosphorolysis, typically within a hexameric assembly. It is produced by Gammaproteobacteria bacterium and is classified with UniProt keywords Serine/threonine-protein kinase, Metal-binding, and ATP-binding.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 5461, 43, 18542, 12, 2375, 13, 4016, 19, 12556, 2051, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 4346, 22707, 1036, 1927, 1920, 25602, 1935, 18542, 8468, 19, 13143, 4016, 8618, 1040, 16, 43, 6443, 2213, 7138, 4543, 5056, 3115, 3016, 2394, 10084, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 4113, 11, 61, 2559, 17, 22707, 1007, 5062, 13728, 3170, 16, 7201, 2176, 1942, 2347, 2651, 43, 8844, 28155, 1939, 3421, 15208, 1012, 2433, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 18542, 4016, 19, 12556, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 1920, 29491, 4113, 18542, 1040, 19, 58, 16, 6773, 5056, 4585, 8422, 1922, 8604, 17, 2843, 4802, 18, 2176, 17097, 2321, 1920, 4498, 17, 3100, 4050, 1927, 2375, 17, 4182, 1990, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 2496, 16881, 3454, 3421, 6892, 16, 5745, 2651, 43, 25602, 1935, 5957, 18, 2176, 1977, 4152, 2007, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 8468, 19, 13143, 17, 2213, 4016, 16, 6048, 17, 2743, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MTSTPQLSAETIFNAYEELLGLTWLGGKNGRHRPPNRVQVLGKNELAYIEDMGPEDRQDILRKTPPSGFIDNANAQNMPLLVSTEPSPRLIDALQYYLIGVLLTGDAGVGKSEIALELLSRNHRLIADDAVDFMEVRGLGILDVRAMFGETATKRADRLQAETQTRTILGIRVPEVIIPIAPGRNALHDFMEQQQSVMRRNEIPINDVTTDQQKELEQVNAKYPGLALVGHLSLIHIFTSQYCSAIIIADSLTTAMAQRLTEHGVFMEVMGELSRVSPQLLEGRCPEALRKYLRLIVRLEQMGKQAMAQLNLAVLVEAAVRNHIQHMRGK", "metadata": {"id": "A0A972RHC3", "cluster": 18050525, "interpro_all": ["IPR003755", "IPR011104", "IPR011126", "IPR027417", "IPR028979"], "interpro_used": ["IPR027417", "IPR011126", "IPR011104"], "interpro_unused": ["IPR003755", "IPR028979"]}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein is a member of the Protein of unknown function DUF4199 family, which comprises sequences that are currently functionally uncharacterized. It is found in Aquimarina sp. AD1.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 23087, 3416, 16, 2154, 12936, 3709, 1988, 2032, 5077, 9346, 24528, 18, 2176, 1977, 2435, 1922, 10059, 12874, 5572, 1019, 2056, 18, 2041, 1009, 18, 3], "output": "MEKSVKSNAISLGVILGVVLSLVTVLAYTVYQGMYTNWMAGIGLSLMIIVFGIVSAVKSRKLLGGFIDFKKAFTSYLITVAIGTLISTVVTILIYVAVDPDAATAINEQIIESTVGFMEKFGTPESEIEKAVAKMQEENQFSLVNQIKGWFWGMLIYIIIGLLASLAIKKKEPLY", "metadata": {"id": "A0A3A9VPD9", "cluster": 21197631, "interpro_all": ["IPR025250"], "interpro_used": ["IPR025250"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein is associated with the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. Also, the protein is assigned to the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It has been characterized in Ferrovum sp and corresponds to UniProt keyword Lipid metabolism, Metal-binding, and ATP-binding.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 1977, 2458, 1956, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 2258, 2252, 4378, 1922, 20976, 1020, 1989, 2056, 1930, 8852, 1942, 20709, 11121, 2538, 4486, 4714, 16, 6048, 17, 2743, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MEGKVLSQANADPEVKAFFYSAAGFRSAYTGEISLSQHLALVGSLIFVLLVELLNSAIEMGSAAVLLSLVLALMVWVGVLWAPGPKKPAAPRIAAFREEVWVSLILGVISWFLQASVDHTSLEFHPMAKCAKD", "metadata": {"id": "A0A6N9SN34", "cluster": 22844317, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR033718", "IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein has a DUF6973 domain that is found in uncharacterized bacterial proteins, including the putative protein RhsE. This module is predicted to adopt a globular structure consisting of five $\\alpha$-helices and is likely distantly related to Wnt domains. It is native to Bacteroidota bacterium.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 2258, 43, 4855, 17136, 8528, 1010, 3418, 1988, 1977, 2435, 1922, 24528, 4543, 2697, 16, 2710, 1920, 6770, 2213, 3617, 4127, 18, 2052, 9059, 1977, 4396, 1942, 14103, 43, 20975, 3170, 7600, 1927, 3628, 8, 38, 4595, 8, 17, 12789, 1930, 1977, 3205, 29448, 2712, 1942, 7028, 4682, 18, 2176, 1977, 6196, 1942, 24323, 7336, 14061, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MNPTLKEGAEFEEKAMAYIENRLLKESISAYKLRLTLSGLSKTESDDAPEPDFPGFVTTILALEAVVKQKTNLGKTFSAEAYQGQIRELKKTLATTWLNDETADISYPDPDRERLFAVFAALRLASHFLVVTRGGDEGDAFRHVYVNVLMRRWLGKNLARDIGTLYEIIRPLDVLDWPEMSRRTAAFIENSSNEMEPEKKGYTGMLKAFDNQQEQELAFLKPAEAERNELETWEVFTTPLEEVMEIDGTLLARKYAIDEQKRLYPNSGNEPRHRAMDLHNNYVGYDSQYDALRGHWL", "metadata": {"id": "A0A3D4IIS6", "cluster": 26828307, "interpro_all": ["IPR054246"], "interpro_used": ["IPR054246"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is a member of the Protein kinase-like domain superfamily, which modifies other proteins by chemically adding phosphate groups. This enzymatic activity is fundamental to most signaling and regulatory processes in the eukaryotic cell. It is present in Metarhizium guizhouense (strain ARSEF 977). The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2213, 4016, 17, 3189, 3418, 13975, 16, 2154, 25436, 2303, 2697, 2007, 13944, 8013, 5413, 2671, 18, 2052, 8145, 2455, 1977, 8829, 1942, 2501, 3197, 1930, 4948, 4028, 1922, 1920, 10825, 2024, 18, 2176, 1977, 2481, 1922, 5880, 5004, 2061, 2457, 3194, 2061, 15492, 4480, 12, 3943, 9896, 7726, 5749, 1027, 13, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MLGFADFGPTRNDPRYEFSIFEDHTAQHAKRNPPFHVLQDVTEPEIAREYLPQDARVVMTTNGRRPRFIHGHWKDIEQVPAAVVVKQTPQTASFKFSLNSTIICECYFAPFEDDITIANSGPGSLEYGRLFGGRLSQDGVKKTYDLTFETPTPTVNKSENSTTTAPSGLKRKFDEFLGKTMTTAPNKCRRNTSDAFVSASSSQEHDSQQRPAKAPKAPSRGQPEEDCGSTAVVGNAQITLAYNRSEPPRPFRLTIRPRHSMPGQVTASTESYSVSNVTSIPSLGRSMFTSTKRRTGGIVALRVPRDVMSKDAIPKLAAEWKALRDVLSRLRSPWIIDFLGADARFLAIFTKFAYSRLPEEMDSSYHFKGRPEDGVAMCLGITSALVYLHDTMRIRHGHISANVFQGRCESKSWI", "metadata": {"id": "A0A0B4GEZ4", "cluster": 27907017, "interpro_all": ["IPR011009"], "interpro_used": ["IPR011009"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein has a M23ase beta-sheet core domain that constitutes the catalytic center of zinc-dependent metallopeptidases involved in bacterial peptidoglycan hydrolysis and remodeling. This structural motif coordinates a zinc ion to facilitate specific activities, such as glycyl-glycine endopeptidase cleavage, which are essential for cell wall metabolism, growth, and virulence. Additionally, this conserved beta-sheet architecture is found in select sugar permeases and eukaryotic chemotaxins involved in neurite formation. Furthermore, the protein can be placed in the Duplicated hybrid motif superfamily, which forms a structural domain consisting of a half-barrel $\\beta$-sheet arrangement found in bacterial glucose-permease-like enzymes. This motif is integral to domain IIa of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) for sugar uptake and phosphorylation, and is also present in peptidoglycan hydrolases like *Staphylococcus aureus* LytM. Furthermore, the protein is grouped in the Bacterial cell wall metabolism enzyme family, which encompasses murein hydrolase activators, endopeptidases, and transglycosylases critical for cell wall dynamics. These proteins facilitate cell division and expansion by activating hydrolases for septal cleavage or remodeling peptidoglycan structures such as polyglycine interpeptide bridges. Additionally, some members contribute to virulence by degrading host proteins like elastin or assisting in spore cortex maturation. It is native to Ruminiclostridium papyrosolvens DSM 2782 and features UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 6056, 6675, 4127, 4666, 17, 11130, 4728, 3418, 1988, 14879, 1920, 6804, 4102, 1927, 7997, 17, 3100, 8969, 24897, 1036, 3286, 1922, 4543, 24183, 9128, 1930, 8378, 18, 2052, 4346, 5219, 10675, 43, 7997, 4755, 1942, 6628, 2487, 4209, 16, 2427, 1966, 4235, 2199, 17, 10646, 16239, 9626, 2410, 9200, 6404, 16, 2154, 2032, 4415, 1958, 2024, 4821, 4714, 16, 2905, 16, 1930, 9304, 18, 4950, 16, 2052, 5305, 4666, 17, 11130, 9335, 1977, 2435, 1922, 8702, 9523, 6191, 2319, 1930, 10825, 12776, 17234, 1036, 3286, 1922, 15912, 3337, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 19479, 5249, 5219, 13975, 16, 2154, 4952, 43, 4346, 3418, 7600, 1927, 43, 4768, 17, 19560, 8, 38, 4666, 8, 17, 11130, 13002, 2435, 1922, 4543, 3817, 17, 6191, 2051, 17, 3189, 5038, 18, 2052, 5219, 1977, 12328, 1942, 3418, 17433, 1927, 1920, 8078, 9356, 18425, 12631, 2010, 30, 9523, 8078, 9961, 2433, 12, 8618, 13, 1958, 9523, 5047, 1930, 4050, 16, 1930, 1977, 2222, 2481, 1922, 24183, 30337, 3189, 14, 13452, 8849, 14, 7518, 15375, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 4543, 2024, 4821, 4714, 4113, 3416, 16, 2154, 21569, 6185, 14818, 20748, 15497, 16, 16239, 9626, 2410, 30413, 16, 1930, 2127, 17038, 4879, 18801, 24605, 1918, 4140, 1958, 2024, 4821, 5565, 18, 2144, 2697, 6628, 2024, 8451, 1930, 7013, 2007, 8019, 30337, 1958, 16458, 6404, 2014, 8378, 24183, 4061, 2427, 1966, 16115, 19602, 2053, 2107, 9626, 2410, 2261, 18142, 18, 4950, 16, 2673, 4678, 4672, 1942, 9304, 2007, 18192, 4423, 2697, 3189, 22684, 2014, 27840, 1922, 18445, 4997, 7655, 18, 2176, 1977, 6196, 1942, 22631, 24410, 17414, 9734, 3860, 5134, 2204, 14937, 2099, 10964, 21928, 1028, 1930, 4075, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTKKGIKKKIIITGSVLLMPLGTGSNPIVMAKGLDIPAGFLSIANKAATENGDNFTNEIIPEVLGKAKTCNPDSLPDSLGPIPKSKIITTTVQKKQNNDDSKQPATTSTEIQYTYSHSDDFGAQRTFGGDRAHENDFGGNIVGVLTDKDTYFYYAHDVLGYVGNTGYGPPGTSGMFITHLHLQIGIKLLDQFRITLHEEANVGGGDFLIFFLMIMFTQRSIEFAFFLTLSAGAANFNPKEIYSIYSKYYNDLKVDGTEAGSENDQPQYEGNDIIADGGVPIVSITDGVIRDMNWMRGFNTAFHEGDRVKAGEGQKKRFYISPYNIVAY", "metadata": {"id": "F1TH01", "cluster": 28071574, "interpro_all": ["IPR050570", "IPR011055", "IPR016047"], "interpro_used": ["IPR016047", "IPR011055", "IPR050570"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein should include a MrpA C-terminal/MbhD domain that constitutes part of the proton translocation module within the membrane-bound hydrogenase (MBH) complex. This integral membrane component contains three transmembrane helices and corresponds to the C-terminal region of the MrpA antiporter subunit and Nqo10 of Complex I. It is native to Thermococcus sp. LS2 and is described by UniProt keywords Cell membrane and Transmembrane helix.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 3066, 3951, 43, 27997, 1019, 45, 17, 4262, 19, 5667, 6518, 3418, 1988, 14879, 3131, 1927, 1920, 8433, 7849, 9059, 2651, 1920, 3260, 17, 4124, 6201, 2051, 12, 5667, 1023, 13, 2796, 18, 2052, 12328, 3260, 4594, 5461, 2559, 9117, 12789, 1930, 8852, 1942, 1920, 45, 17, 4262, 3031, 1927, 1920, 27997, 1019, 2246, 24095, 5903, 1930, 27798, 1008, 1927, 2796, 51, 18, 2176, 1977, 6196, 1942, 7967, 4879, 2437, 1957, 2056, 18, 6639, 1028, 1930, 1977, 2910, 2007, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 3], "output": "MIEIHLGFSAVQAIAYAIAFSALLIFAISKTERYEVVLILSLALMLGFVASYLAVTEKDLLKAVYILMAPDIVLAYIAIAVGIY", "metadata": {"id": "A0A8J8DLB0", "cluster": 1198961, "interpro_all": ["IPR025383"], "interpro_used": ["IPR025383"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein has a tRNA-binding domain that binds tRNA to facilitate aminoacylation, often directing the substrate to the active site of enzymes like methionyl-, phenylalanyl-, and tyrosyl-tRNA synthetases. It is also present in export-related chaperones and proteins such as yeast ARC1, where it mediates complex formation and may exhibit catalytic activity. Additionally, the protein should feature a tRNA synthetase B5-domain domain that is located in the beta subunit of phenylalanine-tRNA synthetase and binds DNA through a winged helix-turn-helix motif. This domain enables the enzyme to influence cellular processes via DNA binding, distinct from its canonical aminoacylation function. Moreover, the protein contains a Ferrodoxin-fold anticodon-binding domain that specifically recognizes the anticodon of cognate tRNAs within bacterial and mitochondrial Phenylalanine-tRNA synthetases. This domain adopts a canonical double split $\\alpha+\\beta$ motif with an RNA recognition fold topology to facilitate genetic code translation. It is expressed in Enterobacteriaceae endosymbiont of Plateumaris consimilis and is annotated with UniProt keywords Nucleotide-binding, Cytoplasm, and Ligase.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 10089, 17, 2743, 3418, 1988, 6876, 10089, 1942, 6628, 3835, 14645, 1943, 16, 3868, 23258, 1920, 4510, 1942, 1920, 3500, 3200, 1927, 5038, 3189, 2295, 2001, 2199, 17, 16, 7971, 8056, 16323, 1024, 17, 16, 1930, 6578, 2199, 17, 10089, 18185, 1036, 18, 2176, 1977, 2222, 2481, 1922, 12660, 17, 2712, 18098, 1930, 2697, 2427, 1966, 5688, 9952, 1009, 16, 2597, 2176, 10412, 2796, 3337, 1930, 2278, 5987, 6804, 2455, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 10089, 18185, 24365, 17, 3418, 3418, 1988, 1977, 4810, 1922, 1920, 4666, 5903, 1927, 17388, 17, 10089, 18185, 1930, 6876, 2678, 2596, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 18, 2052, 3418, 10217, 1920, 4113, 1942, 4039, 3689, 4028, 3454, 2678, 2743, 16, 4493, 2037, 2496, 9452, 3835, 14645, 1943, 2347, 18, 3950, 16, 1920, 2213, 5461, 43, 20976, 22389, 10960, 17, 3728, 11693, 28615, 17, 2743, 3418, 1988, 4475, 16197, 1920, 11693, 28615, 1927, 15786, 20770, 2651, 4543, 1930, 4596, 17388, 17, 10089, 18185, 1036, 18, 2052, 3418, 24032, 43, 9452, 4825, 10030, 8, 38, 4595, 15, 38, 4666, 8, 5219, 1956, 1925, 3146, 5708, 3728, 13678, 1942, 6628, 3299, 7815, 6410, 18, 2176, 1977, 3198, 1922, 25192, 22868, 19077, 2001, 1031, 1927, 5500, 18202, 1937, 2134, 17315, 1937, 1930, 1977, 10633, 1956, 20709, 11569, 5489, 17, 2743, 16, 5239, 16, 1930, 11905, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MIYVYSLKMIYVFLNNLNKNMIKLSELWLREWITYNNIELLDNIFIGQVIDCQFNNNKNIYNLTIDIGKNKLYKIKSNAINCSLYKKYIYNQKFNFLLQSEGLLCSKKMLGLKDNIRSNYLQLNDNILYINIPYNRSDCLSIMGIARDLSTKIKNDNYLFKFPYEDYLTKNKQNNIINCVIQNVDLQNKIPFLIEQRLQRSGILISNNNPLLNISNYINLELGYPVYFYDLNKIKITLLKNTLIIKDKEKILSIPILAQNKEVIIDKNTKNILLECFFLDTMTDPLIQKKILIRTINLILKIYGGKRSKIKVVNTDNYINNFLTLKTIKLNFKKIKQILGFVIKLKTDMNCIIQIPSWRYDIKIEADIIEEIIRIYGYNNIPNKHIKLNLIEKNINDNNRFFKSNEVINYSFINPKIQYLIFPKEKFIKLCNPISIEMSVMRTSLLCGLINNIIYNQNRQQKSLMFGGIINGKLHEEHWSLSNKNVDFYDLKGDIECIFDLLGKISKIEFRSISDINFLHPINENTVLFELECNEILNHTETIIKTISNLPLNRRDISLIVKENIPFINIIQECKSFTISFIIQDNTHTLKDKEINDIIQLCINKLKIKFKIILRDKNYDFNSEQLTMLGFEVEKIEPICKIKIKNKIKIIFATVNSDKNHILILNNNAKIGQNAYKVHINENVNKYNLSYFYKGDIYIKEYKNINDNVLIDTNNNADNLSNQYKIFNLFSHLYQRGLTDKIFNIMNKLGFKIINITKIKNFLINKGYNLRFFEIGLCFKINKKLEFGISQKYKGSSIYLNNSFIGYIGVIHPYIQTYLGNFSIKQIIDINLFDVYQGINIPKGYK", "metadata": {"id": "A0A6H2F337", "cluster": 2299759, "interpro_all": ["IPR045864", "IPR005146", "IPR009061", "IPR005121", "IPR036690", "IPR012340", "IPR045060", "IPR004532", "IPR020825", "IPR041616", "IPR002547", "IPR005147"], "interpro_used": ["IPR002547", "IPR005147", "IPR005121"], "interpro_unused": ["IPR009061", "IPR020825", "IPR041616", "IPR005146", "IPR004532", "IPR012340", "IPR045060", "IPR045864", "IPR036690"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein is classified under the Vacuolar protein sorting-associated protein Vta1-like family, which facilitates multivesicular body (MVB) biogenesis and sorting by interacting with and regulating AAA ATPases such as Vps4 and SKD1. These proteins are essential for intracellular trafficking, with specific homologues functioning in plant basal resistance and mammalian HIV viral release. Furthermore, the protein contains a Vta1, C-terminal domain that acts as a dimerization module and promotes the ATP-dependent double ring assembly of Vps4. This domain stimulates Vps4 ATPase activity, playing a critical role in the multivesicular body (MVB) pathway. Furthermore, the protein carries a Vta1/callose synthase, N-terminal domain that functions in multivesicular body (MVB) formation as a component of class E vacuolar protein sorting proteins like Vta1. In plants, this domain is also present in callose synthases, where it contributes to callose synthesis at the forming cell plate during cytokinesis. It is derived from Pichia californica and is linked to UniProt keywords Membrane, Endosome, and Cytoplasm.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 21582, 2213, 11404, 17, 2458, 2213, 17838, 1009, 17, 3189, 3416, 16, 2154, 11374, 5738, 18522, 18021, 5148, 1005, 3362, 12, 5963, 1014, 13, 13008, 1930, 11404, 2007, 8615, 1956, 1930, 6773, 13835, 28132, 2427, 1966, 14851, 1006, 1930, 3097, 7240, 18, 2144, 2697, 2032, 4415, 1958, 4776, 9604, 16, 1956, 2487, 18541, 7295, 1922, 4496, 5342, 3554, 1930, 6492, 3525, 4324, 4012, 18, 3677, 16, 1920, 2213, 5461, 43, 17838, 1009, 16, 45, 17, 4262, 3418, 1988, 8016, 1966, 43, 13640, 9059, 1930, 7383, 1920, 4498, 17, 3100, 4825, 6335, 5957, 1927, 14851, 1006, 18, 2052, 3418, 11803, 14851, 1006, 9444, 2455, 16, 14797, 43, 4140, 2770, 1922, 1920, 5738, 18522, 18021, 5148, 1005, 3362, 12, 5963, 1014, 13, 3374, 18, 3677, 16, 1920, 2213, 16252, 43, 17838, 1009, 19, 4567, 2217, 8921, 16, 56, 17, 4262, 3418, 1988, 4088, 1922, 5738, 18522, 18021, 5148, 1005, 3362, 12, 5963, 1014, 13, 3337, 1966, 43, 4594, 1927, 2921, 47, 21582, 2213, 11404, 2697, 3189, 17838, 1009, 18, 1922, 4793, 16, 2052, 3418, 1977, 2222, 2481, 1922, 4567, 2217, 8921, 1036, 16, 2597, 2176, 7624, 1942, 4567, 2217, 4271, 2019, 1920, 7402, 2024, 5500, 2409, 20825, 18, 2176, 1977, 3595, 2037, 7271, 7969, 1019, 9939, 6102, 1930, 1977, 4624, 1942, 20709, 11569, 3260, 16, 22321, 16, 1930, 5239, 18, 3], "output": "MSESETPPFEDPLGTIPQAATKLISPFIKRGKELLESKLHLQDAEVAEYIEILLNYIESIMKEINTNNLTEIINDKVKIKTVVNFKAFLDFIQVLNLWPDLYTQNLHDFHNQIKYYITPQDESELSQFISEPSKDDTSQLSTLSPTLSSQYISDNKEAEESVNGNEDSWASNCSEKENNEQKAPVVPAKPPTIPSKPVIKYTAVNQTQDKQHILESKILAISALNYEDIETAITELQGALKLLRGEHTAQPLISYYCYLYSAQLISFKLILSFSLSIFNKSFNEINMHTSSAKFHSSRILKDIKANRDPNDIDDDDDDDDDHIYNNNSKKDVEEIWTKSDIMSNAQRKAKF", "metadata": {"id": "A0A9P6WKG4", "cluster": 2628211, "interpro_all": ["IPR044538", "IPR039431", "IPR023175", "IPR041212"], "interpro_used": ["IPR044538", "IPR041212", "IPR039431"], "interpro_unused": ["IPR023175"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein is associated with the RNA methyltransferase RlmH family, which is predicted to function as an S-adenosyl-L-methionine (AdoMet)-dependent methyltransferase based on structural homology. These enzymes likely catalyze the transfer of methyl groups to RNA substrates for regulatory modification. In addition, the protein is included in the tRNA (guanine-N1-)-methyltransferase, N-terminal superfamily, which represents the N-terminal domain of SPOUT superfamily enzymes, including the tRNA:Gm18 methyltransferase TrmH. This domain is characterized by a rare \u03b1/\u03b2 knot structure that poses a significant folding challenge. Moreover, the protein is included in the Alpha/beta knot methyltransferases superfamily, which encompasses enzymes containing a deep, rare \u03b1/\u03b2 knot structural domain essential for RNA methylation. This fold is characteristic of S-adenosyl-L-methionine (SAM)-dependent enzymes, including the SPOUT and EMG1/NEP1 families, facilitating the modification of RNA substrates. It is native to Sporomusa sp. KB1 and is annotated with UniProt keywords Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 3146, 16478, 11929, 22316, 3416, 16, 2154, 1977, 4396, 1942, 2347, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 12, 2041, 14080, 13, 17, 3100, 16478, 2454, 1990, 4346, 9039, 18, 2144, 5038, 3205, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 3146, 6249, 1958, 4948, 6295, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 10089, 12, 16904, 17, 13007, 17, 13, 17, 16478, 16, 56, 17, 4262, 13975, 16, 2154, 4972, 1920, 56, 17, 4262, 3418, 1927, 18055, 1984, 13975, 5038, 16, 2710, 1920, 10089, 30, 28673, 1025, 16478, 28402, 1023, 18, 2052, 3418, 1977, 4378, 2007, 43, 5844, 160, 19, 161, 26646, 3170, 1988, 17274, 43, 2228, 10328, 6013, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4595, 19, 4666, 26646, 28253, 13975, 16, 2154, 21569, 5038, 3165, 43, 6515, 16, 5844, 160, 19, 161, 26646, 4346, 3418, 4415, 1958, 3146, 5547, 18, 2052, 3728, 1977, 6293, 1927, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5038, 16, 2710, 1920, 18055, 1984, 1930, 13952, 1009, 19, 26046, 1009, 5767, 16, 12440, 1920, 6295, 1927, 3146, 6249, 18, 2176, 1977, 6196, 1942, 9130, 1947, 28553, 2056, 18, 6633, 1009, 1930, 1977, 10633, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 3], "output": "MKITIAAIGCKLDIVEFAEERMPDNPAVRPGSYLIVLDVAGQAMGGQSDITFIIGGAFGLSAEVAAAALLVEQIYRAFKISRGEPYHWKIKEKYLTAGIQEFLKRLPPYSSAEKIQALTREGERLLKSSEQLSARFDSLALKERLSFSKMTFTHQMIRL", "metadata": {"id": "A0A562GIG5", "cluster": 3884522, "interpro_all": ["IPR029028", "IPR003742", "IPR029026"], "interpro_used": ["IPR003742", "IPR029026", "IPR029028"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein features a Cadherin-like domain that mediates calcium-dependent cell-cell adhesion through homophilic interactions, serving as a primary structural component of adherens junctions. These extracellular repeats form rigid rod-like structures upon binding calcium ions, facilitating tissue morphogenesis and precise cell sorting. It is produced by Scylla paramamosain (Mud crab).", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 8875, 17, 3189, 3418, 1988, 10412, 5016, 17, 3100, 2024, 17, 2024, 6141, 2596, 16350, 24888, 3742, 3719, 16, 13915, 1966, 43, 3065, 4346, 4594, 1927, 30050, 11245, 18, 2144, 5329, 9569, 2386, 12383, 6275, 17, 3189, 4061, 4073, 2743, 5016, 6982, 16, 12440, 2960, 15328, 1930, 8162, 2024, 11404, 18, 2176, 1977, 4152, 2007, 2160, 10196, 1019, 3167, 1976, 5360, 1921, 12, 23910, 25493, 13, 18, 3], "output": "MQWWRAAGWGWQLFGVRTEEAEGHVFPLAPLDYEDPRHAAGFSFLVQVTDRGVEGFANHLHIDSARVKLALLNINDNPPVFARPHAQLTLREDAHLGTLLATLPAHDPDEMKNVTKDYKTLYKNPLSGRGGGGGGGGEGGGRGEGEGGGGEEVVEVVVVAVAVVVMEQERMAIMEWNARVEQGKWN", "metadata": {"id": "A0AAW0V0J8", "cluster": 4376860, "interpro_all": ["IPR002126", "IPR015919"], "interpro_used": ["IPR002126"], "interpro_unused": ["IPR015919"]}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein should feature a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. Also, the protein should include a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. Furthermore, the protein is included in the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. It occurs in Lactobacillus sp. CBA3605 and exhibits UniProt keyword tags Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 3066, 5961, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 2176, 5110, 1922, 18134, 2056, 18, 26853, 5677, 15264, 1930, 9826, 20709, 11121, 2538, 14392, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MTEEKIALFTIFGGTGDLAQRKLYIGTARRPWTDEHYHQIITDSLASLHADPATVDAQHYVTLKQLSEKLDQQYGLQGNRIFYLAMTPNGFNRVIIEKPFGHDYDSEMIQNISAIRFGNNIWESLWNNRYISNSGALRDMVQNHILQILSLLTMDQPAEIATNFVRGQYAPTDEAKGYRQEDKISPESNFRWSGVPFYVRTGKRLADKFTRIDVVFKRPVVVEPTEGFELRMNAKCVGQGFATTNSPEAYERLLHDALNGDATNFTHWQENYQPGTMGPTASDDLLKRDGNDWIYKGPSLFKLYQKGYLQAHFAVSKFASHFYYQSHDVTAPNFFGTIAQHLKSENILAKELNDQLTATFNENQIYRIDHYLGKVQITLSEKLGVEERAVYYDNVEFTENDIDVEKVKALRSLRPYKPTDTFVAGKVMIDNNIFNHDDNPDQTPDNGLEPNVLTINPVKLDFDHDSEATAVAYSWKFVDVIQKYWDEHTPDFP", "metadata": {"id": "A0A2R3JMW9", "cluster": 4639554, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR022674", "IPR019796", "IPR036291"], "interpro_unused": ["IPR001282", "IPR022675"]}, "task_type": "infilling"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein is assigned to the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. Additionally, the protein is classified under the Gfo/Idh/MocA oxidoreductase family, which comprises enzymes that catalyze diverse NAD(P)H-dependent redox reactions essential for cellular metabolism. Members of this family exhibit varied substrate specificities, participating in processes ranging from plant cell wall degradation and biliverdin reduction to the oxidation of UDP-GlcNAc. Furthermore, the protein should feature a Gfo/Idh/MocA-like oxidoreductase N-terminal domain that functions as the NAD(P)-binding Rossmann fold component of enzymes involved in diverse redox reactions, including carbohydrate and biliverdin metabolism. While primarily associated with oxidoreductase activity, this structural family also encompasses non-enzymatic regulatory proteins such as the galactose metabolic regulator Gal80. It is found in uncultured bacterium. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 6304, 1942, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 9281, 1037, 19, 26944, 19, 2661, 3375, 27388, 3416, 16, 2154, 12936, 5038, 1988, 18170, 6445, 6577, 12, 58, 13, 50, 17, 3100, 9366, 5298, 4415, 1958, 3689, 4714, 18, 4678, 1927, 2052, 3416, 5987, 6760, 4510, 18764, 16, 9505, 1922, 4028, 6485, 2037, 4496, 2024, 4821, 4877, 1930, 5088, 3482, 22816, 3378, 1942, 1920, 6638, 1927, 18500, 17, 15397, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 9281, 1037, 19, 26944, 19, 2661, 3375, 17, 3189, 27388, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6577, 12, 58, 13, 17, 2743, 18215, 8890, 3728, 4594, 1927, 5038, 3286, 1922, 6445, 9366, 5298, 16, 2710, 10590, 1930, 5088, 3482, 22816, 4714, 18, 2679, 5985, 2458, 1956, 27388, 2455, 16, 2052, 4346, 3416, 2222, 21569, 2447, 17, 8145, 4948, 2697, 2427, 1966, 1920, 15996, 4487, 7888, 5179, 4476, 18, 2176, 1977, 2435, 1922, 5269, 21058, 14061, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MDVKSLISKRFDVDHAFEAYEELENNKSVLGILIDYPNQNLSHKMQSSVTIYDKKSAQNKVKIDNVSVGFLGAGNYGANILAPAFQKAGVNLQSVMSSQGVSAKRLAKKCGFKSALTDDQMIYDDDKINTVVIATRHNAHADQVIRALEKNKHVFVEKPLAICLDDLAKIKFAYENKNNLLMIGFNRRFSPLIQTMKKLLSTEKMPKSFMMTVNAGAIPQTHWAQDIAVGGGRIIGEACHFIDLLRYLAGNP", "metadata": {"id": "K2D1V9", "cluster": 5160804, "interpro_all": ["IPR000683", "IPR051450", "IPR036291"], "interpro_used": ["IPR036291", "IPR051450", "IPR000683"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein is grouped in the Bacterial iron-siderophore binding family, which acts as the periplasmic solute-binding component of ABC transporters involved in iron acquisition. Members of this family specifically bind iron-siderophore complexes, such as ferric citrate, enterobactin, and ferrichrome, and deliver them to membrane permeases for translocation into the cytoplasm. This function is essential for bacterial survival and virulence in iron-limited environments. Furthermore, the protein should feature a ABC transporter periplasmic binding domain that functions as a high-affinity receptor for bacterial import systems, specifically targeting substrates such as cobalamin (vitamin B12) and iron-siderophore complexes. It captures ligands within a cleft formed by two \u03b1/\u03b2 subdomains and delivers them to the transmembrane permease for cellular uptake. It is identified in Mobilicoccus pelagius NBRC 104925 and has UniProt annotations Signal.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 1977, 10809, 1922, 1920, 4543, 5680, 17, 22940, 11082, 2743, 3416, 16, 2154, 8016, 1966, 1920, 24334, 19661, 17, 2743, 4594, 1927, 7219, 10538, 3286, 1922, 5680, 6165, 18, 4678, 1927, 2052, 3416, 4475, 4566, 5680, 17, 22940, 11082, 5048, 16, 2427, 1966, 20247, 11599, 16, 5553, 14357, 2268, 16, 1930, 20247, 6570, 2225, 16, 1930, 3971, 3581, 1942, 3260, 6191, 2319, 1958, 7849, 2460, 1920, 5239, 18, 2052, 2347, 1977, 4415, 1958, 4543, 3298, 1930, 9304, 1922, 5680, 17, 3892, 8114, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 7219, 9054, 24334, 2743, 3418, 1988, 4088, 1966, 43, 2149, 17, 5173, 3148, 1958, 4543, 2582, 3771, 16, 4475, 5133, 6249, 2427, 1966, 18477, 3717, 12, 6111, 17492, 13, 1930, 5680, 17, 22940, 11082, 5048, 18, 2176, 20008, 6908, 2651, 43, 14649, 5333, 2007, 2288, 160, 19, 161, 30103, 1930, 30070, 3581, 1942, 1920, 9117, 6191, 2051, 1958, 3689, 5047, 18, 2176, 1977, 2899, 1922, 20407, 5670, 2437, 1957, 7874, 29284, 1957, 8789, 15618, 8824, 11884, 1015, 1930, 2258, 20709, 15010, 2733, 18, 3], "output": "MSRTLAITLSLTATLGLAACGSPTDEKAAATGAAQVPRNPQRVVALDNTSFETLQAFGITPVLDVGNHREPKLEVVAQARPDLIVGGKRFEKVTDDLQKLSSRDYVADLKKQTTTIGEIFGRQADAKALNDALDASVAKAVAAGRIGALLQPLPMTEVFGTTPNSESVHQDSSLSPETIAAKNPDVMIVMDKAWKNTTFAKNGDIVYLRDTFYTTEGIQAYTDAYTRIAETLQRASSSPDAQGTLTVASKGGDVAAPKGLLPKDLDAWKKDPNVPVVDLAPEVEKAAKATSGQTVFLANHNGGKIDNRDAAVAKPGETVTPASRTIEAQ", "metadata": {"id": "H5UUL5", "cluster": 5599634, "interpro_all": ["IPR002491", "IPR051313"], "interpro_used": ["IPR051313", "IPR002491"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein should have a Flp pilus assembly protein RcpC/CpaB domain that serves as an inner membrane auxiliary component of the Tad machinery involved in the assembly of type IVb pili. It interacts with TadB and the ATPase TadZ, and contains tandem \u03b2-clip structures that may modify Flp pilin or bind carbohydrates. Also, the protein belongs to the Pilus assembly, Flp-type CpaB family, which comprises the CpaB protein involved in the assembly of Flp-type pili. Members of this family are similar to the FlgA protein involved in bacterial flagellum biosynthesis. In addition, the protein carries a SAF domain that adopts a structural \u03b2-clip fold and is found in a diverse range of proteins, including antifreeze proteins, flagellar assembly factors such as FlgA, and CpaB pilus components. It has been detected in Bradyrhizobium quebecense and has UniProt annotations Signal.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 3066, 2162, 43, 25714, 7547, 1957, 5957, 2213, 7399, 7693, 19, 22675, 1014, 3418, 1988, 10634, 1966, 1925, 6671, 3260, 21549, 4594, 1927, 1920, 17857, 10853, 3286, 1922, 1920, 5957, 1927, 2601, 4370, 1014, 7547, 1033, 18, 2176, 9034, 1956, 17857, 1014, 1930, 1920, 9444, 17857, 1011, 16, 1930, 5461, 10361, 161, 17, 18709, 4061, 1988, 2278, 11675, 25714, 7547, 1921, 2014, 4566, 16282, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 7547, 1957, 5957, 16, 25714, 17, 2601, 22675, 1014, 3416, 16, 2154, 12936, 1920, 22675, 1014, 2213, 3286, 1922, 1920, 5957, 1927, 25714, 17, 2601, 7547, 1033, 18, 4678, 1927, 2052, 3416, 2032, 2551, 1942, 1920, 2300, 4223, 2213, 3286, 1922, 4543, 7030, 10757, 8132, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 4345, 3418, 1988, 24032, 43, 4346, 161, 17, 18709, 3728, 1930, 1977, 2435, 1922, 43, 6445, 3109, 1927, 2697, 16, 2710, 12244, 2329, 6931, 2697, 16, 24154, 5957, 2790, 2427, 1966, 2300, 4223, 16, 1930, 22675, 1014, 7547, 1957, 4178, 18, 2176, 2258, 2252, 3330, 1922, 20152, 5004, 2061, 23156, 26180, 4480, 1930, 2258, 20709, 15010, 2733, 18, 3], "output": "MDKARILVLAIAGCAGLAALYLASGSQAVKPEDLQWQTWPAATASASFMRRDSNAEAIKDGSGFMAAILPTGMRAVSTEISPETGAPDRSGADIVNSEVILTNVRVLAIDQAPKEKDQTETLARARQSGVLSLALRSIADGDTINVIRFGVANQATMQKDDKPAPAPPVAQLPTVDILVAKTDIGLGDVTGSIARAPFIQGEPIREQKLVKAGGFILPNDRVDVLLSKRDKNGTNALIGKTVTLELKPENNAPETRTDDNRQRR", "metadata": {"id": "A0A974AAR3", "cluster": 7357967, "interpro_all": ["IPR017592", "IPR031571", "IPR013974"], "interpro_used": ["IPR031571", "IPR017592", "IPR013974"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Function:\nThe protein is assigned to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. In addition, the protein possesses a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein should contain a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is produced by Monoglobus pectinilyticus and is classified with UniProt keywords Isoprene biosynthesis and Transferase.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 4152, 2007, 8914, 4365, 2389, 1957, 22422, 2869, 2002, 1957, 1930, 1977, 5947, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MVKSITEKCSAKINIAIVGIFDVITISLKDEKGIEIAGSDINMPVDEGCDIYIEKHIPMGAGMAGGSSDAAGVIKKLGADVPFCVMGGCALAEGIGECYLIAKPRQSISTKWVYEHLDYNNKPVPFMGNILENSAVQICPQVNVYKAEMLRELAVKAYKEFKLRHSDADGVWVLADVLGKYPNGYHEVRMIMTQSNLAWKAANEFFKAIKFDGNGLNKLFDSPLSLEERMKMGRLTVLPELPEVNLDIDKIISGIKSGDLKKIQNLGADIAMMSGSGSAVFGMFDD", "metadata": {"id": "A0A2K9P3C2", "cluster": 8672106, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR014721", "IPR036554", "IPR020568"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nIt is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is native to Cyanobacteria bacterium HKST-UBA05 and contains UniProt keyword associations Membrane, Transmembrane, and Transmembrane helix.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 6196, 1942, 21897, 14061, 13595, 2156, 17, 4803, 1019, 15264, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "PLGICQLSQWAGVQGLLMLAGVFLGPAALGGIRVVMHLASPINLHHGYRAMRTYLANFGLILGGSMALALLGICVFKDGLISRLYSQQYLAYGHLMYWFSAYLANFAATVATFALYAVLAKPYGDTAVMMALVCNQLILNAMFVMVFARQNRKHLAAYAANLGAGKTSVIEAVGQRLTTTFTDQHYYHLRPRMLNYNSKVGALSGYDQPHKQPPRYWLRVLPQKDARSLVIFDRYVHDLLVDTARFRLSLPEGVIRAILRLVPLPDLIVVLYRNLARDGRGKVVAVDALGQVEETAQEVTALILAQAQLAEARPEKEAVITQGTQNFVPTEASRLLLVVSVATHTLTYYLRTIEQTRPLAWGQPKEGVVVAFLGPDGCGTLVSLVKLLYFVLDYYLGDGSAQCFHDRKQELSLEELERQISC", "metadata": {"id": "A0A956Q3M6", "cluster": 9575192, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that can perform the following function: The protein features a NifU N-terminal domain that acts as a scaffold for iron-sulphur (FeS) cluster assembly, facilitating the maturation of the nitrogenase complex and other metalloproteins. It binds an iron atom to generate a transient cluster that is subsequently transferred to recipient apoproteins. This domain operates within the nitrogen fixation (NIF) system but is also conserved in organisms that do not fix nitrogen. It is produced by Kouleothrix aurantiaca.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 17719, 1032, 56, 17, 4262, 3418, 1988, 8016, 1966, 43, 7281, 1958, 5680, 17, 13528, 1949, 12, 18097, 13, 4377, 5957, 16, 12440, 1920, 7655, 1927, 1920, 6634, 2051, 2796, 1930, 2303, 14558, 1036, 18, 2176, 6876, 1925, 5680, 6761, 1942, 5655, 43, 6809, 4377, 1988, 1977, 5326, 6311, 1942, 10664, 11466, 22163, 1036, 18, 2052, 3418, 22460, 2651, 1920, 6634, 7938, 12, 17719, 13, 2433, 2308, 1977, 2222, 5305, 1922, 7373, 1988, 2608, 2084, 4011, 6634, 18, 2176, 1977, 4152, 2007, 6235, 3466, 2195, 3027, 1039, 11826, 10402, 10973, 18, 3], "output": "MDDMYREVILEHYKHPHNAGTLEAADITHED", "metadata": {"id": "A0A0P9D7X1", "cluster": 10609504, "interpro_all": ["IPR002871"], "interpro_used": ["IPR002871"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a polypeptide chain that performs the following role: The protein should contain a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Furthermore, the protein should include a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Additionally, the protein features a Helicase/UvrB, N-terminal domain that serves as a conserved component of enzymes involved in DNA processing and repair. It is characteristically found in the N-terminus of helicases, the HsdR subunit of type I restriction endonucleases, the Res subunit of type III endonucleases, and the UvrB subunit of the UvrABC system. It is identified in Brevibacterium epidermidis and is described by UniProt keywords Excision nuclease, DNA excision, and DNA repair. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 5531, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 4950, 16, 1920, 2213, 4075, 43, 15318, 19, 5819, 16007, 16, 56, 17, 4262, 3418, 1988, 10634, 1966, 43, 5305, 4594, 1927, 5038, 3286, 1922, 2678, 4587, 1930, 5059, 18, 2176, 1977, 6293, 2169, 2435, 1922, 1920, 56, 17, 7822, 1927, 29919, 16, 1920, 18926, 1005, 5903, 1927, 2601, 51, 7587, 18697, 1036, 16, 1920, 1995, 5903, 1927, 2601, 4337, 18697, 1036, 16, 1930, 1920, 5819, 16007, 5903, 1927, 1920, 5819, 5524, 8284, 2433, 18, 2176, 1977, 2899, 1922, 3022, 2165, 7972, 2341, 18842, 1989, 27348, 1930, 1977, 2910, 2007, 20709, 11569, 10940, 16230, 16, 2678, 10940, 16, 1930, 2678, 5059, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MSSERPLPAIGHRPDVTREVAPFEVVSEYSPSGDQPTAIKEISERLDAGERDIVLLGATGTGKSATTAWLIEQVQRPTLIMAPNKTLAAQLANEFRQLLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSSINDEVERLRHSATNSLLTRRDVVVVSTVSCIYGLGTPEEYVDRMVTLHKGDECDRDELLKRFVSMQYARNDMAFTRGTFRVRGDTVEIIPQYEELALRIEFFGDEIESLQTLHPLTGEIVRDEDTIHVFPASHYVAGENRMATAISGIEDELQKRLSEFESQNKLLEAQRLKMRTTYDLEMMESMGFTSGIENYSRHIDGRAPGSAPNCLLDYFPEDFLLVIDESHVTVPQIGGMYEGDMSRKRTLVEHGFRLPSAMDNRPLKFDEFRERVGQSVYLSATPGNFELGNANGYVQQIIRPTGLVDPEIKVKPTKGQIDDLLDEIRTRVDANERVLVTTLTKKMAEDLTDYLLEHDVRVQYLHSDVDTLRRVELL", "metadata": {"id": "A0A9D2ZWK9", "cluster": 10760172, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR004807", "IPR041471"], "interpro_used": ["IPR014001", "IPR001650", "IPR006935"], "interpro_unused": ["IPR027417", "IPR004807", "IPR041471"]}, "task_type": "autoregressive"} {"instruction": "The protein should include a Alpha-galactosidase NEW3 domain that is typically found in bacterial galactosidases, though its specific functional role remains uncharacterized. Additionally, the protein carries a Forkhead-associated (FHA) domain that functions as a phosphopeptide recognition module, displaying specificity for phosphothreonine-containing epitopes and phosphotyrosine. This 11-stranded beta-sandwich structure facilitates protein-protein interactions in diverse bacterial and eukaryotic regulatory proteins, including kinases and transcription factors, to mediate processes such as DNA repair, signal transduction, and protein degradation. Additionally, the protein is classified under the Cellular Process Regulator and RNA Processing Protein family, which regulates diverse cellular activities ranging from glutamate metabolism to RNA processing. Members modulate the Krebs cycle by inhibiting 2-oxoglutarate dehydrogenase and influence cell proliferation and splicing by inhibiting protein phosphatase 1, while also associating with the spliceosome to facilitate pre-mRNA splicing and microRNA biogenesis. It is native to Chloroflexota bacterium and corresponds to UniProt keyword Transferase.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 3066, 3951, 43, 4595, 17, 15782, 2814, 1010, 3418, 1988, 1977, 5745, 2435, 1922, 4543, 15782, 1036, 16, 4170, 2496, 2487, 3183, 2770, 4497, 24528, 18, 4950, 16, 1920, 2213, 16252, 43, 29548, 17, 2458, 12, 11912, 1019, 13, 3418, 1988, 4088, 1966, 43, 8078, 9626, 2410, 2261, 5708, 9059, 16, 13867, 4896, 1958, 8078, 5856, 1021, 12530, 17, 3165, 11427, 1930, 29552, 18, 2052, 2513, 17, 10338, 4666, 17, 18038, 3170, 11374, 2213, 17, 2213, 3719, 1922, 6445, 4543, 1930, 10825, 4948, 2697, 16, 2710, 7784, 1930, 3213, 2790, 16, 1942, 8265, 4028, 2427, 1966, 2678, 5059, 16, 2733, 8201, 16, 1930, 2213, 4877, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 3689, 2585, 7888, 1930, 3146, 4587, 2213, 3416, 16, 2154, 7014, 6445, 3689, 4209, 6485, 2037, 7627, 4714, 1942, 3146, 4587, 18, 4678, 8480, 1920, 25362, 4048, 2007, 7918, 22, 17, 18588, 16542, 17488, 9294, 1930, 4039, 2024, 4031, 1930, 8490, 2007, 7918, 2213, 8167, 21, 16, 2679, 2222, 26284, 1956, 1920, 10708, 4283, 1942, 6628, 2097, 17, 3616, 8490, 1930, 14084, 13008, 18, 2176, 1977, 6196, 1942, 10107, 18222, 7336, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 13763, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MSSPSQGGGAAPKVIVIDPGGSRRLPVTLTTARRHARIDWDGQRATVTDLGSSNGTNVGDARLLAHSFIQLEPPEGVMQQAQASASANVPPPPPPPPGPGQPPPGSTGTAGSTGAAGGMFESGRIRVTLVANTGTLVDHLTVSVEGVPSAWVKAPEVPSQLNPGVRARSRENPNETGAAVALWTVLPGLTLGRVEGNDIVLPHDSVSAQDWRPGDWLNIGPFPYVTTNPVPGLQQAAGAQESNTLTLTPGQPAVVRVNAQTTVVLQVNVARVAQNRSGDYPVT", "metadata": {"id": "A0A3A0AG22", "cluster": 11500664, "interpro_all": ["IPR018905", "IPR050923", "IPR000253", "IPR013783", "IPR008984"], "interpro_used": ["IPR018905", "IPR000253", "IPR050923"], "interpro_unused": ["IPR008984", "IPR013783"]}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: It is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Moreover, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Moreover, the protein is assigned to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is present in Oscillospiraceae bacterium and is classified with UniProt keywords Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 2481, 1922, 7799, 3106, 11979, 1972, 3336, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 3], "output": "MAAVFSHRSVLLDECIEGLAIKPEGVYVDGTAGGGGHSYHIAERLTTGRLIAIDRDEAAIAAATARLSPFSERATVYRSNFSEVSHVLDDLGIDTIDGMLLDLGVSSYQLDTAERGFSYQADAPLDMRMDRRNEKTAYTVVNTYSEEALKNILFTYGEEKFSARIARKIVQAREIAPIATTKELSDLIKSAMPAAAREGGHHPAKRSFQAIRIEVNGELDAIVPALKGAMARLNRGGRLAVITFHSLEDRIVKQAFAEMAEGCTCPKSLPICVCGHKPVAKIITRKPILPSAVELEENPRSRSAKLRVAEKL", "metadata": {"id": "A0A928F543", "cluster": 13197157, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR023397", "IPR002903"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein falls within the Winged helix-like DNA-binding domain superfamily, which encompasses diverse DNA-binding proteins including transcriptional regulators, helicases, and endonucleases that utilize a winged helix-turn-helix motif for sequence-specific recognition. This domain engages the DNA major groove via a recognition helix while loop structures known as wings contact the minor groove or backbone, often serving as a scaffold for protein-protein interactions. Also, the protein has a Winged helix DNA-binding domain that facilitates specific DNA recognition through a modified helix-turn-helix structural motif. It is typically found in proteins with currently uncharacterized biological roles, likely contributing to transcriptional regulation or nucleic acid binding. It is derived from Kutzneria albida DSM 43870.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 12920, 1919, 7864, 17, 3189, 2678, 17, 2743, 3418, 13975, 16, 2154, 21569, 6445, 2678, 17, 2743, 2697, 2710, 5224, 9098, 16, 29919, 16, 1930, 18697, 1036, 1988, 12561, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 1958, 3244, 17, 2487, 5708, 18, 2052, 3418, 11580, 1036, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 2679, 5881, 4061, 3171, 1966, 28297, 5217, 1920, 5857, 15920, 2014, 10787, 16, 3868, 13915, 1966, 43, 7281, 1958, 2213, 17, 2213, 3719, 18, 2222, 16, 1920, 2213, 2258, 43, 12920, 1919, 7864, 2678, 17, 2743, 3418, 1988, 11374, 2487, 2678, 5708, 2596, 43, 4795, 7864, 17, 5165, 17, 7864, 4346, 5219, 18, 2176, 1977, 5745, 2435, 1922, 2697, 1956, 5077, 24528, 3933, 5456, 16, 3205, 8739, 1942, 5224, 3640, 2014, 11079, 2687, 2743, 18, 2176, 1977, 3595, 2037, 11352, 15982, 3239, 2126, 5311, 9532, 10964, 29873, 4618, 18, 3], "output": "MATPDLDPLLLDPTRLSIVALLASTEWAEFRWVRDLVGLSDSALSKQITNLSDSGHQALRAHVAALNQIVEQSQRAGSTHRAEEPSALANPGYVEVKKGYVGKRPRTWLN", "metadata": {"id": "W5WKP8", "cluster": 16609240, "interpro_all": ["IPR036388", "IPR027395", "IPR036390"], "interpro_used": ["IPR036388", "IPR027395"], "interpro_unused": ["IPR036390"]}, "task_type": "infilling"} {"instruction": "The protein falls within the TRAP transporter solute receptor DctP family, which constitutes the substrate-binding protein (SBP) component of the tripartite ATP-independent periplasmic (TRAP) transporter system in prokaryotes. These receptors bind specific extracellular solutes, such as sialic acid, and undergo a characteristic domain closure to deliver the substrate to the integral membrane transport complex for uptake across the cytoplasmic membrane. It is native to Rhodospirillales bacterium and is linked to UniProt keywords Signal. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 10947, 9054, 19661, 3148, 22936, 1034, 3416, 16, 2154, 14879, 1920, 4510, 17, 2743, 2213, 12, 12345, 13, 4594, 1927, 1920, 8027, 24707, 4498, 17, 3484, 24334, 12, 10947, 13, 9054, 2433, 1922, 28149, 18, 2144, 4086, 4566, 2487, 5329, 27993, 16, 2427, 1966, 20436, 2687, 16, 1930, 4978, 43, 6293, 3418, 10408, 1942, 3971, 1920, 4510, 1942, 1920, 12328, 3260, 4860, 2796, 1958, 5047, 3436, 1920, 6823, 3260, 18, 2176, 1977, 6196, 1942, 11490, 3106, 23576, 11560, 3955, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 2733, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MKKLLITSMLVGALAGGFATVAKAAEFTIKYAHVGPVTSDDQVAGEFLKSFLEARSNGRIAVEIYPGAQLGNFREMIEQVQLNTLELTHTTVGGIASFFPELQVTDIPYMMNGDAIAENIAQSAFFDDVREEILKKTGNVRLVAVGNTGRWRNFFTTKKLIKSASDMAGVKMRTINSPLQIEFIKSLGGNPTPVAWGELYTSLQTGVVEGTKNAATDIIPTKMYEAVKYVTLDEHAYLFAFWWMSDQWLKKLPADLQDLVIDGVQQTAMVQSDWNKEYDARALKEFQGFGGTVYVPTPEERATFVAARDKMKVWFVEKYGDTWLKKFEKAVADAESQVSSKISRVIGR", "metadata": {"id": "A0A973AHK6", "cluster": 16890554, "interpro_all": ["IPR018389", "IPR004682", "IPR038404"], "interpro_used": ["IPR018389"], "interpro_unused": ["IPR004682", "IPR038404"]}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein possesses a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. Also, the protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is produced by Cloacimonadota bacterium and is annotated with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 14465, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 4152, 2007, 12596, 28278, 3947, 12595, 3857, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSKGRLITFEGSEGAGKSTQVKALKKYLVSLKIRSLLLSPDSGDFSDETELFMMLAARAEHVESLVLPSYGRGIDIKTISQMNAFAIKGRYPDLTVRAAKTGSLDRIESAALSFHQNVREDIQTLESEIKERVLKLLKYENGYKVVCTFEPGGGSDLCKLSRGEIVICDRFIDSSVAYQGVMDIDPVIGLKGFMSLAQEGERYFVVDASL", "metadata": {"id": "A0A2A5AKM5", "cluster": 18773439, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR018094", "IPR039430"]}, "task_type": "infilling"} {"instruction": "Give me the sequence of a polypeptide chain with the following function. The function of the polypeptide chain is The protein contains a Small GTP-binding domain that functions as a molecular switch by binding and hydrolyzing GTP to regulate diverse cellular processes, including signal transduction, vesicle transport, and protein biosynthesis. It is found in the Ras superfamily of small GTPases as well as within larger proteins such as translation elongation factors. Moreover, the protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is present in Ectocarpus sp. CCAP 1310/34 and is connected to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 7031, 2142, 1920, 3244, 1927, 43, 13022, 4659, 1956, 1920, 2894, 2347, 18, 1920, 2347, 1927, 1920, 13022, 4659, 1977, 1920, 2213, 5461, 43, 2858, 9319, 17, 2743, 3418, 1988, 4088, 1966, 43, 3272, 6195, 2007, 2743, 1930, 7222, 9046, 9319, 1942, 5741, 6445, 3689, 4028, 16, 2710, 2733, 8201, 16, 11502, 4860, 16, 1930, 2213, 8132, 18, 2176, 1977, 2435, 1922, 1920, 6520, 13975, 1927, 2858, 18390, 1966, 2486, 1966, 2651, 4327, 2697, 2427, 1966, 6410, 9971, 2790, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2481, 1922, 7495, 7095, 1034, 1957, 2056, 18, 13980, 1034, 11389, 1008, 19, 3540, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MNENIGRGLGETEDALRLVERLGDSLYLHGNPWIMPPEGVVEAGLTAVKRYLVDVREAKKAGADVTSLQLLKVVLVGSASAGKTSLMHSIIAGRGSPTEGTPAQASTVGMELRPCQLQDTKVEFFDCAGQVDYAGMHQTFLTRRALYLLVVDITKYHGVDDLDKAIHDDIMRWLYYLYLRAPGSTVVLVANKCDGSIDKFAETAERIQRRVRELVAVWHEARGLRGRSKGHVTDLTLLPGMSRVSCQEKGSPEASGLPALIALISRQAATAIHVPPAWDLALEVIGALRASCNPIAAARDKLGLPNPLPADGVADVHAFAFISKDELSRKWRSVVDNLRDDVPAAMISNWESALEGALWISDFAGHTLRVDGGDGIFLDVLWLSKCLSPILSHKLKNQPFENRWLWMRDDLAGDGILRREFALHIWRESVGEVVMESEEVAEALFSVLIKLGVALPMGRRTLLAHSDRSTPTAPSDVSGSNDMLVIMRLSETCNEHQRTLFDGLASKMPRDRVTLKWEFDKAGPPYGLIERLIASCHVLGEVETGACWRYGAVFQSHDMRFVEGRNVRFYKIALSMTSYNESERVFTAKVFGPLDSERVWVAIRYVASAMINLSKEWPGVLWTGWLDCEKHPSQHLYMASSVEARVGDPLLPAAAPDARRCDCLLEPGGVLRLAVEELGPVIDTGKDPFEGLSDEDTEDPEETVTCNCVREAFGHWLPHAWRTAKWLFGLAVVLFTTAVVAGIVEDKETLWKSSLGVCCVLMVFSVVASVFAYCGDREQGQSGGQHGTPEDVVAAFA", "metadata": {"id": "A0A6H5K8T1", "cluster": 19472625, "interpro_all": ["IPR027417", "IPR005225"], "interpro_used": ["IPR005225", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein should feature a Flagellar hook-length control protein-like, C-terminal domain that regulates the length of the bacterial flagellar hook or type III secretion system substructures. It functions as a molecular ruler that detects when the hook reaches its optimal length, subsequently terminating hook assembly and triggering the switch to filament export. Additionally, the protein is grouped in the Flagellar hook-length control family, which regulates bacterial flagellar assembly by determining the length of the hook structure that connects the basal body to the filament. These proteins possess a two-domain architecture with a central hinge region, a structural feature essential for precise hook sizing and effective bacterial motility. In addition, the protein is assigned to the FliK-like, C-terminal domain superfamily, which comprises the C-terminal region of proteins involved in flagellar assembly and operation. This domain is critical in FliK for detecting optimal flagellar hook length to trigger the switch from hook to filament export, and is also present in the chemotaxis protein MotD, which is required for flagellar motor rotation. It is present in Marinomonas sp. TW1.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 3066, 5961, 43, 24154, 17185, 17, 3471, 2285, 2213, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 7014, 1920, 3471, 1927, 1920, 4543, 24154, 17185, 2014, 2601, 4337, 5512, 2433, 28876, 2352, 18, 2176, 4088, 1966, 43, 3272, 8728, 1005, 1988, 19998, 2469, 1920, 17185, 14698, 2496, 5419, 3471, 16, 5326, 5475, 2287, 17185, 5957, 1930, 14074, 1920, 6195, 1942, 10797, 12660, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 24154, 17185, 17, 3471, 2285, 3416, 16, 2154, 7014, 4543, 24154, 5957, 2007, 7426, 1920, 3471, 1927, 1920, 17185, 3170, 1988, 26414, 1920, 5342, 3362, 1942, 1920, 10797, 18, 2144, 2697, 7150, 43, 2288, 17, 3418, 9335, 1956, 43, 4101, 20484, 3031, 16, 43, 4346, 5961, 4415, 1958, 8162, 17185, 5998, 9046, 1930, 3655, 4543, 9254, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2300, 3815, 17, 3189, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 12936, 1920, 45, 17, 4262, 3031, 1927, 2697, 3286, 1922, 24154, 5957, 1930, 7277, 18, 2052, 3418, 1977, 4140, 1922, 2300, 3815, 1958, 9227, 5419, 24154, 17185, 3471, 1942, 6086, 1920, 6195, 2037, 17185, 1942, 10797, 12660, 16, 1930, 1977, 2222, 2481, 1922, 1920, 16884, 2213, 12798, 1007, 16, 2154, 1977, 3414, 1958, 24154, 4842, 8891, 18, 2176, 1977, 2481, 1922, 13081, 11873, 3947, 1934, 2056, 18, 2249, 1009, 18, 11586, 5655, 3581, 18, 3], "output": "MRTDSNTLLPIASGSASKKSSMEDFNRAKDVMSGSKYDDKHRVVHADEQRKPSVTVTSKTTTSAPQSKAVDTQSDNSEPGSVKVGEQLSGEASPETNNTTKGEEAQLLGENVVEDQIAQNADELLSVVEGGQTKVSLNEASGNGSQTENALLDNGSVVQQPSVQGLSGVNAPVDALLSDQVTEAPLLEGSDLERLNESGSQTMAPGQDVVAGSDEELSWVLDQMSSTPRKKSAGLAGAGLALGVAGKLNADSTNGSAELRKKEHEAMLGRMAGNVDAKIDDVGGLSSPPGHPNWAAEMGQKVAWVAREGGHTAHIRLDPPTQINFVAATAQARDLLEGQMGRLRDMLAQQGMDLSRAEVDVSQQDASGEEADDVMPGVMSYVSATGVDYYANRVPEKQGAAFSSDKLSHQRTKDDRINTSEQAPVGTQSTVSGADQAGESGKKLAGSIAAGALAKSSEAGVAKLNIALTSDEVHQQGLMNPTPQEFGQVAMPVDGKASGQVIVMAPVAAAVATGVASPDGVVTGLLAEASEAERVTDLLQEADLTLDDMIGNEPLSFNQQIGRAAATVGVASQLAGANQSLNMAMSVELGSLTVKVSVDSDSNTQKDAGQTRVANNSDGKGD", "metadata": {"id": "A0A166K9N5", "cluster": 21692195, "interpro_all": ["IPR021136", "IPR052563", "IPR038610"], "interpro_used": ["IPR021136", "IPR052563", "IPR038610"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence be if I wanted a polypeptide chain capable of the following function: The protein should contain a Serine/threonine-protein kinase active site that catalyzes the transfer of the gamma phosphate from ATP to serine or threonine residues on protein substrates, utilizing a conserved aspartic acid residue essential for enzymatic activity. This reversible phosphorylation regulates diverse cellular processes, including division, proliferation, and apoptosis. Furthermore, the protein is categorized in the Protein kinase-like domain superfamily, which modifies other proteins by chemically adding phosphate groups. This enzymatic activity is fundamental to most signaling and regulatory processes in the eukaryotic cell. It has been characterized in Umbelopsis vinacea and contains UniProt keyword associations Transferase.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 8468, 19, 13143, 17, 2213, 4016, 3500, 3200, 1988, 17097, 1920, 3856, 1927, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 2014, 13143, 4248, 1990, 2213, 6249, 16, 10232, 43, 5305, 23047, 2687, 6181, 4415, 1958, 8145, 2455, 18, 2052, 10743, 4050, 7014, 6445, 3689, 4028, 16, 2710, 8451, 16, 4031, 16, 1930, 4091, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 4016, 17, 3189, 3418, 13975, 16, 2154, 25436, 2303, 2697, 2007, 13944, 8013, 5413, 2671, 18, 2052, 8145, 2455, 1977, 8829, 1942, 2501, 3197, 1930, 4948, 4028, 1922, 1920, 10825, 2024, 18, 2176, 2258, 2252, 4378, 1922, 25589, 1938, 8369, 11132, 22076, 1930, 5461, 20709, 11121, 2538, 5253, 13763, 18, 3], "output": "MDISNEDLEVQKQEIEIHRSLVKSSRIARLVSHFETEQYLFLVLEYIQGMDLYWWILHKNDHYDSATGRNLDTLERLTVLSNLFVQCLEAVHFIHTKKIAHRDLKPENFLITLDQSIKLIDFGLATTEHYPTDFDCGSKPYMSFECHNPDNPHYDAFQADIWSLGIIFINLFWHRSPWSRPDNSCPAYKSFTQHPTDFLVERFDGMSRTVATFLSDRVFCSENKGRVKIAEWKAWCKNLVKLLSDDTCNRPTTPKKTIGFLPLTISLSNVRNNSAKAKESALSARLRRSSFFSMLPPSPILSPGKRGHESNDTYFPSRIDHQYSKSWSQELDFDAEESEMDFSEPISFADTPQTSEDETKKEGQDDNDSGFGSDEPDSTAPQSFLSPRSPAAAASSDEQQPMKTVPKYIPPAKRRNHIPDIRGSSKRYSISSTQTAQPSSVGGQGYHVGAHQRRPFAPPQPTWRHRNQQQQRHEPWQKSNHPFTKPSNGMRNSPPSLLKTNDKIPAYPVLVYTPPHRTSKPLASASVSLFNNRMPGMTTHKSLADSSSVVQDYKPAAVDDMEMSEMDVVFGETPPPVERRNHLTKGAISDFGKLLRSIARDRSQ", "metadata": {"id": "A0A8H7PW16", "cluster": 23766644, "interpro_all": ["IPR011009", "IPR000719", "IPR008271"], "interpro_used": ["IPR008271", "IPR011009"], "interpro_unused": ["IPR000719"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has the following function: The protein is classified under the Metallo-dependent phosphatase-like superfamily, which encompasses a diverse group of enzymes, including purple acid phosphatases and DNA repair nucleases, that catalyze the hydrolysis of phosphate esters. These proteins utilize a conserved binuclear metal center, typically composed of manganese, iron, or zinc ions coordinated by histidine, aspartate, and asparagine residues, to facilitate functions ranging from nucleotide metabolism to signal transduction. Also, the protein possesses a Calcineurin-like, phosphoesterase domain that functions as the catalytic center in diverse enzymes, ranging from nucleotidases and sphingomyelin phosphodiesterases to nucleases like Mre11. This domain adopts a fold comprising two sandwiched $\\beta$-sheets flanked by $\\alpha$-helices, which coordinate a binuclear metal center essential for hydrolyzing phosphoester bonds. In addition, the protein falls within the Diadenosine polyphosphate hydrolase family, which catalyzes the hydrolysis of diadenosine polyphosphates, particularly Ap4A, into either two ADP molecules or a combination of AMP and ATP. These enzymes exhibit symmetrical or asymmetrical activity to modulate nucleotide metabolism and regulate cellular processes sensitive to nucleotide levels. It has been characterized in Gammaproteobacteria bacterium 45_16_T64. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 8969, 1037, 17, 3100, 8167, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 5038, 16, 2710, 14308, 2687, 19131, 1930, 2678, 5059, 29305, 16, 1988, 18170, 1920, 9128, 1927, 5413, 16785, 18, 2144, 2697, 12561, 43, 5305, 8768, 13821, 6048, 4102, 16, 5745, 7179, 1927, 19516, 16, 5680, 16, 2014, 7997, 6982, 11651, 2007, 13873, 16, 12878, 16, 1930, 23677, 4248, 16, 1942, 6628, 4088, 6485, 2037, 5489, 4714, 1942, 2733, 8201, 18, 2222, 16, 1920, 2213, 14465, 43, 19555, 17, 3189, 16, 8078, 8342, 2051, 3418, 1988, 4088, 1966, 1920, 6804, 4102, 1922, 6445, 5038, 16, 6485, 2037, 2797, 4090, 2319, 1930, 28057, 24821, 1036, 1942, 29305, 3189, 26460, 18, 2052, 3418, 24032, 43, 3728, 10351, 2288, 18038, 1919, 8, 38, 4666, 8, 17, 14685, 20185, 2007, 8, 38, 4595, 8, 17, 12789, 16, 2154, 11865, 43, 8768, 13821, 6048, 4102, 4415, 1958, 7222, 9046, 8078, 8342, 9031, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 25141, 5233, 7506, 11769, 11787, 20748, 3416, 16, 2154, 17097, 1920, 9128, 1927, 25141, 5233, 7506, 11769, 11787, 1036, 16, 4443, 2100, 9458, 16, 2460, 3108, 2288, 9828, 4206, 2014, 43, 3921, 1927, 3681, 1930, 4498, 18, 2144, 5038, 5987, 20410, 2014, 27184, 2455, 1942, 8480, 5489, 4714, 1930, 5741, 3689, 4028, 4532, 1942, 5489, 2428, 18, 2176, 2258, 2252, 4378, 1922, 7034, 9218, 1021, 10296, 14061, 3607, 41, 2641, 41, 20762, 1006, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MKIEVFEENTCGADFVCSDIHGHFSLLERQLEAVKFNKSVDRLFCLGDLIDRGDESHRVIHYLSQPWFHSILGNHELMLIDAFESESEHVRRQWGYWGGDWADDLDEDQLQQYYDVLVTLPMAIELAVSSTQVVGLVHAELPMICDWRDVKRELENKPSADNLTNTALLHGMMWNKNQMRSAEAIRGVLPAVENIDHVFHGHTILNEITTVSNRTFLDLGSYETGVIGLISPLDYIEG", "metadata": {"id": "A0A1Y5GZC8", "cluster": 2422477, "interpro_all": ["IPR050126", "IPR004843", "IPR029052"], "interpro_used": ["IPR029052", "IPR004843", "IPR050126"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein should have a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. Furthermore, the protein includes a Rho termination factor, RNA-binding domain that binds single-stranded RNA to facilitate the disengagement of newly transcribed RNA from its DNA template. It features an N-terminal OB-type fold with an indented face that serves as the primary binding site and supports the formation of a functional hexameric complex. In addition, the protein incorporates a ATPase alpha/beta subunit nucleotide-binding domain that forms the central structural component of the catalytic or regulatory subunits in F-, V-, and A-type ATPases, as well as flagellar ATPases and termination factor Rho. It binds nucleotides to drive ATP synthesis or hydrolysis through conformational changes linked to the complex's rotary motor mechanism, coupling chemical energy with proton translocation. It is derived from Gemmatimonadota bacterium and exhibits UniProt keyword tags ATP-binding, Helicase, and Hydrolase. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 3066, 2162, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 3677, 16, 1920, 2213, 5921, 43, 10585, 12462, 2991, 16, 3146, 17, 2743, 3418, 1988, 6876, 2957, 17, 10338, 3146, 1942, 6628, 1920, 28347, 8909, 1927, 7471, 10078, 3146, 2037, 2496, 2678, 7662, 18, 2176, 4075, 1925, 56, 17, 4262, 2384, 17, 2601, 3728, 1956, 1925, 2063, 12871, 6171, 1988, 10634, 1966, 1920, 3065, 2743, 3200, 1930, 7825, 1920, 3337, 1927, 43, 3183, 25602, 1935, 2796, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 9444, 4595, 19, 4666, 5903, 5489, 17, 2743, 3418, 1988, 4952, 1920, 4101, 4346, 4594, 1927, 1920, 6804, 2014, 4948, 6991, 1922, 48, 17, 16, 64, 17, 16, 1930, 43, 17, 2601, 28132, 16, 1966, 2486, 1966, 24154, 28132, 1930, 12462, 2991, 10585, 18, 2176, 6876, 9519, 1942, 9265, 4498, 4271, 2014, 9128, 2596, 8523, 2840, 4624, 1942, 1920, 2796, 11, 61, 23548, 4842, 2856, 16, 7590, 4399, 3844, 1956, 8433, 7849, 18, 2176, 1977, 3595, 2037, 10607, 3368, 2265, 12502, 22389, 3857, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 15318, 16, 1930, 20748, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MPAVASRSLSDRNGAHCTTRSFRMTERKRPIRRSRTSGTPSPDAGGDDNPYLDAPSAPAPRDAAPPPPTAGAPDEAPRPRRGRPPRRPAADAAADASASIERDAPPAPPAPLAESRPEPRHTSRSAPRAEPMAPPAFFDPAAERPRLDSADRYDRAFDRPANPPAGSAERPEPRPDRPFGDRPERPDRPDRGGRPRDRGRHRNERGDRGPRGDRTDGGNGAQVGGQAAPQDRPDRGPDRGGDRGDRNGPDRGGDASLRRNGRRGRNRFRRGGAGGDGRPASGAEGAVERAPSVPSTPAVVDGTMTGWFDPSRDGGFVRRAINSYLPDPTDPFVPAALVRLHQLRRSDKLDATFGRDSRGRHVIIEVQQLNDGSPVVLEKRADFNTLTASYPDRKLTLETGRPAKTGPELTRRAIDLIAPIGYGQRALIVAPARAGKTTLLQAIVEGVAINHPEAALLVLLVDERPEEVSEMITWGYGEVVASSFDMPPKRHVEVAEMTLERARRLVEQGKDVVIVLDSITRLARAYNTVERGTGRTMSGGLDSNAMQKPKAFFGSARMIAPQHGGGSLTIISTALVETGSRMDDVIFEEFKGTGNCEIKLDRSLADRRIFPAFDIGTSGTRREEKLYRPDQLEKVHLLRRGLHQLPPQAGMEWLIKRIAATTNNDSLLDGL", "metadata": {"id": "A0A2G4FV94", "cluster": 3091024, "interpro_all": ["IPR003593", "IPR000194", "IPR012340", "IPR027417", "IPR041703", "IPR011113", "IPR004665"], "interpro_used": ["IPR003593", "IPR011113", "IPR000194"], "interpro_unused": ["IPR027417", "IPR041703", "IPR012340", "IPR004665"]}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, the protein belongs to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It has been characterized in Aneurinibacillus soli and is linked to UniProt keywords Cytoplasm and rRNA processing.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 2258, 2252, 4378, 1922, 19071, 5572, 26073, 10401, 5277, 1036, 2638, 1033, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 1930, 9067, 4587, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MFHHITVLHEEAVDGLNIKPGGIYVDCTLLTEGARLISIDQDDTALAAARERLAPYMDHHITQVDGVLFDLGVSSPQLDEAERGFSYTIVNEWEESEIASIIFKYGEEKFARRIAREVELIKRGIPAPARRTGGHPAKRTFQAIRILAPGGRTSVITFHSLEDRICKQTYLKILTRKPIIPTDVEQEENRRARSAKLRVAEKLAKGGAGHSSLIASRVTLVKSNFRRIKQILHDLYNAEAALDMRMDQQQELTAICLERARKPIETTEELAVNDELNAFKEALEDSIEMQEYSKGCICPPGLPQCACGQKPT", "metadata": {"id": "A0A0U5AUQ1", "cluster": 3093677, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein contains a YGX type MBG domain that is found in a variety of bacterial extracellular proteins. This domain represents a structural variant of the standard MBG domain, distinguished by the replacement of the characteristic N-terminal YDG motif with a YGX sequence. Moreover, the protein should feature a Fibronectin type III domain that serves as a versatile structural module in extracellular matrix proteins, cell-surface receptors, and enzymes. It adopts a conserved seven-stranded beta-sandwich fold and frequently mediates cell adhesion and protein-protein interactions, often binding integrins via an Arg-Gly-Asp (RGD) motif. Moreover, the protein contains a Leucine-rich repeat that folds into a characteristic horseshoe shape to provide a versatile structural framework for protein-protein interactions. Found in organisms ranging from viruses to eukaryotes, this motif typically utilizes its concave beta-sheet face to bind ligands, such as alpha-helices, and is involved in diverse processes including signal transduction, cell adhesion, and immune response. It has been characterized in Thioflexithrix psekupsensis and is connected to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 5461, 43, 67, 1029, 1039, 2601, 5667, 1029, 3418, 1988, 1977, 2435, 1922, 43, 5386, 1927, 4543, 5329, 2697, 18, 2052, 3418, 4972, 43, 4346, 6031, 1927, 1920, 2970, 5667, 1029, 3418, 16, 12080, 2007, 1920, 7619, 1927, 1920, 6293, 56, 17, 4262, 67, 18641, 5219, 1956, 43, 67, 1029, 1039, 3244, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 12848, 2601, 4337, 3418, 1988, 10634, 1966, 43, 20425, 4346, 9059, 1922, 5329, 4526, 2697, 16, 2024, 17, 3154, 4086, 16, 1930, 5038, 18, 2176, 24032, 43, 5305, 5260, 17, 10338, 4666, 17, 18038, 3728, 1930, 5467, 10412, 2024, 6141, 1930, 2213, 17, 2213, 3719, 16, 3868, 2743, 15563, 3454, 1925, 4582, 17, 3376, 17, 4138, 12, 18797, 13, 5219, 18, 3950, 16, 1920, 2213, 5461, 43, 12624, 17, 5536, 6865, 1988, 16231, 2460, 43, 6293, 15638, 10647, 1021, 5989, 1942, 3394, 43, 20425, 4346, 6465, 1958, 2213, 17, 2213, 3719, 18, 2435, 1922, 7373, 6485, 2037, 6241, 1942, 15021, 16, 2052, 5219, 5745, 18127, 2496, 26019, 4666, 17, 11130, 6171, 1942, 4566, 6908, 16, 2427, 1966, 4595, 17, 12789, 16, 1930, 1977, 3286, 1922, 6445, 4028, 2710, 2733, 8201, 16, 2024, 6141, 16, 1930, 3743, 2644, 18, 2176, 2258, 2252, 4378, 1922, 15331, 18222, 1953, 3027, 1039, 5971, 1040, 25372, 8134, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTSHLKNSTARFTRWLSSGSGRHFVPLRSQQRANWLGLTAVLWLSLWTSQAYALSCSAGNFQGKDYTQAVSPVGMGIPESSEAAEIGGELAGIALDEGLGGGSAFLSYGTCSDASCNSYITPSQYKSGVRYYFQNTSAGGGKQVFSCEWYGSAWLGQYYFKNARMDVPGVVDRYTAQNASGAIVPNQVTATDAIDANPVVTCTPALTSYLPVGKNTISCTAKDASNNVSGTVSFVTEVLKANQSSSLTPVYSASGPCSVNSSGVVSVSGTGNCAITATHPGNGYFNEASDGTQRFDINPSFTLGVTGGGSGNPVKLTTRLSPNVCFVALPNTLYVFGAGTCKVEAFQDGNASFKVGEKAYGNPAFRVRATSSVPPYLLNYSTTGVCSNSGNLITLTGVGTCTVTVAVAATSAYDATSATLAQLTLASTGGTSGEPIVYSATGTCSVSGDVVTFTEGLCEVTANQAGNTNYNAAAPVSRSLVFAKANQTGGQFPVSATGGASGNPVTYSAAGCSISGTTVTITPGTLCNVTASQAGNVDSGAIVTNCNSTAVTGVPVGDCQALLALYNSTGGANWTTKTNWNTNSAVSTWYTGTLPSELGNLTGLIQLGLMDNNLTGTIPPELGQLPSLGYVYLRGNKLSGEIPSQLGNLSALSDLSLDGNQLRTLSLANNKLNGAIPSQLGNAPLLSSLNLSNNQLSGAIPVELSPYFPGMPPNLSLGYNALTDETSGTATARQADWRDTQTAPPTGITANVLSATSIALSWTPMLYQSDSGYYQVQYATTATVNGLKPGTTYYFVVTGYTGDTIDVTSDPSAEISATTTALNHTQTLTFPTLGNLTSGPCSVTGNEVTATGVGTCTVTASQAGNGQYSAATSAERSFEIAKLAQAIDFPFASGNCTVSGDQVTANDAGMCTVTASQAGDAQYNAASDVVRSFDMSKIAQSITFAALPSVEYSASGVCSVTGGVLSVNSAGTCTVTASQPGDTLHAAATPVSHSFTVTPSEGALAFEPTGAITYTSITPETCSVSGNTVNILQAGLCQLTAEQAADVNTPVAQASVELPAFGATSYEGFVRSETETVLSGTLAFTTTAPTPVIAGSYDINASGLTSPNYTISYLPGKLTVPVVEGQSGVISVKLTGQPGGIATVTLTPDNFVSLGASAAGQPITLSFDANNWDTVQNVTVYSGVTEMTVRTIIYDNDPGVVIQPYSETLNLIEGGTAGQYTLRLSSIPIQAADETALQMKYIQVTAIDDSVFSNVPALITHSITTGDGVGYTNALAIAPVTVNITDNDPGVVIKSAPVSPVTVLLSYDSKQLAVSQSQLIFAADATASTAQTITVTAIDDSIYLESNTLESVSVAIGDKAVAPPLPPPPSPPPVVEVPAPSNLQISSTVEGNVLVWNASTAALTWTDTVRVGITECDRAYTYSVRNMAGGVRSNEVTGTIPCVLEEPKEDITDPDPNTDATDNTDTTLPNTDATDNTDTPPPNTDATDNTDTPPPNTDATDNTDTPPPNTDGTDNTDNTDPDNPHSGDSETELDLSALIRMIPGFENLSVEQLADGELLFTAPDKSVMAAFVILSNERPTLVLSLSNGVILRTVPGLMPKAPWESVLAALGIKMTGMQSGGNWLFEGHGISYTPMPCDSGAVSLTFEHDGMKYQQNLHPALADMAMVQTYLQQNAGVQLEPRGQGELGVEGTAIKDSDKDFSLSYPNGMQQSTCITSPLESSNAESTSRKKAQSAPAVEESKEEAEATQWLDPYQARYYPANGTYLGYHTTDGHFYLYQPELYGENPYLVGKLSELLFLAQEAGFGTKEGSLPGGGSVCYCDLMVYGGSKSGGSIKYRDAVNTKIIMSPSIQYRYYAWVTFYPINNIELGESAPALNVSLPARTVQTITFDTVPEKTADDPASAMLEFEVKKAVVSLSLAEDISVLKGNQLINFPALDRASVSNINFPAISSSSISYNAAADVTQSIQISAVQVYNGRVSSLYLNSNNLSLSGQIPVALANLSQQLNLSELLLSNNRLTGTIPDLSKIPLGGPYDLAGVTADKTATGYPNDTQILNASASSGLAVSYSVLQETAPGSSQTLTATASSGLTVNYSDISYGQPAPTLSATVTPATLIDSPSYANLNFTVTAKRDGAVVINPVALSVWVADASIQEGSPGGIGLMVTEMEDAPVDDTIPHGTKWSFIKATLNGSVTMTLTPDTRLQTDVTTVTFAPSSISAVEGGATGSYSISLNVEGAHSSSIHHSIKIGDGASAKDSHGYYIYRSDKKDQVFANPTEDSGGVIIPVQPDVTDNMDNTENPNDATDPEETNSQTPSFKLSADGSGASMWPEWNIQRVADETPLGLMLYPHWSLVPNAGSGSFNISPKADYERVMNWAEAYFSEILPAP", "metadata": {"id": "A0A251X5T9", "cluster": 6630154, "interpro_all": ["IPR037160", "IPR003961", "IPR036116", "IPR013783", "IPR001611", "IPR032675", "IPR041286"], "interpro_used": ["IPR041286", "IPR003961", "IPR001611"], "interpro_unused": ["IPR032675", "IPR036116", "IPR037160", "IPR013783"]}, "task_type": "infilling"} {"instruction": "The protein features a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein is a member of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It originates from Endomicrobiia bacterium and is connected to UniProt keyword Isoprene biosynthesis and Transferase.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 4075, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 22970, 2037, 16239, 4913, 15129, 3907, 1019, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 26690, 1021, 8132, 1930, 13763, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MKIYLKAPAKINFFLEIKNKRADGYHNLLTKNTISLECNDKSLYAYKTNIVYKAAMAVKKHYNTSSDAASTLKALAKLWNIKTKKDELEQIATPLKSAGKLNIVLVNPGFDVLTADIYKKIKFPLTNQAKIRLEEFIFPNYPEILEIKRVLNKLCCASLMSGSCGWKIWFVTTIDTSFHSLFPSTQSQSSGIVESIMQTVSLYDELSFEDKGVKIYLKKEIPIGSGLGGGKLGADVPFFLTGGTALCEGIGEIVTHIIKNLIFNNSFNKKEAFKSCFNGATVFGILDSDAKTEKLKSRLNR", "metadata": {"id": "A0A9P3AV53", "cluster": 7054998, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "infilling"} {"instruction": "Generate a complete amino acid sequence given the following functional description of a protein that will be able to perform the described role. The desired function is: The protein is categorized in the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. It is produced by Cladocopium goreaui.", "tokenized_instruction": [2, 5655, 43, 4080, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 1977, 10234, 1922, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2176, 1977, 4152, 2007, 23415, 24724, 10984, 1989, 20380, 5376, 15444, 18, 3], "output": "MKSKEKHLYLCLTIPTTDTEFNGIVTELREVFAAVHILPANERRKGNQDLKQKRTRKVEHVQNVGSSLVDRLLKLRGESGSVKSHRWRDPSPSKKLGLQRHVFGLNVPTVLRETLLVELTMVRFLAHDDDGAPSPVVDDEPEEEAEAVEVEAKKEERAGRSKIATLAARLCADQCLGLRSKTWNAGSEGQRREQQRGLITFSVCRSIVLKPLKKSVRHAMPRGGRPGLRRAWMLPSVCIIVELLARRPKLLGFGTVSNLDPFKSRAASSLSSLSPAERELERKLRSASEWEVVDAAVSSYTGNSSRIYVLAMNAAIHYDQLLQGASLYRKCKESCQQDSFCYSTALRIFGQLEDTERVCEVYQEALKDCGLNGHLAMSRISAAARVADVKTVAQVLDQMESRRVDIDLYHLTSAIRACSDFESKERHLVAEYFFTQIHELRLQPDTAVFSSMVATQWQAPLPVIDSLYIDMKNMQVEPDKLFAELYLTTVLQKPRGQIWDRNNKFLESVLQNKPLDRVKAAQNALLDFHDANVTLSRLCKDIDYVLRQRYKPPDSHDPYL", "metadata": {"id": "A0A9P1DWG3", "cluster": 8966180, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein includes a YegS/DAGK C-terminal domain that forms the C-terminal structural component of lipid kinases, including bacterial diacylglycerol kinase and eukaryotic sphingosine kinase. It adopts a beta-sandwich fold related to NAD kinases and helps form the active site cleft for the phosphorylation of substrates like phosphatidylglycerol. Furthermore, the protein is assigned to the Diacylglycerol/lipid kinase family, which comprises enzymes that catalyze the phosphorylation of lipids, including the conversion of diacylglycerol (DAG) to phosphatidic acid and phosphatidylglycerol kinase activity. Predominantly found in bacteria where they recycle DAG for lipoteichoic acid synthesis, these kinases show specificity for long-chain DAGs, while eukaryotic members may regulate sphingoid base production and cold stress responses. Also, the protein incorporates a Diacylglycerol kinase, catalytic domain that catalyzes the phosphorylation of diacylglycerol (DAG) to phosphatidic acid, thereby modulating the balance between these signaling lipids. This conserved catalytic region is present in various lipid kinases, including ceramide and sphingosine kinases, across bacteria and mammals. It occurs in Desulfobacteraceae bacterium and is associated with UniProt keywords Phospholipid biosynthesis, Magnesium, and ATP-binding.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 5921, 43, 5293, 4874, 19, 18815, 1040, 45, 17, 4262, 3418, 1988, 4952, 1920, 45, 17, 4262, 4346, 4594, 1927, 4486, 7784, 16, 2710, 4543, 29527, 4016, 1930, 10825, 26113, 4016, 18, 2176, 24032, 43, 4666, 17, 18038, 3728, 2712, 1942, 6577, 7784, 1930, 12612, 2386, 1920, 3500, 3200, 14649, 1958, 1920, 4050, 1927, 6249, 3189, 10951, 18207, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 29527, 19, 4486, 4016, 3416, 16, 2154, 12936, 5038, 1988, 18170, 1920, 4050, 1927, 8238, 16, 2710, 1920, 7309, 1927, 29527, 12, 18815, 13, 1942, 2766, 8525, 1935, 2687, 1930, 10951, 18207, 4016, 2455, 18, 7700, 2435, 1922, 4802, 2597, 2611, 12381, 1021, 18815, 1958, 3178, 7229, 2108, 8643, 2687, 4271, 16, 2144, 7784, 2146, 4896, 1958, 2815, 17, 4659, 18815, 1036, 16, 2679, 10825, 4678, 2278, 5741, 13502, 2642, 5170, 3372, 1930, 6685, 3071, 3387, 18, 2222, 16, 1920, 2213, 19683, 43, 29527, 4016, 16, 6804, 3418, 1988, 17097, 1920, 4050, 1927, 29527, 12, 18815, 13, 1942, 2766, 8525, 1935, 2687, 16, 6113, 10871, 1920, 6766, 2192, 2144, 3197, 8238, 18, 2052, 5305, 6804, 3031, 1977, 2481, 1922, 3425, 4486, 7784, 16, 2710, 16926, 1930, 26113, 7784, 16, 3436, 4802, 1930, 9902, 18, 2176, 5110, 1922, 30311, 5883, 9914, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 14608, 8132, 16, 13148, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MHTVAIVNPAAGGGPPTPVWWTAGPRHAEHLAFEVINGLWREAEGVLPSVRLGVSLREKLATALAGPCASVDVGACFGFDAAVIQRLNSQRLKLRGDGEAVATEALLFAAGIGTSFGGGMRVWGERMGRLELLRLFPKIYSGRHGTTPIELEIRPRALRIACAGVKTRAFRKLAGLAAALGEGPAKARREGVERVVVVGGDGTLGIVPVGTGCDYGRNFRLSGMDGRPYPRVFLNVLGRLPYLFATLREMLRAGGCTVTGTVITPDGRLDAGRFQLLGHPKVRSRLARSAALSAAPAAWVEAEGELI", "metadata": {"id": "A0A3N5YGW5", "cluster": 11529676, "interpro_all": ["IPR017438", "IPR005218", "IPR001206", "IPR050187", "IPR016064", "IPR045540"], "interpro_used": ["IPR045540", "IPR005218", "IPR001206"], "interpro_unused": ["IPR050187", "IPR017438", "IPR016064"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein incorporates a Ribosomal RNA small subunit methyltransferase E (RsmE) methyltransferase domain that catalyzes the specific methylation of uridine-1498 in 16S rRNA within the 30S ribosomal subunit using S-adenosyl-L-methionine (AdoMet) as a donor. This C-terminal catalytic module features a deep trefoil knot structure responsible for cofactor binding and enzymatic activity. It typically functions in a dimeric configuration to facilitate proper substrate recognition and catalysis. Moreover, the protein is categorized in the PUA-like superfamily, which constitutes a conserved RNA-binding motif with a pseudo-barrel fold found across archaea, bacteria, and eukaryotes. This domain is integral to enzymes involved in ribosome biogenesis, translation, and the post-transcriptional modification of tRNA and rRNA. Also, it is part of the Alpha/beta knot methyltransferases superfamily, which encompasses enzymes containing a deep, rare \u03b1/\u03b2 knot structural domain essential for RNA methylation. This fold is characteristic of S-adenosyl-L-methionine (SAM)-dependent enzymes, including the SPOUT and EMG1/NEP1 families, facilitating the modification of RNA substrates. It is present in Galactobacter valiniphilus and is connected to UniProt keyword Cytoplasm and rRNA processing.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 19683, 43, 11196, 3146, 2858, 5903, 16478, 47, 12, 4366, 3870, 13, 16478, 3418, 1988, 17097, 1920, 2487, 5547, 1927, 26104, 17, 14094, 1025, 1922, 11209, 9067, 2651, 1920, 27755, 11196, 5903, 2193, 61, 17, 29283, 17, 54, 17, 12417, 12, 2041, 14080, 13, 1966, 43, 6282, 18, 2052, 45, 17, 4262, 6804, 9059, 4075, 43, 6515, 2171, 15282, 1970, 26646, 3170, 5061, 1958, 15155, 2743, 1930, 8145, 2455, 18, 2176, 5745, 4088, 1922, 43, 18150, 9674, 1942, 6628, 3405, 4510, 5708, 1930, 15408, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 6612, 1019, 17, 3189, 13975, 16, 2154, 14879, 43, 5305, 3146, 17, 2743, 5219, 1956, 43, 11520, 17, 19560, 3728, 2435, 3436, 21501, 16, 4802, 16, 1930, 15021, 18, 2052, 3418, 1977, 12328, 1942, 5038, 3286, 1922, 12794, 13008, 16, 6410, 16, 1930, 1920, 2753, 17, 5224, 6295, 1927, 10089, 1930, 9067, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 4595, 19, 4666, 26646, 28253, 13975, 16, 2154, 21569, 5038, 3165, 43, 6515, 16, 5844, 160, 19, 161, 26646, 4346, 3418, 4415, 1958, 3146, 5547, 18, 2052, 3728, 1977, 6293, 1927, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5038, 16, 2710, 1920, 18055, 1984, 1930, 13952, 1009, 19, 26046, 1009, 5767, 16, 12440, 1920, 6295, 1927, 3146, 6249, 18, 2176, 1977, 2481, 1922, 9479, 5883, 2326, 11566, 24888, 5277, 1036, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MSRQAFLDPAAAAGVAVGESFELSAAEAHHAKVKRVRQGELEAEAGVLLRVLAEELDDAAARPRFVLVQALSKQDRDLQAIVRWKDDRAAKAHAKWEHQVAAAVKQSRRSTLPPVEGGLMLVLHEAATVPLLEALGTPGDPERPGAGTEVLFVVTHVLRASTAGSVALVLLLQAYGAFGAPATAPRPPATDQIDVVDGAGRRLVCEVVESCVEIGIDAVIPWQADRSALVSSKSLAARAAEVTAAGPEGGISDAELAALEAAGARTVVLG", "metadata": {"id": "A0A399JDS1", "cluster": 12984455, "interpro_all": ["IPR029028", "IPR015947", "IPR006700", "IPR046886", "IPR046887", "IPR029026"], "interpro_used": ["IPR046886", "IPR015947", "IPR029028"], "interpro_unused": ["IPR029026", "IPR006700", "IPR046887"]}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein should contain a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Also, the protein should contain a UvrB, YAD/RRR-motif-containing domain that is located at the C-terminus of the ultraviolet resistance protein B (UvrB), playing a role in mutational resistance against UV light. This approximately 40-amino acid region is characterized by the presence of conserved YAD and RRR sequence motifs. Additionally, the protein incorporates a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. It is derived from marine metagenome and contains UniProt keyword associations DNA damage, Excision nuclease, and DNA repair.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 3066, 5531, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 5819, 16007, 16, 26169, 1007, 19, 5162, 1005, 17, 5219, 17, 3165, 3418, 1988, 1977, 4810, 2019, 1920, 45, 17, 7822, 1927, 1920, 17077, 3554, 2213, 44, 12, 5819, 16007, 13, 16, 14797, 43, 2770, 1922, 13736, 3554, 3316, 5819, 3696, 18, 2052, 3993, 3040, 17, 3835, 2687, 3031, 1977, 4378, 2007, 1920, 2990, 1927, 5305, 26169, 1007, 1930, 5162, 1005, 3244, 8277, 18, 4950, 16, 1920, 2213, 19683, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2176, 1977, 3595, 2037, 10789, 16552, 2225, 1930, 5461, 20709, 11121, 2538, 5253, 2678, 4293, 16, 10940, 16230, 16, 1930, 2678, 5059, 18, 3], "output": "LGATGTGKTFTIAHVIVEHGRPTLVMSHNKTLYYDYYQPEAYVPATDTYIEKDASINEDIERLRLRATSSLMVDYKSLMLHLEVGSEISRRDMLKGLVDIQYKRNDYLFERGKFRVRWGDEIERITRFDPLTGEVISTLNRTAIYPASHYVTRRRTIEEIEAQRLEQRTKFDIEMMLQIGTCPGIENYSRYTSQRQSGEPQINGMYKGDRSRKLTLIEHGFRLPSALDNRPLKFDEWAELVPRTIYVSQIIRPTGLVDPPVDVRPVKGQVDDLLAEIRDRETKGERVLVSVGVRVRYMHSEVDTIERMEILRSLRLGKIDVLVGIDADKEGFLRDARSLIQTIGRTARNVNMKRCLDETSRRREVQIAHNEEHGIKPESIQKSLEAAQLYGELKSLFPNNAVEYFVSEREDVIVVASVSCIYGLGNPGDTVEVFPAYEEQAIRVELAPLIREELHDHVAVLRTQEKLLRPACLLDYFPSDFLTIVDESHVSIATPGDWELDRVSGVVIETTLTKRMAEDLSEYLQNLLREGLDLPEVSLVAILGKAIMYADKVTAS", "metadata": {"id": "A0A382EK07", "cluster": 13258618, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR014001", "IPR024759", "IPR001650"], "interpro_unused": ["IPR041471", "IPR006935", "IPR027417", "IPR004807"]}, "task_type": "infilling"} {"instruction": "Function:\nThe protein carries a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. Moreover, it is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein is included in the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. It has been detected in Pseudomonadota bacterium and contains UniProt keyword associations ATP-binding, Nucleotide biosynthesis, and Transferase.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 16252, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2176, 2258, 2252, 3330, 1922, 11520, 3947, 12595, 3857, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MTAASEHPGRGAFITLEGVEGSGKSTNLAFVAEREVLLAGDPGSMPPLTELLLMFAARAAHLRELVWPALIASLEASVQGAFRPDLTLLLDASWQGTRTRRDQRGTADLDRARGEPGRFRVIDAGCELPEVQEALSRALDVFLESFQKSIASDLRAAGKTVVMTREPGGVPVAERIREQGQWVVCDRFTDASYAYQGGGRGLPVTLRFELEGRDFFDRVRACY", "metadata": {"id": "A0A6H9I3Q3", "cluster": 15574454, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR039430", "IPR027417", "IPR018094"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We aim to build a protein that does the following:\nThe protein is associated with the Nucleic acid-binding, OB-fold superfamily, which utilizes a conserved five-stranded $\\beta$-barrel motif to bind single-stranded nucleic acids or oligosaccharides. This versatile domain is found in diverse proteins, including ribosomal subunits, DNA ligases, and toxins, where it plays essential roles in DNA replication, repair, and translation. Moreover, the protein should feature a TRAM domain that adopts a simple $\\beta$-barrel fold and is predicted to bind tRNA to deliver RNA-modifying enzymatic domains to their targets. This module is characteristically found in translation machinery proteins, including the TRM2 and miaB families of tRNA-modifying enzymes and archaeal RNA chaperones. Additionally, the protein is associated with the Ribosomal protein uS12 methylthiotransferase RimO family, which is a radical S-adenosylmethionine enzyme that catalyzes the post-translational methylthiolation of the aspartate residue at position 88 in ribosomal protein uS12. This modification is found in many bacterial species. It has been detected in Armatimonadetes bacterium Cent15-Ar3.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 1977, 2458, 1956, 1920, 11079, 2687, 17, 2743, 16, 2384, 17, 3728, 13975, 16, 2154, 18127, 43, 5305, 3628, 17, 10338, 8, 38, 4666, 8, 17, 19560, 5219, 1942, 4566, 2957, 17, 10338, 11079, 4576, 2014, 22012, 18, 2052, 20425, 3418, 1977, 2435, 1922, 6445, 2697, 16, 2710, 11196, 6991, 16, 2678, 22423, 16, 1930, 13599, 16, 2597, 2176, 5705, 4415, 5456, 1922, 2678, 5158, 16, 5059, 16, 1930, 6410, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 23179, 3418, 1988, 24032, 43, 5288, 8, 38, 4666, 8, 17, 19560, 3728, 1930, 1977, 4396, 1942, 4566, 10089, 1942, 3971, 3146, 17, 12691, 8145, 4682, 1942, 2310, 4845, 18, 2052, 9059, 1977, 6293, 2169, 2435, 1922, 6410, 10853, 2697, 16, 2710, 1920, 28402, 1028, 1930, 24173, 1014, 5767, 1927, 10089, 17, 12691, 5038, 1930, 22367, 3146, 18098, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 11196, 2213, 2022, 3112, 4963, 22523, 14165, 14764, 1037, 3416, 16, 2154, 1977, 43, 6917, 61, 17, 29283, 23568, 11215, 4113, 1988, 17097, 1920, 2753, 17, 8414, 4963, 22523, 10173, 1929, 1927, 1920, 12878, 6181, 2019, 3507, 5744, 1922, 11196, 2213, 2022, 3112, 18, 2052, 6295, 1977, 2435, 1922, 3086, 4543, 3038, 18, 2176, 2258, 2252, 3330, 1922, 6011, 1968, 3947, 2873, 14652, 14061, 3208, 3962, 17, 2245, 1010, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "SQEPGTPSHDMPGQVQEISLEVNESWIGRSLKVLVEAQQFVFFKGEARPGDLVDVEVKSRKKMEPLRMAPPKAPQSQKVKEDRYHQLMSLQDGWLIGRSHRDAPDIDGTEAEPYDLFGQQVGSSV", "metadata": {"id": "A0A254QG72", "cluster": 19663103, "interpro_all": ["IPR012340", "IPR005840", "IPR002792"], "interpro_used": ["IPR012340", "IPR002792", "IPR005840"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein is classified under the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. Additionally, the protein is grouped in the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It occurs in Desulfofustis sp and carries UniProt keyword assignments Cell inner membrane, Transferase, and Phospholipid metabolism. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 5110, 1922, 30311, 4199, 2892, 1937, 2056, 1930, 16252, 20709, 11121, 2538, 18306, 2024, 6671, 3260, 16, 13763, 16, 1930, 14608, 4714, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MDKPKSKKGMARLVAALRYSLQGIVACYRNEEAFRQEVIVFGVLLVVIILMPVSGMIKLMLFSINSLVLIVELLNSAVEAIVDRVSPEYDELAGRAKDMGSAAVLLSLIAAAAVWAYALYQVI", "metadata": {"id": "A0A7Y2UPB0", "cluster": 21046923, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR033718", "IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein is assigned to the Mevalonate kinase family, which plays a key role in the synthesis of isopentanyl pyrophosphate, a common intermediate for pathways including cholesterol biosynthesis. It is also involved in mevalonate catabolism and is found across eukaryotes, archaea, and bacteria. Also, the protein should have a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is derived from Candidatus Agrococcus pullicola and is associated with UniProt keywords Cytoplasm and Transferase.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 6304, 1942, 1920, 21750, 20807, 5791, 1021, 4016, 3416, 16, 2154, 5705, 43, 3834, 2770, 1922, 1920, 4271, 1927, 10301, 10653, 16323, 1024, 24937, 16, 43, 3059, 6129, 1958, 3873, 2710, 5463, 8132, 18, 2176, 1977, 2222, 3286, 1922, 21750, 20807, 5791, 1021, 19480, 1930, 1977, 2435, 3436, 15021, 16, 21501, 16, 1930, 4802, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 3595, 2037, 14550, 1031, 1957, 25277, 4879, 2437, 1957, 10875, 29902, 1930, 1977, 2458, 1956, 20709, 11569, 5239, 1930, 13763, 18, 3], "output": "TATAVARVRQRRDHRPAFVDSRIEKLADLTHSAAEACQAGSIHLVGAAMNEGQEALADLGVSSNSLDRLVESARDAGAVGAKLTGGGMGGCIIALAPTGGADALAAELRSAGATRTWISTMEAAA", "metadata": {"id": "A0A9D1YWD6", "cluster": 22324542, "interpro_all": ["IPR013750", "IPR036554", "IPR006205"], "interpro_used": ["IPR006205", "IPR013750"], "interpro_unused": ["IPR036554"]}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein contains a Internalin B-like, B-repeat repeat that facilitates protein-protein interactions, likely by binding host cell receptors to enhance downstream signaling via the receptor tyrosine kinase Met. Comprising 70 to 78 residues, this domain occurs in varying copy numbers in *Listeria* internalins and other bacterial proteins, serving as a structural module for host-pathogen recognition and invasion. Moreover, the protein is categorized in the Listeria-Bacteroides repeat domain superfamily, which comprises a conserved core region of approximately 43 residues typically arranged in tandem arrays within bacterial surface proteins. These repeats are characteristic of *Listeria* internalins, playing a role in host cell invasion, and are also found in varying copy numbers in *Tannerella* and other bacterial species. It is native to Bifidobacterium aemilianum.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 5461, 43, 4495, 1921, 44, 17, 3189, 16, 44, 17, 6865, 6865, 1988, 11374, 2213, 17, 2213, 3719, 16, 3205, 2007, 2743, 4423, 2024, 4086, 1942, 4826, 5863, 3197, 3454, 1920, 3148, 6941, 4016, 2130, 18, 10351, 3895, 1942, 5440, 4248, 16, 2052, 3418, 5110, 1922, 7155, 6983, 4630, 1922, 14, 23914, 14, 4495, 2925, 1930, 2303, 4543, 2697, 16, 13915, 1966, 43, 4346, 9059, 1958, 4423, 17, 7055, 5708, 1930, 6254, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 23914, 17, 27978, 6865, 3418, 13975, 16, 2154, 12936, 43, 5305, 4728, 3031, 1927, 3993, 3941, 4248, 5745, 14940, 1922, 10361, 10517, 2651, 4543, 3154, 2697, 18, 2144, 9569, 2032, 6293, 1927, 14, 23914, 14, 4495, 2925, 16, 14797, 43, 2770, 1922, 4423, 2024, 6254, 16, 1930, 2032, 2222, 2435, 1922, 7155, 6983, 4630, 1922, 14, 22669, 1959, 11560, 1019, 14, 1930, 2303, 4543, 3038, 18, 2176, 1977, 6196, 1942, 21724, 12022, 10194, 7395, 12191, 24961, 18, 3], "output": "MDEENGAVTWQATNIQIDDVVTYKFKHEAHVWLSGIDVATLQSDVDITIDDGEILGDYMPTGNALPTRTGHCLSWVYASNDMEWTMEYDGSGSNTQDATVGSAYGAILESMAPAYTRTHNWLSGWSQQADGSGPTDGHSPATCVEYVNPDGASMVPGPTAPSQAGAVFRTQDVKWARDRRTVPFAQEGGVTPSIVPAVSADGLVLKEHWTPNPHDVNFHHHDWNLVADTLPDNDLDLYAQWLKQRKVTFD", "metadata": {"id": "A0A366K8R8", "cluster": 23689855, "interpro_all": ["IPR013378", "IPR042229"], "interpro_used": ["IPR013378", "IPR042229"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein belongs to the Putative beta barrel porin-7 family, which comprises proteins predicted to form transmembrane beta-barrel channels, initially identified in *Rhodopirellula baltica*. These proteins likely function as porins to facilitate the diffusion of solutes across the outer membrane. It is produced by Planctomycetales bacterium.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 14440, 1942, 1920, 6770, 4666, 19560, 4572, 1921, 17, 27, 3416, 16, 2154, 12936, 2697, 4396, 1942, 2386, 9117, 4666, 17, 19560, 5628, 16, 6370, 2899, 1922, 14, 11490, 2011, 2952, 11560, 5617, 4641, 21788, 14, 18, 2144, 2697, 3205, 2347, 1966, 4572, 2925, 1942, 6628, 1920, 6601, 1927, 27993, 3436, 1920, 7642, 3260, 18, 2176, 1977, 4152, 2007, 4720, 2341, 13386, 3949, 1918, 14061, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MRVSWTNRHGLVALTATLVVLQGVGQTKAQFAPLGNPQNQNQVYTPSQYQAYPQIPAYQPVSQAQVPAYGQVAPRYATPQYTAMAYQPHSAPPIEAMPTEVQGGGYPEAGVGCNNSTGCATGGCATGGYGYNTFSNECYGNYGNCGHGGQLLGCRTGCPLAFSTPTGNVPPYYPTDTETVLTTSNVDIGYQGGAEVRFGATLGGCGYDSCGGGACGTCCGCGPTHAWEVVYWGIFDDSATSIVTDLTTDANRVYGNVWYDYGPPTVDNTAPYDVEVRSFTTRSTFSAQNIELNLLRLPTICGGGGCGFRSDYERMDTNGTGFLAYNAEVDNQLIGFQLGCNGSYRMGRCGRWALMDSPTGGVVRFANGTQSTFNVESDKDDVAMIGELRLGGSYQYSCNQIPTAFITPDQVGKVASNGSLLLHGLQAGVECTYQAQAAPQTQAYQPQVQVQPQNTTPQYTACQAAPAVNYDSYPGRRWFGGVYGLLMERDDANCVRAFGGYSPCGDACGGGSMMDFRGLEYNPGTGYRSVSNCSRYEVTTLAGARFMRFDEDFYHCNSNVGIYGNHIEVHQWWRFYGGWRVIGVSGIALATD", "metadata": {"id": "A0A954XIU4", "cluster": 24410869, "interpro_all": ["IPR011446"], "interpro_used": ["IPR011446"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence of a protein with the following function look like? Here is the function: The protein falls within the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein should include a AAA domain, group 14 domain that belongs to the AAA superfamily and features a characteristic P-loop motif for nucleotide binding. It typically functions as an ATPase, utilizing energy from ATP hydrolysis to drive conformational changes for the remodeling of macromolecules. It originates from Candidatus Ornithospirochaeta avicola.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 1920, 2213, 12182, 2651, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 13835, 3418, 16, 2210, 2607, 3418, 1988, 14440, 1942, 1920, 13835, 13975, 1930, 4075, 43, 6293, 58, 17, 5881, 5219, 1958, 5489, 2743, 18, 2176, 5745, 4088, 1966, 1925, 9444, 16, 10232, 3844, 2037, 4498, 9128, 1942, 9265, 8523, 2840, 1958, 1920, 8378, 1927, 20625, 18, 2176, 22970, 2037, 14550, 1031, 1957, 23685, 3106, 10602, 25588, 9215, 22731, 4879, 5148, 18, 3], "output": "MYISRKVDREFEKIIENNDAILIYGFFKSGKSTLLRNALKKRKEKTIILTAKESAYEKNLLAFAEKADRLISVEKTSSLFSLFSLFNEREEKVIFVIEEIENIRKQEDEIKRMLKERGENTKIILTTASLDFYNDLSSSRYLDKCSFIPTFEYSEAESFYSKLNSKDKLLFYSVFGSLPYVNMLINEEESLKKNIRNIFIAKSSPIHPYMLYEITKNIGKRSYAYDILSELGSEYKTYSDLLPSLYQENNGLLDKQLSVLLGEGLIEKINPINKIGNRKSRYYCIKDGAVAFYYSYIYPYLDEISELSEKEFFELHVERELGLFTDRMISRALNSYFKRTYMADESGIFDDDGVVFNSSFLKNGEYTLTFIRTNDGKMTSDEAEGIKCKYKKAFFSLNGFDFNAFDVELLSPKDLYKERI", "metadata": {"id": "A0A9D1PUP7", "cluster": 25503494, "interpro_all": ["IPR041682", "IPR027417"], "interpro_used": ["IPR027417", "IPR041682"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein is included in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It occurs in Staphylococcus lloydii and contains UniProt keyword associations ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 5110, 1922, 13452, 26911, 2584, 3907, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MPKVIGLTGGIATGKSTVSEVLSVHGFKIVDADVASRKAVEKGSEGLANVKAAFGDDAIDENGEMDRAYVGDVVFNQPEKRLELNEIVHPIVHDIMEKEKNDYLNEGYNVIMDIPLLFENELQDTVDEVWLVYTSESIQIDRLMERNNLSLEDAKARVLSQISIDKKRRMADHVIDNRDSKLDLKQNLESFLIEQGYIDEAEHL", "metadata": {"id": "A0A7T1FAF0", "cluster": 27687076, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Furthermore, it is part of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, the protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is identified in Leptospira johnsonii and contains UniProt keyword associations Cytoplasm and rRNA processing. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 2899, 1922, 24060, 11979, 13890, 3907, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 1930, 9067, 4587, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MENELEPVHYSVLYREILSFFLSVFDKDRELLFLDGTAGEGGHSLLLLEQFPNSKLVLVDRDSVMLSRAQARLSAHSSRVIPIEANFSDLDLEFLNGFGITNPPDGILLDLGISTFHLLHAGRGFSFRENEPLDMRLSSSGGISAEDVINTYPEKALSKIFYEYGEERWTKKIVEAILERRRHARIGYSGDLAQLVSRVIPRKFWPPGRHPATRVFQALRIEVNQELLHIEIGVKKLLDLVAKGGLLQVISFHSLEDRIIKNLFRDYARNGEAKLLTKKPVLPTEAETKENPASRSAKLRVIHKSLPTDTEDEEEDEEE", "metadata": {"id": "A0A2P2D372", "cluster": 3380937, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein should contain a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. Moreover, the protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is found in Pseudoxanthomonas winnipegensis and is classified with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 3066, 5531, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2435, 1922, 11520, 11414, 4905, 25808, 9259, 14383, 29449, 6541, 8134, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSPRPLEHRHFLSLEGGEGAGKGGTPLAERMRDIVLQPGDEALAPEAELLGAWVVSDRFTDSSYAYQVHGRGLDRALVRARTAGRDLWPDRIEREQDDFFERVREGYRRRVAAAVREAVQAWLDTQATSALGAIRETLQAAGHEVLLTREPLMFAARAQHVQRVIAPALAREDLEQRVVHVAPALTLLLDLDVRVGAQAFPQRFRVIDAAQSPQD", "metadata": {"id": "A0A4Q8LFN1", "cluster": 4069763, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR018094", "IPR039430"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein belongs to the Heterochromatin-associated chromo domain-containing protein family, which facilitates the formation and maintenance of heterochromatin by specifically recognizing and binding to methylated histone H3 lysine-9 residues to mediate epigenetic gene repression. Members also contribute to kinetochore assembly essential for chromosome segregation, DNA damage response recruitment, and RNA interference pathways including piRNA-mediated transposon silencing. Also, the protein incorporates a Chromo shadow domain that mediates homodimerization and interacts with PxVxL motif-containing proteins to facilitate heterochromatin formation. It is distantly related to the chromodomain and functions in association with it to organize chromatin structure. Also, the protein should include a Chromo domain that mediates chromatin organization and gene repression by targeting proteins to specific nuclear sites via interactions with methylated histone tails or RNA. This conserved module, structurally defined by an OB-fold with three $\\beta$-strands packed against an $\\alpha$-helix, is critical for the assembly of heterochromatin complexes and transcriptional silencing. It is native to Parthenolecanium corni and corresponds to UniProt keyword Nucleus.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 14440, 1942, 1920, 18933, 17, 2458, 3233, 1037, 3418, 17, 3165, 2213, 3416, 16, 2154, 11374, 1920, 3337, 1930, 6291, 1927, 18933, 2007, 4475, 15667, 1930, 2743, 1942, 11882, 6632, 8170, 9082, 17, 29, 4248, 1942, 8265, 8542, 2359, 10084, 18, 4678, 2222, 4672, 1942, 21563, 5957, 4415, 1958, 5597, 12707, 16, 2678, 4293, 2644, 6067, 16, 1930, 3146, 8703, 3873, 2710, 13774, 2175, 17, 3434, 18808, 8343, 18, 2222, 16, 1920, 2213, 19683, 43, 3233, 1037, 24655, 3418, 1988, 10412, 21189, 2466, 1930, 9034, 1956, 15194, 1020, 19776, 5219, 17, 3165, 2697, 1942, 6628, 18933, 3337, 18, 2176, 1977, 29448, 2712, 1942, 1920, 3233, 17166, 1930, 4088, 1922, 3279, 1956, 2176, 1942, 25681, 6338, 3170, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 3233, 1037, 3418, 1988, 10412, 6338, 5901, 1930, 2359, 10084, 2007, 5133, 2697, 1942, 2487, 4254, 3402, 3454, 3719, 1956, 11882, 6632, 18103, 2014, 3146, 18, 2052, 5305, 9059, 16, 12171, 3608, 2007, 1925, 2384, 17, 3728, 1956, 2559, 8, 38, 4666, 8, 17, 13214, 15827, 3316, 1925, 8, 38, 4595, 8, 17, 7864, 16, 1977, 4140, 1958, 1920, 5957, 1927, 18933, 5048, 1930, 5224, 8343, 18, 2176, 1977, 6196, 1942, 3131, 22467, 7794, 13578, 12856, 1033, 1930, 8852, 1942, 20709, 11121, 2538, 5607, 18, 3], "output": "MSANEEPYFGERVVPTSRYTWETVDNVHCQDLIDEYELLFDEAETDPSFDEAETGPRRWTSSSKAPKVHKMMNTKQKTVERKYQKNLKAEKIVGVQKRGDTIFTKVKEANINFKDIQEGKRLRSDGREMYFIKWKRHTNWGTSSFDEADTGSSCDEAETGPYSMSSLMANSRKRCLSKGLLLPKRNSKARQTVGVKKRGKTIFIWQGIPKVSLVLSEVACKTFPHLLLDFY", "metadata": {"id": "A0AAN9TH70", "cluster": 5256219, "interpro_all": ["IPR016197", "IPR000953", "IPR023780", "IPR008251", "IPR051219"], "interpro_used": ["IPR051219", "IPR008251", "IPR023780"], "interpro_unused": ["IPR000953", "IPR016197"]}, "task_type": "infilling"} {"instruction": "I want to make a polypeptide chain that will have the following function description: The protein should feature a DUF6697 domain that is found in fungi and currently lacks a characterized biological function. It is found in Bondarzewia mesenterica and exhibits UniProt keyword tags Coiled coil. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 13022, 4659, 1988, 2832, 2162, 1920, 2894, 2347, 8418, 30, 1920, 2213, 3066, 5961, 43, 4855, 17136, 7093, 1027, 3418, 1988, 1977, 2435, 1922, 10520, 1930, 5077, 13012, 43, 4378, 3933, 2347, 18, 2176, 1977, 2435, 1922, 5403, 1933, 6931, 17045, 1019, 16234, 1019, 1930, 9826, 20709, 11121, 2538, 14392, 17524, 9121, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MATHRASHSQGSTVDIERQRINWEQLNIYSNQQEDEIESLKKENDVLKRKILALEAKFKDRDRAITSVSRQRVDLDRGRSSLEPISQRDFLVPVKDGSRSSSSKPVRDRKAHSVKSRRATPARASSAARSARTSTHGDGQNTHHDVVDRAGRRAMPQFILDDRMSLRWYDLPQFQASFLVQPAKRGLFRKVYESISKRQSKHRGSADSYSPTPESFPGFLALNNISCPNLPTQPGQPGLCFAFLRSAKDMMTSSGDAGVYLVVRMSTKAWLYMGQYRAANPFFLTREEWTSQPDEVRQAWAKYVATSSRPAMNLMQLRAQIHLSILLDREPTEEKLGLFMRNKRVLVKDGIPIRDVINAWDHGWAMMKISAIECIGYDAEYQSRIGELKADDNSLASDGDEDVDDREDTEYEF", "metadata": {"id": "A0A4S4M834", "cluster": 8531253, "interpro_all": ["IPR046520"], "interpro_used": ["IPR046520"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. In addition, the protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, the protein is associated with the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It occurs in Parvimonas micra and corresponds to UniProt keyword Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 5110, 1922, 19995, 1980, 9259, 17020, 1019, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 3], "output": "MEFNHIPIMLNEVIDNLNIKPNGIYVKNGKLICVDQDEEALSVARDRLLKISDNVLFYDIGVSSYQIDNGQRGFSYMIDAPLDMRIFYNYGEEKWTKRIVEFIVNYRKEKLIEKRVFQAIRIEVNRELEVIRKVIDRIVKDSFKELARGCICPKELYVCVCNNKPRNPRSKSSKLRICSKIDLTVGGAGHSTEILRRIKSNFENFKEILDYFGIDKVDGVLLMDRDLKKSAFDVVNYYNSEDLEYTTFELVDIIERAIPKAVRAKGGHPAPDIVERLNKNGRLCVITFHSLEKIKILTKKPLVPSEEEMN", "metadata": {"id": "A0A0B4S0U0", "cluster": 10133387, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR023397", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, the protein is assigned to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, the protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It has been characterized in Burkholderia contaminans and is annotated with UniProt keywords Cytoplasm and rRNA processing.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 2258, 2252, 4378, 1922, 18359, 18681, 2126, 9712, 2075, 1930, 1977, 10633, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MGNELQHRTVLLDEAVESVLARLAPGGRLIAFDKDPRAIETAQGIEDAGVEKVSGVLLDLGVSSPQVDDPAGESAAEWLARASVQELTEVIRDYGEERFAFQIAKAVGHVVKTREKGKDPATRTFQAVVLDAALSLLEQGGRLVVISFHSLEDRIVKRFMLKIVSRQFPSEAEVAANPRARSAVMRIAERVTPLVTRPDGIYVDGTFGRGGHSRARFSIVHDSFASMRDALAARRGFSFRADGPLDMRMDPTRLVARRAESDRLGPLDTTGELAQIIRIHVNQELADLQQAHASAPAVDRRLPIRAVDLPSPP", "metadata": {"id": "A0A2S5E0L5", "cluster": 10610794, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein carries a Rhodanese-like domain that functions as a sulfurtransferase involved in cyanide detoxification or serves as a versatile structural module in a diverse superfamily of proteins. It constitutes the catalytic core of Cdc25 phosphatases and appears as a non-catalytic regulatory element in MAPK-phosphatases, ubiquitin C-terminal hydrolases, and various stress response proteins. Furthermore, the protein belongs to the Thiosulfate sulfurtransferase domain-containing protein family, which facilitates sulfur metabolism by transferring sulfur from thiosulfate to other molecules using a catalytic cysteine residue typically found in the C-terminal of two rhodanese domains. Members of this family function as sulfotransferases to generate thiosulfate, detoxify cyanide into thiocyanate, or contribute to the post-transcriptional thiolation of tRNA. Additionally, the protein incorporates a Thiosulphate sulfurtransferase conserved site that catalyzes the transfer of a sulfane sulfur atom from thiosulfate to cyanide, producing sulfite and thiocyanate via a mechanism involving a catalytic cysteine residue. This activity is critical for cyanide detoxification and the formation of iron-sulfur complexes in both vertebrate mitochondria and various bacterial species. It is produced by Bordetella sp. N and carries UniProt keyword assignments Repeat.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 16252, 43, 11490, 4484, 1021, 17, 3189, 3418, 1988, 4088, 1966, 43, 12585, 9961, 3286, 1922, 26164, 18169, 2014, 10634, 1966, 43, 20425, 4346, 9059, 1922, 43, 6445, 13975, 1927, 2697, 18, 2176, 14879, 1920, 6804, 4728, 1927, 23149, 19131, 1930, 5107, 1966, 43, 2447, 17, 6804, 4948, 6149, 1922, 7859, 17, 19131, 16, 6526, 45, 17, 4262, 30337, 16, 1930, 3425, 3071, 2644, 2697, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 15331, 19028, 2010, 12585, 9961, 3418, 17, 3165, 2213, 3416, 16, 2154, 11374, 12585, 4714, 2007, 21902, 12585, 2037, 15331, 19028, 2010, 1942, 2303, 4206, 2193, 43, 6804, 8666, 6181, 5745, 2435, 1922, 1920, 45, 17, 4262, 1927, 2288, 11490, 4484, 1021, 4682, 18, 4678, 1927, 2052, 3416, 2347, 1966, 5141, 14165, 1036, 1942, 5655, 15331, 19028, 2010, 16, 15289, 5169, 26164, 2460, 15331, 13796, 20660, 1021, 16, 2014, 4672, 1942, 1920, 2753, 17, 5224, 13914, 1943, 1927, 10089, 18, 4950, 16, 1920, 2213, 19683, 43, 15331, 20490, 13857, 2722, 2057, 12585, 9961, 5305, 3200, 1988, 17097, 1920, 3856, 1927, 43, 5141, 2516, 12585, 6761, 2037, 15331, 19028, 2010, 1942, 26164, 16, 7144, 5141, 2394, 1930, 15331, 13796, 20660, 1021, 3454, 43, 2856, 5884, 43, 6804, 8666, 6181, 18, 2052, 2455, 1977, 4140, 1958, 26164, 18169, 1930, 1920, 3337, 1927, 5680, 17, 12585, 5048, 1922, 2321, 13416, 6489, 1930, 3425, 4543, 3038, 18, 2176, 1977, 4152, 2007, 7570, 3695, 2057, 11560, 1019, 2056, 18, 56, 1930, 16252, 20709, 11121, 2538, 18306, 6865, 18, 3], "output": "MATFELATPDWLARHIGQEDIVLVDTRPAADGPALARLQAVLTWSLSALGIAPTSRVVVAGAQNEVNAVDAWTGERVTAAPAVAATPFTVTPQARVIDARSREEFSGQRSNAGRTGRVPGARFWDTSRELAADGRFAAAAQLAQLAGHTGAAVYPASWNEWGTSDKFPVESAAADYWAGHIPGARHLEPSLFAVTRTARVAWALAYAGVEHIVLLDGGAYLATADEVLAAVQAQAQPAGVPAVKDVVAADERAIVYCGGGGRAARTFIAL", "metadata": {"id": "A0A0S1Y0T7", "cluster": 11183844, "interpro_all": ["IPR001763", "IPR036873", "IPR051126", "IPR001307"], "interpro_used": ["IPR001763", "IPR051126", "IPR001307"], "interpro_unused": ["IPR036873"]}, "task_type": "infilling"} {"instruction": "The protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein has a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Moreover, the protein carries a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is expressed in Dialister sp and corresponds to UniProt keyword Isoprene biosynthesis and Transferase.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3950, 16, 1920, 2213, 16252, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 3198, 1922, 7588, 7263, 2056, 1930, 8852, 1942, 20709, 11121, 2538, 26690, 1021, 8132, 1930, 13763, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MGIMMITEKAYAKINLTLSVGERREDGYHEIDSVMHISLSIKEGLAPGGKANLMWEAAELFFRETGFSGGAHMELVKQIPSEALSLAALADMGARLGADVPFCVAGGCRRCEGIGEKLTPLAGWEGLPLYGLLDVCPRRRAGTAESCIKALKNKDRAALMASLSNDFEDVLFKAETSGSAFFLMAGNEVQQRKLAAKIKEERPQWYVGTAETILSISLCDEVTLTEAGGGMGGGSSDAAAVLRGLNRMTGQQVIVRPGVSISTGKAVLGETFSYLSSLCKKAMMTG", "metadata": {"id": "A0A3D5K9K1", "cluster": 11683679, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR013750", "IPR006204"], "interpro_unused": ["IPR014721", "IPR036554", "IPR020568"]}, "task_type": "infilling"} {"instruction": "The protein is categorized in the Protein polyglycylase TTLL10 family, which functions as a polyglycylase that modifies target proteins by generating glycine side chains on the \u03b3-carboxyl groups of specific glutamate residues. It acts as an elongase toward alpha- and beta-tubulin, requiring prior monoglycylation to extend the chain, whereas it can initiate glycylation de novo on non-tubulin substrates such as NAP1. In addition, the protein can be placed in the Tubulin-tyrosine ligase/Tubulin polyglutamylase family, which catalyzes the ATP-dependent post-translational modification of the carboxy-terminal tails of tubulins and other specific target proteins. These enzymes function as tyrosine ligases or generate amino acid side chains on glutamate residues, regulating microtubule properties essential for neuronal network organization, centriole stability, axoneme motility, and mitosis. It is derived from Opisthorchis viverrini.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 16115, 19602, 15499, 7382, 11560, 2930, 3416, 16, 2154, 4088, 1966, 43, 16115, 19602, 15499, 1988, 25436, 2758, 2697, 2007, 9155, 10646, 4159, 7835, 1990, 1920, 162, 17, 9943, 2671, 1927, 2487, 7627, 4248, 18, 2176, 8016, 1966, 1925, 7846, 2051, 4205, 4595, 17, 1930, 4666, 17, 9332, 16, 8887, 3432, 8914, 17038, 13796, 6055, 1942, 9676, 1920, 4659, 16, 3417, 2176, 2112, 11051, 4235, 3017, 2028, 9441, 1990, 2447, 17, 9332, 6249, 2427, 1966, 14290, 1009, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 9332, 17, 6941, 11905, 19, 9332, 16115, 26697, 27302, 2051, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 2753, 17, 8414, 6295, 1927, 1920, 15750, 17, 4262, 18103, 1927, 9332, 1036, 1930, 2303, 2487, 2758, 2697, 18, 2144, 5038, 2347, 1966, 6941, 22423, 2014, 5655, 3835, 2687, 4159, 7835, 1990, 7627, 4248, 16, 6773, 10544, 3879, 4415, 1958, 5121, 3504, 5901, 16, 23348, 2456, 5057, 16, 9980, 17800, 9254, 16, 1930, 12611, 18, 2176, 1977, 3595, 2037, 7976, 2156, 10647, 15618, 17210, 3548, 5385, 11566, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "VNHIPNCGRYQLRYGRAPSVSMAFFAAYEILTNKLGLLLSLREYERHDFFPETYIADDPVERD", "metadata": {"id": "A0A1S8WPN5", "cluster": 12765864, "interpro_all": ["IPR004344", "IPR027752"], "interpro_used": ["IPR027752", "IPR004344"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. In addition, the protein carries a Methyltransferase type 11 domain that functions as an S-adenosyl-L-methionine (SAM)-dependent enzyme with a Rossmann-like $\\alpha/\\beta$ fold, catalyzing the transfer of methyl groups to diverse nucleophilic acceptors. It acts on substrates ranging from small molecules and lipids to proteins, playing critical roles in the biosynthesis of ubiquinone, biotin, and ergosterol, as well as in chromatin regulation and arsenite detoxification. Furthermore, the protein is a member of the Ubiquinone biosynthesis O-methyltransferase family, which functions as an O-methyltransferase catalyzing two distinct steps in the ubiquinone (Coenzyme Q) biosynthetic pathway. This family includes the bacterial enzyme UbiG and the mitochondrial enzyme COQ3. It has been detected in Rhizobium sp. BK602.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 16478, 2601, 2513, 3418, 1988, 4088, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 4113, 1956, 43, 18215, 8890, 17, 3189, 8, 38, 4595, 19, 38, 4666, 8, 3728, 16, 29601, 1920, 3856, 1927, 4963, 2671, 1942, 6445, 24456, 27916, 18, 2176, 8016, 1990, 6249, 6485, 2037, 2858, 4206, 1930, 8238, 1942, 2697, 16, 14797, 4140, 5456, 1922, 1920, 8132, 1927, 5582, 22123, 16, 8622, 16, 1930, 11949, 23030, 16, 1966, 2486, 1966, 1922, 6338, 3640, 1930, 29466, 18169, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 5582, 22123, 8132, 57, 17, 16478, 3416, 16, 2154, 4088, 1966, 1925, 57, 17, 16478, 29601, 2288, 4493, 5983, 1922, 1920, 5582, 22123, 12, 22051, 59, 13, 14041, 3374, 18, 2052, 3416, 5921, 1920, 4543, 4113, 4803, 1950, 1930, 1920, 4596, 4113, 25147, 1010, 18, 2176, 2258, 2252, 3330, 1922, 13458, 23156, 2056, 18, 13702, 5127, 1028, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MSEAAKSTIDQSEVDRFSANFGRDPKSARPLEGLRVLDIGCGGGLLSASTHAKASGVPVDYRAVTAEQMEVVEHVADVEFFLTTCAKMVRPGGAENVLRWLPRGTHQYEKLVRPEEIQDRWNLSKDMDVNYMLLAKRGEMAAEWWSPTGKFKPLHKFNPVRLAYIRDHACEEPVARMGAAVVGADPSEKNIGILAEAGETFDIVLNLMFVATINRTMKAAALAIFAEKPLAASGLDIIARTGVFYSPL", "metadata": {"id": "A0A7W5SMN4", "cluster": 14252118, "interpro_all": ["IPR013216", "IPR029063", "IPR010233"], "interpro_used": ["IPR029063", "IPR013216", "IPR010233"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein is classified under the Endolytic murein transglycosylase family, which functions as a peptidoglycan terminase that endolytically cleaves nascent peptidoglycan strands to terminate their elongation. Structurally, members of this family feature an extended N-terminus topped by a globular head domain containing a conserved cleft that likely serves as the active site. It is present in Methylococcaceae bacterium and carries UniProt keyword assignments Cell membrane, Transmembrane, and Lyase.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 16239, 1954, 2002, 6185, 14818, 2127, 17038, 4879, 18801, 24605, 1021, 3416, 16, 2154, 4088, 1966, 43, 24183, 5475, 2051, 1988, 16239, 1954, 3497, 23839, 16861, 24183, 13214, 1942, 26767, 2310, 9971, 18, 12171, 16, 4678, 1927, 2052, 3416, 5961, 1925, 6091, 56, 17, 7822, 3700, 7438, 2007, 43, 20975, 4469, 3418, 3165, 43, 5305, 14649, 1988, 3205, 10634, 1966, 1920, 3500, 3200, 18, 2176, 1977, 2481, 1922, 4963, 26941, 9914, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 2024, 3260, 16, 9117, 16, 1930, 23928, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MKRKIFARLSSIFLALILWFYFAYKTVLTTPAFQNNCTIEIEKGDVNPLWLKVLAYRQQIVHKLKVGEYELTANLTIPEILTIFAEGKSKKYAIQKNQNIQSTLSKEFTDISSQLEMTEKHPEGWIFPDTYFFMQAVLTEEWQNKDQNLPYKTPHEALIMASIIEKETGAKNQTDPTVIYGMGDKYQGNIRASDLTTPTPYNTYPDKDENLYFVAKGDGSHQFSKTISEHNKAVNTFQKRKKSFTKVTDKLVAQGLVITFPEGWNLKEVLQEEKHTTDISILKRAYNKERQMIAGVFTRRLAKGMLLVIQGLPPTPIAMPGREAIYAALH", "metadata": {"id": "A0A936GK82", "cluster": 14825548, "interpro_all": ["IPR003770"], "interpro_used": ["IPR003770"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: The protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein contains a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. Furthermore, the protein can be placed in the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. It is found in Flavobacteriales bacterium and features UniProt keywords Metal-binding.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 2176, 1977, 2435, 1922, 7732, 15229, 1918, 14061, 1930, 4075, 20709, 11569, 6048, 17, 2743, 18, 3], "output": "MSSIKKDLVLAELKKINEIEIDLNIKNPTLQYKKKVEDTIKIKINFNILKKEGLPKIKGDQIPGVKNIFAIAVALSELGHKVGVIDADIYGPSMHXMFDVKVLSIGFFTDAQQAVVWRGPMAGTGDIHLSLVQSXPLTGAVVVSTPQPVIGLIENMSYFSPKELPENKYYIFGKSGVKREAADAGRPAVLQDNTPISNTVNLPPTKKVDITHKKGCSFTKLGDNDLSSDSIKNLLVFGIKSLTEIFTECGIASGKGGVGKSTVTANLVDAVPXAVEVEGKRRMSPPENXGSKALNQLLWDAHWGEIDYLLVDXPPDXALADVKKGVNMFQMPSIDVNLSEKMNIEFLGEIPIVQSVFMXLASKIDHQIKKRN", "metadata": {"id": "A0A2E8TJZ4", "cluster": 16072460, "interpro_all": ["IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR027417", "IPR000808", "IPR033756"], "interpro_unused": ["IPR019591", "IPR044304"]}, "task_type": "infilling"} {"instruction": "Generate a protein according to these design specifications: The protein is grouped in the RelB/DinJ antitoxin family, which functions as the labile antitoxin component in bacterial type II toxin-antitoxin systems, neutralizing cognate toxins such as RelE or YafQ. These proteins typically utilize an N-terminal ribbon-helix-helix (RHH) motif to dimerize and bind DNA, thereby autoregulating operon transcription while forming a heterotetrameric complex that inhibits the toxin's lethal activity. Also, the protein includes a Stability determinant domain that acts as the antitoxin component in the prokaryotic type II toxin-antitoxin module paaR2-paaA2-parE2, predominantly found in proteobacteria. It belongs to the RelB-antitoxin family but lacks DNA-binding capabilities, instead neutralizing the ParE2 toxin by wrapping around it using a structure of two $\\alpha$-helices and defined loops. Moreover, the protein is classified under the Arc-type ribbon-helix-helix superfamily, which forms a structural domain with a ribbon-helix-helix topology consisting of four helices in an open array of two hairpins. It functions as a DNA-binding module in transcriptional repressors and regulators, including bacteriophage P22 Mnt and Arc proteins, CopG, and nickel-responsive regulators. It is present in Marinobacter sp. C1S70.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2139, 1014, 19, 11687, 1013, 10310, 9754, 3416, 16, 2154, 4088, 1966, 1920, 22001, 10310, 9754, 4594, 1922, 4543, 2601, 2890, 9165, 17, 10310, 9754, 3771, 16, 12130, 15786, 13599, 2427, 1966, 2956, 2014, 26169, 1038, 1055, 18, 2144, 2697, 5745, 12561, 1925, 56, 17, 4262, 25149, 17, 7864, 17, 7864, 12, 3617, 1023, 13, 5219, 1942, 7632, 2606, 1930, 4566, 2678, 16, 6113, 24643, 4765, 15675, 3213, 2679, 7402, 43, 19732, 28959, 17118, 2796, 1988, 7042, 1920, 9165, 11, 61, 10470, 2455, 18, 2222, 16, 1920, 2213, 5921, 43, 5057, 12483, 3418, 1988, 8016, 1966, 1920, 10310, 9754, 4594, 1922, 1920, 21545, 2601, 2890, 9165, 17, 10310, 9754, 9059, 22692, 9746, 17, 22692, 8398, 17, 2096, 14806, 16, 7700, 2435, 1922, 22266, 18, 2176, 14440, 1942, 1920, 2139, 1014, 17, 10310, 9754, 3416, 2308, 13012, 2678, 17, 2743, 13693, 16, 5974, 12130, 1920, 2096, 14806, 9165, 2007, 4573, 5041, 4760, 2176, 2193, 43, 3170, 1927, 2288, 8, 38, 4595, 8, 17, 12789, 1930, 3608, 11109, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 9952, 17, 2601, 25149, 17, 7864, 17, 7864, 13975, 16, 2154, 4952, 43, 4346, 3418, 1956, 43, 25149, 17, 7864, 17, 7864, 13678, 7600, 1927, 3006, 12789, 1922, 1925, 4437, 6472, 1927, 2288, 14565, 1036, 18, 2176, 4088, 1966, 43, 2678, 17, 2743, 9059, 1922, 5224, 26446, 1930, 9098, 16, 2710, 24613, 29243, 5890, 1031, 1930, 9952, 2697, 16, 3725, 1029, 16, 1930, 16541, 17, 8487, 9098, 18, 2176, 1977, 2481, 1922, 13081, 11873, 7972, 2341, 1915, 2056, 18, 8817, 1036, 4618, 18, 3], "output": "MLHVRVDDELKADAAEKLASFGLTVSDAVRILLTRVTKEGGLPVGLTADPEAHDAWFRDKVKEALADARPTVPHQQVMDEAQALIDRKRRRA", "metadata": {"id": "U7P095", "cluster": 16495355, "interpro_all": ["IPR013321", "IPR048851", "IPR007337"], "interpro_used": ["IPR007337", "IPR048851", "IPR013321"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein carries a Ferlin C-terminal domain that defines the C-terminal region of proteins belonging to the ferlin family, including dysferlin, myoferlin, otoferlin, and fer-1-like proteins. Additionally, the protein is categorized in the Ferlin family, which facilitates vesicle and membrane fusion events, typically utilizing a series of tandem C2 domains and a C-terminal transmembrane anchor. These proteins are critical for physiological processes such as muscle repair and auditory function, with defects linked to muscular dystrophy, deafness, and infertility. It is found in Calypte anna (Anna's hummingbird) (Archilochus anna) and has UniProt annotations Repeat. What would its protein sequence look like?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 16252, 43, 4635, 7782, 45, 17, 4262, 3418, 1988, 16737, 1920, 45, 17, 4262, 3031, 1927, 2697, 10588, 1942, 1920, 4635, 7782, 3416, 16, 2710, 3890, 2070, 7782, 16, 15924, 2070, 7782, 16, 7608, 28079, 7782, 16, 1930, 4635, 17, 21, 17, 3189, 2697, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 4635, 7782, 3416, 16, 2154, 11374, 11502, 1930, 3260, 5289, 3916, 16, 5745, 10232, 43, 4696, 1927, 10361, 8453, 4682, 1930, 43, 45, 17, 4262, 9117, 13333, 18, 2144, 2697, 2032, 4140, 1958, 5005, 4028, 2427, 1966, 3760, 5059, 1930, 8401, 2347, 16, 1956, 6007, 4624, 1942, 12330, 19321, 16, 25371, 16, 1930, 15446, 18, 2176, 1977, 2435, 1922, 2570, 16314, 1021, 5112, 1019, 12, 5112, 1019, 11, 61, 2490, 9069, 14052, 1007, 13, 12, 5594, 1970, 2694, 1957, 5112, 1019, 13, 1930, 2258, 20709, 15010, 6865, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "GSIELKLHDMVRAAKSSEHCSIRMAQEEAAPRCSIFRNKRMRGWWPFIKLQDQEDEDMFPLQGKVEAEFHLLTMEEAEKNPVGLGRKEPE", "metadata": {"id": "A0A091IE27", "cluster": 22031872, "interpro_all": ["IPR037721", "IPR032362"], "interpro_used": ["IPR032362", "IPR037721"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein is grouped in the TSP type-3 repeat superfamily, which comprises calcium-binding domains found in extracellular multifunctional thrombospondins. These repeats lack typical secondary structure and are instead organized around a stabilizing core of calcium ions encapsulated by conserved aspartate-rich motifs. Furthermore, the protein should include a Domain of unknown function DUF7901 domain that is likely involved in carbohydrate binding within bacterial proteins. It is predicted to adopt a $\\beta$-sandwich structure with significant topological similarity to galactose-binding lectin-like domains, such as that of the *Clostridium difficile* surface protein Cwp84. Also, the protein should have a EF-Hand 1 calcium binding site that coordinates calcium ions in a pentagonal bipyramidal configuration using a conserved twelve-residue loop. This binding event triggers a conformational shift that activates or inactivates the target protein. It has been characterized in Planctomycetes bacterium DG_20.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10809, 1922, 1920, 14733, 2601, 17, 23, 6865, 13975, 16, 2154, 12936, 5016, 17, 2743, 4682, 2435, 1922, 5329, 20136, 16379, 3508, 2315, 2925, 18, 2144, 9569, 3630, 5939, 4067, 3170, 1930, 2032, 5974, 11275, 4760, 43, 14384, 4728, 1927, 5016, 6982, 15358, 2007, 5305, 12878, 17, 5536, 8277, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 3418, 1927, 5435, 2347, 4855, 1038, 9364, 6924, 3418, 1988, 1977, 3205, 3286, 1922, 10590, 2743, 2651, 4543, 2697, 18, 2176, 1977, 4396, 1942, 14103, 43, 8, 38, 4666, 8, 17, 18038, 3170, 1956, 2228, 16365, 6796, 1942, 15996, 17, 2743, 13468, 17, 3189, 4682, 16, 2427, 1966, 1988, 1927, 1920, 14, 21156, 19148, 14, 3154, 2213, 13198, 1034, 11068, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 8485, 17, 3897, 21, 5016, 2743, 3200, 1988, 10675, 5016, 6982, 1922, 43, 9412, 13481, 8446, 3553, 25238, 1923, 9674, 2193, 43, 5305, 12367, 17, 6181, 5881, 18, 2052, 2743, 4817, 11847, 43, 8523, 5950, 1988, 9094, 2014, 22331, 1036, 1920, 2758, 2213, 18, 2176, 2258, 2252, 4378, 1922, 4720, 2341, 25148, 14061, 9665, 41, 2036, 18, 3], "output": "MRGLNGETQAAPAQNNGGTIKNQHLPDLDSTGIDVVNSWYTLGGDGYILAEDFLCTESGYITQIDFWGSWAADIPAGEPAPLYSHPGDNLWNYTTAPGECVGSLYAETPGEGFMEPPDAYYYPADFNVWQFSCPIPEGAAVPPIAFGWKSSVEHLYDDGVWYRGTEPVNPDDWGELRYPPGHPWAGSSLDLSFQIWGEPEATEACCYPDGSCADEPDDTCIDADPLCCDDLGGVPLGAGTCSAPEACCFLDGSCMDLDPLICAAGYGGAPGGVDTVCLGDNNGNEIDDACELQVKPFYCGDTDGDAYEDVTAASTWVGGYECCNGIDDDGDTYIDGLDPQCGGLTNQDGAPWYQTDDWDDGDDDGDGLIDEDPKNDFDDDGDCPFQGDCWTSTLYGGCMEYCDEDPANGFLGFDNDQDGLVDEDGYGPLCEEQGQGVDDDGDTMVDEDPLDSPMAFWAEEGGAAVVKWEQPPDLDPTGIDVNATDIKLADDFPCTQSGEISQIDFWGSLSIHENIPAGGDPPYSHPGAQVWGYSIQCMVYREGAVPGYEGWLDPATGWYEPFGDTYVWRYECPIPEGERFDYYWGWKTTPIQDWPAILDDAVWYSGTPEWTDIWYPYSHQWSEYSLDLAFRIWTQEEATGHEVYEPHYLVKEVLLNRYRVDALEDGKNTCNDLLDNDGDDLVDANDPDCLEEHLWAEGGLHACSDGWDNGMLFAEPDGLVDADDPDCQTLTEVSDGVHWYVKPPTDSPWLEDHPQCGQYYTTDPDRYAKCVPCKIEHPTLDPVGPVNEYCGELVLNPGYCIAADSTPGVHKELDIHQATDPLGTAWWQLYPDNYYPESYYLWELTSWEDNGNGILDYSDQIDMELYYDPYGGLGKAWFHVDEVTETVCLEWDDGTDWNEKWPYTGETCDIRTWTDNDPYGVVSISDWLEISCPDFTQGEYVWLHVMDVGWDLWLSQKVVKEHQFDLSCEGETSLHKFELEMEMLVACMEWEPGDVDNLVVPNPDGMANGNTWDVDVCDSEIQTVYVDVTHGIWDFGEVLYGANYPSDFTLLADKIEWPVLMSSPATDPEYGTESEWTQTGYCTDTIDNDGDGFYDADDAGCQTPENLHAYGTCSDGLDNDKNGADDMDASKTPEHMQFPWTCNDGIDNDKDNACDDVGGCGTGLPAEPDDNGDGAPDCSPEQLKKVPPPVACASPLDNLYTPGPGNPLTVSRDLVLHCFQAANPYPTEFILAYMRPAGVHEVDLYTDNDFALDYFDGEASCPDGTSDLEVLAWNFTYDSHTGPLAGQPVAVLLEKWLNIPPGCDGSLTISKSETVVIPAGVWYTEHANGHEATFPDDWNQGPATLTPGNEVEELGANYYLTLEESTSVWEDEVFDIYCREPTDPGEDVVFAFRNFLSHRYWPDECDPDVSNNWATHQIVVEVPMDTDGDTVDGAGDACDCDSDNGGTPDGQEILRDGTEPLDETDDKALDTLDTDSDGALNWEEYWCGSDVNDDCGDDCNEFPILMFPANINMPIKQGVINPKPFQCRYDLDPDSWINAQDILMLPARVLPSMPKKCTNPQEMYPGGDPYNVTFRLSFHEQFYQEVGNIYWLNVQAVLDDPLTCGGVPQGPQTMCTVLEACWLAEIPEADLEKVDQIDEDPDPYMSGQSWPWNAGRFDFNGNTMIDACEDYAGWLGDEMPYGGYEPYEGDPGAVAFDVQEEGNTYWLDVHAYPLEEGPEPWVVATDTKEIDAPDVECKNEDDFITVAVDLGYRTHNMHLIEPGGIDPYWLGYAICIEPLTGSIDWPYGIIQNKLEPYEGEPVVDPNPENNLEEYSPGLGISNLGGDSDGDGWVTDSLDPKCWDKDGDGYSYVDEDLLFNGWLPQAGDTEFIYLYGNGDLSVGLEIVSDFHTFVEETVNTSKNIHSGGNTVYVRGLDDPDSPDDTDNCMYVPNPGQEDYDHPPPGTLDAWAYDPNIDCWANAAD", "metadata": {"id": "A0A0S7YJD2", "cluster": 22987719, "interpro_all": ["IPR057223", "IPR018247", "IPR028974"], "interpro_used": ["IPR028974", "IPR057223", "IPR018247"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Moreover, the protein is grouped in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is produced by Armatimonadota bacterium and is associated with UniProt keywords Cytoplasm and rRNA processing.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 4152, 2007, 6011, 1968, 3947, 12595, 3857, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MSAYHKPVMLSECLDALNLAPGRRVVDGTLGGGGHARAIAEKIAPGGVLLALSVRLRQVNFAEIAGAVAAEGIGGVDGVLLDLGVSSHQLDTADRGFAFRYVGPLDMRTLPEAQLARIFFEYGEESRSRRIAAEIVTRRRTKPFVTTEDEIHPATKVFQALRIAVNRELDVLEAVLRGAASVLAPGGRLVVMSYHPDPTPRAEPILTVLTKKPVVPTDTETRANPRARSAKLRVAERRESQDQDADAIAEATRTLADGLGTVMNRDDSDTQTAADLVNLVDTVRATMPYNTRAGSLEDRIVKNIFAELSGKRVETDL", "metadata": {"id": "A0A926GP34", "cluster": 23202650, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein is a member of the Spermadhesin, CUB domain superfamily, which comprises extracellular and membrane-associated proteins featuring a conserved beta-sandwich jelly-roll fold primarily utilized for protein-protein interactions and oligomerization. These domains are critical for substrate recognition and ligand binding\u2014often in a calcium-dependent manner\u2014within diverse biological contexts such as complement activation, tissue repair, and fertilization. Structurally, the motif typically contains four conserved cysteines forming disulphide bridges and serves as the defining unit of spermadhesins and a regulatory module in various peptidases. Moreover, the protein includes a CUB domain that functions as an extracellular structural motif, utilizing a \u03b2-sandwich jelly-roll fold to mediate protein-protein interactions, oligomerization, and substrate recognition. Frequently found in peptidases and developmentally regulated proteins, it facilitates diverse processes ranging from complement activation to cell adhesion by binding specific partners, often including collagen-like regions. It has been detected in Pocillopora damicornis (Cauliflower coral) (Millepora damicornis) and is associated with UniProt keywords Disulfide bond.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 6283, 24604, 29473, 16, 11585, 3418, 13975, 16, 2154, 12936, 5329, 1930, 3260, 17, 2458, 2697, 29931, 43, 5305, 4666, 17, 18038, 8988, 11560, 1012, 17, 12970, 3728, 5985, 7079, 1958, 2213, 17, 2213, 3719, 1930, 17371, 18, 2144, 4682, 2032, 4140, 1958, 4510, 5708, 1930, 5207, 2743, 230, 3868, 1922, 43, 5016, 17, 3100, 5222, 230, 2651, 6445, 3933, 11144, 2427, 1966, 5508, 2936, 16, 2960, 5059, 16, 1930, 14493, 18, 12171, 16, 1920, 5219, 5745, 5461, 3006, 5305, 22446, 7402, 2054, 23138, 2261, 18142, 1930, 10634, 1966, 1920, 11266, 5344, 1927, 6283, 24604, 29473, 1036, 1930, 43, 4948, 9059, 1922, 3425, 24050, 1036, 18, 3950, 16, 1920, 2213, 5921, 43, 11585, 3418, 1988, 4088, 1966, 1925, 5329, 4346, 5219, 16, 10232, 43, 161, 17, 18038, 8988, 11560, 1012, 17, 12970, 3728, 1942, 8265, 2213, 17, 2213, 3719, 16, 17371, 16, 1930, 4510, 5708, 18, 5467, 2435, 1922, 24050, 1036, 1930, 23130, 4335, 2697, 16, 2176, 11374, 6445, 4028, 6485, 2037, 5508, 2936, 1942, 2024, 6141, 2007, 2743, 2487, 7228, 16, 3868, 2710, 5621, 17, 3189, 3451, 18, 2176, 2258, 2252, 3330, 1922, 18660, 22538, 21086, 3787, 5670, 1005, 11110, 12, 20200, 12191, 9893, 1915, 17358, 13, 12, 4736, 2128, 8846, 3787, 5670, 1005, 11110, 13, 1930, 1977, 2458, 1956, 20709, 11569, 11830, 5403, 18, 3], "output": "MNLFFLNDPITDGDLSFTAGNSSEVNLNGWSGYFWSPNFPNNFPTNRKSTWNITVPSEKIIKLIFLKFTLVTGESDDCAGAAQDSARVFISNVASHGGKPGDFEICGQKLPPPVYSDGNFLQVTFESRDTVNKGFNASFEAIDRDPPNPIKEGGIEILGTPRFIPVKCYSLNESLRVLFVSDDTIMDFDGLGATYKRLNHSPPICPREVIPLSGSGKISSLNYPMSNYTMYTNCTWKITGSASQKIKFAFTDFALSPCAANCNSDSCSYVELYDGGSTSSPFLARFCDGSILNETLSKGHEMFVRFYSGKTADRGFEAEYHVSYDGHKKLEK", "metadata": {"id": "A0A3M6U359", "cluster": 23672948, "interpro_all": ["IPR000859", "IPR035914"], "interpro_used": ["IPR035914", "IPR000859"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein is grouped in the Carbohydrate-binding-like fold superfamily, which typically functions as a carbohydrate-binding module within enzymes such as glycosyl hydrolases and rhamnogalacturonase B. Structurally, these domains consist of a seven-stranded \u03b2-sandwich with a Greek key topology and are often located at the C-terminal end of the protein. It occurs in Planctomycetales bacterium and exhibits UniProt keyword tags Carboxypeptidase, Protease, and Signal.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10809, 1922, 1920, 10590, 17, 2743, 17, 3189, 3728, 13975, 16, 2154, 5745, 4088, 1966, 43, 10590, 17, 2743, 9059, 2651, 5038, 2427, 1966, 20067, 30337, 1930, 23120, 27395, 10366, 2051, 44, 18, 12171, 16, 2144, 4682, 3149, 1927, 43, 5260, 17, 10338, 161, 17, 18038, 1956, 43, 27568, 3834, 13678, 1930, 2032, 3868, 4810, 2019, 1920, 45, 17, 4262, 2482, 1927, 1920, 2213, 18, 2176, 5110, 1922, 4720, 2341, 13386, 3949, 1918, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 15750, 9626, 2410, 9200, 16, 7154, 16, 1930, 2733, 18, 3], "output": "MRQRTHHVAVIAALLGVATWQAAIAAEPVTSAGQPHTDAQVLLVAQNGAGVQPGVYHLASAGHGGMVRVWQARQAPPNAPLWMTGLVALAIALPLTLANKSGSTRDLALTQDGSLQGQVFPRAATTDANGKFQFAHDAALIATGPIQRGQGGAWNN", "metadata": {"id": "A0A954UTX4", "cluster": 24250223, "interpro_all": ["IPR013784"], "interpro_used": ["IPR013784"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that has the following function: The protein carries a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. In addition, the protein should contain a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. Additionally, the protein is classified under the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. It is identified in Mesorhizobium sp. M7A.F.Ca.US.006.04.2.1 and exhibits UniProt keyword tags Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 2176, 1977, 2899, 1922, 23577, 5004, 2061, 23156, 2056, 18, 55, 13827, 18, 48, 18, 2332, 18, 2022, 18, 12791, 18, 5228, 18, 22, 18, 21, 1930, 9826, 20709, 11121, 2538, 14392, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MSQERSDTLVLFGATGDLAHKKIFPALYQMVAKGTLTEPVIGVAFDAWDLKQLQARARDGIVNALGKIDEKAFAKFASLLRYVSGDYRDGATFEKLKSALGTAQRPLHYMAVPPTMFETVVQGLEQSGTAHGARLMVEKPFGHDLQSARWLNRVLHLVFDEQSIFRIDHYLGKEAIQNLLYFRFANSFLEPIWNRNYVESVQITMAEDFGVEGRGRFYDDVGCIRDVIENHLLNILLLLAMEPPVGRSADDLIDEKVQVLRAIRTLTKDDVVRGQFTGYLTEPGVAPNSPVETFAAVRFFVDTWRWQDVPFFIRAGKNMPVHVTEVVVRLKRPPLDVFDPIKPADQNYVRFRIDPQVVIAIGAQRKAPGDDMIGEQVELTALDDSKGDMPPYERLIGDAMNGNGQLFTRQDASELAWRIVGPVLGDTTPPHLYEPLTWGPADVMAGFGPPNGWIDPVK", "metadata": {"id": "A0A436CND0", "cluster": 25361689, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR019796", "IPR022674", "IPR036291"], "interpro_unused": ["IPR022675", "IPR001282"]}, "task_type": "autoregressive"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein can be placed in the UBA-like superfamily, which adopts a compact three-helical bundle fold with a conserved hydrophobic surface patch to mediate protein-protein interactions in diverse cellular processes including the ubiquitin/proteasome pathway, DNA excision-repair, and cell signaling. This superfamily encompasses functionally distinct domains such as the TS-N domain of elongation factor Ts, which catalyzes EF-Tu recycling during translation, and the C-terminal domain of TAP/NXF1, which binds FG nucleoporins to facilitate nuclear export. It has been characterized in Paragonimus westermani.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4803, 1019, 17, 3189, 13975, 16, 2154, 24032, 43, 13726, 2559, 17, 11514, 14142, 3728, 1956, 43, 5305, 7919, 3154, 7504, 1942, 8265, 2213, 17, 2213, 3719, 1922, 6445, 3689, 4028, 2710, 1920, 6526, 19, 9993, 3374, 16, 2678, 10940, 17, 5059, 16, 1930, 2024, 3197, 18, 2052, 13975, 21569, 9346, 4493, 4682, 2427, 1966, 1920, 4894, 17, 56, 3418, 1927, 9971, 2991, 4894, 16, 2154, 17097, 8485, 17, 9037, 13977, 2409, 6410, 16, 1930, 1920, 45, 17, 4262, 3418, 1927, 10167, 19, 27578, 5739, 16, 2154, 6876, 13320, 2797, 7540, 5572, 1036, 1942, 6628, 4254, 12660, 18, 2176, 2258, 2252, 4378, 1922, 8202, 3827, 8635, 23084, 9195, 14874, 1033, 18, 3], "output": "MYDQCLLQTNEMHLFKLITPCTKVEITRWNVPETEVSLWDLLIKKLERMLRMPFEKLHLSWFDGRDFCAIHGPVDLHDAMEFMQNHPGVDGCSRIFVSRDETAHSLIFSSALNESGSFDNDQDIPSRIASPSSDFDYRSSVRAVTSPRIFRRSEPTDLIPPSIVRRPVMHNHNVERTNSAPNWSSVGREPLQSSAQVETTPVDLDENDESVNQAVTTLQTMGFHQEPQLLRKLILQYEGDINKIIDTLEHTP", "metadata": {"id": "A0A8T0DY42", "cluster": 26088109, "interpro_all": ["IPR009060"], "interpro_used": ["IPR009060"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein is classified under the Amino acid/polyamine transporter I family, which comprises integral membrane proteins responsible for the uptake of amino acids, polyamines, and related compounds such as methylthioribose. Members of this family, part of the amino acid-polyamine-organocation (APC) superfamily, typically possess up to 12 transmembrane segments and include various bacterial and fungal permeases. Additionally, the protein is grouped in the Amino acid-polyamine-organocation superfamily, which comprises membrane transport proteins that facilitate the symport or antiport of amino acids, polyamines, and organocations such as arginine, ornithine, and GABA. These transporters are characterized by transmembrane helices forming a central substrate-binding cavity and play critical roles in biological processes ranging from acid resistance and energy conversion to virulence. It is identified in Mycoplasma sp. Mirounga ES2805-ORL and is associated with UniProt keywords Cell membrane and Transmembrane helix. Generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1988, 2258, 1920, 2894, 3879, 30, 1920, 2213, 1977, 5947, 2441, 1920, 3835, 2687, 19, 27883, 9054, 51, 3416, 16, 2154, 12936, 12328, 3260, 2697, 5061, 1958, 1920, 5047, 1927, 3835, 4576, 16, 27883, 1036, 16, 1930, 2712, 4300, 2427, 1966, 4963, 22523, 6658, 29258, 1021, 18, 4678, 1927, 2052, 3416, 16, 3131, 1927, 1920, 3835, 2687, 17, 27883, 17, 3090, 5980, 12, 9187, 13, 13975, 16, 5745, 7150, 2353, 1942, 2369, 9117, 7492, 1930, 3951, 3425, 4543, 1930, 8697, 6191, 2319, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 3835, 2687, 17, 27883, 17, 3090, 5980, 13975, 16, 2154, 12936, 3260, 4860, 2697, 1988, 6628, 1920, 29148, 2718, 2014, 2246, 2272, 1927, 3835, 4576, 16, 27883, 1036, 16, 1930, 3090, 28636, 2427, 1966, 9732, 16, 26918, 16, 1930, 7992, 18, 2144, 10538, 2032, 4378, 2007, 9117, 12789, 7402, 43, 4101, 4510, 17, 2743, 8568, 1930, 3918, 4140, 5456, 1922, 3933, 4028, 6485, 2037, 2687, 3554, 1930, 3844, 7309, 1942, 9304, 18, 2176, 1977, 2899, 1922, 22313, 2056, 18, 3138, 2125, 4223, 2376, 4839, 15264, 17, 2014, 1024, 1930, 1977, 2458, 1956, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MIKSEYKRKKLSSIAIMFVVMGTSIGAGIFFKAKNIADNSQQNFIMAIFSWIIAAIAVISMSLSLVEITSVENEDLSIIGWNKIFNNKLIYKMSKNFMLYLFMPLTFLFIPFLIVMFLQNSIAILSNSNSATFNTNFDWLIWFLITLSTTIYFLVITTFFAKIGSIQNLVTFVIKFIPIILVIIIGLVLIFTNNHSEISLKFNGKSVKELSKGASISNINGIGAAFGLFISISSVFFTYDGFYAGLGLQSEMKHPRHTPIVVLSGLILTTIIYLSVAISLSLNGGDISSLHDNFAKLVGKKSARITLGIINLTITIGIIGVLNNLSMWTPRFIQKLINRNEVLFSSYFKRKFNSQNKPIAGLLYSFMIIIPVITIFTLIGVYAYLPDSNLSKYGEGMDSLYNFLQLITNWCPLFSFLFVTLAIMGGLINRKTNKIATKKTKYFKASAWISIIIIFLSLFVVIILPFIDLVLLYQVENLASETKLIISRIATVVSLLIFVVFTTISTFIEIKIENNKKIFSN", "metadata": {"id": "A0A975A306", "cluster": 26246174, "interpro_all": ["IPR002293", "IPR050367"], "interpro_used": ["IPR002293", "IPR050367"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein includes a Phospho-N-acetylmuramoyl-pentapeptide transferase conserved site that constitutes key structural regions within the bacterial enzyme MraY, which is essential for peptidoglycan cell wall biosynthesis. This site participates in catalyzing the formation of the first lipid intermediate, undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-pentapeptide, from UDP-MurNAc-pentapeptide and undecaprenyl-phosphate. Also, the protein is grouped in the Glycosyl transferase, family 4 family, which comprises UDP-GlcNAc/MurNAc:polyisoprenol-P transferases that catalyze the transfer of phosphorylated sugars to lipid carriers. Members include eukaryotic N-acetylglucosamine-1-phosphate transferases critical for N-linked glycosylation and bacterial phospho-N-acetylmuramoyl-pentapeptide-transferases that initiate peptidoglycan cell wall biosynthesis. It occurs in Neisseria sicca and is annotated with UniProt keywords Transmembrane, Cell division, and Membrane. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 5921, 43, 8078, 17, 56, 17, 6894, 23010, 29085, 10921, 17, 9412, 24010, 13763, 5305, 3200, 1988, 14879, 3834, 4346, 3451, 2651, 1920, 4543, 4113, 24564, 1012, 16, 2154, 1977, 4415, 1958, 24183, 2024, 4821, 8132, 18, 2052, 3200, 17241, 1922, 29601, 1920, 3337, 1927, 1920, 2561, 4486, 6129, 16, 3075, 19384, 20367, 2199, 17, 20661, 2609, 2247, 1024, 17, 56, 17, 6894, 23010, 29085, 10921, 17, 9412, 24010, 16, 2037, 18500, 17, 6185, 16608, 17, 9412, 24010, 1930, 3075, 19384, 20367, 2199, 17, 5413, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 20067, 13763, 16, 3416, 24, 3416, 16, 2154, 12936, 18500, 17, 15397, 19, 6185, 16608, 30, 4286, 23854, 20367, 1945, 17, 58, 13763, 1036, 1988, 18170, 1920, 3856, 1927, 7199, 15592, 1942, 4486, 8974, 18, 4678, 3951, 10825, 56, 17, 6894, 22988, 17454, 17, 21, 17, 5413, 13763, 1036, 4140, 1958, 56, 17, 4624, 12082, 1930, 4543, 8078, 17, 56, 17, 6894, 23010, 29085, 10921, 17, 9412, 24010, 17, 13763, 1036, 1988, 11051, 24183, 2024, 4821, 8132, 18, 2176, 5110, 1922, 28356, 18339, 16022, 3375, 1930, 1977, 10633, 1956, 20709, 11569, 9117, 16, 2024, 8451, 16, 1930, 3260, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MFLWLAHFSNWLSGLNIFQYTTFRAVMAALTALAFSLLLGPWTIRKLTQLKVGQAVRTDGPQTHLIKNGTPTMGGSLILTAITVSTLLWGNWANPYIWILLGVLLATGALGFYDDWRKVVYKDPNGVSPKFKMVWQSSVAIIAALALFYLASNSSNNILIVPFFKQVALPLGVVGFVVLTYLTIVGTSNAVNLTDGLDGLAAFPVVLVAAGLAIFAYASGHSQFAQYLQLPYVAGANEVVIFCTAMCGACLGFLWFNAYPAQVFMGDVGALALGAALGTVAVIVRQEFVLVIMGGLFVVEAVSVMLQVGWYKKTKKRIFLMAPIHHHYEQKGWKETQVVVRFWIITIVLVLIGLSTLKIR", "metadata": {"id": "A0A2I1XCR9", "cluster": 140370, "interpro_all": ["IPR000715", "IPR003524", "IPR018480"], "interpro_used": ["IPR018480", "IPR000715"], "interpro_unused": ["IPR003524"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein should contain a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. Additionally, the protein is assigned to the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. It is produced by Klebsiella pneumoniae and carries UniProt keyword assignments Oxidoreductase.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 5531, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 2176, 1977, 4152, 2007, 23556, 12238, 1930, 16252, 20709, 11121, 2538, 18306, 27388, 18, 3], "output": "MKEKIDEGLWDTLSGRLEFCNINYFAMPPSPLARSVKGWAPPVNQRPGRRVFLDVNDTSGFTRLGEMLDQKNRVTKRSLMPSQRAWSWKNRSAPRWK", "metadata": {"id": "A0A377TV77", "cluster": 1650334, "interpro_all": ["IPR022674", "IPR036291"], "interpro_used": ["IPR022674", "IPR036291"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein carries a Hydroxyacylglutathione hydrolase C-terminal domain that forms the C-terminal region of hydroxyacylglutathione hydrolase enzymes and facilitates substrate binding through an interface with the catalytic domain. Furthermore, the protein carries a Metallo-beta-lactamase domain that adopts a characteristic \u03b1-\u03b2/\u03b2-\u03b1 sandwich fold and typically binds two zinc ions to catalyze diverse hydrolytic reactions, including the breakdown of S-D-lactoyl-glutathione by glyoxalase II family members. Beyond enzymatic activity, this domain is essential for natural transformation in bacteria like *Neisseria gonorrhoeae*, where it likely functions as a transporter for DNA uptake. Additionally, the protein should include a Hydroxyacylglutathione hydrolase MBL domain that catalyzes the hydrolysis of S-D-lactoylglutathione to D-lactate and regenerates glutathione in the second step of the glyoxalase system. This metallo-beta-lactamase fold domain contains a binuclear zinc-binding active site and exhibits broad specificity for hydrolyzing various glutathione thiol esters into their corresponding carboxylic acids. It is expressed in Calocera viscosa (strain TUFC12733) and is connected to UniProt keyword Metal-binding.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 16252, 43, 8275, 14645, 16542, 2183, 7253, 20748, 45, 17, 4262, 3418, 1988, 4952, 1920, 45, 17, 4262, 3031, 1927, 8275, 14645, 16542, 2183, 7253, 20748, 5038, 1930, 11374, 4510, 2743, 2596, 1925, 6854, 1956, 1920, 6804, 3418, 18, 3677, 16, 1920, 2213, 16252, 43, 8969, 1037, 17, 4666, 17, 23023, 3418, 1988, 24032, 43, 6293, 160, 17, 161, 19, 161, 17, 160, 18038, 3728, 1930, 5745, 6876, 2288, 7997, 6982, 1942, 18170, 6445, 26702, 5298, 16, 2710, 1920, 13630, 1927, 61, 17, 46, 17, 5641, 10921, 17, 9153, 2007, 3376, 23859, 2051, 2890, 3416, 4678, 18, 6844, 8145, 2455, 16, 2052, 3418, 1977, 4415, 1958, 4613, 7002, 1922, 4802, 3189, 14, 28356, 18339, 27702, 6802, 3336, 14, 16, 2597, 2176, 3205, 4088, 1966, 43, 9054, 1958, 2678, 5047, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 8275, 14645, 16542, 2183, 7253, 20748, 21007, 3418, 1988, 17097, 1920, 9128, 1927, 61, 17, 46, 17, 5641, 10921, 16542, 2183, 7253, 1942, 46, 17, 9456, 1930, 26362, 1036, 9153, 1922, 1920, 2812, 3537, 1927, 1920, 3376, 23859, 2051, 2433, 18, 2052, 8969, 1037, 17, 4666, 17, 23023, 3728, 3418, 5461, 43, 8768, 13821, 7997, 17, 2743, 3500, 3200, 1930, 9826, 4949, 4896, 1958, 7222, 9046, 3425, 9153, 13914, 16785, 2460, 2310, 3980, 18708, 4576, 18, 2176, 1977, 3198, 1922, 2570, 1994, 7124, 23722, 5735, 12, 3943, 9037, 8815, 16513, 6498, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 6048, 17, 2743, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MRVVPVPNQADNYAYLLIDEATQKAAVLDPYDVGKVKRYAQKEGVELESVGNLEFAREYPGVTVIGGSTAVPALTKKVEDGDEFTIGEDISVKCLTGDTLFQAGCGRFFEGNAAEMHKALSYLGTLPDSTIVYNGHEYTNTSMKFGKHVNVFMRLTSAAVQKATGETDQVTAMKKLRELKNNFRGLTTHHHHDHSGATPCHTQDSICYYATSKSKPEQPGLVFDPENPAFQKLDNLVKTEEQTCGKSTIADEKSW", "metadata": {"id": "A0A167Q5I4", "cluster": 2488810, "interpro_all": ["IPR035680", "IPR032282", "IPR017782", "IPR001279", "IPR036866"], "interpro_used": ["IPR032282", "IPR001279", "IPR035680"], "interpro_unused": ["IPR036866", "IPR017782"]}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: The protein carries a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Moreover, the protein carries a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Additionally, the protein features a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. It is found in Alphaproteobacteria bacterium TMED62 and corresponds to UniProt keyword DNA repair, DNA damage, and SOS response.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 16252, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 3950, 16, 1920, 2213, 16252, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 4950, 16, 1920, 2213, 4075, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2176, 1977, 2435, 1922, 4595, 9218, 1021, 10296, 14061, 22377, 1007, 8166, 1930, 8852, 1942, 20709, 11121, 2538, 2678, 5059, 16, 2678, 4293, 16, 1930, 17668, 2644, 18, 3], "output": "MLKINKNSINELFPTEKKGCFELINKKERDQVLLGVTGSGKTFTMANVEMKTLFPKNAVEYFVSYYDYYQPEAYDRLRHSATRSMFERKDVIIVASVSCIYGVNDQVSRDNLVKNLINMQYKRNNLSFNRGNIDKSWKIEFFGDTIENIYEVDPLTGRKISNLTTIRIKKDLEIRLSELEREKKLIEAQRGSCQGIENYSRYLSGRNPGEPPPTLFEYIGMYKGDFSRKTTLSEHGFRLPSCKDNRPLKFEGIFTEQVIRPTGLVDPTCKVKPAKNQIDDLLMAENISDFLKENAIKVKYLHSDIDTVQRMEIIRDLRLECSLVAILDADREGFLRSKTSLIQTIGRYADTITKSIKEALSETDRRRKKTKSIENLVDDITQKDKNIREDDKEIKNGKAADIRDEISKIEKNELNISNFKPAGDQKHAISELISGLIQSVQRPALIMAPNKTLAAQLYGVPRTDTFIEKDSSINEHILGPVETYSKMIIDVKRVQGDILEIFPAHLEVYANSHYITAKPTLKTAITQLEQRTKYDLEMLVTTPDNSLLFIDESHVTVPQIGEEWEFMRPKTIFISATPGDWELNKTNEIQKVILKNERVLVTTLTKKGEFDVLVGINLLREGLDIPAARNINGTVLIQIEWNKENNITPKSVHNLKKYIKQLKIEMYKEAEDLNFE", "metadata": {"id": "A0A1Z8VRT6", "cluster": 2610671, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001650", "IPR014001", "IPR001943"], "interpro_unused": ["IPR004807", "IPR036876", "IPR041471", "IPR024759", "IPR027417", "IPR006935"]}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein should include a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein contains a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Furthermore, the protein is associated with the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is produced by Desulfosarcina ovata subsp. ovata and is associated with UniProt keywords Isoprene biosynthesis and Transferase.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 5461, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 4152, 2007, 30311, 5360, 15618, 4058, 12329, 3857, 19615, 18, 12329, 3857, 1930, 1977, 2458, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MTVTVHAPAKINLFLRITGKRSDGYHELSQVACAHPAVPEDSSNLVARAAALFFETAFAGCPPLGGGMGSSDAAAVLVALNRHFGLPLTHTTLQAVGLATGIGEQLAAFPYLAPWTALLVYPGVLSKFHFNGRFFRLDEHLVNDLEPVTESAFPVITEIKRLLQAHGAKGAMMSGSYKVLCGNQQRQNWTLYIADLLISVMCPVALYDTVTITFGDDDGIRIHIEKRIPVGAGLGGARIGADVPFFIFGAPAAISTAWVYKNLNLRLTKDEKKGSAVFGLYADRDRAESA", "metadata": {"id": "A0A5K8AJ56", "cluster": 2618415, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein is included in the GHMP kinase, C-terminal domain superfamily, which encompasses the C-terminal structural component of ATP-dependent enzymes involved in amino acid, isoprene, and carbohydrate metabolism. This domain adopts a central alpha-beta plait fold that cooperates with the N-terminal domain to create a nucleotide-binding pocket. While primarily found in homoserine, galacto-, and mevalonate kinases, it is also present in structurally related diphosphomevalonate decarboxylases. Furthermore, the protein should include a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein is a member of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is derived from Polynucleobacter meluiroseus and exhibits UniProt keyword tags Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 21569, 1920, 45, 17, 4262, 4346, 4594, 1927, 4498, 17, 3100, 5038, 3286, 1922, 3835, 2687, 16, 26690, 1021, 16, 1930, 10590, 4714, 18, 2052, 3418, 24032, 43, 4101, 4595, 17, 4666, 5606, 1932, 3728, 1988, 23230, 1036, 1956, 1920, 56, 17, 4262, 3418, 1942, 7762, 43, 5489, 17, 2743, 10154, 18, 2679, 5985, 2435, 1922, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 16, 2176, 1977, 2222, 2481, 1922, 12171, 2712, 11791, 2609, 2225, 4701, 8870, 23922, 1036, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 3595, 2037, 15176, 2626, 5883, 4221, 15444, 5652, 1957, 1930, 9826, 20709, 11121, 2538, 14392, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MTDVGHTLELHTPAKLNLFLHIVGRRADGYHLLQSAFQLIDWCDVLNLKLIPENEIRRIDPIPGVPAESDLVVRAAQLIKAYCGVRTGVEIRLQKNIPMGAGLGGGSSDAAATLIGLNQLWHLNLDQATLCRLGLSLGADVPFFIFGSNAFVEGIGEKMQAISLELQNFLVIFPNQAIATALIFQDPELTRDRAPITIDGFVASPLLNQTNDCQTVAVRICPEVKHALDWISQTLPGSTPRMSGSGSSVFTALDPKTDLANLENHLQNLPKGWVGRVVGGLNKNPAYNLISSE", "metadata": {"id": "A0A240DYT5", "cluster": 3697191, "interpro_all": ["IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR036554", "IPR006204", "IPR004424"], "interpro_unused": ["IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Furthermore, the protein is categorized in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is expressed in Parcubacteria group bacterium CG1_02_39_15 and exhibits UniProt keyword tags Cytoplasm and rRNA processing.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 3198, 1922, 2096, 18021, 7972, 2341, 18339, 2210, 14061, 7294, 1009, 41, 5725, 41, 3886, 41, 2461, 1930, 9826, 20709, 11121, 2538, 14392, 5239, 1930, 9067, 4587, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MVHIPVLQKEVIKYLEPKPNENLIDCTIGEAGHTLIKNIECRISNIEYKKRLILVCDNFANLGMSSWHLEKSGRGFSFLKREPLDMRYNPESIEKILREYGQESFAREIAKNIIEFRKIKPKRFHHKKLHPATKTFQALRIAVNDELNNLVKGLSQALKFLQERKIEILTKKPIAPSLEEIKINPRSRSAKLRVGQKSAILEKNGPRGKVLGIDQDPEMEEIVKKENFKLVKGILFDLPLTAEKIVNYWSAPEPIKTTSLLVELVKKAVTLENGGRLAVISFHSLEDRIVKN", "metadata": {"id": "A0A1J4WG68", "cluster": 5680034, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a polypeptide chain that performs the following role: The protein is categorized in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein contains a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein has a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is native to Bacillota bacterium (Firmicutes bacterium) and is described by UniProt keywords Isoprene biosynthesis and Transferase. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10234, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 5461, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 6196, 1942, 8175, 22538, 3857, 14061, 12, 24474, 14061, 13, 1930, 1977, 2910, 2007, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MMRESIFIKAPAKINLSLDIIGRRPDGFHLVEMVMQTISLCDHITLEAADGAIHLHCSHPFVPAGSGNIVWKAAHLLKSTYGSAEMGAVITVEKHIPVSAGLGGGSSDAAAVLKGLNELWDLRLSPAQLAELGLRLGADVPFCLQGGTALARGIGEELTPVAPPPSLWVVLLKPNMGVSTGEVYREFVQGRVRTRPDTQRLVSALEAGDYQAMAESMANVLESVTFRRFPILRRLKQKALELGALAAMMSGSGPTIFALTPEYKRAAAIYNRLRHQVEFAHITTFWEE", "metadata": {"id": "A0A971AN74", "cluster": 9843612, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein features a Cupin-like domain 8 domain that shares structural similarity to the JmjC domain, suggesting a potential role in histone demethylation or oxidative catalysis. It likely adopts the conserved beta-barrel fold characteristic of the cupin superfamily. In addition, the protein incorporates a JmjC domain that adopts a cupin fold to coordinate Fe(II) and alpha-ketoglutarate, functioning as a metalloenzyme involved in chromatin remodeling. This catalytic domain primarily acts as a histone demethylase conserved from yeast to humans, although some variants display hydroxylase activity involved in processes such as tRNA modification. It is expressed in Mizuhopecten yessoensis (Japanese scallop) (Patinopecten yessoensis) and carries UniProt keyword assignments Cytoplasm.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 14967, 1921, 17, 3189, 3418, 28, 3418, 1988, 16495, 4346, 6796, 1942, 1920, 16097, 30271, 3418, 16, 3783, 43, 2889, 2770, 1922, 6632, 20254, 2014, 5163, 15408, 18, 2176, 3205, 24032, 1920, 5305, 4666, 17, 19560, 3728, 6293, 1927, 1920, 14967, 1921, 13975, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 16097, 30271, 3418, 1988, 24032, 43, 14967, 1921, 3728, 1942, 11865, 2650, 12, 2890, 13, 1930, 4595, 17, 21471, 16542, 17488, 16, 7295, 1966, 43, 8969, 6802, 1022, 9318, 3286, 1922, 6338, 8378, 18, 2052, 6804, 3418, 5985, 8016, 1966, 43, 6632, 21732, 2051, 5305, 2037, 5688, 1942, 5209, 16, 2876, 2673, 4936, 4434, 16324, 2455, 3286, 1922, 4028, 2427, 1966, 10089, 6295, 18, 2176, 1977, 3198, 1922, 29953, 28721, 4907, 2341, 1917, 11633, 2204, 8134, 12, 10405, 7350, 6012, 1034, 13, 12, 2091, 11873, 3920, 2777, 11633, 2204, 8134, 13, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 18, 3], "output": "MEAETYLLTEQPAVLHNTMVNWPSSSWTPEFLGEQLSQPLSCKVTPLSIGRALMETECIQESVSLSDFVQWLRGQVSGDNPLQKYDRNTFSCYLDYKYMQEIFTTKPELLKAVCWESVGLEGRDGTASTLWMGSEGAYTNCHYDAYGYNLVAQIFGRKRWVLFPPSDTQHLYPTRIPFEESSIFSQVDVKHPDLKLHPKVKLTSVHEVILEPGQILYVPRHWWHYVECLEPAISVNTWVELAADTESRFEEAITRNLFSSLWCSHIDMKKQGMNDCHQLGAVGAQQEGANTQEWINPKEEIWDNRRNMFVLSEAYKAIEGDKSGGDGCTTTDCGLVTSDTPDCTTDDRERNLKIFARHFRGKTVIFLPKGRVQGSVIQNKDKNSKPIQGEYFNISSEISSKTVKKPHLHLREKEHGIFYCDDENYKMSTAQNWNREDKLSEKTYHQPTQKIPVKSTNLFLKRNQSGEVYSDQSCAAKVSKLTSQSSEELLTDRVMMKTISRPDTKFNSRNVTSNRPCNTLIKTCLRCNNQDCDGQVCRSRTVAPSPSEISLTAVTPQPFMTWHSVCKCGDKNSDKDENQRGSRILNATLDNSSLDNKLDTDKEVSYYQRETCRYCVGDSHTSELTNQSNTGEQVNPIKTLTFEEFVMCATHPDVIHTIAKVIRNNMTGD", "metadata": {"id": "A0A210R5F8", "cluster": 10835319, "interpro_all": ["IPR041667", "IPR003347"], "interpro_used": ["IPR041667", "IPR003347"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein possesses a Longin domain that exerts a regulatory function within membrane-trafficking machinery, typically characterizing the N-terminus of VAMP family SNARE proteins. It adopts a profilin-like globular fold consisting of a five-stranded antiparallel beta-sheet sandwiched by alpha-helices. This domain is conserved across all eukaryotes and is essential for coordinating vesicular transport. Furthermore, the protein is classified under the Longin-like domain superfamily, which adopts a profilin-like fold composed of a five-stranded antiparallel beta-sheet sandwiched by alpha-helices and serves as a regulatory module in membrane trafficking. This domain is conserved across eukaryotes and is integral to proteins involved in SNARE-mediated fusion, ER-to-Golgi transport, and clathrin-mediated endocytosis. It originates from Terrestrivirus sp and is classified with UniProt keywords Lipoprotein, Palmitate, and Prenylation.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 14465, 43, 2815, 1921, 3418, 1988, 14235, 43, 4948, 2347, 2651, 3260, 17, 9604, 10853, 16, 5745, 15772, 1920, 56, 17, 7822, 1927, 27324, 3416, 19146, 2697, 18, 2176, 24032, 43, 4851, 1921, 17, 3189, 20975, 3728, 7600, 1927, 43, 3628, 17, 10338, 28892, 4666, 17, 11130, 18038, 1919, 2007, 4595, 17, 12789, 18, 2052, 3418, 1977, 5305, 3436, 2136, 15021, 1930, 1977, 4415, 1958, 19355, 16168, 4860, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2815, 1921, 17, 3189, 3418, 13975, 16, 2154, 24032, 43, 4851, 1921, 17, 3189, 3728, 7179, 1927, 43, 3628, 17, 10338, 28892, 4666, 17, 11130, 18038, 1919, 2007, 4595, 17, 12789, 1930, 10634, 1966, 43, 4948, 9059, 1922, 3260, 9604, 18, 2052, 3418, 1977, 5305, 3436, 15021, 1930, 1977, 12328, 1942, 2697, 3286, 1922, 19146, 17, 3434, 5289, 16, 2668, 17, 1942, 17, 10277, 4860, 16, 1930, 17053, 17, 3434, 11914, 18, 2176, 22970, 2037, 17974, 1997, 19913, 2056, 1930, 1977, 5947, 1956, 20709, 11569, 9694, 16, 22047, 16, 1930, 9972, 3017, 18, 3], "output": "MVKVLNISIYKYDEENPIRLRLAVKCTSPGTRQTIEIDDITFVTDKLYPKINAYRILSQVLNVKEDKIGSELRYDWLDDLLMKCKKMDASSMNDEEFSYNYFSRMYTSKIYEIINFSTDFVTHTYVAQYNNNFLGASYSKNGNLISINI", "metadata": {"id": "A0A3G4ZQG4", "cluster": 11200492, "interpro_all": ["IPR011012", "IPR010908"], "interpro_used": ["IPR010908", "IPR011012"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that can perform the following function: The protein belongs to the ACP-like superfamily, which comprises four-helix bundle proteins that serve as essential carriers for acyl intermediates in biosynthetic pathways including fatty acid, polyketide, and non-ribosomal peptide synthesis. These proteins typically utilize a phosphopantetheine prosthetic group attached to a conserved serine residue, acting as a swinging arm to tether and transport activated fatty acids or amino acids between enzymatic active sites. Moreover, the protein includes a Phosphopantetheine binding ACP domain that serves as a central carrier for acyl intermediates during the synthesis of fatty acids, polyketides, and non-ribosomal peptides. It forms a four-helical bundle and covalently attaches a phosphopantetheine prosthetic group to a conserved serine residue, utilizing it as a 'swinging arm' to shuttle activated substrates between enzymatic active sites. It is native to Legionellales bacterium RIFCSPHIGHO2_12_FULL_37_14. Give the amino acid chain.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 18543, 17, 3189, 13975, 16, 2154, 12936, 3006, 17, 7864, 14142, 2697, 1988, 7120, 1966, 4415, 8974, 1958, 11337, 12386, 1922, 14041, 3873, 2710, 5934, 2687, 16, 4286, 18540, 2261, 16, 1930, 2447, 17, 11196, 4207, 4271, 18, 2144, 2697, 5745, 12561, 43, 8078, 6528, 2057, 20536, 2053, 19019, 2210, 8765, 1942, 43, 5305, 8468, 6181, 16, 8290, 1966, 43, 24775, 1941, 6011, 1942, 13893, 1930, 4860, 4128, 5934, 4576, 2014, 3835, 4576, 2192, 8145, 3500, 3402, 18, 3950, 16, 1920, 2213, 5921, 43, 8078, 6528, 2057, 20536, 2053, 2743, 18543, 3418, 1988, 10634, 1966, 43, 4101, 9685, 1958, 11337, 12386, 2409, 1920, 4271, 1927, 5934, 4576, 16, 4286, 18540, 3726, 16, 1930, 2447, 17, 11196, 5320, 18, 2176, 4952, 43, 3006, 17, 11514, 14142, 1930, 16590, 5823, 1918, 43, 8078, 6528, 2057, 20536, 2053, 19019, 2210, 1942, 43, 5305, 8468, 6181, 16, 10232, 2176, 1966, 43, 11, 24775, 1941, 6011, 11, 1942, 23814, 4128, 6249, 2192, 8145, 3500, 3402, 18, 2176, 1977, 6196, 1942, 27836, 5870, 2612, 14061, 12424, 2792, 24888, 2509, 5265, 41, 2369, 41, 4125, 41, 3191, 41, 2607, 18, 7031, 1920, 3835, 2687, 4659, 18, 3], "output": "MLILFTDLQALITEVIPTVDVATFDSSLTFTEAGMDSLDVFSFFMKVEAKYGFSIPEHDFGKMNTFQDVLNYSNSLLSMDVT", "metadata": {"id": "A0A1G0WY51", "cluster": 11534583, "interpro_all": ["IPR036736", "IPR009081"], "interpro_used": ["IPR036736", "IPR009081"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Function:\nThe protein belongs to the MFS transporter superfamily, which constitutes a ubiquitous group of secondary carriers that transport small solutes across membranes in response to chemiosmotic ion gradients. Characterized by a core structure of twelve transmembrane helices forming a central channel, these proteins function as uniporters, symporters, or antiporters to facilitate the movement of diverse substrates. It has been characterized in bacterium and features UniProt keywords Transmembrane helix.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 14440, 1942, 1920, 23778, 9054, 13975, 16, 2154, 14879, 43, 15498, 2210, 1927, 4067, 8974, 1988, 4860, 2858, 27993, 3436, 5726, 1922, 2644, 1942, 2975, 14356, 12492, 2002, 4755, 12741, 18, 4378, 2007, 43, 4728, 3170, 1927, 12367, 9117, 12789, 7402, 43, 4101, 4999, 16, 2144, 2697, 2347, 1966, 15943, 2718, 2045, 16, 29148, 2718, 2045, 16, 2014, 2246, 24095, 1036, 1942, 6628, 1920, 5829, 1927, 6445, 6249, 18, 2176, 2258, 2252, 4378, 1922, 14061, 1930, 4075, 20709, 11569, 9117, 7864, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MSSLKFFKLLSTFAINIISVFIPAIIYILFAFLRIFLDLIFKKWLLRYIEVNFIAGIVLAALFHAFALTFTLVPENSLYATMILQYLDQSFLLIFVLIIYSSGAIPSVLQNVEHEQKKSKTRIFLCCGAVIKTDPSAVNTALFYAVSYLQKLFIIIRIIPVILYFFSVSLKKDDSNYGRVKIYENIGNIIGIISGGLLFIKDIREMKRVGLVVKPSNEIIKED", "metadata": {"id": "A0A7V6J221", "cluster": 15752250, "interpro_all": ["IPR036259"], "interpro_used": ["IPR036259"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the polypeptide chain function: The protein possesses a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein is categorized in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is identified in Treponema bryantii and exhibits UniProt keyword tags Isoprene biosynthesis and Transferase. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 14465, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 2899, 1922, 2171, 21851, 6666, 26949, 10402, 1033, 1930, 9826, 20709, 11121, 2538, 14392, 26690, 1021, 8132, 1930, 13763, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MEHEISGWAYAKINFGLRVLPGRADGFHGIESIFQTVDLFDELTLTVTAEKGCFVHCSDMELPENNTLTKAYNAFCKVVDCEVPGVKVELKKGIPSGGGLGGGSSDAAALVRMLEKLCNVRLSDSDLDNIAAETGSDVFFFMHCDEQGRGCALVSGRGEVVKKIHGREDLFLVLIFPKVSSSTKEAYALVDEAFAGGKVLVSPEFDELELVYRKPPENWTFINTFTPVISKKYEEIGRAIEALKALNCNYAQMSGSGSTVFGVFASRQLAESAVEKLADSWNCKLARTV", "metadata": {"id": "A0A1H9HW27", "cluster": 17265390, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein includes a Helicase-associated domain that may bind nucleic acids and is typically found in multiple copies within helicase proteins. This short domain is predicted to structurally consist of three $\\alpha$-helices. It has been detected in Seminavis robusta and is linked to UniProt keywords ATP-binding, Hydrolase, and Nucleotide-binding. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 1925, 3835, 2687, 3244, 1988, 2469, 16318, 2460, 43, 2213, 22665, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 15318, 17, 2458, 3418, 1988, 2278, 4566, 11079, 4576, 1930, 1977, 5745, 2435, 1922, 3137, 9425, 2651, 15318, 2697, 18, 2052, 3662, 3418, 1977, 4396, 1942, 12171, 3149, 1927, 2559, 8, 38, 4595, 8, 17, 12789, 18, 2176, 2258, 2252, 3330, 1922, 19381, 9188, 1036, 5786, 1019, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 16, 20748, 16, 1930, 5489, 17, 2743, 18, 7031, 1920, 3244, 18, 3], "output": "MPNQVRTWEENYAQLVAYKKERGDCMVPLRYAQDKILGKWVSTQRESRYVLKPERKELLDSIGFEWHPRQRRSDDKWNGMFKRLLEYREKNDLATVFSANKEDPELVKWCCNQREYSGRGLLNEERYNRLRDVGFPVRPLQKSVQAKREQDQQQIAPPEGNISNASTDSNQKAKKKKIKKMNLSPAVLDVNKTAATKISRFLTEENEQDEEDATTTPPTPSPAPTIVPSADLIATTSGSGTARRRSWLESYAALAGFKGQHGHCRVPIQYKQDKQLGIWVGEQKKKKFLMSDERREKLEELGFTWANPRGKQWSVMFEKLREYREEHPQNFKPKNFNLRKWLESQRHAILDGSLSRECADKLRSIGYDFSDEIKTLDSQDSMTESEGGEGEEEDSSIEAISSTEDSQSIMPPKKKRQVSVLSEPGTAPDAVAEDTPMGDVAESLLSLSAPGGSKPPSRKNSDDATKSTPPKKKQKTSPSLIEHQFLPPPPPELPVVPPTEDKAADTAKRQHYNTRGVGLFMGTDAAASMARGGMSSSAHGGALAANNVLPVEQMLALQQGRATGRMGINNANINNASAMMTQQLQQQHPWQQHRGPQQPVHPPPPTKSELDDLQLADLYLLLVKEIGPHRR", "metadata": {"id": "A0A9N8DB27", "cluster": 19199924, "interpro_all": ["IPR005114"], "interpro_used": ["IPR005114"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a protein with the following function: The protein includes a IQ motif binding site that forms a basic amphipathic helix to recruit EF-hand proteins, including calmodulin and myosin light chains. This motif frequently serves as a substrate for protein kinase C phosphorylation and regulates functions in diverse proteins such as myosins and neuromodulin. It is present in Acorus calamus (Sweet flag) and carries UniProt keyword assignments Calmodulin-binding. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 8338, 5219, 2743, 3200, 1988, 4952, 43, 5937, 26747, 21494, 7864, 1942, 5608, 8485, 17, 3897, 2697, 16, 2710, 17537, 1930, 10863, 3696, 7835, 18, 2052, 5219, 5467, 10634, 1966, 43, 4510, 1958, 2213, 4016, 45, 4050, 1930, 7014, 4088, 1922, 6445, 2697, 2427, 1966, 10863, 1036, 1930, 25409, 3392, 18, 2176, 1977, 2481, 1922, 2000, 1924, 1957, 2570, 1976, 1957, 12, 15190, 7030, 13, 1930, 16252, 20709, 11121, 2538, 18306, 17537, 17, 2743, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MQSPERKIVKEKKRWGLRRLRHGEANSLIPLKSNPSSIEKILRDAEGDVKRPILPSQHVRKAQNTHIQLPPEKEEVQRPLVSLQQRIVPGRTTKYATPVIRDLFEFAATRIQAVYRGYMARKNYRAHKGLVKLQRLVRSQGVKDQTSNALRFTTMLVRIQSQIQSMRLQKVEMQSMERRRMPRTRETKAGFGKFSVTQPMYNGFLFEQYERDLQQEEWDDSVKRKMEGVIKRERAMAFAYSHQLSKGLRKLDPKTFNDSLDVATPRSSQSLRVTSTAAASKKKRVRRNNIRSRYGGGGGNDSPMSCPPPSATPNYMAQTASAKAKVIPMGSLKCNRGSSMNSVGGSSVDSTASLPALLLIGRGFK", "metadata": {"id": "A0AAV9F010", "cluster": 19971775, "interpro_all": ["IPR000048"], "interpro_used": ["IPR000048"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein is categorized in the Nucleotide cyclase superfamily, which encompasses catalytic domains found in adenylyl, guanylyl, and diguanylate cyclases responsible for synthesizing cyclic nucleotide second messengers. These domains share a core ferredoxin-like fold, though the specific nucleotide-binding mode differs between subtypes such as the GGDEF domain and adenylate cyclases. Also, the protein should include a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. In addition, the protein contains a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. It has been characterized in Triatoma dimidiata (Kissing bug) (Meccus dimidiatus) and contains UniProt keyword associations Magnesium, Lyase, and ATP-binding.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 10234, 1922, 1920, 5489, 16526, 13975, 16, 2154, 21569, 6804, 4682, 2435, 1922, 27802, 16, 13504, 25671, 16, 1930, 4325, 13785, 9075, 16526, 1036, 5061, 1958, 25292, 9821, 5489, 2812, 16716, 1036, 18, 2144, 4682, 7948, 43, 4728, 25304, 22389, 10960, 17, 3189, 3728, 16, 4170, 1920, 2487, 5489, 17, 2743, 5754, 11457, 2192, 8160, 2427, 1966, 1920, 12358, 3695, 1038, 3418, 1930, 23052, 16526, 1036, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 2176, 2258, 2252, 4378, 1922, 5083, 8286, 3368, 3363, 14773, 3857, 12, 19752, 1941, 25761, 13, 12, 10685, 6973, 3363, 14773, 1031, 1957, 13, 1930, 5461, 20709, 11121, 2538, 5253, 13148, 16, 23928, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MSSVLSLAVVSVFLRLGFILKLLLMLVVAGIHYGLFISQPLFRGYYYGIANDSLTYVPWELKLAVAISCVTALLHVLDRQVEFTTRTDYQWRAKLLIEQEEVETMRGINKILLENILPAHVAHLFLTKNTSQELYHERYNSIAVMFASIPNYKEFYDENDVNKQGLECLRLLNEIICDFDKLLLKPKFSCIEKIKTIGSTYMLASGLEPGKEDARGKATRQRDHSVISLVEFAVALMNLLDQINKESFQRFKLRIGLNHGPVIAGVVGAQKPQYDIWGNTVNVASRMDSCGVMGRIQVTEDTAKILMSNGYECESRGLTYVKGKGN", "metadata": {"id": "A0A0V0GBY9", "cluster": 20037067, "interpro_all": ["IPR001054", "IPR018297", "IPR029787"], "interpro_used": ["IPR029787", "IPR001054", "IPR018297"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein contains a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Also, the protein includes a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Also, the protein should have a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. It is found in Ignavibacteria bacterium RIFOXYC2_FULL_35_21 and is annotated with UniProt keywords DNA repair, Cytoplasm, and Excision nuclease. Can you generate the amino acid sequence corresponding to this polypeptide chain?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 13022, 4659, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2222, 16, 1920, 2213, 5921, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2176, 1977, 2435, 1922, 12046, 9188, 7972, 2341, 18339, 14061, 12424, 7221, 8054, 41, 4125, 41, 3259, 41, 2900, 1930, 1977, 10633, 1956, 20709, 11569, 2678, 5059, 16, 5239, 16, 1930, 10940, 16230, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MNKFELVSSYKPSGDQPKAINELMEGLARGDKHQVLLGVTGSGKTFTISNVIQEIQKPTLVISPNKTLAAQLYSEFKAFFPNNAVEYFISYYDYYQPEAYIPTTDTYIEKDFSINDEIDRLRLRTTSSIVEGRNDVIVVASVSCIYSIGRKEDFLAYIFPLKVGQKITRQDLLYKLTDLHYSRNDYEFSRGTFRVRGDVVDVIPAYEDQTALRIELFGDEIEKLTYVDALTGKTKSATESIVLYPAKLFVTPEDRLLDAMTAIREELIERLKVLRSQDKLIEAQRLEQRTLFDLEMMKEVGYCSGIENYSMHLTGRNFGETPECLFHYFPEDYLLIIDESHVTVPQLRAMYNGDRSRKQTLVEHGFRLPSALENRPLKFDEFESLVNKAIYVSATPGPYELDKTAGAIVEQVIRPTGLLDPEISIRPVRNQIDDLLNEIHLRTAKGERVLVTTLTKRMSEDLTEYLQNLQIKVAYIHSDVETLERVEIIRNLRIGENDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRSERSLMQTAGRTARNVNGLVILYADKVTRSMQALLEETNRRRELQVQYNEEHNINPQTVYKSLDEILSATSVADIQVQREKRLEYIQEKKIRKAAEPLVKYLTNEQRGELTEQLFLEMKEAARQLDFERAAELRDEIQRLKAASEIAGKKRKKSK", "metadata": {"id": "A0A1G0WTQ5", "cluster": 23653168, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001650", "IPR001943", "IPR014001"], "interpro_unused": ["IPR004807", "IPR036876", "IPR041471", "IPR024759", "IPR027417", "IPR006935"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein has a NodB homology domain that serves as the catalytic core in carbohydrate esterase family 4 (CE4) enzymes and PuuE proteins. Adopting a deformed (\u03b2/\u03b1)8 barrel fold, this domain typically catalyzes the metal-dependent deacetylation of polysaccharides such as chitin and peptidoglycan, or functions as a metal-independent allantoinase in PuuE variants. Additionally, the protein is associated with the Glycoside hydrolase/deacetylase, beta/alpha-barrel superfamily, which encompasses a structural domain found in enzymes such as alpha-mannosidases, 4-alpha-glucanotransferases, and polysaccharide deacetylases. This domain typically features a seven-stranded beta/alpha barrel fold that supports catalytic activities involved in the hydrolysis or deacetylation of carbohydrate substrates. It occurs in Anaerolineales bacterium. What would its protein sequence look like?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 2258, 43, 3889, 1014, 9039, 3418, 1988, 10634, 1966, 1920, 6804, 4728, 1922, 10590, 26389, 3416, 24, 12, 5827, 1006, 13, 5038, 1930, 6612, 2182, 2697, 18, 20478, 43, 28466, 12, 161, 19, 160, 13, 28, 19560, 3728, 16, 2052, 3418, 5745, 17097, 1920, 6048, 17, 3100, 23764, 1927, 18686, 2427, 1966, 16588, 1930, 24183, 16, 2014, 4088, 1966, 43, 6048, 17, 3484, 2136, 26182, 11413, 1922, 6612, 2182, 4936, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 7533, 2261, 20748, 19, 19489, 16, 4666, 19, 4595, 17, 19560, 13975, 16, 2154, 21569, 43, 4346, 3418, 2435, 1922, 5038, 2427, 1966, 4595, 17, 7338, 12224, 1036, 16, 24, 17, 4595, 17, 18798, 14165, 1036, 16, 1930, 17167, 19489, 1036, 18, 2052, 3418, 5745, 4075, 43, 5260, 17, 10338, 4666, 19, 4595, 19560, 3728, 1988, 7825, 6804, 4209, 3286, 1922, 1920, 9128, 2014, 23764, 1927, 10590, 6249, 18, 2176, 5110, 1922, 11381, 8419, 3955, 14061, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "MTPSPRLLLTIDYESWFAPSRRYDFLPPETRYQLDGERSRHALDPILEIFDDSKVTFYLVGEMVGWFPELPEKISKAGHEVGFHCHIHRRLNDAKEIEKDLIASSDWIQQYNARGYRAPMINTVEEVYPLLARHNFTYSSSQYAPAGVTVDKGGVWEIPVSTLPLLSTPTRFTAPRHMNLKLVTGGEFPYGSSFTSGLFRRTVYKIIERDLKAGKSPVIFLHPYEIVTPKGYPQNFIVDMIHHPLLFPFTFNKSKFLKDLLKNFPASTMQDYVNEL", "metadata": {"id": "A0A935A9F6", "cluster": 27318537, "interpro_all": ["IPR011330", "IPR002509"], "interpro_used": ["IPR002509", "IPR011330"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein is grouped in the Alpha/beta knot methyltransferases superfamily, which encompasses enzymes containing a deep, rare \u03b1/\u03b2 knot structural domain essential for RNA methylation. This fold is characteristic of S-adenosyl-L-methionine (SAM)-dependent enzymes, including the SPOUT and EMG1/NEP1 families, facilitating the modification of RNA substrates. In addition, the protein belongs to the RNA methyltransferase RlmH family, which is predicted to function as an S-adenosyl-L-methionine (AdoMet)-dependent methyltransferase based on structural homology. These enzymes likely catalyze the transfer of methyl groups to RNA substrates for regulatory modification. In addition, the protein is grouped in the tRNA (guanine-N1-)-methyltransferase, N-terminal superfamily, which represents the N-terminal domain of SPOUT superfamily enzymes, including the tRNA:Gm18 methyltransferase TrmH. This domain is characterized by a rare \u03b1/\u03b2 knot structure that poses a significant folding challenge. It has been detected in Synechococcus sp. MEDNS5 and corresponds to UniProt keyword Cytoplasm and rRNA processing. What would its protein sequence look like?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 10809, 1922, 1920, 4595, 19, 4666, 26646, 28253, 13975, 16, 2154, 21569, 5038, 3165, 43, 6515, 16, 5844, 160, 19, 161, 26646, 4346, 3418, 4415, 1958, 3146, 5547, 18, 2052, 3728, 1977, 6293, 1927, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5038, 16, 2710, 1920, 18055, 1984, 1930, 13952, 1009, 19, 26046, 1009, 5767, 16, 12440, 1920, 6295, 1927, 3146, 6249, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 3146, 16478, 11929, 22316, 3416, 16, 2154, 1977, 4396, 1942, 2347, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 12, 2041, 14080, 13, 17, 3100, 16478, 2454, 1990, 4346, 9039, 18, 2144, 5038, 3205, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 3146, 6249, 1958, 4948, 6295, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 10089, 12, 16904, 17, 13007, 17, 13, 17, 16478, 16, 56, 17, 4262, 13975, 16, 2154, 4972, 1920, 56, 17, 4262, 3418, 1927, 18055, 1984, 13975, 5038, 16, 2710, 1920, 10089, 30, 28673, 1025, 16478, 28402, 1023, 18, 2052, 3418, 1977, 4378, 2007, 43, 5844, 160, 19, 161, 26646, 3170, 1988, 17274, 43, 2228, 10328, 6013, 18, 2176, 2258, 2252, 3330, 1922, 26734, 8256, 2056, 18, 2242, 3355, 1015, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "MNISRCRIIAVGKVRKGWVQEGVALYLKRLQGLQVVELKDSTPEKEAEAIRSSLRADEWPVMLMEQGTPLASIPFAQQLERLGNERLAFVIGGADGLTDELKAAARWQLSLSPMTFPHELARLLLLEQLFRAQTILQGSPYHRA", "metadata": {"id": "A0A7G8HIG8", "cluster": 28028857, "interpro_all": ["IPR029028", "IPR003742", "IPR029026"], "interpro_used": ["IPR029028", "IPR003742", "IPR029026"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein should feature a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Moreover, the protein should contain a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Moreover, the protein should contain a UvrB, YAD/RRR-motif-containing domain that is located at the C-terminus of the ultraviolet resistance protein B (UvrB), playing a role in mutational resistance against UV light. This approximately 40-amino acid region is characterized by the presence of conserved YAD and RRR sequence motifs. It has been characterized in Candidatus Accumulibacter meliphilus and carries UniProt keyword assignments SOS response, DNA excision, and DNA repair.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 5819, 16007, 16, 26169, 1007, 19, 5162, 1005, 17, 5219, 17, 3165, 3418, 1988, 1977, 4810, 2019, 1920, 45, 17, 7822, 1927, 1920, 17077, 3554, 2213, 44, 12, 5819, 16007, 13, 16, 14797, 43, 2770, 1922, 13736, 3554, 3316, 5819, 3696, 18, 2052, 3993, 3040, 17, 3835, 2687, 3031, 1977, 4378, 2007, 1920, 2990, 1927, 5305, 26169, 1007, 1930, 5162, 1005, 3244, 8277, 18, 2176, 2258, 2252, 4378, 1922, 14550, 1031, 1957, 4020, 13004, 7972, 2341, 1915, 4221, 6285, 1970, 1957, 1930, 16252, 20709, 11121, 2538, 18306, 17668, 2644, 16, 2678, 10940, 16, 1930, 2678, 5059, 18, 3], "output": "LIDPVLIVRPASSQIDDLLSEIRLRVGRGERVLVTTLTKRMSEYLHSDIDTVERVEIIRDLRLGKFDVLVGINLLREGLDIPEVSLVAILDADKEDRVTGSMSRAIAETERRRLKQIAFNAAHGIVPKGISKRITDIIDGVYDLDDARAMSEKQLARELKRLEKEMLEYARNLEFEKAAAARDELFRIRQQVFGISGEQANIEGDLTEYLSEHEVRVRGFLRSERSLIQTIGRAARHLNGTAILYARELKAAQQQANYE", "metadata": {"id": "A0A369XJK9", "cluster": 1643618, "interpro_all": ["IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR024759"], "interpro_used": ["IPR001650", "IPR001943", "IPR024759"], "interpro_unused": ["IPR004807", "IPR027417", "IPR036876"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein is grouped in the Winged helix-like DNA-binding domain superfamily, which encompasses diverse DNA-binding proteins including transcriptional regulators, helicases, and endonucleases that utilize a winged helix-turn-helix motif for sequence-specific recognition. This domain engages the DNA major groove via a recognition helix while loop structures known as wings contact the minor groove or backbone, often serving as a scaffold for protein-protein interactions. In addition, the protein features a RNA polymerase sigma-70 region 2 domain that serves as the primary interface for binding the core RNA polymerase beta-prime clamp and recognizing the -10 promoter sequence. As the most conserved region of the sigma factor, it utilizes C-terminal aromatic residues to mediate DNA strand separation and facilitate transcription initiation. Also, the protein incorporates a RNA polymerase sigma-70-like domain that reversibly associates with the core RNA polymerase complex to form a holoenzyme essential for transcription initiation. It mediates specific promoter recognition, typically binding the -35 region via a helix-turn-helix motif, to direct the expression of distinct regulons in bacteria and plant plastids. It originates from Aeromicrobium phragmitis and is classified with UniProt keywords Transcription regulation.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 1977, 10809, 1922, 1920, 12920, 1919, 7864, 17, 3189, 2678, 17, 2743, 3418, 13975, 16, 2154, 21569, 6445, 2678, 17, 2743, 2697, 2710, 5224, 9098, 16, 29919, 16, 1930, 18697, 1036, 1988, 12561, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 1958, 3244, 17, 2487, 5708, 18, 2052, 3418, 11580, 1036, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 2679, 5881, 4061, 3171, 1966, 28297, 5217, 1920, 5857, 15920, 2014, 10787, 16, 3868, 13915, 1966, 43, 7281, 1958, 2213, 17, 2213, 3719, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 3146, 6479, 5139, 17, 3895, 3031, 22, 3418, 1988, 10634, 1966, 1920, 3065, 6854, 1958, 2743, 1920, 4728, 3146, 6479, 4666, 17, 13476, 10209, 1930, 15667, 1920, 17, 2119, 4465, 3244, 18, 1966, 1920, 2501, 5305, 3031, 1927, 1920, 5139, 2991, 16, 2176, 18127, 45, 17, 4262, 10761, 4248, 1942, 8265, 2678, 5984, 7106, 1930, 6628, 3213, 6035, 18, 2222, 16, 1920, 2213, 19683, 43, 3146, 6479, 5139, 17, 3895, 17, 3189, 3418, 1988, 26778, 14162, 1956, 1920, 4728, 3146, 6479, 2796, 1942, 2386, 43, 20403, 14896, 4415, 1958, 3213, 6035, 18, 2176, 10412, 2487, 4465, 5708, 16, 5745, 2743, 1920, 17, 3259, 3031, 3454, 43, 7864, 17, 5165, 17, 7864, 5219, 16, 1942, 3083, 1920, 2294, 1927, 4493, 3052, 2101, 1922, 4802, 1930, 4496, 19754, 1036, 18, 2176, 22970, 2037, 6049, 22980, 3821, 1989, 17252, 11431, 3678, 1930, 1977, 5947, 1956, 20709, 11569, 3213, 3640, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MSAATIMNPTSEAAWRDDLVTRHVALAKSLANRYTSRVGLVRAAHRYDPSRGPFAAFAAPTILGEIKHELQARINAARADLEAEAGGEVDLAQIAEHLGEDIIESTDANGRDTVTDLHGEEDANFTRVENVVLRLRFVDELSQRQIARILGTSQMQVCRRLRRVLSQLRGDMAAGVEYEDLKQVALHFRDAEWAIRPPRRLQEEVRSAASVHHCFSSLAPLVSKLDPDDREL", "metadata": {"id": "A0A3L8PNQ2", "cluster": 3977817, "interpro_all": ["IPR014284", "IPR007627", "IPR007630", "IPR013325", "IPR013324", "IPR036388"], "interpro_used": ["IPR036388", "IPR007627", "IPR014284"], "interpro_unused": ["IPR007630", "IPR013325", "IPR013324"]}, "task_type": "infilling"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein possesses a Domain of unknown function DUF4124 domain that is currently functionally uncharacterized but is predicted to adopt an immunoglobulin-like (Ig-like) fold. It is produced by Chitinimonas taiwanensis DSM 18899 and is classified with UniProt keywords Signal.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 3418, 1927, 5435, 2347, 4855, 10432, 19943, 3418, 1988, 1977, 5077, 9346, 24528, 2308, 1977, 4396, 1942, 14103, 1925, 11837, 17, 3189, 12, 7021, 17, 3189, 13, 3728, 18, 2176, 1977, 4152, 2007, 16588, 1980, 9259, 12760, 8134, 10964, 16359, 6576, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 3], "output": "MRLLILLLPLLALPASATVYQCLHKGEISYQDNPCPGATPPLKSPPSKAATRSDTLADIALPEPSIPPGPPRALAAGAEIVLVSGYESETRQVRVDLDRPGKRVLLVLSSYHAIDWLVVPSARTQLSAVLYSKTASDGEASVKAGKAARYPVTLPYSYEADNKHFVQILAHLNGWFGRSSVDSFHGAYSLARQVSIRQPDAPNPMLTLQGPAAQNLPSQLEFGLWNTEQQLEPWTVNGPHSGRKQGYRDIGLQTWDETGKVMYTLENDQLVRSERRSGKRESFALPGTFPRLSWPTALAYDTRRHIVTLSSLGGEGLLYRFNARSGKWLDYRSLDNLDLNALSYDAKADRYMGWSSEGSLVFLSHACQLQTTRRILDQLSGFGRGYDRGNESMPRLALYASSPEVALVRIEAGVVEQVWHYNFNSGKATLSYSARQP", "metadata": {"id": "A0A1K2H7C1", "cluster": 4073001, "interpro_all": ["IPR025392"], "interpro_used": ["IPR025392"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein possesses a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. Additionally, the protein carries a RuvB AAA lid domain that is found at the C-terminus of the RuvB protein and functions as part of the RuvABC resolvasome. It drives branch migration to resolve Holliday junctions targeted by RuvA during genetic recombination and DNA repair. Also, the protein belongs to the Holliday junction branch migration complex subunit RuvB family, which functions as an ATP-dependent 5'-3' helicase that drives the branch migration of Holliday junctions. It assembles into hexameric rings and interacts with the junction-binding protein RuvA to promote the translocation of recombination intermediates along DNA. It is produced by Phycisphaerales bacterium and is described by UniProt keywords ATP-binding and Hydrolase. Can you generate the amino acid sequence corresponding to this polypeptide chain?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 13022, 4659, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 4950, 16, 1920, 2213, 16252, 43, 7212, 1020, 1014, 13835, 13096, 3418, 1988, 1977, 2435, 2019, 1920, 45, 17, 7822, 1927, 1920, 7212, 1020, 1014, 2213, 1930, 4088, 1966, 3131, 1927, 1920, 7212, 7302, 8284, 24321, 10916, 2225, 18, 2176, 15435, 6089, 5049, 1942, 13818, 14451, 27539, 11245, 5154, 2007, 7212, 7302, 2409, 3299, 7827, 1930, 2678, 5059, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 14451, 27539, 6910, 6089, 5049, 2796, 5903, 7212, 1020, 1014, 3416, 16, 2154, 4088, 1966, 1925, 4498, 17, 3100, 25, 11, 17, 23, 11, 15318, 1988, 15435, 1920, 6089, 5049, 1927, 14451, 27539, 11245, 18, 2176, 17421, 1036, 2460, 25602, 1935, 12750, 1930, 9034, 1956, 1920, 6910, 17, 2743, 2213, 7212, 7302, 1942, 5527, 1920, 7849, 1927, 7827, 12386, 4231, 2678, 18, 2176, 1977, 4152, 2007, 25511, 9119, 29164, 3955, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 1930, 20748, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MATERWISAEQRAPEEDVSNQALRPRHLDEYIGQRDLVERLRIAIEAARRRGEALEHVLLHGPPGLGKTTLAHVIAQEMGSAVHVTSGPALTRGTDLVGALTNMQPNDVLFIDEIHRLPVAVEEFIYPAMEDGRIDIAIDSGMNARTLTIRLKAFTLIGATTRAGLLSSPLRSRFGLTHHLQYYPAEDLLTILARSAGLLGIEAAGEALMSIAKRSRGTPRIANRLLRRVRDYA", "metadata": {"id": "A0A955EJC2", "cluster": 7031006, "interpro_all": ["IPR003593", "IPR041445", "IPR004605", "IPR027417", "IPR008824"], "interpro_used": ["IPR003593", "IPR041445", "IPR004605"], "interpro_unused": ["IPR008824", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: It is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein belongs to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is produced by Luminiphilus syltensis NOR5-1B and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 4152, 2007, 16410, 6285, 1970, 1957, 29311, 2777, 8362, 3990, 1015, 17, 5462, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MTYCVGVTGGIGSGKSAVTDRLAALGITVVDADVAAREIVAPGQPALDEIREHFGPGVIQADGNLDRAQLRKIVFENPKQRKQLEAITHPRIRDQLASQLNSATSPYVILASPLLLESGQNSFADHVVVVDVPESVQLERTMARDNNDAALVEKIMAAQLPRPERLANADTVIDNSGTLEALDEQVVQLHQTLLRLAQQSPQ", "metadata": {"id": "B8KR40", "cluster": 8470405, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein includes a RNA polymerase sigma-70 region 2 domain that serves as the primary interface for binding the core RNA polymerase beta-prime clamp and recognizing the -10 promoter sequence. As the most conserved region of the sigma factor, it utilizes C-terminal aromatic residues to mediate DNA strand separation and facilitate transcription initiation. Also, the protein possesses a RNA polymerase sigma-70-like domain that reversibly associates with the core RNA polymerase complex to form a holoenzyme essential for transcription initiation. It mediates specific promoter recognition, typically binding the -35 region via a helix-turn-helix motif, to direct the expression of distinct regulons in bacteria and plant plastids. Also, the protein has a Ankyrin repeat that mediates protein-protein interactions through tandemly repeated helix-loop-helix modules which stack to form an L-shaped structure. This versatile motif is found in diverse eukaryotic proteins, including transcriptional initiators, cell-cycle regulators, cytoskeletal components, and signal transducers. It is found in Chloroflexota bacterium and has UniProt annotations ANK repeat and Transcription regulation.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 3146, 6479, 5139, 17, 3895, 3031, 22, 3418, 1988, 10634, 1966, 1920, 3065, 6854, 1958, 2743, 1920, 4728, 3146, 6479, 4666, 17, 13476, 10209, 1930, 15667, 1920, 17, 2119, 4465, 3244, 18, 1966, 1920, 2501, 5305, 3031, 1927, 1920, 5139, 2991, 16, 2176, 18127, 45, 17, 4262, 10761, 4248, 1942, 8265, 2678, 5984, 7106, 1930, 6628, 3213, 6035, 18, 2222, 16, 1920, 2213, 14465, 43, 3146, 6479, 5139, 17, 3895, 17, 3189, 3418, 1988, 26778, 14162, 1956, 1920, 4728, 3146, 6479, 2796, 1942, 2386, 43, 20403, 14896, 4415, 1958, 3213, 6035, 18, 2176, 10412, 2487, 4465, 5708, 16, 5745, 2743, 1920, 17, 3259, 3031, 3454, 43, 7864, 17, 5165, 17, 7864, 5219, 16, 1942, 3083, 1920, 2294, 1927, 4493, 3052, 2101, 1922, 4802, 1930, 4496, 19754, 1036, 18, 2222, 16, 1920, 2213, 2258, 43, 28336, 6865, 1988, 10412, 2213, 17, 2213, 3719, 2596, 10361, 1954, 5116, 7864, 17, 5881, 17, 7864, 10803, 2154, 10496, 1942, 2386, 1925, 54, 17, 9132, 3170, 18, 2052, 20425, 5219, 1977, 2435, 1922, 6445, 10825, 2697, 16, 2710, 5224, 23467, 1036, 16, 2024, 17, 4048, 9098, 16, 14787, 4178, 16, 1930, 2733, 26307, 18, 2176, 1977, 2435, 1922, 10107, 18222, 7336, 14061, 1930, 2258, 20709, 15010, 9808, 6865, 1930, 3213, 3640, 18, 3], "output": "MPTETVSATAAHVRLLQSPEATQQARHEAFAALVAAYQDMACGYALAQLGNWPAAQDAAQDAFILAYQQIGQLHEPAAFGAWLKRIVWSQCSRTQRAPVTEPLPADELGLCAPDDAQPAVASEAAAWRQQVLAAVQALPAHERDAVLLYYIDGYAPREVAAFLEISEPALRKRLQRARDHLREAMMDLLRDSLAAERPSRDDAFLRAVQLATTLEEAAVEAQIAVLEAALVDGIDVNAAGASGQTLLHWAARQGNLEALTLLLRNGADPALLDRLGRTPLRVALDAGQSRAADLLRRWAARHTAPEPQEPRP", "metadata": {"id": "A0A971U3W6", "cluster": 9604386, "interpro_all": ["IPR002110", "IPR036770", "IPR039425", "IPR014284", "IPR007627", "IPR013249", "IPR013325", "IPR013324", "IPR036388"], "interpro_used": ["IPR007627", "IPR014284", "IPR002110"], "interpro_unused": ["IPR039425", "IPR013249", "IPR036770", "IPR036388", "IPR013325", "IPR013324"]}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein is categorized in the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. Also, the protein possesses a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. Also, the protein carries a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. It is expressed in Buchnera aphidicola (Cinara splendens) and corresponds to UniProt keyword Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase. Generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1988, 2258, 1920, 2894, 3879, 30, 1920, 2213, 1977, 10234, 1922, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 2222, 16, 1920, 2213, 14465, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 2222, 16, 1920, 2213, 16252, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 2176, 1977, 3198, 1922, 25485, 3239, 1019, 27040, 29902, 12, 10510, 9041, 12002, 5233, 1036, 13, 1930, 8852, 1942, 20709, 11121, 2538, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MLLKKNYDLIIFGATGDLAQKKLFPALYQLEKKKYLISSMQIIGVSRTNYTIEEYLNIIYNSLKKFLNENIQPFIWKLLKKRFIFITIDINQIQSFTKLIPYLKKKNSTIINYLAVSSDMFEKIFKGLSLIKLNTLNSKIIVEKPIGKSLSTFLIIEKSMKKYFFEKNIFRIDHYLGKKTILNLIKLKFFNPIFNKYLNKSYIDHVQITLSESIGIENRWNYFDNTGQTIDMVQNHMLQIISIFAMKIPKLFNRKNICNEKIKILKSLRIINKKNIHNYVSLGQYSSGKINNHTVKAYVNEKQAQKNSSTETFVAIKLYIDTKQWKNIPFYIRTGKRLFKKSSKIVIFFKNQHNTLFKNKYIHSTSNRMTINLQPILEMISKNKTKESQLNSNITYKKNKLFNDDKNLFFKNNSLKEYERLLLEIVQNRQFLFVQQKEVIHAWKWIDPIIQAYKSCPKLLQYYTSGTWGPQSAFNLIKKDKKKWDNN", "metadata": {"id": "A0A451DE94", "cluster": 9844902, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR036291", "IPR019796", "IPR022674"], "interpro_unused": ["IPR001282", "IPR022675"]}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein should have a Psq-type DNA-binding HTH domain that mediates DNA binding through a helix-turn-helix structure of approximately 50 amino acids. It is characteristic of the eukaryotic Pipsqueak protein family found in vertebrates, insects, nematodes, and fungi, where it can occur in tandem repeats. Furthermore, the protein carries a HTH CenpB-type DNA-binding domain that mediates specific DNA binding in eukaryotic centromere proteins and transposases via a helix-turn-helix motif. It employs a three-helix bundle structure where the third helix interacts with the DNA major groove, notably recognizing the CENP-B box within centromeric alpha-satellite DNA. In addition, the protein incorporates a DDE superfamily endonuclease domain that typically catalyzes DNA cleavage and strand transfer reactions through a mechanism involving three metal-coordinating carboxylate residues. Although primarily associated with transposable elements, this fold is also utilized by the inner kinetochore protein CENP-B for specific centromere sequence binding, despite the loss of catalytic residues and endonuclease activity in that context. It has been detected in Hirsutella minnesotensis 3608.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 3066, 2162, 43, 2742, 1055, 17, 2601, 2678, 17, 2743, 5334, 1023, 3418, 1988, 10412, 2678, 2743, 2596, 43, 7864, 17, 5165, 17, 7864, 3170, 1927, 3993, 2761, 3835, 4576, 18, 2176, 1977, 6293, 1927, 1920, 10825, 6556, 1036, 5089, 2220, 2213, 3416, 2435, 1922, 14976, 16, 13340, 16, 19669, 16, 1930, 10520, 16, 2597, 2176, 2112, 4704, 1922, 10361, 9569, 18, 3677, 16, 1920, 2213, 16252, 43, 5334, 1023, 19990, 1014, 17, 2601, 2678, 17, 2743, 3418, 1988, 10412, 2487, 2678, 2743, 1922, 10825, 22242, 2697, 1930, 12935, 2319, 3454, 43, 7864, 17, 5165, 17, 7864, 5219, 18, 2176, 22620, 43, 2559, 17, 7864, 14142, 3170, 2597, 1920, 4563, 7864, 9034, 1956, 1920, 2678, 3044, 15920, 16, 7388, 15667, 1920, 19990, 17, 44, 5758, 2651, 25790, 4595, 17, 14199, 2678, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 6758, 1021, 13975, 18697, 3418, 1988, 5745, 17097, 2678, 6404, 1930, 5984, 3856, 5298, 2596, 43, 2856, 5884, 2559, 6048, 17, 19355, 20877, 4248, 18, 2876, 5985, 2458, 1956, 12935, 2115, 5362, 16, 2052, 3728, 1977, 2222, 7079, 2007, 1920, 6671, 21563, 2213, 19990, 17, 44, 1958, 2487, 22242, 3244, 2743, 16, 4281, 1920, 3257, 1927, 6804, 4248, 1930, 18697, 2455, 1922, 1988, 4491, 18, 2176, 2258, 2252, 3330, 1922, 15086, 20490, 2057, 11560, 1019, 21457, 7229, 3355, 1937, 15533, 1025, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MSSPINSRENDIDNAVFEVLDGLSIAAASRDFDVPENSQRLSQRQEQELINWILAEEAAGRPPSKRNVQAFAQLIAVLGSDDRPIGHNWVEEAFRDFYERLDREIKTKSVGSNRIYNIDETGIAEGETQAGKVASILECVSATGRRLTPVVVLTGTNLQGQWFPENFPSWKYDCNPSGWLVLDGASSHVTIDFMHTAWKHHVQLLFLPAHSSHITQPLDVGVFSPLNTFYRQQFAFSKTNIQAGFRAAGIFPTNVERPLATLTRSDQSEGPNEAPRMPKKQKINKRAQTDLLRRDLDGIDRGFRTVATKAGHALDQKNHLITSLKTQNTYLQAQLEAQKPAAVPDIVKARNQAAGAAEEHTERHGSTIEEDAMESARTDQEDMMFTFQVRTTLRRRLQGGTTNRDSKNRFIARHEEIKTKVSRGVPSVRTLHSTVGSSLTKHSTKTTGSSREWSNGEIALKWLEEVFLPETKPEIPSLWRIAGLVDFSINAPRQKQRFLRAYAAGSEENKEWWTPKDSKEVTGRKAVKKNPNDTF", "metadata": {"id": "A0A0F7ZXE3", "cluster": 11154661, "interpro_all": ["IPR050863", "IPR004875", "IPR009057", "IPR006600", "IPR007889", "IPR036397"], "interpro_used": ["IPR007889", "IPR006600", "IPR004875"], "interpro_unused": ["IPR050863", "IPR009057", "IPR036397"]}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein carries a LIS1 homology (LisH) motif conserved site that functions as a protein-binding module in eukaryotic proteins involved in microtubule dynamics, cell migration, and chromosome segregation. Predicted to adopt a two $\\alpha$-helix fold, this motif contributes to regulation by mediating dimerization or by binding cytoplasmic dynein and microtubules directly. In addition, the protein possesses a CTLH domain that forms a predicted $\\alpha$-helical sequence often located immediately adjacent to the LisH motif in eukaryotic proteins regulating microtubule dynamics, nucleokinesis, and chromosome segregation. It is frequently associated with WD-40 or Kelch domains in multi-domain proteins but can also occur independently in specific contexts, such as in the yeast protein RMD5. Moreover, the protein has a TPL/SMU1, LisH-like dimerisation domain that contains a lissencephaly homologous (LisH) motif to facilitate N-terminal protein dimerization. This domain is conserved in eukaryotes and functions in diverse contexts, ranging from transcriptional corepression during plant development (e.g., TOPLESS) to pre-mRNA splicing as a component of the spliceosome (e.g., SMU1). It is expressed in Monopterus albus (Swamp eel) and is described by UniProt keywords Mitochondrion, Repeat, and WD repeat.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 16252, 43, 19620, 1009, 9039, 12, 19620, 1023, 13, 5219, 5305, 3200, 1988, 4088, 1966, 43, 2213, 17, 2743, 9059, 1922, 10825, 2697, 3286, 1922, 10544, 5565, 16, 2024, 5049, 16, 1930, 5597, 12707, 18, 4396, 1942, 14103, 43, 2288, 8, 38, 4595, 8, 17, 7864, 3728, 16, 2052, 5219, 7624, 1942, 3640, 2007, 10239, 13640, 2014, 2007, 2743, 6823, 18188, 1930, 12444, 4103, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 13960, 1023, 3418, 1988, 4952, 43, 4396, 8, 38, 4595, 8, 17, 11514, 3244, 3868, 4810, 6183, 6811, 1942, 1920, 19620, 1023, 5219, 1922, 10825, 2697, 6773, 10544, 5565, 16, 2797, 11172, 1937, 16, 1930, 5597, 12707, 18, 2176, 1977, 5467, 2458, 1956, 17907, 17, 3040, 2014, 16080, 2072, 4682, 1922, 2779, 17, 3418, 2697, 2308, 2112, 2222, 4704, 6407, 1922, 2487, 11144, 16, 2427, 1966, 1922, 1920, 5688, 2213, 10625, 1007, 1015, 18, 3950, 16, 1920, 2213, 2258, 43, 6213, 1024, 19, 2426, 24396, 16, 19620, 1023, 17, 3189, 7632, 6284, 3418, 1988, 5461, 43, 19620, 17221, 26547, 8725, 12, 19620, 1023, 13, 5219, 1942, 6628, 56, 17, 4262, 2213, 13640, 18, 2052, 3418, 1977, 5305, 1922, 15021, 1930, 4088, 1922, 6445, 11144, 16, 6485, 2037, 5224, 4728, 3124, 2409, 4496, 2740, 12, 47, 18, 49, 18, 16, 3700, 5427, 13, 1942, 2097, 17, 3616, 8490, 1966, 43, 4594, 1927, 1920, 10708, 4283, 12, 47, 18, 49, 18, 16, 2426, 24396, 13, 18, 2176, 1977, 3198, 1922, 8914, 2410, 25822, 5311, 1957, 12, 3476, 3456, 11150, 1024, 13, 1930, 1977, 2910, 2007, 20709, 11569, 30017, 16, 6865, 16, 1930, 17907, 6865, 18, 3], "output": "MQANGAGQGQESSELSCINSAQNGESSNNVGTSNGSSTGPSSGTLTASTASGSEIRLIGQHLRGLGLNQTVDLLMQESGCRLEHPSATKFRNHVMESGLSWDLLRMKFLLLQQKYLEYLEDGKVLEALQVLRGEDLRAKAEWEGKGTASRCRLLDKLQTYLPPSVMLPPRRLHNTKLDSSLDSVSLLIDHVCSRKQFPCYTHQLATGSKDTTVIIWQVDLESHQLKLLRTLEGHAYGVSYLAPDDCSELWLWNVQTGELRTKMSQSHEDSLTSVADGNLLDSWEGVRVQCLWCLSDGRTVLASDTHQRIEDHPIMSFTVSKNGRLALLNVATQGVHGVTQGFYTIHSCFGGHNEDFIASGSEDHKVYIWHRRGESDDGTVRIWGPAPFLDSQENCSKMDSTATGTHSNGLISSTDNGASSLKKKKRLSQADEDVGEWEKVGLGLLWLHKSKHFDRRGVLTPLKYNTDRIHVLSGYLMCSHAEQTLLRQAVELQRDRCLYILTEHCNEVWFCKFSNDGTKWSPDDTYLIACGWNPDGKRFVTGGQRGQFYQCDLRGYNFEDLTDRNIVQLWDLQDRVLVRKYQLPIAELTGHTRTINCVSWNPAIPGLMASA", "metadata": {"id": "A0A3Q3R131", "cluster": 11610603, "interpro_all": ["IPR006595", "IPR006594", "IPR054532", "IPR015943", "IPR036322", "IPR001680", "IPR051350"], "interpro_used": ["IPR006594", "IPR006595", "IPR054532"], "interpro_unused": ["IPR051350", "IPR036322", "IPR001680", "IPR015943"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein carries a Ubiquitin-associated (UBA) domain that mediates protein-protein interactions by binding to ubiquitin via a conserved hydrophobic surface patch. This compact three-helix bundle is commonly found in proteins associated with the ubiquitin-proteasome pathway, DNA excision-repair, and cell signaling. Additionally, the protein can be placed in the UBA-like superfamily, which adopts a compact three-helical bundle fold with a conserved hydrophobic surface patch to mediate protein-protein interactions in diverse cellular processes including the ubiquitin/proteasome pathway, DNA excision-repair, and cell signaling. This superfamily encompasses functionally distinct domains such as the TS-N domain of elongation factor Ts, which catalyzes EF-Tu recycling during translation, and the C-terminal domain of TAP/NXF1, which binds FG nucleoporins to facilitate nuclear export. It is found in Microthyrium microscopicum. Please provide the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 7762, 30, 1920, 2213, 16252, 43, 6526, 17, 2458, 12, 4803, 1019, 13, 3418, 1988, 10412, 2213, 17, 2213, 3719, 2007, 2743, 1942, 6526, 3454, 43, 5305, 7919, 3154, 7504, 18, 2052, 13726, 2559, 17, 7864, 14142, 1977, 5384, 2435, 1922, 2697, 2458, 1956, 1920, 6526, 17, 9993, 3374, 16, 2678, 10940, 17, 5059, 16, 1930, 2024, 3197, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4803, 1019, 17, 3189, 13975, 16, 2154, 24032, 43, 13726, 2559, 17, 11514, 14142, 3728, 1956, 43, 5305, 7919, 3154, 7504, 1942, 8265, 2213, 17, 2213, 3719, 1922, 6445, 3689, 4028, 2710, 1920, 6526, 19, 9993, 3374, 16, 2678, 10940, 17, 5059, 16, 1930, 2024, 3197, 18, 2052, 13975, 21569, 9346, 4493, 4682, 2427, 1966, 1920, 4894, 17, 56, 3418, 1927, 9971, 2991, 4894, 16, 2154, 17097, 8485, 17, 9037, 13977, 2409, 6410, 16, 1930, 1920, 45, 17, 4262, 3418, 1927, 10167, 19, 27578, 5739, 16, 2154, 6876, 13320, 2797, 7540, 5572, 1036, 1942, 6628, 4254, 12660, 18, 2176, 1977, 2435, 1922, 7666, 30338, 3027, 1989, 10372, 1989, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MEYDCAIGSSNIYVENDSSESEKEPQMIGDRNAKSFDVVINLPDTHEFDLVSGLSWEKPQRYVSDSILKRNDISLVDEHGNRLKTIFLEWLLSEPSGSSVKSGNFTILPDEAMTHDAIANWSSTKELEDDVALQAVNRIERARIRGLQRRGTDSRTSPSSGKFPSSTHKRYRRPINDDGEEDEEFESLPEQSKTAKNKSRATHDSKGWASDLESLRIQHEPLIPPALLDDSEYQKQIASRTGERQGDDEVRPTNPFIDSQGRITSPWFSETQEGRYPVEIADEDFASAPEESRGRGITNLPYHSRQASEEPYVDQLRQLNDMGFYESEHNVKALRKSGGKVQRAVEHLLSGDF", "metadata": {"id": "A0A6A6UG73", "cluster": 14380188, "interpro_all": ["IPR015940", "IPR009060"], "interpro_used": ["IPR015940", "IPR009060"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein contains a Cro/C1-type, helix-turn-helix domain that functions as a DNA-binding module within transcriptional regulators found in bacteriophages, prokaryotes, and eukaryotes. This motif typically employs a specific recognition helix to bind the DNA major groove, often operating within a dimer to control gene expression, such as the regulation of phage lysogeny and lytic growth. Additionally, the protein is associated with the Lambda repressor-like, DNA-binding domain superfamily, which functions as a transcriptional regulator controlling critical genetic switches such as bacteriophage lysogeny and bacterial sporulation. This domain typically adopts a four-helix closed folded leaf topology, a variation of the helix-turn-helix motif, to mediate specific DNA binding and interactions with RNA polymerase. Structural analogs of this fold are also conserved in eukaryotic POU transcription factors and the N-terminal domain of the metabolic enzyme cyanase. It is produced by Anoxybacter fermentans.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 5461, 43, 9442, 19, 8817, 17, 2601, 16, 7864, 17, 5165, 17, 7864, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 9059, 2651, 5224, 9098, 2435, 1922, 24613, 1036, 16, 28149, 16, 1930, 15021, 18, 2052, 5219, 5745, 22620, 43, 2487, 5708, 7864, 1942, 4566, 1920, 2678, 3044, 15920, 16, 3868, 8654, 2651, 43, 7632, 1942, 2285, 2359, 2294, 16, 2427, 1966, 1920, 3640, 1927, 10503, 3629, 27791, 1930, 17033, 2905, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 18279, 14434, 17, 3189, 16, 2678, 17, 2743, 3418, 13975, 16, 2154, 4088, 1966, 43, 5224, 7888, 7138, 4140, 3299, 21529, 2427, 1966, 24613, 3629, 27791, 1930, 4543, 23647, 18, 2052, 3418, 5745, 24032, 43, 3006, 17, 7864, 8047, 16318, 6998, 13678, 16, 43, 4516, 1927, 1920, 7864, 17, 5165, 17, 7864, 5219, 16, 1942, 8265, 2487, 2678, 2743, 1930, 3719, 1956, 3146, 6479, 18, 4346, 13204, 1927, 2052, 3728, 2032, 2222, 5305, 1922, 10825, 28398, 3213, 2790, 1930, 1920, 56, 17, 4262, 3418, 1927, 1920, 4487, 4113, 10208, 2051, 18, 2176, 1977, 4152, 2007, 28976, 10465, 7972, 2341, 1915, 17748, 2075, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MDYDNLKDKKKLMGESYISAWKNGHRLIPTLYIHKISEIGKKIAKARKLKNMQYIDLAKKAKAEELEKIAEELNLTSIEAIIQQIKFDIEMYRLAFLLKEHNIKNKELAKILNVSEYFGVPVSYLMGEDIENHWQKTGIAPIRLSQIERGIIKVDELTIDFESCIEEIKKLCVKIGVSDE", "metadata": {"id": "A0A3Q9HQY7", "cluster": 15177951, "interpro_all": ["IPR001387", "IPR010982"], "interpro_used": ["IPR001387", "IPR010982"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given the following functional description of a protein, generate a complete amino acid sequence that performs the described role. The desired function is: The protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein carries a RecF/RecN/SMC, N-terminal domain that functions in essential chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, and DNA repair. This domain facilitates the formation of heterodimeric SMC complexes and higher-order structures required for chromatin dynamics and epigenetic silencing. It is also central to the activity of RecF and RecN proteins in DNA metabolism and recombination. Additionally, the protein is a member of the Chromosome partition protein MukB/SMC family, which is essential for chromosome condensation, segregation, and cell cycle progression. These proteins function as V-shaped homodimers characterized by large intramolecular coiled-coil regions and a hinge domain. They facilitate chromosome organization by introducing negative DNA supercoiling to condense DNA during cell division. It is derived from Enterorhabdus sp. P55 and exhibits UniProt keyword tags ATP-binding, Coiled coil, and Cytoplasm.", "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 16, 5655, 43, 4080, 3835, 2687, 3244, 1988, 17436, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 16252, 43, 2090, 1038, 19, 2090, 1022, 19, 16312, 16, 56, 17, 4262, 3418, 1988, 4088, 1922, 4415, 9220, 2127, 19666, 16, 2710, 5597, 16112, 16, 14611, 17, 28829, 21275, 16, 1930, 2678, 5059, 18, 2052, 3418, 11374, 1920, 3337, 1927, 30194, 16312, 5048, 1930, 2580, 17, 3238, 4061, 3414, 1958, 6338, 5565, 1930, 8542, 8343, 18, 2176, 1977, 2222, 4101, 1942, 1920, 2455, 1927, 2090, 1038, 1930, 2090, 1022, 2697, 1922, 2678, 4714, 1930, 7827, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 5597, 11334, 2213, 8975, 11228, 19, 16312, 3416, 16, 2154, 1977, 4415, 1958, 5597, 16112, 16, 12707, 16, 1930, 2024, 4048, 4380, 18, 2144, 2697, 2347, 1966, 64, 17, 9132, 29227, 4378, 2007, 3103, 18083, 17524, 17, 9121, 3451, 1930, 43, 20484, 3418, 18, 2611, 6628, 5597, 5901, 2007, 13930, 3136, 2678, 26936, 13697, 1942, 11637, 1021, 2678, 2409, 2024, 8451, 18, 2176, 1977, 3595, 2037, 5553, 20846, 1957, 2056, 18, 18974, 1015, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 17524, 9121, 16, 1930, 5239, 18, 3], "output": "MYLKSLVLKGFKSFADRSVMALEPGITAVVGPNGSGKSNISDAVLWVLGERNAKHLRGQAMEDVIFAGSSARKPTGLAEVDLVLDNSDGTLPIDYDEVAITRRMYRNGESEYLINGTVARRMDVLEILHDSGLGTGTHSIISQGSLDSILQSKPEDRRALIEEAAGVLKHKQRKAKSERKLASMDQHLARARDVVAEVERQLGPLSRKAKKARTYQELAGELADVSLRLAVDDLRTLQRAWDGSQEKEAALAADMEAKRAAIEAAEAAVEELQERIRLDSVDAGELSRQYRAAAAAVERFDSAALVMHERRRAATARAGEIELEIEAAQARRAAAEAELRGA", "metadata": {"id": "A0A7K3L474", "cluster": 16463195, "interpro_all": ["IPR050308", "IPR027417", "IPR003395"], "interpro_used": ["IPR027417", "IPR003395", "IPR050308"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence of a protein with the following function look like? Here is the function: The protein is assigned to the Ribonuclease Z/Hydroxyacylglutathione hydrolase-like superfamily, which comprises proteins sharing a duplicated $\\beta(4)-\\alpha-\\beta-\\alpha$ fold that typically bind two zinc ions to facilitate hydrolytic activity. This group includes glyoxalase II thiolesterases, which convert S-D-lactoyl-glutathione to glutathione and D-lactic acid, and competence proteins required for natural transformation and DNA uptake in species such as *Neisseria gonorrhoeae*. It has been characterized in Compsopogon caeruleus.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 18347, 2051, 68, 19, 8275, 14645, 16542, 2183, 7253, 20748, 17, 3189, 13975, 16, 2154, 12936, 2697, 10763, 43, 19479, 8, 38, 4666, 12, 24, 13, 17, 38, 4595, 17, 38, 4666, 17, 38, 4595, 8, 3728, 1988, 5745, 4566, 2288, 7997, 6982, 1942, 6628, 26702, 2455, 18, 2052, 2210, 5921, 3376, 23859, 2051, 2890, 13914, 8342, 2319, 16, 2154, 14450, 61, 17, 46, 17, 5641, 10921, 17, 9153, 1942, 9153, 1930, 46, 17, 16562, 2687, 16, 1930, 12939, 2697, 3414, 1958, 4613, 7002, 1930, 2678, 5047, 1922, 3038, 2427, 1966, 14, 28356, 18339, 27702, 6802, 3336, 14, 18, 2176, 2258, 2252, 4378, 1922, 2059, 2204, 7056, 3827, 1022, 2332, 29755, 1957, 18, 3], "output": "GRRRNSVLPVLQQEFPGPVRANYGYNLEMLRPGVFAVWDGAYFAMIVKGSDRISFFDFPQNPFARSDVVVGSRMVDAGLEILDGEVPDHIDMVYSHDHYDHFGSSQVAYSELIGLFPSAVIRIWSSWQVKNRLESRQSQDTPIRAPIPTEIIE", "metadata": {"id": "A0A7S1T960", "cluster": 19233978, "interpro_all": ["IPR036866"], "interpro_used": ["IPR036866"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein is included in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, the protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Furthermore, the protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It originates from Flavonifractor sp. An4 and is classified with UniProt keywords Cytoplasm and rRNA processing.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 22970, 2037, 12094, 1974, 5524, 2341, 1924, 2056, 18, 1925, 1006, 1930, 1977, 5947, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MSETGFSHKPVLLAECIEALNIRPDGIYLDVDRDQAALNAAEERLAQWRDKVTLVHSNSSPQLDDGSRGFSYMADAPLDMRLRRILWQYGEERYSSAIAGAIVRAREKALREKQHPAKRSFQAIRIAVNDELGSVDKMVRSLEDRIVKNGLAEYAKGCTCPPDFPVCGPEELEENPRARSAKLRVAEKLRERGTLGRAGHSREIVKRLTSGRLICFCELDAILDKLGLEGVDGMLFDLGVMDQSDGLTARIVVNEWPQEEKPVETTLELVDIIKGAMPASAVPRLNPGGRLAVISFHSVCGKKPQIKLITRKPIVS", "metadata": {"id": "A0A1Y4A329", "cluster": 21371087, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a protein with the following function: The protein should have a AbiU2-like HEPN domain that functions as a component of the AbiU2 abortive infection system to provide anti-bacteriophage defense and limit the spread of viral infection. It occurs in Bradyrhizobium sp. cir1. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 13127, 1032, 1028, 17, 3189, 3357, 1022, 3418, 1988, 4088, 1966, 43, 4594, 1927, 1920, 13127, 1032, 1028, 11380, 2185, 2909, 2433, 1942, 3394, 2246, 17, 24613, 9720, 1930, 4411, 1920, 6441, 1927, 4324, 2909, 18, 2176, 5110, 1922, 20152, 5004, 2061, 23156, 2056, 18, 3252, 1009, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MPSPLPIEDRIERAAQLVLRSRIFFDIWFYFEGADTRPHLLDTMNEFSEFFRFAPHAHFVAFVVSVAALFEKRRDTITLPALSREMARAGMLSPQAYSEVEALISHAEPLAGKVTILRHNAFAHRSARISYDDIFKAAAITPAQMRELTEIALKVANALLRARGHQEQFFNELAREDAETMMRVLQSATHNG", "metadata": {"id": "A0A7W6SQH3", "cluster": 21867808, "interpro_all": ["IPR040704"], "interpro_used": ["IPR040704"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein is included in the MgtC/SapB/SrpB/YhiD family, which comprises a group of bacterial transmembrane proteins, including the representative members MgtC, SapB, SrpB, and YhiD. In addition, the protein features a MgtC/SapB/SrpB/YhiD N-terminal domain that serves as a bacterial virulence factor required for growth in low-magnesium environments and survival within macrophages. It is hypothesized to regulate membrane potential by activating the Na+/K+-ATPase. Furthermore, the protein should have a Domain of unknown function DUF4010 domain that is found in putative membrane proteins from archaea and bacteria. It is produced by [Flexibacter] sp. ATCC 35208 and is classified with UniProt keywords Cell membrane and Transmembrane helix.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2786, 6916, 19, 9235, 1014, 19, 19939, 1014, 19, 67, 7969, 1007, 3416, 16, 2154, 12936, 43, 2210, 1927, 4543, 9117, 2697, 16, 2710, 1920, 5051, 4678, 2786, 6916, 16, 9235, 1014, 16, 19939, 1014, 16, 1930, 67, 7969, 1007, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 2786, 6916, 19, 9235, 1014, 19, 19939, 1014, 19, 67, 7969, 1007, 56, 17, 4262, 3418, 1988, 10634, 1966, 43, 4543, 9304, 2991, 3414, 1958, 2905, 1922, 2330, 17, 13148, 8114, 1930, 3298, 2651, 5205, 18, 2176, 1977, 7149, 1942, 5741, 3260, 2889, 2007, 8019, 1920, 4049, 15, 19, 53, 15, 17, 9444, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 3418, 1927, 5435, 2347, 4855, 10432, 6924, 1008, 3418, 1988, 1977, 2435, 1922, 6770, 3260, 2697, 2037, 21501, 1930, 4802, 18, 2176, 1977, 4152, 2007, 37, 5795, 26073, 2341, 1915, 39, 2056, 18, 11037, 26902, 13895, 1930, 1977, 5947, 1956, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 3], "output": "MDEFMHLDAAPIALKMAVSTGIGMLVGMERKWSQKEAGIRTFSIVALLGMLSAVISEQFIIISMIGVFLLVIAINARSLLAERQVEITTSAALIVNCVLGILVGLGHIFTPVAGAIVMTMLLAWKSELNKFAGGLLPSEIRSAILLGLIGFVIYPILPDKYIDRWELFNPSDAWISIIAIAGIGFVNYVFLRIFSTGGLYLGAVFGGLVNSSATVAEMSSRVQTSGLTSKMTTLCMLTTIAMFARNLVIATLFSPASLSSTLIPLLAMSIVAALFIWRDKIHETKITEDTGTLKLASPISLPKVLWFGLLFILIQVGGTLLTRVFGSYGLLATGVFGGLVSSASTTAAAATMAMHNRISPALAGNVAILSSLASAVVNLPLVWKNIQDKGVVRKLTIELMVVLGVGIILVILDRIFQLSEMLLKL", "metadata": {"id": "A0A1V2BCA5", "cluster": 25530273, "interpro_all": ["IPR025105", "IPR003416", "IPR049177"], "interpro_used": ["IPR003416", "IPR049177", "IPR025105"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein includes a Peptidase M48 domain that functions as the catalytic region of zinc-dependent integral membrane metalloproteases, including CAAX prenyl proteases. It typically localizes to the endoplasmic reticulum or Golgi to proteolytically remove the C-terminal three residues from farnesylated proteins, utilizing a characteristic HExxH motif within a deep substrate-binding cleft. It is found in Cohaesibacter celericrescens and corresponds to UniProt keyword Hydrolase, Metal-binding, and Transmembrane helix.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 5921, 43, 24050, 21397, 1025, 3418, 1988, 4088, 1966, 1920, 6804, 3031, 1927, 7997, 17, 3100, 12328, 3260, 28629, 2319, 16, 2710, 20951, 1039, 9972, 2199, 12447, 18, 2176, 5745, 18440, 1942, 1920, 13355, 12279, 2014, 10277, 1942, 12712, 2169, 7989, 1920, 45, 17, 4262, 2559, 4248, 2037, 24281, 4336, 2697, 16, 10232, 43, 6293, 7142, 1039, 1023, 5219, 2651, 43, 6515, 4510, 17, 2743, 14649, 18, 2176, 1977, 2435, 1922, 3757, 3336, 12924, 7972, 2341, 1915, 15765, 3383, 2808, 22749, 1930, 8852, 1942, 20709, 11121, 2538, 20748, 16, 6048, 17, 2743, 16, 1930, 9117, 7864, 18, 3], "output": "MTQASNDTHSLATAIHRFVLSGKNLWCVTAFVVFGTARGLYHFVQEFNLYLHSNPMELVRWLGGVVAQFELVSILFIAHYRRFSRPIGASLTQNKQAGAATRELLARVGYFSVGRVFFAPKGQVSRLLKGKPAENQTKTLTFFMVHEYAHSIYVFVFLSLLGPVLLLGSALASSSPMGPLLTVPLSLTVFLLFCREFFADQAAFTFVPDAENPYGLQTDLRRPDAICALSNNISGSLHARNLLVFFWGVAFSIRTLYILVAPKDWCFSILAFDLMRPTFPWVLTLLSILAVEIAGPGLFGAPGLILLLTFFFACFYLGIKKLVKMRKSEPRRTGQLLKRLLLRFMIQPFLRHFITLEFLNTGLVVNTMLLGMLCLGVVTRFALVTTQGALIVFVMTGIMHLVLTDMLASARRSVLAIFYLMLRCVAYWARNKLDKIELNLEQMICRGVATLFLMMTVLHSLDSARGRSILDLSAWAVTGVFKDIQTPIIREGLVSNAFAVTKDNLANSVFLVVISSVALCFYGMWVSYIKAYERDQHRQGYAAALAAFFVLYRCLPKRPPQLLKAVYWDAFSNENAQLMGLAPGNAVEYFVVCVVVLLFCFLYHQYKNFFVVNRQAPVSWDFLIGLVRTSDLPSALIVGVIS", "metadata": {"id": "A0A2N5XUQ0", "cluster": 26712263, "interpro_all": ["IPR001915"], "interpro_used": ["IPR001915"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that can perform the following function: The protein should contain a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. In addition, the protein should feature a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Also, the protein contains a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It originates from Biomphalaria glabrata (Bloodfluke planorb) (Freshwater snail) and has UniProt annotations Transmembrane helix, Magnesium, and Glycoprotein. Give the amino acid chain.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 2222, 16, 1920, 2213, 5461, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 22970, 2037, 4071, 6256, 6148, 29866, 12, 2877, 5842, 3324, 4720, 4174, 13, 12, 18762, 15929, 13, 1930, 2258, 20709, 15010, 9117, 7864, 16, 13148, 16, 1930, 11424, 18, 7031, 1920, 3835, 2687, 4659, 18, 3], "output": "MANLPLALANVGRNIHFEDSYTLSRDEKHMSSSRDANGCASAHPSEVSLDFEATNTATLVKCRNHNSNGDVERSIFNNGVVPPDAGHGESPPSTPATLRQHVTHEERLSSISSQLALFRDSSAEPSSSDPNSKEKTLSLKRVKGSFNDLDLEKLYKDYTVRSKFPLVVMYLAVLTFATLVLLLLTASQIEKEAKSIGRLVILCLTLILFISLLIVILRFRQKSFISQPTRLAFTIVAVTTLSIIIYFILGYDERTPTSDVPALFYTVVVSYMVLPLSRKWMVISGTVIILAHLLTTTLVILLNPKDRHNDLPAQLLCTLLTLVCANVFGLSHRFLSEIVHRRAFLEARNSVDSMIKLEKEKQQQDELLVSCIPSNLITEIKKDLQENMREPRPTIFHDLYVERYDNVSILYADIVNFTPLASECTAAELVKMLNELFGRFDQLASKSNCMRIKILGDCYYCVSGVPSADKNHALNCVRMGLRMLDAIRDVREATGVDVDMRIGVHTGSVLCGVLGLRKWQYDVWSDDVTIANHMESGGLPGRVHISRQTLDFLEGEYEVEEGRGHERSVFLAENKIETYLVIPVERRHARDRKLGKTRYHLSGLRKSLRVSKFLETWGVDKPFANLKTSSMVSKVLSLTSLALIDSNFMMNSAGIDQGLMAADKQQQEEINMRLQERLNNINNSSFHSHPDAEMHPVTLRFLDQSAENSFSKQSDDMFSFYVIPAFVIFFIIFIIQAIMLPRVTVLFVTSTLGILFFTALTAVCLCNKIHIFRYCHKFLDIFTHISTTIGNTSYIRVLFSLSCEVLIFFTSTISMAYCQAQEFTKNCSDNVNVTMEAGTALCSYPSYYLLCFLLAFTSYSIFIQISFIIKFLFLGAMFSLNTILVHVVRWQIFDTYDYMFCNTSPHGFSLKVETSLCIAVVLFTMHFLDRQMEFANRLGHLFKLQFQQETEQVKMMAAINKIVLENIIPAHVIAYYLRTSRKHEDLYHESCSDVCVMFASIPNFKDFYQQTKTNGEGLECIRVLNEIISDFDLLLIKKHQEVEKIKTIGSTYMAATGLHTGSRKNEDDMSWEKNIVALIEFSLAMIGTLDLINRHSFNEFSLRIGANHGPVIAGVIGARKPQYDIWGDTVNVASRMDSSGVSGKIQVTEETAAVLIKNGYSLEYRGLTKVKGKAPMKTFFILDRRPFVDPKDRLIELTRL", "metadata": {"id": "A0A9W3AWD3", "cluster": 28626580, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR009398", "IPR029787"], "interpro_used": ["IPR009398", "IPR018297", "IPR001054"], "interpro_unused": ["IPR032628", "IPR030672", "IPR029787"]}, "task_type": "autoregressive"} {"instruction": "The protein should feature a TonB, C-terminal domain that interacts with the N-terminal TonB box of outer membrane transporters to facilitate the active uptake of iron-siderophore complexes. This domain positions itself within the transporter barrel to transduce energy required for the translocation of the iron complex across the outer membrane. It is expressed in bacterium and is connected to UniProt keyword Transmembrane helix. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 16501, 1014, 16, 45, 17, 4262, 3418, 1988, 9034, 1956, 1920, 56, 17, 4262, 16501, 1014, 5758, 1927, 7642, 3260, 10538, 1942, 6628, 1920, 3500, 5047, 1927, 5680, 17, 22940, 11082, 5048, 18, 2052, 3418, 6490, 6999, 2651, 1920, 9054, 19560, 1942, 30334, 3844, 3414, 1958, 1920, 7849, 1927, 1920, 5680, 2796, 3436, 1920, 7642, 3260, 18, 2176, 1977, 3198, 1922, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9117, 7864, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MRSNFQKPILGITLVISMVIHVVLILAVPSIRMVPSSSGVPSSSSGEYTEVQLIGTEEVQAPVSSQENLLAEVQKTGRVTQEVPTKLDVTEPEPAPLKKPDLLAKAQDLQNKNRDTEGKALEDSSEERSSQPSKPLPDLTSLKVTNPERLPEEATRDRISKVGEPTSKETPQLKDPISTVPEQKLQTTLKQPQALPQPQDPAPVPRAPGMPDTLSEAVPLPKEEASSKRPVPESSLTASNPNPVQPEQVDKRPEGEVPLDPTVHKETPIQLKDPMAAIPEQEIKPVLKRPGPAVKSQDPAPPLQAPEMPIALPEQAPLPREADSSKVQIPDLSKPGPVFVQPDQAGQIAKSEVPVEQSAKETPQSKDKTPAKLEDPLLTQEGLKPQRPEPTSEEPIGSLRPPSETIPQVVQKEPAPEQERSKQTQVKQRTVELENKTDLQVRKDDPEVKPGEGDKETPGVKDKVLVLAEQTAPEKLPPSEKNRTSPEEPAPVVQAPVEVSGTNGDQGVPTLAQESSKKRKMVENLQVAPPAVRPEVGAVRESSLPDAVSSPSLTTPKEVPETQDPVALAPPAPTIRKNTSAPPMTSESLPLGEALAYNMGFRTATVPGQGLPSELGSSKSSPVPGLGDLNPAEPQKNSFGVPRPKEEVKREAVRDPKASVLPPPLADPGHKEGLAIPLPKSPPAKFQIQGPAGTREIIFQPNPPKVDIHVEGDVVLKFWILPDGTVGRVIPLKKVDAQLEQAAINYIQKWRFAPLPGNVPQEEEWGIIPIKYKLK", "metadata": {"id": "A0A7V3XE22", "cluster": 28773711, "interpro_all": ["IPR006260", "IPR037682"], "interpro_used": ["IPR037682"], "interpro_unused": ["IPR006260"]}, "task_type": "autoregressive"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein is assigned to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. In addition, the protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Furthermore, it is part of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is present in Acidimicrobiaceae bacterium and is connected to UniProt keyword Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 1977, 6304, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 2481, 1922, 2687, 1980, 1935, 15129, 19476, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 3], "output": "MARSHGSRRFAARVSRPVHRWRRLVTASGSDPLHSSNQNQLGRTFSHEPVMLKEVLDTFASLREGLFVDATVGGGGHAEALLTDSANRNLLGLDRDLAAVLATRKRLRDFDNRIEIVHCRFDEISGLSQLAEVELSGALFDLGVSSHQLDTADRGFSYRLDSDLDMRMDTSAALDAYQVVNNYSERELASIIRAYSDERFAGRIAAAIISQRPISSTLELADVVRGAVPAAARRTGRHPAMRTFQAIRIEVNSELDLIKPALNQIIERLRPGGRIVVLSYHSGEDRIVKQVLREAADGLCVCPSTLPCICGSEPNVKLLRRKVTRPSTDEVNRNPRSASARFRAAERLSAGEA", "metadata": {"id": "A0A2D9RS10", "cluster": 878401, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein belongs to the The Peptidase M8, leishmanolysin family, which comprises metallopeptidases sharing a thermolysin-like fold, including the abundant GPI-anchored surface endopeptidase of *Leishmania* parasites. These enzymes function as virulence factors adapted to acidic host environments or, in chordates, as developmental regulators such as invadolysin and the left-right patterning protein CIROP. It has been characterized in Dictyostelium firmibasis and is connected to UniProt keyword Membrane, Transmembrane, and Signal.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 1920, 24050, 55, 1025, 16, 14251, 23872, 3416, 16, 2154, 12936, 8969, 24897, 1036, 10763, 43, 7967, 19010, 1921, 17, 3189, 3728, 16, 2710, 1920, 7437, 17497, 17, 17199, 3154, 16239, 9626, 2410, 9200, 1927, 14, 18344, 14, 9687, 18, 2144, 5038, 2347, 1966, 9304, 2790, 8461, 1942, 9931, 4423, 8114, 2014, 16, 1922, 22015, 2209, 16, 1966, 5878, 9098, 2427, 1966, 26908, 23872, 1930, 1920, 3506, 17, 3659, 16060, 2213, 3252, 2011, 18, 2176, 2258, 2252, 4378, 1922, 29060, 18092, 12191, 1989, 15384, 26073, 8362, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 2733, 18, 3], "output": "MQKIIYLSIVLLVVSLFLISIGFSSPTLFNNNNNENENYSNKLLQRHNNNNVDKNINNIINKGYQKMVDGLKLKSQFHYDEDKYMKRAMEKQQTNPLGYKCQHDSIVQKRIEKVKNNLKESSNNNQNNMKTSEKLVKDAKTLEAAANTVSSTSQPIRFQFDTSYITGTKDQYACHNVGDVISVGGSSNAVKPCQPDGSVDVCLYTCTEADVQTTQLQNFYKNNIIETIKEVFQSRLLVRNPQNSFTFNPTATDGTCDYGVSIPESYYTTGIQNTDIYVWVTSRPTSSNNTIAYAFACDYDTSNNILGRPRAASINFNPMFFSPFIGAENSISFNEYVRVGIHEMTHALGFSSSFFDSYVKPNTNDVIRDGVGAAQTFEFSGKTPSGEKYTVSKAAIYSDNVVNFGKQHYGCQGLTYQELEDFGGSGTAGSHWEARTAGEEYMLGFVSPIMPITDLSFNLLLDSGWYEIVTNSSEPLVWGRGLGCDFVQKPCSTETWNYQGYFCTENGATSCTGTRMGKGVCKIVQGQNDWQPMYQHLNNPKLVGYNLAADGCPFYSVQDDNVYCFDTSKQSTANSQIYEEYCEDCRCFEFKDPNDNSIQQSCWEQRCGSNGLQIKINNNWIDCPDSQTVVSSNVTVVCPTGYTICGGEPKPIVLVGGNPATIILPYFILIISLITLSYLLI", "metadata": {"id": "A0AAN7UHN1", "cluster": 1157280, "interpro_all": ["IPR001577"], "interpro_used": ["IPR001577"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein is a member of the The prokaryotic-type Ku family, which is predicted to mediate the repair of DNA double-strand breaks through a mechanism similar to eukaryotic non-homologous end-joining (NHEJ). These proteins typically function as homodimers that bind to DNA ends by forming a ring-like structure with a highly charged central channel, allowing the DNA to pass through without direct base contacts. Moreover, the protein should contain a Ku70/Ku80 DNA-binding domain that forms the central \u03b2-barrel structure of the Ku heterodimer, serving to recognize and bind DNA double-strand breaks. This interaction is essential for initiating the non-homologous end-joining pathway to maintain genomic integrity. In addition, the protein is included in the SPOC-like, C-terminal domain superfamily, which comprises proteins with a closed \u03b2-barrel fold involved in transcriptional regulation and DNA repair. This domain is found in Spen proteins, such as SHARP, which function as transcriptional repressors in Notch and nuclear receptor signaling, as well as in the Ku70/Ku80 heterodimer, which binds DNA double-strand breaks to facilitate non-homologous end-joining. It is expressed in Acidobacteriota bacterium.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 1920, 21545, 17, 2601, 11352, 3416, 16, 2154, 1977, 4396, 1942, 8265, 1920, 5059, 1927, 2678, 4825, 17, 5984, 13065, 2596, 43, 2856, 2551, 1942, 10825, 2447, 17, 8725, 2482, 17, 15836, 12, 19576, 13, 18, 2144, 2697, 5745, 2347, 1966, 29227, 1988, 4566, 1942, 2678, 9618, 2007, 7402, 43, 6335, 17, 3189, 3170, 1956, 43, 3626, 9516, 4101, 4999, 16, 7201, 1920, 2678, 1942, 4675, 2596, 2979, 3083, 5170, 9070, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 11352, 4618, 19, 11352, 4476, 2678, 17, 2743, 3418, 1988, 4952, 1920, 4101, 161, 17, 19560, 3170, 1927, 1920, 11352, 15672, 16, 13915, 1942, 9967, 1930, 4566, 2678, 4825, 17, 5984, 13065, 18, 2052, 2835, 1977, 4415, 1958, 12410, 1920, 2447, 17, 8725, 2482, 17, 15836, 3374, 1942, 6698, 4935, 7996, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 18055, 1030, 17, 3189, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 12936, 2697, 1956, 43, 8047, 161, 17, 19560, 3728, 3286, 1922, 5224, 3640, 1930, 2678, 5059, 18, 2052, 3418, 1977, 2435, 1922, 6077, 1022, 2697, 16, 2427, 1966, 11707, 16, 2154, 2347, 1966, 5224, 26446, 1922, 8091, 1930, 4254, 3148, 3197, 16, 1966, 2486, 1966, 1922, 1920, 11352, 4618, 19, 11352, 4476, 15672, 16, 2154, 6876, 2678, 4825, 17, 5984, 13065, 1942, 6628, 2447, 17, 8725, 2482, 17, 15836, 18, 2176, 1977, 3198, 1922, 2687, 5883, 3940, 3857, 14061, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MAARPTWKGFMKISLVNECQTRIQQKRWCPKCEREDGRRGHGQGASLFRAALLPRARRPDGLRVLRRHSIPVRVFPATDSAASISFNQLHAGIDARHRPRPVHRRGRDRSD", "metadata": {"id": "A0A2V8GE47", "cluster": 3691686, "interpro_all": ["IPR006164", "IPR009187", "IPR016194"], "interpro_used": ["IPR009187", "IPR006164", "IPR016194"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein features a YoaP-like domain that forms a conserved feature typically located at the C-terminus of bacterial and archaeal proteins, such as *Bacillus subtilis* YoaP. This approximately 40-amino acid region is characterized by a single completely conserved alanine residue of potential functional importance. It originates from Clostridium scindens (strain JCM 10418 / VPI 12708).", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 4075, 43, 7419, 2026, 17, 3189, 3418, 1988, 4952, 43, 5305, 5961, 5745, 4810, 2019, 1920, 45, 17, 7822, 1927, 4543, 1930, 22367, 2697, 16, 2427, 1966, 14, 14587, 14745, 14, 7419, 2026, 18, 2052, 3993, 3040, 17, 3835, 2687, 3031, 1977, 4378, 2007, 43, 2957, 5796, 5305, 10504, 6181, 1927, 2889, 3183, 4737, 18, 2176, 22970, 2037, 21156, 14975, 5233, 1036, 12, 3943, 14904, 1035, 8824, 3928, 19, 9314, 1033, 10899, 13895, 13, 18, 3], "output": "MRFPVIKTARWLQKAVEILSEKKFEKIAKRRAAVKTIPGRTCPFAFTSYCLFYDGKFLTN", "metadata": {"id": "A0A844F7Y9", "cluster": 7328098, "interpro_all": ["IPR025685"], "interpro_used": ["IPR025685"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein is classified under the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. In addition, the protein should include a RmlD-like substrate binding domain that binds a sugar nucleotide substrate to facilitate the final step of dTDP-L-rhamnose synthesis. This domain functions within the RmlD enzyme to produce a precursor for L-rhamnose, a saccharide required for virulence in certain bacteria. Also, the protein is classified under the dTDP-4-dehydrorhamnose reductase family, which typically catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose, a precursor essential for bacterial cell wall components like lipopolysaccharides. Members of this family also include the regulatory subunit MAT2B, which modulates S-adenosylmethionine synthesis, and enzymes involved in the biosynthesis of antibiotics such as oleandomycin. It is found in Rhodospirillaceae bacterium TMED167 and is classified with UniProt keywords Oxidoreductase.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 10625, 4184, 17, 3189, 4510, 2743, 3418, 1988, 6876, 43, 9523, 5489, 4510, 1942, 6628, 1920, 3948, 3537, 1927, 7711, 10274, 17, 54, 17, 23120, 2217, 4271, 18, 2052, 3418, 4088, 2651, 1920, 10625, 4184, 4113, 1942, 5074, 43, 7897, 1958, 54, 17, 23120, 2217, 16, 43, 14175, 2205, 3695, 3414, 1958, 9304, 1922, 4908, 4802, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 7711, 10274, 17, 24, 17, 28936, 5004, 17652, 2217, 11386, 3416, 16, 2154, 5745, 17097, 1920, 3378, 1927, 7711, 10274, 17, 26, 17, 16333, 17, 54, 17, 7518, 1039, 1037, 17, 24, 17, 7142, 8658, 1942, 4307, 7711, 10274, 17, 54, 17, 23120, 2217, 16, 43, 7897, 4415, 1958, 4543, 2024, 4821, 4178, 3189, 15614, 1036, 18, 4678, 1927, 2052, 3416, 2222, 3951, 1920, 4948, 5903, 2888, 9385, 16, 2154, 13112, 61, 17, 29283, 23568, 11215, 4271, 16, 1930, 5038, 3286, 1922, 1920, 8132, 1927, 7560, 2427, 1966, 12188, 24922, 4636, 18, 2176, 1977, 2435, 1922, 11490, 3106, 23576, 11560, 9914, 14061, 22377, 7240, 6038, 1930, 1977, 5947, 1956, 20709, 11569, 27388, 18, 3], "output": "MIIILGASGVIGSQLHSMARDRGETIIGTYHSQPYPRLQKFDMLQDSLLDTMPQLASSDTVVVLSAYTNPNWIFENSRRAHDLNVIATCRIIDEAISRGAQIVFPSTEIIFADQDDGHTEDSIPNPSTVYAQQKTEVEAYLQANVQNAIIARTGWNVXTDPQSXCPITNTRHALLSGNAKMARDNWFTLTDVSDTCSVLLDLIQNKRHGTFHVTANPPISRIELAEEIMASSSVRDIMSYEKINFTDLPFPEPRPASAWLRNTKVTLETGHHFSPPLGTIKQKVSIIEKHLSDPEGMSR", "metadata": {"id": "A0A1Z9JHB4", "cluster": 14144391, "interpro_all": ["IPR005913", "IPR036291", "IPR029903"], "interpro_used": ["IPR036291", "IPR029903", "IPR005913"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "It is part of the Alpha/beta knot methyltransferases superfamily, which encompasses enzymes containing a deep, rare \u03b1/\u03b2 knot structural domain essential for RNA methylation. This fold is characteristic of S-adenosyl-L-methionine (SAM)-dependent enzymes, including the SPOUT and EMG1/NEP1 families, facilitating the modification of RNA substrates. In addition, the protein is assigned to the RNA methyltransferase RlmH family, which is predicted to function as an S-adenosyl-L-methionine (AdoMet)-dependent methyltransferase based on structural homology. These enzymes likely catalyze the transfer of methyl groups to RNA substrates for regulatory modification. In addition, the protein is grouped in the tRNA (guanine-N1-)-methyltransferase, N-terminal superfamily, which represents the N-terminal domain of SPOUT superfamily enzymes, including the tRNA:Gm18 methyltransferase TrmH. This domain is characterized by a rare \u03b1/\u03b2 knot structure that poses a significant folding challenge. It is expressed in Tetragenococcus muriaticus 3MR10-3 and is associated with UniProt keywords Cytoplasm and rRNA processing.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 2176, 1977, 3131, 1927, 1920, 4595, 19, 4666, 26646, 28253, 13975, 16, 2154, 21569, 5038, 3165, 43, 6515, 16, 5844, 160, 19, 161, 26646, 4346, 3418, 4415, 1958, 3146, 5547, 18, 2052, 3728, 1977, 6293, 1927, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5038, 16, 2710, 1920, 18055, 1984, 1930, 13952, 1009, 19, 26046, 1009, 5767, 16, 12440, 1920, 6295, 1927, 3146, 6249, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 3146, 16478, 11929, 22316, 3416, 16, 2154, 1977, 4396, 1942, 2347, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 12, 2041, 14080, 13, 17, 3100, 16478, 2454, 1990, 4346, 9039, 18, 2144, 5038, 3205, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 3146, 6249, 1958, 4948, 6295, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 10089, 12, 16904, 17, 13007, 17, 13, 17, 16478, 16, 56, 17, 4262, 13975, 16, 2154, 4972, 1920, 56, 17, 4262, 3418, 1927, 18055, 1984, 13975, 5038, 16, 2710, 1920, 10089, 30, 28673, 1025, 16478, 28402, 1023, 18, 2052, 3418, 1977, 4378, 2007, 43, 5844, 160, 19, 161, 26646, 3170, 1988, 17274, 43, 2228, 10328, 6013, 18, 2176, 1977, 3198, 1922, 12470, 2432, 8256, 6185, 3801, 24375, 23445, 7011, 1008, 17, 23, 1930, 1977, 2458, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MIQGIQEYIRRLQGYTKIQLVEVADEKAPENLSETEILFALAIEGKNLSSEAFAKQIDQLTTQGKSDLTFVLMRLILVEQIYRSFRINRGEAYHKALVKEKEGKRILAKVRDTEFIGGSLGLSAEVLQRSNAQLSFGNMTYPHQ", "metadata": {"id": "A0A091C9F9", "cluster": 16554149, "interpro_all": ["IPR029028", "IPR003742", "IPR029026"], "interpro_used": ["IPR029028", "IPR003742", "IPR029026"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\nThe protein contains a Domain of unknown function DUF4325 domain that is functionally uncharacterised. This domain is found predominantly in bacteria, though it is also present in some archaea. It originates from Omnitrophica bacterium (Omnitrophota bacterium).\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 5461, 43, 3418, 1927, 5435, 2347, 4855, 10432, 6763, 1015, 3418, 1988, 1977, 9346, 23229, 3495, 18, 2052, 3418, 1977, 2435, 7700, 1922, 4802, 16, 4170, 2176, 1977, 2222, 2481, 1922, 2673, 21501, 18, 2176, 22970, 2037, 18825, 3032, 24888, 3375, 14061, 12, 18825, 3032, 2102, 7336, 14061, 13, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MKEIKINIFDGELSYNRIVKGLEEKDVFLNAAIGQLYNKYGSPFLRERLKVKAKIDASIKEALGDEEQIGSTAAVSSEKVILNFTNIELVTSTENMAKEDLELLKKVVERAKEYFKD", "metadata": {"id": "A0A949F1C9", "cluster": 17868420, "interpro_all": ["IPR025474"], "interpro_used": ["IPR025474"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein features a ABC-2 type transporter transmembrane domain that constitutes the integral membrane component of ATP-binding cassette (ABC) transport systems, typically comprising six transmembrane helices. It assembles into homo- or hetero-oligomeric channels that interact with cytosolic ATPase subunits to facilitate the ATP-dependent translocation of diverse substrates, including toxins and macromolecules, across the membrane. It is native to Phycisphaerae bacterium and has UniProt annotations Transmembrane helix.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 4075, 43, 7219, 17, 22, 2601, 9054, 9117, 3418, 1988, 14879, 1920, 12328, 3260, 4594, 1927, 4498, 17, 2743, 12992, 12, 7219, 13, 4860, 3771, 16, 5745, 10351, 3798, 9117, 12789, 18, 2176, 17421, 1036, 2460, 16350, 17, 2014, 19732, 17, 19206, 5628, 1988, 6310, 1956, 9410, 9444, 6991, 1942, 6628, 1920, 4498, 17, 3100, 7849, 1927, 6445, 6249, 16, 2710, 13599, 1930, 20625, 16, 3436, 1920, 3260, 18, 2176, 1977, 6196, 1942, 25511, 9119, 29164, 3336, 14061, 1930, 2258, 20709, 15010, 9117, 7864, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MRKALTVAWREFKHTAMTKAFLFLTESNNTPLVGTVVVLAEDDVLEEITIQIERGNTTLTEVLEKLSDITIIEGNPSELDSIKAQVRDGIYKGVIVVPDSTVSPNHTDILTSATSRAVVDARLKRLSHNAEIQDNEIARRIIPMAFMMLLWIATFTEKSNKVMEVLLSAVSPMQLLGGKILGQAGVSAVILLAFALGDLVPVLHLVLFAIYFVIAYFMIATIMIMLVMVIPMIIWPVLSEHPNGMLATITSFTVTASTEPIAIWQIVLSIGVLMQGKPPSILQLAKWIRQGGAIVMPLLMMGLFIVVVPLPDAITNDPIASALLATAPKTQNGNEDKIEIFIPSSFPAAIRDLIRRPRATATRLSNDGSGQYLLTTTIELLMYGSAVMAGAAVGSAVNELRDAQSLMGPPPLLPFVMILRGVGIVSVVAMIWMCARIFRI", "metadata": {"id": "A0A9E1T674", "cluster": 18093980, "interpro_all": ["IPR013525"], "interpro_used": ["IPR013525"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein is classified under the Fe-S cluster assembly domain superfamily, which facilitates the mobilization, assembly, and transfer of iron-sulfur clusters to recipient apoproteins. Members of this superfamily function within the ISC, SUF, and NIF pathways, often acting as scaffold proteins that transiently bind Fe and S atoms to synthesize [2Fe-2S] or [4Fe-4S] cofactors. These domains are critical for maturing proteins involved in electron transfer, redox catalysis, and nitrogen fixation across bacteria and eukaryotes. Moreover, the protein should include a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. Furthermore, it is part of the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. It occurs in Candidatus Carbobacillus altaicus and carries UniProt keyword assignments ATP-binding, Hydrolase, and Metal-binding.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2650, 17, 61, 4377, 5957, 3418, 13975, 16, 2154, 11374, 1920, 14586, 16, 5957, 16, 1930, 3856, 1927, 5680, 17, 12585, 5859, 1942, 10664, 11466, 22163, 1036, 18, 4678, 1927, 2052, 13975, 2347, 2651, 1920, 23924, 16, 2020, 1038, 16, 1930, 17719, 3873, 16, 3868, 8290, 1966, 7281, 2697, 1988, 12145, 4566, 2650, 1930, 61, 9030, 1942, 15541, 37, 13775, 1021, 17, 20759, 39, 2014, 37, 15338, 1021, 17, 26814, 39, 21362, 18, 2144, 4682, 2032, 4140, 1958, 2888, 4729, 2697, 3286, 1922, 4995, 3856, 16, 9366, 15408, 16, 1930, 6634, 7938, 3436, 4802, 1930, 15021, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 2176, 5110, 1922, 14550, 1031, 1957, 3697, 14357, 8898, 8387, 5504, 6973, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 16, 20748, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MLKTRALKQALKKVIDPELGENIEWKKDGHLHLTIALTSPLCPLTEAIQEQLSNDKKKALADRLMDRHIVSNQLMAKIYQGVGKSTLTANLAIAFAEQGLKVIVIDAMTVPPLAYGVRWMSLGLFQEVYWGDLDLLLIDMPPGTGDMALDVAEIAERAAGMSKLAKSQAEVTLLGIIEGGGASVAEALNVPLLAQIPFAPRGQTLWLMIESRVHLEQVRVDLGMVERIIEKTVRLTFPQSPPKVEITWGEKNPLLRILTIMSGKGGVIDADMYGYTLPRLVGLKGARNLPVLWRGPMLGKTLRHFANELFPKKRYDVIVTTPEKEASYNMSYHICHHCGEKEALFGVGLYVHQPILKEPMIHLA", "metadata": {"id": "A0A2R6Y0W1", "cluster": 24547454, "interpro_all": ["IPR034904", "IPR002744", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR034904", "IPR002744", "IPR033756"], "interpro_unused": ["IPR019591", "IPR027417", "IPR044304"]}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein should have a Insertion element IS402-like domain that functions as a putative transposase belonging to the IS4/IS5 family of insertion sequences. Found primarily in prokaryotes such as *Burkholderia cepacia*, it likely mediates the transposition of mobile genetic elements. Additionally, the protein is classified under the Transposase_6_like family, which functions as a transposase to facilitate the movement of insertion sequences within the genome. These enzymes catalyze the specific recognition, cleavage, and rejoining of DNA strands required for strand transfer and insertion into new genomic locations. It is native to Actinoplanes sp. TBRC 11911.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 3066, 2162, 43, 7413, 6149, 1977, 25079, 17, 3189, 3418, 1988, 4088, 1966, 43, 6770, 12935, 2051, 10588, 1942, 1920, 1977, 1006, 19, 1977, 1015, 3416, 1927, 7413, 3709, 18, 2435, 5985, 1922, 28149, 2427, 1966, 14, 18359, 18681, 2126, 17008, 20243, 14, 16, 2176, 3205, 10412, 1920, 22596, 1927, 8785, 3299, 5362, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 12935, 2051, 41, 26, 41, 3189, 3416, 16, 2154, 4088, 1966, 43, 12935, 2051, 1942, 6628, 1920, 5829, 1927, 7413, 3709, 2651, 1920, 3843, 18, 2144, 5038, 18170, 1920, 2487, 5708, 16, 6404, 16, 1930, 12677, 9024, 1941, 1927, 2678, 13214, 3414, 1958, 5984, 3856, 1930, 7413, 2460, 2814, 4935, 7183, 18, 2176, 1977, 6196, 1942, 4718, 3513, 4484, 2056, 18, 5152, 15618, 11022, 3242, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MAAGGSTTVRSFPGSCFRERTGIWQRIAERLRLDTEMGDPQWTLGINSSVALSAHPRTDVRAHLVYGTLLVDEDTRVLPITLREGRDAAFKMPTDADSLLSVTTTTGAPRTGIPWRDLPARFGSWKTVYLRKRRWALDGTIRAHQHAAGTRHQRPADAYFRTSMRVPLPTISAPRVLGVDDFALSGRCMPWPTRRSAFMPNVQRNVHAGVLAI", "metadata": {"id": "A0A7Y0PDZ4", "cluster": 25198931, "interpro_all": ["IPR025161", "IPR052909"], "interpro_used": ["IPR025161", "IPR052909"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein should feature a Crp-type HTH domain that functions as a C-terminal DNA-binding winged helix-turn-helix (wHTH) motif within transcription regulators of the Crp-Fnr family. These regulators typically act as activators or repressors to control processes such as virulence, nitrogen fixation, and respiration in response to diverse intracellular signals like cAMP, redox state, and oxidative stress. Furthermore, the protein is categorized in the Winged helix-like DNA-binding domain superfamily, which encompasses diverse DNA-binding proteins including transcriptional regulators, helicases, and endonucleases that utilize a winged helix-turn-helix motif for sequence-specific recognition. This domain engages the DNA major groove via a recognition helix while loop structures known as wings contact the minor groove or backbone, often serving as a scaffold for protein-protein interactions. Additionally, the protein has a Cyclic nucleotide-binding domain that functions as a regulatory module by binding the second messengers cAMP or cGMP. Characterized by a fold containing three $\\alpha$-helices and an eight-stranded antiparallel $\\beta$-barrel, it modulates the activity of proteins such as dependent protein kinases, cyclic nucleotide-gated ion channels, and prokaryotic transcription factors. It occurs in Devosia equisanguinis and carries UniProt keyword assignments Transcription regulation.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 3066, 5961, 43, 8833, 17, 2601, 5334, 1023, 3418, 1988, 4088, 1966, 43, 45, 17, 4262, 2678, 17, 2743, 12920, 1919, 7864, 17, 5165, 17, 7864, 12, 2003, 1963, 13, 5219, 2651, 3213, 9098, 1927, 1920, 8833, 17, 9945, 1005, 3416, 18, 2144, 9098, 5745, 4033, 1966, 15497, 2014, 26446, 1942, 2285, 4028, 2427, 1966, 9304, 16, 6634, 7938, 16, 1930, 11695, 1922, 2644, 1942, 6445, 4776, 4771, 3189, 6225, 16, 9366, 3360, 16, 1930, 5163, 3071, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 12920, 1919, 7864, 17, 3189, 2678, 17, 2743, 3418, 13975, 16, 2154, 21569, 6445, 2678, 17, 2743, 2697, 2710, 5224, 9098, 16, 29919, 16, 1930, 18697, 1036, 1988, 12561, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 1958, 3244, 17, 2487, 5708, 18, 2052, 3418, 11580, 1036, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 2679, 5881, 4061, 3171, 1966, 28297, 5217, 1920, 5857, 15920, 2014, 10787, 16, 3868, 13915, 1966, 43, 7281, 1958, 2213, 17, 2213, 3719, 18, 4950, 16, 1920, 2213, 2258, 43, 9821, 5489, 17, 2743, 3418, 1988, 4088, 1966, 43, 4948, 9059, 2007, 2743, 1920, 2812, 16716, 1036, 6225, 2014, 15958, 18, 4378, 2007, 43, 3728, 3165, 2559, 8, 38, 4595, 8, 17, 12789, 1930, 1925, 5066, 17, 10338, 28892, 8, 38, 4666, 8, 17, 19560, 16, 2176, 13112, 1920, 2455, 1927, 2697, 2427, 1966, 3100, 2213, 7784, 16, 9821, 5489, 17, 12336, 4755, 5628, 16, 1930, 21545, 3213, 2790, 18, 2176, 5110, 1922, 4251, 27545, 1019, 3009, 6509, 2029, 18402, 1937, 1930, 16252, 20709, 11121, 2538, 18306, 3213, 3640, 18, 3], "output": "MAEHHNSLRSAQTSMANYPEAYDDALRRAAIFDAMSNTHRHAILAQATVLELGAGQIWQKDDTSQDFCLLVSGRLRMQQETSDGLRHIARYVLSGDVFEMPHDLDAEPQIAAAACADSTVLIWSNPVWTSLLAQDVLLSSNTARALTHILRETQTRVRQIATQDVEQRLANAVLGLLDRASQPVKGGLAIDFPIGRKDFADMIGTTQTTVSRIVSTWETKGFLRTGKFKFEVTNIAQLRAYAAGLDRNSPARFANQRKQARLALA", "metadata": {"id": "A0A447I6A7", "cluster": 25927112, "interpro_all": ["IPR000595", "IPR018490", "IPR012318", "IPR014710", "IPR036388", "IPR036390"], "interpro_used": ["IPR012318", "IPR036388", "IPR000595"], "interpro_unused": ["IPR014710", "IPR018490", "IPR036390"]}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein possesses a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. Additionally, the protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It originates from Nitrospirillum amazonense and is classified with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 14465, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 22970, 2037, 16665, 10984, 3027, 11560, 1989, 23498, 4480, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MATGRFITLEGGEGAGKSTQIRLLAQALTDRGLEVVTTREPGGGSDGNAARHENVEALVRPALARGAWVLCDRYVDSTMAYQGYAMGVDRGVLADLHRLSTDRYERMGMAFHERLRQGFLDIAAHDPGRCAVIDATGDIATIQARLLGVVERRLGPLGRAAAAGIRALLVAGDTPWQRLTEALLHGGLMPDLTLVLDLPVEAGLARAGSRPGAE", "metadata": {"id": "A0A560GD97", "cluster": 2929371, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "infilling"} {"instruction": "Give me the sequence of a polypeptide chain with the following function. The function of the polypeptide chain is It is part of the Alpha/beta knot methyltransferases superfamily, which encompasses enzymes containing a deep, rare \u03b1/\u03b2 knot structural domain essential for RNA methylation. This fold is characteristic of S-adenosyl-L-methionine (SAM)-dependent enzymes, including the SPOUT and EMG1/NEP1 families, facilitating the modification of RNA substrates. Moreover, the protein carries a tRNA/rRNA methyltransferase (SpoU type) domain that functions as a 2'-O-methyltransferase acting on tRNA and rRNA substrates. It specifically catalyzes the methylation of conserved nucleotides in the peptidyl transferase center of the large ribosomal RNA, a modification required for the formation of functional large ribosomal subunits. Moreover, the protein is associated with the tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL family, which catalyzes the S-adenosyl-L-methionine-dependent methylation of the ribose 2'-OH group at the wobble position of specific leucyl-tRNA isoacceptors. This enzyme specifically modifies nucleotide 34 (cytidine or uridine) to facilitate accurate codon recognition during translation. It occurs in Succinivibrio dextrinosolvens and corresponds to UniProt keyword Cytoplasm and tRNA processing.", "tokenized_instruction": [2, 7031, 2142, 1920, 3244, 1927, 43, 13022, 4659, 1956, 1920, 2894, 2347, 18, 1920, 2347, 1927, 1920, 13022, 4659, 1977, 2176, 1977, 3131, 1927, 1920, 4595, 19, 4666, 26646, 28253, 13975, 16, 2154, 21569, 5038, 3165, 43, 6515, 16, 5844, 160, 19, 161, 26646, 4346, 3418, 4415, 1958, 3146, 5547, 18, 2052, 3728, 1977, 6293, 1927, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5038, 16, 2710, 1920, 18055, 1984, 1930, 13952, 1009, 19, 26046, 1009, 5767, 16, 12440, 1920, 6295, 1927, 3146, 6249, 18, 3950, 16, 1920, 2213, 16252, 43, 10089, 19, 9067, 16478, 12, 18055, 1032, 2601, 13, 3418, 1988, 4088, 1966, 43, 22, 11, 17, 57, 17, 16478, 8290, 1990, 10089, 1930, 9067, 6249, 18, 2176, 4475, 17097, 1920, 5547, 1927, 5305, 9519, 1922, 1920, 3431, 2199, 13763, 4102, 1927, 1920, 3103, 11196, 3146, 16, 43, 6295, 3414, 1958, 1920, 3337, 1927, 3183, 3103, 11196, 6991, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 10089, 12, 2702, 5802, 19, 26104, 17, 22, 11, 17, 57, 17, 13, 17, 16478, 28402, 1024, 3416, 16, 2154, 17097, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 5547, 1927, 1920, 17870, 22, 11, 17, 5622, 2210, 2019, 1920, 26334, 6936, 1952, 3507, 1927, 2487, 9906, 2199, 17, 10089, 4911, 22790, 2133, 18, 2052, 4113, 4475, 25436, 5489, 3540, 12, 2702, 5802, 2014, 26104, 13, 1942, 6628, 6305, 8905, 5708, 2409, 6410, 18, 2176, 5110, 1922, 13791, 2068, 3693, 3940, 20256, 5572, 1951, 10131, 3355, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 10089, 4587, 18, 3], "output": "MINIVLYQPEMPGNAGNIIRLAVNCGAKLHFIGPLGFYLDNERLMRAGLDYHELCNLTVHVNFQTFMETQKPKRLIASTSKAHLSHVDFKFEDGDYVIFGREKEGLADEVYNVVPQEHRIKIPMAPNSRCLNLSNSVAVVAYEAWRQLGFENALV", "metadata": {"id": "A0A662ZQL8", "cluster": 4070307, "interpro_all": ["IPR029028", "IPR001537", "IPR016914", "IPR029026"], "interpro_used": ["IPR029028", "IPR001537", "IPR016914"], "interpro_unused": ["IPR029026"]}, "task_type": "autoregressive"} {"instruction": "\"The protein is grouped in the Ankyrin repeat-containing domain superfamily, which functions as a versatile protein-protein interaction module defined by tandem repeats of a \u03b22-\u03b12 structural motif. Predominantly found in eukaryotes, these domains mediate molecular recognition in diverse biological processes, including transcriptional regulation, cell-cycle control, cytoskeletal organization, and signal transduction. Moreover, the protein should have a Ankyrin repeat that mediates protein-protein interactions through tandemly repeated helix-loop-helix modules which stack to form an L-shaped structure. This versatile motif is found in diverse eukaryotic proteins, including transcriptional initiators, cell-cycle regulators, cytoskeletal components, and signal transducers. It is native to Anas zonorhyncha (Eastern spot-billed duck) and corresponds to UniProt keyword ANK repeat, Cytoplasm, and Nucleus.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 1977, 10809, 1922, 1920, 28336, 6865, 17, 3165, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 2213, 17, 2213, 2835, 9059, 3608, 2007, 10361, 9569, 1927, 43, 11157, 17, 13213, 4346, 5219, 18, 7700, 2435, 1922, 15021, 16, 2144, 4682, 8265, 3272, 5708, 1922, 6445, 3933, 4028, 16, 2710, 5224, 3640, 16, 2024, 17, 4048, 2285, 16, 14787, 5901, 16, 1930, 2733, 8201, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 28336, 6865, 1988, 10412, 2213, 17, 2213, 3719, 2596, 10361, 1954, 5116, 7864, 17, 5881, 17, 7864, 10803, 2154, 10496, 1942, 2386, 1925, 54, 17, 9132, 3170, 18, 2052, 20425, 5219, 1977, 2435, 1922, 6445, 10825, 2697, 16, 2710, 5224, 23467, 1036, 16, 2024, 17, 4048, 9098, 16, 14787, 4178, 16, 1930, 2733, 26307, 18, 2176, 1977, 6196, 1942, 7381, 1036, 26533, 14514, 2304, 25588, 12, 11562, 9177, 17, 11376, 1919, 26856, 13, 1930, 8852, 1942, 20709, 11121, 2538, 9808, 6865, 16, 5239, 16, 1930, 5607, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MTEEPRLFKLARRGQLELLKDALRGGDAAGHLHLLAWLLEELELDMEVANVDYKRSYLLAKGACVDALKRGDWTPLMMACTRQNLEVIKDGWNCFHIASREGHGQVLSYLLAASPSCWDCRDAVELLLERCGYEPDSRDNCGVTPFMDDALGAQALHRAAVTAQDGTALHYAAKEGHTDTIRTLLSLGADLEAKTARGTPELSCVYANGSWCSLTCQNPFFFHFCVFELAVLGPSPCGKKLQHSSGLFSARLIPLISPNISQKSKLSQNEAVQGGQRCGRSGDTLLHLAARHPLHEAASAGHGECVKDLVEHGANPLLKNTESTTRRTPLHTAAMHGALQHGHVDIARLLLEKHGACPTAVAIRFLVAELGVGVNERATALRLDGKGRSGKLLAHPPCIFLFFFFQKGSHSAGLSDVLILHEALISL", "metadata": {"id": "A0A8B9V4G1", "cluster": 6241588, "interpro_all": ["IPR002110", "IPR036770"], "interpro_used": ["IPR036770", "IPR002110"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is grouped in the Protein kinase-like domain superfamily, which modifies other proteins by chemically adding phosphate groups. This enzymatic activity is fundamental to most signaling and regulatory processes in the eukaryotic cell. It originates from Rhodospirillaceae bacterium.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 2213, 4016, 17, 3189, 3418, 13975, 16, 2154, 25436, 2303, 2697, 2007, 13944, 8013, 5413, 2671, 18, 2052, 8145, 2455, 1977, 8829, 1942, 2501, 3197, 1930, 4948, 4028, 1922, 1920, 10825, 2024, 18, 2176, 22970, 2037, 11490, 3106, 23576, 11560, 9914, 14061, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MSFLKNLGKVVKILPPSGNAIVRNDGSISWFDWEHCGCQLDKDILTKYINLFKSSNSTISAQQKQWWKRDYCLEFDRLTSPLTPWLQEISVYLKTVIDEIALNDALIVVPDTFIKWDARARSSIDDLVWFLGDEWISTHQYFFIHGTLHICGRLAQILRHKGNQMGITRREARNLADKASEWANFD", "metadata": {"id": "A0A2E4BRD5", "cluster": 7650240, "interpro_all": ["IPR011009"], "interpro_used": ["IPR011009"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein contains a Ubiquitin specific protease (USP) catalytic domain that functions as a deubiquitinating enzyme to hydrolyze isopeptide bonds between ubiquitin molecules, thereby reversing protein ubiquitination. It adopts a conserved \"open hand\" fold stabilized by a zinc-binding motif and houses a Cys-His-Asp/Asn catalytic triad responsible for substrate cleavage. This activity regulates critical cellular pathways, including protein degradation, trafficking, and the DNA damage response. Additionally, the protein should have a Ubiquitin specific protease conserved site that forms the catalytic core of peptidase family C19 deubiquitinating enzymes, specifically encompassing the active site cysteine and histidine residues. These motifs are structurally positioned within the thumb and palm subdomains to facilitate the hydrolysis of isopeptide bonds between ubiquitin molecules, thereby reversing protein ubiquitination. In addition, the protein possesses a MATH/TRAF domain that functions as a protein-protein interaction module, facilitating self-association and recognition of specific receptor sequences. Adopting an antiparallel beta-sandwich fold, this domain is essential for trimerization and signal transduction in intracellular TRAF proteins, including interaction with TNF receptors, and plays a structural role in extracellular meprin metallopeptidases. It is present in Naegleria gruberi (Amoeba) and is connected to UniProt keyword Hydrolase, Thiol protease, and Ubl conjugation pathway. Can you generate the amino acid sequence corresponding to this polypeptide chain?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 13022, 4659, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 6526, 2487, 7154, 12, 14277, 13, 6804, 3418, 1988, 4088, 1966, 43, 29436, 2287, 4113, 1942, 7222, 6931, 10301, 8253, 9031, 2192, 6526, 4206, 16, 6113, 26526, 2213, 11758, 18, 2176, 24032, 43, 5305, 6, 4437, 3897, 6, 3728, 12017, 2007, 43, 7997, 17, 2743, 5219, 1930, 23407, 43, 4998, 17, 4167, 17, 4138, 19, 15118, 6804, 21845, 5061, 1958, 4510, 6404, 18, 2052, 2455, 7014, 4140, 3689, 3873, 16, 2710, 2213, 4877, 16, 9604, 16, 1930, 1920, 2678, 4293, 2644, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 6526, 2487, 7154, 5305, 3200, 1988, 4952, 1920, 6804, 4728, 1927, 24050, 3416, 8817, 1026, 29436, 2287, 5038, 16, 4475, 17527, 1920, 3500, 3200, 8666, 1930, 13873, 4248, 18, 2144, 8277, 2032, 12171, 11814, 2651, 1920, 22362, 1930, 15516, 30103, 1942, 6628, 1920, 9128, 1927, 10301, 8253, 9031, 2192, 6526, 4206, 16, 6113, 26526, 2213, 11758, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 8250, 19, 14803, 3418, 1988, 4088, 1966, 43, 2213, 17, 2213, 2835, 9059, 16, 12440, 3543, 17, 3279, 1930, 5708, 1927, 2487, 3148, 3709, 18, 20478, 1925, 28892, 4666, 17, 18038, 3728, 16, 2052, 3418, 1977, 4415, 1958, 20085, 2466, 1930, 2733, 8201, 1922, 4776, 14803, 2697, 16, 2710, 2835, 1956, 4705, 4086, 16, 1930, 5705, 43, 4346, 2770, 1922, 5329, 17257, 5572, 8969, 24897, 1036, 18, 2176, 1977, 2481, 1922, 4049, 6541, 3823, 2126, 2398, 24118, 1033, 12, 27714, 1019, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 20748, 16, 13914, 7154, 16, 1930, 4803, 1024, 14122, 3374, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MKMTDEYDLSDSDDEMMQDTEEDRGFSAEEERKLALRQQELDEAAQYYEPIDESKEGVYHVKSFDANTEKVRWKADFSKMAQKQYSPTFTIAGNHEFRLLVFPRGNQVPCISLYLDTNNSQEIKLVRFQVSILNQKDIRESHSQDAEKRYGPNDVDWGFKEFIELKKVNPDVGFISTSGIVYFEMVIHICTQPYLIDPISYDSRKETGFAGLQNQGATCYMNSLLQTLYLLTYFRKSVYKMPIDENEKPQDSIPLALMRVFFRLQFDKGAVDTKELTKSFGWDTIDSFLQHDVQEFARVLIDNLEKKMEKTDQKEVMRQIFEGMCKNYIKCINVDYESSRKEPFYDLQLNVKGCKNVAESFDQYILEETLQGENQYQAEGHGLQDAKKGTNFLKLPPVLMLHLKRFEYDYIRDLIYKINDRYEFPLEIDLGKYLSEDSEQKKEDNTYVLFSVLVHSGDVSGGHYYNFARPYINEDRWFKFDDEKVYEVNESLAVQDNYGGEAKKSKMFWLSSNPNSVYKKFTNAYMLLYIRKSAISNMIAPVEVDEIPSHLEERFQKDRDERERKKREKLEAAKYCNIKIVTDDDIKKSVEKTGSGLVEFEDVEPIKFLREGTFAELKEQIETLYGIKAEQQRFWKWQKRQNHTLRPDAIIKPADDASTIERKYPYVKHQQAPPVELYLEVSKQTYSYQKDDEECVVHFPEPAQRYILLFIKEYNPEERKLNFVGTVYADMLSEVSEVIPSIKALIGADEDDDIHIVEEIKPKMIDDVRIDQSFKDAQLQSGDILAVQRVPKGTDLSKYPIPTAKSYYDYLNNRVSVEIRKLEDPLKNVAVVELLKNMEYKELTDKLGSALEVDGNFLRLTGHHPYSEGPLEQPFKSNSGSTLKDMINIGQTPQKILYYEILDEPIFNVENKKELIVTWMNSKCQDVEKFKFLLYPDQKVNDLKQLIEAKVNGRREIENSTIVISQISNFKISKLLTGEELIKTLATNKGETIRAEEILNEELSIITSSHNLTENTRILQVQHICKETTGYRLFGNPSVLVVKTEETLGDVKKRLQDKLQVRDIDYKRYKFYFIVNMKIKDALEDDSLLFCELFDKEKQSTNVDVVLALEHKDPTPKARWYEKPIVIKN", "metadata": {"id": "D2VYU4", "cluster": 8722321, "interpro_all": ["IPR002083", "IPR038765", "IPR050164", "IPR001394", "IPR008974", "IPR024729", "IPR029346", "IPR018200", "IPR028889"], "interpro_used": ["IPR028889", "IPR018200", "IPR002083"], "interpro_unused": ["IPR024729", "IPR050164", "IPR038765", "IPR008974", "IPR029346", "IPR001394"]}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein should include a Neuraminidase-like domain that functions as a pH-sensitive electrostatic lock within the TcA subunit of tripartite Tc toxin complexes in bacterial pathogens. Structurally homologous to neuraminidases, this domain regulates the complex by opening at high or low pH values. Additionally, the protein features a Tc toxin complex TcA, C-terminal TcB-binding domain that mediates interaction with the TcB subunit to assemble the functional Tc toxin complex found in bacteria like *Photorhabdus luminescens*. This binding event triggers the opening of a $\\beta$-propeller gate, facilitating the perforation of host endosomal membranes and the translocation of toxic enzymes. Furthermore, the protein possesses a ABC toxin, N-terminal domain domain that is located N-terminal to the neuraminidase domain in pore-forming toxins from fungi and bacteria. This region serves as a component of orally active toxin complexes, such as the *Yersinia entomophaga* YenA2 subunit, which exhibits potent insecticidal activity against Coleoptera and Lepidoptera larvae. It is found in Acidobacteriota bacterium.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 3066, 3951, 43, 29831, 17, 3189, 3418, 1988, 4088, 1966, 43, 2087, 17, 4532, 12452, 12756, 2651, 1920, 13828, 5903, 1927, 8027, 24707, 5283, 9165, 5048, 1922, 4543, 7741, 18, 12171, 8725, 1942, 29831, 1036, 16, 2052, 3418, 7014, 1920, 2796, 2007, 9497, 2019, 2149, 2014, 2330, 2087, 2851, 18, 4950, 16, 1920, 2213, 4075, 43, 5283, 9165, 2796, 13828, 16, 45, 17, 4262, 5283, 1014, 17, 2743, 3418, 1988, 10412, 2835, 1956, 1920, 5283, 1014, 5903, 1942, 17421, 1920, 3183, 5283, 9165, 2796, 2435, 1922, 4802, 3189, 14, 10066, 5004, 13385, 1957, 16410, 1918, 22749, 14, 18, 2052, 2743, 4817, 11847, 1920, 9497, 1927, 43, 8, 38, 4666, 8, 17, 5062, 13728, 11898, 16, 12440, 1920, 17018, 1927, 4423, 16514, 5726, 1930, 1920, 7849, 1927, 6161, 5038, 18, 3677, 16, 1920, 2213, 14465, 43, 7219, 9165, 16, 56, 17, 4262, 3418, 3418, 1988, 1977, 4810, 56, 17, 4262, 1942, 1920, 29831, 3418, 1922, 8554, 17, 7402, 13599, 2037, 10520, 1930, 4802, 18, 2052, 3031, 10634, 1966, 43, 4594, 1927, 12950, 3500, 9165, 5048, 16, 2427, 1966, 1920, 14, 29323, 14102, 27521, 4965, 1019, 14, 5293, 2175, 1028, 5903, 16, 2154, 9826, 6828, 15350, 7161, 2455, 3316, 21481, 21244, 1930, 28820, 21244, 8784, 18, 2176, 1977, 2435, 1922, 2687, 5883, 3940, 3857, 14061, 18, 3], "output": "MKLQGRNLHNGDQGEDVSLLQKELEILGFHLIAKARDTEITPKIFGPHTLVAIREIQEKAGLPVTGVVDEATARVINERVDGTTGGGGGGGKGPFVVKGRITTADGQPAPRVRVRAFDRGLRSEKMLGETLSGAAGDYEIRYRQEDLRKPDRGAADLLVRALPQGSPAVESAVRFRASRTETIDLVLASLGPSEYELLLAALSGVLEGVAPKDLTTAEVLHLAGLLGREPAHVGFAVSAERLAGSTGLPASVFYAFARRGLPSALPSLLAQPLDRLQRELEAALGANLVPATLRNRLPEILDLLRELILRQASVTPTGGFSLTDLLATVLPSEQVRRRFLDLYIRHRGPIRDFWANLHNNPEFAQPGAVEALQLTLQLGVLSGNHLPLVQALQQRGVRTARDLARISGADWQSLIDQHGVPPSTPGANASERAANYRGAIQQLVDAAFPTAALGRELAADPAGDAGAKAFFSDHPDFEFGTVPVRQLLGGQPAGEAVLQQLEGMERIFQVTPGYAPVKALIDAGFDSASRIAQEGPDTFVRRFATTFGGPAEALQVFERADHNTAVVSTVFGAYAPPFWRDRPGVIVSGPVDPDTDPDWRSLFGSLDLCACRHCRSVLSAAAYLDDLLGTLQKWNVAAALRSRRPDLFALELSCANTDTTLPYIDLVNELLESAVLPSSLPVRTEGTAAELRIQPQVLSSAAYEKLRGEHYPWGLPFDLWETEAGLYLDRLGTRRHELMAAFRNSETPSGVAIAANRLGLNATELGLLTRPVPAASAWELYGFASEGAWLQDLSGVAEFLKRTGLSYGELAELLRLRLVNPDHGIDIQPKATANPDTCDPEELEIHSWSPTRLDLLQRFVRLRRRIGWTAWELDRTIAALQPGTIDGDLLVALARLGQLSRELRLPPRKLLVFYGRIDTYVYLDGVDRPLYNELFLNPAVYKAPEGQAHPLALGPDLGELEHTGRRLAEPAPAAVLRGALSLSEADWNTLLADPLAAGDGKLTLWNVTRLTRTVFLARGLRLPVADLLRLLPFSGESPFSEAAPGDLAVLGHTLDFVATVRKLRESGVPLAETFLLLTGARDPASPATPPDEALAKLLTDLRTALQDVIVTTSAQTDPDGSLTARALTLLEWEPALIENVMATLLGRQPYAEPLPELPKDLEFPLVLAGKVSYDKEAKALRFQGPMSKEDHQVLSDLATGDDYRSAVQKLYDAPRTLILKHLGSFGLTAADVAAMFDDPAAPAATLAARFDRLLGPLQALLRRTQSKAITLETVGTALGLDAATAESLLGTWLRAPSLQAPAGTKEPILQALLDPDFIAGDPSAFQRLVESLSLAFRAAYVLQRLGLDSRDLPVLFRRAAAGGWLDLNELPLEATAESPQLFAAWVHLLDVVRLRNRLPRQQPPLLDLLERALAASPGPATVSGPPESFLADLAALTGWRREDLQHLAGQAATAGSLGLRFPEDWRTGEAFARIADCFDLLRRLGAKADEAATWSQDGIQEAAVLRLRQILKTRTEGAAWIEIAGPLRDSLREKQRDALVAFLVPRPDAAKNQRWTDVNGLFSHFLIDVEMSSCQLTSRLKQALSSVQLFVQRCLMNLEEGIHLPQEAPGEWQWRKSYRVWEANRKVYLYPENWIEPELRDDKSPFFQELENELLQGDVTDAAVEQAVRAYLDKLHDVGRLLLVAMCLGPEISPTLHVFGRTRGEPRQYFYRRWVGRTTWTPWEPVNVHVEGDHLIPIVHNRRLYLFWALFTAVPDENQTSGTAAKKHWEIRLAWSERRNGKWTPKKETEEALSPFLGSEDLKLPLRPDGLPFKDSFRFRADSQGGRLRVRLYGLFEFRRGGSATSFPAGLYPLSAWLLLPCDGTLELLPQVSNQEEVVLVPQNTYVQAERFRQGTLFGWFFIGQNTDDELALFEGPFVAAESPDETGQRRKDFNVLATTPGTFELLFPHHTPQPDAWQPFFYQDDRQTFFVLPEVSGADVGQEQSWGRGDVNLGQIGALSFNTATPSLGIANRNLAESAQDVAEVTIWTEFSFPEPQPQITLTFHLFHHPQVCRFIEALEAGGMAALFGQPARETDVPIFDGNAYKPLPVVNKPYPVEAMDFCPGGACSLYNWELFFHIPLLVADRLSKNQRFEEARRWFHFIFDPTDATAGADPHRFWKFKPFAEDSACDPSLDLLRLLGRREPLTSRERAALDRQIGQWQEHPFQPHAIARLRWSAYQKTVVMKYLDNLIAWGDNLFQRDTLETLNEATQLYVLAADILGNRPREIPPRHEAAAGSHDHPASGASPLAFLENLLPGRVGTEITWGSPTVAGPSFPGPAATPPSPASLFGQAGSFCLPGNEKLSGYWDTVADRLFKIRHCMNIEGIVRQLPLFEPPIDPALLVRAAAAGLDPGTVLSGLAVPRPPYRFATLAQKATELCSEVKALGAALLSALEKKDAEELALLRSGHELALLGAVRQVKEQQVAEAETALAALRAGREVVNKRWQYYRDIKQHSLWELSQMGLMVTTAALQFISKNIEAGAAVVQTAVPDAIVGGAGSMGTPVALVAEGGTKKAETGSRAAKVFQVLAEVSSLSAQMVGLEAGFQRRWDEWKLQERLAEQELLQLDQQILAAEIRHEITRKELDNHDLQVENAREMDAAMREKFTNRELYAWMVGQISGIYFQSYRLAHDVARRAERAYRHELALPNSNFIQFGSWDSLKKGLLAGERLFHDVKRLEVAYLDQHRRELEITKHVSVARLDPLALVELRRTGSCIVRLPEALFDLDFPGHYLRRIKTVSVSVPCVTGPYTGVPCTLTLLRSTVRHGSTLLNDSYRRQEDDPRFTDNLGAIESVATSSGQNDSGLFETNLRDERFLPFEGAGVISEWQIELPAEFRSFDYDTISDVLLHLRYTARSGGKRLADQVKTELSQALNEMARSQGEQGLAQLISVRHDMPTEWHRFLQGPAESSGFRKLTLDLGKERFPYLFATSPELRITGIELFLQGEQDLGDDEASLFALTLSPPGGEEKTLTRVAWEGLLRAVHGPAPQNGLGPWTLRIQGQPLHNVLVVCHYTVAPEADSNRPRSSSSSSSR", "metadata": {"id": "A0A355EY41", "cluster": 9153000, "interpro_all": ["IPR046839", "IPR041079", "IPR002477", "IPR036365", "IPR036366", "IPR040840"], "interpro_used": ["IPR041079", "IPR040840", "IPR046839"], "interpro_unused": ["IPR036365", "IPR036366", "IPR002477"]}, "task_type": "autoregressive"} {"instruction": "The protein should feature a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Furthermore, the protein possesses a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Additionally, the protein should include a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. It has been characterized in Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253) and corresponds to UniProt keyword Cytoplasm, SOS response., and DNA damage. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 3677, 16, 1920, 2213, 14465, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2176, 2258, 2252, 4378, 1922, 7570, 3695, 2057, 11560, 1019, 22224, 3062, 19333, 12, 3943, 9100, 4460, 19, 11037, 6813, 1019, 17, 4804, 1027, 19, 10409, 1030, 11824, 3786, 13, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 16, 17668, 2644, 18, 16, 1930, 2678, 4293, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MTAPGFVEFPDSPFHLYQPYPPAGDQPGAIDALTEGVSDGLMFQTLLGVTGSGKTYTMANMIARLGRPALVLAPNKTLAAQLYAEMREFFPRNAVEYFVSYYDYYQPEAYVPTRDLFIEKDSSINEHIEQMRLSATKSLLERRDTVIVGTVSCIYGIGNPGDYHAMVLILRTGDRISRREVLARLVAMQYTRNDADFTRGVFRVRGETIDIFPAESPELALRLTLFDDEIESLELFDPLTGRVRQKLPRFTVYPGSHYVTPRETVLRAIETIKEELRERLAQLIADGKLVEAQRLEQRTRFDLEMLQELGFCKGIENYSRHLSGAAPGEPPPTLIDYLPADALMFIDESHVTIGQLGGMYRGDRSRKETLVQYGFRLPSALDNRPLRLEEFEARMRQCVFVSATPAAYEQEHADNVVEQVVRPTGLVDPIVEVRPAHTQVDDLLGEIHKRAALQERVLVTTLTKRMAEDLTDFLSEHGVRVRYLHSDIDTVERVEIIRDLRLGVFDVLVGISLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNLNGRAILYADRITDSMRRAIDETERRRAKQIQHNTDHGITARGVSKAVRELIDGVVAPAGHDALESAVPAEVLTDEKAMAREIRRLEKLMMDHARNLEFEQAAAARDALNALKSRLLLDGVG", "metadata": {"id": "Q7W8V6", "cluster": 9614325, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR014001", "IPR001650", "IPR001943"], "interpro_unused": ["IPR027417", "IPR036876", "IPR041471", "IPR006935", "IPR024759", "IPR004807"]}, "task_type": "autoregressive"} {"instruction": "Give me a peptide sequence capable of: It is part of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Moreover, the protein can be placed in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, the protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It has been characterized in Slackia faecicanis and is associated with UniProt keywords Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 2258, 2252, 4378, 1922, 18548, 12940, 2126, 5685, 1940, 13611, 1937, 1930, 1977, 2458, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 3], "output": "MTGEYRHIPVLLDECLEQARLKPQHTFVDATLGGAGHSSEVAQRLGSQGLLIGIDQDDMALTAAGARLKALGSDDLPQIELLRGNFGNLDELLLEAEVPGIDAILFDLGVSSPQLDFPSRGFSFKEDAPLDMRMDPGNQTTTAAELVNTLDAAELARIIRDYSDEKWASRIAQFIVAAREREPIETSGQLVEIIKAAIPASARRAGGHPAKRTFQALRIEVNSELSVLRSGLEAAVRWLNPKGRILVISYHSLEDRVVKEVFADYARTCTCPPGLPVCACGANPALKIVTRKPILPTPEEIERNPRARSAKLRVAEKIR", "metadata": {"id": "A0A3N0ADM0", "cluster": 10037338, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: It is part of the Pyridoxal phosphate-dependent transferase, major domain superfamily, which forms the large catalytic component with a 3-layer \u03b1/\u03b2/\u03b1 sandwich topology in enzymes that utilize pyridoxal 5'-phosphate (PLP) as a cofactor. Through a Schiff base linkage with an active site lysine, members of this superfamily facilitate diverse chemical transformations, including transamination, decarboxylation, and deamination, which are essential for the biosynthesis and catabolism of amino acids and neurotransmitters. In addition, the protein falls within the Kynureninase family, which functions as a pyridoxal-5'-phosphate (PLP)-dependent enzyme catalyzing the hydrolytic cleavage of L-kynurenine or 3-hydroxykynurenine to yield L-alanine and anthranilic or 3-hydroxyanthranilic acid. This reaction constitutes a key step in the L-tryptophan catabolic pathway involved in NAD biosynthesis across bacteria, fungi, and vertebrates. Structurally, the enzyme belongs to subgroup IVa of the aminotransferase superfamily. Also, the protein is assigned to the Pyridoxal phosphate-dependent transferase, small domain superfamily, which comprises the complex $\\alpha/\\beta$ structural domain found in enzymes such as aspartate aminotransferase and DOPA decarboxylase. These proteins utilize pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze diverse reactions, including transamination, decarboxylation, and deamination, playing a vital role in amino acid biosynthesis and neurotransmitter metabolism. It is expressed in Mesocestoides corti (Flatworm) and has UniProt annotations Cytoplasm, Hydrolase, and Pyridine nucleotide biosynthesis. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 2176, 1977, 3131, 1927, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 3044, 3418, 13975, 16, 2154, 4952, 1920, 3103, 6804, 4594, 1956, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 18038, 13678, 1922, 5038, 1988, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 18, 2596, 43, 25214, 5170, 8611, 1956, 1925, 3500, 3200, 9082, 16, 4678, 1927, 2052, 13975, 6628, 6445, 4399, 18510, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 2154, 2032, 4415, 1958, 1920, 8132, 1930, 19480, 1927, 3835, 4576, 1930, 21012, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 23523, 24684, 11413, 3416, 16, 2154, 4088, 1966, 43, 24828, 23859, 17, 25, 11, 17, 5413, 12, 21453, 13, 17, 3100, 4113, 29601, 1920, 26702, 6404, 1927, 54, 17, 23523, 24684, 2053, 2014, 23, 17, 8275, 6716, 1022, 24684, 2053, 1942, 4307, 54, 17, 10504, 1930, 14228, 16692, 1935, 2014, 23, 17, 8275, 7744, 17182, 10029, 2687, 18, 2052, 3227, 14879, 43, 3834, 3537, 1922, 1920, 54, 17, 13489, 22112, 3374, 3286, 1922, 6577, 8132, 3436, 4802, 16, 10520, 16, 1930, 14976, 18, 12171, 16, 1920, 4113, 14440, 1942, 6200, 4370, 1019, 1927, 1920, 15817, 13975, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 2858, 3418, 13975, 16, 2154, 12936, 1920, 2796, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3418, 2435, 1922, 5038, 2427, 1966, 12878, 15817, 1930, 19428, 23922, 18, 2144, 2697, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 1942, 18170, 6445, 5298, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 14797, 43, 8970, 2770, 1922, 3835, 2687, 8132, 1930, 15223, 4714, 18, 2176, 1977, 3198, 1922, 23577, 3707, 4575, 3726, 18964, 1033, 12, 9778, 16620, 13, 1930, 2258, 20709, 15010, 5239, 16, 20748, 16, 1930, 19604, 5489, 8132, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MESLEALASALDGSDPLKEFRQRFILPTLKALKGPVGETNGHTEEANNGDIDSGVIYLCTNSLGLPPKATGENLAKVLDAWGSLGVLSHTKGISPTEISDIRPKQLLAEFLVGAKFEEVAVMESLTANIHTLVSSFFVPKGKKSRILIEKNSFPSDYYAIESQLYVKGVDKSALIELDLRPNGKYLSTEEIVEEIKRHGEVLAFVWLPGVQYLTGQMLDIRRITAAVHEYCDCPIGWDLAHAVGNVPLSLHDWKVDCATWCGYKYLCGSPGGYSAIFVHEKHHLKAGSHVPTDKHAYGPSMSGWWGHRYSTRFQMTNKMETEAGADAYRRSCPSMLLNSALTSALEVFAEAGGMKPIREKSIKLTNFLENLLTNGPYALPPDSLEIITPADPDSRGSQLSLKINVDVDKLYRRLIDRGVVCDTRKPCYVRVAPFALYTSFTDVLKAAKIIHEEVNDLIDDNC", "metadata": {"id": "A0A0R3U8C5", "cluster": 12781715, "interpro_all": ["IPR010111", "IPR015424", "IPR015421", "IPR015422"], "interpro_used": ["IPR015421", "IPR010111", "IPR015422"], "interpro_unused": ["IPR015424"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein should contain a BURP domain that is found at the C-terminus of various plant proteins and serves as a putative motif for localization within the cell wall matrix or structural integration. It is associated with diverse physiological roles, ranging from developmental processes like seed coat differentiation and pollen maturation to stress responses involving drought and aluminum tolerance. Also, the protein is associated with the Polygalacturonase-associated BURP domain-containing protein family, which regulates plant cell size and growth and includes non-catalytic subunits of polygalacturonase. These proteins are characterized by a unique C-terminal BURP domain and can function as chaperones facilitating protein transport through the secretory pathway. It originates from Arabidopsis suecica (Swedish thale-cress) (Cardaminopsis suecica) and has UniProt annotations Apoplast, Secreted, and Signal. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 3066, 5531, 43, 4598, 1034, 3418, 1988, 1977, 2435, 2019, 1920, 45, 17, 7822, 1927, 3425, 4496, 2697, 1930, 10634, 1966, 43, 6770, 5219, 1958, 5363, 2651, 1920, 2024, 4821, 4526, 2014, 4346, 7122, 18, 2176, 1977, 2458, 1956, 6445, 5005, 5456, 16, 6485, 2037, 5878, 4028, 3189, 4861, 15642, 4155, 1930, 12206, 7655, 1942, 3071, 3387, 5884, 12309, 1930, 16874, 6555, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 16115, 23276, 10366, 2051, 17, 2458, 4598, 1034, 3418, 17, 3165, 2213, 3416, 16, 2154, 7014, 4496, 2024, 3081, 1930, 2905, 1930, 5921, 2447, 17, 6804, 6991, 1927, 16115, 23276, 10366, 2051, 18, 2144, 2697, 2032, 4378, 2007, 43, 5008, 45, 17, 4262, 4598, 1034, 3418, 1930, 2112, 2347, 1966, 18098, 12440, 2213, 4860, 2596, 1920, 11518, 3374, 18, 2176, 22970, 2037, 8900, 2020, 1940, 6102, 12, 15110, 15717, 1021, 17, 18401, 1036, 13, 12, 9429, 19143, 2523, 1937, 2020, 1940, 6102, 13, 1930, 2258, 20709, 15010, 11466, 2030, 2197, 16, 8366, 16, 1930, 2733, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MNNIEATLFLCFFCIFSSSNVHFAGAKQTAGNITPSENPFTPKAYLIRYWNNHINGDSPKPSFFLSKASPLTAVDSTRFASLASNHALNTHHSDFCSAAKLFCFPELAAHSLEKHGDDVNFAAYSGKNFTNYGSDRLSGADSFKNYSGGDNIAVDSFRRYSRNSAGHDDGFINYAGEVNVADQSFTTYATGTTGGSGEFTNYNTDANEPNGRFTSYSDKANGRSQTFTTYSENGNTGDQSFTSYSKNGNGAPNEFSGYGTGSNVVNTGFTKYGESANGANDSFTSYGENGNVPVNEFKGYGDGGNGAVYGFKNYRDQSNIGVDSFSSYAKNSNNEKVNFVNYGKSFNLGSDNFTGYGQDNVGGNVSFKTYGQGQSFKVYTKDGVVFAHYSNNVSSNGKTVNKWVEEGKFFREAMLKEGTLMQMPDIKDKMPKRTFLPRNIVKNLPFSSSAIGEIWRVFGAGENSSMAGIISSAVSECERPASHGETKRCVGSAEDMIDFATSVLGRGVVVRTTENVVGSKKKVVIGRVNGINGGDVTRAVSCHQSLYPYLLYYCHSVPRVRVYETDLLDPKSLEKINHGVAICHIDTSAWSPSHGAFLALGSGPGQIEVCHWIFENDMTWNIID", "metadata": {"id": "A0A8T2HHE3", "cluster": 13181132, "interpro_all": ["IPR004873", "IPR051897"], "interpro_used": ["IPR004873", "IPR051897"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein incorporates a Domain of unknown function DUF58 domain that characterizes a family of prokaryotic proteins with currently undefined biological roles. It appears in both eubacteria and archaebacteria, and is sometimes found in proteins that also contain a Von Willebrand factor type A domain. It is derived from Chloroflexota bacterium and is associated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 3418, 1927, 5435, 2347, 4855, 17968, 1025, 3418, 1988, 26735, 43, 3416, 1927, 21545, 2697, 1956, 5077, 26687, 3933, 5456, 18, 2176, 5107, 1922, 2321, 4791, 7972, 2341, 18339, 1930, 13470, 7972, 2341, 18339, 16, 1930, 1977, 8929, 2435, 1922, 2697, 1988, 2222, 5531, 43, 14147, 30067, 2991, 2601, 43, 3418, 18, 2176, 1977, 3595, 2037, 10107, 18222, 7336, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MNRITFLGVLVWGGLLLGLGLLNGLLLTLLIPLVVYILAGLFFSPAEPQFQISRLVNTDRASEDLHLTSFLPDGLKALEGEKEYALFLPRDKTIEIDHTVTGARGYYGLPDITVTSRDPFDLFQRPQTPPLKRIAIRPNRTRTFSGQVPARIGGPGVEFFGLREYQTGDSLRWIDWILDARFRVNVKYADQSLFEHGVMATASLAETFLRTGNRVGLLLYGSLLDWTTLGNSLVFGSMENLPTRLFPSNSQLVIISPLMDGDEGMLLGLRARGYQILVVSPNIASVERGLLLNKLRQAGIFVMDWDVNTTFENAAHAALNNVPLWYQTAGLLPGEEVSIQLSLRNNGTDQQTRVPAPGRVFFINTTARHSNILFTKIFEQERVVDVGLYPAYGKVQRERIMRSLARAPISFERPLLEDNENVALAAR", "metadata": {"id": "A0A6N6KTA4", "cluster": 14252542, "interpro_all": ["IPR002881"], "interpro_used": ["IPR002881"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein according to these design specifications: The protein should include a Fibronectin type III domain that serves as a versatile structural module in extracellular matrix proteins, cell-surface receptors, and enzymes. It adopts a conserved seven-stranded beta-sandwich fold and frequently mediates cell adhesion and protein-protein interactions, often binding integrins via an Arg-Gly-Asp (RGD) motif. Additionally, the protein can be placed in the Immunoglobulin-like fold superfamily, which comprises domains characterized by a beta-sandwich of seven or more strands arranged in a Greek-key topology, facilitating protein-protein interactions often via beta-sheet interfaces. These domains are ubiquitous in animal proteins, playing critical roles in immune recognition, cell adhesion, and structural integrity in muscle proteins such as titin. It originates from Streptomyces katrae and exhibits UniProt keyword tags Signal, Polysaccharide degradation, and Hydrolase.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 3066, 3951, 43, 12848, 2601, 4337, 3418, 1988, 10634, 1966, 43, 20425, 4346, 9059, 1922, 5329, 4526, 2697, 16, 2024, 17, 3154, 4086, 16, 1930, 5038, 18, 2176, 24032, 43, 5305, 5260, 17, 10338, 4666, 17, 18038, 3728, 1930, 5467, 10412, 2024, 6141, 1930, 2213, 17, 2213, 3719, 16, 3868, 2743, 15563, 3454, 1925, 4582, 17, 3376, 17, 4138, 12, 18797, 13, 5219, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 11837, 17, 3189, 3728, 13975, 16, 2154, 12936, 4682, 4378, 2007, 43, 4666, 17, 18038, 1927, 5260, 2014, 2253, 13214, 14940, 1922, 43, 27568, 17, 3834, 13678, 16, 12440, 2213, 17, 2213, 3719, 3868, 3454, 4666, 17, 11130, 14857, 18, 2144, 4682, 2032, 15498, 1922, 4027, 2697, 16, 14797, 4140, 5456, 1922, 3743, 5708, 16, 2024, 6141, 16, 1930, 4346, 7996, 1922, 3760, 2697, 2427, 1966, 7090, 1921, 18, 2176, 22970, 2037, 22874, 14164, 5524, 1021, 1930, 9826, 20709, 11121, 2538, 14392, 2733, 16, 17167, 4877, 16, 1930, 20748, 18, 3], "output": "MKLGNLFAVAVLMTPLPFVGMAQPAWAHPTHTVAITGALVVENNPVFGKGSRITRHVFREVNLTHGDPKESFLFVQCAGGESRGELRVTVDLIESDRVTVSALLNFFEGSTCGSTDLEEFQRWNGSIAAGESVKVGLEAYNHEFQSNDGAVANFTVTHNVPERPAKPTDVRARAVRVLCVPRLPCSGKKEVVVKWVDNSVNEIGYSIRDTTTGETVGLPANTTEFTWSGLDPQVKHCFLVRANGDAEVSEWSAPIRAILPGQLSSCA", "metadata": {"id": "A0A0F4J100", "cluster": 15079749, "interpro_all": ["IPR003961", "IPR036116", "IPR013783"], "interpro_used": ["IPR003961", "IPR013783"], "interpro_unused": ["IPR036116"]}, "task_type": "autoregressive"} {"instruction": "\"It is part of the Protein-tyrosine phosphatase-like, PTPLA family, which is thought to function in the development, differentiation, and maintenance of various tissue types. Members of this family share the core protein tyrosine phosphatase (PTPase) structure but are distinguished by the substitution of the conserved catalytic arginine with a proline at the active site, suggesting a modified enzymatic mechanism or regulatory role compared to canonical PTPases. It is produced by Cavia porcellus (Guinea pig) and is annotated with UniProt keywords Lipid biosynthesis, Lyase, and Transmembrane.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 2176, 1977, 3131, 1927, 1920, 2213, 17, 6941, 8167, 17, 3189, 16, 14990, 5148, 3416, 16, 2154, 1977, 6212, 1942, 2347, 1922, 1920, 2740, 16, 4155, 16, 1930, 6291, 1927, 3425, 2960, 3584, 18, 4678, 1927, 2052, 3416, 7948, 1920, 4728, 2213, 6941, 8167, 12, 14990, 2051, 13, 3170, 2308, 2032, 12080, 2007, 1920, 6636, 1927, 1920, 5305, 6804, 9732, 1956, 43, 12958, 2019, 1920, 3500, 3200, 16, 3783, 43, 4795, 8145, 2856, 2014, 4948, 2770, 2452, 1942, 9452, 14990, 2319, 18, 2176, 1977, 4152, 2007, 9879, 2126, 4572, 9631, 1957, 12, 12938, 5445, 13, 1930, 1977, 10633, 1956, 20709, 11569, 4486, 8132, 16, 23928, 16, 1930, 9117, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "WLVIAVGLVRAYLAKGSYHSLYYSIEKPLKFFQSSVVLTSFQVMSRVFLIWAVTHSVKEVQTEDSVLLFVTAWTIPYLIKWARYTLFIVLYPMGVSGELLTIYAALPFVRQAGLYSISYIPLFPQLYFHMIHQRRKVLSRTEEHKKFETGALLEILHCAIGIVPTEIIRYSFYTFSLLNHLSLPNKYNFSFDYYAFLILIMI", "metadata": {"id": "A0A286Y1W3", "cluster": 16547727, "interpro_all": ["IPR007482"], "interpro_used": ["IPR007482"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein is assigned to the Urease accessory protein UreD family, which mediates the activation of the urease enzyme and the assembly of its nickel metallocenter as part of the UreD-UreF-UreG-urease complex. This family includes orthologues such as *Helicobacter pylori* UreH and the fungal homologue URE4 from *Cryptococcus neoformans*, which contributes to host brain invasion and meningoencephalitis. It is identified in Staphylococcus pseudintermedius and carries UniProt keyword assignments Chaperone, Cytoplasm, and Nickel insertion.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 10505, 4127, 15954, 2213, 6794, 1007, 3416, 16, 2154, 10412, 1920, 2936, 1927, 1920, 10505, 4127, 4113, 1930, 1920, 5957, 1927, 2496, 16541, 8969, 26907, 1915, 1966, 3131, 1927, 1920, 6794, 1007, 17, 6794, 1038, 17, 6794, 1029, 17, 10505, 4127, 2796, 18, 2052, 3416, 5921, 11382, 2291, 2427, 1966, 14, 22293, 10665, 14, 6794, 1023, 1930, 1920, 8697, 17986, 6794, 1006, 2037, 14, 11829, 8256, 24276, 14, 16, 2154, 7624, 1942, 4423, 3068, 6254, 1930, 10286, 29159, 3678, 18, 2176, 1977, 2899, 1922, 13452, 6050, 9185, 5476, 1957, 1930, 16252, 20709, 11121, 2538, 18306, 14044, 16, 5239, 16, 1930, 16541, 7413, 18, 3], "output": "MAISKWTGELDLTFKHDGRRTVNGKTYFQGGLKVIRPTYLNGSPHPTMFLINLGGGFVDGDRYRMTVHFEPRTHAILTTQGATIVFKTLEDKVEQYQTFQLDDESFMEFISDPIIGYSEAKFYQVNQFHLSPTASMFYTDILTPGYDKEGRQFNYHYLHLKNEIYVDEKLVVFDNLKLDTQKNKVTHMGYMEGFTHMASCFYISPGVNQKAVEAVQEVVTPYIDEHCRVGVTLLPTHGLTFRILAYSTDVIQRVIHAVHQYVMETYHEEDAQFLRKY", "metadata": {"id": "A0A7T7SWM3", "cluster": 17099116, "interpro_all": ["IPR002669"], "interpro_used": ["IPR002669"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein is assigned to the Zinc finger C2H2 superfamily, which comprises stable, zinc-coordinated $\\beta/\\beta/\\alpha$ motifs that primarily function as DNA-binding domains in eukaryotic transcription factors. These versatile scaffolds typically interact with the DNA major groove in tandem clusters, but can also be adapted to bind RNA, proteins, or lipids to regulate diverse cellular processes. In addition, the protein should contain a Zinc finger C2H2-type domain that functions as a classical DNA-binding motif, typically found in eukaryotic transcription factors where it interacts with the DNA major groove using a conserved $\\beta/\\beta/\\alpha$ fold coordinated by a zinc ion. These domains frequently appear in tandem arrays to facilitate specific recognition of nucleic acids, proteins, or lipids, acting as stable scaffolds for diverse biological activities ranging from gene transcription to chromatin remodeling. It is found in Serinus canaria (Island canary) (Fringilla canaria) and corresponds to UniProt keyword Zinc-finger, Repeat, and Nucleus.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 1977, 6304, 1942, 1920, 7997, 8497, 8453, 6951, 13975, 16, 2154, 12936, 4700, 16, 7997, 17, 11651, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 8277, 1988, 5985, 2347, 1966, 2678, 17, 2743, 4682, 1922, 10825, 3213, 2790, 18, 2144, 20425, 10603, 5745, 6310, 1956, 1920, 2678, 3044, 15920, 1922, 10361, 5859, 16, 2308, 2112, 2222, 1998, 8461, 1942, 4566, 3146, 16, 2697, 16, 2014, 8238, 1942, 5741, 6445, 3689, 4028, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 7997, 8497, 8453, 6951, 17, 2601, 3418, 1988, 4088, 1966, 43, 8445, 2678, 17, 2743, 5219, 16, 5745, 2435, 1922, 10825, 3213, 2790, 2597, 2176, 9034, 1956, 1920, 2678, 3044, 15920, 2193, 43, 5305, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 3728, 11651, 2007, 43, 7997, 4755, 18, 2144, 4682, 5467, 3267, 1922, 10361, 10517, 1942, 6628, 2487, 5708, 1927, 11079, 4576, 16, 2697, 16, 2014, 8238, 16, 8290, 1966, 4700, 10603, 1958, 6445, 3933, 4209, 6485, 2037, 2359, 3213, 1942, 6338, 8378, 18, 2176, 1977, 2435, 1922, 2375, 22214, 2112, 6148, 12, 10269, 2112, 2141, 13, 12, 9081, 2029, 10888, 2112, 6148, 13, 1930, 8852, 1942, 20709, 11121, 2538, 7997, 17, 8497, 16, 6865, 16, 1930, 5607, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "XPNSRPKPHRSLLGTGNYDVFHPKILEFHPQIPKFNTTIPEFNPKIPKFRPQFKIPKFHPKIPEFNPKIPKFHPKTLEFHPKTLEFHPQIPKFPNFRPQNSRFSPPQRQGRETRDGGVTMPQRLYLRPRPPPAEPGPSHLQHTWTHPYSTAKLVLGGRSGAPGAPGEAEKPGEDEEDEEEDEDLPACPACHKSFKRTWELLSHQVVHTEARPFTCVHTEERPHRCDLCGKRFKRSSNLQEHRRIHPAANALLLHRRHRCEDKPHTCGVCGKRDRPFRCALCGKAFKQSNALASHERVGKAFKQSSLTWAIPPAGSHRNVVMAALEFNPKIPKIPEFNPQIPDFYPKIPKFHSNPKILEFRPKIPQLYPQIPKPHHAPQPGASLQVRPSPGDPSTSHLRRPGAPGLESPSPEPGEATPGFVQLIDERGVHLEIRQVIVADKPFQHLCRATFKRHSDFKSHALSGQRPFTCPRCCGKDFFTYGHSLKVHERVHTGHTGERPFACRTC", "metadata": {"id": "A0A8C9MKZ9", "cluster": 18437525, "interpro_all": ["IPR036236", "IPR013087"], "interpro_used": ["IPR036236", "IPR013087"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Moreover, the protein has a GtrA/DPMS transmembrane domain that serves as an integral membrane component involved in cell surface polysaccharide synthesis and protein glycosylation. Typically comprising four transmembrane helices arranged as dimers, it is implicated in the translocation of lipid-linked sugars and forms the membrane-anchoring region of enzymes like dolichol-phosphate mannosyltransferase (DPMS). This domain facilitates processes such as O-antigen modification, teichoic acid glycosylation, and the formation of dolichol phosphate mannose donors. It is produced by marine sediment metagenome and has UniProt annotations Transmembrane helix.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3950, 16, 1920, 2213, 2258, 43, 30441, 1019, 19, 5679, 2800, 9117, 3418, 1988, 10634, 1966, 1925, 12328, 3260, 4594, 3286, 1922, 2024, 3154, 17167, 4271, 1930, 2213, 12082, 18, 5745, 10351, 3006, 9117, 12789, 14940, 1966, 13351, 16, 2176, 1977, 6835, 1922, 1920, 7849, 1927, 4486, 17, 4624, 15592, 1930, 4952, 1920, 3260, 17, 20816, 3031, 1927, 5038, 3189, 17837, 2108, 1945, 17, 5413, 7338, 25566, 12, 5679, 2800, 13, 18, 2052, 3418, 11374, 4028, 2427, 1966, 57, 17, 4730, 6295, 16, 3602, 2108, 8643, 2687, 12082, 16, 1930, 1920, 3337, 1927, 17837, 2108, 1945, 5413, 17936, 8276, 18, 2176, 1977, 4152, 2007, 10789, 10363, 16552, 2225, 1930, 2258, 20709, 15010, 9117, 7864, 18, 3], "output": "YKFIICKSGTWSFVFWFNFSSFQNNKFITRIKTNNYIINYHWTFRHKKSTNKNVVVGWFKYLGNSAIGDGTDLVVLAFLTEVFGMWYMLSALLASGVASIIKYSIANKLIWKEKKRTAKDEDYEWVSFFKGLPWQKRWKRIIANIVKDFAEIPNGSAGKLLDIGCGSSPQGLLINHDDYVGFDINNSKIRYMNGKHLLNHNSFITGGFDEIQDMVLAESQDTVICIEVIEHLKHMEVVRQGLKVMHNKLKPNGKLILATPNFGGFRGKWMDKLYGIFQKGAYKDEHQLKFNLPTLKELCEEMGFQYIESKIPSGADMICLFQKVG", "metadata": {"id": "A0A0F9D0Q5", "cluster": 19294571, "interpro_all": ["IPR007267", "IPR029063"], "interpro_used": ["IPR029063", "IPR007267"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: It is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein belongs to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is found in Halobacteriovorax sp and has UniProt annotations ATP-binding, Cytoplasm, and Transferase. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2435, 1922, 23226, 7972, 2341, 18842, 2579, 18897, 2056, 1930, 2258, 20709, 15010, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MRTLKNKYISKTKEQRLYEQDIPTIGLTGGIATGKTSVSKYLEEKGLAVICADKLVKSIYAQPATIEFINQDYPSAIKNNEIDFKKLREIFFSDKEIQKKIEHYIYAKMPNAYLDAVSKFHDPGILIYDVPLLFEKGLDQKVDLSILVYASPEIQVKRLMNRDGISKELALNIISKQISIDEKKEKSDFIVDNSQTLENSFSQIDQLLELLLEN", "metadata": {"id": "A0A2D5YQU4", "cluster": 20617071, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The desired role of my protein is: The protein incorporates a Radical SAM domain that utilizes a [4Fe-4S] cluster to reductively cleave S-adenosylmethionine (SAM) into a 5'-deoxyadenosyl radical, initiating diverse catalytic reactions. Adopting a TIM barrel fold, it coordinates the iron-sulfur cluster via a conserved CxxxCxxC motif to facilitate processes such as methylation, isomerization, and sulfur insertion. Found in all domains of life, it functions in the biosynthesis of DNA precursors, vitamins, and antibiotics, often providing oxygen-independent reaction mechanisms. Furthermore, the protein contains a Elp3/MiaA/NifB-like, radical SAM core domain that functions as the catalytic center for a diverse superfamily of enzymes utilizing S-adenosylmethionine to generate radical intermediates. It supports complex chemical transformations, including methylthiotransfer, peptide cyclization, and the biosynthesis of essential cofactors such as biotin, lipoyl groups, and the FeMo-cofactor. In addition, the protein should contain a Radical SAM N-terminal domain that constitutes the N-terminal region of bacterial and archaeal radical SAM proteins. While the specific function of this domain is unknown, it is associated with enzymes that catalyze diverse reactions such as methylations, isomerizations, ring formations, and anaerobic oxidations. It originates from Porphyra umbilicalis (Purple laver) (Red alga). Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 19683, 43, 6917, 2235, 3418, 1988, 18127, 43, 37, 15338, 1021, 17, 26814, 39, 4377, 1942, 23335, 1954, 21252, 61, 17, 29283, 23568, 11215, 12, 2235, 13, 2460, 43, 25, 11, 17, 16333, 10185, 11731, 6917, 16, 12410, 6445, 6804, 5298, 18, 20478, 43, 2267, 19560, 3728, 16, 2176, 10675, 1920, 5680, 17, 12585, 4377, 3454, 43, 5305, 5639, 14710, 1030, 14710, 1030, 5219, 1942, 6628, 4028, 2427, 1966, 5547, 16, 27027, 16, 1930, 12585, 7413, 18, 2435, 1922, 2136, 4682, 1927, 3308, 16, 2176, 4088, 1922, 1920, 8132, 1927, 2678, 10416, 16, 18818, 16, 1930, 7560, 16, 3868, 5453, 4612, 17, 3484, 3227, 3531, 18, 3677, 16, 1920, 2213, 5461, 43, 2349, 7170, 19, 24173, 1019, 19, 17719, 1014, 17, 3189, 16, 6917, 2235, 4728, 3418, 1988, 4088, 1966, 1920, 6804, 4102, 1958, 43, 6445, 13975, 1927, 5038, 10232, 61, 17, 29283, 23568, 11215, 1942, 5655, 6917, 12386, 18, 2176, 7825, 2796, 4399, 18510, 16, 2710, 4963, 22523, 8435, 2070, 16, 4207, 25267, 16, 1930, 1920, 8132, 1927, 4415, 21362, 2427, 1966, 8622, 16, 3178, 10921, 2671, 16, 1930, 1920, 3210, 1037, 17, 15155, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 6917, 2235, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 3031, 1927, 4543, 1930, 22367, 6917, 2235, 2697, 18, 2679, 1920, 2487, 2347, 1927, 2052, 3418, 1977, 5435, 16, 2176, 1977, 2458, 1956, 5038, 1988, 18170, 6445, 5298, 2427, 1966, 5547, 1036, 16, 27027, 1036, 16, 6335, 3337, 1036, 16, 1930, 12554, 6638, 1036, 18, 2176, 22970, 2037, 17376, 3553, 1019, 15078, 1937, 12, 14308, 21875, 1915, 13, 12, 2312, 4326, 1019, 13, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MSNSGHVILYSCLNDTPGVLADRSYLPASDMVAALGRARQPLFAVESKRPLAAFDAVVMPVHYELGALNCLELLALGGIPLTWAAREAADAEAGRPRWSVADGSVPLVIAGGTTLTSNPEPYADFLDAVLLGDGEDVLPAVASTIARCLASPTPLSREDVLLRLAAVPGVYVPRFYEVYTSTGAVRAVRGDVPRRPSRQVATPQPRRALALVPAMGTVHDRLVVEVRRGCTRGCRFCAPGMLTRPARDVPPADVAAAVRDGVAKTGYNEFSLLSLSCSDYLSLPAVGLGLKNELRDMNIGLSLPSQRVDRFDDNIAALSGGLRKSGLTFAVEAGTQRLRDVVNKDLTYAQLEAGVRTAVAAGWRQVKLYFMMGLPSETDDDVLAIADTIRALQRAVRLPNGQRLAVHVTVSALIPKPHTPFQWHNVSSEELDRKRGLVIKSFSRMRDVKVMVASWRIHSLEDFLSRGDRRASAVVLRARELGVGADAWWMDEKGAHATWVQAIADCGLSPQYRAMEAGSWDIMNPAIMPQEVVRGKRGWYDFAKTKGVDFKTLNPKGAAATKGDGVAAAAVTAAVTEAAAGGAAVEEGGSLLDRPLPWDHIDTGVDKGWLRDELMRALTGTLTPDCSFSDCSECGVCGSARGNNVVSEPPPIPAFEGNWRPDTTKANTLRLALAKRGDASLLSHLDTFRLFDRALRRARMPIAYSGGFHPKPRIAAASALPFGATADAELFDFTFTTHVSAADFTAAFAPQLTPGFSVVAVEELDDKAATVAHRMRAAEYVVGVYLATDGEALVDGSGEADADAPVPAVAVDAGMAAAQSTPAASATMTVAVDTQADATAAAAAPAPATRAEDIDWPALVADTLAMDACVVTRATNGGKGQNTRAVDLRSRLFGLSLAAPADAAPVLRHVGPADWPAGAVALTATVLSSNDGALSPDDLVELLRVGAGGRLPGLELLHAHRRGLVLASEAEVAAAAAVAKAATRARRKEREAAAEVAADAKAARKAAGAAAAAARAEAANEATA", "metadata": {"id": "A0A1X6NMC8", "cluster": 25309606, "interpro_all": ["IPR018768", "IPR006638", "IPR045784", "IPR007197", "IPR023404"], "interpro_used": ["IPR007197", "IPR006638", "IPR045784"], "interpro_unused": ["IPR018768", "IPR023404"]}, "task_type": "autoregressive"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein can be placed in the Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II superfamily, which encompasses proteins sharing a seven-bladed beta-propeller structure, including bacterial inhibitors of beta-lactamases and eukaryotic regulators of nuclear processes. Specific members include BLIP-II, which competitively binds enzymes like TEM-1 to inhibit antibiotic resistance, and RCC1, a guanine nucleotide exchange factor for Ran that mediates spindle formation and nucleocytoplasmic transport. Also, the protein should include a Regulator of chromosome condensation (RCC1) repeat that functions as a guanine-nucleotide dissociation stimulator (GDS) for the nuclear GTP-binding protein Ran, promoting the exchange of GDP for GTP. Structurally, these repeats form a seven-bladed beta-propeller domain that facilitates binding to chromatin. It is native to Trifolium pratense (Red clover) and is annotated with UniProt keywords Receptor.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 7888, 1927, 5597, 16112, 21, 19, 4666, 17, 23023, 17, 4106, 2213, 2890, 13975, 16, 2154, 21569, 2697, 10763, 43, 5260, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 16, 2710, 4543, 4472, 1927, 4666, 17, 23023, 1036, 1930, 10825, 9098, 1927, 4254, 4028, 18, 2487, 4678, 3951, 2266, 2049, 17, 2890, 16, 2154, 10362, 1954, 6876, 5038, 3189, 2775, 17, 21, 1942, 2875, 7267, 3554, 16, 1930, 13253, 1009, 16, 43, 16904, 5489, 6818, 2991, 1958, 2845, 1988, 10412, 10716, 3337, 1930, 2797, 3107, 11302, 4860, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 7888, 1927, 5597, 16112, 12, 13253, 1009, 13, 6865, 1988, 4088, 1966, 43, 16904, 17, 5489, 9182, 24052, 12, 29650, 13, 1958, 1920, 4254, 9319, 17, 2743, 2213, 2845, 16, 7356, 1920, 6818, 1927, 15217, 1958, 9319, 18, 12171, 16, 2144, 9569, 2386, 43, 5260, 17, 22707, 1007, 4666, 17, 5062, 13728, 3418, 1988, 11374, 2743, 1942, 6338, 18, 2176, 1977, 6196, 1942, 13453, 30438, 21227, 2777, 4127, 12, 2312, 12596, 2004, 13, 1930, 1977, 10633, 1956, 20709, 11569, 3148, 18, 3], "output": "MDGAVQHGVAGCGGVLRGQHGNIVGYVLQDRETSTIQSCTVKALPSQRVRSVVAGSRNSLAICHDGKSKWIPCQWGSGEDGQLGIGTNEDKEWV", "metadata": {"id": "A0A2K3MIY5", "cluster": 25316402, "interpro_all": ["IPR009091", "IPR000408"], "interpro_used": ["IPR009091", "IPR000408"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein is included in the Vacuolar protein sorting-associated protein 13 family, which mediates lipid transfer between membranes at organelle contact sites to regulate mitochondrial lipid homeostasis and membrane morphogenesis. These phospholipid-binding proteins stabilize junctions, such as ER-mitochondria contact sites, and are essential for vacuolar protein delivery and lysosomal degradation. In addition, the protein should feature a VPS13-like middle region domain that acts as a channel to mediate the bulk transfer of glycerolipids between membranes at organelle contact sites. Found in VPS13 proteins, this domain facilitates the bridging of organelles like the ER, mitochondria, and endosomes during processes such as vesicle fusion, autophagy, and actin regulation. It is derived from Desmophyllum pertusum.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 1977, 3063, 1922, 1920, 21582, 2213, 11404, 17, 2458, 2213, 2590, 3416, 16, 2154, 10412, 4486, 3856, 2192, 5726, 2019, 19309, 5217, 3402, 1942, 5741, 4596, 4486, 7622, 1930, 3260, 15328, 18, 2144, 14608, 17, 2743, 2697, 13448, 11245, 16, 2427, 1966, 2668, 17, 6489, 5217, 3402, 16, 1930, 2032, 4415, 1958, 21582, 2213, 4868, 1930, 12097, 4877, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 14851, 3633, 17, 3189, 5576, 3031, 3418, 1988, 8016, 1966, 43, 4999, 1942, 8265, 1920, 9390, 3856, 1927, 9244, 2049, 3753, 2192, 5726, 2019, 19309, 5217, 3402, 18, 2435, 1922, 14851, 3633, 2697, 16, 2052, 3418, 11374, 1920, 17908, 1927, 14487, 3189, 1920, 2668, 16, 6489, 16, 1930, 14978, 2409, 4028, 2427, 1966, 11502, 5289, 16, 6661, 16, 1930, 4718, 3640, 18, 2176, 1977, 3595, 2037, 17489, 13384, 1989, 7548, 1957, 1989, 18, 3], "output": "MEASSLSLVQTPVGSSRWSVSPNCCEGANPDHPEYSFTKLHQEALLKPSSIFQPKLLPRHSALLLLIALSTQYAHQSQSIDKDEIQIEVTAKLGGIGVTVTSVDGDLSHVIVGGLSAYCVVRDSRTEIVSIVNQEVFNLQQLRNMEAADVKFQMGIGCIRVVFLNKFVMNLLATIQNLQTQSSRISLSVSIQAPLIVIPVSSTSHDALVANVVVDNMVVELSSVQLSRAVMTDGENIGATRLVLEPASLAVYVALHAVKIWKLPVRASVLQHQLQSEDVWDSVKFSFKIEEVSASLVWDSSSLVSRGLAAGNGGNRKRGRTIRKSSTFKSTQQLCCLWNSLRYKALICHEHPKAQSDGKKKKEVIASMKNLSVLDSTPGALYPKEFLNKFQKAKDAMEYARKSAAESATLGHLSVANTFNLAHDGEDPGGSDARNLSPWYHDVPDIDVMGRVFWKESAKPSGQQVLQRAQTW", "metadata": {"id": "A0A9W9ZW78", "cluster": 25975206, "interpro_all": ["IPR026847", "IPR056747"], "interpro_used": ["IPR026847", "IPR056747"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein should feature a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein should contain a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Additionally, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is produced by Deltaproteobacteria bacterium and is described by UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 4152, 2007, 9649, 9218, 1021, 10296, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MFSAPAKINLCLHVLGRRADGYHELRMVMQQINLCDRIRILVGAGDGVTVGCSGVDLAEGTENIAARAARLILREAGVRAVVDIEIDKKIPVAAGLGGGSSDAAAVLKAVNGMLALGFDDFALAKMGLSLGADVPFFIRGGAALAEGIGERLRPFSIRPDVGYLLVNPGFAVSTAWVYRNLVLTSKGDEANLARFVGCYSGLLRLLHNDLEKVTLTYYPVLKDIKKRLLKAGADGALMSGSGPTVFGLFRDRAAARRAGEELARTTSWQVFPAEPCS", "metadata": {"id": "A0A971JBB5", "cluster": 27234908, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR014721", "IPR036554", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence for a protein with the following function: The protein is included in the Macro domain-like superfamily, which functions primarily by recognizing ADP-ribose derivatives to regulate ADP-ribosylation in chromatin biology, DNA repair, and viral pathogenesis. This superfamily shares a mixed \u03b1/\u03b2 fold and encompasses both the metabolite-binding Macro domain found in histone macroH2A and PARPs, as well as the DNA-binding N-terminal domain of leucine aminopeptidases. It originates from Mytilus galloprovincialis (Mediterranean mussel).", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1958, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 10133, 3418, 17, 3189, 13975, 16, 2154, 4088, 5985, 2007, 15667, 9828, 17, 17870, 8383, 1942, 5741, 9828, 17, 29117, 3017, 1922, 6338, 7256, 16, 2678, 5059, 16, 1930, 4324, 6559, 18, 2052, 13975, 16495, 43, 4985, 160, 19, 161, 3728, 1930, 21569, 2321, 1920, 9483, 17, 2743, 10133, 3418, 2435, 1922, 6632, 10133, 6951, 1019, 1930, 12007, 1036, 16, 1966, 2486, 1966, 1920, 2678, 17, 2743, 56, 17, 4262, 3418, 1927, 12624, 3835, 9626, 2410, 30413, 18, 2176, 22970, 2037, 3057, 2583, 1957, 9354, 12964, 11800, 3349, 19337, 12, 16825, 26874, 1938, 13, 18, 3], "output": "MNLVRFRYGDLLTISDVDVICHQVNCLTTKPHGLSKYIADEIPWSDIYSKRRSVRSRNLAVEKDRGVPGSIRRLGRVVCFQAQWDFGGPKEGRRISPHVDSRENREKWFKNCLYELGLMEEQKIGMPFKLGCGLAKGHWPTYLKMIKNYSQNENDIPISRRLYSLAPG", "metadata": {"id": "A0A8B6D5K5", "cluster": 27630426, "interpro_all": ["IPR043472"], "interpro_used": ["IPR043472"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein carries a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. In addition, the protein should include a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. Furthermore, the protein is a member of the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. It originates from Gammaproteobacteria bacterium and is connected to UniProt keyword Hydrolase and Metal-binding.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 16252, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 2176, 22970, 2037, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 20748, 1930, 6048, 17, 2743, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MTQITEQLVLGALRNVREPELHKDLVTLNMIRDIKIKGDDVAFTNCNDVLAQIGVKHVDINWISEVPADQRIIDQLQVTFHNTIAISSGKGGVGAGVGLLDADIYGPNIPLMMGVDRLPRSTGDKIIPAFAHGIWRGPMIHSAIKQFLTDVDWGQLDYLIIDLPPGTGDAQLTLAQQEVALADALRGLKMFEKLEVPILGIIENMGPYVDPVSGQKIAFFGEGGGGDAGKPIVVGKPDSAAGVALKAIAQQVAARISVLNLEDIVLTTPACPLTAQMEKGKSTVAANLAVALAKMVRLMSMAFLMNPDQPVSVPLTGAVIVSTPQRMADRLQVPFLGSVPLDPSVREG", "metadata": {"id": "A0A916H523", "cluster": 297576, "interpro_all": ["IPR034904", "IPR002744", "IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR000808", "IPR002744", "IPR033756"], "interpro_unused": ["IPR034904", "IPR044304", "IPR019591", "IPR027417"]}, "task_type": "infilling"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein is assigned to the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. Moreover, the protein is assigned to the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Also, the protein has a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. It has been detected in Fusarium langsethiae and contains UniProt keyword associations Metal-binding, ATP-binding, and Magnesium.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 2222, 16, 1920, 2213, 2258, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 2176, 2258, 2252, 3330, 1922, 24470, 5646, 4646, 7969, 3336, 1930, 5461, 20709, 11121, 2538, 5253, 6048, 17, 2743, 16, 4498, 17, 2743, 16, 1930, 13148, 18, 3], "output": "MSSEQAFGVTPPISVQLPTEAELRQSDALLEELKRQKTFESPAETAKREEVLIRNARGRVFTYGSYRLGVYGPGSDIDTLIVAPRYVTREDYFKYFPDLLVSMAPRGISIDLIFSRIIQKQLAPDLKDLKDSGLLRGLDEAELRSLNGTRVTTFKNALRAIKLWAQRRAVYANIMGFPGGVAWAMLVARVCQLYPKATPAVIVNKFFLVRVWNPKLYKGDTFHLMPVITPAYPSMCATFNITRSSMTIINRELKRALQIKYYISVISAAKTKESHTIWSGYVESKVRMLVQKLEQHQSIALAHKEIESVQEGSLDFLCKEDAAEPTTIKIEPAVAELPIKAENGENGLTVKSEPAVSGATDVYTTTHYIGLELAAGAKSLDLSYQVEEFKELCTSWQKYKDDLFENGEKKPQKKSAAKGAANNKKRGPPEETPPPAKRQQSSIAAAGASIQIICDAFVRRVAEEKEPKNEVLDAITDMAVVTDAFVPIIKFEYFDEILTLVPEQSISQWRWPQPVLLKPIEGGPLPVSESIMVGTRPWGDLFAKHSFFTSGYPFNKGYERHHLCQNETTEDNGPITAEPIKSETPNDTKLSETKDVVSIGIQHVRNFNLPDDV", "metadata": {"id": "A0A0M9EUE5", "cluster": 1182466, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR011068", "IPR043519", "IPR007012"], "interpro_unused": ["IPR007010", "IPR048840", "IPR014492"]}, "task_type": "infilling"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein is grouped in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It occurs in Limosilactobacillus reuteri (strain DSM 20016) (Lactobacillus reuteri) and contains UniProt keyword associations ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 5110, 1922, 2784, 27545, 5148, 2341, 14357, 8898, 1964, 4834, 1033, 12, 3943, 10964, 4797, 1016, 13, 12, 18134, 1964, 4834, 1033, 13, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MTKIVGLTGGIATGKTTVSNILRQAGIPVIDADQVARQVQTPDSVGLTRIVKVFGPKVLLPTGELNRPALAKIVFNDKEALKKLNEILQPLIYDAIFVQADTLKKQGIPLVVLDVPLLFEQHYDEDCDYVVVVYTDPQTQLKRLMARDHCSKKEAQARIAAQMPLSEKEARADFKINNNGDQVALQKQVASLINQLKAK", "metadata": {"id": "A5VKX8", "cluster": 3057676, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a polypeptide chain with the following function: The protein has a NurA domain that functions as a nuclease with both single-stranded endonuclease and 5'-3' exonuclease activities on single-stranded and double-stranded DNA substrates. It was originally identified in the hyperthermophilic archaeon *Sulfolobus acidocaldarius*. It is expressed in Altiarchaeales archaeon and has UniProt annotations Coiled coil. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 23870, 1019, 3418, 1988, 4088, 1966, 43, 16230, 1956, 2321, 2957, 17, 10338, 18697, 1930, 25, 11, 17, 23, 11, 24966, 4209, 1990, 2957, 17, 10338, 1930, 4825, 17, 10338, 2678, 6249, 18, 2176, 1982, 10398, 2899, 1922, 1920, 19144, 12492, 24888, 3742, 13470, 1916, 14, 5141, 26356, 26835, 2687, 5000, 3825, 3027, 1957, 14, 18, 2176, 1977, 3198, 1922, 8387, 9475, 25588, 5243, 1918, 13470, 1916, 1930, 2258, 20709, 15010, 17524, 9121, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MGRYDLWLRKYEEKKKLILEEIQTYRLELKRVIEQLKEKNLFTKIDEKRKIDATICFIDGGDAIKELLGASIYLIKASALVLEKRSDKLSNERFLRDLDFGVLEYEENNKERVELLRCLMEFQLGRDCIKKFNPDFLLMDGSLYVNANKRYSQPKLVIKHRALFNSLLKEAEKNGTKLIGVSEDSRSRVLVNYLTNRYNLKIPRFITDSTLIKITAKDNICKSITFKPLADGSEKDYEFQTFYLQPTPLANPLRIDVPDLGYDIEEIASLVYNLSLGSRSYGYPIGLHLAHLDAKVEAFEMEWCTKQLAKVLEQDELFSVMLRKTRRELRPKIRYEK", "metadata": {"id": "A0A497S0L8", "cluster": 3084663, "interpro_all": ["IPR018977"], "interpro_used": ["IPR018977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein is included in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, the protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. In addition, the protein is categorized in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It has been characterized in Sphingobacteriales bacterium 41-5 and corresponds to UniProt keyword Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 2258, 2252, 4378, 1922, 13502, 15229, 1918, 14061, 4353, 17, 25, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 3], "output": "MAEKKQIQKLPTEENEEVYHVPVLLSEAIEGLNIKPDKLVAFDQDADAEANLPNDARIIFVPQNFRHLKRFLRLHGIFDAALDMRMDRRQPITAFSVVQHYSEQQLVRNNFQLQTIDGFKNAVRGIVKGNPNKALKEMLVQGKEVLKVGGRLAVITFHSIEDRLVKNFFRAGSFDKKPVVAAAEELKKNKRSRSAKLRVAEKKGIYVDCTFGGGGHSKAILERLGKTGTGVDGILADLGVSSHQFDEADRGFSTRHKMFEQYGEVTNAKTLAKTIVDYFAQVFQALRIEVNEEMEEKEENPFLNTSTESGLKIIT", "metadata": {"id": "A0A1Q3K7A9", "cluster": 3339525, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein has a Xylanolytic transcriptional activator regulatory domain that serves a regulatory function within fungal zinc cluster transcription factors, connecting the N-terminal DNA-binding domain to the C-terminal acidic region. It is essential for the activity of proteins like XlnR, which modulate the expression of cellulolytic and xylanolytic genes, as well as D-xylose catabolism, in response to D-xylose availability. In addition, the protein is included in the ABC-transporter-regulating transcription factor-like family, which comprises fungal transcription factors that regulate the expression of genes involved in azole resistance and drug response. Members of this family also activate gluconeogenic enzymes and control biosynthetic gene clusters for various secondary metabolites, including toxins and pigments. It has been characterized in Fonsecaea monophora and exhibits UniProt keyword tags Coiled coil. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 2258, 43, 23665, 6586, 5224, 9518, 4948, 3418, 1988, 10634, 43, 4948, 2347, 2651, 8697, 7997, 4377, 3213, 2790, 16, 15031, 1920, 56, 17, 4262, 2678, 17, 2743, 3418, 1942, 1920, 45, 17, 4262, 9931, 3031, 18, 2176, 1977, 4415, 1958, 1920, 2455, 1927, 2697, 3189, 11764, 16964, 16, 2154, 8480, 1920, 2294, 1927, 18485, 6586, 1930, 23665, 6586, 2628, 16, 1966, 2486, 1966, 46, 17, 21055, 19480, 16, 1922, 2644, 1942, 46, 17, 21055, 6855, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 7219, 17, 9054, 17, 6773, 3213, 2991, 17, 3189, 3416, 16, 2154, 12936, 8697, 3213, 2790, 1988, 5741, 1920, 2294, 1927, 2628, 3286, 1922, 27381, 1952, 3554, 1930, 2838, 2644, 18, 4678, 1927, 2052, 3416, 2222, 6980, 22296, 3880, 5038, 1930, 2285, 14041, 2359, 5859, 1958, 3425, 4067, 6926, 16, 2710, 13599, 1930, 23756, 18, 2176, 2258, 2252, 4378, 1922, 23160, 4127, 3375, 5376, 20401, 8846, 1930, 9826, 20709, 11121, 2538, 14392, 17524, 9121, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MASMMNSAAPFEEWPQSEQSLAPRKLYPGAMRRRRADQRACDSCRYRKIKVSIPRPNLSLVGRGDRNLSCHVNIRDSVMSGIDVHAQAVFRLRLSARPAATHLLQGARTRREDQIVRLTEKLAATEDRVKSLSEGQERTQACLSRFVDCSDDCRASQGSASFSGVGYANNMAGGLNPRRNDELAPSRHFSLAPPSSLSTSPPTQLHHSDGEPHNSQFFGPTSGVVFASAIKDFIQRQGGPGHVSSSSIFQTALHSSDTRVPSSDGEMSKAAPLLTLLPRRQQALQLLDIYRVHVQEYTPVLPWPSVLDKFARLYDRPVRSGCKSDFIKDFVLLNAVWSIGSQLTEESEAVQESDKNEVRSGWRFFSLARDHYDLAAPKYDLDDAAICLLMSIYLQGASLLNTCWVYVGLTARIIQDLGLHIRPTNQLVTPAQVEVRNRLFWGTYLVDRKIALTLGRTVALLDEECSVDLPRDVDPATFGGSDSTEILRVSVQTCSKLRDIINFTPSPNHQERDMTFLFEMDSALSQYWEDYPLRMKDFSQPDAYDPSCLKVLCILMQARLTTMRHFTDTSLNKDFRKWCFTRSVQISLVTLQTVNTLSRTDDWERKTALFCSGVVYGHIFRAALVLALAGSKFAEDLDTPAERHRFSTLWEFLRAASSRRTSVLKYLQLLEVLAKALGTPLGEDGLSRTTPAPASQVNSDQQSLLGGPRVGGPVGMPPTMHDLTNSNSRLQSRTEYPGQETGMPMGRSTRTLFPANDLRMGYNPPPEMPEAPSSAEDSGLGTNSAPQTVDFDWELFDQIMDCDSSAFPTFPLGLDMDGFDM", "metadata": {"id": "A0A177ERC2", "cluster": 4324189, "interpro_all": ["IPR050987", "IPR007219"], "interpro_used": ["IPR007219", "IPR050987"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein has a Adrift-type ribose 2-O-methyltransferase domain that catalyzes the 2'-O-methylation of the ribose on the second transcribed nucleotide of mRNA and snRNA 5'-ends to form the cap2 structure. This domain is characteristic of cap methyltransferase 2 enzymes in higher eukaryotes and viruses, and acts as a critical factor for nerve pathfinding in *Drosophila*. Furthermore, the protein features a Ribosomal RNA methyltransferase FtsJ domain that functions as an S-adenosylmethionine-dependent enzyme responsible for the 2'-O-methylation of RNA, specifically targeting conserved residues like U2552 in 23S rRNA. It adopts a methyltransferase fold containing a catalytic triad and modifies the RNA substrate within the context of the assembled 50S ribosomal subunit during late-stage ribosome maturation. Furthermore, the protein is classified under the mRNA Cap 2'-O-Ribose Methyltransferase family, which catalyzes the S-adenosyl-L-methionine-dependent methylation of the ribose 2'-O position at the 5'-cap of mRNAs and small nuclear RNAs. By producing cap1 and cap2 structures, these enzymes enhance translation efficiency and influence the interferon response, with some viral members utilizing this mechanism to modify late viral transcripts. It is native to Ceratina calcarata.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 2258, 43, 25622, 2794, 17, 2601, 17870, 22, 17, 57, 17, 16478, 3418, 1988, 17097, 1920, 22, 11, 17, 57, 17, 5547, 1927, 1920, 17870, 1990, 1920, 2812, 10078, 5489, 1927, 3616, 1930, 11970, 2175, 25, 11, 17, 9618, 1942, 2386, 1920, 2853, 1028, 3170, 18, 2052, 3418, 1977, 6293, 1927, 2853, 16478, 22, 5038, 1922, 2580, 15021, 1930, 6241, 16, 1930, 8016, 1966, 43, 4140, 2991, 1958, 5507, 2450, 19906, 2117, 1922, 14, 8273, 14, 18, 3677, 16, 1920, 2213, 4075, 43, 11196, 3146, 16478, 17022, 1013, 3418, 1988, 4088, 1966, 1925, 61, 17, 29283, 23568, 11215, 17, 3100, 4113, 5061, 1958, 1920, 22, 11, 17, 57, 17, 5547, 1927, 3146, 16, 4475, 5133, 5305, 4248, 3189, 15823, 7054, 1028, 1922, 3020, 1036, 9067, 18, 2176, 24032, 43, 16478, 3728, 3165, 43, 6804, 21845, 1930, 25436, 1920, 3146, 4510, 2651, 1920, 4491, 1927, 1920, 10151, 2761, 1036, 11196, 5903, 2409, 5058, 17, 3587, 12794, 7655, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 3616, 2853, 22, 11, 17, 57, 17, 17870, 16478, 3416, 16, 2154, 17097, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 5547, 1927, 1920, 17870, 22, 11, 17, 57, 3507, 2019, 1920, 25, 11, 17, 2853, 1927, 8806, 1930, 2858, 4254, 8624, 18, 2007, 7144, 2853, 1009, 1930, 2853, 1028, 4061, 16, 2144, 5038, 4826, 6410, 5034, 1930, 4039, 1920, 10001, 2644, 16, 1956, 2673, 4324, 4678, 10232, 2052, 2856, 1942, 11675, 5058, 4324, 6247, 18, 2176, 1977, 6196, 1942, 6580, 3248, 1019, 2799, 9041, 3857, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MEAHEQTKKQNLTASNNYFDENEIEFERVTQLFNKRFTLVNNELYSQELKKELNGVKNCLNNYDLDKWQLHTKLRNSAKNVIPREIVSSFPLIPLDYIWRNDNYFKSIHLCEAPGAFVTSLNHWLQTNVIDDDRFIRHTLDYWYFGEDNTGNIMTLNNFTGLIKHSVPHEQESVLTHLHFCETLAALHLLAAGGSFLLKIFTMFECNTICLLYLLACCFTNVSVCTNFKRPVNITSYLEKLKEYYECDPKTAIFNESDIPRYFIEKIINCDAFLSMRQIQRSVADKYIKDYKIRKLGKDEEIIGNASYNERCEKQHLAYFDRMESFYKDIEKVEIYLSHNDIKKVSYLFEKLPKLNSIFKYPLWSVPELLKSNIQPELLTQAWCKFHPDMHWDWTAMTLNPYYEGNSVSTMKDIFLVTADGSVDCADVPAITKPATSKEGNSEVYVSNFFKTHQCSVIQNNIDTFNNYNYIMSLKPANFNPCKVSMQG", "metadata": {"id": "A0AAJ7NGL2", "cluster": 5742655, "interpro_all": ["IPR025807", "IPR050851", "IPR002877", "IPR029063"], "interpro_used": ["IPR025807", "IPR002877", "IPR050851"], "interpro_unused": ["IPR029063"]}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein is categorized in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It occurs in Bacillota bacterium (Firmicutes bacterium) and contains UniProt keyword associations ATP-binding, Cytoplasm, and Transferase.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 5110, 1922, 8175, 22538, 3857, 14061, 12, 24474, 14061, 13, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MKYSGLYVIGLTGGIASGKSTVSRMLRELGAVIIDADEVSREVVSPGFGDKEALDKLDSIIHPLVMARVEETLAELSRESVEGKEGTGEQENAVGMEGVAQQEGLNVKVVVLDAPLLFEVGADKLVDEVWVVSVDPETQMERLIRRNGYSKTENRGDPESTRKQVLALWQEVRRKIRRIAMQTVGWRRVVDAFGPGILRPDGTINRRKLGGMVMVKMEDAGEKRSAGEGQVERSRKKALSRISSQMPLPEKERLSDVVID", "metadata": {"id": "A0A7C7DHG9", "cluster": 8144752, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein is associated with the Sodium:neurotransmitter symporter family, which mediates the high-affinity re-uptake of neurotransmitters into presynaptic nerve terminals and glial cells to terminate synaptic signaling. These integral membrane proteins typically contain 12 transmembrane helices and utilize the co-transport of sodium and chloride ions to drive the uptake of substrates like GABA, dopamine, serotonin, and glycine against their concentration gradients. It originates from Caenorhabditis remanei (Caenorhabditis vulgaris) and has UniProt annotations Metal-binding and Transmembrane helix.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 1977, 2458, 1956, 1920, 5227, 30, 15223, 29148, 2718, 1915, 3416, 16, 2154, 10412, 1920, 2149, 17, 5173, 1964, 17, 5047, 1927, 21012, 2460, 13111, 5507, 13805, 1930, 10786, 2094, 1942, 26767, 6251, 3197, 18, 2144, 12328, 3260, 2697, 5745, 5531, 2369, 9117, 12789, 1930, 12561, 1920, 2081, 17, 4860, 1927, 5227, 1930, 9140, 6982, 1942, 9265, 1920, 5047, 1927, 6249, 3189, 7992, 16, 7964, 16, 11153, 16, 1930, 10646, 3316, 2310, 3110, 12741, 18, 2176, 22970, 2037, 22418, 2500, 2516, 1033, 12, 22418, 22621, 13, 1930, 2258, 20709, 15010, 6048, 17, 2743, 1930, 9117, 7864, 18, 3], "output": "MQRKKIPETTVTTGTTTTISKSMTPTAPSTTQTTQTTNTTTTTKKVNEKKTDRGRKAYKIINFVINPSTGFTDFNFINWATLGAVAICWVALPYIIIVILMIRGITLDGAANGLYYLWGEPDFAFLINMRTWTDAMTQYNWYRVSFTVVFFQKKLKHFDAFLLVLCDTLMSLLGATAVFATLGFLAKQQDVPVPKVISQMPIPYLWHGLFFLMLLLLGMSTEIVIVEIVCSCLSDAVSLTFFTLGLVMTTDIFGWFVAALPFFAIPWFAISTILKYRRENQKIGDQMAEAEPGDDDVEIVDADEDGDESYLEHFEPPKADDERDNEANFRPDQFASIVLIRGMKMIGKLSYFTVIICFSLSIGQGGLMNIASYNKKSIKDGHALAFIVYTEARFGYLRRHRWVTVLIPLRTAFMLQKQHPSYDRISERWPEWK", "metadata": {"id": "E3NBK2", "cluster": 10262397, "interpro_all": ["IPR000175", "IPR037272"], "interpro_used": ["IPR000175"], "interpro_unused": ["IPR037272"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein should have a 3-hydroxyacyl-CoA dehydrogenase conserved site that catalyzes the conversion of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA during fatty acid metabolism. This domain features an N-terminal NAD-binding region and is often found as part of a multifunctional enzyme complex, coupled with enoyl-CoA hydratase and isomerase activities in eukaryotic mitochondria and peroxisomes as well as bacteria. Additionally, the protein is a member of the 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily, which functions as the dimerization module in enzymes catalyzing the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate. This domain facilitates the assembly of the active dimer, often by threading through the partner subunit to contribute to the substrate-binding site or by forming stabilizing salt bridges between monomers. Structurally, it resembles dimerization domains found in diverse oxidoreductases, including mannitol 2-dehydrogenase and glycerol-3-phosphate dehydrogenase. It has been characterized in Ancylostoma ceylanicum.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 3066, 2162, 43, 23, 17, 8275, 14645, 17, 10027, 9294, 5305, 3200, 1988, 17097, 1920, 7309, 1927, 23, 17, 8275, 14645, 17, 10027, 1942, 23, 17, 18588, 14645, 17, 10027, 2409, 5934, 2687, 4714, 18, 2052, 3418, 4075, 1925, 56, 17, 4262, 6577, 17, 2743, 3031, 1930, 1977, 3868, 2435, 1966, 3131, 1927, 43, 20136, 4113, 2796, 16, 6416, 1956, 2066, 10921, 17, 10027, 22420, 3857, 4127, 1930, 25510, 4209, 1922, 10825, 6489, 1930, 28990, 1966, 2486, 1966, 4802, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 26, 17, 8078, 22988, 8870, 9294, 17, 3189, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 4088, 1966, 1920, 13640, 9059, 1922, 5038, 29601, 1920, 5163, 22429, 1943, 1927, 26, 17, 8078, 22988, 8870, 1942, 5216, 8658, 25, 17, 5413, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 3500, 7632, 16, 3868, 2007, 18205, 1941, 2596, 1920, 8240, 5903, 1942, 4672, 1942, 1920, 4510, 17, 2743, 3200, 2014, 2007, 7402, 14384, 7012, 18142, 2192, 13256, 18, 12171, 16, 2176, 17602, 13640, 4682, 2435, 1922, 6445, 27388, 1036, 16, 2710, 20915, 22, 17, 9294, 1930, 9244, 17, 23, 17, 5413, 9294, 18, 2176, 2258, 2252, 4378, 1922, 10315, 2199, 28009, 1019, 5827, 2199, 19510, 1989, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "LTFSGITTICEGDSTLLTVSGNIPQSQFVWEGNVPGNQYMSFQNCPQVTDSILVTVNAVPTVTAPADVQICKGEQFNAAVYPNLGCISEVDSFYVDVLASCSIEVPNTAPEVVEQAKSLIYGEALRIYEEGIADFATIDWAMTELGGFRMGPFTLMDYYKPSFTQKRHFEAGYLGRKSGRGYYNYAEGAVQPEPVKDPVTGQQIAKDIDLAMTNGIHGKPFLSVNQFVFLNDLYIKVNIVAPSGNTYVYVTGPAESTVYWDSTGSVTGTSVTLTAVEKYDSWKKITVLCKDTPGFIVNRVARPFIGNDINYTVTESVFTAFYFDPRVDRILVMLFNEAIDALFLNIAS", "metadata": {"id": "A0A0D6L430", "cluster": 10919139, "interpro_all": ["IPR006180", "IPR006108", "IPR008927"], "interpro_used": ["IPR006180", "IPR008927"], "interpro_unused": ["IPR006108"]}, "task_type": "infilling"} {"instruction": "Target Function: The protein has a Polyketide synthase-like, phosphopantetheine-binding domain that serves as the covalent attachment site for the phosphopantetheine prosthetic group within acyl carrier proteins (ACP) involved in secondary metabolite synthesis. It utilizes a conserved Asp-Ser-Leu (DSL) motif to anchor the prosthetic group to a specific serine residue, creating a \"swinging arm\" that transports activated fatty acid and amino-acid intermediates between active sites. Structurally, the domain forms a four-helix bundle, with the second helix acting as a recognition site for interaction with synthase enzymes. Also, the protein is a member of the Polyketide and Nonribosomal Peptide Biosynthesis Enzymes family, which comprises multifunctional enzymes responsible for the iterative assembly of complex secondary metabolites, including polyketides, nonribosomal peptides, and hybrid compounds. These proteins utilize precursors such as acetyl-CoA, malonyl-CoA, and amino acids to catalyze condensation, reduction, and cyclization reactions, ultimately producing bioactive natural products like antibiotics, mycotoxins, and pigments. In addition, the protein incorporates a Phosphopantetheine attachment site, which covalently anchors a phosphopantetheine prosthetic group to a conserved serine residue, typically found within an Asp-Ser-Leu motif. This modification acts as a flexible 'swinging arm' essential for tethering and transporting activated fatty acid and amino-acid intermediates between catalytic domains in acyl carrier proteins and associated multienzyme complexes. It has been detected in Volvox africanus.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 2258, 43, 4286, 18540, 2261, 8921, 17, 3189, 16, 8078, 6528, 2057, 20536, 2053, 17, 2743, 3418, 1988, 10634, 1966, 1920, 13577, 8576, 3200, 1958, 1920, 8078, 6528, 2057, 20536, 2053, 19019, 2210, 2651, 11337, 9685, 2697, 12, 18543, 13, 3286, 1922, 4067, 9483, 4271, 18, 2176, 18127, 43, 5305, 4138, 17, 2375, 17, 10632, 12, 4473, 1024, 13, 5219, 1942, 13333, 1920, 19019, 2210, 1942, 43, 2487, 8468, 6181, 16, 11124, 43, 6, 24775, 1941, 6011, 6, 1988, 4860, 1036, 4128, 5934, 2687, 1930, 3835, 17, 2687, 12386, 2192, 3500, 3402, 18, 12171, 16, 1920, 3418, 4952, 43, 3006, 17, 7864, 14142, 16, 1956, 1920, 2812, 7864, 8290, 1966, 43, 5708, 3200, 1958, 2835, 1956, 8921, 5038, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 4286, 18540, 2261, 1930, 22060, 2023, 4969, 4207, 8132, 5038, 3416, 16, 2154, 12936, 20136, 5038, 5061, 1958, 1920, 16266, 5957, 1927, 2796, 4067, 6926, 16, 2710, 4286, 18540, 3726, 16, 22060, 2023, 4969, 5320, 16, 1930, 5249, 4300, 18, 2144, 2697, 12561, 10416, 2427, 1966, 6894, 17, 10027, 16, 3054, 12831, 17, 10027, 16, 1930, 3835, 4576, 1942, 18170, 16112, 16, 3378, 16, 1930, 25267, 5298, 16, 8676, 7144, 13570, 4613, 4461, 3189, 7560, 16, 5078, 20223, 16, 1930, 23756, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 8078, 6528, 2057, 20536, 2053, 8576, 3200, 16, 2154, 16590, 27127, 43, 8078, 6528, 2057, 20536, 2053, 19019, 2210, 1942, 43, 5305, 8468, 6181, 16, 5745, 2435, 2651, 1925, 4138, 17, 2375, 17, 10632, 5219, 18, 2052, 6295, 8016, 1966, 43, 9964, 11, 24775, 1941, 6011, 11, 4415, 1958, 23991, 1930, 27038, 4128, 5934, 2687, 1930, 3835, 17, 2687, 12386, 2192, 6804, 4682, 1922, 11337, 9685, 2697, 1930, 2458, 2779, 14896, 5048, 18, 2176, 2258, 2252, 3330, 1922, 2984, 15525, 1039, 7050, 1957, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "SHMAALHAVASGDDAAAAAATTSSPAVVGSSVSPDAPLMSSGLDSLGAVELRNALSEFIAAQLGAGSETGSRKVRGRRAREEVEAVVQEAVRGEGRLGVQLPSTLVFDYPTPAAV", "metadata": {"id": "A0A8J4FAE9", "cluster": 11092309, "interpro_all": ["IPR036736", "IPR050091", "IPR020806", "IPR009081", "IPR006162"], "interpro_used": ["IPR020806", "IPR050091", "IPR006162"], "interpro_unused": ["IPR009081", "IPR036736"]}, "task_type": "infilling"} {"instruction": "Give me a peptide sequence capable of: The protein features a tRNA(Ile)-lysidine/2-thiocytidine synthase N-terminal domain that adopts a dinucleotide-binding fold structure resembling P-loop ATP pyrophosphatases. This PP-loop superfamily member typically serves as the ATP-binding component in enzymes involved in tRNA modifications, such as lysidine or 2-thiocytidine synthesis. In addition, the protein is categorized in the tRNA(Ile)-lysidine synthase family, which catalyzes the ATP-dependent modification of cytidine to lysidine at the wobble position of tRNA(Ile). This essential modification alters the anticodon specificity from methionine to isoleucine, enabling the correct decoding of the AUA codon in bacteria and eukaryotic organelles. The enzyme typically features a conserved N-terminal PP-loop motif involved in ATP binding. Also, the protein can be placed in the Rossmann-like alpha/beta/alpha sandwich fold superfamily, which adopts a characteristic three-layer architecture serving as a scaffold for diverse enzymatic activities, particularly nucleotide binding and transfer. This group includes the catalytic domains of Class I aminoacyl-tRNA synthetases and nucleotidylyl transferases, alongside ATP pyrophosphatases, electron transfer flavoproteins, and DNA photolyases. It originates from Bdellovibrio sp. CG10_big_fil_rev_8_21_14_0_10_47_8 and is associated with UniProt keywords Ligase and tRNA processing.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 4075, 43, 10089, 12, 9940, 13, 17, 3629, 5802, 19, 22, 17, 15331, 27932, 5802, 8921, 56, 17, 4262, 3418, 1988, 24032, 43, 21302, 17, 2743, 3728, 3170, 18994, 58, 17, 5881, 4498, 20661, 2609, 18135, 18, 2052, 4108, 17, 5881, 13975, 7210, 5745, 10634, 1966, 1920, 4498, 17, 2743, 4594, 1922, 5038, 3286, 1922, 10089, 6920, 16, 2427, 1966, 3629, 5802, 2014, 22, 17, 15331, 27932, 5802, 4271, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 10089, 12, 9940, 13, 17, 3629, 5802, 8921, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 6295, 1927, 2702, 5802, 1942, 3629, 5802, 2019, 1920, 26334, 6936, 1952, 3507, 1927, 10089, 12, 9940, 13, 18, 2052, 4415, 6295, 13714, 1920, 11693, 28615, 4896, 2037, 12417, 1942, 25398, 16, 12180, 1920, 5550, 20749, 1927, 1920, 5759, 1019, 8905, 1922, 4802, 1930, 10825, 14487, 18, 1920, 4113, 5745, 4075, 43, 5305, 56, 17, 4262, 4108, 17, 5881, 5219, 3286, 1922, 4498, 2743, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 18215, 8890, 17, 3189, 4595, 19, 4666, 19, 4595, 18038, 3728, 13975, 16, 2154, 24032, 43, 6293, 2559, 17, 4757, 9335, 13915, 1966, 43, 7281, 1958, 6445, 8145, 4209, 16, 4443, 5489, 2743, 1930, 3856, 18, 2052, 2210, 5921, 1920, 6804, 4682, 1927, 2921, 51, 3835, 14645, 17, 10089, 18185, 1036, 1930, 2797, 4090, 25671, 13763, 1036, 16, 17764, 4498, 20661, 2609, 18135, 16, 4995, 3856, 7732, 14070, 16, 1930, 2678, 10066, 1954, 2319, 18, 2176, 22970, 2037, 5238, 20783, 2165, 2377, 3940, 2056, 18, 7294, 2930, 41, 9769, 41, 3313, 41, 5197, 41, 28, 41, 2900, 41, 2607, 41, 20, 41, 2119, 41, 4261, 41, 28, 1930, 1977, 2458, 1956, 20709, 11569, 11905, 1930, 10089, 4587, 18, 3], "output": "MSMMPKDLSSGSKMIEIHRMEPWNSTEHQIYRQFSSAEKSWQGASLLMAVSGGLDSMVLLSVMCRLATAEKWRLGVVFVHHGDAGVSGIQKAYRDQALELVRAAAARFHLPFFSSHSETFLESEEEMRNFRKKEVEKIRQAQNFEFSVWAHHQQDFVETQVLRLIR", "metadata": {"id": "A0A2H0WEU8", "cluster": 14076998, "interpro_all": ["IPR014729", "IPR011063", "IPR012094"], "interpro_used": ["IPR011063", "IPR012094", "IPR014729"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein is assigned to the Leo1-like protein family, which functions as a core component of the RNA polymerase II-associated Paf1 complex. This complex facilitates transcription elongation and regulates gene expression processes, including histone modification and transcript site selection. It is produced by Talaromyces rugulosus (Penicillium rugulosum).", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 2071, 8098, 17, 3189, 2213, 3416, 16, 2154, 4088, 1966, 43, 4728, 4594, 1927, 1920, 3146, 6479, 2890, 17, 2458, 16545, 1009, 2796, 18, 2052, 2796, 11374, 3213, 9971, 1930, 7014, 2359, 2294, 4028, 16, 2710, 6632, 6295, 1930, 5291, 3200, 4367, 18, 2176, 1977, 4152, 2007, 11571, 15186, 23148, 11677, 1957, 12, 25142, 2457, 23148, 11677, 1989, 13, 18, 3], "output": "MSSSEDEDVRRPGRNARGRLSDDEGNASEMDQNNDADDKDDLFGSDSDGGLNELPDRTLNDPELDSGDDEGRYDRTGDRMDLADDGDEGGYEETLKVMDLSLGRAPEPQSTNQEVYTMEMPNFLALETEEFRPETYVAPPYSTAATSLCWRYDPKDASQLQSNVRIVQWEDGSLTLQLASNPKEQYRIASKPLAPLDKAGNYDPSLDTHTYLAAAAETASVFKITSHLTHQLKPLPTSSVTDDAIQRLQENLVAAGATNRLNSYGSGIAIIDINEDPELAGKRAEAAERLKMREDRKRQQYADREQNKTARRPTYRSSRGGLTAAGLEDDDGMLATRPMKKRPRPNRRGEIYSDDEEDQGRHRQDSYEVDDFVADDDEELEEVEDASGSLPDDEADAEGESDVERPAQSPPRRTVAGDAGSPPARKKNRYRVEDDDEEE", "metadata": {"id": "A0A7H8QU03", "cluster": 14861759, "interpro_all": ["IPR007149"], "interpro_used": ["IPR007149"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein includes a MaoC-like dehydratase domain that exhibits (R)-specific enoyl-CoA hydratase activity. This conserved catalytic region is found in multifunctional enzymes, such as peroxisomal hydratase-dehydrogenase-epimerase and fatty acid synthase beta subunits, where it is responsible for hydratase function. Moreover, the protein can be placed in the UPF0336/Enoyl-CoA hydratase-related family, which participates in lipid metabolism through the hydration of enoyl-CoA substrates and 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity. These enzymes play critical roles in mitochondrial fatty acid synthesis, membrane lipid composition, and the production of biopolyesters like polyhydroxyalkanoates. In addition, the protein is associated with the HotDog domain superfamily, which adopts a characteristic fold comprising a seven-stranded antiparallel \u03b2-sheet wrapping around a central \u03b1-helix to support diverse catalytic and regulatory functions. Members primarily act as thioesterases and thiol ester dehydratase-isomerases in fatty acid metabolism and degradation pathways, while specific non-catalytic bacterial homologs serve as transcriptional regulators of fatty acid biosynthesis. It is native to Fasciola gigantica (Giant liver fluke).", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 21178, 1030, 17, 3189, 11725, 7234, 3418, 1988, 9826, 12, 60, 13, 17, 2487, 2066, 10921, 17, 10027, 22420, 3857, 4127, 2455, 18, 2052, 5305, 6804, 3031, 1977, 2435, 1922, 20136, 5038, 16, 2427, 1966, 28765, 22420, 3857, 4127, 17, 9294, 17, 13872, 9213, 2051, 1930, 5934, 2687, 8921, 4666, 6991, 16, 2597, 2176, 1977, 5061, 1958, 22420, 3857, 4127, 2347, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2353, 1038, 12962, 5677, 19, 2066, 10921, 17, 10027, 22420, 3857, 4127, 17, 2712, 3416, 16, 2154, 17241, 1922, 4486, 4714, 2596, 1920, 16561, 1927, 2066, 10921, 17, 10027, 6249, 1930, 23, 17, 8275, 14645, 17, 37, 11337, 17, 9685, 17, 2213, 39, 11725, 7234, 2455, 18, 2144, 5038, 3918, 4140, 5456, 1922, 4596, 5934, 2687, 4271, 16, 3260, 4486, 5128, 16, 1930, 1920, 3372, 1927, 20864, 26558, 26934, 3189, 4286, 8535, 10465, 5135, 9286, 2209, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 9529, 22389, 1029, 3418, 13975, 16, 2154, 24032, 43, 6293, 3728, 10351, 43, 5260, 17, 10338, 28892, 161, 17, 11130, 4573, 5041, 4760, 43, 4101, 160, 17, 7864, 1942, 3373, 6445, 6804, 1930, 4948, 4088, 18, 4678, 5985, 4033, 1966, 30215, 2319, 1930, 13914, 9603, 11725, 7234, 17, 25510, 1036, 1922, 5934, 2687, 4714, 1930, 4877, 3873, 16, 2679, 2487, 2447, 17, 6804, 4543, 14279, 7120, 1966, 5224, 9098, 1927, 5934, 2687, 8132, 18, 2176, 1977, 6196, 1942, 29990, 10173, 24407, 9482, 1019, 12, 15041, 3568, 2848, 3324, 13, 18, 3], "output": "MVAFTHLTGDTNSLHLVDADCTCSGPFGRPVVHGILTLGLVSCLLGTHFPGPGCLLHSLNCQFTAPLYPDEECIVHAEVAEVQGRRVTFHVRVVASRRETV", "metadata": {"id": "A0A504ZA63", "cluster": 15153409, "interpro_all": ["IPR029069", "IPR002539", "IPR050965"], "interpro_used": ["IPR002539", "IPR050965", "IPR029069"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the polypeptide chain function: The protein should contain a Cro/C1-type, helix-turn-helix domain that functions as a DNA-binding module within transcriptional regulators found in bacteriophages, prokaryotes, and eukaryotes. This motif typically employs a specific recognition helix to bind the DNA major groove, often operating within a dimer to control gene expression, such as the regulation of phage lysogeny and lytic growth. Also, the protein is assigned to the Lambda repressor-like, DNA-binding domain superfamily, which functions as a transcriptional regulator controlling critical genetic switches such as bacteriophage lysogeny and bacterial sporulation. This domain typically adopts a four-helix closed folded leaf topology, a variation of the helix-turn-helix motif, to mediate specific DNA binding and interactions with RNA polymerase. Structural analogs of this fold are also conserved in eukaryotic POU transcription factors and the N-terminal domain of the metabolic enzyme cyanase. It is derived from Sphingomonas endophytica. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 3066, 5531, 43, 9442, 19, 8817, 17, 2601, 16, 7864, 17, 5165, 17, 7864, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 9059, 2651, 5224, 9098, 2435, 1922, 24613, 1036, 16, 28149, 16, 1930, 15021, 18, 2052, 5219, 5745, 22620, 43, 2487, 5708, 7864, 1942, 4566, 1920, 2678, 3044, 15920, 16, 3868, 8654, 2651, 43, 7632, 1942, 2285, 2359, 2294, 16, 2427, 1966, 1920, 3640, 1927, 10503, 3629, 27791, 1930, 17033, 2905, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 18279, 14434, 17, 3189, 16, 2678, 17, 2743, 3418, 13975, 16, 2154, 4088, 1966, 43, 5224, 7888, 7138, 4140, 3299, 21529, 2427, 1966, 24613, 3629, 27791, 1930, 4543, 23647, 18, 2052, 3418, 5745, 24032, 43, 3006, 17, 7864, 8047, 16318, 6998, 13678, 16, 43, 4516, 1927, 1920, 7864, 17, 5165, 17, 7864, 5219, 16, 1942, 8265, 2487, 2678, 2743, 1930, 3719, 1956, 3146, 6479, 18, 4346, 13204, 1927, 2052, 3728, 2032, 2222, 5305, 1922, 10825, 28398, 3213, 2790, 1930, 1920, 56, 17, 4262, 3418, 1927, 1920, 4487, 4113, 10208, 2051, 18, 2176, 1977, 3595, 2037, 13502, 10480, 19771, 4274, 1019, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MKEQAEFADWADFPARLRLARRQLGLNQTDFAAIGSVSLNSQGKYEAGLTEPSASYFASLAAAGVDVHWLLTGQRSAGALDEDLSIVVDAIAPLSGDQRAAILAVIHAFAS", "metadata": {"id": "A0A7X0J9K2", "cluster": 17069817, "interpro_all": ["IPR001387", "IPR010982"], "interpro_used": ["IPR001387", "IPR010982"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein incorporates a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, it is part of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is produced by Oxalicibacterium faecigallinarum and is described by UniProt keywords Isoprene biosynthesis and Transferase.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 19683, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 4152, 2007, 20829, 3349, 7972, 2341, 18842, 1989, 5685, 1940, 1950, 2214, 4058, 24277, 1930, 1977, 2910, 2007, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MTRVLNNCAAPAKLNLFLHVVGRRADGYHLLQGVPAESDLVIRAARLLQTAIIARGSDAATTLLALNHLWQAGFSREELMQIGVKAMQAVDTPSRWFVVIEPGVSVPTQQIFADFLGAATSFGKNDLQVVAEKLFPPIADAVKWLQQALDQVPAQWKAWKARALDHHPLAQLLQSSVFQLIDRGDVLHFSLRDDEAICRSTELAAKTPVGVDIAVEKKLPMGGGLGGGSLGADVPFFIFGRNAFVEGIGEAETGLTRDTKVVKIFGEARMTGSGACVFCGFTDERQADA", "metadata": {"id": "A0A8J3AYU8", "cluster": 17242014, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR006204", "IPR004424"], "interpro_unused": ["IPR020568", "IPR014721", "IPR036554"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein is classified under the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It originates from Selenomonas sp. oral taxon 136 and corresponds to UniProt keyword ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 22970, 2037, 12427, 10480, 2056, 18, 4726, 19278, 12990, 1930, 8852, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MRIIGLTGGIACGKSTVSKAYVELFGPEIVTPEGTLDRAEIARRVFSDTVLRDKMNARVHPEAGWDALTNDTWVVTLPPEEQLARLAEKCMRADVVIDNSGTREETKERVEKLWETYLGRAMLKDCGACIVDADAIAHELSQPNQPIFHIIRAAAEDRLDAAHMDGTAVVVLDVPLLFLLARDHTMDEAEARARIAAQMP", "metadata": {"id": "A0A109WCW4", "cluster": 19694867, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein is classified under the Cytochrome P450, E-class, group IV family, which consists of haem-containing mono-oxygenases that typically function within two-component systems dependent on NADPH:P450 reductase for electron transfer. This group encompasses diverse enzymes, including the CYP7, CYP8, and CYP51 subfamilies, that play critical roles in cholesterol metabolism, steroid biosynthesis, and the production of fungal mycotoxins. Additionally, the protein possesses a Cytochrome P450 conserved site that centers on a highly conserved cysteine residue responsible for binding the haem iron cofactor essential for mono-oxygenase activity. This site facilitates the oxidation of diverse substrates, including steroids, fatty acids, and xenobiotics, playing critical roles in detoxification and biosynthetic pathways across all kingdoms of life. The catalytic process utilizes electrons from redox partners to split molecular oxygen and insert a single atom into the substrate. It is derived from Aegilops tauschii subsp. strangulata (Goatgrass) and is connected to UniProt keyword Metal-binding, Monooxygenase, and Heme.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 9387, 12088, 16, 47, 17, 2921, 16, 2210, 4370, 3416, 16, 2154, 7543, 1927, 7105, 17, 3165, 8914, 17, 25298, 1036, 1988, 5745, 2347, 2651, 2288, 17, 4594, 3771, 3100, 1990, 11908, 30, 12088, 11386, 1958, 4995, 3856, 18, 2052, 2210, 21569, 6445, 5038, 16, 2710, 1920, 6120, 1027, 16, 6120, 1025, 16, 1930, 6120, 7912, 24167, 16, 1988, 3918, 4140, 5456, 1922, 5463, 4714, 16, 9507, 8132, 16, 1930, 1920, 3372, 1927, 8697, 5078, 20223, 18, 4950, 16, 1920, 2213, 14465, 43, 9387, 12088, 5305, 3200, 1988, 7365, 1990, 43, 3626, 5305, 8666, 6181, 5061, 1958, 2743, 1920, 7105, 5680, 15155, 4415, 1958, 8914, 17, 25298, 2455, 18, 2052, 3200, 11374, 1920, 6638, 1927, 6445, 6249, 16, 2710, 13039, 16, 5934, 4576, 16, 1930, 29821, 1036, 16, 14797, 4140, 5456, 1922, 18169, 1930, 14041, 3873, 3436, 2136, 13543, 1036, 1927, 3308, 18, 1920, 6804, 2585, 18127, 14354, 2037, 9366, 7228, 1942, 10030, 3272, 4612, 1930, 12844, 43, 2957, 6761, 2460, 1920, 4510, 18, 2176, 1977, 3595, 2037, 18025, 1970, 4001, 7462, 14920, 3907, 19615, 18, 9402, 2029, 5617, 3857, 12, 8838, 27458, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 6048, 17, 2743, 16, 8914, 13966, 16, 1930, 10954, 18, 3], "output": "ECQEPCKVLGFDVLKGTQVIRPERFESGAGVDVDFRGTDLASVELPFASMLLHFDWNLLLRPSLRVPLPTSPPHVNTWALGRDERSWGPDAAEFFELLPFGAGRRMCPGMAFGEAPNISNPAEFDMTEQIGVTARRKA", "metadata": {"id": "A0A452XFJ4", "cluster": 22778650, "interpro_all": ["IPR052306", "IPR001128", "IPR017972", "IPR002403", "IPR036396"], "interpro_used": ["IPR002403", "IPR017972"], "interpro_unused": ["IPR052306", "IPR001128", "IPR036396"]}, "task_type": "infilling"} {"instruction": "The protein possesses a ABC transporter-like, ATP-binding domain that utilizes the energy from ATP hydrolysis to power the transmembrane transport of diverse substrates, ranging from ions to macromolecules. It features conserved Walker A and B motifs, a Q-loop, and a signature sequence that form the nucleotide-binding site, typically functioning within a dimer. This module interacts with transmembrane domains to couple ATP-driven conformational changes to the import of nutrients or the export of toxins and membrane components. Also, the protein should have a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. Also, the protein is assigned to the ABCF protein family, which comprises ribosome-associated ATPases within the ABC transporter superfamily that lack transmembrane domains and function in translational control. These proteins facilitate translation elongation by driving the ATP-dependent release of deacylated tRNA from the ribosomal E-site and stimulating aminoacyl-tRNA binding, while bacterial members can confer macrolide resistance via ribosome protection. Additionally, they are implicated in ribosome biogenesis, quality control pathways, and cellular stress responses. It originates from Saccharothrix sp. CB00851 and has UniProt annotations Coiled coil. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 7219, 9054, 17, 3189, 16, 4498, 17, 2743, 3418, 1988, 18127, 1920, 3844, 2037, 4498, 9128, 1942, 4215, 1920, 9117, 4860, 1927, 6445, 6249, 16, 6485, 2037, 6982, 1942, 20625, 18, 2176, 4075, 5305, 20138, 43, 1930, 44, 8277, 16, 43, 59, 17, 5881, 16, 1930, 43, 9983, 3244, 1988, 2386, 1920, 5489, 17, 2743, 3200, 16, 5745, 7295, 2651, 43, 7632, 18, 2052, 9059, 9034, 1956, 9117, 4682, 1942, 15116, 4498, 17, 6446, 8523, 2840, 1942, 1920, 2582, 1927, 11312, 2014, 1920, 12660, 1927, 13599, 1930, 3260, 4178, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 7219, 1038, 2213, 3416, 16, 2154, 12936, 12794, 17, 2458, 28132, 2651, 1920, 7219, 9054, 13975, 1988, 3630, 9117, 4682, 1930, 2347, 1922, 8414, 2285, 18, 2144, 2697, 6628, 6410, 9971, 2007, 9228, 1920, 4498, 17, 3100, 4012, 1927, 30097, 13796, 15793, 10089, 2037, 1920, 11196, 47, 17, 3200, 1930, 9868, 3835, 14645, 17, 10089, 2743, 16, 2679, 4543, 4678, 2112, 7909, 23929, 2261, 3554, 3454, 12794, 6202, 18, 4950, 16, 2611, 2032, 6835, 1922, 12794, 13008, 16, 3455, 2285, 3873, 16, 1930, 3689, 3071, 3387, 18, 2176, 22970, 2037, 14175, 15742, 5856, 2416, 2056, 18, 5529, 23789, 7912, 1930, 2258, 20709, 15010, 17524, 9121, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MSETCVVVSGMSFSWPDDTPVFADLSCTVPTGRTGLVAPNGAGKTTLLKLIAGELRPSAGSVTVDGVLGYLPQDLPLTGEPTVAEVLGVAPVLRALAAVESGDVAEKHFTTIGNDWDVEERTRAQLDRLGLGELGLDRSLATLSGGQVVSLGLAAQLLKRPDVLLLDEPTNNLDLAARHKLYEVLDDWSGCLLVVSHDRALLDRVDRVAEIESGEVRYYGGNFTEYERAVEAAREVAEKNVRNVEQELKREKREMQQARERAARRASTAARNLGNAGLPRIFAGTMKRNAQESAGKANGTHAARVSAAKAKLDEAERALRDEQKITLELPQTAVPAGRTLFLGERLRAAFGGRELFAGEGVDLAIRGPERIALTGGNGAGKSTLLRIVHGDLEPDSGDVKRADGRIAYLSQRLDLLDSTRTVAENLAAAAPAMPPAQRMNLLARFLFRGSRAHLPVGVLSGGERLRATLACVLFAEPAPQLLLLDEPTNNLDLLSTGQLERALNAYQGAFVVVSHDERFLSEIGVDRRLRLDGGRLLETAAPTTSG", "metadata": {"id": "A0A1Q4X1B3", "cluster": 22922906, "interpro_all": ["IPR003593", "IPR003439", "IPR050611", "IPR027417"], "interpro_used": ["IPR003439", "IPR003593", "IPR050611"], "interpro_unused": ["IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein possesses a CHAT domain that is structurally related to the peptidase clan CD, a family that includes caspases. Named for its association with Caspase, HetF, and Tprs, this domain is implicated in proteolytic processes or signaling pathways involving these motifs. It is found in Orbilia ellipsospora.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 14465, 43, 20560, 3418, 1988, 1977, 12171, 2712, 1942, 1920, 24050, 6958, 1022, 2464, 16, 43, 3416, 1988, 5921, 18535, 18, 10314, 1958, 2496, 3279, 1956, 6186, 16, 21997, 1038, 16, 1930, 22288, 1036, 16, 2052, 3418, 1977, 6835, 1922, 12712, 4028, 2014, 3197, 3873, 5884, 2144, 8277, 18, 2176, 1977, 2435, 1922, 11158, 25600, 25467, 3508, 8846, 18, 3], "output": "MDMEADFKRLLEGIRKQDGFQRFLMEPEFWSDAILVEQHRIRSLNLVALEWLWDVIAQPILEALGITTSPKENTEYSEDSDETVLDRVISSYSVSIRALLLVSMAKTEDQLDLPFAKENNDFMAAAEHHSIVVINVSPGLHESDIKANLKSIKNGDELEVWWPRICWIPIGELCQLPLHAAGRLHDLRMPELVHSSNNA", "metadata": {"id": "A0AAV9WWD7", "cluster": 23064204, "interpro_all": ["IPR024983"], "interpro_used": ["IPR024983"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein carries a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. Also, the protein falls within the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is present in Actinomycetes bacterium and is described by UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 16252, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2481, 1922, 4718, 25148, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MSARRGRLIALEGGEASGKSTQARVLAASLGALLTHEPGGTEIGRRIRAVVLAPDLGDLDARAEALLMAADRAQHVAEVVEPALARGTDVVTDRFAGSSLAYQGFGRGLDVEEVRRLSTWAAGGLEADLVVLLEVPLDIAARRRTAADDRMEAEGAAFHARVADGYRALAAAQPDRWVVVDGDGPPGDVAERVSKVVADKLGTRP", "metadata": {"id": "A0A538JIP5", "cluster": 23986426, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "autoregressive"} {"instruction": "The protein can be placed in the Photosystem I assembly protein Ycf3 family, which acts as a chaperone-like factor essential for the stable assembly of the photosystem I (PSI) complex. By guiding the correct organization of PSI subunits, these proteins ensure the proper functioning of the machinery responsible for the light-dependent reactions of photosynthesis. Furthermore, the protein is associated with the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. Additionally, the protein carries a Tetratricopeptide repeat that mediates protein-protein interactions and the assembly of multiprotein complexes. This motif consists of tandem 34-amino acid residues adopting a helix-turn-helix arrangement, which stacks to form a right-handed superhelical structure involved in diverse processes such as cell cycle regulation and protein folding. It is expressed in Chloroflexi bacterium OLB15 and has UniProt annotations Receptor and TPR repeat. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8811, 2405, 51, 5957, 2213, 22386, 10892, 3416, 16, 2154, 8016, 1966, 43, 14044, 17, 3189, 2991, 4415, 1958, 1920, 4700, 5957, 1927, 1920, 8811, 2405, 51, 12, 14748, 13, 2796, 18, 2007, 19096, 1920, 5550, 5901, 1927, 14748, 6991, 16, 2144, 2697, 6486, 1920, 3405, 7295, 1927, 1920, 10853, 5061, 1958, 1920, 3696, 17, 3100, 5298, 1927, 18133, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 4950, 16, 1920, 2213, 16252, 43, 12470, 3319, 21305, 6865, 1988, 10412, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 18, 2052, 5219, 7543, 1927, 10361, 3540, 17, 3835, 2687, 4248, 20478, 43, 7864, 17, 5165, 17, 7864, 13002, 16, 2154, 20836, 1942, 2386, 43, 3659, 17, 17105, 3356, 23285, 2046, 3170, 3286, 1922, 6445, 4028, 2427, 1966, 2024, 4048, 3640, 1930, 2213, 10328, 18, 2176, 1977, 3198, 1922, 10107, 18222, 1033, 14061, 2865, 5090, 1015, 1930, 2258, 20709, 15010, 3148, 1930, 22288, 6865, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "LIAQEGTPNPDAVAGATLFDESDYEAAFPFLLRAGYANPADGDNMRRLLVTALRTGNYGYANFANNYLNQFAPEAWDEITAETDAALAADSDDEGAAIVAAWMGVGTPEGQALIDRVFAFDSDSAIGHDLLGFQKFFTGDIEGALASFETALLLAGHGYPHIAADVAWVFAYQAGQPERAIEIITQAIEMEPEFALLYNIRGGFYQQIGDTDAALSDFDQALTLNPADFQSQNARGRVLQELGDFEAAYDEYASVLATFPLSPSAMNGLLYVAIEAHLPIDPLIDARDLVEADSVLTVDTPYTGMMTANRVVRLPITGDPGDYTITVRASDPMTLDPVLLIANGDNIPLALHDDIDSSGAQADGAYNSQITRTAEAGEVYVAYIFHGGAGSEGEFTVTLEPAVS", "metadata": {"id": "A0A136L3M4", "cluster": 24525256, "interpro_all": ["IPR011990", "IPR019734", "IPR050498"], "interpro_used": ["IPR050498", "IPR011990", "IPR019734"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein is classified under the Large ribosomal subunit protein uL29 family, which functions as a structural component of the large ribosomal subunit located on the surface near the polypeptide exit channel. It stabilizes the ribosomal architecture through interactions with 23S rRNA and forms part of the protein ring surrounding the tunnel exit to support the emergence of nascent chains. Furthermore, this protein participates in the formation of binding sites for the translocon and the trigger factor chaperone, facilitating the processing and transport of synthesized proteins. It is native to Microgenomates bacterium OLB23 and is linked to UniProt keywords Ribonucleoprotein and Ribosomal protein.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 3103, 11196, 5903, 2213, 3570, 4539, 3416, 16, 2154, 4088, 1966, 43, 4346, 4594, 1927, 1920, 3103, 11196, 5903, 4810, 1990, 1920, 3154, 4931, 1920, 13022, 14185, 4999, 18, 2176, 19658, 1920, 11196, 9335, 2596, 3719, 1956, 3020, 1036, 9067, 1930, 4952, 3131, 1927, 1920, 2213, 6335, 7510, 1920, 16403, 14185, 1942, 3373, 1920, 10400, 1927, 16861, 7835, 18, 3677, 16, 2052, 2213, 17241, 1922, 1920, 3337, 1927, 2743, 3402, 1958, 1920, 12930, 1916, 1930, 1920, 6086, 2991, 14044, 16, 12440, 1920, 4587, 1930, 4860, 1927, 6653, 2697, 18, 2176, 1977, 6196, 1942, 12517, 19824, 29187, 14061, 2865, 8520, 1010, 1930, 1977, 4624, 1942, 20709, 11569, 18347, 6657, 1930, 11196, 2213, 18, 3], "output": "MKSKELQKLKDQSAQELMLSAQKLKEEIARMGIEGSINKPKNTNALGKKKQELAVVLTILNEKSQ", "metadata": {"id": "A0A136KQM2", "cluster": 27063974, "interpro_all": ["IPR001854", "IPR036049"], "interpro_used": ["IPR001854"], "interpro_unused": ["IPR036049"]}, "task_type": "autoregressive"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein carries a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. In addition, it is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein belongs to the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. It is produced by Candidatus Methylomirabilota bacterium and features UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 16252, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2176, 1977, 4152, 2007, 14550, 1031, 1957, 4963, 1947, 11979, 12039, 7336, 14061, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 11586, 5655, 3581, 18, 3], "output": "MRGVLITVEGVEGSGKTTQCERLSEPDGTRLGSAIRGLFEQEMAARQQHVTEIIRPALQRGAVVVTIRDLNALATGGVTPDLTLLLDLDPEKMDLAFHRRVREGYLEIADVARAVEELLERRGAGRGAGQWLHARGFEVVLTSGSPTPLTQTFLFSDRYADATLAYQGWGGGMDLEAAGMSRIGGRALDAFARAEKNRVRVLDAARDAATLH", "metadata": {"id": "A0AAV6CM46", "cluster": 177661, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR039430", "IPR027417", "IPR018094"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein should contain a SleB cell wall hydrolase domain that functions as a cortex-lytic enzyme involved in spore germination. It is typically deposited in the spore cortex in an inactive form during sporulation and is subsequently activated to hydrolyze the peptidoglycan layer, facilitating the outgrowth of the vegetative cell. It occurs in Bdellovibrionales bacterium.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 3066, 5531, 43, 4565, 1014, 2024, 4821, 20748, 3418, 1988, 4088, 1966, 43, 4997, 17, 17033, 4113, 3286, 1922, 18445, 14609, 18, 2176, 1977, 5745, 10199, 1922, 1920, 18445, 4997, 1922, 1925, 9078, 2386, 2409, 23647, 1930, 1977, 5326, 4128, 1942, 7222, 6931, 1920, 24183, 4757, 16, 12440, 1920, 15040, 1927, 1920, 18823, 2024, 18, 2176, 5110, 1922, 5238, 20783, 2165, 2377, 12778, 1918, 14061, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MSWLLGISLAFLGCQTSLHHYDDFTTVHADCSSNNPGDCMACALQGEAANVTKARGQFEGMRKRGKRKISRRVRKVTRQILKSREKKWYEKRRCEKQEIGDHIFYNANKCELSRRQLLANQQTSQGIYAVGVTIMTRAKGKLENICKTHFWAPRAQKRLRRSKPFWATH", "metadata": {"id": "A0A958MH56", "cluster": 270232, "interpro_all": ["IPR011105", "IPR042047"], "interpro_used": ["IPR011105"], "interpro_unused": ["IPR042047"]}, "task_type": "infilling"} {"instruction": "The protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein incorporates a Methyltransferase domain 25 domain that functions as a methyltransferase enzyme responsible for transferring methyl groups. Structurally, it belongs to a clan of Rossmann-fold domains, indicating it likely utilizes S-adenosylmethionine (SAM) as a cofactor for catalysis. Also, the protein belongs to the Methyltransferase Superfamily family, which catalyzes the transfer of methyl groups from S-adenosyl-L-methionine to various substrates, including aklanonic acid and demethylmenaquinol. These enzymes are crucial for the biosynthesis of antibiotics, secondary metabolites such as gliotoxin, and essential components of cell membranes and bacterial electron transport chains. It is found in Nocardioides jishulii.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 19683, 43, 16478, 3418, 2637, 3418, 1988, 4088, 1966, 43, 16478, 4113, 5061, 1958, 21902, 4963, 2671, 18, 12171, 16, 2176, 14440, 1942, 43, 6958, 1022, 1927, 18215, 8890, 17, 3728, 4682, 16, 4168, 2176, 3205, 18127, 61, 17, 29283, 23568, 11215, 12, 2235, 13, 1966, 43, 15155, 1958, 15408, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 16478, 13975, 3416, 16, 2154, 17097, 1920, 3856, 1927, 4963, 2671, 2037, 61, 17, 29283, 17, 54, 17, 12417, 1942, 3425, 6249, 16, 2710, 4464, 17576, 3490, 2687, 1930, 21732, 19047, 15287, 18402, 1945, 18, 2144, 5038, 2032, 6608, 1958, 1920, 8132, 1927, 7560, 16, 4067, 6926, 2427, 1966, 6534, 11140, 16, 1930, 4415, 4178, 1927, 2024, 5726, 1930, 4543, 4995, 4860, 7835, 18, 2176, 1977, 2435, 1922, 9812, 3082, 12363, 14280, 6150, 13004, 1033, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MTVVTDAQADPRTPGQRIDQRGRAELEFVVALRTGMTGALRPKVRRRIEESGVVEAAAAHRFQAASLRWSREISTPRGVEAFDRRRELLEPMATPSAPVEDLTDGDVPRYWTYEFHATEGGKIYGGGGDIFALRRAFADRAPADTYADIVDLGCGTGQYTLKLAEAYPEARITALDLSQAAERTGLPDESADLVTSYILLHEMPPHAIKSVFAEAYRLLRPGGHVHFGDVGAYATRAATTDIAEIAREAGFVDVERYELLPGGHPMGTTARKPLQEDVLAPETGIDTADIVAVREAVDPWDGHDHMGFVHHEMVYQYLLTSELNYAQRRAEDAGLDISFRRASGYDAWNDDWDAEHGNEPWWRL", "metadata": {"id": "A0A4U2YIF4", "cluster": 4744482, "interpro_all": ["IPR041698", "IPR050508", "IPR029063"], "interpro_used": ["IPR029063", "IPR041698", "IPR050508"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "\"The protein belongs to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Also, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is derived from Nocardioidaceae bacterium and is described by UniProt keywords ATP-binding, Cytoplasm, and Transferase.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 14440, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3595, 2037, 9812, 3082, 2642, 9914, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MMRVGLTGGIGSGKSSVSRLLAERGAVVVDADLLAGPDMLTESGELDRTAMGERVFGDDRARARLEQIIHPRVHDIPLLVETGQADRFDAVIVVDAPVDVQLQRLTGTRGVADHVIENAGTLDDLRAAVDAVWAQLTDRVSASGDEAGRFRDVVAAGTTGLAEIVVEFVRARAAEIESASPPDAIVMGEEEARSRISAQTTRERRLA", "metadata": {"id": "A0A7W0M385", "cluster": 7008373, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein has a Dynein heavy chain, tail domain that functions as the flexible N-terminal scaffold for heavy chain dimerization and the binding of intermediate and light chains to form the basal cargo-binding unit. This domain enables the assembly of the dynein motor complex, facilitating ATP-dependent movement along microtubules for processes such as organelle transport and mitosis. It has been detected in Argulus foliaceus. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 18188, 7881, 4659, 16, 5281, 3418, 1988, 4088, 1966, 1920, 9964, 56, 17, 4262, 7281, 1958, 7881, 4659, 13640, 1930, 1920, 2743, 1927, 6129, 1930, 3696, 7835, 1942, 2386, 1920, 5342, 14713, 17, 2743, 5344, 18, 2052, 3418, 10217, 1920, 5957, 1927, 1920, 18188, 4842, 2796, 16, 12440, 4498, 17, 3100, 5829, 4231, 12444, 1958, 4028, 2427, 1966, 19309, 4860, 1930, 12611, 18, 2176, 2258, 2252, 3330, 1922, 25883, 5277, 1036, 25783, 8565, 1036, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "NMKLNFSDLTTPAQIQAVAGSLETLPLVEEVVHYWIAQLDKILVENQQIRQETEEVGPRTEIQYWKHHLAKFDTLVEQLKSTKVTNTIQVLVVAKSKLLMKWRMVQNEIIDIWNESFDNVKYLTSMQKFFEPLYHCDPE", "metadata": {"id": "A0A7R9X7N9", "cluster": 8521507, "interpro_all": ["IPR026983", "IPR013594"], "interpro_used": ["IPR013594"], "interpro_unused": ["IPR026983"]}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein falls within the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein is associated with the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It has been characterized in Desulforamulus hydrothermalis Lam5 = DSM 18033 and carries UniProt keyword assignments ATP-binding, Cytoplasm, and Transferase.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 12182, 2651, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 2258, 2252, 4378, 1922, 30311, 8846, 23010, 5277, 1036, 26959, 1937, 8282, 1015, 33, 10964, 8585, 6498, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MLIGLTGNIASGKSTVAKYLKELGAQVIVNSFGPGILHEDGTLNRAKLASVIFQDAAAKEKLENSSFKKSHPGGILVLEAPLLIEAGWHKSVDQVWLVTVDPQLQLQRLSQMPQEEKKKFAHVIINNAGSPSDLQRQVQAIWHSLPAGYDADQVARQVVLPHSPALKEIILHPRIADAINRQIILRDKLTPEQARQRMA", "metadata": {"id": "K8DXH5", "cluster": 10175533, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein belongs to the Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily, which comprises enzymes sharing a TIM $\\beta/\\alpha$-barrel fold that catalyze key reactions in central carbon metabolism involving phosphoenolpyruvate (PEP) and pyruvate. Notable members, including pyruvate kinase and phosphoenolpyruvate carboxylase, mediate processes such as phosphate transfer to ADP and carbon fixation. Structurally, this domain often coordinates metal ions and facilitates oligomeric assembly, such as the formation of swapped dimers or tetramers, to regulate enzymatic activation. Also, the protein incorporates a Pyruvate kinase barrel domain that constitutes the catalytic core responsible for the final, rate-limiting step of glycolysis. Comprising a $\\beta$/$\\alpha$-barrel with an inserted $\\beta$-barrel, this domain facilitates the magnesium- and potassium-dependent conversion of phosphoenolpyruvate to pyruvate and the concomitant phosphorylation of ADP to ATP. Furthermore, the protein belongs to the Pyruvate kinase, C-terminal domain superfamily, which constitutes the regulatory 3-layer $\\alpha/\\beta/\\alpha$ sandwich domain of pyruvate kinase, an enzyme responsible for the ATP-generating final step of glycolysis. This domain contains the allosteric binding site for effectors such as fructose 1,6-bisphosphate, playing a critical role in modulating the conversion of phosphoenolpyruvate to pyruvate in response to metabolic signals. It occurs in Acer yangbiense and has UniProt annotations ATP-binding, Metal-binding, and Transferase.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 14440, 1942, 1920, 11867, 19, 8078, 9356, 18425, 12631, 2010, 4016, 17, 3189, 3418, 13975, 16, 2154, 12936, 5038, 10763, 43, 2267, 8, 38, 4666, 19, 38, 4595, 8, 17, 19560, 3728, 1988, 18170, 3834, 5298, 1922, 4101, 5056, 4714, 5884, 8078, 9356, 18425, 12631, 2010, 12, 9110, 13, 1930, 11867, 18, 11892, 4678, 16, 2710, 11867, 4016, 1930, 8078, 9356, 18425, 12631, 2010, 29073, 16, 8265, 4028, 2427, 1966, 5413, 3856, 1942, 9828, 1930, 5056, 7938, 18, 12171, 16, 2052, 3418, 3868, 10675, 6048, 6982, 1930, 11374, 19206, 5957, 16, 2427, 1966, 1920, 3337, 1927, 3476, 6688, 13351, 2014, 26568, 16, 1942, 5741, 8145, 2936, 18, 2222, 16, 1920, 2213, 19683, 43, 11867, 4016, 19560, 3418, 1988, 14879, 1920, 6804, 4728, 5061, 1958, 1920, 3948, 16, 2769, 17, 8051, 3537, 1927, 13393, 18, 10351, 43, 8, 38, 4666, 8, 19, 8, 38, 4595, 8, 17, 19560, 1956, 1925, 9103, 8, 38, 4666, 8, 17, 19560, 16, 2052, 3418, 11374, 1920, 13148, 17, 1930, 9057, 17, 3100, 7309, 1927, 8078, 9356, 18425, 12631, 2010, 1942, 11867, 1930, 1920, 8537, 4050, 1927, 9828, 1942, 4498, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 11867, 4016, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 14879, 1920, 4948, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 18038, 3418, 1927, 11867, 4016, 16, 1925, 4113, 5061, 1958, 1920, 4498, 17, 9155, 3948, 3537, 1927, 13393, 18, 2052, 3418, 5461, 1920, 14772, 2743, 3200, 1958, 13066, 2427, 1966, 15102, 21, 16, 26, 17, 29443, 16, 14797, 43, 4140, 2770, 1922, 10871, 1920, 7309, 1927, 8078, 9356, 18425, 12631, 2010, 1942, 11867, 1922, 2644, 1942, 4487, 4771, 18, 2176, 5110, 1922, 8298, 1005, 12662, 3821, 4480, 1930, 2258, 20709, 15010, 4498, 17, 2743, 16, 6048, 17, 2743, 16, 1930, 13763, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MIKSPWPTCAKATNVADVVLDGTNCVMLSGESIFKEMIRSTTLPMSPLESLASSTVRIANKAKLVAKYRPAIPISATEKGLCQPSDAAVAFHNIEAAYVNKICIVKVVGAYQELAAKIMHRICINAGSSLDYGALSVATNAEVIVEAAMK", "metadata": {"id": "A0A5C7H507", "cluster": 11379511, "interpro_all": ["IPR001697", "IPR015813", "IPR040442", "IPR015793", "IPR036918"], "interpro_used": ["IPR015813", "IPR015793", "IPR036918"], "interpro_unused": ["IPR001697", "IPR040442"]}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein carries a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Additionally, the protein can be placed in the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Furthermore, the protein is categorized in the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. It has been detected in Xylaria multiplex and is described by UniProt keywords Transmembrane, Transmembrane helix, and mRNA processing.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 2176, 2258, 2252, 3330, 1922, 9639, 6148, 12710, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 16, 9117, 7864, 16, 1930, 3616, 4587, 18, 3], "output": "METTEKTWGITKPISSALPTPAESHSTTQLLEELRRQNTFETASETKKREKVINDLQRIADEFVRKVARAKEPHNEVLIRDARGEVFTYGSYCLGVYGPGSDIDTLVTAPRYVSRDDYFKYFPDLLKEMAPPSAITNLTAVEEAFVPIIKFEYWGISIDLIFSRIATLTQFPPRNQLQLTSNEYLRGLDDRELRSLNGTRVTREILNLVPEQSTFRTALRAIKLWAQRRAIYANIIGFPGGVVWAMMVARVCQLYPKATSATIVAKFFLVMKGWPWPIPVQLKHMEDGPLNVRVWNPKIYKSDSFHLMPVITPAYPQMCATFNITKSTKAIIQRELERGVELTDKILGSELPWKDLFMKHTFFTQDHKYYLAVIAMSITKEAHKIWSGFVESKVRILVGELERHPSVALARPYNKGFERQHLTKTDEESAEVQNGSLLYAAKDEKDLADTTAAKEGNGTGVDTNTQGLKGTVEDTSQPRRTYTTTHYIGLELAEGAKSLDLSYQVNTFKQMCSEWEKHSAELNSLSVQHVKNINLPEDVFEPGEVRPTRPLRKPVANGTAPVTQRKRTAPAEGHPPPPAKRQQSSAAAAG", "metadata": {"id": "A0A7C8MG26", "cluster": 12049941, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR007012", "IPR043519", "IPR011068"], "interpro_unused": ["IPR014492", "IPR007010", "IPR048840"]}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein should include a PRC-barrel domain that adopts an all $\\beta$-barrel fold and serves as a versatile regulatory module in processes ranging from photosynthesis to RNA metabolism. It is essential for RimM-mediated 16S rRNA processing and ribosomal maturation in bacteria, while stand-alone forms facilitate FtsZ-based cell division in archaea. Also, the protein belongs to the PRC-barrel-like superfamily, which defines an approximately 80-residue all $\\beta$-barrel domain utilized in diverse biological processes including photosynthesis and RNA metabolism. This fold appears in the bacterial ribosome maturation factor RimM, archaeal cell division proteins CdpB1 and CdpB2, and the cytoskeletal CKK domain of CAMSAP proteins. It is identified in Arboricoccus pini and corresponds to UniProt keyword Signal.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 3066, 3951, 43, 29134, 17, 19560, 3418, 1988, 24032, 1925, 2136, 8, 38, 4666, 8, 17, 19560, 3728, 1930, 10634, 1966, 43, 20425, 4948, 9059, 1922, 4028, 6485, 2037, 18133, 1942, 3146, 4714, 18, 2176, 1977, 4415, 1958, 14764, 1035, 17, 3434, 11209, 9067, 4587, 1930, 11196, 7655, 1922, 4802, 16, 2679, 2924, 17, 4298, 4952, 6628, 27497, 17, 2454, 2024, 8451, 1922, 21501, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 29134, 17, 19560, 17, 3189, 13975, 16, 2154, 16737, 1925, 3993, 3729, 17, 6181, 2136, 8, 38, 4666, 8, 17, 19560, 3418, 7079, 1922, 6445, 3933, 4028, 2710, 18133, 1930, 3146, 4714, 18, 2052, 3728, 5107, 1922, 1920, 4543, 12794, 7655, 2991, 14764, 1035, 16, 22367, 2024, 8451, 2697, 26707, 5090, 1930, 26707, 8520, 16, 1930, 1920, 14787, 6394, 1040, 3418, 1927, 4934, 5735, 1034, 2697, 18, 2176, 1977, 2899, 1922, 19590, 5670, 2437, 1957, 8701, 1033, 1930, 8852, 1942, 20709, 11121, 2538, 2733, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MRVCPSLLLCLLLASLPALGSPAASSEGASARPPPQAAAILPVDAVDLELDLESGEVTHFVVKTGGFMGVGGTAFLLGAAQMQNLVVLPEAEDPVRATEDASPPPPERAEEGLPGSPTGRFPGRASQLLNKPVLGIDGKSLGTIVRRAVRWAPDGALRTDMT", "metadata": {"id": "A0A212R6E9", "cluster": 13093411, "interpro_all": ["IPR027275", "IPR011033"], "interpro_used": ["IPR027275", "IPR011033"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein carries a Amidohydrolase-related domain that functions as the metal-dependent catalytic core for a diverse superfamily of hydrolases, including adenine deaminase, dihydroorotase, and the urease alpha subunit. These enzymes catalyze the hydrolysis of carbon-nitrogen bonds, contributing to critical processes such as purine metabolism and nitrogen source utilization. Moreover, the protein can be placed in the Metal-dependent hydrolase superfamily, which comprises a diverse group of hydrolytic enzymes characterized by a (\u03b2/\u03b1)8-barrel (TIM barrel) fold coordinating mono- or binuclear transition metal ions within the active site. These enzymes utilize these metal centers to catalyze the hydrolysis of a broad spectrum of substrates involved in fundamental metabolic processes. It is found in Verrucomicrobiia bacterium.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 16252, 43, 28813, 8601, 21524, 17, 2712, 3418, 1988, 4088, 1966, 1920, 6048, 17, 3100, 6804, 4728, 1958, 43, 6445, 13975, 1927, 30337, 16, 2710, 15643, 27955, 16, 11842, 30232, 3857, 4127, 16, 1930, 1920, 10505, 4127, 4595, 5903, 18, 2144, 5038, 18170, 1920, 9128, 1927, 5056, 17, 6634, 9031, 16, 8739, 1942, 4140, 4028, 2427, 1966, 19700, 4714, 1930, 6634, 4585, 8422, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 6048, 17, 3100, 20748, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 26702, 5038, 4378, 2007, 43, 12, 161, 19, 160, 13, 28, 17, 19560, 12, 2267, 19560, 13, 3728, 19355, 8914, 17, 2014, 8768, 13821, 4832, 6048, 6982, 2651, 1920, 3500, 3200, 18, 2144, 5038, 12561, 2144, 6048, 7365, 1942, 18170, 1920, 9128, 1927, 43, 4949, 5648, 1927, 6249, 3286, 1922, 8829, 4487, 4028, 18, 2176, 1977, 2435, 1922, 3566, 3176, 13055, 1935, 15129, 3907, 1019, 14061, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "QRADLEGVRWALASDIGGGRAAGNGSATFTRALYRSTDLDYIAVKASPETLCAASADAVLRVVEGECLFSCPYLSMLDVMASFVRQNQKGADIQGLGDRKGSFTPGKSVISPFETDRDQFDCLVSTT", "metadata": {"id": "A0A960SER8", "cluster": 14424593, "interpro_all": ["IPR006680", "IPR032466"], "interpro_used": ["IPR006680", "IPR032466"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein I want to design has this role: The protein carries a Signal transduction response regulator, receiver domain that functions as a phosphorylation-activated switch within two-component systems to couple environmental sensing with cellular adaptation. It accepts a phosphoryl group from a cognate sensor histidine kinase, inducing a conformational change that activates an associated effector domain to regulate gene expression. Additionally, the protein should feature a LytTR DNA-binding domain that functions as the DNA-binding component of bacterial transcriptional regulators in the algR/agrA/lytR family. This potential winged helix-turn-helix (wHTH) domain mediates the regulation of physiological processes such as cell autolysis. In addition, it is part of the Transcriptional regulatory protein LytR-like family, which comprises DNA-binding response regulators and sensory transduction proteins containing a LytTR domain. These proteins, such as LytR and LytT, typically utilize a potential winged helix-turn-helix motif to regulate gene expression associated with processes like cell autolysis. It originates from Saprospiraceae bacterium. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 16252, 43, 2733, 8201, 2644, 7888, 16, 12608, 3418, 1988, 4088, 1966, 43, 4050, 17, 4128, 6195, 2651, 2288, 17, 4594, 3771, 1942, 15116, 4813, 9306, 1956, 3689, 7810, 18, 2176, 5861, 1036, 43, 12556, 2210, 2037, 43, 15786, 6443, 13873, 4016, 16, 7834, 43, 8523, 3185, 1988, 9094, 1925, 2458, 7917, 3418, 1942, 5741, 2359, 2294, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 7518, 3519, 1005, 2678, 17, 2743, 3418, 1988, 4088, 1966, 1920, 2678, 17, 2743, 4594, 1927, 4543, 5224, 9098, 1922, 1920, 4326, 1005, 19, 23171, 1019, 19, 7518, 1997, 3416, 18, 2052, 2889, 12920, 1919, 7864, 17, 5165, 17, 7864, 12, 2003, 1963, 13, 3418, 10412, 1920, 3640, 1927, 5005, 4028, 2427, 1966, 2024, 5728, 27004, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 5224, 4948, 2213, 7518, 1997, 17, 3189, 3416, 16, 2154, 12936, 2678, 17, 2743, 2644, 9098, 1930, 6893, 8201, 2697, 3165, 43, 7518, 3519, 1005, 3418, 18, 2144, 2697, 16, 2427, 1966, 7518, 1997, 1930, 7518, 3519, 16, 5745, 12561, 43, 2889, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 1942, 5741, 2359, 2294, 2458, 1956, 4028, 3189, 2024, 5728, 27004, 18, 2176, 22970, 2037, 9235, 5424, 11979, 1972, 3336, 14061, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MKLTCLIIDDEPLARKILEKYVSRISAIELMASFDNAIDASVYITEHNPDIIFLDIRMPEMSGLEMLKIIQHPPEVILTSAYSEYGVESYDYEVFDYLLKPIPFERFMKTITKLIDSITPTHHDEILPIDHITVKDGKKQIQVKLKDIHYIQAYGNYLKIFTKEKQFLSRMKMSVMEALLPMTHFVRIHKSYIVSLLYVEHTGGNEIILKSGKELPLSKYYKRSAKERLG", "metadata": {"id": "A0A7Y2MSD2", "cluster": 16567835, "interpro_all": ["IPR011006", "IPR046947", "IPR007492", "IPR001789"], "interpro_used": ["IPR001789", "IPR007492", "IPR046947"], "interpro_unused": ["IPR011006"]}, "task_type": "autoregressive"} {"instruction": "The protein includes a GTP binding domain that contains five conserved structural motifs to bind guanosine triphosphate (GTP). It is present in a diverse array of proteins, such as the developmentally regulated DRG, the essential bacterial OBG, and ferrous iron transport protein B, indicating a broad role in cellular regulation and transport. Additionally, the protein carries a TrmE-type guanine nucleotide-binding domain that functions as a P-loop GTPase molecular switch to facilitate tRNA modification. It adopts a canonical Ras-like fold that dimerizes in a potassium-dependent manner and utilizes conformational changes driven by GTP hydrolysis to modify uridine bases at the tRNA wobble position. Moreover, the protein contains a Small GTP-binding domain that functions as a molecular switch by binding and hydrolyzing GTP to regulate diverse cellular processes, including signal transduction, vesicle transport, and protein biosynthesis. It is found in the Ras superfamily of small GTPases as well as within larger proteins such as translation elongation factors. It is found in Alphaproteobacteria bacterium ADurb.Bin438 and carries UniProt keyword assignments Hydrolase, Cytoplasm, and tRNA processing. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 5921, 43, 9319, 2743, 3418, 1988, 5461, 3628, 5305, 4346, 8277, 1942, 4566, 24870, 17978, 12, 9319, 13, 18, 2176, 1977, 2481, 1922, 43, 6445, 6472, 1927, 2697, 16, 2427, 1966, 1920, 23130, 4335, 14801, 16, 1920, 4415, 4543, 2384, 1029, 16, 1930, 26739, 5680, 4860, 2213, 44, 16, 4168, 43, 4949, 2770, 1922, 3689, 3640, 1930, 4860, 18, 4950, 16, 1920, 2213, 16252, 43, 28402, 1021, 17, 2601, 16904, 5489, 17, 2743, 3418, 1988, 4088, 1966, 43, 58, 17, 5881, 14809, 3272, 6195, 1942, 6628, 10089, 6295, 18, 2176, 24032, 43, 9452, 6520, 17, 3189, 3728, 1988, 7632, 4517, 1922, 43, 9057, 17, 3100, 5222, 1930, 18127, 8523, 2840, 6446, 2007, 9319, 9128, 1942, 11675, 26104, 11137, 2019, 1920, 10089, 26334, 6936, 1952, 3507, 18, 3950, 16, 1920, 2213, 5461, 43, 2858, 9319, 17, 2743, 3418, 1988, 4088, 1966, 43, 3272, 6195, 2007, 2743, 1930, 7222, 9046, 9319, 1942, 5741, 6445, 3689, 4028, 16, 2710, 2733, 8201, 16, 11502, 4860, 16, 1930, 2213, 8132, 18, 2176, 1977, 2435, 1922, 1920, 6520, 13975, 1927, 2858, 18390, 1966, 2486, 1966, 2651, 4327, 2697, 2427, 1966, 6410, 9971, 2790, 18, 2176, 1977, 2435, 1922, 4595, 9218, 1021, 10296, 14061, 2041, 5223, 18, 8768, 7514, 1025, 1930, 16252, 20709, 11121, 2538, 18306, 20748, 16, 5239, 16, 1930, 10089, 4587, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MYNEKDTIYALATIKGKAGVAVIRVSGTKSKEVLKIICKKENLTPRMMTNTLFYDSEEIVDKGLVVFFENPKSFTGEDVLELHIHSSLAVIKRLSKVLGEIEGVRLADRGEFSRRAVMNNKMDLTEAEGLIDLINAETEFQRKIALKQYSGEQRKLFEEWKEDLTKSLAWIEAYLDFPEEEVSEDVTVSIQNLINKLSTAISTMLSTKSNGEAIRTGYKIAIIGKPNAGKSSLLNALTKRNVAIVSDIEGTTRDVIEAYIDLDGYPITFLDTAGIRNSEDIIEAEGVRRALEVAKDADLILYLKPISDFSTDDFEKDFNQSNVLKVLTKSDLPYMVMNDNSDRDDFIKCSVKAPHGVDNLMKAISEKISNDLSDINDTLLTRERHRQALKSCLDNLFGQRTIIYSH", "metadata": {"id": "A0A1V5LDZ1", "cluster": 17257787, "interpro_all": ["IPR031168", "IPR006073", "IPR018948", "IPR004520", "IPR027368", "IPR025867", "IPR027417", "IPR005225", "IPR027266"], "interpro_used": ["IPR006073", "IPR031168", "IPR005225"], "interpro_unused": ["IPR025867", "IPR027417", "IPR027266", "IPR004520", "IPR027368", "IPR018948"]}, "task_type": "autoregressive"} {"instruction": "The protein should feature a 2Fe-2S ferredoxin iron-sulphur binding site that coordinates a 2Fe-2S cluster via four conserved cysteine residues to mediate electron transfer in diverse metabolic reactions. This motif is integral to photosynthetic electron transport chains and bacterial dioxygenase systems, where it typically adopts an \u03b1 + \u03b2 fold with three of the coordinating cysteines arranged on an extruded loop. In addition, the protein has a 2Fe-2S ferredoxin-type iron-sulfur binding domain that functions as an electron transfer module in biological redox systems by ligating a 2Fe-2S cluster via four conserved cysteine residues. Characterized by a beta-grasp fold, this domain appears in ferredoxins and various metabolic enzymes across plants, animals, and bacteria. Also, the protein should have a Molybdenum cofactor sulfurase, C-terminal (MOSC) domain that functions as a sulfur carrier to catalyze the conversion of the molybdenum cofactor from its oxo form to a sulfurylated form. It adopts a $\\beta$-barrel structure and utilizes a strictly conserved cysteine residue to accept sulfur from NifS-like enzymes and deliver it for the synthesis of diverse metal-sulfur clusters required by enzymes such as xanthine dehydrogenase. It is expressed in Aliivibrio wodanis.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 13775, 1021, 17, 20759, 25304, 22389, 10960, 5680, 17, 13528, 1949, 2743, 3200, 1988, 10675, 43, 13775, 1021, 17, 20759, 4377, 3454, 3006, 5305, 8666, 4248, 1942, 8265, 4995, 3856, 1922, 6445, 4487, 5298, 18, 2052, 5219, 1977, 12328, 1942, 16068, 4995, 4860, 7835, 1930, 4543, 23652, 10465, 2432, 2051, 3771, 16, 2597, 2176, 5745, 24032, 1925, 160, 15, 161, 3728, 1956, 2559, 1927, 1920, 19355, 22446, 14940, 1990, 1925, 2821, 4421, 5881, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 13775, 1021, 17, 20759, 25304, 22389, 10960, 17, 2601, 5680, 17, 12585, 2743, 3418, 1988, 4088, 1966, 1925, 4995, 3856, 9059, 1922, 3933, 9366, 3771, 2007, 3650, 2287, 43, 13775, 1021, 17, 20759, 4377, 3454, 3006, 5305, 8666, 4248, 18, 4378, 2007, 43, 4666, 17, 22815, 3728, 16, 2052, 3418, 5107, 1922, 25304, 22389, 10960, 1036, 1930, 3425, 4487, 5038, 3436, 4793, 16, 3555, 16, 1930, 4802, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 2629, 16924, 5233, 1989, 15155, 12585, 2051, 16, 45, 17, 4262, 12, 7500, 1030, 13, 3418, 1988, 4088, 1966, 43, 12585, 9685, 1942, 18170, 1920, 7309, 1927, 1920, 2629, 16924, 5233, 1989, 15155, 2037, 2496, 18588, 2386, 1942, 43, 12585, 4336, 2386, 18, 2176, 24032, 43, 8, 38, 4666, 8, 17, 19560, 3170, 1930, 18127, 43, 14470, 5305, 8666, 6181, 1942, 5861, 12585, 2037, 17719, 1036, 17, 3189, 5038, 1930, 3971, 2176, 1958, 1920, 4271, 1927, 6445, 6048, 17, 12585, 5859, 3414, 2007, 5038, 2427, 1966, 26059, 9294, 18, 2176, 1977, 3198, 1922, 15356, 2068, 3693, 3940, 26334, 3825, 11110, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MDASVSQINSVSNLSNINVFPVKSIAGISLPSAQVEKQGLQCDRRFMVASLNGKMITALHFTFDELEMKEIDTTVWSDTFTAYSTTEEANQWFSSILGTEAQLLFSGQQSNRMREKIQSSHHTMAQFRTNLVVSGNEAFIEDSWKRIRIGEVEFEVVKPCQRCILTTVNPNTAQYHPNKEPLKTFSTFNEGTIRIGDKIEVLETKEKEYYADSNKHAVTSVTIQDKQTDTVSEEITISLNGHLFKGNCGACRVTLESGEVEQEDSPALNQNLKEAGMILACCSIPKSDIEVIDRTHPQMVKIKAIIEPDGLVLCYPGLIDTNVSFADGYPLLVISEASLAELNKRSRADDSGNVYFGQNLVAKTQDPLLNQAEAAGLSINNSCRAGL", "metadata": {"id": "A0A090I9E8", "cluster": 17507497, "interpro_all": ["IPR036010", "IPR001041", "IPR006058", "IPR012675", "IPR005302", "IPR005303", "IPR011037"], "interpro_used": ["IPR006058", "IPR001041", "IPR005302"], "interpro_unused": ["IPR036010", "IPR005303", "IPR011037", "IPR012675"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: It is part of the Outer membrane protein/outer membrane enzyme PagP, beta-barrel superfamily, which forms a transmembrane \u03b2(8,10)-barrel structure found in a diverse range of bacterial outer membrane proteins. This domain serves as a structural scaffold for proteins such as OmpA, OmpX, and NspA, as well as for the outer membrane enzyme PagP. It has been detected in Fibrella aestuarina BUZ 2. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 2176, 1977, 3131, 1927, 1920, 7642, 3260, 2213, 19, 7642, 3260, 4113, 17869, 1034, 16, 4666, 17, 19560, 13975, 16, 2154, 4952, 43, 9117, 161, 12, 28, 16, 2119, 13, 17, 19560, 3170, 2435, 1922, 43, 6445, 3109, 1927, 4543, 7642, 3260, 2697, 18, 2052, 3418, 10634, 1966, 43, 4346, 7281, 1958, 2697, 2427, 1966, 21921, 1019, 16, 21921, 1039, 16, 1930, 16672, 1019, 16, 1966, 2486, 1966, 1958, 1920, 7642, 3260, 4113, 17869, 1034, 18, 2176, 2258, 2252, 3330, 1922, 15121, 11560, 1019, 12893, 1031, 12169, 5572, 1019, 3168, 1011, 22, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MKSLYILFLLSLCNISVVDGQGLAFKWKEAIGDWHIGVNLSTTRYCGDLSERYGFNHLQLGWAAEGHLRYRVSERFCVRTDIGFYSLRGDQQYTKNRTNYLRFTTTNPSVIAGLQWNVRSIEYNQHNIPHFWVGAGATYLNPRADYNGTTYSLPALQTEKVAYNRIAGQFVLGGGMPFTLNKKSQLRLEARYTYILSDYVDDVSGTYADKSGSPALDQVLADRRREYGLTPNAVGGQRGNPLRNDGYFALTLQYAVKRSTP", "metadata": {"id": "I0KG25", "cluster": 18601213, "interpro_all": ["IPR011250"], "interpro_used": ["IPR011250"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Target Function: The protein should contain a Rieske [2Fe-2S] iron-sulphur domain that functions as a high-potential redox center by binding a [2Fe-2S] cluster coordinated by two cysteine and two histidine residues. It serves as a critical electron transfer component in the mitochondrial cytochrome bc1 complex and chloroplast cytochrome b6f complex, as well as in bacterial non-heme iron oxygenase systems involved in aromatic hydrocarbon degradation. It has been detected in Actinomycetota bacterium and is described by UniProt keywords Iron-sulfur and Metal-binding.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 3066, 5531, 43, 11280, 1918, 3324, 37, 13775, 1021, 17, 20759, 39, 5680, 17, 13528, 1949, 3418, 1988, 4088, 1966, 43, 2149, 17, 2889, 9366, 4102, 2007, 2743, 43, 37, 13775, 1021, 17, 20759, 39, 4377, 11651, 2007, 2288, 8666, 1930, 2288, 13873, 4248, 18, 2176, 10634, 1966, 43, 4140, 4995, 3856, 4594, 1922, 1920, 4596, 9387, 6452, 1009, 2796, 1930, 17471, 9387, 11750, 1038, 2796, 16, 1966, 2486, 1966, 1922, 4543, 2447, 17, 10954, 5680, 25298, 3771, 3286, 1922, 10761, 21638, 4877, 18, 2176, 2258, 2252, 3330, 1922, 4718, 13386, 19446, 3857, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 5680, 17, 12585, 1930, 6048, 17, 2743, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MTFTPLIARDELVEGQAQQVRLEGRHEEFSLALGEVDIDDKTIECERHGPVEAYATRQVNGVVEVDLPVLAVVLLGSDVYVLSDRCSALFSLETGAAVTFPATQ", "metadata": {"id": "A0A965JTK9", "cluster": 20154912, "interpro_all": ["IPR017941", "IPR036922"], "interpro_used": ["IPR017941"], "interpro_unused": ["IPR036922"]}, "task_type": "infilling"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein is assigned to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is produced by Saprospiraceae bacterium and is described by UniProt keywords Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 4152, 2007, 9235, 5424, 11979, 1972, 3336, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 5239, 1930, 9067, 4587, 18, 3], "output": "MNNSYHHIPVLLTPSVDALIGNPSGVYIDATLGGAGHSRAILNRLVGLNLPQDDRFVWIKSNFKYLKKYMEYYKIEMLDGVLADLMNSSQPLRAIDILQQYSEVQLTTIFFEYGELTNAKKIAQAIIQKRNKWMAQLFQALRIEVNQELSSLEMLLQEATDLLKKDGKLVVISYHSLEDRFSSWSKHAIVPDEKELEENSRSRSAKMRVGIKADKNATLFGFDQDDAGVSSFHFDEDQRGFSFQSQYPLDMRDRKNRRWDSCIAFANWADAFVYGMVKNWMKQEKNVDLIYGKKDFL", "metadata": {"id": "A0A936VT89", "cluster": 24161776, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR023397", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should have a Glycosyltransferase 2-like domain that catalyzes the transfer of sugar moieties from activated nucleotide donors, such as UDP-glucose or GDP-mannose, to specific acceptor molecules to form glycosidic bonds. This domain participates in the biosynthesis of diverse structures, including cellulose, dolichol phosphate, and teichoic acids. It occurs in Bacillota bacterium (Firmicutes bacterium) and carries UniProt keyword assignments Carotenoid biosynthesis, Transmembrane, and Transmembrane helix. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 3066, 2162, 43, 20067, 9961, 22, 17, 3189, 3418, 1988, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 5489, 8276, 16, 2427, 1966, 18500, 17, 3817, 2014, 15217, 17, 17936, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2052, 3418, 17241, 1922, 1920, 8132, 1927, 6445, 4061, 16, 2710, 12343, 16, 17837, 2108, 1945, 5413, 16, 1930, 3602, 2108, 8643, 4576, 18, 2176, 5110, 1922, 8175, 22538, 3857, 14061, 12, 24474, 14061, 13, 1930, 16252, 20709, 11121, 2538, 18306, 23779, 8132, 16, 9117, 16, 1930, 9117, 7864, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MILLSLLYFFVFLVLALAVKAYPVKSRSHNLFFSVIVPFRNERRHLGPLLDSLKKQSHRDREFIFVNDHSDDGGEDLLAGQELTLLHLHDEYGKLAALAKGSHVANGEYLVFCDADCSPKWNWLKTLNKRVHEDAVLFAGFVEIEESAFFTLDMFMLIGIASGLDFFHIPSSCAGGNLVVRRDVYESFLDELDSENSLTEDTLLLHTIYKKGWGNSFFFFDPDTVIRTRGYASAKEFIRQRIRWLKGGYRLDLRLFVFLAFIFVSHLLFLLHPLYLIPAAAGQYIFLRTLLKRFHRTKLLYLFPFYFFFHIVYTILSGILFLFLSGEVEWKGRKY", "metadata": {"id": "A0A9D0M6Y5", "cluster": 24719080, "interpro_all": ["IPR001173", "IPR029044"], "interpro_used": ["IPR001173"], "interpro_unused": ["IPR029044"]}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein is assigned to the RNase H-like EbsB-related family, which is implicated in bacterial cell surface processes such as the expression of receptors for mating aggregate formation. Despite their structural relationship to ribonucleases, these proteins may lack RNase H activity and instead function as cell wall hydrolases or participate in the synthesis and assembly of the cell envelope. Additionally, the protein has a Ribonuclease H domain that specifically recognizes and hydrolyzes the RNA strand of RNA-DNA heteroduplexes. This type-I domain is widely distributed across all kingdoms of life and functions as a critical component of retroviral reverse transcriptases, where it degrades the RNA template during viral replication. It originates from Microthlaspi erraticum.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 1977, 6304, 1942, 1920, 9843, 50, 17, 3189, 19183, 1014, 17, 2712, 3416, 16, 2154, 1977, 6835, 1922, 4543, 2024, 3154, 4028, 2427, 1966, 1920, 2294, 1927, 4086, 1958, 11786, 12405, 3337, 18, 4281, 2310, 4346, 3303, 1942, 18347, 2319, 16, 2144, 2697, 2278, 3630, 9843, 50, 2455, 1930, 5974, 2347, 1966, 2024, 4821, 30337, 2014, 7352, 1922, 1920, 4271, 1930, 5957, 1927, 1920, 2024, 11262, 18, 4950, 16, 1920, 2213, 2258, 43, 18347, 2051, 50, 3418, 1988, 4475, 16197, 1930, 7222, 20887, 1920, 3146, 5984, 1927, 3146, 17, 2678, 11330, 3481, 29140, 18, 2052, 2601, 17, 51, 3418, 1977, 5673, 6533, 3436, 2136, 13543, 1036, 1927, 3308, 1930, 4088, 1966, 43, 4140, 4594, 1927, 16599, 5267, 13335, 1036, 16, 2597, 2176, 28004, 1920, 3146, 7662, 2409, 4324, 5158, 18, 2176, 22970, 2037, 7666, 7806, 13432, 1033, 3781, 2479, 1989, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MLFTCSVPRQIWAMSDFPFLENGFGESVYAKKKFPWVLWFIWKNRNNFFFENKSFDTRKVMGKITKEMEMWFLVKRWRPPPKPWLKCNVGSVWSEEKQMDGFAWVLRDEEGTVLLCLTWAAESLISHGVKRVVFAAGDSDLVGALSRLMTNSDHLLTQCKNEKLHQDIAQKVEEECDAELAENHTKIHSRRSWMAIKSKSECSFR", "metadata": {"id": "A0A6D2KYL9", "cluster": 24949312, "interpro_all": ["IPR052929", "IPR002156"], "interpro_used": ["IPR052929", "IPR002156"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Furthermore, the protein falls within the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Moreover, the protein is associated with the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is found in Nitrospirota bacterium and exhibits UniProt keyword tags Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 2435, 1922, 16665, 10984, 6843, 1019, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 5239, 1930, 9067, 4587, 18, 3], "output": "MVHVPVMLNEIVEALRVKRSGIYVRKAEGECTLIGMDRDEEALEIAGKRLKDYDVQLMYKEVDGILLDLGLSTLQLKAEGRGFSFLRANIVNEYPEKDLANVLWKYGEERFSTIKTCKELALIIEKAVKRRGRIHPATRAFQTLRILLGPKGRLCVLSYHSLEDRIVKPLTPQKEERDANPSSRSAKLRVAEKLDGTVGLGGHAEGILKDNFSNMEDAVKGLGDDPLDMRMDTAQELTARKIARAIVNARQRKEVNKELTLLSMALDAGINHSFKDMAKKGVLTIITKR", "metadata": {"id": "A0A7C1A4N8", "cluster": 26288203, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR023397", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is assigned to the Large ribosomal subunit protein eL32 family, which stabilizes the tertiary structure of the large ribosomal subunit by extending a finger-like projection into the RNA core to interact with the \"kink-turn\" motif of 23S rRNA. Found in archaea and eukaryotes, this protein does not participate in forming the ribosomal active sites but may function extraribosomally as a nuclear transcriptional regulator. It is produced by Trichonephila clavata (Joro spider) (Nephila clavata) and is classified with UniProt keywords Ribonucleoprotein and Ribosomal protein. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 1977, 6304, 1942, 1920, 3103, 11196, 5903, 2213, 2349, 6763, 3416, 16, 2154, 19658, 1920, 10832, 3170, 1927, 1920, 3103, 11196, 5903, 2007, 12140, 43, 8497, 17, 3189, 11244, 2460, 1920, 3146, 4728, 1942, 6310, 1956, 1920, 6, 30322, 17, 5165, 6, 5219, 1927, 3020, 1036, 9067, 18, 2435, 1922, 21501, 1930, 15021, 16, 2052, 2213, 3731, 2084, 7352, 1922, 7402, 1920, 11196, 3500, 3402, 2308, 2278, 2347, 8324, 3027, 29258, 4229, 1954, 1966, 43, 4254, 5224, 7888, 18, 2176, 1977, 4152, 2007, 10477, 18128, 19167, 19887, 5499, 12, 7420, 1931, 26376, 13, 12, 7737, 19167, 19887, 5499, 13, 1930, 1977, 5947, 1956, 20709, 11569, 18347, 6657, 1930, 11196, 2213, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "LVVNFNVHVLRVNLLHVTGIMSPLPLNHCKIVKKRVKKFTRHQSDRYGKIKLNWRKPKVLIIEYVDDLRVSVRCLKLVMEVVKKTKHLLLMVSEKFNVRNIKELECLMMCNRRFCAEINHAVSSKKRKAIVERAQQLCIRVINANADCVLKKMNKLNQYFVIVAFVSCFFKCWETISF", "metadata": {"id": "A0A8X6LGG4", "cluster": 27084761, "interpro_all": ["IPR001515", "IPR036351"], "interpro_used": ["IPR001515"], "interpro_unused": ["IPR036351"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to these design specifications: The protein incorporates a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. Furthermore, the protein includes a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. Moreover, the protein should feature a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. It is derived from Stichopus japonicus (Sea cucumber) and features UniProt keywords Magnesium, Metal-binding, and ATP-binding.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 19683, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 3677, 16, 1920, 2213, 5921, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 2176, 1977, 3595, 2037, 14243, 20855, 1957, 18913, 1957, 12, 9309, 18242, 22660, 13, 1930, 4075, 20709, 11569, 13148, 16, 6048, 17, 2743, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MATLQQRMLWHGKGAHGKEVSPTHLRDFERGGSSMKDYISEIFLLMALLTLFLLFVVTCADAVALKFYRLMGLLIWLSLMVAIYIVYALHLKPDVFPVGDLGLIIFTILTLYMMLPLSTKGAILAGWTTCIPHIILMFAGEFWIPANQLSNGTDSSQNQSIPEPEPEPSSTTQGCASNFSVRLVISILLLICANFVGCCHKLLLDVVLRKTFFDTRTCIESRVKLEYEQAQQEQLLLSVLPAHLAAEMRTEMMERVRDPAMTPMPPRQNHSTTHFHNLYIKRHKNVSILYADIVGFTALASGCSPPELVKTLNELFGKFDQLAEAHNCMRIKILGDCYYCVSGLPISRPGHAANCVQMGLDMCQSINCVRDATDVNINMRVGVHTGNVLCGVLGLKKWQYDVWSHDVTLANHMESSGKPGRVHITKTTLDSLNGKYDVEPAYGRERSDFIKELNMETFFIINPRSMLSQNNSTEGVVENGHNGNHQQMSSQRASIRMARYLETWGADTPFSTGSVAPIPRGIGISGLTVLNTCLFPYTVADHSTRIHRKSVMFEKRVNERLLEAIEAINFKKSEDIHRGTMLFRQPNYEQKFSRLPDPLFRYALLALNVVLLCILVGQGLNYHCHDEHLHYALGSFALVFVVFVTVLAFSNSWKCLDNSPFPIFAKHLAKDKWLQKVLGSVCLVLILAVPLIYLGLNTPDPEMRIFNPAVELKQLKQKQGRDHDAGCHSLRRCTGCQINGCVSKVMFAVTWPAYSSPTPTHPTPPPLLPSPPPHHYYHLSLARSSGLFDL", "metadata": {"id": "A0A2G8KG48", "cluster": 27727638, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR009398", "IPR029787"], "interpro_used": ["IPR001054", "IPR009398", "IPR018297"], "interpro_unused": ["IPR032628", "IPR029787"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein carries a Zinc finger, C2H2, LYAR-type domain that is found in LYAR proteins involved in the regulation of cell growth. This motif typically forms a stable scaffold to facilitate specific interactions with target molecules. Additionally, the protein is grouped in the Cell growth-regulating nucleolar protein family, which features a C2H2, LYAR-type zinc finger and mediates the processing of pre-rRNA precursors into mature 18S and 28S rRNAs. These proteins also function as transcriptional repressors, specifically regulating the gamma-globin promoter and oxidative stress response genes. It is produced by Phytomonas sp. Hart1 and features UniProt keywords Nucleus, Zinc-finger, and Metal-binding.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 16252, 43, 7997, 8497, 16, 8453, 6951, 16, 7518, 1933, 17, 2601, 3418, 1988, 1977, 2435, 1922, 7518, 1933, 2697, 3286, 1922, 1920, 3640, 1927, 2024, 2905, 18, 2052, 5219, 5745, 4952, 43, 4700, 7281, 1942, 6628, 2487, 3719, 1956, 2758, 4206, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2024, 2905, 17, 6773, 23770, 2213, 3416, 16, 2154, 4075, 43, 8453, 6951, 16, 7518, 1933, 17, 2601, 7997, 8497, 1930, 10412, 1920, 4587, 1927, 2097, 17, 9067, 10416, 2460, 6665, 17659, 1930, 3158, 1036, 9067, 1036, 18, 2144, 2697, 2222, 2347, 1966, 5224, 26446, 16, 4475, 6773, 1920, 7034, 17, 18938, 4465, 1930, 5163, 3071, 2644, 2628, 18, 2176, 1977, 4152, 2007, 25512, 3947, 1934, 2056, 18, 21558, 1009, 1930, 4075, 20709, 11569, 5607, 16, 7997, 17, 8497, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MVSFTCNRCHDVVKKPKVLGHSNMCRSSGFTCVDCMEVRCSVNGNPKRPATPGDASDSEVKAVRPRPRMPNLSDSDSENSDDRREAGGHLSMDAQDRREESTNRDQPSPTRIQSNAQVKEKTSRPCSPTSSEVADVVVDILGEHPERTSMRPKDLSKELVNRYSRRIAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGASQNRYDMHFDVHSVKLHTACITEVDKYQGQWKQWVHGKKSTKRPREEDAGDTSGTDCVVPTFVLGSAKSVRHAXXXXXXXXXXXXXX", "metadata": {"id": "W6L2J0", "cluster": 27905070, "interpro_all": ["IPR039999", "IPR014898", "IPR036236"], "interpro_used": ["IPR014898", "IPR039999"], "interpro_unused": ["IPR036236"]}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein is associated with the Pyridoxal phosphate-dependent transferase, major domain superfamily, which forms the large catalytic component with a 3-layer \u03b1/\u03b2/\u03b1 sandwich topology in enzymes that utilize pyridoxal 5'-phosphate (PLP) as a cofactor. Through a Schiff base linkage with an active site lysine, members of this superfamily facilitate diverse chemical transformations, including transamination, decarboxylation, and deamination, which are essential for the biosynthesis and catabolism of amino acids and neurotransmitters. Also, the protein is grouped in the Kynureninase family, which functions as a pyridoxal-5'-phosphate (PLP)-dependent enzyme catalyzing the hydrolytic cleavage of L-kynurenine or 3-hydroxykynurenine to yield L-alanine and anthranilic or 3-hydroxyanthranilic acid. This reaction constitutes a key step in the L-tryptophan catabolic pathway involved in NAD biosynthesis across bacteria, fungi, and vertebrates. Structurally, the enzyme belongs to subgroup IVa of the aminotransferase superfamily. In addition, the protein is classified under the Pyridoxal phosphate-dependent transferase, small domain superfamily, which comprises the complex $\\alpha/\\beta$ structural domain found in enzymes such as aspartate aminotransferase and DOPA decarboxylase. These proteins utilize pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze diverse reactions, including transamination, decarboxylation, and deamination, playing a vital role in amino acid biosynthesis and neurotransmitter metabolism. It is produced by Gammaproteobacteria bacterium and is connected to UniProt keyword Hydrolase and Pyridine nucleotide biosynthesis.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 1977, 2458, 1956, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 3044, 3418, 13975, 16, 2154, 4952, 1920, 3103, 6804, 4594, 1956, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 18038, 13678, 1922, 5038, 1988, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 18, 2596, 43, 25214, 5170, 8611, 1956, 1925, 3500, 3200, 9082, 16, 4678, 1927, 2052, 13975, 6628, 6445, 4399, 18510, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 2154, 2032, 4415, 1958, 1920, 8132, 1930, 19480, 1927, 3835, 4576, 1930, 21012, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 23523, 24684, 11413, 3416, 16, 2154, 4088, 1966, 43, 24828, 23859, 17, 25, 11, 17, 5413, 12, 21453, 13, 17, 3100, 4113, 29601, 1920, 26702, 6404, 1927, 54, 17, 23523, 24684, 2053, 2014, 23, 17, 8275, 6716, 1022, 24684, 2053, 1942, 4307, 54, 17, 10504, 1930, 14228, 16692, 1935, 2014, 23, 17, 8275, 7744, 17182, 10029, 2687, 18, 2052, 3227, 14879, 43, 3834, 3537, 1922, 1920, 54, 17, 13489, 22112, 3374, 3286, 1922, 6577, 8132, 3436, 4802, 16, 10520, 16, 1930, 14976, 18, 12171, 16, 1920, 4113, 14440, 1942, 6200, 4370, 1019, 1927, 1920, 15817, 13975, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 2858, 3418, 13975, 16, 2154, 12936, 1920, 2796, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3418, 2435, 1922, 5038, 2427, 1966, 12878, 15817, 1930, 19428, 23922, 18, 2144, 2697, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 1942, 18170, 6445, 5298, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 14797, 43, 8970, 2770, 1922, 3835, 2687, 8132, 1930, 15223, 4714, 18, 2176, 1977, 4152, 2007, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 20748, 1930, 19604, 5489, 8132, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MNKYNLAYAQELDSQDPLRAMSLGLAPKLAREYVLEFLDAWQQRGVKGHFEGDYPWMPYNDEVVMMNSLTANLHLMMVSFYQPQGKRTKILQENMLLWQPRQNEELLNHKDLYQLIEQQGDEVLDMKTITEKAHAKGIKVGFDLAHAVGNIVAGCFVHQQHAHNTELNRFAGWWGHDKATRFKVLSLAAIRGSFDTIKMAGGIKALRKKSLKLMAEHQRGCQLSLMINKQTISDLGIDGKTIRVAPVPLYNSFADIYHFVRILKECLVRAQFTIPKQKNGEEEYYFTGNHEFLTAQAAALIGAKLEDHAFPSDHYAVSSQIKHHGLDEIALILLPGVQYYTGQELSLHDWQADFACWCSYKYLNAGAGSMENNFQPIASAEGWQLSNPPTQYMFDLLAQELSDKITIITPVFNRIEAKGVTTDWREPNV", "metadata": {"id": "A0A2A4VQX3", "cluster": 28268673, "interpro_all": ["IPR010111", "IPR015424", "IPR015421", "IPR015422"], "interpro_used": ["IPR015421", "IPR010111", "IPR015422"], "interpro_unused": ["IPR015424"]}, "task_type": "infilling"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein is grouped in the Ubiquinone biosynthesis O-methyltransferase family, which functions as an O-methyltransferase catalyzing two distinct steps in the ubiquinone (Coenzyme Q) biosynthetic pathway. This family includes the bacterial enzyme UbiG and the mitochondrial enzyme COQ3. Moreover, the protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It has been characterized in Legionella israelensis.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 5582, 22123, 8132, 57, 17, 16478, 3416, 16, 2154, 4088, 1966, 1925, 57, 17, 16478, 29601, 2288, 4493, 5983, 1922, 1920, 5582, 22123, 12, 22051, 59, 13, 14041, 3374, 18, 2052, 3416, 5921, 1920, 4543, 4113, 4803, 1950, 1930, 1920, 4596, 4113, 25147, 1010, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 2258, 2252, 4378, 1922, 27836, 5870, 19187, 8134, 18, 3], "output": "MNESTIDLQEISKFEQHAKDWWDPDGPLKTLHDINPLGLLTEAMARKGANCMGVDAEKNVIEVAKSHAASQKDLALSYHSVAIEDHPELVLQHSARVLKPGGWLFLSTINRSLKAYVGVILAAEYLLGLLPRDADLNIKDMKGMRYNPFLRTAVLTSDVSVNYLFACQKSERLEFILMHQSLGGKKVLDVGCGGVQDENFDIVTCMEMLEHVQKQTHDYNKLIKPSELAQFV", "metadata": {"id": "A0A0W0W344", "cluster": 1601563, "interpro_all": ["IPR029063", "IPR010233"], "interpro_used": ["IPR010233", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein should include a TPL/SMU1, LisH-like dimerisation domain that contains a lissencephaly homologous (LisH) motif to facilitate N-terminal protein dimerization. This domain is conserved in eukaryotes and functions in diverse contexts, ranging from transcriptional corepression during plant development (e.g., TOPLESS) to pre-mRNA splicing as a component of the spliceosome (e.g., SMU1). Additionally, the protein contains a CTLH domain that forms a predicted $\\alpha$-helical sequence often located immediately adjacent to the LisH motif in eukaryotic proteins regulating microtubule dynamics, nucleokinesis, and chromosome segregation. It is frequently associated with WD-40 or Kelch domains in multi-domain proteins but can also occur independently in specific contexts, such as in the yeast protein RMD5. Additionally, the protein includes a LIS1 homology (LisH) motif conserved site that functions as a protein-binding module in eukaryotic proteins involved in microtubule dynamics, cell migration, and chromosome segregation. Predicted to adopt a two $\\alpha$-helix fold, this motif contributes to regulation by mediating dimerization or by binding cytoplasmic dynein and microtubules directly. It is native to Oncorhynchus kisutch (Coho salmon) (Salmo kisutch) and is linked to UniProt keywords Mitochondrion, Repeat, and WD repeat.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 3951, 43, 6213, 1024, 19, 2426, 24396, 16, 19620, 1023, 17, 3189, 7632, 6284, 3418, 1988, 5461, 43, 19620, 17221, 26547, 8725, 12, 19620, 1023, 13, 5219, 1942, 6628, 56, 17, 4262, 2213, 13640, 18, 2052, 3418, 1977, 5305, 1922, 15021, 1930, 4088, 1922, 6445, 11144, 16, 6485, 2037, 5224, 4728, 3124, 2409, 4496, 2740, 12, 47, 18, 49, 18, 16, 3700, 5427, 13, 1942, 2097, 17, 3616, 8490, 1966, 43, 4594, 1927, 1920, 10708, 4283, 12, 47, 18, 49, 18, 16, 2426, 24396, 13, 18, 4950, 16, 1920, 2213, 5461, 43, 13960, 1023, 3418, 1988, 4952, 43, 4396, 8, 38, 4595, 8, 17, 11514, 3244, 3868, 4810, 6183, 6811, 1942, 1920, 19620, 1023, 5219, 1922, 10825, 2697, 6773, 10544, 5565, 16, 2797, 11172, 1937, 16, 1930, 5597, 12707, 18, 2176, 1977, 5467, 2458, 1956, 17907, 17, 3040, 2014, 16080, 2072, 4682, 1922, 2779, 17, 3418, 2697, 2308, 2112, 2222, 4704, 6407, 1922, 2487, 11144, 16, 2427, 1966, 1922, 1920, 5688, 2213, 10625, 1007, 1015, 18, 4950, 16, 1920, 2213, 5921, 43, 19620, 1009, 9039, 12, 19620, 1023, 13, 5219, 5305, 3200, 1988, 4088, 1966, 43, 2213, 17, 2743, 9059, 1922, 10825, 2697, 3286, 1922, 10544, 5565, 16, 2024, 5049, 16, 1930, 5597, 12707, 18, 4396, 1942, 14103, 43, 2288, 8, 38, 4595, 8, 17, 7864, 3728, 16, 2052, 5219, 7624, 1942, 3640, 2007, 10239, 13640, 2014, 2007, 2743, 6823, 18188, 1930, 12444, 4103, 18, 2176, 1977, 6196, 1942, 5595, 14514, 2304, 2072, 1957, 8191, 20490, 8888, 12, 3757, 1037, 9590, 13, 12, 3370, 12492, 8191, 20490, 8888, 13, 1930, 1977, 4624, 1942, 20709, 11569, 30017, 16, 6865, 16, 1930, 17907, 6865, 18, 3], "output": "SNNNKRSSAIKLVIVSSLTPEGAGGLGAAIGSAANGAGQGQDSENVNGLSTTNNGNSVSNNDGIPAPAASNNTVSSDLGLNQTVDLLMQESGCRLEHPSATKFRNHVPSAIVVSPTVLQLRMKFLLLQQKYLECLEDAKVLEYNTERIHILSGYLMCSHAEDLRAKAEPPSVMLPPRRLQTLLRQAVELQRERCLYHNTKLDSGQILTEHCNEVWFCKFSNDGTKLATQLKLMKTLEGHAYGVSYLAWSPDDTYLIACGTKMSQSHEDSLTSVAWNPDGKRFVTGGQRGRVQCLWCLGDARTVLASDTHRNIVQEDHPIMSFTVSKNGRLALLNVATQGRKYQGVTQGFYTIHSCFGGHNEDFIASGSLTGHSRTVNCVSWNPVVPGLLADAEGLNGTDLFDWSSYFNLLAPTLHHSVTNTLASVALSCLNNSERNGESSSAGEAHTDANSVKKKKRLSQSEEDVIRLIGQHLHVEGEWDKAESDLNELKALMHSALQVLRAELTPLKWEGKGTASRTKLLDKLQTYLLDSVSLLLDHACSRKQFPCYTQGSKDTTVIVWHVNTSHPDDCSELWLWNVQTGELRQFYQCDLDGNLLDSWEGVQRIRGYNFEDLTDVHLWDLHDRVLVEDHKVYIWHRRSELPIAESASDDGTVRIWGPAPFLDVQ", "metadata": {"id": "A0A8C7DD29", "cluster": 2347974, "interpro_all": ["IPR006595", "IPR006594", "IPR054532", "IPR015943", "IPR036322", "IPR001680", "IPR051350"], "interpro_used": ["IPR054532", "IPR006595", "IPR006594"], "interpro_unused": ["IPR015943", "IPR001680", "IPR036322", "IPR051350"]}, "task_type": "infilling"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein is categorized in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is found in Clostridiales bacterium and is described by UniProt keywords Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 2435, 1922, 17938, 26890, 1918, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 5239, 1930, 9067, 4587, 18, 3], "output": "MSSYHTPVLLNEVISGLNIKSNGIYVDGTVGGGGHSREIFKLLDKNGLLICNDIDIEAIEEAKREIPSSKNIIYINDNYKNLVSNLHNLNIEKVDGVLLDLGVSSHQIDDAARGFSYMIDAPLDMRMSKDTDITAYDVVNGYSYEELVEILFSYGEEKYSRFIAKQIIKSREINPIKTTTELADITKKAYQIKNNYGSGHPAKKTFQAIRIEVNKELEKLSECIVSLTRLLKRGGRICIISFHSLEDRIVKQTFVELEKSCICDKMSPICTCNKKSEIEILTKKPLTASAKEIENNSRSKSAKLRIAQKK", "metadata": {"id": "A0A7C6TP54", "cluster": 6280585, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein is grouped in the Cof family, which constitutes a bacterial subgroup of the Haloacid Dehydrogenase (HAD) superfamily that functions as phosphatases, likely acting on phosphorylated sugars. Members such as *E. coli* Cof and YbiV catalyze the hydrolysis of substrates like HMP-PP or sugar phosphates, displaying broad specificity in vitro. These enzymes typically exist as monomers containing an $\\alpha/\\beta$ hydrolase domain with a Rossmann fold, with the active site located at the inter-domain interface. Furthermore, the protein belongs to the HAD superfamily, which encompasses enzymes such as phosphatases, P-type ATPases, and dehalogenases involved in diverse cellular processes ranging from amino acid biosynthesis to detoxification. These proteins share a conserved \u03b1/\u03b2-hydrolase fold similar to the Rossmann fold, featuring a core domain and a variable cap domain that allows for structural and functional variation. Additionally, the protein is grouped in the HAD-superfamily hydrolase, subfamily IIB family, which functions as a group of aspartate-nucleophile hydrolases within the Haloacid Dehalogenase (HAD) superfamily characterized by a distinct Class II insertion domain. It encompasses enzymes involved in carbohydrate metabolism, including trehalose-6-phosphatase, sucrose-phosphatase, phosphomannomutase, and Cof-like hydrolases. It has been characterized in Lachnospiraceae bacterium.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2081, 1038, 3416, 16, 2154, 14879, 43, 4543, 6200, 1927, 1920, 23226, 29272, 9294, 12, 2430, 13, 13975, 1988, 4088, 1966, 19131, 16, 3205, 8290, 1990, 7199, 15592, 18, 4678, 2427, 1966, 14, 47, 18, 5178, 14, 2081, 1038, 1930, 21000, 2068, 18170, 1920, 9128, 1927, 6249, 3189, 5833, 1034, 17, 4108, 2014, 9523, 26473, 16, 13867, 4949, 4896, 1922, 3596, 18, 2144, 5038, 5745, 5516, 1966, 13256, 3165, 1925, 8, 38, 4595, 19, 38, 4666, 8, 20748, 3418, 1956, 43, 18215, 8890, 3728, 16, 1956, 1920, 3500, 3200, 4810, 2019, 1920, 2107, 17, 3418, 6854, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 2430, 13975, 16, 2154, 21569, 5038, 2427, 1966, 19131, 16, 58, 17, 2601, 28132, 16, 1930, 2028, 7289, 2404, 2319, 3286, 1922, 6445, 3689, 4028, 6485, 2037, 3835, 2687, 8132, 1942, 18169, 18, 2144, 2697, 7948, 43, 5305, 160, 19, 161, 17, 20748, 3728, 2551, 1942, 1920, 18215, 8890, 3728, 16, 29931, 43, 4728, 3418, 1930, 43, 4650, 2853, 3418, 1988, 5731, 1958, 4346, 1930, 3183, 4516, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2430, 17, 13975, 20748, 16, 16227, 19795, 3416, 16, 2154, 4088, 1966, 43, 2210, 1927, 12878, 17, 2797, 28335, 30337, 2651, 1920, 23226, 29272, 2028, 7289, 2404, 2051, 12, 2430, 13, 13975, 4378, 2007, 43, 4493, 2921, 2890, 7413, 3418, 18, 2176, 21569, 5038, 3286, 1922, 10590, 4714, 16, 2710, 23995, 17, 26, 17, 8167, 16, 8819, 17, 8167, 16, 8078, 8890, 1947, 26455, 4127, 16, 1930, 2081, 1038, 17, 3189, 30337, 18, 2176, 2258, 2252, 4378, 1922, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 18, 3], "output": "MNRIKLIAFDLDGTLLKDNKELAPETMEALRQAAEAGICLVPTTGRLYDGVPEELRTQPFIRYVIAANGAEVYDAKEKKSLYRAELTPEEVRRFFDAVRDVPAIVGCYKGGQGLMGREDMEKMEAFAARGLFRMMRRVYTQVEDLEAYLLETGETVQKLMLFFADLEERVRVLKSMREELSDLAVSSSVENNIEVNAAAAHKGAALRFLYRHLQIERTETAAFGDGSNDVSMLMEAGVGIAMENACQEAKKAADRITLSNEQNGVAHMIKEFLNEAAV", "metadata": {"id": "A0A7U9NCN2", "cluster": 7170732, "interpro_all": ["IPR000150", "IPR036412", "IPR006379", "IPR023214"], "interpro_used": ["IPR000150", "IPR023214", "IPR006379"], "interpro_unused": ["IPR036412"]}, "task_type": "autoregressive"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein features a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. Furthermore, the protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein is associated with the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. It is produced by Lentisphaerota bacterium and features UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2176, 1977, 4152, 2007, 10226, 3508, 20051, 6843, 1019, 14061, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MTGHFITFEGPEGSGKSTHIRRLASRLRAAAHDVVVTREPGGTSLGEAIRGLLQHDAAGESPVPRAEALLFCASRAQLVQTVIRPALARGAWVLADRFADSTFAYQGFGRGFALADLQAANAFATGGLVPELTLLLDLDEAAGRRRLAERHGPKAAADRFEREPHDFHARLREGFLTLAAAEPERILVIPTGRAEDAVADDIWQAVTTRFPGAPGAT", "metadata": {"id": "A0A7X7RIF4", "cluster": 7485220, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR039430", "IPR027417", "IPR018094"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Function:\nThe protein should include a GmrSD restriction endonuclease C-terminal domain that functions as a DNA nicking nuclease within modification-dependent restriction systems to defend against phage infection. Belonging to the HNH nuclease superfamily and containing a conserved HXXP motif, this domain targets and cleaves DNA carrying specific epigenetic marks, such as glucosylated hydroxymethylcytosine or phosphorothioate modifications. Also, the protein should include a GmrSD restriction endonucleases, N-terminal domain that functions as the nucleotide binding, recognition, and hydrolysis module within the GmrSD family of Type IV modification-dependent restriction enzymes. Found in proteins such as BrxU and SspE, this domain facilitates NTPase activity required to recognize and cleave DNA containing specific modifications, such as 5-methylcytosine or phosphorothioates, providing defense against bacteriophage infection. It is native to Pseudomonadota bacterium.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 3066, 3951, 43, 5711, 5675, 1007, 7587, 18697, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 2678, 12657, 1941, 16230, 2651, 6295, 17, 3100, 7587, 3771, 1942, 30178, 10249, 3316, 10503, 2909, 18, 10588, 1942, 1920, 9888, 1023, 16230, 13975, 1930, 3165, 43, 5305, 22721, 1039, 1034, 5219, 16, 2052, 3418, 4845, 1930, 23839, 2678, 8215, 2487, 8542, 13387, 16, 2427, 1966, 3351, 22756, 29078, 27932, 7506, 2014, 3421, 17809, 25120, 6920, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 5711, 5675, 1007, 7587, 18697, 1036, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 5489, 2743, 16, 5708, 16, 1930, 9128, 9059, 2651, 1920, 5711, 5675, 1007, 3416, 1927, 2601, 4370, 6295, 17, 3100, 7587, 5038, 18, 2435, 1922, 2697, 2427, 1966, 2387, 1039, 1032, 1930, 19715, 1021, 16, 2052, 3418, 11374, 29676, 2051, 2455, 3414, 1942, 9967, 1930, 21252, 2678, 3165, 2487, 6920, 16, 2427, 1966, 25, 17, 4963, 27932, 7506, 2014, 3421, 17809, 25120, 1036, 16, 5453, 9720, 3316, 24613, 2909, 18, 2176, 1977, 6196, 1942, 11520, 3947, 12595, 3857, 14061, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MFPGLFTAPLRIVELFSDPFRFTVPSYQRRYAWTVKEAGQLLDDILLALGGEGPLFPRNLEIVDGQQRLITVTILLAVLRDLAAADGASHYSKLQELIRTYVLNPRACLQSPTDIVLEPCMEAMLEVRNHFMAEMQALTIADRQRIRMFSVLNDRGRPLARKDIIKAEVLGGVPPERAATLIEQWRAAEQRLGSDYDRSVMQEAGGSEAFVSNVLLPNAEAYDIIRRAHHEGAPESAEITRLLRYQMLKFLQVVEPFAYSLRLLCIGAGKRATRFAAVLAALEDGSIFDPERSPCLLTSDEQRHILLRLNDELAGEPQNLDPVDWTVEHILPQSPGRNGLWREWFPDNDERELLTQSLGNLVLVRRISTFDTWTPDQVRAREERFIEIISRIWRLDLSAMRRGDDLEMARRRRRAVDPVEPDYFFGAILLTDSGVHADWRKGPTVGKSQNGDHTHRLQLQGSDDAFFLDYLLNRCHAVVIVTTDVDHGHAFLSHLRVIEGRGRLPIIAGILNWLGSSEWVPATMKWFSLHRCDPATYNLRNLHERHPQTCKLVNQNDRASNQDFFRKKAIYFKHAQGDMPVITRE", "metadata": {"id": "A0A2W4RJ59", "cluster": 7858126, "interpro_all": ["IPR011089", "IPR004919"], "interpro_used": ["IPR011089", "IPR004919"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein has a Domain of unknown function DUF6894 domain that represents a small structural unit found mainly in alphaproteobacteria. It features a fold composed of a four-stranded \u03b2-sheet packed against an \u03b1-helix, though its specific biological function remains unknown. It has been characterized in Sphingomonas sp. Leaf343. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 3418, 1927, 5435, 2347, 4855, 17136, 9485, 1006, 3418, 1988, 4972, 43, 2858, 4346, 5344, 2435, 4994, 1922, 4595, 9218, 1021, 10296, 18, 2176, 4075, 43, 3728, 7179, 1927, 43, 3006, 17, 10338, 161, 17, 11130, 15827, 3316, 1925, 160, 17, 7864, 16, 4170, 2496, 2487, 3933, 2347, 4497, 5435, 18, 2176, 2258, 2252, 4378, 1922, 13502, 10480, 2056, 18, 6998, 29059, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MPHLFLNLENHNGLQPDTEGRDFDTVDAAIAEAGRTAGQVLAEDIAAGRTPVRIRVLIDDAAGQRQATLESFIEVKR", "metadata": {"id": "A0A0Q5PQN8", "cluster": 8335321, "interpro_all": ["IPR054189"], "interpro_used": ["IPR054189"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein is grouped in the Ubiquinone biosynthesis O-methyltransferase family, which functions as an O-methyltransferase catalyzing two distinct steps in the ubiquinone (Coenzyme Q) biosynthetic pathway. This family includes the bacterial enzyme UbiG and the mitochondrial enzyme COQ3. In addition, the protein belongs to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Moreover, the protein should contain a Methyltransferase type 11 domain that functions as an S-adenosyl-L-methionine (SAM)-dependent enzyme with a Rossmann-like $\\alpha/\\beta$ fold, catalyzing the transfer of methyl groups to diverse nucleophilic acceptors. It acts on substrates ranging from small molecules and lipids to proteins, playing critical roles in the biosynthesis of ubiquinone, biotin, and ergosterol, as well as in chromatin regulation and arsenite detoxification. It has been detected in Mytilus galloprovincialis (Mediterranean mussel) and contains UniProt keyword associations Membrane, Mitochondrion, and Mitochondrion inner membrane.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 5582, 22123, 8132, 57, 17, 16478, 3416, 16, 2154, 4088, 1966, 1925, 57, 17, 16478, 29601, 2288, 4493, 5983, 1922, 1920, 5582, 22123, 12, 22051, 59, 13, 14041, 3374, 18, 2052, 3416, 5921, 1920, 4543, 4113, 4803, 1950, 1930, 1920, 4596, 4113, 25147, 1010, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 16478, 2601, 2513, 3418, 1988, 4088, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 4113, 1956, 43, 18215, 8890, 17, 3189, 8, 38, 4595, 19, 38, 4666, 8, 3728, 16, 29601, 1920, 3856, 1927, 4963, 2671, 1942, 6445, 24456, 27916, 18, 2176, 8016, 1990, 6249, 6485, 2037, 2858, 4206, 1930, 8238, 1942, 2697, 16, 14797, 4140, 5456, 1922, 1920, 8132, 1927, 5582, 22123, 16, 8622, 16, 1930, 11949, 23030, 16, 1966, 2486, 1966, 1922, 6338, 3640, 1930, 29466, 18169, 18, 2176, 2258, 2252, 3330, 1922, 3057, 2583, 1957, 9354, 12964, 11800, 3349, 19337, 12, 16825, 26874, 1938, 13, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 30017, 16, 1930, 30017, 6671, 3260, 18, 3], "output": "MTSLRLCHKCFTVLSHTRTQQYQLIKICGKVLQNNPRSCQNSIATQSSRFNSTSTADSPNAHTTIDQDEHHKFTKLASHWWDEKGEFYALHSMNRLRIPLIRDAFVDASDKASKIFPLKDKLILDVGSGGGIIAEPLARLGATVTGIDMVEENVRIAQTHIFQDPEISGRVNYIHGAVEDLPEEGKYDAVVASEVVEHVSDVDMFISSCCKLIKPGGYFFMTTLNKTNASYLLAVLGAEHLLRIVPPGTHDWNKFIPPEDLQLSLEQNGMTVRLLHGMCYNPVINRWSWISNTTINYAMYAVKSTQPLHSHDTIEQTDY", "metadata": {"id": "A0A8B6CP59", "cluster": 8740033, "interpro_all": ["IPR013216", "IPR029063", "IPR010233"], "interpro_used": ["IPR010233", "IPR029063", "IPR013216"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein is associated with the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Furthermore, the protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is found in Agromyces mariniharenae and has UniProt annotations Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 2435, 1922, 25277, 14930, 3707, 13081, 8635, 28476, 11496, 1021, 1930, 2258, 20709, 15010, 5239, 1930, 9067, 4587, 18, 3], "output": "MDIERIHTPVMLERTVELLAPAIRQEGAALVDATLGMGGHSRAFLERFPELTVIGLDRDTDALGIARERLAAFGDRARFVHTVYDGIAEAIRSEGFDEVQGVLFDLGVSSLQLDRAERGFAYAKDAPLDMRMDSTRGRTAADVIAESSEQELRRIFQEYGEEKLAQRYARAIVRARAEEPITRSGQLVAILTDATPVAVQRQGHPAKRVFQALRIEVNEELSVLQRAMPAALDSIALGGRIVVLAYQSLEDRIVKRVLQAASTSSAPPGLPMELPEHKPQFRLLVRGAELASESEQAENPRAKPVRMRAAERVRRPS", "metadata": {"id": "A0A5S4V3J9", "cluster": 9979282, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR023397", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein incorporates a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein should contain a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Additionally, the protein is classified under the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is native to Peptoniphilus asaccharolyticus DSM 20463 and features UniProt keywords Isoprene biosynthesis and Transferase.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 19683, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 6196, 1942, 23045, 13339, 24888, 5277, 1036, 15634, 2437, 28476, 29370, 10964, 16368, 7576, 1930, 4075, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MKSYAKINLSLDVVSKREDGYHNIASIFNFDSDMELPEENTVTKAYRVLTEYMERDLPVSVKLHKNIPTNRIYDLNLSTDDLRKLGVKVGADVPFMIGGETALCEGIGDLITKEVYSQMNIRDERIDFKSLEMSLKNGNLTEISKYLRSALMSGSGSTVYGLFDNEDDLKKAYDKFKKLYKNTYMVNLIMQRIDIYDEMEIEKSEKGAGLAGGSANAATLFEEIDLDINFSKLKALIINPGFEISSNDMENVVFKKYKEVENIKEELLKHTQ", "metadata": {"id": "A0A1W1UHX6", "cluster": 14277858, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "infilling"} {"instruction": "The protein belongs to the Diedel family, which functions as an insect immune response protein that acts as a negative regulator of the JAK/STAT signaling pathway following septic injury. Homologues present in insect DNA viruses, such as *Baculoviridae*, serve to suppress the host immune deficiency (IMD) pathway. It is native to Megalurothrips usitatus (bean blossom thrips).\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 8545, 1938, 3416, 16, 2154, 4088, 1966, 1925, 11422, 3743, 2644, 2213, 1988, 8016, 1966, 43, 3136, 7888, 1927, 1920, 10108, 19, 3156, 3197, 3374, 2894, 13927, 4047, 18, 18541, 2481, 1922, 11422, 2678, 6241, 16, 2427, 1966, 14, 23011, 14127, 10828, 14, 16, 7120, 1942, 4400, 1920, 4423, 3743, 6179, 12, 2042, 1007, 13, 3374, 18, 2176, 1977, 6196, 1942, 20418, 5277, 6843, 6570, 5689, 2022, 9909, 1031, 1957, 12, 21266, 16635, 5590, 1947, 8481, 5689, 13, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MIRPVQFFATVCVLASALDVTTAVCCPNEVMKLQTEASNVERLLWASVTSEDLRPSLSAVSRDFRESGFHCNCDGGCITGRQFDVPTIGEQPLSFYCDKDVPADLDKDVMNLIKHRDCTCSNAVHRDLQNASDPIYCEKGMVYCEVDIRRVKSFGVTTSLSFTLGAGAGLSQKDRDPRRLFRDAHQAQVLQIDCRHCHSAAAEPPQLLRDPARLRAKDQRGRHHSRRQAVRLPEYRCADGRHVGSLDVCSVGPCNFRHTSGDYTLSVTEVEGPEDRVVRDDGHRDGLPLHGTGRRRHLAPH", "metadata": {"id": "A0AAV7X9D1", "cluster": 16917498, "interpro_all": ["IPR025061"], "interpro_used": ["IPR025061"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a polypeptide chain that performs the following role: The protein carries a Pleckstrin homology (PH) domain that targets proteins to cellular membranes through high-affinity binding to phosphoinositides, particularly those with vicinal phosphate groups. This modular fold facilitates signal transduction and cytoskeletal organization by recruiting proteins to the plasma membrane and enabling interactions with partners such as G-proteins and Protein Kinase C. Also, the protein can be placed in the PH-like domain superfamily, which comprises a diverse group of modular domains, including Pleckstrin homology (PH), PTB, EVH1, and FERM domains, that share a conserved structural fold consisting of a partly opened \u03b2-barrel capped by an \u03b1-helix. These domains primarily function in cellular signaling and subcellular targeting by mediating specific interactions with membrane phospholipids, phosphotyrosines, or peptide motifs. It is native to Aplanochytrium stocchinoi. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 16252, 43, 6483, 12940, 2156, 5572, 9039, 12, 2087, 13, 3418, 1988, 4845, 2697, 1942, 3689, 5726, 2596, 2149, 17, 5173, 2743, 1942, 23546, 1036, 16, 4443, 2690, 1956, 8159, 2526, 5413, 2671, 18, 2052, 16078, 3728, 11374, 2733, 8201, 1930, 14787, 5901, 2007, 17040, 2697, 1942, 1920, 3582, 3260, 1930, 12180, 3719, 1956, 7228, 2427, 1966, 49, 17, 2697, 1930, 2213, 4016, 45, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2087, 17, 3189, 3418, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 16078, 4682, 16, 2710, 6483, 12940, 2156, 5572, 9039, 12, 2087, 13, 16, 19562, 16, 2180, 8600, 16, 1930, 20620, 4682, 16, 1988, 7948, 43, 5305, 4346, 3728, 7600, 1927, 43, 10028, 16645, 161, 17, 19560, 22069, 2007, 1925, 160, 17, 7864, 18, 2144, 4682, 5985, 2347, 1922, 3689, 3197, 1930, 11309, 5133, 2007, 10239, 2487, 3719, 1956, 3260, 15619, 16, 29552, 1036, 16, 2014, 4207, 8277, 18, 2176, 1977, 6196, 1942, 18373, 9286, 2072, 2355, 3027, 1989, 13046, 2437, 7969, 11873, 1033, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MCRPVRKEGYLCVKTETDEKISWNLRYFVLARNLTYLQSKENYINKAEKGTPFDLTTYTCFQNRDCLTEVCIRSLGNRCIDLRAETEEEAREWQIQLTGTDNIKCE", "metadata": {"id": "A0A7S3PKS6", "cluster": 16930822, "interpro_all": ["IPR011993", "IPR001849"], "interpro_used": ["IPR001849", "IPR011993"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein should have a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein is grouped in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Moreover, the protein has a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is found in Nitrospira sp. CG24E and has UniProt annotations Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3950, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 2435, 1922, 16665, 10984, 5524, 2056, 18, 7294, 4561, 1021, 1930, 2258, 20709, 15010, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MHDPSAIDWKSTPSREAVISSQPSPSEITVFAPAKINVILRILDRRPDGFHNLWSIMQTVALEDEVQIRLCADRQDIQLRCDAAQLAADQSNLVYRAATVVLAQARQSIGLDIELRKRIPMGAGLGGGSSDAAATIIGLNRLLQLEWSPTQMAEVGQSLGSDVPFFLFAPSAYVAGRGETVQPIVVEGVRWVVLVNPGFGVNTKWAYQELAATRTAVTPLSTVQQELGRQSRVDWAQLVATAENDFEAPVFATHEKLREIKRSLLDHGAEIALLSGSGATVFGLFADEARARLAQAQFMSKNGMKIFVVPTCSGPLVWR", "metadata": {"id": "A0A525WGA9", "cluster": 17097024, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein belongs to the MFS transporter superfamily, which constitutes a ubiquitous group of secondary carriers that transport small solutes across membranes in response to chemiosmotic ion gradients. Characterized by a core structure of twelve transmembrane helices forming a central channel, these proteins function as uniporters, symporters, or antiporters to facilitate the movement of diverse substrates. Also, the protein falls within the Transmembrane secretion effector family, which comprises transport proteins responsible for the secretion of specific substrates. Members of this family include proteins that export the ferric chelator enterobactin and those involved in antibiotic resistance mechanisms. It is found in Streptococcus oralis SK313 and corresponds to UniProt keyword Cell membrane and Transmembrane helix.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 14440, 1942, 1920, 23778, 9054, 13975, 16, 2154, 14879, 43, 15498, 2210, 1927, 4067, 8974, 1988, 4860, 2858, 27993, 3436, 5726, 1922, 2644, 1942, 2975, 14356, 12492, 2002, 4755, 12741, 18, 4378, 2007, 43, 4728, 3170, 1927, 12367, 9117, 12789, 7402, 43, 4101, 4999, 16, 2144, 2697, 2347, 1966, 15943, 2718, 2045, 16, 29148, 2718, 2045, 16, 2014, 2246, 24095, 1036, 1942, 6628, 1920, 5829, 1927, 6445, 6249, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 9117, 5512, 7917, 3416, 16, 2154, 12936, 4860, 2697, 5061, 1958, 1920, 5512, 1927, 2487, 6249, 18, 4678, 1927, 2052, 3416, 3951, 2697, 1988, 12660, 1920, 20247, 28914, 5553, 14357, 2268, 1930, 2690, 3286, 1922, 7267, 3554, 3531, 18, 2176, 1977, 2435, 1922, 15746, 4726, 1937, 3097, 6800, 1010, 1930, 8852, 1942, 20709, 11121, 2538, 2024, 3260, 1930, 9117, 7864, 18, 3], "output": "MKVFIQNRDFRQLTINQWISMVGDTIFYLAFLNYVADTISETVPQVLQIFMGVLADFQHHRVLKYTVISFVKFVLYSIVALSDTLSYFSGAMLTPIFIRIIGKEHLTEAIGFKQLSIQFISLLNALAFLIAFVGILFIKNDLLKVEKTINYQFQSSKLIWNLDRVIFILFIVSISQAVINVTVPISTLFASFAPLAILLILSLSGQPFSLWLVFFICLMNLSTVSLVRTISNILGGVLLGIEGLSIKSFCQHL", "metadata": {"id": "F9Q3N8", "cluster": 18938072, "interpro_all": ["IPR036259", "IPR010290"], "interpro_used": ["IPR036259", "IPR010290"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is classified under the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein should include a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Additionally, the protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It has been characterized in Armatimonadota bacterium and carries UniProt keyword assignments Isoprene biosynthesis and Transferase. The above text is a description of the function of my protein. What amino acid sequence corresponds to this functional description?", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 2258, 2252, 4378, 1922, 6011, 1968, 3947, 12595, 3857, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 26690, 1021, 8132, 1930, 13763, 18, 1920, 3538, 5316, 1977, 43, 8418, 1927, 1920, 2347, 1927, 3057, 2213, 18, 4663, 3835, 2687, 3244, 8852, 1942, 2052, 3183, 8418, 35, 3], "output": "MIRMVAPAKVNLFLAIQCRRADGFHELETVFQAIDLADVIELETSPEGIHMTSDWPGLPAGKGNLCWRAAALLAESAGTSKGVEIRLNKKIPPGAGLGGGSSDAAAVLLGLNRLWELHLSPEELQTRAASLGADVSFFLQGGTALGKGRGEVLSALPTPHLWFVIGWPGVTLSTSAVYQDWDKQPSAGNTKLSEMLSALEATEASGIAAALRNDLEDTTLRLCPACAELKSTLLERGCSGALVSGSGAAVFGIARDKELADEVTAALSRRGLWARSASSLSSSETL", "metadata": {"id": "A0A9E5TD45", "cluster": 24480223, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR013750", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "I want to make a polypeptide chain that will have the following function description: The protein should feature a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein is associated with the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein carries a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It has been detected in Eubacterium sp. CAG:115 and is annotated with UniProt keywords Isoprene biosynthesis and Transferase. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 13022, 4659, 1988, 2832, 2162, 1920, 2894, 2347, 8418, 30, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 16252, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 2258, 2252, 3330, 1922, 4791, 7972, 2341, 18842, 1989, 2056, 18, 13415, 30, 10709, 1930, 1977, 10633, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MRTASGIRIYKLNAYAKLNLYLDITGRRDDGYHLLETVMQSISLADEVTVVVSAGNGITLSVSREDIPTDGRNTAFRAAELFLEKAGASGSVCIDIEKRIPSGAGMGGGSADAAAVLKALNTAFGEPLSESELLGIAAQVGADVPFCLIGGTKLCRGIGEQMSDIPVTEGVFLVVKPEFGCPTGEAYRKYDESPLEIHGGLERFIAGLPRNYAPEMYSVFQKLYSDRRIEDICARLTALGAKGAMLTGSGSAVFGVFDNEANAKRASGEFPGCFTAVSGCVREGVSITEREVL", "metadata": {"id": "R5LLF5", "cluster": 25846666, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR004424", "IPR013750"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein should feature a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein possesses a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It has been detected in Clostridiales bacterium and features UniProt keywords Isoprene biosynthesis and Transferase. Generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1988, 2258, 1920, 2894, 3879, 30, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 2258, 2252, 3330, 1922, 17938, 26890, 1918, 14061, 1930, 4075, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MIKLRTTAPAKINLTLDVLDRRPDGYHNLSTIMHQVPLEDEIEVMIGQGEGIRATTNLPFIRAETNIAAKAARLFIDELGKLVRISEKNTGILIDIRKRIPVGAGLGGGSANAAAVLKLLNEYFGSPFDEKSLVDIGARVGADVPFCLIGGCALCEGIGEIMTPLARIPSCYIVIVKPRASISTAQLFSEYTVAKSQVRPDTAGAVNALKAGDLCGISSRVFNVLEEVAVKKIKGISEIKRVLMRNGALGASMSGSGSAVFGIFDDKGAADSAASFFEKSHSQVFMLRCE", "metadata": {"id": "A0A970JM71", "cluster": 27009635, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein includes a Thioredoxin domain that functions as a ubiquitous protein disulphide oxidoreductase, utilizing a conserved active site with two cysteines to facilitate reversible redox reactions. It mediates electron transfer in NADPH-dependent pathways and serves as a core component of enzymes like protein disulphide isomerases (PDI) and bacterial Dsb proteins, where it catalyzes the formation and rearrangement of disulphide bonds during protein folding. Also, the protein is a member of the Thioredoxin-like superfamily, which encompasses a diverse group of redox-active proteins characterized by a conserved $\\alpha$/$\\beta$/$\\alpha$ structural fold and a CXXC active site motif. These enzymes primarily facilitate electron transfer via thiol-disulfide exchange reactions to maintain cellular redox homeostasis, assist in protein folding through disulfide bond formation or isomerization, and participate in signaling pathways like the glutathione/glutaredoxin system. It is present in Planctomycetaceae bacterium.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 5921, 43, 23684, 3418, 1988, 4088, 1966, 43, 15498, 2213, 2054, 23138, 2261, 27388, 16, 10232, 43, 5305, 3500, 3200, 1956, 2288, 22446, 1942, 6628, 10743, 9366, 5298, 18, 2176, 10412, 4995, 3856, 1922, 11908, 17, 3100, 3873, 1930, 10634, 1966, 43, 4728, 4594, 1927, 5038, 3189, 2213, 2054, 23138, 2261, 25510, 1036, 12, 20506, 13, 1930, 4543, 15136, 2697, 16, 2597, 2176, 17097, 1920, 3337, 1930, 14154, 1927, 2054, 23138, 2261, 9031, 2409, 2213, 10328, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 23684, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 9366, 17, 3500, 2697, 4378, 2007, 43, 5305, 8, 38, 4595, 8, 19, 8, 38, 4666, 8, 19, 8, 38, 4595, 8, 4346, 3728, 1930, 43, 5639, 21487, 3500, 3200, 5219, 18, 2144, 5038, 5985, 6628, 4995, 3856, 3454, 13914, 17, 11830, 6818, 5298, 1942, 6698, 3689, 9366, 7622, 16, 6589, 1922, 2213, 10328, 2596, 11830, 5403, 3337, 2014, 27027, 16, 1930, 7352, 1922, 3197, 3873, 3189, 1920, 9153, 19, 19406, 1919, 9754, 2433, 18, 2176, 1977, 2481, 1922, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 18, 11586, 5655, 3581, 18, 3], "output": "MGTDDGSKWQIAVVALLIGAGIGLNVIDRSVPVVVKFGAEWCGPCRSMDEKPELARHYGVSSIPRTFLRADDLESWLADNAGIHRLRNQSNPTPPDDRWFQAHQELEKLRSRVSGFHLVEINVFVDGQLVSDLRGSR", "metadata": {"id": "A0A954EYT3", "cluster": 27892798, "interpro_all": ["IPR036249", "IPR013766"], "interpro_used": ["IPR013766", "IPR036249"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to make a polypeptide chain that will have the following function description: The protein belongs to the Peptidase M19 family, which comprises zinc-dependent metalloenzymes, such as renal dipeptidase, that hydrolyze a wide range of dipeptides. These homodimeric, GPI-anchored proteins are involved in the metabolism of glutathione and possess a catalytic domain structurally related to the urease fold. In addition, the protein belongs to the Metal-dependent hydrolase superfamily, which comprises a diverse group of hydrolytic enzymes characterized by a (\u03b2/\u03b1)8-barrel (TIM barrel) fold coordinating mono- or binuclear transition metal ions within the active site. These enzymes utilize these metal centers to catalyze the hydrolysis of a broad spectrum of substrates involved in fundamental metabolic processes. It has been characterized in Lachnospiraceae bacterium. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 13022, 4659, 1988, 2832, 2162, 1920, 2894, 2347, 8418, 30, 1920, 2213, 14440, 1942, 1920, 24050, 8510, 1026, 3416, 16, 2154, 12936, 7997, 17, 3100, 8969, 6802, 1022, 16367, 16, 2427, 1966, 4604, 9137, 18877, 16, 1988, 7222, 6931, 43, 4743, 3109, 1927, 9137, 11536, 18, 2144, 21189, 1935, 16, 17497, 17, 17199, 2697, 2032, 3286, 1922, 1920, 4714, 1927, 9153, 1930, 7150, 43, 6804, 3418, 12171, 2712, 1942, 1920, 10505, 4127, 3728, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 6048, 17, 3100, 20748, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 26702, 5038, 4378, 2007, 43, 12, 161, 19, 160, 13, 28, 17, 19560, 12, 2267, 19560, 13, 3728, 19355, 8914, 17, 2014, 8768, 13821, 4832, 6048, 6982, 2651, 1920, 3500, 3200, 18, 2144, 5038, 12561, 2144, 6048, 7365, 1942, 18170, 1920, 9128, 1927, 43, 4949, 5648, 1927, 6249, 3286, 1922, 8829, 4487, 4028, 18, 2176, 2258, 2252, 4378, 1922, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MTAIYPYIDLHCDTLPCAWRQGRSTLLELTDTMTDLRKLRTGRCLAQCFAIFMPSIDRISNSPDYPGDEAYIEALYRIFIQTGQEHSDIFTRVETADDLAALPASGKLGGILTMEDGRAVLGRLENLRRFYDMGVRILALLWNHANCFGAPNSPDPAVMGTGLTDFGKEAVEYMEHLGMGIDVSHLSDGGFWDVVRLTKKPFFATHSNCRALNPHPRSMTDEMIRALADKGGVMGVNFYPAFLYEDLSRPDSTIDGIAAQLRHRINVGGLECAAVGTDFDGIDGDLEIPDASHMPRLFEELARRGFTADELEHIAYRNAERVLKDIL", "metadata": {"id": "A0A939Y8A4", "cluster": 462593, "interpro_all": ["IPR032466", "IPR008257"], "interpro_used": ["IPR008257", "IPR032466"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given the following functional description of a protein, generate a complete amino acid sequence that performs the described role. The desired function is: The protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein is included in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is found in Gammaproteobacteria bacterium RIFCSPHIGHO2_12_FULL_41_20 and has UniProt annotations ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 16, 5655, 43, 4080, 3835, 2687, 3244, 1988, 17436, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2435, 1922, 7034, 9218, 1021, 10296, 14061, 12424, 2792, 24888, 2509, 5265, 41, 2369, 41, 4125, 41, 4353, 41, 2036, 1930, 2258, 20709, 15010, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MFVVGLTGGIGSGKSTVARLFAKHGITIIDADEIARQLTAPDQPALQQIVAHFGNAILLEDGSLNRYKLRRIIFDNTENRSWLEQLLHPLIRKQMQQRIQAATSAYCIAMIPLLLESTPNPLIQRILVVDTPEEYQIQRVQKRDQSPPTEIASIVKTQINREKRLAAADDVITNQGSANDLIPQVEKLHQLYIKLSKV", "metadata": {"id": "A0A1G0HBH7", "cluster": 713466, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein has a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein falls within the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein possesses a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It occurs in Kryptobacter tengchongensis and is described by UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 2258, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 5110, 1922, 6203, 16314, 5883, 5656, 5813, 10647, 2029, 8134, 1930, 1977, 2910, 2007, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MDRIKLFSPAKINIGLRVLRKRVDGYHDIEFESDSDEIPRGFENLCLKAVRIFFESPVGAGLGGGSSNSATVLKGLNILFNVGADDDHLCGRGEIIEPIDVKVPYKIVIVYPGVKISTAWAVENVKNPAALRELIGNDFEELVFSHYPVVIDEDKLKSTFSGDLMWYLVTIFHEVKLFDEIEMEIYDEIEFGIHSGVRIYLKKRIEIGSLIGSDVPFFIKGGTAYATYENLKLKGHEGEESLKKIFEDVKRKLYKLGSVFSLMSGSGSAVFGFFEE", "metadata": {"id": "A0A916LJW0", "cluster": 798123, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR004424", "IPR013750"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein is assigned to the Ankyrin repeat-containing domain superfamily, which functions as a versatile protein-protein interaction module defined by tandem repeats of a \u03b22-\u03b12 structural motif. Predominantly found in eukaryotes, these domains mediate molecular recognition in diverse biological processes, including transcriptional regulation, cell-cycle control, cytoskeletal organization, and signal transduction. Moreover, the protein carries a Ankyrin repeat that mediates protein-protein interactions through tandemly repeated helix-loop-helix modules which stack to form an L-shaped structure. This versatile motif is found in diverse eukaryotic proteins, including transcriptional initiators, cell-cycle regulators, cytoskeletal components, and signal transducers. It occurs in Spongospora subterranea and corresponds to UniProt keyword ANK repeat.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 28336, 6865, 17, 3165, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 2213, 17, 2213, 2835, 9059, 3608, 2007, 10361, 9569, 1927, 43, 11157, 17, 13213, 4346, 5219, 18, 7700, 2435, 1922, 15021, 16, 2144, 4682, 8265, 3272, 5708, 1922, 6445, 3933, 4028, 16, 2710, 5224, 3640, 16, 2024, 17, 4048, 2285, 16, 14787, 5901, 16, 1930, 2733, 8201, 18, 3950, 16, 1920, 2213, 16252, 43, 28336, 6865, 1988, 10412, 2213, 17, 2213, 3719, 2596, 10361, 1954, 5116, 7864, 17, 5881, 17, 7864, 10803, 2154, 10496, 1942, 2386, 1925, 54, 17, 9132, 3170, 18, 2052, 20425, 5219, 1977, 2435, 1922, 6445, 10825, 2697, 16, 2710, 5224, 23467, 1036, 16, 2024, 17, 4048, 9098, 16, 14787, 4178, 16, 1930, 2733, 26307, 18, 2176, 5110, 1922, 19513, 9890, 1019, 13329, 5385, 2516, 1019, 1930, 8852, 1942, 20709, 11121, 2538, 9808, 6865, 18, 3], "output": "RSTALHLAVRSPREHVAMFLLEKGANPAIRDESGNTALHAAVLNLRINIVRKILHINSAAKGWSQTIINFLGRNPIDLQNHEGHTALHLALRSQSFFVISAGMILLENGANPALVDRLGMTALHAAAANGLVNTVIKILDINPNLINL", "metadata": {"id": "A0A0H5QTI5", "cluster": 1227254, "interpro_all": ["IPR002110", "IPR036770"], "interpro_used": ["IPR036770", "IPR002110"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that has the following function: The protein features a Adenylate cyclase, N-terminal domain that comprises the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase. Furthermore, the protein should have a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Furthermore, the protein contains a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It is produced by Cacopsylla melanoneura and is connected to UniProt keyword Lyase, Magnesium, and ATP-binding. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 23052, 16526, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 56, 17, 4262, 5329, 3031, 1930, 1920, 2561, 9117, 25, 17, 26, 4675, 3031, 1927, 23052, 16526, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 3677, 16, 1920, 2213, 5461, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 1977, 4152, 2007, 19107, 9196, 11560, 1019, 5313, 2290, 9280, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 23928, 16, 13148, 16, 1930, 4498, 17, 2743, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MEAGTSDQIFPKSFKDAVLERLFQTYSVKQKRSAIECYLLASVLFNLQNLVLIVDVNSVHFVHSLVFLTVNIFIFLWCRFSSKPFWSVIPHVTWGLSLLQVLVHMGLQVYPHTSRDYLGWILLISFFIYATLPVELQMCRLLSIVSCIVYILVILLIHHLTDSSTSSQPFLFRQICTNVILLVSANILGQMCFTMSEKEQRTAFLETRQCLEMRLVIEEQSAEQERLLLSVLPEHVAVKMRQDLGESFDSQFKKIYMSRHENVSILYADIVGFTAISSTYSASELVKILNELFARFDRLSEKYNQLRIKILGDCYYCISGAPEERPDHAILSVHMGLSMVKAIKYVQQTTNSPVDMRVGIHTGAVLAGVLGQRQWQFDVYSKDVELANKMESSGLPGRVHISEKTLCYIDGNFEVEPAFGENREETLRQAGLKTYFIVNTIIPFKDESGGRYDVENYQDFKDDEIVAENNIEKTRAREDSEDFKMRLKKDVMERDLSKYTGIFSKRKLSINCKGYNQHKDSVSNSKMALASGPIILFFITIAKMFVLPWNPRALITIILNVLIFIVVLAVAIVPSLPQSLTGALEGRILGLNDSLILRQCMGAFVSLLIFLVNIIYMLLCEDSSSLIPISSNITSPIPHNCSLSEISSTPLCVFPSYYSMFCILILITVILHGQNTFPQKCVLLSIMLAVQIGSNVLFVQESMYCERYFSSIYEGGNPQFGMLGPSTLLLFVSLSLTFLAFYMEKASKVLFVWKKEVESQKETASDIRRRNEALVYNILPPHVAAHFLGNRKRQHEELYSQSYAEVGVLFASMPNFSEFYCEDDVNKQGLECLRFLNEVISDFDALLEVPKFKEVIKIKTIGSTYMAASGLDPNFVTLIKPTDPIEVRWKHLDVLIEFAIELKKALTGINENSFNHFVLKMGVNHGPITAGVIGARKPHYDIWGNTVNVASRMESTGRAGFIQVTEETMLILQHFGYMFEQRGLVSVKGKGQLMTYYLLGKNTSGTHHPYESTIMEPLKEVDEEHEKAEEINETNLTLELDETNETEELLKKEDVQNGVIVPSSNE", "metadata": {"id": "A0A8D8ULE8", "cluster": 2875197, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR029787"], "interpro_used": ["IPR032628", "IPR018297", "IPR001054"], "interpro_unused": ["IPR030672", "IPR029787"]}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein falls within the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. In addition, the protein features a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. Also, the protein should have a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. It has been characterized in Bacillus cereus VD048 and corresponds to UniProt keyword Hydrolase and Metal-binding.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 12182, 2651, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 2176, 2258, 2252, 4378, 1922, 14587, 29533, 13411, 14743, 1025, 1930, 8852, 1942, 20709, 11121, 2538, 20748, 1930, 6048, 17, 2743, 18, 3], "output": "MTIMEGMCMMITHEQIMNALSHVEDPELHKSIVELNMVRNIKIDGTEVGLEDIEDSLRNIGASKVSLTFGSMTPEERAALTASLKKEARTETGMPSMLRPDSGVRFITVTSGKGGVGKGILDADIYGFSIPAMMETNEKPTMIDQTAIPVVSHGVKIMSMGFFTEGNNPVMWRGPDYLLLDLPPGTGDVAIDVAAMIPQAKEIIVTTPHNVASFVASRVGVMAKLFGKGGGEMLAEQLQTEVIAQIPFAKREENNGSCVYDEDSLVGEMFTSLAEDLIYNGVVLTIQGCPLKAKIQQSTVTINLATALASMGKKVMLNKWIQNFLANTHWGELHTKHDILGIVENMAYYEEQDGSRNY", "metadata": {"id": "J8HC22", "cluster": 4353702, "interpro_all": ["IPR034904", "IPR002744", "IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR033756", "IPR000808", "IPR002744"], "interpro_unused": ["IPR027417", "IPR019591", "IPR034904", "IPR044304"]}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein contains a Rhs repeat-associated core domain that forms a conserved structural element often found in large proteins containing FG-GAP or Rhs repeats, such as secreted bacterial insecticidal toxins and eukaryotic teneurins. It is also present in the N-terminal region of shorter, uncharacterized proteins across bacteria and eukaryotes. In addition, the protein is categorized in the Type VI secretion system VgrG/RHS family, which comprises components of the bacterial type VI secretion (T6SS) and contact-dependent growth inhibition (CDI) systems essential for interbacterial competition and virulence. These proteins often function as structural spikes at the secretion tip to deliver effectors or exhibit intrinsic enzymatic activities, such as actin cross-linking, ADP-ribosylation, and nuclease functions, that disrupt target cell processes. They typically feature a conserved N-terminal region for secretion and a variable C-terminal domain harboring toxic activity. It is found in Bacteroidetes bacterium CG2_30_33_31.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 5461, 43, 3617, 1036, 6865, 17, 2458, 4728, 3418, 1988, 4952, 43, 5305, 4346, 6149, 3868, 2435, 1922, 3103, 2697, 3165, 13320, 17, 5750, 2014, 3617, 1036, 9569, 16, 2427, 1966, 8366, 4543, 15350, 7161, 13599, 1930, 10825, 5656, 3708, 5572, 1036, 18, 2176, 1977, 2222, 2481, 1922, 1920, 56, 17, 4262, 3031, 1927, 7310, 16, 24528, 2697, 3436, 4802, 1930, 15021, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 2601, 3070, 5512, 2433, 19458, 1005, 1029, 19, 3617, 1036, 3416, 16, 2154, 12936, 4178, 1927, 1920, 4543, 2601, 3070, 5512, 12, 20762, 5590, 13, 1930, 5217, 17, 3100, 2905, 3523, 12, 19238, 13, 3771, 4415, 1958, 2107, 7972, 2341, 18339, 1024, 9682, 1930, 9304, 18, 2144, 2697, 3868, 2347, 1966, 4346, 14533, 2019, 1920, 5512, 7933, 1942, 3971, 13066, 2014, 5987, 7598, 8145, 4209, 16, 2427, 1966, 4718, 3567, 17, 9486, 16, 9828, 17, 29117, 3017, 16, 1930, 16230, 4088, 16, 1988, 12512, 2758, 2024, 4028, 18, 2611, 5745, 5961, 43, 5305, 56, 17, 4262, 3031, 1958, 5512, 1930, 43, 4650, 45, 17, 4262, 3418, 12827, 6161, 2455, 18, 2176, 1977, 2435, 1922, 26808, 14061, 7294, 1028, 41, 2627, 41, 3401, 41, 3470, 18, 3], "output": "MVDIDVNVATINADVETIALDLVALLEYRVEELRYTSINNFESDMYFYNTDLPIAIGMGSSSWITDASGAVNQHLNIPYTFSGKEKDAETGYSYFGARYYAYVANNPIIYYDPDGRIIGIVVTSMANKPGASKQGHMMKEYEKIVKNGNVIWPESYSSPNYVYYSHSEKSLDELLNAGKDRGNGYDRITSLNNVNADQEAEYEFATNNCASFSINSINHFFGNIINDKTAMDRPNHEFNPMQVIDIKAENKLLLGSEGYENRSNTCAQIEWGNVTLPEPILQYLPFGEDYICQRNSSWYDSDISIWLSVDPLSSIYPTLSPAIIVGNDDIGYHLFSLEDPTGHAKDYYMSLNAPGTANFLKFMQSQTGDDFINKITKDTHNWSVIQDGKN", "metadata": {"id": "A0A1J5AQI5", "cluster": 4702664, "interpro_all": ["IPR022385", "IPR050708"], "interpro_used": ["IPR022385", "IPR050708"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: It is part of the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. It has been detected in Parvularcula sp and is connected to UniProt keyword Coiled coil, Transmembrane, and Membrane.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 2176, 1977, 3131, 1927, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2176, 2258, 2252, 3330, 1922, 19995, 2168, 18021, 5148, 2056, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 17524, 9121, 16, 9117, 16, 1930, 3260, 18, 3], "output": "MAVLLTALGAVADILSLEGRVPQFGFALAAGAMLVFGAMILFRWRGAVSAAQSATDTRETGLIRGALLDDPYAKNLPTPCSRNKICIVVAPLADDDATATIEYPQTEHVIASLSALIRLAPIRIGGELMGDRARNNQEAILRARAWLESQQADVLIHGRVVRADEILELRLIGSLPSDFTVDFGSVLAAEIARTVDQFLTSERYAVDVIEPIVARLAPLAEDLPDALPANVKGQELDKAVAFYRRGLSQTSLEDWPYQWGNGHNNLGVALASLGDRRADSQLLEEAAAAFENQGDTYRMLGDLKRDTGLLRRAEASLKNAMIVFTREDEPAGWAMSQTNLGLVYRSLARQRETEPLSWAVIQNNLAEALLTQGELTGDKTVLTQALAAIDAALEEVSQTQFRQQWTSAQNKLEEAARVHERLLTALNRTEAPLEWARIQNNLGNDLRIIAATESGTDKLRRAIAQSQSNLGAALSLLSRRESDPALREEALAAYQAALEVATRTTAPMQWARTQFNLASTREAIRLYREVLEVARKETEPVIWAAVQRSLGSALREVAIRERDLTLYEASLAAIEASLEIRTRERFPELWLTGDVDRISGGVEAYRHFITGQSKDDDPLDWAQHHYLIGIFSLKVAAATDETAAWRYVEEAFRQAERSLDEERYREAASIAESVSLDAIRLIAPDQSDPRELEDQVAEFGNQACWYRAKAIEISGAARDFRWLQSSHSLAYLWMVTGEVRDDREMLQRSSEAFKALLADSSTAAFPEIQQEIERDAARAAAMLNNFSVCAVPFVVSIAAAGVLGFESFGDMQSPVEGGANRTRYNLTEKIYAVLISYADALSVIGEQGVRNSAAAGYLKDSSPFGWALARNESKSENLAAAIAAYRNALEKTANHGNILLTLGELDGDPSAAFKAALEERTRERTPLDWLKSQVGDNEPNLEDVTSTQLSLASTLFGLGEARSDALRRHAPQEWLMATYYLANAAGIVDLAEADCRRAIDLWKSDKSTG", "metadata": {"id": "A0A2E1XAB1", "cluster": 9526934, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Furthermore, the protein is classified under the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. In addition, the protein falls within the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It has been characterized in Candidatus Falkowbacteria bacterium CG10_big_fil_rev_8_21_14_0_10_39_11 and is linked to UniProt keywords Cytoplasm and rRNA processing.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 2258, 2252, 4378, 1922, 14550, 1031, 1957, 29236, 8323, 1018, 7972, 2341, 18339, 14061, 7294, 2930, 41, 9769, 41, 3313, 41, 5197, 41, 28, 41, 2900, 41, 2607, 41, 20, 41, 2119, 41, 3886, 41, 2513, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 1930, 9067, 4587, 18, 11586, 5655, 3581, 18, 3], "output": "MKKLGNIIMRLHKKTQITSPKNEVLESLNPDANQDFIDGTLGGGGHALLGLDWDKDAVERVQVRLKKYDNNVVLINDSSFDGILLDLGLSLDQLKASGRGFTFQQDEPLDTSLETLFREYGEEGQAGAIAKAIVTKRKTNPATKVFQALRIAVNQEFDNIQSVITDFKMESTSCICPKELPQCVCLHKARVKLVNRSAKLRVVEKLDVMKLQNVTNNYKKNSASWEFKFMTVHDSVLLEEILKRILPNGRSYIRIKKHVYENGFMRYSVDNELTAAEIVNSYSQEETIDRTVQLVDLIKEVKGMNPWTRAIELLNPGGRLAIITFHSLEDRIVKEYRKPITPSDKELQDNRRS", "metadata": {"id": "A0A2H0V7R4", "cluster": 10517729, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein should feature a Glycosyl transferase, family 1 domain that catalyzes the transfer of sugar moieties from activated UDP-, ADP-, GDP-, or CMP-linked donors to specific acceptor molecules, forming glycosidic bonds. This enzymatic activity is essential for diverse biosynthetic processes, including the synthesis of glycogen, bacterial lipopolysaccharides, and human GPI anchors. It is identified in Synergistaceae bacterium. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 1925, 3835, 2687, 3244, 1988, 2469, 16318, 2460, 43, 2213, 22665, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 20067, 13763, 16, 3416, 21, 3418, 1988, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 18500, 17, 16, 9828, 17, 16, 15217, 17, 16, 2014, 28738, 17, 4624, 8276, 1942, 2487, 12641, 4206, 16, 7402, 7533, 12546, 9031, 18, 2052, 8145, 2455, 1977, 4415, 1958, 6445, 14041, 4028, 16, 2710, 1920, 4271, 1927, 13302, 16, 4543, 15614, 1036, 16, 1930, 2616, 17497, 27127, 18, 2176, 1977, 2899, 1922, 8722, 25879, 1972, 3336, 14061, 18, 7031, 1920, 3244, 18, 3], "output": "MYWERFFKKSAANPIRYAKMLMKHTIYRNKNVYLLCAGAYAAKDAAIIGAYPGKTYKWGYFTDTKRPDFEELYGKKEKETVTLLWSGRFLYFKHPEKAILLLKKLLENGYDCRLKMIGNGPMFRKINNLANKLHLTEKNHFFGNAFSFAS", "metadata": {"id": "A0A971VI36", "cluster": 11811576, "interpro_all": ["IPR001296"], "interpro_used": ["IPR001296"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein is grouped in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Furthermore, the protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is produced by Wenzhouxiangella sediminis and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 4152, 2007, 2038, 1022, 19902, 18068, 5285, 11560, 1019, 6276, 1980, 15472, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MLVALTGGVASGKTSVSDRLSSPGLNRVVEAFGPEILDSSGALDRRALRERVFARPEARADYVVLVVPLLVESGLFKDADRVVVVDVPESVQIERLVERDNVDRSQADVLDNSGSIEELMEATDELYEKLTRLSRRPPRAPRMPARGVPVVDTDLIARQVVAPGERLEAILHPLIEKEARRQVALHREESMLAAQATRPNRLAAAT", "metadata": {"id": "A0A3E1KBB6", "cluster": 11921586, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein belongs to the ATP synthase subunit ATP5MJ family, which comprises hydrophobic mitochondrial proteins that function as regulators of mitochondrial ATP synthesis. It is derived from Catagonus wagneri (Chacoan peccary) and is classified with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 4498, 8921, 5903, 4498, 1015, 1035, 1013, 3416, 16, 2154, 12936, 7919, 4596, 2697, 1988, 2347, 1966, 9098, 1927, 4596, 4498, 4271, 18, 2176, 1977, 3595, 2037, 3115, 5164, 1957, 27592, 1033, 12, 13297, 4879, 1928, 13494, 15339, 1012, 13, 1930, 1977, 5947, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MLQSLIKKIWIPRKPCYRCTGKRRKALKVLNPESAHGHHIQVYQAIWGGMGLTVFIIYKI", "metadata": {"id": "A0A8C3WZD0", "cluster": 13268182, "interpro_all": ["IPR012574"], "interpro_used": ["IPR012574"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein is classified under the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. In addition, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Also, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It has been detected in Coprococcus sp. OM04-5BH and corresponds to UniProt keyword Cytoplasm and rRNA processing. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 5947, 2441, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 2258, 2252, 3330, 1922, 3725, 4104, 15648, 1957, 2056, 18, 7254, 14743, 17, 7807, 1023, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MEFVHKSVLLNETIENLNIKPDGIYVDGTLGGAGHSYEICKRLSDRGRLIGIDQDKDAIAAATERLKPFSDRVTIVRNNYCNFKSILDELNISAVDGMLLDLGVSSYQLDNVDRGFTYRADAPLDMRMDDRQDKTAKDIVNGYSERELFRIIHEFGEDKYAKSIAYHICRYRENKTIETTEELNDIIRGSIPAKARNGKGHPSKQTFQAIRIELNKELEVLTNSIDDMIKSLKPGGRLCIITFHSLEDRIVKNAFRKNENPCICPPNFPVCTCGRVSLGHVVTRKPIVPGEEELEENSRAKSSKLRVFERV", "metadata": {"id": "A0A417T184", "cluster": 14076849, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein is associated with the Short-chain dehydrogenase/reductase (SDR) family, which comprises a large and diverse group of NAD- or NADP-dependent oxidoreductases. These enzymes typically possess a conserved coenzyme-binding domain and a variable substrate-binding domain that determines catalytic specificity. Furthermore, the protein is assigned to the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. Moreover, the protein is assigned to the Short-chain dehydrogenases/reductases family, which catalyzes NAD(P)(H)-dependent oxidoreduction of diverse substrates, including fatty acids, steroids, and aromatic compounds. These enzymes play critical roles in metabolic processes such as fatty acid elongation, bile acid metabolism, and polyhydroxybutyrate biosynthesis, typically utilizing a conserved Rossmann fold for cofactor binding. It occurs in Betaproteobacteria bacterium.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 3662, 17, 4659, 9294, 19, 11386, 12, 4035, 1005, 13, 3416, 16, 2154, 12936, 43, 3103, 1930, 6445, 2210, 1927, 6577, 17, 2014, 24221, 17, 3100, 27388, 1036, 18, 2144, 5038, 5745, 7150, 43, 5305, 22051, 17, 2743, 3418, 1930, 43, 4650, 4510, 17, 2743, 3418, 1988, 13554, 6804, 4896, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 3662, 17, 4659, 9294, 1036, 19, 11386, 1036, 3416, 16, 2154, 17097, 6577, 12, 58, 13, 12, 50, 13, 17, 3100, 24056, 2681, 1927, 6445, 6249, 16, 2710, 5934, 4576, 16, 13039, 16, 1930, 10761, 4300, 18, 2144, 5038, 3918, 4140, 5456, 1922, 4487, 4028, 2427, 1966, 5934, 2687, 9971, 16, 9619, 2687, 4714, 16, 1930, 4286, 8535, 10465, 16119, 16128, 8132, 16, 5745, 10232, 43, 5305, 18215, 8890, 3728, 1958, 15155, 2743, 18, 2176, 5110, 1922, 4666, 9218, 1021, 10296, 14061, 18, 3], "output": "MDLHLKGKNVLLVGASLGVGLEAAVMFAGEGANLMLASRSEERLRRAVAWVTTESGNRNVHFVVGDIRERDSHARMVNAAVEKLGTIDVLVNNAGAAMSNPNPEMTDELWTEALNYKLLGYIRTTMAAFPVMRKNGGGVIINVIGGTGREPYSWTSSTGVVNAALLNFTKTTATQYAAAGVRVNAINPRQIDTKRLSDFRTLEPTGYAATIAEIPMGRVGRPEEVASLIVFLASDRASFVTGTAIDVDGGATRSVSF", "metadata": {"id": "A0A9D6SQD3", "cluster": 15040162, "interpro_all": ["IPR036291", "IPR050259", "IPR002347"], "interpro_used": ["IPR002347", "IPR036291", "IPR050259"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein should contain a Transposase DDE domain that catalyzes efficient DNA transposition by coordinating metal ions via a conserved triad of carboxylate residues. This domain facilitates the enzymatic cleavage of DNA at specific sites followed by a strand transfer reaction. Moreover, the protein has a Transposase InsH, N-terminal domain that constitutes the N-terminal region of the InsH transposase associated with the insertion sequence element IS5A. Found in *Escherichia coli* and related bacteria and archaea, it contributes to the transposition of these mobile genetic elements. It has been detected in Pseudonocardia endophytica.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 3066, 5531, 43, 12935, 2051, 6758, 1021, 3418, 1988, 17097, 5807, 2678, 22596, 2007, 19355, 6048, 6982, 3454, 43, 5305, 21845, 1927, 20877, 4248, 18, 2052, 3418, 11374, 1920, 8145, 6404, 1927, 2678, 2019, 2487, 3402, 3489, 2007, 43, 5984, 3856, 3227, 18, 3950, 16, 1920, 2213, 2258, 43, 12935, 2051, 2346, 1023, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 3031, 1927, 1920, 2346, 1023, 12935, 2051, 2458, 1956, 1920, 7413, 3244, 6149, 1977, 9422, 18, 2435, 1922, 14, 10210, 5178, 14, 1930, 2712, 4802, 1930, 21501, 16, 2176, 7624, 1942, 1920, 22596, 1927, 2144, 8785, 3299, 5362, 18, 2176, 2258, 2252, 3330, 1922, 11520, 11873, 15339, 7408, 1019, 19771, 4274, 1019, 18, 3], "output": "MGLNYVTGDREQRFLLAPDMRDWLAPEHLCWFPAVMVAVLLYAYCTGVRSSRQIQRRCLEQIDYRILAAGAVFVDSLRLCAEAGLVSLGAIAVDGTKELGKQISAILAEAAEIDAAEDAASDQDHQSESGPAVDPAARTRLEVVAADRAARFEARSAQLNAARAAKGLTDPDSRPMQSRHGRVQGFNAQTVTTAGQIGITEPIDALVADAGYWRAENVNASHPDLARPDGPTLYIGKPSEATTTALVEQMTARLKTDTGKKMMGIRQLSRRGLVAARAEWKLIAATHNLLKLYRATAIVIDVVEALDLDAFHRSYRADGHGRAAYDLAPDHVTLARFRARHADALAIAANASIDRNRTSEALRRAALDAARQRLEQPPRQFRPRARDEAPKPGTTTNIVAAEVSTDSNDVAQLAPMLSATRAGLTAAAVARHGRRGKPRQDRMRSTSVEPVFGQIKHGR", "metadata": {"id": "A0A4R1HKD9", "cluster": 15293426, "interpro_all": ["IPR025668", "IPR008490"], "interpro_used": ["IPR025668", "IPR008490"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein sequence for a protein with the following function: The protein is a member of the Winged helix-like DNA-binding domain superfamily, which encompasses diverse DNA-binding proteins including transcriptional regulators, helicases, and endonucleases that utilize a winged helix-turn-helix motif for sequence-specific recognition. This domain engages the DNA major groove via a recognition helix while loop structures known as wings contact the minor groove or backbone, often serving as a scaffold for protein-protein interactions. Also, the protein should contain a S-layer protein, outer domain domain that forms the exterior structural component of the archaeal surface layer (S-layer), contributing to the assembly of a protective paracrystalline envelope. This region typically surrounds an inserted central domain and aids in maintaining cell integrity and shape in organisms such as *Pyrococcus* and *Methanocaldococcus*. Furthermore, the protein possesses a ArsR-like helix-turn-helix domain that acts as the DNA-binding component of prokaryotic, metal-regulated homodimeric repressors. Characterized by a winged helix topology, this domain typically regulates gene expression by dissociating from DNA upon binding specific metal ions. It is native to Candidatus Nanohalarchaeota archaeon.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1958, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 12920, 1919, 7864, 17, 3189, 2678, 17, 2743, 3418, 13975, 16, 2154, 21569, 6445, 2678, 17, 2743, 2697, 2710, 5224, 9098, 16, 29919, 16, 1930, 18697, 1036, 1988, 12561, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 1958, 3244, 17, 2487, 5708, 18, 2052, 3418, 11580, 1036, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 2679, 5881, 4061, 3171, 1966, 28297, 5217, 1920, 5857, 15920, 2014, 10787, 16, 3868, 13915, 1966, 43, 7281, 1958, 2213, 17, 2213, 3719, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 61, 17, 4757, 2213, 16, 7642, 3418, 3418, 1988, 4952, 1920, 2897, 18842, 1924, 4346, 4594, 1927, 1920, 22367, 3154, 4757, 12, 61, 17, 4757, 13, 16, 8739, 1942, 1920, 5957, 1927, 43, 6337, 13344, 6907, 2156, 2214, 2053, 11262, 18, 2052, 3031, 5745, 13097, 1036, 1925, 9103, 4101, 3418, 1930, 8494, 1922, 8231, 2024, 7996, 1930, 5989, 1922, 7373, 2427, 1966, 14, 18446, 4879, 2437, 1957, 14, 1930, 14, 17348, 5000, 22389, 4879, 2437, 1957, 14, 18, 3677, 16, 1920, 2213, 14465, 43, 9896, 1005, 17, 3189, 7864, 17, 5165, 17, 7864, 3418, 1988, 8016, 1966, 1920, 2678, 17, 2743, 4594, 1927, 21545, 16, 6048, 17, 4335, 21189, 1935, 26446, 18, 4378, 2007, 43, 12920, 1919, 7864, 13678, 16, 2052, 3418, 5745, 7014, 2359, 2294, 2007, 7296, 2287, 2037, 2678, 4073, 2743, 2487, 6048, 6982, 18, 2176, 1977, 6196, 1942, 14550, 1031, 1957, 9788, 7289, 3983, 3336, 7336, 13470, 1916, 18, 3], "output": "MLYLKYCMKLNNLCLLKKNEADRTPFLLKELDSKNTKILSANAINILEILSEKEMYPKEIARVLGMNEQKVYYYVNNLKKAGLVDVVGEKTYGGLTARYFSATSDGAFVLWKKKDAEKTKTEGKENPLSVFSKNSFSNTIFVLGAPMHHGKQMAKAEDEKLAILIALFAGSFSKSCSVSLSNVKYDIDMTENDLKKNLIIIGGPAINKTTALINRHLAVKFLKKDDFYYALYSAISRKKYSDENCGFIEKIINPFNKYSAILVLGGRRSTGTEAAVFFLINKFKSFEAGNQYNKNIFSKIVKGFDEDNDGIVDKAEELE", "metadata": {"id": "A0A662QVB2", "cluster": 17194807, "interpro_all": ["IPR011991", "IPR022651", "IPR036388", "IPR036390"], "interpro_used": ["IPR036388", "IPR022651", "IPR011991"], "interpro_unused": ["IPR036390"]}, "task_type": "autoregressive"} {"instruction": "The protein is assigned to the Transmembrane protein 255 family, which comprises eukaryotic proteins of unknown function that are typically between 241 and 349 amino acids in length. It is expressed in Hemibagrus wyckioides and is linked to UniProt keywords Transmembrane helix.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 6304, 1942, 1920, 9117, 2213, 19915, 3416, 16, 2154, 12936, 10825, 2697, 1927, 5435, 2347, 1988, 2032, 5745, 2192, 21616, 1930, 26925, 3835, 4576, 1922, 3471, 18, 2176, 1977, 3198, 1922, 28881, 7972, 2299, 1957, 24622, 12940, 3940, 3726, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 7864, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MQQPSVSEPDPSEQYSKRRCTARTGNVAVAGYYSGIILSFGTFLGIVGLNVVENCAIVDGIVAAEYIDRRPLMEGRCEFYASSSGYAYDNKSNTCYCCDLYSCESPGYHAHYFEFTGVSWSDVVLNVLGVFLGIITAAILGAFKDLVPAVPSQMSPRPAAPAYPNYPVPLQHLNSYPAASPSQPSPEVPVSPSEESQPQMLTPNAPSLYPHSLGPFEKPPPYACMWCTVALHALSIIILLIGLMAATRRPMLVASIIFISLGVISCFFYYTEVMCQNYNQDCKLKVSCWDVVHLYRLLPHILYNPTQHVVTYAGFCPSGQALPPSNSNPAVPSQSSCPDTSGY", "metadata": {"id": "A0A9D3N354", "cluster": 19254145, "interpro_all": ["IPR028014"], "interpro_used": ["IPR028014"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is included in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Moreover, the protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is derived from Nodularia spumigena CENA596 and is associated with UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3595, 2037, 21106, 2126, 2056, 28851, 2432, 1019, 14585, 28059, 10352, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MNKRIIGLTGGIATGKTTVANYLASAYNLPYGEQILLPDGSLNREKLGTIIFAQPDERHWIESLTLLLVIPLLFEAQMTDLVTEIWVVRCSELQQLQRLIQAARANIVLDNSSTLESLLKEIDVAFAMNIQDNISVFDADIYARDAVAVGSPILNAIAQRIHPYVVERFEQAIIAKSSSPRNHLTPIQAQARINSQLSLSEK", "metadata": {"id": "A0A166KYM4", "cluster": 21193531, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We aim to build a protein that does the following:\nThe protein is classified under the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. In addition, the protein falls within the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It is derived from uncultured Gammaproteobacteria bacterium and features UniProt keywords Phospholipid metabolism, Transferase, and Transmembrane helix.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 1977, 5947, 2441, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 1977, 3595, 2037, 5269, 21058, 7034, 9218, 1021, 10296, 14061, 1930, 4075, 20709, 11569, 14608, 4714, 16, 13763, 16, 1930, 9117, 7864, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MKNEATGLKRISNAFGFSMQGLKICYQSEAAFRQELWFGVVLISNSAIESVVDRIGDEYHALSGVAKDMGSAAVWLSLVLVLITWIIILILAFWLKESAIERVLLIAPVFLVLIVEVL", "metadata": {"id": "A0A5E5PJJ4", "cluster": 21653462, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR033718", "IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "I am designing a protein that has the following properties: The protein falls within the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. In addition, the protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is found in Microtus ochrogaster (Prairie vole) and is connected to UniProt keyword Transmembrane helix, Transferase, and ATP-binding. Generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1988, 2258, 1920, 2894, 3879, 30, 1920, 2213, 12182, 2651, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2435, 1922, 7666, 1957, 18129, 6405, 7092, 12, 21227, 23576, 1021, 2984, 1021, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9117, 7864, 16, 13763, 16, 1930, 4498, 17, 2743, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MTVDTEGEHVSKSSARPRPPPPALAADAWPSFPVPPIPLAGRPIGVHARASLLFAASRAVSAAEVGLAAEAEAESEPRYPPAKPAVRTACALAEEESQAVVAHQPCGPVLTRPECLLTTGFSSLVEQLIGKCADCPVLSGSFSACLLSPGKMFLVGLTGGIASGKSSVIQVFQQLGCAVIDVDVIARHVVQPGYPAHRRIVEAFGTEVLLENGDIDRKVLGDLIFNQPDRRQLLNSITHPEIRKEMMKETFKYFLRGYRYVILDIPLLFETKKLLKYMKHTVVVYCDRDTQLARLMKRNSLSREDAEARINAQLPLKDKARMANHVLDNSGEWSLTRRQVILLHAKLERSMEYLPLRLGFLTGLAGIASLLYLLTRYLLPSP", "metadata": {"id": "A0A8J6GKN7", "cluster": 22622615, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein is classified under the Immunoglobulin-like fold superfamily, which comprises domains characterized by a beta-sandwich of seven or more strands arranged in a Greek-key topology, facilitating protein-protein interactions often via beta-sheet interfaces. These domains are ubiquitous in animal proteins, playing critical roles in immune recognition, cell adhesion, and structural integrity in muscle proteins such as titin. It originates from Dehalococcoidia bacterium and is described by UniProt keywords Signal.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 11837, 17, 3189, 3728, 13975, 16, 2154, 12936, 4682, 4378, 2007, 43, 4666, 17, 18038, 1927, 5260, 2014, 2253, 13214, 14940, 1922, 43, 27568, 17, 3834, 13678, 16, 12440, 2213, 17, 2213, 3719, 3868, 3454, 4666, 17, 11130, 14857, 18, 2144, 4682, 2032, 15498, 1922, 4027, 2697, 16, 14797, 4140, 5456, 1922, 3743, 5708, 16, 2024, 6141, 16, 1930, 4346, 7996, 1922, 3760, 2697, 2427, 1966, 7090, 1921, 18, 2176, 22970, 2037, 2028, 7289, 26941, 2642, 2126, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 2733, 18, 3], "output": "MSKMMNTCYRILAILSIIAISASCTAAPPATNPASTVSNANLKLKVIDIVGIHEWTPLQENTLNCALEGQASSSNALKYSWSAEQGTISGDGKEVKWAAPETPGDYKITVQVSDASGDNAIFSKSFKVTTNP", "metadata": {"id": "A0A3N5Z038", "cluster": 22820276, "interpro_all": ["IPR013783"], "interpro_used": ["IPR013783"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence for a protein with the following function: The protein should contain a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Additionally, it is part of the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. In addition, the protein can be placed in the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. It has been characterized in Pseudovirgaria hyperparasitica and is classified with UniProt keywords Magnesium, Manganese, and ATP-binding.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1958, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 2176, 2258, 2252, 4378, 1922, 11520, 3026, 13279, 2126, 28239, 13130, 21788, 1930, 1977, 5947, 1956, 20709, 11569, 13148, 16, 19516, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MAAPEIRQWGQNPPISTALPTEQENQLNAALIDELKRENNFERPEETEKRVEILNTFQKVTEEFVKLVGRNKGLAQSAIDNAGGKVFTYGSYRLGVYGPGSDIDTLIVAPKHCTRDDFFQLFPELLAKMSRADAIDEMTPVPDAHVPVISLEYCGISIDLIFAPLAISSVPMSLDLKDKNLLKGLSDTDLRSVNGSRVTDEILTLVPQVKTFRHALRAVKLWAQRRAVYANVMGFPGGVAWAMMVARVCQLYPMAPGSVLVSKFFNLMKSWPWPRPIMLKDMDDGPIQQKVWNPQIYPGDRRHLMPVITPAFPSMCATHNITPSTQKIILRELSRASDITNEIFMGRKAWKDLFRRHTFFTEGYKYYLSIVAASRTKDAQSIWSGLVQSRLRRLVTGIEVSDASVELAHPFNKGFERVHQCKTDEEVEMTLQGSLKFQVKEVKTETTEDTKDIKQAVVAEGSTENVEMPNKTLGEVNSDGVRTIYSTTFYVGIELEEGAKSLDISYPVGEFKRNCTDWPQYNDELNSLRIVHTRNYDLPDDVFEPGEVRPSRKKKATSRSNGQSASKRNVGEAGLDGTNGHPAKRQQSSTGVSTAAG", "metadata": {"id": "A0A6A6W4Z6", "cluster": 23887635, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR007012", "IPR011068", "IPR043519"], "interpro_unused": ["IPR014492", "IPR007010", "IPR048840"]}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein contains a HPr kinase/phosphorylase, C-terminal domain that functions as the catalytic core of the bifunctional enzyme HprK/P, regulating carbon source utilization in Gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 on the phosphocarrier protein HPr and its dephosphorylation via phosphorolysis, typically within a hexameric assembly. Also, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein features a HPr(Ser) kinase/phosphorylase, N-terminal domain that constitutes the structural blades of the hexameric HPr serine/threonine kinase PtsK, a sensor protein controlling bacterial carbon catabolite repression. This domain facilitates the assembly of the enzyme's three-bladed propeller structure, allowing it to function within a multicomponent phosphorelay system. It occurs in Xanthomonas dyei and has UniProt annotations Transferase, Multifunctional enzyme, and Metal-binding.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 5461, 43, 18542, 4016, 19, 12556, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 1920, 29491, 4113, 18542, 1040, 19, 58, 16, 6773, 5056, 4585, 8422, 1922, 8604, 17, 2843, 4802, 18, 2176, 17097, 2321, 1920, 4498, 17, 3100, 4050, 1927, 2375, 17, 4182, 1990, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 2496, 16881, 3454, 3421, 6892, 16, 5745, 2651, 43, 25602, 1935, 5957, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 4075, 43, 18542, 12, 2375, 13, 4016, 19, 12556, 2051, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 4346, 22707, 1036, 1927, 1920, 25602, 1935, 18542, 8468, 19, 13143, 4016, 8618, 1040, 16, 43, 6443, 2213, 7138, 4543, 5056, 3115, 3016, 2394, 10084, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 4113, 11, 61, 2559, 17, 22707, 1007, 5062, 13728, 3170, 16, 7201, 2176, 1942, 2347, 2651, 43, 8844, 28155, 1939, 3421, 15208, 1012, 2433, 18, 2176, 5110, 1922, 15213, 10480, 8347, 1033, 1930, 2258, 20709, 15010, 13763, 16, 20136, 4113, 16, 1930, 6048, 17, 2743, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MNTSITARELFDQQRDKLALRWVAGQKGEHREIQAGSNNAAWLDSLDARQRWETIEKIIQVQPLALAISKNQSCPEDLRAAADESNTPLWISPKRGHLHGVFMEIYSIGVLITGEAGSGKSELALELLSRGHRLVADDAPELLQDLLEVRGLGVLNVRDMFGDTAVKKNKYLRLIVHLTRPMTEPTPSGYERLTGDSGSRHVLDLAATRLHILRTKGIDPAAMFIARHSNLLERRTPRRPSLAGYLNVIYPNKVQILGTEELELLNHLSYHLARTLAPRVTPEFTQIAPDVLDGTCDVPLITLPVMPGRNLAVLTE", "metadata": {"id": "A0A2S7C993", "cluster": 24398655, "interpro_all": ["IPR003755", "IPR011104", "IPR011126", "IPR027417", "IPR028979"], "interpro_used": ["IPR011104", "IPR027417", "IPR011126"], "interpro_unused": ["IPR003755", "IPR028979"]}, "task_type": "infilling"} {"instruction": "What would the protein sequence be if I wanted a protein that could perform the following function: The protein is associated with the Ankyrin repeat-containing domain superfamily, which functions as a versatile protein-protein interaction module defined by tandem repeats of a \u03b22-\u03b12 structural motif. Predominantly found in eukaryotes, these domains mediate molecular recognition in diverse biological processes, including transcriptional regulation, cell-cycle control, cytoskeletal organization, and signal transduction. In addition, the protein includes a Ankyrin repeat that mediates protein-protein interactions through tandemly repeated helix-loop-helix modules which stack to form an L-shaped structure. This versatile motif is found in diverse eukaryotic proteins, including transcriptional initiators, cell-cycle regulators, cytoskeletal components, and signal transducers. It has been detected in Latescibacterota bacterium and exhibits UniProt keyword tags ANK repeat.", "tokenized_instruction": [2, 4663, 2962, 1920, 2213, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 28336, 6865, 17, 3165, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 2213, 17, 2213, 2835, 9059, 3608, 2007, 10361, 9569, 1927, 43, 11157, 17, 13213, 4346, 5219, 18, 7700, 2435, 1922, 15021, 16, 2144, 4682, 8265, 3272, 5708, 1922, 6445, 3933, 4028, 16, 2710, 5224, 3640, 16, 2024, 17, 4048, 2285, 16, 14787, 5901, 16, 1930, 2733, 8201, 18, 1922, 2459, 16, 1920, 2213, 5921, 43, 28336, 6865, 1988, 10412, 2213, 17, 2213, 3719, 2596, 10361, 1954, 5116, 7864, 17, 5881, 17, 7864, 10803, 2154, 10496, 1942, 2386, 1925, 54, 17, 9132, 3170, 18, 2052, 20425, 5219, 1977, 2435, 1922, 6445, 10825, 2697, 16, 2710, 5224, 23467, 1036, 16, 2024, 17, 4048, 9098, 16, 14787, 4178, 16, 1930, 2733, 26307, 18, 2176, 2258, 2252, 3330, 1922, 5058, 12709, 26073, 2341, 6506, 3857, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 9808, 6865, 18, 3], "output": "MQQRHTPLHSAACENAIETAELLITQGAEINAKNDKGRTPLHDAAETDATATAELLLKQGAEVNAESDDGLTPLHIATNHNAAETAELLNRYGGRE", "metadata": {"id": "A0A9E4BXA8", "cluster": 24748255, "interpro_all": ["IPR002110", "IPR036770"], "interpro_used": ["IPR036770", "IPR002110"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein carries a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein should include a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein belongs to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It has been characterized in Firmicutes bacterium CAG:345 and has UniProt annotations Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 16252, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 2258, 2252, 4378, 1922, 24474, 14061, 13415, 30, 22920, 1930, 2258, 20709, 15010, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MIIKAQAKLNLAIDLIGKRNDGYHDIDMISIPLELHDCLEIDEISFGNETFITADDVSLVCDKSNTVHKAFNIMKERYDIKKPYRIQIYKNIPTQAGLAGGSADAACLINGLNYSKKLNVSKEELAKIGLEIGADVPYCIYNVPARVQGIGDKIIPIKGEYNFFVLIVKPQEGLKTAEVYQKSDDIEIEYHPDIEGLSKLLTQNPTIDQIAPYLYNGLRPAAENLCPEIITILDNMKKIGLCACEMSGSGSACFALTQNEKELDKAYKYFQKLGYTAIKTIATNHPHTSKDFFKRLFHINKYEI", "metadata": {"id": "R6YZQ4", "cluster": 26190943, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR036554", "IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Moreover, it is part of the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It has been characterized in Pedobacter cryophilus and carries UniProt keyword assignments Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 2258, 2252, 4378, 1922, 5296, 5883, 18164, 7969, 5277, 1036, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 3], "output": "MMSNYHIPVMLKECIDALDIQPSGVYVDVTFGGGGHSKEIMKHLGDDGVLVAFDQVFIDQNFRYLKNNLRMHDLLPVNGILADLGVSSHQFDVPERGFSAKKVVNEYSEDQLHKIFGIYGEIQNAKSLAKAVVTSRLAKPIETIADLKSAIAKVNQEMEALKEFLEQTVDVLASGGRLVVMSYHSLEDRLVGNEIKPFDLVVKKSITASEDEIKINNRARSARLRIAVKRDVDAQKNVIADERFTRFDADLDMRMDQAGSLTLIPKGKENKYLAQVFQALRIEKNFMAKGKFSGTVEKDFF", "metadata": {"id": "A0A4U1C0D8", "cluster": 26649561, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR023397", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein is associated with the Thioredoxin-like ferredoxin family, which comprises iron-sulfur proteins predicted to function in redox sensing and electron transfer within fungi, plants, and bacteria. These proteins adopt a ferredoxin-like fold and bind Fe-S clusters through a distinct active site motif typically containing two cysteines and two histidines. Specific members, such as yeast Apd1, are involved in cellular defense against hydroxyurea and actin patch localization. Also, the protein falls within the Thioredoxin-like superfamily, which encompasses a diverse group of redox-active proteins characterized by a conserved $\\alpha$/$\\beta$/$\\alpha$ structural fold and a CXXC active site motif. These enzymes primarily facilitate electron transfer via thiol-disulfide exchange reactions to maintain cellular redox homeostasis, assist in protein folding through disulfide bond formation or isomerization, and participate in signaling pathways like the glutathione/glutaredoxin system. It originates from Gammaproteobacteria bacterium.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 1977, 2458, 1956, 1920, 23684, 17, 3189, 25304, 22389, 10960, 3416, 16, 2154, 12936, 5680, 17, 12585, 2697, 4396, 1942, 2347, 1922, 9366, 9306, 1930, 4995, 3856, 2651, 10520, 16, 4793, 16, 1930, 4802, 18, 2144, 2697, 14103, 43, 25304, 22389, 10960, 17, 3189, 3728, 1930, 4566, 2650, 17, 61, 5859, 2596, 43, 4493, 3500, 3200, 5219, 5745, 3165, 2288, 22446, 1930, 2288, 13873, 1036, 18, 2487, 4678, 16, 2427, 1966, 5688, 23313, 1009, 16, 2032, 3286, 1922, 3689, 9720, 3316, 8275, 16648, 1930, 4718, 7504, 5363, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 23684, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 9366, 17, 3500, 2697, 4378, 2007, 43, 5305, 8, 38, 4595, 8, 19, 8, 38, 4666, 8, 19, 8, 38, 4595, 8, 4346, 3728, 1930, 43, 5639, 21487, 3500, 3200, 5219, 18, 2144, 5038, 5985, 6628, 4995, 3856, 3454, 13914, 17, 11830, 6818, 5298, 1942, 6698, 3689, 9366, 7622, 16, 6589, 1922, 2213, 10328, 2596, 11830, 5403, 3337, 2014, 27027, 16, 1930, 7352, 1922, 3197, 3873, 3189, 1920, 9153, 19, 19406, 1919, 9754, 2433, 18, 2176, 22970, 2037, 7034, 9218, 1021, 10296, 14061, 18, 3], "output": "MRWVASRGSDYEAVREIDVLTADLIPMRENVYFVCTNGQRDFCCARYGTTHLGGHRFAPNVLTLPQGVLYGRVDVDDVNAFVTTIESGDLSRPHVRGVEALLDVREDRVLFQTNLGEEEIQIQKSSIPYKLLQVAVISSLRTFTQLVGPHNVAFTPKRIADSYPIPLFLLVQNIPEEGHAPRLLIAEDWMLPTFEGLKELVGERVWQRSAFPPEAQFAELQVTGRTFGHVVDDEMLLRSGFRFN", "metadata": {"id": "A0A920S3T6", "cluster": 27401742, "interpro_all": ["IPR009737", "IPR036249"], "interpro_used": ["IPR009737", "IPR036249"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein belongs to the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. Additionally, it is part of the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. It has been detected in Alphaproteobacteria bacterium ADurb.Bin438 and features UniProt keywords Metal-binding, Transmembrane helix, and Transferase. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 2176, 2258, 2252, 3330, 1922, 4595, 9218, 1021, 10296, 14061, 2041, 5223, 18, 8768, 7514, 1025, 1930, 4075, 20709, 11569, 6048, 17, 2743, 16, 9117, 7864, 16, 1930, 13763, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MKATEKGIKRIFNAFKYSYSGFISSFKSEEAFRQDLLFCLIFFVIALFLPCDVISKIILIFPLVLIIIMELVNTAIETVVDRISEEYHELSKKAKDIGSLLVLLSFVFRAGVWFFMILSFI", "metadata": {"id": "A0A1V5LEG8", "cluster": 27910873, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR000829", "IPR033718"], "interpro_unused": ["IPR036945"]}, "task_type": "autoregressive"} {"instruction": "I want to generate an amino acid sequence for a protein. The protein should have the function The protein features a DNA polymerase III alpha subunit finger domain that constitutes the \"finger\" structural component of the catalytic alpha subunit, contributing to the characteristic right-hand architecture of the enzyme. It functions in concert with palm and thumb domains to position the DNA template and incoming nucleotides during replication. Additionally, the protein carries a PHP domain that functions as a histidinol phosphatase or is implicated in pyrophosphate hydrolysis within bacterial DNA polymerase III alpha-subunits and family X DNA polymerases. This domain adopts a distorted (\u03b1/\u03b2)7 barrel fold and utilizes conserved histidine and aspartate residues for metal ion coordination. Moreover, the protein features a Bacterial DNA polymerase III alpha subunit NTPase domain that constitutes a conserved region within the catalytic alpha chain of the DNA polymerase III holoenzyme. This subunit functions as the primary DNA polymerase responsible for the majority of replicative synthesis in bacteria. It occurs in Nakamurella multipartita (strain ATCC 700099 / DSM 44233 / CIP 104796 / JCM 9543 / NBRC 105858 / Y-104) (Microsphaera multipartita) and contains UniProt keyword associations Nucleotidyltransferase, DNA-directed DNA polymerase, and DNA replication.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 4075, 43, 2678, 6479, 4337, 4595, 5903, 8497, 3418, 1988, 14879, 1920, 6, 8497, 6, 4346, 4594, 1927, 1920, 6804, 4595, 5903, 16, 8739, 1942, 1920, 6293, 3659, 17, 3897, 9335, 1927, 1920, 4113, 18, 2176, 4088, 1922, 21799, 1956, 15516, 1930, 22362, 4682, 1942, 3507, 1920, 2678, 7662, 1930, 22201, 9519, 2409, 5158, 18, 4950, 16, 1920, 2213, 16252, 43, 24939, 3418, 1988, 4088, 1966, 43, 27507, 22816, 1945, 8167, 2014, 1977, 6835, 1922, 24937, 9128, 2651, 4543, 2678, 6479, 4337, 4595, 17, 6991, 1930, 3416, 66, 2678, 20910, 18, 2052, 3418, 24032, 43, 22797, 12, 160, 19, 161, 13, 27, 19560, 3728, 1930, 18127, 5305, 13873, 1930, 12878, 4248, 1958, 6048, 4755, 9478, 18, 3950, 16, 1920, 2213, 4075, 43, 4543, 2678, 6479, 4337, 4595, 5903, 29676, 2051, 3418, 1988, 14879, 43, 5305, 3031, 2651, 1920, 6804, 4595, 4659, 1927, 1920, 2678, 6479, 4337, 20403, 14896, 18, 2052, 5903, 4088, 1966, 1920, 3065, 2678, 6479, 5061, 1958, 1920, 4827, 1927, 20604, 4271, 1922, 4802, 18, 2176, 5110, 1922, 14510, 1976, 2027, 11560, 1019, 20677, 5263, 9909, 12, 3943, 11037, 11851, 13192, 1026, 19, 10964, 4044, 24082, 19, 12998, 8824, 9364, 1016, 19, 14904, 1035, 3002, 7514, 19, 8789, 15618, 7991, 10025, 1025, 19, 67, 17, 8824, 13, 12, 6592, 4151, 7124, 20677, 5263, 9909, 13, 1930, 5461, 20709, 11121, 2538, 5253, 2797, 4090, 2199, 9961, 16, 2678, 17, 6554, 2678, 6479, 16, 1930, 2678, 5158, 18, 3], "output": "MTDVRDEFVHLHVHGEHSHQDGISRADDLVEAAVRHGQPALALTDHGSIGGAWRFGQAAAQAGIKPIIGVEAYLAIGDRALRGSRPVPRDLLGADGGGAGADAEVGFKKQTYEHLTVLAATGEGFGNLSRLTADASRHVYHRPRMDYTSLAAHSAGLIGLTGCVSGPVAGALLRDGTRQPDGTVFDGRAAAKQAIITLRDIFGRDRLFVEVMDHGIAAERRVTEQLFDLARRAGLKTLFTNDSHYTNADDAPLHDLWLCIGETTRQGAGKPPFKITDTNRWRFTGTGYHLRSTAEMYALAGGDDRAVRALRNTLLVADMIEDRVLPESRIRLPRYDRLGAFTCAAELLRSLVDDGAGERWGADWRAARPDVANRIDHELAVINQLGFVDYFLIVREALYAARGAGYRTGPGRGSAAGSAVSYALRIVDVDPLANGLLFERFLDPTRAEMPDIDSDLDRAGQQWVFRYLSERWGADRVARIGAPGYTRARASIRDAARAIVPGHAAIQVGNQLAAKVPPTAPTLAGLIDPTNPDGEALRAAVPTDPDHQAVLDSAVGIEGLVKQAGVHACGVVVSSEPLPPLVPLRQVTADDGQPIWVTDWDVHDLADLGLVKIDFLGLRTLDVIDAAVAQIRASTGTDIDPEHLADEPGDPRAEAVWTMLGAGRTSGVFQLESASMAGLCERARPRSIDDLSAILALWRPGPISAGFPDLFAARQTGADTVDYSIFTTDPAEERALRTVLDTTQGLIVYQEQIMQIGALVAGFGPTLTSKLRKAVSKKDAAAMTEIGERFLVGAARDVTDDGAAKQPFARSTARALWAGIKGAGAYSFNKSHSRAYAELTWQTAWLKASYLPQFAAALLACTDSADKRAAALMDLRSEQVTVLGPSVNHGADVTSCDRHGVVRLGLSEIAGVGSAGAAIVRERTHGGDYTDLHNLYRRVRVPDAAGSGDTRPLSASTLLALVESGALDQFGPRMGLAALIGSVKSPDPVPVPDMEWPTLERSIRERRVLGTALSSNPLRAAKETVHAWRTPDFQRRPTPVHKVPAADGADILTLGVLASIDVRISAGRERAGIVIEGSRSQLAGIIWPTQYAQITSGRGIPPIGSIVAVRGRVRMVEAQRHADPRSDTATSDDPTADAAVTDLRKELTVYDLWTVQMPDDTRPLPPARTLMSILTAAPITVAEPAVDSLPDAADRGADSDAGTADETQDEPSGRAIACPTPVTGRRDGPDASTVGRRDSHLVVVVDGGRPDDPPGPSIAATDQDLRVDVLCVRSGRGLPVDDLATMALLTGQSFGHLVSGPAKKGVQMAIAAAPTWTRTAVLRSRDGADRLTIVVVPRDWRPGLATGITLTARGAHLPGVQALVACTRPVQADPIDVARLRAPGLLPVFDLPVGTVDRAAETAFSQAFGKAPSTGLPAGGVA", "metadata": {"id": "C8X8N9", "cluster": 1090979, "interpro_all": ["IPR011708", "IPR041931", "IPR040982", "IPR004805", "IPR029460", "IPR004013", "IPR003141", "IPR016195"], "interpro_used": ["IPR040982", "IPR004013", "IPR011708"], "interpro_unused": ["IPR016195", "IPR004805", "IPR041931", "IPR003141", "IPR029460"]}, "task_type": "autoregressive"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein should have a Ribosomal RNA-processing protein 14, N-terminal domain that constitutes the N-terminal region of Rrp14, a protein required for the synthesis of the 60S ribosomal subunit and the processing of precursor rRNA during ribosome biogenesis. In addition, the protein features a Ribosomal RNA-processing protein 14/surfeit locus protein 6, C-terminal domain that serves as a structural component of the nucleolar matrix with strong nucleic acid binding capabilities. This domain is constitutively present in nucleolar substructures and is implicated in ribosomal RNA processing. Also, the protein should have a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. It is identified in Diutina rugosa (Yeast) (Candida rugosa) and corresponds to UniProt keyword mRNA processing, ATP-binding, and Magnesium.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 3066, 2162, 43, 11196, 3146, 17, 4587, 2213, 2607, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 3031, 1927, 5162, 5113, 1006, 16, 43, 2213, 3414, 1958, 1920, 4271, 1927, 1920, 3276, 1036, 11196, 5903, 1930, 1920, 4587, 1927, 7897, 9067, 2409, 12794, 13008, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 11196, 3146, 17, 4587, 2213, 2607, 19, 3014, 12638, 6730, 2213, 26, 16, 45, 17, 4262, 3418, 1988, 10634, 1966, 43, 4346, 4594, 1927, 1920, 23770, 4526, 1956, 3206, 11079, 2687, 2743, 13693, 18, 2052, 3418, 1977, 11744, 2481, 1922, 23770, 28876, 2352, 1930, 1977, 6835, 1922, 11196, 3146, 4587, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 2176, 1977, 2899, 1922, 2137, 10574, 1019, 23148, 5360, 12, 5688, 13, 12, 14550, 23148, 5360, 13, 1930, 8852, 1942, 20709, 11121, 2538, 3616, 4587, 16, 4498, 17, 2743, 16, 1930, 13148, 18, 3], "output": "MTDTASFGVTAPISVANPTPAENAINDALIKELKLRNSFEPESATRRRAEVLGTLQKMAEEFVYRVSKRKNMSEGMARDAGGKIFTFGSYRLGVYGPGSDIDALVVVPRHVSRADFFDEFPKLLNERPELEEMTPVPDAFVPIIKLEYGGISIDLICARLDVSRVPVTLTLEDKNLLRNVDEKDLRSLNGTRVTDEILKLVPKLTVFKHALRCIKMWAQQRAIYGNVSGFPGGVAWAMLVARICQLYPNAVGAVIVDRVFNIYHQWSWPQPVVLKKIEDGPLQVRVWNPTLYAGDRHHLMPVITPSYPSMCATHNIGQSTFKVIMEEFKRGKEIMADIIAGKKTWADLFERHKFFHKYKFYLCVVASTYGTSDQHALYSGMVESKVRLLVQRLENVAGVELAHPYVKSFDNDYFCDSKEQASQIVASYGDLSGEKLAANVATKRESDSQVEVHLTKFFVGLNVDVDKCGGDKKLDIQQPCGDFMNICKTWTEFDPKINGINIKKVRVYDLPNDVFVEGEERPVRVSKRKRVVAKGEGAKRPKSESIKNHSSAFDGLLSLIPAKYYYDDATQDQWKQKKKSKQEQRQNKRAKLDPSSKDSADDYANGHASAKHVKDNKAKKGKPVKLPGAATLRGPVPVAKASNDDEDDDESESSDSSMALDSVTVFDDNGDEVEDASEAAEDDAAVEIQTANDDDATTTDESHSVKEKAKNAKAQLSEQERKAREEKLAALRQRLTSKISQMKEKRKAVGSKAEGAPKSRQQILEERKRKAELRKKRKREEEEEQADDSDSDNDDNDNDNDNEVNDADEVGAKDSTFFGNIVFNDGTRVTSDLTKLRNTAEKRKKKGPANNDIKAHLAILEKKKERFAKLSPEQQQKELEKEKWQKVMTQAEGVKLKDDEKLLKKALKRKEKQKLKSEREWQERTQTVKDTKAARQKRREENLQARRDAKGVRGKKKKQLPRLKKFTGIVNKAGGKTGGKAGGKKRAGFEGSAKSKKK", "metadata": {"id": "A0A642UTQ1", "cluster": 2249600, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR029190", "IPR029188"], "interpro_used": ["IPR029188", "IPR029190", "IPR007012"], "interpro_unused": ["IPR007010", "IPR043519", "IPR048840", "IPR011068"]}, "task_type": "autoregressive"} {"instruction": "The protein is a member of the Teichoic Acid Biosynthesis Enzymes family, which catalyzes the polymerization of glycerol phosphate or ribitol phosphate units to form the main chain of major teichoic acids in the bacterial cell wall. These enzymes transfer phosphate units from cytidine diphosphate-activated donors to a growing polymer chain attached to a disaccharide linkage unit, functioning either as primases that initiate the process or as polymerases that extend the chain. Furthermore, the protein is assigned to the CDP-glycerol glycerophosphotransferase, C-terminal domain superfamily, which represents the Rossmann-fold containing region of TagF-like enzymes responsible for wall teichoic acid biosynthesis in Gram-positive bacteria. These enzymes catalyze the polymerization of the teichoic acid main chain by sequentially transferring glycerol-phosphate units from CDP-glycerol to a lipid linkage unit attached to the peptidoglycan. It is produced by Geodermatophilus pulveris and is linked to UniProt keywords Cell membrane and Membrane.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 1920, 3602, 2108, 8643, 2687, 8132, 5038, 3416, 16, 2154, 17097, 1920, 11486, 1927, 9244, 5413, 2014, 5216, 8148, 5413, 5701, 1942, 2386, 1920, 2730, 4659, 1927, 3044, 3602, 2108, 8643, 4576, 1922, 1920, 4543, 2024, 4821, 18, 2144, 5038, 3856, 5413, 5701, 2037, 2702, 5802, 23266, 17, 4128, 8276, 1942, 43, 6552, 4593, 4659, 8765, 1942, 43, 2054, 9466, 8611, 5344, 16, 7295, 3108, 1966, 2610, 2319, 1988, 11051, 1920, 2585, 2014, 1966, 20910, 1988, 9676, 1920, 4659, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 26707, 17, 9244, 7757, 8630, 14165, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 4972, 1920, 18215, 8890, 17, 3728, 3165, 3031, 1927, 5218, 1038, 17, 3189, 5038, 5061, 1958, 4821, 3602, 2108, 8643, 2687, 8132, 1922, 8604, 17, 2843, 4802, 18, 2144, 5038, 18170, 1920, 11486, 1927, 1920, 3602, 2108, 8643, 2687, 2730, 4659, 2007, 14985, 21902, 9244, 17, 5413, 5701, 2037, 26707, 17, 9244, 1942, 43, 4486, 8611, 5344, 8765, 1942, 1920, 24183, 18, 2176, 1977, 4152, 2007, 14136, 2179, 3368, 27747, 7969, 5277, 1036, 3784, 2004, 1937, 1930, 1977, 4624, 1942, 20709, 11569, 2024, 3260, 1930, 3260, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MHHRLQHVARVVGRRALDRLNAAVPKREQLLLNLYVVVLLTHPANAVATRVREVLGARVRVYRRSVVLTHPVYDSARLARRQTVVNVWHGMPIKAIGRLLGVPPESVVVLHSPRIEHLCQGHRGGGGVSSAPLLSPDGAARLGELLARRRGVLELTDTVLEAAGVGIYEVLAEADALVTDVLDAYTADRPLLLDPYETWTPGPPLADEQVRELLMSARSGGLATRVLAFAGVRRPPSASPDTDASLPPLLEACRDVEGRRGSFGAVWQYLRSDGRQDVVLADWTLASSGFYRPLLAEAADVWERVAVDRSAYDRVFVWMPTFRGREPECLLVLRRHPYEARAVPLSVPSSVWLDFLLLDRPIVIWFPDDDLLAALDAVATGEDPFRLRRR", "metadata": {"id": "A0A239BSQ9", "cluster": 2255270, "interpro_all": ["IPR007554", "IPR043148", "IPR043149", "IPR051612"], "interpro_used": ["IPR051612", "IPR043148"], "interpro_unused": ["IPR007554", "IPR043149"]}, "task_type": "infilling"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, the protein can be placed in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Also, the protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is derived from Oscillospiraceae bacterium and corresponds to UniProt keyword Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 3595, 2037, 7799, 3106, 11979, 1972, 3336, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 3], "output": "MEFSHKSVLLNETIEALNIKPNGIYADGTAGGAGHSLEIAKRLTDGRLYALDRDPDAVKTASERLKGYNAEVIKSNFSEMQEVLNKRGVTGVDGILLDLGVSSYQLDNAERGFSYRQNAPLDMRMSKSGISAADIVNTYSKEELVRILRDYGEEKFAFKIADRIISEREKAPIDTTLKLADIISSAVPARARRDGHPTRKSFQAIRIAVNGELDCLETGIDKAFNLLNKDGVLSIITFHSLEDRXXHSLEDRMVKQKFKEYCTGCICPPDFPVCVCGRKPQGRLLTKKPIEPTAEEINENQRSRSAKLRVIIKNE", "metadata": {"id": "A0A354M7X3", "cluster": 2839507, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein is included in the Protein of unknown function DUF1579 family, which comprises paralogous hypothetical proteins of uncharacterized function identified in bacterial species including *Rhodopirellula baltica* and *Agrobacterium tumefaciens*. It has been detected in Acidobacteria bacterium SCN 69-37.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 5739, 5071, 1026, 3416, 16, 2154, 12936, 16188, 2080, 15148, 2697, 1927, 24528, 2347, 2899, 1922, 4543, 3038, 2710, 14, 11490, 2011, 2952, 11560, 5617, 4641, 21788, 14, 1930, 14, 26896, 30258, 25018, 14, 18, 2176, 2258, 2252, 3330, 1922, 2687, 10296, 14061, 14870, 5349, 17, 3191, 18, 3], "output": "MNPTTEHQWLTRLVGDWTFSLPAPKIDDARVTTIEGTETYRALGPLWVIGDAVAPLADGGLSESRMALGWDPQRRRFVGTRILSTTPSLWVYDGEGDPDGRRLRLYTEGPATEGATHSEPLLDVIAFVDANSRTLTRHTKAADGSWTAVLTVEYRRR", "metadata": {"id": "A0A1E3Y297", "cluster": 4437227, "interpro_all": ["IPR011473"], "interpro_used": ["IPR011473"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein includes a Nephrocystin 3-like, N-terminal domain that functions as a P-loop like NACHT NTPase found in diverse eukaryotic and bacterial proteins. It is integral to proteins such as Nephrocystin-3 and ANKRD50, supporting roles in ciliary development, Wnt signaling inhibition, endosomal trafficking, and toxin biosynthesis. Additionally, the protein contains a Ankyrin repeat that mediates protein-protein interactions through tandemly repeated helix-loop-helix modules which stack to form an L-shaped structure. This versatile motif is found in diverse eukaryotic proteins, including transcriptional initiators, cell-cycle regulators, cytoskeletal components, and signal transducers. In addition, the protein should have a NACHT nucleoside triphosphatase domain that functions as a predicted NTPase module containing seven conserved motifs, including Walker A and B sites for ATP or GTP binding. Found in animals, fungi, and bacteria, it frequently associates with ligand-sensing or effector domains, such as LRR and CARD, to mediate signal transduction. It occurs in Dendryphion nanum and is annotated with UniProt keywords ANK repeat. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 5921, 43, 7737, 4104, 29764, 23, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 43, 58, 17, 5881, 3189, 15343, 1031, 29676, 2051, 2435, 1922, 6445, 10825, 1930, 4543, 2697, 18, 2176, 1977, 12328, 1942, 2697, 2427, 1966, 7737, 4104, 29764, 17, 23, 1930, 9808, 8544, 3382, 16, 6184, 5456, 1922, 17542, 2740, 16, 7028, 3197, 3523, 16, 16514, 9604, 16, 1930, 9165, 8132, 18, 4950, 16, 1920, 2213, 5461, 43, 28336, 6865, 1988, 10412, 2213, 17, 2213, 3719, 2596, 10361, 1954, 5116, 7864, 17, 5881, 17, 7864, 10803, 2154, 10496, 1942, 2386, 1925, 54, 17, 9132, 3170, 18, 2052, 20425, 5219, 1977, 2435, 1922, 6445, 10825, 2697, 16, 2710, 5224, 23467, 1036, 16, 2024, 17, 4048, 9098, 16, 14787, 4178, 16, 1930, 2733, 26307, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 15343, 1031, 18015, 14051, 2609, 7234, 3418, 1988, 4088, 1966, 43, 4396, 29676, 2051, 9059, 3165, 5260, 5305, 8277, 16, 2710, 20138, 43, 1930, 44, 3402, 1958, 4498, 2014, 9319, 2743, 18, 2435, 1922, 3555, 16, 10520, 16, 1930, 4802, 16, 2176, 5467, 14162, 1956, 5207, 17, 9306, 2014, 7917, 4682, 16, 2427, 1966, 13947, 1930, 9429, 16, 1942, 8265, 2733, 8201, 18, 2176, 5110, 1922, 10240, 11397, 2001, 3529, 1989, 1930, 1977, 10633, 1956, 20709, 11569, 9808, 6865, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MAEGLAIAASVIAVIQLTDRIANAVNFYVETLRDDLPSDLRVILSETAALKTVFEKLHSEVDETVAKTLAGPVNDCKKALQALKDLLPTKSTQTQGCSPKVGKMRAALFSIKWSFKETKVNKLLDNISRHKATIQLVLTKGSLTQDQLRDVFNWLEHTNPSPLHNQACEQFTPGTAEWVCRMPEWTDWIEARFRCLWIHGIPGAGKTVLISHLIKQLKCHRHNPSSTKVALVYYYCYYGRNQDEAAPFLRWLLNQLCRQSNVVPKSLYKLYKAGTEATVAEILLVVLEMIVHFDKIYVVIDALDESSPRGKLLDVIHKLATNKNCAKIQTLVSSREYPEIEKVLNTFATPVSMDNEFVRQDIRLCVHSLLRSKNAFRHWPITLFDEVEEALSTGAQGMFRWAVCQVDVLRRLKGDRTVIEKSLKDLPKTLDDIYDRIFLLIDEEERLYALHALLWIVNTASRHSSHNSGRIISTQVLPIAAVKSTSRFNTNYRDRFYDFEILADLLGCLIRETTDSKVVLAHYTVKEYLYSSNISTVLTNITSIPPSSLRNVVVEAMFDEVLAMENFEVCMDAPKILMQLEGFCVMKLLEYLKEGMIDTHNDDYVSLSLDLLDPSKSHYISLLKITGLVNASKGFGNAGFLRMEMWAVHSNGSPLAIRAFHLSNIDLLTGPAEARLSLLEKLSTQPLYHEALHESLSLQFCSNSKVDGSKQSYFQGTLAEWNPGLALSLYESANNSNFLPSNYGSDLMLLCAAHKGRQICCRSVNEPCELKRLLETGISPDFAKHSVTPLQIATLCCDFEAVKLLLEAGADPNRSGIGQVDEGSSIDLRDPDGCIQSHSRVSFNFFCRYYQEIELHNFGFYFKKGDFRSTEDENDRAEIEKLLLQFGAKEIGNIPTLEAGSGKKSPFGGTNSRCFFCKESAPE", "metadata": {"id": "A0A9P9EJZ1", "cluster": 4800698, "interpro_all": ["IPR002110", "IPR036770", "IPR007111", "IPR056884", "IPR027417", "IPR031348"], "interpro_used": ["IPR056884", "IPR002110", "IPR007111"], "interpro_unused": ["IPR031348", "IPR036770", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein is associated with the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Additionally, the protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein includes a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. It is found in Achromobacter anxifer and contains UniProt keyword associations ATP-binding, Nucleotide biosynthesis, and Transferase.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 1977, 2458, 1956, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 5921, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 2176, 1977, 2435, 1922, 28216, 13777, 7972, 2341, 1915, 24400, 2070, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MTTRGRFITLEGVDGAGKSTHTVPGGTPLGEKLRALLLSDPMGLDTEPALARGAWVVCDRYTDATYAWMQAGSPDRTWLFEGAAFFERTREAYHARAAGLRELLGQAAWIADFLRAQGLDVVSTRETLLMFAARCEHLRQVIEYQGGGRGLGAARVAALEDDVPLEVARARLADAREPDRFERKADPERIRIVDSTQTIAQVRAGLE", "metadata": {"id": "A0A6S7EV23", "cluster": 7191890, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR018094", "IPR027417", "IPR039430"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Function:\nThe protein is categorized in the The ARFGAP/RecO-like zinc finger superfamily, which features a characteristic C4-type zinc finger motif, functions as a GTPase-activating protein (GAP) that promotes the hydrolysis of GTP bound to ADP ribosylation factors (ARFs) to facilitate vesicle uncoating and Golgi maintenance. Additionally, this structural fold is found in RecO proteins, where it participates in DNA repair and damage avoidance pathways. In addition, the protein should contain a Arf GTPase-activating protein domain that regulates ADP-ribosylation factors (ARFs) by facilitating GTP hydrolysis, which is essential for membrane uncoating and Golgi maintenance. This domain is structurally distinct from other GAPs, featuring a characteristic zinc finger motif coordinated by four cysteines. Unlike classical GAPs, it does not supply a catalytic arginine finger to the active site, suggesting an indirect role in GTPase hydrolysis. In addition, the protein is assigned to the Arf-GAP domain and FG repeat-containing protein family, which facilitates vesicular transport processes, particularly during acrosome biogenesis, and contributes to RNA trafficking or localization. Members of this family can act as cofactors for HIV-1 Rev to promote viral RNA export and utilize FG repeats for nucleocytoplasmic transport or cellular scaffolding roles. It has been characterized in Piptocephalis cylindrospora and is linked to UniProt keywords Metal-binding and Zinc-finger.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 1920, 13720, 19823, 19, 29326, 17, 3189, 7997, 8497, 13975, 16, 2154, 4075, 43, 6293, 10872, 17, 2601, 7997, 8497, 5219, 16, 4088, 1966, 43, 14809, 17, 8019, 2213, 12, 5750, 13, 1988, 7383, 1920, 9128, 1927, 9319, 4124, 1942, 9828, 29117, 3017, 2790, 12, 13720, 1036, 13, 1942, 6628, 11502, 20732, 2287, 1930, 10277, 6291, 18, 4950, 16, 2052, 4346, 3728, 1977, 2435, 1922, 29326, 2697, 16, 2597, 2176, 17241, 1922, 2678, 5059, 1930, 4293, 11700, 3873, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 13720, 14809, 17, 8019, 2213, 3418, 1988, 7014, 9828, 17, 29117, 3017, 2790, 12, 13720, 1036, 13, 2007, 12440, 9319, 9128, 16, 2154, 1977, 4415, 1958, 3260, 20732, 2287, 1930, 10277, 6291, 18, 2052, 3418, 1977, 12171, 4493, 2037, 2303, 11349, 16, 29931, 43, 6293, 7997, 8497, 5219, 11651, 2007, 3006, 22446, 18, 7945, 8445, 11349, 16, 2176, 3731, 2084, 9042, 43, 6804, 9732, 8497, 1942, 1920, 3500, 3200, 16, 3783, 1925, 6354, 2770, 1922, 14809, 9128, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 13720, 17, 5750, 3418, 1930, 13320, 6865, 17, 3165, 2213, 3416, 16, 2154, 11374, 16168, 4860, 4028, 16, 4443, 2409, 25992, 2225, 13008, 16, 1930, 7624, 1942, 3146, 9604, 2014, 5363, 18, 4678, 1927, 2052, 3416, 2112, 4033, 1966, 21362, 1958, 3525, 17, 21, 5197, 1942, 5527, 4324, 3146, 12660, 1930, 12561, 13320, 9569, 1958, 2797, 3107, 11302, 4860, 2014, 3689, 22582, 5456, 18, 2176, 2258, 2252, 4378, 1922, 6556, 4575, 9175, 1937, 15460, 28988, 1019, 1930, 1977, 4624, 1942, 20709, 11569, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MAINLDERNIKFPPRVFPDGRMIRELLRLQDNRQCFDCTFHRELAHRVKPISTSRFTVAEVALLKNGGNAVAAEVWMARWGRCKWADPAKLPSTHTPPSSSASSVTTSSASSISSQRSMEGSSLRSPTSPLALTSGKVVYDRFSGGGGVGRGSRLDQASGGRESPSTLGLTYSTASTSPTYGPQVDSEGPAKAPHHANMMNQTFICEQCAQDRLPADLGDHGAMRRYFRDKYVLRSGSGGSLHGSGGKGSSSGRTTPPPLVPTVVTSECSPVPTK", "metadata": {"id": "A0A4P9XZZ8", "cluster": 10872122, "interpro_all": ["IPR052248", "IPR037278", "IPR001164", "IPR038508"], "interpro_used": ["IPR037278", "IPR001164", "IPR052248"], "interpro_unused": ["IPR038508"]}, "task_type": "infilling"} {"instruction": "The protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, the protein is categorized in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is present in Proteiniclasticum aestuarii and is associated with UniProt keywords Cytoplasm and rRNA processing. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 2481, 1922, 2213, 24410, 4054, 1989, 12893, 1031, 12169, 21094, 1930, 1977, 2458, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MEFKHVSVLLEECIEALNIKENGIYVDCTLGGAGHTKEILKRLRDGKLIGIDQDTDALNNARDILKDYDNVVLVHSNFENIGKIIEEHAPQGVDGILMDLGVSSYQLDEGERGFSYMKDAPLDMRMNREDVLSAYDVVNGYEEADIARVIRDYGEEKFAKRIAGFIVKAREEKPIATTHELVDIIKAAIPAKARREGPHPAKRTFQAIRIEVNRELTIIRDTILDAVEGLKPEGRLAIITFHSLEDRIVKNTYKELMFPCTCPTSMPCICGKTATVKILTRKPILPGEEEIEENPRSRSAKLRVLEKI", "metadata": {"id": "A0A939HAJ8", "cluster": 13989632, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR023397", "IPR002903"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein contains a Methanocaldococcus jannaschii dihydropteroate synthase-like, MBL-fold metallo hydrolase domain that functions primarily in folate biosynthesis by acting as a dihydropteroate synthase to catalyze the formation of 7,8-dihydropteroate. This domain belongs to the MBL-fold metallo-hydrolase superfamily and is also found in certain ferredoxin-like proteins. Furthermore, the protein is grouped in the Ribonuclease Z/Hydroxyacylglutathione hydrolase-like superfamily, which comprises proteins sharing a duplicated $\\beta(4)-\\alpha-\\beta-\\alpha$ fold that typically bind two zinc ions to facilitate hydrolytic activity. This group includes glyoxalase II thiolesterases, which convert S-D-lactoyl-glutathione to glutathione and D-lactic acid, and competence proteins required for natural transformation and DNA uptake in species such as *Neisseria gonorrhoeae*. Additionally, the protein belongs to the Metallo-beta-lactamase domain-containing protein family, which participates in cofactor biosynthesis by catalyzing the metal-dependent condensation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate with 4-(beta-D-ribofuranosyl)-aminobenzene-5'-phosphate to form a tetrahydromethanopterin precursor. Additionally, these enzymes can utilize alternative arylamine substrates to synthesize related compounds. It is native to Bacillota bacterium (Firmicutes bacterium).", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 5461, 43, 17348, 5000, 22389, 4879, 2437, 1957, 7626, 3676, 19519, 1033, 11842, 2410, 6506, 2010, 8921, 17, 3189, 16, 21007, 17, 3728, 8969, 1037, 20748, 3418, 1988, 4088, 5985, 1922, 13761, 8132, 2007, 8290, 1966, 43, 11842, 2410, 6506, 2010, 8921, 1942, 18170, 1920, 3337, 1927, 27, 16, 28, 17, 11842, 2410, 6506, 2010, 18, 2052, 3418, 14440, 1942, 1920, 21007, 17, 3728, 8969, 1037, 17, 20748, 13975, 1930, 1977, 2222, 2435, 1922, 4908, 25304, 22389, 10960, 17, 3189, 2697, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 18347, 2051, 68, 19, 8275, 14645, 16542, 2183, 7253, 20748, 17, 3189, 13975, 16, 2154, 12936, 2697, 10763, 43, 19479, 8, 38, 4666, 12, 24, 13, 17, 38, 4595, 17, 38, 4666, 17, 38, 4595, 8, 3728, 1988, 5745, 4566, 2288, 7997, 6982, 1942, 6628, 26702, 2455, 18, 2052, 2210, 5921, 3376, 23859, 2051, 2890, 13914, 8342, 2319, 16, 2154, 14450, 61, 17, 46, 17, 5641, 10921, 17, 9153, 1942, 9153, 1930, 46, 17, 16562, 2687, 16, 1930, 12939, 2697, 3414, 1958, 4613, 7002, 1930, 2678, 5047, 1922, 3038, 2427, 1966, 14, 28356, 18339, 27702, 6802, 3336, 14, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 8969, 1037, 17, 4666, 17, 23023, 3418, 17, 3165, 2213, 3416, 16, 2154, 17241, 1922, 15155, 8132, 2007, 29601, 1920, 6048, 17, 3100, 16112, 1927, 26, 17, 29078, 17, 27, 16, 28, 17, 11842, 2410, 16654, 24937, 1956, 24, 17, 12, 4666, 17, 46, 17, 21857, 29579, 11731, 13, 17, 3835, 29386, 17, 25, 11, 17, 5413, 1942, 2386, 43, 21196, 23568, 9286, 2410, 16654, 7897, 18, 4950, 16, 2144, 5038, 2112, 12561, 5012, 15578, 3812, 6249, 1942, 15541, 2712, 4300, 18, 2176, 1977, 6196, 1942, 8175, 22538, 3857, 14061, 12, 24474, 14061, 13, 18, 3], "output": "QSFGSDFELLVGTNFNREYLEKNRIDPILINEDTKEISPGVYRFYTYNGLDYELDCFTDEVVIVMEVIEAVRTRFNKPIHCIIGGTHLVEADDVRLERTFQYLKKAEERFFVNSTGTSISFERGFFNPKYGNNNGAWEYLGSVLTNFPRTSEFEKPNKKAGLVVLLGCSHPGLVNILKGLNLPLLGISHCTGEKATEY", "metadata": {"id": "A0A355FPS0", "cluster": 16163688, "interpro_all": ["IPR041712", "IPR052926", "IPR036866"], "interpro_used": ["IPR041712", "IPR036866", "IPR052926"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence be if I wanted a protein that could perform the following function: The protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein incorporates a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. It has been characterized in Alphaproteobacteria bacterium and is described by UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2176, 2258, 2252, 4378, 1922, 4595, 9218, 1021, 10296, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MPGFFITFEGGEGSGKTTQINKLAESLNAAGYKVVTTREPGGTPESEKIRQLLVQRDGGNWSPMAEALMFFAARLMLYQKIIKPALDEGKIVICDRFTDSTRAYQGYGHDLGFDVIDELKHIALGDAEPNLTFILDIDPKSGIERAQERLSSQKINAERREDRFEKLDLSFHQRLREGFLQIAKREPQRCVIVDAAQTIEHMAQSILQTALKRLEERLEERKG", "metadata": {"id": "A0A962J622", "cluster": 17178362, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR027417", "IPR018095"], "interpro_unused": ["IPR018094", "IPR039430"]}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is a member of the RNA methyltransferase RlmH family, which is predicted to function as an S-adenosyl-L-methionine (AdoMet)-dependent methyltransferase based on structural homology. These enzymes likely catalyze the transfer of methyl groups to RNA substrates for regulatory modification. Additionally, the protein is included in the Alpha/beta knot methyltransferases superfamily, which encompasses enzymes containing a deep, rare \u03b1/\u03b2 knot structural domain essential for RNA methylation. This fold is characteristic of S-adenosyl-L-methionine (SAM)-dependent enzymes, including the SPOUT and EMG1/NEP1 families, facilitating the modification of RNA substrates. Also, the protein can be placed in the tRNA (guanine-N1-)-methyltransferase, N-terminal superfamily, which represents the N-terminal domain of SPOUT superfamily enzymes, including the tRNA:Gm18 methyltransferase TrmH. This domain is characterized by a rare \u03b1/\u03b2 knot structure that poses a significant folding challenge. It is native to Streptococcus mitis 29/42 and is annotated with UniProt keywords Cytoplasm and rRNA processing.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 3146, 16478, 11929, 22316, 3416, 16, 2154, 1977, 4396, 1942, 2347, 1966, 1925, 61, 17, 29283, 17, 54, 17, 12417, 12, 2041, 14080, 13, 17, 3100, 16478, 2454, 1990, 4346, 9039, 18, 2144, 5038, 3205, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 3146, 6249, 1958, 4948, 6295, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4595, 19, 4666, 26646, 28253, 13975, 16, 2154, 21569, 5038, 3165, 43, 6515, 16, 5844, 160, 19, 161, 26646, 4346, 3418, 4415, 1958, 3146, 5547, 18, 2052, 3728, 1977, 6293, 1927, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5038, 16, 2710, 1920, 18055, 1984, 1930, 13952, 1009, 19, 26046, 1009, 5767, 16, 12440, 1920, 6295, 1927, 3146, 6249, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 10089, 12, 16904, 17, 13007, 17, 13, 17, 16478, 16, 56, 17, 4262, 13975, 16, 2154, 4972, 1920, 56, 17, 4262, 3418, 1927, 18055, 1984, 13975, 5038, 16, 2710, 1920, 10089, 30, 28673, 1025, 16478, 28402, 1023, 18, 2052, 3418, 1977, 4378, 2007, 43, 5844, 160, 19, 161, 26646, 3170, 1988, 17274, 43, 2228, 10328, 6013, 18, 2176, 1977, 6196, 1942, 15746, 3263, 1937, 3230, 19, 3858, 1930, 1977, 10633, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MKIKVVTVGKLKEKYLKDGIAEYSKRIESENQKILEIEGQRILSKVGDRDFVIVGFSTLTFIIGGSLGLAQDVKKRANEQIYRAFTIQQGSPYHKSRFAKLEMIELADEKTPDKASLAIEGKTFSSEEFSKQLEEASIKLSVSFGRLTLPHQLMRLVLV", "metadata": {"id": "S7Z909", "cluster": 20534661, "interpro_all": ["IPR029028", "IPR003742", "IPR029026"], "interpro_used": ["IPR003742", "IPR029028", "IPR029026"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein falls within the Allene oxide cyclase/Dirigent protein superfamily, which comprises plant-specific proteins that exert stereochemical control over cyclization reactions. Members include allene oxide cyclases involved in jasmonate biosynthesis and wound response, as well as dirigent proteins that impart stereoselectivity on phenoxy radical-coupling to yield lignans during secondary metabolism. In addition, the protein should include a Allene oxide cyclase barrel-like domain that functions as a spirotetronate cyclase or Diels-Alderase involved in the biosynthesis of antibiotics. Structurally comprised of two eight-stranded antiparallel \u03b2-barrels, it mediates spiro-conjugate synthesis in pathways producing compounds such as pyrroindomycins. It is derived from Streptomyces sp. CB01883 and is connected to UniProt keyword Signal.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 12182, 2651, 1920, 23260, 1021, 7491, 16526, 19, 17393, 6419, 1031, 2213, 13975, 16, 2154, 12936, 4496, 17, 2487, 2697, 1988, 10788, 26692, 11402, 2285, 2338, 25267, 5298, 18, 4678, 3951, 23260, 1021, 7491, 16526, 1036, 3286, 1922, 30014, 8870, 8132, 1930, 6376, 2644, 16, 1966, 2486, 1966, 17393, 6419, 1031, 2697, 1988, 2754, 5263, 26692, 4127, 25419, 8158, 1990, 3037, 7221, 6917, 17, 7590, 1942, 4307, 12975, 2075, 2409, 4067, 4714, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 23260, 1021, 7491, 16526, 19560, 17, 3189, 3418, 1988, 4088, 1966, 43, 22075, 28959, 8870, 16526, 2014, 8769, 4668, 17, 11174, 7124, 4127, 3286, 1922, 1920, 8132, 1927, 7560, 18, 12171, 8842, 1927, 2288, 5066, 17, 10338, 28892, 161, 17, 19560, 1036, 16, 2176, 10412, 22075, 17, 13074, 4271, 1922, 3873, 7144, 4300, 2427, 1966, 6487, 1931, 2762, 7928, 1036, 18, 2176, 1977, 3595, 2037, 22874, 2056, 18, 5529, 6924, 7331, 1010, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MMVRRMRAVGLIGAETGRDGKTAKVIKVSVGNETIGSGDILDARGKVIGSFASVLDLPEGQIMFHSRQKAGENPFVDLGNREQAVTITLTAKRVAAATVLLAPAESSLAAGTNRLTRVRVLELGGPQPVECTVTQHEPPVTMLQCLTAAVTGGTGAYVGAGGTAT", "metadata": {"id": "A0A1Q5KBU2", "cluster": 23083631, "interpro_all": ["IPR044859", "IPR041013"], "interpro_used": ["IPR044859", "IPR041013"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the polypeptide chain function: The protein is associated with the Nucleotide cyclase superfamily, which encompasses catalytic domains found in adenylyl, guanylyl, and diguanylate cyclases responsible for synthesizing cyclic nucleotide second messengers. These domains share a core ferredoxin-like fold, though the specific nucleotide-binding mode differs between subtypes such as the GGDEF domain and adenylate cyclases. Additionally, the protein has a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. In addition, the protein should include a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It is derived from Anopheles christyi and features UniProt keywords ATP-binding, cAMP biosynthesis, and Repeat. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 5489, 16526, 13975, 16, 2154, 21569, 6804, 4682, 2435, 1922, 27802, 16, 13504, 25671, 16, 1930, 4325, 13785, 9075, 16526, 1036, 5061, 1958, 25292, 9821, 5489, 2812, 16716, 1036, 18, 2144, 4682, 7948, 43, 4728, 25304, 22389, 10960, 17, 3189, 3728, 16, 4170, 1920, 2487, 5489, 17, 2743, 5754, 11457, 2192, 8160, 2427, 1966, 1920, 12358, 3695, 1038, 3418, 1930, 23052, 16526, 1036, 18, 4950, 16, 1920, 2213, 2258, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 1977, 3595, 2037, 24945, 20898, 16582, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 6225, 8132, 16, 1930, 6865, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MRFLTTERFLIDVAFLVVFVIGQIMHSQQTEITRRLDFIWKLQATEEKEDMEHLQAYNRKLLANILPVHVADHFLMREKNIEEIYHEQCDTVCVMFASIPNFSEFYIELEGNNEGVECLRLLNEIIVDFDELLGLERFRYVEKIKTTGSTYMAASGLTANSCDKNDFQHVIAMMDYALELFQKITDVNEHSFNNFRMRIGINIGPVVAGVIGTRKPQYDIWGNAVNVASRMDSTGLMDHIQVTEDVYQIVKDQGYNLTCRGTVNVKGKGTMITYLMPGLVKDPPN", "metadata": {"id": "A0A182JXV2", "cluster": 24779552, "interpro_all": ["IPR001054", "IPR018297", "IPR029787"], "interpro_used": ["IPR029787", "IPR018297", "IPR001054"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein should include a YqaJ viral recombinase domain that functions as a processive, Mg(2+)-dependent alkaline exonuclease to digest linear double-stranded DNA, with a preference for 5'-phosphorylated ends. This oligomeric domain constitutes the exonuclease component of the two-part SynExo viral recombinase system. In addition, the protein belongs to the PD-(D/E)XK endonuclease-like domain superfamily, which comprises enzymes sharing a conserved core fold that catalyze the ATP- or magnesium-dependent exonucleolytic cleavage of DNA. These domains typically function within larger helicase-nuclease complexes, such as bacterial RecBCD or viral exonucleases, to process genomic ends and generate substrates essential for the initiation of recombinational repair and DNA replication. Additionally, the protein features a Lambda-type exonuclease domain that functions as a 5' to 3' exonuclease, digesting double-stranded DNA to generate 3' single-stranded overhangs involved in recombination. This domain is characteristic of bacteriophage genomes and integrated prophage regions within prokaryotic organisms. It is native to freshwater metagenome.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 67, 1055, 1019, 1013, 4324, 21366, 3418, 1988, 4088, 1966, 43, 2585, 2320, 16, 2786, 12, 22, 15, 13, 17, 3100, 10746, 24966, 1942, 20808, 4258, 4825, 17, 10338, 2678, 16, 1956, 43, 8308, 1958, 25, 11, 17, 7199, 9618, 18, 2052, 19206, 3418, 14879, 1920, 24966, 4594, 1927, 1920, 2288, 17, 3131, 2540, 2783, 1037, 4324, 21366, 2433, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 3203, 17, 12, 46, 19, 47, 13, 66, 1040, 18697, 17, 3189, 3418, 13975, 16, 2154, 12936, 5038, 10763, 43, 5305, 4728, 3728, 1988, 18170, 1920, 4498, 17, 2014, 13148, 17, 3100, 7049, 2626, 6586, 6404, 1927, 2678, 18, 2144, 4682, 5745, 2347, 2651, 4327, 15318, 17, 16230, 5048, 16, 2427, 1966, 4543, 2090, 8284, 1007, 2014, 4324, 24966, 1036, 16, 1942, 2585, 4935, 9618, 1930, 5655, 6249, 4415, 1958, 1920, 6035, 1927, 7827, 1923, 5059, 1930, 2678, 5158, 18, 4950, 16, 1920, 2213, 4075, 43, 18279, 17, 2601, 24966, 3418, 1988, 4088, 1966, 43, 25, 11, 1942, 23, 11, 24966, 16, 20808, 1941, 4825, 17, 10338, 2678, 1942, 5655, 23, 11, 2957, 17, 10338, 27538, 1036, 3286, 1922, 7827, 18, 2052, 3418, 1977, 6293, 1927, 24613, 7313, 1930, 6714, 8839, 2170, 3451, 2651, 21545, 7373, 18, 2176, 1977, 6196, 1942, 18762, 16552, 2225, 18, 3], "output": "MRDFRIGGSEAAAACGINPYTKWGQVLEPVLRDELRQTLGIIEPDGFLFQDGDLCLVELKTVGLNGASAWKRMYFGCLVGGQRFITRTLDEAPAPDGTDGTTNALKLLYPAARKASEVEEDRIIQELKMQMGDASNATVRGVTVATWRFEACLTTTTFRRFALKSRIALWLDKTGKQPLPEAGEAAEWTPATLAEVRPADLPEWVQGTDDDSVPITYQVQAQVYMAITGADFDPKVWATILSLLIEFKDLVDRHAETVELPEHKWPLVEQARKARDANTSRTGTDTDKLKAEHPEA", "metadata": {"id": "A0A6J5Z8S5", "cluster": 200898, "interpro_all": ["IPR017482", "IPR011604", "IPR011335", "IPR019080"], "interpro_used": ["IPR019080", "IPR011604", "IPR017482"], "interpro_unused": ["IPR011335"]}, "task_type": "infilling"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein should feature a FlgA SAF domain that forms the conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA, which is required for P-ring assembly in bacteria. It adopts a $\\beta$-clip fold structurally similar to Type III antifreeze proteins. Also, the protein is categorized in the Flagellar protein FlgA family, which functions as a chaperone essential for the assembly of the flagellar P-ring. It is required for flagellar biosynthesis and motility, and plays a significant role in biofilm formation in species such as *Campylobacter*. Furthermore, the protein contains a SAF domain that adopts a structural \u03b2-clip fold and is found in a diverse range of proteins, including antifreeze proteins, flagellar assembly factors such as FlgA, and CpaB pilus components. It is expressed in Gammaproteobacteria bacterium and is linked to UniProt keywords Signal, Periplasm, and Cilium.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 2300, 4223, 4345, 3418, 1988, 4952, 1920, 5305, 45, 17, 4262, 3031, 1927, 1920, 24154, 5342, 3362, 58, 17, 6335, 3337, 2213, 2300, 4223, 16, 2154, 1977, 3414, 1958, 58, 17, 6335, 5957, 1922, 4802, 18, 2176, 24032, 43, 8, 38, 4666, 8, 17, 18709, 3728, 12171, 2551, 1942, 2601, 4337, 12244, 2329, 6931, 2697, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 24154, 2213, 2300, 4223, 3416, 16, 2154, 4088, 1966, 43, 14044, 4415, 1958, 1920, 5957, 1927, 1920, 24154, 58, 17, 6335, 18, 2176, 1977, 3414, 1958, 24154, 8132, 1930, 9254, 16, 1930, 5705, 43, 2228, 2770, 1922, 9638, 3337, 1922, 3038, 2427, 1966, 14, 22657, 14, 18, 3677, 16, 1920, 2213, 5461, 43, 4345, 3418, 1988, 24032, 43, 4346, 161, 17, 18709, 3728, 1930, 1977, 2435, 1922, 43, 6445, 3109, 1927, 2697, 16, 2710, 12244, 2329, 6931, 2697, 16, 24154, 5957, 2790, 2427, 1966, 2300, 4223, 16, 1930, 22675, 1014, 7547, 1957, 4178, 18, 2176, 1977, 3198, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 2733, 16, 20171, 16, 1930, 28997, 18, 3], "output": "MDIMKNTYLTTVLIIFLTLSLTANASGSKFASHEKIRTAARQFLVEKANKLGFQDFTVEVGHLDNRLKLPTCDSELTAKGGNNKLPGNISIAVRCNSDKPWKIYIQASVKAYKSIYVARSPIARGEIVRKSNLKMAKQDVTSLNGNYFTDINLINGHIAKRLIRENQAIKSYMLAKSKVIKRGEYVMIIAETSGISIKMKGKALNDATIGEHVRVKNMNSKRIIEGTAIRSGVVKINI", "metadata": {"id": "A0A7C1UVF6", "cluster": 299113, "interpro_all": ["IPR017585", "IPR039246", "IPR041231", "IPR013974"], "interpro_used": ["IPR017585", "IPR039246", "IPR013974"], "interpro_unused": ["IPR041231"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has the following function: The protein is a member of the Secondary Metabolite Biosynthesis Regulators family, which functions as a group of transcription factors that regulate the expression of gene clusters involved in the biosynthesis of diverse secondary metabolites, including antibiotics and mycotoxins. These regulators typically contain a C6 finger domain and control specific pathways for compounds such as neosartoricin and viridicatumtoxin, while also participating in efflux pump regulation and detoxification. Furthermore, the protein possesses a Xylanolytic transcriptional activator regulatory domain that serves a regulatory function within fungal zinc cluster transcription factors, connecting the N-terminal DNA-binding domain to the C-terminal acidic region. It is essential for the activity of proteins like XlnR, which modulate the expression of cellulolytic and xylanolytic genes, as well as D-xylose catabolism, in response to D-xylose availability. Moreover, the protein should feature a Zn(2)Cys(6) fungal-type DNA-binding domain that functions as a transcriptional regulator in fungi by utilizing a cysteine-rich motif to facilitate zinc-dependent DNA binding. It forms a binuclear zinc cluster where two zinc atoms are coordinated by six cysteine residues, establishing the molecular basis for specific DNA recognition. This domain is found in proteins involved in diverse metabolic and biosynthetic pathways, including galactose, arginine, and pyrimidine metabolism. It occurs in Botrytis fragariae and contains UniProt keyword associations Metal-binding and Nucleus. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 4067, 9483, 8132, 9098, 3416, 16, 2154, 4088, 1966, 43, 2210, 1927, 3213, 2790, 1988, 5741, 1920, 2294, 1927, 2359, 5859, 3286, 1922, 1920, 8132, 1927, 6445, 4067, 6926, 16, 2710, 7560, 1930, 5078, 20223, 18, 2144, 9098, 5745, 5531, 43, 12822, 8497, 3418, 1930, 2285, 2487, 3873, 1958, 4300, 2427, 1966, 11724, 5735, 7446, 18151, 1921, 1930, 2787, 12546, 9576, 4575, 10960, 16, 2679, 2222, 9505, 1922, 11247, 8912, 3640, 1930, 18169, 18, 3677, 16, 1920, 2213, 14465, 43, 23665, 6586, 5224, 9518, 4948, 3418, 1988, 10634, 43, 4948, 2347, 2651, 8697, 7997, 4377, 3213, 2790, 16, 15031, 1920, 56, 17, 4262, 2678, 17, 2743, 3418, 1942, 1920, 45, 17, 4262, 9931, 3031, 18, 2176, 1977, 4415, 1958, 1920, 2455, 1927, 2697, 3189, 11764, 16964, 16, 2154, 8480, 1920, 2294, 1927, 18485, 6586, 1930, 23665, 6586, 2628, 16, 1966, 2486, 1966, 46, 17, 21055, 19480, 16, 1922, 2644, 1942, 46, 17, 21055, 6855, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 7230, 12, 22, 13, 4998, 12, 26, 13, 8697, 17, 2601, 2678, 17, 2743, 3418, 1988, 4088, 1966, 43, 5224, 7888, 1922, 10520, 2007, 10232, 43, 8666, 17, 5536, 5219, 1942, 6628, 7997, 17, 3100, 2678, 2743, 18, 2176, 4952, 43, 8768, 13821, 7997, 4377, 2597, 2288, 7997, 9030, 2032, 11651, 2007, 3798, 8666, 4248, 16, 11810, 1920, 3272, 4859, 1958, 2487, 2678, 5708, 18, 2052, 3418, 1977, 2435, 1922, 2697, 3286, 1922, 6445, 4487, 1930, 14041, 3873, 16, 2710, 15996, 16, 9732, 16, 1930, 21611, 4714, 18, 2176, 5110, 1922, 12499, 6907, 3600, 4145, 6148, 1021, 1930, 5461, 20709, 11121, 2538, 5253, 6048, 17, 2743, 1930, 5607, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "LSCTNCRRRKIRCNKTTNPCIPCQASGTECIFPTRIRNPRPRQSNPKSRDAELLKRISHLESLVSRIDATKLLGEDGQVEDEVRSNTPSSGPRPHRSFTSPSQKFNDNAHEIGFVPGRLDHQFADFIKRQETESIYTHDGFWTRLSEEIDGLKQLIENPSDDEDENSGSTATSPASKYDYPSQFVFDSKVTSSNIIIPYPSVEHRNILFDFYLKNVHPMVVTVHKSTSHLMVNSSSELLDPNTGRHKFKSLEASTFSMYLAAVTSMSNEECLEFLDEERQILVTRYKTATEIALQESDFLNSVEIVTLQALMTYIAAMRSHDRSRSVWAFIGLAVRLARGIGLHRDGSNQPFDVEMRRRVWWSLVVLDTRASEDRGTETMITDGSFDTKMPANINDEDISVNSTTSPVDRMGFTSMTFACITMTVSGIGLRMNFVPTRLDAPVLTTEQKEQMIKGFTDKVESTYLAGADPNDPRFFWFCRVSRLLSLKLWLVTQYPLQRRKSTHRVLPRGQSLRTAMAYLNLMEEMWEHGPSKGWLWFFQTYVPWHAIAVALAELCAEPTGTLADQAWEVIEFHYNKWSEYVADTKDGMIWRPVKNLLKRARAARRRERGLSDSQASTTPTAISNSNMYSPAPNLGAEFSPIMPENNNYRQPSTIGQVDPIGQNTYGAMGFDLPIPMGSTPIDTNMTSPLPIPDGYTNAHWNEFIFGLGTVGGDAPQHPEMWG", "metadata": {"id": "A0A1S6R556", "cluster": 1644870, "interpro_all": ["IPR050613", "IPR007219", "IPR036864", "IPR001138"], "interpro_used": ["IPR050613", "IPR007219", "IPR001138"], "interpro_unused": ["IPR036864"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein is grouped in the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. Furthermore, the protein carries a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. Moreover, the protein falls within the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is found in Gammaproteobacteria bacterium and is annotated with UniProt keywords Metal-binding. Please provide the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 7762, 30, 1920, 2213, 1977, 10809, 1922, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 3677, 16, 1920, 2213, 16252, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 3950, 16, 1920, 2213, 12182, 2651, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2435, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 6048, 17, 2743, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MLLNATDMHLKVTNQELLDPLEKDGLKLNSRGFISAEKMPVIWRGPMVRGAVMQLMAQTNWGKLDYLIVDTPPGTGDVQLTLLQKIALSAAIVVTTPQDIAVADTMKGIEMLKKLNLPILGLIENMSYFEPKDSKKRYYLYGKGGAKTLSKEYQLDLLGEVPQFEFEESNLTNQNMEISKILDLIASKVVKKLDSMSSKNKSLIPQVNK", "metadata": {"id": "A0A920J3Y4", "cluster": 2515034, "interpro_all": ["IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR033756", "IPR000808", "IPR027417"], "interpro_unused": ["IPR019591", "IPR044304"]}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein should contain a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein is grouped in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein should feature a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It has been characterized in Lysobacter sp and is connected to UniProt keyword Isoprene biosynthesis and Transferase.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 2258, 2252, 4378, 1922, 3629, 5883, 2056, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 26690, 1021, 8132, 1930, 13763, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MSASGWSSWPAPAKLNLFLRITGRRSDGYHELQTVFGAIVRVGASAFGVSAQQDLAVRAAILLQKSANVCEGVDIGFGGGSSDAATVLVALNRLWNTGLSTLEWAEGVGEALVPVMLPPAWYVIAEPGVHCPTSGDTRSARLGNAFEPVLRAREPAVEATLASREAAQAALRMLPSDLRCRLVAGAQVSPLHRALARTRLLEWGDLIHLRLRPDTVVKRIPEGGLARLGLHLGADVPVFVHGCNALLFGSPDLTRDSPALKMADFVAGAALSQVGDARLTGSGSGCFVEF", "metadata": {"id": "A0A522Y358", "cluster": 6647929, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR020568", "IPR036554", "IPR014721"]}, "task_type": "infilling"} {"instruction": "The protein contains a Domain of unknown function DUF6471 domain that is found predominantly in Proteobacteria and is predicted to function as a DNA-binding module. This region is defined by a conserved KxxRG motif and a highly conserved leucine residue. It is derived from Pseudomonadota bacterium.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 5461, 43, 3418, 1927, 5435, 2347, 4855, 17136, 6106, 1009, 3418, 1988, 1977, 2435, 7700, 1922, 22266, 1930, 1977, 4396, 1942, 2347, 1966, 43, 2678, 17, 2743, 9059, 18, 2052, 3031, 1977, 3608, 2007, 43, 5305, 53, 14710, 1005, 1029, 5219, 1930, 43, 3626, 5305, 12624, 6181, 18, 2176, 1977, 3595, 2037, 11520, 3947, 12595, 3857, 14061, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MAGKQQDKAELARRDISYKELARLLPDEVDITEKTQPGRRTDRLRYYYAEASRILNYVQLKTKINRGSFSAGFFIKVLRAIGAMH", "metadata": {"id": "A0A2W4TJI2", "cluster": 7257721, "interpro_all": ["IPR045526"], "interpro_used": ["IPR045526"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein carries a Munc13 homology 1 domain that functions as a key regulator of membrane trafficking, specifically mediating vesicle priming and maturation during exocytosis. Predicted to adopt an $\\alpha$-helical structure, it is frequently flanked by C2 domains and is essential for synaptic transmission and the secretion of large dense-core vesicles across diverse eukaryotes. Furthermore, the protein is classified under the Protein unc-13 homologue family, which functions in plants to control the tethering of the proton ATPase AHA1 to the plasma membrane, a process essential for stomatal opening in response to low carbon dioxide and light. These proteins contain two Munc13 homology domains that likely mediate exocytotic priming analogous to synaptic transmission in animals. In addition, the protein possesses a Mammalian uncoordinated homology 13, domain 2 (MHD2) domain that regulates membrane trafficking and vesicle exocytosis, particularly in the context of synaptic vesicle priming and maturation. Predicted to form an $\\alpha$-helical structure, this conserved module is typically found alongside MHD1 and C2 domains in Munc13 and CAPS family proteins essential for secretory pathways. It is derived from Chlorella desiccata (nom. nud.).\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 16252, 43, 30403, 3633, 9039, 21, 3418, 1988, 4088, 1966, 43, 3834, 7888, 1927, 3260, 9604, 16, 4475, 10239, 11502, 11794, 1930, 7655, 2409, 18904, 18, 4396, 1942, 14103, 1925, 8, 38, 4595, 8, 17, 11514, 3170, 16, 2176, 1977, 5467, 20185, 2007, 8453, 4682, 1930, 1977, 4415, 1958, 6251, 5303, 1930, 1920, 5512, 1927, 3103, 10472, 17, 4728, 8319, 3436, 6445, 15021, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2213, 5269, 17, 2590, 17986, 3416, 16, 2154, 4088, 1922, 4793, 1942, 2285, 1920, 23991, 1927, 1920, 8433, 9444, 22844, 1009, 1942, 1920, 3582, 3260, 16, 43, 2585, 4415, 1958, 23075, 9497, 1922, 2644, 1942, 2330, 5056, 15422, 1930, 3696, 18, 2144, 2697, 5531, 2288, 30403, 3633, 9039, 4682, 1988, 3205, 8265, 18930, 27932, 3153, 11794, 12464, 1942, 6251, 5303, 1922, 3555, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 6492, 20732, 2538, 4597, 9039, 2590, 16, 3418, 22, 12, 5146, 9091, 13, 3418, 1988, 7014, 3260, 9604, 1930, 11502, 18904, 16, 4443, 1922, 1920, 4491, 1927, 6251, 11502, 11794, 1930, 7655, 18, 4396, 1942, 2386, 1925, 8, 38, 4595, 8, 17, 11514, 3170, 16, 2052, 5305, 9059, 1977, 5745, 2435, 17764, 5146, 7240, 1930, 8453, 4682, 1922, 30403, 3633, 1930, 7070, 3416, 2697, 4415, 1958, 11518, 3873, 18, 2176, 1977, 3595, 2037, 4891, 5870, 23843, 5499, 12, 9684, 18, 28416, 18, 13, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MQSHVESAVGDRRLLLRHALQEYKDKGGQIAFPQINKRGKLDLIVMCSAAGSLNNSILSRLPSNNSQEHPSSAAGGAGGGIDEREMQMLAFQIFVSACGSKASPALLQTVRAQLEIGEALGKDLTTVTQLANKNQSFRSFAAWRSGIASVISKSLEHAAAHSWVSQQGGDAAKSGAPARSLLASLRGSEEATRRLAGNITGGDLTFPMGLSIQVAEMLLCGVFDSLDEGQFVPEAQELLSGMWVHFRQYMASKETSLLHAGVLLAQSATGTAANSSAADAHTSFANTGEMQVLLEFLRSIYGLQNDKNNNDAGAFEGMLTRCIKASRTALLATETSALLHVERNQFVPILRQYQPAAAAIAADTLHELATIHASVDLESELMAEIAAHGGAGASQQLPPPWGAVQRITWLDRIMAEEDWSPVVQQRGATSRSAVEVLKVMDDAVDTLFGMGKYCKMSLASVGTADSLVPPAPPLTRFKKDLAESAEVEAMGGSSGIKSVTNKVGAAGVMYDTLVVRANSMYYLATKTSDLEALVKEKWHAAQEEEVSADAASLRFITLKLVCGDLRSAIFKDLYAFHVEYSRIQSILEEVDGALGMLLHVLLDGGPNRLFTLQDMPILLEDFEQLRAMFFAEGAGLDPMSLDTKALITASKTTKKQPLKASAGSAEGILDPETVLRVLCHRADYEPNVFSASVSRSFAALSFPTSATKATKQGGVRRMEANPVGCSGFDGWLMDALDVPLVLNIEGTSQRKSLPHLQIPSMAINGISSLSTIDALVTLLQIVPSSAFLRRMDVCEADDYEETEYFAAARGVLLSSNVWPQLGISPQMNSALAFTSKVLDALSAEASTALSDYVGAAFARRAAEVHNQVALEEDYGAKMLTWLISVNCLTKSVAPLLHNWAQQQVSNMYGIAVPASVVNALVDGMDAVLQLVTSWLPSLTQDQQSRILFRGTGFLNGAVASAAEGVDNICEMLDEGLAPRMAGHVCKTLSAAVTAVGKLCLPLENALYTASKFLKKDHKIPKKL", "metadata": {"id": "A0A8T2W6W4", "cluster": 8424171, "interpro_all": ["IPR014770", "IPR014772", "IPR008528"], "interpro_used": ["IPR014770", "IPR008528", "IPR014772"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein possesses a DnaT DNA-binding domain that cooperatively binds single-stranded DNA (ssDNA), a function essential for primosomal protein activity in DNA replication. This domain adopts a three-helix bundle structure stabilized by a specific N-terminal loop and forms a spiral filament assembly upon DNA binding. It is identified in Salmonella enterica subsp. enterica serovar Java.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 2678, 1031, 2678, 17, 2743, 3418, 1988, 13350, 1954, 6876, 2957, 17, 10338, 2678, 12, 15063, 13, 16, 43, 2347, 4415, 1958, 2610, 4969, 2213, 2455, 1922, 2678, 5158, 18, 2052, 3418, 24032, 43, 2559, 17, 7864, 14142, 3170, 12017, 2007, 43, 2487, 56, 17, 4262, 5881, 1930, 4952, 43, 17366, 10797, 5957, 4073, 2678, 2743, 18, 2176, 1977, 2899, 1922, 11681, 24847, 19615, 18, 24847, 28353, 13149, 7302, 18, 3], "output": "MAGDWIKMRADLHTHPKVVRMASALKADRLRIVGGLHSSAETLDDLIGFPGFARAMMAVGWLEEDGESLVIPRFEAHKRTREEKRREDLKDKTPHIGDEKNQPVDNSGGEEPDPHATNSVTPDSWTPDPDFTKRAALWGVNLKTDVTPFELADFITYQKLARSVQLSRSKPARTQQRDVNAVPEPDSEIPPGFRGAWCLFDVHSVDGFLDGYNGQSAKRRAQDADRKRNVRKASASEADKDGYAPPGGSGSLGKFTMWKAEGKAFHHDQWQ", "metadata": {"id": "A0A5U8K0E9", "cluster": 10740044, "interpro_all": ["IPR040480"], "interpro_used": ["IPR040480"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me a peptide sequence capable of: The protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein contains a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. Additionally, the protein falls within the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. It is found in Lysobacter silvisoli and is annotated with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 5461, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2176, 1977, 2435, 1922, 3629, 5883, 4059, 7400, 8436, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSLQVQPRLITLEGGEGAGKSTVLAALREALAATGAEVLCTREPGGTPLAEQIRGLLLDTHHEPATPEAELLLVFAGRAQHVSETVLPALRRGAWVVSDRFTDASYAYQGEGRGLDPEFIAELERRVVGIEPALTLLLDVPVAIGLQRARGRGAADRIEAEREDFFERVRAGYRARAQSQPQRFHVIDASQPADVVAAEAVARVRRLLEAGA", "metadata": {"id": "A0A371K242", "cluster": 12394172, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR027417", "IPR039430", "IPR018094"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "\"The protein is a member of the Translation protein, beta-barrel domain superfamily, which comprises a circularly permuted \u03b2-barrel fold found in key translation initiation and elongation factors like EF-Tu, eEF1A, and EF-G. This domain facilitates the transport of aminoacyl-tRNA and ribosomal translocation, often interacting with the switch 2 region to stabilize domain orientations during GTP-dependent conformational changes. Furthermore, the protein carries a Ribosome maturation factor RimM, PRC barrel domain that facilitates the final assembly of the 30S ribosomal subunit head region and the efficient processing of 16S rRNA. This domain binds specifically to ribosomal protein uS19 and free 30S subunits, assisting in late-stage maturation and preventing the accumulation of precursor rRNA forms. Also, the protein can be placed in the Ribosome maturation factor RimM family, which functions as a 30S ribosomal subunit-binding protein implicated in the processing of 16S ribosomal RNA. Broadly distributed across bacteria and plant chloroplasts, this factor facilitates ribosome maturation and is frequently associated with translation-related genes such as trmD. It occurs in Gammaproteobacteria bacterium and is classified with UniProt keywords Chaperone, Cytoplasm, and Ribosome biogenesis.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 1977, 43, 7210, 1927, 1920, 6410, 2213, 16, 4666, 17, 19560, 3418, 13975, 16, 2154, 12936, 43, 10262, 1954, 7187, 3072, 161, 17, 19560, 3728, 2435, 1922, 3834, 6410, 6035, 1930, 9971, 2790, 3189, 8485, 17, 9037, 16, 11150, 21952, 16, 1930, 8485, 17, 49, 18, 2052, 3418, 11374, 1920, 4860, 1927, 3835, 14645, 17, 10089, 1930, 11196, 7849, 16, 3868, 8615, 1956, 1920, 6195, 22, 3031, 1942, 13448, 3418, 16450, 2409, 9319, 17, 3100, 8523, 2840, 18, 3677, 16, 1920, 2213, 16252, 43, 12794, 7655, 2991, 14764, 1035, 16, 29134, 19560, 3418, 1988, 11374, 1920, 3948, 5957, 1927, 1920, 27755, 11196, 5903, 4469, 3031, 1930, 1920, 5807, 4587, 1927, 11209, 9067, 18, 2052, 3418, 6876, 4475, 1942, 11196, 2213, 2022, 4136, 1930, 3294, 27755, 6991, 16, 27840, 1922, 5058, 17, 3587, 7655, 1930, 8444, 1920, 4858, 1927, 7897, 9067, 4952, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 12794, 7655, 2991, 14764, 1035, 3416, 16, 2154, 4088, 1966, 43, 27755, 11196, 5903, 17, 2743, 2213, 6835, 1922, 1920, 4587, 1927, 11209, 11196, 3146, 18, 11984, 6533, 3436, 4802, 1930, 4496, 24627, 16, 2052, 2991, 11374, 12794, 7655, 1930, 1977, 5467, 2458, 1956, 6410, 17, 2712, 2628, 2427, 1966, 28402, 1007, 18, 2176, 5110, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 14044, 16, 5239, 16, 1930, 12794, 13008, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MGRLGAARGLQGWLRVKSFADPPEQLENYRTWNLLVNDQCREMRDAAEELRGAEIRVKRADLPPAGEKEWYWADLEGLEVRNLEGRPLQGERRRLIPFVQGSRVREVDLQARRLIVDWDPADTLRRLRITPRGLECRLDGIETGRVRGLMATGANDVLIV", "metadata": {"id": "A0A6B1EHX6", "cluster": 12465497, "interpro_all": ["IPR011033", "IPR056792", "IPR011961", "IPR002676", "IPR036976", "IPR009000"], "interpro_used": ["IPR009000", "IPR056792", "IPR011961"], "interpro_unused": ["IPR011033", "IPR002676", "IPR036976"]}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein features a DUF2281 domain that is found in putative uncharacterized proteins, though some members are described as transcriptional regulators of the Xre family. It is expressed in Candidatus Melainabacteria bacterium HGW-Melainabacteria-1.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 4075, 43, 4855, 6680, 4839, 1009, 3418, 1988, 1977, 2435, 1922, 6770, 24528, 2697, 16, 4170, 2673, 4678, 2032, 2910, 1966, 5224, 9098, 1927, 1920, 15507, 1021, 3416, 18, 2176, 1977, 3198, 1922, 14550, 1031, 1957, 4221, 2005, 20013, 2341, 18339, 14061, 7175, 1018, 17, 4221, 2005, 20013, 2341, 18339, 17, 21, 18, 3], "output": "MLDDRKLLADIHSLPPGDQSEVIDFISRLKARHVSQAEATHPSSTQPVSQAVSPLGAMKGLILHMADDFDEPLNDFAEYMA", "metadata": {"id": "A0A2N1UXU8", "cluster": 13541461, "interpro_all": ["IPR018739"], "interpro_used": ["IPR018739"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein incorporates a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Also, the protein incorporates a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Moreover, the protein should contain a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. It has been detected in Lactobacillus paragasseri and carries UniProt keyword assignments DNA excision, DNA damage, and Excision nuclease.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2222, 16, 1920, 2213, 19683, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2176, 2258, 2252, 3330, 1922, 18134, 8202, 4223, 5590, 18842, 1930, 16252, 20709, 11121, 2538, 18306, 2678, 10940, 16, 2678, 4293, 16, 1930, 10940, 16230, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MIRRQKNKKFELVSKFQPAGDQEQAIKKLTDGFENGENVVAKLNKPTLVISHNKTLVGQLYGEFKEFFPKNAVDYFVSYYDYYQPEAYVPQSDTYIEKDVIVVASVSCIYGLGDPREYAASVVSISEGQEISRDVLLRDLVNIQYDRNDIDFQRGRFRFFGDEIDRIVEVDSLTGEVIGEREQVSIFPATHFVTNEQIMQRALASIKDEMNIQVKKFEGEGQRTTYDMEMMSEVGYTNGIENYSRHMEGRKAGQPPHTLLDFFPDDARKQTLIDYGFRLPSALDNRPLKLEEFEKHVNQIMYVSATPGDYELNQTKGQIDDLVGEINKRIDRDERVFVTTLTKKMAEDLTDYLKDLGIKVRYLVLIGINLLREGIDVPEVSLVAILDADKEGFLRSTRPLVQTIGRAARNSTDSMREAIDATERRRSLQMKFNKEHGITPKTIVKPIRDVISITKDSDIKTLTAQMQEAAKKLDFEEAANLRDAIMDLQKQVHEKKKKAQILEGATGTGKTFTMADSSINDEIDQLRHKTTSDLMSRNVRGDVVEIFPAGYSDHAFRVEKLLEAQRIKFLILIDESHATMPELKAMYNGDRDHKVEQIIRPTGLLDPEIEVRPIHSDIKTLERLEIIRDLRLGKFDNGKVIMYADSIEKENKESFADLNFDELTKKQKQTM", "metadata": {"id": "A0A6B2FV30", "cluster": 15833577, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001650", "IPR014001", "IPR001943"], "interpro_unused": ["IPR004807", "IPR024759", "IPR036876", "IPR006935", "IPR027417", "IPR041471"]}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein falls within the SCF complex F-box component family, which functions as a subunit of SCF (SKP1-cullin-F-box) E3 ubiquitin ligase complexes to mediate the ubiquitination and subsequent proteasomal degradation of target proteins. These proteins regulate diverse plant developmental processes, including meristem and floral organ identity, cell proliferation, and culm strength, while also contributing to vascular bundle formation and environmental stress responses. Additionally, the protein possesses a F-box associated beta-propeller domain that is typically found C-terminal to an F-box motif in plant proteins and serves as a subunit of SCF E3 ubiquitin ligase complexes. It facilitates the ubiquitination of target proteins, marking them for degradation. Furthermore, the protein belongs to the Galactose oxidase/kelch, beta-propeller superfamily, which constitutes a structural $\\beta$-propeller domain utilized in diverse enzymatic and cytoskeletal functions. Members include the copper-dependent galactose oxidase, which catalyzes the stereospecific oxidation of primary alcohols to aldehydes, and kelch-repeat proteins that often mediate protein-protein interactions or actin cross-linking. It occurs in Durio zibethinus (Durian). Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 12437, 2796, 48, 17, 5758, 4594, 3416, 16, 2154, 4088, 1966, 43, 5903, 1927, 12437, 12, 3097, 5113, 17, 22859, 1921, 17, 48, 17, 5758, 13, 10968, 6526, 11905, 5048, 1942, 8265, 1920, 11758, 1930, 4521, 19308, 4877, 1927, 2758, 2697, 18, 2144, 2697, 5741, 6445, 4496, 5878, 4028, 16, 2710, 29842, 1930, 20741, 3090, 6833, 16, 2024, 4031, 16, 1930, 6710, 1035, 4568, 16, 2679, 2222, 8739, 1942, 4541, 14142, 3337, 1930, 4813, 3071, 3387, 18, 4950, 16, 1920, 2213, 14465, 43, 48, 17, 5758, 2458, 4666, 17, 5062, 13728, 3418, 1988, 1977, 5745, 2435, 45, 17, 4262, 1942, 1925, 48, 17, 5758, 5219, 1922, 4496, 2697, 1930, 10634, 1966, 43, 5903, 1927, 12437, 10968, 6526, 11905, 5048, 18, 2176, 11374, 1920, 11758, 1927, 2758, 2697, 16, 23471, 3581, 1958, 4877, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 15996, 10488, 19, 16080, 2072, 16, 4666, 17, 5062, 13728, 13975, 16, 2154, 14879, 43, 4346, 8, 38, 4666, 8, 17, 5062, 13728, 3418, 7079, 1922, 6445, 8145, 1930, 14787, 4088, 18, 4678, 3951, 1920, 9541, 17, 3100, 15996, 10488, 16, 2154, 17097, 1920, 26692, 19302, 6638, 1927, 3065, 21773, 1942, 25075, 16, 1930, 16080, 2072, 17, 6865, 2697, 1988, 3868, 8265, 2213, 17, 2213, 3719, 2014, 4718, 3567, 17, 9486, 18, 2176, 5110, 1922, 2335, 3940, 28666, 5873, 22523, 1022, 1957, 12, 2335, 3122, 13, 18, 7031, 1920, 3244, 18, 3], "output": "MKQVNFSPRKAMVSFISNQTLDVVANLDIPSFTDDPISINILGHCNGIICLCDCFSGILLWNIATKEFKILPMCPFEGPPSSENTIDVAGLGYDSKRDEYKVIRIDTFWEGDFDKVPRGNRVALYNLTTDSWRKLNDNLTAEFFHSYRNYQVYSNGFYHCLADVDSEELLLSFDMSNEVFVTTPFPDGRLDGCYDVWVLGELGLKNSWTKLFTIESLPPATTPLGVGSDGEIFLVNEESKFLAWHHRENKEIKTLQFEGTALELAMYAESLVSFRGGTAFNH", "metadata": {"id": "A0A6P5YKX9", "cluster": 16278905, "interpro_all": ["IPR017451", "IPR011043", "IPR050796"], "interpro_used": ["IPR050796", "IPR017451", "IPR011043"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein belongs to the Leucine-rich repeat domain superfamily, which forms a right-handed beta-alpha superhelix that typically adopts an arc or horseshoe shape to provide a structural framework for protein-protein interactions. Found in diverse proteins from viruses to eukaryotes, including tyrosine kinase receptors and virulence factors, this domain facilitates processes such as signal transduction, immune responses, and cell adhesion. It occurs in Termitomyces sp. J132.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14440, 1942, 1920, 12624, 17, 5536, 6865, 3418, 13975, 16, 2154, 4952, 43, 3659, 17, 17105, 4666, 17, 4595, 3356, 23285, 2416, 1988, 5745, 24032, 1925, 9952, 2014, 15638, 10647, 1021, 5989, 1942, 3394, 43, 4346, 6465, 1958, 2213, 17, 2213, 3719, 18, 2435, 1922, 6445, 2697, 2037, 6241, 1942, 15021, 16, 2710, 6941, 4016, 4086, 1930, 9304, 2790, 16, 2052, 3418, 11374, 4028, 2427, 1966, 2733, 8201, 16, 3743, 3387, 16, 1930, 2024, 6141, 18, 2176, 5110, 1922, 2576, 8752, 14930, 3707, 2056, 18, 52, 15288, 18, 3], "output": "MLNNRLTPMLLSSICRLSLEQLPYKNSPPLLFCHVCRPWRQLALATPELWCHLNEFWLSRSKHHPLCFRFSLDRVPDQRWALAFKDQLRGVSFDGIEPLKCLEAVDLRIRGYIMEMYPILPDKVPSLSMLSLSYPDFHCGKIKLISLLAWHEILRMTPHLQKCYVGLCLFYADHEESEEILTPCLGMVFTGVVCPNLTRFVVKSSSVQTNAQGLKQLQLLRQDIDASSVLVVLLILPALEDLFVPKLKKFNLGVIRYDRLQRDVPTFSAAIYSASTRVVERMTRATLLVDEDHEMDLWKAKHLLSNVNWKNPLISGENTWVRWKKEMGLWHQEIFIHTYHTSDNSRILEATPESFKAPRRGVRKFKEILTFPFRSNLRELEIDVASNEHEDNDSDLNVPWRQMTHLCLHEEHDIAKLPQVHMEHLQELEVSNALSGIEKQLTLCSSLDCAGNHDKLLRALAVRDDADAIKSRWCWKRQRKCLKQVKRGLSFRAEVHSAR", "metadata": {"id": "A0A0L6WQN2", "cluster": 16825063, "interpro_all": ["IPR032675"], "interpro_used": ["IPR032675"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should feature a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Additionally, the protein falls within the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Moreover, the protein should contain a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is found in Bacteroidetes bacterium ADurb.BinA395 and is linked to UniProt keywords Isoprene biosynthesis and Transferase.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 2435, 1922, 26808, 14061, 2041, 5223, 18, 8768, 12779, 8803, 1930, 1977, 4624, 1942, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MIVHPNAKINIGLNITGLLPNGYHSIETVFYPVNVYDHLKLSIDGKPENNLVIKAWQLLRDEYKIAPVKIFLEKNIPMGAGLGEKLKHLAAKLGADCPFFIDNQPVFAQGKGDKFHPLKLSLKNFYLVLYAETVPKKPEFPLQELVKKPIEEWKYFIKNDFEESIETGAVYASMSGSGSAVYGIFYDRPVRNGYFDNYFFSIVPLSIEPIPKAAENQFVVKGGGSSDAAFMLKTLNDLFQLDIDRVKPDIHIATANAFKRYPLIAEIKQKLY", "metadata": {"id": "A0A1V5F4F3", "cluster": 17167581, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR020568", "IPR036554", "IPR014721"]}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: The protein should have a DNA methylase, N-6 adenine-specific, conserved site that specifically methylates the amino group at the C-6 position of adenines in DNA using S-adenosyl-L-methionine (SAM) as a methyl donor. Found in bacterial restriction-modification systems, this domain contains a conserved N-terminal motif (Asp/Asn-Pro-Pro-Tyr/Phe) likely involved in substrate binding or catalytic activity. In addition, the protein should feature a MmeI-like, C-terminal domain that forms the C-terminal helical bundle structure in Type IIL restriction-modification enzymes like MmeI. This structural module follows the target recognition domain in proteins that integrate DNA recognition, methyltransferase, and endonuclease activities within a single polypeptide. In addition, the protein possesses a MmeI-like, helicase spacer domain that acts as a multi-helical linker connecting the N-terminal endonuclease domain to the DNA-methyltransferase domain in Type IIL restriction-modification enzymes. This structural module plays a critical role in correctly positioning the endonuclease cleavage domain to facilitate precise DNA strand scission. It is native to Rathayibacter sp. VKM Ac-2759 and has UniProt annotations Plasmid.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 3066, 2162, 43, 2678, 4963, 2051, 16, 56, 17, 26, 15643, 17, 2487, 16, 5305, 3200, 1988, 4475, 4963, 2209, 1920, 3835, 2210, 2019, 1920, 45, 17, 26, 3507, 1927, 15643, 1036, 1922, 2678, 2193, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1966, 43, 4963, 6282, 18, 2435, 1922, 4543, 7587, 17, 6295, 3771, 16, 2052, 3418, 5461, 43, 5305, 56, 17, 4262, 5219, 12, 4138, 19, 15118, 17, 1965, 17, 1965, 17, 9036, 19, 10422, 13, 3205, 3286, 1922, 4510, 2743, 2014, 6804, 2455, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 2489, 14209, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 4952, 1920, 45, 17, 4262, 11514, 14142, 3170, 1922, 2601, 2890, 1024, 7587, 17, 6295, 5038, 3189, 2489, 14209, 18, 2052, 4346, 9059, 6052, 1920, 2758, 5708, 3418, 1922, 2697, 1988, 13780, 2678, 5708, 16, 16478, 16, 1930, 18697, 4209, 2651, 43, 2957, 13022, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 2489, 14209, 17, 3189, 16, 15318, 17060, 3418, 1988, 8016, 1966, 43, 2779, 17, 11514, 11040, 15031, 1920, 56, 17, 4262, 18697, 3418, 1942, 1920, 2678, 17, 16478, 3418, 1922, 2601, 2890, 1024, 7587, 17, 6295, 5038, 18, 2052, 4346, 9059, 5705, 43, 4140, 2770, 1922, 10329, 12158, 1920, 18697, 6404, 3418, 1942, 6628, 8162, 2678, 5984, 30198, 2001, 18, 2176, 1977, 6196, 1942, 3067, 2722, 16582, 7972, 2341, 1915, 2056, 18, 26855, 1035, 2000, 17, 18821, 1026, 1930, 2258, 20709, 15010, 5609, 18, 3], "output": "MNEAKLLAFVDNQDLRELFITELGWNNPDQPDGYKGLRIWFCAELPARRIQRTLDELIGQNSHERLVIFADAKLLVHRHIVGEADAHMAKQLSTIAIDFDEDISLVELARLMSSLYTWLVEANYNEHEATLFLARDIFLQFLVDDTDDAELHLRLTELFLALDTPKNMQQLPPEFRRDLIAACHFDWSLISPAVFGSMFQLRTIEPLFLNDLRNRLIENWDSIAGLNRLQTYLGSLRFLDPRRRELDLASGTDRRYQGTFDVTGDIRVTLDHFFGIEHLANQRMAQDFGVAPDRLPISIDDVLIFGNPPYLGHKERSAAQTADMKVAWGKLKRAKFAFVTTNSIVQGFSVSYLFGPLFADGWRIRFAHRPVGFDKERSTPQLFTYERPNSKPVEVTVDRIEDMGVVSSGSNPIDFGHLIFSDATKRVIEKDDADPSDLTVSPILRERVNALALDRAASDRAATKRLANLSGLFGEPDTVIGMKLYSSADPDGTTLAIASSSLFADWQQPLPRLSSDDRRSLVNAAQAIKEARHNLPEMSRLTFSIFRLDPYSTLLERQRHLLSRYAQMTHRCKFEVEGHAYSLTQIADRRQEWRWPRRAQLGGANLTKMRAAFDEEAQQASVKALLFVLFADDSNMWSRESPLTKFPYVNGGLYAERLELRPLPATVKSKEARRSGGEHYTTEENIACGCGNFLIVAYRELRALELDLIVIDEWPARIAEVAMLLMDAPKILHANALREDWKQLVGKAYFGYLDFVTSWHAKCLVFFAGTFAWTSEAPDPAGVHTVISPYLIDASDVVVVPRNQPLSPIARKYIRKFANGDEFINGKTRWCLWLRDRQPVAQFVAFPQTFSEHRKYCTVGDMQLVGGRLESRLSFSINLVWNNYLSEMYKEGLGSEELLRAHMSLD", "metadata": {"id": "A0A6P1FI80", "cluster": 17752472, "interpro_all": ["IPR002052", "IPR046818", "IPR046819", "IPR046816", "IPR046820", "IPR050953", "IPR029063"], "interpro_used": ["IPR002052", "IPR046818", "IPR046819"], "interpro_unused": ["IPR029063", "IPR050953", "IPR046816", "IPR046820"]}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\nThe protein should include a PatA-like, N-terminal domain that regulates heterocyst pattern formation in bacteria such as *Nostoc* sp. It is specifically required for the differentiation of intercalary heterocysts, playing a critical role in spatial developmental patterning distinct from terminal heterocyst formation. It is native to Deltaproteobacteria bacterium.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 3066, 3951, 43, 2917, 1019, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 7014, 27804, 2298, 3114, 3337, 1922, 4802, 2427, 1966, 14, 9291, 4575, 1030, 14, 2056, 18, 2176, 1977, 4475, 3414, 1958, 1920, 4155, 1927, 19014, 2141, 27804, 29664, 16, 14797, 43, 4140, 2770, 1922, 5067, 5878, 16060, 4493, 2037, 4262, 27804, 2298, 3337, 18, 2176, 1977, 6196, 1942, 9649, 9218, 1021, 10296, 14061, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MVASKVTSKNQTMSGKTITISPKVSSLGPDVLILEKFASQKPGTTGKILLGGGILTAIHGETLRRLFFDAGALRLASSTSKSELLGEASMRVGEALVKKGLCTTTDIFRMICKQVEEIFMLELPAFLSIDTSALLLDAAKRIDEISYFKQPLEADFLGRCDGLKTIGKIGEETGISDVLTEQISRENISVIVSHFNSIIETINSYLNNAIAEGEIPEGIVIDEMGRLNEHSVADAISNSSCSYLPKKSQQQLSVIVHSMIQKVASRGFVTCDDENLVRFWQDQAGEWEVKGEGWIADVIGLIANSKWSVLVRENLVSRNHLEEILKETGFSVILMDSGWYYFTETSEKKIPGTGIILRRKRRTFPPRMFEAMKMAYQLLERGYVEIYLTEPQNLKNLVTIERNIKGENKISWLVNSLTRYVFFVLF", "metadata": {"id": "A0A7C5LFR6", "cluster": 18054816, "interpro_all": ["IPR025497"], "interpro_used": ["IPR025497"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein should feature a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. It is identified in Verrucomicrobia bacterium Tous-C9LFEB and carries UniProt keyword assignments ATP-binding, Nucleotide biosynthesis, and Transferase.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2176, 1977, 2899, 1922, 3566, 3176, 13055, 1935, 15129, 2126, 14061, 1942, 1957, 17, 19224, 1024, 10140, 1014, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MKPHFITLEGSEACGKSTQITREPGGTALGETLRHLLKHAPEGRGMCAEAELAGGWVISDRFGDSTTVYQGVARKLAPADVASINHLDLDPEEAKRRLLRRPRPVGQATDRMEDQPADFFDRSAAGKLNEVEETIWSLVSHAFSLERLKARLEARGDTVLLLLFTASRAQLCREVIAPTLAFAMGAIRPSLTIVVREGYRALAQAEPDRVKLI", "metadata": {"id": "A0A2A2R2H6", "cluster": 19817038, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR027417", "IPR018095"], "interpro_unused": ["IPR018094", "IPR039430"]}, "task_type": "infilling"} {"instruction": "I want to generate an amino acid sequence for a protein. The protein should have the function The protein should feature a THAP-type zinc finger domain that mediates zinc-dependent, sequence-specific DNA binding in animal transcription factors and transposases. This ~90-residue module features a C2CH consensus motif and a characteristic loop-helix-loop insertion essential for recognizing specific nucleotide targets. It is native to Amblyomma americanum (Lone star tick) and exhibits UniProt keyword tags Metal-binding and Zinc-finger.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 3066, 5961, 43, 21513, 1034, 17, 2601, 7997, 8497, 3418, 1988, 10412, 7997, 17, 3100, 16, 3244, 17, 2487, 2678, 2743, 1922, 4027, 3213, 2790, 1930, 12935, 2319, 18, 2052, 72, 3865, 17, 6181, 9059, 4075, 43, 8453, 2072, 7076, 5219, 1930, 43, 6293, 5881, 17, 7864, 17, 5881, 7413, 4415, 1958, 15667, 2487, 5489, 4845, 18, 2176, 1977, 6196, 1942, 26441, 1947, 3368, 5339, 1989, 12, 10969, 1021, 3632, 12085, 13, 1930, 9826, 20709, 11121, 2538, 14392, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 3], "output": "GKTCAVLVCKNCDRDLKIWDETVCPLHNPELHKDCPCMRPFSMHNFPRGEHNKLVRKRWIANLQRKGFDPGNFARVCSIHFVDGRPTPDNPYPTLHLGTPTVPFKSRSELKARVVISPRLKMSPKRVLEASRTDSIATQQRQAHPITTSSLGKASGASRTDSVATYQRPAHAIATYQRLPRVKTNPEGVSEASHTDSIATSQRPAHPIATYQRSPRRNEKGTLASCLTYW", "metadata": {"id": "A0A0C9SBM0", "cluster": 22094545, "interpro_all": ["IPR006612"], "interpro_used": ["IPR006612"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want a protein that has the function: The protein can be placed in the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Moreover, the protein contains a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Moreover, the protein is a member of the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. It is native to Tolypocladium capitatum and corresponds to UniProt keyword ATP-binding, Magnesium, and Metal-binding. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 3950, 16, 1920, 2213, 5461, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 2176, 1977, 6196, 1942, 21930, 2085, 5406, 21913, 21361, 1031, 1989, 1930, 8852, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 13148, 16, 1930, 6048, 17, 2743, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MPGEQVCGVTPPISVALPTEQEKRASDALIEELRRQKTFESPSDTQKRHKVLESLQNICDEFVKRVARKKEPKNETLIKNARGKVFTYGSFRLGVFGPGSDIDTLIVAPKYVTRDDYFEYFPDMLVDMAPKGTITNLTVVTDAFVPIIKFEYSGISIDLIFSRLIQKQLSPDLQDLKDSGLLRGLDEAELRSLNGTRVTDEILNLVPEQSTFKLALRAIKLWAQRRAVYANIMGFPGGVAWAMLVARVCQLYPKAATSVIVNKFFLVMGQWRWPQPVLLKPIESGPLPVRVWNPKAYKGDSFHLMPVITPAYPSMCATFNITRSSMTIINQELQRGLELTESIMVSKRPWSDLFVKHTFFTMDYKYYISVTTASKDKEAHKVWSGYVESKIRMLVQKLELHQSIALARAFNKGYDRRHRCNDNAQIAQVQEGSLDFVIKPDDIDTGTDNNANKKQEPAEDREGSQPPFPADVYTTTHYIGLELEKSKYLLKAKSLDLSYQVDEFKTLCTQWNRYKDELQPLVSIGIQHVRNVNLPDDVFEAGEAKPQKKGARGNLNGKKRGASEDNPPPPAKRPQTSVVAAG", "metadata": {"id": "A0A2K3Q9L4", "cluster": 22769784, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR043519", "IPR007012", "IPR011068"], "interpro_unused": ["IPR014492", "IPR007010", "IPR048840"]}, "task_type": "autoregressive"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: It is part of the Electron transport accessory-like domain superfamily, which comprises proteins with an SH3-like $\\beta$ topology and a characteristic 3-10 helical turn that participate in electron transport, regulation, and catalysis. Members include photosystem I accessory proteins that modulate ferredoxin interactions, the regulatory alpha chain of ferredoxin thioredoxin reductase, and enzymes such as nitrile hydratase and R67 dihydrofolate reductase. Additionally, it is part of the Photosystem I PsaE, reaction centre subunit IV family, which acts as a stromal subunit of the photosystem I reaction centre involved in electron transfer. This polypeptide adopts a five-stranded beta-sheet fold similar to SH3 domains and facilitates complex formation with ferredoxin and ferredoxin-oxidoreductase. It is found in Spirodela intermedia (Intermediate duckweed) and has UniProt annotations Membrane and Photosynthesis.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 2176, 1977, 3131, 1927, 1920, 4995, 4860, 15954, 17, 3189, 3418, 13975, 16, 2154, 12936, 2697, 1956, 1925, 18824, 17, 3189, 8, 38, 4666, 8, 13678, 1930, 43, 6293, 23, 17, 2119, 11514, 5165, 1988, 7352, 1922, 4995, 4860, 16, 3640, 16, 1930, 15408, 18, 4678, 3951, 8811, 2405, 51, 15954, 2697, 1988, 8480, 25304, 22389, 10960, 3719, 16, 1920, 4948, 4595, 4659, 1927, 25304, 22389, 10960, 23684, 11386, 16, 1930, 5038, 2427, 1966, 8214, 2383, 22420, 3857, 4127, 1930, 22098, 1027, 11842, 27851, 11386, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 8811, 2405, 51, 10203, 1021, 16, 3227, 8141, 5903, 4370, 3416, 16, 2154, 8016, 1966, 43, 9709, 5903, 1927, 1920, 8811, 2405, 51, 3227, 8141, 3286, 1922, 4995, 3856, 18, 2052, 13022, 24032, 43, 3628, 17, 10338, 4666, 17, 11130, 3728, 2551, 1942, 18824, 4682, 1930, 11374, 2796, 3337, 1956, 25304, 22389, 10960, 1930, 25304, 22389, 10960, 17, 27388, 18, 2176, 1977, 2435, 1922, 22075, 16878, 1019, 11213, 1019, 12, 6129, 26856, 29775, 13, 1930, 2258, 20709, 15010, 3260, 1930, 18133, 18, 3], "output": "MCIQCYVGAPLLSRYNGVGAATPPPSCVRAVAVSEAAAAANPPPIGPKRGTQVKILRRESYWFNGQGHYANVSTNNYSLDEIQEVKLLLPSWKRMKWAEVRYVSYVGSVVAVDQVISLPGRGPLQ", "metadata": {"id": "A0A7I8J8X8", "cluster": 23193735, "interpro_all": ["IPR008990", "IPR003375"], "interpro_used": ["IPR008990", "IPR003375"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein is classified under the Fatty acid oxidation complex subunit alpha family, which constitutes the alpha subunit of the mitochondrial trifunctional enzyme responsible for the latter stages of long-chain fatty acid beta-oxidation. Members of this family exhibit 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities, catalyzing the conversion of enoyl-CoA to 3-oxoacyl-CoA to generate energy. Additionally, these proteins possess monolysocardiolipin acyltransferase activity, facilitating the acylation of monolysocardiolipin into the key mitochondrial phospholipid cardiolipin. In addition, the protein is a member of the 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily, which functions as the dimerization module in enzymes catalyzing the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate. This domain facilitates the assembly of the active dimer, often by threading through the partner subunit to contribute to the substrate-binding site or by forming stabilizing salt bridges between monomers. Structurally, it resembles dimerization domains found in diverse oxidoreductases, including mannitol 2-dehydrogenase and glycerol-3-phosphate dehydrogenase. Also, the protein incorporates a 3-hydroxyacyl-CoA dehydrogenase conserved site that catalyzes the conversion of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA during fatty acid metabolism. This domain features an N-terminal NAD-binding region and is often found as part of a multifunctional enzyme complex, coupled with enoyl-CoA hydratase and isomerase activities in eukaryotic mitochondria and peroxisomes as well as bacteria. It occurs in Crocinitomicaceae bacterium and is described by UniProt keywords Lipid degradation, Lipid metabolism, and Lyase.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 5934, 2687, 6638, 2796, 5903, 4595, 3416, 16, 2154, 14879, 1920, 4595, 5903, 1927, 1920, 4596, 13453, 20839, 4113, 5061, 1958, 1920, 6296, 5143, 1927, 2815, 17, 4659, 5934, 2687, 4666, 17, 6638, 18, 4678, 1927, 2052, 3416, 5987, 23, 17, 8275, 14645, 17, 10027, 13872, 9213, 2051, 1930, 23, 17, 8275, 14645, 17, 10027, 9294, 4209, 16, 29601, 1920, 7309, 1927, 2066, 10921, 17, 10027, 1942, 23, 17, 18588, 14645, 17, 10027, 1942, 5655, 3844, 18, 4950, 16, 2144, 2697, 7150, 9150, 2012, 9641, 29802, 11337, 9961, 2455, 16, 12440, 1920, 11337, 1943, 1927, 9150, 2012, 9641, 29802, 2460, 1920, 3834, 4596, 14608, 21129, 8257, 1921, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 26, 17, 8078, 22988, 8870, 9294, 17, 3189, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 4088, 1966, 1920, 13640, 9059, 1922, 5038, 29601, 1920, 5163, 22429, 1943, 1927, 26, 17, 8078, 22988, 8870, 1942, 5216, 8658, 25, 17, 5413, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 3500, 7632, 16, 3868, 2007, 18205, 1941, 2596, 1920, 8240, 5903, 1942, 4672, 1942, 1920, 4510, 17, 2743, 3200, 2014, 2007, 7402, 14384, 7012, 18142, 2192, 13256, 18, 12171, 16, 2176, 17602, 13640, 4682, 2435, 1922, 6445, 27388, 1036, 16, 2710, 20915, 22, 17, 9294, 1930, 9244, 17, 23, 17, 5413, 9294, 18, 2222, 16, 1920, 2213, 19683, 43, 23, 17, 8275, 14645, 17, 10027, 9294, 5305, 3200, 1988, 17097, 1920, 7309, 1927, 23, 17, 8275, 14645, 17, 10027, 1942, 23, 17, 18588, 14645, 17, 10027, 2409, 5934, 2687, 4714, 18, 2052, 3418, 4075, 1925, 56, 17, 4262, 6577, 17, 2743, 3031, 1930, 1977, 3868, 2435, 1966, 3131, 1927, 43, 20136, 4113, 2796, 16, 6416, 1956, 2066, 10921, 17, 10027, 22420, 3857, 4127, 1930, 25510, 4209, 1922, 10825, 6489, 1930, 28990, 1966, 2486, 1966, 4802, 18, 2176, 5110, 1922, 9442, 3665, 8752, 4913, 9914, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 4486, 4877, 16, 4486, 4714, 16, 1930, 23928, 18, 3], "output": "MNNDFFRLEIENGIATIWIDSKNDKMNIVSPTLIGDFEEVFNEVNQNNQIQGAILISAKKDFIAGADIKSFKGEKVGDFQPTSRKGHAMLQAIQDSKKPIVAAIHGTCYGLGTEISLACHARICTDDTKTKMALPEVKLGLLPGAGGTQRLPRLVGLAKSLDIMLTGKNVFAYPAKKMGLVDEVVHHSKLHRAAKTLVSKMNNGKFQRKPIKKSLVEKLLDSSLGRGVVFSQARKKTLKATKGNYPAPIAIIECVEAGLKKGLKNGYEKEVVLFEELMLSDVSKALRNLFFTTTEKKKNPYNVKPKNTDRIAVLGAGFMGGGITDVSVNNGMDVILKDLSEDMIQSSKSTIWKGLKRKLKRKQLKDTEAKTIVQRAVGQTDFKGFQGVDVVIEAIVENMEIKQKVIKELETVCHEDFIFASNTSSLPLTEMSKAAKKPENVIGMHYFSPVPKMPLLEIIKTDQTSEETLATCYEIGKRQGKTCIVVNDMPGFYVNRILCPYLIEGLLMIEEGVRIEDIDGALTSLGMPIGPITLLDEVGIDVGAHVMSGNMAQLLKGREGFKINYSMPKMFEAGLHGRKAKKGFYNYAMKKGRLRKTSPNQGRISTFWKSIP", "metadata": {"id": "A0A920KEZ7", "cluster": 26443236, "interpro_all": ["IPR006180", "IPR006176", "IPR006108", "IPR008927", "IPR029045", "IPR001753", "IPR050136", "IPR036291"], "interpro_used": ["IPR050136", "IPR008927", "IPR006180"], "interpro_unused": ["IPR006108", "IPR029045", "IPR006176", "IPR001753", "IPR036291"]}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is produced by Symploca sp. SIO3C6.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 4152, 2007, 29148, 6012, 3375, 2056, 18, 5998, 8583, 24304, 18, 3], "output": "MSLKTSDQGLEVIDALRRKKGWCKSAITWADYANVAQSTLKRFWRKEPILEENFKAICQAVGVQNWPPVETSCFQEILQPGALIRIKAPRKMGKTRLMQKIFAHAQDHNYQTVTLNLLWVEASVLTDLWDPDTSSNDNCTAFLEECILSQLDTPLVLGLDNVDWIFQHPAVASDFFRLLRSWHDEAKSYDLLKNLRLPEFTPQQVLSFAQRYGLDWQSPQVEQLMALIGGHPYLIQQALEAIKRYPNLCLQQLLDSEYLQQDSELIAAMEKVVTSDHAIQLSADQAFKLHSMGLVQWQGDEVESSCRLYHLYFRNQLRGIQVLSSQDIIDYQQSPSLPEEISEVSHYINRNKFLRCLCHRISRRLKLKNQVSEILIVVHSTEVYIPLNINHSPFNVGLSIGASTASSIYRNHLRALW", "metadata": {"id": "A0A6P0K529", "cluster": 27460401, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the polypeptide chain function: The protein is included in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein should include a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein should include a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It originates from Myxococcales bacterium and is linked to UniProt keywords Isoprene biosynthesis and Transferase. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 22970, 2037, 21464, 11748, 1918, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MNLGLRLVGRREDGYHLLESLFAPIDLHDEVEVELGGSGSEGVHLELAPIPADRMPPALAAVTAGPDNLVVRAAVAFLRAASLTRSVEIRLDKRIPAGAGLGGGSSDAAAVLRALNALVDRPLPAAELARVALGLGADVPFFLAPIPSFVSGIGECIEPLEGLPGLDLVVANPGISLATAEVYRAADALGSALTRPGAGSTMRAFSRLRAASDPSGSVPRVSGIGPRSLQPSIRDLLVNDLEPAARRLCPPITRLAQRLAEMGAMAVSLSGSGATVFGVFASADAARRAADRLREAGAEIGGVVWVRATRILSGTDALDR", "metadata": {"id": "A0A955UFN8", "cluster": 28684706, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR020568", "IPR036554", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein contains a EGF-like domain that functions as a structural motif in the extracellular regions of membrane-bound and secreted proteins to mediate protein-protein interactions. This domain is characterized by a fold stabilized by six conserved cysteine residues forming disulfide bonds and frequently contains a calcium-binding site essential for biological activity. Furthermore, the protein has a PAN/Apple domain that functions as a protein-protein interaction module, mediating binding to partners such as high molecular weight kininogen, Factor XIIa, platelets, and heparin. This cysteine-rich domain typically adopts a characteristic fold stabilized by disulfide bonds and is often found in the N-terminal region of plasma serine proteases. In addition, the protein is grouped in the Concanavalin A-like lectin/glucanase domain superfamily, which adopts a characteristic $\\beta$-sandwich fold of 12-14 strands to support diverse carbohydrate-recognition and catalytic activities. This versatile structural scaffold is found in a wide range of proteins, including legume and animal lectins, glycosyl hydrolases, neurotoxins, and molecular chaperones such as calnexin. It has been detected in Nematostella vectensis (Starlet sea anemone) and is classified with UniProt keywords ATP-binding, Nucleotide-binding, and Transmembrane helix.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 5461, 43, 4451, 17, 3189, 3418, 1988, 4088, 1966, 43, 4346, 5219, 1922, 1920, 5329, 3451, 1927, 3260, 17, 4124, 1930, 8366, 2697, 1942, 8265, 2213, 17, 2213, 3719, 18, 2052, 3418, 1977, 4378, 2007, 43, 3728, 12017, 2007, 3798, 5305, 8666, 4248, 7402, 11830, 9031, 1930, 5467, 5461, 43, 5016, 17, 2743, 3200, 4415, 1958, 3933, 2455, 18, 3677, 16, 1920, 2213, 2258, 43, 3797, 19, 19663, 3418, 1988, 4088, 1966, 43, 2213, 17, 2213, 2835, 9059, 16, 10239, 2743, 1942, 7228, 2427, 1966, 2149, 3272, 3388, 3498, 3522, 2432, 16, 2991, 11551, 2126, 16, 10097, 16, 1930, 9962, 18, 2052, 8666, 17, 5536, 3418, 5745, 24032, 43, 6293, 3728, 12017, 2007, 11830, 9031, 1930, 1977, 3868, 2435, 1922, 1920, 56, 17, 4262, 3031, 1927, 3582, 8468, 12447, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2499, 7241, 4701, 1921, 43, 17, 3189, 13468, 19, 18798, 2051, 3418, 13975, 16, 2154, 24032, 43, 6293, 8, 38, 4666, 8, 17, 18038, 3728, 1927, 2369, 17, 2607, 13214, 1942, 3373, 6445, 10590, 17, 5708, 1930, 6804, 4209, 18, 2052, 20425, 4346, 7281, 1977, 2435, 1922, 43, 4743, 3109, 1927, 2697, 16, 2710, 6703, 16120, 1930, 4027, 25607, 16, 20067, 30337, 16, 9124, 21269, 16, 1930, 3272, 18098, 2427, 1966, 2570, 28700, 1921, 18, 2176, 2258, 2252, 3330, 1922, 13000, 18092, 11560, 1019, 23098, 8134, 12, 3632, 6088, 9309, 9860, 3947, 1021, 13, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 17, 2743, 16, 1930, 9117, 7864, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MDLYVACVSTRNSFFPEQSEFCFIREDEGFTAILLTIVLLGQTRSQVARLDCKKVGNFQHYEKDKMLAGHVITSLEMKANTGAESFTCQLNNATKKSSSSGLVTSSEGFAYYDADKNPHPDSCESDSYTCVCGYGTQGKHCEKWSEPHLESRLDLTICFAVLLKKVASALFTFEDENQNEILSMETRNRSDSVGRKISMMVDLSTSHTPLETGGSQILTAKTIRGFEDISSFTISVWFTTSIDNFTKTLRKQGVSPNLIIVVDIFYLSELFTHTSTSLTSGWYHLALSFPGRLVIGQKQETFSVLANQKADSYCEKNAASVKAINEKYGYQADTLSSKGTCIPGHAMWQSTEPGLSLIWAAFLVTMGTVHTSLLDCVDECLTEIRCKSINISCASLPCRNGGLCAVQEAGVKNYAEVSLTFGVSNVMTSRMNMEINIRLKVSAVEDVDFLLRYKPSTTGACFSYRTADQADVLRVDLEKTTSRVKSYMNGINLAVDEVSHLGPVCVVNAASPRRALFDQLIGDTTRQWRCYG", "metadata": {"id": "A7T3J8", "cluster": 68539, "interpro_all": ["IPR013320", "IPR000742", "IPR003609"], "interpro_used": ["IPR000742", "IPR003609", "IPR013320"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein should contain a ATP-grasp fold domain that catalyzes the ATP-dependent ligation of a carboxylate-containing molecule to an amino or thiol group-containing molecule, predominantly contributing to macromolecular synthesis. This domain features two $\\alpha$-$\\beta$ subdomains that grasp the ATP molecule and utilizes conserved phosphate and Mg(2+) binding motifs to activate substrates. Furthermore, the protein belongs to the ATP-dependent Amino Acid Ligase family, which catalyzes the ATP-dependent formation of dipeptides that serve as precursors for bioactive compounds like bacilysin and dapdiamides. These enzymes function within biosynthetic gene clusters and display specific substrate recognition for amino acids such as alanine or arginine to generate molecules used in microbial defense. It is derived from Actinobacteria bacterium OK074 and carries UniProt keyword assignments ATP-binding. Can you generate the amino acid sequence corresponding to this polypeptide chain?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 13022, 4659, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 4498, 17, 22815, 3728, 3418, 1988, 17097, 1920, 4498, 17, 3100, 11102, 1927, 43, 20877, 17, 3165, 5388, 1942, 1925, 3835, 2014, 13914, 2210, 17, 3165, 5388, 16, 7700, 8739, 1942, 21815, 4271, 18, 2052, 3418, 4075, 2288, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 30103, 1988, 22815, 1920, 4498, 5388, 1930, 18127, 5305, 5413, 1930, 2786, 12, 22, 15, 13, 2743, 8277, 1942, 6980, 6249, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 4498, 17, 3100, 3835, 2687, 11905, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 3337, 1927, 9137, 11536, 1988, 7120, 1966, 10416, 1958, 13570, 4300, 3189, 8175, 2869, 6777, 1930, 8243, 7408, 20381, 18, 2144, 5038, 2347, 2651, 14041, 2359, 5859, 1930, 4434, 2487, 4510, 5708, 1958, 3835, 4576, 2427, 1966, 10504, 2014, 9732, 1942, 5655, 4206, 2251, 1922, 7293, 9720, 18, 2176, 1977, 3595, 2037, 29130, 14061, 12167, 14099, 1006, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MQRYVVVVDGYHLRAGDNRGFSSAFRARGVIPVAVMSTPVPLEKFVKKSTWHPEDFEAVHFYDGDFDSILAVVRDYDPIGIVAENEAGVELAADLVDALMPERGNVPGTAVDQRNKGNMIEALERAGVPAPKTISTDDPEAVARWIQDTGMAGKPLIVKPPASAGTDNVHLVDAGEDWRPYFDLIMGRVNGFNLRNDTVIVQEYLEGLEYIVDLYSVDGRHGLVDACVYAKHDRGTRIGIYDVADFLPPDHPDMAVLADYVKRAADAVGIRNGSTHAEVIMTTAGPRLVELAARYSGSCMMLSGSLATGDNQIERTVRHLLDGAFTPSFDLVMEVRTLWLCADFAGEVRRMDVLEPIRSLPTVDSMAIPSEGTNVPMTNDVTTSLGWVIQGAPDWEAIEKDSARIRELERTWNACNIESGSPTT", "metadata": {"id": "A0A0N1FY47", "cluster": 7040544, "interpro_all": ["IPR052032", "IPR011761"], "interpro_used": ["IPR011761", "IPR052032"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein falls within the Rho GTPase-activating Guanine Nucleotide Exchange Factor family, which utilizes Dbl-homology (DH) domains to catalyze nucleotide exchange for Rho GTPases, such as RAC1 and RHOA, thereby driving actin cytoskeleton reorganization. These proteins play a critical role in neuronal development, regulating axonal outgrowth, dendrite formation, and synaptic plasticity, as well as contributing to cell migration, adipogenesis, and myogenesis. It is produced by Bursaphelenchus okinawaensis and is connected to UniProt keyword Guanine-nucleotide releasing factor.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 12182, 2651, 1920, 10585, 14809, 17, 8019, 16904, 5489, 6818, 2991, 3416, 16, 2154, 18127, 6594, 1024, 17, 9039, 12, 6781, 13, 4682, 1942, 18170, 5489, 6818, 1958, 10585, 18390, 16, 2427, 1966, 13981, 1930, 14289, 16, 6113, 9228, 4718, 11612, 18062, 18, 2144, 2697, 3918, 43, 4140, 2770, 1922, 5121, 2740, 16, 6773, 10623, 15040, 16, 21222, 3337, 16, 1930, 6251, 8771, 16, 1966, 2486, 1966, 8739, 1942, 2024, 5049, 16, 21089, 16, 1930, 15924, 13349, 18, 2176, 1977, 4152, 2007, 13579, 2575, 29476, 2072, 1957, 12167, 4058, 13956, 8134, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 16904, 17, 5489, 13182, 2991, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MSTIELIDSIENKHSVTLPGIPEGFVDVANQRIKVRDLSHILVSRDSRSQLTFEEYQILLAYLFQLIIDRRTDKWSAVRVLFSYLMVSFENDFEVIDCVEVEHEDQLDIFAFISGLRTSDGNPILTFPVPPLDEDGAKKDKKGYV", "metadata": {"id": "A0A811LT04", "cluster": 9619593, "interpro_all": ["IPR051336"], "interpro_used": ["IPR051336"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should have a Glycosyltransferase 2-like domain that catalyzes the transfer of sugar moieties from activated nucleotide donors, such as UDP-glucose or GDP-mannose, to specific acceptor molecules to form glycosidic bonds. This domain participates in the biosynthesis of diverse structures, including cellulose, dolichol phosphate, and teichoic acids. Also, the protein belongs to the Glycosyltransferase 2 family, which catalyzes the transfer of sugar moieties from activated donors like UDP-glucose to lipid or carbohydrate acceptors, facilitating the assembly of N-linked glycans, O antigens, and 6-O-methylglucose lipopolysaccharides. Certain members play a critical role in bacterial virulence by modifying lipid A, thereby conferring resistance to polymyxin and cationic antimicrobial peptides. It occurs in Phycisphaerae bacterium.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 3066, 2162, 43, 20067, 9961, 22, 17, 3189, 3418, 1988, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 5489, 8276, 16, 2427, 1966, 18500, 17, 3817, 2014, 15217, 17, 17936, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2052, 3418, 17241, 1922, 1920, 8132, 1927, 6445, 4061, 16, 2710, 12343, 16, 17837, 2108, 1945, 5413, 16, 1930, 3602, 2108, 8643, 4576, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 20067, 9961, 22, 3416, 16, 2154, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 8276, 3189, 18500, 17, 3817, 1942, 4486, 2014, 10590, 27916, 16, 12440, 1920, 5957, 1927, 56, 17, 4624, 15509, 16, 57, 7769, 16, 1930, 26, 17, 57, 17, 4963, 22988, 2217, 15614, 1036, 18, 4908, 4678, 3918, 43, 4140, 2770, 1922, 4543, 9304, 2007, 12691, 4486, 43, 16, 6113, 21510, 3554, 1942, 3491, 28330, 1930, 15175, 8003, 5320, 18, 2176, 5110, 1922, 25511, 9119, 29164, 3336, 14061, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MYLAVIPAFNENNSIANIVQETRRSGAIVLHHSKNRGVGAAMITGIAYPWLIHPIRVGRADWVLGSRFLQGPPANTSLIKHLGNKFFTFITALNRKALLALDLRSEFTYTQKYVDQVIVVDDSSRDNTQELARAQKLKPDIVVTLDADGQHNPKDIGILAGVKLTDTQTGFR", "metadata": {"id": "A0A967V7U4", "cluster": 11071530, "interpro_all": ["IPR001173", "IPR050256", "IPR029044"], "interpro_used": ["IPR001173", "IPR050256"], "interpro_unused": ["IPR029044"]}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: It is part of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Also, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. In addition, the protein falls within the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It has been detected in Candidatus Levybacteria bacterium RIFCSPLOWO2_12_FULL_37_14 and contains UniProt keyword associations Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 2258, 2252, 3330, 1922, 14550, 1031, 1957, 10157, 16924, 2422, 2126, 14061, 12424, 2792, 2030, 1971, 5265, 41, 2369, 41, 4125, 41, 3191, 41, 2607, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 1930, 9067, 4587, 18, 3], "output": "MSDFHKSVLLKETIAGLRVEKNEKYIDAGGKVLGIDVDKDAIAYVKSKKPESLTLARGSHQIDSVTRGFSFQNEGPLDMRMDRELTRAWAISNAIVRARSIKPIETTTDLAKIVLKALGLLKENGRLCVISFHSLEDRIVKKKFLEFEPIIPTEDEIEGNKRARSAKLRIFSAKGGSALGTLGGGGHSFEILRLNFRDIDKIALLNNFGKVAGIIFDLGVSGVRALDLIKILTKGELSEIFTKFGEEAIGGKSKKVFQALRIAVNDELNSILEALPEKGMGRIITKK", "metadata": {"id": "A0A1F6KVF1", "cluster": 11458407, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein should include a CRISPR type III-associated protein domain that functions as a component of the Type III RAMP family within the prokaryotic CRISPR-Cas defense system against foreign genetic elements. It includes subunits such as Csm3 and Cmr4 that interact with CRISPR RNA to form surveillance complexes. Furthermore, it is part of the CRISPR-associated protein TM1795 family, which constitutes a component of the CRISPR-Cas prokaryotic defense mechanism against foreign genetic elements. This family specifically represents the highly conserved N-terminal region of Cas proteins, such as TM1795 found in *Thermotoga maritima*. It is present in bacterium and exhibits UniProt keyword tags Antiviral defense.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 3066, 3951, 43, 12509, 2601, 4337, 17, 2458, 2213, 3418, 1988, 4088, 1966, 43, 4594, 1927, 1920, 2601, 4337, 18682, 3416, 2651, 1920, 21545, 12509, 17, 4373, 9720, 2433, 3316, 12400, 3299, 5362, 18, 2176, 5921, 6991, 2427, 1966, 30141, 1010, 1930, 17831, 1006, 1988, 6310, 1956, 12509, 3146, 1942, 2386, 7889, 5048, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 12509, 17, 2458, 2213, 5072, 25229, 1015, 3416, 16, 2154, 14879, 43, 4594, 1927, 1920, 12509, 17, 4373, 21545, 9720, 2856, 3316, 12400, 3299, 5362, 18, 2052, 3416, 4475, 4972, 1920, 3626, 5305, 56, 17, 4262, 3031, 1927, 4373, 2697, 16, 2427, 1966, 5072, 25229, 1015, 2435, 1922, 14, 7967, 4575, 4223, 13081, 2265, 1019, 14, 18, 2176, 1977, 2481, 1922, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 10129, 9720, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MSYTSLWSKIQEELKNRNLLFRIECETLGIHEGIRPSKIKGYLRWWSRVLELSKFGQSKFFINVRYEVKDEAKRFGEEIENFEKSDFFKENNINIEIDFNPARLSIKYTKNEIVKLSNNNIDVKEKEKKVDLKLNSNIYAPLVNASYLRIGGYNARPYSIVNPDLMDYKMADKKVGKYLGSEEKEKLISDYTNALIRFKFNSKKKNDIQNLKEKLIEHESKNDVKEKKKRESKDAL", "metadata": {"id": "A0A7V2I042", "cluster": 12610968, "interpro_all": ["IPR007522", "IPR005537"], "interpro_used": ["IPR005537", "IPR007522"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\nThe protein carries a Spore germination GerAC-like, C-terminal domain that likely serves as a component of the inner spore membrane germination apparatus in Firmicutes. It is implicated in mediating the spore's germination response to L-alanine. It has been detected in Gottfriedia solisilvae and is described by UniProt keywords Lipoprotein, Palmitate, and Signal.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 16252, 43, 18445, 14609, 9559, 1948, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 3205, 10634, 1966, 43, 4594, 1927, 1920, 6671, 18445, 3260, 14609, 11161, 1922, 24474, 18, 2176, 1977, 6835, 1922, 10239, 1920, 18445, 11, 61, 14609, 2644, 1942, 54, 17, 10504, 18, 2176, 2258, 2252, 3330, 1922, 14643, 27807, 13272, 2126, 2638, 1937, 1970, 7302, 1021, 1930, 1977, 2910, 2007, 20709, 11569, 9694, 16, 22047, 16, 1930, 2733, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MKTFKKLRVIILISFLAGISMLKDEYKLFLQIPQPSQGTIKTKIVILHLKVIVFEKKLAQKGMNDLISGFMRSRDVSPKATEPEGTALLEYFEKNAGWNPQIALTSVWMTYRSIKSTLVEQVGSAVIKKGKLVEEINSDGKIEVTHDGSVLILSNKMKHKSKFKNERTGDTSLGSIKNDMEKLLTNRFNKMFTKIQDSEADILLTMDFQVQVDIQNGGNLITHSTLSACWDNKDINHRVLPVVLGTGKTISQAVDKISTNMESSVDLMVAICDDDIGLFFSKMKQSHSYTQDVAIPMLKIGETLLFNAFNDESNNAYLKSKLKLKVSILETGLGQYYRNKIPRKELKNWRSKYYSK", "metadata": {"id": "A0A8J3AJM8", "cluster": 13362704, "interpro_all": ["IPR008844", "IPR046953", "IPR038501"], "interpro_used": ["IPR046953"], "interpro_unused": ["IPR008844", "IPR038501"]}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein should include a Tetratricopeptide repeat that mediates protein-protein interactions and the assembly of multiprotein complexes. This motif consists of tandem 34-amino acid residues adopting a helix-turn-helix arrangement, which stacks to form a right-handed superhelical structure involved in diverse processes such as cell cycle regulation and protein folding. Furthermore, the protein should have a Histidine kinase domain that functions as the catalytic core of two-component signal transduction systems, orchestrating cellular responses to environmental stimuli. It undergoes ATP-dependent autophosphorylation on a conserved histidine residue within a homodimer before transferring the high-energy phosphoryl group to an aspartate residue on a partner response regulator protein. This domain contains a dimerization interface and a structurally distinct ATP-binding cleft defined by conserved nucleotide-binding motifs. Moreover, the protein is classified under the Sensor Histidine Kinase Two-Component System family, which functions as the sensory component of signal transduction pathways to detect environmental stimuli such as oxygen levels or cell wall stress. These kinases autophosphorylate a conserved histidine residue and transfer the phosphoryl group to a response regulator, thereby modulating gene expression for processes like sporulation, biofilm formation, and antibiotic resistance. Some members also exhibit phosphatase activity to fine-tune the signaling response. It is present in Taibaiella chishuiensis and exhibits UniProt keyword tags Two-component regulatory system, Membrane, and Transmembrane helix.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 3066, 3951, 43, 12470, 3319, 21305, 6865, 1988, 10412, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 18, 2052, 5219, 7543, 1927, 10361, 3540, 17, 3835, 2687, 4248, 20478, 43, 7864, 17, 5165, 17, 7864, 13002, 16, 2154, 20836, 1942, 2386, 43, 3659, 17, 17105, 3356, 23285, 2046, 3170, 3286, 1922, 6445, 4028, 2427, 1966, 2024, 4048, 3640, 1930, 2213, 10328, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 13873, 4016, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 2288, 17, 4594, 2733, 8201, 3771, 16, 21991, 2287, 3689, 3387, 1942, 4813, 5458, 18, 2176, 14928, 4498, 17, 3100, 22009, 1990, 43, 5305, 13873, 6181, 2651, 43, 21189, 3119, 21902, 1920, 2149, 17, 3844, 12556, 2210, 1942, 1925, 12878, 6181, 1990, 43, 8240, 2644, 7888, 2213, 18, 2052, 3418, 5461, 43, 13640, 6854, 1930, 43, 12171, 4493, 4498, 17, 2743, 14649, 3608, 2007, 5305, 5489, 17, 2743, 8277, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 6443, 13873, 4016, 2288, 17, 4594, 2433, 3416, 16, 2154, 4088, 1966, 1920, 6893, 4594, 1927, 2733, 8201, 3873, 1942, 4277, 4813, 5458, 2427, 1966, 4612, 2428, 2014, 2024, 4821, 3071, 18, 2144, 7784, 20369, 9075, 43, 5305, 13873, 6181, 1930, 3856, 1920, 12556, 2210, 1942, 43, 2644, 7888, 16, 6113, 10871, 2359, 2294, 1958, 4028, 3189, 23647, 16, 9638, 3337, 16, 1930, 7267, 3554, 18, 2673, 4678, 2222, 5987, 8167, 2455, 1942, 8882, 17, 23703, 1920, 3197, 2644, 18, 2176, 1977, 2481, 1922, 27896, 7972, 19918, 7368, 6150, 15444, 8134, 1930, 9826, 20709, 11121, 2538, 14392, 2288, 17, 4594, 4948, 2433, 16, 3260, 16, 1930, 9117, 7864, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MIPVYTRLLLLLFTCIACKAGAQDNFQLSANRPAMSNREIHTRTALGAAIQNHNIPEATEAYSHIVTLYNNRGEYEMLPTIYNSFANRFQRTGQYDSSMAYYYNAIAVIEGVLQIVGDYPNALVYLDKAEKITRQIKYMHLLRKYNFLQWKHLALSNLGATHHAEGHNKEALRFLNYKEAESYLLQSISTAEQKHIARDITEGHRIISEQLKDSIESQATKHDISNLEIKYRTAQKDKELIVALLLAAIAALLYSMYRSNWHQQRFQEEKFRNLEQEQEIGGMLASIKMNLQAIQDEQPQLQQLAGINKVSLTKQNLRGALLQYSENNSNSLLQIALQYDVKELVQNIVKHAGANYAVIQLMLHESSLSIIVELQGYLACSSVIGKGTTIHIEFDFLKLKNLLIDSAIARATAQSDTAMPMFRAYTFAKDVLRIAEARNMKGNDTPVNRNSLATLYTNLSALVLINKGNTLNSMDQLDASIRNLDEALAIAKEAISLKGDVDPNYQNTNIALLGKVYLALGLYAATHEYHKAYEHQYRYIKELQISRQNAQIKQKNLWIVGVSAGQLRAMMKGEEKERIRIAQDLHDGIGGMLADTVTEVRKTAHNLMPDAEAMPKNAELFIYRIIQDNGGGFDTGRATTGAGLQNIRKKVET", "metadata": {"id": "A0A2P8DDI8", "cluster": 13780419, "interpro_all": ["IPR036890", "IPR005467", "IPR050482", "IPR011712", "IPR011990", "IPR019734"], "interpro_used": ["IPR019734", "IPR005467", "IPR050482"], "interpro_unused": ["IPR011712", "IPR011990", "IPR036890"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that has the following function: The protein contains a Ribosome-binding factor A conserved site that associates specifically with free 30S ribosomal subunits to facilitate the efficient processing of 16S rRNA. Found primarily in bacteria and plant chloroplasts, this domain is located in the second half of the protein and is essential for ribosome maturation. Also, the protein falls within the K homology domain-like, alpha/beta superfamily, which comprises RNA-binding modules that adopt a characteristic two-layer \u03b1/\u03b2 fold found in diverse prokaryotic and eukaryotic regulatory proteins. These domains can function independently or cooperatively to bind RNA substrates and are integral to complexes such as the ribosome, Era GTPases, and the NusA transcription factor. It originates from Candidatus Phytoplasma pini and features UniProt keywords Cytoplasm and Ribosome biogenesis. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 12794, 17, 2743, 2991, 43, 5305, 3200, 1988, 14162, 4475, 1956, 3294, 27755, 11196, 6991, 1942, 6628, 1920, 5807, 4587, 1927, 11209, 9067, 18, 2435, 5985, 1922, 4802, 1930, 4496, 24627, 16, 2052, 3418, 1977, 4810, 1922, 1920, 2812, 4768, 1927, 1920, 2213, 1930, 1977, 4415, 1958, 12794, 7655, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 53, 9039, 3418, 17, 3189, 16, 4595, 19, 4666, 13975, 16, 2154, 12936, 3146, 17, 2743, 10803, 1988, 14103, 43, 6293, 2288, 17, 4757, 160, 19, 161, 3728, 2435, 1922, 6445, 21545, 1930, 10825, 4948, 2697, 18, 2144, 4682, 2112, 2347, 6407, 2014, 13350, 1954, 1942, 4566, 3146, 6249, 1930, 2032, 12328, 1942, 5048, 2427, 1966, 1920, 12794, 16, 14821, 18390, 16, 1930, 1920, 13232, 5735, 3213, 2991, 18, 2176, 22970, 2037, 14550, 1031, 1957, 25512, 15403, 1019, 8701, 1033, 1930, 4075, 20709, 11569, 5239, 1930, 12794, 13008, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MNPNIANNKIKMRANLIHKLLINIVNDVIENEEIEHITINGVNLSNDLSFCTVFYSILNKDDHTSSLLKKILEENKKEIRAQLASKIRNMKKIPQLIFQYDNSLNYGEKIDKLLETIKK", "metadata": {"id": "A0A559KJ35", "cluster": 15049185, "interpro_all": ["IPR015946", "IPR000238", "IPR023799", "IPR020053"], "interpro_used": ["IPR020053", "IPR015946"], "interpro_unused": ["IPR023799", "IPR000238"]}, "task_type": "autoregressive"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein should have a Aminotransferase class V domain that functions as a pyridoxal-phosphate (PLP)-dependent catalytic module found in aminotransferases and related enzymes such as cysteine desulfurase. This domain facilitates enzymatic transformations by covalently binding the PLP cofactor to a conserved lysine residue. In addition, it is part of the Pyridoxal phosphate-dependent transferase, small domain superfamily, which comprises the complex $\\alpha/\\beta$ structural domain found in enzymes such as aspartate aminotransferase and DOPA decarboxylase. These proteins utilize pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze diverse reactions, including transamination, decarboxylation, and deamination, playing a vital role in amino acid biosynthesis and neurotransmitter metabolism. Additionally, the protein is classified under the Pyridoxal phosphate-dependent transferase, major domain superfamily, which forms the large catalytic component with a 3-layer \u03b1/\u03b2/\u03b1 sandwich topology in enzymes that utilize pyridoxal 5'-phosphate (PLP) as a cofactor. Through a Schiff base linkage with an active site lysine, members of this superfamily facilitate diverse chemical transformations, including transamination, decarboxylation, and deamination, which are essential for the biosynthesis and catabolism of amino acids and neurotransmitters. It occurs in Basidiobolus meristosporus CBS 931.73.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 3066, 2162, 43, 15817, 2921, 64, 3418, 1988, 4088, 1966, 43, 24828, 23859, 17, 5413, 12, 21453, 13, 17, 3100, 6804, 9059, 2435, 1922, 15817, 1036, 1930, 2712, 5038, 2427, 1966, 8666, 30311, 9280, 4127, 18, 2052, 3418, 11374, 8145, 18510, 2007, 16590, 2743, 1920, 21453, 15155, 1942, 43, 5305, 9082, 6181, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 2858, 3418, 13975, 16, 2154, 12936, 1920, 2796, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3418, 2435, 1922, 5038, 2427, 1966, 12878, 15817, 1930, 19428, 23922, 18, 2144, 2697, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 1942, 18170, 6445, 5298, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 14797, 43, 8970, 2770, 1922, 3835, 2687, 8132, 1930, 15223, 4714, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 3044, 3418, 13975, 16, 2154, 4952, 1920, 3103, 6804, 4594, 1956, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 18038, 13678, 1922, 5038, 1988, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 18, 2596, 43, 25214, 5170, 8611, 1956, 1925, 3500, 3200, 9082, 16, 4678, 1927, 2052, 13975, 6628, 6445, 4399, 18510, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 2154, 2032, 4415, 1958, 1920, 8132, 1930, 19480, 1927, 3835, 4576, 1930, 21012, 18, 2176, 5110, 1922, 2726, 13756, 2389, 19574, 24108, 9890, 1957, 16341, 6156, 1009, 18, 5356, 18, 3], "output": "MDPSLASLRQIPFGQSARKLYAARREWLDRSEKNPDKWLRHDYNGVNSVVRSLNFKPEEKVVYFSTTDSQRLSLVEVQVDFPFKDEDLLKQVGELLDVPALLFPFVELNKLFKSRGITVADFFVTNIHKWGQSSRPCALLISHGYETRSFYEDFQWTGTEERILRYIHELAVKGGQKVATILGTELPLSAQHGDKHIRQLAVTLLQKFNVPLEPGYTNLNNGSFGTVPLYVEFQQYERVRDEVADYVGAEKENLVFVQNATYNAVKQLLFYLRREPNIKLAIVDAISSLVDGAHAYGQIPLKLEECGYATKKQQMNIHPSSTDLSQIMSVSAALAYRKAIGVIGDEHQIPAMVNVR", "metadata": {"id": "A0A1Y1YKY1", "cluster": 16155184, "interpro_all": ["IPR000192", "IPR015424", "IPR015421", "IPR015422"], "interpro_used": ["IPR000192", "IPR015422", "IPR015421"], "interpro_unused": ["IPR015424"]}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein can be placed in the DNA recombination-mediator protein A family, which mediates natural bacterial transformation by binding cooperatively to single-stranded DNA (ssDNA) and facilitating RecA loading to catalyze homologous recombination. It overcomes the barrier imposed by SSB proteins to promote filament formation and interacts with ComE to regulate competence shut-off. It originates from Idiomarina sp.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2678, 7827, 17, 11370, 2213, 43, 3416, 16, 2154, 10412, 4613, 4543, 7002, 2007, 2743, 13350, 1954, 1942, 2957, 17, 10338, 2678, 12, 15063, 13, 1930, 12440, 21534, 6693, 1942, 18170, 8725, 7827, 18, 2176, 9063, 1036, 1920, 7104, 16125, 2007, 22228, 2697, 1942, 5527, 10797, 3337, 1930, 9034, 1956, 10449, 1942, 5741, 12939, 14413, 17, 4013, 18, 2176, 22970, 2037, 11407, 2954, 5572, 1019, 2056, 18, 3], "output": "MNQQDVCILLGLNRANQEIRKAARELKSTSEVIDRWGQSLKPVDAKWVKATLAWQESSNQGVIGFYDHEYPDRLRQIDDPPWLLFYQGRAELINATGIAIVGSRKAS", "metadata": {"id": "A0A2E9H4R4", "cluster": 17810833, "interpro_all": ["IPR003488"], "interpro_used": ["IPR003488"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein falls within the Nucleic acid-binding, OB-fold superfamily, which utilizes a conserved five-stranded $\\beta$-barrel motif to bind single-stranded nucleic acids or oligosaccharides. This versatile domain is found in diverse proteins, including ribosomal subunits, DNA ligases, and toxins, where it plays essential roles in DNA replication, repair, and translation. Additionally, the protein includes a Telomeric single stranded DNA binding POT1/Cdc13 domain that adopts an OB fold to bind single-stranded telomeric DNA, regulating telomere length, replication, and capping. It functions as a component of the shelterin complex to protect chromosome ends from attack by DNA-repair mechanisms. It is derived from Salinomyces thailandicus.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 12182, 2651, 1920, 11079, 2687, 17, 2743, 16, 2384, 17, 3728, 13975, 16, 2154, 18127, 43, 5305, 3628, 17, 10338, 8, 38, 4666, 8, 17, 19560, 5219, 1942, 4566, 2957, 17, 10338, 11079, 4576, 2014, 22012, 18, 2052, 20425, 3418, 1977, 2435, 1922, 6445, 2697, 16, 2710, 11196, 6991, 16, 2678, 22423, 16, 1930, 13599, 16, 2597, 2176, 5705, 4415, 5456, 1922, 2678, 5158, 16, 5059, 16, 1930, 6410, 18, 4950, 16, 1920, 2213, 5921, 43, 19951, 2957, 10338, 2678, 2743, 2543, 1009, 19, 7137, 3633, 3418, 1988, 24032, 1925, 2384, 3728, 1942, 4566, 2957, 17, 10338, 19951, 2678, 16, 6773, 12025, 3471, 16, 5158, 16, 1930, 23565, 18, 2176, 4088, 1966, 43, 4594, 1927, 1920, 27624, 1921, 2796, 1942, 9145, 5597, 9618, 2037, 8926, 2007, 2678, 17, 5059, 3531, 18, 2176, 1977, 3595, 2037, 30128, 29249, 17445, 24375, 18, 3], "output": "MEDKIQIQSLAPGTAPPRDQSIRAVVTLAWPFSSSTRQCALLSAEAVAKSRVGIGDEVTLSLGGAVWAEQGDETARTPGNSVGGELVFARQLAAGTATGTPLPRAVGGLRQSLGESTVPIYSSPAFALEHDADEGIKKDLRSSFSGVGQWRYATRSPSPVKDVQHFDLEVELERVQKELPTTPDQIFSSPKTRSPIAAAEPPQPPAPDGVTIGDMPGVQQQVSQLFADTSRIGEEAAARNSPTTPELRAVPNSALPLPSPFPVEGAQPSLRHPDLTSPPQPQKDPERQGSQPRSGIDGTFKIPFEKSSEEQSHAFSLMRDAGQAPPRPVASTPVKLPPSTFSLDGEGSSASLHPVTPAPQYKSLFGFRTSPEPQPSPTVHEEPPEKRNEPVLGWTDTAPSSPMKEPEIAETQFPDRVDDAISSPPRVQEKVQRERIADETEPPKAARNSQESEADILATQHHESFRRPEEAAGAAVHDHLKQTQRPSALQINEKQAAENAIDRISPGTGYRSATSSDHVDERSTAIDVSRPLPTSQLNEAAEQTESSPTPQPQSMLQNQPTLSEQLNQGGSVHFPATEQVPAAAESEGGEEEHEVDDVTQNEPSPARPIDTTDLEESATLQDAANLDKSIDGAMLHEIGVQQEATSTEDDDRDLAETLSSPRYSAHADDSPKDISRDETQESLQTSSSVASRTPSSASASLPQTEVIEIGSSSPASAETVPSPITAESLEPTFESQNVPAENRTTTQVRIIDQSPGAQNLLSFDTTRPTDQVSEIARAAAEEDTRQETDDSMMPEASQHFSTQSPISNLPDMSTSAVISPALTQETSQQFETQIPISDVPDVSYPTLPLSPLASQPRFESQAIQKEQTLNDKTNQKQPEIQEQPLDSASTQGDLIPGRMLGTLESNGAHKQPTSSGGEQEQAPEVVESHKVEQDASPGPKKKTTFSPKRSSTAAIETPNTPPQTENEQVHLRSTHFAAEQVGKGLKKTPSSGIVTSTGYYTPLPRLEEHLNSSSQQGSNANTVDVLAVVVNSGPRDYYTIFRIAEPSTTSQSSVRVEVFRPWKAKLPVAEQPYLLSTDTSAWCVWRHGSTQATQSFVDQPGWALQRSSGASSSHSSWLVMHSEGNKQQVGEEMDGDVDGLVSPDLTARLLADPDFRLRTRGGQVRVRFTGPSLRIGRDGGEVDISLDAPPSPQKASRGKRMRLSGDSFLDSAYDPFPDAGDVQVSDIEMLDQVHEENMPPPPLSKLRMPETLRVPVRSVENGQEVDQIGDQNVDSSAQAPSSQNQTKVAHMFQSESRMAKSTPQSTPQSQRERVMSQTRFDDVFPVAIKRRLKTDELAFADVDRDGSKQDRAPPDATVIDLDSNSDVVIEEIQLPLAAQVGYDAGTSIEPEVASSPPIGDSQDGFLGSLSTQPTGNGTDTLAQLIQAEMDQEMEEVRSAADTDVEMSTHVHDDFDGTADKVSQKPSSVALRTASTPDVEQAVVGMKLSDPVNSTLYQDKSQTINELDAATELKDLVSRPGATAEPESWLQEDNEQSKDGLPLTPQLTQAASGVLEMPEQNLTLAHQARAPARKSFGSRLSGVPDVISAWAVRDVQEGDAVGPPETPSTKPPERAKGVGDVVLLRDFTVKSRQRSVREEVKGPPVELGDDERKHAKVLRE", "metadata": {"id": "A0A4U0TRY4", "cluster": 18676482, "interpro_all": ["IPR012340", "IPR011564"], "interpro_used": ["IPR012340", "IPR011564"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein contains a Domain of unknown function DUF5641 domain that is found in a range of retrotransposon polyproteins. Furthermore, the protein carries a Integrase zinc-binding domain that coordinates zinc ions and is found in a wide variety of integrase proteins responsible for viral genome integration. Moreover, the protein should feature a Integrase catalytic core domain that catalyzes the insertion of viral or transposon DNA into a host genome by performing 3' end processing and strand transfer reactions. Adopting an RNase H-like fold, it utilizes a conserved DD35E motif to coordinate magnesium ions required for these enzymatic activities. It occurs in Galendromus occidentalis (western predatory mite).", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 5461, 43, 3418, 1927, 5435, 2347, 4855, 17968, 8760, 1009, 3418, 1988, 1977, 2435, 1922, 43, 3109, 1927, 27181, 1916, 6240, 10355, 18, 3677, 16, 1920, 2213, 16252, 43, 27252, 7997, 17, 2743, 3418, 1988, 10675, 7997, 6982, 1930, 1977, 2435, 1922, 43, 4743, 5386, 1927, 27252, 2697, 5061, 1958, 4324, 3843, 7122, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 27252, 6804, 4728, 3418, 1988, 17097, 1920, 7413, 1927, 4324, 2014, 18808, 2678, 2460, 43, 4423, 3843, 2007, 8219, 23, 11, 2482, 4587, 1930, 5984, 3856, 5298, 18, 20478, 1925, 9843, 50, 17, 3189, 3728, 16, 2176, 18127, 43, 5305, 6758, 5798, 1021, 5219, 1942, 11865, 13148, 6982, 3414, 1958, 2144, 8145, 4209, 18, 2176, 5110, 1922, 5179, 2200, 2018, 1957, 2708, 5314, 19337, 12, 4540, 20648, 1012, 24688, 13, 18, 3], "output": "METTQMARRVIRCLRTKKRNSVAEILASANISESKTSLPPGRHYDTELITHPDLSEEDIDAEVESSENFHDELARVVARLTVAKNKAAVSTSVSEMFRSARESTVPQASTPARSTELRKLSRVNDPFDVSGLRKLSTTVQRNVKVLATMGIQLMSLAPSLKSSLEAALPVQLKRQLEEQLKILSPASNRTTDNDEQPLENLSTKTPDIYSEEVLQMIEFLKVRVADLEDSRTLDSARTRNRTPEHSRQTVAAAAVKNRRPKFQPRPCLFCMTPDHNSSKRKADIPVEQRREILRGNRNPCGICGSKLHYSSMHEPDDKRGECATGASPTNDTLLMTIEVFIVNGGSRIPVRESPVQRARLNIQAFKDPHTFDAQRFSIRIGFLELQAPRRVTQDLLAFRTHAGWAIQSAALAEPAGDLERLWTIDAIGIDDGASTTFSAGEQAALNQLAEGITYDGTRYTLQQRPESYQRYDDEIMKLVHSGYASEVTGVLEGVVSEIDGSYFIPHHSKSVAEHLACHGIESWNPSQDCFQFCIRDLAQLAESQKSLTKRLVLRLVASVFDPLEWLAPFILRGKLTVQQMWQEFRFPRQYAPSNQRTVAHRLHIFCDASTRSYACAAYLQTLLENGSSDFSLIMSKSRLAPKIRLTLPRALGFERISFYTDSSIASFWALSRSSVDQWFFISGDKNIADLATRGIPAKIQTASEEWWFGPSWLRLDAVQVETRNTVAFDDVFRPLIDLERFSTAARAIRVMSYILKFIDISRKRQIPTVAECAVRSGDRVPSTSKLAAFRLFIDTHGVLRARTRLDRGSAFTYDEKNPIFIPGCSRFATLLILDTHRIGRQIIKALLAKCVTCRRKHSRPSSQVEAPSPDERAEFVAPFAAGSLDSCGPLFGRIKKETEKMYIALFTCSASYPSCRLLVSDNARSFTKAATDIKRVFNTVKNPEVRELLAGRKIEWKFICPRAPWQGGMYERLVGTVAEFRTIVAEMTAIVNARPISHVSSDVDEPLPLTPAQFLRGGPQQLVKRTAYLESLAARWHREYLLQLRSANCPRGSEQEPYAVGEVCLLREENVPRIRWSLVRIEDTHMVDPEYLLALIRPMIAIILAGLLDAERDSLLARREFREKQCAESALGPAKASADQRSRQKGRCVRCFRAAPALASECQRLFLDSGSSLTFIRPAVRQLLGPTPDAASPRVAAIADVCCVPFPKTADLSELPNNKSIALQRAERKIGLSPTLNLDEGKTLKVLGVTWEMQWDEEITGELMVEFAQWVSEFQAFLELLAALIGTRLKTFLVENMENPERQPASQPRLKLSKLASKAETVLIRTVQQQHLFEELNAHFGVNTVLSFLRRRFWIVRTRAVHLEVVPSMSAIQTHLALRRFLASTKTLGRSFVSYECAPLAQILPLDRLGPDGALPGDELRR", "metadata": {"id": "A0AAJ7WJ49", "cluster": 18772711, "interpro_all": ["IPR040676", "IPR001584", "IPR041588", "IPR008042", "IPR012337", "IPR036397"], "interpro_used": ["IPR040676", "IPR041588", "IPR001584"], "interpro_unused": ["IPR036397", "IPR012337", "IPR008042"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Additionally, the protein is included in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, the protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It occurs in Bacteroidetes/Chlorobi group bacterium ChocPot_Mid and is linked to UniProt keywords Cytoplasm and rRNA processing.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 5110, 1922, 26808, 19, 10107, 3821, 2210, 14061, 4551, 10020, 1991, 41, 3953, 1930, 1977, 4624, 1942, 20709, 11569, 5239, 1930, 9067, 4587, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MAKKKKKSVSDLNLERSEYEVKKPDGKYIDGTLGGGGHSGEILRRLSPRGSLYSFDKDRLRLINECFSKACSITGVEGGLDESRRGFSYRKDSSLDMRFGDYGEEPFAHRIARRIMLQRRAEESVPEQHRSKSLSRVFQAFRIAVNNELESYHSLEDRIVKSFFKERAVKKAQIKSDSNPRARSAKMRVAEVVFFYHLPVMLSKACDFLEQAISFCREKFWGELQRGEESFDGILLDLGLSSRQPDGKTAEEILHAAKEEEIIAILRFPFKTTFALRSVVVLYDTLHNCLPIMSDGAKIVVIDLTKSVPLLKILTPKPVLPDDDEIAR", "metadata": {"id": "A0A3N0ZTB0", "cluster": 22993599, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR002903", "IPR029063"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein contains a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Moreover, the protein is associated with the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein features a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It has been characterized in Ignavibacteriaceae bacterium and features UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 5461, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 4075, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 2258, 2252, 4378, 1922, 12046, 9188, 7972, 2341, 18339, 1972, 3336, 14061, 1930, 4075, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MKLIINSPAKINFGLFITEKRSDGFHNIETVYYPLELCDEVVIQACDRHIIETDSDELNKAGFENNLIFKAILLMEKKSGKKLPARISLKKRIPLGAGLGGGSSNAASVLLGLNDLFRLGYGKKELEVFGAELGSDVPFFIHPYPSFGEGRGEILTELEFELTGSLVVVNPGIFISTSEAYAGCRVGAAGYNLRELNKRKISDYKELRMSVKNVFEDTVFVNHPEIAELKEQFYDNGAEFALMSGSGSTVFGIFNNNEKAEAFVRTLPQNYFVFSQEL", "metadata": {"id": "A0A6N6SQ96", "cluster": 24628927, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR004424", "IPR013750"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to these design specifications: The protein is included in the Aldolase-type TIM barrel superfamily, which forms a TIM \u03b2/\u03b1 barrel fold that typically covers the entire protein structure. This superfamily includes metabolic enzymes such as class I aldolases, class I DAHP synthases, class II fructose-bisphosphate aldolases, and 5-aminolevulinate dehydratase. Furthermore, the protein has a Orotidine 5'-phosphate decarboxylase active site that catalyzes the decarboxylation of orotidine 5'-phosphate (OMP) to uridine 5'-monophosphate (UMP), marking the final step in de novo pyrimidine biosynthesis. This catalytic center is located in the N-terminal region and relies on an essential, highly conserved lysine residue for enzymatic function. Furthermore, the protein can be placed in the Ribulose-phosphate binding barrel superfamily, which is characterized by a parallel \u03b2-sheet barrel fold containing a phosphate-binding site. This structural motif is utilized by diverse enzymes, including D-ribulose-5-phosphate 3-epimerase, decarboxylases, and proteins involved in histidine and tryptophan biosynthesis pathways. It is native to Chitinophaga japonensis (Flexibacter japonensis) and contains UniProt keyword associations Lyase.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 1977, 3063, 1922, 1920, 11174, 21524, 17, 2601, 2267, 19560, 13975, 16, 2154, 4952, 43, 2267, 161, 19, 160, 19560, 3728, 1988, 5745, 10272, 1920, 5346, 2213, 3170, 18, 2052, 13975, 5921, 4487, 5038, 2427, 1966, 2921, 51, 11174, 21524, 1036, 16, 2921, 51, 3692, 15870, 8921, 1036, 16, 2921, 2890, 15102, 17, 29443, 11174, 21524, 1036, 16, 1930, 25, 17, 3835, 1952, 1020, 3392, 2010, 11725, 7234, 18, 3677, 16, 1920, 2213, 2258, 43, 25027, 10873, 25, 11, 17, 5413, 23922, 3500, 3200, 1988, 17097, 1920, 22429, 1943, 1927, 25027, 10873, 25, 11, 17, 5413, 12, 21921, 13, 1942, 26104, 25, 11, 17, 21363, 12, 8736, 1034, 13, 16, 23471, 1920, 3948, 3537, 1922, 2028, 9441, 21611, 8132, 18, 2052, 6804, 4102, 1977, 4810, 1922, 1920, 56, 17, 4262, 3031, 1930, 12850, 1990, 1925, 4415, 16, 3626, 5305, 9082, 6181, 1958, 8145, 2347, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 5216, 8658, 17, 5413, 2743, 19560, 13975, 16, 2154, 1977, 4378, 2007, 43, 6110, 161, 17, 11130, 19560, 3728, 3165, 43, 5413, 17, 2743, 3200, 18, 2052, 4346, 5219, 1977, 7079, 2007, 6445, 5038, 16, 2710, 46, 17, 5216, 8658, 17, 25, 17, 5413, 23, 17, 13872, 9213, 2051, 16, 23922, 1036, 16, 1930, 2697, 3286, 1922, 13873, 1930, 13489, 8132, 3873, 18, 2176, 1977, 6196, 1942, 16588, 4965, 1019, 5604, 2290, 3355, 1937, 12, 5795, 26073, 2341, 1915, 5604, 2290, 3355, 1937, 13, 1930, 5461, 20709, 11121, 2538, 5253, 23928, 18, 3], "output": "MNRQELVGLIKERQSYLCVGLDTDIQKIPKHLLSYPDPVFAFNKAIIDATKDLCVAYKINTAFYECMGIRGWESLQRTVEYIPSGIFTIADAKRGDIGNTATQYAKTFFDTYKFDAVTVAPYMGEDSVAPFLSFNEKWAIVLGLTSNEGSKDFQLQKVGEEYLYEKVIRTVMEWGTPDNLMFVVGATQTAQLAAVRQLAPDHFFLVPGVGAQGGSLQEISSLAMNKDCGLLVNASRAIIYAGNGEDFATDARNAALQYQQEMSEYLEQAVAG", "metadata": {"id": "A0A562SM46", "cluster": 25490163, "interpro_all": ["IPR013785", "IPR018089", "IPR011995", "IPR001754", "IPR011060"], "interpro_used": ["IPR013785", "IPR018089", "IPR011060"], "interpro_unused": ["IPR011995", "IPR001754"]}, "task_type": "autoregressive"} {"instruction": "Give me a peptide sequence capable of: The protein is associated with the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Moreover, the protein is classified under the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It occurs in Alkalibaculum bacchi and is described by UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 1977, 2458, 1956, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 5110, 1922, 25178, 7972, 18021, 5277, 1035, 8175, 19519, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MKIYGLTGSIATGKSTVSNILREYCNAKIIDADLLARKAVEPDSIGLEKITEEFGPSILLPDGTLNRKKLGDIVFGSSHAIKILNNIVHPEVAKLYNEVADQYRTQGYEAILYDCPLLIEEKLTDTVDEVILVVSSEDAQLERLMARNNLTEDEAIKRIESQMNIKDKIPYGDYLIYNDGDYDQLKDAVIYLGREILKIGKLKVNKGDTF", "metadata": {"id": "A0A366IFZ5", "cluster": 26134862, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein falls within the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Additionally, the protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It has been characterized in Dehalococcoidia bacterium and has UniProt annotations ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 12182, 2651, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 2258, 2252, 4378, 1922, 2028, 7289, 26941, 2642, 2126, 14061, 1930, 2258, 20709, 15010, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MLVIGLTGGIGTGKSEVSRREVVAAFGESILGPSDEIDRKRLGAIIAEMVKEKIDLLRQQGEDLVVLEAAVLINNLSEEEAVSRIRSQLSHEEEIKFLWADRVKGKVEILREWGATVIDADLVGHEAYRPHSPAWFNDADARARLNSMMHPRMEAGWNSLVDEVWVTHSPEGEVINRLRQRERAKHAHVTVRNSGSMDELL", "metadata": {"id": "A0A9E4KSH4", "cluster": 28970816, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein contains a Phycobilisome linker domain that mediates the structural assembly of phycobilisomes in cyanobacteria and red algae by connecting trimeric and hexameric phycobiliprotein discs. It acts as a scaffold to organize these units into peripheral rods or core cylinders, essential for the formation and integrity of the light-harvesting supercomplex. It is found in Compsopogon caeruleus and features UniProt keywords Plastid, Membrane, and Thylakoid.\nPredict the masked amino acids to fulfill this.", "tokenized_instruction": [2, 1958, 43, 7471, 4609, 2213, 16, 2496, 2347, 1977, 28668, 2007, 1920, 2894, 30, 1920, 2213, 5461, 43, 25511, 17428, 12191, 2204, 3870, 11040, 3418, 1988, 10412, 1920, 4346, 5957, 1927, 25511, 17428, 12191, 2204, 21085, 1922, 21897, 1930, 2312, 17721, 2007, 15031, 29177, 1930, 25602, 1935, 25511, 17428, 8257, 5684, 16380, 18, 2176, 8016, 1966, 43, 7281, 1942, 25681, 2144, 5701, 2460, 5009, 19330, 2014, 4728, 20163, 1036, 16, 4415, 1958, 1920, 3337, 1930, 7996, 1927, 1920, 3696, 17, 17318, 26936, 6588, 2592, 18, 2176, 1977, 2435, 1922, 2059, 2204, 7056, 3827, 1022, 2332, 29755, 1957, 1930, 4075, 20709, 11569, 19754, 16, 3260, 16, 1930, 30193, 14288, 1960, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "RLGNAAGELEVDRVLATAYAQVFGDAAVLVRANVGAAETFRRMVYLENSPHSFIDTMCRRLLGRAPLNQEEVAEYIDAFGEDTVPFTKFPSYLDDDHIRTTSILQSSSSNSKCVTSLGSDADAAVSNAEEMLREGMISVRGFISMLCRSERHLLILSEEGFEAEVDSYIESQVESTWLAGASEFLS", "metadata": {"id": "A0A7S1TI70", "cluster": 1045159, "interpro_all": ["IPR001297", "IPR038255"], "interpro_used": ["IPR001297"], "interpro_unused": ["IPR038255"]}, "task_type": "infilling"} {"instruction": "I am designing a protein with the following function: The protein should contain a Transcription regulator HTH, GntR domain that functions as a bacterial DNA-binding module, typically located at the N-terminus, to regulate transcription across diverse biological processes. It adopts a conserved winged helix-turn-helix fold consisting of a three-helical bundle and a small beta-sheet. Also, the protein should include a UbiC transcription regulator-associated (UTRA) domain that functions as a conserved ligand-binding module to modulate bacterial transcription factor activity. By binding small molecules such as sugar phosphates and urocanate, it regulates operon expression, exemplified by the histidine utilization repressor which blocks gene transcription in the absence of an inducer. Moreover, the protein is included in the Bacterial HTH-type transcriptional regulator family, which typically functions as a repressor to control gene expression involved in metabolic pathways, virulence, and stress adaptation. These proteins utilize a helix-turn-helix (HTH) motif to bind specific DNA regions, often regulating operons for substrate uptake and degradation in response to environmental effector molecules. It has been detected in Streptomyces sp. 1-11 and exhibits UniProt keyword tags Transcription regulation. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 3213, 7888, 5334, 1023, 16, 9005, 1997, 3418, 1988, 4088, 1966, 43, 4543, 2678, 17, 2743, 9059, 16, 5745, 4810, 2019, 1920, 56, 17, 7822, 16, 1942, 5741, 3213, 3436, 6445, 3933, 4028, 18, 2176, 24032, 43, 5305, 12920, 1919, 7864, 17, 5165, 17, 7864, 3728, 7600, 1927, 43, 2559, 17, 11514, 14142, 1930, 43, 2858, 4666, 17, 11130, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 4803, 1935, 3213, 7888, 17, 2458, 12, 8812, 1019, 13, 3418, 1988, 4088, 1966, 43, 5305, 5207, 17, 2743, 9059, 1942, 8480, 4543, 3213, 2991, 2455, 18, 2007, 2743, 2858, 4206, 2427, 1966, 9523, 26473, 1930, 14984, 8337, 2010, 16, 2176, 7014, 15675, 2294, 16, 22236, 2007, 1920, 13873, 8422, 14434, 2154, 7644, 2359, 3213, 1922, 1920, 3905, 1927, 1925, 18027, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4543, 5334, 1023, 17, 2601, 5224, 7888, 3416, 16, 2154, 5745, 4088, 1966, 43, 14434, 1942, 2285, 2359, 2294, 3286, 1922, 4487, 3873, 16, 9304, 16, 1930, 3071, 7810, 18, 2144, 2697, 12561, 43, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 4566, 2487, 2678, 3451, 16, 3868, 6773, 28748, 1958, 4510, 5047, 1930, 4877, 1922, 2644, 1942, 4813, 7917, 4206, 18, 2176, 2258, 2252, 3330, 1922, 22874, 2056, 18, 21, 17, 2513, 1930, 9826, 20709, 11121, 2538, 14392, 3213, 3640, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MVSETGPQRPKYQRIADDLKAAIESGVYGPGDRLPGESALAGQYDVAVLTARQALKILRIEGLVETKKGAGARVIEFRPIRRHGIQRLAREQWGAGKSIWSADEERPVTIDVRVDTVAAPPHVARMLEVEENDRVCARSRRFILDDRSVMLATSYLPLDLVDGTAIMRVDTGEGGAYARLAEIGHAPAHFREEIRCRLPVAEEAEGLGMPLERPVIKVCRTAFDAELRAVEVNEMTMDSAAYVLEYKFDA", "metadata": {"id": "A0A510TQC6", "cluster": 1135282, "interpro_all": ["IPR050679", "IPR028978", "IPR000524", "IPR011663", "IPR036388", "IPR036390"], "interpro_used": ["IPR000524", "IPR011663", "IPR050679"], "interpro_unused": ["IPR028978", "IPR036388", "IPR036390"]}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein should contain a Planctomycete-type cytochrome c domain that facilitates electron transfer via a heme cofactor bound to a conserved N-terminal motif. This region contains the characteristic C-x-x-C-H sequence typical of c-type cytochromes and is primarily found in Planctomycetes, Verrucomicrobia, and Bacteroidetes. It originates from Bacteroidales bacterium.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 4720, 2341, 13386, 11555, 17, 2601, 9387, 45, 3418, 1988, 11374, 4995, 3856, 3454, 43, 10954, 15155, 4124, 1942, 43, 5305, 56, 17, 4262, 5219, 18, 2052, 3031, 5461, 1920, 6293, 45, 17, 66, 17, 66, 17, 45, 17, 50, 3244, 5939, 1927, 45, 17, 2601, 9387, 1036, 1930, 1977, 5985, 2435, 1922, 4720, 2341, 25148, 16, 3566, 3176, 13055, 1935, 15129, 2126, 16, 1930, 26808, 18, 2176, 22970, 2037, 24323, 3955, 14061, 18, 3], "output": "MKINKIYLFLFTVLLIITVSWVISCTHTADISNLPEVCFEGDVLPVFKNSHSVVPGNPLASKVYKAIIATTGENKMPPDRPLSIENRIMIRLWIERACFTRDILPVLVSRCASTGCHDAITHKEGYIFASYTTAMKAVTPGNPGGTAEIDSIGRWISYGALNENCGEICDTINPVTFSGTIWPVIQSSCTGCHASNGLLIKSLNGTGVPRMPPAGFFSACRIRQFEIWIRNGFLNNSCSISGCHDGSGESGMVLNNYLDIQGARLTVCPDGTGNGTGGDPYVNPSKLYKVIKLTSGEEKMPPAGSSQLTSGTAPSGNISLTSYNNVAAV", "metadata": {"id": "A0A352MF52", "cluster": 4793519, "interpro_all": ["IPR011429"], "interpro_used": ["IPR011429"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein should include a HPr kinase/phosphorylase, C-terminal domain that functions as the catalytic core of the bifunctional enzyme HprK/P, regulating carbon source utilization in Gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 on the phosphocarrier protein HPr and its dephosphorylation via phosphorolysis, typically within a hexameric assembly. Furthermore, the protein carries a HPr(Ser) kinase/phosphorylase, N-terminal domain that constitutes the structural blades of the hexameric HPr serine/threonine kinase PtsK, a sensor protein controlling bacterial carbon catabolite repression. This domain facilitates the assembly of the enzyme's three-bladed propeller structure, allowing it to function within a multicomponent phosphorelay system. Moreover, the protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It has been detected in hydrothermal vent metagenome and is linked to UniProt keywords Metal-binding, Transferase, and Magnesium.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 18542, 4016, 19, 12556, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 1920, 29491, 4113, 18542, 1040, 19, 58, 16, 6773, 5056, 4585, 8422, 1922, 8604, 17, 2843, 4802, 18, 2176, 17097, 2321, 1920, 4498, 17, 3100, 4050, 1927, 2375, 17, 4182, 1990, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 2496, 16881, 3454, 3421, 6892, 16, 5745, 2651, 43, 25602, 1935, 5957, 18, 3677, 16, 1920, 2213, 16252, 43, 18542, 12, 2375, 13, 4016, 19, 12556, 2051, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 4346, 22707, 1036, 1927, 1920, 25602, 1935, 18542, 8468, 19, 13143, 4016, 8618, 1040, 16, 43, 6443, 2213, 7138, 4543, 5056, 3115, 3016, 2394, 10084, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 4113, 11, 61, 2559, 17, 22707, 1007, 5062, 13728, 3170, 16, 7201, 2176, 1942, 2347, 2651, 43, 8844, 28155, 1939, 3421, 15208, 1012, 2433, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 2258, 2252, 3330, 1922, 26959, 14654, 16552, 2225, 1930, 1977, 4624, 1942, 20709, 11569, 6048, 17, 2743, 16, 13763, 16, 1930, 13148, 18, 3], "output": "MNIPATVRDLFDIFKDKLSLEWVAGEAGGNRRLKGELPEALSQPLAGQLNNIHPNRIQVIGPAELAYLAELGKNSHHDIIDKLFWGLPAAVILANGSDVDAEFIEYAERTNTPLLRSPLPDNKLLSNLQYYLTRALADCTTLHGVFLEVLGMGVLLTGDPAVGKSELALELITRGHRLIADDAPEFSRMAPDILTGSCPPLLQHFLEVRGLGILNIRDMFGDSAIKKEKYLRLIITMKRLSQDELSQIDRLQGSHSTRELLGISTPEVTIPVAPGRSLAILVETAVRQHIHRRKGYDASVDFIERQQKMIFENEAKKKKSQL", "metadata": {"id": "A0A3B1AHY5", "cluster": 8923043, "interpro_all": ["IPR003755", "IPR011104", "IPR011126", "IPR027417", "IPR028979"], "interpro_used": ["IPR011104", "IPR011126", "IPR027417"], "interpro_unused": ["IPR003755", "IPR028979"]}, "task_type": "autoregressive"} {"instruction": "I am designing a polypeptide chain with the following function: The protein should contain a Carboxyltransferase subdomain C and D domain that forms the C-terminal portion of the carboxyltransferase component in biotin-dependent enzymes like urea carboxylase and urea amidolyase, facilitating the ATP-dependent carboxylation of urea. In proteins such as 5-oxoprolinase subunit B (PxpB), this domain complexes with the N-terminal subdomains but lacks the conserved residues necessary for carboxyltransferase catalytic activity. Moreover, the protein is grouped in the Cyclophilin-like domain superfamily, which constitutes the $\\beta$-barrel core of cyclophilin-type peptidyl-prolyl cis-trans isomerases involved in protein folding. This domain catalyzes the isomerization of peptide bonds preceding proline residues and is also found in the C-terminus of various bacterial proteins. Additionally, the protein belongs to the 5-oxoprolinase subunit B family, which catalyzes the ATP-dependent conversion of 5-oxoproline to L-glutamate. Widely distributed in bacteria, this protein contains a carboxyltransferase domain and functions as an inhibitor of sporulation kinase A (KinA) in *Bacillus subtilis*. It has been characterized in Spirochaeta isovalerica and is connected to UniProt keyword ATP-binding and Hydrolase. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 9943, 9961, 27517, 45, 1930, 46, 3418, 1988, 4952, 1920, 45, 17, 4262, 7717, 1927, 1920, 9943, 9961, 4594, 1922, 8622, 17, 3100, 5038, 3189, 10505, 29073, 1930, 10505, 28813, 26558, 2051, 16, 12440, 1920, 4498, 17, 3100, 9943, 1943, 1927, 10505, 18, 1922, 2697, 2427, 1966, 25, 17, 18588, 15743, 11413, 5903, 44, 12, 15194, 16752, 13, 16, 2052, 3418, 5048, 1956, 1920, 56, 17, 4262, 30103, 2308, 13012, 1920, 5305, 4248, 4680, 1958, 9943, 9961, 6804, 2455, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 20585, 7969, 7782, 17, 3189, 3418, 13975, 16, 2154, 14879, 1920, 8, 38, 4666, 8, 17, 19560, 4728, 1927, 20585, 7969, 7782, 17, 2601, 3431, 2199, 17, 3192, 2199, 5848, 17, 2127, 25510, 1036, 3286, 1922, 2213, 10328, 18, 2052, 3418, 17097, 1920, 27027, 1927, 4207, 9031, 12141, 12958, 4248, 1930, 1977, 2222, 2435, 1922, 1920, 45, 17, 7822, 1927, 3425, 4543, 2697, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 25, 17, 18588, 15743, 11413, 5903, 44, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 7309, 1927, 25, 17, 18588, 15743, 2053, 1942, 54, 17, 7627, 18, 5673, 6533, 1922, 4802, 16, 2052, 2213, 5461, 43, 9943, 9961, 3418, 1930, 4088, 1966, 1925, 4106, 1927, 23647, 4016, 43, 12, 3498, 1019, 13, 1922, 14, 14587, 14745, 14, 18, 2176, 2258, 2252, 4378, 1922, 22075, 25588, 9215, 4911, 28144, 3133, 1019, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 1930, 20748, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MYVQNLGDGSLSFVIGDRIDRETSRRILKLYKTMKNSSLPGELSIYDIVPSYCSLTFHFDPLKTDCVVMEEELWPVIASQLRKAKSSSGKGKSFHIPVIYRGEDLNRVSRLTGLTVKQIIRRHTYPSYQVAMIGFRPHFPYLIGLDRKLATRRLDTPRLKICAGSVGIGGSQTGVYPEDSPGGWNIIGYTDPQLLKELSPGDTLKFCEVSRL", "metadata": {"id": "A0A841RCB5", "cluster": 9500410, "interpro_all": ["IPR003833", "IPR029000", "IPR010016"], "interpro_used": ["IPR003833", "IPR029000", "IPR010016"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Give me a peptide sequence capable of: The protein is grouped in the Papain-like cysteine peptidase superfamily, which encompasses enzymes that utilize a conserved Cys-His-Asn catalytic triad to perform proteolysis. These members typically adopt a structural fold consisting of a single alpha-helix and four strands of antiparallel beta-sheet. It is found in Vecturithrix granuli.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 1977, 10809, 1922, 1920, 3860, 2005, 17, 3189, 8666, 24050, 13975, 16, 2154, 21569, 5038, 1988, 12561, 43, 5305, 4998, 17, 4167, 17, 15118, 6804, 21845, 1942, 2385, 15439, 18, 2144, 4678, 5745, 14103, 43, 4346, 3728, 7600, 1927, 43, 2957, 4595, 17, 7864, 1930, 3006, 13214, 1927, 28892, 4666, 17, 11130, 18, 2176, 1977, 2435, 1922, 23098, 18330, 5856, 2416, 9015, 1033, 18, 3], "output": "MNINTDNKKMRHYYKYFICKPKWKTFIAGLFAIVFLWLGSSHYFHLTPIQLAKQGSRVIIVPVFAKLYAEDKKSAELLRQNSWIGESNVISSSSLESWKHIEAQVPGFRFLGGNGSNENIQRDIPFIYESMNAQYLVELREHYQLDQLIMEAPDEYHAMLRLGAWVGTRWDHGIDPVPQGITIPHPLDIIQAGENGSKFWCEVAAKVTVNAATALGWPARLVTASRDGYTWEHALAELWSNQHRKWFVMDTDFNIVYEANGIPLSAFELCHNGLELQKTKQLYTREIAPPKPSLPLIDLLPFYRYIHIDLRNDWYSRRLRRGSPAGGDLATWWTARPSFGNILTAKIRVDHQKKFDWPVNSVNIYARSLDSSQNPPLLNIGLFGYSPFFKTFQISVDDRTWHDTKSGHDSFHLLPGKHSVKARVMTMTEQAGPVYEIQFQFF", "metadata": {"id": "A0A081C4B1", "cluster": 13196950, "interpro_all": ["IPR038765"], "interpro_used": ["IPR038765"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is associated with the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Also, the protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein should feature a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. It has been detected in Branchiibius sp. NY16-3462-2 and is associated with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 2176, 2258, 2252, 3330, 1922, 6089, 3907, 3821, 1957, 2056, 18, 8932, 3672, 17, 26955, 1028, 17, 22, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MPGFFLVFEGGDGAGKTTQLTALREALADTGREIVVTREPGGTPVGQAIRDVLLHGEHVAPRAEALLFAADRAHHVATVVRPALERDAIVLQDRYLDSSIAYQGAGRELAAEDVRGLSLWGTEGLLPDLTVLLDVPAETGRERRGEVHDRLEQEADDFHGRVREHFLGLAAAEPQRYLVLDATRPADELAKDIEAAARERLA", "metadata": {"id": "A0A151C2J2", "cluster": 14958716, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR018094", "IPR027417", "IPR039430"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein falls within the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. Furthermore, the protein has a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. Additionally, the protein should have a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. It is identified in Candidatus Egerieousia excrementavium and features UniProt keywords Hydrolase and Metal-binding.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 3677, 16, 1920, 2213, 2258, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 2176, 1977, 2899, 1922, 14550, 1031, 1957, 7282, 18842, 1021, 2080, 2126, 9394, 2017, 9188, 1989, 1930, 4075, 20709, 11569, 20748, 1930, 6048, 17, 2743, 18, 3], "output": "MTESKQIEDVLRGVVHPASDKNVVELDMIEAKLVFPRPDALASSIKAACKKAVEDAFPGKLEVDQIQLENVDKIIAVASGKGGVGKSTVAVNLAVTLARMMTGTEGETPQVYLPEGYKEGDNTELIIPIEKYGVKWMSLKQMILQVKWDELDYLLLDLPPGTGDIHISLVHDIPDVEKGINLFRNPNINKPIYGLVENMAWFTPEELPENRYYPIVQSIRECGDNGEPSAVRPGPVFDAFVKIAEQLIRCEEDGDVHKIKFYTVEIMELVREKRAHKAKGYKVGLADADVYGPSIPKIGYFAAPEQALIWRGPMACNALTGAIVVSTPQAVALSIFGKDGCRKMAEKYNVPLLGQI", "metadata": {"id": "A0A9D9DLR3", "cluster": 15358060, "interpro_all": ["IPR034904", "IPR002744", "IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR033756", "IPR002744", "IPR000808"], "interpro_unused": ["IPR019591", "IPR034904", "IPR044304", "IPR027417"]}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein should have a PBP domain that functions as a ligand-binding module within the periplasmic binding domain superfamily. It is often structurally associated with helix-turn-helix domains, facilitating the coupling of solute recognition to transcriptional regulation or signal transduction. In addition, the protein is assigned to the Phosphate-binding ABC transporter substrate-binding family, which serves as the high-affinity receptor of the PstSACB complex to mediate the uptake of inorganic phosphate. Some members are implicated in host cell adhesion and virulence, while others are inhibited by arsenate and pyrophosphate. It is found in Anaerolineae bacterium.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 3066, 2162, 43, 22574, 3418, 1988, 4088, 1966, 43, 5207, 17, 2743, 9059, 2651, 1920, 24334, 2743, 3418, 13975, 18, 2176, 1977, 3868, 12171, 2458, 1956, 7864, 17, 5165, 17, 7864, 4682, 16, 12440, 1920, 7590, 1927, 19661, 5708, 1942, 5224, 3640, 2014, 2733, 8201, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 5413, 17, 2743, 7219, 9054, 4510, 17, 2743, 3416, 16, 2154, 10634, 1966, 1920, 2149, 17, 5173, 3148, 1927, 1920, 16910, 5735, 18598, 2796, 1942, 8265, 1920, 5047, 1927, 13849, 5413, 18, 2673, 4678, 2032, 6835, 1922, 4423, 2024, 6141, 1930, 9304, 16, 2679, 4991, 2032, 5069, 2007, 21290, 2010, 1930, 24937, 18, 2176, 1977, 2435, 1922, 11381, 8419, 3336, 14061, 18, 3], "output": "MTSFRRTIALMLVALVLLTTFAPGLSLRAQDSNTVTADGSALVAKVIEAAKTAYLVTAPEAKIEIAVSGTEGGFEKFCEGSLDLALAYGAISDQAAAACAAKNVQFTELLLGYDAAVVAVNSTSPARCLSLDQFNILLSPSASGVNQWASVDSTLGEGAISTVLAPPEDAQTRFLFDRLIAGEGLRADLTVVATPAEMISQISADIAAVGLMTLADFNANTDGKTTRALQVRSGTACIDANALNIDEARYPAVESLYVYVNLASLDRQPVVDFLNFVLGAEGKKQVTSSGYSVAGSLLYDRGREYVSAKRAGRTFSRIQRLNISADQTGSITVGGSSTVHALLSKVNGAFTPRFSGIAINLTTYDSANALADLCAGIADVVGVSRKATDAELAICQSADIAPIQLTLGSEALVLAVNSTNTFAQCLTLDEVNKVFNAKTAPKKWSEVKDGFPETDLMPVLPSVGAMENDLLLVRVAKDQIAPIMREDGVKNDDALFRAAGVQNVDGGITFLKYSDFKKSSSKVNVVKIDGGNGCVEPTEATIGDGTYAFSYPNYLLVNPKSFVRPEMRAYTWFLLSDDTLTLLNSSGLTGTDTVGITGLRDGVLDLFEKAETPAATATPSAETPAPTAETPAETPAPTVETPAPTVETPAPTAETP", "metadata": {"id": "A0A916CXW0", "cluster": 17158220, "interpro_all": ["IPR024370", "IPR050811"], "interpro_used": ["IPR024370", "IPR050811"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has the following function: The protein is assigned to the Glutamine synthetase/guanido kinase catalytic domain superfamily, which comprises enzymes sharing a common structural fold essential for nitrogen and energy metabolism. This family includes glutamine synthetase, which catalyzes the condensation of glutamate and ammonia, as well as ATP:guanido phosphotransferases (such as creatine and arginine kinase) that mediate the reversible transfer of phosphate between ATP and phosphogens. Additionally, the protein carries a Glutamine synthetase, catalytic domain that functions as the C-terminal active center of glutamine synthetase enzymes, playing an essential role in nitrogen metabolism by catalyzing the condensation of glutamate and ammonia to form glutamine. This domain is conserved across three enzyme classes (GSI, GSII, and GSIII) that adopt distinct oligomeric structures ranging from hexamers to dodecamers in both prokaryotes and eukaryotes. It is present in Stylonychia lemnae (Ciliate) and is linked to UniProt keywords Ligase. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 9959, 18185, 19, 13504, 15072, 4016, 6804, 3418, 13975, 16, 2154, 12936, 5038, 10763, 43, 3059, 4346, 3728, 4415, 1958, 6634, 1930, 3844, 4714, 18, 2052, 3416, 5921, 9959, 18185, 16, 2154, 17097, 1920, 16112, 1927, 7627, 1930, 14880, 16, 1966, 2486, 1966, 4498, 30, 13504, 15072, 8078, 18580, 12, 2427, 1966, 17784, 1930, 9732, 4016, 13, 1988, 8265, 1920, 10743, 3856, 1927, 5413, 2192, 4498, 1930, 8078, 7470, 18, 4950, 16, 1920, 2213, 16252, 43, 9959, 18185, 16, 6804, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 3500, 4102, 1927, 9959, 18185, 5038, 16, 14797, 1925, 4415, 2770, 1922, 6634, 4714, 2007, 29601, 1920, 16112, 1927, 7627, 1930, 14880, 1942, 2386, 9959, 18, 2052, 3418, 1977, 5305, 3436, 2559, 4113, 7190, 12, 5022, 1033, 16, 5022, 3907, 16, 1930, 5022, 10831, 13, 1988, 14103, 4493, 19206, 4061, 6485, 2037, 25602, 1036, 1942, 12621, 19384, 27306, 1922, 2321, 28149, 1930, 15021, 18, 2176, 1977, 2481, 1922, 26435, 14186, 19519, 1019, 15551, 26243, 12, 15714, 2057, 13, 1930, 1977, 4624, 1942, 20709, 11569, 11905, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MESTQNLAQSDNQNQEEQYDHVILSWQPYNGMRHAHLTRKEIYDQRDQKSQIAIVPALMLFMPMTHDVLLPNYPIPNLLDGIIMKPDHSSFKILKVGGNTESGTKSVNIGFVNCSFNYKDMSLCDYCPRNLVKRAILALQQKHNISVKIGYEIEFNVLDMDGKPINKHSGLNLDALLKQSDVLIRISNELNSQGVRVLNMHKESSHGQYEIVLDYDDVLKSIDNYNFAIQVIKQNFQREGKQISLLPRPFENQFCNGLHIHMSIWRDGKNILGDSAGQHLLTVEGQQFMAGILEHSSAINHFLAPSPNSMKRIQSHMCAGTFKIWGLENRDAILRLIQTDSVEGRPTHFELKALDHTANQCFALASVLVAATNGLDKEMKLPQPVNDVPLFIPEDAWQEKGITILPQTYEDRKVAVYSEENKVLLEFFGKPLIDNIFLISDEDFKELDGKSISEQFELLNSKF", "metadata": {"id": "A0A078BDJ3", "cluster": 26478883, "interpro_all": ["IPR014746", "IPR008146"], "interpro_used": ["IPR014746", "IPR008146"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The desired role of my protein is: The protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. In addition, the protein is assigned to the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. In addition, the protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is identified in Sulfuriroseicoccus oceanibius and features UniProt keywords Cytoplasm and rRNA processing. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 2899, 1922, 12585, 10602, 4127, 5670, 2437, 1957, 13563, 2023, 11519, 1930, 4075, 20709, 11569, 5239, 1930, 9067, 4587, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MPDECIAALQPAEGKVIADLTLGGGGHTERLLEAGATVYGFDQDLEAIQFASERLARFGSRFIPVHSNFCGIERELTLRGVEHLDGVLIDLGVSSRQLDAPERGFSFMREGPLDMRMDANDPTMQTAADLVNTWEAEELARIFFQYGEEKFSRKIAREIVSYRSLHPFQTTLELADLIERVVPKRGPKHPATRVFQALRIAVNHEMSVLEQTLDALPRMLGDGGRLAIITFHSLEDRMVKLDFRKRSQEMLDHESWPEPRPNPDYAYRLVKRKPLLPTDEEIRVNPRSRSAKVRVAERLPRK", "metadata": {"id": "A0A7T7F459", "cluster": 269265, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR029063", "IPR002903", "IPR023397"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein is associated with the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It originates from Phycisphaerales bacterium and features UniProt keywords Cytoplasm and rRNA processing.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 22970, 2037, 25511, 9119, 29164, 3955, 14061, 1930, 4075, 20709, 11569, 5239, 1930, 9067, 4587, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MCTPDQGDGLARHVPVLVNQVSQLLSPPPCGTVVDLTIGQAGHSLVLGSRLGPDGVLVGIDVDFAQVGDLLRGKGIDAVDVMLADLGFSSGQVGDPQSGLSFLSDAPLDMRLDRSIQTTAADIVNDIARLIVERRKLKPICTTKELAELVCAAYRGRRHLRIHPATRTFQALRIAVNRELDNLQALLDQAPFRSRAQTGQYKVLTKRPIRPDPQEIAANRRARSARLRIAERIQRALDHARTVLRSLDCKVILIRGNTDEQVLADLIYRYGEDRLSRRTLLRSGGRFGVISFHSLEDRLVKQD", "metadata": {"id": "A0A7C3XE28", "cluster": 892621, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is associated with the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein should feature a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. It is found in Sphingomonas sp. YR710 and is associated with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2176, 1977, 2435, 1922, 13502, 10480, 2056, 18, 13031, 9948, 1008, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MSGRFISLEGGEGVGKSTQVRRLAEALRARGIDVIETREPGGSAGAEAIRRLLLEGAGDRWTAPTEALLFAAARADHVARTIGPAVTAGKWVLSDRYLDSSIAYQGGADGLGEEAIRTLHGIGSGGYLPDRTLLLALPAGDAVARAAARDRDGADRIGGREDAYHARVADSFDRLAAAEPDRFRRIDAVGAPEAVTNRLIAAIADLL", "metadata": {"id": "A0A1G6V8V0", "cluster": 4058987, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR027417", "IPR018095"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is included in the Ricin B-like lectin superfamily, which functions as a carbohydrate-recognition module typically binding simple sugars such as galactose or lactose. This domain is characterized by three QxW repeats arranged around a pseudo-threefold axis and is frequently found in plant and bacterial AB-toxins, glycosidases, and proteases. Moreover, the protein includes a Glycosyl hydrolase family 30, TIM-barrel domain that functions as a glucosylceramidase to hydrolyze the glucosidic bonds of glucosylceramide and synthetic beta-glucosides. This catalytic domain is characteristic of mammalian acid beta-glucosidases, and its dysfunction is linked to the lysosomal storage disorder Gaucher disease. Furthermore, the protein is categorized in the Glycoside hydrolase superfamily, which hydrolyses glycosidic bonds between carbohydrates or between a carbohydrate and a non-carbohydrate moiety using a conserved catalytic TIM \u03b2/\u03b1 barrel domain. Widespread across all groups of organisms including viruses, this superfamily encompasses a diverse range of enzymes, including alpha-amylases, beta-glucosidases, and chitinases. It occurs in Thalassiosira oceanica (Marine diatom) and carries UniProt keyword assignments Signal.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 27417, 44, 17, 3189, 13468, 13975, 16, 2154, 4088, 1966, 43, 10590, 17, 5708, 9059, 5745, 2743, 5288, 15592, 2427, 1966, 15996, 2014, 21021, 18, 2052, 3418, 1977, 4378, 2007, 2559, 59, 1039, 1018, 9569, 14940, 4760, 43, 11520, 17, 23109, 5432, 1930, 1977, 5467, 2435, 1922, 4496, 1930, 4543, 2186, 17, 13599, 16, 7533, 30413, 16, 1930, 12447, 18, 3950, 16, 1920, 2213, 5921, 43, 20067, 20748, 3416, 2627, 16, 2267, 17, 19560, 3418, 1988, 4088, 1966, 43, 3351, 11731, 2337, 25238, 2051, 1942, 7222, 6931, 1920, 3351, 27545, 7408, 1030, 9031, 1927, 3351, 11731, 2337, 5482, 1930, 6830, 4666, 17, 28507, 1036, 18, 2052, 6804, 3418, 1977, 6293, 1927, 6492, 2687, 4666, 17, 24755, 1036, 16, 1930, 2496, 5273, 1977, 4624, 1942, 1920, 12097, 7451, 4770, 4357, 21956, 2573, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 7533, 2261, 20748, 13975, 16, 2154, 21686, 1918, 7533, 12546, 9031, 2192, 16282, 2014, 2192, 43, 10590, 1930, 43, 2447, 17, 10590, 11804, 2193, 43, 5305, 6804, 2267, 161, 19, 160, 19560, 3418, 18, 9360, 3436, 2136, 2671, 1927, 7373, 2710, 6241, 16, 2052, 13975, 21569, 43, 6445, 3109, 1927, 5038, 16, 2710, 4595, 17, 19139, 1036, 16, 4666, 17, 24755, 1036, 16, 1930, 16588, 2319, 18, 2176, 5110, 1922, 20338, 14356, 11979, 13563, 6102, 12, 10789, 24149, 1947, 13, 1930, 16252, 20709, 11121, 2538, 18306, 2733, 18, 3], "output": "MSREGYDSIPAASPPAEAAEHEDEHPPEIGRESSHHQPTRYIALASIETNPPTRLCEVYTRDKFSLIQTSLSEPSKQWSEVACVHHNEPYSPKEESKGSTPSASIDVDFAKIAASELLFGKEYGLGYSLGRTHINSCDFCVESYSFDDTDQDFTLSNFDDEVTHDVESGKESEYGMRIIASPWSPPPWLKAPTYEDVDGALHAEKMTGSALPVCIRDGVGKDSKYNEPEFPAPWDACAYDPASEGEFIANHLGPQLRESHPNVKILIFDHNKDHINTWARWYAGGMDRLLDGAQGQANLHRFTSLLEMMEVKKDHVLLGSEACHCPSTGYAGGDLNIAWASNGFIEWNLILDSIGGPNHLGNMCDSPLLAVPHRALDAVGIPDQMDFEVAGHPFGDVHGDSKTRQMFYYVGHITRYVRPGSRAVYGLVDGGGGGPGERTFRPAGQDVAGGGINRQEWKLNEHKQLQVFGHDWLGAPTSSCLSKRASKDFDGLMGRANIVLKNTKADRSMSCLSVLLKSDAGANGPRGGGPGEHRRLRPGVRRRGHVPDDRLAVPPGGRVRHVRDGRQLEDCGGPQRGGQLCQLRAEGQGESILRQTWVCFGGGGEHVCVNSCPFELRGGVVYIGESYMAGHFVSTECLCLSLLLLILAYVVGKSTSAETVQLPQEIYPNRPPILGFGGAFTEATALNFMSLNDEARGVMVEMMLQATKVSKESYPAKSWALFFDKFITAYANHGVDLYGVTIQHLLDEKHPASKYIDGTAVHRAERNAHTILADLAGGEELHAEGVSSKFLDLGIAVQDLARDGIEVTLWPCEGSTLGSCNITEGSSGLYEVVPLEDKPVRVGLRRRDGGDILVTPGRLESSHVGINSTALHSNNCTGLEGYLFCFLI", "metadata": {"id": "K0S439", "cluster": 5791365, "interpro_all": ["IPR001139", "IPR033453", "IPR017853", "IPR035992"], "interpro_used": ["IPR035992", "IPR033453", "IPR017853"], "interpro_unused": ["IPR001139"]}, "task_type": "infilling"} {"instruction": "Target Function: The protein is grouped in the Ribonuclease H-like superfamily, which encompasses a diverse group of polynucleotidyl transferases that share a conserved 3-layer $\\alpha/\\beta/\\alpha$ catalytic fold. Members of this superfamily utilize a similar mechanism to perform critical nucleic acid processing functions, ranging from RNA degradation and DNA exonuclease activity to retroviral integration and Holliday junction resolution. Additionally, the protein has a Ribonuclease H domain that specifically recognizes and hydrolyzes the RNA strand of RNA-DNA heteroduplexes. This type-I domain is widely distributed across all kingdoms of life and functions as a critical component of retroviral reverse transcriptases, where it degrades the RNA template during viral replication. It is expressed in Oleoguttula mirabilis and is classified with UniProt keywords Endonuclease and Hydrolase.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 18347, 2051, 50, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 15176, 2626, 4090, 2199, 13763, 1036, 1988, 7948, 43, 5305, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 6804, 3728, 18, 4678, 1927, 2052, 13975, 12561, 43, 2551, 2856, 1942, 2385, 4140, 11079, 2687, 4587, 4088, 16, 6485, 2037, 3146, 4877, 1930, 2678, 24966, 2455, 1942, 16599, 7122, 1930, 14451, 27539, 6910, 4885, 18, 4950, 16, 1920, 2213, 2258, 43, 18347, 2051, 50, 3418, 1988, 4475, 16197, 1930, 7222, 20887, 1920, 3146, 5984, 1927, 3146, 17, 2678, 11330, 3481, 29140, 18, 2052, 2601, 17, 51, 3418, 1977, 5673, 6533, 3436, 2136, 13543, 1036, 1927, 3308, 1930, 4088, 1966, 43, 4140, 4594, 1927, 16599, 5267, 13335, 1036, 16, 2597, 2176, 28004, 1920, 3146, 7662, 2409, 4324, 5158, 18, 2176, 1977, 3198, 1922, 12188, 2021, 1984, 1031, 5617, 3138, 3836, 1937, 1930, 1977, 5947, 1956, 20709, 11569, 18697, 1930, 20748, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MSPDGRRFLLAEYFDRPQTLSNDDVEARAGGFTNLSTTLQPLIVACDGGCRYVGNVNAFAAIGVLMPQDSSKPTPQRAELFAALRALQTAMNAMTNLIHRWRQNGYMSDRNGCPVADRELYWQLEKAVWWVPRKDNTAADKLARAPLAAEDNRRKALLAAKETDADEDTAKRIRLHQRPVLPLPTRPNQYFQAPNSIYVQAQAWVASPPMPIPPPMLAPQPTYRYTLPSIPALAPQPAYRYTLPTIPALAPLPPPPLPVLTTASPATPLQTATKFFHNIAQFFGWRTFVDCDCSYHDNCSCHFVGAGSSFNVSERIKDHGWIPAVKTVVLKTDNLNLVTGLHHQHGVETLFLHAKRKRGSPESQQPPMMMPPPAAPVQPLPALPPPTTHIQYPQLPMLAYSTYSPATLAAPVVTYSAPVQFGH", "metadata": {"id": "A0AAV9JKZ0", "cluster": 6422912, "interpro_all": ["IPR050092", "IPR012337", "IPR002156", "IPR036397"], "interpro_used": ["IPR012337", "IPR002156"], "interpro_unused": ["IPR050092", "IPR036397"]}, "task_type": "infilling"} {"instruction": "Function:\nThe protein can be placed in the Insect cuticle protein family, which functions as a key structural component of the arthropod exoskeleton, interacting with chitin to define the mechanical properties of the cuticle. Members of this family typically feature hydrophobic tetrapeptide repeats and a conserved R&R consensus motif that facilitates chitin binding through a non-cysteine-containing domain. It has been detected in Psylliodes chrysocephalus and is classified with UniProt keywords Signal.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 11422, 25420, 2213, 3416, 16, 2154, 4088, 1966, 43, 3834, 4346, 4594, 1927, 1920, 21680, 1986, 24602, 20133, 30119, 16, 8615, 1956, 16588, 1942, 7425, 1920, 5821, 3879, 1927, 1920, 25420, 18, 4678, 1927, 2052, 3416, 5745, 5961, 7919, 28000, 8253, 9569, 1930, 43, 5305, 60, 10, 60, 7076, 5219, 1988, 11374, 16588, 2743, 2596, 43, 2447, 17, 8666, 17, 3165, 3418, 18, 2176, 2258, 2252, 3330, 1922, 2742, 10196, 13025, 1918, 21367, 1994, 2128, 7289, 1957, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MLNKAVAVFLACLAFTLAAPATEDRTTTAVKGSQRGHAPTKKDTVIKKTTITTVEKPTETLSDNSHVTITHLGNDHSYESVSHTVGSHESGANPTVIVHKVPTTSSSHSEDWSQAKNAHFQFATQVDDHINGNYQQKAETRQGGVLYGKVLPTHMTQRTGDASVQTLMDGYLVDYKINENDIGSSKRQSPASSRDGQGDVQRLIEELERNNVVSSSEELLNKLKNEEVHSSNNFENSAEFQQYSYDDGFFWTTVYYKADKNGFVVTKRE", "metadata": {"id": "A0A9P0GFF1", "cluster": 8909810, "interpro_all": ["IPR000618"], "interpro_used": ["IPR000618"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein carries a Peptidase M13 N-terminal domain that is found in zinc-dependent metallopeptidases of the neprilysin family, functioning as part of enzymes involved in the proteolytic processing of diverse physiological substrates like neuropeptides and vasoactive peptides. These proteins regulate biological processes ranging from cardiovascular development and blood pressure control in mammals to nutrient digestion in bacteria. In addition, the protein possesses a Peptidase M13, C-terminal domain that constitutes the extracellular catalytic unit of M13 family metallopeptidases, featuring a thermolysin-like fold and a conserved HEXXH active site motif. This oligopeptidase domain exhibits broad substrate specificity to regulate critical physiological functions, ranging from mammalian cardiovascular control and neuropeptide signaling to bacterial nutrient digestion. Also, the protein is associated with the Metallopeptidase, catalytic domain superfamily, which functions as the enzymatic core of various metallopeptidases responsible for hydrolyzing peptide bonds. This domain is structurally defined by a three-layer \u03b1-\u03b2-\u03b1 sandwich fold that typically scaffolds the metal-dependent active site. It is present in Bdellovibrionales bacterium and is associated with UniProt keywords Metalloprotease, Metal-binding, and Hydrolase.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 24050, 28534, 56, 17, 4262, 3418, 1988, 1977, 2435, 1922, 7997, 17, 3100, 8969, 24897, 1036, 1927, 1920, 26046, 3027, 19010, 1921, 3416, 16, 7295, 1966, 3131, 1927, 5038, 3286, 1922, 1920, 12712, 4587, 1927, 6445, 5005, 6249, 3189, 26839, 1930, 26613, 5320, 18, 2144, 2697, 5741, 3933, 4028, 6485, 2037, 5321, 2740, 1930, 2877, 3772, 2285, 1922, 9902, 1942, 8708, 9379, 1922, 4802, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 24050, 28534, 16, 45, 17, 4262, 3418, 1988, 14879, 1920, 5329, 6804, 5344, 1927, 28534, 3416, 8969, 24897, 1036, 16, 29931, 43, 7967, 19010, 1921, 17, 3189, 3728, 1930, 43, 5305, 7142, 1039, 1023, 3500, 3200, 5219, 18, 2052, 15039, 9626, 2410, 9200, 3418, 9826, 4949, 4510, 4896, 1942, 5741, 4140, 5005, 4088, 16, 6485, 2037, 6492, 5321, 2285, 1930, 21908, 3197, 1942, 4543, 8708, 9379, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 8969, 24897, 16, 6804, 3418, 13975, 16, 2154, 4088, 1966, 1920, 8145, 4728, 1927, 3425, 8969, 24897, 1036, 5061, 1958, 7222, 9046, 4207, 9031, 18, 2052, 3418, 1977, 12171, 3608, 2007, 43, 2559, 17, 4757, 160, 17, 161, 17, 160, 18038, 3728, 1988, 5745, 10603, 1920, 6048, 17, 3100, 3500, 3200, 18, 2176, 1977, 2481, 1922, 5238, 20783, 2165, 2377, 12778, 1918, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 28629, 2051, 16, 6048, 17, 2743, 16, 1930, 20748, 18, 3], "output": "MSKLALLSSVIVFVATLLSCNHPQRQINAANAETPDASTGQQALLTQNLVIPERRDFPVNVKLDPCNDFYEYACSGALADFSLPDDKSAYTFAFNDSHERVKRKKMAFIDSVANKKVSPRLAQVRDVYQSCLNEKRQVTDEQEWVAQVKADLAQINSHEELAQYIVQRWNAGSPSFLGLGDIPNQKNSLKNDAYFDVDVMQLNHRKLYEKEDVKQAYTELVSAFLITIGETQQISARAKKVVDLEQAFSQVYPTPEEFRALINEDRYVSRESLVAKYPAFHLDQVFAPLSASVPLRDLSPEATAYLHEQFVKGDLQTLKDLVAVQSLYSTLDDAYPEFYDQKFQFSHKYLGGPAVRKPRDQRCADYTFRKFAKEIDADMVQEMFPDFSKEKFVALLEKVRKEMIHRIKSNEWLSDAGRKGALKKMERLGYQVVTPNTEAEWDFLPVKTYDNASFLNNVVIFNKMMIEKTYDDLSKDRNKDVWGMGPLTVNAYYSAMDNKFVMPIGILQYPFYDQNLPEHVNMGAVGVVVGHEIGHAIDDKGAQYDGDGALNNWMTEEDLKHFKEMGQKLGVYYAAEEHNPELTMGENIGDLSGLTFAYDAAFGKKAATQKQKQEFFLQYARAWCQSIRPKFREQMLRNDYHSQQPQRVNLPIKHLTGFYEAYQCKAGDNMYVAPKDRVQIW", "metadata": {"id": "A0A958QFR0", "cluster": 9264232, "interpro_all": ["IPR024079", "IPR000718", "IPR018497", "IPR042089", "IPR008753"], "interpro_used": ["IPR008753", "IPR018497", "IPR024079"], "interpro_unused": ["IPR042089", "IPR000718"]}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein should feature a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. It has been characterized in Mesorhizobium sp. B2-4-16 and is linked to UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2176, 2258, 2252, 4378, 1922, 23577, 5004, 2061, 23156, 2056, 18, 11054, 17, 24, 17, 2641, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MASGFFITFEGGEGAGKSTQIERLARAVRHVLLSGAAEPFGPKMEAILFAAGSIVLCDRFIDSSRVYQGVTGGLDADFMKPAEGLKRAAARRGAGDAADRFEKETLAIASADPDTVENVVTAAVFAALEDRMPAQRIETAPARMRAKKYEVLVSREPGGSPGAEARSDHVEQVIRPAVERALEAVAINGMMPDMTLIFDIDHRRRREAFLAIAEAEPERCIVVD", "metadata": {"id": "A0A503LGD8", "cluster": 11880059, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR027417", "IPR018095"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "infilling"} {"instruction": "It is part of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Additionally, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is produced by Porticoccaceae bacterium and is annotated with UniProt keywords ATP-binding, Cytoplasm, and Transferase. I want a protein with the function described above.", "tokenized_instruction": [2, 2176, 1977, 3131, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 4152, 2007, 9260, 5670, 2437, 9914, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MNPLNRFVVGLTGGIGSGKSTAAKHFEKLGAEVINADIIARDSVSSGSHALLKIKQHFGKKIVDKKGNLERSKLREIIFEDTSEKLWLENLLHPIIREKIILDINNASGCYVLLESPLLFETNQYKLVNVVLLIDVPEEMQIIRASQRDKATINEIKKIINTQMPRSXKIKLSTYIADNTKSEDDLKKXVDYYHRKFSXLARNSCNL", "metadata": {"id": "A0A2E2SCG0", "cluster": 12372848, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein carries a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Furthermore, the protein features a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Also, the protein incorporates a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. It has been characterized in Thermotoga petrophila (strain ATCC BAA-489 / DSM 13996 / JCM 10882 / RKU-10) (Thermotoga naphthophila) and is associated with UniProt keywords DNA excision, SOS response, and DNA damage. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 16252, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 3677, 16, 1920, 2213, 4075, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2222, 16, 1920, 2213, 19683, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2176, 2258, 2252, 4378, 1922, 7967, 4575, 4223, 16901, 7766, 12, 3943, 11037, 6813, 1019, 17, 3427, 1026, 19, 10964, 13316, 10352, 19, 14904, 1035, 9123, 11715, 19, 21179, 1032, 17, 2119, 13, 12, 7967, 4575, 4223, 23330, 7766, 13, 1930, 1977, 2458, 1956, 20709, 11569, 2678, 10940, 16, 17668, 2644, 16, 1930, 2678, 4293, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MFKLVSEFEPTGDQPQAIEKLVEGLNRGMRFQTLLGVTGSGKTFTMANVIARVNRPALVISPNKTLAAQLYQEFKAFFPENRVEFFISYYDYYQPEAYIPTKDLYIEKNADINDVIVRMRMSTLKSVRTRRDVVVVASVSCIYATGDPNDFDRMNINLAVGDRIDVLELAERLARIGYQRTEDVSLSGCFRLKGDTVEIYPTYQDEGIRIEFFGDEVDSITLIDRFNRTTLEHLDKIIIYPAVEFITTEEKLKRAVESIREELNERLSELKKQGKILEYERLKQRTLNDIELLETMGYCPGIENYSRHFDGRKPGEPPYTLLDYFDKDFIVFIDESHITVPQLRAMYNGDRSRKKNLVEYGFRLPSAYDNRPLTFEEFLKKTGQIIFVSATPGDFELSISEQVVEQIIRPTGLVDPEVEVRPTAGQVDDLVNEIVKVKERGERALVTVLTKKTAELLSEHLTELGIRSLYLHSELDAIERVEVLKKLRRGDVDVVVGVNLLREGLDLPEVSLVAIMDADVEGFLRSETTLIQIIGRTARNINGKVIMYADRITNAMKRAIEETNRRRRIQLEYNKKHGITPRSVIKPLEIEVFEQFMVKEEPERYGDTVKNIFEMKKTLSPEEYMAVLEEEMYRAASELRYEDAAALRDELFRIREEIKKKKGL", "metadata": {"id": "D2C854", "cluster": 12801753, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR014001", "IPR001650", "IPR001943"], "interpro_unused": ["IPR004807", "IPR024759", "IPR036876", "IPR027417", "IPR041471", "IPR006935"]}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein is categorized in the Histidine kinase/HSP90-like ATPase superfamily, which comprises a diverse range of ATP-binding proteins functioning in signal transduction, DNA repair and topology, and protein folding. Notable members include histidine kinases, DNA gyrase B, topoisomerases, and HSP90, all sharing a core two-layer \u03b1/\u03b2 structure with an 8-stranded mixed \u03b2-sheet. Moreover, the protein should have a Histidine kinase domain that functions as the catalytic core of two-component signal transduction systems, orchestrating cellular responses to environmental stimuli. It undergoes ATP-dependent autophosphorylation on a conserved histidine residue within a homodimer before transferring the high-energy phosphoryl group to an aspartate residue on a partner response regulator protein. This domain contains a dimerization interface and a structurally distinct ATP-binding cleft defined by conserved nucleotide-binding motifs. In addition, it is part of the Sensor Histidine Kinase Regulatory family, which functions as the sensory component of two-component signal transduction pathways to mediate adaptation to environmental stimuli. These proteins autophosphorylate upon activation and transfer the phosphate group to downstream response regulators, thereby modulating gene expression, cell division, virulence, and osmosensing. In cyanobacteria, specific members are essential for regulating circadian rhythms and photosystem dynamics through complex formation and synchronization with light-dark cycles. It is expressed in Chloroflexota bacterium and is connected to UniProt keyword Transferase and Two-component regulatory system.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10234, 1922, 1920, 13873, 4016, 19, 12254, 17, 3189, 9444, 13975, 16, 2154, 12936, 43, 6445, 3109, 1927, 4498, 17, 2743, 2697, 7295, 1922, 2733, 8201, 16, 2678, 5059, 1930, 13678, 16, 1930, 2213, 10328, 18, 11892, 4678, 3951, 13873, 7784, 16, 2678, 9430, 2051, 44, 16, 20294, 1036, 16, 1930, 12254, 16, 2136, 10763, 43, 4728, 2288, 17, 4757, 160, 19, 161, 3170, 1956, 1925, 28, 17, 10338, 4985, 161, 17, 11130, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 13873, 4016, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 2288, 17, 4594, 2733, 8201, 3771, 16, 21991, 2287, 3689, 3387, 1942, 4813, 5458, 18, 2176, 14928, 4498, 17, 3100, 22009, 1990, 43, 5305, 13873, 6181, 2651, 43, 21189, 3119, 21902, 1920, 2149, 17, 3844, 12556, 2210, 1942, 1925, 12878, 6181, 1990, 43, 8240, 2644, 7888, 2213, 18, 2052, 3418, 5461, 43, 13640, 6854, 1930, 43, 12171, 4493, 4498, 17, 2743, 14649, 3608, 2007, 5305, 5489, 17, 2743, 8277, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 6443, 13873, 4016, 4948, 3416, 16, 2154, 4088, 1966, 1920, 6893, 4594, 1927, 2288, 17, 4594, 2733, 8201, 3873, 1942, 8265, 7810, 1942, 4813, 5458, 18, 2144, 2697, 20369, 9075, 4073, 2936, 1930, 3856, 1920, 5413, 2210, 1942, 5863, 2644, 9098, 16, 6113, 10871, 2359, 2294, 16, 2024, 8451, 16, 9304, 16, 1930, 9405, 6642, 6777, 1029, 18, 1922, 21897, 16, 2487, 4678, 2032, 4415, 1958, 6773, 10507, 16622, 1930, 8811, 2405, 5565, 2596, 2796, 3337, 1930, 17692, 1956, 3696, 17, 6190, 6355, 18, 2176, 1977, 3198, 1922, 10107, 18222, 7336, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 13763, 1930, 2288, 17, 4594, 4948, 2433, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "GEVEELARIESGGRQLFAERQHVTIRTEVAADLPFVSGEAPDSSVVVSVRREADEVTASVAFYKADRSRTSGGGTGLGLAIEHEGATFIIGLPIAVSATSEPVHGAHLDDVDLGRVAEETAERLRPAQLGQVFANLIHNAVKFSPDRGIGISAADLPRIFERARHVVEGHGGRIVAESV", "metadata": {"id": "A0A522B3I1", "cluster": 15072890, "interpro_all": ["IPR036890", "IPR005467", "IPR050736", "IPR004358"], "interpro_used": ["IPR036890", "IPR005467", "IPR050736"], "interpro_unused": ["IPR004358"]}, "task_type": "infilling"} {"instruction": "The protein features a Domain of unknown function DUF6780 domain that is functionally uncharacterised but is typically located at the C-terminus of fungal proteins. It spans 48 to 62 amino acids and contains a conserved WxRHxAAxK motif that may be important for its function. In addition, the protein has a Sigma-54 interaction domain ATP-binding site 1 binding site that functions as an atypical P-loop motif to facilitate ATPase activity. This site drives the conformational changes required for bacterial regulatory proteins to interact with the alternative sigma-54 factor during transcriptional activation. Also, the protein should feature a Septin-type guanine nucleotide-binding (G) domain that functions as a GTP-dependent molecular switch to drive the assembly of septin monomers into cytoskeletal filaments and scaffolds. This domain binds and hydrolyzes guanine nucleotides to regulate the formation of homo- and hetero-oligomeric complexes essential for cytokinesis, vesicle trafficking, and diffusion barrier formation. Its structure features a conserved P-loop for nucleotide interaction and unique secondary elements that distinguish it from canonical Ras-like domains. It originates from Cytospora paraplurivora and is associated with UniProt keywords GTP-binding. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 4075, 43, 3418, 1927, 5435, 2347, 4855, 17136, 7950, 1008, 3418, 1988, 1977, 9346, 23229, 3495, 2308, 1977, 5745, 4810, 2019, 1920, 45, 17, 7822, 1927, 8697, 2697, 18, 2176, 23658, 3427, 1942, 5374, 3835, 4576, 1930, 5461, 43, 5305, 65, 10024, 1023, 11414, 3013, 1040, 5219, 1988, 2278, 1998, 2715, 1958, 2496, 2347, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 5139, 17, 4584, 2835, 3418, 4498, 17, 2743, 3200, 21, 2743, 3200, 1988, 4088, 1966, 1925, 10834, 58, 17, 5881, 5219, 1942, 6628, 9444, 2455, 18, 2052, 3200, 15435, 1920, 8523, 2840, 3414, 1958, 4543, 4948, 2697, 1942, 6310, 1956, 1920, 5012, 5139, 17, 4584, 2991, 2409, 5224, 2936, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 8394, 1921, 17, 2601, 16904, 5489, 17, 2743, 12, 49, 13, 3418, 1988, 4088, 1966, 43, 9319, 17, 3100, 3272, 6195, 1942, 9265, 1920, 5957, 1927, 8394, 1921, 13256, 2460, 14787, 11855, 1930, 10603, 18, 2052, 3418, 6876, 1930, 7222, 20887, 16904, 9519, 1942, 5741, 1920, 3337, 1927, 16350, 17, 1930, 19732, 17, 19206, 5048, 4415, 1958, 20825, 16, 11502, 9604, 16, 1930, 6601, 7104, 3337, 18, 2496, 3170, 4075, 43, 5305, 58, 17, 5881, 1958, 5489, 2835, 1930, 5008, 4067, 5362, 1988, 7279, 2176, 2037, 9452, 6520, 17, 3189, 4682, 18, 2176, 22970, 2037, 5521, 21086, 22224, 5277, 3027, 15525, 5524, 1930, 1977, 2458, 1956, 20709, 11569, 9319, 17, 2743, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MLPTRGPASGISEVSSRRGSMTASIPDEIASQALTLSEELEPQQSSGMLDSGTAPQLVMPSIKMPSRRPFTDEGKRIGRLKVLVAGDSGVGKTALIKAMVQSCEHIVHVDPIAPQSSYLGQRSSPRRGRFKPSKNIDSTSQTSEIFASTKPYPEWWSDLDDFRLLKRRKSMGDLVLDRNICFVDTPGYSDGASSMEMIAPVIRYVESHFEKVQSNASPDPDMLGMLGGDGGNQVDVVFYLIQNKPRPADIKYLQMLAPLTNVIPLLAQSDTMTPEAIAQSKTRIRSELLEAGIRPFSFNVSSVGLSGRSEPTYPYAISSTTGSDHDIMDASLLMSPDYVRPLVQSELATLVEQVFCENGASWLRHAAAKKYLQWKSDKPTQSRDLYRPMTLPGGPSTALVASEHLTSPLGATSQYSLARIADHTQREERMAQIRLANWATDLQRSLTNERARYEALARGERAIWLTEKLNECVQDGSLVPVGGQGRDRSVSRLREKIGQRLARGRSQSTSTMQHQDPLGLLQVASRLKANGWVVLEVLGSMGILGGVAIWVSRQGWHISAVGWAVEQWSEFWNGDR", "metadata": {"id": "A0AAN9TWM9", "cluster": 16707601, "interpro_all": ["IPR046707", "IPR030379", "IPR027417", "IPR025662"], "interpro_used": ["IPR046707", "IPR025662", "IPR030379"], "interpro_unused": ["IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein belongs to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Moreover, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It has been detected in Moorella thermoacetica (strain ATCC 39073 / JCM 9320) and is annotated with UniProt keywords ATP-binding, Cytoplasm, and Transferase..", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 2258, 2252, 3330, 1922, 22728, 11560, 1019, 7967, 13722, 1019, 12, 3943, 11037, 23450, 8966, 19, 14904, 1035, 6156, 3520, 13, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 18, 3], "output": "MFIIGLTGGIASGKSTVAGILKDLGAIIIDTDRVAREVVAPGRPAYREIVAAFGPRVLRPDGQLDRPALARIIFNDATARELLNAITHPRIRELVQKRLEDLRRANPEAIVVIEAPLLFEAGMEGMVDAVWAVTAPAPVRLKRLMARDKLSLAEAESRLRAQGEETARLRRATRVIPTGGDLEATRASVRAAWQELQRHLADDPEPGGAPWV", "metadata": {"id": "Q2RHF1", "cluster": 17116794, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein is grouped in the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. In addition, the protein is assigned to the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, the protein can be placed in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It has been detected in Candidatus Kuenenbacteria bacterium HGW-Kuenenbacteria-1 and corresponds to UniProt keyword Cytoplasm and rRNA processing. Generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1988, 2258, 1920, 2894, 3879, 30, 1920, 2213, 1977, 10809, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 2258, 2252, 3330, 1922, 14550, 1031, 1957, 11352, 2880, 17046, 2422, 2126, 14061, 7175, 1018, 17, 11352, 2880, 17046, 2422, 2126, 17, 21, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 1930, 9067, 4587, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MHIPVLLNEVIENLNIQPNQNFIDCTFGDGGHTMAILKKNKPNGIVVGIDLNIKKFEAKERLILINDNFANLGKIIDQLRSDAKFQSAFWQIKFHGILLDLGFSSRQLEEDERGFSFQKDEFLDMRFNKLDTDLTAEKIINTYPEKELANIFWKYGEEKYSRYIAKIIIQERKKQKIYTTKQLADLIYKISKLKTKNSKFNAKHYIHPATKVFQALRIIVNNELENLKQVLPQAIKILEPKGKICVISFHSLEDRIVKQFFKQESKNCICPSEFPQCICNHKTTLKIITKKIIVPTFEEIKKNPRSRSAKMRVAEKLAF", "metadata": {"id": "A0A2N1UNX2", "cluster": 18781151, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein has a NAD-dependent epimerase/dehydratase domain that utilizes NAD as a cofactor to catalyze diverse chemical reactions on nucleotide-sugar substrates. This structural motif is characteristic of enzymes involved in carbohydrate metabolism, including UDP-galactose 4-epimerase which interconverts UDP-galactose and UDP-glucose. In addition, the protein is a member of the UDP-glucuronic acid decarboxylase-like family, which comprises short-chain dehydrogenase/reductase (SDR) enzymes that catalyze the NAD-dependent decarboxylation of UDP-glucuronic acid to yield UDP-xylose, a precursor for various polysaccharides and glycoproteins. These proteins share a Rossmann-fold NAD(P)H binding domain and are found across eukaryotes and bacteria. The family also includes bacterial homologues that specifically convert UDP-N-acetylglucosaminuronic acid to UDP-N-acetylxylosamine. In addition, it is part of the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. It has been characterized in Paenibacillus sp. J31TS4 and corresponds to UniProt keyword Lyase.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 2258, 43, 6577, 17, 3100, 13872, 9213, 2051, 19, 11725, 7234, 3418, 1988, 18127, 6577, 1966, 43, 15155, 1942, 18170, 6445, 4399, 5298, 1990, 5489, 17, 9523, 6249, 18, 2052, 4346, 5219, 1977, 6293, 1927, 5038, 3286, 1922, 10590, 4714, 16, 2710, 18500, 17, 15996, 24, 17, 13872, 9213, 2051, 2154, 8590, 12766, 24916, 18500, 17, 15996, 1930, 18500, 17, 3817, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 18500, 17, 17102, 1935, 2687, 23922, 17, 3189, 3416, 16, 2154, 12936, 3662, 17, 4659, 9294, 19, 11386, 12, 4035, 1005, 13, 5038, 1988, 18170, 1920, 6577, 17, 3100, 22429, 1943, 1927, 18500, 17, 17102, 1935, 2687, 1942, 4307, 18500, 17, 21055, 16, 43, 7897, 1958, 3425, 18686, 1930, 16268, 18, 2144, 2697, 7948, 43, 18215, 8890, 17, 3728, 6577, 12, 58, 13, 50, 2743, 3418, 1930, 2032, 2435, 3436, 15021, 1930, 4802, 18, 1920, 3416, 2222, 5921, 4543, 18541, 1988, 4475, 14450, 18500, 17, 56, 17, 6894, 22988, 5360, 8547, 21280, 2687, 1942, 18500, 17, 56, 17, 6894, 10465, 6012, 5735, 25157, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 2176, 2258, 2252, 4378, 1922, 25726, 8635, 7972, 10401, 5277, 1036, 2056, 18, 52, 6800, 1973, 1006, 1930, 8852, 1942, 20709, 11121, 2538, 23928, 18, 3], "output": "MKVLVTGGAGFIGSHLVEALLSGGHGHIFVQGKVEDRRLMEELMQSVDLVVHALANQVKVVFASTSEIYGKSEQLPYAKALEEHLCVGYAGRGLAVTIARYALRGEPIPVYGDGTQSRCFTYIDDTIRGIMQLAQKIKILTGSDSPIVRIPYRESRVLGFSPSVELEEGLLRTIAWYRARQEDEQVVTIDDLSAGSERVFFGEASRDLAAVLGVKTCVENPLKVIEGNLDGTRNVLELKEDSDRVLGSTFKNRWCYATFNAYGPRAASSPYGNVIPKFITATLLSMEARHNGEVFNIGSNQSVTALGEHYEDTPNRIPDLTKS", "metadata": {"id": "A0A919Z9K6", "cluster": 20667871, "interpro_all": ["IPR001509", "IPR036291", "IPR044516"], "interpro_used": ["IPR001509", "IPR044516", "IPR036291"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein is a member of the Small ribosomal subunit protein bS16 family, which constitutes a structural component of the small ribosomal subunit in bacteria, chloroplasts, and mitochondria. These proteins decorate the rRNA core to organize and stabilize its tertiary structure, thereby facilitating mRNA-directed protein synthesis. It is expressed in Phycisphaerales bacterium and is described by UniProt keywords Ribonucleoprotein and Ribosomal protein.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2858, 11196, 5903, 2213, 8242, 3672, 3416, 16, 2154, 14879, 43, 4346, 4594, 1927, 1920, 2858, 11196, 5903, 1922, 4802, 16, 24627, 16, 1930, 6489, 18, 2144, 2697, 23038, 2010, 1920, 9067, 4728, 1942, 25681, 1930, 13448, 2496, 10832, 3170, 16, 6113, 12440, 3616, 17, 6554, 2213, 4271, 18, 2176, 1977, 3198, 1922, 25511, 9119, 29164, 3955, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 18347, 6657, 1930, 11196, 2213, 18, 3], "output": "MVVLRFKRFGRIHRPTYRLCAADKRCPRNGTVIEELGWFDPAGPEGKQFEFNMERVAHWFKMGAQPSQTAANMIKKAGGTIPAAAIKALLVRSKVSKHPKPVVVATPAAAAEETPKGE", "metadata": {"id": "A0A964VCJ8", "cluster": 20890076, "interpro_all": ["IPR000307", "IPR023803"], "interpro_used": ["IPR000307"], "interpro_unused": ["IPR023803"]}, "task_type": "autoregressive"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein is classified under the Winged helix-like DNA-binding domain superfamily, which encompasses diverse DNA-binding proteins including transcriptional regulators, helicases, and endonucleases that utilize a winged helix-turn-helix motif for sequence-specific recognition. This domain engages the DNA major groove via a recognition helix while loop structures known as wings contact the minor groove or backbone, often serving as a scaffold for protein-protein interactions. Additionally, the protein should feature a DeoR-type HTH domain that functions as a DNA-binding helix-turn-helix module within prokaryotic transcriptional regulators of sugar and nucleoside catabolism. Typically located at the N-terminus, it mediates specific DNA recognition to repress operon expression, a process often modulated by phosphorylated metabolic intermediates. These regulators frequently oligomerize to bind multiple operators simultaneously, potentially facilitating DNA looping. It is expressed in Candidatus Nealsonbacteria bacterium CG_4_10_14_0_8_um_filter_37_14 and features UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 1977, 5947, 2441, 1920, 12920, 1919, 7864, 17, 3189, 2678, 17, 2743, 3418, 13975, 16, 2154, 21569, 6445, 2678, 17, 2743, 2697, 2710, 5224, 9098, 16, 29919, 16, 1930, 18697, 1036, 1988, 12561, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 1958, 3244, 17, 2487, 5708, 18, 2052, 3418, 11580, 1036, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 2679, 5881, 4061, 3171, 1966, 28297, 5217, 1920, 5857, 15920, 2014, 10787, 16, 3868, 13915, 1966, 43, 7281, 1958, 2213, 17, 2213, 3719, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 2028, 1924, 17, 2601, 5334, 1023, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 7864, 17, 5165, 17, 7864, 9059, 2651, 21545, 5224, 9098, 1927, 9523, 1930, 18015, 19480, 18, 5745, 4810, 2019, 1920, 56, 17, 7822, 16, 2176, 10412, 2487, 2678, 5708, 1942, 9055, 15675, 2294, 16, 43, 2585, 3868, 9985, 2007, 7199, 4487, 12386, 18, 2144, 9098, 5467, 13034, 2606, 1942, 4566, 3137, 20480, 7159, 16, 5063, 12440, 2678, 5881, 1941, 18, 2176, 1977, 3198, 1922, 14550, 1031, 1957, 2069, 2472, 1916, 7972, 2341, 18339, 14061, 7294, 41, 24, 41, 2119, 41, 2607, 41, 20, 41, 28, 41, 8736, 41, 6199, 41, 3191, 41, 2607, 1930, 4075, 20709, 11569, 3213, 3640, 18, 3], "output": "MDSNHFFQLTLGVYRVTELFPKGEPLKLKIREKALEILSDLVLASPNPGVKRLEDAAPAINKNIKIIADFFDLAQSQKWIDSRNFLVLKREYNKIKQNIETELGGIGYRQDSKVKDGDPSEISSNQLFPRQKRIIDILKQNGGAQAGEILKSFEKLSKRTLRRDLGRLVREGMIERVGRCNKVFYKLPTLS", "metadata": {"id": "A0A2M7R6N9", "cluster": 21006111, "interpro_all": ["IPR001034", "IPR036388", "IPR036390"], "interpro_used": ["IPR036388", "IPR001034"], "interpro_unused": ["IPR036390"]}, "task_type": "autoregressive"} {"instruction": "The protein can be placed in the Thiolase-like superfamily, which is characterized by a 3-layer \u03b1/\u03b2/\u03b1 structural topology that typically occurs as a duplicated pseudo-dyad. This family encompasses a diverse group of condensing enzymes, including thiolases involved in fatty acid oxidation and synthases such as chalcone synthase and beta-ketoacyl-ACP synthase that drive fatty acid and polyketide biosynthesis. Furthermore, the protein incorporates a Thiolase, N-terminal domain that contains a conserved active site cysteine responsible for forming an acyl-enzyme intermediate during the metabolism of acyl-CoA thioesters. It functions within both acetoacetyl-CoA thiolases and 3-ketoacyl-CoA thiolases, facilitating pathways such as fatty acid beta-oxidation, steroid biogenesis, and poly beta-hydroxybutyrate synthesis. Also, the protein contains a Thiolase, C-terminal domain 2 domain that constitutes the C-terminal region of CoA-dependent thiolase enzymes involved in lipid metabolism across all cellular organisms. This structural element folds into a four-stranded antiparallel beta-sheet with alpha-helices packed on one side. It originates from Deltaproteobacteria bacterium.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 13914, 2051, 17, 3189, 13975, 16, 2154, 1977, 4378, 2007, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 4346, 13678, 1988, 5745, 5110, 1966, 43, 19479, 11520, 17, 28679, 18, 2052, 3416, 21569, 43, 6445, 2210, 1927, 11637, 1941, 5038, 16, 2710, 13914, 2319, 3286, 1922, 5934, 2687, 6638, 1930, 8921, 1036, 2427, 1966, 29343, 12334, 1021, 8921, 1930, 4666, 17, 21471, 14645, 17, 18543, 8921, 1988, 9265, 5934, 2687, 1930, 4286, 18540, 2261, 8132, 18, 3677, 16, 1920, 2213, 19683, 43, 13914, 2051, 16, 56, 17, 4262, 3418, 1988, 5461, 43, 5305, 3500, 3200, 8666, 5061, 1958, 7402, 1925, 11337, 17, 4113, 6129, 2409, 1920, 4714, 1927, 11337, 17, 10027, 30215, 1036, 18, 2176, 4088, 2651, 2321, 4118, 15365, 3152, 1024, 17, 10027, 13914, 2319, 1930, 23, 17, 21471, 14645, 17, 10027, 13914, 2319, 16, 12440, 3873, 2427, 1966, 5934, 2687, 4666, 17, 6638, 16, 9507, 13008, 16, 1930, 4286, 4666, 17, 8275, 16119, 16128, 4271, 18, 2222, 16, 1920, 2213, 5461, 43, 13914, 2051, 16, 45, 17, 4262, 3418, 22, 3418, 1988, 14879, 1920, 45, 17, 4262, 3031, 1927, 10027, 17, 3100, 13914, 2051, 5038, 3286, 1922, 4486, 4714, 3436, 2136, 3689, 7373, 18, 2052, 4346, 6149, 16231, 2460, 43, 3006, 17, 10338, 28892, 4666, 17, 11130, 1956, 4595, 17, 12789, 15827, 1990, 2340, 4159, 18, 2176, 22970, 2037, 9649, 9218, 1021, 10296, 14061, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MEEEMDVYVSGVGLTKFGKSKEPLEKIMAEAAGLALKEAQREKVESNFATLLADTIGLTGIPSTRVETASSTGAGAFEMTHLPTSKTTRILSGVIDRTERRYGATMPAFAALIAQRYAHESANGALNPYAQFRKPITREDYLSSQIISYPLRLYDCAPITDGAVSHRASLTSFNSTKEAALKAYRMAQLNPSEIQFAEVHDAFEERITHLRGRLPINPSGGLKSRGHPVGASGLAQGLAQSIGGLGNNNFVIILERSDRKKVYGKGWRPEYQPEEGMGILETFTILHHPPEGFRSPLALGFIHLKGGGRIVLFEPREGLYVFYRLTLWNRLKLWLKREKRVKKDAIFIGVMNVEEFVGTGFYAVASGYMKNVLVLAGEKQLSISKLEEILAQVAIKNHAALLLTSEPTSIKVTGIGHATDTLATPFEIIGTEDLGFFTPGEGWKAVLVEIVFQLRGEAGEERQLEKAEIIQTVSKSSLPPPSMACNPEYKNPKSLKIGRK", "metadata": {"id": "A0A7V4PNN7", "cluster": 21669449, "interpro_all": ["IPR012340", "IPR016039", "IPR055140", "IPR020616"], "interpro_used": ["IPR016039", "IPR020616", "IPR055140"], "interpro_unused": ["IPR012340"]}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nIt is part of the GHMP kinase, C-terminal domain superfamily, which encompasses the C-terminal structural component of ATP-dependent enzymes involved in amino acid, isoprene, and carbohydrate metabolism. This domain adopts a central alpha-beta plait fold that cooperates with the N-terminal domain to create a nucleotide-binding pocket. While primarily found in homoserine, galacto-, and mevalonate kinases, it is also present in structurally related diphosphomevalonate decarboxylases. Additionally, the protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. In addition, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is expressed in Acholeplasmataceae bacterium and contains UniProt keyword associations Isoprene biosynthesis and Transferase.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 2176, 1977, 3131, 1927, 1920, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 21569, 1920, 45, 17, 4262, 4346, 4594, 1927, 4498, 17, 3100, 5038, 3286, 1922, 3835, 2687, 16, 26690, 1021, 16, 1930, 10590, 4714, 18, 2052, 3418, 24032, 43, 4101, 4595, 17, 4666, 5606, 1932, 3728, 1988, 23230, 1036, 1956, 1920, 56, 17, 4262, 3418, 1942, 7762, 43, 5489, 17, 2743, 10154, 18, 2679, 5985, 2435, 1922, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 16, 2176, 1977, 2222, 2481, 1922, 12171, 2712, 11791, 2609, 2225, 4701, 8870, 23922, 1036, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 3198, 1922, 3546, 2456, 15403, 26317, 5376, 1021, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 26690, 1021, 8132, 1930, 13763, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MIEEKAHAKLNLALDVVGKREDGYHELKMIMIPLALHDVVLKTIETMKRTFHVDQGVHVKLTKHIPIGAGLGGGSANILENLENIALELGSDTLFCLYERPAFIYGRGDQYLFAAYRGRHRPKRFERLFRLYLNEHYQAFFRKTYNALLKSTFFVLDGDNISTKKPKRNEKNTIKGLKTRPKSLTFSPHPDIVVECDVEIPDNHAATIRGLNRLWQLDQPFIDMPPIKEIELFSCDQAVSTKTVTTMKAYPAVKAHYKRLKKDHPTVRMTGSG", "metadata": {"id": "A0A651DKN4", "cluster": 21826652, "interpro_all": ["IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR036554", "IPR006204", "IPR004424"], "interpro_unused": ["IPR014721", "IPR020568"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein should feature a Septin-type guanine nucleotide-binding (G) domain that functions as a GTP-dependent molecular switch to drive the assembly of septin monomers into cytoskeletal filaments and scaffolds. This domain binds and hydrolyzes guanine nucleotides to regulate the formation of homo- and hetero-oligomeric complexes essential for cytokinesis, vesicle trafficking, and diffusion barrier formation. Its structure features a conserved P-loop for nucleotide interaction and unique secondary elements that distinguish it from canonical Ras-like domains. Also, the protein should include a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Additionally, the protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is native to Colletotrichum simmondsii and is connected to UniProt keyword GTP-binding, Metal-binding, and mRNA processing. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 3066, 5961, 43, 8394, 1921, 17, 2601, 16904, 5489, 17, 2743, 12, 49, 13, 3418, 1988, 4088, 1966, 43, 9319, 17, 3100, 3272, 6195, 1942, 9265, 1920, 5957, 1927, 8394, 1921, 13256, 2460, 14787, 11855, 1930, 10603, 18, 2052, 3418, 6876, 1930, 7222, 20887, 16904, 9519, 1942, 5741, 1920, 3337, 1927, 16350, 17, 1930, 19732, 17, 19206, 5048, 4415, 1958, 20825, 16, 11502, 9604, 16, 1930, 6601, 7104, 3337, 18, 2496, 3170, 4075, 43, 5305, 58, 17, 5881, 1958, 5489, 2835, 1930, 5008, 4067, 5362, 1988, 7279, 2176, 2037, 9452, 6520, 17, 3189, 4682, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 6196, 1942, 5549, 4575, 3319, 24315, 1035, 2328, 18885, 12924, 1033, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9319, 17, 2743, 16, 6048, 17, 2743, 16, 1930, 3616, 4587, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MSAFGTSDTGRPQSTYSGEVAQQFIMPTINVPSRRPFTEAGKGLGRLKLLVAGVGKTALIRTITQSCSHIVHVDPTVPVAMASKGFLPAKTMPNSPPISQGTFQITETLASTKPYPSWWKDSAFSSPTPAPIQPEDTILDRNICLVDTPGYQETCRPTDTMGQVSQYVESYLQKSRLDGLEDPDVLKTISGSGGLLVDAVLYMIPSSGLSATDIHYLRQLDALTNIIPLIAHADTLTLEQTAAAKKHIAQQLAEADLGLFSFDPSTDGVGEQHIYAASSELVSDSEVMDASLLMSSEYEVIAHLERICDEFVKRVARKREAGNEALIRDARGKIFTYGSFRLGVFGPGSDIDTLVVAPKYVTRADYFEIFPNLLKEMAPPGSITDMAVVADAFVPIIKFEFDGISIDLIFSRIAMLKQLNKDFTVQDSGLLRGLDEAELRSLNGTRVTDEILSLVPEESTFKLALRAIKLWAQRRAIYANIMGFPGGVAWAMLVARVCQLYPKAASSVIVNKFFHIMRRWPWPQPVLLKHVEGGPLQVRVWNPKLYKGDQFHLMPVITPAYPSMCATYNITRSAMTVIQQELSRGCDITDNIMLGKSPWSDLFVKHTFFTKGYKYYISVITASTDKEAHKIWSGYVESKVRVLVQGLEQHQSIALAHAFNKGYERRHRCTNEAEISQVQAGSFSFLAKDSDVKEEDFEQEGKIEKVQPVETKPDLSGIPGLKTEPTDDAHGLKTEENETQPGVKTEGVKSEDEISKAPSQIPKHNPYTDVFTTTHYIGLTLSEGAKSLDLSYQVENFKALCTQWEKYDAVLNSLNVQHVRSFNLPDDVFEANETKPQKPQKKRVIPNANGAAQIKKRSASEENQEPPAKRQQASVTAAG", "metadata": {"id": "A0A135TR55", "cluster": 22266028, "interpro_all": ["IPR030379", "IPR043519", "IPR011068", "IPR027417", "IPR007012", "IPR048840", "IPR007010"], "interpro_used": ["IPR030379", "IPR007012", "IPR027417"], "interpro_unused": ["IPR048840", "IPR011068", "IPR007010", "IPR043519"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe protein is a member of the Bacterial tyrosine recombinase XerC/XerD complex family, which catalyzes site-specific DNA cutting and rejoining to facilitate critical genomic transactions. These enzymes function primarily in chromosome segregation by resolving bacterial chromosome dimers into monomers, ensuring proper cell division and plasmid stability. Additionally, members of this family mediate bacteriophage integration and excision, as well as regulate gene expression via DNA segment inversion. Also, the protein is grouped in the Integrase-like, catalytic domain superfamily, which mediates unidirectional site-specific recombination between DNA recognition sequences, such as phage and bacterial attachment sites. This superfamily encompasses the catalytic core of tyrosine recombinases, characterized by an alpha3-beta3-alpha4 fold and a conserved tyrosine residue responsible for strand cleavage. Members include lambda integrase, Cre, and XerD, which utilize this domain to facilitate DNA integration and excision events. Furthermore, the protein has a Integrase catalytic domain that cleaves DNA substrates through a series of staggered cuts to facilitate site-specific recombination. This activity proceeds via a mechanism in which a conserved catalytic tyrosine residue forms a transient covalent linkage with the DNA substrate. It is produced by Deltaproteobacteria bacterium and has UniProt annotations DNA recombination.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 4543, 6941, 21366, 27833, 1030, 19, 27833, 1007, 2796, 3416, 16, 2154, 17097, 3200, 17, 2487, 2678, 14589, 1930, 12677, 9024, 1941, 1942, 6628, 4140, 4935, 2127, 19666, 18, 2144, 5038, 2347, 5985, 1922, 5597, 12707, 2007, 20412, 4543, 5597, 13351, 2460, 13256, 16, 14435, 3405, 2024, 8451, 1930, 5609, 5057, 18, 4950, 16, 4678, 1927, 2052, 3416, 8265, 24613, 7122, 1930, 10940, 16, 1966, 2486, 1966, 5741, 2359, 2294, 3454, 2678, 5367, 14825, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 27252, 17, 3189, 16, 6804, 3418, 13975, 16, 2154, 10412, 28250, 3200, 17, 2487, 7827, 2192, 2678, 5708, 3709, 16, 2427, 1966, 10503, 1930, 4543, 8576, 3402, 18, 2052, 13975, 21569, 1920, 6804, 4728, 1927, 6941, 21366, 1036, 16, 4378, 2007, 1925, 4595, 1010, 17, 4666, 1010, 17, 4595, 1006, 3728, 1930, 43, 5305, 6941, 6181, 5061, 1958, 5984, 6404, 18, 4678, 3951, 18279, 27252, 16, 3478, 16, 1930, 27833, 1007, 16, 2154, 12561, 2052, 3418, 1942, 6628, 2678, 7122, 1930, 10940, 3916, 18, 3677, 16, 1920, 2213, 2258, 43, 27252, 6804, 3418, 1988, 23839, 2678, 6249, 2596, 43, 4696, 1927, 23891, 3312, 7752, 25865, 1942, 6628, 3200, 17, 2487, 7827, 18, 2052, 2455, 20737, 3454, 43, 2856, 1922, 2154, 43, 5305, 6804, 6941, 6181, 4952, 43, 6809, 13577, 8611, 1956, 1920, 2678, 4510, 18, 2176, 1977, 4152, 2007, 9649, 9218, 1021, 10296, 14061, 1930, 2258, 20709, 15010, 2678, 7827, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MIALNISNTKIAQVGEYLYPEEAELIMWETGGRVSEVLSLTVEDIDVVNNVLYLITLERRNVPKRKVYLFPESTLCRDLQDYVVTHVWHLLADTRPNRRPGLSVSLGIRKLKGAVNRLGHTSVTSTEVYAGLTDKARKEMIDRCINACPNERDRLILRTKRKDKRGRKVGEKRKVRPISNKLELRDWVFQGGCRNEGIEGQVSTPVWPHLWRHGAAMNMLERIGSLPVVQMQ", "metadata": {"id": "A0A661PGF0", "cluster": 23246254, "interpro_all": ["IPR011010", "IPR013762", "IPR002104", "IPR050090"], "interpro_used": ["IPR050090", "IPR013762", "IPR002104"], "interpro_unused": ["IPR011010"]}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein is categorized in the WD40/YVTN repeat-like-containing domain superfamily, which features repeating motifs of approximately 40 residues that fold into a seven- or eight-bladed beta-propeller structure composed of four-stranded beta-sheets. This architecture typically serves as a rigid scaffold for mediating diverse protein-protein interactions and facilitating the assembly of multi-protein complexes. Furthermore, the protein falls within the Quinoprotein amine dehydrogenase, beta chain-like superfamily, which forms a 7-bladed beta-propeller structure serving as a scaffold for the active site in enzymes such as quinohemoprotein amine dehydrogenase and methylamine dehydrogenase. This domain corresponds to the beta and heavy chains of these respective complexes and shares structural similarity with the YVTN repeats found in archaeal surface layer proteins. It is produced by Corynebacterium sp. 366. Can you generate the amino acid sequence corresponding to this polypeptide chain?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 13022, 4659, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 17907, 4241, 19, 67, 25641, 1022, 6865, 17, 3189, 17, 3165, 3418, 13975, 16, 2154, 4075, 21763, 8277, 1927, 3993, 3040, 4248, 1988, 3728, 2460, 43, 5260, 17, 2014, 5066, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 7179, 1927, 3006, 17, 10338, 4666, 17, 14685, 18, 2052, 9335, 5745, 10634, 1966, 43, 12383, 7281, 1958, 10239, 6445, 2213, 17, 2213, 3719, 1930, 12440, 1920, 5957, 1927, 2779, 17, 2213, 5048, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 9012, 6657, 13610, 9294, 16, 4666, 4659, 17, 3189, 13975, 16, 2154, 4952, 43, 27, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 13915, 1966, 43, 7281, 1958, 1920, 3500, 3200, 1922, 5038, 2427, 1966, 9012, 2977, 1987, 6657, 13610, 9294, 1930, 4963, 3812, 9294, 18, 2052, 3418, 8852, 1942, 1920, 4666, 1930, 7881, 7835, 1927, 2144, 7025, 5048, 1930, 16495, 4346, 6796, 1956, 1920, 67, 25641, 1022, 9569, 2435, 1922, 22367, 3154, 4757, 2697, 18, 2176, 1977, 4152, 2007, 2233, 17151, 7972, 2341, 18842, 1989, 2056, 18, 26725, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MKNLLHTPTLRKTATRMSVAVLAVAGLGLSSCGSSLPGLPDGDTQDQGAPSVADLPMKAVDSPQAQSDSVAGSVARGVFADADVKDGNTANFRSAAFGPLGDNAHESSQSIGVLAGSSLLIASPGDAKARSVSVPDDCTDIATSGAGVALACGSSLIEYTAEGKEARKVDTKGTVRSGTFTADGLGAYSTSDSDKVYFFDAEGKTVGDDIVSKDLDRSVLVQPHDGPQRVAMIDRTRTSINDVAPADKAYNAALRIGQGVGQVAASASTDGVVVASDTRQDQLLIYTMNDVVRLHQSTPTGHSPFAVTWDSQRNLAWVSTTADNTLTAFDITTGVPVAVADMATLANIAAVYPTGDHGLMLLSKNGDVQTIEASAIDTAVKKNADKPSTQYPVKKIAGE", "metadata": {"id": "A0A6I0FCS1", "cluster": 23505078, "interpro_all": ["IPR011044", "IPR015943"], "interpro_used": ["IPR015943", "IPR011044"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein includes a 3-dehydroquinate synthase, N-terminal domain that adopts a Rossmann-fold structure to bind NAD+ in an inverted orientation and contributes to the formation of the enzyme's active site cleft. It facilitates the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate to 3-dehydroquinate and orthophosphate, a critical step in the shikimate pathway for aromatic amino acid biosynthesis. Additionally, the protein possesses a 3-dehydroquinate synthase C-terminal domain that contains the key catalytic and Zn2+-binding residues required to convert 3-deoxy-D-arabino heptulosonic 7 phosphate into dehydroquinate. This alpha-helical module functions within the shikimate pathway for aromatic amino acid biosynthesis, existing either in isolation or as part of the pentafunctional AROM polypeptide. In addition, the protein can be placed in the Dehydroquinate Synthase family, which catalyzes the cyclization of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ), a pivotal step in the shikimate pathway. This enzymatic activity is essential for the biosynthesis of aromatic amino acids in bacteria, fungi, and plants. It is found in Planomicrobium sp. CPCC 101110 and is associated with UniProt keywords Zinc, Metal-binding, and Amino-acid biosynthesis.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 5921, 43, 23, 17, 28936, 11072, 2010, 8921, 16, 56, 17, 4262, 3418, 1988, 24032, 43, 18215, 8890, 17, 3728, 3170, 1942, 4566, 6577, 15, 1922, 1925, 12344, 7148, 1930, 7624, 1942, 1920, 3337, 1927, 1920, 4113, 11, 61, 3500, 3200, 14649, 18, 2176, 11374, 1920, 7309, 1927, 23, 17, 16333, 17, 46, 17, 20790, 1037, 17, 20662, 11677, 8870, 27, 17, 5413, 1942, 23, 17, 28936, 11072, 2010, 1930, 17266, 10647, 3508, 2722, 2057, 16, 43, 4140, 3537, 1922, 1920, 20837, 7369, 23874, 3374, 1958, 10761, 3835, 2687, 8132, 18, 4950, 16, 1920, 2213, 14465, 43, 23, 17, 28936, 11072, 2010, 8921, 45, 17, 4262, 3418, 1988, 5461, 1920, 3834, 6804, 1930, 21061, 15, 17, 2743, 4248, 3414, 1942, 14450, 23, 17, 16333, 17, 46, 17, 20790, 1037, 20662, 11677, 3490, 27, 5413, 2460, 28936, 11072, 2010, 18, 2052, 4595, 17, 11514, 9059, 4088, 2651, 1920, 20837, 7369, 23874, 3374, 1958, 10761, 3835, 2687, 8132, 16, 6124, 3108, 1922, 7152, 2014, 1966, 3131, 1927, 1920, 9412, 2624, 20839, 8981, 13022, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 28936, 11072, 2010, 8921, 3416, 16, 2154, 17097, 1920, 25267, 1927, 23, 17, 16333, 17, 46, 17, 20790, 1037, 17, 20662, 11677, 8870, 27, 17, 5413, 12, 3692, 15870, 13, 1942, 28936, 11072, 2010, 12, 6781, 1055, 13, 16, 43, 13637, 3537, 1922, 1920, 20837, 7369, 23874, 3374, 18, 2052, 8145, 2455, 1977, 4415, 1958, 1920, 8132, 1927, 10761, 3835, 4576, 1922, 4802, 16, 10520, 16, 1930, 4793, 18, 2176, 1977, 2435, 1922, 4720, 22980, 3821, 1989, 2056, 18, 21816, 1030, 9447, 24307, 1930, 1977, 2458, 1956, 20709, 11569, 7997, 16, 6048, 17, 2743, 16, 1930, 3835, 17, 2687, 8132, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MKLLRVEADQPYNVHIGHERGLLDAADRIVVVADAQVARLHMSGEQAKSVETFMDCHTFLLKEGCSRKSLLTFMRGIPYIQIPTTILAHDSAVGGLLRTLPAHEIRSGMAEVIKHAFISNEDWLLIAAHLEKGIAVKAAIVEEDEFEGGTLAHALEGHFGYGKLTHGEAVACRKNGYPLQKLNEVAFEEILPFMPFLEAIDENRAEKVYLELCAMIGGVVFSLFKEDYEYLLRYLQEYDVSILTVPLAFGGGAVGDVAGFVASKTAINHALGKNMIGTFYQPKAVLYDIQELLEITDFSSLSDEEVRKYLNFGHLGMAYALRLSNHPQLDPFLVWKKDKKSSKGSLSFVLLEKTGA", "metadata": {"id": "A0A5C5USG5", "cluster": 24225039, "interpro_all": ["IPR050071", "IPR016037", "IPR030963", "IPR030960", "IPR056179"], "interpro_used": ["IPR030960", "IPR056179", "IPR050071"], "interpro_unused": ["IPR030963", "IPR016037"]}, "task_type": "infilling"} {"instruction": "I want to design a protein that has the following function: The protein is categorized in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Additionally, the protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is derived from Myxococcales bacterium and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3595, 2037, 21464, 11748, 1918, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MRIVGLTGGIATGKSSVGRILTGLGVEVIDADRVAREVVEPGQPTLAALVQALGPEILDADGRLDRPAMREAIANDPEVKATLDRITHPAIRTAIAQRLVQLGESGAEAAVVDAALMVETGSHALYPQVIVVSCHPDTQLERLIGRDGMAPDAARRLVATQMPLAEKERYATVVVRNDGTPEELEAAVRAAWAELTS", "metadata": {"id": "A0A955YDQ7", "cluster": 24754128, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein has a ATPase alpha/beta subunit nucleotide-binding domain that forms the central structural component of the catalytic or regulatory subunits in F-, V-, and A-type ATPases, as well as flagellar ATPases and termination factor Rho. It binds nucleotides to drive ATP synthesis or hydrolysis through conformational changes linked to the complex's rotary motor mechanism, coupling chemical energy with proton translocation. Additionally, the protein should feature a Rho termination factor, RNA-binding domain that binds single-stranded RNA to facilitate the disengagement of newly transcribed RNA from its DNA template. It features an N-terminal OB-type fold with an indented face that serves as the primary binding site and supports the formation of a functional hexameric complex. Moreover, the protein should contain a AAA+ ATPase domain that utilizes energy from ATP hydrolysis to drive the conformational remodeling of macromolecules, facilitating processes such as protein unfolding, complex assembly, and DNA replication. This module is structurally characterized by an N-terminal P-loop NTPase subdomain with a Rossmann fold and Walker motifs, coupled to a C-terminal alpha-helical subdomain. It functions as a molecular motor in diverse cellular contexts, ranging from membrane fusion to proteolysis. It has been detected in Desulfofustis sp. PB-SRB1 and is associated with UniProt keywords ATP-binding, Transcription termination, and Transcription.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 9444, 4595, 19, 4666, 5903, 5489, 17, 2743, 3418, 1988, 4952, 1920, 4101, 4346, 4594, 1927, 1920, 6804, 2014, 4948, 6991, 1922, 48, 17, 16, 64, 17, 16, 1930, 43, 17, 2601, 28132, 16, 1966, 2486, 1966, 24154, 28132, 1930, 12462, 2991, 10585, 18, 2176, 6876, 9519, 1942, 9265, 4498, 4271, 2014, 9128, 2596, 8523, 2840, 4624, 1942, 1920, 2796, 11, 61, 23548, 4842, 2856, 16, 7590, 4399, 3844, 1956, 8433, 7849, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 10585, 12462, 2991, 16, 3146, 17, 2743, 3418, 1988, 6876, 2957, 17, 10338, 3146, 1942, 6628, 1920, 28347, 8909, 1927, 7471, 10078, 3146, 2037, 2496, 2678, 7662, 18, 2176, 4075, 1925, 56, 17, 4262, 2384, 17, 2601, 3728, 1956, 1925, 2063, 12871, 6171, 1988, 10634, 1966, 1920, 3065, 2743, 3200, 1930, 7825, 1920, 3337, 1927, 43, 3183, 25602, 1935, 2796, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 13835, 15, 9444, 3418, 1988, 18127, 3844, 2037, 4498, 9128, 1942, 9265, 1920, 8523, 8378, 1927, 20625, 16, 12440, 4028, 2427, 1966, 2213, 17490, 16, 2796, 5957, 16, 1930, 2678, 5158, 18, 2052, 9059, 1977, 12171, 4378, 2007, 1925, 56, 17, 4262, 58, 17, 5881, 29676, 2051, 27517, 1956, 43, 18215, 8890, 3728, 1930, 20138, 8277, 16, 6416, 1942, 43, 45, 17, 4262, 4595, 17, 11514, 27517, 18, 2176, 4088, 1966, 43, 3272, 4842, 1922, 6445, 3689, 11144, 16, 6485, 2037, 3260, 5289, 1942, 15439, 18, 2176, 2258, 2252, 3330, 1922, 30311, 4199, 2892, 1937, 2056, 18, 5242, 17, 4581, 5090, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 3213, 12462, 16, 1930, 3213, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MNLAELKLKKIEELVKLARELNGGKLRGNGVLEILPDGFGFLRAPDYNYLPGPDDGFVRSPKESERYLALLKVESVNFDPPEAVKEWQPKDYSMRIIDMFAPIGKGQRGIVHNHKETYLIVLLIDERPEEVTEMQRSMVIEKAKRLVEHKKDVIILLDSIGGVEANALHRPKRFFGAARNIEEGGSLSILATALIETGSKMDKMADKRIFPAIDIKRSGTRKEDLLLEPAVLPADSMEFLLDKLKQHKTNIDFLDAMNGVEGFSGMRKQELIFAILQAQASNDIYVSPSQIRRLNLSTGDVIQKTLFGNLTPLHPEEKFVLLIVAPPRTGKTVLMQKIANSVAEAEVVSSTFDEPPQRHIQVAETRLARAYNTVTPASGKILSEVIFEEFKGTGNMELILDRNRVWILRKLLAAMN", "metadata": {"id": "V4J238", "cluster": 25709385, "interpro_all": ["IPR003593", "IPR000194", "IPR011129", "IPR012340", "IPR027417", "IPR011112", "IPR041703", "IPR036269", "IPR011113", "IPR004665"], "interpro_used": ["IPR000194", "IPR011113", "IPR003593"], "interpro_unused": ["IPR011129", "IPR041703", "IPR011112", "IPR036269", "IPR004665", "IPR027417", "IPR012340"]}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein should feature a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein should contain a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Additionally, the protein is categorized in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is found in Acidithiobacillus ferrivorans and exhibits UniProt keyword tags Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 2435, 1922, 2687, 1953, 3940, 7972, 10401, 5277, 1036, 12210, 2068, 8846, 3355, 1930, 9826, 20709, 11121, 2538, 14392, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MSENYPAPAKLNLMLRVVDQRSDGYHELQTVFQFIDLADQLQFDSRPAGQFSRSGGPEGVPEADDLSIRAAKCLADVGAVHEGVHIHIDKILPMGGGIGGGSSDAATTLIVLNRLWRTGLRREELMEIGASLGADVPVFIFGRSAWAEGVGERLQLLDALPESHYVLLHPQVFVSTREIFTAPELTRHHVPSTIGAFLGGATENTLEPTVCARYPEVEHGARWLKNQGVHDVRLTGSGACVFGLVADNISAQQIAARVPAPWRAWSVRGCNKHPLYELAEQ", "metadata": {"id": "A0A060UMG4", "cluster": 26619362, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR014721", "IPR036554", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "The desired role of my protein is: The protein belongs to the Peptidase A25 family, which initiates the degradation of small acid-soluble proteins during bacterial spore germination. This aspartic-type endopeptidase functions as a homotetramer and exhibits specificity for acidic and hydrophobic residues at the cleavage site. Additionally, the protein belongs to the Peptidase HybD-like domain superfamily, which encompasses proteolytic enzymes such as HybD and the germination protease of Gram-positive bacteria. These proteins are characterized by a structural core consisting of a twisted five-stranded \u03b2-sheet surrounded by \u03b1-helices and function in specific peptide hydrolysis events. It occurs in Clostridiales bacterium and is classified with UniProt keywords Zymogen. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 14440, 1942, 1920, 24050, 8595, 1015, 3416, 16, 2154, 18637, 1920, 4877, 1927, 2858, 2687, 17, 6622, 2697, 2409, 4543, 18445, 14609, 18, 2052, 23047, 17, 2601, 16239, 9626, 2410, 9200, 4088, 1966, 43, 16350, 28959, 8835, 1930, 9826, 4896, 1958, 9931, 1930, 7919, 4248, 2019, 1920, 6404, 3200, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 24050, 4527, 13602, 17, 3189, 3418, 13975, 16, 2154, 21569, 12712, 5038, 2427, 1966, 4527, 13602, 1930, 1920, 14609, 7154, 1927, 8604, 17, 2843, 4802, 18, 2144, 2697, 2032, 4378, 2007, 43, 4346, 4728, 7600, 1927, 43, 16985, 1919, 3628, 17, 10338, 161, 17, 11130, 16006, 2007, 160, 17, 12789, 1930, 2347, 1922, 2487, 4207, 9128, 3916, 18, 2176, 5110, 1922, 17938, 26890, 1918, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 15856, 2404, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MARKKQQFLNFSHNIFMKNGNFRLDMAEESADFLKIDVKTAQKRVGENVTVRVTCVQKDEESRALNRDKGKYITVDAEKNVAYPSVKRDVTAAVKDAIRNLSSKAFRERPRVLVAGLGNRYVAADAIGPKTADNIETAGKTEMYAISTGIYAMTGLESATIIRAVARETKANLVIVVDTLATAKPMRVFRSFQLTDAGLEPGSATQAGRDKINFESVGVPVIAIGVPTCVYARQIVLDTLEKSGGLSLAKKYEITHEILKENVSALYSPKDSEAAATVAAEIIKDAINGTFQGKTH", "metadata": {"id": "A0A3D5WSB4", "cluster": 4160099, "interpro_all": ["IPR023430", "IPR005080"], "interpro_used": ["IPR005080", "IPR023430"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein should include a HPr kinase/phosphorylase, C-terminal domain that functions as the catalytic core of the bifunctional enzyme HprK/P, regulating carbon source utilization in Gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 on the phosphocarrier protein HPr and its dephosphorylation via phosphorolysis, typically within a hexameric assembly. In addition, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein should feature a HPr(Ser) kinase/phosphorylase, N-terminal domain that constitutes the structural blades of the hexameric HPr serine/threonine kinase PtsK, a sensor protein controlling bacterial carbon catabolite repression. This domain facilitates the assembly of the enzyme's three-bladed propeller structure, allowing it to function within a multicomponent phosphorelay system. It originates from Thioflexithrix psekupsensis and exhibits UniProt keyword tags Metal-binding, Transferase, and Multifunctional enzyme.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 3066, 3951, 43, 18542, 4016, 19, 12556, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 1920, 29491, 4113, 18542, 1040, 19, 58, 16, 6773, 5056, 4585, 8422, 1922, 8604, 17, 2843, 4802, 18, 2176, 17097, 2321, 1920, 4498, 17, 3100, 4050, 1927, 2375, 17, 4182, 1990, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 2496, 16881, 3454, 3421, 6892, 16, 5745, 2651, 43, 25602, 1935, 5957, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 18542, 12, 2375, 13, 4016, 19, 12556, 2051, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 4346, 22707, 1036, 1927, 1920, 25602, 1935, 18542, 8468, 19, 13143, 4016, 8618, 1040, 16, 43, 6443, 2213, 7138, 4543, 5056, 3115, 3016, 2394, 10084, 18, 2052, 3418, 11374, 1920, 5957, 1927, 1920, 4113, 11, 61, 2559, 17, 22707, 1007, 5062, 13728, 3170, 16, 7201, 2176, 1942, 2347, 2651, 43, 8844, 28155, 1939, 3421, 15208, 1012, 2433, 18, 2176, 22970, 2037, 15331, 18222, 1953, 3027, 1039, 5971, 1040, 25372, 8134, 1930, 9826, 20709, 11121, 2538, 14392, 6048, 17, 2743, 16, 13763, 16, 1930, 20136, 4113, 18, 3], "output": "MQLISVVELYESCADSLTLHWVAGRTGSKRHVGYLNLIHPHQIQVISLYELAYLLASVIVVDSHATDDLKEYAEKYQVPLFVLHGVFMDVLGMGVLIMGRSGTGKSNVINGACAMAGMNPFLEVRGLGILNVQALFGNSDRLQGDYRVRRVLGVDIPEISLPVAAGRDDFCERQQQAMQDNSTRFNTFNILLRVDEKLADALTRPVYQETLKQLFENDNSQLPGEHVINYLHTTFAGLLAQRTTELALELVSRGHRLIADDAPEFCRVSPSIKTENQLRLIVMLEQMSEERLKSINLAVLLESAVRNHSLKEQGYNAA", "metadata": {"id": "A0A251X4H9", "cluster": 4160443, "interpro_all": ["IPR003755", "IPR011104", "IPR011126", "IPR027417", "IPR028979"], "interpro_used": ["IPR011104", "IPR027417", "IPR011126"], "interpro_unused": ["IPR028979", "IPR003755"]}, "task_type": "infilling"} {"instruction": "I am designing a protein with the following function: The protein can be placed in the Cobalamin biosynthesis CobD/CbiB family, which functions in the synthesis of vitamin B12 and porphyrins by converting cobyric acid to cobinamide. This enzyme specifically catalyzes the addition of aminopropanol to the F carboxylic group of the precursor molecule. It is derived from candidate division MSBL1 archaeon SCGC-AAA382C18 and has UniProt annotations Cell membrane, Transmembrane helix, and Transmembrane. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 18477, 3717, 8132, 22528, 1007, 19, 5529, 2023, 3416, 16, 2154, 4088, 1922, 1920, 4271, 1927, 6111, 17492, 1930, 24944, 1036, 2007, 15025, 22528, 19872, 2687, 1942, 22528, 4058, 16408, 1021, 18, 2052, 4113, 4475, 17097, 1920, 2459, 1927, 3835, 20194, 4296, 1942, 1920, 48, 18708, 2210, 1927, 1920, 7897, 5388, 18, 2176, 1977, 3595, 2037, 6610, 8451, 3012, 3450, 1009, 13470, 1916, 2160, 5813, 17, 13835, 4745, 10866, 3928, 1930, 2258, 20709, 15010, 2024, 3260, 16, 9117, 7864, 16, 1930, 9117, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MSLINPSNSIYELIILSSAIIIDFLIGEFPEKIHPTVWIGKLANFLKSKLKGERGRVDIAGGVILTLLTFTIFVIPIYLLSILLVELYWIAYIFIMSLILMSTFAIRSMENHILRIITAIEDNNLEEAREKTSLIVSRDTSELDTEEIVSASIESTCESITDGIISPFFYFIFLGVPGAVGFRVVNTLDSMFGYKNSEMKDFGWGPANLDTLLGFIPARLTAFMMVPSAWFLGEDWKEAMRCASKESGKTSSINSGWPMAAAAGALNAKLEKQDHYILGENNQPPTPDHALRAIKIMKVSTLLFTLITMGVISIPLL", "metadata": {"id": "A0A133VJD7", "cluster": 6221717, "interpro_all": ["IPR004485"], "interpro_used": ["IPR004485"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to these design specifications: The protein is a member of the Armadillo-like helical superfamily, which is characterized by a multi-helical fold arranged in a right-handed superhelix that provides an extensive solvent-accessible surface for binding large substrates such as proteins and nucleic acids. This superfamily encompasses structurally related domains with low sequence similarity, including Armadillo, HEAT, and Pumilio repeats, which function in diverse processes ranging from nuclear transport to RNA binding. Furthermore, the protein incorporates a PBS lyase HEAT-like repeat that forms a bi-helical motif to bind tetrapyrrole phycobilins, facilitating their covalent attachment to apophycobiliproteins during light-harvesting complex assembly. Found in cyanobacteria and red algae, this domain is central to the function of phycobiliprotein lyases and proteins coordinating phycobilisome degradation. Additionally, the protein is included in the Armadillo-type fold superfamily, which forms a multi-helical domain consisting of two curved layers of alpha-helices arranged in a right-handed superhelix. This structural arrangement creates an extensive solvent-accessible surface that facilitates the binding of large substrates, including proteins and nucleic acids. It is produced by Candidatus Solincola sediminis.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 6011, 2713, 11560, 1037, 17, 3189, 11514, 13975, 16, 2154, 1977, 4378, 2007, 43, 2779, 17, 11514, 3728, 14940, 1922, 43, 3659, 17, 17105, 3356, 23285, 2416, 1988, 4558, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 2427, 1966, 2697, 1930, 11079, 4576, 18, 2052, 13975, 21569, 12171, 2712, 4682, 1956, 2330, 3244, 6796, 16, 2710, 6011, 2713, 11560, 1037, 16, 5631, 16, 1930, 13532, 5912, 1037, 9569, 16, 2154, 2347, 1922, 6445, 4028, 6485, 2037, 4254, 4860, 1942, 3146, 2743, 18, 3677, 16, 1920, 2213, 19683, 43, 4429, 23928, 5631, 17, 3189, 6865, 1988, 4952, 43, 2273, 17, 11514, 5219, 1942, 4566, 28000, 3553, 15828, 25511, 17428, 7782, 1036, 16, 12440, 2310, 13577, 8576, 1942, 11466, 25818, 4879, 12039, 16979, 7229, 2925, 2409, 3696, 17, 17318, 2796, 5957, 18, 2435, 1922, 21897, 1930, 2312, 17721, 16, 2052, 3418, 1977, 4101, 1942, 1920, 2347, 1927, 25511, 17428, 8257, 5684, 23928, 1036, 1930, 2697, 19355, 25511, 17428, 12191, 2204, 3870, 4877, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 6011, 2713, 11560, 1037, 17, 2601, 3728, 13975, 16, 2154, 4952, 43, 2779, 17, 11514, 3418, 7600, 1927, 2288, 19299, 7458, 1927, 4595, 17, 12789, 14940, 1922, 43, 3659, 17, 17105, 3356, 23285, 2416, 18, 2052, 4346, 13002, 15628, 1925, 6475, 7596, 17, 10551, 3154, 1988, 11374, 1920, 2743, 1927, 3103, 6249, 16, 2710, 2697, 1930, 11079, 4576, 18, 2176, 1977, 4152, 2007, 14550, 1031, 1957, 2638, 4006, 10173, 6276, 1980, 15472, 18, 3], "output": "MKILGFDLKRLRARGGLERIIRKLDDPERENRARAAEALGDTQDTRAVEALIKALDDEWLLVRATAAESLGKIADPRAVDPLIVSLRDSDEYVRKDAAEALGRIKDARATDALAKALEDDWMTVRAAAAKALGNIAEESSTQALMRALHDPEPLVRKEAAAAVQKIGNTEPLIQALKNEDDNLRCQAILALGEIGAGEAVSPLISCLKDSTVEVAISAAEALGKIGDSRAQLPLLELLQDERVQVRGRAVEALGLTGGSEVAKPLKEILKNDKDPYLRDEAYRALEQLKKRDLRVD", "metadata": {"id": "A0A1F2WNT4", "cluster": 9404957, "interpro_all": ["IPR011989", "IPR016024", "IPR004155"], "interpro_used": ["IPR011989", "IPR004155", "IPR016024"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein is grouped in the Translation protein, beta-barrel domain superfamily, which comprises a circularly permuted \u03b2-barrel fold found in key translation initiation and elongation factors like EF-Tu, eEF1A, and EF-G. This domain facilitates the transport of aminoacyl-tRNA and ribosomal translocation, often interacting with the switch 2 region to stabilize domain orientations during GTP-dependent conformational changes. Furthermore, the protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein has a Translation initiation factor IF-2, domain 3 domain that constitutes a structural component of bacterial initiation factor 2, facilitating the GTP-dependent binding of initiator methionyl-tRNA to the ribosomal small subunit. This domain adopts an $\\alpha/\\beta/\\alpha$ fold with a core formed by a four-stranded parallel $\\beta$-sheet. It is found in Boletus reticuloceps and carries UniProt keyword assignments GTP-binding and Protein biosynthesis.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 6410, 2213, 16, 4666, 17, 19560, 3418, 13975, 16, 2154, 12936, 43, 10262, 1954, 7187, 3072, 161, 17, 19560, 3728, 2435, 1922, 3834, 6410, 6035, 1930, 9971, 2790, 3189, 8485, 17, 9037, 16, 11150, 21952, 16, 1930, 8485, 17, 49, 18, 2052, 3418, 11374, 1920, 4860, 1927, 3835, 14645, 17, 10089, 1930, 11196, 7849, 16, 3868, 8615, 1956, 1920, 6195, 22, 3031, 1942, 13448, 3418, 16450, 2409, 9319, 17, 3100, 8523, 2840, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 2258, 43, 6410, 6035, 2991, 2647, 17, 22, 16, 3418, 23, 3418, 1988, 14879, 43, 4346, 4594, 1927, 4543, 6035, 2991, 22, 16, 12440, 1920, 9319, 17, 3100, 2743, 1927, 23467, 2295, 2001, 2199, 17, 10089, 1942, 1920, 11196, 2858, 5903, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 1956, 43, 4728, 5333, 2007, 43, 3006, 17, 10338, 6110, 8, 38, 4666, 8, 17, 11130, 18, 2176, 1977, 2435, 1922, 10608, 27228, 18905, 1994, 9431, 1930, 16252, 20709, 11121, 2538, 18306, 9319, 17, 2743, 1930, 2213, 8132, 18, 3], "output": "MLSRQLHAQILKHATFPPPEPAFVNCTRPPSHARSQFKGGHGNKAAVTLATQQIDDADADNAPTAEAKPGFSAFGALAIEGDGGIGKTKKDKKKAKKVQEDFDEPLDEELNADGLTPIISSAPPVPSAEPEPKKKVQAEAKKSAAAEGAPVDTTVIAPSSSSALLASHSEGNAVAGAGLSGLDSRAGDTGAESLYLLIGPFFLRVANLLSALPRQSTLVCVVQRRPFSLFASSSVSDPLFLRLSSSSVRFAFSSNLCFSSIIAFNAIIPPFFLFAVGAGAGAAAGAGTAPPPSWPSPSSSSFPNFESEGAGTDAAALAPAIKEDWDASSEDERCLQMEKRKDPQMNLPKTIRKKAEAAKRRAKAHEAALAERSKDNLCSPVCCILNVQEGEAGGITRQIDAMKTKTTVLNKYVCYRMGNKNTNLQGAHFAISPFLSLISCMASNHKHSSPSAYLEIDPFIIALNEIDRMFWWEAVQKTMLAFGEQGLTAVLHCENKDFARNVSLVPTSEIAGEGIYLSELECTVLEVKVVEGLGTTIGVVLSNGILRESDKIVVCVKAALGVKVDLMEGVMSDQTSLLNSIDKSGRGVSVQASTLGSLEALLHKKDIMHMAAMLERAKGLAVVLAFDVPVDMDAEWLAEEMGIKIFVKRRDAAPQAFWPCRLKTIAAFCIIPAGNALTKLIIGTPLTDGPPEVDENEDFGGLMCAIKQADGDEDGDTGPKILDKKEKEKLKKSLTPSAVFGSSAGAGDGEAYYQQRASRTVANSHFMMYLSSSAFSSSSAADASSSLLPFFASASAQADLKQCQGPISSPPGHVDTGKTKLLDKIRQSCLSLTLLATNRSPIYAVVETPDGAFLESLAKQKRSVQRKFKDRPDMIMLLVDLTQQRMSDRLMVASDLEKAVADSQLLVVGPDNDEEFLKVSKIPVPGINIGPIHEADIIYHLFDVFTAYNEIME", "metadata": {"id": "A0A8I2YDR8", "cluster": 9660297, "interpro_all": ["IPR027417", "IPR015760", "IPR023115", "IPR036925", "IPR009000"], "interpro_used": ["IPR009000", "IPR027417", "IPR023115"], "interpro_unused": ["IPR015760", "IPR036925"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that has this function description: The protein is a member of the Hydrogenase maturation factor HypA/HybF family, which acts as a metallochaperone to deliver nickel to the active sites of enzymes such as hydrogenase, urease, and guanidine hydrolase. These proteins coordinate nickel for transport and utilize a conserved C-terminal zinc-binding site to stabilize the protein fold during the maturation process. It originates from Anatilimnocola aggregata and is annotated with UniProt keywords Metal-binding. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 2052, 2347, 8418, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 6201, 2051, 7655, 2991, 2483, 1019, 19, 4527, 19781, 3416, 16, 2154, 8016, 1966, 43, 8969, 2694, 6748, 2290, 1942, 3971, 16541, 1942, 1920, 3500, 3402, 1927, 5038, 2427, 1966, 6201, 2051, 16, 10505, 4127, 16, 1930, 13504, 5802, 20748, 18, 2144, 2697, 11865, 16541, 1958, 4860, 1930, 12561, 43, 5305, 45, 17, 4262, 7997, 17, 2743, 3200, 1942, 13448, 1920, 2213, 3728, 2409, 1920, 7655, 2585, 18, 2176, 22970, 2037, 6289, 5912, 18044, 23338, 1019, 5206, 5499, 1930, 1977, 10633, 1956, 20709, 11569, 6048, 17, 2743, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MHEWSFARKLLQQATGICHANGARHCLEVRVQIGPLSGIEATLLESAFEQLASDHELAPTRLVIERTPLVVRCRDCAAESELSDFDFYCRLCGGRAVQVVAGDQLQLVSVTVDDAALMIKGTT", "metadata": {"id": "A0A517YAM7", "cluster": 9739664, "interpro_all": ["IPR000688"], "interpro_used": ["IPR000688"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein is categorized in the Transposase, L1 family, which mediates the retrotransposition of LINE-1 elements through reverse transcriptase and nucleic acid chaperone activities. These proteins preferentially bind and mobilize their own transcripts, while members such as L1TD1 also play a critical role in regulating stemness, embryonic stem cell self-renewal, and cancer cell proliferation. It occurs in Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) and is classified with UniProt keywords Coiled coil. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 10234, 1922, 1920, 12935, 2051, 16, 7554, 3416, 16, 2154, 10412, 1920, 27181, 2092, 1927, 2823, 17, 21, 5362, 2596, 5267, 13335, 1930, 11079, 2687, 14044, 4209, 18, 2144, 2697, 10662, 4566, 1930, 20407, 2606, 2310, 6614, 6247, 16, 2679, 4678, 2427, 1966, 7554, 1031, 7240, 2222, 3918, 43, 4140, 2770, 1922, 6773, 25128, 16, 7231, 4402, 2024, 3543, 17, 14498, 16, 1930, 2539, 2024, 4031, 18, 2176, 5110, 1922, 14545, 12862, 1937, 12, 4540, 6958, 2172, 1007, 23707, 13, 12, 4059, 20028, 1019, 12862, 1937, 13, 1930, 1977, 5947, 1956, 20709, 11569, 17524, 9121, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "LTLRWKNIWARQLQYPEQTETTTEPFNPQLQMAQAQELAQLLGPLLDQKLASIKESMVEILQQVTNQTQRMTEAEQRISTLEDELDKAQKSIDLQQHKIIIMADKIDDLENRSRRNNLRLVGIPESVKGTELEQLLKIELPKMLNMEEARSHYLIERYHRIGPPPLKDSNRPRQIIFKLLNYADKMNILAAYRKTKDLHYQDHHIMLFQDFSCKEFSKVCQALINRNINFSLMYPAKLKIFLPSGTRIFNDPLEASTFREYSDLYPLGKKEDTYT", "metadata": {"id": "A0A6I8QT02", "cluster": 11869945, "interpro_all": ["IPR004244"], "interpro_used": ["IPR004244"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Functionally defined as:\nThe protein can be placed in the Homeodomain-like superfamily, which comprises transcription factors and DNA-binding proteins that utilize a conserved helix-turn-helix (HTH) motif to interact with the DNA major groove. These proteins are ubiquitous across all domains of life and play critical roles in gene regulation through specific hydrogen bonding and hydrophobic contacts. In addition, the protein contains a TetR-type DNA-binding HTH domain that functions as a transcriptional regulator in bacteria and archaea, typically acting as a homodimeric repressor to control susceptibility to hydrophobic antibiotics and detergents. It structurally comprises an N-terminal helix-turn-helix motif with an inverse orientation to facilitate DNA binding. Additionally, the protein is classified under the HTH-type, TetR-like transcriptional regulator family, which comprises predominantly bacterial DNA-binding proteins that utilize a helix-turn-helix (HTH) motif to repress gene expression. These regulators control diverse physiological processes ranging from antibiotic resistance and lipid metabolism to osmotic stress response and cell division, as exemplified by the nucleoid occlusion factor SlmA. It is derived from Syntrophomonadaceae bacterium and is annotated with UniProt keywords Transcription regulation.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4502, 17166, 17, 3189, 13975, 16, 2154, 12936, 3213, 2790, 1930, 2678, 17, 2743, 2697, 1988, 12561, 43, 5305, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 6310, 1956, 1920, 2678, 3044, 15920, 18, 2144, 2697, 2032, 15498, 3436, 2136, 4682, 1927, 3308, 1930, 3918, 4140, 5456, 1922, 2359, 3640, 2596, 2487, 6201, 11463, 1930, 7919, 9070, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 5575, 17, 2601, 2678, 17, 2743, 5334, 1023, 3418, 1988, 4088, 1966, 43, 5224, 7888, 1922, 4802, 1930, 21501, 16, 5745, 8290, 1966, 43, 21189, 1935, 14434, 1942, 2285, 6461, 1942, 7919, 7560, 1930, 15814, 1036, 18, 2176, 12171, 12936, 1925, 56, 17, 4262, 7864, 17, 5165, 17, 7864, 5219, 1956, 1925, 9526, 7148, 1942, 6628, 2678, 2743, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 5334, 1023, 17, 2601, 16, 5575, 17, 3189, 5224, 7888, 3416, 16, 2154, 12936, 7700, 4543, 2678, 17, 2743, 2697, 1988, 12561, 43, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 9055, 2359, 2294, 18, 2144, 9098, 2285, 6445, 5005, 4028, 6485, 2037, 7267, 3554, 1930, 4486, 4714, 1942, 13951, 3071, 2644, 1930, 2024, 8451, 16, 1966, 22236, 2007, 1920, 2797, 2642, 10543, 2991, 2788, 3368, 18, 2176, 1977, 3595, 2037, 14913, 2789, 20050, 7324, 1972, 3336, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 3213, 3640, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MEGKGLPDRIKKAAVSEIKKYGFRRFTMDDLAAQELITAILSDEFEQEAARIATIVAKDEHWFDREANLFFPEQAKLIENRYSIIKQQYTFLLINQNCSRIIEQSKGISLVQRLEEIKKILFFGVIRREWRLKVSKKTIYKSFASKLNELVDLCAEGRFSPALLEQEGLSKGHIQPDIHLDLLVIIMDEL", "metadata": {"id": "A0A971PBA4", "cluster": 13882655, "interpro_all": ["IPR009057", "IPR050109", "IPR001647"], "interpro_used": ["IPR009057", "IPR001647", "IPR050109"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein possesses a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. Furthermore, the protein is classified under the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is native to Rhodospirillaceae bacterium and contains UniProt keyword associations ATP-binding, Nucleotide biosynthesis, and Transferase.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 14465, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 6196, 1942, 11490, 3106, 23576, 11560, 9914, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MKPPPTSGKFITLEGGEGAGKTTQIKLLADFLKAGGLDPIITREPGGSPEALLNFAARLEHVRETIEPALTAGRWVLCDRFADSTVAYQGYGHDLFQPDLTVILDIPVDEGLARTRNREQAEGSREDRYERMNPERCVVIDAAQEPETVHAEIRAVVGQRLKVALAAAEVIRSLLVEGAVDRWQPMTGRAAIDELHRLVLGYDEGFHQRLRDGFLDIARR", "metadata": {"id": "A0A2D6JXV8", "cluster": 15871483, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein has a UvrD-like helicase, ATP-binding domain that functions as the catalytic ATP-binding component of Superfamily 1 helicases, utilizing ATP hydrolysis to drive DNA unwinding, typically with 3'-5' polarity. This domain adopts a RecA-like core structure and undergoes conformational swiveling to support essential processes such as DNA repair, replication, and recombination. Moreover, the protein is classified under the DNA helicase, UvrD/REP type family, which catalyzes the ATP-dependent unwinding of double-stranded DNA into single-stranded DNA. This family includes both UvrD and Rep helicases, with Rep proteins functioning as dimers composed of four structural domains. It is native to Chrysiogenia bacterium.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 2258, 43, 5819, 8544, 17, 3189, 15318, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4498, 17, 2743, 4594, 1927, 13975, 21, 29919, 16, 10232, 4498, 9128, 1942, 9265, 2678, 26801, 16, 5745, 1956, 23, 11, 17, 25, 11, 12432, 18, 2052, 3418, 24032, 43, 21534, 17, 3189, 4728, 3170, 1930, 14928, 8523, 19532, 2035, 1941, 1942, 3373, 4415, 4028, 2427, 1966, 2678, 5059, 16, 5158, 16, 1930, 7827, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2678, 15318, 16, 5819, 8544, 19, 3073, 2601, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 26801, 1927, 4825, 17, 10338, 2678, 2460, 2957, 17, 10338, 2678, 18, 2052, 3416, 5921, 2321, 5819, 8544, 1930, 3073, 29919, 16, 1956, 3073, 2697, 7295, 1966, 13351, 7179, 1927, 3006, 4346, 4682, 18, 2176, 1977, 6196, 1942, 21367, 3940, 2432, 2126, 14061, 18, 11586, 5655, 3581, 18, 3], "output": "MSDEQQIRLRDGEARELARSSFEHPIVLEAGAGTGKTATLVTISRGGDADARIFADEVAVRVADRIAAITFTERAAAEMKERIAEILTVRAKHLLAVLDHFFVGTIHAFCRRLLAQYALPAGVHPGFVLADRLQEVYGDPGDENLLALAAMGWGPAEIVEALGELIRGGVPASELAAPLEAFIGLAAGPLAEGKGNLNAARSVLEALGTLATRLANVSEAGELRDLALIEDEVQAAAAPLAARIRHLQSLDPDLLPRACVALRELLGNVQARLRAAGDEVLRGHVRQRFDQLLVDEFQDTDPVQYEIIEYLALDGPSFERPWRGADLGAYARFIARVKDEGGEIHSLQVNFRSVPAILSEVARVLTWCLGPGWARAAEDLRGFAAVLRGEGIVGLELERFEEPLVDADEGMSNSLIEDVEALAHDPYAPELVKQAAEVDVKRLREWGEGKLNKTESKALAGEGIETFAALLRDTRDLLGLFLIGDPKQSIYG", "metadata": {"id": "A0A958BHV9", "cluster": 16741936, "interpro_all": ["IPR000212", "IPR027417", "IPR014016"], "interpro_used": ["IPR027417", "IPR014016", "IPR000212"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein has a Tf2-1-like, SH3-like domain that forms the C-terminal region of the Tf2-1 polyprotein in the fission yeast *Schizosaccharomyces pombe*. This domain is associated with gypsy-like retrotransposons, a group of mobile genetic elements widely distributed among eukaryotes. It has been characterized in Paspalum notatum var. saurae.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 2258, 43, 6406, 1028, 17, 21, 17, 3189, 16, 18824, 17, 3189, 3418, 1988, 4952, 1920, 45, 17, 4262, 3031, 1927, 1920, 6406, 1028, 17, 21, 6240, 5684, 1922, 1920, 16150, 5688, 14, 7071, 5360, 2437, 28476, 29249, 22168, 14, 18, 2052, 3418, 1977, 2458, 1956, 8415, 9196, 17, 3189, 27181, 2101, 16, 43, 2210, 1927, 8785, 3299, 5362, 5673, 6533, 2706, 15021, 18, 2176, 2258, 2252, 4378, 1922, 9233, 13797, 1989, 2084, 9576, 4953, 18, 4611, 9280, 1021, 18, 3], "output": "MAKLNESISVWRLIFGNFGTILVLWVGTRSSRDYEILADWLQERDVMIRMFAVGESVFLKLQPYVQSSLAPSVAYTRSFPSIVVFIPPFMSRNVLFIRAPRNGLTGWQQQAVVKQHLHRAKHRMKKQVDKGRTERSNQKLAFKFFGPFQIVAKCG", "metadata": {"id": "A0AAQ3T950", "cluster": 18762012, "interpro_all": ["IPR056924"], "interpro_used": ["IPR056924"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein possesses a MASE11 domain that functions as a predicted transmembrane sensor involved in signal transduction. It is frequently associated with sensor histidine kinases and intracellular signaling modules, including PAS, GAF, GGDEF, EAL, and HD-GYP domains. It is present in Chloroflexaceae bacterium and is annotated with UniProt keywords Coiled coil and Transmembrane helix.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 14465, 43, 9955, 12474, 1009, 3418, 1988, 4088, 1966, 43, 4396, 9117, 6443, 3286, 1922, 2733, 8201, 18, 2176, 1977, 5467, 2458, 1956, 6443, 13873, 7784, 1930, 4776, 3197, 10803, 16, 2710, 9233, 16, 4357, 1038, 16, 12358, 3695, 1038, 16, 11377, 1024, 16, 1930, 4515, 17, 8415, 1034, 4682, 18, 2176, 1977, 2481, 1922, 10107, 18222, 9914, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 17524, 9121, 1930, 9117, 7864, 18, 3], "output": "MANLLHATTTSRTWREQALLRAMRVIFWVLAPIFVYAFWAFTLNIRYHTRAAALLTILYVAGSFWLINNGVPGIGLTMGIIFWGFTAEWLIIPTRLDARMYTDGWLFLLWFVQSIIGGAALAQLNQELEQRIAERTAELRQQQALFQAFLDNITLSHQSVIGTLFSALLLFSCWASRIYLLVFVVVAALVLNMRAALVVWLLTVGLVFAIVLLVRSFQRTLHIAETNQ", "metadata": {"id": "A0A968N960", "cluster": 19944590, "interpro_all": ["IPR048437"], "interpro_used": ["IPR048437"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein possesses a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. Moreover, the protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is expressed in Algimonas arctica and contains UniProt keyword associations ATP-binding, Nucleotide biosynthesis, and Transferase. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3198, 1922, 4326, 1980, 9259, 23937, 1019, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MAGQFITFEGGEGAGKTTQAKMLADALEKVGVETILTREPGGTFGAESIRKLVLEGTDDRWSGMTELLLMYAARLDHVEKLIKPALQRGAWVISDRFSDSSLAYQGYARDLGADRVRSVHDVVMEGFNPDLTLVFDMDVYLSLKRVETRAAQDDEVLTRFDKAGQAFHTTIREAYLDIAKNEPARVKVVDADGSRQAVHSRILNALTAKYPEFAGKLGGA", "metadata": {"id": "A0A8J3CLS8", "cluster": 21792755, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence of a protein with the following function look like? Here is the function: The protein can be placed in the Papain-like cysteine peptidase superfamily, which encompasses enzymes that utilize a conserved Cys-His-Asn catalytic triad to perform proteolysis. These members typically adopt a structural fold consisting of a single alpha-helix and four strands of antiparallel beta-sheet. It has been detected in Fusarium solani (Filamentous fungus) and is classified with UniProt keywords Coiled coil.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 8120, 3189, 35, 3410, 1977, 1920, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 3860, 2005, 17, 3189, 8666, 24050, 13975, 16, 2154, 21569, 5038, 1988, 12561, 43, 5305, 4998, 17, 4167, 17, 15118, 6804, 21845, 1942, 2385, 15439, 18, 2144, 4678, 5745, 14103, 43, 4346, 3728, 7600, 1927, 43, 2957, 4595, 17, 7864, 1930, 3006, 13214, 1927, 28892, 4666, 17, 11130, 18, 2176, 2258, 2252, 3330, 1922, 24470, 2638, 8150, 12, 18706, 16461, 13, 1930, 1977, 5947, 1956, 20709, 11569, 17524, 9121, 18, 3], "output": "MNSPPTERSAAVELHFPTTHDERVFWLDQAWKGPWFPVDARIGWLGTDSSLAFYMVRITHAAIDRGIPLASLWDAESPHGHLRRAVMKESAILKDSEGSHPHLLTPDIVTEVYEIMMASEKTASNNTPSEHPSDKSDDGDSIDLPPPPQAQATTTARFKPFSKTEHEFQLKRPIEHQDGLSAMPLHVRHEDQSSPLKRIFRTTTYVSSGTAGQKPTAEVPPITGIATQEEPIDKNRRFQPAPEAYMGSPDLSTRPETFVSPNGLLQPPSSPMQSPEHSLLPYVSSPPADEPLNKAPTPTSPITPTKKRKRAMVSVPSTPTRAVKGERLTGPLTVEKILRQLTCDVQLTDDVVELVCQAIVVEHGGDNVRLLSPLWFEADEPSSLPQTIRNLDQEQTICFPIHHKFPKHWTMGVARVTADQVVLTFHDSMQCSERANTVRRRFGAWMEAVRLKQPLVFQTKECTLQKDATSCGVHAAVCLRRDLRKETCCDPIEPFLEKRAMLEGLRTVRETSPIHSTTFPLLRELRSRQSLGADASIVSTPCRGGSAMPVTARQESEVQVIQPQMGLGYVLDGLSLETLQDRLKDAETRLDEAINARDNAQDTLRELELSQRLIHDMYPRIITYVRSRGINMDEYSDATMAVQRNSMPKGLDQGEIFQQRRNIMGDFLKASEREGVDHTLAAIRENQAQVFADIGNTQQILDQRNEEITSVESEVASLQEICEAKKALEKYSGPDWLAYFQSMQGL", "metadata": {"id": "A0A9P9HDB1", "cluster": 22967886, "interpro_all": ["IPR038765"], "interpro_used": ["IPR038765"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein should have a Tetratricopeptide repeat that mediates protein-protein interactions and the assembly of multiprotein complexes. This motif consists of tandem 34-amino acid residues adopting a helix-turn-helix arrangement, which stacks to form a right-handed superhelical structure involved in diverse processes such as cell cycle regulation and protein folding. Furthermore, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein incorporates a NB-ARC domain that functions as a signaling motif in bacteria and eukaryotes, regulating critical pathways such as plant disease resistance and animal cell death. Structurally belonging to the AAA+ ATPase superfamily, it is proposed to bind and hydrolyze ATP to induce conformational changes that drive the assembly of oligomeric signaling complexes. It is found in Stackebrandtia nassauensis (strain DSM 44728 / CIP 108903 / NRRL B-16338 / NBRC 102104 / LLR-40K-21).\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 3066, 2162, 43, 12470, 3319, 21305, 6865, 1988, 10412, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 18, 2052, 5219, 7543, 1927, 10361, 3540, 17, 3835, 2687, 4248, 20478, 43, 7864, 17, 5165, 17, 7864, 13002, 16, 2154, 20836, 1942, 2386, 43, 3659, 17, 17105, 3356, 23285, 2046, 3170, 3286, 1922, 6445, 4028, 2427, 1966, 2024, 4048, 3640, 1930, 2213, 10328, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 19683, 43, 8789, 17, 9952, 3418, 1988, 4088, 1966, 43, 3197, 5219, 1922, 4802, 1930, 15021, 16, 6773, 4140, 3873, 2427, 1966, 4496, 2573, 3554, 1930, 4027, 2024, 3539, 18, 12171, 10588, 1942, 1920, 13835, 15, 9444, 13975, 16, 2176, 1977, 4211, 1942, 4566, 1930, 7222, 6931, 4498, 1942, 4769, 8523, 2840, 1988, 9265, 1920, 5957, 1927, 19206, 3197, 5048, 18, 2176, 1977, 2435, 1922, 10496, 13495, 17182, 18314, 2126, 7312, 5735, 2182, 3355, 1937, 12, 3943, 10964, 29146, 4839, 19, 12998, 9123, 5124, 1010, 19, 5214, 1005, 1024, 44, 17, 15199, 4745, 19, 8789, 15618, 10049, 15231, 19, 10748, 1005, 17, 3040, 1040, 17, 2900, 13, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MGHLTRVRLDPSRAREVDDLIAYLRRLRIEAGGMSIRDIQRGIRELRLTIHSCFQPGRKRLNVDTVTDIAAVLGLNDDGVALLRQGCQLVMDRVSRSLVVTHDLDRVLDMTASRPPDDAPLVITIEGMAGVGKTTLAQRVCQELESLGDGYDTRLSVDLRGYDPTEPGADPDPSERREHYARLLAERRALILLDNAADETQLRPILLSVSPSTILVTSRRRLHDLDGAADTDATAATRLVHLCRQLPIELAAVGSQLASKPDWSLSDHVERLKVMPSFDISRPQRLFRLLALHPGREFTDDTAAVLSDLPPAKTGELLRSLFDEHLLLCPTEGRYQFHDSIRDHYRQRLAEDADPAWIQAERSNLMACLHLHGHDEGIIALVAALHPRLRTMGYYDDVEADALSGLAEIARLTGQPRRAEDLFRRVLVIRRQIADHDGEAHALRGLAQVSAGRDFVAAADYYRQEIARIFEDYATVEANARSILEICRRVGNRIGEAHALCGLGTAFARTGDHEAATTSCRRALSICLDAHDDADTARDAFTQAREIGSAIGDRAGEAHATFGLAEVARLNGDDREALALVADAQPVAQGDRDAARAHWEEALVLATRHALPQTARLRAKLDGQNASHDPPFSAKRGVPDSAPSVATRADIAAAAATFTGRRAVIRGFLVHLGMSPQHIDGLSRLPLEPLSIDDALDLLRRLDPSGRVAFAVSYQNQSAAADFATTLVHQEEPASGQRAAQGRVLRIGNHTVLRLAQAIGDRGAALDLHRRNGNGPGEAETLWGLLIGNRRGAVRAWRGLGEAALFQDLDDDPCTVLALDLRGDMAV", "metadata": {"id": "D3PWH2", "cluster": 23956306, "interpro_all": ["IPR002182", "IPR027417", "IPR011990", "IPR019734"], "interpro_used": ["IPR019734", "IPR027417", "IPR002182"], "interpro_unused": ["IPR011990"]}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that can perform the following function: The protein possesses a Transcription regulator LuxR, C-terminal domain that functions as a DNA-binding helix-turn-helix (HTH) motif to regulate transcription, primarily acting as an activator within the LuxR/FixJ family. This module forms a four-helical bundle that binds the DNA major groove and mediates dimerization, typically in response to N-terminal domain signals such as phosphorylation or quorum-sensing autoinducer binding. Additionally, the protein is a member of the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. Also, the protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It has been characterized in Actinokineospora alba. Give the amino acid chain.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 3213, 7888, 17851, 1005, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 5741, 3213, 16, 5985, 8290, 1966, 1925, 9518, 2651, 1920, 17851, 1005, 19, 4011, 1013, 3416, 18, 2052, 9059, 4952, 43, 3006, 17, 11514, 14142, 1988, 6876, 1920, 2678, 3044, 15920, 1930, 10412, 13640, 16, 5745, 1922, 2644, 1942, 56, 17, 4262, 3418, 4771, 2427, 1966, 4050, 2014, 28481, 17, 9306, 27485, 4600, 1005, 2743, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 2258, 2252, 4378, 1922, 4718, 7189, 9890, 1019, 5311, 1019, 18, 7031, 1920, 3835, 2687, 4659, 18, 3], "output": "MADVAASGWVPELVALREAPHNLAAELSSFVGRERELAELTDAIAGTRMLTLTGAGGCGKSRVAHRVGRALLPRFPDGVWWVGLATLSGRDELEQALAHVIGVRPAPGRRALDSVAAHLASRRVLLIMDNCEHVLDEAARVAETLVGDCPGVTVLATSREPLRTDGETDWRVPSLSLPTAAPAESDAVRLFVERARQVRPGFQLDDANADAVARICRELDGIPLAIELAATRLRMLSVDQLADALGERFRVLTDGTRTSLTQHRTLRASVDWSHDLLSDAERTLLRRLGVFRGGFTLDAATRVCAGDRIQAGAVFELLAALVDKSLVQAEDHGPVVRYRLLETIRQYALERLAAAGETDRVLDRHRDAYLALAEDLAPKVNSPRQLEVLGLLDPEAANFVQAIDRAAAGESETALWLCVALTGWWQGRGRFGQGLACLRTALAASDQPSVPRVRALWGRAFLLALTGEFADALPVAQQVLTEAEQLSDLETVGRTRWLLGMLVFFPAPADCREQLERSLELATAHGDTYGAAVCAMSIAYSYLHQNDLRQAEPWSRRAMRQAQAVGQLDLIAWCHGATAWAHHVRAEFDLCRREALAAIRCARSIGDIMSEISATCAISQADVGGGHPERALERLTAARQRALSLGAGFILPAAVACTGWAHAAQGRLDEAAACLEDLIREGAGGYSYALGFACAGLAEVYRLRGERADEVGGRALELAVYNGDRLSMAATQLTLGRVAGARGEWAQAQRTHHEALSVVVADGYAVLLPSALEALAEDAAGLGRPLDATRILAAAASARTALGVVDWLPRREQTAALSDRLRTELGDEPHAAATTEGARLSADEAVAFVSRARGARKRPADGWESLTPTELDVARHAADGLTNPQIAERMFITRGTVKSHLAHIYAKLGLRNRAELAAELARRT", "metadata": {"id": "A0A1H0F1N6", "cluster": 24917724, "interpro_all": ["IPR027417", "IPR016032", "IPR011990", "IPR000792", "IPR036388"], "interpro_used": ["IPR000792", "IPR011990", "IPR027417"], "interpro_unused": ["IPR036388", "IPR016032"]}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein has a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein possesses a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is found in bacterium and is associated with UniProt keywords Isoprene biosynthesis and Transferase. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 2435, 1922, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MITIKAYAKINLCLRVLGRRPDGYHELETLFQQIDLCDTLLFSEADQALTVTTSHADCPADEKNIVYRAADLLRRCSGCQSGVHIHIEKHIPMGAGLGGGSSDAAAALMGLNRLWRLNLDDALLHQLASQLGADVAFFLHGGSALGTGRGEQLQPLRLPLDYYGVLVYPRFPISTAWAYQNLKLNLTNSPKRSKFYSFDDLVNDRESWQQGFTNDLEKVVFEEYPELDRLREQLATAGAFFSRMSGSGSCIYGLYETRARAEKAFLGVGTSYQRFLFSPISTHANPAETV", "metadata": {"id": "A0A7X8MD74", "cluster": 25366832, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR014721", "IPR020568", "IPR036554"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein belongs to the Dehydroquinate Synthase family, which catalyzes the cyclization of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ), a pivotal step in the shikimate pathway. This enzymatic activity is essential for the biosynthesis of aromatic amino acids in bacteria, fungi, and plants. Additionally, the protein should have a 3-dehydroquinate synthase C-terminal domain that contains the key catalytic and Zn2+-binding residues required to convert 3-deoxy-D-arabino heptulosonic 7 phosphate into dehydroquinate. This alpha-helical module functions within the shikimate pathway for aromatic amino acid biosynthesis, existing either in isolation or as part of the pentafunctional AROM polypeptide. Furthermore, the protein carries a 3-dehydroquinate synthase, N-terminal domain that adopts a Rossmann-fold structure to bind NAD+ in an inverted orientation and contributes to the formation of the enzyme's active site cleft. It facilitates the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate to 3-dehydroquinate and orthophosphate, a critical step in the shikimate pathway for aromatic amino acid biosynthesis. It originates from Phascolarctobacterium succinatutens CAG:287 and contains UniProt keyword associations Nucleotide-binding, Cobalt, and Amino-acid biosynthesis. Please provide the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 7762, 30, 1920, 2213, 14440, 1942, 1920, 28936, 11072, 2010, 8921, 3416, 16, 2154, 17097, 1920, 25267, 1927, 23, 17, 16333, 17, 46, 17, 20790, 1037, 17, 20662, 11677, 8870, 27, 17, 5413, 12, 3692, 15870, 13, 1942, 28936, 11072, 2010, 12, 6781, 1055, 13, 16, 43, 13637, 3537, 1922, 1920, 20837, 7369, 23874, 3374, 18, 2052, 8145, 2455, 1977, 4415, 1958, 1920, 8132, 1927, 10761, 3835, 4576, 1922, 4802, 16, 10520, 16, 1930, 4793, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 23, 17, 28936, 11072, 2010, 8921, 45, 17, 4262, 3418, 1988, 5461, 1920, 3834, 6804, 1930, 21061, 15, 17, 2743, 4248, 3414, 1942, 14450, 23, 17, 16333, 17, 46, 17, 20790, 1037, 20662, 11677, 3490, 27, 5413, 2460, 28936, 11072, 2010, 18, 2052, 4595, 17, 11514, 9059, 4088, 2651, 1920, 20837, 7369, 23874, 3374, 1958, 10761, 3835, 2687, 8132, 16, 6124, 3108, 1922, 7152, 2014, 1966, 3131, 1927, 1920, 9412, 2624, 20839, 8981, 13022, 18, 3677, 16, 1920, 2213, 16252, 43, 23, 17, 28936, 11072, 2010, 8921, 16, 56, 17, 4262, 3418, 1988, 24032, 43, 18215, 8890, 17, 3728, 3170, 1942, 4566, 6577, 15, 1922, 1925, 12344, 7148, 1930, 7624, 1942, 1920, 3337, 1927, 1920, 4113, 11, 61, 3500, 3200, 14649, 18, 2176, 11374, 1920, 7309, 1927, 23, 17, 16333, 17, 46, 17, 20790, 1037, 17, 20662, 11677, 8870, 27, 17, 5413, 1942, 23, 17, 28936, 11072, 2010, 1930, 17266, 10647, 3508, 2722, 2057, 16, 43, 4140, 3537, 1922, 1920, 20837, 7369, 23874, 3374, 1958, 10761, 3835, 2687, 8132, 18, 2176, 22970, 2037, 18421, 12709, 4362, 2341, 12022, 13791, 1926, 2696, 3355, 13415, 30, 22891, 1930, 5461, 20709, 11121, 2538, 5253, 5489, 17, 2743, 16, 20773, 16, 1930, 3835, 17, 2687, 8132, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MKKIHVALGAHAYDIEIAAGLLPQVGSKVAALLPKARKAAIISDTNVAPLYAAKLQASLEEAGLVVHKVVIEAGEQSKNMQVLSDVLEQLAAAGLTRTDVVLTLGGGVVGDLGGFAAASFMRGIAFVQIPTSLLAQIDSSVGGKVAVDLKAGKNLAGAFYQPKAVFIDTDLLATLSTRFLHDGLAEAIKYGCIKDAALFEKIAGYADDAELLADIDSVVATCCAIKARIVEQDEFDTGLRMLLNFGHTLGHAVEQHFGYSSFTHGEGVAIGMYQLTKRTEELGMTAKGSAERIKSVLEKYNLPLTAGVEKAQLLDTMARDKKKNGNSITLIILQQIGEGVLQKVDWQEVPKYLG", "metadata": {"id": "R6WZF7", "cluster": 25523983, "interpro_all": ["IPR050071", "IPR016037", "IPR030963", "IPR030960", "IPR056179"], "interpro_used": ["IPR050071", "IPR056179", "IPR030960"], "interpro_unused": ["IPR016037", "IPR030963"]}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein has a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. In addition, the protein possesses a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Furthermore, the protein incorporates a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. It is derived from Subtercola sp. PAMC28395 and carries UniProt keyword assignments Cytoplasm, Hydrolase, and SOS response.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 2258, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 3677, 16, 1920, 2213, 19683, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2176, 1977, 3595, 2037, 13329, 3234, 10173, 2056, 18, 11888, 8054, 11368, 8803, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 16, 20748, 16, 1930, 17668, 2644, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MEPTRSVRPFEVISDYTPSGDQPAAVAELTARINAGEWLIEAVQRPTLVLAHNKTLAAQLATEFREYQPEAYVPQTDTFIEKDSSINSEVERLRHSTTNSLLSRRDQYMKAMMALQVGMKVDRDWLIRKFISVRGDTIEIIPMYEELAIRIEMFGDEIEALYTLHPLTGDIVIQEELAERLTQLEREGKLLEAQRLRMRTTFDLEMMQQIGFTSPGEAPHCLLDYFPDDFLVVIDESHVTVPQIGAMYLDNRPLRWNEFNDRVGQKVYLSATPGKYEMPSKGQIDDLLEEIRIRVAKDERILVTTLTKKMAEELTDFMAEHGVRVSELRAGVYDVLVGINLLREGLDLPEVSLVAILDADKEGFLRRNVSGEVHMYADVMTASMTRAIEETNRRREKQVAYNLERITEMLAREGADTAALLAGRNSKKKSPTPNLRREGIAAAGAAGELKFELAARLRDELGDLKHELRQMEKAGHITDVVLLGATGTGKSATTALMPNNAVEYFVSYYDYVVVVSTVSCIYGLGTPEMQYQRNDIDFSRGNFRRKMDSISVFPGSHYVADTNVMHRAIGTGIENYSRHIDGRQEGDSSRKRTLVEHGFRLPSAGIADGVVEQIIRPTGLIDPEIIVKRYLHSDVDTLRRVELLSSTSLIQTIGRAAGVDPQPLRKKINDANELESLIADLNDQMMT", "metadata": {"id": "A0A975SFV5", "cluster": 26043374, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR001943", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001650", "IPR001943", "IPR014001"], "interpro_unused": ["IPR024759", "IPR004807", "IPR041471", "IPR006935"]}, "task_type": "infilling"} {"instruction": "\"The protein falls within the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. Moreover, the protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein possesses a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. It originates from Clostridium sp. JS66 and is annotated with UniProt keywords Metal-binding.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 12182, 2651, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 14465, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 2176, 22970, 2037, 21156, 2056, 18, 16883, 7283, 1930, 1977, 10633, 1956, 20709, 11569, 6048, 17, 2743, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MSNCNSCPSGDSCTKDKEKCMIENNPMNSIKNVIGVMSGKGGYKVGILDADITGPSVPRLLGLKDKNAEVREKIIYPVETEDKIKVISGAVKQFWTDVLWGELDYLIIDMPPGTGDVALTVSMIVSKAINMARKMDIKVLGVVENMSYIVCPDCNKKIKLELPMVSEICNLSSCGCENSSESLDELFNPIVTNILKKFGVGKSTISVMIAKQLRKSMSLNLLIEDENEPVIWRGPIVMQSIPINGLVMVSVPQDLFNGESIDKFLEEADLELLG", "metadata": {"id": "A0AAU0NWI0", "cluster": 26320401, "interpro_all": ["IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR033756", "IPR027417", "IPR000808"], "interpro_unused": ["IPR019591", "IPR044304"]}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein possesses a Peptidase M56 domain that functions as a metallopeptidase characterized by a conserved HEXXH active site motif. It is exemplified by the BlaR1 protein, where it acts as a potential penicillin-binding component required for the induction of beta-lactamase. Furthermore, the protein should include a TonB, C-terminal domain that interacts with the N-terminal TonB box of outer membrane transporters to facilitate the active uptake of iron-siderophore complexes. This domain positions itself within the transporter barrel to transduce energy required for the translocation of the iron complex across the outer membrane. Furthermore, the protein is grouped in the TonB-dependent transporter energy transducer family, which interacts with outer membrane receptors to transduce energy from the cytoplasmic membrane for the high-affinity uptake of specific substrates into the periplasm. These proteins are essential for nutrient utilization and are also implicated in bacterial virulence and bacteriophage infection. It originates from Bacteroidales bacterium and is associated with UniProt keywords Cell inner membrane, Transmembrane helix, and Protein transport.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 14465, 43, 24050, 24862, 1016, 3418, 1988, 4088, 1966, 43, 8969, 24897, 4378, 2007, 43, 5305, 7142, 1039, 1023, 3500, 3200, 5219, 18, 2176, 1977, 22236, 2007, 1920, 18208, 7011, 2213, 16, 2597, 2176, 8016, 1966, 43, 2889, 9957, 17, 2743, 4594, 3414, 1958, 1920, 4408, 1927, 4666, 17, 23023, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 16501, 1014, 16, 45, 17, 4262, 3418, 1988, 9034, 1956, 1920, 56, 17, 4262, 16501, 1014, 5758, 1927, 7642, 3260, 10538, 1942, 6628, 1920, 3500, 5047, 1927, 5680, 17, 22940, 11082, 5048, 18, 2052, 3418, 6490, 6999, 2651, 1920, 9054, 19560, 1942, 30334, 3844, 3414, 1958, 1920, 7849, 1927, 1920, 5680, 2796, 3436, 1920, 7642, 3260, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 16501, 1014, 17, 3100, 9054, 3844, 14848, 3416, 16, 2154, 9034, 1956, 7642, 3260, 4086, 1942, 30334, 3844, 2037, 1920, 6823, 3260, 1958, 1920, 2149, 17, 5173, 5047, 1927, 2487, 6249, 2460, 1920, 20171, 18, 2144, 2697, 2032, 4415, 1958, 8708, 8422, 1930, 2032, 2222, 6835, 1922, 4543, 9304, 1930, 24613, 2909, 18, 2176, 22970, 2037, 24323, 3955, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 2024, 6671, 3260, 16, 9117, 7864, 16, 1930, 2213, 4860, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MSAQELILGRLLPIAVAIAVFWIVYRLLFTNSNRIKFSLKQNMFGGIVLDQVAIAADESTPLVEAAAQHYSIWQIISIIYFVGVGSQKEKCGSYTAVYTGKEQGSFSFLNYAFFPDKSIDKEIVRHEISHISHHHSWDIELQCIHEYQADRDVVDAGANKRDYMMLILQQCTAVDFSRISNNFSLILWRLLVTLPVLAVMLVANTNATAKEQLADNNSEATVIANGDIKTEAMMKFIQENTVYPENAKKKGIGGKTFVSFTIEKDGSITNVMPKWTPGKVKGKTVRVNFVMPFVFKAPQKNRYYILMSIIFALALPLLGVLIGRGSPEMLISLLLLMFKLFKIFLLVVKVFIEIMMVLQWFNPFIYMLKRTKKRIKMITKSEKTKGLWNIQQSKDSIYEAGDVEVMPQFPGGDKVLRGCDKECDAEAVRVVKS", "metadata": {"id": "A0A939VLH2", "cluster": 28682233, "interpro_all": ["IPR008756", "IPR051045", "IPR006260", "IPR037682"], "interpro_used": ["IPR008756", "IPR037682", "IPR051045"], "interpro_unused": ["IPR006260"]}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein falls within the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein is a member of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is expressed in Thermoanaerobacteraceae bacterium SP2 and carries UniProt keyword assignments ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 3198, 1922, 7967, 7241, 6506, 7972, 2341, 7124, 1972, 3336, 14061, 29611, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MKVIGLTGGIASGKSTISMLLKNRGAVIIDADKIAREIMTPGKPVWHAVIEHFGREILLDGKNIDRKKLGRIVFSDPKLLETLNSITHPAIVQEIKERLDYYRHKNEKVVVVDAALLLEIGLDSLVDEVWVVVVDEKNQLKRLMDREKGMDLEEARNRIRAQMPLDEKIKMADKIIDNSGSIEETERQIDELWREIELSWQKKLQQY", "metadata": {"id": "A0A3A9K080", "cluster": 605605, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein is included in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It originates from Moorena sp. SIO3G5 and is annotated with UniProt keywords ATP-binding and Transferase.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 22970, 2037, 22728, 2175, 2056, 18, 5998, 8583, 1029, 1015, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 1930, 13763, 18, 3], "output": "KLHPAGKRRSSDLNRKGHPYVRDRFQSELDTIVAPTVILCSAEQQLRRIQKRDRISKEQAQARINSQALIQQVSTALASNPYHPYFLGEIIFSNPAERQWLEQQIVIPLLFEAKMTDLVTEIWVVSLPLQQKIALADLVLDNSSTQE", "metadata": {"id": "A0A6P0MEI2", "cluster": 4178372, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should feature a GmrSD restriction endonuclease C-terminal domain that functions as a DNA nicking nuclease within modification-dependent restriction systems to defend against phage infection. Belonging to the HNH nuclease superfamily and containing a conserved HXXP motif, this domain targets and cleaves DNA carrying specific epigenetic marks, such as glucosylated hydroxymethylcytosine or phosphorothioate modifications. Furthermore, the protein has a GmrSD restriction endonucleases, N-terminal domain that functions as the nucleotide binding, recognition, and hydrolysis module within the GmrSD family of Type IV modification-dependent restriction enzymes. Found in proteins such as BrxU and SspE, this domain facilitates NTPase activity required to recognize and cleave DNA containing specific modifications, such as 5-methylcytosine or phosphorothioates, providing defense against bacteriophage infection. It is native to Acidovorax sp. 99.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 5711, 5675, 1007, 7587, 18697, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 2678, 12657, 1941, 16230, 2651, 6295, 17, 3100, 7587, 3771, 1942, 30178, 10249, 3316, 10503, 2909, 18, 10588, 1942, 1920, 9888, 1023, 16230, 13975, 1930, 3165, 43, 5305, 22721, 1039, 1034, 5219, 16, 2052, 3418, 4845, 1930, 23839, 2678, 8215, 2487, 8542, 13387, 16, 2427, 1966, 3351, 22756, 29078, 27932, 7506, 2014, 3421, 17809, 25120, 6920, 18, 3677, 16, 1920, 2213, 2258, 43, 5711, 5675, 1007, 7587, 18697, 1036, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 5489, 2743, 16, 5708, 16, 1930, 9128, 9059, 2651, 1920, 5711, 5675, 1007, 3416, 1927, 2601, 4370, 6295, 17, 3100, 7587, 5038, 18, 2435, 1922, 2697, 2427, 1966, 2387, 1039, 1032, 1930, 19715, 1021, 16, 2052, 3418, 11374, 29676, 2051, 2455, 3414, 1942, 9967, 1930, 21252, 2678, 3165, 2487, 6920, 16, 2427, 1966, 25, 17, 4963, 27932, 7506, 2014, 3421, 17809, 25120, 1036, 16, 5453, 9720, 3316, 24613, 2909, 18, 2176, 1977, 6196, 1942, 2687, 2579, 18897, 2056, 18, 4922, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MQANPRSISELFNSQLRYVVPMFQRLDVAEKAALRIAKKETSPHYLGALIIEGVKPTSPREVLARQLDWKSIDKPLTRYLENADPDVMDRTSGSKAEVAKRHPLVFIGRKRKPEPRTTVLTAASDAETVAFNLLQAVQEDFSVVNSQGRPLSQSDLLRSLIFMRAEKEKQNRDQIAGRSYSRLDLGLRYFLIAKTGQLIDARRVNEEYVRDELADFVKHGDVYARYESSPTSTLPSTDLRRLEAGLDDQQLSKCLAMVESFIARRVFLNDENRTKLLSGGGGTRRWPTDQEVVEHAISKPVYNVLRNKKTEKMEIEPNLQIEHVLPQTWWTHWSLQGKAYLEFKYFEESIRQRNSAIHMLGNLSLVNRHLNPRYFSNCKEWDEQAISVRSKILGEAICSIWPRYVWQQSPQWETLWEKRFLVIDGQQRLTTLQLLLCAFRDPEEEVFKLWPTTLNREIYKSVLSNLVEAYLYFHNQISSWIDEITLSDGDDSQEIFYSLFDEYWSKFETPFWSLEVKRRQWISSKPPRYASIFADFDVSTALPLVMFLEEYNKFFVEIVGNLLGKRGDDVAPALRSTSALRLILERLELSQIPELIGRYPYYATDEKAGSNQAFTIKLDEYRNSILRLN", "metadata": {"id": "A0A2U1DNQ9", "cluster": 4294031, "interpro_all": ["IPR011089", "IPR004919"], "interpro_used": ["IPR011089", "IPR004919"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein should feature a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Furthermore, the protein possesses a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein is a member of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is present in Verrucomicrobiota bacterium and carries UniProt keyword assignments Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3677, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 2481, 1922, 3566, 3176, 13055, 1935, 15129, 3940, 3857, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MKILSAAKINLTLEILGRRPDGFHEVATWMLPIGLYDSVEIELASQSSFYPNLPELKGDRSNLIIQAAQVFNQAASLDTQYAIHLEKKIPVGAGLGGGSSNAAATLRLLNDLHGCPFDTRRLEELAAILGSDVAFFIGGRSAWCTGRGEQIEPRAFPDALWVSLFKPRFAVSTAGAYSAYTRLAAGCKRGQEIETAWGTFRNDLEPAVFPKYLFLRLVKDWLNQQPESLFALMSGSGATIFAIVRSQSEGETLQGRFRDEFGEQTWSTVCEMNVKNRSGRFGENENDDADEDVER", "metadata": {"id": "A0A950FZ93", "cluster": 6409792, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR006204", "IPR004424"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nIt is part of the dCTP deaminase family, which catalyzes the deamination of dCTP to form dUTP, a critical intermediate in nucleotide metabolism that serves as a precursor for thymidine synthesis. While typically monofunctional, some members of this family function as bifunctional enzymes that also possess dUTP diphosphatase activity to further process dUTP into dUMP. Furthermore, the protein falls within the dUTPase-like superfamily, which represents a distorted barrel domain found in deoxyuridine triphosphate nucleotidohydrolases and CTP deaminases. Also, the protein should have a Trimeric dUTPase domain that catalyzes the hydrolysis of dUTP into dUMP and pyrophosphate, essential for preventing dUTP incorporation into DNA and providing precursors for dTTP synthesis. This domain folds into an eight-stranded jelly-roll beta-barrel and assembles into a homotrimer with active sites located at the subunit interfaces. It is found in Bacteroidota bacterium and carries UniProt keyword assignments Membrane, Transmembrane, and Transmembrane helix.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 2176, 1977, 3131, 1927, 1920, 22936, 1034, 27955, 3416, 16, 2154, 17097, 1920, 30097, 8547, 1943, 1927, 22936, 1034, 1942, 2386, 28024, 16, 43, 4140, 6129, 1922, 5489, 4714, 1988, 10634, 1966, 43, 7897, 1958, 16253, 4271, 18, 2679, 5745, 8914, 15802, 16, 2673, 4678, 1927, 2052, 3416, 2347, 1966, 29491, 5038, 1988, 2222, 7150, 28024, 11791, 2609, 7234, 2455, 1942, 2520, 2585, 28024, 2460, 17751, 1034, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 28024, 2051, 17, 3189, 13975, 16, 2154, 4972, 43, 22797, 19560, 3418, 2435, 1922, 16333, 23864, 17978, 2797, 4090, 8601, 21524, 1036, 1930, 25639, 27955, 1036, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 29177, 28024, 2051, 3418, 1988, 17097, 1920, 9128, 1927, 28024, 2460, 17751, 1034, 1930, 24937, 16, 4415, 1958, 8444, 28024, 8629, 2460, 2678, 1930, 5453, 10416, 1958, 11504, 1034, 4271, 18, 2052, 3418, 16231, 2460, 1925, 5066, 17, 10338, 8988, 11560, 1012, 17, 12970, 4666, 17, 19560, 1930, 17421, 1036, 2460, 43, 16350, 1997, 5770, 1956, 3500, 3402, 4810, 2019, 1920, 5903, 14857, 18, 2176, 1977, 2435, 1922, 24323, 7336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MSFLNSDEIEKNLDNLFTKDFDKNLIECGCYELRLGNDPQIIIPSGQFALLTTKETLGLTSDFFGLISIKAGIKFKGLVNISDIVLDKDQRVFPIWFGKFTTPETKPYNNSHNNFDQNKITSKDIMDVSGKIPSPASLSKKLKLCIVFWNTTLNNLNILRNDVKEEKQMLLEIKDSVKAERQKFKIHFDSLKNNSKYYISSDGKGSKKISDQNGFHVDPGFKGILKFSVYNAGARNYTNIALGAVSLLTLLSGIVVT", "metadata": {"id": "A0A9E0UPI6", "cluster": 6808034, "interpro_all": ["IPR011962", "IPR036157", "IPR033704"], "interpro_used": ["IPR011962", "IPR036157", "IPR033704"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein carries a CAAX prenyl protease 2/Lysostaphin resistance protein A-like domain that functions as an integral membrane endoprotease, specifically a type II CAAX prenyl protease localized to the endoplasmic reticulum. It mediates the cleavage of the carboxyl-terminal three amino acids from farnesylated and geranylgeranylated CaaX proteins, including Ras family GTPases and nuclear lamins. This all-\u03b1 domain belongs to the glutamate intramembrane protease (IMP) family and utilizes conserved glutamate and histidine residues for catalysis. Additionally, the protein features a EF-hand domain that functions as a calcium-binding motif characterized by a twelve-residue loop flanked by two alpha-helices. Upon coordinating calcium ions, it undergoes a conformational change that triggers the activation or inactivation of target proteins, often occurring in pairs or higher copy numbers. Additionally, the protein contains a EF-Hand 1 calcium binding site that coordinates calcium ions in a pentagonal bipyramidal configuration using a conserved twelve-residue loop. This binding event triggers a conformational shift that activates or inactivates the target protein. It has been detected in Chrysotila carterae (Marine alga) (Syracosphaera carterae) and has UniProt annotations Signal.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 20951, 1039, 9972, 2199, 7154, 22, 19, 3629, 2259, 2575, 1921, 3554, 2213, 43, 17, 3189, 3418, 1988, 4088, 1966, 1925, 12328, 3260, 16239, 9218, 18013, 1021, 16, 4475, 43, 2601, 2890, 20951, 1039, 9972, 2199, 7154, 6579, 1942, 1920, 13355, 12279, 18, 2176, 10412, 1920, 6404, 1927, 1920, 9943, 17, 4262, 2559, 3835, 4576, 2037, 24281, 4336, 1930, 9559, 12804, 4938, 12804, 1981, 20951, 1039, 2697, 16, 2710, 6520, 3416, 18390, 1930, 4254, 7962, 1036, 18, 2052, 2136, 17, 160, 3418, 14440, 1942, 1920, 7627, 9857, 8591, 7154, 12, 2754, 13, 3416, 1930, 18127, 5305, 7627, 1930, 13873, 4248, 1958, 15408, 18, 4950, 16, 1920, 2213, 4075, 43, 8485, 17, 3897, 3418, 1988, 4088, 1966, 43, 5016, 17, 2743, 5219, 4378, 2007, 43, 12367, 17, 6181, 5881, 20185, 2007, 2288, 4595, 17, 12789, 18, 4073, 19355, 5016, 6982, 16, 2176, 14928, 43, 8523, 3185, 1988, 11847, 1920, 2936, 2014, 8005, 1927, 2758, 2697, 16, 3868, 6966, 1922, 5803, 2014, 2580, 6983, 4630, 18, 4950, 16, 1920, 2213, 5461, 43, 8485, 17, 3897, 21, 5016, 2743, 3200, 1988, 10675, 5016, 6982, 1922, 43, 9412, 13481, 8446, 3553, 25238, 1923, 9674, 2193, 43, 5305, 12367, 17, 6181, 5881, 18, 2052, 2743, 4817, 11847, 43, 8523, 5950, 1988, 9094, 2014, 22331, 1036, 1920, 2758, 2213, 18, 2176, 2258, 2252, 3330, 1922, 21367, 13323, 5148, 17302, 20938, 12, 10789, 4326, 1019, 13, 12, 11458, 20682, 3508, 20051, 5524, 17302, 20938, 13, 1930, 2258, 20709, 15010, 2733, 18, 3], "output": "MVALAVSLASAAAAFQAHSVWQPQQTQQVRFASGLQPHVRPRVASNLISAKVEEKERTATFPDLSSLGDAITGKDNGKKNNKPSSPPSAPFLNKRLFAQLVLSQLTIGGFANIQSNGATWATLVQNSHFGSPAALALGVAAALPLIGLGRVIEESDSEDLASINLSTDLIAYSLFGKNTQPAFALAASAFMCTLTGVVEETVFRGQVMPNLFNWLAANNWVDSAAQGLAFAGVLSSVLFAAGHLNFGGGLRNLVSAEARTLFTLQFFNGLTFATLYGLTGDLTAPIIAHALYDLSALYGTHLRVTKQLSYAEEQAGGRPKTPMDAARRTFYLMDRNKDGFVSPRELRIGLYFFGIIPPRSFSDKLFGNVDIDGDGRISEREFLRQLKSNVEDGKSPEEAAGNAMKRSVLGVQM", "metadata": {"id": "A0A7S4B6P6", "cluster": 6981428, "interpro_all": ["IPR011992", "IPR018247", "IPR002048", "IPR003675"], "interpro_used": ["IPR003675", "IPR002048", "IPR018247"], "interpro_unused": ["IPR011992"]}, "task_type": "autoregressive"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein should feature a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. Also, the protein should have a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Moreover, the protein should have a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It is found in Cinara cedri and is linked to UniProt keywords Transmembrane helix, Magnesium, and cAMP biosynthesis.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 3066, 5961, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 1977, 2435, 1922, 10510, 9041, 19424, 3027, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 7864, 16, 13148, 16, 1930, 6225, 8132, 18, 3], "output": "MHSETSSLHTLTTKQTKNKELWLRAIHRIHSQKRRNQQVDLPKVNSVSNITTDTFDDTDHNTNNTSQIPVEYTEPVFKKGRVYKGIYCPTLTNSFREPSLELSYQRYSHRQRQKSLIIVNFVDLTLKAVLAGIWLFPTLNENHNHSHRALWTCLTMFANLTVCLLGWWKCFANNYLQWAAVFTWCFINVQGFVWESYGQGSREYLVWYVLFIVFVTYAMLPLPLKWCILAGCSTALLHILITSYTKSSKEKNALCVARQLTAISLLYAAVNFAGMYTKYLTDRSQRKAFLETHRSTEARFKTQKENEQQEKLLLSVLPDFVAREIIKDIASETDKGPFMPNQFHRIYIHRYENVSILFADIKGFTEWASRTCAQELVRVLNDLFANFDKLAAENHCLRIKLLGDCYYCVSGLPQTRQDHAVCCVEMGLHMINAIKDVRNNLNVDLNMRIGIHSGSVLCGVLGLRKWQFDVWSYDVTLANHLESGGIPGRVHISKATLDCLEEAYDTEPGHGEDRDAYLRDHSIETFLIKEQEPCRGHRKLQKINSTRPRLWSDEKLSFNSNAQKLISPKIEDYIDDNKCNEWTPEIPFENLNTSDQELEADDNECVTPITIEGDVEHAEDIMDHCIEVESNERMRNENIDRWTLRFKQPEIETKFCQLREDMFKSNMACCFIIWLFVVCCQTIMLPRCMKLLVALTFTTVVLCAALTLVMAEEFMHLPSALQRMSSILVQNRFRRTMFICAVVGLICFSSTLSLIFTPNEHLIRKKSSLTTFVNDGDVGEETDRKARLRRDVTEEESSNDCVHPEYLVFTWVLCLIALATTLKLYFLVKTFLASLMVAVYTGLTSLAYPQVFSQNDGTDHRAMPLSSQMLLLLIVFLVLVAYHARLVEVTSRLDFLWKREAERELTEMRETRTNNRQLLRNILPDHVAHHFLSSARRHTTDELYSQSIDKVGVMFASIPNFTEFYSEDINKGMECIRLLNEIIADFDELLSETKFSSIEKIKTVGASYMAASGLNPSVKDGEDEYGHLCALVDFALAMKQCLQDVNVHSFNNFQLRVGISCGALVGGVIGARKPVYDIWGNTVNEASRMDSTGTMGRIQVPESTAKILMDRGYETEFRGSIAVKGKGEMNTHFVVGKKGAVANNLSRQSSQISSLATVVYGMVQARRRQNTVKKRHFNRECASTNNTNIFCRVFLASISLKGAETLNGWLYRVLEMWLECCQGESRQQKSHV", "metadata": {"id": "A0A5E4N4Z7", "cluster": 10085573, "interpro_all": ["IPR001054", "IPR018297", "IPR032628", "IPR030672", "IPR009398", "IPR029787"], "interpro_used": ["IPR009398", "IPR018297", "IPR001054"], "interpro_unused": ["IPR032628", "IPR030672", "IPR029787"]}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein is grouped in the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. It is identified in Haptolina ericina.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2176, 1977, 2899, 1922, 29683, 8261, 1019, 2668, 6915, 1019, 18, 3], "output": "AQNGGTDGAQNGGTDAGDGMASSGTAPVELSGELDLATEGWRLVHSSEWGRARDLLAPLAASPNLLARCALAACCLHLAEKRMAAKDTAGGKALAIEAVEHAKAAASLDPSSSLALVWLGQTIQVRAKATEGGMGQGKVCAEMVGCWERAVLLDPTDPHPLHLLGSFASQVSSMNGASYAILRRISPGLKKYTSDDALNYLQKSEALQPNPPAQYSVTNCSLIGQILLQRKNKAEARAWFLKATVDSGVPQSCKLDETAKGARATAQKKLASC", "metadata": {"id": "A0A7S3F1E9", "cluster": 10429428, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein is a member of the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. Also, the protein is assigned to the Fe-S cluster assembly domain superfamily, which facilitates the mobilization, assembly, and transfer of iron-sulfur clusters to recipient apoproteins. Members of this superfamily function within the ISC, SUF, and NIF pathways, often acting as scaffold proteins that transiently bind Fe and S atoms to synthesize [2Fe-2S] or [4Fe-4S] cofactors. These domains are critical for maturing proteins involved in electron transfer, redox catalysis, and nitrogen fixation across bacteria and eukaryotes. Additionally, the protein possesses a MIP18 family-like domain that functions in the maturation and transfer of iron-sulfur (Fe-S) clusters. This domain is central to the cytosolic iron-sulfur protein assembly (CIA) machinery and bacterial SufT-like proteins, often serving as an Fe-S cluster carrier. It is present in Bacteroides faecis and is classified with UniProt keywords ATP-binding, Hydrolase, and Metal-binding.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2650, 17, 61, 4377, 5957, 3418, 13975, 16, 2154, 11374, 1920, 14586, 16, 5957, 16, 1930, 3856, 1927, 5680, 17, 12585, 5859, 1942, 10664, 11466, 22163, 1036, 18, 4678, 1927, 2052, 13975, 2347, 2651, 1920, 23924, 16, 2020, 1038, 16, 1930, 17719, 3873, 16, 3868, 8290, 1966, 7281, 2697, 1988, 12145, 4566, 2650, 1930, 61, 9030, 1942, 15541, 37, 13775, 1021, 17, 20759, 39, 2014, 37, 15338, 1021, 17, 26814, 39, 21362, 18, 2144, 4682, 2032, 4140, 1958, 2888, 4729, 2697, 3286, 1922, 4995, 3856, 16, 9366, 15408, 16, 1930, 6634, 7938, 3436, 4802, 1930, 15021, 18, 4950, 16, 1920, 2213, 14465, 43, 15070, 3928, 3416, 17, 3189, 3418, 1988, 4088, 1922, 1920, 7655, 1930, 3856, 1927, 5680, 17, 12585, 12, 2650, 17, 61, 13, 5859, 18, 2052, 3418, 1977, 4101, 1942, 1920, 9410, 5680, 17, 12585, 2213, 5957, 12, 24748, 13, 10853, 1930, 4543, 2020, 2794, 17, 3189, 2697, 16, 3868, 13915, 1966, 1925, 2650, 17, 61, 4377, 9685, 18, 2176, 1977, 2481, 1922, 27978, 5685, 1940, 1937, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 20748, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MTLYPKLILDALATVRYPGTGKNLVEAEMVADNLRIDGMTVSTAIHTYVSPDVQVTITTESKQAARPEVGKLLPQVKNIIGVSANLAVALAKLGYKVGLLDADIFGPSMPKMFQVEDARPYAEKIDGRDLLWRGGMASNALKQLIGDADWGDLDYFLIDLPPGTSDIHLTVVQTLAMTGAINDKVNVPILGLVENMAWFTPAELPENKYYIFGKEGAKKLAEEMNVPLLGEDTVTGRAFLSLAASVVRQVDRRNIEMAPTKIVEMHKFSLIFEKPTDPFMKSMLKAAEISSGKGGVGKSTIIPVEKYGVKLLSIGFFVDPDQATVVSTPQAVALADARKGINMFTQIPIVQSICEGGDNGTPVALD", "metadata": {"id": "A0A3E5GMC3", "cluster": 15998094, "interpro_all": ["IPR034904", "IPR002744", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR033756", "IPR034904", "IPR002744"], "interpro_unused": ["IPR044304", "IPR019591", "IPR027417"]}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein should include a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Moreover, the protein has a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein is included in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It originates from Holdemanella biformis and features UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3950, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 22970, 2037, 9038, 17119, 5870, 10740, 2076, 1937, 1930, 4075, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MQVQARAKINLALDVVERMDNGYHSLDMIMAPISICEGMKLPESNTVSKMIQVLKDTYHLDSSFKVSIKKHIPAQAGKMEGIEETEENLYEITKQVGADVPFCIHDKWARVKGIGVVVVKPDFGISTANAFSKWKESRPFHPDVDLVESSIREENMMDMEDAGLVRILMSGSGSSMLGFSVDEDVILNAYEQLKEKYDFVKIIHVGGYDEIEIEKSDCDMVELGGGSADAAAVCKAILEKITPIESDWKFDDLLYQTMANALEPIAFEIEPELNQVK", "metadata": {"id": "A0A413CX89", "cluster": 17452745, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR006204", "IPR004424"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "infilling"} {"instruction": "\"The protein has a Adenylate cyclase, N-terminal domain that comprises the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase. It is found in Probosciger aterrimus (Palm cockatoo).\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 2258, 43, 23052, 16526, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 56, 17, 4262, 5329, 3031, 1930, 1920, 2561, 9117, 25, 17, 26, 4675, 3031, 1927, 23052, 16526, 18, 2176, 1977, 2435, 1922, 2680, 17413, 4938, 30280, 18858, 12579, 12, 15516, 11379, 8286, 1037, 13, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "SNVLIFSCTNIVGQETRECIQARLHSQRENAKQEDMMFHKIYIQKHDNVCTHYPAEVSQRQAFQQQERLLLSVLPRHVAMEMKADIN", "metadata": {"id": "A0A7K5FHG6", "cluster": 17784245, "interpro_all": ["IPR032628"], "interpro_used": ["IPR032628"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein carries a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. Moreover, the protein belongs to the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. Additionally, the protein carries a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. It has been detected in Burkholderia singularis and carries UniProt keyword assignments Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 16252, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 4950, 16, 1920, 2213, 16252, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 2176, 2258, 2252, 3330, 1922, 18359, 18681, 2126, 21233, 1937, 1930, 16252, 20709, 11121, 2538, 18306, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 3], "output": "MHTDSSFTFVLFGGTGDLSMRKIVAVARGAADRDAYLGWVEEHVKPHAAKAARIVYVKLDASRAQDYALLRDAVDKLAAVGLNEGARIVLEKPLGYDLRSSNAINEPVQNLLALRFGNALFEPLWRREWVESFYDNTGALRDMVQNHLLQLLSIVAMEPPHSMDSDSDQRDIGKVAVRGQYHAGVIKGAQVPAYATEPGVEIENWRWAGVPFFLRTGKRLADRVAEIVVNFLVIRLQPNESIRLYCLAKQPGEGMNLAAYQRLLLDVINGRLALFVRRDEQAGTWGPAAASAMLAQHGTCWLEEENLPALFEAHRANMLAEAGRIGSAFDEAAWRSFLESGIRVFYLATGPSLFVPICNALDAVGEIFAEEQIYRIDHYLGKIQITIAEELGVEARGDVRDEKLRVLRALKPVKPDSQTETFVALKVRPVPHSALGPTALRAGANRSVHLDLAFDQFFKEGQMEEAAWRWVEPILNEWARSMKPPKPYA", "metadata": {"id": "A0A103DWY0", "cluster": 18260621, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR022674", "IPR036291", "IPR019796"], "interpro_unused": ["IPR001282", "IPR022675"]}, "task_type": "infilling"} {"instruction": "The protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. In addition, the protein is assigned to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is expressed in Oceanobacillus limi and contains UniProt keyword associations ATP-binding, Cytoplasm, and Transferase. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 3198, 1922, 13563, 14357, 8898, 2784, 1033, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MALIIGLTGSIASGKSTVSHMFHDLNIPVVDADKISREVVNRGEKAYQEIIDVFGEGILTKSKIIDRKKLGAIIFKDETKRNQLNGIVHPAVRERMLEKRDTYVEAGEKCIVLDIPLLFESKLTHFVDKTLVVFVDEDVQLQRLMERDGYTEEEADQRIQSQIPVKEKAKLADAVINNNGTINETNQQLKQILHDWQVL", "metadata": {"id": "A0A1I0EGQ4", "cluster": 19952464, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein should contain a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. In addition, the protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is produced by Pseudomonadota bacterium and is annotated with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 4152, 2007, 11520, 3947, 12595, 3857, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MKGRFVTFEGGEGTGKSTQLRLLADYLRTKGINAVATKEPGGTPTGQELRRILVTGDKDKFDATAEALLYFADRHIHMTQKVWPEMEQGAWVLSDRFADSTVAYQYYGYDKRVSKENLDCLYNIAVGDFKPDLTVILDIDPEIGLARSFKKADGMNVKELRFEGRELAFHQRLRRGFLEIAEQEPQRCIVLDADKSIEALHEEIVRVITERFGL", "metadata": {"id": "A0A942ZGC5", "cluster": 20692790, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein is associated with the Winged helix-like DNA-binding domain superfamily, which encompasses diverse DNA-binding proteins including transcriptional regulators, helicases, and endonucleases that utilize a winged helix-turn-helix motif for sequence-specific recognition. This domain engages the DNA major groove via a recognition helix while loop structures known as wings contact the minor groove or backbone, often serving as a scaffold for protein-protein interactions. Furthermore, the protein should include a Transcription regulator LuxR, C-terminal domain that functions as a DNA-binding helix-turn-helix (HTH) motif to regulate transcription, primarily acting as an activator within the LuxR/FixJ family. This module forms a four-helical bundle that binds the DNA major groove and mediates dimerization, typically in response to N-terminal domain signals such as phosphorylation or quorum-sensing autoinducer binding. Also, it is part of the Signal transduction response regulator C-terminal effector superfamily, which functions as the DNA-binding output domain in bacterial two-component systems to regulate gene expression. Structurally defined by a three-helical bundle, this domain binds DNA or RNA polymerase in response to environmental stimuli\u2014such as quorum signals or osmotic stress\u2014following the phosphorylation of the associated N-terminal receiver domain. It has been detected in Streptomyces sp. NBC_00304. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 2458, 1956, 1920, 12920, 1919, 7864, 17, 3189, 2678, 17, 2743, 3418, 13975, 16, 2154, 21569, 6445, 2678, 17, 2743, 2697, 2710, 5224, 9098, 16, 29919, 16, 1930, 18697, 1036, 1988, 12561, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 1958, 3244, 17, 2487, 5708, 18, 2052, 3418, 11580, 1036, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 2679, 5881, 4061, 3171, 1966, 28297, 5217, 1920, 5857, 15920, 2014, 10787, 16, 3868, 13915, 1966, 43, 7281, 1958, 2213, 17, 2213, 3719, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 3213, 7888, 17851, 1005, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 5741, 3213, 16, 5985, 8290, 1966, 1925, 9518, 2651, 1920, 17851, 1005, 19, 4011, 1013, 3416, 18, 2052, 9059, 4952, 43, 3006, 17, 11514, 14142, 1988, 6876, 1920, 2678, 3044, 15920, 1930, 10412, 13640, 16, 5745, 1922, 2644, 1942, 56, 17, 4262, 3418, 4771, 2427, 1966, 4050, 2014, 28481, 17, 9306, 27485, 4600, 1005, 2743, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 2733, 8201, 2644, 7888, 45, 17, 4262, 7917, 13975, 16, 2154, 4088, 1966, 1920, 2678, 17, 2743, 6647, 3418, 1922, 4543, 2288, 17, 4594, 3771, 1942, 5741, 2359, 2294, 18, 12171, 3608, 2007, 43, 2559, 17, 11514, 14142, 16, 2052, 3418, 6876, 2678, 2014, 3146, 6479, 1922, 2644, 1942, 4813, 5458, 230, 2427, 1966, 28481, 4771, 2014, 13951, 3071, 230, 2894, 1920, 4050, 1927, 1920, 2458, 56, 17, 4262, 12608, 3418, 18, 2176, 2258, 2252, 3330, 1922, 22874, 2056, 18, 8789, 1030, 41, 10438, 14743, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MSSDSGTPPRPAVEPSPAPPGSPAAAPSDSVRSSLARLQEDLRRADDSLARLLGQWQPHADGEPEQPIEYWQGHEAQARRLYELEYSARTSLLVFQSGANTVAPVPSTLVTPTPTPPPADGPEPALRKDGNPTAAYRVVVDRDFLSEPAALHALDERLAAGHQVRVVDQPLIKLVVADGETAMVQVEGGRSMVLGPPVVLLAVELFEAVWRRSRPYLREDGDLSPKDRRLLQLMLSGLTDAATAHQLGTSPRTVQRRLRALMDVAAVSSRVQLGWYAMRNNWV", "metadata": {"id": "A0AAU4PJU4", "cluster": 22189364, "interpro_all": ["IPR016032", "IPR000792", "IPR036388"], "interpro_used": ["IPR036388", "IPR000792", "IPR016032"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein falls within the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Furthermore, the protein should feature a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. Additionally, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is identified in Gammaproteobacteria bacterium and is classified with UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 12182, 2651, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2899, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSIGKLISFEGIEGVGKSTTISSIESLRNILLNNKSNISPEAELLLLFSMRSQHIKEIIKPKLDQGNWVLCDRFLKKIKLLIDNFTDNVIPDITLFFDLPYNLAKQRFPKNKKKDRFENLEDSFFENKSRIKRIDSDCSKKEVCDQIKFILENKFKDFLLRKYLEDNGITVYCTREPGGTKYGIDASIAYQGFGKKIDEDVYKGYIYQLN", "metadata": {"id": "A0A2E2WUN2", "cluster": 22533482, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR018094", "IPR039430", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein contains a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. Moreover, it is part of the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. Moreover, the protein should include a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. It is derived from Candidatus Cloacimonas sp. SDB and features UniProt keywords Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 2176, 1977, 3595, 2037, 14550, 1031, 1957, 12596, 28278, 3947, 1934, 2056, 18, 4035, 1014, 1930, 4075, 20709, 11569, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 3], "output": "MIVIFGASGDLTRKKLIPALYNLFKKGTLAENIGSNEIDPEFISYLTYYPTDFRKFYLAVGPDLFQPIIDIIKQLGISRKKVVFEKPFGFDLGEMVQNILVFRFANSIFEQIWNRDFIEKVEITISENAGALRDMMQNHLLQLLALTAMNPPISMQADDIRDEYESYRQEIEKPDSVTETYAALTLNIDEAEINLIIKDVTCRLFSRERKIKNLPNTITLRIQGMDLQQVKMDFCHKCEFGPNTPEAYESLLYKIIDPIRQQKKQLSFYQEGSEVFTDSIICLARKKFSTEDFIESLQLPDINLLQTVLSKEEETISATELNDCISKTFNEKEIYRIDHYLGKEAAGIGRRAEYYVVKVLRKVKTLNFKVAQAKWQGVPFELKTGKKLAQRYPNEGIMVKFNAKIPGAEIMEGDQTLFTRWDSVEASW", "metadata": {"id": "A0A0Q0VL65", "cluster": 24305061, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR019796", "IPR036291", "IPR022674"], "interpro_unused": ["IPR001282", "IPR022675"]}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: It is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein is associated with the DNA Replication and Repair Clamp Loader Complex family, which functions as a key component of DNA replication and repair machinery by utilizing ATPase activity to load sliding clamps, such as PCNA, onto DNA. These proteins ensure the processivity of DNA polymerases delta and epsilon during template elongation and contribute to chromatin assembly and sister chromatid cohesion. Additionally, specific members regulate developmental processes such as plant trichome branching. It is identified in Polaromonas vacuolata and carries UniProt keyword assignments Nucleotidyltransferase and Transferase.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 2678, 5158, 1930, 5059, 10209, 4019, 1915, 2796, 3416, 16, 2154, 4088, 1966, 43, 3834, 4594, 1927, 2678, 5158, 1930, 5059, 10853, 2007, 10232, 9444, 2455, 1942, 4019, 17324, 10209, 1036, 16, 2427, 1966, 14381, 16, 6131, 2678, 18, 2144, 2697, 6486, 1920, 2585, 10794, 1927, 2678, 20910, 9649, 1930, 22206, 2409, 7662, 9971, 1930, 4672, 1942, 6338, 5957, 1930, 14611, 28829, 21275, 18, 4950, 16, 2487, 4678, 5741, 5878, 4028, 2427, 1966, 4496, 10477, 2225, 13898, 18, 2176, 1977, 2899, 1922, 5676, 10480, 26684, 5499, 1930, 16252, 20709, 11121, 2538, 18306, 2797, 4090, 2199, 9961, 1930, 13763, 18, 3], "output": "MNQRTLAPWLQTQLTSLLSQRGHAWLLSGPSGLGQFDLALALARAHLCEKATPQGACGVCASCHAVDVHTHADLCMLMPEALSLELGWPLDEKTQSDLDSKKRKPSKEIKVDAAREAVSFTQYTRSRGATKVVLVFPSERMNGITANTLLKTLEEPPGAVQFILATEAAHQLLPTIRSRCQTHTMLWPDTAQGLAWLAEISLAQRGDDGPANKKAGKLPTQDDLQTLLAAAGGRPADALAWVLSGQAEQIAQGWQALPKAMAKGDVSALSDLLPSQAVDALQKLCHDVWAVRSGSEPRFFRRQDLPPSDKTGLTSHYALSAWARELSTTARTVEHPYNAGLMLEYLASRAKLALAAS", "metadata": {"id": "A0A6H2H9D0", "cluster": 25249585, "interpro_all": ["IPR050238", "IPR027417"], "interpro_used": ["IPR027417", "IPR050238"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the polypeptide chain function: The protein carries a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. Additionally, the protein should have a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. Furthermore, the protein is assigned to the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. It occurs in Sphingobium subterraneum and features UniProt keywords Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 16252, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 2176, 5110, 1922, 13502, 23156, 13329, 5385, 2516, 1989, 1930, 4075, 20709, 11569, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MALVGVSHHDSDDEQLRQALDEFVKDDANWPWLRSRIRYLKGDFADSTMYQALGSQLTGNAIFYLATAPAFFGTVVNQLGDAGLLNETDGFRRVVIEKPFGTDLASAQALNRQILSRASESQIYRIDHFLGKETVQNIMVTRFGNTMIEAVWNNRYVDHVQITAAEAVTVGTRGRFYDATGALRDMVPNHLFQLLALIAMEPPISFDADAIRTEKEKVIAAIRPIDPTEAIRGRYCSGAIAGKAVSAYLDEPDVDPASRTETFAALKLHVETWRWSGVPFYLRTGKALATRDTEIVVQFRDVPLALFQETVVDRLPPNRLVVQIQPDEGISLEFVVKRPGLVVNTAPVAMDFRYRDHFDVGHQTGYETLLYDVQSGDQTLFQRAAQIEGGWRAVQPLLDLWAQGTPEEYAAGSAGPESADALMHRSHRRWHHLG", "metadata": {"id": "A0A841J480", "cluster": 25684227, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR019796", "IPR022674", "IPR036291"], "interpro_unused": ["IPR001282", "IPR022675"]}, "task_type": "autoregressive"} {"instruction": "I want a protein that has the function: The protein features a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein is included in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein incorporates a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is produced by Peptoclostridium phage phiCDIF1296T and corresponds to UniProt keyword Transferase. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 4075, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 19683, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 4152, 2007, 23045, 5406, 17414, 9734, 10503, 17971, 9547, 1974, 18253, 1016, 1031, 1930, 8852, 1942, 20709, 11121, 2538, 13763, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MDFIRLKSRAKINLSIDVLGKRQDGYHFVEMIMQTIDLYDIVKIKELDEDEIKVKSTSLDIPLDEDNIVYKAAKILKNKFYIKKGVEIFIEKNIPVAAGMAGGSSNAAAVLVGLNHLWELRLSEDELKEIGLNLGADVPFCISGRPALAQGIGEKLTNIKGLPCDTNILICKPDLFVSTKEVYQGLDLNNIKKRPNNKYLIECLKSEDIKAVSESMVNILENVTIGKHKEISDIKQVMMKNNALGSMMSGSGPTVFGLFKNKEDALIGKKELLKKYKQVYVVNSSQKGVEICGEFN", "metadata": {"id": "A0A125YE57", "cluster": 27609203, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR004424", "IPR013750"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that will have the following function: The protein carries a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Moreover, the protein includes a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein is classified under the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is expressed in Elusimicrobiota bacterium and exhibits UniProt keyword tags Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3950, 16, 1920, 2213, 5921, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 3198, 1922, 2349, 24327, 4913, 15129, 3940, 3857, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MKGLSVLSRAKVNLFLEVTGRRPDGYHDLLTLFARINLADSLTLRPSAKPGIRLSVVNKSNFVPIPQEKNLAWRAADAFYRGFRLEPALDIRLVKRIPAGAGLGGGSSNAAAVLEGLSRLHRRRSPADRRRLARLAAGLGSDVPFFLAGSVFCEGRGRGEKLKALALKPGRHTLVLYFPGFQVPTPGVYAALERPGPAAVSVSRRDYRRLIKAMFSGAGPAAWAPLMRNRLEDPVLPARPAIARARARLSAAGAAGAMMSGSGSTVFAAAGSRAEAARLARALKPCKGMVFLAEFA", "metadata": {"id": "A0A7V8AGK5", "cluster": 2088841, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR006204", "IPR004424"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein belongs to the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. Moreover, the protein is assigned to the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It has been detected in Olavius sp. associated proteobacterium Delta 1 and is linked to UniProt keywords Metal-binding, Cell membrane, and ATP-binding.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 2258, 2252, 3330, 1922, 2865, 9188, 1957, 2056, 18, 2458, 2174, 12022, 9649, 21, 1930, 1977, 4624, 1942, 20709, 11569, 6048, 17, 2743, 16, 2024, 3260, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MGKAKESVLRHIGKAFIWSATGIKAAWKNELAFRVEAIIIIILIPLGIWLGNSAAERALLIASCLLILIIELLNSAVEAVVDRIGTEQHELSGRAKDMGSAAAFFAMLTAGIVWALIAYERFWG", "metadata": {"id": "A0A6J4X9P0", "cluster": 3657116, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR033718", "IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein possesses a DnaT DNA-binding domain that cooperatively binds single-stranded DNA (ssDNA), a function essential for primosomal protein activity in DNA replication. This domain adopts a three-helix bundle structure stabilized by a specific N-terminal loop and forms a spiral filament assembly upon DNA binding. It is identified in Synechococcaceae cyanobacterium SM1_2_3.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 2678, 1031, 2678, 17, 2743, 3418, 1988, 13350, 1954, 6876, 2957, 17, 10338, 2678, 12, 15063, 13, 16, 43, 2347, 4415, 1958, 2610, 4969, 2213, 2455, 1922, 2678, 5158, 18, 2052, 3418, 24032, 43, 2559, 17, 7864, 14142, 3170, 12017, 2007, 43, 2487, 56, 17, 4262, 5881, 1930, 4952, 43, 17366, 10797, 5957, 4073, 2678, 2743, 18, 2176, 1977, 2899, 1922, 26734, 26941, 9914, 26898, 7972, 2341, 18842, 1989, 2426, 1009, 41, 22, 41, 23, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MDLDWVPNETAFNELQTSGIPVEFIAQSLHEFRAYQQQEQRRHDRSEARSRVSGLPQNQSGRQRRETVTERFAPKTRLQPTSPGTEGLMPARAIAALWARFSHAATWAKALANLTADDLARGLHACLDRAAWLSRGEKKPDWNPEFIRQTRHQFAYQNERYERFAAGLDTGNDAELYGNRWVSVYGEALSADGILQPV", "metadata": {"id": "A0A846SW22", "cluster": 4682100, "interpro_all": ["IPR040480"], "interpro_used": ["IPR040480"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein is categorized in the Sialidase superfamily, which hydrolyses non-reducing, terminal sialic acid linkages in substrates such as glycoproteins, glycolipids, and polysaccharides. These enzymes, also known as neuraminidases, share conserved \u03b2-sheet motifs and play diverse roles ranging from lysosomal catabolism in mammals to facilitating viral transport and release from host cells. It is native to Actinomadura soli and is annotated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 12952, 9200, 13975, 16, 2154, 21686, 1918, 2447, 17, 5526, 16, 4262, 20436, 2687, 19949, 1922, 6249, 2427, 1966, 16268, 16, 14193, 2049, 3753, 16, 1930, 18686, 18, 2144, 5038, 16, 2222, 3171, 1966, 29831, 1036, 16, 7948, 5305, 161, 17, 11130, 8277, 1930, 3918, 6445, 5456, 6485, 2037, 12097, 19480, 1922, 9902, 1942, 12440, 4324, 4860, 1930, 4012, 2037, 4423, 2094, 18, 2176, 1977, 6196, 1942, 4718, 2954, 10015, 5524, 2638, 1033, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTPTGKPDDDHDVERPDPGQPAQAPPPPQWLNEQPGSAAQLLPEYDGEEAEPESDAGSSEASEGESSGSGSGMNEAMHTVVLGGRSPAPGTGPSDEGTPGADAAQPPSPAPPVGQPPSTGVPPATSTDIPAPPPFPFAQEMPDATQVQAAAPPPFPYAQEMPDATRAEPFPSQQPSAPPQPTRGRPPASPSQSPPAHEPFPYAQQIPGAPAPAAHEPFPYAQEIPGTPPGQPAAEPFPWAQQIPGAAQPGQPGQDAVQPLAPPPAIEEPWRTQGRQARTRRSIKKPLLIGVAVLAVAGMAAAGVLVVPGLIEGDGEDEGGKGAKLAAALFPVSGAARTDGRDQKITDVAAVGSTVVAVGGETDALNARGIFLASSDGGRTFKSVTQQGTDGGAAPPGGIPDAVGGSSRGWVAIGSLPGLRGAVWTSENGLEWRRQPDAVGDAFGKGNRVRRIVATDTGYLAIGENSRKGDFTDSQPAVWLSGDGRRWEARVGDQIGVQVSNGKFALVEAAASGNVILLEGLVTPDSGKPGPYRVVWRSEDGGRTWSTSDVPVPKGSRGLMVGGGQAGFLAMREIQSSGRLYGQAFTSKDGKSWTKAGALRTSDYKRTGRVIGDGGGYAAVVVRGRDVMLSRSADGAAWKDAGTAEAKPGREFSGAALAGGQAIIGGREPGGGDMDPMLGVWDAAGTAVPVDLTKIPGVIRPDHSVRSAGATDGLAVAVGSARGDAAVWSSQDGGSWKPAQGLGAAFTRPGPQQLNDVAGGAAGWLAVGYDQAVPRRPLVVTSKDGATWEAADSATAFAGGKDGTPITYAAAAGNAGYVIVGTQGFSAAAWFSKDLKNWVPGAGADPRTLRGAKGAAHWMFDVTAGPSGYAAVGGVQDAKGNQPSVWSSSDGRRWTAQQLPLPGGVTAGHLTHVAARGNTLVTTGIAATAQGLNWLGYVSTDGGRSWRPLASPSGDAVVSVTALTATPKGFAATGTTGSAGATDVVSWTSADGSSWATATPGGTGLGGVGDQEITGLAAFKNTLLGVGRSVDGNGDQPVLWSRAS", "metadata": {"id": "A0A5C4J6U5", "cluster": 5087117, "interpro_all": ["IPR036278"], "interpro_used": ["IPR036278"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein is classified under the Rhodococcus equi virulence-associated protein family, which comprises plasmid-encoded virulence factors found in the pulmonary pathogen *Rhodococcus equi*. These proteins, particularly VapA, function to inhibit phagosome maturation, thereby promoting intracellular bacterial survival within the host. It has been characterized in Bacillus fungorum. Generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1988, 2258, 1920, 2894, 3879, 30, 1920, 2213, 1977, 5947, 2441, 1920, 11490, 8256, 3009, 1033, 9304, 17, 2458, 2213, 3416, 16, 2154, 12936, 5609, 17, 7905, 9304, 2790, 2435, 1922, 1920, 5352, 7055, 14, 11490, 8256, 3009, 1033, 14, 18, 2144, 2697, 16, 4443, 16697, 1019, 16, 2347, 1942, 2875, 8476, 4283, 7655, 16, 6113, 7356, 4776, 4543, 3298, 2651, 1920, 4423, 18, 2176, 2258, 2252, 4378, 1922, 14587, 29602, 17279, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MDEKPNVSQLEMDERVARDLKQLLNGTLKPEEIDRMITQAKTNTKYHAEFRALGAIFYTHYWVWTPDADSPYAKFNGDAGGINGIGQAGEGDIYTNDREALINNTTSFAYLGVAGVYFSIYFYDKHSNLLGHFQAGGIGTAGAGGGTGKWTRTPPELKD", "metadata": {"id": "A0A2G6QEJ9", "cluster": 6350283, "interpro_all": ["IPR008810", "IPR038625"], "interpro_used": ["IPR008810"], "interpro_unused": ["IPR038625"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein can be placed in the Winged helix-like DNA-binding domain superfamily, which encompasses diverse DNA-binding proteins including transcriptional regulators, helicases, and endonucleases that utilize a winged helix-turn-helix motif for sequence-specific recognition. This domain engages the DNA major groove via a recognition helix while loop structures known as wings contact the minor groove or backbone, often serving as a scaffold for protein-protein interactions. In addition, the protein should have a LysR, HTH, N-terminal domain that serves as the DNA-binding module of bacterial LysR-type transcriptional regulators (LTTRs), utilizing a helix-turn-helix fold to recognize specific promoter sequences. It typically functions within a homotetrameric complex to repress or activate genes involved in diverse metabolic and physiological processes, often in response to conformational changes triggered by small-molecule effectors. Furthermore, the protein has a LysR substrate-binding domain that constitutes the C-terminal effector-binding region of prokaryotic LysR-type transcriptional regulators (LTTRs), facilitating oligomerization and ligand sensing. Upon binding diverse effectors ranging from amino acids to reactive oxygen species, this domain undergoes conformational changes that modulate the regulator's interaction with DNA and RNA polymerase to control gene expression. It is expressed in Alkalibacter rhizosphaerae and is linked to UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 12920, 1919, 7864, 17, 3189, 2678, 17, 2743, 3418, 13975, 16, 2154, 21569, 6445, 2678, 17, 2743, 2697, 2710, 5224, 9098, 16, 29919, 16, 1930, 18697, 1036, 1988, 12561, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 1958, 3244, 17, 2487, 5708, 18, 2052, 3418, 11580, 1036, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 2679, 5881, 4061, 3171, 1966, 28297, 5217, 1920, 5857, 15920, 2014, 10787, 16, 3868, 13915, 1966, 43, 7281, 1958, 2213, 17, 2213, 3719, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 3629, 1005, 16, 5334, 1023, 16, 56, 17, 4262, 3418, 1988, 10634, 1966, 1920, 2678, 17, 2743, 9059, 1927, 4543, 3629, 1005, 17, 2601, 5224, 9098, 12, 3457, 1997, 1036, 13, 16, 10232, 43, 7864, 17, 5165, 17, 7864, 3728, 1942, 9967, 2487, 4465, 3709, 18, 2176, 5745, 4088, 2651, 43, 16350, 28959, 17118, 2796, 1942, 9055, 2014, 6980, 2628, 3286, 1922, 6445, 4487, 1930, 5005, 4028, 16, 3868, 1922, 2644, 1942, 8523, 2840, 9436, 2007, 2858, 17, 5388, 13066, 18, 3677, 16, 1920, 2213, 2258, 43, 3629, 1005, 4510, 17, 2743, 3418, 1988, 14879, 1920, 45, 17, 4262, 7917, 17, 2743, 3031, 1927, 21545, 3629, 1005, 17, 2601, 5224, 9098, 12, 3457, 1997, 1036, 13, 16, 12440, 17371, 1930, 5207, 9306, 18, 4073, 2743, 6445, 13066, 6485, 2037, 3835, 4576, 1942, 6079, 4612, 3038, 16, 2052, 3418, 14928, 8523, 2840, 1988, 8480, 1920, 7888, 11, 61, 2835, 1956, 2678, 1930, 3146, 6479, 1942, 2285, 2359, 2294, 18, 2176, 1977, 3198, 1922, 25178, 7972, 2341, 1915, 13458, 2609, 29164, 3336, 1930, 1977, 4624, 1942, 20709, 11569, 3213, 3640, 18, 3], "output": "MMDFMQIKYFILVAQYSSFSKAANDAYTTQSNVSKQIAHLEEELGVKLFERNTRQVQLTPQGAYFYKEINRLLNHLDDIVKNVKTMDVNRSGTLKVGLHGQLAMDIIAPGLFYLFQDRYPDIDLQIVSMGFKNLRANLLNETLDVILTFSFEQQNNKSISHFVVSRSTPRIYYLKELFEDRTPIFEDFKQMPLVSLDNEESKPAIAYIDEICKINQLEFKNHIRINSMETMKFYLESGLGVAILGCSYQIANSKKLGYIDIPKVPYLIGTDAIWVKNNMNPALELFVDVLKECICDKNTKDQSLST", "metadata": {"id": "A0A974XIZ1", "cluster": 7307382, "interpro_all": ["IPR005119", "IPR000847", "IPR036388", "IPR036390"], "interpro_used": ["IPR036388", "IPR000847", "IPR005119"], "interpro_unused": ["IPR036390"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein includes a Septum formation-related domain that is predicted to play a role in septum formation during cell division. This feature is typically found in proteins associated with the cytokinetic machinery required for cellular separation. It occurs in Ilumatobacter coccineus (strain NBRC 103263 / KCTC 29153 / YM16-304) and is classified with UniProt keywords Signal.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 5921, 43, 17026, 3337, 17, 2712, 3418, 1988, 1977, 4396, 1942, 3918, 43, 2770, 1922, 17026, 3337, 2409, 2024, 8451, 18, 2052, 5961, 1977, 5745, 2435, 1922, 2697, 2458, 1956, 1920, 6137, 2002, 10853, 3414, 1958, 3689, 7106, 18, 2176, 5110, 1922, 2614, 23813, 4575, 7972, 2341, 1915, 28014, 2053, 1957, 12, 3943, 8789, 15618, 9373, 4684, 1010, 19, 14331, 6916, 24608, 3786, 19, 23143, 3672, 17, 23490, 13, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 3], "output": "MSAPRRPSSVLATLLVAAIGIAACGGGSDDDAPPATDPPTSDEPVGTEPPATMPTPPVTCGEKVELLPPPQQNAPRDEADFEATLARFCLPDVASYTGESFEDPVECWVTMTAERSLVGSIAEVGLDAALGDASMVDEQLDSFDIVRLDPCDAEGVEQVVAFCDAAVADTTVDMISSTVAVVYPDEIGWTVAEQRGAACVHDSEFAGFVTPPDSDLPTDPIEAEILVTELCAPTVSEFGDDINCWVVVGSPGALDAAIAEVGLEAAMGEHRLGFVVDCTTPDALMAVGLVSVDDDGPWPGDDSLSVDPTSVSGTFPNEIGWEALGRRYISCDAVPASVTAVPDTATSETAPPPTDPPVTDPPATDGEYAVVDCDEPHDSELVSLKDLSVVTVEIGFVSPTPLGTFLSSLEPGDCYVPLESRAYPGQDELVDEAFALAYIDTGDAEPVCAIQIPSEGHDPVDCAEPYLGGRDLSTSGVGVGFDANTGLGEPIIAELDPGTCFTFAPDTYDPLRAIRFDLCSAVLAET", "metadata": {"id": "A0A6C7EAQ1", "cluster": 9058961, "interpro_all": ["IPR026004"], "interpro_used": ["IPR026004"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein carries a Zinc finger, AD-type domain that functions as a protein-protein interaction module capable of forming homodimers, distinct from typical DNA-binding zinc fingers. Found primarily at the N-terminus of arthropod C2H2 proteins, this domain adopts an atypical treble-cleft-like zinc-coordinating fold. Moreover, the protein should feature a Zinc finger C2H2-type domain that functions as a classical DNA-binding motif, typically found in eukaryotic transcription factors where it interacts with the DNA major groove using a conserved $\\beta/\\beta/\\alpha$ fold coordinated by a zinc ion. These domains frequently appear in tandem arrays to facilitate specific recognition of nucleic acids, proteins, or lipids, acting as stable scaffolds for diverse biological activities ranging from gene transcription to chromatin remodeling. Moreover, the protein is categorized in the Zinc finger C2H2 superfamily, which comprises stable, zinc-coordinated $\\beta/\\beta/\\alpha$ motifs that primarily function as DNA-binding domains in eukaryotic transcription factors. These versatile scaffolds typically interact with the DNA major groove in tandem clusters, but can also be adapted to bind RNA, proteins, or lipids to regulate diverse cellular processes. It is derived from Ladona fulva (Scarce chaser dragonfly) (Libellula fulva) and contains UniProt keyword associations Metal-binding, Repeat, and Transcription regulation.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 16252, 43, 7997, 8497, 16, 2041, 17, 2601, 3418, 1988, 4088, 1966, 43, 2213, 17, 2213, 2835, 9059, 7131, 1927, 7402, 29227, 16, 4493, 2037, 5939, 2678, 17, 2743, 7997, 18233, 18, 2435, 5985, 2019, 1920, 56, 17, 7822, 1927, 21680, 1986, 8453, 6951, 2697, 16, 2052, 3418, 24032, 1925, 10834, 2171, 7272, 17, 14649, 17, 3189, 7997, 17, 19355, 3728, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 7997, 8497, 8453, 6951, 17, 2601, 3418, 1988, 4088, 1966, 43, 8445, 2678, 17, 2743, 5219, 16, 5745, 2435, 1922, 10825, 3213, 2790, 2597, 2176, 9034, 1956, 1920, 2678, 3044, 15920, 2193, 43, 5305, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 3728, 11651, 2007, 43, 7997, 4755, 18, 2144, 4682, 5467, 3267, 1922, 10361, 10517, 1942, 6628, 2487, 5708, 1927, 11079, 4576, 16, 2697, 16, 2014, 8238, 16, 8290, 1966, 4700, 10603, 1958, 6445, 3933, 4209, 6485, 2037, 2359, 3213, 1942, 6338, 8378, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 7997, 8497, 8453, 6951, 13975, 16, 2154, 12936, 4700, 16, 7997, 17, 11651, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 8277, 1988, 5985, 2347, 1966, 2678, 17, 2743, 4682, 1922, 10825, 3213, 2790, 18, 2144, 20425, 10603, 5745, 6310, 1956, 1920, 2678, 3044, 15920, 1922, 10361, 5859, 16, 2308, 2112, 2222, 1998, 8461, 1942, 4566, 3146, 16, 2697, 16, 2014, 8238, 1942, 5741, 6445, 3689, 4028, 18, 2176, 1977, 3595, 2037, 17786, 12502, 5257, 7302, 12, 16937, 22948, 1005, 24579, 1916, 15972, 13, 12, 9954, 1992, 5617, 5257, 7302, 13, 1930, 5461, 20709, 11121, 2538, 5253, 6048, 17, 2743, 16, 6865, 16, 1930, 3213, 3640, 18, 3], "output": "MFLSTEEMESSNLFNSCRLCLCESERLLLQFKVCKTDRYPHLICCPCLDKLTDFKNKVMVKEDQYSLGSENFKPVSIKDEMESDVEANYSQVTYEVAQLSRQVDDSDTKSDLAVMDLRKTRTNEDCHSLLLVESCVLSQHSQRNRSLEATGQSSKFFKGGGETSEVQDEFYKRERPYECEECGWRFVKKPFECEECGWRFRYKGQLTRHQKSVTHHRIHTGEKPFACQKCSSSFAQSGDLVKHKHFRVHSGQKPYPCDECERRFLCEKRFLRRSSLVMHMRTHTGVRPYSCRETECDKRFSTSGDLKRHMNVHTKINIFEVNGRHGYAAAEVITDIFKDQCINAKLTYEEEKEAEDLSINRISKNEKHQEELVTERERPFQNNGSSLSQLQQKLHTRNNPTQLDKHLQIHSTHNGEKAFVCEVCGKCFARKSSLERIHSGEKPFPCHECGKMFAQSSDLAASTCDLNRHKMSHRGYKPNACKCGKTFPQRSGLVTHLRVHSGERPYPC", "metadata": {"id": "A0A8K0JUR7", "cluster": 9887963, "interpro_all": ["IPR012934", "IPR036236", "IPR013087"], "interpro_used": ["IPR012934", "IPR013087", "IPR036236"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to make a protein that can have this function: The protein should have a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Also, the protein features a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Also, the protein features a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. It originates from Marinovum sp and is annotated with UniProt keywords Cytoplasm, DNA excision, and Excision nuclease. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 3066, 2162, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2222, 16, 1920, 2213, 4075, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2222, 16, 1920, 2213, 4075, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2176, 22970, 2037, 13081, 22243, 1989, 2056, 1930, 1977, 10633, 1956, 20709, 11569, 5239, 16, 2678, 10940, 16, 1930, 10940, 16230, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MTASVPVTNTDDLRARLKLEGGKAFVLQTEFEPAGDQPTAISELVQGVQGGEHNQVLLGATGTGKTFTMAKVIEQTQRPALILAPNKTLAAQLYGEFKGFFPENAVEYFVSYYDYYQPEAYVARSDTFIEKESQINEQIDRMRHAATRALLERDDVIIVASVSCIYGIGSVETYGAMTQDLQAGQSYDQRQIIADLVAQQYRRNDQAFQRGAFRVRGDALEIFPAHLDDRAWRLSFFGDDLENITEFDPLTGEKTQVLDQVRVYANSHYVTPKPTINQAIINIKKELRQRLDQLVGDGKLLEAQRLEQRTNFDIEMLEATGVCNGIENYSRYLTGRAPGEPPPTLFEFIPDHALVFADESHVSVPQIGGMYKGDYRRKFTLAEHGFRLPSCMDNRPLKFEEWDAMRPQTVYVSATPASWELEQTGGIFTEQVIRPTGLLDPKIEIRPVEMQVDDLLDEVRKVAQDGFRTLCTTLTKRMAEDLTEYMHEQGIRVRYMHSEIDTIERIEILRDLRLGAFDVLIGINLLREGLDIPECGLVAILDADKEGFLRSETSLVQTIGRAARNADGRVIMYADRITGSMERAIGETQRRRAKQNAYNIKHDITPATVKKNVEDILAGLYKGDTDQSRVTATIDAPLSGSNLNAVLEGLRTDMRKAAENLEFEEAARLRDEVKRLEAVDLAVADDPLARQFVIEAAGEAAKASSGRSTAGRPGQRGGNVRRKRR", "metadata": {"id": "A0A2D5CMP5", "cluster": 14205559, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001650", "IPR001943", "IPR014001"], "interpro_unused": ["IPR004807", "IPR036876", "IPR006935", "IPR027417", "IPR024759", "IPR041471"]}, "task_type": "autoregressive"} {"instruction": "Given the following functional description of a protein, generate a complete amino acid sequence that performs the described role. The desired function is: The protein is included in the Metal-dependent hydrolase superfamily, which comprises a diverse group of hydrolytic enzymes characterized by a (\u03b2/\u03b1)8-barrel (TIM barrel) fold coordinating mono- or binuclear transition metal ions within the active site. These enzymes utilize these metal centers to catalyze the hydrolysis of a broad spectrum of substrates involved in fundamental metabolic processes. In addition, the protein has a TatD-related deoxyribonuclease conserved site that belongs to a superfamily of metalloenzymes, typically exhibiting DNase activity or functioning as a hydrolase in enzymes such as allantoinase. Also, it is part of the 3'-5' ssDNA/RNA exonuclease TatD-like family, which comprises metalloenzymes, often adopting a TIM-barrel fold, that primarily function as 3'-5' exonucleases processing single-stranded DNA or RNA. These proteins play roles in DNA repair, as seen in bacterial TatD, as well as chromosomal segregation and cell cycle progression in eukaryotes. Notably, despite being encoded within the bacterial Tat operon, these nucleases are not involved in the Twin-Arginine Translocation protein export pathway. It is native to Vitreoscilla sp. (strain C1) and has UniProt annotations Metal-binding.", "tokenized_instruction": [2, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 16, 5655, 43, 4080, 3835, 2687, 3244, 1988, 17436, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 1977, 3063, 1922, 1920, 6048, 17, 3100, 20748, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 26702, 5038, 4378, 2007, 43, 12, 161, 19, 160, 13, 28, 17, 19560, 12, 2267, 19560, 13, 3728, 19355, 8914, 17, 2014, 8768, 13821, 4832, 6048, 6982, 2651, 1920, 3500, 3200, 18, 2144, 5038, 12561, 2144, 6048, 7365, 1942, 18170, 1920, 9128, 1927, 43, 4949, 5648, 1927, 6249, 3286, 1922, 8829, 4487, 4028, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 10687, 1007, 17, 2712, 26405, 13261, 5305, 3200, 1988, 14440, 1942, 43, 13975, 1927, 8969, 6802, 1022, 16367, 16, 5745, 12196, 12861, 2455, 2014, 7295, 1966, 43, 20748, 1922, 5038, 2427, 1966, 2136, 26182, 11413, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 23, 11, 17, 25, 11, 15063, 19, 3146, 24966, 10687, 1007, 17, 3189, 3416, 16, 2154, 12936, 8969, 6802, 1022, 16367, 16, 3868, 20478, 43, 2267, 17, 19560, 3728, 16, 1988, 5985, 2347, 1966, 23, 11, 17, 25, 11, 24966, 1036, 4587, 2957, 17, 10338, 2678, 2014, 3146, 18, 2144, 2697, 3918, 5456, 1922, 2678, 5059, 16, 1966, 3945, 1922, 4543, 10687, 1007, 16, 1966, 2486, 1966, 9220, 12707, 1930, 2024, 4048, 4380, 1922, 15021, 18, 7388, 16, 4281, 3301, 7905, 2651, 1920, 4543, 10687, 15675, 16, 2144, 29305, 2032, 2084, 3286, 1922, 1920, 13392, 17, 9732, 7849, 2213, 12660, 3374, 18, 2176, 1977, 6196, 1942, 16986, 17413, 11560, 1019, 2056, 18, 12, 3943, 8817, 13, 1930, 2258, 20709, 15010, 6048, 17, 2743, 18, 3], "output": "MLIDSHCHLNFPDLMNRLPEVLDNMAANDVRQALAISVSRDTYTQVQALADAHEHIFCTVGVHPDEENAAEFLAEEMIAIAQAQPKVVGIGETGLDYHWCKGDLTWQHDRFRAHIQAANATKLPLIIHTRDAGHDTLDVLRAEKAHGGVIHCFTEDVAFARGALDLGFYISFSGIVTFKNAQQIQEAAKFVPQDRILVETDAPFLAPVPKRGKTNEPAYVKHTAEFLAQLRGETFAEVEQYSCDNFYRLFDQVPRIDKAFI", "metadata": {"id": "A0A6M4CB52", "cluster": 14754968, "interpro_all": ["IPR018228", "IPR032466", "IPR001130", "IPR015991"], "interpro_used": ["IPR032466", "IPR018228", "IPR001130"], "interpro_unused": ["IPR015991"]}, "task_type": "autoregressive"} {"instruction": "Target Function: The protein belongs to the CCB3/YggT family, which includes components of the System IV cytochrome c biogenesis pathway essential for heme attachment in oxygenic photosynthesis. Members such as YlmG are implicated in chloroplast and cyanobacterial division, while the related protein YggT supports bacterial growth in the absence of major potassium uptake systems. It is found in SAR202 cluster bacterium and corresponds to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 14440, 1942, 1920, 4928, 13965, 19, 67, 14276, 3416, 16, 2154, 5921, 4178, 1927, 1920, 2433, 4370, 9387, 45, 13008, 3374, 4415, 1958, 10954, 8576, 1922, 4612, 1935, 18133, 18, 4678, 2427, 1966, 12111, 9759, 2032, 6835, 1922, 17471, 1930, 21897, 1024, 8451, 16, 2679, 1920, 2712, 2213, 67, 14276, 7825, 4543, 2905, 1922, 1920, 3905, 1927, 3044, 9057, 5047, 3771, 18, 2176, 1977, 2435, 1922, 9851, 18406, 4377, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MGLVQLIHFVFNPILINIYDILAQITEPILGVVIIVLQIIHEVLIAALSTLFYLAILGRIILSFIIPMMGGRPPVRKIIPTVGMLDFSPL", "metadata": {"id": "A0A6A0JLB6", "cluster": 16045433, "interpro_all": ["IPR003425"], "interpro_used": ["IPR003425"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein is grouped in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Moreover, the protein should contain a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It occurs in Persicitalea jodogahamensis and is annotated with UniProt keywords Isoprene biosynthesis and Transferase.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 1977, 10809, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 5110, 1922, 3096, 19753, 2603, 1019, 7420, 22389, 4223, 8527, 8134, 1930, 1977, 10633, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MVTFPNAKINIGLNIVGKRPDGFHNLESCFYPVGWADALEILPQTDWQDSNLCLKAYRLLAEDFALPPVSIHLLKAVPIGAGLGDISTENQQKYARSLGSDCAFFIENKPMYCFGKGDQFHISTAEAYSGITPRVPTQDLRELLQKPIGQWRDFVKNDFEEASMSGSGSTVYGIFDHEPDPANNFQNSTVWKGELNHHQVVSFTSSGLSIPGNGGSADAAFTIKALNQLFSLEETSLRLTGKWILLVNPGLSLFKNHSVLPQIKAKIYDLGAQY", "metadata": {"id": "A0A8J3G7L6", "cluster": 17788851, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein contains a PAS-associated C-terminal (PAC) domain that contributes to the formation of the conserved 3D PAS fold by stabilizing the region carboxy-terminal to PAS repeats. This structural motif supports the diverse regulatory functions of the associated PAS domain, including protein dimerization, light sensing, and signal transduction in circadian rhythms and bacterial histidine kinases. In addition, the protein should include a Histidine kinase domain that functions as the catalytic core of two-component signal transduction systems, orchestrating cellular responses to environmental stimuli. It undergoes ATP-dependent autophosphorylation on a conserved histidine residue within a homodimer before transferring the high-energy phosphoryl group to an aspartate residue on a partner response regulator protein. This domain contains a dimerization interface and a structurally distinct ATP-binding cleft defined by conserved nucleotide-binding motifs. Additionally, the protein should have a PAS domain that functions as a versatile signal sensor module in signaling proteins across archaea, bacteria, and eukaryotes. This domain detects diverse stimuli, often through the binding of cofactors like heme or flavin, and frequently associates with PAC domains to form a conserved 3D fold. It has been detected in Haloarcula rubra and is annotated with UniProt keywords Transferase.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 5461, 43, 9233, 17, 2458, 45, 17, 4262, 12, 6866, 13, 3418, 1988, 7624, 1942, 1920, 3337, 1927, 1920, 5305, 5050, 9233, 3728, 2007, 14384, 1920, 3031, 15750, 17, 4262, 1942, 9233, 9569, 18, 2052, 4346, 5219, 7825, 1920, 6445, 4948, 4088, 1927, 1920, 2458, 9233, 3418, 16, 2710, 2213, 13640, 16, 3696, 9306, 16, 1930, 2733, 8201, 1922, 10507, 16622, 1930, 4543, 13873, 7784, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 13873, 4016, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 2288, 17, 4594, 2733, 8201, 3771, 16, 21991, 2287, 3689, 3387, 1942, 4813, 5458, 18, 2176, 14928, 4498, 17, 3100, 22009, 1990, 43, 5305, 13873, 6181, 2651, 43, 21189, 3119, 21902, 1920, 2149, 17, 3844, 12556, 2210, 1942, 1925, 12878, 6181, 1990, 43, 8240, 2644, 7888, 2213, 18, 2052, 3418, 5461, 43, 13640, 6854, 1930, 43, 12171, 4493, 4498, 17, 2743, 14649, 3608, 2007, 5305, 5489, 17, 2743, 8277, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 9233, 3418, 1988, 4088, 1966, 43, 20425, 2733, 6443, 9059, 1922, 3197, 2697, 3436, 21501, 16, 4802, 16, 1930, 15021, 18, 2052, 3418, 19998, 6445, 5458, 16, 3868, 2596, 1920, 2743, 1927, 21362, 3189, 10954, 2014, 26758, 16, 1930, 5467, 14162, 1956, 6866, 4682, 1942, 2386, 43, 5305, 5050, 3728, 18, 2176, 2258, 2252, 3330, 1922, 23226, 5332, 5617, 10010, 5524, 1930, 1977, 10633, 1956, 20709, 11569, 13763, 18, 3], "output": "MTGGENRHQTILEQIRDGVYTLDSSGEILVGAPVSKVLTDADVEKCLSIIRTLLTASGDSIPCDLHLALLPAEDGEFQGTVGVVRDIRILRHDLSNAMTVILGRVQQLEDLIETSEKVQQIHHIHNDMADQQGSLKLCSEVDIPSDAHAATGHEELVTTAFINLQIRIEDNGPGIPSEERDVLEMACSGDIRFDDDISQGTAVLMEFPRAAASDQTWVNETAVENFDIGYTRDDRSDERESGRCEIRLQTNRKQREQRLDVLNGVDPEFQPAIDAIRERGEELVESIVDDFRVNYPAVDFIENAIEHNDSDQPLVLVTIQKDPDRIGSESQLRHSMGLGLWLASWSVT", "metadata": {"id": "A0AAW4PT89", "cluster": 18236931, "interpro_all": ["IPR036890", "IPR005467", "IPR001610", "IPR000014", "IPR000700", "IPR035965", "IPR052162", "IPR004358"], "interpro_used": ["IPR000700", "IPR005467", "IPR000014"], "interpro_unused": ["IPR036890", "IPR004358", "IPR001610", "IPR035965", "IPR052162"]}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein possesses a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Moreover, it is part of the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Also, the protein falls within the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. It is derived from Friedmanniomyces endolithicus and is described by UniProt keywords Metal-binding, Magnesium, and ATP-binding.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 2176, 1977, 3595, 2037, 26086, 8635, 29249, 16239, 12191, 22523, 6973, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 16, 13148, 16, 1930, 4498, 17, 2743, 18, 3], "output": "MAAERQWGVTPAFSSDPPSAGDLKLNDLLVSELKAQNNFAPASDTEKREAIITKLKGEVYTYGSYRLGVYGPASDVDTLMVAPKHVTRDDFFDLMPDLLRQSTAPGEITNLVPVPGISTPIIKLTSDKVDLADDSILRGLDEVDRRCVNGTRVTNRILQLVPQTKTFRLALRAIKLWAQKRAIYRVCQLYPKAVAPLLVQRFFFIIQRWNWPKPVFLQHKEESSLQLREWDSTKTVMMREFKRAEEIIKDIYDTGKPWSTLFERHDFFTRRYKHYICVNTAAKDQNAHDASVELVQPFTKGFDRVHLCNGEQQLEKTLDGSLEFQVKATETVATEVLATNGEANVKKEDGPQRVYTMTYYIGIGLREGATALDISTPVQNFQGECTAWPGYDADTKPVRPKRKPKATTNGASPADNKRSFSNSGLDEATASAKRRQSANTTNGTEGGLLRQMVQTVGKKKGLPQDILDVAGIRGVDIDLIFSSLQLSSLGNIVGFPGGVAYAILVAPNTYRGDAAHLMPILTPAVPSMNTAHTVTRWAGLVQSRIKRLMAGIEGSDANDGHADVKAQIAQSDTDGVMHSIRIKHIRSYDLPADVFVPGE", "metadata": {"id": "A0AAN6H6N9", "cluster": 18324220, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR007012", "IPR043519", "IPR011068"], "interpro_unused": ["IPR014492", "IPR007010", "IPR048840"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: It is part of the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. Also, the protein can be placed in the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Moreover, the protein carries a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. It is found in Lachancea mirantina and is described by UniProt keywords Metal-binding, Manganese, and mRNA processing. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 2176, 1977, 3131, 1927, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 3950, 16, 1920, 2213, 16252, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 2176, 1977, 2435, 1922, 7511, 15409, 1972, 1019, 3138, 10402, 2175, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 16, 19516, 16, 1930, 3616, 4587, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MSGQKTLGVTGPISAAGPTAAENKLNDALVQELKREGSFETEAETQKRIQVLAVMQELAQKFVFEVSKSKNMSDGMAKDAGGKIFTFGSYRLGVHGPGSDLDTLIVVPKHVTREDFFTVMDRLLRERPELEEIAPVPDAFVPIFKIKFSGISIDMLCARLDVPQVPLTLTLADKNLLRNLDEKDLRALNGTRVTDEILQLVPKPTAFKTALRAIKLWASRRAVYGNVFGFPGGVAWAMLVARICQLYPNACGGVIVARFFHILTKWNWPQPVLLKPIEDGPLQVRVWNPRIYAQDRSHKMPVITPAYPSMCATHNINESTKTVILRELERGAQITNDIFTNKKSWSELFQKHDFFYRYKFYLTVMASTKGSDEQHLKWSGLVESKLRLLVQKLEVLNGIKLVHPFVKPFECTYLYKTDEECSKIVDNYGTSKTEGVLKQFIEKTDANAQEETVKASKQVHITTLYIGLDVVAEGKKQIDIHVPCSDFFNLCRSFSEYDDPDTYSLMIKYVKLHDLPDTVYAEGEERPVKHSKRKKQDKPHKKAKKPKSTVAELEEPENDDKRPTKASDNINVATAVTPLADRAS", "metadata": {"id": "A0A1G4K2M0", "cluster": 18692007, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR011068", "IPR043519", "IPR007012"], "interpro_unused": ["IPR014492", "IPR007010", "IPR048840"]}, "task_type": "autoregressive"} {"instruction": "The protein is classified under the STAS domain superfamily, which serves as a regulatory module in bacterial anti-sigma factor antagonists and a cytoplasmic domain in SLC26 anion transporters. It often possesses NTP-binding or weak NTPase activity to facilitate conformational changes and protein-protein interactions, such as binding acyl carrier proteins. Mutations within this domain compromise transporter function and are associated with human pathologies like Pendred's syndrome and diastrophic dysplasia. It occurs in Pontibacter chinhatensis. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 1920, 23891, 1036, 3418, 13975, 16, 2154, 10634, 1966, 43, 4948, 9059, 1922, 4543, 2246, 17, 5139, 2991, 10515, 1930, 43, 6823, 3418, 1922, 12150, 4684, 10985, 10538, 18, 2176, 3868, 14465, 29676, 17, 2743, 2014, 5015, 29676, 2051, 2455, 1942, 6628, 8523, 2840, 1930, 2213, 17, 2213, 3719, 16, 2427, 1966, 2743, 11337, 9685, 2697, 18, 3527, 2651, 2052, 3418, 15386, 9054, 2347, 1930, 2032, 2458, 1956, 2616, 14407, 3189, 26127, 3510, 11, 61, 4741, 1930, 8455, 7325, 14095, 18, 2176, 5110, 1922, 15065, 4397, 2422, 6790, 2722, 2777, 8362, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MVLSSTPFHHLEHYPAHNVVVSQWYGPCSSQEYRNTLMQFLHLIEEMRIPYAIADRRLLPPMPVEDNRWTLNEYLEKFLRLPLKRFAFINSFDPVAERQIHRFLENNKNTVFPFEMRVFDDLTSAYDWLITGKERH", "metadata": {"id": "A0A1I2YN15", "cluster": 21403645, "interpro_all": ["IPR036513"], "interpro_used": ["IPR036513"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein is assigned to the Ubiquinone biosynthesis O-methyltransferase family, which functions as an O-methyltransferase catalyzing two distinct steps in the ubiquinone (Coenzyme Q) biosynthetic pathway. This family includes the bacterial enzyme UbiG and the mitochondrial enzyme COQ3. Also, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. It is derived from Legionella norrlandica.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 5582, 22123, 8132, 57, 17, 16478, 3416, 16, 2154, 4088, 1966, 1925, 57, 17, 16478, 29601, 2288, 4493, 5983, 1922, 1920, 5582, 22123, 12, 22051, 59, 13, 14041, 3374, 18, 2052, 3416, 5921, 1920, 4543, 4113, 4803, 1950, 1930, 1920, 4596, 4113, 25147, 1010, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2176, 1977, 3595, 2037, 27836, 5870, 3990, 1005, 4702, 6102, 18, 3], "output": "MTQIKSTIDVQEVNKFAQLANYWWDANGPLKTLHDINEARFKFISQHINLQDLRVLDVGCGGGILCETMAKAGAHVTGIDAERETVQVAKEHAQKVHLDIDYFSSTIEEYEAQSFDVVTCMEMLEHVQNPELVIQHCKRLLKPDGLLFLSTISRTLKAYLGAIIAAEYILNLLPRQTHDYVKFIKPSELATMARQYDFKVIDMKGLCYNPFTRKASLAPDVSVNYIIALK", "metadata": {"id": "A0A0A2SS66", "cluster": 22694588, "interpro_all": ["IPR029063", "IPR010233"], "interpro_used": ["IPR010233", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: The protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Additionally, the protein should include a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Also, the protein is categorized in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is present in Cyanobacteria bacterium UBA11367 and carries UniProt keyword assignments Isoprene biosynthesis and Transferase. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 2481, 1922, 21897, 14061, 4803, 4904, 22744, 1027, 1930, 16252, 20709, 11121, 2538, 18306, 26690, 1021, 8132, 1930, 13763, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MRSYSLIAPAKINLYLEILGDRADGYHELVMILQSIDLADKIDIRAIGTQGIQVHCEDAEVPLDQTNLAYRAAKLMADNFPDTFAQFGGVEINIKKNIPVAAGLAGGSTDAAAVLVGLDMMWQLGLTQPELQDLAAKLGSDVPFCLAGGTAIATGRGEELDPLPSVDSLYVVLAKYRNLAVSTPWAYQTYRSQFGDGYIRDAHSLEARAQRIHSGPIVQAIMNHKMGEIGKLLYNDLEKVVLPNYPQVLELRKAFENSGALGTMMSGSGPTVFALCESEGEAQRILQEVRKGISAPDLGFWVSRFSNHGIQVI", "metadata": {"id": "A0A352XCD9", "cluster": 25968684, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR006204", "IPR013750", "IPR004424"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein can be placed in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. In addition, the protein should feature a SAM-dependent methyltransferase TRM5/TYW2-type domain that functions as an S-adenosylmethionine-dependent enzyme involved in tRNA methylation. This domain is characteristic of Trm5 and Tyw2 proteins, which utilize SAM as a cofactor to modify transfer RNA. It is native to Rhinocladiella mackenziei CBS 650.93.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 2235, 17, 3100, 16478, 28402, 1015, 19, 6227, 1018, 1028, 17, 2601, 3418, 1988, 4088, 1966, 1925, 61, 17, 29283, 23568, 11215, 17, 3100, 4113, 3286, 1922, 10089, 5547, 18, 2052, 3418, 1977, 6293, 1927, 28402, 1015, 1930, 6227, 1018, 1028, 2697, 16, 2154, 12561, 2235, 1966, 43, 15155, 1942, 11675, 3856, 3146, 18, 2176, 1977, 6196, 1942, 14066, 5406, 2713, 5870, 24306, 4389, 2621, 1033, 16341, 18529, 18, 6156, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MESDATRTRPKFERKSRSEKRLANPLVKGIVAFCAAEASIPAQMSRGTSDFQCETSRSSLQVSLSFSDLPKRYTLYAPLLLLSELFKCIAEEGFAGLGVSRIAVNAPIAAEENGEEVNPTDSDTEVQVPSQKRRQHILRSPSGLVPVYGDWGPQPRQIPSPKTQHRGIMQCWAPLYTMFSRGNVSEKARILGLASPPALDEPIEAVDVIDFYVGIGYFAFCYLACRVRRVWGWVRVDEDGKLVGMGVKELVERVVGVQGDTIGAGNESGRGNEERADVIKCVAFLGDNKWADKVMREPTSGGSWENAIRMVTGSYNQGKGGWLHVHENVDIGRIDEMKGNVSCVHVEEVKTYAPGVMHCVFDIEIKANGAKRGIVIATNEEGASSSLAHNFPTRNPRWRDFYNALSQPERNEPERPEAWAGKYPSIRPDPDVHDKDLTTMTGRLLLTDPTTRDFSEAFWTSTPASTSPSAGEKAEIGGRFPGLDINPWSIEGLRRGCERNGWGCVVNVRNGGRMAKGTENVGGARVRCEFDGQERGLNVRHVNLGLLIVQGIERLASREAGREGNQRTHWV", "metadata": {"id": "A0A0D2FQD8", "cluster": 26206165, "interpro_all": ["IPR030382", "IPR029063"], "interpro_used": ["IPR029063", "IPR030382"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein should include a Phospholipid/glycerol acyltransferase domain that mediates acyl transfer reactions in diverse enzymes involved in phospholipid biosynthesis and membrane biogenesis. This domain is notably found in bacterial glycerol-phosphate acyltransferases and in mitochondrial tafazzins, where it facilitates the remodeling of cardiolipin required for oxidative phosphorylation. It is identified in Porphyromonadaceae bacterium COT-184 OH4590. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 3066, 3951, 43, 14608, 19, 9244, 11337, 9961, 3418, 1988, 10412, 11337, 3856, 5298, 1922, 6445, 5038, 3286, 1922, 14608, 8132, 1930, 3260, 13008, 18, 2052, 3418, 1977, 7388, 2435, 1922, 4543, 9244, 17, 5413, 11337, 18580, 1930, 1922, 4596, 19063, 3408, 22030, 3355, 16, 2597, 2176, 11374, 1920, 8378, 1927, 21129, 8257, 1921, 3414, 1958, 5163, 4050, 18, 2176, 1977, 2899, 1922, 17376, 5134, 3947, 7324, 1972, 3336, 14061, 17150, 17, 16053, 5622, 6803, 5124, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MWLEKKIFSLLGWKAEIKIDLPDKCVACIAPHTSNWDFFYCVMFKEAYRIQVNFLIKEEWTKSIVGGIIHRLGGIGVRRDKSQSSTDIYAKVFDNHKVMRIAITPEGTRSANKDWKLGFYYIALKANVPIILVSLDYKTKTLTIDRLIVPNGDVDTQMAEIKAHYKGVTARYPDRFLI", "metadata": {"id": "A0A0A2EL40", "cluster": 26294998, "interpro_all": ["IPR002123"], "interpro_used": ["IPR002123"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that has the following function: The protein is associated with the Uracil phosphoribosyltransferase/Adenine phosphoribosyltransferase family, which catalyzes the conversion of uracil or adenine and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) to UMP or AMP and diphosphate within nucleotide salvage pathways. These enzymes facilitate energy-efficient nucleotide pool maintenance and are typically allosterically activated by GTP. Moreover, the protein should include a Phosphoribosyltransferase domain that catalyzes the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP) by a nitrogen-containing nucleophile to yield an alpha-1 substituted ribose-5'-phosphate and free pyrophosphate. This domain is essential for nucleotide synthesis and salvage pathways and features a conserved PRPP binding motif. Moreover, the protein is associated with the Phosphoribosyltransferase-like superfamily, which encompasses enzymes such as phosphoribosyltransferases (PRTases) and phosphoribosylpyrophosphate synthetase-like proteins. These domains typically catalyze the transfer of phosphoribosyl groups to specific substrates, playing a central role in nucleotide biosynthesis and salvage pathways. It has been characterized in Mycobacterium talmoniae and has UniProt annotations Magnesium, Allosteric enzyme, and GTP-binding. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 22761, 3421, 2023, 25566, 19, 15643, 3421, 2023, 25566, 3416, 16, 2154, 17097, 1920, 7309, 1927, 22761, 2014, 15643, 1930, 25, 17, 8078, 17, 4595, 17, 46, 17, 17870, 21, 17, 23266, 12, 11533, 1034, 13, 1942, 8736, 1034, 2014, 3681, 1930, 23266, 2651, 5489, 17577, 3873, 18, 2144, 5038, 6628, 3844, 17, 5807, 5489, 5562, 6291, 1930, 2032, 5745, 14772, 2169, 4128, 2007, 9319, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 3421, 2023, 25566, 3418, 1988, 17097, 1920, 9514, 1927, 1920, 4595, 17, 21, 11, 17, 24937, 1927, 25, 17, 3421, 2023, 11731, 17, 4595, 17, 21, 17, 24937, 12, 11533, 1034, 13, 2007, 43, 6634, 17, 3165, 2797, 28335, 1942, 4307, 1925, 4595, 17, 21, 11798, 17870, 17, 25, 11, 17, 5413, 1930, 3294, 24937, 18, 2052, 3418, 1977, 4415, 1958, 5489, 4271, 1930, 17577, 3873, 1930, 4075, 43, 5305, 11533, 1034, 2743, 5219, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 3421, 2023, 25566, 17, 3189, 13975, 16, 2154, 21569, 5038, 2427, 1966, 3421, 2023, 25566, 1036, 12, 2033, 3857, 4127, 1036, 13, 1930, 3421, 2023, 11731, 18425, 15707, 18185, 17, 3189, 2697, 18, 2144, 4682, 5745, 18170, 1920, 3856, 1927, 3421, 2023, 11731, 2671, 1942, 2487, 6249, 16, 14797, 43, 4101, 2770, 1922, 5489, 8132, 1930, 17577, 3873, 18, 2176, 2258, 2252, 4378, 1922, 16389, 11571, 3947, 7955, 1930, 2258, 20709, 15010, 13148, 16, 14772, 4113, 16, 1930, 9319, 17, 2743, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MEVRVLDHPLAAARLTTLRDHRTGSAAFRAALRDLTLMLVYEATRGLRCERITVRTPLVETVGAVLAAPPLLVPVLRAGLGMVDQAHALLPEARVGFVGVVRDEDTHLPVPYLASLPTDLTGQPVMVLDPMLATGGSMTHTLGVLVDRGATDITVLCVVVAPEGLAALEKTAPGVRLFTAAVDERLNEDAYIVPGLGDAGDRQFGPR", "metadata": {"id": "A0A1S1NLH8", "cluster": 9647808, "interpro_all": ["IPR000836", "IPR029057", "IPR034332", "IPR050054", "IPR005765"], "interpro_used": ["IPR050054", "IPR000836", "IPR029057"], "interpro_unused": ["IPR034332", "IPR005765"]}, "task_type": "autoregressive"} {"instruction": "The protein belongs to the Protein kinase-like domain superfamily, which modifies other proteins by chemically adding phosphate groups. This enzymatic activity is fundamental to most signaling and regulatory processes in the eukaryotic cell. In addition, the protein should include a Protein kinase domain that functions as the conserved catalytic core responsible for transferring the gamma phosphate from ATP to serine, threonine, or tyrosine residues on substrate proteins. This phosphorylation event induces conformational changes that regulate diverse cellular processes, such as proliferation, differentiation, and apoptosis. Moreover, the protein incorporates a MORN repeat that functions as a putative lipid-binding module to facilitate membrane occupation and recognition. Structurally composed of a beta-hairpin followed by a short loop, these repeats are ubiquitous in eukaryotes and prokaryotes and often occur in tandem arrays in proteins such as junctophilins. It is present in Pseudocohnilembus persalinus (Ciliate) and features UniProt keywords Transferase.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 2213, 4016, 17, 3189, 3418, 13975, 16, 2154, 25436, 2303, 2697, 2007, 13944, 8013, 5413, 2671, 18, 2052, 8145, 2455, 1977, 8829, 1942, 2501, 3197, 1930, 4948, 4028, 1922, 1920, 10825, 2024, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 2213, 4016, 3418, 1988, 4088, 1966, 1920, 5305, 6804, 4728, 5061, 1958, 21902, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 16, 13143, 16, 2014, 6941, 4248, 1990, 4510, 2697, 18, 2052, 4050, 4817, 6387, 8523, 2840, 1988, 5741, 6445, 3689, 4028, 16, 2427, 1966, 4031, 16, 4155, 16, 1930, 4091, 18, 3950, 16, 1920, 2213, 19683, 43, 2803, 1022, 6865, 1988, 4088, 1966, 43, 6770, 4486, 17, 2743, 9059, 1942, 6628, 3260, 16805, 1930, 5708, 18, 12171, 7179, 1927, 43, 4666, 17, 14565, 3489, 2007, 43, 3662, 5881, 16, 2144, 9569, 2032, 15498, 1922, 15021, 1930, 28149, 1930, 3868, 4704, 1922, 10361, 10517, 1922, 2697, 2427, 1966, 7269, 2341, 25117, 1036, 18, 2176, 1977, 2481, 1922, 11520, 4879, 11619, 2383, 17010, 1957, 3096, 18130, 1957, 12, 15714, 2057, 13, 1930, 4075, 20709, 11569, 13763, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MGNQESTGGQEDPQQILDSLTVIKKFTDQRFNTTEQEEHKNNLAKYQERLQLQHPNTVQLLKNSLEKEIQARKGLAFLQKNGIAHNCIRSSTIYFNEEGQPKVTDPTVPSGIYLAPSLMEALEQQNWSPEHNEFKSDVFSFNYADGSFLSQQLENRLIQFSQRYSQDLTQLMLKTEQNSPEKDQNQDQIQSQNQSPEQQKFSQYSAQNQSPQQQRQQLSQLPPQQNLQQSYQQGNGPASFMMKDQPDLGSSKNNAPQENIAGPNQEEVQDQEYHQQSQEQPQQQQQNNNYYQQQQSQVQQQSQNQVPQQQQSNNYYKPYQQQEIQPQQQKEQDYIPLPGEKKVQPQYQQYQQQQGQQSSITNTYTASSYQIPYNNNQSASNQYQQSYQQANQTQTYTNSYTSPYQGYYQSSQQVPQQQQVGVENYQNGSRYEGEKLNGQRHGSGKFYYQDNGGLYDGNWRYNKMHGKFQGFGVLYNENPAVLQGNFDYKDFDLVEEFWTRYDGEFNDDNKSGNFKKDFVSGQGTFYTSNQQIIRGIWENNKLVQTLGDSSLVEHKETKQQFILREMEQQAFFSEGELWNAMGGAIQVFMQLNNFATTCQDQENGMTLLSMGLLENLDDCYEDHRFDFLQLEEILISQPQQHQEHNVSNQSPDENIGNEIGGNYQEDYSQSYQQSQITQSNTYSNQNLESILNKYSNTGSQQKQQQPQQQLGGLNINNTNSNKNLNDQKDLQKQPQYQQSTQIQQNTQSSNIEQKEYVGILYYASGKKAYDGDWVEDKEGYGTLYLSNNEKF", "metadata": {"id": "A0A0V0QDU8", "cluster": 806844, "interpro_all": ["IPR011009", "IPR003409", "IPR000719"], "interpro_used": ["IPR011009", "IPR000719", "IPR003409"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein should have a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, it is part of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Additionally, the protein contains a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is expressed in Bacteroides sp. A1C1 and corresponds to UniProt keyword Isoprene biosynthesis and Transferase. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 4950, 16, 1920, 2213, 5461, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 3198, 1922, 27978, 2056, 18, 21372, 1009, 1930, 8852, 1942, 20709, 11121, 2538, 26690, 1021, 8132, 1930, 13763, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MLTFPNAKINLGLNITEKRPDGYHNLETIFYPVPIEDALEINILNEGNRKFRLHQAGLEIEGEAESNLVVKAYKLLDDQFNLPPVDIHLFKHIPSGAGLGGGSADAAFMLKLLNNKFELGLPDDTLEEYAAKLGADCAFFIKNRPTYAEGIGNIFSPLPLSLKGYRIWLVKPDIFVSTRDAFAKIKPHHPEMSLKEIAQLPVEEWNGRMVNDFEESVFPQFPTIGEIKEEMYRQGAVYASMSGSGSSVYGLFKEDAVLPEVDFGEKAFVYKGRFTDV", "metadata": {"id": "A0A4P6RDA8", "cluster": 1360807, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: The protein contains a Adenylate cyclase conserved domain that forms part of the N-terminal cytoplasmic region in membrane-bound adenylate cyclase isoforms. This conserved segment is not required for the catalytic production of cAMP from ATP but is present in isoforms regulated by factors such as G proteins, kinases, and calmodulin. Furthermore, the protein should have a Adenylyl cyclase class-4/guanylyl cyclase conserved site that catalyzes the synthesis of cyclic GMP (cGMP) from GTP, facilitating intracellular signaling through cGMP-dependent kinases and ion channels. This catalytic domain is present in both soluble cytoplasmic heterodimers and membrane-bound receptors that mediate diverse physiological responses, including vascular smooth muscle relaxation and retinal photo-transduction. Moreover, the protein carries a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It is produced by Leptobrachium leishanense (Leishan spiny toad) and contains UniProt keyword associations Repeat, ATP-binding, and Glycoprotein. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 5461, 43, 23052, 16526, 5305, 3418, 1988, 4952, 3131, 1927, 1920, 56, 17, 4262, 6823, 3031, 1922, 3260, 17, 4124, 23052, 16526, 7963, 18, 2052, 5305, 5367, 1977, 2084, 3414, 1958, 1920, 6804, 3372, 1927, 6225, 2037, 4498, 2308, 1977, 2481, 1922, 7963, 4335, 2007, 2790, 2427, 1966, 49, 2697, 16, 7784, 16, 1930, 17537, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 27802, 16526, 2921, 17, 24, 19, 13504, 25671, 16526, 5305, 3200, 1988, 17097, 1920, 4271, 1927, 9821, 18033, 12, 15958, 13, 2037, 9319, 16, 12440, 4776, 3197, 2596, 15958, 17, 3100, 7784, 1930, 4755, 5628, 18, 2052, 6804, 3418, 1977, 2481, 1922, 2321, 6622, 6823, 21523, 1930, 3260, 17, 4124, 4086, 1988, 8265, 6445, 5005, 3387, 16, 2710, 4541, 6689, 3760, 9157, 1930, 6943, 10066, 17, 8201, 18, 3950, 16, 1920, 2213, 16252, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 1977, 4152, 2007, 16976, 2389, 5524, 19519, 1989, 19768, 15409, 4480, 12, 19768, 15409, 7707, 1012, 1942, 2015, 13, 1930, 5461, 20709, 11121, 2538, 5253, 6865, 16, 4498, 17, 2743, 16, 1930, 11424, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MPSKGKYFIKDSEDWVITHALYEKYQCISQHYPLLLILLFVVATACVTLIALFFASNHDPSKHLALLITVFLALVIFCALYVLVYTESFLQKWLQVFSVLIYVCLLAIGYVLIYDPEDVHTWDQVPFFLFITFSVYTTLPLGMRACLIASALSGTSHIIAISITVMLSRDKDHDSIAFQESLLLSVLPVYISMEMKLAIQDRLKESNDNRQPDKNFHSLYVKRHQNVSILYADIVGFTRLASDCSPKELVVMLNELFGKFDQIAKENECMRIKILGDCYYCVSGLPVSLPNNAKNCVKMGLDMCNAIKKVREATGADINMRVGVHSGNVLCGVIGLRKWQFDVWSHDVSLANRMESAGVPGRVHITEATLKHLNGAYKVEEGHGDLRDPYLKEMDIKTYLIIDPMSKEHQSQNNHISRPRVNDGLKVRPSVRMTRYLESWGAARPFSHFDHSENTNTEVLIPNGKPKPEIQLQRPCNADRNNSQKKNQEGELHERMMDAIDGLSSAKPWFWKSEDFYVFLLFFTDEGLEKEYRTIRIPKIRNYFLCAAVVFLCIFLIQILVMPRTTTLGISFGVVSLLMFFLVLMCYADKFVNFCDTSVSRVLCTVMEKVEERPLLRVPLAALTIGVLLVIAIINLPLQKIQNCNVSTVETDISCQSIPYYIYCCILAFIACSMFLRMSFELKILLLSAAFIVYNIIIFHTGHFKNDLPSNSTGILKDLQKMSCFYLSLFYLTLVLLARQVDYYSRLDCLWKKKFREEDEEIGTMENLNRLLLENVLPAHVAAYFIDNSKMNEDLYHQSYDCVCVMFASVPEFKVFYTECDVNKEGLECLRLLNEIIADFDELLMKPKFSGVEKIKTIGSTYMAAAGLTVTQGQENNQDQEKQNAQIGIMVEYAMALMVKLDGINRHSFNNFRLRVGINHGPVIAGVIGAKKPQYDIWGNTVNVASRMETTGELGKIQTTEETCHILESLGYACECRGLINVKGKGELRTYFVCTDMAKSQTVGMN", "metadata": {"id": "A0A8C5PZ03", "cluster": 2813614, "interpro_all": ["IPR001054", "IPR018297", "IPR030672", "IPR009398", "IPR029787"], "interpro_used": ["IPR009398", "IPR018297", "IPR001054"], "interpro_unused": ["IPR029787", "IPR030672"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein is associated with the Protein of unknown function DUF4169 family, which consists of proteins with currently uncharacterized biological roles. It is expressed in hydrothermal vent metagenome. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 2458, 1956, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 22548, 3416, 16, 2154, 7543, 1927, 2697, 1956, 5077, 24528, 3933, 5456, 18, 2176, 1977, 3198, 1922, 26959, 14654, 16552, 2225, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MANIINFNKAGKKIAKIKQEKQAGKNRARFGQKKPAKRIIKKEIKALKDHLDAHKISDKDDNGDKERS", "metadata": {"id": "A0A3B1B3R4", "cluster": 8151135, "interpro_all": ["IPR025227"], "interpro_used": ["IPR025227"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want a protein that has the function: The protein has a Calponin homology (CH) domain that functions as a cytoskeletal interaction module, primarily binding F-actin to regulate cell contractility and structural organization. Often found in tandem pairs to form a stable actin-binding domain, this four-helix bundle structure can also mediate localization to microtubule plus-ends or facilitate signal transduction depending on the protein context. It has been characterized in Anaeramoeba ignava (Anaerobic marine amoeba) and carries UniProt keyword assignments Cell projection, Cilium, and Flagellum. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 2258, 43, 15946, 6655, 9039, 12, 2016, 13, 3418, 1988, 4088, 1966, 43, 14787, 2835, 9059, 16, 5985, 2743, 48, 17, 4718, 1942, 5741, 2024, 17862, 1930, 4346, 5901, 18, 3868, 2435, 1922, 10361, 5803, 1942, 2386, 43, 4700, 4718, 17, 2743, 3418, 16, 2052, 3006, 17, 7864, 14142, 3170, 2112, 2222, 8265, 5363, 1942, 10544, 5390, 17, 9618, 2014, 6628, 2733, 8201, 6362, 1990, 1920, 2213, 4491, 18, 2176, 2258, 2252, 4378, 1922, 11381, 1976, 6802, 7972, 12046, 15777, 12, 12554, 10789, 27714, 1019, 13, 1930, 16252, 20709, 11121, 2538, 18306, 2024, 11244, 16, 28997, 16, 1930, 7030, 10757, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MSRISPQTRALLLRISYNKDIQYLKQNDQEEIKKVSTTDLLIRWTNLLTQSSITDISQLSDCLILGKLIAYLTETSLNKQLQTEQSLQKRASIFFDLLKNAGLKAVFSAEDLTNGNENEILKILAQMFLWKSGLPLKERPKTPTEQSAEKKSNIQDILSRIKQKSKSPINQMISHKETKTETTQNEETQTKSNSKAKISNFHLSKRNSNKKKSIAFSNFIRKK", "metadata": {"id": "A0A9Q0RE25", "cluster": 10165663, "interpro_all": ["IPR001715", "IPR036872"], "interpro_used": ["IPR001715"], "interpro_unused": ["IPR036872"]}, "task_type": "autoregressive"} {"instruction": "Function:\nThe protein possesses a Adenylate cyclase, N-terminal domain that comprises the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase. It is present in Tetraodon nigroviridis (Spotted green pufferfish) (Chelonodon nigroviridis).\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 14465, 43, 23052, 16526, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 56, 17, 4262, 5329, 3031, 1930, 1920, 2561, 9117, 25, 17, 26, 4675, 3031, 1927, 23052, 16526, 18, 2176, 1977, 2481, 1922, 12470, 12268, 17452, 14127, 18596, 12, 21268, 4524, 6612, 3429, 14422, 13, 12, 11749, 23557, 28615, 17452, 14127, 18596, 13, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MSWFSGFLVARVDDRKSAWGERNGPRYMSCLRDPDAMEPPSGAPLHQHHRGGVHYGKRGGALGEGVGLKSVDLGFEDGDLTDCWLSRKLERLYQRYFFRLNQSSLTIPVGRHGAVHGADGGVGAGVRRADGGAQERLRGNLVVRVLHLHHLHSAAREDEGLWKQVSANVLIFLCTNIIGICTHYPAEVSQRQAFQETRRLLLSVLPRHVAMEMKADINAKKEDMMFHKIYIQKHDNVKKPNRKGGSSLCNAGAVGGGGNFGVRCGWQEDRVVRVFQSKKFQVQPQRLPPGLHVDGQLPGDRRPGGGAERVLSVIHVVTTWHINQEDPFGYIQARLHLQRENQQQE", "metadata": {"id": "H3DQA2", "cluster": 11279942, "interpro_all": ["IPR032628"], "interpro_used": ["IPR032628"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein is classified under the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. In addition, the protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is expressed in Okeania sp. SIO3B5 and is connected to UniProt keyword ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3198, 1922, 12167, 5376, 10306, 2056, 18, 5998, 8583, 24462, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MRLIGLTGGIGTGKTTVSNYLGSLILENIVEHYGADILLPNGNLNRQKLGEHPYVRDRFEQNIQQFIVKNNQLGYHTSEGYPTAVTNTSLQQQIERLIQRDRLTQEQAYSTLEILLKQVDSAIANSSSPENKTYHLPIWDADIYARQAVQPIVFNNQEELFWLEKQIVLVVPLLFEAKMTDLVTEIWTRINHQMPLEDKCQQADIVLDNS", "metadata": {"id": "A0A6L9ZRH4", "cluster": 12356667, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein belongs to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is produced by Leucoagaricus sp. SymC.cos and carries UniProt keyword assignments Transmembrane helix, ATP-binding, and Membrane.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 4152, 2007, 9906, 6952, 13279, 24375, 2056, 18, 2985, 1030, 18, 4890, 1930, 16252, 20709, 11121, 2538, 18306, 9117, 7864, 16, 4498, 17, 2743, 16, 1930, 3260, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MLWQVMGHWLRGEKWCVLDVPLLIEGSAEIQLQRLMLRDGSTHVEYADTVIDNSGSRAELEEQVIAFINKMNKLAAWTLARRNLFSRRNRKRAPLWKFVGLVVVVYCEDASARLNSQLPIATKETGQARWLLSWLIPPVGIV", "metadata": {"id": "A0A137QCA0", "cluster": 12520199, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein is a member of the Lambda repressor-like, DNA-binding domain superfamily, which functions as a transcriptional regulator controlling critical genetic switches such as bacteriophage lysogeny and bacterial sporulation. This domain typically adopts a four-helix closed folded leaf topology, a variation of the helix-turn-helix motif, to mediate specific DNA binding and interactions with RNA polymerase. Structural analogs of this fold are also conserved in eukaryotic POU transcription factors and the N-terminal domain of the metabolic enzyme cyanase. Moreover, the protein falls within the HigA family, which comprises short, bacterial helix-turn-helix proteins that function as the antitoxin in the hig (host inhibition of growth) system. These proteins neutralize the cognate HigB killer protein, preventing its toxic effects on the host. It occurs in Acidobacteriota bacterium and contains UniProt keyword associations Membrane, Transmembrane, and Transmembrane helix. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 18279, 14434, 17, 3189, 16, 2678, 17, 2743, 3418, 13975, 16, 2154, 4088, 1966, 43, 5224, 7888, 7138, 4140, 3299, 21529, 2427, 1966, 24613, 3629, 27791, 1930, 4543, 23647, 18, 2052, 3418, 5745, 24032, 43, 3006, 17, 7864, 8047, 16318, 6998, 13678, 16, 43, 4516, 1927, 1920, 7864, 17, 5165, 17, 7864, 5219, 16, 1942, 8265, 2487, 2678, 2743, 1930, 3719, 1956, 3146, 6479, 18, 4346, 13204, 1927, 2052, 3728, 2032, 2222, 5305, 1922, 10825, 28398, 3213, 2790, 1930, 1920, 56, 17, 4262, 3418, 1927, 1920, 4487, 4113, 10208, 2051, 18, 3950, 16, 1920, 2213, 12182, 2651, 1920, 21340, 1019, 3416, 16, 2154, 12936, 3662, 16, 4543, 7864, 17, 5165, 17, 7864, 2697, 1988, 2347, 1966, 1920, 10310, 9754, 1922, 1920, 21340, 12, 4423, 3523, 1927, 2905, 13, 2433, 18, 2144, 2697, 25885, 1920, 15786, 21340, 1014, 16644, 2213, 16, 8444, 2496, 6161, 2564, 1990, 1920, 4423, 18, 2176, 5110, 1922, 2687, 5883, 3940, 3857, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 7031, 1920, 3244, 18, 3], "output": "MLRKPIEIDTRFVPPWTGAIMLWPFILYRPGQRTPRTAMYMHYLWRQCLRCWVLPWLLCYLILGLFYLPRKRWWQHPLQIYAHAVSAGVREQLRLVGKEGRTVAIPNTVGGGCAREGGPPGHPGELIGKMFLNGLGFTEEEFSGRLGASPESLRAVLQGDEAVTADFALRLERVTRVGADFWLALQHRHDQWQVTQSERAAAIEALEPLPLAT", "metadata": {"id": "A0A9E4J5E7", "cluster": 15892887, "interpro_all": ["IPR010982", "IPR013430"], "interpro_used": ["IPR010982", "IPR013430"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "It is part of the Type II secretion system protein GspE, N-terminal superfamily, which constitutes the N-terminal domain of general secretory system II protein E members typically involved in Type IV pilus biogenesis. Some members of this group also participate in other processes, such as cellular aggregation in *Myxococcus xanthus*. Structurally, the domain features an extra C-terminal helix that packs against a shorter N-terminal helix. It is present in Bacteroidetes bacterium QS_8_64_10.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 2176, 1977, 3131, 1927, 1920, 2601, 2890, 5512, 2433, 2213, 5022, 9626, 16, 56, 17, 4262, 13975, 16, 2154, 14879, 1920, 56, 17, 4262, 3418, 1927, 3335, 11518, 2433, 2890, 2213, 47, 4678, 5745, 3286, 1922, 2601, 4370, 7547, 1957, 13008, 18, 2673, 4678, 1927, 2052, 2210, 2222, 7352, 1922, 2303, 4028, 16, 2427, 1966, 3689, 7883, 1922, 14, 21464, 8256, 15213, 1957, 14, 18, 12171, 16, 1920, 3418, 4075, 1925, 8324, 45, 17, 4262, 7864, 1988, 5464, 1036, 3316, 43, 7310, 56, 17, 4262, 7864, 18, 2176, 1977, 2481, 1922, 26808, 14061, 15178, 41, 28, 41, 4723, 41, 2119, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MSALEDLFGNFSSGNGDDSAAGSSGDDEKQTDWDDPDLKALQHSLEEQREDAAGQASSASPDRDEVQDESGDDGEGEDLRRAMATSTDEDDAPAAGDDASARLNWLVDFVGEEDAPPPAEDGSLDDMAGIFHNKVLMGLLQRDAVDVTQAVRAVRQKKRQPDRANAEGIRHAEITENRPTTEFLETVLAVLPTPVRKQFMYLGLPTHPYVKDFVEGLDVEVELRYAPEATISECIEDVQKVEAVAQETQGLADGETSETDEDDDVSSDDDETVAARADAPADDEQTPDAADSHPDKEPETRHPRDDDTDRQQFGPEAPPPDKEAGDASAIESDPDDAEALLDDVLDTAAREKITSLFEQDDAATRQSTDAEDHLAALYETDSGKEEKEDVDFEADEPTESTPADEPSKANDEEAVSRRAPLWDVLANLPDVDSQEVFVEALPYAFEVDEEAVQQHLVVASHYDGLSTGPLGELLQARDESATDAPAAPAPPAEEDE", "metadata": {"id": "A0A2T2U6K8", "cluster": 17978126, "interpro_all": ["IPR037257"], "interpro_used": ["IPR037257"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein possesses a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein is a member of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is found in Chthoniobacterales bacterium and is annotated with UniProt keywords Isoprene biosynthesis and Transferase.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 2435, 1922, 2016, 1963, 13339, 5883, 3955, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MQLRAPAKVNLSFRILHRREDGFHEIETLMAPVSLYDDINIARLPAERGIEMATGLRIELRKGIPHGAGLGGGSSDAASTLLGLNELLGAALSLAELAELGGRIGARLQRELPLLLLKPQFGVPTSWAYSRWTDSRELPHVGYKRQDLLVQPETGAALMSGSGSTVFAVLREHSDADALAQRAKMEVDPGLWTSACATIAAAFTCDDSSLPLGEENLIVKAARLFLSAVSSDVPFFIFRSAAVCSGRGEKVRAFAGETFFNDLERPVFEKHLFLSHLKMW", "metadata": {"id": "A0A838N093", "cluster": 18822061, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR004424", "IPR006204"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein should include a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. Moreover, the protein contains a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Additionally, the protein includes a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. It occurs in Planctomycetaceae bacterium and contains UniProt keyword associations Cytoplasm, DNA damage, and SOS response.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 3066, 3951, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 3950, 16, 1920, 2213, 5461, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 4950, 16, 1920, 2213, 5921, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2176, 5110, 1922, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 16, 2678, 4293, 16, 1930, 17668, 2644, 18, 11586, 5655, 3581, 18, 3], "output": "MIEKRQFELVSEFDPAGDQPQAIEALVNGINSGQRNQVLMGVTGSGKTFTMANVIERIQKSEFKSFFPRNAVNYFVSYYDYYQPEAYIPQRDIYIEKDASINEEIDRLASVSSIYGLGSPEDYKEMMVSAAKGQIIQRDELLRKLIDIQYERNDVGFERTKFRVRGDCVEDQLSIIDPTTGESIQTLENIFIYPAKHFVMPEQRIESAVRAIRDLNARTRYDVEMLQEVGYCPGVENYSRHLAGRKEGEPPDTLAMWAGDRSRKSTLVDHGFRLPSALDNRPLTFEEWEGKSRSAVFVSATPNDYELEQSPARGQVTHLLEQIRERAAAGDRVLVTALTKRLAEDLSDFFEQEGVKCKWLHSVGVNLLREGLDLPEVSLVAILDADKEGFLRSETSLIQTIGRSARNVNAKVILRRRELQEEFNKKHGITPETIKKNIQSGIETEAAAHIQANAAVGRTNDEDIAAEQMEFERAAALRDRIIQMQDLIGKRISDVEVESYTAKRGHSRKKKASQKVPRPKRGPTLVISHNKTLAAQLYRLASTSSLVSRDDVIIVIWPSYEEFAYRIELWGDEIELREQLALFKDEGKLLEAQRYDFFPDDFLLFVDESHVSVPQVRSGEVVEQVIRPTGLLDPIIEVVELDAFERVELLRDLRAGRFEALYADKVTNSMRRAIDETQITQDYINDLEKEMMA", "metadata": {"id": "A0A3C0WH63", "cluster": 19001783, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR014001", "IPR001943", "IPR001650"], "interpro_unused": ["IPR024759", "IPR036876", "IPR027417", "IPR041471", "IPR004807", "IPR006935"]}, "task_type": "infilling"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein features a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Moreover, the protein is assigned to the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. Furthermore, it is part of the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. It occurs in Aspergillus homomorphus (strain CBS 101889) and is described by UniProt keywords Nucleus, mRNA processing, and Manganese.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 2176, 5110, 1922, 17604, 16350, 12492, 11119, 24315, 1036, 12, 3943, 16341, 9447, 7331, 1026, 13, 1930, 1977, 2910, 2007, 20709, 11569, 5607, 16, 3616, 4587, 16, 1930, 19516, 18, 3], "output": "MTAPPARQWGVTPPISTALPTPDELAANDDLISELKAQNNFESPAETERRQQVLQLLQRVALEFVKVVSRKKGLSPAAVEAAGGKILTYGSYRLGVYGPGSDIDTLVVGPKHVVIDDFFSDFPPVLERLAPPGAIEKMTPVPDAFVPIIKMELSGISIDLIFARLIVPSVPMSLDLKNNDYLRGLDEKEVRSLNGTRVTDQILELVPQQKTFRLALRAIKLWAQQRAIYANVVGFPGGVAWAMLVARVCQLYPQATGSVIVGKFFRIMTKWAWPQPVLLKPIEDGPLQMKVWNPKIYNGDRFHLMPIITPAYPSMCATHNVSVSTKTVILRELQRGGDIVDKIFTKQLNWNDLFKRHTFFTQDYKYYLSITASSRTKEAESVWSGLVESKIRHLVGALDRKATIAVAHPFPKGFERVHKVSSEEEIEAVKTGSTKYQDREIKTETTDETKDAAHEAAAQNGAENREVPATEEKAAEDTRVMYTATYYIGLELKPLEPGASRSLDISSDAQLFKSLCTAWPGYQPEVMDVAITHVRSFDLPDDVFQPGEKKPLRPKKKIIKRSDASGQKRTIDSLDDASHPAAKRQVTSNGVSNGVASAASTPA", "metadata": {"id": "A0A395I925", "cluster": 19567333, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR007012", "IPR043519", "IPR011068"], "interpro_unused": ["IPR014492", "IPR048840", "IPR007010"]}, "task_type": "autoregressive"} {"instruction": "The protein should feature a Domain of unknown function DUF58 domain that characterizes a family of prokaryotic proteins with currently undefined biological roles. It appears in both eubacteria and archaebacteria, and is sometimes found in proteins that also contain a Von Willebrand factor type A domain. It has been detected in Acidobacteria bacterium RIFCSPLOWO2_12_FULL_66_21. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 3418, 1927, 5435, 2347, 4855, 17968, 1025, 3418, 1988, 26735, 43, 3416, 1927, 21545, 2697, 1956, 5077, 26687, 3933, 5456, 18, 2176, 5107, 1922, 2321, 4791, 7972, 2341, 18339, 1930, 13470, 7972, 2341, 18339, 16, 1930, 1977, 8929, 2435, 1922, 2697, 1988, 2222, 5531, 43, 14147, 30067, 2991, 2601, 43, 3418, 18, 2176, 2258, 2252, 3330, 1922, 2687, 10296, 14061, 12424, 2792, 2030, 1971, 5265, 41, 2369, 41, 4125, 41, 4970, 41, 2900, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MPRTPIGGRVGERLGSGTGSSLEFQDYRPYAPGDDLRHVDWAAYARSELLAVRLYREEVAPRIDLVLDISRSMAVTEQKLRAYGELSGLLACACTSTVADTRIITTSAVQPQPLHVPEDIERVLVCDAGLSALEEVHLPFRRRSLRVVVSDFLFPHDADVLVSRLARDSALLTIVQLTLREEAEPVVEGARRLVDVEDRGELDMVIDEGAIRDYRARFSRLRLGLSRAARRAGARFAHVVAGTPIRSVARELAAAGILESC", "metadata": {"id": "A0A1F2TWS8", "cluster": 19751431, "interpro_all": ["IPR002881"], "interpro_used": ["IPR002881"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein is a member of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein possesses a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Furthermore, the protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is identified in Cyanobacteria bacterium UBA8530 and has UniProt annotations Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 14465, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 2899, 1922, 21897, 14061, 4803, 1019, 10025, 4294, 1930, 2258, 20709, 15010, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MASNEVLHVKAPAKINLFLAIGARRPDGFHDLETIFHAIELCDELSFRKTKESFRITCLAPDVPTDSSNLIWKAAELLKKEKGCSFGCEVELKKKVPMGAGLGGGSSDAAATLRALDRLWETHSTRGELERMAAKLGSDVPFFLGKGTALGKGRGEILESLPSLPELFLVVALPQVRISTPWAYARLDEMPARRHFSIAPMLEALKKGSLSEIAQSLGNSFEEALFPSLPILADLKKKLLSSGALGASLSGSGSAMFGLYENEEKAKRAADGLRAEGFTAYPLTPSLSPRCASTDG", "metadata": {"id": "A0A355UVX8", "cluster": 20803759, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR013750", "IPR006204"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein includes a Kinesin-like KIF1-type domain that is conserved in kinesin-like proteins, specifically members of the kinesin-3 family such as KIF1, KIF13, KIF28, and unc-104. This feature is approximately 50 amino acids in length. It is present in Strongylocentrotus purpuratus (Purple sea urchin).", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 5921, 43, 19378, 17, 3189, 18177, 1009, 17, 2601, 3418, 1988, 1977, 5305, 1922, 19378, 17, 3189, 2697, 16, 4475, 4678, 1927, 1920, 19378, 17, 23, 3416, 2427, 1966, 18177, 1009, 16, 18177, 3633, 16, 18177, 4839, 16, 1930, 5269, 17, 8824, 18, 2052, 5961, 1977, 3993, 2761, 3835, 4576, 1922, 3471, 18, 2176, 1977, 2481, 1922, 3206, 2199, 26907, 6843, 1957, 25945, 9280, 1031, 1957, 12, 14308, 9309, 3674, 28964, 13, 18, 3], "output": "MNSKWLFLPRDDMFRQSLAKLREDVVKANALIREANFLGEEMGKQTEFRVTLQIPVCNLTPNRKRGAIVSELAIQVKRKDRGTQIWSVEKLENKIIDMRDMYNDRKDEGIPLKDEESESLRKLSFFESQVHFPSLTLFPPLTLFPHHSLFPSHILVLTCNGIR", "metadata": {"id": "A0A7M7PJ44", "cluster": 20861351, "interpro_all": ["IPR022140"], "interpro_used": ["IPR022140"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein is categorized in the Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid superfamily, which encompasses enzymes sharing a characteristic alpha-alpha barrel fold composed of mostly antiparallel helices. Members function as protein prenyltransferases that transfer farnesyl or geranylgeranyl groups to CaaX motifs to facilitate membrane anchoring, or as terpenoid cyclases involved in the biosynthesis of cholesterol, antibiotics, and toxins. Moreover, the protein should include a Squalene cyclase, N-terminal domain that forms the N-terminal portion of integral membrane enzymes, such as lanosterol synthase and hopene synthase, which utilize an alpha 6-alpha 6 barrel fold. These enzymes catalyze the complex cationic cyclization of linear triterpenes, including squalene and 2,3-oxidosqualene, into fused ring compounds essential for sterol and hopanoid biosynthesis. In addition, the protein is a member of the Squalene hopene cyclase family, which functions as an integral membrane enzyme to directly cyclize squalene into hopanoid products involved in triterpenoid biosynthesis. Predominantly found in bacteria, these enzymes generate lipids that modulate membrane fluidity and permeability similarly to eukaryotic sterols. It has been detected in Phycisphaerae bacterium and is linked to UniProt keywords Isomerase and Repeat.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 6005, 17125, 2642, 16526, 1036, 19, 2213, 9972, 2199, 9961, 4595, 17, 4595, 8184, 2642, 13975, 16, 2154, 21569, 5038, 10763, 43, 6293, 4595, 17, 4595, 19560, 3728, 7179, 1927, 6969, 28892, 12789, 18, 4678, 2347, 1966, 2213, 9972, 2199, 18580, 1988, 3856, 24281, 2199, 2014, 9559, 12804, 4938, 12804, 2671, 1942, 20951, 1039, 8277, 1942, 6628, 3260, 20816, 16, 2014, 1966, 6005, 17125, 2642, 16526, 1036, 3286, 1922, 1920, 8132, 1927, 5463, 16, 7560, 16, 1930, 13599, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 4687, 2603, 2912, 16526, 16, 56, 17, 4262, 3418, 1988, 4952, 1920, 56, 17, 4262, 7717, 1927, 12328, 3260, 5038, 16, 2427, 1966, 19027, 23030, 8921, 1930, 12737, 2912, 8921, 16, 2154, 12561, 1925, 4595, 26, 17, 4595, 26, 19560, 3728, 18, 2144, 5038, 18170, 1920, 2796, 15175, 25267, 1927, 4258, 5083, 1967, 17125, 1918, 16, 2710, 4687, 2603, 2912, 1930, 22, 16, 23, 17, 3618, 1951, 2048, 2603, 2912, 16, 2460, 10305, 6335, 4300, 4415, 1958, 20408, 1930, 11089, 9286, 1960, 8132, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 4687, 2603, 2912, 12737, 2912, 16526, 3416, 16, 2154, 4088, 1966, 1925, 12328, 3260, 4113, 1942, 4103, 3637, 2606, 4687, 2603, 2912, 2460, 11089, 9286, 1960, 4461, 3286, 1922, 5083, 1967, 17125, 2642, 8132, 18, 7700, 2435, 1922, 4802, 16, 2144, 5038, 5655, 8238, 1988, 8480, 3260, 29555, 1930, 8828, 4852, 1942, 10825, 29991, 18, 2176, 2258, 2252, 3330, 1922, 25511, 9119, 29164, 3336, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 25510, 1930, 6865, 18, 3], "output": "MTTTSTRVDRERLTASLSAAQTALLAQQRDDGHFCGELEGDSILESEYLLMKFILRQEHAARPDGSPGRATLEKIAEQLRRQQRPDGGWGQYPGSGVDLSATVKAYFALKLMGDDPTLEAMQAARAVIRANGGAEHCNSFTNFYLAALGQVPWSAVPAIPPEIVFLPRWSYFHLDTVSAWTRTMIMPLSIVATLQPTRRLETTDGIDELFIDEEERRRLTASRTPDRWSRFFLGIDRLLKIAGSGMPLRRIALRRVERWILARAGQDGPAATDGLGAIFPPMVSIQIALDALGYEPEHPARVRAEAELDALFIDDGTAIRIQPCFSPVWDTGIALYALTDCGMTEADEPACAAAAWLRAKECRHVGDWHRNVRGEVEPSGWYFEYHNAWYPDVDDTAMVAMSLRRTGGAANRRASARGVAWMLAMQNDDGGWAAFDRTRDRAILERIPFADHNAMQDPSCPDITGRVLECLAWHGLRRDHPAIDRAVAYIRSHQEPDGAFFGRWGVNYLYGTWQAVVGPVRCGIDPAEPWLERAGAWVRSVQQPDGGFGETANSYVDPAFRGQGPATASQTAWAAMTLLALAGPHDDAVERAMSWLMTHQLDERRAADPEENPDGDPAGSWAETQFTGTGFPEVFYLRYHLYRLYFPLMALGRYRAALQAAGEERPALKVRPKVVVG", "metadata": {"id": "A0A947FZK5", "cluster": 21525498, "interpro_all": ["IPR006400", "IPR032696", "IPR032697", "IPR018333", "IPR008930"], "interpro_used": ["IPR008930", "IPR032697", "IPR006400"], "interpro_unused": ["IPR032696", "IPR018333"]}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein is associated with the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. In addition, the protein should have a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein should feature a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is found in Planctomycetes bacterium RBG_16_64_12 and has UniProt annotations Isoprene biosynthesis and Transferase. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 1977, 2458, 1956, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 2435, 1922, 4720, 2341, 25148, 14061, 6160, 1029, 41, 2641, 41, 4723, 41, 2369, 1930, 2258, 20709, 15010, 26690, 1021, 8132, 1930, 13763, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MHLHRSPSGWVVHAPAKLNLFFEVLARRDDGYHEIETLVYPINLYDTLFFKEDASGQIKFGLERVSGVWGPKGSGLGEVPLGADNLVVRAAELLRRRCGAPRGAVVRLVKRIPSAAGLGGGSSDAAAALAAANAAWGLGRSAAQLGSLAAELGSDVPSFFAGGPAVCRGRGEQVQAAGDLGMLHFVVVRPPVGLSTAEVYETCRPAARPRPLAPLLDALARGDVARAGRLLFNRLEPAARELSPWIHRVESELARLDLLGHGMTGSGSCYFGLCRHARHAGRVARHLQAKGIGVAFPVRGSR", "metadata": {"id": "A0A1G3AD38", "cluster": 25007527, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "autoregressive"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein includes a FPG/IleRS-type zinc finger domain that functions as a C-terminal DNA-binding motif in base excision repair enzymes and isoleucyl tRNA synthetases. In repair enzymes like Fpg and Endonuclease VIII, it coordinates a zinc ion to facilitate the recognition and flipping of oxidized purines and pyrimidines, supporting N-glycosylase and AP lyase activities. Additionally, the protein includes a Zinc finger, DNA glycosylase/AP lyase-type domain that facilitates DNA binding in bifunctional enzymes involved in the base excision repair of oxidative damage. Found in proteins such as Fpg and Endonuclease VIII (Nei), this motif stabilizes the recognition complex to support the excision of oxidized bases, such as 8-oxoguanine, and subsequent AP lyase-mediated backbone cleavage. It is derived from Williamsia sp. 1135 and is classified with UniProt keywords Metal-binding and Zinc-finger.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 5921, 43, 23833, 19, 9940, 5675, 17, 2601, 7997, 8497, 3418, 1988, 4088, 1966, 43, 45, 17, 4262, 2678, 17, 2743, 5219, 1922, 5170, 10940, 5059, 5038, 1930, 24467, 1978, 2199, 10089, 18185, 1036, 18, 1922, 5059, 5038, 3189, 23833, 1930, 18697, 18675, 16, 2176, 10675, 43, 7997, 4755, 1942, 6628, 1920, 5708, 1930, 16405, 9219, 1927, 11339, 19700, 1036, 1930, 21611, 1036, 16, 6184, 56, 17, 20067, 2051, 1930, 2100, 23928, 4209, 18, 4950, 16, 1920, 2213, 5921, 43, 7997, 8497, 16, 2678, 20067, 2051, 19, 2100, 23928, 17, 2601, 3418, 1988, 11374, 2678, 2743, 1922, 29491, 5038, 3286, 1922, 1920, 5170, 10940, 5059, 1927, 5163, 4293, 18, 2435, 1922, 2697, 2427, 1966, 23833, 1930, 18697, 18675, 12, 2069, 1033, 13, 16, 2052, 5219, 19658, 1920, 5708, 2796, 1942, 3373, 1920, 10940, 1927, 11339, 11137, 16, 2427, 1966, 28, 17, 18588, 11056, 7290, 16, 1930, 4521, 2100, 23928, 17, 3434, 10787, 6404, 18, 2176, 1977, 3595, 2037, 16092, 2126, 2056, 18, 11549, 1015, 1930, 1977, 5947, 1956, 20709, 11569, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 11586, 5655, 3581, 18, 3], "output": "MSKSGNPESIYRRILDDIGGTAWSASQEVRHVERSLAGSAFAFSGGKLERFSGYFSRRKCQRPPRQGNGTCRIVSGVETAVLELHSYGREGLPCHRCGALIRREAFMNRSSFVC", "metadata": {"id": "A0A1X1BB43", "cluster": 25066577, "interpro_all": ["IPR000214", "IPR010663"], "interpro_used": ["IPR010663", "IPR000214"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein is classified under the Peptidase S1C family, which encompasses serine peptidases and non-peptidase homologues, including the bacterial protease Do and magnetosome-associated proteins like MamE and MamO. These members function in biomineralization by promoting magnetite nucleation, localizing proteins to the magnetosome, and facilitating crystal maturation through proteolytic activity. Moreover, the protein is classified under the Chloroplastic and Bacterial Serine Proteases family, which comprises peptidase S1C serine proteases that function in the degradation of abnormal exported proteins, propeptide processing, and protein maturation. These enzymes contribute to stress resistance and virulence, often exhibiting dual chaperone activity to assist in refolding misfolded proteins. Many members utilize PDZ domains to regulate proteolytic activity and determine substrate specificity, such as binding to C-terminal Tyr-X-Phe sequences. Furthermore, the protein is associated with the Peptidase S1 (PA clan) chymotrypsin-like fold superfamily, which encompasses a diverse range of serine and cysteine proteases found in viruses, prokaryotes, and eukaryotes. These enzymes are structurally characterized by two six-stranded antiparallel beta-barrels that form a central cleft housing the catalytic machinery responsible for proteolytic activity. It originates from Anaerolineae bacterium and corresponds to UniProt keyword Signal.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 1977, 5947, 2441, 1920, 24050, 25480, 3416, 16, 2154, 21569, 8468, 24050, 1036, 1930, 2447, 17, 24050, 18541, 16, 2710, 1920, 4543, 7154, 2608, 1930, 14634, 4283, 17, 2458, 2697, 3189, 20272, 1021, 1930, 20272, 1037, 18, 2144, 4678, 2347, 1922, 4071, 29384, 2007, 7356, 17637, 2057, 17254, 16, 29507, 2697, 1942, 1920, 14634, 4283, 16, 1930, 12440, 6561, 7655, 2596, 12712, 2455, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 17471, 1935, 1930, 4543, 8468, 12447, 3416, 16, 2154, 12936, 24050, 25480, 8468, 12447, 1988, 2347, 1922, 1920, 4877, 1927, 4552, 20721, 2697, 16, 5062, 8253, 4587, 16, 1930, 2213, 7655, 18, 2144, 5038, 4672, 1942, 3071, 3554, 1930, 9304, 16, 3868, 12196, 7064, 14044, 2455, 1942, 6589, 1922, 28306, 20303, 2697, 18, 3086, 4678, 12561, 17755, 4682, 1942, 5741, 12712, 2455, 1930, 3415, 4510, 4896, 16, 2427, 1966, 2743, 1942, 45, 17, 4262, 9036, 17, 66, 17, 10422, 3709, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24050, 4062, 12, 3838, 6958, 1022, 13, 27799, 17, 3189, 3728, 13975, 16, 2154, 21569, 43, 6445, 3109, 1927, 8468, 1930, 8666, 12447, 2435, 1922, 6241, 16, 28149, 16, 1930, 15021, 18, 2144, 5038, 2032, 12171, 4378, 2007, 2288, 3798, 17, 10338, 28892, 4666, 17, 19560, 1036, 1988, 2386, 43, 4101, 14649, 13178, 1920, 6804, 10853, 5061, 1958, 12712, 2455, 18, 2176, 22970, 2037, 11381, 8419, 3336, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 2733, 18, 3], "output": "MRVNKRKSLALSMVAAITARLTSNTALPTTTSVIRLDGPLPVNSVTIEVVSQATSPFGRQQVQQGLGSGFVWDTKGNVVFSDGTTAAATLVAADPQSDLAVIKVALAGCGAVATAAGLPAATSVAALQNAFENVYDEVNPSVIVTNNHVIDGATQIT", "metadata": {"id": "A0A7C3YD38", "cluster": 26560876, "interpro_all": ["IPR051201", "IPR009003", "IPR043504", "IPR001940"], "interpro_used": ["IPR001940", "IPR051201", "IPR043504"], "interpro_unused": ["IPR009003"]}, "task_type": "infilling"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein contains a Leucine rich repeat 4 repeat that functions as a structural motif primarily involved in mediating protein-protein interactions and molecular recognition, typically forming a solenoid shape to facilitate binding with diverse partners. In addition, the protein has a Copper amine oxidase-like, N-terminal domain that forms the structural stalk of mushroom-shaped copper amine oxidase homodimers, facilitating the oxidation of primary amines to aldehydes via a copper ion and topaquinone cofactor. This domain adopts a fold consisting of a five-stranded antiparallel beta-sheet twisted around an alpha-helix and is also observed in related enzymes such as cell wall hydrolases and amidases. Furthermore, the protein features a Leucine-rich repeat, typical subtype repeat that folds into a characteristic horseshoe shape to provide a versatile structural framework for protein-protein interactions. It features a parallel beta-sheet on its concave face ideal for binding alpha-helical ligands, facilitating diverse biological processes including signal transduction, cell adhesion, and immune responses. This domain is found in a wide range of proteins, such as tyrosine kinase receptors and virulence factors, across organisms from viruses to eukaryotes. It is derived from Clostridium sp. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 5461, 43, 12624, 5536, 6865, 24, 6865, 1988, 4088, 1966, 43, 4346, 5219, 5985, 3286, 1922, 10239, 2213, 17, 2213, 3719, 1930, 3272, 5708, 16, 5745, 7402, 43, 12168, 20815, 5989, 1942, 6628, 2743, 1956, 6445, 7228, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 9541, 13610, 10488, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 4952, 1920, 4346, 19447, 1927, 21903, 17, 9132, 9541, 13610, 10488, 29227, 16, 12440, 1920, 6638, 1927, 3065, 20739, 1942, 25075, 3454, 43, 9541, 4755, 1930, 3700, 15287, 18402, 2290, 15155, 18, 2052, 3418, 24032, 43, 3728, 7600, 1927, 43, 3628, 17, 10338, 28892, 4666, 17, 11130, 16985, 1919, 4760, 1925, 4595, 17, 7864, 1930, 1977, 2222, 2528, 1922, 2712, 5038, 2427, 1966, 2024, 4821, 30337, 1930, 28813, 2319, 18, 3677, 16, 1920, 2213, 4075, 43, 12624, 17, 5536, 6865, 16, 5939, 8856, 6865, 1988, 16231, 2460, 43, 6293, 15638, 10647, 1021, 5989, 1942, 3394, 43, 20425, 4346, 6465, 1958, 2213, 17, 2213, 3719, 18, 2176, 4075, 43, 6110, 4666, 17, 11130, 1990, 2496, 26019, 6171, 8950, 1958, 2743, 4595, 17, 11514, 6908, 16, 12440, 6445, 3933, 4028, 2710, 2733, 8201, 16, 2024, 6141, 16, 1930, 3743, 3387, 18, 2052, 3418, 1977, 2435, 1922, 43, 4743, 3109, 1927, 2697, 16, 2427, 1966, 6941, 4016, 4086, 1930, 9304, 2790, 16, 3436, 7373, 2037, 6241, 1942, 15021, 18, 2176, 1977, 3595, 2037, 21156, 2056, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MKRIISIFLLIVVLITAFQGLALAEDKPIKVFIDGIGFETNPPATILNGTTYVPLFPLCEVLGAEVNIIENGSNVTYVITREMTNKKLELAPGNDFVKVNDKIVKIAVPPVLNMVWSETNEKVTVVPIKFVVEELGGVVLWDQKGGRIIADSCKPIVFEDENLEAAVREIIKIPEGEFYKSDVASVQTLIISEREISSIEGLQYFENLSYLDITENSVTDLTPIRNLTNLSNLLISGNPVVDYSPVVKIFSALKQRDFDIRISIYEQKIKSAVQAKLNKKDSNFTVEEILKVKELDLSGRGLSDLQGLQYLVNLTDLDLSDNNISDLQHIKCLDGLKRLVLDSNSIESLDYLINLNALEELSLKNNNINDISVLSKLVSLKKLNLSNNKIFNIDPLKNLTGLKELYISDNYIDDFSPVNEYYLDIELKDFETYIEIVQRFYIGKKNYYVNNREKEMDIAPMIKNGRTFLPIRYVSETLGAVVGWDDVEKKVTVRLNDTTIELWIGKDIARVNGEEVPVDEAPFIHEGRTVLPLRFVGENLNMKVGWNDEEKEVTLYNSTYVENHPEEFLE", "metadata": {"id": "A0A7X8MHL8", "cluster": 26652278, "interpro_all": ["IPR012854", "IPR001611", "IPR025875", "IPR003591", "IPR032675", "IPR036582", "IPR050836"], "interpro_used": ["IPR025875", "IPR012854", "IPR003591"], "interpro_unused": ["IPR001611", "IPR032675", "IPR050836", "IPR036582"]}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: The protein is categorized in the Aerotolerance-related protein BatD family, which confers tolerance to oxygen in *Bacteroides* species. These proteins typically contain up to three membrane-spanning regions to facilitate survival in oxidative environments. It is expressed in Vibrio tapetis subsp. tapetis and has UniProt annotations Transmembrane helix. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10234, 1922, 1920, 6049, 11099, 3823, 2152, 17, 2712, 2213, 11579, 1007, 3416, 16, 2154, 16556, 6555, 1942, 4612, 1922, 14, 27978, 14, 3038, 18, 2144, 2697, 5745, 5531, 2353, 1942, 2559, 3260, 17, 13346, 3451, 1942, 6628, 3298, 1922, 5163, 8114, 18, 2176, 1977, 3198, 1922, 23280, 19688, 3600, 19615, 18, 19688, 3600, 1930, 2258, 20709, 15010, 9117, 7864, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MASISQRNRVLLVIQTICLVLVFTFSAAINAKQLSSVKEQVSISAWLANEEEPDLAAKFYVNEQVKLYIEVSTPTWFSAGTRISYIDVPNAIVKQSNQLATNYTTREKGQTWSKQRWEITLFAQQVGRYEIPPTTVSVTVADENRQKLALEFVTPRIMFEAVTPTELADPSKPWFSATKARIHQTWQKSDDVLKVGDSITRTVMIDATDTLSIFLPSTISTDSTEYYQNFAAPNQLSDQQSRGSYHAKRVEQRTYVVQKGGELVFPEQQFVWWNSKTKTQQVLTLPEHRFQIKHTFVSFVQQYQKAIVVALSALGGAIILIGWMIRYYRHRPLPELACLLNLLRLQHWPQVRAVVYQRLRNKTGLLALSGYQAHDQWQRHSQQLQTEVTSRYVVTWIWFQMKNRANKSRKFVFKCLNL", "metadata": {"id": "A0A2N8ZIP1", "cluster": 28247075, "interpro_all": ["IPR025738"], "interpro_used": ["IPR025738"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "\"The protein should include a AAA-type ATPase core domain that functions as a molecular motor, coupling ATP binding and hydrolysis to conformational changes that remodel or translocate target substrates. It typically assembles into oligomeric ring structures, often hexamers, containing conserved Walker A and B motifs essential for enzymatic activity. This module drives diverse cellular processes, such as protein unfolding and DNA processing, by mechanically manipulating macromolecules. Furthermore, the protein is grouped in the AAA ATPase domain-containing protein family, which utilizes ATP hydrolysis to drive the unfolding of substrate proteins and the disassembly of protein complexes. These proteins are integral to protein quality control pathways, including endoplasmic reticulum-associated degradation (ERAD), and participate in diverse cellular processes such as organelle biogenesis, vesicle fusion, and cell division. Also, the protein includes a PUB (or PUG) domain that functions as a AAA ATPase binding module, commonly found in peptide N-glycanase and other proteins associated with the ubiquitin-proteasome system. It adopts an \u03b1(2)-\u03b2-\u03b1(2)-\u03b1(2)-\u03b1 fold characterized by a cluster of helices with a small antiparallel \u03b2-sheet on one side. It is produced by Pelagomonas calceolata.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 3066, 3951, 43, 13835, 17, 2601, 9444, 4728, 3418, 1988, 4088, 1966, 43, 3272, 4842, 16, 7590, 4498, 2743, 1930, 9128, 1942, 8523, 2840, 1988, 7456, 1938, 2014, 26377, 2758, 6249, 18, 2176, 5745, 17421, 1036, 2460, 19206, 6335, 4061, 16, 3868, 25602, 1036, 16, 3165, 5305, 20138, 43, 1930, 44, 8277, 4415, 1958, 8145, 2455, 18, 2052, 9059, 15435, 6445, 3689, 4028, 16, 2427, 1966, 2213, 17490, 1930, 2678, 4587, 16, 2007, 17841, 23107, 20625, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 13835, 9444, 3418, 17, 3165, 2213, 3416, 16, 2154, 18127, 4498, 9128, 1942, 9265, 1920, 17490, 1927, 4510, 2697, 1930, 1920, 20702, 1927, 2213, 5048, 18, 2144, 2697, 2032, 12328, 1942, 2213, 3455, 2285, 3873, 16, 2710, 13355, 12279, 17, 2458, 4877, 12, 14827, 13, 16, 1930, 7352, 1922, 6445, 3689, 4028, 2427, 1966, 19309, 13008, 16, 11502, 5289, 16, 1930, 2024, 8451, 18, 2222, 16, 1920, 2213, 5921, 43, 3080, 12, 2014, 6612, 1029, 13, 3418, 1988, 4088, 1966, 43, 13835, 9444, 2743, 9059, 16, 5384, 2435, 1922, 4207, 56, 17, 15060, 2051, 1930, 2303, 2697, 2458, 1956, 1920, 6526, 17, 9993, 2433, 18, 2176, 24032, 1925, 160, 12, 22, 13, 17, 161, 17, 160, 12, 22, 13, 17, 160, 12, 22, 13, 17, 160, 3728, 4378, 2007, 43, 4377, 1927, 12789, 1956, 43, 2858, 28892, 161, 17, 11130, 1990, 2340, 4159, 18, 2176, 1977, 4152, 2007, 7874, 10421, 3947, 1934, 2799, 1021, 10173, 3857, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MSLGSLPRDALDALETIASNLQREPHNAKFRTLAALAGLGFVKRDDAMTLETIDMRAVERTLAAVKPPPKQAWGTQRSPSPKKPPKPRAPLDAERNRVTAREMQGGPRWEDRLILLYGPPGCGKGLLAACLATEWGRGDLVTVHGAELRLAPCVLLVRGLELNDCGDALMDLKGPDDRVIVIVTCSVLPTDQLLNVPMPSSFERSRLVASCLSRSSGSDSPAPPYDIRRNASRRKPRASVLESDFDMVLDAVPSLDAITPAAERALRAADGDESEATPVKRGIRRLSNAAVQRRLGSHAARAAKNTEGITWNVVDTTMPSRPNTSWDDVVGLGQVKTELQQISEFSRSKSEAKRFYDRARSTPSRRRRALRSRATEGLAAFDVDDLAGQMLGFAPRAVVRVVDAATLAPNREASDGLVCDWGDALAWR", "metadata": {"id": "A0A7S3ZTS7", "cluster": 28583974, "interpro_all": ["IPR050168", "IPR003959", "IPR027417", "IPR036339", "IPR018997"], "interpro_used": ["IPR003959", "IPR050168", "IPR018997"], "interpro_unused": ["IPR036339", "IPR027417"]}, "task_type": "infilling"} {"instruction": "Here is the protein function: The protein falls within the Duplicated hybrid motif superfamily, which forms a structural domain consisting of a half-barrel $\\beta$-sheet arrangement found in bacterial glucose-permease-like enzymes. This motif is integral to domain IIa of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) for sugar uptake and phosphorylation, and is also present in peptidoglycan hydrolases like *Staphylococcus aureus* LytM. Additionally, the protein contains a M23ase beta-sheet core domain that constitutes the catalytic center of zinc-dependent metallopeptidases involved in bacterial peptidoglycan hydrolysis and remodeling. This structural motif coordinates a zinc ion to facilitate specific activities, such as glycyl-glycine endopeptidase cleavage, which are essential for cell wall metabolism, growth, and virulence. Additionally, this conserved beta-sheet architecture is found in select sugar permeases and eukaryotic chemotaxins involved in neurite formation. Also, the protein is included in the Bacterial cell wall metabolism enzyme family, which encompasses murein hydrolase activators, endopeptidases, and transglycosylases critical for cell wall dynamics. These proteins facilitate cell division and expansion by activating hydrolases for septal cleavage or remodeling peptidoglycan structures such as polyglycine interpeptide bridges. Additionally, some members contribute to virulence by degrading host proteins like elastin or assisting in spore cortex maturation. It is produced by Actinomycetota bacterium and corresponds to UniProt keyword Signal. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 12182, 2651, 1920, 19479, 5249, 5219, 13975, 16, 2154, 4952, 43, 4346, 3418, 7600, 1927, 43, 4768, 17, 19560, 8, 38, 4666, 8, 17, 11130, 13002, 2435, 1922, 4543, 3817, 17, 6191, 2051, 17, 3189, 5038, 18, 2052, 5219, 1977, 12328, 1942, 3418, 17433, 1927, 1920, 8078, 9356, 18425, 12631, 2010, 30, 9523, 8078, 9961, 2433, 12, 8618, 13, 1958, 9523, 5047, 1930, 4050, 16, 1930, 1977, 2222, 2481, 1922, 24183, 30337, 3189, 14, 13452, 8849, 14, 7518, 15375, 18, 4950, 16, 1920, 2213, 5461, 43, 6056, 6675, 4127, 4666, 17, 11130, 4728, 3418, 1988, 14879, 1920, 6804, 4102, 1927, 7997, 17, 3100, 8969, 24897, 1036, 3286, 1922, 4543, 24183, 9128, 1930, 8378, 18, 2052, 4346, 5219, 10675, 43, 7997, 4755, 1942, 6628, 2487, 4209, 16, 2427, 1966, 4235, 2199, 17, 10646, 16239, 9626, 2410, 9200, 6404, 16, 2154, 2032, 4415, 1958, 2024, 4821, 4714, 16, 2905, 16, 1930, 9304, 18, 4950, 16, 2052, 5305, 4666, 17, 11130, 9335, 1977, 2435, 1922, 8702, 9523, 6191, 2319, 1930, 10825, 12776, 17234, 1036, 3286, 1922, 15912, 3337, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4543, 2024, 4821, 4714, 4113, 3416, 16, 2154, 21569, 6185, 14818, 20748, 15497, 16, 16239, 9626, 2410, 30413, 16, 1930, 2127, 17038, 4879, 18801, 24605, 1918, 4140, 1958, 2024, 4821, 5565, 18, 2144, 2697, 6628, 2024, 8451, 1930, 7013, 2007, 8019, 30337, 1958, 16458, 6404, 2014, 8378, 24183, 4061, 2427, 1966, 16115, 19602, 2053, 2107, 9626, 2410, 2261, 18142, 18, 4950, 16, 2673, 4678, 4672, 1942, 9304, 2007, 18192, 4423, 2697, 3189, 22684, 2014, 27840, 1922, 18445, 4997, 7655, 18, 2176, 1977, 4152, 2007, 4718, 13386, 19446, 3857, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 2733, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MPHINPRIKRTVTTVALLAALMSIQSFSGAASIHAATIHAAKMPPNLGPHTEHRWSWPTEPSHRVIGRYDPPIHNWLPGHRGIDLAGKTGQSIYAAGSGRVTFAGTLANKDVVVITHGSLRTTYEPVSAVVEVDQQVSKGELIGYLVPGASHCASATSVHCLHWGLKRGHLYLNPLRLVQPRVRLLPLWQN", "metadata": {"id": "A0A6I2X6B0", "cluster": 1736764, "interpro_all": ["IPR050570", "IPR011055", "IPR016047"], "interpro_used": ["IPR011055", "IPR016047", "IPR050570"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein includes a Leucine-rich repeat that folds into a characteristic horseshoe shape to provide a versatile structural framework for protein-protein interactions. Found in organisms ranging from viruses to eukaryotes, this motif typically utilizes its concave beta-sheet face to bind ligands, such as alpha-helices, and is involved in diverse processes including signal transduction, cell adhesion, and immune response. Furthermore, the protein is grouped in the Arabidopsis Inactive Receptor-like Kinases family, which functions in signal transduction and cellular communication, often acting as scaffolds or recognition receptors despite predominantly lacking catalytic kinase activity. These proteins regulate diverse plant processes including early zygote development, secondary cell wall formation, and immunity against pathogens like *Pseudomonas syringae* via interactions involving leucine-rich repeats and calmodulin binding. It has been detected in Arcella intermedia and features UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 5921, 43, 12624, 17, 5536, 6865, 1988, 16231, 2460, 43, 6293, 15638, 10647, 1021, 5989, 1942, 3394, 43, 20425, 4346, 6465, 1958, 2213, 17, 2213, 3719, 18, 2435, 1922, 7373, 6485, 2037, 6241, 1942, 15021, 16, 2052, 5219, 5745, 18127, 2496, 26019, 4666, 17, 11130, 6171, 1942, 4566, 6908, 16, 2427, 1966, 4595, 17, 12789, 16, 1930, 1977, 3286, 1922, 6445, 4028, 2710, 2733, 8201, 16, 2024, 6141, 16, 1930, 3743, 2644, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 8900, 9078, 3148, 17, 3189, 7784, 3416, 16, 2154, 4088, 1922, 2733, 8201, 1930, 3689, 6396, 16, 3868, 8290, 1966, 10603, 2014, 5708, 4086, 4281, 7700, 7046, 6804, 4016, 2455, 18, 2144, 2697, 5741, 6445, 4496, 4028, 2710, 3120, 16160, 7229, 2740, 16, 4067, 2024, 4821, 3337, 16, 1930, 7611, 3316, 7741, 3189, 14, 13461, 19468, 3336, 14, 3454, 3719, 5884, 12624, 17, 5536, 9569, 1930, 17537, 2743, 18, 2176, 2258, 2252, 3330, 1922, 9952, 5870, 11213, 1019, 1930, 4075, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MKDFYDATDGVHWARGNWTFSGVDPCALNWDGVTCSSGHVILLILPKRNVSGSIPSSIGNLTKLQKLDLSFNALVSTIPSSLSTLRDLEQIRFQSNSLTGTIPPSLGLLPKLDTLLLQVNQLTGSIPSSLGSLSHLSELNLSSNSLCGGCFVMNKSVDCVLTGIELDCSCNTLPDSCLFSCSNPLICPDPTNSPSSDTSIPAPIPSSLYVTPIPPPSPSPSPSLSPSPSPSPDPVSITPITPPSPSPTPISTITLSPPTQPQPIPTPHPQPTPPPPGKCSNGAQEGLCVSGNTTLNLNNTALHFMNITNGTITIIGNLSTTSLFLTNSQLDITGSYIVQNVSIEVDGTITIKNDMRFQSGWIVYESLGSRILVYGKVDLGETVLVVDLHQQEITTGEYIVLEAPNQSIVGVPNLVFKNKDPQQCSKTTTEIHRIKVFFMPCGRDEGVPVYTIVGGVIGGLFGLICLAGSFWVWFSPRYQDIKMDHFKSLIELQKKHQRV", "metadata": {"id": "A0A6B2L230", "cluster": 6532888, "interpro_all": ["IPR050994", "IPR001611", "IPR032675"], "interpro_used": ["IPR001611", "IPR050994"], "interpro_unused": ["IPR032675"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein falls within the Antirestriction family, which comprises bacterial ArdA proteins that protect unmodified plasmids from host restriction systems during conjugation. This activity enables the incoming DNA to evade degradation in the recipient bacterium and acquire cognate modifications. In addition, the protein is grouped in the Antirestriction protein ArdA, domain 3 superfamily, which forms the C-terminal region of the bacterial ArdA protein, facilitating plasmid evasion of host restriction systems during conjugation. Structurally, this domain comprises a three-stranded beta-sheet and three alpha-helices, incorporating a winged helix-turn-helix component. Despite resembling nucleotide-binding folds, it exhibits a reversed surface potential, indicating it does not bind DNA directly but contributes to the structural integrity of the antirestriction dimer. It is expressed in Phascolarctobacterium sp.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 2246, 2808, 3319, 1929, 3416, 16, 2154, 12936, 4543, 2245, 3825, 2697, 1988, 9145, 18602, 8069, 2037, 4423, 7587, 3771, 2409, 14122, 18, 2052, 2455, 10217, 1920, 22201, 2678, 1942, 28917, 4877, 1922, 1920, 10664, 14061, 1930, 13174, 15786, 6920, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2246, 2808, 3319, 1929, 2213, 2245, 3825, 16, 3418, 23, 13975, 16, 2154, 4952, 1920, 45, 17, 4262, 3031, 1927, 1920, 4543, 2245, 3825, 2213, 16, 12440, 5609, 25092, 1927, 4423, 7587, 3771, 2409, 14122, 18, 12171, 16, 2052, 3418, 12936, 43, 2559, 17, 10338, 4666, 17, 11130, 1930, 2559, 4595, 17, 12789, 16, 12553, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 4594, 18, 4281, 18994, 5489, 17, 2743, 16231, 16, 2176, 9826, 43, 9432, 3154, 2889, 16, 4168, 2176, 3731, 2084, 4566, 2678, 4103, 2308, 7624, 1942, 1920, 4346, 7996, 1927, 1920, 2246, 2808, 3319, 1929, 7632, 18, 2176, 1977, 3198, 1922, 18421, 12709, 4362, 2341, 12022, 2056, 18, 3], "output": "MLEIFVTNLSKYNAGELVGKWLSLPMDEEELTAALEEIGGEEQFISDYETSLDLRIGEHEDVFALNEQAQEFEDLEDWEQDIVQAYLEAFGGDLQGALNKYDDCTFYPGMSLIDVAYEIVEDCYDLPEVAQRYFDYDAFARDLGYDGYVEVSNGVICAN", "metadata": {"id": "A0A316S4H6", "cluster": 6975133, "interpro_all": ["IPR009899", "IPR041895", "IPR041893"], "interpro_used": ["IPR009899", "IPR041893"], "interpro_unused": ["IPR041895"]}, "task_type": "autoregressive"} {"instruction": "The protein possesses a Autotransporter beta-domain domain that functions as the C-terminal integral membrane beta-barrel in bacterial autotransporters, mediating the type V secretion of the passenger domain through the outer membrane. Furthermore, the protein should have a Autotransporter-associated beta strand repeat that facilitates the efficient transport of virulence factors to the bacterial surface. Also known as the Passenger-associated Transport Repeat (PATR), this motif likely adopts a $\\beta$-helical structure within the passenger domain, utilizing conserved glycines to enable the flexibility required for folding-driven secretion. It is typically found in bacteria associated with subtilisin-type protease domains and polymorphic outer-membrane protein repeats. Moreover, the protein features a Phosphatidic acid phosphatase type 2/haloperoxidase domain that functions as a type 2 phosphatidic acid phosphatase (PAP2) to dephosphorylate phosphatidate into diacylglycerol for lipid synthesis and signaling, or acts as a vanadium-dependent haloperoxidase to catalyze halide oxidation. This domain features a core 5-helical bundle structure with conserved residues for binding phosphate or vanadate cofactors. It occurs in Acinetobacter boissieri.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 5728, 5412, 24095, 4666, 17, 3418, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 12328, 3260, 4666, 17, 19560, 1922, 4543, 5728, 5412, 24095, 1036, 16, 10239, 1920, 2601, 64, 5512, 1927, 1920, 29240, 3418, 2596, 1920, 7642, 3260, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 5728, 5412, 24095, 17, 2458, 4666, 5984, 6865, 1988, 11374, 1920, 5807, 4860, 1927, 9304, 2790, 1942, 1920, 4543, 3154, 18, 2222, 3171, 1966, 1920, 29240, 17, 2458, 4860, 6865, 12, 2917, 1005, 13, 16, 2052, 5219, 3205, 24032, 43, 8, 38, 4666, 8, 17, 11514, 3170, 2651, 1920, 29240, 3418, 16, 10232, 5305, 10646, 1036, 1942, 8675, 1920, 10569, 3414, 1958, 10328, 17, 6446, 5512, 18, 2176, 1977, 5745, 2435, 1922, 4802, 2458, 1956, 14745, 1921, 17, 2601, 7154, 4682, 1930, 14240, 7642, 17, 3260, 2213, 9569, 18, 3950, 16, 1920, 2213, 4075, 43, 2766, 8525, 1935, 2687, 8167, 2601, 22, 19, 24980, 19883, 3418, 1988, 4088, 1966, 43, 2601, 22, 2766, 8525, 1935, 2687, 8167, 12, 3860, 1028, 13, 1942, 13517, 9075, 2766, 8525, 2010, 2460, 29527, 1958, 4486, 4271, 1930, 3197, 16, 2014, 8016, 1966, 43, 7409, 21913, 17, 3100, 24980, 19883, 1942, 18170, 4217, 2261, 6638, 18, 2052, 3418, 4075, 43, 4728, 25, 17, 11514, 14142, 3170, 1956, 5305, 4248, 1958, 2743, 5413, 2014, 7409, 24675, 21362, 18, 2176, 5110, 1922, 27182, 4078, 2348, 3453, 1033, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MKFQLSRLTVAIGLTLQSTVLFADTTPTATGAQILDKNVRLSVDVARSRTAIQEVQAYEIQILKKETGAFTTVNGIPKEAYTGSVADKGNGLGAKNAYNYPRPFRQMLDGQDLKSILGFPSGHTNAGYLAALSVAYVVPQQAGIHSPLDVIGGRMHATYYTIQGLLNNADLRRNATVSACYDSTDLNQRYTQYQTNKALYDKYTLIETRYPYLTANQRRDLLQTTSNARGGVLDQKTTINMNATDGGLSASDVWLNDISRNTWSGGTQLLAGTLIGSNGSAMTGSGTLYKQGTGLLNYTGDGSGFTGTTRVQTTIVESSGTLQGAGKLQNLQVLQGGTIQANSATSSGIDVSGRTQINAANVLLNSTNGVTGRFATVKSAYSFLTPQIGYTANTQRFNSVAQTANQYQVANSIESLGLGNSLYNLVAKQSYASLAVNATQDLLATTDFVAAQKYQTQPYLWLNSYGRQFGELPLNNQSSLGLVLGQGKGTAKVADNGFTAKDNNSQLGLYGVQRQINSTGLNSQANANLDVYSLQGFAEYGKSFQEQGADIANLYGTKSTNNMTFTGLGWQHALGDTQGQTTLQFNRASSYKVNGSEIAQAGQFASQSHSNEGTLKLDYRFISVKSGVDVLSGFNNLWKPGATWNTGDRQDANYAVLTALGPLQNTNNNLGQLVNLVNAVRYPASTTPQPSLVARVPATGQGDGQADLVLRAGEMGYSRVLYQQAQSFFATQCGGFANAFTAIGDTTLTPIVPDNAEVNGLGYDTLNLYKAANGYGAFNGQGQLEKTGTGSLTLVGFGQGAIFNQANLVLNHNTTESLANTNGQLNVTNRLNGDLTQSLNRLSVSGDLTLNQGTLKVLTQVGLGSEYNLLSEYVIVTLQLLRNDSDQARQSYNRLSGEGNNRAVDVSDSSYKNYGAVVGRYADENSNAIFGLFGRWGDVSFKPTALPISPYARLAHVVTQTTLGLKANYDFNLGSKPVTAQFDLAKVDVGVSTKLTNQLSFGLNY", "metadata": {"id": "A0A1G6GJC7", "cluster": 7210524, "interpro_all": ["IPR001011", "IPR005546", "IPR036709", "IPR013425", "IPR036938", "IPR000326", "IPR011050"], "interpro_used": ["IPR005546", "IPR013425", "IPR000326"], "interpro_unused": ["IPR036709", "IPR011050", "IPR001011", "IPR036938"]}, "task_type": "infilling"} {"instruction": "The protein I want to design has this role: The protein falls within the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. It has been characterized in Frankia nepalensis. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 12182, 2651, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2176, 2258, 2252, 4378, 1922, 14542, 2126, 23717, 8134, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MPWRHAPARHTDPYLGAAGRAGQTGLPRQATEKLGPDHGRAVILLAGADELMHHDPATAASWLTTASDLLPRTDPRRYDAQLLLAGAHLLLGRPDETRRGLRALVPQPTAPRASARFALYHGRASRLLDRRREARALFENGLRTADGDTGDVVPLHTEIAELALEDLDLPTAVWYAAAAAGLARGLADRTGEAGALAVLSLARLHAGDAAPARVAATAATAAAALIDAAPDAELIRDLASLRRLGAAESALDRLPDAERHLARGLTLSYDTGQAHVRGELLTSLAQVQLRRGCFQHALGSLTEARRAVLPGDVARAALIETTYAEVAPRSWPAWTSGTAARNRPPAPDGRE", "metadata": {"id": "A0A937RF81", "cluster": 8171502, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a complete amino acid sequence given the following functional description of a protein that will be able to perform the described role. The desired function is: The protein belongs to the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. Moreover, the protein is assigned to the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. It originates from Campylobacter coli and corresponds to UniProt keyword Transferase, Cell inner membrane, and Lipid metabolism.", "tokenized_instruction": [2, 5655, 43, 4080, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 1927, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2910, 2770, 18, 1920, 9465, 2347, 1977, 30, 1920, 2213, 14440, 1942, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 2176, 22970, 2037, 22657, 5178, 1930, 8852, 1942, 20709, 11121, 2538, 13763, 16, 2024, 6671, 3260, 16, 1930, 4486, 4714, 18, 3], "output": "MKPKYHLLNNARYALEGILALLKNEMAFRLELCVIIPAIIFSFFLDVSLLEHLFLIVVLILILIAEALNSAIEACVDLITNEWHEKAKVAKDCASAAVFFSVCLALFIWGFILGKLWL", "metadata": {"id": "A0A644SCH0", "cluster": 8232305, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR000829", "IPR033718"], "interpro_unused": ["IPR036945"]}, "task_type": "autoregressive"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein can be placed in the GHMP kinase, C-terminal domain superfamily, which encompasses the C-terminal structural component of ATP-dependent enzymes involved in amino acid, isoprene, and carbohydrate metabolism. This domain adopts a central alpha-beta plait fold that cooperates with the N-terminal domain to create a nucleotide-binding pocket. While primarily found in homoserine, galacto-, and mevalonate kinases, it is also present in structurally related diphosphomevalonate decarboxylases. In addition, the protein is a member of the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. In addition, the protein has a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. It is native to Aerophobetes bacterium and is described by UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 21569, 1920, 45, 17, 4262, 4346, 4594, 1927, 4498, 17, 3100, 5038, 3286, 1922, 3835, 2687, 16, 26690, 1021, 16, 1930, 10590, 4714, 18, 2052, 3418, 24032, 43, 4101, 4595, 17, 4666, 5606, 1932, 3728, 1988, 23230, 1036, 1956, 1920, 56, 17, 4262, 3418, 1942, 7762, 43, 5489, 17, 2743, 10154, 18, 2679, 5985, 2435, 1922, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 16, 2176, 1977, 2222, 2481, 1922, 12171, 2712, 11791, 2609, 2225, 4701, 8870, 23922, 1036, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2176, 1977, 6196, 1942, 6049, 2688, 16248, 14652, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MVKKNNYDLKLFSPAKVNLFFRVLKKRSDGYHEIASLMQAIDFGDTLSFSLSNKDAFTCSDPSLPMDRSNLIVKAINLFKRQTGKKFSLKLHLDKKIPMGAGLGGGSSNAATTLHALDRLLKTNLTTDALIKMGEMLGADVPFFFSKGTAYCTGIGEILEDIVCKPMNFILAKPKALSLSTPLVYKNCKIDAVSKTSPSFFRKRYTEDFFNFIQVLVNDLEYPAFKLEKTLFRFKKELEELGFNKVIMTGSGTAFMCFGKMQIPSLSDVLFYKVSSISKCSASWYPSK", "metadata": {"id": "A0A2A4YKE4", "cluster": 9207287, "interpro_all": ["IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR036554", "IPR004424", "IPR006204"], "interpro_unused": ["IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "The protein has a Serine/threonine-protein kinase active site that catalyzes the transfer of the gamma phosphate from ATP to serine or threonine residues on protein substrates, utilizing a conserved aspartic acid residue essential for enzymatic activity. This reversible phosphorylation regulates diverse cellular processes, including division, proliferation, and apoptosis. Additionally, the protein possesses a Zinc-ribbon domain that constitutes the full length of the archaeal large ribosomal subunit protein eL40. It also forms the N-terminal region of the eukaryotic serine/threonine-protein kinase VRK3 and bacterial membrane-associated proteins such as TcaA. In addition, the protein falls within the Protein kinase-like domain superfamily, which modifies other proteins by chemically adding phosphate groups. This enzymatic activity is fundamental to most signaling and regulatory processes in the eukaryotic cell. It has been detected in Leptospiraceae bacterium and contains UniProt keyword associations Transferase and Transmembrane helix.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 8468, 19, 13143, 17, 2213, 4016, 3500, 3200, 1988, 17097, 1920, 3856, 1927, 1920, 7034, 5413, 2037, 4498, 1942, 8468, 2014, 13143, 4248, 1990, 2213, 6249, 16, 10232, 43, 5305, 23047, 2687, 6181, 4415, 1958, 8145, 2455, 18, 2052, 10743, 4050, 7014, 6445, 3689, 4028, 16, 2710, 8451, 16, 4031, 16, 1930, 4091, 18, 4950, 16, 1920, 2213, 14465, 43, 7997, 17, 25149, 3418, 1988, 14879, 1920, 4125, 3471, 1927, 1920, 22367, 3103, 11196, 5903, 2213, 2349, 4241, 18, 2176, 2222, 4952, 1920, 56, 17, 4262, 3031, 1927, 1920, 10825, 8468, 19, 13143, 17, 2213, 4016, 12110, 16098, 1930, 4543, 3260, 17, 2458, 2697, 2427, 1966, 13828, 1019, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 2213, 4016, 17, 3189, 3418, 13975, 16, 2154, 25436, 2303, 2697, 2007, 13944, 8013, 5413, 2671, 18, 2052, 8145, 2455, 1977, 8829, 1942, 2501, 3197, 1930, 4948, 4028, 1922, 1920, 10825, 2024, 18, 2176, 2258, 2252, 3330, 1922, 24060, 11979, 1972, 3336, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 13763, 1930, 9117, 7864, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MNTCPNCQNKIPEKAKFCPVMLQKVLEPEFKIDKKLAIGGMAKVYIGEQPSLDRKEARTIAKVHHPNIIHVIHSGVSDLKSKKGETVFRFVDVLKFTEKILSGLQSAHEKGIVVDFGIAKILNSVAKTSAGTMIGVGIMLYEMLVGETPFAGDNSFTIVNETFIKELQPENLNHIQSILEKACAKQKEDAYNVVTETKQKFGLKLAVVIVSICALVGEVKLGCWVSSIYGKASINEKSLVQGQEVVTNGWIFGSKENTTFRFREKKEGKKHKIIFEVSKIIGIVKGSDLSQKTETKFRVDVRDKVSSSLKKSNWTEEEIAKSDYQPILEDLKSKRNIEKNWSELGLVKIATSTSHQTQNVKKEFMKRRREADELVYISRSEIEKLKRIGKIKRKEPNVLILKNGEKVAGLVYEPRNKVESIEFFEQCGSSFMEEIDHDLLVVVKVMLEQYAKDKDVQERFLLSRPYFVMEYMEGGSLSDFHRDIKPDNILLHSNDEPVITADYMSPEQCKGDPLIDGRSDIYSNKHIAENIPSVTHKFSSLGHRYQTADEFMLALKQLRHEIAGSIGYYFFQKQKKANEAKLSVKTTYNKTFADFQISDTTLEVIGEIIYDIRKIGPNQEIEIITPENIELIKGNVSIRPAIAEKFEEGKTTKMSKPGDKASVELTDVSKKAKDFSFEFKMEQLSYESKNIPELIRRKNKENEKVLSKPGIYTVETVNGEVENY", "metadata": {"id": "A0A960VYC6", "cluster": 10461682, "interpro_all": ["IPR011009", "IPR000719", "IPR008271", "IPR026870"], "interpro_used": ["IPR008271", "IPR026870", "IPR011009"], "interpro_unused": ["IPR000719"]}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein belongs to the Nucleotide cyclase superfamily, which encompasses catalytic domains found in adenylyl, guanylyl, and diguanylate cyclases responsible for synthesizing cyclic nucleotide second messengers. These domains share a core ferredoxin-like fold, though the specific nucleotide-binding mode differs between subtypes such as the GGDEF domain and adenylate cyclases. Moreover, the protein features a Adenylyl cyclase class-3/4/guanylyl cyclase domain that constitutes the conserved Class III catalytic core responsible for synthesizing cyclic nucleotides, such as cGMP from GTP, to act as intracellular second messengers. This domain plays a critical role in eukaryotic signal transduction by activating kinases and regulating ion channels, while in bacteria, it contributes to anti-phage immunity through the synthesis of specific signaling molecules. It is native to Leptidea sinapis and is classified with UniProt keywords Membrane, Lyase, and Metal-binding. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 5489, 16526, 13975, 16, 2154, 21569, 6804, 4682, 2435, 1922, 27802, 16, 13504, 25671, 16, 1930, 4325, 13785, 9075, 16526, 1036, 5061, 1958, 25292, 9821, 5489, 2812, 16716, 1036, 18, 2144, 4682, 7948, 43, 4728, 25304, 22389, 10960, 17, 3189, 3728, 16, 4170, 1920, 2487, 5489, 17, 2743, 5754, 11457, 2192, 8160, 2427, 1966, 1920, 12358, 3695, 1038, 3418, 1930, 23052, 16526, 1036, 18, 3950, 16, 1920, 2213, 4075, 43, 27802, 16526, 2921, 17, 23, 19, 24, 19, 13504, 25671, 16526, 3418, 1988, 14879, 1920, 5305, 2921, 4337, 6804, 4728, 5061, 1958, 25292, 9821, 9519, 16, 2427, 1966, 15958, 2037, 9319, 16, 1942, 4033, 1966, 4776, 2812, 16716, 1036, 18, 2052, 3418, 5705, 43, 4140, 2770, 1922, 10825, 2733, 8201, 2007, 8019, 7784, 1930, 6773, 4755, 5628, 16, 2679, 1922, 4802, 16, 2176, 7624, 1942, 2246, 17, 10503, 7611, 2596, 1920, 4271, 1927, 2487, 3197, 4206, 18, 2176, 1977, 6196, 1942, 16976, 27830, 3132, 2026, 1937, 1930, 1977, 5947, 1956, 20709, 11569, 3260, 16, 23928, 16, 1930, 6048, 17, 2743, 18, 7031, 1920, 3244, 18, 3], "output": "MADACVDSSKQTRFHEMHVQRHNNVSILYADIVNFTPLSERLSASDLVKTLNELFGRFDQIAQENQCMRIKILGDCYYCVSGLPVSRPNHAYNCVNMGLQMIDAIRFVREATGFNVDMRIGIHTGNVLCGVLGLRKWQFDVWSDDLGGRFEVEPGDGASREGYLADHKVETYLIVPPKKLSENGRLSVCTIDRKASIVSSICQDVSPTRPRENISPATSQHSIVEQEVPRVMRAESIRSPGNLCRRASSVKGDVLKAVAFENNNFTNSDAMGNGGVVTKPKSRSGSIIGAISPIIGTATPGIPNRSRPSSKMTKYVECWGADKPFANITDSTLAKNIGISSLAMIEQHLLPQKTCCDCSNNSEGMSRVTLWFKNTQQEYQYREQADNQFKYNVACACALFLLIAFIQLLTGVILYASFGPTAATLLLFVYLSWYDGRCPGRGMSLLPDSPDMYTDNCTKPGQIVASNCYIRLTVFVVTVVLIAACAVINLVRSILDFILKIKYMI", "metadata": {"id": "A0A5E4QBQ9", "cluster": 11872786, "interpro_all": ["IPR001054", "IPR029787"], "interpro_used": ["IPR029787", "IPR001054"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein is classified under the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Additionally, it is part of the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Also, the protein is classified under the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It is found in bacterium and is classified with UniProt keywords Cytoplasm and rRNA processing.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 1977, 5947, 2441, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 1977, 2435, 1922, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 5239, 1930, 9067, 4587, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MNYHVPVMLREVIDFLDPKPGAVYVDATLGTGGHTEIILKRGGRVIGNFSKLNQVLDGLKLETVKGIIYDLGTNLVQLENPERGFSLYRDRLREIIRNYGEERWAKRIARKIVKERKSKPIETTLQLAHITKTFQALRIVVNDELDSLKDSLKGVITYLEPGGRIIVLLTKKPLVPTEVEIKGNPRARSAKLRVAERIPLREKIDVDQEVLNIAKERLARFGERITYIHTGPLDMRMDRSLPITCQDLVNNLPEDVEETVFWKGCHKKKGDIHLASFHSLEDRIAKHTFLEWAKSDPPLVKI", "metadata": {"id": "A0A350D914", "cluster": 12168817, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein possesses a Protein DA1-like domain that functions as a ubiquitin-activated metalloendopeptidase to limit final seed and organ size by restricting cell proliferation. It utilizes a conserved HEXXH motif to cleave and inactivate proliferation-promoting substrates, including specific E3 ligases, deubiquitinases, and transcription factors. It occurs in Helianthus annuus (Common sunflower).", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 14465, 43, 2213, 3692, 1009, 17, 3189, 3418, 1988, 4088, 1966, 43, 6526, 17, 4128, 8969, 6802, 10249, 24897, 1942, 4411, 3948, 4861, 1930, 3090, 3081, 2007, 20571, 2024, 4031, 18, 2176, 18127, 43, 5305, 7142, 1039, 1023, 5219, 1942, 21252, 1930, 22331, 4031, 17, 7356, 6249, 16, 2710, 2487, 10968, 22423, 16, 29436, 2319, 16, 1930, 3213, 2790, 18, 2176, 5110, 1922, 3091, 19196, 24315, 1036, 5112, 25901, 1036, 12, 3059, 8147, 9893, 1915, 13, 18, 3], "output": "MEKRMQTECKLRLGQGASKELTIASVLKTAILVLYVFRGCREFNVAIIKEKNVIITSSGIRRPRIDGSWFVGMRTRHHKLTCRCEV", "metadata": {"id": "A0A9K3EHY1", "cluster": 14097375, "interpro_all": ["IPR022087"], "interpro_used": ["IPR022087"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. Moreover, the protein is included in the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Additionally, it is part of the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. It is identified in Verrucomicrobiota bacterium and contains UniProt keyword associations Cytoplasm and rRNA processing.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 2176, 1977, 2899, 1922, 3566, 3176, 13055, 1935, 15129, 3940, 3857, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 1930, 9067, 4587, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MGAAYAAVEPASESPEQPFYKLMADGTLGGGGHTEALLKAGATVKGIDRDADARAYFGDIATLAQVRGWERLDGILLDLGVLDMRMGGDGPTAADLVNNWSSEREKLKFERTSHLADGIEKLLGRRGRLGELRRFLKVAPDLLKPGGRLVKQTFRDASKEEIDRPEWPAPQPNPGRNSRSRSSRLRVVEKIQNLAHHESILLEEVVQFLQPVAGANERLARFGDRFEAVEGRSSHQLDCGDRGFSFRLDGPEAELRQIFWDLGEEKFARKIAAWIINHPATKVFQALRMEVNDEAIITFHSLEDRIYVYRLLTRKGIAPGGQEIA", "metadata": {"id": "A0A946GAR8", "cluster": 14999029, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR023397", "IPR029063", "IPR002903"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that has the following function: The protein should have a Phosphotransferase system, enzyme I N-terminal domain that functions as the catalytic region responsible for transferring a phosphoryl group to the phosphoryl carrier protein HPr within the bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS). This domain, also known as EIN, reversibly interacts with HPr to facilitate the coupled phosphorylation and translocation of carbohydrates across the membrane. Also, the protein contains a PEP-utilising enzyme conserved site that identifies a family of structurally related enzymes, including PPDK, PEP synthase, and PTS Enzyme I, which catalyze the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) via a phospho-histidine intermediate. This C-terminal region is associated with essential metabolic processes such as carbon fixation in plants, gluconeogenesis, and bacterial sugar transport. In addition, the protein is a member of the Phosphoenolpyruvate-dependent sugar PTS enzyme family, which facilitates the concomitant phosphorylation and translocation of sugar substrates across the cell membrane as a key component of the phosphotransferase system (PTS). These proteins typically function as Enzyme I, transferring a phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) via a conserved central histidine. Structurally, they are characterized by an N-terminal HPr binding site, a central catalytic domain, and a C-terminal pyruvate-binding domain. It is present in Elusimicrobia bacterium RIFOXYB2_FULL_48_7 and contains UniProt keyword associations Magnesium, Metal-binding, and Cytoplasm. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 8078, 9961, 2433, 16, 4113, 51, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 3031, 5061, 1958, 21902, 43, 12556, 2210, 1942, 1920, 12556, 9685, 2213, 18542, 2651, 1920, 4543, 8078, 9356, 18425, 12631, 2010, 30, 9523, 8078, 9961, 2433, 12, 8618, 13, 18, 2052, 3418, 16, 2222, 3171, 1966, 16101, 1022, 16, 26778, 9034, 1956, 18542, 1942, 6628, 1920, 6416, 4050, 1930, 7849, 1927, 16282, 3436, 1920, 3260, 18, 2222, 16, 1920, 2213, 5461, 43, 9110, 17, 4009, 4007, 4113, 5305, 3200, 1988, 14133, 43, 3416, 1927, 12171, 2712, 5038, 16, 2710, 20450, 1040, 16, 9110, 8921, 16, 1930, 8618, 4113, 51, 16, 2154, 18170, 1920, 3856, 1927, 43, 12556, 2210, 2037, 8078, 9356, 18425, 12631, 2010, 12, 9110, 13, 3454, 43, 8078, 17, 13873, 6129, 18, 2052, 45, 17, 4262, 3031, 1977, 2458, 1956, 4415, 4487, 4028, 2427, 1966, 5056, 7938, 1922, 4793, 16, 25680, 16, 1930, 4543, 9523, 4860, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 8078, 9356, 18425, 12631, 2010, 17, 3100, 9523, 8618, 4113, 3416, 16, 2154, 11374, 1920, 8537, 4050, 1930, 7849, 1927, 9523, 6249, 3436, 1920, 2024, 3260, 1966, 43, 3834, 4594, 1927, 1920, 8078, 9961, 2433, 12, 8618, 13, 18, 2144, 2697, 5745, 2347, 1966, 4113, 51, 16, 21902, 43, 12556, 2210, 2037, 8078, 9356, 18425, 12631, 2010, 12, 9110, 13, 1942, 1920, 12556, 9685, 2213, 12, 18542, 13, 3454, 43, 5305, 4101, 13873, 18, 12171, 16, 2611, 2032, 4378, 2007, 1925, 56, 17, 4262, 18542, 2743, 3200, 16, 43, 4101, 6804, 3418, 16, 1930, 43, 45, 17, 4262, 11867, 17, 2743, 3418, 18, 2176, 1977, 2481, 1922, 2349, 24327, 4913, 15129, 2126, 14061, 12424, 7221, 8520, 41, 4125, 41, 3427, 41, 27, 1930, 5461, 20709, 11121, 2538, 5253, 13148, 16, 6048, 17, 2743, 16, 1930, 5239, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MFILEKRKNKLELHGTPITSRVVIGEAYLFKQIDINGLLKNRYSLTDREISYELEKLGHALRKSKMQLEAARLQADNKTGKAAGGIFEAYICIIGDEVFLQKIKNNITEQRAAADYIIAKEIELLANASLASETNEITKNTLLTTLDIYYRLLRDLLNVEQVNHDFLRNTDNPVILVAERLVPSDIVSIKKEKVLGIIIEEGNPTSHVAILLKALKIPAIINVSGAGVLIKTGDVVALSGITGNIIVNPEKEELEDIKYKKSVYDQKNLKTAENKNLPCLTKDNIKIILEANVSTLEDAEDAFLNGAEGVGLVRSEIFYMTLEKIPSVEEEADFYKKLIICGKNKPITIRLLDIGADKNLPYLASIHEDNPELGTRGIRFLLKNTDLLKKQVMSILNASKTGPQPLVKILIPFVTTINDVDEAVKIIEEIAKEMGVNRDTYQIGIMVEIPAAALAINQFIHKVDFVSIGTNDLAQYVFAADRENNELNNYQQIYHPVVLGLIKSVADCARLNKKAVTVCGEIASDPVGASLLVGLGIQSLSMNPSAIPEIREALSGKYYKDLKIFADKALTCQDSSGILTLWNTFSSN", "metadata": {"id": "A0A1F9XLQ4", "cluster": 16743274, "interpro_all": ["IPR008279", "IPR050499", "IPR000121", "IPR023151", "IPR036637", "IPR024692", "IPR006318", "IPR008731", "IPR036618", "IPR015813", "IPR040442"], "interpro_used": ["IPR008731", "IPR023151", "IPR050499"], "interpro_unused": ["IPR006318", "IPR015813", "IPR036618", "IPR040442", "IPR036637", "IPR000121", "IPR024692", "IPR008279"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein falls within the Translation initiation factor 1A (eIF-1A) family, which is required for the maximal rate of protein biosynthesis. It functions by enhancing ribosome dissociation into subunits and stabilizing the binding of the initiator Met-tRNA to 40S ribosomal subunits, with homologues present in both eukaryotes and archaea. In addition, the protein belongs to the Nucleic acid-binding, OB-fold superfamily, which utilizes a conserved five-stranded $\\beta$-barrel motif to bind single-stranded nucleic acids or oligosaccharides. This versatile domain is found in diverse proteins, including ribosomal subunits, DNA ligases, and toxins, where it plays essential roles in DNA replication, repair, and translation. Moreover, the protein is grouped in the Probable RNA-binding protein EIF1AD family, which functions as a putative RNA-binding protein involved in the cellular response to oxidative stress. Members of this family contain an S1-like domain and nuclear localization signals, and interact with glyceraldehyde 3-phosphate dehydrogenase (GAPDH). It is derived from Brassica carinata (Ethiopian mustard) (Abyssinian cabbage).", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 12182, 2651, 1920, 6410, 6035, 2991, 5123, 12, 9493, 17, 5123, 13, 3416, 16, 2154, 1977, 3414, 1958, 1920, 7275, 2769, 1927, 2213, 8132, 18, 2176, 4088, 2007, 9221, 12794, 9182, 2460, 6991, 1930, 14384, 1920, 2743, 1927, 1920, 23467, 2130, 17, 10089, 1942, 29805, 11196, 6991, 16, 1956, 18541, 2481, 1922, 2321, 15021, 1930, 21501, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 11079, 2687, 17, 2743, 16, 2384, 17, 3728, 13975, 16, 2154, 18127, 43, 5305, 3628, 17, 10338, 8, 38, 4666, 8, 17, 19560, 5219, 1942, 4566, 2957, 17, 10338, 11079, 4576, 2014, 22012, 18, 2052, 20425, 3418, 1977, 2435, 1922, 6445, 2697, 16, 2710, 11196, 6991, 16, 2678, 22423, 16, 1930, 13599, 16, 2597, 2176, 5705, 4415, 5456, 1922, 2678, 5158, 16, 5059, 16, 1930, 6410, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 12584, 3146, 17, 2743, 2213, 9493, 6146, 1007, 3416, 16, 2154, 4088, 1966, 43, 6770, 3146, 17, 2743, 2213, 3286, 1922, 1920, 3689, 2644, 1942, 5163, 3071, 18, 4678, 1927, 2052, 3416, 5531, 1925, 4062, 17, 3189, 3418, 1930, 4254, 5363, 4771, 16, 1930, 6310, 1956, 22447, 23, 17, 5413, 9294, 12, 9747, 13, 18, 2176, 1977, 3595, 2037, 19503, 6102, 2279, 4058, 3857, 12, 18847, 1022, 4902, 2211, 13, 12, 2186, 2012, 6777, 3122, 11026, 7972, 2106, 13, 18, 3], "output": "MDAKGENSLALFPAKFRESMWIRRGSFIVCKVLFFEQIRLLQKSPEWPEIFRDAKPVPPLEANTNRLRPFGVQCDAETDSGSDSDSVVIDHTGKEKAQESGSKVTSADESSQIPIPQDDDIDLSDESDDGMP", "metadata": {"id": "A0A8X7UTY3", "cluster": 16774300, "interpro_all": ["IPR039294", "IPR012340", "IPR001253"], "interpro_used": ["IPR001253", "IPR012340", "IPR039294"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein according to these design specifications: The protein should include a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. In addition, the protein carries a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Moreover, the protein can be placed in the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. It is native to Rikenellaceae bacterium and contains UniProt keyword associations Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 3066, 3951, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2176, 1977, 6196, 1942, 11280, 11341, 5870, 1972, 3336, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MIVYPKAKINIGLRIIEKRSDGFHDLETFFFPVEMSDILEVRESNKVSMFHYGAAIDSLPEDNICLKAYNSIKKDFNLPPVEIHLYKRIPVGAGLGGGSSDAANTLIALKKLFSLSIDDQGLAEYAAKVGSDCPFFVYSSTLETAKGEGMLAKGRGEILTKIAIPQLEGVKIQIEKPPVFISTAEAYKGVTPNKSTAGLNELLSMPLESWKNNIVNDFEKSIFKKYPIIEEYKNKMYDKGALYASMSGSGSAVFGIFR", "metadata": {"id": "A0A359H3Z5", "cluster": 20531715, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR006204", "IPR004424"], "interpro_unused": ["IPR020568", "IPR036554", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "Give me the sequence of a polypeptide chain with the following function. The function of the polypeptide chain is The protein is associated with the Tetratricopeptide-like helical domain superfamily, which adopts a multi-helical, right-handed superhelical fold that presents an extensive solvent-accessible surface for binding large substrates like proteins and nucleic acids. These domains primarily mediate protein-protein interactions and the assembly of multiprotein complexes involved in diverse biological processes ranging from cell cycle regulation to protein transport. It occurs in Myxococcales bacterium 68-20 and corresponds to UniProt keyword Transmembrane, Transmembrane helix, and Signal.", "tokenized_instruction": [2, 7031, 2142, 1920, 3244, 1927, 43, 13022, 4659, 1956, 1920, 2894, 2347, 18, 1920, 2347, 1927, 1920, 13022, 4659, 1977, 1920, 2213, 1977, 2458, 1956, 1920, 12470, 3319, 21305, 17, 3189, 11514, 3418, 13975, 16, 2154, 24032, 43, 2779, 17, 11514, 16, 3659, 17, 17105, 3356, 23285, 2046, 3728, 1988, 8178, 1925, 6475, 7596, 17, 10551, 3154, 1958, 2743, 3103, 6249, 3189, 2697, 1930, 11079, 4576, 18, 2144, 4682, 5985, 8265, 2213, 17, 2213, 3719, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 3286, 1922, 6445, 3933, 4028, 6485, 2037, 2024, 4048, 3640, 1942, 2213, 4860, 18, 2176, 5110, 1922, 21464, 11748, 1918, 14061, 5117, 17, 2036, 1930, 8852, 1942, 20709, 11121, 2538, 9117, 16, 9117, 7864, 16, 1930, 2733, 18, 3], "output": "MKTRRIAAAVLFTLLPATVSLPAWSQQDDAITVQARARFKEGVEAFDKGKYEEARLAFLQAYALKKHPSVLLNLAQSSAKSNHPLDAAKYFQQFLKEATSASPQQRKDAETGLAEVRQKLGRIEVVAPAGTEISLDDQGKVGTMPMEALDVEPGSHTVKSPTQSVTVIAVVGQKVEARLGMPAAPAAVAPITAPPPSTEPTGEATEPALGPTPPADHGPSKRTNLLVPPKNMTPVYIGLGAAGFGAVSAIVFGLFKADAQDKADVVANQIRTAAAQRNIPAQGVCNSASAPAEFATACKTLVDNNDKVDTNAAIANVSLAVMGAGLVFAGAWYLTAPKRGASAPQTARAPQPPIVTPWAGWNTGGVSVAGQF", "metadata": {"id": "A0A1M3NDT7", "cluster": 22639338, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a polypeptide chain that performs the following role: The protein contains a 3-dehydroquinate synthase C-terminal domain that contains the key catalytic and Zn2+-binding residues required to convert 3-deoxy-D-arabino heptulosonic 7 phosphate into dehydroquinate. This alpha-helical module functions within the shikimate pathway for aromatic amino acid biosynthesis, existing either in isolation or as part of the pentafunctional AROM polypeptide. Furthermore, the protein is included in the Dehydroquinate Synthase family, which catalyzes the cyclization of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ), a pivotal step in the shikimate pathway. This enzymatic activity is essential for the biosynthesis of aromatic amino acids in bacteria, fungi, and plants. Moreover, the protein should have a 3-dehydroquinate synthase, N-terminal domain that adopts a Rossmann-fold structure to bind NAD+ in an inverted orientation and contributes to the formation of the enzyme's active site cleft. It facilitates the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate to 3-dehydroquinate and orthophosphate, a critical step in the shikimate pathway for aromatic amino acid biosynthesis. It is derived from Psychrobacillus sp. FJAT-21963 and is annotated with UniProt keywords Nucleotide-binding, Lyase, and Cytoplasm. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 5461, 43, 23, 17, 28936, 11072, 2010, 8921, 45, 17, 4262, 3418, 1988, 5461, 1920, 3834, 6804, 1930, 21061, 15, 17, 2743, 4248, 3414, 1942, 14450, 23, 17, 16333, 17, 46, 17, 20790, 1037, 20662, 11677, 3490, 27, 5413, 2460, 28936, 11072, 2010, 18, 2052, 4595, 17, 11514, 9059, 4088, 2651, 1920, 20837, 7369, 23874, 3374, 1958, 10761, 3835, 2687, 8132, 16, 6124, 3108, 1922, 7152, 2014, 1966, 3131, 1927, 1920, 9412, 2624, 20839, 8981, 13022, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 28936, 11072, 2010, 8921, 3416, 16, 2154, 17097, 1920, 25267, 1927, 23, 17, 16333, 17, 46, 17, 20790, 1037, 17, 20662, 11677, 8870, 27, 17, 5413, 12, 3692, 15870, 13, 1942, 28936, 11072, 2010, 12, 6781, 1055, 13, 16, 43, 13637, 3537, 1922, 1920, 20837, 7369, 23874, 3374, 18, 2052, 8145, 2455, 1977, 4415, 1958, 1920, 8132, 1927, 10761, 3835, 4576, 1922, 4802, 16, 10520, 16, 1930, 4793, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 23, 17, 28936, 11072, 2010, 8921, 16, 56, 17, 4262, 3418, 1988, 24032, 43, 18215, 8890, 17, 3728, 3170, 1942, 4566, 6577, 15, 1922, 1925, 12344, 7148, 1930, 7624, 1942, 1920, 3337, 1927, 1920, 4113, 11, 61, 3500, 3200, 14649, 18, 2176, 11374, 1920, 7309, 1927, 23, 17, 16333, 17, 46, 17, 20790, 1037, 17, 20662, 11677, 8870, 27, 17, 5413, 1942, 23, 17, 28936, 11072, 2010, 1930, 17266, 10647, 3508, 2722, 2057, 16, 43, 4140, 3537, 1922, 1920, 20837, 7369, 23874, 3374, 1958, 10761, 3835, 2687, 8132, 18, 2176, 1977, 3595, 2037, 3463, 15129, 13707, 5277, 1036, 2056, 18, 23726, 1926, 17, 18343, 7576, 1930, 1977, 10633, 1956, 20709, 11569, 5489, 17, 2743, 16, 23928, 16, 1930, 5239, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MIIPVRTKDSTYEVHLGENILKAFCDRNTEGFEKADKIVVITDENVWGLHRDYFDDNFSFNYQVHLVPNGEACKTFDSYFNVQTFLLQENCSRNSILLALGGGAVGDLTGFVASTFMRGIPFIQIPTTILAHDSAVGGKTAINHPNGKNMIGAFYQPKEVLYDFHFLNTLPKSEVRSGLAEVIKHALISDITWSNDFLKLESIDVIQKEELLVWLEKGIRVKARIVELDEKEKSYRKYLNFGHTYGHAIEATVGYGKITHGEAVMIGMIPALMLSEIYGEVKAGYARDVYKLAKKLEYNFQHVLNSPFDQLATFMLKDKKTTNGELHFALLNHIGDPFIQIVTMDEVKKCDDLLRKWIKEEI", "metadata": {"id": "A0A0Q3W2L2", "cluster": 24010477, "interpro_all": ["IPR050071", "IPR016037", "IPR030963", "IPR030960", "IPR056179"], "interpro_used": ["IPR056179", "IPR050071", "IPR030960"], "interpro_unused": ["IPR030963", "IPR016037"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein features a HAD-superfamily hydrolase, subfamily IIIA domain that functions as an aspartate-nucleophile hydrolase, encompassing enzymes such as histidinol-phosphatase and DNA 3-phosphatase. Structurally distinct due to the lack of insertion domains between catalytic motifs, it often constitutes the phosphatase component of bifunctional systems involved in histidine biosynthesis or polynucleotide kinase activities. Moreover, the protein has a Polynucleotide 3'-phosphatase domain that catalyzes the magnesium-dependent dephosphorylation of DNA 3'-phosphates, a critical step in repairing single-strand breaks caused by radiation or oxidative damage. Often linked to a DNA 5'-kinase domain, this HAD-superfamily member features distinct catalytic motif variations that may facilitate interaction with the DNA phosphate backbone. Also, the protein is classified under the Polynucleotide kinase 3 phosphatase family, which plays a key role in the repair of single-strand DNA breaks induced by DNA-damaging agents such as gamma radiation and camptothecin. It originates from Phellinidium pouzarii.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 4075, 43, 2430, 17, 13975, 20748, 16, 16227, 23876, 3418, 1988, 4088, 1966, 1925, 12878, 17, 2797, 28335, 20748, 16, 17527, 5038, 2427, 1966, 27507, 22816, 1945, 17, 8167, 1930, 2678, 23, 17, 8167, 18, 12171, 4493, 2810, 1942, 1920, 3630, 1927, 7413, 4682, 2192, 6804, 8277, 16, 2176, 3868, 14879, 1920, 8167, 4594, 1927, 29491, 3771, 3286, 1922, 13873, 8132, 2014, 15176, 15274, 4016, 4209, 18, 3950, 16, 1920, 2213, 2258, 43, 15176, 15274, 23, 11, 17, 8167, 3418, 1988, 17097, 1920, 13148, 17, 3100, 16881, 1927, 2678, 23, 11, 17, 26473, 16, 43, 4140, 3537, 1922, 5059, 1941, 2957, 17, 5984, 13065, 4189, 2007, 5442, 2014, 5163, 4293, 18, 3868, 4624, 1942, 43, 2678, 25, 11, 17, 4016, 3418, 16, 2052, 2430, 17, 13975, 7210, 4075, 4493, 6804, 5219, 6740, 1988, 2278, 6628, 2835, 1956, 1920, 2678, 5413, 10787, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 15176, 15274, 4016, 23, 8167, 3416, 16, 2154, 5705, 43, 3834, 2770, 1922, 1920, 5059, 1927, 2957, 17, 5984, 2678, 13065, 2719, 2007, 2678, 17, 15939, 4820, 2427, 1966, 7034, 5442, 1930, 6225, 4575, 20536, 3665, 18, 2176, 22970, 2037, 10422, 11560, 11566, 7408, 1989, 28398, 12813, 21094, 18, 3], "output": "MAMAQNLHAVVFPKKLPFLLTSTCLFGENLAPALRSKIAAFDLDYWNKKVPQVLKEVHDSGYSIVFFSNQCLHDKKLKQFMIFAATAKDMYRKPMPGMWLAVEKLAKDAGKSGTDRKFAENLDLKFSTPEVNKLFPGDDNTNKDKKTRQYYLTLLYRALCLPLLSERTTPDTKPERKKTVNWVFEGNSHEERFWRMWLQIDGKLFDRSSDAAAPVESIGPFHWGTVIKWSASKNGTDWEWRLKIPSIAKSLPDVPTIDRPNSFFVGDAAGRKGDFEYFLNKAPQPYTLQGVHAKSLGVPIRSSVELAWHNNLVPYLAFSSFAQGYEEPTVEEGFQDV", "metadata": {"id": "A0A4S4LAS0", "cluster": 25137031, "interpro_all": ["IPR036412", "IPR006549", "IPR023214", "IPR027417", "IPR013954", "IPR006551"], "interpro_used": ["IPR006549", "IPR006551", "IPR013954"], "interpro_unused": ["IPR023214", "IPR027417", "IPR036412"]}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein contains a Poly(A) polymerase, central domain domain that functions as a template-independent RNA polymerase to catalyze the specific incorporation of ATP at the 3' end of mRNA. This catalytic core shares structural homology with other nucleotidyl transferases and is essential for eukaryotic mRNA stability, nuclear export, and translation initiation. Moreover, the protein can be placed in the Nucleotidyltransferase, class I-like, C-terminal superfamily, which constitutes the C-terminal structural domain of class I enzymes, including eukaryotic poly(A) polymerases and archaeal tRNA CCA-adding enzymes. This domain adopts an $\\alpha/\\beta$ sandwich fold reminiscent of the RNA-recognition motif, contributing to the architecture necessary for nucleotide transfer. Moreover, the protein can be placed in the Nucleotidyltransferase superfamily, which comprises Pol beta-like enzymes that catalyze nucleotide addition via a conserved two-metal ion mechanism coordinated by carboxylate residues. This diverse group includes DNA polymerases, RNA-modifying enzymes such as PolyA polymerases and CCA-adding enzymes, as well as nucleotidyltransferases involved in protein regulation and antibiotic resistance. It originates from Ambispora leptoticha and is described by UniProt keywords Metal-binding, Magnesium, and Membrane.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 4286, 12, 43, 13, 6479, 16, 4101, 3418, 3418, 1988, 4088, 1966, 43, 7662, 17, 3484, 3146, 6479, 1942, 18170, 1920, 2487, 8629, 1927, 4498, 2019, 1920, 23, 11, 2482, 1927, 3616, 18, 2052, 6804, 4728, 16495, 4346, 9039, 1956, 2303, 2797, 4090, 2199, 13763, 1036, 1930, 1977, 4415, 1958, 10825, 3616, 5057, 16, 4254, 12660, 16, 1930, 6410, 6035, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2797, 4090, 2199, 9961, 16, 2921, 51, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 4346, 3418, 1927, 2921, 51, 5038, 16, 2710, 10825, 4286, 12, 43, 13, 20910, 1930, 22367, 10089, 13980, 17, 8013, 5038, 18, 2052, 3418, 24032, 1925, 8, 38, 4595, 19, 38, 4666, 8, 18038, 3728, 20395, 1927, 1920, 3146, 17, 5708, 5219, 16, 8739, 1942, 1920, 9335, 4680, 1958, 5489, 3856, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2797, 4090, 2199, 9961, 13975, 16, 2154, 12936, 2492, 4666, 17, 3189, 5038, 1988, 18170, 5489, 2459, 3454, 43, 5305, 2288, 17, 6048, 4755, 2856, 11651, 2007, 20877, 4248, 18, 2052, 6445, 2210, 5921, 2678, 20910, 16, 3146, 17, 12691, 5038, 2427, 1966, 4286, 1019, 20910, 1930, 13980, 17, 8013, 5038, 16, 1966, 2486, 1966, 2797, 4090, 2199, 18580, 3286, 1922, 2213, 3640, 1930, 7267, 3554, 18, 2176, 22970, 2037, 6168, 1937, 21086, 16976, 3153, 2722, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 16, 13148, 16, 1930, 3260, 18, 3], "output": "MTENTNGYGKIWVFSEYFILSLGQTLECFKVTPPRSLSLNPQQDWRIQHLGVTPPIALSQPTPREFEVTDSLLEELKEQGTFESEEESKRREVVLGKLDKIVKDFVKQICRKKNLSEADANEAGGKIFTFGSYRLGADIDTLCVVPRHVVREDFFTEMHEALRCRNEVTELTSVTDAYVPVIKMKFQNIPIDLVFASLGVSKVPDDLDLQDNSLLKNLDETCIRSLNGSRVTDEILRLVPNIPAFRTSLRCIKLWAKRRAIYSNIMGFFGGVAWAMLVARICQLYPNAIAGAIVSRFFRIMYQWNWPQPVLLKPIEEGPLQVRVWNPKLYPIDRSHLMPIITPAYPSMCATHNVTSSTKKIIENEFKRAAEIADKVMVGTGKWNELFAKHDFFMRYRYYLQIIASSDSPERQLKWAGMVESKIRHLITKLELVENLSLAHPFVNGFEKVQYCRNDQEQSDIAYGMFDNNNSAEVNTAAQSQDNVRRIYTTTFYIGLFIEPRSTGATAPRQLDISWPISEFTKMVKSWDKYDEQTMAIVVNNVKRNALPADVFEDGEPRPIRRKSPRATPGSPRATPGKNKFLNTTTTGTEQPNKKRRGSNDTVMSAFDQVNLNNNEPILNGSENLTTLSPATPPTASFDQHVRQTVKSGP", "metadata": {"id": "A0A9N8ZPR3", "cluster": 1337745, "interpro_all": ["IPR043519", "IPR011068", "IPR007012", "IPR048840", "IPR007010", "IPR014492"], "interpro_used": ["IPR007012", "IPR011068", "IPR043519"], "interpro_unused": ["IPR048840", "IPR014492", "IPR007010"]}, "task_type": "autoregressive"} {"instruction": "Here is the protein function: The protein is categorized in the GlcG-related carbohydrate metabolism protein family, which functions in carbohydrate metabolism and transport, particularly in the utilization and regulation of cellular glucose levels. These proteins contribute to overall energy homeostasis by processing glucose and glucose-derived molecules through various biochemical pathways. Also, the protein is classified under the Corrinoid adenosyltransferase PduO/GlcC-like family, which comprises bacterial and fungal proteins with a Roadblock/LC7-like fold that perform diverse catalytic and regulatory functions. Members include PduO, an enzyme that converts cob(I)alamin to adenosylcobalamin, as well as regulatory proteins involved in glycolate pathway control, heme binding, and formaldehyde sensing. It is present in Olivibacter sp. LS-1. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 19954, 1029, 17, 2712, 10590, 4714, 2213, 3416, 16, 2154, 4088, 1922, 10590, 4714, 1930, 4860, 16, 4443, 1922, 1920, 8422, 1930, 3640, 1927, 3689, 3817, 2428, 18, 2144, 2697, 4672, 1942, 3399, 3844, 7622, 2007, 4587, 3817, 1930, 3817, 17, 3595, 4206, 2596, 3425, 6503, 3873, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2233, 5572, 2642, 29283, 9961, 3203, 22914, 19, 19954, 1030, 17, 3189, 3416, 16, 2154, 12936, 4543, 1930, 8697, 2697, 1956, 43, 13009, 3450, 2602, 19, 5236, 1027, 17, 3189, 3728, 1988, 2385, 6445, 6804, 1930, 4948, 4088, 18, 4678, 3951, 3203, 22914, 16, 1925, 4113, 1988, 21420, 22528, 12, 51, 13, 10527, 8547, 1942, 29283, 4879, 5949, 3717, 16, 1966, 2486, 1966, 4948, 2697, 3286, 1922, 14193, 2010, 3374, 2285, 16, 10954, 2743, 16, 1930, 14325, 9306, 18, 2176, 1977, 2481, 1922, 26195, 26073, 2341, 1915, 2056, 18, 6639, 17, 21, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MEINLNESRQVVQQARAKAIQLNVNVNIAILDTAGHLKTFERMDDAFLGSMDIAIKKAKTASLFRTSSENVGEYLKPEAGTYGMVNTNNGLVGFAGGLPILKDKRIIGYIGVSGGAVSEDLQIATAGAEIFNQN", "metadata": {"id": "A0A5C0ZP20", "cluster": 3045757, "interpro_all": ["IPR052517", "IPR005624", "IPR038084"], "interpro_used": ["IPR052517", "IPR005624"], "interpro_unused": ["IPR038084"]}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein should include a Hemolysin-type calcium-binding conserved site that binds calcium ions within a parallel beta-roll structure formed by tandem nonapeptide repeats. Found in Gram-negative bacterial secreted proteins like hemolysins and metallopeptidases, this domain facilitates calcium-mediated interactions with host cells such as erythrocytes. Additionally, the protein includes a von Willebrand factor, type A domain that mediates the formation of multiprotein complexes and interacts with a wide array of ligands to facilitate cell adhesion, migration, and signal transduction. Commonly found in extracellular proteins like integrins and collagens, this versatile module also functions intracellularly in processes such as transcription and DNA repair. Furthermore, the protein possesses a RTX calcium-binding nonapeptide repeat that binds calcium ions to form a parallel beta-roll structure. These Asp-rich repeats are found in Gram-negative bacterial proteins, such as toxins and metallopeptidases, where they facilitate Type I secretion by folding in the extracellular environment to prevent backsliding and accelerate transport. It is expressed in Gammaproteobacteria bacterium and corresponds to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 3066, 3951, 43, 3243, 23872, 17, 2601, 5016, 17, 2743, 5305, 3200, 1988, 6876, 5016, 6982, 2651, 43, 6110, 4666, 17, 12970, 3170, 5333, 2007, 10361, 2447, 24010, 9569, 18, 2435, 1922, 8604, 17, 3136, 4543, 8366, 2697, 3189, 3243, 23872, 1036, 1930, 8969, 24897, 1036, 16, 2052, 3418, 11374, 5016, 17, 3434, 3719, 1956, 4423, 2094, 2427, 1966, 14161, 18, 4950, 16, 1920, 2213, 5921, 43, 14147, 30067, 2991, 16, 2601, 43, 3418, 1988, 10412, 1920, 3337, 1927, 20677, 5684, 5048, 1930, 9034, 1956, 43, 4743, 6472, 1927, 6908, 1942, 6628, 2024, 6141, 16, 5049, 16, 1930, 2733, 8201, 18, 5384, 2435, 1922, 5329, 2697, 3189, 15563, 1930, 5621, 1036, 16, 2052, 20425, 9059, 2222, 4088, 26511, 1922, 4028, 2427, 1966, 3213, 1930, 2678, 5059, 18, 3677, 16, 1920, 2213, 14465, 43, 29839, 5016, 17, 2743, 2447, 24010, 6865, 1988, 6876, 5016, 6982, 1942, 2386, 43, 6110, 4666, 17, 12970, 3170, 18, 2144, 4138, 17, 5536, 9569, 2032, 2435, 1922, 8604, 17, 3136, 4543, 2697, 16, 2427, 1966, 13599, 1930, 8969, 24897, 1036, 16, 2597, 2611, 6628, 2601, 51, 5512, 2007, 10328, 1922, 1920, 5329, 3515, 1942, 4625, 3231, 1036, 12191, 2117, 1930, 15947, 4860, 18, 2176, 1977, 3198, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MAGALSLNIKTTSTDIDEGGKGGKSTLVTEDSFTVSVSEVADSPTLSVQNAIGVEDAGRADDGEISPENAIALNIQSASEIPDGVQLYSDGNVISINDGSATLSSDQLSNLTLVPVENSHVDFALTVTATSTESNGDSIQSAALQLPVSISPIADVPSISVASSNEDGSSLIKLDLSAQSPDNDVDDNGDVITNGDGSQATVGMFAGVDDEGNTSWVLSESELANVYMTPPADAVDEVTISFKVTTVDVDSDDNSTDVRVTETPVTLQIAATDSIETDEGSDAISLGLSTAIVDGDANEQSYVQISGVPEGARLSAGASEVLEDGSTVWNVPTSEIDNLDFVGGKDFSDVFTLTTVNPVADEVVISDSTSMGQEGNEIPLNLNISLTDTDGSETLTITFSDVPEGATISDGVNNYAADADGKIEVSNLGQIELGVEAVSVDSNGVTTDQLDTAATSTLTIDIAAQNSGFTDASDLTVNVGDYSATADGIEVPLSVSGIEMVDTDGSEIGGLVIEINPAETPNYQQILSNLTVSTTDVDKLEGEIGVTATTIELSTGETTSLFATTEVSEFTTDAANAQDDKTLAADEDTSIDLNLELNNGAETVAISQQAVSIVIVDENGDVDTTVHHADMDSSNAVTMTQTEFEALSIKPANNSDTDFDLSVSSTAYEVDQSLNVIEGIDGTEDAPEVSIELGDPNLTTDNTYEYDLDITATLTDTDGSESIQEITVSNLPSGATLSSGTNNGDGSWSLTADQLDGLTLTSVDGVSTTTSEAVAETVEIDSGTMTPTVDVMQPSNDHTPTISGSAEANSTVTISDTDGNEIGSSATDANGQWSYEFSDDLDDDTAIVVTATDETGVASTDEDSVVVIDPLANDSDSDGDQFSLTSVESPVMHNGVNVGTAEIVDGKIQFTPTDGMDALGEDEVANVSFNYSVTDQYGDLSEIQVSGTGHDTGNTIVLYNAEGQQVASTNVQADGTWTANIADEDNGVRIEVSAKEIHPNGVVSDASNSVNTLQDNESSVVDSITVADDNANDGLVVDGGDGIDTVKFTGNDNEVDIDLAAQTATVGDDTIDVLNVESVYGSDKADTITGDDANNKLFGDDGAGDSTNDNDSLFGDAGNDAIHGGVGDDTLSGGSGDDELHGGADTDTAVFSGNQSDYTITEDKDSQTLTITDNRDGSPDGIDVVHSDVEKLQFSDDSANQVAENVAIGTSTGVTLKATDADGDAISYSVEGDVPFTVGNDGVVVTSGDIDFESKQSYTFDVKATSADGTTSTESITINVKDILGDMINGADAGVTVTGLFEQGSSNNLLDGIDDALVTSNSHKLGNYWPDNENQTGYNYMGGHDWFEDHGITQAGNDLDGSYIYYKPYENLENSVISTNEDTSITITSESLLSNDTDANNDTLTISSVQEASHGSVEINDDGNIVFTPDENYHGEATLEVDSVNDVITQVTDSDSSTNEVAENVANGAKTGVTLSATDADGEAVTYSIVDDVPFSVDSNGVIVTDGDIDFESKESEDIDADGVTLDLNLISSNKEVKSQGQGNLGSKPEGLENIENISDDSILFNNFDTATDYGGDDDLNVHIAGNMNRSIDLGDGDNILINIDGNQNRNIEMGDGDNRLDVDGNSSNIFMRDGDDSIRVGGNLNLSVDLNGGDNTLDVKGNAGGNIYSDKGNDTVIVGGNANRNISTLTLKSNSNRRIYAEEGDDTIVLDGSVGDYIMGGSGNDSIVLNHYSKADWDSNRDNIQGRVKEFENIKFNDGEVIGDESAFSTEDTTNNVPDDTVSVEDKDGNELTVSQGQVNVPVQSGVATTIVLTTSEQLSASDMSDITGSVTSTENKTNASKTATDALGHDISQVTDSDDSNNSEDGDAIQYSVDSDSFTVNENGEIVTAKVLDFETKESYTFDVTATSADGSTSTETVTIDVADLDDNLTPSSKPEVQTLSLGSAETSDLSLTEAAIAEIVDKYDSMGDVNVNVIQFWGNGNEVSGWQDADSEVSLYTNKSGTDPEQGLSAQAVFVFSDGNSYGAYETDFEKITGDGSSWNQFIADNNVDLHSIGINVRSLSDLDTIASAGDHDPQYVADVSDLASTIESINNVSGGDGEISVDSITIGGVTYNSESFPEGGLNTDEGAVLHLDFESGIYTYRASDDSVTSDISETFTVSVSDEDGDSTDVKVTVNVDVDDTGDVSKVEASSEQSFTGIDVENGLDNFESNADKSYSKDASSEIKGTRGDDDIFIGKDANKEIELGDGGNDSLYIVDDAKKEIKAGDGDDQIYIGDKAEKEISLEDGDDYLAIGGDAKNEIKAGDGDDYITVGKKAEKEISLDGNDYVVVGDDVNETIDGGAGTDSIELKAYSREDYDDNKDDIQENIENFENIKFSDGSVIGDSSAFESNSITGYEYPISIKANLVDTLSSGIDNYDGSWSLTSEQLEGLSLTIPDTETTSFNLSVAVTTTESNGGDTSVTTLTTSITPGQDAGITTIETAGGAGDDAFTGGKGDDTFFHGGEGGWTDIIHLDATADPNADPNDPWTITVDGEEVDYDLAAKALDLDPDSSGVVSLSDGSQLTFDGVDKIEWGNGSIDTDGSETVTIEISETLTYMLEDIPSGAVLVKVETEELESGGAGQINLSAQAFNYDLASGDFTSSEVQAVEISLDSLGDLTITAPASFSISVNIQGLEGTTVSYNGEAIGEARDPSLSSQGGAEERIGAITLDDIPAGAQINAQTIAIDLSAVAIPQDAEEFDIGVTATNKSAAASFDVLINQDPSAVDDADSSATIQVNVTGLDNDNPAPAISDVVDVHGSNASDDYIFTGREDDTIHGGAGDDEIIGDHSYLNDGKVTFDSLQSHDVSAVTDIDQENVGPDATDDLTINITGATDLSAIDGIVTFSDGSVGVIDYISNGGYAGESSFTYTIIDGNGGSDTATVYTFDVTATSADGSTSTQEITIDVTDIVEIDNNAQQITTGSGDDTVGDGDDTVYIQGNTGGQINLGDGDDYETTIGIKATQADTDGSETLSEVTIVAENSDVGTYTGITLKATDSSSTNVTFIVDVSSSMSNAMDSYDGTQPDADNVVPEVTTASVTGKVKEASVSTANIDVDDNVYIGDDAEKEIDLGSGDGDDYLSVGKATYKEITAGDGSESISEIVVSGFPSSAVSGGDGDDTYFFNPFDGNDE", "metadata": {"id": "A0A9D8A1Q7", "cluster": 3825284, "interpro_all": ["IPR049531", "IPR041498", "IPR002126", "IPR015919", "IPR041690", "IPR018511", "IPR001343", "IPR013783", "IPR050174", "IPR011049", "IPR002035", "IPR036465"], "interpro_used": ["IPR018511", "IPR002035", "IPR001343"], "interpro_unused": ["IPR002126", "IPR049531", "IPR036465", "IPR041690", "IPR050174", "IPR015919", "IPR013783", "IPR011049", "IPR041498"]}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein should have a Polymerase beta, nucleotidyltransferase domain that adopts a nucleotidyltransferase fold and is typically found in polyvalent proteins and polymorphic toxin systems, such as NTox45. In addition, the protein possesses a HTH ArsR-type DNA-binding domain that functions as a winged helix-turn-helix (wHTH) module within prokaryotic ArsR/SmtB family transcriptional regulators. These repressors control heavy metal resistance operons by binding promoter DNA and dissociating in the presence of specific ions like arsenic, zinc, or cadmium. This metal-sensing mechanism allows for the inducible transcription of detoxification and efflux systems. Also, the protein incorporates a ArsR-like helix-turn-helix domain that acts as the DNA-binding component of prokaryotic, metal-regulated homodimeric repressors. Characterized by a winged helix topology, this domain typically regulates gene expression by dissociating from DNA upon binding specific metal ions. It is present in Nanoarchaeota archaeon. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 6479, 4666, 16, 2797, 4090, 2199, 9961, 3418, 1988, 24032, 43, 2797, 4090, 2199, 9961, 3728, 1930, 1977, 5745, 2435, 1922, 4286, 28144, 4905, 2697, 1930, 14240, 9165, 3771, 16, 2427, 1966, 5891, 2325, 6803, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 5334, 1023, 9896, 1005, 17, 2601, 2678, 17, 2743, 3418, 1988, 4088, 1966, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 12, 2003, 1963, 13, 9059, 2651, 21545, 9896, 1005, 19, 2426, 27414, 3416, 5224, 9098, 18, 2144, 26446, 2285, 7881, 6048, 3554, 28748, 2007, 2743, 4465, 2678, 1930, 7296, 2287, 1922, 1920, 2990, 1927, 2487, 6982, 3189, 14241, 16, 7997, 16, 2014, 17203, 18, 2052, 6048, 17, 9306, 2856, 5731, 1958, 1920, 9376, 3213, 1927, 18169, 1930, 11247, 3771, 18, 2222, 16, 1920, 2213, 19683, 43, 9896, 1005, 17, 3189, 7864, 17, 5165, 17, 7864, 3418, 1988, 8016, 1966, 1920, 2678, 17, 2743, 4594, 1927, 21545, 16, 6048, 17, 4335, 21189, 1935, 26446, 18, 4378, 2007, 43, 12920, 1919, 7864, 13678, 16, 2052, 3418, 5745, 7014, 2359, 2294, 2007, 7296, 2287, 2037, 2678, 4073, 2743, 2487, 6048, 6982, 18, 2176, 1977, 2481, 1922, 9788, 3983, 3336, 7336, 13470, 1916, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MIEGRQWEIISILAKGDKTPTEIAGIMKISLPGLHRHLMELERAGMIKKGNSTKGKTRPYTTYTIGTGFLYFAKAMKGNAEQGFIEADENVKAQLSIWAIPQKEYHYYLESFWWQMQEFIEDIDVIAIFGSVAKGNAREGSDIDILLLVKKEVKKFENRFGTIAVGKKGKKAMVMAQVFETNDFKNSLEEGSKFAEEVIKSHKGIYDPNEILPGLTQSSA", "metadata": {"id": "A0A7J4QBQ5", "cluster": 3980338, "interpro_all": ["IPR011991", "IPR001845", "IPR043519", "IPR041633", "IPR052548", "IPR036388", "IPR036390"], "interpro_used": ["IPR041633", "IPR001845", "IPR011991"], "interpro_unused": ["IPR036390", "IPR036388", "IPR043519", "IPR052548"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nIt is part of the Kynureninase family, which functions as a pyridoxal-5'-phosphate (PLP)-dependent enzyme catalyzing the hydrolytic cleavage of L-kynurenine or 3-hydroxykynurenine to yield L-alanine and anthranilic or 3-hydroxyanthranilic acid. This reaction constitutes a key step in the L-tryptophan catabolic pathway involved in NAD biosynthesis across bacteria, fungi, and vertebrates. Structurally, the enzyme belongs to subgroup IVa of the aminotransferase superfamily. Also, the protein belongs to the Pyridoxal phosphate-dependent transferase, small domain superfamily, which comprises the complex $\\alpha/\\beta$ structural domain found in enzymes such as aspartate aminotransferase and DOPA decarboxylase. These proteins utilize pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze diverse reactions, including transamination, decarboxylation, and deamination, playing a vital role in amino acid biosynthesis and neurotransmitter metabolism. In addition, it is part of the Pyridoxal phosphate-dependent transferase, major domain superfamily, which forms the large catalytic component with a 3-layer \u03b1/\u03b2/\u03b1 sandwich topology in enzymes that utilize pyridoxal 5'-phosphate (PLP) as a cofactor. Through a Schiff base linkage with an active site lysine, members of this superfamily facilitate diverse chemical transformations, including transamination, decarboxylation, and deamination, which are essential for the biosynthesis and catabolism of amino acids and neurotransmitters. It is found in Actinomadura livida and exhibits UniProt keyword tags Hydrolase and Pyridine nucleotide biosynthesis.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 2176, 1977, 3131, 1927, 1920, 23523, 24684, 11413, 3416, 16, 2154, 4088, 1966, 43, 24828, 23859, 17, 25, 11, 17, 5413, 12, 21453, 13, 17, 3100, 4113, 29601, 1920, 26702, 6404, 1927, 54, 17, 23523, 24684, 2053, 2014, 23, 17, 8275, 6716, 1022, 24684, 2053, 1942, 4307, 54, 17, 10504, 1930, 14228, 16692, 1935, 2014, 23, 17, 8275, 7744, 17182, 10029, 2687, 18, 2052, 3227, 14879, 43, 3834, 3537, 1922, 1920, 54, 17, 13489, 22112, 3374, 3286, 1922, 6577, 8132, 3436, 4802, 16, 10520, 16, 1930, 14976, 18, 12171, 16, 1920, 4113, 14440, 1942, 6200, 4370, 1019, 1927, 1920, 15817, 13975, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 2858, 3418, 13975, 16, 2154, 12936, 1920, 2796, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3418, 2435, 1922, 5038, 2427, 1966, 12878, 15817, 1930, 19428, 23922, 18, 2144, 2697, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 1942, 18170, 6445, 5298, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 14797, 43, 8970, 2770, 1922, 3835, 2687, 8132, 1930, 15223, 4714, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 3044, 3418, 13975, 16, 2154, 4952, 1920, 3103, 6804, 4594, 1956, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 18038, 13678, 1922, 5038, 1988, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 18, 2596, 43, 25214, 5170, 8611, 1956, 1925, 3500, 3200, 9082, 16, 4678, 1927, 2052, 13975, 6628, 6445, 4399, 18510, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 2154, 2032, 4415, 1958, 1920, 8132, 1930, 19480, 1927, 3835, 4576, 1930, 21012, 18, 2176, 1977, 2435, 1922, 4718, 2954, 10015, 5524, 15260, 9532, 1930, 9826, 20709, 11121, 2538, 14392, 20748, 1930, 19604, 5489, 8132, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MTAEDEARRLDAADPLPTLRGEAGNSLGLQPRAVAGRLREELDDWARLAVEAHTEARRPWVDAMNSLTVNLHLMMASFYRPAGDRTRIVIEDSAFAAVVRLRPRPGEDDLRTEDVVAFLGREGDTVALVLRAAGAAVGWDLAHAAGNVPLRLHDWDVDFAAWCTYKYLNSGKLAGWWGTDPAVRFRMDPDISPPASADAWQLSNPPIMALAPVLTGYLADRLAETRARIITPADPAARREPDVLRLAPAPLYCTFHDCHRAAEALRDLVFLVPPAPGGAYEEAAYFYHELLREPAARLVGALPHEVVPSDSYAVASQAVHHGLDPALGGVNYLTGQLMDMPAITKAGPGAVAGCFVHERHVRDASVPASLEIFDRVGMAALRAKSERLGAQLSLQVDDAGGLVRRLAQDRGVVADA", "metadata": {"id": "A0A7W7MYB3", "cluster": 4246725, "interpro_all": ["IPR010111", "IPR015424", "IPR015421", "IPR015422"], "interpro_used": ["IPR010111", "IPR015422", "IPR015421"], "interpro_unused": ["IPR015424"]}, "task_type": "infilling"} {"instruction": "The protein should have a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. Also, the protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It has been characterized in Moraxella catarrhalis (Branhamella catarrhalis) and carries UniProt keyword assignments ATP-binding, Nucleotide biosynthesis, and Transferase.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 3066, 2162, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 2258, 2252, 4378, 1922, 2803, 10031, 5148, 13248, 5004, 19337, 12, 30344, 8527, 5870, 13248, 5004, 19337, 13, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MQGKFISFEGTEGIQVVRTREPGGSELNMNADTEILLMFAARSSTVAYQGFGRYHGKQAALLDVVTGMQRAAKRSAADRLEANDIAFFEANGTVAEVAARIDTALGLDGVGKTTAIEALITRLVDRAEQLRQLFLNPNADHLHQVILPAIKSGKWVVSDRFFDAKIELLIEQFVPIYPDVTLWLDRVYQGLAYQHSHHPNRIHRID", "metadata": {"id": "A0A198WN45", "cluster": 5336994, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein can be placed in the Snail/Krueppel C2H2-type zinc-finger family, which functions as a transcriptional regulator that typically acts as a repressor by binding to E-box motifs. These proteins modulate the activity of basic helix-loop-helix (bHLH) transcription factors to control diverse developmental processes, including neuronal differentiation, mesoderm formation, and epithelial-mesenchymal transition. Also, the protein should have a Zinc finger C2H2-type domain that functions as a classical DNA-binding motif, typically found in eukaryotic transcription factors where it interacts with the DNA major groove using a conserved $\\beta/\\beta/\\alpha$ fold coordinated by a zinc ion. These domains frequently appear in tandem arrays to facilitate specific recognition of nucleic acids, proteins, or lipids, acting as stable scaffolds for diverse biological activities ranging from gene transcription to chromatin remodeling. Furthermore, the protein falls within the Zinc finger C2H2 superfamily, which comprises stable, zinc-coordinated $\\beta/\\beta/\\alpha$ motifs that primarily function as DNA-binding domains in eukaryotic transcription factors. These versatile scaffolds typically interact with the DNA major groove in tandem clusters, but can also be adapted to bind RNA, proteins, or lipids to regulate diverse cellular processes. It occurs in Timema poppense (Walking stick) and is described by UniProt keywords Metal-binding, Nucleus, and Repeat.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 15929, 19, 6203, 2182, 9434, 1938, 8453, 6951, 17, 2601, 7997, 17, 8497, 3416, 16, 2154, 4088, 1966, 43, 5224, 7888, 1988, 5745, 8016, 1966, 43, 14434, 2007, 2743, 1942, 47, 17, 5758, 8277, 18, 2144, 2697, 8480, 1920, 2455, 1927, 5937, 7864, 17, 5881, 17, 7864, 12, 24735, 13, 3213, 2790, 1942, 2285, 6445, 5878, 4028, 16, 2710, 5121, 4155, 16, 20985, 3337, 16, 1930, 4944, 17, 9152, 4832, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 7997, 8497, 8453, 6951, 17, 2601, 3418, 1988, 4088, 1966, 43, 8445, 2678, 17, 2743, 5219, 16, 5745, 2435, 1922, 10825, 3213, 2790, 2597, 2176, 9034, 1956, 1920, 2678, 3044, 15920, 2193, 43, 5305, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 3728, 11651, 2007, 43, 7997, 4755, 18, 2144, 4682, 5467, 3267, 1922, 10361, 10517, 1942, 6628, 2487, 5708, 1927, 11079, 4576, 16, 2697, 16, 2014, 8238, 16, 8290, 1966, 4700, 10603, 1958, 6445, 3933, 4209, 6485, 2037, 2359, 3213, 1942, 6338, 8378, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 7997, 8497, 8453, 6951, 13975, 16, 2154, 12936, 4700, 16, 7997, 17, 11651, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 8277, 1988, 5985, 2347, 1966, 2678, 17, 2743, 4682, 1922, 10825, 3213, 2790, 18, 2144, 20425, 10603, 5745, 6310, 1956, 1920, 2678, 3044, 15920, 1922, 10361, 5859, 16, 2308, 2112, 2222, 1998, 8461, 1942, 4566, 3146, 16, 2697, 16, 2014, 8238, 1942, 5741, 6445, 3689, 4028, 18, 2176, 5110, 1922, 2367, 3368, 2640, 11179, 1021, 12, 9109, 19774, 13, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 16, 5607, 16, 1930, 6865, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MDLTNVIFVSNLYRKNRDKYNCDDYSKSPYKCDICSKYFKFKSILKNHLISHVRLMVEHRPHKCDVCGKFFKLNKILKSHIHLISHGEHRPHDKNFKNKTILKTHLVTHSELITHGEHRPHKCDVCGKCLKPNTSLKSHLITFTNVIFVASVSKRRLILKGIHLFMVNMDERSELLPLGIEVSTLSSSLPFIKEEIKYTKNINIKSHLLTQSEQRITKLKPSLKPFSLLITHSEHRPHKCDVCGKCFKEKHKLKHRPHKCDVCGKFFKLNKILKSHHATLNLISPVIVNTDLANLLFDKLTSTMKCECNEEDN", "metadata": {"id": "A0A7R9DB68", "cluster": 6933134, "interpro_all": ["IPR050527", "IPR036236", "IPR013087"], "interpro_used": ["IPR050527", "IPR013087", "IPR036236"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me a peptide sequence capable of: The protein carries a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. In addition, the protein should feature a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Additionally, the protein should have a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. It is expressed in Chloroflexota bacterium and features UniProt keywords DNA excision, Excision nuclease, and Cytoplasm.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 16252, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2176, 1977, 3198, 1922, 10107, 18222, 7336, 14061, 1930, 4075, 20709, 11569, 2678, 10940, 16, 10940, 16230, 16, 1930, 5239, 18, 3], "output": "MDRPSGRAPFELVLPWDLAGDQPRASEALTRGLREGMRSQTLRGVTGSGKTVTMAKVIADAGRPALVLAHNKTLAAQLYGEFKEFFPKNAVQYFVSYYDYYQPEAYIARSDTYIEKDSSRNEEIDRMRHAATRALFERRDVLIVASVSCIYGLGAPVDYGAVTVRLNKGERVRRDTVLRHLVDIQYERTNSDLVRGKFRVMGDTLEVQPSYEELAIRVEFFGDDVERITELDPLTGEVLAERDRIDIYPARHFVTPREKLMEAIRDIEAELVERVTELEANGRLLEAQRLRQRTNFDLEMMRETGSCAGIENYSRHLARRPAGSRPWTLLDYFPPDFLMFVDESHISIPQVHGMWGGDRSRKQILVEYGFRLPSALDNRPLTFEEFEARLDQTIFVSATPSAYEVQRSGQVVDQIIRPTGLIDPEIDVRRTDGQIDDLLAELRLRVDRGQRALVTTLTKKMAEDLADYLREMGVKVQYLHSEIETIERVEILRDLRLGVFDVVVGVNLLREGIDLPEVTLVAILDADKEGYLRSEGSLIQVIGRAARHVEGRVIMYADRVTASMRAAIDETERRREVQLAFNKEHGIDPQTVVKAIRDVGMRLREVAEVEGVYEKGGRPIAAGELPKDELARLIKDLELQMKTAAKELAFEKAAALRDEIVDLRGLLVLQSGPEGLDDSAMPTGPRTTQRVMGRRRGS", "metadata": {"id": "A0A536C5B0", "cluster": 8828358, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR014001", "IPR001650", "IPR001943"], "interpro_unused": ["IPR036876", "IPR006935", "IPR041471", "IPR004807", "IPR024759", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein should feature a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. Also, the protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It originates from Zobellella endophytica and features UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 3066, 5961, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 22970, 2037, 11906, 21512, 5870, 19771, 4274, 1019, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSQFIVIEGLEGAGKSTVQRHVVAWLEARGLTVMTTREPGGTPLAEKMRALVKEVHDEPLTMEAELLLMYAARVQLVKTRIQPSLAAGTWVVGDRHDLSSQAYQGGGRGLDRHLIDQIKLAVLGNFAPDLTLYLDIDPALGLQRARARGELDRIELEQLDFFERTRARYLELVQADPRIVQLDGSQSPERVRADVIHCLEQHLCIPG", "metadata": {"id": "A0A2P7RCA3", "cluster": 9092150, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR018095", "IPR027417"], "interpro_unused": ["IPR039430", "IPR018094"]}, "task_type": "autoregressive"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein should include a Glycosyltransferase 2-like domain that catalyzes the transfer of sugar moieties from activated nucleotide donors, such as UDP-glucose or GDP-mannose, to specific acceptor molecules to form glycosidic bonds. This domain participates in the biosynthesis of diverse structures, including cellulose, dolichol phosphate, and teichoic acids. It originates from Actinomycetes bacterium and features UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 3066, 3951, 43, 20067, 9961, 22, 17, 3189, 3418, 1988, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 5489, 8276, 16, 2427, 1966, 18500, 17, 3817, 2014, 15217, 17, 17936, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2052, 3418, 17241, 1922, 1920, 8132, 1927, 6445, 4061, 16, 2710, 12343, 16, 17837, 2108, 1945, 5413, 16, 1930, 3602, 2108, 8643, 4576, 18, 2176, 22970, 2037, 4718, 25148, 14061, 1930, 4075, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTHDGRRWLDHCLRSLDRQSYPVMDVVVVDVAGAALGRRRHTVMRTPSPFGFGGAVNWALDRLRSLDPGSAIVGPKVVSWDEPALLEEVGWSTDRFGHDSGQRDLAREVFHVTSTCMLVRKSVFYRLNGWDTYSVEVNPAARVRHAAALIHRSRRIAWGSTRYLLWLVPQLFLLAFAEMAGYLVVRQPRAALQVLGARRVQRSRKIPDGSLRRFRVPAAIRMRSYIARRSDRLEAVSGPRALIGMLLVLGLRDSLHAPSVSVGELLPFPEGALILGVFPVLTLGSAVLAQKLLVVCLALAAAVGGAYAAALAYTAGPIGYAGLRAGRLGALVFGAALPPRRTRGRAFTARGEMGRIALGCGVSALGEARGGPGRGRVFNLAAAFGGIAAGWSPSSVTYSAAFSDVSAASVLLAQLPAGGSPMGPTLGAIGLTVALWASGRAPSLMASPVAVGGALERLSQAGRQGVAAAAFLALLAALAAASSDIAALLGSQVVGEDAGKVLWVGEQTEFGPSLLRSSGELSEGAGRGIARSVASVEAGATDRAGRELAPWDIRFISQRDLSLVSDEPGYLLLASAGAPPGPRPDSSPAGPGEAPLQSPDAELLLFIHDDVALDPDSVEHMVRRMGYHGLEEGERKMRAFCEDLDLCWRARLAGMRRNRFRAVAKNSSALRLLGWNLAALPSTLPARTRALLAGTWGPVRAGSRVIPAITTMFQAYAQRWSGLGHAEAAPPALAYRLTAAWAAEGRAGRLAPYVVSALARLCGPPAFVPASLVLYSGVAVLAGLSGALGFLLPWSASWLHPGGPLFRLLELVLAGVAALATSRGPQRRSALFLWACEAGVLAALAWAVLAGLVVPPLAGGAYTPGRAQGGATGPERLTGAQGPVLSDIFPVVSTSGAPGHDRSSWL", "metadata": {"id": "A0A7W1D6T1", "cluster": 12320779, "interpro_all": ["IPR001173", "IPR050834", "IPR029044"], "interpro_used": ["IPR001173"], "interpro_unused": ["IPR029044", "IPR050834"]}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is assigned to the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Furthermore, the protein incorporates a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Also, the protein has a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. It is present in Buchnera aphidicola (Aphis aurantii) and is associated with UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 3677, 16, 1920, 2213, 19683, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 2222, 16, 1920, 2213, 2258, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 2176, 1977, 2481, 1922, 25485, 3239, 1019, 27040, 29902, 12, 12274, 1937, 11826, 10402, 1033, 13, 1930, 1977, 2458, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MIYTWPSPAKINLFLYVTGIRSDGYHYIQSLFQFLNYKKLFLNSENIIIKAANLLKSKALNYKKTNCITLGAKIFLNNKLWKTKFTLQELAEFGLEIGSDIPAFVIGKTSIVEGIGEILHPIQRKEKWYNSSNQKKSIQFLLKSPFKNDFENIVSNKFKKIKKLLSILSPYAPLSAQKIFSLLPKNMQGFIAKSVNTSPLHHIFYEKNNHIFNGDTLKIIPNNTGNIELFFEKKIPIGSGLGGGSSNAATVLIVLLVVYPEIHILTKNIFSSFLLTRMTGTGSCVFAEFNDK", "metadata": {"id": "A0AAU6W5R4", "cluster": 13272181, "interpro_all": ["IPR013750", "IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR013750"], "interpro_unused": ["IPR036554", "IPR014721", "IPR020568"]}, "task_type": "infilling"} {"instruction": "The protein is included in the Siphovirus Gp157 family, which comprises viral and bacterial proteins homologous to the Gp157 protein of the *Streptococcus thermophilus* SFi bacteriophage. These proteins are thought to confer increased resistance to bacteriophage infection in host bacteria. It occurs in Prokaryotic dsDNA virus sp.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 20978, 10647, 11074, 4882, 16151, 3416, 16, 2154, 12936, 4324, 1930, 4543, 2697, 8725, 1942, 1920, 4882, 16151, 2213, 1927, 1920, 14, 15746, 7967, 24888, 5277, 1036, 14, 6347, 1033, 24613, 18, 2144, 2697, 2032, 6212, 1942, 7909, 2502, 3554, 1942, 24613, 2909, 1922, 4423, 4802, 18, 2176, 5110, 1922, 21545, 16397, 3413, 2056, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MPKLYELAEEFDEIYREIEDKLISCVKVLKTLNAEADVCRSEYVKECMLSSGMLRVKSSLFNISIADNPPAVDIKLAIERGEEVPGATLVRSQGVRIRSEANPDEDFSDDLKERLRKAEGNFEADRLTKRARSFARNADSLKDVFDIDNIPEEFTVAVPRKVSKA", "metadata": {"id": "A0A516LF12", "cluster": 14566139, "interpro_all": ["IPR008840"], "interpro_used": ["IPR008840"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\nThe protein possesses a TetR-type DNA-binding HTH domain that functions as a transcriptional regulator in bacteria and archaea, typically acting as a homodimeric repressor to control susceptibility to hydrophobic antibiotics and detergents. It structurally comprises an N-terminal helix-turn-helix motif with an inverse orientation to facilitate DNA binding. Moreover, the protein is assigned to the HTH-type, TetR-like transcriptional regulator family, which comprises predominantly bacterial DNA-binding proteins that utilize a helix-turn-helix (HTH) motif to repress gene expression. These regulators control diverse physiological processes ranging from antibiotic resistance and lipid metabolism to osmotic stress response and cell division, as exemplified by the nucleoid occlusion factor SlmA. Also, the protein is grouped in the Homeodomain-like superfamily, which comprises transcription factors and DNA-binding proteins that utilize a conserved helix-turn-helix (HTH) motif to interact with the DNA major groove. These proteins are ubiquitous across all domains of life and play critical roles in gene regulation through specific hydrogen bonding and hydrophobic contacts. It is found in Rothia dentocariosa (strain ATCC 17931 / CDC X599 / XDIA) and is connected to UniProt keyword Transcription regulation.\nIt currently has masked regions that need to be filled. Provide the exact amino acids.", "tokenized_instruction": [2, 43, 2213, 1977, 3414, 1942, 2385, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 5575, 17, 2601, 2678, 17, 2743, 5334, 1023, 3418, 1988, 4088, 1966, 43, 5224, 7888, 1922, 4802, 1930, 21501, 16, 5745, 8290, 1966, 43, 21189, 1935, 14434, 1942, 2285, 6461, 1942, 7919, 7560, 1930, 15814, 1036, 18, 2176, 12171, 12936, 1925, 56, 17, 4262, 7864, 17, 5165, 17, 7864, 5219, 1956, 1925, 9526, 7148, 1942, 6628, 2678, 2743, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 5334, 1023, 17, 2601, 16, 5575, 17, 3189, 5224, 7888, 3416, 16, 2154, 12936, 7700, 4543, 2678, 17, 2743, 2697, 1988, 12561, 43, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 9055, 2359, 2294, 18, 2144, 9098, 2285, 6445, 5005, 4028, 6485, 2037, 7267, 3554, 1930, 4486, 4714, 1942, 13951, 3071, 2644, 1930, 2024, 8451, 16, 1966, 22236, 2007, 1920, 2797, 2642, 10543, 2991, 2788, 3368, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 4502, 17166, 17, 3189, 13975, 16, 2154, 12936, 3213, 2790, 1930, 2678, 17, 2743, 2697, 1988, 12561, 43, 5305, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 1942, 6310, 1956, 1920, 2678, 3044, 15920, 18, 2144, 2697, 2032, 15498, 3436, 2136, 4682, 1927, 3308, 1930, 3918, 4140, 5456, 1922, 2359, 3640, 2596, 2487, 6201, 11463, 1930, 7919, 9070, 18, 2176, 1977, 2435, 1922, 21149, 2126, 12547, 7095, 14356, 1019, 12, 3943, 11037, 16182, 6800, 19, 7137, 66, 7308, 1026, 19, 66, 7408, 1019, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3213, 3640, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MERTATATKGTIPMPDTPNPARRPGRTGKTQRKEEVAQRAGVSKGTVYYNFGSKKTMIDRLLQYGTHLLVESMISTALTYLHEHRGFTRLWVSEVWKGLDAWTDSMVDNRQEILDFIESQVIFGATFMLAMDREIHGVQRSIEDSTRAVMLVFDGYIRHLFTATMEIMEHRGSAHVSISEASVAQSDPREGLRKSRALRSRYTIDTAQDTRALALS", "metadata": {"id": "E3H1J2", "cluster": 15699294, "interpro_all": ["IPR009057", "IPR050109", "IPR001647", "IPR036271"], "interpro_used": ["IPR001647", "IPR050109", "IPR009057"], "interpro_unused": ["IPR036271"]}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that will be able to perform the following function: It is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, it is part of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is produced by Senegalia massiliensis and is described by UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 4152, 2007, 6964, 11253, 12191, 1019, 3411, 29044, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MGQNKIKIIGLTGGIATGKTTVKNILIKYGYKVIDADEISREVVKKNKPAYKDIVDFFGKDVLNSNDEINREKLGGIIFNKKDLRNKLNEIVHPRVYESIRNNIYKYIKENQKVIFIDIPLLIEVRKRLEKEKIIFDEIWLIYLNKDEQIKRLMNRDRYTFKEAMSRINAQIDIDEKIKYCDIVIDNSRDIEHTKRQLKVALSKNDFM", "metadata": {"id": "A0A845QW55", "cluster": 18679794, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein belongs to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Additionally, the protein belongs to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is expressed in Cyanobacteria bacterium RM1_2_2 and features UniProt keywords ATP-binding, Cytoplasm, and Transferase.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 14440, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 3198, 1922, 21897, 14061, 10625, 1009, 41, 22, 41, 22, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MLPRIIGLTGGVGMGKTTVSDYLQNAYGLPVLDADLYAREMLLPTGHLDRTRLGEIVFGSAPERLWLEQQIAVLVIPLLFEARMTDLVTEIWVVHSADGQQVERLQIEQADVVLENSSTPEALFRQVDQALGFSAVEPGSQVLAKIMERYGTSHPYVRDQLEAGLRQLAAQGQTTRRDQLSLQQIRARINSQMPIAKK", "metadata": {"id": "A0A969T2V6", "cluster": 19822436, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein possesses a Molybdopterin oxidoreductase, 4Fe-4S domain that functions as an electron-transfer component within the molybdenum or tungsten bis-MGD oxidoreductase family. It is present in a diverse range of enzymes, including nitrate reductases, formate dehydrogenases, and dimethyl sulfoxide reductases, where it facilitates redox reactions essential for anaerobic respiration and other metabolic pathways. Also, the protein includes a Molybdopterin dinucleotide-binding domain that binds molybdopterin dinucleotide cofactors in oxidoreductases, including formylmethanofuran dehydrogenase and DMSO reductase. It interacts with the 2-amino pyrimidone ring of the cofactor to support enzymatic activity, such as the reduction of CO2 to methane in methanogenic archaea. Furthermore, the protein is assigned to the Prokaryotic molybdopterin-containing oxidoreductase family, which catalyzes diverse redox reactions involving electron transfer to or from quinones, utilizing molybdopterin and iron-sulfur clusters as cofactors. These enzymes function in critical metabolic processes such as nitrate reduction, formate oxidation, and arsenic detoxification, often facilitating anaerobic respiration in the bacterial periplasm or contributing to electron transfer within mitochondrial Complex I. It is found in Pseudomonas sp. FW507-12TSA and corresponds to UniProt keyword Metal-binding.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 14465, 43, 2629, 16924, 22389, 2410, 16654, 27388, 16, 15338, 1021, 17, 26814, 3418, 1988, 4088, 1966, 1925, 4995, 17, 3856, 4594, 2651, 1920, 2629, 16924, 5233, 1989, 2014, 26530, 24690, 7266, 17, 2786, 1007, 27388, 3416, 18, 2176, 1977, 2481, 1922, 43, 6445, 3109, 1927, 5038, 16, 2710, 12628, 11386, 1036, 16, 25741, 9294, 1036, 16, 1930, 9780, 20139, 11386, 1036, 16, 2597, 2176, 11374, 9366, 5298, 4415, 1958, 12554, 11695, 1930, 2303, 4487, 3873, 18, 2222, 16, 1920, 2213, 5921, 43, 2629, 16924, 22389, 2410, 16654, 21302, 17, 2743, 3418, 1988, 6876, 2629, 16924, 22389, 2410, 16654, 21302, 21362, 1922, 27388, 1036, 16, 2710, 29285, 23568, 9286, 29579, 9294, 1930, 7731, 11386, 18, 2176, 9034, 1956, 1920, 22, 17, 3835, 17015, 15726, 6335, 1927, 1920, 15155, 1942, 3373, 8145, 2455, 16, 2427, 1966, 1920, 3378, 1927, 6333, 1942, 18863, 1922, 17348, 3880, 21501, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 21545, 2629, 16924, 22389, 2410, 16654, 17, 3165, 27388, 3416, 16, 2154, 17097, 6445, 9366, 5298, 5884, 4995, 3856, 1942, 2014, 2037, 25093, 1036, 16, 10232, 2629, 16924, 22389, 2410, 16654, 1930, 5680, 17, 12585, 5859, 1966, 21362, 18, 2144, 5038, 2347, 1922, 4140, 4487, 4028, 2427, 1966, 12628, 3378, 16, 25741, 6638, 16, 1930, 14241, 18169, 16, 3868, 12440, 12554, 11695, 1922, 1920, 4543, 20171, 2014, 8739, 1942, 4995, 3856, 2651, 4596, 2796, 51, 18, 2176, 1977, 2435, 1922, 13461, 2056, 18, 16451, 3382, 1027, 17, 2369, 1973, 1019, 1930, 8852, 1942, 20709, 11121, 2538, 6048, 17, 2743, 18, 3], "output": "MTKTLHHRACHLCEAICGLTLEITEEPGSGPRITSIKGDDPDRLRHPVRRVGNEWQPIEWDEAFALVAERLADIQYGLMTHSNYFLGQLKSRNRFSATSVDQLPQHLASYLMYGHGLLLPIPDITVPDVEKRLKAIQARGGKVVVIDPRRSETAAMADQHLFIRPGGDVALLFVREAISPFTPEAMSPLCAIPAPQIRQLAREFASADRAVCYGNLVTGNLDRVGGALCTEPALDLVAATSGGHFNAWQSRVSGLPEYVAGNPVLSTPNGRRLEQALDGLEFMVSIDLYINETTRYADLILPSTSALENDHYDTTFNMLHDWEIFVGLAKAFAARTGNSLKPTMAPAQMIDLGLRAGPYGPNLAQRLKTENRRIQAAPAAIMADLQRFAAQPVPQVDELLLIGRRHVLMHPQDLTQRGLRDGQRVRISSRVGTVEVEVLASADMMPGVSGQPGCSANDLTDERHLDALSGNAALNGVPVKVVAAPQDSFSRGHICPKAVALQDIQDQRHGKDAVATYQGNPSVHNDHTDFMLILGGNPLASNGSIMGLLNSIFLDGPMRDSHLQVDGLAQRMGVSTQAFGTLCHWLLQLLGGELPVSALAEEMLTEGEGQVRALVTFAVRNVSRFNRAILPKPEGADGAPLKLSLATLDLHPHGIDLGPLQRSNNSWMHNYHRLVKGKPRHQLVSLPHGWGHARPGVQMEIA", "metadata": {"id": "A0AA92H3Y9", "cluster": 23372450, "interpro_all": ["IPR006657", "IPR006656", "IPR006963", "IPR050123"], "interpro_used": ["IPR006963", "IPR006657", "IPR050123"], "interpro_unused": ["IPR006656"]}, "task_type": "infilling"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein should include a Signal transduction histidine kinase dimerisation and phosphoacceptor domain that facilitates homodimerisation and histidine autophosphorylation within two-component signal transduction systems. This domain forms a four-helical bundle structure that catalyzes the transfer of a phosphate from ATP to a conserved histidine, and subsequently to an aspartate residue on a response regulator. Additionally, the protein contains a GAF domain that functions as a versatile signaling module structurally related to the PAS domain. It regulates diverse cellular processes by binding small ligands, such as cyclic nucleotides (cAMP and cGMP) to control phosphodiesterases and cyclases, or by acting as a light-sensing chromophore-binding region in phytochromes and transcriptional activators. Furthermore, the protein possesses a Histidine kinase domain that functions as the catalytic core of two-component signal transduction systems, orchestrating cellular responses to environmental stimuli. It undergoes ATP-dependent autophosphorylation on a conserved histidine residue within a homodimer before transferring the high-energy phosphoryl group to an aspartate residue on a partner response regulator protein. This domain contains a dimerization interface and a structurally distinct ATP-binding cleft defined by conserved nucleotide-binding motifs. It is present in Halieaceae bacterium and carries UniProt keyword assignments Coiled coil, Transferase, and Two-component regulatory system.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 2733, 8201, 13873, 4016, 7632, 6284, 1930, 8078, 22790, 1924, 3418, 1988, 11374, 21189, 6284, 1930, 13873, 22009, 2651, 2288, 17, 4594, 2733, 8201, 3771, 18, 2052, 3418, 4952, 43, 3006, 17, 11514, 14142, 3170, 1988, 17097, 1920, 3856, 1927, 43, 5413, 2037, 4498, 1942, 43, 5305, 13873, 16, 1930, 5326, 1942, 1925, 12878, 6181, 1990, 43, 2644, 7888, 18, 4950, 16, 1920, 2213, 5461, 43, 4357, 1038, 3418, 1988, 4088, 1966, 43, 20425, 3197, 9059, 12171, 2712, 1942, 1920, 9233, 3418, 18, 2176, 7014, 6445, 3689, 4028, 2007, 2743, 2858, 6908, 16, 2427, 1966, 9821, 9519, 12, 6225, 1930, 15958, 13, 1942, 2285, 24821, 1036, 1930, 16526, 1036, 16, 2014, 2007, 8290, 1966, 43, 3696, 17, 9306, 25801, 17, 2743, 3031, 1922, 25512, 2072, 4191, 1036, 1930, 5224, 15497, 18, 3677, 16, 1920, 2213, 14465, 43, 13873, 4016, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 2288, 17, 4594, 2733, 8201, 3771, 16, 21991, 2287, 3689, 3387, 1942, 4813, 5458, 18, 2176, 14928, 4498, 17, 3100, 22009, 1990, 43, 5305, 13873, 6181, 2651, 43, 21189, 3119, 21902, 1920, 2149, 17, 3844, 12556, 2210, 1942, 1925, 12878, 6181, 1990, 43, 8240, 2644, 7888, 2213, 18, 2052, 3418, 5461, 43, 13640, 6854, 1930, 43, 12171, 4493, 4498, 17, 2743, 14649, 3608, 2007, 5305, 5489, 17, 2743, 8277, 18, 2176, 1977, 2481, 1922, 4217, 2621, 9914, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 17524, 9121, 16, 13763, 16, 1930, 2288, 17, 4594, 4948, 2433, 18, 3], "output": "MDPDIKHLQDPNFATAMLSMVRTGSDCKSPSDVAWQVCDSIQNGLCLDDIILYLMNDDSTELIQAAAAGPKKSPDRNISNPIRIPVGHGIVGSVAETGHAEIIDDTSVDGRYILDDAHRLSEISVPIIQSGRLIGVLDSETDPKGYYTSDHLARLELMASVASPHILRVMAEINLENVSRRKNQLEQIAAQQTQVKEQLNAMETWLSRESINLTQTLHHELRTPLNAIMGISEILDDICNRGDPSEKELIPFASMLKRSGQDLLDRITDLLEVPRLSGNDRLSSTGLQEVDVALLLGKIHSRLTHNAEKSEMQIELDVQASGAALACDPVALSRVICYLIDNATKFSSNAAVLVRLVVDESGKPQEIAVIDQGIGIERAQIDRIFEPFLQLDQGLTRRYGGLGLGLPIARRLCRDMGFTLAVDSHPGRGSCFSVKFC", "metadata": {"id": "A0A9E1P3U4", "cluster": 25431649, "interpro_all": ["IPR003018", "IPR029016", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR050736", "IPR004358"], "interpro_used": ["IPR003661", "IPR003018", "IPR005467"], "interpro_unused": ["IPR050736", "IPR036890", "IPR029016", "IPR036097", "IPR004358"]}, "task_type": "autoregressive"} {"instruction": "The desired role of my protein is: The protein is a member of the Succinate dehydrogenase/fumarate reductase type B transmembrane subunit family, which functions as the hydrophobic cytochrome b component of the succinate dehydrogenase and fumarate reductase complexes. These mono-haem proteins typically contain three transmembrane regions and conserved histidine residues that bind the haem group, serving to anchor the catalytic flavoprotein and iron-sulphur subunits to the membrane. Moreover, the protein possesses a Peptidase M3A/M3B catalytic domain that functions as a metallopeptidase to cleave medium-sized peptides across archaea, bacteria, and eukaryotes. This domain adopts a thermolysin-like fold and constitutes the active site of enzymes such as thimet oligopeptidase, neurolysin, and mitochondrial intermediate peptidase. Additionally, the protein is grouped in the Neurolysin/Thimet oligopeptidase, domain 2 superfamily, which represents an alpha orthogonal bundle domain found in zinc-dependent metallopeptidases such as neurolysin and thimet oligopeptidase. These enzymes metabolize small bioactive peptides, exhibiting overlapping but distinct substrate recognition and cleavage specificities. It is expressed in Clydaea vesicula and corresponds to UniProt keyword Metalloprotease, Metal-binding, and Heme. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 19234, 9294, 19, 28343, 11386, 2601, 44, 9117, 5903, 3416, 16, 2154, 4088, 1966, 1920, 7919, 9387, 44, 4594, 1927, 1920, 19234, 9294, 1930, 28343, 11386, 5048, 18, 2144, 8914, 17, 7105, 2697, 5745, 5531, 2559, 9117, 3451, 1930, 5305, 13873, 4248, 1988, 4566, 1920, 7105, 2210, 16, 13915, 1942, 13333, 1920, 6804, 7732, 6657, 1930, 5680, 17, 13528, 1949, 6991, 1942, 1920, 3260, 18, 3950, 16, 1920, 2213, 14465, 43, 24050, 12123, 1019, 19, 12123, 1014, 6804, 3418, 1988, 4088, 1966, 43, 8969, 24897, 1942, 21252, 3649, 17, 12177, 5320, 3436, 21501, 16, 4802, 16, 1930, 15021, 18, 2052, 3418, 24032, 43, 7967, 19010, 1921, 17, 3189, 3728, 1930, 14879, 1920, 3500, 3200, 1927, 5038, 2427, 1966, 7566, 14578, 15039, 9626, 2410, 9200, 16, 20325, 2012, 1921, 16, 1930, 4596, 6129, 24050, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 20325, 2012, 1921, 19, 7566, 14578, 15039, 9626, 2410, 9200, 16, 3418, 22, 13975, 16, 2154, 4972, 1925, 4595, 15581, 14142, 3418, 2435, 1922, 7997, 17, 3100, 8969, 24897, 1036, 2427, 1966, 20325, 2012, 1921, 1930, 7566, 14578, 15039, 9626, 2410, 9200, 18, 2144, 5038, 3074, 2606, 2858, 13570, 5320, 16, 12196, 8984, 2308, 4493, 4510, 5708, 1930, 6404, 18764, 18, 2176, 1977, 3198, 1922, 2111, 2584, 24145, 5634, 16058, 1019, 1930, 8852, 1942, 20709, 11121, 2538, 28629, 2051, 16, 6048, 17, 2743, 16, 1930, 10954, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MNFGLHFKRSFTPLIAKQYGVNFTKATASSLIYSQREGFNSSTKSNFEQPESFVKSQKLGRPMSPITIYKPQITSVLSISSRVTGAGLGVGIYGFAALYSFNLLDPTAFVSLVHSFPVLVGLAKAAIAYPVAFHSANGIRHLKPTPLQSIFDNQEYFRKKELNSDIKTGIFQYEHLQTPMDFETIVKIRTKQADKLVDLVCKADSIEEIKKTVKRLDRLSDMICSVVDMAEVIRHIHPSKKMAEAANAAHVALSNYLNRLNTHQKLYEALGKAVNNPAVQSLMSEQEKRVGALLTMDFENSGIHMPAETRKKFVELNDLVLELGQEFVTNSNPSVAYIEVENPYKALAGIPVKVIASISKKQKAIIPIGSNISYLILKKCENEETRKAVFIALNSGSKSQVECLDLMLKTRGELARLLSKKSYAELHLSDKMAKNPENVMKFLLSLSSKHKSRMEKDKLRLQDLKRSHTQDKLAVLQPWDRYFYAQYFSPNDMSVGGNEDPFHKAPQHEINDTLSRFFSVGNTFEGLSRLFSALYGVKFVPGTIHKGETWHPDVRKLEVIDEVKGKIGVVYCDVFSRDTAEVRKYENAAHFTVRCSRRIDQDENLNIDGVGDKENDILRNAAAEINVNEKEECKVYQMPIVVLVTSFYKSKHAPSLLSLSEVETLFHEMGHAMHSMLARSDFQHISGTRCAMDFVEVPSILTEFFAKDPLVLCSFAEDYETGEKLSPSVLSSYRKASNALESLENQHQIQLAILDQVYHAPENSELFIAGNKNFSSTDILRAVQNKVGVFPYTEGTAWQIQFSHLLTYGSSYYSYFWSRMWAQRLYQELFSKQITEQYGKKSLGNADKDFPSVDMIEILGKNGWRDSGQIVKTEILEVGGGRDPSIGNKLGLSKVLGNLNSDDFDLYK", "metadata": {"id": "A0AAD5XVT0", "cluster": 25976650, "interpro_all": ["IPR033851", "IPR024079", "IPR024077", "IPR045090", "IPR001567", "IPR034804", "IPR014314", "IPR000701"], "interpro_used": ["IPR000701", "IPR001567", "IPR024077"], "interpro_unused": ["IPR024079", "IPR034804", "IPR033851", "IPR014314", "IPR045090"]}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein can be placed in the PIN-like domain superfamily, which functions as a ribonuclease structurally defined by a 3-layer \u03b1/\u03b2/\u03b1 core and conserved acidic residues. These domains participate in eukaryotic nonsense-mediated mRNA decay and rRNA processing, or act as the toxic VapC component in prokaryotic VapBC toxin-antitoxin systems. It is found in Candidatus Contendobacter odensis Run_B_J11. Can you generate the amino acid sequence corresponding to this polypeptide chain?", "tokenized_instruction": [2, 51, 2150, 12144, 1922, 14246, 43, 13022, 4659, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8701, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 18347, 2051, 12171, 3608, 2007, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 4728, 1930, 5305, 9931, 4248, 18, 2144, 4682, 7352, 1922, 10825, 19605, 17, 3434, 3616, 9310, 1930, 9067, 4587, 16, 2014, 4033, 1966, 1920, 6161, 16697, 1030, 4594, 1922, 21545, 16697, 8284, 9165, 17, 10310, 9754, 3771, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 4257, 10249, 5883, 4426, 8134, 4747, 41, 44, 41, 52, 3242, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MKNSVYLDTTIPSYLFDERESINTHIKTTQKWWTEESSKFDIWISEETLNEVAEGNYPRKDEILRFISSIPILSPEKQIIDIAQIYLDNYVMPRVLKGDALHLAYASFYKIDFLLTWNCNHLANANKKQHIRIMNTRLNLATPEIVTPLELFAETNDDYQ", "metadata": {"id": "A0A7U7J5C8", "cluster": 28681963, "interpro_all": ["IPR029060"], "interpro_used": ["IPR029060"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein can be placed in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein is a member of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is produced by Stagnimonas aquatica and contains UniProt keyword associations ATP-binding, Cytoplasm, and Transferase.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 4152, 2007, 23891, 3223, 1980, 9259, 15849, 1019, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MSLAIGLTGGVASGKSYVQGLFAELGVPIIEADDVGRAVVQPGEPALAEIAARFERVFQDAAALRELEAITHPHIRARLRAWRDAQTAPYCLLSAAILLESGMSTLPLARAMLARQWTRAERLARADDLIDNPEPAGDLRPAVLALHRRYLGLAGGADMLLADGHLNRPRMRVSRVLVVDAPEQDQLSRLIRRDGIAE", "metadata": {"id": "A0A3N0VKW4", "cluster": 174028, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein has a Zinc finger C2H2-type domain that functions as a classical DNA-binding motif, typically found in eukaryotic transcription factors where it interacts with the DNA major groove using a conserved $\\beta/\\beta/\\alpha$ fold coordinated by a zinc ion. These domains frequently appear in tandem arrays to facilitate specific recognition of nucleic acids, proteins, or lipids, acting as stable scaffolds for diverse biological activities ranging from gene transcription to chromatin remodeling. Moreover, the protein belongs to the Zinc finger C2H2 superfamily, which comprises stable, zinc-coordinated $\\beta/\\beta/\\alpha$ motifs that primarily function as DNA-binding domains in eukaryotic transcription factors. These versatile scaffolds typically interact with the DNA major groove in tandem clusters, but can also be adapted to bind RNA, proteins, or lipids to regulate diverse cellular processes. Also, it is part of the C2H2-type zinc-finger protein AZF1/2/3-like family, which comprises plant transcription repressors that function primarily under abiotic stress conditions such as drought, cold, and high salinity. Belonging to the C1-2i subclass, these proteins negatively regulate abscisic acid and auxin signaling pathways and play roles in root development and nutrient stress responses. It is produced by Medicago truncatula (Barrel medic) (Medicago tribuloides) and is described by UniProt keywords Metal-binding and Transcription regulation. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 2258, 43, 7997, 8497, 8453, 6951, 17, 2601, 3418, 1988, 4088, 1966, 43, 8445, 2678, 17, 2743, 5219, 16, 5745, 2435, 1922, 10825, 3213, 2790, 2597, 2176, 9034, 1956, 1920, 2678, 3044, 15920, 2193, 43, 5305, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 3728, 11651, 2007, 43, 7997, 4755, 18, 2144, 4682, 5467, 3267, 1922, 10361, 10517, 1942, 6628, 2487, 5708, 1927, 11079, 4576, 16, 2697, 16, 2014, 8238, 16, 8290, 1966, 4700, 10603, 1958, 6445, 3933, 4209, 6485, 2037, 2359, 3213, 1942, 6338, 8378, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 7997, 8497, 8453, 6951, 13975, 16, 2154, 12936, 4700, 16, 7997, 17, 11651, 8, 38, 4666, 19, 38, 4666, 19, 38, 4595, 8, 8277, 1988, 5985, 2347, 1966, 2678, 17, 2743, 4682, 1922, 10825, 3213, 2790, 18, 2144, 20425, 10603, 5745, 6310, 1956, 1920, 2678, 3044, 15920, 1922, 10361, 5859, 16, 2308, 2112, 2222, 1998, 8461, 1942, 4566, 3146, 16, 2697, 16, 2014, 8238, 1942, 5741, 6445, 3689, 4028, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 8453, 6951, 17, 2601, 7997, 17, 8497, 2213, 6352, 5739, 19, 22, 19, 23, 17, 3189, 3416, 16, 2154, 12936, 4496, 3213, 26446, 1988, 2347, 5985, 2441, 16596, 3071, 2961, 2427, 1966, 12309, 16, 6685, 16, 1930, 2149, 15805, 18, 10588, 1942, 1920, 8817, 17, 25359, 17625, 16, 2144, 2697, 7191, 5741, 23006, 1937, 1935, 2687, 1930, 16243, 3197, 3873, 1930, 3918, 5456, 1922, 5904, 2740, 1930, 8708, 3071, 3387, 18, 2176, 1977, 4152, 2007, 3935, 10421, 7847, 1926, 5617, 12, 19560, 3935, 13, 12, 3935, 10421, 14521, 1944, 12363, 13, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 1930, 3213, 3640, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MYSSSSPSHDHSFHQKPKTNNQSLQKTRYPSFSFVESSTTNDAGKENPEKKIIWRFSYSVAHNHNDVVKQKKHSCDVCNKVFTSNKALNGHMRCHCRQNGPTVAAPSFEKQQPCRRRRYMNIDDDDDDVIETVAEILLQLSRMGYEDVNHRGAKRKNLSCNMMDDNEKKKRKKKEQGVLLTSGGHDIEEKKTINEGETELGSKVVKNVDLNELSSDDNEGETELGSKVVKNVDLNELPSDDNEGEAELGSKDVKNFDLNELPSDDNEGETESGSKVVKNLDLNELPSDEFEDKTN", "metadata": {"id": "A0A072VNE8", "cluster": 281683, "interpro_all": ["IPR044653", "IPR036236", "IPR013087"], "interpro_used": ["IPR013087", "IPR036236", "IPR044653"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Target Function: The protein should contain a Helicase, C-terminal domain-like domain that serves as the conserved C-terminal module in superfamily 1 and 2 helicases involved in DNA and RNA unwinding. Characterized by a parallel $\\alpha$-$\\beta$ topology, this domain is found in diverse enzymes across all domains of life, including the DEAD-box RNA helicase eIF4A. Also, the protein has a UVR domain that mediates protein-protein interactions, particularly the coiled-coil association between UvrB and UvrC required for DNA strand incision during nucleotide excision repair. This motif is also present in bacterial and chloroplastic Clp ATPases, where it likely facilitates similar subunit interactions. Also, the protein should feature a Helicase superfamily 1/2, ATP-binding domain that functions as the catalytic core for Superfamily 1 and 2 helicases, utilizing Walker A and B motifs to bind and hydrolyze ATP for the energy-dependent separation of double-stranded nucleic acids. This RecA-like structural module is found in a wide range of viral, bacterial, and eukaryotic proteins involved in DNA replication, repair, recombination, and RNA metabolism. It occurs in Butyricimonas virosa and is annotated with UniProt keywords SOS response, Cytoplasm, and DNA repair.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 3066, 5531, 43, 15318, 16, 45, 17, 4262, 3418, 17, 3189, 3418, 1988, 10634, 1966, 1920, 5305, 45, 17, 4262, 9059, 1922, 13975, 21, 1930, 22, 29919, 3286, 1922, 2678, 1930, 3146, 26801, 18, 4378, 2007, 43, 6110, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 13678, 16, 2052, 3418, 1977, 2435, 1922, 6445, 5038, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 9535, 17, 5758, 3146, 15318, 15718, 1019, 18, 2222, 16, 1920, 2213, 2258, 43, 5819, 1005, 3418, 1988, 10412, 2213, 17, 2213, 3719, 16, 4443, 1920, 17524, 17, 9121, 3279, 2192, 5819, 16007, 1930, 5819, 15618, 3414, 1958, 2678, 5984, 11773, 2409, 5489, 10940, 5059, 18, 2052, 5219, 1977, 2222, 2481, 1922, 4543, 1930, 17471, 1935, 18017, 28132, 16, 2597, 2176, 3205, 11374, 2551, 5903, 3719, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 15318, 13975, 21, 19, 22, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 13975, 21, 1930, 22, 29919, 16, 10232, 20138, 43, 1930, 44, 8277, 1942, 4566, 1930, 7222, 6931, 4498, 1958, 1920, 3844, 17, 3100, 7106, 1927, 4825, 17, 10338, 11079, 4576, 18, 2052, 21534, 17, 3189, 4346, 9059, 1977, 2435, 1922, 43, 4743, 3109, 1927, 4324, 16, 4543, 16, 1930, 10825, 2697, 3286, 1922, 2678, 5158, 16, 5059, 16, 7827, 16, 1930, 3146, 4714, 18, 2176, 5110, 1922, 2308, 19872, 1980, 9259, 2787, 5360, 1930, 1977, 10633, 1956, 20709, 11569, 17668, 2644, 16, 5239, 16, 1930, 2678, 5059, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MFKLTSAFEPTGDQPEAIKELTQGLLDEVPGQVLLGVTGSGKTFTIANVIQEVQRNAVEYFVSYYDYYQPEAYLPTTNTYIEKDLMINDEIDKLRLRTTASLLSGIIYLQKGQKIARNQLLRRLVDALYVNNELEFKRGSFRYRIEFWDDEIDRITSFSPQTGKTIDEMENLNIYPANLFVTDKATVDFLNSIGKHFEAKRLDERVKYDVEMIRELGYCSGIENYSRYLDGRAAGSHVTLPQVRAMYGGDRSRKQSLVEYGFRLPAAFDNRPLTFEEFEANTGQTIYVSATPADLDPEIEVVPSKNQIDHLINEIQKRIEINEKVLVTTLTKRTLERVQIIENLRKGVIDVIVGVNLLREGLDMPEVSLVAILDADKEGFLRAARNLNGKVIMYADTITRSMQETINETQYRREKQMEYNLQHGITPTQIRKSTESVLKEKMLQKTKAAMQKAAKEMDFLEAARLRDEMFKLEETIKRLNSPTLILSHNKTLAAQLYGEFKAFFPERRDVIVISSVSCLYGMADPTAFGSNAKGETVDIFPAIETFEGMALAKAIHDIEHDLVVQVRPFCLLDYFPQDFLLVVDEYELEKCNGVVVEQIIRPTGIMAEELSKYLDRIRIKCQYIHSDVDSTRSLIQTSGRTSRAYIEEEHVNLAADPVTAYMSKPELE", "metadata": {"id": "A0A412X696", "cluster": 1084973, "interpro_all": ["IPR006935", "IPR014001", "IPR001650", "IPR027417", "IPR001943", "IPR036876", "IPR004807", "IPR041471", "IPR024759"], "interpro_used": ["IPR001650", "IPR001943", "IPR014001"], "interpro_unused": ["IPR004807", "IPR041471", "IPR024759", "IPR006935", "IPR036876", "IPR027417"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein belongs to the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. Also, the protein is classified under the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It is expressed in Kosakonia sacchari and is linked to UniProt keywords Transferase, Cell inner membrane, and Metal-binding.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 1977, 3198, 1922, 23818, 14288, 10306, 14175, 2205, 1930, 1977, 4624, 1942, 20709, 11569, 13763, 16, 2024, 6671, 3260, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MQSSDPCATGKYSHGKTGIARIVSTLIYSRDGFLMITALVVNVSGVERALLLAVCFISLLVELLAKDMGSTAQTTALLMVAVVWGVILLALTAVHGEAAFRQLLVLHSVNSAIEAVVDRISLERHPLSKN", "metadata": {"id": "A0A1G4XUB0", "cluster": 3042678, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR033718", "IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein is categorized in the Polysaccharide biosynthesis protein family, which comprises integral membrane proteins involved in the production of polysaccharides. Members include RfbX, a component of the O antigen biosynthesis pathway, and SpoVB, which is required for spore cortex biosynthesis. In addition, the protein is assigned to the Polysaccharide Biosynthesis and Transport family, which functions as a flippase or transporter to facilitate the movement of lipid-linked saccharide precursors from the inner to the outer leaflet of the cytoplasmic membrane. These proteins are essential for assembling cell surface structures such as N-glycans, peptidoglycan, and lipopolysaccharides, thereby contributing to biofilm formation, structural integrity, and bacterial pathogenicity. It has been detected in Saprospirales bacterium and is classified with UniProt keywords Cell membrane and Transmembrane helix.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 1977, 10234, 1922, 1920, 17167, 8132, 2213, 3416, 16, 2154, 12936, 12328, 3260, 2697, 3286, 1922, 1920, 3372, 1927, 18686, 18, 4678, 3951, 7751, 1014, 1039, 16, 43, 4594, 1927, 1920, 57, 4730, 8132, 3374, 16, 1930, 18055, 1020, 1014, 16, 2154, 1977, 3414, 1958, 18445, 4997, 8132, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 17167, 8132, 1930, 4860, 3416, 16, 2154, 4088, 1966, 43, 16405, 5506, 2014, 9054, 1942, 6628, 1920, 5829, 1927, 4486, 17, 4624, 14175, 2205, 3695, 10416, 2037, 1920, 6671, 1942, 1920, 7642, 20097, 1927, 1920, 6823, 3260, 18, 2144, 2697, 2032, 4415, 1958, 26358, 2024, 3154, 4061, 2427, 1966, 56, 17, 15509, 16, 24183, 16, 1930, 15614, 1036, 16, 6113, 8739, 1942, 9638, 3337, 16, 4346, 7996, 16, 1930, 4543, 15903, 18, 2176, 2258, 2252, 3330, 1922, 9235, 5424, 7118, 1918, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MGLNREFLVNIILLVVINLLIKPLYLFGIDARVQNIVGGIQNFNSRLIAQDRDKIIFHFPRILGSKVLLGLIFIIVTTLAATLFIYLRTNISALGMYRKDSYISAIDKLIMIIILGYLTWAYTIACIVAFAIVLPKVKERWIVFSWSYLLKLVKKSAPFALVILLVAIYLRIYAAAYRFFEAAGMLAYLFGALLLPMYSTLMGKKESVASLTLTSLRMIRHDLMTFIYDDATTYYGKILIYMMLAFFAVAISHIYGAMIFILGAILNVSLNLWLIPLKGAEGAAIATVATQLLVTISQICLAHSQMKLQINYSLIMALSILFCLGISLLLGVVDKNMLSTLQKQNAESTENFGLYFALFNFIFLFQVINDPFLIGYDLSELNMLILIAVNFFLAFYPDLESFTIYWFIYGQMIIDGVMLERLLDDNGLQAGLVISMTILVTLVVYMAKGSLKELNIIAKSIVFGFLCTISAILWHNSGLYWTIS", "metadata": {"id": "A0A350IBV4", "cluster": 3191158, "interpro_all": ["IPR050833", "IPR002797"], "interpro_used": ["IPR002797", "IPR050833"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe protein is categorized in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. In addition, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It has been detected in Bifidobacterium catenulatum PV20-2 and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 2258, 2252, 3330, 1922, 21724, 12022, 3115, 1917, 5617, 1031, 1989, 5774, 3520, 17, 22, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MVIRIGLTGGIAAGKSTVSTKLRELGAVLGSIGLQRIAECFGPDALTDRGDLNRAWMAEHVFSGADAERKRKILDAVVVHDIPLLAEVIDSIPFEFDHIVTVEAPEQVRVSRMMTTRGMSESQAWRLAIADEVIDSTQPLEQMFEHIDMLMKQWRTEARVDYDLLARHVVEPGIEHPLIYELAVQLEHEAVEADCQNRVNHQSSVEQ", "metadata": {"id": "A0A0A7I235", "cluster": 3350074, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein falls within the Interferon alpha-inducible protein IFI6/IFI27-like family, which mediates interferon-induced apoptosis through pro-apoptotic factors such as IFI6 and ISG12. These proteins contribute to cell death pathways, often by localizing to the mitochondria and perturbing normal mitochondrial function. It has been detected in Rhinolophus ferrumequinum (Greater horseshoe bat) and corresponds to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 10001, 4595, 17, 9376, 2213, 29784, 1016, 19, 29784, 4282, 17, 3189, 3416, 16, 2154, 10412, 10001, 17, 2719, 4091, 2596, 1965, 17, 6353, 2790, 2427, 1966, 29784, 1016, 1930, 22443, 3112, 18, 2144, 2697, 4672, 1942, 2024, 3539, 3873, 16, 3868, 2007, 29507, 1942, 1920, 6489, 1930, 8589, 1941, 2791, 4596, 2347, 18, 2176, 2258, 2252, 3330, 1922, 14066, 26356, 2102, 1957, 12210, 16120, 11072, 1989, 12, 3430, 15638, 10647, 1021, 11579, 13, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MALPGLRSRGKALCYIQKGSTLVHARKQEDESPQSSSAGSTPGRPPQGPPPGPDGHGSDSTDPPPKDGGRNFSRTAAIVAAGVTTGAVAVGAAPVVLGAMGFTGAGIAASSLAAKMMSAAAVANGGGVAAGSLVATLQSAGAAGLSLSSNILLGLTGFSFGGWLGSKATSSSPPPGPSTEAEGGPHVGGDSPGPQNDSPPNDKPPASPNCSEKDEK", "metadata": {"id": "A0A671ED04", "cluster": 4067799, "interpro_all": ["IPR009311", "IPR038213"], "interpro_used": ["IPR009311"], "interpro_unused": ["IPR038213"]}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein includes a Glycosyltransferase RgtA/B/C/D-like domain that functions as a glycosyltransferase involved in the modification of the lipopolysaccharide (LPS) inner core. This domain is typically found in bacteria such as *Rhizobium leguminosarum*, where it contributes to the biosynthesis and structural integrity of the cell envelope. It has been characterized in Rhodospirillales bacterium and contains UniProt keyword associations Membrane, Transmembrane, and Transmembrane helix.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 5921, 43, 20067, 9961, 9372, 3857, 19, 44, 19, 45, 19, 46, 17, 3189, 3418, 1988, 4088, 1966, 43, 20067, 9961, 3286, 1922, 1920, 6295, 1927, 1920, 15614, 12, 5887, 13, 6671, 4728, 18, 2052, 3418, 1977, 5745, 2435, 1922, 4802, 2427, 1966, 14, 13458, 23156, 6703, 5101, 5360, 24277, 14, 16, 2597, 2176, 7624, 1942, 1920, 8132, 1930, 4346, 7996, 1927, 1920, 2024, 11262, 18, 2176, 2258, 2252, 4378, 1922, 11490, 3106, 23576, 11560, 3955, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MKNLFPPVTIAAFLCFGIIAIQLLWQKPEPRGTGQSGEVPQPDNYIVPAYPALLAAIAVFDPLSLILIQAVLLAGATLFTFNAYRHLNPRPAFAYTALVCLLAVGLQARCLVTALRSKGAQSWLAVGAVIGLGALIRPSTFYLVFMMIPVVLFATRSRNVLIVDSLSFTGSYGGITLAQRVAYNAMTPVEWGVALIYIEAYQRLDFSTQNGFYRIGNTALMAEALSRAGGPQGLTGVLIKDRGLWVAKYVGLAAILLLIPVVTGLWRQGRAKNFLILASPYNYSLVIIYAALFAYAGFYIWDRVNRAPTSTAINQDQVDERFYLVLAHDLYEFGVFTSATARPEMRKQMRCAVGPIGDCMATILATSILPDGLSLAAFMVLAGVRGSIAMLIGFTIVLTPWILWLPDFGDSLAASLFPWILAHPLTHIATTIPIFLFFLMAGFHAGISINIPR", "metadata": {"id": "A0A2D9HZ83", "cluster": 4648318, "interpro_all": ["IPR038731"], "interpro_used": ["IPR038731"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein incorporates a Twin-arginine translocation pathway signal sequence conserved site that targets fully folded proteins, such as redox enzymes with complex cofactors, for export across energy-transducing membranes in bacteria, archaea, and chloroplasts. This N-terminal peptide contains a characteristic motif with invariant twin-arginine residues that directs the protein to the Tat translocase machinery, facilitating the secretion of substrates that have already acquired their tertiary structure. In addition, the protein possesses a SsuA/THI5-like domain that is proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine in NMT1/THI5 family proteins. It also functions as the aliphatic sulfonate-binding component of the SsuA transport system. It is identified in Bradyrhizobium sp. Leo121.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 19683, 43, 13392, 17, 9732, 7849, 3374, 2733, 3244, 5305, 3200, 1988, 4845, 5437, 16318, 2697, 16, 2427, 1966, 9366, 5038, 1956, 2796, 21362, 16, 1958, 12660, 3436, 3844, 17, 5925, 1941, 5726, 1922, 4802, 16, 21501, 16, 1930, 24627, 18, 2052, 56, 17, 4262, 4207, 5461, 43, 6293, 5219, 1956, 17004, 13392, 17, 9732, 4248, 1988, 28351, 1920, 2213, 1942, 1920, 10687, 12930, 2051, 10853, 16, 12440, 1920, 5512, 1927, 6249, 1988, 2162, 6064, 5815, 2310, 10832, 3170, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 4577, 12169, 19, 7566, 1015, 17, 3189, 3418, 1988, 1977, 4211, 1942, 1998, 3414, 1958, 1920, 8132, 1927, 1920, 21611, 11804, 1927, 26901, 1922, 2943, 6613, 19, 7566, 1015, 3416, 2697, 18, 2176, 2222, 4088, 1966, 1920, 22234, 26265, 2010, 17, 2743, 4594, 1927, 1920, 4577, 12169, 4860, 2433, 18, 2176, 1977, 2899, 1922, 20152, 5004, 2061, 23156, 2056, 18, 2071, 8098, 4716, 18, 3], "output": "MISRRAFVSGFGGAMATAALQPSIVLAQAGGKPLRITHAVTSLAYMQSYIANQNGYFNQAGLTAQIIDTGGGGPDVQLVLGGRAEMTVNDGAQILPALQQGQKLTCVLSLLNRSIVNATISKTAAAKYGVTEAMPLADKLGRMKGMKIGVTRPGALTWQLARFNLVSVGLNPDKDAQIVAVGGPPALAAALENGAVDLIYISMPIGEKLIREGKAISFINNARGEDPKLANFMMEGLWTTPDYLAANRPTIKAAVTAYQKASDFIRTSAPEAVVAALMPALGSLGEAVLLDSVKRIHPAVSETGKITSAEFDTTQALLKMNGFLNTPFVIADVFDGSFTKV", "metadata": {"id": "A0A4Q7G0A8", "cluster": 5434120, "interpro_all": ["IPR015168", "IPR006311"], "interpro_used": ["IPR006311", "IPR015168"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the polypeptide chain function: The protein is included in the IS1016-like transposase family, which catalyzes the movement of specific insertion elements within bacterial genomes by cutting and rejoining DNA sequences. These proteins facilitate genomic rearrangements and horizontal gene transfer, contributing to genetic variation and adaptation. It is derived from Capitella teleta (Polychaete worm). Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 1977, 13100, 1016, 17, 3189, 12935, 2051, 3416, 16, 2154, 17097, 1920, 5829, 1927, 2487, 7413, 5362, 2651, 4543, 7313, 2007, 14589, 1930, 12677, 9024, 1941, 2678, 3709, 18, 2144, 2697, 6628, 4935, 13955, 1930, 8743, 2359, 3856, 16, 8739, 1942, 3299, 4516, 1930, 7810, 18, 2176, 1977, 3595, 2037, 2853, 2394, 11560, 1019, 10304, 3857, 12, 25754, 3336, 2057, 11055, 13, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MTVRAFYGFIMDTSVLFEWLRDFGLIKRTRYCPVCKEAMKLKKVPDERLSDGCIWRCDRKIGGKRRGKEISVRHSSWFSHSKMTLSEILELTFWWVRGDKQDVIMNETGHGEHTLVDWGNFMRECCLVYLEKFGNLGKIGGEGVIVEIDESKFGKRKYRGNLVEGSWVIGGRERDNPKKCFFEVVEN", "metadata": {"id": "R7U9G0", "cluster": 5669941, "interpro_all": ["IPR053164"], "interpro_used": ["IPR053164"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a polypeptide chain that performs the following role: The protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It has been characterized in Acidobacteriota bacterium. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 2258, 2252, 4378, 1922, 2687, 5883, 3940, 3857, 14061, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MNTAAHHQIGIEVGGLPVLVHTQDQKFCDQLAKYYAGFVSHSGVARFHFEVEQLAQAPDPGAEISVEVRDGIWSVRRADFTAECNPSAGSAKIRQSAGTHSFDSVLRIIHTLALADEGGFLLHAASALRNGRAFIFSGVSGAGKTTLARMAPSDATILTDEVSYVRRLDGRFEACGTPFAGELARAGANTSAPVDTLLFLQQGPENRIEEMNKQEALQRLLRNILFFAADPELVTKLFETANKFLESIPVRRLTFQPEPDVWSLIQ", "metadata": {"id": "A0A2V9NWH4", "cluster": 6125844, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein can be placed in the Ribosomal RNA small subunit methyltransferase H family, which catalyzes the N4-methylation of cytidine 1402 in the 16S rRNA. This modification fine-tunes the ribosomal P-site structure to enhance interaction with the mRNA codon and improve translation decoding fidelity. Furthermore, the protein is associated with the S-adenosyl-L-methionine-dependent methyltransferase superfamily, which utilizes the cofactor S-adenosyl-L-methionine (SAM) to catalyze the transfer of methyl groups to a wide variety of substrates such as proteins, nucleic acids, lipids, and small molecules. Members typically share a conserved core structure, often a Rossmann-like fold featuring a central seven-stranded beta-sheet and a characteristic GxGxG motif for cofactor binding. Also, the protein is a member of the S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily, which serves as a recognition module in bacterial SAM-dependent methyltransferases to determine methyl acceptor selectivity. This domain adopts a central alpha orthogonal structure, distinguishing it from simpler recognition motifs found in related enzymes. It has been characterized in Planctomycetes bacterium GWF2_39_10 and carries UniProt keyword assignments Cytoplasm and rRNA processing.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 11196, 3146, 2858, 5903, 16478, 50, 3416, 16, 2154, 17097, 1920, 27982, 17, 5547, 1927, 2702, 5802, 8949, 1028, 1922, 1920, 11209, 9067, 18, 2052, 6295, 8882, 17, 23703, 1036, 1920, 11196, 58, 17, 3200, 3170, 1942, 4826, 2835, 1956, 1920, 3616, 8905, 1930, 3326, 6410, 20749, 14013, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 13975, 16, 2154, 18127, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 1942, 43, 4743, 5386, 1927, 6249, 2427, 1966, 2697, 16, 11079, 4576, 16, 8238, 16, 1930, 2858, 4206, 18, 4678, 5745, 7948, 43, 5305, 4728, 3170, 16, 3868, 43, 18215, 8890, 17, 3189, 3728, 29931, 43, 4101, 5260, 17, 10338, 4666, 17, 11130, 1930, 43, 6293, 26615, 1029, 1039, 1029, 5219, 1958, 15155, 2743, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 16, 24564, 1018, 16, 5708, 3418, 13975, 16, 2154, 10634, 1966, 43, 5708, 9059, 1922, 4543, 2235, 17, 3100, 28253, 1942, 3415, 4963, 12641, 9008, 18, 2052, 3418, 24032, 43, 4101, 4595, 15581, 3170, 16, 15589, 2176, 2037, 20552, 5708, 8277, 2435, 1922, 2712, 5038, 18, 2176, 2258, 2252, 4378, 1922, 4720, 2341, 25148, 14061, 8997, 6680, 41, 3886, 41, 2119, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 1930, 9067, 4587, 18, 3], "output": "MHDTTNDLLHKPVMVEEVLDYLNPQTGQVIKIKPNGLLIGIDKDMEILQIAKQHIEVLRQAGTDKVNGVLLDLGTSSLQFDQAERGFSFSKEKLEELFSKYGEERWSRRIARAILKEENDTGIHPATRVFQALRIAVNKELESLEVFLNKIHNYMTVGARIVILTKKPITPGEAEIERNIRCRSAKLRAAERIIDCTVGGGGHASKIMSSEIGNIFKLYHADYSEIDGPLDMRMDRSQGITAKDLVHRLSEQTSTRQLANIIERAVPRGKSKIVISFHSLEDRIVKNKFSERAKQNIFQ", "metadata": {"id": "A0A1G2XMR1", "cluster": 7532513, "interpro_all": ["IPR002903", "IPR023397", "IPR029063"], "interpro_used": ["IPR002903", "IPR029063", "IPR023397"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein includes a GHMP kinase, C-terminal domain that functions as the C-terminal component of ATP-dependent enzymes in the GHMP superfamily, including homoserine, galacto-, and mevalonate kinases. This domain contributes to a nucleotide-binding fold via a central alpha-beta plait structure and participates in isoprene and amino acid biosynthesis as well as carbohydrate metabolism. Additionally, the protein is a member of the Ribosomal protein uS5 domain 2-type superfamily, which encompasses proteins sharing a distinctive $\\alpha/\\beta$ fold often utilized for nucleotide binding and processing. This domain is integral to translational machinery, RNA processing complexes, and DNA repair enzymes, while also forming the core structure of GHMP kinases and Hsp90 chaperones. Furthermore, the protein is classified under the Small ribosomal subunit protein uS5 domain 2-type fold superfamily, which features a left-handed \u03b2-\u03b1-\u03b2 structure utilized in diverse nucleic acid-binding proteins and GHMP family kinases. This domain serves as a key component in translational machinery and DNA repair enzymes, such as MutL and DNA gyrase B, while also facilitating ATP-dependent phosphoryl transfer in metabolic enzymes like galactokinase and mevalonate kinase. It is derived from Candidatus Zhuqueibacterota bacterium 4484_188 and contains UniProt keyword associations Transferase.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 5921, 43, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 45, 17, 4262, 4594, 1927, 4498, 17, 3100, 5038, 1922, 1920, 6101, 6588, 13975, 16, 2710, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 18, 2052, 3418, 7624, 1942, 43, 5489, 17, 2743, 3728, 3454, 43, 4101, 4595, 17, 4666, 5606, 1932, 3170, 1930, 17241, 1922, 26690, 1021, 1930, 3835, 2687, 8132, 1966, 2486, 1966, 10590, 4714, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 11196, 2213, 2022, 1015, 3418, 22, 17, 2601, 13975, 16, 2154, 21569, 2697, 10763, 43, 15308, 8, 38, 4595, 19, 38, 4666, 8, 3728, 3868, 7079, 1958, 5489, 2743, 1930, 4587, 18, 2052, 3418, 1977, 12328, 1942, 8414, 10853, 16, 3146, 4587, 5048, 16, 1930, 2678, 5059, 5038, 16, 2679, 2222, 7402, 1920, 4728, 3170, 1927, 6101, 6588, 7784, 1930, 12254, 18098, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2858, 11196, 5903, 2213, 2022, 1015, 3418, 22, 17, 2601, 3728, 13975, 16, 2154, 4075, 43, 3506, 17, 17105, 161, 17, 160, 17, 161, 3170, 7079, 1922, 6445, 11079, 2687, 17, 2743, 2697, 1930, 6101, 6588, 3416, 7784, 18, 2052, 3418, 10634, 1966, 43, 3834, 4594, 1922, 8414, 10853, 1930, 2678, 5059, 5038, 16, 2427, 1966, 2446, 1024, 1930, 2678, 9430, 2051, 44, 16, 2679, 2222, 12440, 4498, 17, 3100, 12556, 3856, 1922, 4487, 5038, 3189, 9479, 18655, 1930, 21750, 20807, 5791, 1021, 4016, 18, 2176, 1977, 3595, 2037, 14550, 1031, 1957, 19533, 5089, 26073, 2341, 6506, 3857, 14061, 29877, 1006, 41, 16359, 1930, 5461, 20709, 11121, 2538, 5253, 13763, 18, 3], "output": "MFQLDLSVPEMIRLAARVGSDVPFFIPGKTALVKGRGEVVVPVRFLTDYRILLVLPNVQLSTAEIYKKFEMNLTKYAHHVKFEAVILGIRNLEDLNYYLYNDLEQVAQTVYPELAGIRERLLASGAAYVSLTGSGSAMYGLYHKESDLEAVGELFSPDFRVYAAQPVT", "metadata": {"id": "A0A1V4RMP0", "cluster": 7878107, "interpro_all": ["IPR013750", "IPR036554", "IPR020568", "IPR014721"], "interpro_used": ["IPR013750", "IPR020568", "IPR014721"], "interpro_unused": ["IPR036554"]}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence be if I wanted a protein that could perform the following function: The protein is classified under the 4-diphosphocytidyl-2C-methyl-D-erythritol kinase family, which functions as a key enzyme in the non-mevalonate pathway for isoprenoid biosynthesis. Belonging to the GHMP kinase superfamily, these proteins participate in the deoxyxylulose phosphate pathway of terpenoid production and are essential for chloroplast development. Also, the protein contains a GHMP kinase N-terminal domain that functions as the ATP-binding module in galacto-, homoserine, mevalonate, and phosphomevalonate kinases. It contains a conserved Gly/Ser-rich region essential for catalyzing the phosphorylation of these substrates. Furthermore, the protein can be placed in the GHMP kinase, C-terminal domain superfamily, which encompasses the C-terminal structural component of ATP-dependent enzymes involved in amino acid, isoprene, and carbohydrate metabolism. This domain adopts a central alpha-beta plait fold that cooperates with the N-terminal domain to create a nucleotide-binding pocket. While primarily found in homoserine, galacto-, and mevalonate kinases, it is also present in structurally related diphosphomevalonate decarboxylases. It has been detected in Acidimicrobiaceae bacterium and is classified with UniProt keywords Isoprene biosynthesis and Transferase.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 24, 17, 11791, 2609, 3107, 19743, 17, 6921, 17, 4963, 17, 46, 17, 6549, 3027, 4575, 1024, 4016, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 2447, 17, 21750, 20807, 5791, 1021, 3374, 1958, 26690, 2642, 8132, 18, 10588, 1942, 1920, 6101, 6588, 4016, 13975, 16, 2144, 2697, 7352, 1922, 1920, 16333, 10465, 5277, 6012, 4127, 5413, 3374, 1927, 6005, 17125, 2642, 3372, 1930, 2032, 4415, 1958, 17471, 2740, 18, 2222, 16, 1920, 2213, 5461, 43, 6101, 6588, 4016, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 9059, 1922, 9479, 1037, 17, 16, 16350, 26337, 16, 21750, 20807, 5791, 1021, 16, 1930, 8078, 3870, 4701, 8870, 7784, 18, 2176, 5461, 43, 5305, 3376, 19, 2375, 17, 5536, 3031, 4415, 1958, 29601, 1920, 4050, 1927, 2144, 6249, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 6101, 6588, 4016, 16, 45, 17, 4262, 3418, 13975, 16, 2154, 21569, 1920, 45, 17, 4262, 4346, 4594, 1927, 4498, 17, 3100, 5038, 3286, 1922, 3835, 2687, 16, 26690, 1021, 16, 1930, 10590, 4714, 18, 2052, 3418, 24032, 43, 4101, 4595, 17, 4666, 5606, 1932, 3728, 1988, 23230, 1036, 1956, 1920, 56, 17, 4262, 3418, 1942, 7762, 43, 5489, 17, 2743, 10154, 18, 2679, 5985, 2435, 1922, 16350, 26337, 16, 9479, 1037, 17, 16, 1930, 21750, 20807, 5791, 1021, 7784, 16, 2176, 1977, 2222, 2481, 1922, 12171, 2712, 11791, 2609, 2225, 4701, 8870, 23922, 1036, 18, 2176, 2258, 2252, 3330, 1922, 2687, 1980, 1935, 15129, 19476, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 26690, 1021, 8132, 1930, 13763, 18, 3], "output": "MENTVRTNKGVKVISPAKLTLSLRIIGRREDGYHFIESEMVTIDLIDTVFFKKGVRKVTYEGEYPIKPHAEEDLILKALNFLDIDSEVTVSKSIPPQGGLGGGSGNAAAVLRYFGYTDLKKAVKLGADVPFNIKGGRARVGGIGENIEPLTYKEKTFTLLTPDVGCSTIEVYKKWDQLGGPKGENGNDLEQAALEVHPELSQWRDKLEQHTGLTPKLAGSGSTWXVEGYFPGQGFITARTLPAFDETSPSKL", "metadata": {"id": "A0A2E6E3D4", "cluster": 8448710, "interpro_all": ["IPR036554", "IPR006204", "IPR004424", "IPR020568", "IPR014721"], "interpro_used": ["IPR004424", "IPR006204", "IPR036554"], "interpro_unused": ["IPR020568", "IPR014721"]}, "task_type": "autoregressive"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein should feature a Helix-turn-helix domain, group 17 domain that functions as a DNA-binding module typically found in bacteriophage excisionases, such as the Xis protein from Salmonella phage P22. It facilitates the specific DNA recognition events required for the excision of the phage genome from the host chromosome. It is present in Bacteroidia bacterium.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 3066, 5961, 43, 7864, 17, 5165, 17, 7864, 3418, 16, 2210, 2752, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 9059, 5745, 2435, 1922, 24613, 10940, 2319, 16, 2427, 1966, 1920, 11551, 1036, 2213, 2037, 11681, 10503, 29243, 18, 2176, 11374, 1920, 2487, 2678, 5708, 3916, 3414, 1958, 1920, 10940, 1927, 1920, 10503, 3843, 2037, 1920, 4423, 5597, 18, 2176, 1977, 2481, 1922, 24323, 2126, 14061, 18, 3], "output": "MSNINNPFIAVSSKLEASPAKDRIYSLVSAKNIPHETKSEFLKKIKDTILRRLDEIDERLIGGIDLACEVLKGIYSKQTSKRGKMLVFSEKVLLEWVTENKK", "metadata": {"id": "A0A9E0AIH9", "cluster": 9758925, "interpro_all": ["IPR041657"], "interpro_used": ["IPR041657"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein includes a Transcription regulator HTH, AraC- type, HTH domain that binds DNA via a helix-turn-helix motif to regulate transcription in bacteria. Typically situated towards the C-terminus, this domain is found in a diverse family of proteins, including SoxS and VirF, where it facilitates specific genomic interactions to control gene expression. Additionally, the protein should contain a Signal transduction response regulator, receiver domain that functions as a phosphorylation-activated switch within two-component systems to couple environmental sensing with cellular adaptation. It accepts a phosphoryl group from a cognate sensor histidine kinase, inducing a conformational change that activates an associated effector domain to regulate gene expression. Also, the protein should have a HTH domain AraC-type conserved site that functions as a DNA-binding motif in bacterial transcriptional regulators, most of which act as positive factors. This region comprises two helix-turn-helix subdomains that bind the major groove of DNA, structurally inducing a bend in the double helix. It has been detected in Thiospirochaeta perfilievii and is classified with UniProt keywords Transcription regulation and Two-component regulatory system.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 5921, 43, 3213, 7888, 5334, 1023, 16, 20289, 1030, 17, 2601, 16, 5334, 1023, 3418, 1988, 6876, 2678, 3454, 43, 7864, 17, 5165, 17, 7864, 5219, 1942, 5741, 3213, 1922, 4802, 18, 5745, 18287, 5681, 1920, 45, 17, 7822, 16, 2052, 3418, 1977, 2435, 1922, 43, 6445, 3416, 1927, 2697, 16, 2710, 9149, 1036, 1930, 2787, 1038, 16, 2597, 2176, 11374, 2487, 4935, 3719, 1942, 2285, 2359, 2294, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 2733, 8201, 2644, 7888, 16, 12608, 3418, 1988, 4088, 1966, 43, 4050, 17, 4128, 6195, 2651, 2288, 17, 4594, 3771, 1942, 15116, 4813, 9306, 1956, 3689, 7810, 18, 2176, 5861, 1036, 43, 12556, 2210, 2037, 43, 15786, 6443, 13873, 4016, 16, 7834, 43, 8523, 3185, 1988, 9094, 1925, 2458, 7917, 3418, 1942, 5741, 2359, 2294, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 5334, 1023, 3418, 20289, 1030, 17, 2601, 5305, 3200, 1988, 4088, 1966, 43, 2678, 17, 2743, 5219, 1922, 4543, 5224, 9098, 16, 2501, 1927, 2154, 4033, 1966, 2843, 2790, 18, 2052, 3031, 12936, 2288, 7864, 17, 5165, 17, 7864, 30103, 1988, 4566, 1920, 3044, 15920, 1927, 2678, 16, 12171, 7834, 43, 20672, 1922, 1920, 4825, 7864, 18, 2176, 2258, 2252, 3330, 1922, 15331, 3508, 10602, 25588, 9215, 5294, 5912, 9488, 3907, 1930, 1977, 5947, 1956, 20709, 11569, 3213, 3640, 1930, 2288, 17, 4594, 4948, 2433, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MIKTLIVDDEPNIREGLKIVIEWEKLGFQVVGEAASGVEALRKIEELQPAKELNISFIILSGHGEFSMAKQALNLGVNDYLLKPVDEDELTEALIKLKKDKFSSISLPEIKRLFKIDNQISFYYVIVDSRGNIPVDTIKGLIQKTLPSNSTISLHSINIYLMDLISFVYKETLKEVSIYLGTKKRNLYELKDSMDEAVIASVHRYYRESGIIIDYNNIQHEVTRSINNLVNYFLDQYLSAHIIYLHLNRLLNRVLESVQKLGGDSEKIIHKADFIIKINKLKNKSSLGLELKEYIDVNFRENLSLKCVADKFNVNPAYLGQVFKKETLLLQSNIKIYEVAQSVGYMDVNYFMKKFERQFSTTPKQYRKNYNKSIKIVVITDVKMPKMSGLELAAECVKRHHSEPIYLQAQFDQLLSSNREREKKHMCGSYGFMIHSTMLKDYNLDFCDEYSETQYIDDILNGVLDRDRGRESQIYLYSLPNKIEGLMDVVLNIGTSFNSYFHTLRLNEASK", "metadata": {"id": "A0A5C1Q9V0", "cluster": 9818543, "interpro_all": ["IPR011006", "IPR009057", "IPR051552", "IPR018060", "IPR018062", "IPR001789", "IPR020449"], "interpro_used": ["IPR020449", "IPR001789", "IPR018062"], "interpro_unused": ["IPR009057", "IPR051552", "IPR011006", "IPR018060"]}, "task_type": "infilling"} {"instruction": "The protein should include a Twin-arginine translocation pathway signal sequence conserved site that targets fully folded proteins, such as redox enzymes with complex cofactors, for export across energy-transducing membranes in bacteria, archaea, and chloroplasts. This N-terminal peptide contains a characteristic motif with invariant twin-arginine residues that directs the protein to the Tat translocase machinery, facilitating the secretion of substrates that have already acquired their tertiary structure. It has been detected in Myxococcales bacterium.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 3066, 3951, 43, 13392, 17, 9732, 7849, 3374, 2733, 3244, 5305, 3200, 1988, 4845, 5437, 16318, 2697, 16, 2427, 1966, 9366, 5038, 1956, 2796, 21362, 16, 1958, 12660, 3436, 3844, 17, 5925, 1941, 5726, 1922, 4802, 16, 21501, 16, 1930, 24627, 18, 2052, 56, 17, 4262, 4207, 5461, 43, 6293, 5219, 1956, 17004, 13392, 17, 9732, 4248, 1988, 28351, 1920, 2213, 1942, 1920, 10687, 12930, 2051, 10853, 16, 12440, 1920, 5512, 1927, 6249, 1988, 2162, 6064, 5815, 2310, 10832, 3170, 18, 2176, 2258, 2252, 3330, 1922, 21464, 11748, 1918, 14061, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MSRRPVSRRAPLRAVDGDVPLDELREFLSADLFGFGPPPTRGDDTASPGVSAALPADADFGLEADFEVPADPGFKNRLREKLWELVESRA", "metadata": {"id": "A0A956A0I4", "cluster": 11803619, "interpro_all": ["IPR006311"], "interpro_used": ["IPR006311"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein is associated with the UPF0208 family, which consists of uncharacterised proteins found in bacteria. It is found in Mannheimia haemolytica (Pasteurella haemolytica) and is classified with UniProt keywords Cell inner membrane, Membrane, and Transmembrane. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 1977, 2458, 1956, 1920, 2353, 1038, 11636, 13895, 3416, 16, 2154, 7543, 1927, 23229, 3495, 2697, 2435, 1922, 4802, 18, 2176, 1977, 2435, 1922, 24615, 2126, 7105, 26656, 12, 24868, 5870, 7105, 26656, 13, 1930, 1977, 5947, 1956, 20709, 11569, 2024, 6671, 3260, 16, 3260, 16, 1930, 9117, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MLSLFDAGQRYLNTLPNQKKLANFMPDYHIIRLVKFSSKVMPAFACFALVWQYCFTDPTQSILANSVLTAVFAISIPFQGLYWLGKRARSPLSLSLLEWYESLRQKLISAQVKLEENTSGTFFPRFCKFTQASRRDLGR", "metadata": {"id": "A0A378N929", "cluster": 12687893, "interpro_all": ["IPR007334"], "interpro_used": ["IPR007334"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein should have a Parallel beta-helix repeat-2 repeat that stacks to form a right-handed parallel beta-helix structure involved in carbohydrate binding and sugar hydrolysis. This motif is homologous to the tandem repeats found in the periplasmic C-5 mannuronan epimerase AlgA of *Pseudomonas aeruginosa*. Additionally, the protein is a member of the Pectin lyase fold/virulence factor superfamily, which comprises proteins sharing a parallel $\\beta$-helix topology that function primarily as microbial virulence factors and carbohydrate-degrading enzymes. Members include pectin and pectate lyases that cleave plant cell wall components, as well as adhesins like pertactin and viral tailspike proteins. It is found in Altimarinota bacterium (Gracilibacteria bacterium). Please provide the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 7762, 30, 1920, 2213, 3066, 2162, 43, 6110, 4666, 17, 7864, 6865, 17, 22, 6865, 1988, 20836, 1942, 2386, 43, 3659, 17, 17105, 6110, 4666, 17, 7864, 3170, 3286, 1922, 10590, 2743, 1930, 9523, 9128, 18, 2052, 5219, 1977, 8725, 1942, 1920, 10361, 9569, 2435, 1922, 1920, 24334, 45, 17, 25, 7338, 10366, 1928, 13872, 9213, 2051, 4326, 1019, 1927, 14, 13461, 10830, 14, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 22422, 23928, 3728, 19, 9304, 2991, 13975, 16, 2154, 12936, 2697, 10763, 43, 6110, 8, 38, 4666, 8, 17, 7864, 13678, 1988, 2347, 5985, 1966, 7293, 9304, 2790, 1930, 10590, 17, 18192, 5038, 18, 4678, 3951, 22422, 1930, 13494, 3857, 2057, 23928, 1036, 1988, 21252, 4496, 2024, 4821, 4178, 16, 1966, 2486, 1966, 5315, 2925, 3189, 7548, 11686, 1930, 4324, 18103, 10984, 3324, 2697, 18, 2176, 1977, 2435, 1922, 8387, 12874, 5572, 7336, 14061, 12, 24689, 10401, 26073, 2341, 18339, 14061, 13, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MYLDSSNNNILDNIQTSDNKSYGIYLRASSNNILNNIQTYNNSIH", "metadata": {"id": "A0A3D5YG04", "cluster": 13591786, "interpro_all": ["IPR022441", "IPR011050"], "interpro_used": ["IPR022441", "IPR011050"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a polypeptide chain with the following function: The protein should feature a Transglutaminase-like domain that catalyzes calcium-dependent acyl-transfer reactions to cross-link proteins through the formation of proteinase-resistant epsilon-(gamma-glutamyl)lysine isopeptide bonds. This post-translational modification utilizes peptidyl glutamine residues as acyl donors and primary amines as acceptors. In addition, the protein incorporates a Protein-glutamine gamma-glutamyltransferase-like, C-terminal domain that contributes to essential cell wall functions and bacterial viability in prokaryotes, often in concert with a transglutaminase core. It contains a conserved TXXE motif and is required for the survival of organisms such as *Pseudomonas aeruginosa*. Furthermore, the protein can be placed in the Bacterial transglutaminase-like family, which exhibits periplasmic transglutaminase activity to catalyze the formation of isopeptide bonds between glutamine and lysine residues. These enzymes are crucial for bacterial viability, potentially contributing to cell wall maintenance by stabilizing protein assemblies through post-translational modification. It is expressed in Chthoniobacter flavus Ellin428 and contains UniProt keyword associations Membrane, Transmembrane, and Transmembrane helix. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 2127, 16542, 15848, 17, 3189, 3418, 1988, 17097, 5016, 17, 3100, 11337, 17, 3856, 5298, 1942, 3567, 17, 3300, 2697, 2596, 1920, 3337, 1927, 16172, 17, 4910, 22206, 17, 12, 7034, 17, 25345, 13, 9082, 10301, 8253, 9031, 18, 2052, 2753, 17, 8414, 6295, 18127, 3431, 2199, 9959, 4248, 1966, 11337, 8276, 1930, 3065, 20739, 1966, 27916, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 2213, 17, 9959, 7034, 17, 25345, 9961, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 7624, 1942, 4415, 2024, 4821, 4088, 1930, 4543, 6432, 1922, 28149, 16, 3868, 1922, 21799, 1956, 43, 2127, 16542, 15848, 4728, 18, 2176, 5461, 43, 5305, 10117, 1039, 1021, 5219, 1930, 1977, 3414, 1958, 1920, 3298, 1927, 7373, 2427, 1966, 14, 13461, 10830, 14, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4543, 2127, 16542, 15848, 17, 3189, 3416, 16, 2154, 9826, 24334, 2127, 16542, 15848, 2455, 1942, 18170, 1920, 3337, 1927, 10301, 8253, 9031, 2192, 9959, 1930, 9082, 4248, 18, 2144, 5038, 2032, 6608, 1958, 4543, 6432, 16, 5063, 8739, 1942, 2024, 4821, 6291, 2007, 14384, 2213, 16137, 2596, 2753, 17, 8414, 6295, 18, 2176, 1977, 3198, 1922, 2016, 1963, 13339, 5883, 7732, 1957, 20430, 1921, 6852, 1025, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MDIFRHSRYSSNVATAPLVGMIIALAAAVIPMGEKVAGWVICGFFAACIARLIFNRPGARLPSLPLKLLLFAGSVGGVAFNYGSAVGIEPGFSILVALVGLKLIEANGPRDFHVLGLLAFFLALCDLFFSQDLLRWLYVAIIVLLVLATLVRFHRGTSPGSYSRSTWLAMRLLLQALPIAVLLFLFFPRVYGGFRFQFSQSLMNIGGMSDRLSPGSMSSIALNSDVVFRADFPDGNIPPMSSMYWRGGVLWRGDELTWVLGPFFSRTEYQPAPMSGPKIRQRISLQPHGGRWLFALDRPMEMHGASYLPGGVLQSKRAILSRYRYEVTSLPEDRQTKLPSDQMRAALDLPAHLSPRVKALVASWKAESKNPAKIVEAALRYFRHERFTYTLQPGSYSDANALDEFLFERRQGFCEHYAAAFATLMRVAGVPSRVVIGYHAGEYNSLGKYVIVRQSDAHAWCEVWLQNVGWQRIDPTDVIAPDRISSNLESYLESHTSQSDATSGERSLAATGWREIQHDLQLAWDSLNYQWDLHILNFDEDAQMNFLMLLGLGSVSWASILIWVLIATALFVGGLSFFLRRSRSTVDKVGRGYAGFCHALARAGLPREPWEGAQHFAARAAAHFPEQAELIGRISQLYIELRYGRGEASAAHFLTAVRQLPRFSVKSGT", "metadata": {"id": "B4D786", "cluster": 14618635, "interpro_all": ["IPR052901", "IPR038765", "IPR025403", "IPR021878", "IPR002931"], "interpro_used": ["IPR002931", "IPR025403", "IPR052901"], "interpro_unused": ["IPR038765", "IPR021878"]}, "task_type": "autoregressive"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein falls within the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Also, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein should have a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. It has been detected in Burkholderiales bacterium and exhibits UniProt keyword tags ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 2176, 2258, 2252, 3330, 1922, 18359, 18681, 2086, 1918, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MQTASRGRFITFEGVDGAGKSTQIEALAQTLRQHRVAVVRTREPGGTPLGEALRTIMLGQAMDPLTESLLMFAARREHVAQVIEPALAGSQWVLCDRFTDASYAYQGAGRGVPADRLDVLAGWVHGRLQPDLTVLVDIDPDQARQRRAQVRAADRFETESAAFFQAVRSAYLARAAAEPARFLVVDGGAPAPVVTSKILERLSQWLR", "metadata": {"id": "A0A2N9LFD7", "cluster": 16061588, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR018094", "IPR027417", "IPR039430"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein is associated with the B-cell differentiation antigen CD72 family, which comprises membrane proteins expressed primarily in B cells that regulate proliferation and differentiation. These proteins contain an extracellular C-type lectin-like domain (CTLD) and a cytoplasmic immunoreceptor tyrosine-based inhibition motif (ITIM) that mediates inhibitory signaling. They are implicated in immune tolerance and the regulation of autoimmune diseases such as systemic lupus erythematosus (SLE). In addition, the protein should include a C-type lectin-like domain that typically functions as a calcium-dependent carbohydrate-recognition module to mediate immune responses, cell trafficking, and pathogen defense. Stabilized by conserved disulfide bonds, this versatile fold is also utilized in non-sugar binding contexts to facilitate protein-protein interactions, such as those seen in snake venom phospholipase A2 inhibitors. Furthermore, the protein is classified under the C-type lectin fold superfamily, which encompasses a versatile structural domain originally characterized by calcium-dependent carbohydrate binding but capable of mediating diverse protein-protein, protein-lipid, and protein-nucleic acid interactions. This fold appears in a wide array of functional contexts, ranging from immune system receptors and cell adhesion molecules to bacterial toxins and extracellular matrix components like collagen. It originates from Podarcis muralis (Wall lizard) (Lacerta muralis) and is associated with UniProt keywords Coiled coil, Secreted, and Transmembrane helix.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 44, 17, 2024, 4155, 4730, 2464, 10180, 3416, 16, 2154, 12936, 3260, 2697, 3198, 5985, 1922, 44, 2094, 1988, 5741, 4031, 1930, 4155, 18, 2144, 2697, 5531, 1925, 5329, 45, 17, 2601, 13468, 17, 3189, 3418, 12, 13960, 1007, 13, 1930, 43, 6823, 8613, 3342, 1924, 6941, 17, 2454, 3523, 5219, 12, 2176, 1980, 13, 1988, 10412, 5431, 3197, 18, 2611, 2032, 6835, 1922, 3743, 6555, 1930, 1920, 3640, 1927, 8904, 3902, 2427, 1966, 5510, 13711, 22045, 12, 4565, 13, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 45, 17, 2601, 13468, 17, 3189, 3418, 1988, 5745, 4088, 1966, 43, 5016, 17, 3100, 10590, 17, 5708, 9059, 1942, 8265, 3743, 3387, 16, 2024, 9604, 16, 1930, 7055, 9720, 18, 12017, 2007, 5305, 11830, 9031, 16, 2052, 20425, 3728, 1977, 2222, 7079, 1922, 2447, 17, 9523, 2743, 11144, 1942, 6628, 2213, 17, 2213, 3719, 16, 2427, 1966, 2690, 3945, 1922, 24044, 15540, 17570, 8595, 4472, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 45, 17, 2601, 13468, 3728, 13975, 16, 2154, 21569, 43, 20425, 4346, 3418, 10398, 4378, 2007, 5016, 17, 3100, 10590, 2743, 2308, 7131, 1927, 10239, 6445, 2213, 17, 2213, 16, 2213, 17, 4486, 16, 1930, 2213, 17, 11079, 2687, 3719, 18, 2052, 3728, 5107, 1922, 43, 4743, 6472, 1927, 3183, 11144, 16, 6485, 2037, 3743, 2433, 4086, 1930, 2024, 6141, 4206, 1942, 4543, 13599, 1930, 5329, 4526, 4178, 3189, 5621, 18, 2176, 22970, 2037, 10181, 5332, 1937, 6185, 19337, 12, 4821, 26932, 2211, 13, 12, 7511, 3062, 1019, 6185, 19337, 13, 1930, 1977, 2458, 1956, 20709, 11569, 17524, 9121, 16, 8366, 16, 1930, 9117, 7864, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "DSGRFLWRRSSSKVLSVCPNLPTALQLFQYYGKVYCSFPSPFPKPEEEKAPSSLEPAKGPRRQTYYAAVALLAVSRQFGEASQAHAANSSALAQRIRTKEESLAQAREMLREATLLRQDQGRLEEKNREMETNLTHARSCQQIGCCPPQWKLFRWKCLWISAEKRTWEESELQRSQVLMNSLRSTSFWIGLQGIRRWVDNSLYSGETTEEELAYENVQGALFFFATTVGFAVGYWQVSKAGLEHAREELRRAECNLKTDCAKNESLLLILRGPWSAE", "metadata": {"id": "A0A670INM1", "cluster": 18547344, "interpro_all": ["IPR001304", "IPR016186", "IPR039689", "IPR016187"], "interpro_used": ["IPR039689", "IPR001304", "IPR016187"], "interpro_unused": ["IPR016186"]}, "task_type": "infilling"} {"instruction": "I want a protein that has the function: The protein features a NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site that constitutes the largest component of the complex I iron-sulphur (IP) fragment. It plays a central role in electron transport by binding two 4Fe-4S clusters, designated N-3 and N-4. Moreover, the protein should include a NADH:ubiquinone oxidoreductase subunit G iron-sulphur binding domain that coordinates a [4Fe-4S] cluster via a specialized histidine-cysteine motif situated between two alpha-helices. This domain primarily functions within the G subunit of respiratory complex I to facilitate electron transfer coupled to proton translocation, but it is also found in formate dehydrogenase complexes involved in the reduction of CO2 to formate. Furthermore, the protein possesses a Molybdopterin oxidoreductase, 4Fe-4S domain that functions as an electron-transfer component within the molybdenum or tungsten bis-MGD oxidoreductase family. It is present in a diverse range of enzymes, including nitrate reductases, formate dehydrogenases, and dimethyl sulfoxide reductases, where it facilitates redox reactions essential for anaerobic respiration and other metabolic pathways. It has been detected in Myxococcales bacterium and contains UniProt keyword associations 2Fe-2S, Translocase, and Iron-sulfur. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 4075, 43, 14261, 30, 5582, 22123, 27388, 16, 4089, 30493, 5903, 16, 5305, 3200, 1988, 14879, 1920, 7585, 4594, 1927, 1920, 2796, 51, 5680, 17, 13528, 1949, 12, 5416, 13, 5302, 18, 2176, 5705, 43, 4101, 2770, 1922, 4995, 4860, 2007, 2743, 2288, 15338, 1021, 17, 26814, 5859, 16, 10176, 56, 17, 23, 1930, 56, 17, 24, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 14261, 30, 5582, 22123, 27388, 5903, 49, 5680, 17, 13528, 1949, 2743, 3418, 1988, 10675, 43, 37, 15338, 1021, 17, 26814, 39, 4377, 3454, 43, 11021, 13873, 17, 8666, 5219, 18287, 2192, 2288, 4595, 17, 12789, 18, 2052, 3418, 5985, 4088, 2651, 1920, 49, 5903, 1927, 5481, 2796, 51, 1942, 6628, 4995, 3856, 6416, 1942, 8433, 7849, 16, 2308, 2176, 1977, 2222, 2435, 1922, 25741, 9294, 5048, 3286, 1922, 1920, 3378, 1927, 6333, 1942, 25741, 18, 3677, 16, 1920, 2213, 14465, 43, 2629, 16924, 22389, 2410, 16654, 27388, 16, 15338, 1021, 17, 26814, 3418, 1988, 4088, 1966, 1925, 4995, 17, 3856, 4594, 2651, 1920, 2629, 16924, 5233, 1989, 2014, 26530, 24690, 7266, 17, 2786, 1007, 27388, 3416, 18, 2176, 1977, 2481, 1922, 43, 6445, 3109, 1927, 5038, 16, 2710, 12628, 11386, 1036, 16, 25741, 9294, 1036, 16, 1930, 9780, 20139, 11386, 1036, 16, 2597, 2176, 11374, 9366, 5298, 4415, 1958, 12554, 11695, 1930, 2303, 4487, 3873, 18, 2176, 2258, 2252, 3330, 1922, 21464, 11748, 1918, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 13775, 1021, 17, 20759, 16, 12930, 2051, 16, 1930, 5680, 17, 12585, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MIEMPVIVTFTVRSNWSFAFAATKVNVVVVERGVGRDGPPTLGCLGFRAKTVEPWLTWRKVAPCTLHESVTVSPDRTALADAVKDWIERAPPPSPPSSSPPHAVIQPAISALHTIKLRCMKSSSLPNVHPVPTYGSVPSSQGTPPYPIPRGFGHPIVREGARKVLPPQVIADRLLRVMPKFTLDGRELEAAPGRTVIEAAADVGIEIPHYCWHPHLSIAANCRMCLVEIENAPKLMPACEVKVRDGMVVQSKSPKVLDAREAVMEFLLVNHPIDCPICDQAGECKLQDYYMAHDRSGTRFREVKVVKNKAVTLGPWVMLDEERCINCTRCVRFMDEVAKNPQLGQFDRGDRAVIGTFPGQPFDDPYSLNTVEICPVGALTSRDFRFKVRSWFLKSTESVCAGCARGCNIQIDHYNHEVQRYRGRDNRAVNKGWLCDEGRLSYKRIHDPETQLTVPHRREDDGRFVPISWDEAADRVRALLARHVGADESKLGMSVSPQCTNEGITALVELSESLLRADTFAILGRADWRSDEILRVADQNPNRAGAEQVFEAYSLFDEGPEALQRVLSTGRVETLLMLGTDHPTNDDAWLETVEASEVIAFTSNWDPTALRARIVLPMTSFAEQDGTWINVQGRLQRIQRAIRPINGRKSEVEAVHWIAQMVAPNAEWSLRNWLNAFNALKKRVPSLEPVKPLKLLPWGATLEEPSVDGAPRAVSTPA", "metadata": {"id": "A0A968SX84", "cluster": 19947891, "interpro_all": ["IPR036010", "IPR001041", "IPR006656", "IPR006963", "IPR000283", "IPR054351", "IPR019574", "IPR050123"], "interpro_used": ["IPR000283", "IPR019574", "IPR006963"], "interpro_unused": ["IPR050123", "IPR006656", "IPR054351", "IPR001041", "IPR036010"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to these design specifications: The protein should contain a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. Moreover, the protein should include a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. Furthermore, the protein is assigned to the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. It is produced by Vibrio sp. RC586 and is annotated with UniProt keywords Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 3066, 5531, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 2176, 1977, 4152, 2007, 23280, 2056, 18, 7399, 7532, 1016, 1930, 1977, 10633, 1956, 20709, 11569, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 3], "output": "MVIPENSSIVIFGASGDLTYRKLIPALYHLYASQQLPKSFAILGVSRTEYSDESYREKLKRSLQELEKTEPAALEAFMQHVHYQALNTAEVADYQHLANRLDTLANNYQFEQRNTLFYLATPPSLYGVIPTCLAAHGLNDESQGWKRLIIEKPFGYDLQSAQELDVEIHRHFKEHQIYRIDHYLGKETVQNLLVFRFANGMFEPLWNRNFIDYVEITGAEFLGVEERGGYYDGSGAVRDMFQNHLLQVLAMVGMEPPAAINADSIRNEVNKVLQSLQPLSESDLRNNLVLGQYTESEVRGQFLPSYRNEPGVAADSRTETYVALKMFINNWRWNGVPFYVRSGKRLPTRVTEVVIHFKRTPHPVFGQNAPENKLIIRIQPDEGILMSFGLKEPGAGFKAKEVSMNFHYASLEQIKMLTAYERLLLDALNGDATLFARTDAVEACWKFVQPILDFKQDPQSLYGYACGTWGPKESDDLLRRDGREWRFPCKNLTNTDYCEL", "metadata": {"id": "D0IHJ0", "cluster": 20485862, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR019796", "IPR022674", "IPR036291"], "interpro_unused": ["IPR001282", "IPR022675"]}, "task_type": "autoregressive"} {"instruction": "I need a polypeptide chain that performs the following role: The protein is associated with the NAD(P)-binding domain superfamily, which facilitates the binding of NAD or NADP cofactors through a conserved core Rossmann-type fold consisting of a three-layered \u03b1/\u03b2/\u03b1 structure. This domain is integral to the function of a wide array of metabolic enzymes, including alcohol and lactate dehydrogenases, as well as regulatory components in potassium channels and transcriptional repressors. Additionally, the protein contains a Glucose-6-phosphate dehydrogenase, NAD-binding domain that serves as the cofactor-binding component of G6PDH, facilitating the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the first step of the pentose phosphate pathway. This activity generates NADPH, which is essential for maintaining cellular redox homeostasis and supporting reductive processes in bacteria and eukaryotes. Furthermore, the protein features a Glucose-6-phosphate dehydrogenase active site that catalyses the reduction of glucose-6-phosphate to gluconolactone 6-phosphate, the first step in the pentose phosphate pathway. This region contains a highly conserved lysine residue that functions as a reactive nucleophile essential for enzymatic activity. It is expressed in Enterococcus faecium EnGen0180 and is linked to UniProt keywords Carbohydrate metabolism, Glucose metabolism, and Oxidoreductase. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 2458, 1956, 1920, 6577, 12, 58, 13, 17, 2743, 3418, 13975, 16, 2154, 11374, 1920, 2743, 1927, 6577, 2014, 24221, 21362, 2596, 43, 5305, 4728, 18215, 8890, 17, 2601, 3728, 7600, 1927, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3170, 18, 2052, 3418, 1977, 12328, 1942, 1920, 2347, 1927, 43, 4743, 6472, 1927, 4487, 5038, 16, 2710, 4284, 1930, 9456, 9294, 1036, 16, 1966, 2486, 1966, 4948, 4178, 1922, 9057, 5628, 1930, 5224, 26446, 18, 4950, 16, 1920, 2213, 5461, 43, 3817, 17, 26, 17, 5413, 9294, 16, 6577, 17, 2743, 3418, 1988, 10634, 1966, 1920, 15155, 17, 2743, 4594, 1927, 25631, 1023, 16, 12440, 1920, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 1922, 1920, 2561, 3537, 1927, 1920, 9412, 2217, 5413, 3374, 18, 2052, 2455, 12399, 11908, 16, 2154, 1977, 4415, 1958, 8231, 3689, 9366, 7622, 1930, 6184, 23335, 4028, 1922, 4802, 1930, 15021, 18, 3677, 16, 1920, 2213, 4075, 43, 3817, 17, 26, 17, 5413, 9294, 3500, 3200, 1988, 13928, 1918, 1920, 3378, 1927, 3817, 17, 26, 17, 5413, 1942, 3351, 23557, 5148, 2341, 2290, 26, 17, 5413, 16, 1920, 2561, 3537, 1922, 1920, 9412, 2217, 5413, 3374, 18, 2052, 3031, 5461, 43, 3626, 5305, 9082, 6181, 1988, 4088, 1966, 43, 6079, 2797, 28335, 4415, 1958, 8145, 2455, 18, 2176, 1977, 3198, 1922, 25390, 5685, 27372, 3814, 1917, 6924, 4476, 1930, 1977, 4624, 1942, 20709, 11569, 10590, 4714, 16, 3817, 4714, 16, 1930, 27388, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MSNEKNVLFTIFGGTGDLAQRKLYPSLFRLYRKGNLGEHFAVIGTARRPWSDEHYREVVKETIRALNPSDEEATTFASHFYYQSHDVNDSTHYQTLKELSDRLDGHYQLNGNRVYYLAMAPQFFGTIVSHLKSQNIMTKNGFNRLIIEKPFGSDYQSAFELNQQIREVFPEQDIFRIDHYLGKEMIQNISAIRFANNIFEAQWNNRYIDNIQITFGENLGVEDRGGYYDHSGALKDMVQNHILQVVALLAMEPPVAFSEKEIRTEKIKALKAIRIYNEEEVLENFVRGQYAQGELDGVQFKGYREEDKVDAQSETETFVAGKFTIDNFRWSGVPFYVRTGKRLTEKGTRINIVFKQVPVNVFKTSVDEPCDDTTLPPNVLTIYIQPTEGFSLSLNGKEVGQGFETEPIKLEFRNSAEMVENSPEAYEKLLLDALNGDGTNFSHWEEVAQSWHIVDVIRKAWDQTQPDFPNYKAGSMGPKAAFELLEKDGFEWIWQPDNWYRERGKLND", "metadata": {"id": "A0A829F263", "cluster": 21116113, "interpro_all": ["IPR001282", "IPR019796", "IPR022675", "IPR022674", "IPR036291"], "interpro_used": ["IPR036291", "IPR022674", "IPR019796"], "interpro_unused": ["IPR001282", "IPR022675"]}, "task_type": "autoregressive"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nIt is part of the Multiheme cytochrome superfamily, which comprises proteins containing multiple covalently bound c-type heme groups that function primarily in electron transfer or as enzymatic active sites. These domains often feature conserved CxxCH motifs and structural arrangements like the di-heme elbow, playing critical roles in processes such as photosynthesis, respiration, and nitrogen metabolism within enzymes like nitrate and nitrite reductases. Furthermore, the protein should contain a Cytochrome c7-like domain that functions as a tri-haem electron transfer unit involved in anaerobic iron respiration. This domain exhibits variable haem coordination and can serve as the NrfH subunit, forming a complex with cytochrome c nitrite reductase NrfA. Additionally, the protein has a Doubled CXXCH motif domain that facilitates haem binding through two copies of the conserved CXXCH sequence. This domain is typically found in multiple repeats within high molecular weight c-type cytochromes. It is produced by Chloroflexota bacterium and carries UniProt keyword assignments Membrane, Transmembrane, and Transmembrane helix.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 2176, 1977, 3131, 1927, 1920, 2779, 20730, 1021, 9387, 13975, 16, 2154, 12936, 2697, 3165, 3137, 16590, 4124, 45, 17, 2601, 10954, 2671, 1988, 2347, 5985, 1922, 4995, 3856, 2014, 1966, 8145, 3500, 3402, 18, 2144, 4682, 3868, 5961, 5305, 5639, 21487, 1023, 8277, 1930, 4346, 19850, 3189, 1920, 2137, 17, 10954, 17621, 16, 14797, 4140, 5456, 1922, 4028, 2427, 1966, 18133, 16, 11695, 16, 1930, 6634, 4714, 2651, 5038, 3189, 12628, 1930, 15988, 11386, 1036, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 9387, 19677, 17, 3189, 3418, 1988, 4088, 1966, 43, 5083, 17, 7105, 4995, 3856, 5344, 3286, 1922, 12554, 5680, 11695, 18, 2052, 3418, 9826, 4650, 7105, 9478, 1930, 2112, 7120, 1966, 1920, 24593, 1023, 5903, 16, 7402, 43, 2796, 1956, 9387, 45, 15988, 11386, 24593, 1019, 18, 4950, 16, 1920, 2213, 2258, 43, 20875, 5639, 21487, 1023, 5219, 3418, 1988, 11374, 7105, 2743, 2596, 2288, 9425, 1927, 1920, 5305, 5639, 21487, 1023, 3244, 18, 2052, 3418, 1977, 5745, 2435, 1922, 3137, 9569, 2651, 2149, 3272, 3388, 45, 17, 2601, 9387, 1036, 18, 2176, 1977, 4152, 2007, 10107, 18222, 7336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 3581, 18, 3], "output": "MRTHGFAHMSLWRSWRRPRRAALLVLLWIGLLLDMVLPSGEILPITVDSAVLHFSAHGQTTEQEIHCQDCHTDYRELQIYYSQTCANCHEEEALKRVDSVHARLLASGKLEAATCVDCVPRIRAVEMCKTCHSTIYEAYLQSVHGRDLLEGNEDVPGCPDCHPAHTIEDPRGDKALMAKYGISTDVFDTYVGDFHGTTVLVFQKTAPGQGTNKAVCIDCHGPDASPNFADSWLGHYRPDWKRYPLVTAVLWFYRIVIPLTLGFFLLYIGLDAQKRLRERKGTPPVRADSGPTVPDWVCLTCHERVGIIVGYPHGTLPVRTHGAHNVRWINREKHPETLAFRVKSPNLCGKCHAHKIMRPEEVGTEEYKANLLQTCRQCH", "metadata": {"id": "A0A972N6M0", "cluster": 23473316, "interpro_all": ["IPR029467", "IPR036280", "IPR051829", "IPR010177"], "interpro_used": ["IPR036280", "IPR029467", "IPR010177"], "interpro_unused": ["IPR051829"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein can be placed in the Fe-S cluster assembly domain superfamily, which facilitates the mobilization, assembly, and transfer of iron-sulfur clusters to recipient apoproteins. Members of this superfamily function within the ISC, SUF, and NIF pathways, often acting as scaffold proteins that transiently bind Fe and S atoms to synthesize [2Fe-2S] or [4Fe-4S] cofactors. These domains are critical for maturing proteins involved in electron transfer, redox catalysis, and nitrogen fixation across bacteria and eukaryotes. Also, the protein possesses a Iron-sulfur cluster carrier protein-like conserved site that is found in ATP-binding proteins, including *Escherichia coli* Mrp and human NBP, which act as scaffolds for iron-sulfur cluster assembly and transfer. This domain is ubiquitously preserved across all cellular organisms, functioning as a core component of the Fe-S cluster biosynthesis machinery. In addition, the protein is included in the Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 family, which encompasses ATP-dependent proteins that function either as scaffolds for iron-sulfur cluster assembly or as regulators of flagellar biosynthesis. Members of this family facilitate the formation and transfer of nascent Fe-S clusters to target enzymes or control flagellum number and placement by activating the SRP-GTPase FlhF. It has been characterized in Deltaproteobacteria bacterium and has UniProt annotations Hydrolase and Metal-binding. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2650, 17, 61, 4377, 5957, 3418, 13975, 16, 2154, 11374, 1920, 14586, 16, 5957, 16, 1930, 3856, 1927, 5680, 17, 12585, 5859, 1942, 10664, 11466, 22163, 1036, 18, 4678, 1927, 2052, 13975, 2347, 2651, 1920, 23924, 16, 2020, 1038, 16, 1930, 17719, 3873, 16, 3868, 8290, 1966, 7281, 2697, 1988, 12145, 4566, 2650, 1930, 61, 9030, 1942, 15541, 37, 13775, 1021, 17, 20759, 39, 2014, 37, 15338, 1021, 17, 26814, 39, 21362, 18, 2144, 4682, 2032, 4140, 1958, 2888, 4729, 2697, 3286, 1922, 4995, 3856, 16, 9366, 15408, 16, 1930, 6634, 7938, 3436, 4802, 1930, 15021, 18, 2222, 16, 1920, 2213, 14465, 43, 5680, 17, 12585, 4377, 9685, 2213, 17, 3189, 5305, 3200, 1988, 1977, 2435, 1922, 4498, 17, 2743, 2697, 16, 2710, 14, 10210, 5178, 14, 27997, 1930, 2616, 8789, 1034, 16, 2154, 4033, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 1930, 3856, 18, 2052, 3418, 1977, 21853, 10502, 3436, 2136, 3689, 7373, 16, 7295, 1966, 43, 4728, 4594, 1927, 1920, 2650, 17, 61, 4377, 8132, 10853, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 7030, 10757, 3200, 17, 7426, 2213, 12111, 1039, 1023, 19, 2650, 17, 61, 4377, 26358, 2991, 8789, 7170, 1015, 3416, 16, 2154, 21569, 4498, 17, 3100, 2697, 1988, 2347, 3108, 1966, 10603, 1958, 5680, 17, 12585, 4377, 5957, 2014, 1966, 9098, 1927, 24154, 8132, 18, 4678, 1927, 2052, 3416, 6628, 1920, 3337, 1930, 3856, 1927, 16861, 2650, 17, 61, 5859, 1942, 2758, 5038, 2014, 2285, 7030, 10757, 2529, 1930, 9555, 2007, 8019, 1920, 19939, 17, 14809, 2300, 1023, 1038, 18, 2176, 2258, 2252, 4378, 1922, 9649, 9218, 1021, 10296, 14061, 1930, 2258, 20709, 15010, 20748, 1930, 6048, 17, 2743, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MFGFGKKTPDLETLLADKHPQVLAELNRLSCPHIGDQIVDLGIVDALRTDRAGKDTRVVVELVLPTPALKDREQLEADVVATVQGVLGADVPVVVESTSDVKPAVQADGQKGALPGIANVILVASGKGGVGKSTVASNLAVALAQLGCKVGLLDADIYGPSAPTMFGIADGTRPGTIPSSDPQRPQIAPLDRYGVKLMSIGFLVDTSTPMVWRGPMIASAAMQLFKDVGWGELDYLVVDMPPGTGDVQLTISQQVIVAGAVIVSTPQDVALADVIRAKAMFDKVSIPCLGVVENMSYFLCDGCNKRHEIFFHGGARQASERMRVPFLGEVPLEAGVVGGGDTGEPVVKKFPQSASARAFLNLAREVATSLAKTAHDNPEALAPPSISISGGSLKGAGGAGGKKPKKGLPVVS", "metadata": {"id": "A0A938QSA8", "cluster": 23618243, "interpro_all": ["IPR034904", "IPR000808", "IPR019591", "IPR044304", "IPR027417", "IPR033756"], "interpro_used": ["IPR034904", "IPR000808", "IPR033756"], "interpro_unused": ["IPR044304", "IPR019591", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "I want to make a polypeptide chain that will have the following function description: It is part of the Putative S-adenosyl-L-methionine-dependent methyltransferase family, which is predicted to catalyze the transfer of methyl groups from the cofactor S-adenosyl-L-methionine (SAM) to various substrates. It is found in Helianthus annuus (Common sunflower). Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 13022, 4659, 1988, 2832, 2162, 1920, 2894, 2347, 8418, 30, 2176, 1977, 3131, 1927, 1920, 6770, 61, 17, 29283, 17, 54, 17, 12417, 17, 3100, 16478, 3416, 16, 2154, 1977, 4396, 1942, 18170, 1920, 3856, 1927, 4963, 2671, 2037, 1920, 15155, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 3425, 6249, 18, 2176, 1977, 2435, 1922, 3091, 19196, 24315, 1036, 5112, 25901, 1036, 12, 3059, 8147, 9893, 1915, 13, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MKYGKQAHEKSDQNWMVVKGEKFVFADAQLLKRQHEQPWKLLRTLLDVGCGVASFSGYLLSSDMIATWLSSII", "metadata": {"id": "A0A9K3ENW1", "cluster": 23938049, "interpro_all": ["IPR004159"], "interpro_used": ["IPR004159"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to this functional description: The protein falls within the 5-formyltetrahydrofolate cyclo-ligase family, which functions as a methenyl-THF synthetase to catalyze the ATP- and magnesium-dependent conversion of 5-formyltetrahydrofolate to 5,10-methenyltetrahydrofolate. While this is the primary activity, the family also includes divergent members, such as plant COG0212-like proteins, that lack this cyclo-ligase activity and may instead play a role in thiamin metabolism. Also, the protein is a member of the NagB/RpiA transferase-like superfamily, which comprises enzymes sharing a common $\\alpha/\\beta$ structural core, including ribose-5-phosphate isomerase A (RpiA), glucosamine-6-phosphate deaminase (NagB), and 6-phosphogluconolactonase (6PGL). These proteins facilitate critical steps in metabolic processes such as the pentose phosphate pathway and N-acetylneuraminate degradation. Furthermore, the protein is classified under the 5-formyltetrahydrofolate cyclo-ligase-like domain superfamily, which comprises single-domain alpha/beta proteins including 5,10-methenyltetrahydrofolate synthetase, an enzyme critical for folate metabolism. These proteins possess a central four-stranded parallel beta-sheet core flanked by helices and include LutC/YkgG homologues that likely act as electron transporters during L-lactate oxidation. It is derived from Thiovulum sp. ES and has UniProt annotations ATP-binding and Metal-binding.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 12182, 2651, 1920, 25, 17, 29285, 28959, 5945, 2584, 28716, 8649, 17009, 17, 11905, 3416, 16, 2154, 4088, 1966, 43, 2295, 8033, 17, 17608, 18185, 1942, 18170, 1920, 4498, 17, 1930, 13148, 17, 3100, 7309, 1927, 25, 17, 29285, 28959, 5945, 2584, 28716, 8649, 1942, 25, 16, 2119, 17, 2295, 8033, 28959, 5945, 2584, 28716, 8649, 18, 2679, 2052, 1977, 1920, 3065, 2455, 16, 1920, 3416, 2222, 5921, 13609, 4678, 16, 2427, 1966, 4496, 17082, 11636, 3112, 17, 3189, 2697, 16, 1988, 3630, 2052, 17009, 17, 11905, 2455, 1930, 2278, 5974, 3918, 43, 2770, 1922, 7566, 3717, 4714, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 14466, 1014, 19, 4822, 2126, 13763, 17, 3189, 13975, 16, 2154, 12936, 5038, 10763, 43, 3059, 8, 38, 4595, 19, 38, 4666, 8, 4346, 4728, 16, 2710, 17870, 17, 25, 17, 5413, 25510, 43, 12, 4822, 2126, 13, 16, 28627, 17, 26, 17, 5413, 27955, 12, 14466, 1014, 13, 16, 1930, 26, 17, 8078, 22988, 23557, 5148, 2341, 9259, 1021, 12, 26, 15209, 1024, 13, 18, 2144, 2697, 6628, 4140, 5983, 1922, 4487, 4028, 2427, 1966, 1920, 9412, 2217, 5413, 3374, 1930, 56, 17, 6894, 2912, 9280, 8547, 2010, 4877, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 25, 17, 29285, 28959, 5945, 2584, 28716, 8649, 17009, 17, 11905, 17, 3189, 3418, 13975, 16, 2154, 12936, 2957, 17, 3418, 4595, 19, 4666, 2697, 2710, 25, 16, 2119, 17, 2295, 8033, 28959, 5945, 2584, 28716, 8649, 18185, 16, 1925, 4113, 4140, 1958, 13761, 4714, 18, 2144, 2697, 7150, 43, 4101, 3006, 17, 10338, 6110, 4666, 17, 11130, 4728, 20185, 2007, 12789, 1930, 3951, 10908, 6916, 19, 67, 23254, 1029, 18541, 1988, 3205, 4033, 1966, 4995, 10538, 2409, 54, 17, 9456, 6638, 18, 2176, 1977, 3595, 2037, 15331, 1020, 7705, 2056, 18, 2376, 1930, 2258, 20709, 15010, 4498, 17, 2743, 1930, 6048, 17, 2743, 18, 3], "output": "MTKEQFRQKGRERISNRERRVLSRKIEKELNRVIYRNQNRNILFYSPLKNEVDISNSLKFWNKRRNVFLPKIGGETFSAIPFRVPLKKSKFGTFEPSGKSKMRNLDIAIVPILGIDSTFRRVGFGKGMYDRFFPKLRKIPFTIFVQNRLNFSKKVLTEKHDIFCDVVLFGKSETNDRFYLKR", "metadata": {"id": "J0V1Q8", "cluster": 25780880, "interpro_all": ["IPR002698", "IPR024185", "IPR037171"], "interpro_used": ["IPR002698", "IPR037171", "IPR024185"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein is a member of the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. Moreover, the protein is categorized in the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. It is produced by Vibrio penaeicida and features UniProt keywords Metal-binding, ATP-binding, and Transmembrane helix.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 2176, 1977, 4152, 2007, 23280, 4959, 3336, 2478, 3825, 1930, 4075, 20709, 11569, 6048, 17, 2743, 16, 4498, 17, 2743, 16, 1930, 9117, 7864, 18, 3], "output": "MKPGATGLTRVVHATSTLTFFLPVTPLEQVAMISVVLLVIIVELLNSAIEAVVDIGSAAVFVALLLAGLVWIGILLLRYSMKGLKAAWINEAAFRQEVVLLAFLRFGSEWNELSGRAKD", "metadata": {"id": "A0AAV5NYW9", "cluster": 27033026, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR000829", "IPR033718"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein should feature a Competence protein ComEA, helix-hairpin-helix domain that functions as an essential component of the DNA uptake machinery in naturally competent bacteria. Comprising two tandem copies of a helix-hairpin-helix motif, this domain likely mediates DNA binding to facilitate the transport of exogenous genetic material into the cytoplasm during transformation. Additionally, the protein should have a Helix-hairpin-helix DNA-binding motif, class 1 domain that mediates non-sequence-specific DNA binding in prokaryotic and eukaryotic proteins, typically those involved in enzymatic activities. It interacts with the DNA phosphate backbone via a conserved loop and the N-terminus of the second helix, rather than engaging the major groove like helix-turn-helix motifs. Moreover, it is part of the Endonuclease/exonuclease/phosphatase family domain-containing protein 1 family, which facilitates DNA processing and the specific uptake of transforming DNA. Although they do not directly bind DNA, these proteins are essential for transporting exogenous genetic material into the cell, thereby driving genomic diversification through transformation. It is derived from Fidelibacterota bacterium.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 3066, 5961, 43, 12939, 2213, 10449, 1019, 16, 7864, 17, 14565, 17, 7864, 3418, 1988, 4088, 1966, 1925, 4415, 4594, 1927, 1920, 2678, 5047, 10853, 1922, 10414, 13527, 4802, 18, 10351, 2288, 10361, 9425, 1927, 43, 7864, 17, 14565, 17, 7864, 5219, 16, 2052, 3418, 3205, 10412, 2678, 2743, 1942, 6628, 1920, 4860, 1927, 8278, 3299, 3485, 2460, 1920, 5239, 2409, 7002, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 7864, 17, 14565, 17, 7864, 2678, 17, 2743, 5219, 16, 2921, 21, 3418, 1988, 10412, 2447, 17, 3244, 17, 2487, 2678, 2743, 1922, 21545, 1930, 10825, 2697, 16, 5745, 2690, 3286, 1922, 8145, 4209, 18, 2176, 9034, 1956, 1920, 2678, 5413, 10787, 3454, 43, 5305, 5881, 1930, 1920, 56, 17, 7822, 1927, 1920, 2812, 7864, 16, 4356, 2254, 15888, 1920, 3044, 15920, 3189, 7864, 17, 5165, 17, 7864, 8277, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 18697, 19, 24966, 19, 8167, 3416, 3418, 17, 3165, 2213, 21, 3416, 16, 2154, 11374, 2678, 4587, 1930, 1920, 2487, 5047, 1927, 13231, 2678, 18, 2876, 2611, 2608, 2084, 4103, 4566, 2678, 16, 2144, 2697, 2032, 4415, 1958, 27038, 8278, 3299, 3485, 2460, 1920, 2024, 16, 6113, 9228, 4935, 20046, 2596, 7002, 18, 2176, 1977, 3595, 2037, 26209, 30466, 2422, 7336, 14061, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MFTAKEKSIIGFLGLSAVIFKALADSIYSAENKPKSKFVNINTANKDELTQLPKIGGKKTLEKIRDKIILKSEDKGFSIIQFKEHKKTDFVVVSKEEKAKHPIKIIKHPKEKNSKIEVPVTAEKIILYRNDFGAFKTVDELVKVKGI", "metadata": {"id": "A0A946EXM8", "cluster": 28175042, "interpro_all": ["IPR004509", "IPR051675", "IPR003583", "IPR010994"], "interpro_used": ["IPR004509", "IPR003583", "IPR051675"], "interpro_unused": ["IPR010994"]}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein belongs to the Diacylglycerol kinase, prokaryotic family, which comprises homo-trimeric integral membrane enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. These enzymes primarily function to recycle diacylglycerols generated during lipopolysaccharide and membrane-derived oligosaccharide biosynthesis back into the phospholipid pool. In addition, the protein is categorized in the DAGK family, which comprises small, multispan membrane enzymes including prokaryotic diacylglycerol kinase and undecaprenol kinase that catalyze the ATP-dependent phosphorylation of diacylglycerol to form phosphatidic acid. These proteins are critical for phospholipid biosynthesis and lipid recycling, supporting essential functions such as biofilm formation, lipoteichoic acid production, and spore stability in bacteria. They are structurally distinct, typically containing three transmembrane domains within a compact 13 to 15 kD scaffold. It is derived from Porticoccaceae bacterium and carries UniProt keyword assignments Lipid metabolism, Cell membrane, and Transmembrane helix.", "tokenized_instruction": [2, 51, 2162, 43, 5740, 2213, 3244, 1956, 17476, 11349, 18, 2454, 1990, 2052, 2347, 16, 5660, 1920, 6814, 3835, 4576, 30, 1920, 2213, 14440, 1942, 1920, 29527, 4016, 16, 21545, 3416, 16, 2154, 12936, 16350, 17, 29177, 12328, 3260, 5038, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2766, 8525, 1935, 2687, 18, 2144, 5038, 5985, 2347, 1942, 12381, 1021, 29527, 1036, 3999, 2409, 15614, 1930, 3260, 17, 3595, 28215, 8132, 3231, 2460, 1920, 14608, 5562, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 18815, 1040, 3416, 16, 2154, 12936, 2858, 16, 13564, 6528, 3260, 5038, 2710, 21545, 29527, 4016, 1930, 3075, 19384, 20367, 1945, 4016, 1988, 18170, 1920, 4498, 17, 3100, 4050, 1927, 29527, 1942, 2386, 2766, 8525, 1935, 2687, 18, 2144, 2697, 2032, 4140, 1958, 14608, 8132, 1930, 4486, 13977, 16, 6184, 4415, 4088, 2427, 1966, 9638, 3337, 16, 3178, 7229, 2108, 8643, 2687, 3372, 16, 1930, 18445, 5057, 1922, 4802, 18, 2611, 2032, 12171, 4493, 16, 5745, 3165, 2559, 9117, 4682, 2651, 43, 13726, 2590, 1942, 2461, 7546, 7281, 18, 2176, 1977, 3595, 2037, 9260, 5670, 2437, 9914, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 4486, 4714, 16, 2024, 3260, 16, 1930, 9117, 7864, 18, 3], "output": "MIEPHERGVAGVLRRRILGASQYSWQGLRACLARSVVELCLLLGAMLVVLIVEVLNSALETAVDLFSRLLSMILFFMVWGFIIALRFTSYRYEEAFRVELLLGALLLPVAFWEPNELAGRSKDQGSAAV", "metadata": {"id": "A0A3B9A8C3", "cluster": 28599177, "interpro_all": ["IPR000829", "IPR033718", "IPR036945"], "interpro_used": ["IPR033718", "IPR000829"], "interpro_unused": ["IPR036945"]}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence be if I wanted a polypeptide chain capable of the following function: The protein is categorized in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein is assigned to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It is present in Lactococcus garvieae and exhibits UniProt keyword tags ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 1977, 2481, 1922, 5641, 8256, 13139, 12248, 3336, 1930, 9826, 20709, 11121, 2538, 14392, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MNKVIGLTGGIASGKSTAVDFLRSQGYPIIDADQVVRELQAPSGALYQAILKEFGPTYFDEDGLLNRRKLGNLIFSKDEAREKLASLQNHIIRQELYKRREALLKDDKVQKPIIMDIPLLIEQAYDGFDEIWLIAVPESIQMERIMSRDNMTQEEAEARIKAQMPLSEKKKYATRIIDSSGTIPETYEKITELLKVVEKRD", "metadata": {"id": "A0A6L2ZXA5", "cluster": 503957, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein carries a Polycystin domain that forms a structural component of group II Transient receptor potential (TRPP) channels, including PKD1 and PKD2. It features a sandwich-like fold comprising a tilted middle layer of five \u03b2-sheets, three \u03b1-helices on one side, and a large loop containing two short antiparallel \u03b2-sheets on the other. Also, the protein incorporates a Polycystin cation channel domain that constitutes the six-transmembrane region responsible for calcium transport, lysosomal exocytosis, and membrane trafficking. This domain facilitates the heterodimeric interaction between Polycystin-1 and Polycystin-2, creating a signaling complex essential for protein stability and normal renal tubulogenesis. Moreover, the protein incorporates a PLAT/LH2 domain that adopts a \u03b2-sandwich structure and mediates membrane attachment via interactions with protein binding partners in lipid-associated contexts. It typically features a conserved surface lysine or arginine residue that facilitates ligand binding, exemplified by the salt bridge formed with procolipase in pancreatic lipase. It occurs in Henosepilachna vigintioctopunctata and is connected to UniProt keyword Transmembrane helix. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 16252, 43, 12043, 29764, 3418, 1988, 4952, 43, 4346, 4594, 1927, 2210, 2890, 6809, 3148, 2889, 12, 7259, 1034, 13, 5628, 16, 2710, 28806, 1930, 26643, 1028, 18, 2176, 4075, 43, 18038, 17, 3189, 3728, 10351, 43, 18322, 1919, 5576, 4757, 1927, 3628, 161, 17, 14685, 16, 2559, 160, 17, 12789, 1990, 2340, 4159, 16, 1930, 43, 3103, 5881, 3165, 2288, 3662, 28892, 161, 17, 14685, 1990, 1920, 2303, 18, 2222, 16, 1920, 2213, 19683, 43, 12043, 29764, 9976, 4999, 3418, 1988, 14879, 1920, 3798, 17, 9117, 3031, 5061, 1958, 5016, 4860, 16, 12097, 18904, 16, 1930, 3260, 9604, 18, 2052, 3418, 11374, 1920, 30194, 2835, 2192, 12043, 29764, 17, 21, 1930, 12043, 29764, 17, 22, 16, 11124, 43, 3197, 2796, 4415, 1958, 2213, 5057, 1930, 2791, 4604, 25860, 3761, 18, 3950, 16, 1920, 2213, 19683, 43, 4474, 19, 9107, 1028, 3418, 1988, 24032, 43, 161, 17, 18038, 3170, 1930, 10412, 3260, 8576, 3454, 3719, 1956, 2213, 2743, 7228, 1922, 4486, 17, 2458, 11144, 18, 2176, 5745, 4075, 43, 5305, 3154, 9082, 2014, 9732, 6181, 1988, 11374, 5207, 2743, 16, 22236, 2007, 1920, 7012, 11925, 5333, 1956, 9823, 6575, 2051, 1922, 6356, 16653, 18, 2176, 5110, 1922, 14618, 2217, 10984, 5148, 2072, 2175, 11505, 2879, 3940, 2341, 2011, 7475, 5499, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9117, 7864, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MDEIEIKIWQDHNPLEIIIEKQYYHIVNVFMVFLYLLYFILLCFSIREVDYTNKSIFFLSDVSRQNLYGYVIVTKTGRAGTTSNVTIRLIGKTAESDAHVLNYPDPLLKILQKGEEDWFFLATKVHLGKILEIELWYDGIGGLPYWYCKSVNIFDVQNDQWYEFRISSLFTIHPKPKIYAREKALDSIRGPSIRVKLLKLLDNLRPDYRIFSLSLRRIDEYRSYVKRLTIMFSIVLAIGFWSIILNGVPHGAPIDSIMRFCEYKLNIFTTSYGIVGSIAAAITHLPIVHIFTVSRLRFSENGSPYRENQPFIVTILCWSVIIILITFNSTFIILCGVWIPTVDAYLWITSVAIGLIFYILVIETISGTLMRFIRGNYDEYEVYVKQKLRRIMIDIEKQRDILYRLLGKYLLRPFLQHLYKPMETSKIKYRLIVEKMKFEVRELIENMVMFVIYTSLMYMVILTNKDHYSVNSNKQISSLMDGSYTKTYSLGDVTTISNLEEYIANTLIVATQSRTWYGKYAVRDPGMTNDYSNKMLGVIRIRQHRSEANSCGVPDIMRFTNRSCNGDYFKSQSFRDYGIRWSLSEPSSSEGRMANVWKFLNSSETGTFPFIGKLGIYTGGGYVAFLGRGMKNSYVNFNYLQHYSWFDVLTRGIFIEFLLYNTNSNVFNSVQFTIEKSVTGYLKIEVKVDTSKMLLVNEKKFTAINTLLGIFVVIVLFLSMKTLMRILRTGVWYFKDVWHLIDIVLISLSYTCIVLYYKRSTKVGALLESLEGVEPRDFVNYFALYRVDHAFTITAALLITVATIKLWLLFRFLLVFKVAERTFSAMFRSLCALFCYHVVSLFAFSFFAYILFVDHLYRFAGMVNTVEFLSELNIRSFSEEERTVLNTPYMGLGYIFYILYSFTVMISNCIYTSMIAIFYSKAKEELSEYHGSYSVKNYLKTQFQFYYNLAKVRLKYLRMKAGGTVGGNYTPVEPKADEHRFADCFTLGIDKLRAMSLVSLCVLKNSNPKRKPLSQRDIRLMTYTLYYLKKIDNNPDDEEEVERFYKADLGGNKVKLIPEFNLTKIEAAASILLGQSQDKTMKDLNINGDDIIRDDIKQGIQHLKNELSLMLETLNKVKIITL", "metadata": {"id": "A0AAW1VHH0", "cluster": 534203, "interpro_all": ["IPR013122", "IPR001024", "IPR036392", "IPR051223", "IPR046791"], "interpro_used": ["IPR046791", "IPR013122", "IPR001024"], "interpro_unused": ["IPR036392", "IPR051223"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein should have a ABC transporter type 1, transmembrane domain MetI-like domain that functions as the membrane-spanning permease subunit of bacterial ABC importers, such as the D-methionine transport system. It is organized around five transmembrane helices and contains a conserved cytoplasmic EAA motif that facilitates interaction with the ATP-binding cassette module to ensure correct complex assembly. Also, the protein is included in the MetI-like superfamily, which comprises proteins structurally homologous to the MetI subunit of the L-methionine ABC transporter. These proteins are organized around a core of five transmembrane helices, a structural fold also observed in the membrane-spanning subunits of molybdate and maltose ABC transporters. Moreover, the protein is included in the ABC transporter permease component family, which functions as the integral membrane subunit of binding-protein-dependent ATP-binding cassette (ABC) transporter complexes. These proteins facilitate the cellular uptake of various substrates, including starch degradation products, sugars such as melibiose and lactose, and osmoprotective compounds like trehalose. It is found in Paenibacillus thalictri and is annotated with UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 7219, 9054, 2601, 21, 16, 9117, 3418, 2130, 1033, 17, 3189, 3418, 1988, 4088, 1966, 1920, 3260, 17, 13346, 6191, 2051, 5903, 1927, 4543, 7219, 2582, 2045, 16, 2427, 1966, 1920, 46, 17, 12417, 4860, 2433, 18, 2176, 1977, 11275, 4760, 3628, 9117, 12789, 1930, 5461, 43, 5305, 6823, 11377, 1019, 5219, 1988, 11374, 2835, 1956, 1920, 4498, 17, 2743, 12992, 9059, 1942, 6486, 5550, 2796, 5957, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2130, 1033, 17, 3189, 13975, 16, 2154, 12936, 2697, 12171, 8725, 1942, 1920, 2130, 1033, 5903, 1927, 1920, 54, 17, 12417, 7219, 9054, 18, 2144, 2697, 2032, 11275, 4760, 43, 4728, 1927, 3628, 9117, 12789, 16, 43, 4346, 3728, 2222, 2528, 1922, 1920, 3260, 17, 13346, 6991, 1927, 2629, 16924, 3825, 2057, 1930, 25902, 7219, 10538, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 7219, 9054, 6191, 2051, 4594, 3416, 16, 2154, 4088, 1966, 1920, 12328, 3260, 5903, 1927, 2743, 17, 2213, 17, 3100, 4498, 17, 2743, 12992, 12, 7219, 13, 9054, 5048, 18, 2144, 2697, 6628, 1920, 3689, 5047, 1927, 3425, 6249, 16, 2710, 12912, 4877, 4461, 16, 15592, 2427, 1966, 4221, 2023, 14356, 1021, 1930, 21021, 16, 1930, 9405, 15305, 4300, 3189, 23995, 18, 2176, 1977, 2435, 1922, 25726, 8635, 7972, 10401, 5277, 1036, 15717, 5847, 3027, 1930, 1977, 10633, 1956, 20709, 11569, 9117, 7864, 18, 3], "output": "MRKWNKRSAKPVKKRKRNRFTGFFFTLPLLLFVGVFTFFGIFYNVYIGFFEWTGIGSKTFIGLDNYIQLFQDSAFYKALGNTVYFLLLTLPASMAIGLLMAVLLNGVWALDGMFKSIFFLPHVIAVVTIGTTFSGIYEPNFGLLNTLLRAAGLNDWAHSWLSDPATSLSAIAAAYIFANAGFYMLIYYTSMLNMEQEIFEAAKIDGAGVVRQFRHIIFPMLTGTHVTLMILGIIFALKVFDLVWIMTEGGPGDATELLSTFLFRESLLKYHTGYSSAISVILLLIAFGYTVVQLRVYNKIRR", "metadata": {"id": "A0A4Q9DKN5", "cluster": 4394637, "interpro_all": ["IPR051393", "IPR000515", "IPR035906"], "interpro_used": ["IPR000515", "IPR035906", "IPR051393"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein is associated with the CAAX motif-specific protease family, which catalyzes the proteolytic cleavage of farnesylated peptides containing the CAAX motif during post-translational modification. These proteins regulate signaling pathways, including those governing bacterial quorum sensing and virulence, through protease-dependent mechanisms. Also, the protein possesses a CAAX prenyl protease 2/Lysostaphin resistance protein A-like domain that functions as an integral membrane endoprotease, specifically a type II CAAX prenyl protease localized to the endoplasmic reticulum. It mediates the cleavage of the carboxyl-terminal three amino acids from farnesylated and geranylgeranylated CaaX proteins, including Ras family GTPases and nuclear lamins. This all-\u03b1 domain belongs to the glutamate intramembrane protease (IMP) family and utilizes conserved glutamate and histidine residues for catalysis. It is found in Halorubrum sp. ASP1 and contains UniProt keyword associations Hydrolase, Metalloprotease, and Transmembrane helix. Please provide the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 7762, 30, 1920, 2213, 1977, 2458, 1956, 1920, 20951, 1039, 5219, 17, 2487, 7154, 3416, 16, 2154, 17097, 1920, 12712, 6404, 1927, 24281, 4336, 5320, 3165, 1920, 20951, 1039, 5219, 2409, 2753, 17, 8414, 6295, 18, 2144, 2697, 5741, 3197, 3873, 16, 2710, 2690, 20012, 4543, 28481, 9306, 1930, 9304, 16, 2596, 7154, 17, 3100, 3531, 18, 2222, 16, 1920, 2213, 14465, 43, 20951, 1039, 9972, 2199, 7154, 22, 19, 3629, 2259, 2575, 1921, 3554, 2213, 43, 17, 3189, 3418, 1988, 4088, 1966, 1925, 12328, 3260, 16239, 9218, 18013, 1021, 16, 4475, 43, 2601, 2890, 20951, 1039, 9972, 2199, 7154, 6579, 1942, 1920, 13355, 12279, 18, 2176, 10412, 1920, 6404, 1927, 1920, 9943, 17, 4262, 2559, 3835, 4576, 2037, 24281, 4336, 1930, 9559, 12804, 4938, 12804, 1981, 20951, 1039, 2697, 16, 2710, 6520, 3416, 18390, 1930, 4254, 7962, 1036, 18, 2052, 2136, 17, 160, 3418, 14440, 1942, 1920, 7627, 9857, 8591, 7154, 12, 2754, 13, 3416, 1930, 18127, 5305, 7627, 1930, 13873, 4248, 1958, 15408, 18, 2176, 1977, 2435, 1922, 23226, 3176, 2377, 1989, 2056, 18, 4138, 1009, 1930, 5461, 20709, 11121, 2538, 5253, 20748, 16, 28629, 2051, 16, 1930, 9117, 7864, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MSQRAGKSPPSVGASRLANSIQSVIGKAGGDLLIAASVAVSGILSIAFWTVTLRMVAVQSVGEVTPVYSIAISNVSVGLGGLLTAVVYFTLSDDEWAYIDVSVPRLSQAKDGLFALLAVVLGVYAVGEVSRYAGVESASHSLVDTVAESGNPEILLWLAVLAFLVVGPAEELVYRNIVQKRLYTNFSGGTAVVVSSMMFALVHFPSYLNGTGGQTLSSLATIFVVALPLGWVFLKTSNLFYPIAVHGAYNAFVYYSLYATAAG", "metadata": {"id": "A0A4V6E426", "cluster": 5339019, "interpro_all": ["IPR052710", "IPR003675"], "interpro_used": ["IPR052710", "IPR003675"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nIt is part of the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. In addition, the protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is identified in Pantoea sp. JKS000250 and is connected to UniProt keyword ATP-binding, Cytoplasm, and Transferase.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 2176, 1977, 3131, 1927, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2899, 1922, 23942, 6802, 1019, 2056, 18, 52, 5297, 6787, 28498, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MPYIVALTGGIGSGKSTIIAREVVGPGTPALQAIQARYGASIVTEQGEEKNWLNALLHPQINARTRELIAQATSPYVLWVVDIDEATQLKRTQQRDHLSVEQAKRIIAAQATRQQLHQRYLRLAATKQDAQAFAASGVDIIDADLMLDRKQLRDIIFQQPPLLVENQLQHQADRVLVVRLACADDIIDNSGEPDDALPQVAE", "metadata": {"id": "A0AAX1DSR6", "cluster": 5362003, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein is assigned to the Pyridoxal phosphate-dependent transferase, small domain superfamily, which comprises the complex $\\alpha/\\beta$ structural domain found in enzymes such as aspartate aminotransferase and DOPA decarboxylase. These proteins utilize pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze diverse reactions, including transamination, decarboxylation, and deamination, playing a vital role in amino acid biosynthesis and neurotransmitter metabolism. Additionally, the protein is grouped in the Kynureninase family, which functions as a pyridoxal-5'-phosphate (PLP)-dependent enzyme catalyzing the hydrolytic cleavage of L-kynurenine or 3-hydroxykynurenine to yield L-alanine and anthranilic or 3-hydroxyanthranilic acid. This reaction constitutes a key step in the L-tryptophan catabolic pathway involved in NAD biosynthesis across bacteria, fungi, and vertebrates. Structurally, the enzyme belongs to subgroup IVa of the aminotransferase superfamily. In addition, the protein belongs to the Pyridoxal phosphate-dependent transferase, major domain superfamily, which forms the large catalytic component with a 3-layer \u03b1/\u03b2/\u03b1 sandwich topology in enzymes that utilize pyridoxal 5'-phosphate (PLP) as a cofactor. Through a Schiff base linkage with an active site lysine, members of this superfamily facilitate diverse chemical transformations, including transamination, decarboxylation, and deamination, which are essential for the biosynthesis and catabolism of amino acids and neurotransmitters. It is expressed in Ectothiorhodospiraceae bacterium and is linked to UniProt keywords Hydrolase and Pyridine nucleotide biosynthesis. Please generate the amino acid sequence for this polypeptide chain.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 13022, 4659, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 2858, 3418, 13975, 16, 2154, 12936, 1920, 2796, 8, 38, 4595, 19, 38, 4666, 8, 4346, 3418, 2435, 1922, 5038, 2427, 1966, 12878, 15817, 1930, 19428, 23922, 18, 2144, 2697, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 1942, 18170, 6445, 5298, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 14797, 43, 8970, 2770, 1922, 3835, 2687, 8132, 1930, 15223, 4714, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 23523, 24684, 11413, 3416, 16, 2154, 4088, 1966, 43, 24828, 23859, 17, 25, 11, 17, 5413, 12, 21453, 13, 17, 3100, 4113, 29601, 1920, 26702, 6404, 1927, 54, 17, 23523, 24684, 2053, 2014, 23, 17, 8275, 6716, 1022, 24684, 2053, 1942, 4307, 54, 17, 10504, 1930, 14228, 16692, 1935, 2014, 23, 17, 8275, 7744, 17182, 10029, 2687, 18, 2052, 3227, 14879, 43, 3834, 3537, 1922, 1920, 54, 17, 13489, 22112, 3374, 3286, 1922, 6577, 8132, 3436, 4802, 16, 10520, 16, 1930, 14976, 18, 12171, 16, 1920, 4113, 14440, 1942, 6200, 4370, 1019, 1927, 1920, 15817, 13975, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 3044, 3418, 13975, 16, 2154, 4952, 1920, 3103, 6804, 4594, 1956, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 18038, 13678, 1922, 5038, 1988, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 18, 2596, 43, 25214, 5170, 8611, 1956, 1925, 3500, 3200, 9082, 16, 4678, 1927, 2052, 13975, 6628, 6445, 4399, 18510, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 2154, 2032, 4415, 1958, 1920, 8132, 1930, 19480, 1927, 3835, 4576, 1930, 21012, 18, 2176, 1977, 3198, 1922, 7495, 17809, 14514, 1986, 3106, 11979, 1972, 3336, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 20748, 1930, 19604, 5489, 8132, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MTNDVFASLEETARAEDARDPLRDVRGQFHIPQHSGGSEQIYLCGNSLGLQPKATAAYVNEVLEDWQQYGVEGHFKAKHAWLPYHEYLTGQTARLVGAKPEEVVAMNSLTVNLHLLMVSFYRPTAARHKILIEKKAFPSDRYAVESQLRYHGYDPAEALVLLEPDDGALISDAAIEDAFERHGEEIALVLIGGVQYYSGQLFDMKRIAELGHSHGCTVGFDLAHAAGNVPLHLHDWDVDFAAWCSYKYLNAGPGSTAGIFVHERHAGRTDIPRFAGWWGHDKETRFQMGTEFVPIPTAESWQLSNPPILPLAALRASLDIFDAHGMEALRTKSEKLTGFLLEALDAACSQYCTVFTPREPARRGCQLSIKVHENGKAVFDALIERGVICDWREPDIIRIAPVPLYNTFQDAFNFVRIFHELLRT", "metadata": {"id": "A0A2E0UMC9", "cluster": 6605171, "interpro_all": ["IPR010111", "IPR015424", "IPR015421", "IPR015422"], "interpro_used": ["IPR015422", "IPR010111", "IPR015421"], "interpro_unused": ["IPR015424"]}, "task_type": "autoregressive"} {"instruction": "I want to make a polypeptide chain that will have the following function description: The protein is included in the G protein-coupled receptor, rhodopsin-like family, which constitutes the extensive Class A group of GPCRs including receptors for hormones, neurotransmitters, and light. These proteins utilize a conserved seven-transmembrane helix architecture to transduce diverse extracellular signals by activating intracellular guanine nucleotide-binding (G) proteins. Additionally, the protein should feature a GPCR, rhodopsin-like, 7TM domain that forms the conserved seven-transmembrane structural core characteristic of Class A G protein-coupled receptors. It transduces diverse extracellular signals, such as hormones, neurotransmitters, and light, into cellular responses by activating intracellular guanine nucleotide-binding (G) proteins. This scaffold supports a wide range of autocrine, paracrine, and endocrine processes by accommodating various ligand structures. It is present in Mesorhabditis belari and is connected to UniProt keyword G-protein coupled receptor and Transducer. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 13022, 4659, 1988, 2832, 2162, 1920, 2894, 2347, 8418, 30, 1920, 2213, 1977, 3063, 1922, 1920, 49, 2213, 17, 6416, 3148, 16, 20586, 17, 3189, 3416, 16, 2154, 14879, 1920, 6475, 2921, 43, 2210, 1927, 17723, 2710, 4086, 1958, 10224, 16, 21012, 16, 1930, 3696, 18, 2144, 2697, 12561, 43, 5305, 5260, 17, 9117, 7864, 9335, 1942, 30334, 6445, 5329, 4771, 2007, 8019, 4776, 16904, 5489, 17, 2743, 12, 49, 13, 2697, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 12542, 16, 20586, 17, 3189, 16, 27, 15375, 3418, 1988, 4952, 1920, 5305, 5260, 17, 9117, 4346, 4728, 6293, 1927, 2921, 43, 49, 2213, 17, 6416, 4086, 18, 2176, 30334, 1036, 6445, 5329, 4771, 16, 2427, 1966, 10224, 16, 21012, 16, 1930, 3696, 16, 2460, 3689, 3387, 2007, 8019, 4776, 16904, 5489, 17, 2743, 12, 49, 13, 2697, 18, 2052, 7281, 7825, 43, 4743, 3109, 1927, 19396, 16, 17515, 16, 1930, 10749, 4028, 2007, 11852, 2287, 3425, 5207, 4061, 18, 2176, 1977, 2481, 1922, 23577, 5004, 13385, 3678, 3262, 2205, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 49, 17, 2213, 6416, 3148, 1930, 14848, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MMDGESPSEVYLFILPIIVTLGLGGNIISLVTIFHSRLRHISANVYLIVLTAADSVFLFGVLLICFKIDFVSWEWCVFVEYILMVASYVSSWATAALTIERYLAIAHPLKHVMFGHVDRWKMLIYWLPIPFILHLFQFINLVPSPANAVDSRKCVLREADYQVVSEFLDVLLCFVLPCAVVVILNLLVMGKVNRERGHFLEQQGKQLEGRRQGGSGSGGFTRILWVVPMVFVILNTPFYCIRMYEAFLVYFTTATAPSVEAETEGQSLYHTVYNAAHYLYYINFASDVVVYAFSSANFRKTVVIAWRRIICPGYDKSRVAKYTITLQDATKTQGFFKEQEASTRSCLISNSTVAHPARRTLSQKESVHPRSLPESHSDADIRMIKSPSKPPHSLSSIVHYHHDLEENVGNGSTAF", "metadata": {"id": "A0AAF3J488", "cluster": 7047908, "interpro_all": ["IPR000276", "IPR017452"], "interpro_used": ["IPR000276", "IPR017452"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein is classified under the Thymidylate kinase family, which catalyzes the ATP- and magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP). This ubiquitous enzyme acts as a critical component of the dTTP biosynthesis pathway required for DNA synthesis, with expression and activity levels often correlated with cell cycle progression and growth. Furthermore, the protein is assigned to the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Also, the protein carries a Thymidylate kinase-like domain that catalyzes the magnesium-dependent phosphorylation of dTMP to dTDP using ATP, or of UMP, CMP, and their deoxy forms in mitochondrial UMP-CMP kinases. This activity is essential for generating nucleotide precursors required for DNA synthesis and cell cycle progression. It is found in Dyella tabacisoli and corresponds to UniProt keyword ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 7330, 19743, 2010, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 1930, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 18, 2052, 15498, 4113, 8016, 1966, 43, 4140, 4594, 1927, 1920, 11504, 1034, 8132, 3374, 3414, 1958, 2678, 4271, 16, 1956, 2294, 1930, 2455, 2428, 3868, 4374, 1956, 2024, 4048, 4380, 1930, 2905, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2222, 16, 1920, 2213, 16252, 43, 7330, 19743, 2010, 4016, 17, 3189, 3418, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 7711, 6588, 1942, 7711, 10274, 2193, 4498, 16, 2014, 1927, 8736, 1034, 16, 28738, 16, 1930, 2310, 16333, 4952, 1922, 4596, 8736, 1034, 17, 28738, 7784, 18, 2052, 2455, 1977, 4415, 1958, 9155, 5489, 10416, 3414, 1958, 2678, 4271, 1930, 2024, 4048, 4380, 18, 2176, 1977, 2435, 1922, 8347, 11560, 1019, 8514, 28278, 2204, 12191, 1930, 8852, 1942, 20709, 11121, 2538, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MSAARGKFISLEGGEGAGKSTLLAGLHEHITAQHVALVQTREPGSRAQLVREVIEPALAAGQWVLCDRFTDASYAYQGGGRGQPLERIAELERWAADGLQPDLTLLLDLRIEVEADAFFERVRSAYRTRAAAEPARFRVIDASQPAVAVLQSAIAALTPLLAEHALGTPLGEAVRAIVLDPARRDMVAEAELLLMFAPVSTGRARAAGRGEAD", "metadata": {"id": "A0A369UN57", "cluster": 10387754, "interpro_all": ["IPR027417", "IPR039430", "IPR018094"], "interpro_used": ["IPR018094", "IPR027417", "IPR039430"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should feature a VPS9 domain that functions as a guanine nucleotide exchange factor (GEF) for Rab5 family GTPases, catalyzing their activation to regulate endocytosis and endosome biogenesis. This domain adopts a layered six $\\alpha$-helix fold that forms the specific binding interface for substrates such as Rab5 and Rab21. Also, the protein incorporates a Ubiquitin system component CUE domain that functions as a dual-specificity motif for recognizing mono- and poly-ubiquitin while binding ubiquitin-conjugating enzymes (UBCs). This domain promotes intramolecular monoubiquitination and plays a structural role in signaling proteins, such as tollip and TAB2, within the IL-1 transduction pathway. In addition, the protein is grouped in the Vacuolar protein sorting-associated protein 9-like family, which utilizes a VPS9 domain to act as a guanine nucleotide exchange factor (GEF) for Rab5 family small G proteins. These proteins are primarily involved in regulating vesicle-mediated vacuolar transport. It is found in Albugo laibachii Nc14.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 14851, 1026, 3418, 1988, 4088, 1966, 43, 16904, 5489, 6818, 2991, 12, 15022, 13, 1958, 28011, 3416, 18390, 16, 29601, 2310, 2936, 1942, 5741, 11914, 1930, 22321, 13008, 18, 2052, 3418, 24032, 43, 19445, 3798, 8, 38, 4595, 8, 17, 7864, 3728, 1988, 4952, 1920, 2487, 2743, 6854, 1958, 6249, 2427, 1966, 28011, 1930, 4673, 4716, 18, 2222, 16, 1920, 2213, 19683, 43, 6526, 2433, 4594, 10200, 3418, 1988, 4088, 1966, 43, 7064, 17, 4896, 5219, 1958, 15667, 8914, 17, 1930, 4286, 17, 6526, 2679, 2743, 6526, 17, 5225, 2287, 5038, 12, 21088, 1036, 13, 18, 2052, 3418, 7383, 18083, 8914, 15571, 1943, 1930, 5705, 43, 4346, 2770, 1922, 3197, 2697, 16, 2427, 1966, 15204, 2049, 1930, 8514, 1028, 16, 2651, 1920, 2614, 17, 21, 8201, 3374, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 21582, 2213, 11404, 17, 2458, 2213, 29, 17, 3189, 3416, 16, 2154, 18127, 43, 14851, 1026, 3418, 1942, 4033, 1966, 43, 16904, 5489, 6818, 2991, 12, 15022, 13, 1958, 28011, 3416, 2858, 49, 2697, 18, 2144, 2697, 2032, 5985, 3286, 1922, 6773, 11502, 17, 3434, 21582, 4860, 18, 2176, 1977, 2435, 1922, 5311, 2215, 1037, 25463, 11097, 3907, 5301, 3745, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MRSSMNNTSSERSKRSFRRDISDLFSKRRGNRESFEGTLHHGTKLLQSMFPAWDLEPLKLVFEAHKFEMEDTIAAILKMNETILPVDFLRLPTECISDTYNEDDEATSDDGIEELKRSVDKDATSELDDIPKAVAPERSDSLAEDDGTLFGRVYTGDLGDVDEDVVHPVLNADQNVRPSIMDTSSIDVIKSRLNLTDAEKRIQHREPHLAFELLTKASEILPLIQPSRMLVDNTMKTDRLISDHEWHLLILKCKNIRQALSIRVVDIETGIVWFTSKRQKDILKLNRKLCKISHRIRETSLPSRLSQTRPSPLTFLNGVALKELHQFLQVPAENMMHPKRTHQLSRQLEQKLQILGGARSIDVLNEIGDLLDGLQEYMLEHRFQEMKQFAERLIKLYTTLKPRNNSYVNILASLDQQTRNDRLYLFISDSIRPELEERICVSVMKSRLQLLRNQSQESFGISASKTSPSNWRSVVRTIKEMDGAFLPWDKLYRAEHAVSSVMEESDSQGYHQASQSEISCQPAGASGTKEELLSVMTQVLLNRLCDPEKRHSEAGYYLATFEAAVHHILSWDKDNFLESPPALSRCTSQAIAKTSNKQSNQNQSQMIEGSQEECLNRQEYTYDAIDGNEPGDAQSIYLEKSYESKVLVAKRQLVFDSVNQKFIPPELRYRNGIISSQELDTLRSYTIRLVNEQEYLNTNAGFAQSQARLLEGFLRSAATLVTRVYVYHTVNDNTSPEGKACLRFPKNVENQQSTNEISSTSKRRDLNHALRKMVVDKEVQFQMARLVACAHQIHAGDDFLPIFIYVLIHCNLDSP", "metadata": {"id": "F0W0N6", "cluster": 11963398, "interpro_all": ["IPR003892", "IPR036871", "IPR003123", "IPR045046", "IPR037191"], "interpro_used": ["IPR003123", "IPR003892", "IPR045046"], "interpro_unused": ["IPR037191", "IPR036871"]}, "task_type": "infilling"} {"instruction": "The protein belongs to the ParB/Sulfiredoxin superfamily, which encompasses proteins sharing a conserved fold characterized by a mixed beta-sheet forming a partly open barrel. Members include ParB, a DNA-binding protein essential for chromosome segregation and nucleoid occlusion, and Sulfiredoxin, a eukaryotic sulfinic acid reductase that lacks the C-terminal helix-turn-helix domain found in ParB. Also, the protein carries a ParB-like N-terminal domain that binds cytidine triphosphate (CTP) to regulate bacterial chromosome partitioning and nucleoid occlusion. It contains a conserved arginine patch essential for function and utilizes CTP binding to stabilize interactions with ParA and modulate affinity for *parS* DNA sites. Specific recognition of *parS* stimulates CTP hydrolysis, driving the segregation of chromosomes to cell poles during division. It has been characterized in Corynebacterium amycolatum and is annotated with UniProt keywords Coiled coil. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 2096, 1014, 19, 5141, 3030, 9754, 13975, 16, 2154, 21569, 2697, 10763, 43, 5305, 3728, 4378, 2007, 43, 4985, 4666, 17, 11130, 7402, 43, 10028, 4437, 19560, 18, 4678, 3951, 2096, 1014, 16, 43, 2678, 17, 2743, 2213, 4415, 1958, 5597, 12707, 1930, 2797, 2642, 10543, 16, 1930, 5141, 3030, 9754, 16, 43, 10825, 5141, 26386, 2687, 11386, 1988, 13012, 1920, 45, 17, 4262, 7864, 17, 5165, 17, 7864, 3418, 2435, 1922, 2096, 1014, 18, 2222, 16, 1920, 2213, 16252, 43, 2096, 1014, 17, 3189, 56, 17, 4262, 3418, 1988, 6876, 2702, 5802, 17978, 12, 25639, 13, 1942, 5741, 4543, 5597, 17615, 1930, 2797, 2642, 10543, 18, 2176, 5461, 43, 5305, 9732, 7504, 4415, 1958, 2347, 1930, 18127, 25639, 2743, 1942, 13448, 3719, 1956, 8202, 1930, 8480, 5173, 1958, 14, 12505, 14, 2678, 3402, 18, 2487, 5708, 1927, 14, 12505, 14, 11803, 25639, 9128, 16, 9228, 1920, 12707, 1927, 8597, 1942, 2024, 24278, 2409, 8451, 18, 2176, 2258, 2252, 4378, 1922, 2233, 17151, 7972, 2341, 18842, 1989, 20306, 4879, 5148, 1031, 1989, 1930, 1977, 10633, 1956, 20709, 11569, 17524, 9121, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MVQVKSVSKHANFYPMLTEEALAELAADIKENGQQSPITVTADGVLLDGRNRLKACEIAGVEPHVTIHEGDDEGAFVRSSNERRHQSTGSRAMSTALSLQADGLRQNGRWVRGAIHGANTEFRVSADGRTWTDAMRQAGVILDERPELAQSVIDGEIALDEAYRQADAKRKVREAEEQRRIEEARDEQKREDSAGRYFDNHQEAKAWLDEKPQGAFPTMREAYAAYMEHDREARRIEAEKRRKEEEFQKQVEESYERAALRLRSFVNSYSQAWGMRTNRNRKEILDKMMPTEREKFEALEGKLGWTTENF", "metadata": {"id": "A0AB37G7G0", "cluster": 12324530, "interpro_all": ["IPR003115", "IPR036086"], "interpro_used": ["IPR036086", "IPR003115"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is grouped in the FAM187A/B family, which comprises the animal proteins FAM187A and FAM187B, though their specific biological functions remain unclear. It is expressed in Parelaphostrongylus tenuis (Meningeal worm) and is described by UniProt keywords Transmembrane, Membrane, and Glycoprotein.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 3011, 19544, 1019, 19, 44, 3416, 16, 2154, 12936, 1920, 4027, 2697, 3011, 19544, 1019, 1930, 3011, 19544, 1014, 16, 4170, 2310, 2487, 3933, 4088, 5555, 6390, 18, 2176, 1977, 3198, 1922, 2096, 15208, 17826, 14342, 26983, 5277, 1036, 5656, 8694, 12, 10286, 5243, 11055, 13, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 16, 3260, 16, 1930, 11424, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MRFFIRGVLHQRRFSDGTTVKIHNEGERLRTTDSNYRLRRSQKPGEQARSIQCMIQRRCDKETMVDRNLTSVDELGEIRVLPVVFTCEMPVDEPTGVQWFSKKKGPILYKTVITQYQVIFQLRPKRGVLGEEGGARPCEQHNEHHNHSARVHPNRMLIALAILDQNCTIAVAGVLKFAPDAINCPNSISDENCAKLYGEAVKLLRYAYACIPGMATHKHDVFYQSLRHTSISDMREAQNASRASLWSDCSKCGEELDYIPKGEFLFGEILPRLPAPVVRRNYLITEGNACKCFENSLAVAFNTAFVDCYITAISGSVVGGLDGVERPDKCGKGIETEAPPYRFDMQLL", "metadata": {"id": "A0AAD5WFF0", "cluster": 13205099, "interpro_all": ["IPR039311"], "interpro_used": ["IPR039311"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein is classified under the Pre-ATP-grasp domain superfamily, which constitutes an N-terminal structural unit that precedes the core ATP-grasp fold in enzymes such as peptide synthetases, biotin carboxylase, and glutathione synthetase. While distinct from the ATP-binding site, this domain is thought to mediate substrate recognition and binding, thereby facilitating the ATP-dependent ligation of carboxylate-containing molecules to amino or thiol groups during macromolecular synthesis. In addition, the protein has a Phosphoribosylglycinamide synthetase N-terminal domain that catalyzes the ATP-dependent ligation of 5-phosphoribosylamine to glycine to form 5'-phosphoribosylglycinamide, constituting the second step of de novo purine biosynthesis. Structurally related to biotin carboxylase, this module functions as a standalone enzyme in bacteria or as part of multifunctional complexes alongside AIRS and GART domains in eukaryotes. It is native to Woeseia sp.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2097, 17, 4498, 17, 22815, 3418, 13975, 16, 2154, 14879, 1925, 56, 17, 4262, 4346, 5344, 1988, 24373, 1920, 4728, 4498, 17, 22815, 3728, 1922, 5038, 2427, 1966, 4207, 18185, 1036, 16, 8622, 29073, 16, 1930, 9153, 18185, 18, 2679, 4493, 2037, 1920, 4498, 17, 2743, 3200, 16, 2052, 3418, 1977, 6212, 1942, 8265, 4510, 5708, 1930, 2743, 16, 6113, 12440, 1920, 4498, 17, 3100, 11102, 1927, 20877, 17, 3165, 4206, 1942, 3835, 2014, 13914, 2671, 2409, 21815, 4271, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 3421, 2023, 11731, 17038, 3665, 5482, 18185, 56, 17, 4262, 3418, 1988, 17097, 1920, 4498, 17, 3100, 11102, 1927, 25, 17, 3421, 2023, 11731, 3812, 1942, 10646, 1942, 2386, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 16, 26033, 1920, 2812, 3537, 1927, 2028, 9441, 19700, 8132, 18, 12171, 2712, 1942, 8622, 29073, 16, 2052, 9059, 4088, 1966, 43, 2924, 20807, 2912, 4113, 1922, 4802, 2014, 1966, 3131, 1927, 20136, 5048, 17764, 4433, 1036, 1930, 13139, 1031, 4682, 1922, 15021, 18, 2176, 1977, 6196, 1942, 26334, 2124, 2126, 2056, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "METKNRVLIVGSGGREHPGNAGTEGEAKTKNVDIKSKNINLVVLAQKIHAFAWKISQSEKVERIFVASPNDIDSLIKFS", "metadata": {"id": "A0A920PHI4", "cluster": 14490339, "interpro_all": ["IPR016185", "IPR000115", "IPR020562"], "interpro_used": ["IPR016185", "IPR020562"], "interpro_unused": ["IPR000115"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: It is part of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Additionally, the protein contains a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. It is found in Rhizobiaceae bacterium and features UniProt keywords ATP-binding, Nucleotide biosynthesis, and Transferase.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 2176, 1977, 3131, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 4950, 16, 1920, 2213, 5461, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2176, 1977, 2435, 1922, 13458, 18311, 1972, 3336, 14061, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 5489, 8132, 16, 1930, 13763, 18, 3], "output": "MPKQGLFVTFEGGEGTGKSVDVLMTREPGGSPGAEAVRMEAVLFAAARNDHVEEIIRPALYQGITGNLEPAFVQNLERVAVNGLRTGDSGEKVEPDRFEKEELDTHEKRAIAEKVFAIIEPLLPIQASRPKEAGKGTQIRLLADRLRRRGHVILSGAAEEYGTRASGAVVLCDRFMDSSRVVVPDCTIILDVPAAEGLRRARREAFLDIAEADPLRCRVVDAGGMPE", "metadata": {"id": "A0A961SVA3", "cluster": 14496740, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR027417", "IPR018095"], "interpro_unused": ["IPR018094", "IPR039430"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein falls within the Phosphatidylglycerol--prolipoprotein diacylglyceryl transferase Lgt family, which serves as an integral membrane enzyme that catalyzes the initial step of post-translational lipid modification. It transfers an n-acyl diglyceride group onto the prospective N-terminal cysteine of prolipoproteins, facilitating their maturation into membrane lipoproteins. It occurs in Halarsenatibacter silvermanii and is linked to UniProt keywords Cell membrane and Transmembrane helix. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 12182, 2651, 1920, 10951, 18207, 17, 17, 3192, 2049, 6657, 25141, 13796, 1024, 14966, 2199, 13763, 12221, 1031, 3416, 16, 2154, 10634, 1966, 1925, 12328, 3260, 4113, 1988, 17097, 1920, 3754, 3537, 1927, 2753, 17, 8414, 4486, 6295, 18, 2176, 19180, 1925, 56, 17, 11337, 4325, 7995, 2261, 2210, 6131, 1920, 6315, 56, 17, 4262, 8666, 1927, 3192, 2049, 14070, 16, 12440, 2310, 7655, 2460, 3260, 18393, 18, 2176, 5110, 1922, 4217, 11005, 5791, 26073, 2341, 1915, 11078, 3862, 3907, 1930, 1977, 4624, 1942, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MDPVAFELRGLSIRWYGIFVTTGILMGLFYVLWQGKKWSYDSEDIIDFLLFGLPITLIGTRLYYVVFNWRYYSNDLRRIIDITSGGLAIHGAIITGILYTFVFVRRRDFDFLEFADLLTPAFLLGLAVGRWGNFANQEAHGGEVSQEFMEIFPGFIREGMYIEGSYYHPAFFYEFIWNTFVFILLVIYTRSRFYSRGKVLALGLGLYSLGRFFIEDIRVDSLYLAGIQIARPVSGAILALCLVFFIRDRKGDTDEK", "metadata": {"id": "A0A1G9JJ62", "cluster": 16041496, "interpro_all": ["IPR001640"], "interpro_used": ["IPR001640"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is included in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Furthermore, the protein contains a Thymidylate kinase conserved site that catalyzes the magnesium-dependent phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) using ATP. This enzymatic activity is a critical step in the biosynthesis of dTTP required for DNA replication and is tightly linked to cell cycle progression and cell growth. It is native to Lachnospiraceae bacterium oral taxon 500 and is connected to UniProt keyword Coiled coil, ATP-binding, and Nucleotide biosynthesis.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3677, 16, 1920, 2213, 5461, 43, 7330, 19743, 2010, 4016, 5305, 3200, 1988, 17097, 1920, 13148, 17, 3100, 4050, 1927, 16253, 25, 11, 17, 21363, 12, 7711, 6588, 13, 1942, 2386, 16253, 25, 11, 17, 23266, 12, 7711, 10274, 13, 2193, 4498, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 8132, 1927, 11504, 1034, 3414, 1958, 2678, 5158, 1930, 1977, 12129, 4624, 1942, 2024, 4048, 4380, 1930, 2024, 2905, 18, 2176, 1977, 6196, 1942, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 4726, 19278, 4599, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 17524, 9121, 16, 4498, 17, 2743, 16, 1930, 5489, 8132, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MFIAIEGMDGSGKSTQIELLRQYFEQRHQQIREILLRPENQAMAARTEALLYAASRAQSYVYQGIARGLGLEAVERINQFAINGRVPDLTIFLFVSQEQALRRKSYPYPRMIIDADAAPAQVHAEIRQRLEQEFGKERQEAVITREPGGTDIGEHVAELIEPALAAGKIVISDRYVVSKAQKELDRLEAESMAFHAKVNQGFRQLAE", "metadata": {"id": "A0A2R3N397", "cluster": 17614544, "interpro_all": ["IPR027417", "IPR039430", "IPR018095", "IPR018094"], "interpro_used": ["IPR027417", "IPR018095"], "interpro_unused": ["IPR018094", "IPR039430"]}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein features a Peptidase M10A, cysteine switch, zinc binding site binding site that coordinates a catalytic zinc ion to drive the degradation of the extracellular matrix. It functions through a cysteine switch mechanism, where a conserved cysteine residue initially chelates the zinc to maintain the enzyme as an inactive zymogen until proteolytic activation. This activity is fundamental to tissue remodeling processes, including wound healing, angiogenesis, and morphogenesis. Moreover, the protein should contain a Ricin B lectin domain that functions as a carbohydrate-binding module, specifically recognizing simple sugars such as galactose or lactose. It is structurally characterized by three homologous QxW repeats arranged around a pseudo-threefold axis and is commonly found in plant and bacterial AB-toxins, glycosidases, and proteases. Additionally, the protein carries a Metallopeptidase domain that functions as a zinc-dependent protease to catalyze peptide bond hydrolysis, often belonging to the metzincin superfamily. It utilizes a divalent cation, typically zinc coordinated by a conserved HEXXH motif, to activate a water molecule for the enzymatic reaction. This domain maintains a specific helical geometry to support metal binding and catalytic activity. It is present in Nocardia bhagyanarayanae and is classified with UniProt keywords Metal-binding, Hydrolase, and Signal.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 4075, 43, 24050, 8510, 1008, 1019, 16, 8666, 6195, 16, 7997, 2743, 3200, 2743, 3200, 1988, 10675, 43, 6804, 7997, 4755, 1942, 9265, 1920, 4877, 1927, 1920, 5329, 4526, 18, 2176, 4088, 2596, 43, 8666, 6195, 2856, 16, 2597, 43, 5305, 8666, 6181, 6370, 11749, 2209, 1920, 7997, 1942, 6698, 1920, 4113, 1966, 1925, 9078, 15856, 2404, 4801, 12712, 2936, 18, 2052, 2455, 1977, 8829, 1942, 2960, 8378, 4028, 16, 2710, 6376, 7872, 16, 8244, 16, 1930, 15328, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 27417, 44, 13468, 3418, 1988, 4088, 1966, 43, 10590, 17, 2743, 9059, 16, 4475, 15667, 5288, 15592, 2427, 1966, 15996, 2014, 21021, 18, 2176, 1977, 12171, 4378, 2007, 2559, 8725, 59, 1039, 1018, 9569, 14940, 4760, 43, 11520, 17, 23109, 5432, 1930, 1977, 5384, 2435, 1922, 4496, 1930, 4543, 2186, 17, 13599, 16, 7533, 30413, 16, 1930, 12447, 18, 4950, 16, 1920, 2213, 16252, 43, 8969, 24897, 3418, 1988, 4088, 1966, 43, 7997, 17, 3100, 7154, 1942, 18170, 4207, 5403, 9128, 16, 3868, 10588, 1942, 1920, 2130, 22030, 15895, 1921, 13975, 18, 2176, 18127, 43, 21610, 9976, 16, 5745, 7997, 11651, 2007, 43, 5305, 7142, 1039, 1023, 5219, 16, 1942, 6980, 43, 3224, 5388, 1958, 1920, 8145, 3227, 18, 2052, 3418, 16566, 43, 2487, 11514, 10869, 1942, 3373, 6048, 2743, 1930, 6804, 2455, 18, 2176, 1977, 2481, 1922, 9812, 13047, 9710, 2006, 12947, 9041, 12947, 3336, 1930, 1977, 5947, 1956, 20709, 11569, 6048, 17, 2743, 16, 20748, 16, 1930, 2733, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MSVQQAPCEPFVHVAEVADTKFGEATPNFGHGGPARARVTGILDADTSTALARYQDFHGLPVTGLFAAIPLRFVRACAWRKTWLTYSFDTGTADIAGDDERTEVAPNQHPDVLIRWGNANCGDTDMTGGVAAHADYPPGCGRDQQVTFIIGAAANSLDLESVALHEIGHILGLQHNDDVEGIRKLYPPTGPLIAKHSSKCLVIAGHSRDNGAEAIQIPMHATNKVLDIRDRSTANRAQVQQWEWWGGGNQRFALEPVGHGYIQFDWWGGDNQRWRIGPAPITSMVSRKVVDIKDLSRAPGVDPLGSGVYRIMIEHSGMCLDVENHSPAGEARIIQWPYKCLTVSGDPDLAGAQLVQRTYEGDGSQLWRLGNVQCFLQRFGYLLEDSKETPESDTATREMMTRPRCGLPDSQAVRNAFVTWAAAAPLAFYGNALPRPVHFNSDDPGALMANEAIAFNTMRRALTWDYFAGKNVIFRIEWVEKGFYKLYRIVAKDSGRVLDVLDRSESNGAKVAQVIQWDYWGGGNQRLRLDPLGTDNQHWLLEKVAFGRVKFVARHSG", "metadata": {"id": "A0A543EXZ3", "cluster": 17699105, "interpro_all": ["IPR024079", "IPR001818", "IPR021190", "IPR021158", "IPR006026", "IPR002477", "IPR036365", "IPR035992", "IPR000772"], "interpro_used": ["IPR021158", "IPR000772", "IPR006026"], "interpro_unused": ["IPR002477", "IPR021190", "IPR001818", "IPR024079", "IPR036365", "IPR035992"]}, "task_type": "infilling"} {"instruction": "The protein should have a Spore germination GerAC-like, C-terminal domain that likely serves as a component of the inner spore membrane germination apparatus in Firmicutes. It is implicated in mediating the spore's germination response to L-alanine. It is produced by Paenibacillus cremeus and carries UniProt keyword assignments Transmembrane helix, Palmitate, and Signal.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 3066, 2162, 43, 18445, 14609, 9559, 1948, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 3205, 10634, 1966, 43, 4594, 1927, 1920, 6671, 18445, 3260, 14609, 11161, 1922, 24474, 18, 2176, 1977, 6835, 1922, 10239, 1920, 18445, 11, 61, 14609, 2644, 1942, 54, 17, 10504, 18, 2176, 1977, 4152, 2007, 25726, 8635, 7972, 10401, 5277, 1036, 3478, 3870, 1957, 1930, 16252, 20709, 11121, 2538, 18306, 9117, 7864, 16, 22047, 16, 1930, 2733, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MSYFERLGGHGGNLKSMKRLHRKNYLAYAIILTGLMMVTTGLDLSPEGNLLLSAQIAVPKAAGEAGGGGGGGTDDTYFVKTAIVFLGHRDVIFIGEQLGKQGFKKFLDEFGRNPISNIRANLFFIEQFSSVEAIRQVHFNGIRDRMTTMVYFKEVMQRDGMRPILQVIREIALFNKSLQVVGFLQEEEAVSVLWASGYLDTQMITEYLSKANGLATVDIKLVLMGKGMLDENDTNLDLFNNRDIRALEKEFNEKVSQRVVNVGEALHRKYPDQWKHMKEDWDKLFPEVEVTVTSQLAIRHIGERGPKGCWDMIEPNQRSVWVGTGKNLEDSFQRIQAKLSRKKYRSAQNFLMEKAELGPKDGAGQNKKMETKGSLSATLHHIKRQIDSTINGKKIHIKMVQKDFGTDVFGF", "metadata": {"id": "A0A559K5V4", "cluster": 18723510, "interpro_all": ["IPR008844", "IPR046953", "IPR038501"], "interpro_used": ["IPR046953"], "interpro_unused": ["IPR038501", "IPR008844"]}, "task_type": "infilling"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein should feature a Zn(2)Cys(6) fungal-type DNA-binding domain that functions as a transcriptional regulator in fungi by utilizing a cysteine-rich motif to facilitate zinc-dependent DNA binding. It forms a binuclear zinc cluster where two zinc atoms are coordinated by six cysteine residues, establishing the molecular basis for specific DNA recognition. This domain is found in proteins involved in diverse metabolic and biosynthetic pathways, including galactose, arginine, and pyrimidine metabolism. In addition, the protein can be placed in the Fungal transcription factor family, which functions as transcriptional regulators in fungi to control diverse metabolic processes including arginine metabolism, lysine biosynthesis, and acriflavine sensitivity. Some members, such as DibT, regulate gene clusters involved in the biosynthesis of secondary metabolites like pestalotiollide B. It is identified in Aplosporella prunicola CBS 121167 and is connected to UniProt keyword Nucleus.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 3066, 5961, 43, 7230, 12, 22, 13, 4998, 12, 26, 13, 8697, 17, 2601, 2678, 17, 2743, 3418, 1988, 4088, 1966, 43, 5224, 7888, 1922, 10520, 2007, 10232, 43, 8666, 17, 5536, 5219, 1942, 6628, 7997, 17, 3100, 2678, 2743, 18, 2176, 4952, 43, 8768, 13821, 7997, 4377, 2597, 2288, 7997, 9030, 2032, 11651, 2007, 3798, 8666, 4248, 16, 11810, 1920, 3272, 4859, 1958, 2487, 2678, 5708, 18, 2052, 3418, 1977, 2435, 1922, 2697, 3286, 1922, 6445, 4487, 1930, 14041, 3873, 16, 2710, 15996, 16, 9732, 16, 1930, 21611, 4714, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8697, 3213, 2991, 3416, 16, 2154, 4088, 1966, 5224, 9098, 1922, 10520, 1942, 2285, 6445, 4487, 4028, 2710, 9732, 4714, 16, 9082, 8132, 16, 1930, 10428, 19814, 9188, 2912, 3802, 18, 2673, 4678, 16, 2427, 1966, 17239, 1031, 16, 5741, 2359, 5859, 3286, 1922, 1920, 8132, 1927, 4067, 6926, 3189, 18171, 20807, 1914, 2201, 2261, 44, 18, 2176, 1977, 2899, 1922, 18373, 9890, 5870, 21692, 29902, 16341, 11844, 21253, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5607, 18, 3], "output": "MVTTDKAVVEPRRKPKSRDGCQRCKIKRLVGRGVACPGYRKLIKWSTKYEAYMPGASRGGEGARGSAFEIVREERPGAGRVRKRGGRGKGGARRREMEECVDTEGRGHPEPNMDAPHTGEPIADLPALEDFPLDMFDLDVPNIDWTTLDVAGEEEAAAPDDIPRLNTPLSRALIRSYARASYPYFQNVCMLYSAFDSSLNPFRSAVARIWDSSPAIFYAIQAMAAAQRQAHATLDDELARVAQGRTSSERALLAILLLGLSAPRLLNPVPPQNVAIVRQNQFFEESLIVPGGGAAAAAGAAATPATASKLLPHPWTGIASHLKHHRNPPNYNNPHPYTLHTQRQACERILVDFGDRNTTKADFVALGEAYRCAGLLELYRVGVGGSGIGGVGGGIGPAGAEVPWGWWWERSNSNSSIGASVAAAPQPRQLPSHSHSPTHHLTSLALHIAASELRLHPQPQPQPRPPERISQARAFVEERLEEFMRRLPRQPLLCMRRLNGGDGEEEEEEEVFWLDVAWERGWLTVMGKCDETKPECRNCLVLGPNQVLEDRALRGGDAGGSADGSGGGGEERGEEAASAVVMGGEEPPLDLPAEPPFEPPAWDDATMEPEYLHDQPPNDPADAEQQQQQQPSPIPPTLIEPGMALVEHLSNTHPAASALGRQLRCWLDCTDLGIANLRAARSLIYYWEMLIGFVSQEGAPGPPLGRWSTCHPQVQTLFAEVGRLIRCERLAAQLEEALLNCSLPREDDMVFPPLLGRRLGSGGACYTPTSTTPFLSLLSHLPPSSGTCSTQPILLVAQNLDFLDLSSSTEECLQPEHLRVREVWWGLDRRVGKGG", "metadata": {"id": "A0A6A6BRF1", "cluster": 22038670, "interpro_all": ["IPR021858", "IPR036864", "IPR001138"], "interpro_used": ["IPR001138", "IPR021858"], "interpro_unused": ["IPR036864"]}, "task_type": "infilling"} {"instruction": "Here is the protein function: The protein is a member of the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. Moreover, the protein is associated with the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. It originates from Stenotrophomonas maltophilia (Pseudomonas maltophilia) (Xanthomonas maltophilia) and contains UniProt keyword associations ATP-binding, Cytoplasm, and Transferase. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 2176, 22970, 2037, 9330, 17330, 10480, 15505, 19740, 12, 13461, 15505, 19740, 13, 12, 15213, 10480, 15505, 19740, 13, 1930, 5461, 20709, 11121, 2538, 5253, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MSRYVVGLTGGIAAGKSEVTRRFEALGIVVADADLAARAVVAAGSPALARIAERFGADMLLADGALDRGRLRAHVFADPAERTALEAITHPAIRLLMQQQCEQAESPYAIAAIPLLTEVGGRKAYPWLDRVLLVDAPEAVQHARLMQRDGIDAALADRMIGAQASRAQRLALADDVVVNDGRPEDLQAQVEQLHARYLGLAGG", "metadata": {"id": "A0A2W6IUC4", "cluster": 22344014, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR027417", "IPR001977"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein is assigned to the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. In addition, the protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is found in Saccharospirillum salsuginis and is annotated with UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2435, 1922, 14175, 15742, 3508, 23576, 11560, 1989, 3370, 20490, 26296, 1937, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MIVGLTGGIGSGKSAAMAVFEKLGIGCVDADVLTEDGLLDRATLRHRIFSDPDEKRWLEGLLHRGCDTSVLIDVPESVQVERVLARDGGSEEQAWAIIRQNMGSLAELESQLVALHKRFVAQSASDVVAREVVEPGQPALSAIADHFGEPLIRTEMQRQLAAQSSPYSVLVAPLLFENDLDQMPREEKLKRADHVVS", "metadata": {"id": "A0A918KQI9", "cluster": 23168016, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein is categorized in the Dephospho-CoA kinase family, which catalyzes the final step in coenzyme A biosynthesis by mediating the ATP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A (dCoA). Members of this family typically adopt a three-domain structure resembling other nucleotide kinases, comprising a nucleotide-binding domain, a substrate-binding $\\alpha$-helical domain, and a lid domain. Furthermore, the protein is grouped in the P-loop containing nucleoside triphosphate hydrolase superfamily, which constitutes the most prevalent nucleotide-binding fold and catalyzes the hydrolysis of the beta-gamma phosphate bond of a bound nucleoside triphosphate, showing a substantial preference for ATP or GTP. The energy generated by this reaction is typically utilized to induce conformational changes in other molecules, thereby driving a diverse range of biological functions. It is identified in Fusobacterium sp. oral taxon 203 and is described by UniProt keywords ATP-binding, Cytoplasm, and Transferase.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2554, 10647, 3508, 10647, 17, 10027, 4016, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 22051, 43, 8132, 2007, 10239, 1920, 4498, 17, 3100, 4050, 1927, 1920, 23, 11, 17, 9420, 2210, 1927, 2554, 10647, 3508, 10647, 4879, 14896, 43, 12, 5330, 6952, 13, 18, 4678, 1927, 2052, 3416, 5745, 14103, 43, 2559, 17, 3418, 3170, 18994, 2303, 5489, 7784, 16, 10351, 43, 5489, 17, 2743, 3418, 16, 43, 4510, 17, 2743, 8, 38, 4595, 8, 17, 11514, 3418, 16, 1930, 43, 13096, 3418, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 58, 17, 5881, 3165, 18015, 17978, 20748, 13975, 16, 2154, 14879, 1920, 2501, 8942, 5489, 17, 2743, 3728, 1930, 17097, 1920, 9128, 1927, 1920, 4666, 17, 7034, 5413, 5403, 1927, 43, 4124, 18015, 17978, 16, 4570, 43, 6317, 8308, 1958, 4498, 2014, 9319, 18, 1920, 3844, 3999, 2007, 2052, 3227, 1977, 5745, 7079, 1942, 4769, 8523, 2840, 1922, 2303, 4206, 16, 6113, 9228, 43, 6445, 3109, 1927, 3933, 4088, 18, 2176, 1977, 2899, 1922, 10630, 12022, 2056, 18, 4726, 19278, 16725, 1930, 1977, 2910, 2007, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 13763, 18, 3], "output": "MIIGLTGGIASGKSTVSKYLAEKGFKVYDADKLDENGNIDRKKLKEIVFENKEKLEKLNGIIHPKVIDFYKFESGIDKFCNKILVIISDYEVQLNRIIERDKINRELAKADVVIENNSSLEDLFKKVERFCETIIAKDISEKKLVQEEIILTFGNKIELKEKNTDEVIIFDVPLLEKIIKSQLSNEERIK", "metadata": {"id": "A0A223AVY9", "cluster": 24745095, "interpro_all": ["IPR001977", "IPR027417"], "interpro_used": ["IPR001977", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is classified under the Cysteine desulfurase family, which comprises homodimeric, pyridoxal-5'-phosphate (PLP)-dependent enzymes that catalyze the conversion of L-cysteine to L-alanine and sulfane sulfur. These proteins serve as central sulfur donors for the biosynthesis of iron-sulfur clusters, tRNA thio-nucleosides, and cofactors such as thiamine and biotin. Moreover, the protein is associated with the Pyridoxal phosphate-dependent transferase, major domain superfamily, which forms the large catalytic component with a 3-layer \u03b1/\u03b2/\u03b1 sandwich topology in enzymes that utilize pyridoxal 5'-phosphate (PLP) as a cofactor. Through a Schiff base linkage with an active site lysine, members of this superfamily facilitate diverse chemical transformations, including transamination, decarboxylation, and deamination, which are essential for the biosynthesis and catabolism of amino acids and neurotransmitters. Also, the protein incorporates a Aminotransferase class V domain that functions as a pyridoxal-phosphate (PLP)-dependent catalytic module found in aminotransferases and related enzymes such as cysteine desulfurase. This domain facilitates enzymatic transformations by covalently binding the PLP cofactor to a conserved lysine residue. It originates from Pacmanvirus S19 and corresponds to UniProt keyword Metal-binding.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 1977, 5947, 2441, 1920, 8666, 30311, 9280, 4127, 3416, 16, 2154, 12936, 21189, 1935, 16, 24828, 23859, 17, 25, 11, 17, 5413, 12, 21453, 13, 17, 3100, 5038, 1988, 18170, 1920, 7309, 1927, 54, 17, 8666, 1942, 54, 17, 10504, 1930, 5141, 2516, 12585, 18, 2144, 2697, 7120, 1966, 4101, 12585, 8276, 1958, 1920, 8132, 1927, 5680, 17, 12585, 5859, 16, 10089, 15331, 17, 18015, 1036, 16, 1930, 21362, 2427, 1966, 26901, 1930, 8622, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24828, 23859, 5413, 17, 3100, 13763, 16, 3044, 3418, 13975, 16, 2154, 4952, 1920, 3103, 6804, 4594, 1956, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 18038, 13678, 1922, 5038, 1988, 12561, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1966, 43, 15155, 18, 2596, 43, 25214, 5170, 8611, 1956, 1925, 3500, 3200, 9082, 16, 4678, 1927, 2052, 13975, 6628, 6445, 4399, 18510, 16, 2710, 2127, 8732, 16, 22429, 1943, 16, 1930, 30097, 8547, 1943, 16, 2154, 2032, 4415, 1958, 1920, 8132, 1930, 19480, 1927, 3835, 4576, 1930, 21012, 18, 2222, 16, 1920, 2213, 19683, 43, 15817, 2921, 64, 3418, 1988, 4088, 1966, 43, 24828, 23859, 17, 5413, 12, 21453, 13, 17, 3100, 6804, 9059, 2435, 1922, 15817, 1036, 1930, 2712, 5038, 2427, 1966, 8666, 30311, 9280, 4127, 18, 2052, 3418, 11374, 8145, 18510, 2007, 16590, 2743, 1920, 21453, 15155, 1942, 43, 5305, 9082, 6181, 18, 2176, 22970, 2037, 6866, 3862, 11074, 4062, 1026, 1930, 8852, 1942, 20709, 11121, 2538, 6048, 17, 2743, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MIYFDNNATTIMPTEVKKAMLEWCNRGNPSAGYALCGIDTCCPEPRDIDNQELLMKAKKNPSKYKIHIVVSAIEHKSIISTIKSYTDRGLVSATFVQPTTSGHIRPEGAINNIQKIGQIAHKHNVPFHCDTVQSFGKFPISPLKDNVDGALIIKQQFLLGYNLQPIIFGSQNEGYRGGTENLPGIGAAFQNIKKYIMTELSKKVPTRQYTAYLHGAKLSVVKRTGTPICNVKMKNSLEKQGIVISVGSAALRISLGDVNTIEEAKKFVQEFLKIINQQLSAREARDMMTEFRKYIGKIFTSGASEANCTVIHGVIDTYSRATGKIPDVEKAITNDTCLVCVMHANNETSFCISFHKLHGPPGITATLLTMKNRKEKNNTSSNKIPAVEIVFLSGLSEYYLPNTLLCNTSDAKASHVLYAMGADDFIRKG", "metadata": {"id": "A0A8F8SP87", "cluster": 27384484, "interpro_all": ["IPR000192", "IPR016454", "IPR015424", "IPR015421", "IPR015422"], "interpro_used": ["IPR016454", "IPR015421", "IPR000192"], "interpro_unused": ["IPR015424", "IPR015422"]}, "task_type": "infilling"}