{"instruction": "Here is the polypeptide chain function: The protein possesses a DUF6534 domain that is found in a large family of fungal integral membrane proteins. It is found in Cristinia sonorae and is associated with UniProt keywords Transmembrane helix. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 14465, 43, 4855, 17136, 3786, 1006, 3418, 1988, 1977, 2435, 1922, 43, 3103, 3416, 1927, 8697, 12328, 3260, 2697, 18, 2176, 1977, 2435, 1922, 29023, 14102, 9337, 8846, 1021, 1930, 1977, 2458, 1956, 20709, 11569, 9117, 7864, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MDSEAVAMKNLPEEILLLLGPMVPHTQLGAVRTADMPSLHVLCRVFRRLTVSVATYDGFRVFVTGWGDSPVLDDIGLFWLSIPVLTGIVACLTQLFYAWRIHQLSERNIWDGLACIQIGHISDLSRSFVFKNIIANLWTGSNVLCDVSITISMLYYLWSAKKRSLAPRSSTTLVRLIKFTVESGLIIAAMTVINLTLFQAIPHTLLYVIIGVPSGKIYSNCLLAVLNSRLLGGRAEVRDQTNTAFVPLDAARYRSNVPWRGTPEPSPSCLTFLSPASQAESASA", "metadata": {"id": "A0A8K0UH65", "cluster": 201545, "interpro_all": ["IPR045339"], "interpro_used": ["IPR045339"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein is included in the Potassium transporter Kch family, which mediates potassium influx and promotes low-affinity K+ uptake. These proteins are essential for the K+-dependent activation of the High-Affinity Ca2+ System (HACS) during the mating pheromone response in budding yeast. It is identified in Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (Yeast) (Saccharomyces elongisporus) and has UniProt annotations 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, 3063, 1922, 1920, 9057, 9054, 14331, 1023, 3416, 16, 2154, 10412, 9057, 12403, 1930, 7383, 2330, 17, 5173, 53, 15, 5047, 18, 2144, 2697, 2032, 4415, 1958, 1920, 53, 15, 17, 3100, 2936, 1927, 1920, 2149, 17, 5173, 5497, 15, 2433, 12, 2118, 2792, 13, 2409, 1920, 11786, 21567, 2644, 1922, 15909, 5688, 18, 2176, 1977, 2899, 1922, 15187, 2179, 29249, 7846, 1937, 2074, 1957, 12, 3943, 11037, 10709, 12962, 19, 16341, 15019, 1015, 19, 14904, 1035, 16877, 1009, 19, 8789, 15618, 14997, 1016, 19, 5214, 1005, 1024, 21000, 17, 27286, 1026, 13, 12, 5688, 13, 12, 16285, 7846, 1937, 2074, 1957, 13, 1930, 2258, 20709, 15010, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MVRDNGGGHLDAERAIKKYDLNVYMWILVLLSFILIAADIYSCLNILVFKKIIFQFVLVIYHWIWALHIYRTRNIALVYLSIDEGNFHDFCCFLTYYELDNAPQIGELNNDILRNIKSIAQTNLNLSIILSFMCLSVVIRDKEANTFKSYCCILINKSVSHAVRIAQLPELDQELPDYTDYTRVFYPSRQFYRRSESSKSQQLNINVSRPLLEEGPLMNRRLSTLQDKNRNRKIIIPPLPLPPPPPRTISTATTTGVAPELTSHKTGQLLETQNMFLQQESLMPSIPKRSYTATLTYMPPQTQQHFQRSFTDPTQMDRIPENPFSSSSIIPPLHPTPRSQGSLYKVTSPSGKSKRKKPDKEEGEEKDNDEVEFEHGLGFYNNEMILTHSITRESLDIIDAYRQEQTKADKNNENDPLSVPYPVRGVSRFFEQSTFDVVKVENFTNYKCTTLFWYFWGTEDYKPYAYSIAKWIFTGCNSICKKIYSIKSYSCFCLLNLIADTPRQVINILTLRYYATGYALFFFRFLFGMIMYVPLKCYLLHHKSKQELLDNGILSREGKNDSEDEIPMQPSFEQLQTQQQEEQVYSTLNNEKEYNLANTTSLPLSSSLSSSFPRNDQTDLYNTAYTGNQFQDTHKHEHDITSTSQLQSDWDKDTDLNASTLYSSQMNSTDLLSNHSTQTGTFTETFSKANRLEDQITYFKEEKPIANEAEQPVGYPRLNLEDVDIVGCQDHQGRGN", "metadata": {"id": "A5E7J1", "cluster": 1262526, "interpro_all": ["IPR031606"], "interpro_used": ["IPR031606"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein is classified under 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. Moreover, the protein possesses 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. In addition, the protein is assigned to the Diverse Substrate Acetyltransferase family, which catalyzes the transfer of an acetyl group from acetyl-CoA to a wide range of substrates, including amino acids, polyamines, and histones. These enzymes regulate critical biological processes such as intracellular polyamine levels for cell growth, chromatin structure via histone modification, and stress responses in plants. It has been characterized in Aegilops tauschii subsp. strangulata (Goatgrass).\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 1977, 5947, 2441, 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, 3950, 16, 1920, 2213, 14465, 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, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 6445, 4510, 22226, 3416, 16, 2154, 17097, 1920, 3856, 1927, 1925, 6894, 2210, 2037, 6894, 17, 10027, 1942, 43, 4743, 3109, 1927, 6249, 16, 2710, 3835, 4576, 16, 27883, 1036, 16, 1930, 15808, 18, 2144, 5038, 5741, 4140, 3933, 4028, 2427, 1966, 4776, 27883, 2428, 1958, 2024, 2905, 16, 6338, 3170, 3454, 6632, 6295, 16, 1930, 3071, 3387, 1922, 4793, 18, 2176, 2258, 2252, 4378, 1922, 18025, 1970, 4001, 7462, 14920, 3907, 19615, 18, 9402, 2029, 5617, 3857, 12, 8838, 27458, 13, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "WLVRPTLRFVIRSNGPWDVRPKILKYRRSGVIDSLKFYFKGKSLYISICAKMAAPTTFSGEAWAELRLADARDVPHIHSLIHQMAEFELLTDLFAATHELLASTILDLSPSPASASADTVGSRRLDLSASSPLADPEAAAFPSGLYVEDIFVRAPWRRRGLGRMMLSAVAGRAAEIGMGRVEWCVLDWNQGAEVFKQWRICRLTGAALDKYKGTGTGSQEEEDAGGKAQGHLVTEQSSNPSCSVSPYPPTPIPPNPGTLFPTPQPAPFTSFTALPRGGGRVTAGFVICFPNYSTFLAKPNAIDFYEGM", "metadata": {"id": "A0A453J136", "cluster": 8036778, "interpro_all": ["IPR016181", "IPR051016", "IPR000182"], "interpro_used": ["IPR016181", "IPR000182", "IPR051016"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The desired role of my protein is: The protein should include a Molybdenum cofactor sulfurase, middle domain that contributes to the sulfuration of the molybdenum cofactor or the reduction of N-oxygenated molecules, depending on the protein context. This structural unit, also known as MOSC_N, is composed of antiparallel beta-sheets and alpha-helices and is frequently located N-terminal to the MOSC domain. Additionally, the protein contains 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. Also, the protein belongs to the Pyruvate kinase-like, insert domain superfamily, which represents the $\\beta$-barrel domain inserted within the catalytic $\\beta/\\alpha$-barrel of pyruvate kinase, an enzyme that generates ATP in the final step of glycolysis. This domain shares a topological fold with the MOSC sulfur-carrier domain and forms part of the structural framework required for the enzyme's allosteric regulation and tetrameric assembly. It is expressed in Fulvimarina manganoxydans. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 3066, 3951, 43, 2629, 16924, 5233, 1989, 15155, 12585, 2051, 16, 5576, 3418, 1988, 7624, 1942, 1920, 12585, 1943, 1927, 1920, 2629, 16924, 5233, 1989, 15155, 2014, 1920, 3378, 1927, 56, 17, 25241, 4206, 16, 6362, 1990, 1920, 2213, 4491, 18, 2052, 4346, 5344, 16, 2222, 3171, 1966, 7500, 1030, 41, 56, 16, 1977, 7179, 1927, 28892, 4666, 17, 14685, 1930, 4595, 17, 12789, 1930, 1977, 5467, 4810, 56, 17, 4262, 1942, 1920, 7500, 1030, 3418, 18, 4950, 16, 1920, 2213, 5461, 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, 2222, 16, 1920, 2213, 14440, 1942, 1920, 11867, 4016, 17, 3189, 16, 12844, 3418, 13975, 16, 2154, 4972, 1920, 8, 38, 4666, 8, 17, 19560, 3418, 9103, 2651, 1920, 6804, 8, 38, 4666, 19, 38, 4595, 8, 17, 19560, 1927, 11867, 4016, 16, 1925, 4113, 1988, 12399, 4498, 1922, 1920, 3948, 3537, 1927, 13393, 18, 2052, 3418, 16495, 43, 16365, 3728, 1956, 1920, 7500, 1030, 12585, 17, 9685, 3418, 1930, 4952, 3131, 1927, 1920, 4346, 6465, 3414, 1958, 1920, 4113, 11, 61, 14772, 3640, 1930, 30442, 5957, 18, 2176, 1977, 3198, 1922, 5257, 2165, 19252, 4058, 18874, 7221, 3825, 3355, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MHLGSIHIYPVKSGRGVDLSHADLQRQGLAGDRRWMVVDRAKRRFLTQREIPSLALLHSELQEDGIILTFGDVGERFVPRPTGEERTKVTIWRDEVDVALADEATHEALSRWLGREVQLVYQDRLERVANAEWAGDAAPVSLADGYPYLITTSASLRDLNSRLVYDGHEPVTMSRFRPNLVIDGAQAWAEDGWETIRVGSLMLDLVKPCARCAITTVDPQEGRFAGDQPLTILREMRMSADRRVPGVLFGWNAVPRSEGRLDVGDRVEVIAHRDTDVVR", "metadata": {"id": "A0A1W2DU48", "cluster": 10764271, "interpro_all": ["IPR005302", "IPR005303", "IPR011037"], "interpro_used": ["IPR005303", "IPR005302", "IPR011037"], "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 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. Furthermore, the protein is included in the Bacterial abhydrolase family, which comprises probable enzymes containing the alpha/beta hydrolase fold that are predicted to catalyze the hydrolysis of a diverse range of substrates, such as esters and lipids. Furthermore, the protein is included in the FrsA esterase family, which catalyzes the hydrolysis of esters, including the degradation of plant cutin and synthetic polyesters like poly(ethylene terephthalate). Members of this family participate in diverse biological processes ranging from quorum quenching and antibiotic biosynthesis to fungal virulence and melanin production. It is native to Planctomycetota 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, 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, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4543, 2186, 8535, 24605, 1021, 3416, 16, 2154, 12936, 12584, 5038, 3165, 1920, 4595, 19, 4666, 20748, 3728, 1988, 2032, 4396, 1942, 18170, 1920, 9128, 1927, 43, 6445, 3109, 1927, 6249, 16, 2427, 1966, 16785, 1930, 8238, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2415, 5735, 26389, 3416, 16, 2154, 17097, 1920, 9128, 1927, 16785, 16, 2710, 1920, 4877, 1927, 4496, 4665, 1921, 1930, 6830, 4286, 26934, 3189, 4286, 12, 13183, 6005, 2128, 19253, 7289, 2010, 13, 18, 4678, 1927, 2052, 3416, 7352, 1922, 6445, 3933, 4028, 6485, 2037, 28481, 16721, 1930, 7267, 8132, 1942, 8697, 9304, 1930, 20850, 3372, 18, 2176, 1977, 6196, 1942, 4720, 2341, 13386, 19446, 3857, 14061, 18, 3], "output": "MDGVTELDLTKSFRAHLEACYAASSRQWTFKGDEASAFRRWRTATRRKLLTLLGGQERARVPLNLRRNVAEETDTFRRERFYYDTRQGLTATAWFVMPKNVKPSVPVVLCPPGHGGGMNQVLLTDSEYKRYPFELVKRGMAVLVPEHIGFGERTGRKGEEKQANHAYFYHSQTLLGQNAMGYLLWDLRRALDVLETLSEVDANRVGCYGLSLGGEMTLFLAACDPRVKVACISGFLCSYGSSFLAEGHCGCGYVFGLGKYLEHEDIAALIAPRPLLVESATRDPIFPVEVAKQTVERLRPLYALCGVPDRIDQDVFEGKHEISGAKAFEWFGKWLASYGG", "metadata": {"id": "A0A938M6Q6", "cluster": 11499780, "interpro_all": ["IPR029058", "IPR025890", "IPR050261"], "interpro_used": ["IPR029058", "IPR025890", "IPR050261"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein should feature a AIG1-type guanine nucleotide-binding (G) domain that functions as a P-loop GTPase molecular switch, hydrolyzing guanine nucleotides to regulate processes ranging from immunity to protein transport. This domain is characteristic of GIMAP/IAN proteins involved in apoptosis and T-cell development, as well as Toc components of the chloroplast protein import machinery. Structurally, it features a central $\\beta$-sheet sandwiched by $\\alpha$-helices, containing five conserved nucleotide-binding motifs and a unique hydrophobic region. Moreover, the protein is assigned to the GTPase GIMA/IAN/Toc family, which encompasses the immunity-associated GIMAP/IAN subfamily involved in regulating apoptosis and T-cell development, and the plant-specific Toc GTPases that function as integral receptors within the chloroplast protein import machinery. These membrane-bound proteins utilize GTP hydrolysis to drive processes ranging from vertebrate immune response to the recognition and translocation of precursor proteins across the outer chloroplast membrane. 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 derived from Microtus ochrogaster (Prairie vole) and is connected to UniProt keyword Coiled coil and GTP-binding.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 9798, 9114, 17, 2601, 16904, 5489, 17, 2743, 12, 49, 13, 3418, 1988, 4088, 1966, 43, 58, 17, 5881, 14809, 3272, 6195, 16, 7222, 9046, 16904, 9519, 1942, 5741, 4028, 6485, 2037, 7611, 1942, 2213, 4860, 18, 2052, 3418, 1977, 6293, 1927, 7217, 11927, 19, 11640, 1022, 2697, 3286, 1922, 4091, 1930, 62, 17, 2024, 2740, 16, 1966, 2486, 1966, 21682, 4178, 1927, 1920, 17471, 2213, 2582, 10853, 18, 12171, 16, 2176, 4075, 43, 4101, 8, 38, 4666, 8, 17, 11130, 18038, 1919, 2007, 8, 38, 4595, 8, 17, 12789, 16, 3165, 3628, 5305, 5489, 17, 2743, 8277, 1930, 43, 5008, 7919, 3031, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 14809, 7217, 3368, 19, 11640, 1022, 19, 21682, 3416, 16, 2154, 21569, 1920, 7611, 17, 2458, 7217, 11927, 19, 11640, 1022, 16227, 3286, 1922, 6773, 4091, 1930, 62, 17, 2024, 2740, 16, 1930, 1920, 4496, 17, 2487, 21682, 18390, 1988, 2347, 1966, 12328, 4086, 2651, 1920, 17471, 2213, 2582, 10853, 18, 2144, 3260, 17, 4124, 2697, 12561, 9319, 9128, 1942, 9265, 4028, 6485, 2037, 13416, 3743, 2644, 1942, 1920, 5708, 1930, 7849, 1927, 7897, 2697, 3436, 1920, 7642, 17471, 3260, 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, 3595, 2037, 7666, 1957, 18129, 6405, 7092, 12, 21227, 23576, 1021, 2984, 1021, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 17524, 9121, 1930, 9319, 17, 2743, 18, 3], "output": "MKDTCTEISRCVLYSCPGPHVSLIKSLFGEAAMRYMIVLFTRNNVIAQCGKRYLAFNNKAVEAEREDQVEDIDRRLRQCLMELEETYAQELTMENLKEKAEENILEYIFKKICAIILVLQLGRFTEEEQKTKDDLEDQSLDDFLGEPNDKLKQLVELIEEMVDRNGGSYFSEKIYAEIKRIERECAHKSEEEKKKRIDSAKKNYDEK", "metadata": {"id": "A0A8J6G8D3", "cluster": 12931993, "interpro_all": ["IPR006703", "IPR045058", "IPR027417"], "interpro_used": ["IPR006703", "IPR045058", "IPR027417"], "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 Aspartate/ornithine carbamoyltransferase superfamily, which encompasses evolutionarily related enzymes, such as ATCase and OTCase, that catalyze the transfer of a carbamoyl group from carbamoyl phosphate to aspartate or ornithine. These proteins play critical roles in de novo pyrimidine biosynthesis, arginine metabolism, and the urea cycle. Members of this family share a similar secondary structure and conserved residues involved in binding the phosphoryl group of carbamoyl phosphate. Also, the protein should feature a Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain that binds the phosphoryl group of carbamoyl phosphate and facilitates subunit trimerization within aspartate carbamoyltransferase (ATCase) and ornithine carbamoyltransferase (OTCase). These enzymes function in pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle by catalyzing the conversion of aspartate or ornithine to carbamoylaspartate or citrulline, respectively. Furthermore, the protein is classified under the Aspartate carbamoyltransferase family, which catalyzes the formation of carbamoyl-aspartate from aspartate and carbamoyl-phosphate as the commitment step of the pyrimidine biosynthesis pathway. Its structural organization varies widely, existing as a standalone oligomer in bacteria\u2014often regulated by CTP\u2014or as a domain within a multifunctional enzyme in eukaryotes. It is present in Candidatus Sungbacteria bacterium RIFCSPLOWO2_01_FULL_54_21.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 12878, 19, 26918, 17742, 10921, 9961, 13975, 16, 2154, 21569, 18584, 2712, 5038, 16, 2427, 1966, 18121, 2051, 1930, 7608, 25792, 16, 1988, 18170, 1920, 3856, 1927, 43, 17742, 10921, 2210, 2037, 17742, 10921, 5413, 1942, 12878, 2014, 26918, 18, 2144, 2697, 3918, 4140, 5456, 1922, 2028, 9441, 21611, 8132, 16, 9732, 4714, 16, 1930, 1920, 10505, 4048, 18, 4678, 1927, 2052, 3416, 7948, 43, 2551, 4067, 3170, 1930, 5305, 4248, 3286, 1922, 2743, 1920, 12556, 2210, 1927, 17742, 10921, 5413, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 12878, 19, 26918, 17742, 10921, 9961, 16, 17742, 10921, 17, 58, 2743, 3418, 1988, 6876, 1920, 12556, 2210, 1927, 17742, 10921, 5413, 1930, 11374, 5903, 20085, 2466, 2651, 12878, 17742, 10921, 9961, 12, 18121, 2051, 13, 1930, 26918, 17742, 10921, 9961, 12, 7608, 25792, 13, 18, 2144, 5038, 2347, 1922, 21611, 8132, 16, 9732, 8132, 16, 1930, 1920, 10505, 4048, 2007, 29601, 1920, 7309, 1927, 12878, 2014, 26918, 1942, 17742, 10921, 13432, 5263, 2010, 2014, 22926, 2053, 16, 2763, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 12878, 17742, 10921, 9961, 3416, 16, 2154, 17097, 1920, 3337, 1927, 17742, 10921, 17, 12878, 2037, 12878, 1930, 17742, 10921, 17, 5413, 1966, 1920, 14373, 3537, 1927, 1920, 21611, 8132, 3374, 18, 2496, 4346, 5901, 10229, 5673, 16, 6124, 1966, 43, 2924, 20807, 2912, 13034, 1922, 4802, 230, 3868, 4335, 2007, 25639, 230, 2014, 1966, 43, 3418, 2651, 43, 20136, 4113, 1922, 15021, 18, 2176, 1977, 2481, 1922, 14550, 1031, 1957, 8147, 22297, 2422, 2126, 14061, 12424, 2792, 2030, 1971, 5265, 41, 3287, 41, 4125, 41, 4584, 41, 2900, 18, 3], "output": "MHILKSQQFSRPLLEAVVRRANEFEVLWRSSSGRYRMRQLFSEKMLFNSFETESVRTHASFCVAGLRLGMDVPPLQGGGRISSEYRNRGESLEDHIKVLNTMGPDVIVLRRPEEGAAERAATVSRVPIINAGDGKGQHPTQAVLDVGTIHQKFGAIDGLSIIIGGDLANGRTARSLAYLLAKFKDVKIMFVSPPELRMKSDVLEYLDKYHVTFTEHEVLEEVIAESKVIYWTRSQHEKADGRVVYEDIERRYCIDAKMMERMQPDAILMHPLPRNEEIHHEVDSDPRAHYFRQTEYSVPIRMALLELALGGNSHAESLAEAA", "metadata": {"id": "A0A1G2LA23", "cluster": 13083160, "interpro_all": ["IPR006132", "IPR006130", "IPR036901", "IPR002082", "IPR006131"], "interpro_used": ["IPR036901", "IPR006132", "IPR002082"], "interpro_unused": ["IPR006131", "IPR006130"]}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that has the following function: The protein is a member 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. Furthermore, the protein can be placed in the Organic radical-activating enzymes family, which creates a glycyl radical in the substrate protein. In addition, the protein has 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. It is found in Firmicutes bacterium ADurb.Bin300 and features UniProt keywords S-adenosyl-L-methionine, Metal-binding, and Pyruvate. 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, 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, 2112, 1998, 5396, 1922, 1920, 6805, 6917, 17, 8019, 5038, 3416, 16, 2154, 15628, 43, 4235, 2199, 6917, 1922, 1920, 4510, 2213, 18, 1922, 2459, 16, 1920, 2213, 2258, 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, 2176, 1977, 2435, 1922, 24474, 14061, 2041, 5223, 18, 8768, 17450, 1930, 4075, 20709, 11569, 61, 17, 29283, 17, 54, 17, 12417, 16, 6048, 17, 2743, 16, 1930, 11867, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MFNKKSHLLIFGKGFNYSEDGPGNRLIYHLKGCNLHCPWCSNPDGLKSEEYEKGTPVDELLKEILSCKPMFFDGGGVTFTGGEILCQADAMENILFQLTENKIHTAVETNASLPSLKRLMPYIDYLIADFKHPNEKKLMQVVGASLLPIKDNLKTRVLSGKPLLVRVPLIHGFNDNDEALEGFTEFFRELSELGAKDSLWFELLKYHEYGREKWEKEGLPYTVKNGFISDKRYNEIMEFFRLRGIAAINT", "metadata": {"id": "A0A1V5S3Y3", "cluster": 15487666, "interpro_all": ["IPR013785", "IPR034457", "IPR007197"], "interpro_used": ["IPR013785", "IPR034457", "IPR007197"], "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 included in 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 is derived from Bdellovibrionales bacterium RIFOXYC1_FULL_39_130.", "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, 3063, 1922, 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, 1977, 3595, 2037, 5238, 20783, 2165, 2377, 12778, 1918, 14061, 12424, 7221, 5800, 41, 4125, 41, 3886, 41, 8761, 18, 3], "output": "MKLPPPKRAFTVLFNGITELRALWDTGATGSMIQGVHGIQLVDTYIVDLIGQTVDILIGMDIISRGDFALTIKFNKQISKIDLQVNGRNKKREIKTPVQVINPLANPPIVIGINKNLIDKLGLKKINAGRILPYNVKASTLEISGGDEKGKTVFSCCYPQLDSKIDFVPSAE", "metadata": {"id": "A0A1F3V5T2", "cluster": 16082742, "interpro_all": ["IPR021109"], "interpro_used": ["IPR021109"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein should have a DEP domain that mediates selective targeting to specific subcellular membranous sites and regulates G-protein signaling pathways. This globular module comprises a three-helix bundle with a beta-hairpin arm and is essential for the function of proteins such as Dishevelled, Egl-10, and Pleckstrin in signal transduction. Furthermore, 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. It is produced by Auanema sp. JU1783.\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, 2554, 3418, 1988, 10412, 5328, 5133, 1942, 2487, 11309, 22890, 3402, 1930, 7014, 49, 17, 2213, 3197, 3873, 18, 2052, 20975, 9059, 12936, 43, 2559, 17, 7864, 14142, 1956, 43, 4666, 17, 14565, 6011, 1930, 1977, 4415, 1958, 1920, 2347, 1927, 2697, 2427, 1966, 14362, 9488, 7667, 16, 25943, 17, 2119, 16, 1930, 6483, 12940, 2156, 5572, 1922, 2733, 8201, 18, 3677, 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, 2176, 1977, 4152, 2007, 5759, 2516, 3368, 2056, 18, 8212, 24761, 1010, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MVDTVFSPWRPLRQLRSGSVDDTPTGRRNNPVFRRQFSQVENSFTGKEAVDFLMEEIPSRFLNGRQVSRENQRFPPSEKIEFRDGNTLYVHAVQPTAKTPKLIAEFENTGMNGGSEENISSASKWDRRTSMSHGNLATLVSTCPSGEGANMLVSPRERRLPDIKPATEEKENQEYVWLSFGKQKKRDPEVRKALGEINRELQYTTSLKYKPSIGSKLSDLDIMNMWKTHLLARLKEELGVEDLSFLNWHVMGYDIKWNLVRLMKYLEQFPFPTGSCNVITYKEFQEVNVFKTICSNLSREPPIIFSIFNEDQKNQSPILPHNKEMETVFGESQPYTRLVDRKMPRFVSNSSMISPDVRFTFSAGKEESIYETLPRIPEKGRLRRRSDRLLEESVDMNDVLGLPGLRCSYRTAPVAFSPKIYNLPRATLNSLLTCVSLVLLSIRTSTRRKLHHLIKFMNKISSLTNCIVSCDEHLSPYQAMDLVSLLMDFEREVFAVDDKNEIPTPTTNVIQFCEKIQHDNYVEQQTAQDDYLMPLLEQIMVMHPDVYRKRFPNDHVFKANKDNGFLRRLFHRNTFKATAMWNDIITSFIDEGPRKKHRCVALLTKFLEKKVINLGGLKRCATPEFLRYKGSPMKCSTFDNIIDEKANIFPPEPEKDSVAALNRRGSVVEKIGSSGVVKSKSDKEEFSSYLSKDECSAILHCSDISDTPIHRLPPAIRTNGISETSPDVVSKIAQMCTPLSSGVSGRNTSNHCLQLEPNSTNRAVLLESLRNLVTEQVREKQRRNLSTAEPGLDPHLKDGDREKKLKQFKK", "metadata": {"id": "A0A9P1MR81", "cluster": 16883043, "interpro_all": ["IPR000591", "IPR036388", "IPR036390"], "interpro_used": ["IPR000591", "IPR036388"], "interpro_unused": ["IPR036390"]}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein is included 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. Furthermore, the protein should feature 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 native to Stephania cephalantha and is classified with UniProt keywords ATP-binding.\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, 3063, 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, 3677, 16, 1920, 2213, 3066, 5961, 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, 6196, 1942, 3537, 15409, 2126, 15221, 7744, 1019, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MVGLIAFLFAFLFEFHVNAIRLPIQKCLLPELSHCLGASRLSCIANIILITFFDPSNIILEKVESSLSFKDKWKRGKPFGRTFMHVYLRFNRYGWEKIGALVNLGAFLPHRCSSRYDPTLKYLGYAPPTDSSNYRSAKVVSFLDAGLMSIARCAELSVLRLAIFYNFRGNDPIQVGKFCHKLFCLIKRALQILISDFGLAKMMPENQEMYVTTKVLGTFGYFDLEYTSTGKLTIQSNVYAFGVVLLELLTRRRAVDLSQGPNDPDMNRSSYNIESITMFANLASHCVRAESTERHSMTDCVKELQMTFHLYFTNSYESFDEPPSSPTNPLGYPIARSGVNVVVVTCTEELAYQQAKEADNLLQKGVIELNLYSSLCEGELFGADLFEAIRLDQNLVLQVRHILTDRKKLRKVI", "metadata": {"id": "A0AAP0P6C1", "cluster": 21436253, "interpro_all": ["IPR011009", "IPR000719", "IPR001245"], "interpro_used": ["IPR011009", "IPR000719"], "interpro_unused": ["IPR001245"]}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein can be placed in the Protein of unknown function DUF2158 family, which comprises predominantly prokaryotic proteins with no currently known function. It is produced by Mucilaginibacter sp. JRF.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 6680, 22633, 3416, 16, 2154, 12936, 7700, 21545, 2697, 1956, 2239, 5077, 3171, 2347, 18, 2176, 1977, 4152, 2007, 3422, 19167, 26296, 26073, 2341, 1915, 2056, 18, 21886, 1038, 18, 3], "output": "MEKIIKVGDVVDENAPRETRLKSGSPQMTVIAISNNYATVSWF", "metadata": {"id": "A0A929PDR0", "cluster": 23385597, "interpro_all": ["IPR019226"], "interpro_used": ["IPR019226"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want a protein that has the function: The protein possesses a DUF5753 domain that serves as a putative ligand-binding region in bacterial transcription regulators, typically associated with an N-terminal helix-turn-helix (HTH) DNA-binding domain. Moreover, 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. Moreover, 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. It is identified in Actinomadura rubteroloni. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 14465, 43, 4855, 17968, 8245, 1010, 3418, 1988, 10634, 1966, 43, 6770, 5207, 17, 2743, 3031, 1922, 4543, 3213, 9098, 16, 5745, 2458, 1956, 1925, 56, 17, 4262, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 2678, 17, 2743, 3418, 18, 3950, 16, 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, 3950, 16, 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, 2176, 1977, 2899, 1922, 4718, 2954, 10015, 5524, 10010, 4947, 13339, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MTGARPPTVRAVQLGRELRYLREEKRLTMEEVGAVTGWSAAKLSRIENARTRATIKDVTALLDLYAAAADRRERLVRLARTARERGWWEAFDGSISESLTTYIGLEDDAARVDAFTSGAFNGLLQTEDYARAVIATAPRPLPPGVVGRRVEVRMRRQARLTGPEPLRLDTVLEEAALRRRIAGPDVMRAQFRYMAEMGERDNVSVRILPFDRGPYPLSALSFSLMRFPGGLRSDVVYLEALSGGAVIEEDEEVFLYTLMWDRLRQLALPEDESRDLLLDLAARF", "metadata": {"id": "A0A2P4UEL9", "cluster": 23410572, "interpro_all": ["IPR001387", "IPR043917", "IPR010982"], "interpro_used": ["IPR043917", "IPR010982", "IPR001387"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein should have a Tc1-like transposase, DDE domain that serves as the catalytic core responsible for transposon mobilization. Adopting an RNase H-like fold with a characteristic DDE motif of acidic residues, it acts as an endonuclease to nick the 5'-end of the transposon DNA. In addition, the protein is grouped in the Ribonuclease H superfamily, which comprises the catalytic domains of diverse polynucleotidyl transferases characterized by a conserved 3-layer $\\alpha/\\beta/\\alpha$ fold. This superfamily includes enzymes such as RNase H, retroviral integrases, transposases, and exonucleases that utilize this domain to catalyze nucleic acid backbone cleavage or transfer during DNA replication, repair, and recombination. Moreover, the protein features a Helitron helicase-like domain domain that facilitates the transposition of eukaryotic Helitron elements via a replicative rolling-circle mechanism. This domain functions as part of a transposase machinery with single-stranded DNA (ssDNA)-specific endonuclease activity, often mobilizing adjacent genes and contributing to genome variability. It is native to Pieris brassicae (White butterfly) (Large white butterfly) and features UniProt keywords Transposable element. 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, 3066, 2162, 43, 5283, 1009, 17, 3189, 12935, 2051, 16, 6758, 1021, 3418, 1988, 10634, 1966, 1920, 6804, 4728, 5061, 1958, 18808, 14586, 18, 20478, 1925, 9843, 50, 17, 3189, 3728, 1956, 43, 6293, 6758, 1021, 5219, 1927, 9931, 4248, 16, 2176, 8016, 1966, 1925, 18697, 1942, 12657, 1920, 25, 11, 17, 2482, 1927, 1920, 18808, 2678, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 18347, 2051, 50, 13975, 16, 2154, 12936, 1920, 6804, 4682, 1927, 6445, 15176, 2626, 4090, 2199, 13763, 1036, 4378, 2007, 43, 5305, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 18, 2052, 13975, 5921, 5038, 2427, 1966, 9843, 50, 16, 16599, 27252, 1036, 16, 12935, 2319, 16, 1930, 24966, 1036, 1988, 12561, 2052, 3418, 1942, 18170, 11079, 2687, 10787, 6404, 2014, 3856, 2409, 2678, 5158, 16, 5059, 16, 1930, 7827, 18, 3950, 16, 1920, 2213, 4075, 43, 3091, 3032, 1022, 15318, 17, 3189, 3418, 3418, 1988, 11374, 1920, 22596, 1927, 10825, 3091, 3032, 1022, 5362, 3454, 43, 20604, 21691, 17, 12233, 2856, 18, 2052, 3418, 4088, 1966, 3131, 1927, 43, 12935, 2051, 10853, 1956, 2957, 17, 10338, 2678, 12, 15063, 13, 17, 2487, 18697, 2455, 16, 3868, 20407, 3903, 6811, 2628, 1930, 8739, 1942, 3843, 5687, 18, 2176, 1977, 6196, 1942, 13306, 1937, 19503, 6102, 1021, 12, 4511, 20883, 15972, 13, 12, 3103, 4511, 20883, 15972, 13, 1930, 4075, 20709, 11569, 12935, 2115, 6149, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MVPTPIEPHQFLQIYFISSMVDQLNVRCNIQGTQQLKRRIIEQLQAFFHANNAVVNMFKTALEQIPSDTHKFVIRADCTPTGEHVRRFNAPTVNDVPAIIVGDPTKSRDIVVQRRSNIMHRVNETHRLYDALQYPIIYWQGQDGYDITLKMVDPTTGISTNKKLSAMNYYAYRMMISTHEENVILKCRRLFQKFAVDMYVKVETERLAFIRFNQAKQRSEDYIHLRDAIHSDGDVQNFERLDDSPIILYRKPTPHARIRSRRYYVRHTVGKVWDDTTVKSRKRAFLEGLSTGAKNPTSKGNRLIVLHIGSDRGFVSDSALVFECKGTGDYHASMNANTFEKWFQEMLPKLEPNSIVVMNNDSYHSRHQEKTPVTSWKKYDIQQSQIHLQRTFLLRTMTQLLEKIKNVKTQYESYVIDEMAKAAGVEILSLPLYNCELNPLELVWADVEGYVARNNTTFQMVDVKKLLQEGLNSITIEKWQNCISHVIKEELKFGGLDSQIDKTVDSFIINKEIRNISGVIEEWASVEQVYERPDRSERARSTPLLFVL", "metadata": {"id": "A0A9P0XDL7", "cluster": 25234595, "interpro_all": ["IPR025476", "IPR036397", "IPR038717"], "interpro_used": ["IPR038717", "IPR036397", "IPR025476"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: 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 native to Ectocarpus siliculosus (Brown alga) (Conferva siliculosa). Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 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, 6196, 1942, 7495, 7095, 1034, 1957, 16105, 11677, 1957, 12, 8084, 4326, 1019, 13, 12, 7909, 7302, 16105, 11677, 1019, 13, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MSSTPAPSDIVRKAAEEDSKASLETWGPEAFARRTRTKIHNLGAPLPPWESKEQRPTPAARGIPKSINIILLGPTGSGKSSLVYTWWRALSGSVTGKEEFLAEHVHDSFLQRLRVGWNAKEGEEARQRAQQQQQQQHKHPALATGASSVAPPTAPGGGALLKAAPRHGTKGLDAFQLQAPDPHRGCTGITVHDTKGQQFFTEEEERFAEQMLQGKVEEGSAVDKQNYKYWFMLGNFGFFSTASLAAAPHVVVLVFDVTLRSFQQMLREPEANELCRCYRKIVRRAAKQGHEVFAVLTHIDAYAPDEDDESTSSDWEEEEEGTEADTEAETATEEGSLEQSAEASPGDGGSEEASSNAQESSLNGHEGVSNAKASSSSGMEHPSNGNESAGAGEFDREAELPGIISLWCEGLSQALGNDPEAPLPKENVFAVQNYHQGSSAQDPVLDLACLECLESVLHAGGRYVDDRYQQQQEGCVIA", "metadata": {"id": "D8LKL3", "cluster": 26622952, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "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 should contain a Integrase zinc-binding domain that coordinates zinc ions and is found in a wide variety of integrase proteins responsible for viral genome integration. Furthermore, the protein is assigned to the Gypsy Retrotransposon Integrase-like family, which mediates the integration of retrotransposon DNA into the host genome to facilitate the replication and mobilization of these mobile genetic elements. Functioning similarly to retroviral integrases, these enzymes recognize specific DNA sequences and catalyze the strand transfer reaction required for genomic insertion. It is found in Tanacetum cinerariifolium (Dalmatian daisy) (Chrysanthemum cinerariifolium) and is linked to UniProt keywords Nucleotidyltransferase, RNA-directed DNA polymerase, 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, 5531, 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, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 8415, 9196, 27181, 1916, 27252, 17, 3189, 3416, 16, 2154, 10412, 1920, 7122, 1927, 27181, 1916, 2678, 2460, 1920, 4423, 3843, 1942, 6628, 1920, 5158, 1930, 14586, 1927, 2144, 8785, 3299, 5362, 18, 7295, 4852, 1942, 16599, 27252, 1036, 16, 2144, 5038, 9967, 2487, 2678, 3709, 1930, 18170, 1920, 5984, 3856, 3227, 3414, 1958, 4935, 7413, 18, 2176, 1977, 2435, 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, 4624, 1942, 20709, 11569, 2797, 4090, 2199, 9961, 16, 3146, 17, 6554, 2678, 6479, 16, 1930, 13763, 18, 3], "output": "MIKKDIPKEELEPRMDGTLCFNDRSWLPCHKSKYSIHLGSDKMYQDLKKLYWWEDMLRAWVINFGKGWVNHLLIVPLVVPLDGLHIDDKLHLVKEPVVIMDFTWERVDQFRKKYPRLFTKTAPSSIAVSYGDLRILIMHKSPNMKANIATYVSKYSTCAKTDEQSERTIQTLEFSYNNSYYARIKRHANEGDIKLLKQNRIPIVKGRWNSRRGLE", "metadata": {"id": "A0A6L2KG66", "cluster": 27371290, "interpro_all": ["IPR052160", "IPR041588"], "interpro_used": ["IPR041588", "IPR052160"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein is a member of the von Willebrand factor A-like domain superfamily, which functions as a versatile protein-interaction module involved in ligand binding and the assembly of multiprotein complexes. Spanning both extracellular proteins like integrins and collagens as well as intracellular machinery, these domains facilitate diverse biological events including cell adhesion, migration, signal transduction, and DNA repair. It is native to Pirellulaceae bacterium.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 14147, 30067, 2991, 43, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 2213, 17, 2835, 9059, 3286, 1922, 5207, 2743, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 18, 13346, 2321, 5329, 2697, 3189, 15563, 1930, 5621, 1036, 1966, 2486, 1966, 4776, 10853, 16, 2144, 4682, 6628, 6445, 3933, 3916, 2710, 2024, 6141, 16, 5049, 16, 2733, 8201, 16, 1930, 2678, 5059, 18, 2176, 1977, 6196, 1942, 13774, 1992, 5617, 1972, 3336, 14061, 18, 3], "output": "MAGRAGKPTRQDRRASVAASRIVQTIGIRASLQDEADETALAVAAALARRRFVATRSGPNAIEVTVRGPQAEPAATATSAVAAVRPRDLVFVVDLRPGSIQAYDAAVLGGLYQDLGYESLAAVDGPLSHAAVPAKYRIEPGDPISVPDPQLPENRRYWLAYLDDLSGAEGLRRGRIEPAQGLYVPLSQHSRHCPPMHQARRGLAEAIYSLAKRNGSDGDPRQALTSDYGSALRAAVRLQPAGVNGSSSGGAAGWRGAEQMIVLVTAAGTEPLRAALERIVEAAPVALVRTMLILVLGLGGVLALVRQAEPSGPSLSAAAAEVAVGRWDAANRAGRGWLARVIAPSSSAMAAESLAAAERLESFPGPDEPLGAPWGAGWDARREKAGAAVIDRQILKLMPRAMSGAKIGYASYVRFMWHLEQVGGGSLRFPPRVEAARDRVAIVSLDWPAGAARVSQLETGLRLADQLLREAERRDGTLNTETRLPDHVVCVGRGATP", "metadata": {"id": "A0A972IHA7", "cluster": 28662368, "interpro_all": ["IPR036465"], "interpro_used": ["IPR036465"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein includes a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. Additionally, the protein is grouped in the Phosphoribosylglycinamide formyltransferase family, which catalyzes the third step in de novo purine biosynthesis by transferring a formyl group from formyl tetrahydrofolate to generate 5'-phosphoribosyl-N-formylglycinamide. While found as a standalone enzyme in prokaryotes, this domain typically occupies the C-terminal region of a multifunctional protein in eukaryotes that also exhibits GAR synthetase and AIR synthetase activities. It is identified in Vampirovibrio sp.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 5921, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3416, 16, 2154, 17097, 1920, 4563, 3537, 1922, 2028, 9441, 19700, 8132, 2007, 21902, 43, 29285, 2210, 2037, 29285, 21196, 27851, 1942, 5655, 25, 11, 17, 3421, 2023, 11731, 17, 56, 17, 29285, 17038, 3665, 5482, 18, 2679, 2435, 1966, 43, 2924, 20807, 2912, 4113, 1922, 28149, 16, 2052, 3418, 5745, 28646, 1920, 45, 17, 4262, 3031, 1927, 43, 20136, 2213, 1922, 15021, 1988, 2222, 9826, 13139, 18185, 1930, 4433, 18185, 4209, 18, 2176, 1977, 2899, 1922, 27324, 10602, 2165, 2377, 3940, 2056, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MSTGDGERKCKLGVLLSGRGSNFQAIHQAIESGQLGKPSAYPSKEEYDTAIVKALKGAEVDLVILAGYTRILGKGMVGGAVHHAVLEAGETQSGCTVHIVTEAVDAQRVLEQEHVLYPNIIGRYIKEQITEQIPFNAEIALVISNKQQAPGLALAQSQGHTTVYLTPVLITAFSKRILNIHPSLLPAYGEGPILGQQTVAVMPKDTPDTL", "metadata": {"id": "A0A952LRH6", "cluster": 9258080, "interpro_all": ["IPR002376", "IPR036477", "IPR004607"], "interpro_used": ["IPR002376", "IPR004607"], "interpro_unused": ["IPR036477"]}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein contains a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. Also, the protein is assigned to the Phosphoribosylglycinamide formyltransferase family, which catalyzes the third step in de novo purine biosynthesis by transferring a formyl group from formyl tetrahydrofolate to generate 5'-phosphoribosyl-N-formylglycinamide. While found as a standalone enzyme in prokaryotes, this domain typically occupies the C-terminal region of a multifunctional protein in eukaryotes that also exhibits GAR synthetase and AIR synthetase activities. It has been detected in Candidatus Zhuqueibacterota bacterium.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 5461, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3416, 16, 2154, 17097, 1920, 4563, 3537, 1922, 2028, 9441, 19700, 8132, 2007, 21902, 43, 29285, 2210, 2037, 29285, 21196, 27851, 1942, 5655, 25, 11, 17, 3421, 2023, 11731, 17, 56, 17, 29285, 17038, 3665, 5482, 18, 2679, 2435, 1966, 43, 2924, 20807, 2912, 4113, 1922, 28149, 16, 2052, 3418, 5745, 28646, 1920, 45, 17, 4262, 3031, 1927, 43, 20136, 2213, 1922, 15021, 1988, 2222, 9826, 13139, 18185, 1930, 4433, 18185, 4209, 18, 2176, 2258, 2252, 3330, 1922, 14550, 1031, 1957, 19533, 5089, 26073, 2341, 6506, 3857, 14061, 18, 3], "output": "MERLKLGVLASGRGSNFAAILRAIEEGRLTAEVFAHWLSPKDYHSPEAYDAAIAQLFDQYEVNFRNRILNIHPALLPSFGGKGMYGIHVHEAVLEYGCKVSGVTVAHRVLEQEHQIYAEAIQLFAEGRIRLEGRRVRIVPRSAGDKILISNREGAGALDVARQHNIVVLAGYLRYITPKFIEKYHIVDEKYDAGPIVLQRCVPVLDDDTPETL", "metadata": {"id": "A0A496U0M8", "cluster": 22140795, "interpro_all": ["IPR002376", "IPR036477", "IPR004607"], "interpro_used": ["IPR002376", "IPR004607"], "interpro_unused": ["IPR036477"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein should contain a Uncharacterised protein family UPF0758 conserved site that is described as a putative JAMM-family deubiquitinating enzyme, although its precise biological function remains to be determined. This domain was previously associated with the radC family. Moreover, the protein should include a RadC-like JAB domain that belongs to the JAB superfamily of metalloproteins and is hypothesized to function as a nuclease. It is widely distributed in bacteria and frequently fused to N-terminal Helix-hairpin-Helix (HhH) domains, helicases, or primases. Additionally, the protein carries a MPN domain that acts as a structural module or a zinc-dependent isopeptidase within multiprotein assemblies such as the 26S proteasome and COP9 signalosome. Catalytic variants containing the JAMM motif coordinate a zinc ion to hydrolyze ubiquitin or ubiquitin-like linkages, while non-catalytic forms lack these coordinating residues and serve scaffolding roles. It originates from Firmicutes bacterium AF36-3BH and features UniProt keywords Hydrolase, Metal-binding, and Metalloprotease.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 23229, 3495, 2213, 3416, 2353, 1038, 14099, 7532, 5305, 3200, 1988, 1977, 2910, 1966, 43, 6770, 16131, 1035, 17, 3416, 29436, 2287, 4113, 16, 2876, 2496, 8162, 3933, 2347, 4497, 1942, 1998, 3180, 18, 2052, 3418, 1982, 3024, 2458, 1956, 1920, 4226, 1030, 3416, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 4226, 1030, 17, 3189, 13149, 1014, 3418, 1988, 14440, 1942, 1920, 13149, 1014, 13975, 1927, 14558, 1036, 1930, 1977, 7149, 1942, 2347, 1966, 43, 16230, 18, 2176, 1977, 5673, 6533, 1922, 4802, 1930, 5467, 10305, 1942, 56, 17, 4262, 7864, 17, 14565, 17, 7864, 12, 9645, 1023, 13, 4682, 16, 29919, 16, 2014, 2610, 2319, 18, 4950, 16, 1920, 2213, 16252, 43, 24255, 3418, 1988, 8016, 1966, 43, 4346, 9059, 2014, 43, 7997, 17, 3100, 10301, 18877, 2651, 20677, 5684, 16137, 2427, 1966, 1920, 27868, 9993, 1930, 3725, 1026, 2733, 4283, 18, 6804, 4936, 3165, 1920, 16131, 1035, 5219, 11865, 43, 7997, 4755, 1942, 7222, 6931, 6526, 2014, 6526, 17, 3189, 19949, 16, 2679, 2447, 17, 6804, 4952, 3630, 2144, 19355, 4248, 1930, 7120, 22582, 5456, 18, 2176, 22970, 2037, 24474, 14061, 2221, 5677, 17, 6341, 1023, 1930, 4075, 20709, 11569, 20748, 16, 6048, 17, 2743, 16, 1930, 28629, 2051, 18, 3], "output": "MDTNNHKGHRKRMRELLYNVIPVADTNDIAHNLIKECGGFVNVFADYICSLGEFIQYYNTEKYNTDFDGKSRECCYMICLDPKNRIINQEMLFEGSFESVVFTHNHPSGILKPSNADLVTTPYLKGSGMNAKINREIKKNNRRDFEKGGFKTWQKHKVLEYHTSKKRLMSIDGVGEKTVFVLNSETSENYLCNLELDVAKVLRSAVKSDASQVQALEHTLFFAGIKMLDHIIVADGKCMSIL", "metadata": {"id": "A0A416CYN4", "cluster": 507608, "interpro_all": ["IPR037518", "IPR025657", "IPR001405", "IPR020891"], "interpro_used": ["IPR020891", "IPR025657", "IPR037518"], "interpro_unused": ["IPR001405"]}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein incorporates 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 contains 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. Moreover, the protein incorporates 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 is expressed in Mucilaginibacter ginsenosidivorans and has UniProt annotations Membrane, Transferase, and Transmembrane helix.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 19683, 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, 5461, 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, 3950, 16, 1920, 2213, 19683, 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, 1977, 3198, 1922, 3422, 19167, 26296, 26073, 2341, 1915, 27601, 27545, 7408, 15525, 17182, 1036, 1930, 2258, 20709, 15010, 3260, 16, 13763, 16, 1930, 9117, 7864, 18, 3], "output": "MAQKRNRSIFNTFGQLSSSLIWMGENKSRPAYILYFKQTIGISSPYLLYFGIVCLSAILSGIGPIPPLDTIELLPKDLVKTIIFLCECSLITLLSSGVIVLTDADNKRIYVSQSIERIIGYTADELPEMIRDMAELKKHPGKNISFVHRIKHKNGDWVWLENEQKKDDFISIASHELKTPVTSLKASLQLLDNVKNDPSSPIVNQRELHLNKTNFRITELMETCCTDIRLSGKRELVLNGNKNIIVWVNNAVKYAPESDTIYLGAEVAGGMAKVSVRDTGPGIEADKMAEIIKKHGGTIGVESESGKGATFWFMLPLYESKNSERYLITLFLVLAATGLKAIFAAFFSAFLADYLFTVAYRQIRQNQLLFKAMIEKGTEGEFIDMPPWALAHPDSITNLLEDEAVKAIVANFYNVSERILMIAKLVTQANRSTEKITSLIEQLLDAGRADEVRIEQVITNLHLFERYYRAGQPAYHNSGLGLGLYISS", "metadata": {"id": "A0A5B8UWU0", "cluster": 1246195, "interpro_all": ["IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR038318", "IPR025201", "IPR052545", "IPR000014", "IPR035965", "IPR013655", "IPR004358"], "interpro_used": ["IPR005467", "IPR013655", "IPR000014"], "interpro_unused": ["IPR003661", "IPR025201", "IPR004358", "IPR038318", "IPR035965", "IPR036890", "IPR036097", "IPR052545"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein should feature a Penicillin-binding protein dimerisation domain that is strongly implicated in the polymerisation of Class B High Molecular Weight Penicillin-Binding Proteins. Located at the N-terminus, this domain adopts a largely disordered \"sugar tongs\" structure. Furthermore, the protein should have a Penicillin-binding protein, transpeptidase domain that catalyzes the cross-linking of peptidoglycan units from lipid intermediates during the final stages of bacterial cell wall biosynthesis. This domain utilizes a conserved active site serine to function as a penicillin-sensitive transpeptidase in biosynthetic enzymes or as an extracellular sensor moiety in regulatory proteins such as BlaR1 and MecR1. Furthermore, it is part of the Class D beta-lactamase/transpeptidase family, which encompasses enzymes involved in bacterial cell wall biosynthesis and antibiotic resistance. Members function as D,D-transpeptidases (penicillin-binding proteins) that catalyze peptidoglycan cross-linking essential for cell integrity and division, or as class D beta-lactamases that hydrolyze beta-lactam antibiotics. It is produced by Intrasporangium oryzae NRRL B-24470 and is linked to UniProt keywords Cell cycle, Cell division, and Membrane.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 3066, 5961, 43, 9957, 17, 2743, 2213, 7632, 6284, 3418, 1988, 1977, 4937, 6835, 1922, 1920, 4593, 6284, 1927, 2921, 44, 2149, 3272, 3388, 9957, 17, 2743, 2697, 18, 4810, 2019, 1920, 56, 17, 7822, 16, 2052, 3418, 24032, 43, 6318, 13885, 6, 9523, 12768, 1036, 6, 3170, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 9957, 17, 2743, 2213, 16, 22796, 18877, 3418, 1988, 17097, 1920, 3567, 17, 9486, 1927, 24183, 5701, 2037, 4486, 12386, 2409, 1920, 3948, 5143, 1927, 4543, 2024, 4821, 8132, 18, 2052, 3418, 18127, 43, 5305, 3500, 3200, 8468, 1942, 2347, 1966, 43, 9957, 17, 4532, 22796, 18877, 1922, 14041, 5038, 2014, 1966, 1925, 5329, 6443, 11804, 1922, 4948, 2697, 2427, 1966, 18208, 7011, 1930, 10685, 7011, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 2921, 46, 4666, 17, 23023, 19, 22796, 18877, 3416, 16, 2154, 21569, 5038, 3286, 1922, 4543, 2024, 4821, 8132, 1930, 7267, 3554, 18, 4678, 2347, 1966, 46, 16, 46, 17, 22796, 18877, 1036, 12, 9957, 17, 2743, 2697, 13, 1988, 18170, 24183, 3567, 17, 9486, 4415, 1958, 2024, 7996, 1930, 8451, 16, 2014, 1966, 2921, 46, 4666, 17, 23023, 1036, 1988, 7222, 6931, 4666, 17, 15294, 7560, 18, 2176, 1977, 4152, 2007, 20362, 21086, 2029, 2457, 27597, 5214, 1005, 1024, 44, 17, 20953, 4618, 1930, 1977, 4624, 1942, 20709, 11569, 2024, 4048, 16, 2024, 8451, 16, 1930, 3260, 18, 3], "output": "MFVAVLFVFTIFAAQLLRIQAFDAAATQAAAMSKRSVKSITPAMRGQAVPAYTVKVDGQPEVVGVSRAAADLAPLLGMDVSELTTLFTRAKTRYVVVKATKTAERIYPTSMALGQIVGFVTPATQKGGGGIELMLDKTLAGSPGTMIAERARDGYDLQWYAQNALAKQVTAVGAESGTAVVIEVATGKIRAAASYPTFDPNDLGKLMTMATALEQKVVTPDTGVIVPSRLPRGGERFKDNEPHGVEDMTATGVIAKSSNMGTERTPVGFPGESRGQLAAASDWTGSRRYTVLFGQGYSVTAIQQAGVFQTIANKGVVVSEDTAVKLSRMMEEVTGENGTASAARIKGYRVAGKTGTADRYDEKLGRYNGFTASFIGYAPGALAGPVFNQVMTYLLERDNTPPSTKSTLDYHVWSKVPLSDSDPKVISDAQARRDGLQILDTNGQVLADSVERYTIAADPKDVNPAVWRQARALGIPGISIIPGSQRVDTPAVNGRDVRLTIDAAHADPKAMGNYAFNDAFEPGSTILIGERVPPPVMDSYYRKFGIGRVPPTLVEGTVNDSGTLVPTPAPTPVRAENPKYVVAVFIQKPSAGMFG", "metadata": {"id": "W9G4R7", "cluster": 7080047, "interpro_all": ["IPR050515", "IPR012338", "IPR005311", "IPR036138", "IPR001460"], "interpro_used": ["IPR005311", "IPR001460", "IPR050515"], "interpro_unused": ["IPR036138", "IPR012338"]}, "task_type": "infilling"} {"instruction": "The protein should feature a Exoribonuclease Xrn1, D2/D3 domain that forms a structural component of the C-terminal extension specific to the cytosolic 5' to 3' exoribonuclease Xrn1. It is suggested to stabilize the N-terminal segment by maintaining the conformation of domain D1, thereby supporting the enzyme's function in the degradation of decapped mRNAs, nonsense-mediated decay, and microRNA decay pathways. Also, the protein belongs to the P-type ATPase, transmembrane domain superfamily, which constitutes the ten-helix membrane-spanning region of P-type (E1-E2) ATPases that utilize ATP hydrolysis to drive the active transport of ions and phospholipids. These transporters alternate between E1 and E2 conformations to pump substrates, including protons, alkali metals, and heavy metals, across bacterial and eukaryotic membranes. It is native to Suillus plorans and carries UniProt keyword assignments 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, 5961, 43, 18930, 3027, 20226, 2626, 2051, 15507, 7301, 16, 8631, 19, 11319, 3418, 1988, 4952, 43, 4346, 4594, 1927, 1920, 45, 17, 4262, 7140, 2487, 1942, 1920, 9410, 25, 11, 1942, 23, 11, 18930, 3027, 20226, 2626, 2051, 15507, 7301, 18, 2176, 1977, 3978, 1942, 13448, 1920, 56, 17, 4262, 5367, 2007, 8231, 1920, 7748, 1927, 3418, 8524, 16, 6113, 6184, 1920, 4113, 11, 61, 2347, 1922, 1920, 4877, 1927, 2344, 6688, 8806, 16, 19605, 17, 3434, 9310, 16, 1930, 14084, 9310, 3873, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 58, 17, 2601, 9444, 16, 9117, 3418, 13975, 16, 2154, 14879, 1920, 5656, 17, 7864, 3260, 17, 13346, 3031, 1927, 58, 17, 2601, 12, 11123, 17, 6602, 13, 28132, 1988, 12561, 4498, 9128, 1942, 9265, 1920, 3500, 4860, 1927, 6982, 1930, 15619, 18, 2144, 10538, 14263, 2192, 11123, 1930, 6602, 12526, 1942, 8912, 6249, 16, 2710, 15948, 16, 25178, 11570, 16, 1930, 7881, 11570, 16, 3436, 4543, 1930, 10825, 5726, 18, 2176, 1977, 6196, 1942, 2020, 8898, 2123, 8846, 3355, 1930, 16252, 20709, 11121, 2538, 18306, 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": "MVLASHHQKNNLGLSIKFELEDWSLFGSLARRQLSSFVNIRTNSQKSSRFWTKEATIWPAIRTSLTHADARVKEVKPWLKLKGVRDLEPVSLFSENLAKVQSDNQESYCEEHPSPRSSETIARYLSTLEPALCFGRQATLIHPQSQVHNQIPRWTSYLILRRHRTVMRNYSIYACTVTIRIVVCFAILAFAFKFDFPPFMVLIIALLNDGTIKTLSADRILPSMTPDSWDSLSVALVTIILETMFFYDKFGVTFNGNPSPSGSNDYQLHMIVYLQVAIISQALTLVTRSHGFFFMERPSVALFGVFCVAQLVSSIIAAYANFGFTQIQAISGGWIGIVWVWNIVWFAPLDWIKFAMKATVIKKLRQHHEAAQAAQAITGVPITCTQSHAASIHES", "metadata": {"id": "A0A9P7DNV4", "cluster": 7254156, "interpro_all": ["IPR023298", "IPR041106"], "interpro_used": ["IPR041106", "IPR023298"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein is classified under the Winged helix DNA-binding domain superfamily, which features a winged helix-turn-helix motif responsible for sequence-specific DNA binding. This domain anchors to the DNA major groove via a recognition helix and interacts with the minor groove or backbone through beta-sheet loops, while frequently facilitating protein-protein interactions via an exposed hydrophobic surface. It has been detected in Limosilactobacillus fermentum (Lactobacillus fermentum).", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 1977, 5947, 2441, 1920, 12920, 1919, 7864, 2678, 17, 2743, 3418, 13975, 16, 2154, 4075, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 5061, 1958, 3244, 17, 2487, 2678, 2743, 18, 2052, 3418, 27127, 1942, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 1930, 9034, 1956, 1920, 5857, 15920, 2014, 10787, 2596, 4666, 17, 11130, 11109, 16, 2679, 5467, 12440, 2213, 17, 2213, 3719, 3454, 1925, 4616, 7919, 3154, 18, 2176, 2258, 2252, 3330, 1922, 2784, 27545, 5148, 2341, 14357, 8898, 17748, 1989, 12, 18134, 17748, 1989, 13, 18, 3], "output": "MAKVKKVRTRGFTQVDNRVVDDPNMSLAGLGLYTYMWRQPDMHELIDLGYVKRERRRDNGQFKGYEYTLFDHPQPNCQNGETVSPNLTNTNLTNDWLNDNKLSSLPEKLGETERQWGMLSTKTKGSLQYKSGLIKYIKKYIESQKAGPEPLKLSASLVKLERRKIDWDYYVTEIAKHFKNGRRSVDSACCFANSENANSRFSTLPITNEGLARQFGPQVVGEGLQAFNENG", "metadata": {"id": "A0A1L7GTL4", "cluster": 7447723, "interpro_all": ["IPR036390"], "interpro_used": ["IPR036390"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein should include 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. In addition, the protein is grouped 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. It is expressed in Candidatus Kaiserbacteria bacterium RIFCSPHIGHO2_02_FULL_55_20.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 3066, 3951, 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, 1922, 2459, 16, 1920, 2213, 1977, 10809, 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, 2176, 1977, 3198, 1922, 14550, 1031, 1957, 30107, 7972, 2341, 18339, 14061, 12424, 2792, 24888, 2509, 5265, 41, 5725, 41, 4125, 41, 4288, 41, 2036, 18, 3], "output": "MTNLPTLAHIVTAATMPHAPSFYRDRYGMRGESALPSIRTWEEVDFFSASSGTGGKPPLFSPRGVVAGYEYRAEWYAMKGPFLSGIHPPHRVQASLRLAAAAGVDGMYVPVFLAAQIAEYLQALGASKRVQYVQEIFPAAAIYASWGMTEVDASPMGIPCRPLAVNEKTVYHLKENIHMDIVNEGELLLTSYPESAAFPLIRYRTGDIGRIVETSCKRHSQPTFTIVGRLRADEVERVLTELNPALERFELHLHQTDTPSGVHYRAVLHVDDGEREGRFEPLQCVPLASSASNQKNRRMITHPIAWHALPRISREDLEARSPLERIFCPLSSFMLQQRERPARVVTLDPNNLHELASEQISNSLIRRLPETLAPLPLKAGSAESDFIKVPGGVAPDTELPALARSVALSLRIGPSFTYA", "metadata": {"id": "A0A1F6DY50", "cluster": 14206332, "interpro_all": ["IPR000873", "IPR042099"], "interpro_used": ["IPR000873", "IPR042099"], "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 can be placed in 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. Also, the protein is included in the Nucleoside triphosphate pyrophosphatase Maf-like protein family, which functions as a \"house-cleaning\" enzyme by hydrolyzing canonical and modified nucleotides, including dTTP, UTP, and 7-methyl-GTP. This pyrophosphatase activity sanitizes the cellular nucleotide pool to prevent the incorporation of noncanonical nucleotides into DNA and is implicated in cell division arrest. It originates from Paracidovorax citrulli (strain AAC00-1) (Acidovorax citrulli) and exhibits UniProt keyword tags Cytoplasm, Hydrolase, and Nucleotide metabolism.", "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, 2112, 1998, 5396, 1922, 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, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 18015, 17978, 20661, 2609, 7234, 16466, 17, 3189, 2213, 3416, 16, 2154, 4088, 1966, 43, 6, 5953, 17, 17833, 6, 4113, 2007, 7222, 9046, 9452, 1930, 4795, 9519, 16, 2710, 11504, 1034, 16, 27412, 16, 1930, 27, 17, 4963, 17, 9319, 18, 2052, 20661, 2609, 7234, 2455, 6867, 2078, 20887, 1920, 3689, 5489, 5562, 1942, 4625, 1920, 8629, 1927, 9341, 9286, 19730, 1923, 9519, 2460, 2678, 1930, 1977, 6835, 1922, 2024, 8451, 8048, 18, 2176, 22970, 2037, 13344, 15072, 15525, 5524, 1039, 22926, 1033, 12, 3943, 19580, 2283, 17, 21, 13, 12, 2687, 2579, 18897, 22926, 1033, 13, 1930, 9826, 20709, 11121, 2538, 14392, 5239, 16, 20748, 16, 1930, 5489, 4714, 18, 3], "output": "MSAPAFPPRPLVLGSTSRYRRELLPGESPRDLALRLAQAKARAVARRHPDAVVIKPGTHERAVAQLQRMRGQTVVFQTAVTVTCAAEIERYLRAEQPYDCAGSAKSEGLGISIRTCRMLRNAGLVLPARLGVPFDVSAPDVDETPQGSDQVADLSGTPLGTGFEATDLAPVEVRFRDLSDELLDAIVSDDPTALVGLPL", "metadata": {"id": "A1TLD3", "cluster": 15417191, "interpro_all": ["IPR029001", "IPR003697"], "interpro_used": ["IPR029001", "IPR003697"], "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 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 Candidatus Binataceae bacterium.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 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, 14550, 1031, 1957, 8768, 26317, 5376, 1021, 14061, 18, 3], "output": "MLYDHGDGTACVLWARTELGYFIRFPELADFLISPAGDRVEYLADGAEVAPETLRHLLIDQVLPTVLSLRGRQAIHATAVMTPSGLCAFTGPSGTGKSTLAAKFLLSGYPTFGDDCLAVEDTGDHIFGAPAYPGLRLWSDSFDSLAGNPISADLDGAKWVSDYSWKYRAFDSESAACFPSDPQPLAIIYRVVRETKADHGACGAPLIEHLSARDGLVELLNASFRLDLVNREILSREFRFFERMALKVPIRRLRMPDDFAALPAVQSAVLNDLATL", "metadata": {"id": "A0A930ZBK2", "cluster": 16055785, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "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 is assigned to the Snake venom C-type lectin-like family, which modulates hemostasis by binding to specific platelet receptors, such as integrins and GPIbalpha, to regulate aggregation and coagulation. These proteins typically function by blocking interactions with agonists like collagen or von Willebrand factor, and may also play roles in cell adhesion, angiogenesis, and immune modulation. Additionally, the protein can be placed in 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. Also, 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 is expressed in Pristionchus entomophagus.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 1977, 6304, 1942, 1920, 24044, 15540, 45, 17, 2601, 13468, 17, 3189, 3416, 16, 2154, 13112, 23963, 2007, 2743, 1942, 2487, 7163, 4086, 16, 2427, 1966, 15563, 1930, 17497, 5949, 4151, 16, 1942, 5741, 7883, 1930, 12441, 18, 2144, 2697, 5745, 2347, 2007, 7472, 3719, 1956, 9849, 3189, 5621, 2014, 14147, 30067, 2991, 16, 1930, 2278, 2222, 3918, 5456, 1922, 2024, 6141, 16, 8244, 16, 1930, 3743, 7145, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 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, 2222, 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, 1977, 3198, 1922, 17618, 2156, 2001, 2072, 1957, 27521, 4965, 1957, 18, 3], "output": "ITSPGFPFNASTPCDYYLMVEEGKKVELEVRLSWNSCCDSLIVYDGYFGGIVMANLTGEVSNTTYTTTTSNIMQVSWVPNGGVNVLGLAVSPKATEATVKRELSPDYSPAPGSVDSPASEPAPATFKQPITPDQNDENREVRLESKDQRLMRNSGNQICRHQRLASEANDTDVIHTFRLRNTKSAGTVGSGPGNARCGNDSHLSHVPLADYRILAGSRHDNSVAESTSTHNQRFLAANALQQPHAFARRKSAETGRPLPILSCSHSLPFNSQIHLVRLLIQQRRITGAV", "metadata": {"id": "A0AAV5TZU7", "cluster": 18700660, "interpro_all": ["IPR000859", "IPR050976", "IPR035914"], "interpro_used": ["IPR050976", "IPR035914", "IPR000859"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein possesses a Type II methyltransferase M.TaqI-like domain that functions as a gamma subtype restriction-modification methylase. It specifically recognizes the double-stranded sequence 5'-TCGA-3' and methylates the adenine residue at the fourth position on both strands to protect the DNA from cleavage by the cognate TaqI endonuclease. 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. It originates from Mesomycoplasma ovipneumoniae.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 2601, 2890, 16478, 55, 18, 11547, 1033, 17, 3189, 3418, 1988, 4088, 1966, 43, 7034, 8856, 7587, 17, 6295, 4963, 2051, 18, 2176, 4475, 16197, 1920, 4825, 17, 10338, 3244, 25, 11, 17, 15931, 17, 23, 11, 1930, 4963, 2209, 1920, 15643, 6181, 2019, 1920, 8776, 3507, 1990, 2321, 13214, 1942, 9145, 1920, 2678, 2037, 6404, 2007, 1920, 15786, 11547, 1033, 18697, 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, 2176, 22970, 2037, 23577, 14930, 2972, 24605, 3368, 24738, 5926, 6114, 1021, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MPKTKPGQKANTLVLIFCPGFEQQAEFNSKQGLTIDPNQGQGDELENNDSIEEKSDKELEKLEGQIKTYYQRILFFSFLTKDKVASLDDILSVPFKRSRLDYKIQNISMLACDESIEPIERAMTSIKKFNRMSESEVITPSKVCDELDIASKSGEYAVALYKRLTSELGYSHENVKDIIYSIPTSSIAYAKVKNDKDEVDYEKISGILKQNKKFSNITLQDEVKAGDKKVLSKQLFPYYTILSMKISSDLSSLIIPARWFTGDAQDKSFLKLREFLKDENTLSDKGGICHFLSSSNHIGDINFVKVLEGEKISTKRNLFLKGLDIVLTDEIQFSVLNTTGRNAFGITGKESIVKTVSSVDIFENACELRCKHNLVRYITEDKVTKNIDIFNIGEPYIGGLKSACTDSLIPIGKFDNLFEAESLQKYLEKSDIDWTKSIVEIDEQLFDKYNLSTEEREHIKKSIKNMDIDEALEEDKKSEQKQDKPIERDENISLSKNLFLDKAIIQKISKSMDMVGLLPEEGLKEIVSNQDKLFTRRFYEILDLNVENIAAMFNAYDLINFAAVIGNPPYQKSIIKEKSNSSLYYYEDTNSIFHHVEIKVRDEEFSSLTEISYKVFISKSAGAPNTDKKVKTKFSRYMISLVKSSQNTTQIVYRFVPMQDFT", "metadata": {"id": "A0AAJ2P5B1", "cluster": 20658400, "interpro_all": ["IPR011639", "IPR029063"], "interpro_used": ["IPR011639", "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 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. Moreover, the protein has 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. Furthermore, the protein has a AMP-binding enzyme, C-terminal domain that functions as a dynamic module in ATP-dependent AMP-binding enzymes, such as Acetyl-coenzyme A synthetase, by undergoing a large rotation to permit both catalytic half-reactions. This structure consists of a central \u03b2-sheet core flanked by \u03b1-helices and is found in eukaryotes, bacteria, and archaea. It is found in Actinomadura sp. WMMB 499.", "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, 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, 3950, 16, 1920, 2213, 2258, 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, 3677, 16, 1920, 2213, 2258, 43, 3681, 17, 2743, 4113, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 5760, 9059, 1922, 4498, 17, 3100, 3681, 17, 2743, 5038, 16, 2427, 1966, 6894, 17, 22051, 43, 18185, 16, 2007, 7258, 43, 3103, 8891, 1942, 11832, 2321, 6804, 4768, 17, 5298, 18, 2052, 3170, 7543, 1927, 43, 4101, 161, 17, 11130, 4728, 20185, 2007, 160, 17, 12789, 1930, 1977, 2435, 1922, 15021, 16, 4802, 16, 1930, 21501, 18, 2176, 1977, 2435, 1922, 4718, 2954, 10015, 5524, 2056, 18, 10177, 17010, 27944, 18, 3], "output": "MRRLVAAPGALAIHDRINRTAVEYPDDRGVALSYRELDLLADGLAARLHEAGVGRGDVVGVCCARSPELIARLRLVLGRARCGVVVTDRPPALRARLPEQRFVRADPDDIAYINFTSGSTGTPKGVPIRHRQLAPISFDAATFEIWGALLNGGTCVLYPSAFLRFSELRKVLEAQRPATLASVGTILTGGEAHSLRHIAAALRHYGPDRIVNAYGTPIQNTRLYLVDGDRLCGAGETGEVWLAGPGGRRERLYRTGDRGRFRPDGAVVFLGRLDDQVKIRHPHVRQSHVVVGATAAGERTLVAFVVPEHEACTAASVREHAALPLSANGKVDRRALLTLHERATGAPVTAPDRPHPNPDETDALFERQAVRTPDATAVVHRERTALLAVLKCGAAYLPFDPDWPDGPADGAAGGAVSGAAPAVSIVRLVHAARYARLDEHARLLVTVVWLTAALFNTIVDEAGPTESTTFATYHPVRALDPDGSPLPIGLSPGYLANPAATRERFVERDINGHRIEPGEVVHHLNLRAELPKYLIPSVIHFC", "metadata": {"id": "A0A5J6U1T7", "cluster": 21217571, "interpro_all": ["IPR010071", "IPR025110", "IPR045851", "IPR020845", "IPR000873"], "interpro_used": ["IPR020845", "IPR010071", "IPR025110"], "interpro_unused": ["IPR045851", "IPR000873"]}, "task_type": "infilling"} {"instruction": "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 identified in Hirschia sp and has UniProt annotations Membrane, Transmembrane, and Transmembrane helix.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 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, 2899, 1922, 15086, 14920, 2126, 2056, 1930, 2258, 20709, 15010, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MSWSISCWGAGPASCPCGASRSLLGLTIKGGLFANAGYPFELATHFRYHLAVASPVLLGLSVVCLNASHVVKMPKNVSVQTRSGQQESDRTARSLSLIWGADIVAIAEAPYDLTLQDWASAFADKPHVWLSPPPLRLEQARMDQLPQSLQPRAWFEAVFRPERGEAGAGGFPGMVKDRNAYIDHVAARVEQLTMSPDVTSFLLAGDWNVTPWAPDFGLPLDHVMVSKGVEPTDYRIGPSIGSDHRPVLAKVTWRAMRLKPVGACLALTGVAGCLLATGLSGPLRMAAIMLVSLLGIVANVDRKREAIAALATLDKAYEHRFPTRIAIASRYPGGLALLFAHPIAPDTRLPGQRIGDARLEASWLNRWPLL", "metadata": {"id": "A0A2E4QVQ6", "cluster": 23091790, "interpro_all": ["IPR036691", "IPR005135"], "interpro_used": ["IPR005135"], "interpro_unused": ["IPR036691"]}, "task_type": "infilling"} {"instruction": "The protein I want to design has this role: The protein falls within the Endonuclease/exonuclease/phosphatase superfamily, which comprises magnesium-dependent enzymes involved in intracellular signaling, DNA repair, and lipid metabolism. Representative members include DNase I, AP endonucleases, and sphingomyelinases, which share a structural core consisting of a beta-sandwich fold and a duplicated alpha+beta motif. It is found in Pisum sativum (Garden pea) (Lathyrus oleraceus). 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, 18697, 19, 24966, 19, 8167, 13975, 16, 2154, 12936, 13148, 17, 3100, 5038, 3286, 1922, 4776, 3197, 16, 2678, 5059, 16, 1930, 4486, 4714, 18, 5051, 4678, 3951, 12861, 51, 16, 2100, 18697, 1036, 16, 1930, 28057, 2319, 16, 2154, 7948, 43, 4346, 4728, 7600, 1927, 43, 4666, 17, 18038, 3728, 1930, 43, 19479, 4595, 15, 4666, 5219, 18, 2176, 1977, 2435, 1922, 17850, 1989, 15036, 1020, 1989, 12, 26981, 20384, 13, 12, 4144, 30338, 3176, 1036, 12188, 5524, 1972, 1957, 13, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MWRASVTLEGNVNFFNTSYPSNHISGSVAEDFDDQLWFFNGIYGFPEEQNKRKTWFLIKELIEKGGDKSHQAIKLCSLADLGFEGYPFTWTNGRREEADIQCHLDMGLASSSFINMFSLMKVFHLARFGSDHTVIRIDLEAPEVEKRNNKIHVFRFEEAWTKNSR", "metadata": {"id": "A0A9D4VI20", "cluster": 23727718, "interpro_all": ["IPR036691"], "interpro_used": ["IPR036691"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein is a member of the EF-hand domain pair superfamily, which functions as a calcium-binding module composed of two adjacent EF-hand units forming a four-helix bundle. This domain coordinates calcium ions in a pentagonal bipyramidal configuration within a twelve-residue loop, serving as a critical regulatory or structural element in diverse proteins such as calmodulin, troponin C, and S100 family members. Also, the protein should have 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. 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. It is present in Phytophthora cactorum. 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, 43, 7210, 1927, 1920, 8485, 17, 3897, 3418, 3715, 13975, 16, 2154, 4088, 1966, 43, 5016, 17, 2743, 9059, 7179, 1927, 2288, 6811, 8485, 17, 3897, 5701, 7402, 43, 3006, 17, 7864, 14142, 18, 2052, 3418, 10675, 5016, 6982, 1922, 43, 9412, 13481, 8446, 3553, 25238, 1923, 9674, 2651, 43, 12367, 17, 6181, 5881, 16, 13915, 1966, 43, 4140, 4948, 2014, 4346, 6149, 1922, 6445, 2697, 2427, 1966, 17537, 16, 18714, 45, 16, 1930, 12678, 3416, 4678, 18, 2222, 16, 1920, 2213, 3066, 2162, 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, 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, 2176, 1977, 2481, 1922, 25512, 2102, 1963, 8846, 9703, 2684, 1989, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MTMTMTTAMAENGEFLTNLTLDGVREGAYMLCKHSDDLLGHHARQVFREKAASMRAENSIYYYLKDLMKEFGSQQHASKIKKTAHGEPQQLVLEAHEFRKLVASDPAFESAIPSDRVDALFHRLECDYQRLLLHRDFVEFCLLDQDQLRLLLFKYRKHLKSLDLTDNEIADTFKRLAPPDGTAMAPELFHAAIMRDLDVVLTTGELTFVMGLMDSDKDGMVKVHDLELLLKDERGAEELIHPPRENGVVGIKISTNSVEEVTLRRDNYIQLLPKLQNESSSSPMHLWFRTAAKEDGKAAISNIKYAASSRDTELVSKGFTCLQQDINRNGAFGKHKYIWTSLVPPSTQMTNEVIDLSLTSGDLSDKHTPRLWIPRHRGFKLVPGNLNEKNPKHGVFLWLRRRRASSTQDLVEPPHIDLTIASPRTRANLHRHIDDLEAQVRKTLRRNCPIDQDCSLNFSRLFEEFDPKKVRTITKQAVLAGIETFGIKLNKKDFQFVWERINPFGAKVIQVGTFGQFLELTDFEIDDVVNALQRTMTTRFGYNVPNYRLIFQSYNTLGDGKLSRSDFQRIFATNQLSFTNSELSKVIQRFDVNKDGIVDYSDFLSYITGICDASARAAGRIADAADEFRLWALEKQNKKLAKDGNIDSASAWRLLKPKHGRLDSETINHILRQRRKRLNAEQIHLLQVLMAPTTNGEVNQAAFHAFVNHVPKKISTMIYELKKLVGSGPVTSDIDEIYNRLNIEANGKLSLVNFAQQLNALAVEKSTRQVDLKDLVYVVQYTGANCGGDGAVLIDRFLAVIRENQDRRNMKSEFVTHYDSPQFLEGVNLLRGELKRCAKTPDGKFDYMVPFRLFDKDNSGQIVLSEFEVAIRELGVDKYLTDQEIKGLMRRFDPNSSGAIDFNEFLRFNLAESSSSSSRRLNISILPDPILQRILEDIIINEQLTTENVGAYCGSIKRMFGIIDKDTTGLVPANRFVETLTEMSIAVPKADMDILVKEFASDDDAGDVQYLRFCEAISQKCQQNVEAQPRLESPPSEILSLLKTLHQQYHQAKQKLEASGHDFDIDRAFGVEKDSAKCIFMSIDDFRDVLWASGVHHPYLREELEAMMNCFQLHQNSGFNVALFKKFLFNGPSAFFAGNSGVLDNHVDRLLGELQAFLSTGKDAGTRLFSLFSELDADVSGFLSHDEFLQLLQRAGFRHFLSSEDEKLLLQFLDTNGDGAISYTEFVTFAKHADEKPKLLVENQSSISALPSPTKSVKGDEAPGSPMLAAQTPASPTQGSSVKDSSTSLQVSSPEKVDERPHAPVLNQMGTLNKLLRPPFPFAKYFSKYRVNQNEARVTVRVFEKVIDKFLDRLVIQRVVYNMKDMDIELLVQAYAVASGDGTKINYEVFLGDITKAQEKAVATGAESDSSSSDSDDELTCSSDEEDRVRMKVSKAVGAALLQTIKHVHKTPAELDALKSLLSTLSKDLAVKKQEAISEKKIYKLLMTLSLRLRNKDVAKLLTCFKTEHYEVVHPDLQFSRSDPADRVTVETASHRLRPNHSEVFKLNFPVIETNLNSKAPGAQLRRIPFRRGEGELRIRHLLNSRVYANALRADSETNSMHGRVNCVP", "metadata": {"id": "A0A8T1CCB6", "cluster": 24575063, "interpro_all": ["IPR011992", "IPR018247", "IPR002048", "IPR052603"], "interpro_used": ["IPR011992", "IPR002048", "IPR018247"], "interpro_unused": ["IPR052603"]}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein has a PGF-CTERM archaeal protein-sorting signal domain that functions as a strictly archaeal C-terminal recognition motif for the archaeosortase enzyme ArtA. This motif facilitates cell surface anchoring via cleavage and lipid modification, such as prenylation, and is typically found in S-layer glycoproteins following a threonine-rich region. Additionally, the protein is a member of 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 is identified in Thermoplasmata archaeon and is annotated with UniProt keywords Membrane and Transmembrane.\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, 2258, 43, 21735, 17, 29486, 23745, 22367, 2213, 17, 11404, 2733, 3418, 1988, 4088, 1966, 43, 14470, 22367, 45, 17, 4262, 5708, 5219, 1958, 1920, 13470, 1951, 2718, 2051, 4113, 6903, 1019, 18, 2052, 5219, 11374, 2024, 3154, 20816, 3454, 6404, 1930, 4486, 6295, 16, 2427, 1966, 9972, 3017, 16, 1930, 1977, 5745, 2435, 1922, 61, 17, 4757, 16268, 2894, 43, 13143, 17, 5536, 3031, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 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, 1977, 2899, 1922, 7967, 15403, 5499, 13470, 1916, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 1930, 9117, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "GTYGLGATVVNGTMEGDGSPGKGSQGYALIRSEAAHDLAVTATPSEVLIGEKTKFDINVYIMNATELQEFHEDYNKLTGMVAATYYIYIRTPDEKHDNLNQEASFDVDKNMTLVFAVEWNGEPLNGTLLIKGVHEVASFVGNITNVTATALGNITFEFKPAADGSIFTDINGEVKVVHPLTGQPCPGLEVSGDFPSGYMVLGKTDAAGEINIVVGLKIVVSSEIQKDKEITITVTVGTTDSNGEIKYKPTEKGNFTITAEKSGYYKATEMVGAILGALGAVLIIRRRRHSYEFTGIKSTEANHNIIVVATFQTPGGDTVYGITRDGEAYGSNLETKVSEGNYTYSGYLDEAGTLATVTVSPSMLVKNVAYENDTYTLAIVNGEAPTIAVEPETVFLAEENLITLLVKNGKVTIGVVPLITGMIKLYVEGDATTRGGKVVEGATVKVGGTKTISISEEEKPSTPGF", "metadata": {"id": "A0A662M362", "cluster": 3861789, "interpro_all": ["IPR013784", "IPR026371"], "interpro_used": ["IPR026371", "IPR013784"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein is included in the Restriction endonuclease, type II, HaeIII family, which functions as a magnesium-dependent component of prokaryotic restriction-modification systems to protect against foreign DNA. These enzymes specifically recognize and catalyze the endonucleolytic cleavage of the double-stranded DNA sequence GG^CC to produce fragments with terminal 5'-phosphates. It is native to Bacteroidales bacterium and is described by UniProt keywords Hydrolase.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 7587, 18697, 16, 2601, 2890, 16, 2118, 14209, 3907, 3416, 16, 2154, 4088, 1966, 43, 13148, 17, 3100, 4594, 1927, 21545, 7587, 17, 6295, 3771, 1942, 9145, 3316, 12400, 2678, 18, 2144, 5038, 4475, 9967, 1930, 18170, 1920, 16239, 1022, 2626, 6586, 6404, 1927, 1920, 4825, 17, 10338, 2678, 3244, 12358, 40, 4928, 1942, 5074, 6535, 1956, 4262, 25, 11, 17, 26473, 18, 2176, 1977, 6196, 1942, 24323, 3955, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 20748, 18, 3], "output": "MPQGDQVKNGKAFEYALASVYADKLREAGVNVTLVNNNALIVANGYFDDFAAEEQERYKEAAFQTLDTMSRLEPGLMAQKGDSDMLYICLNEDGEGKDGDVRDVVFSRNAPSWEIGFSAKNNNDAVKHSRLSSVLDFGESWVGVPCSDDYWNEIEPIFIFLETAKKRLLTWNDLGEKKVSQVYIPMLKAFRKELLKINENNDEIPQKLIRYLVGKYPFYKIIKDDVHNMVIVKAFNIEGELNKTVNGIKPQYKTPKINLPTRIVEFEMKPNSDNTLNMILDGGWEISFRIHNASTHVEQSLKFDIKLLGNPPVLFTQHLFQNPT", "metadata": {"id": "A0A971FUV5", "cluster": 5935458, "interpro_all": ["IPR019059"], "interpro_used": ["IPR019059"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has the following function: The protein possesses a X8 domain that is predicted to function in carbohydrate binding. This domain is characterized by six conserved cysteine residues that likely form three disulfide bridges and is commonly associated with the C-terminus of family 17 glycosyl hydrolases and olive pollen allergens. Also, the protein can be placed in the The plant carbohydrate-binding X8 domain-containing protein family, which utilizes a non-catalytic module to preferentially bind 1,3-beta-glucans and facilitate cell wall remodeling. These proteins are involved in diverse physiological processes, including pollen tube wall re-formation during germination and the regulation of plasmodesmata-mediated cell-to-cell trafficking. It is expressed in Zizania palustris (Northern wild rice) and is linked to UniProt keywords GPI-anchor, Signal, and Glycoprotein. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 66, 1025, 3418, 1988, 1977, 4396, 1942, 2347, 1922, 10590, 2743, 18, 2052, 3418, 1977, 4378, 2007, 3798, 5305, 8666, 4248, 1988, 3205, 2386, 2559, 11830, 18142, 1930, 1977, 5384, 2458, 1956, 1920, 45, 17, 7822, 1927, 3416, 2752, 20067, 30337, 1930, 17546, 12206, 19226, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 1920, 4496, 10590, 17, 2743, 66, 1025, 3418, 17, 3165, 2213, 3416, 16, 2154, 18127, 43, 2447, 17, 6804, 9059, 1942, 10662, 4566, 21, 16, 23, 17, 4666, 17, 18798, 1036, 1930, 6628, 2024, 4821, 8378, 18, 2144, 2697, 2032, 3286, 1922, 6445, 5005, 4028, 16, 2710, 12206, 6723, 4821, 1964, 17, 3337, 2409, 14609, 1930, 1920, 3640, 1927, 3018, 7019, 3368, 3857, 17, 3434, 2024, 17, 1942, 17, 2024, 9604, 18, 2176, 1977, 3198, 1922, 28666, 12813, 10306, 5755, 3894, 1937, 12, 9250, 3576, 8674, 13, 1930, 1977, 4624, 1942, 20709, 11569, 17497, 17, 13333, 16, 2733, 16, 1930, 11424, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MARKNRGDRVAVLLPLMLMMMAFLLLDGISQCEARALSQGKKNTLLDALYKLNFIRTVEPMQLPPPASPARDGDAGSLAAADAGDASSSPFCVNPPNAPSTSTSTPPFTSTPSTPFAPDDQPPPLPPLPPVGASAPPSFEPSPPDSTPILGPPAGSTPGFAPSTPGSAPPSPIFVVPSPPETGPGGGAGGGGEGGGTGGGSGGGGGGGGGGGGGGGGGGGFLPPIVYPPPLAPPLPPGAGQPLWCVAKPTVPDPIIQEAMDYACGSGAACRSILPSGACYQPDTVLAHASFAFNSYWQMTKATGGTCDFGGTATIVTRDPSYEKCQFDLL", "metadata": {"id": "A0A8J5T226", "cluster": 8445623, "interpro_all": ["IPR012946", "IPR044788"], "interpro_used": ["IPR012946", "IPR044788"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein possesses a TLDc domain that confers protection against oxidative stress by influencing the expression of oxygen free-radical scavengers. This highly conserved eukaryotic domain is sufficient to reduce cellular levels of reactive oxygen species (ROS) and provide oxidative resistance. It is derived from Rhizophagus sp. MUCL 43196.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 14465, 43, 10474, 11385, 3418, 1988, 16556, 6202, 3316, 5163, 3071, 2007, 11623, 1920, 2294, 1927, 4612, 3294, 17, 6917, 21433, 1036, 18, 2052, 3626, 5305, 10825, 3418, 1977, 5409, 1942, 4412, 3689, 2428, 1927, 6079, 4612, 3038, 12, 4742, 13, 1930, 3394, 5163, 3554, 18, 2176, 1977, 3595, 2037, 13458, 4965, 1957, 2056, 18, 3422, 1024, 29672, 10352, 18, 3], "output": "MSLIVFKWIDRVTNDRESHYSYKFNLTVTFIKIKGKEEILDGYNPLHIKNIISKIKDKNYEVFNKCEHGPQFGGDIVEGEFSMEDYEVFQIVKKVVVNEREPNSNIFSTILKWIDKVILRGSRDGFTPEKFHELCVGKHNKWESTNSYGKIADRNKMSSSNESIDYEKISYQQDDYEKKLRDS", "metadata": {"id": "A0A372QJA2", "cluster": 9725596, "interpro_all": ["IPR006571"], "interpro_used": ["IPR006571"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is categorized in the Protein of unknown function DUF2933 family, which comprises bacterial proteins of currently uncharacterized function. It is present in Enterococcus dispar ATCC 51266.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 6680, 11436, 1010, 3416, 16, 2154, 12936, 4543, 2697, 1927, 5077, 24528, 2347, 18, 2176, 1977, 2481, 1922, 25390, 9827, 11037, 20094, 7283, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MQWLLLLLCPIMMIFSSELSDLKSKLKMMKGMHSVAKSDNDDPMMKKELENLKAQNEIL", "metadata": {"id": "S1N882", "cluster": 12476327, "interpro_all": ["IPR021682"], "interpro_used": ["IPR021682"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein is assigned to the Enoyl-CoA hydratase, C-terminal superfamily, which represents the alpha-helical C-terminal domain found in enoyl-CoA hydratases and related enzymes. This domain serves a structural role, likely facilitating the trimerisation of the protein complex. Furthermore, the protein contains a Enoyl-CoA hydratase/isomerase conserved site that stabilizes an enolate anion intermediate derived from an acyl-CoA substrate via a characteristic oxyanion hole. Found in the crotonase superfamily, this domain supports diverse catalytic activities, including hydration, isomerization, and dehalogenation, typically within a conserved trimeric structural core. Furthermore, the protein is grouped in the ClpP/crotonase-like domain superfamily, which comprises a diverse group of enzymes sharing a repeated \u03b2/\u03b2/\u03b1 structural unit, including Clp and tail-specific proteases involved in protein degradation, as well as crotonases and biotin-dependent carboxyltransferases. It has been characterized in Mycolicibacterium goodii (Mycobacterium goodii) and exhibits UniProt keyword tags Fatty acid metabolism and Lipid metabolism.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 2066, 10921, 17, 10027, 22420, 3857, 4127, 16, 45, 17, 4262, 13975, 16, 2154, 4972, 1920, 4595, 17, 11514, 45, 17, 4262, 3418, 2435, 1922, 2066, 10921, 17, 10027, 22420, 3857, 4127, 1036, 1930, 2712, 5038, 18, 2052, 3418, 10634, 43, 4346, 2770, 16, 3205, 12440, 1920, 20085, 6284, 1927, 1920, 2213, 2796, 18, 3677, 16, 1920, 2213, 5461, 43, 2066, 10921, 17, 10027, 22420, 3857, 4127, 19, 25510, 5305, 3200, 1988, 19658, 1925, 2066, 8649, 10985, 6129, 3595, 2037, 1925, 11337, 17, 10027, 4510, 3454, 43, 6293, 20004, 8150, 1916, 13356, 18, 2435, 1922, 1920, 9442, 5405, 2051, 13975, 16, 2052, 3418, 7825, 6445, 6804, 4209, 16, 2710, 16561, 16, 27027, 16, 1930, 2028, 7289, 2404, 1943, 16, 5745, 2651, 43, 5305, 29177, 4346, 4728, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 18017, 1034, 19, 9442, 5405, 2051, 17, 3189, 3418, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 5038, 10763, 43, 5116, 161, 19, 161, 19, 160, 4346, 5344, 16, 2710, 18017, 1930, 5281, 17, 2487, 12447, 3286, 1922, 2213, 4877, 16, 1966, 2486, 1966, 9442, 5405, 2319, 1930, 8622, 17, 3100, 9943, 18580, 18, 2176, 2258, 2252, 4378, 1922, 5078, 4485, 26073, 2341, 18842, 1989, 4227, 3907, 12, 16389, 4227, 3907, 13, 1930, 9826, 20709, 11121, 2538, 14392, 5934, 2687, 4714, 1930, 4486, 4714, 18, 3], "output": "MTRQEETTVAQTPALTISEPDQDGILLVIWSEFDDRDDVRVIVVTGEGSAFSAGGDLAFRGIVRGLLDCRKPVVSALEGVAVGAGNAVALMAAFLWPLAMGIQRARGKLLLGEALTGAEAAELAMELAAKIARFDPFAVQATKVSVNGILRQTRAALAAAAPARPSAGDPKLPKNGNRGHEQFTISRPDKLNALREVDHDRLATVQGLTTDDRTRANAWWAADICVAAEDAKIIDGHLAFGASPGDHAGLVYEAVPGGKTLDRHWQTFEASLALEFMCFVNES", "metadata": {"id": "A0A0K0X3R0", "cluster": 12711617, "interpro_all": ["IPR029045", "IPR018376", "IPR001753", "IPR014748"], "interpro_used": ["IPR014748", "IPR018376", "IPR029045"], "interpro_unused": ["IPR001753"]}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: The protein carries 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 is found in Ekhidna sp.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 16252, 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, 1977, 2435, 1922, 20529, 7969, 5806, 2056, 18, 3], "output": "MHKTGSGEGVKPVPAPESAEQLHDRLPFQHFTGLDFPIRSLTAMEASTSSVLRVLLKAKMLFIQYLHNLSKFLLLPRYGTSGSGGWSFVE", "metadata": {"id": "A0A9D5JHQ4", "cluster": 13310060, "interpro_all": ["IPR008490"], "interpro_used": ["IPR008490"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein should have a SnoaL-like domain that functions as a polyketide cyclase, typically involved in catalyzing ring closure steps during polyketide biosynthesis. This domain is structurally characterized by a distorted \u03b1-\u03b2 barrel fold. Furthermore, it is part of the NTF2-like domain superfamily, which constitutes a versatile structural fold characterized by a \u03b2-\u03b1(2)-\u03b2 insertion. This domain scaffolds diverse functional roles, ranging from facilitating nuclear protein transport in NTF2 to supporting enzymatic activity in dioxygenases and structural roles in type IV secretion systems. It occurs in Verrucomicrobiales bacterium and has UniProt annotations Signal.", "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, 3437, 20827, 17, 3189, 3418, 1988, 4088, 1966, 43, 4286, 18540, 2261, 16526, 16, 5745, 3286, 1922, 29601, 6335, 10408, 5983, 2409, 4286, 18540, 2261, 8132, 18, 2052, 3418, 1977, 12171, 4378, 2007, 43, 22797, 160, 17, 161, 19560, 3728, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 5891, 6680, 17, 3189, 3418, 13975, 16, 2154, 14879, 43, 20425, 4346, 3728, 4378, 2007, 43, 161, 17, 160, 12, 22, 13, 17, 161, 7413, 18, 2052, 3418, 10603, 6445, 3183, 5456, 16, 6485, 2037, 12440, 4254, 2213, 4860, 1922, 5891, 6680, 1942, 6184, 8145, 2455, 1922, 23652, 10465, 2432, 2319, 1930, 4346, 5456, 1922, 2601, 4370, 5512, 3771, 18, 2176, 5110, 1922, 3566, 3176, 13055, 1935, 7839, 1918, 14061, 1930, 2258, 20709, 15010, 2733, 18, 3], "output": "MRFLIFVLFSSSALCGAGAAENSISVSDRIEIQDLISRYSHTWDSKDPKGWSDLFVKGGVWTNYFAGKKNKSLGSGDEILAFAEELQGSFRDRGIVTRHHQTNTLLKKKEDGSIEGETVFSVIWQHHDDPLPKLMHSGVYRDVYVKTDEGWKFRVREVRFDHQLFEDEKEPVPDFTLLKERTQAEHRKLGGRTPYFAHYKKGRMELVFIAARHEPKTGSPTHRLIESVMEGFDPECVITEGLYTDEGYSPPPLLRDARRRKVSGNLPEPLYAALLADEKEIPFIGGEPSPSVTTEVLRTVTDDDTDILGYLVVRHLGQVRREQPRAELDNRVKRLLPRMIEQFELETAMNLDQFKSWYEKTTGNPFIAANLDPDDVAPLAVEDPALLKRMGITVMLAREKHLISLEARLLAEHRRVLVIYGSGHLVYE", "metadata": {"id": "A0A800JP34", "cluster": 13638337, "interpro_all": ["IPR032710", "IPR037401"], "interpro_used": ["IPR037401", "IPR032710"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein is classified under 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. Additionally, 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. Moreover, the protein carries a Redoxin domain that functions as the catalytic core of peroxiredoxin, thioredoxin, and glutaredoxin systems to facilitate antioxidant defense and redox regulation. It utilizes a strictly conserved cysteine residue to reduce substrates such as hydrogen peroxide, peroxinitrite, and hydroperoxides. Additionally, this domain modulates the activity of various proteins, including those involved in photosynthetic carbon assimilation and cadmium sensitivity, via thiol redox mechanisms. It is present in Puniceicoccaceae 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, 1977, 5947, 2441, 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, 4950, 16, 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, 3950, 16, 1920, 2213, 16252, 43, 9366, 1921, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 11456, 3030, 9754, 16, 23684, 16, 1930, 19406, 1919, 9754, 3771, 1942, 6628, 7335, 9720, 1930, 9366, 3640, 18, 2176, 18127, 43, 14470, 5305, 8666, 6181, 1942, 4412, 6249, 2427, 1966, 6201, 12316, 16, 11456, 11566, 1997, 2394, 16, 1930, 25461, 29508, 18, 4950, 16, 2052, 3418, 13112, 1920, 2455, 1927, 3425, 2697, 16, 2710, 2690, 3286, 1922, 16068, 5056, 22317, 1930, 17203, 3802, 16, 3454, 13914, 9366, 3531, 18, 2176, 1977, 2481, 1922, 15809, 2927, 5670, 2437, 9914, 14061, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "MHRKPILITAAAAFLGLGLHAEEIRLSLTPEHTEWIEGGHFWGNMRFYNTDLALSTERPAHIHTEPAYDGKVHYGQITLGDAEDASFTFALVTPDAVSGDFQLFLDSKRDGNLANEGDGKFAMVRRMERDGIQAARLSTVVKSEARYADGSKQPYQLLFFGLLNQGELTFGYRRATSMTGSLELDGTTYKVWLVDNDNDAVFNKALDDDNNPVGGGEAGDPLWLITEVDGDQRTVRDARRAFTIGERRLVAEIAPNGTSLVLKPTTRPIPAIRMTAGGAPPAGERPPRPPLLEAGVEAPDFVAVTADGRELRLSDFRGQVVVIDFWATWCGPCLRALPKVDEVARTHTEGVTVLALNVWDNRAAFDRFIETRGDDFAVLFAHDPAGRGAETDIPRTLYNVSGIPTMYVIDADGKVVEGMVGAGGADRLDELIRQALAARS", "metadata": {"id": "A0A651H445", "cluster": 15168766, "interpro_all": ["IPR013740", "IPR036249", "IPR013766", "IPR050553"], "interpro_used": ["IPR050553", "IPR013766", "IPR013740"], "interpro_unused": ["IPR036249"]}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein is associated with the HTH-type Transcriptional Regulator family, which encompasses helix-turn-helix proteins that act as DNA-binding repressors or activators of gene transcription. These regulators modulate diverse processes such as biofilm production, fatty acid metabolism, and antibiotic resistance, often in response to specific environmental signals like fatty acids or cationic lipophilic compounds. Moreover, the protein is a member of 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 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. It is expressed in Sulfuricurvum sp. PD_MW2 and features UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "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, 5334, 1023, 17, 2601, 5224, 7888, 3416, 16, 2154, 21569, 7864, 17, 5165, 17, 7864, 2697, 1988, 4033, 1966, 2678, 17, 2743, 26446, 2014, 15497, 1927, 2359, 3213, 18, 2144, 9098, 8480, 6445, 4028, 2427, 1966, 9638, 3372, 16, 5934, 2687, 4714, 16, 1930, 7267, 3554, 16, 3868, 1922, 2644, 1942, 2487, 4813, 4771, 3189, 5934, 4576, 2014, 15175, 21140, 4300, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 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, 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, 2176, 1977, 3198, 1922, 12585, 1935, 28031, 1989, 2056, 18, 3203, 41, 8825, 1028, 1930, 4075, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTKALELFSKEGFFKSKEILAKDLILYIANILGEEIAKERPETIEYFLRVYLSNREVFQNCCEEGVRSGELKDQDFFSAFGLSLETYEHTIAENIYNALKARYQTTMPTIAEKIGMSVGNLYNYIRKINESPISTQEKIEAIVHMYFRTGMICVSAFVTELMIFFFMGYLGGMVFLNGEQILPK", "metadata": {"id": "A0A2D0I8B1", "cluster": 16165607, "interpro_all": ["IPR009057", "IPR050624", "IPR001647"], "interpro_used": ["IPR050624", "IPR009057", "IPR001647"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that can perform the following function: The protein contains a Allantoicase domain that catalyzes the hydrolysis of allantoate into (S)-ureidoglycolate and urea, facilitating purine degradation for nitrogen utilization. It folds into two repeats with jelly-roll motifs composed of antiparallel beta-sheets, serving as a key enzyme in amphibians and microorganisms but appearing non-functional in mammals. In addition, the protein falls within the Galactose-binding-like domain superfamily, which functions as a versatile ligand-binding module characterized by a $\\beta$-sandwich structure with a jelly roll fold. Found in both eukaryotes and prokaryotes, this domain interacts with diverse targets ranging from cell-surface carbohydrates and phospholipids to membrane-anchored proteins and DNA complexes. It occurs in Mucor circinelloides f. circinelloides (strain 1006PhL) (Mucormycosis agent) (Calyptromyces circinelloides).", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 2136, 26182, 6102, 4127, 3418, 1988, 17097, 1920, 9128, 1927, 2136, 26182, 2010, 2460, 12, 61, 13, 17, 6794, 15072, 17038, 4879, 5148, 2057, 1930, 10505, 16, 12440, 19700, 4877, 1958, 6634, 8422, 18, 2176, 16231, 2460, 2288, 9569, 1956, 8988, 11560, 1012, 17, 12970, 8277, 7179, 1927, 28892, 4666, 17, 14685, 16, 13915, 1966, 43, 3834, 4113, 1922, 22539, 9813, 1930, 11679, 2308, 16905, 2447, 17, 3183, 1922, 9902, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 15996, 17, 2743, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 5207, 17, 2743, 9059, 4378, 2007, 43, 8, 38, 4666, 8, 17, 18038, 3170, 1956, 43, 8988, 11560, 1012, 12970, 3728, 18, 2435, 1922, 2321, 15021, 1930, 28149, 16, 2052, 3418, 9034, 1956, 6445, 4845, 6485, 2037, 2024, 17, 3154, 16282, 1930, 15619, 1942, 3260, 17, 17199, 2697, 1930, 2678, 5048, 18, 2176, 5110, 1922, 3422, 1924, 3624, 2053, 11560, 12363, 48, 18, 3624, 2053, 11560, 12363, 12, 3943, 2813, 1016, 2102, 1024, 13, 12, 3422, 2076, 2773, 2475, 5899, 13, 12, 2570, 16314, 2018, 11535, 3624, 2053, 11560, 12363, 13, 18, 3], "output": "MGNTISSQKHKQLKAKDIKETGFETYTEVSSCHLGGSIELVTDESCGNASNLLKVEKVDRQLNLDDLNEATDGWLTKRHESVGSATITLCNESKIAGLDIDTTGYTDCCPSFANVEGYQTSNMTWQVILPESRINADSHNFYEIKDPNVYSSVRLNIAPGGGIARFRVYGEISPDWSDKSKEYNLASAKLGARIVRWTDQRNANSPNILLDNGTKMSDGWLTPRSKLEKERNDFILLQLATAGTLESIIIDTTGFDKNSPANVFIQGCYSEDVDPHYDTFASWVCLVPQSPVLPGEETTFYFDSVKDPISHIRMHLIPDGGIQQIKVMGKPAEKGTKQQLLIEQAPEVIVIEDTEEDEIMASVLDELHNKSAIEQLNVVHQPPSPPTPRMRIPRATRERNYIYKR", "metadata": {"id": "S2K2B2", "cluster": 17394195, "interpro_all": ["IPR005164", "IPR015908", "IPR008979"], "interpro_used": ["IPR015908", "IPR008979"], "interpro_unused": ["IPR005164"]}, "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 Retrovirus-related Pol polyprotein family, which mediates the replication and integration of retroviral and retrotransposon genetic material into host genomes. This polyprotein encodes multiple enzymatic activities, including a reverse transcriptase for DNA synthesis, an RNase H for RNA degradation, and an integrase for genomic insertion. It also functions as an aspartyl protease that processes Gag and Pol precursors into mature, functional units. Moreover, the protein is included in the Ribonuclease H superfamily, which comprises the catalytic domains of diverse polynucleotidyl transferases characterized by a conserved 3-layer $\\alpha/\\beta/\\alpha$ fold. This superfamily includes enzymes such as RNase H, retroviral integrases, transposases, and exonucleases that utilize this domain to catalyze nucleic acid backbone cleavage or transfer during DNA replication, repair, and recombination. Furthermore, the protein incorporates 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 is found in Austropuccinia psidii MF-1 and features UniProt keywords Transposable element.", "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, 23987, 17, 2712, 2492, 6240, 5684, 3416, 16, 2154, 10412, 1920, 5158, 1930, 7122, 1927, 16599, 1930, 27181, 1916, 3299, 3485, 2460, 4423, 7313, 18, 2052, 6240, 5684, 9937, 3137, 8145, 4209, 16, 2710, 43, 5267, 13335, 1958, 2678, 4271, 16, 1925, 9843, 50, 1958, 3146, 4877, 16, 1930, 1925, 27252, 1958, 4935, 7413, 18, 2176, 2222, 4088, 1966, 1925, 12053, 2199, 7154, 1988, 4028, 9819, 1930, 2492, 10416, 2460, 6665, 16, 3183, 5701, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 18347, 2051, 50, 13975, 16, 2154, 12936, 1920, 6804, 4682, 1927, 6445, 15176, 2626, 4090, 2199, 13763, 1036, 4378, 2007, 43, 5305, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 18, 2052, 13975, 5921, 5038, 2427, 1966, 9843, 50, 16, 16599, 27252, 1036, 16, 12935, 2319, 16, 1930, 24966, 1036, 1988, 12561, 2052, 3418, 1942, 18170, 11079, 2687, 10787, 6404, 2014, 3856, 2409, 2678, 5158, 16, 5059, 16, 1930, 7827, 18, 3677, 16, 1920, 2213, 19683, 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, 1977, 2435, 1922, 7162, 2011, 27186, 2126, 14748, 7408, 1033, 8168, 17, 21, 1930, 4075, 20709, 11569, 12935, 2115, 6149, 18, 3], "output": "MDWVTVLVPGDKENINSFKFIVDRYRRSFRCLPFHKEDTAMDRSQKFTLEFYTNPYYMLGTQFLFYTAYHPQTDGLAERMIQRMDDIIIKDDRENSVEVRLIGEFPRKHLLFPVSLVKPFHNEREDKLPSRRKSHDGKGNRQYLVRSKCRTADKDRWLAEDAIPYGGFDLRRFRSTRRAGTELLFWNNIIFKYGVTKAIISRIFCAYGMEYKDYCQDDTMTQQDKVEVDDSLCPVKKLRL", "metadata": {"id": "A0A9Q3C0N4", "cluster": 18443975, "interpro_all": ["IPR001584", "IPR050951", "IPR012337", "IPR036397"], "interpro_used": ["IPR050951", "IPR036397", "IPR001584"], "interpro_unused": ["IPR012337"]}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein is a member of the Transcriptional Repressor and Histone Methyltransferase family, which acts as a transcriptional regulator and modifies chromatin structure through histone H3 lysine methylation. Members are involved in diverse biological processes, ranging from neural development and oligodendrocyte differentiation to steroidogenesis and spermatid maturation. Also, the protein can be placed 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. Furthermore, 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. It is derived from Petrolisthes manimaculis and is classified with UniProt keywords Membrane, Transmembrane, and Nucleus.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 5224, 14434, 1930, 6632, 16478, 3416, 16, 2154, 8016, 1966, 43, 5224, 7888, 1930, 25436, 6338, 3170, 2596, 6632, 8170, 9082, 5547, 18, 4678, 2032, 3286, 1922, 6445, 3933, 4028, 16, 6485, 2037, 5181, 2740, 1930, 22462, 4155, 1942, 9507, 3761, 1930, 10896, 1960, 7655, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 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, 3677, 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, 2176, 1977, 3595, 2037, 16901, 23747, 20536, 1036, 2323, 12874, 18021, 12191, 1036, 1930, 1977, 5947, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 5607, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MSQRNSVITTHTLIDNLYAFLLCVRGLYFITVTSSTKRSFDVAFLTGAHDTLQSDVPSPAAKSPGVPPSPPRDDPTPGSAFTKVTRSQGAPHASASISSLLGGNKSLAPLLAAPCLLPPGLAPFLPHAIPDRLNNNLVSASEALSRLRSSMYPTDPYKLPFSSLAYPFTPPSQSEALMPPTYSTMAQSAQNVCAKCNISFRMTSDNERLKCTICGETFRERHHLTRHMSAHQDRDGDGDGKTAFNGVMIMAALRGVGGASSPHVSRVGGLKVSPPSVVRSPPCFSAANTLDVLTSSWPEEYLKSQHTLLESKHISDMVSKLGAAAPFLPPPSVSLVYHMRSQHKREADPYKKRR", "metadata": {"id": "A0AAE1NM10", "cluster": 19420345, "interpro_all": ["IPR052296", "IPR036236", "IPR013087"], "interpro_used": ["IPR052296", "IPR036236", "IPR013087"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein according to these design specifications: The protein possesses a YjiS-like domain that forms an arginine-rich region found in proteobacteria, often acting as an inner membrane-associated regulator. It is implicated in diverse functions ranging from the suppression of flagella production and nutrient acquisition to RNA binding roles in oxidative stress defense and photosynthetic complex formation. It is produced by Methylobrevis pamukkalensis.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 14465, 43, 67, 11801, 1036, 17, 3189, 3418, 1988, 4952, 1925, 9732, 17, 5536, 3031, 2435, 1922, 22266, 16, 3868, 8290, 1966, 1925, 6671, 3260, 17, 2458, 7888, 18, 2176, 1977, 6835, 1922, 6445, 4088, 6485, 2037, 1920, 6412, 1927, 26538, 3372, 1930, 8708, 6165, 1942, 3146, 2743, 5456, 1922, 5163, 3071, 9720, 1930, 16068, 2796, 3337, 18, 2176, 1977, 4152, 2007, 4963, 2389, 1936, 7400, 11888, 3711, 7640, 15253, 8362, 18, 3], "output": "MSVTTSSSPSASGSVTALLSLTGRVVAGLRSAYLAWEDRRAVARLQAFDDAMLADIGLTRGDVYGALSLAVTERPSGHLASLAAERRAGSRAQAREIRAALRSDDATVTVDGQVLPKVPLAEQLRHLDRA", "metadata": {"id": "A0A1E3H867", "cluster": 25186420, "interpro_all": ["IPR009506"], "interpro_used": ["IPR009506"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein carries a RNA methyltransferase TrmA active site that catalyzes the S-adenosylmethionine-dependent methylation of uracil residues, such as U54 in tRNA or specific sites in 23S rRNA. This conserved region features a catalytic cysteine that facilitates the reaction by forming a covalent adduct with the C6 position of the target uracil. In addition, 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. Also, the protein is grouped in the (Uracil-5)-methyltransferase family, which catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to the 5-position of uracil residues. Found in bacteria, archaea, and eukaryotes, these Class I methyltransferases adopt a Rossmann-like fold containing a conserved SAM-binding site. It is found in Alphaproteobacteria bacterium and is connected to UniProt keyword 4Fe-4S, Iron-sulfur, and Iron. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 16252, 43, 3146, 16478, 28402, 1019, 3500, 3200, 1988, 17097, 1920, 61, 17, 29283, 23568, 11215, 17, 3100, 5547, 1927, 22761, 4248, 16, 2427, 1966, 63, 5651, 1922, 10089, 2014, 2487, 3402, 1922, 3020, 1036, 9067, 18, 2052, 5305, 3031, 4075, 43, 6804, 8666, 1988, 11374, 1920, 3227, 2007, 7402, 43, 13577, 18533, 1956, 1920, 12822, 3507, 1927, 1920, 2758, 22761, 18, 1922, 2459, 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, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 12, 22761, 17, 25, 13, 17, 16478, 3416, 16, 2154, 17097, 1920, 3856, 1927, 43, 4963, 2210, 2037, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 1942, 1920, 25, 17, 3507, 1927, 22761, 4248, 18, 2435, 1922, 4802, 16, 21501, 16, 1930, 15021, 16, 2144, 2921, 51, 28253, 14103, 43, 18215, 8890, 17, 3189, 3728, 3165, 43, 5305, 2235, 17, 2743, 3200, 18, 2176, 1977, 2435, 1922, 4595, 9218, 1021, 10296, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 15338, 1021, 17, 26814, 16, 5680, 17, 12585, 16, 1930, 5680, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MQRKRRDRARSPRHNEPVSRVDEIVLIERIGHQGDGIGQTDDGSVFVPFTVPGDRIRISRAGNRGVVREIIEPGPDRQTPLCPHFGACGGCGLQHVTGSAYVHWKRQKVRDALAHQGLGDVPIAALIESSPHTRRRTRVTAVRQGRTFRIGYNRRASHQVFALESCPVVEPEIETLFGRLKPLIECLGAGVGRLLISLTNTDTGMDILVTCDPSDDRDLSWQQRAQVSAWAEQVDAARLTFGQEVLIERRAPVVRFSGVNVCPPPGAFLQASCDMERALVDLLRHGVADARSVGDLFAGCGTLTFALAHRARIWAVEGNAAMVGALKSAASRAQGLKSVTTEHRDLFQQPLLAAELDRFDAVVFDPPRAGAAAQAAELAKSSVPRVVGVSCHPASFARDARILCDAGFRLDRVTPIDQFLWSAQIELVGVFSRP", "metadata": {"id": "A0A523FVQ5", "cluster": 25814889, "interpro_all": ["IPR030390", "IPR012340", "IPR029063", "IPR002792", "IPR010280"], "interpro_used": ["IPR030390", "IPR002792", "IPR010280"], "interpro_unused": ["IPR012340", "IPR029063"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that will have the following function: The protein is categorized in the Bacterial Sigma Factor Regulator family, which regulates gene transcription during stress response and sporulation by controlling sigma factor activity. Members typically employ phosphatase and kinase activities to modulate signal transduction pathways, often utilizing PAS domains to sense cellular energy levels or environmental stimuli. In addition, the protein can be placed in the PPM-type phosphatase-like domain superfamily, which catalyzes the Mg2+- or Mn2+-dependent dephosphorylation of phosphoserine and phosphothreonine residues. This domain features a core structure of two beta-sandwich subdomains flanked by alpha-helices and functions as a regulatory module in diverse signaling pathways across prokaryotes and eukaryotes, including stress response and sporulation. It occurs in Bacteroidota bacterium and exhibits UniProt keyword tags Hydrolase, Transmembrane, and Membrane.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 4543, 5139, 2991, 7888, 3416, 16, 2154, 7014, 2359, 3213, 2409, 3071, 2644, 1930, 23647, 2007, 7138, 5139, 2991, 2455, 18, 4678, 5745, 4417, 8167, 1930, 4016, 4209, 1942, 8480, 2733, 8201, 3873, 16, 3868, 10232, 9233, 4682, 1942, 7534, 3689, 3844, 2428, 2014, 4813, 5458, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8748, 17, 2601, 8167, 17, 3189, 3418, 13975, 16, 2154, 17097, 1920, 14756, 15, 17, 2014, 26737, 15, 17, 3100, 16881, 1927, 8078, 26337, 1930, 8078, 5856, 1021, 12530, 4248, 18, 2052, 3418, 4075, 43, 4728, 3170, 1927, 2288, 4666, 17, 18038, 30103, 20185, 2007, 4595, 17, 12789, 1930, 4088, 1966, 43, 4948, 9059, 1922, 6445, 3197, 3873, 3436, 28149, 1930, 15021, 16, 2710, 3071, 2644, 1930, 23647, 18, 2176, 5110, 1922, 24323, 7336, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 20748, 16, 9117, 16, 1930, 3260, 18, 3], "output": "MTKPLKLIASILVYVAIIFSMTIADPEFLKPDVESVIVQPNKSFSLSSEQLSDIEKKRTAFGLVAIICLATGYGLFVRSIGKEYKRRTEIETEMKIAQSIHESLLPKSAVKTDWCEIAGVSLPATEIGGDFYDIIKLSESKILIVIADASGHGTGAGVLSAMTKSSIIQELQHTQSLAEL", "metadata": {"id": "A0A3C1YQF8", "cluster": 26362090, "interpro_all": ["IPR052016", "IPR036457"], "interpro_used": ["IPR052016", "IPR036457"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that can perform the following function: The protein carries a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. Moreover, the protein features a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. It originates from Actinomycetes bacterium.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 3950, 16, 1920, 2213, 4075, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2176, 22970, 2037, 4718, 25148, 14061, 18, 3], "output": "MLSVVVLISGTGSNLLALLKAIDSPLVPVRVVAVGSDGPAPGLAHADLYGVPTFVVERSMFPDRESWAKRLQETIEGYSPDLVALAGFMKILPPAFIKRFSPNLINIHASLLPLFPGAHAVRDTLDAGVTETGATIHVVDEGIDTGPVIFQRTVQVMPGDDVATLHERIKVHERELLIETIIGVAENRIDLASI", "metadata": {"id": "A0A6I3DD68", "cluster": 20093954, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR001555", "IPR002376"], "interpro_unused": ["IPR036477", "IPR004607"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: It is part of the Bacterial Antiviral Defense Nuclease family, which functions as a key component of antiviral systems like Gabija, Retron, and Septu to confer resistance against bacteriophages. These proteins exhibit ATP-dependent or nucleotide-regulated endonuclease and exonuclease activities that target and cleave viral double-stranded DNA or RNA to halt phage 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. In addition, 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 expressed in Methanothrix sp and is connected to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 4543, 10129, 9720, 16230, 3416, 16, 2154, 4088, 1966, 43, 3834, 4594, 1927, 10129, 3771, 3189, 6321, 7483, 1019, 16, 7332, 1022, 16, 1930, 8394, 1032, 1942, 7909, 3554, 3316, 24613, 1036, 18, 2144, 2697, 5987, 4498, 17, 3100, 2014, 5489, 17, 4335, 18697, 1930, 24966, 4209, 1988, 2758, 1930, 21252, 4324, 4825, 17, 10338, 2678, 2014, 3146, 1942, 4217, 1031, 10503, 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, 1922, 2459, 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, 3198, 1922, 17348, 2195, 3027, 1039, 2056, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MKVLIKNLGTVREAEIELKPLTVFVGPNDTEHKKAYEAGTLSHAYPVLEAAINQLLEEGNAKINLIQFFDENWMSKFMGAGQATFDGMEVQMDLHDVYQNLLRGTLLNAFKEKGEPDICFCTKGSFKNKLPLHTIRNFVTGINWLMMPSGSKQDGNRIGTGKKDSVAFMPYPMDNLIKYLELADLIQQEILGGSIGFSKPEPDIAQELAFRPIIYLRYTAMRNDLLVIDEPEMNLQPETTQSQYLVDHLINLMKAAEQEDPKSISGEFILKTLNGDGFIDLETFMGGIPSDPTASAGVTKGTGKKWTAYTVAAIFGYYGWSFDSYINDISKLSAQIRRMPFEEKLSADETGKYVFIFFHIALYHWVYYFQSERTAIFDKTRDEGSYKDRLNQAKNNKNISNTDDKEADSDALLASSMVRELSSLVAQAKLIEFLSMLVNAGLNIIIADAFISKDDVSMYLFEKGTAKDI", "metadata": {"id": "A0A3N9UWL5", "cluster": 3199713, "interpro_all": ["IPR003959", "IPR051396", "IPR027417"], "interpro_used": ["IPR051396", "IPR027417", "IPR003959"], "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 has a Nif11-like leader peptide domain that acts as a conserved N-terminal leader sequence for small ribosomal natural products, including prochlorosins. It typically terminates in a Gly-Gly motif that directs cleavage and export by a specific ABC transporter peptidase. It occurs in Prochlorococcus sp. P1361.", "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, 2258, 43, 17719, 3242, 17, 3189, 17442, 4207, 3418, 1988, 8016, 1966, 43, 5305, 56, 17, 4262, 17442, 3244, 1958, 2858, 11196, 4613, 4461, 16, 2710, 9823, 7806, 30232, 6777, 1036, 18, 2176, 5745, 26767, 1036, 1922, 43, 3376, 17, 3376, 5219, 1988, 28351, 6404, 1930, 12660, 2007, 43, 2487, 7219, 9054, 24050, 18, 2176, 5110, 1922, 9823, 7806, 30232, 4879, 2437, 1957, 2056, 18, 8632, 5677, 1009, 18, 3], "output": "MVAIAKAAGFAITKEDLNTYRQNLSDDSVTFWACKTNYSIDCCSELENVAGGIQKNYQC", "metadata": {"id": "A0A7Y0KVB2", "cluster": 6877071, "interpro_all": ["IPR022516"], "interpro_used": ["IPR022516"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein incorporates 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. Additionally, the protein is a member of 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 Aquarana catesbeiana (American bullfrog) (Rana catesbeiana) and contains UniProt keyword associations Zinc-finger, Metal-binding, and Transcription regulation. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 19683, 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, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 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, 10059, 12415, 1019, 3115, 1918, 5873, 15626, 12, 5339, 14267, 7134, 2021, 13, 12, 2845, 1019, 3115, 1918, 5873, 15626, 13, 1930, 5461, 20709, 11121, 2538, 5253, 7997, 17, 8497, 16, 6048, 17, 2743, 16, 1930, 3213, 3640, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MDPSNPMESSDKSHTMTSDVHLRSMDPSTSEESSDKSHTVTLDVHLRSMDPSNPDEPSDQSHTMTSDDHLRSMCPSNLEESSDKSHTMTSDVHLRSMDPSNPDKPSDQSHTMTSDDHLRSMCPSNLEESSDKSYTMTSDVHLRSMDPSNPEESSYKSHSERPYACSECGKCFATKGKLTTHRKIHSGERPYLCSECGKCFTVKQSLLAHMTKHSSEHPNNFQTVIDVVQIT", "metadata": {"id": "A0A2G9R740", "cluster": 7021416, "interpro_all": ["IPR050331", "IPR036236", "IPR013087"], "interpro_used": ["IPR013087", "IPR036236"], "interpro_unused": ["IPR050331"]}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein should contain a Alcohol dehydrogenase-like, N-terminal domain that functions as the catalytic core for a diverse family of oxidoreductases, including zinc-dependent alcohol dehydrogenases and quinone oxidoreductases. It typically adopts a GroES-like fold to catalyze the reversible oxidation of alcohols to aldehydes or ketones using NAD or NADP cofactors, often utilizing coordinated zinc ions for activity. In addition to enzymatic roles, it can perform structural functions, such as in the mammalian lens protein zeta-crystallin. Also, the protein is a member of the GroES-like superfamily, which adopts a partly open four-stranded $\\beta$-barrel fold found in molecular chaperones and oxidoreductases. Members function as co-chaperones (such as GroES) that partner with GroEL to facilitate ATP-dependent protein folding, or serve as the N-terminal domains of enzymes like alcohol dehydrogenase and ketose reductase. Additionally, it is part of the Cinnamyl alcohol dehydrogenase-like family, which comprises zinc-dependent enzymes that primarily catalyze the NADPH-dependent reduction of cinnamaldehydes to cinnamyl alcohols during plant lignin biosynthesis. These proteins typically assemble as dimers or tetramers containing a C-terminal NAD(P)-binding Rossmann fold, and the family includes diverse members ranging from alkaloid-synthesizing enzymes to microbial aldehyde reductases involved in stress tolerance. It is native to Pythium insidiosum (Pythiosis disease agent).\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, 4284, 9294, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 43, 6445, 3416, 1927, 27388, 1036, 16, 2710, 7997, 17, 3100, 4284, 9294, 1036, 1930, 25093, 27388, 1036, 18, 2176, 5745, 24032, 43, 8947, 1918, 17, 3189, 3728, 1942, 18170, 1920, 10743, 6638, 1927, 21773, 1942, 25075, 2014, 21876, 1036, 2193, 6577, 2014, 24221, 21362, 16, 3868, 10232, 11651, 7997, 6982, 1958, 2455, 18, 1922, 2459, 1942, 8145, 5456, 16, 2176, 2112, 2385, 4346, 4088, 16, 2427, 1966, 1922, 1920, 6492, 8540, 2213, 18943, 17, 24572, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 8947, 1918, 17, 3189, 13975, 16, 2154, 24032, 43, 10028, 4437, 3006, 17, 10338, 8, 38, 4666, 8, 17, 19560, 3728, 2435, 1922, 3272, 18098, 1930, 27388, 1036, 18, 4678, 2347, 1966, 2081, 17, 18098, 12, 2427, 1966, 8947, 1918, 13, 1988, 8240, 1956, 8947, 1938, 1942, 6628, 4498, 17, 3100, 2213, 10328, 16, 2014, 7120, 1966, 1920, 56, 17, 4262, 4682, 1927, 5038, 3189, 4284, 9294, 1930, 21471, 4127, 11386, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 23765, 2199, 4284, 9294, 17, 3189, 3416, 16, 2154, 12936, 7997, 17, 3100, 5038, 1988, 5985, 18170, 1920, 11908, 17, 3100, 3378, 1927, 23765, 8790, 1036, 1942, 23765, 2199, 21773, 2409, 4496, 16965, 8132, 18, 2144, 2697, 5745, 17421, 1966, 13351, 2014, 26568, 3165, 43, 45, 17, 4262, 6577, 12, 58, 13, 17, 2743, 18215, 8890, 3728, 16, 1930, 1920, 3416, 5921, 6445, 4678, 6485, 2037, 29951, 17, 25292, 5038, 1942, 7293, 18727, 11386, 1036, 3286, 1922, 3071, 6555, 18, 2176, 1977, 6196, 1942, 23195, 2457, 2346, 13756, 14740, 12, 23195, 10282, 2573, 5899, 13, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MVVPGNEASVKDLQVGDRVGVGAMGVSCQTAYGGYAEYVRVDANYAFKIPEALFKIPEALPSQSPNKEEQARALGAEDFVVMLDPDAVKRAARSVHALHGELFGVVELAVRRAARAESVERSAGTFGDVRELRDVFTYNATYEDGKDVAAPLLCAGVPVTFSIVTADAPNQHFVAVAREDQLGC", "metadata": {"id": "A0AAD5LLK4", "cluster": 12749329, "interpro_all": ["IPR013154", "IPR047109", "IPR011032"], "interpro_used": ["IPR013154", "IPR011032", "IPR047109"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein is a member of the Cytochrome P450 family, which comprises haem-containing mono-oxygenases found in all kingdoms of life that catalyze the oxidation of a vast array of substrates. Utilizing a heme cofactor and electrons from redox partners, these enzymes play critical roles in the detoxification of xenobiotics, the metabolism of fatty acids and steroids, and the biosynthesis of secondary metabolites. It is found in Trichoderma asperellum (strain ATCC 204424 / CBS 433.97 / NBRC 101777) and is connected to UniProt keyword Iron, Metal-binding, and Oxidoreductase. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 9387, 12088, 3416, 16, 2154, 12936, 7105, 17, 3165, 8914, 17, 25298, 1036, 2435, 1922, 2136, 13543, 1036, 1927, 3308, 1988, 18170, 1920, 6638, 1927, 43, 10983, 6472, 1927, 6249, 18, 10232, 43, 10954, 15155, 1930, 14354, 2037, 9366, 7228, 16, 2144, 5038, 3918, 4140, 5456, 1922, 1920, 18169, 1927, 29821, 1036, 16, 1920, 4714, 1927, 5934, 4576, 1930, 13039, 16, 1930, 1920, 8132, 1927, 4067, 6926, 18, 2176, 1977, 2435, 1922, 10477, 20532, 14176, 10757, 12, 3943, 11037, 16368, 6852, 1006, 19, 16341, 27849, 18, 5749, 19, 8789, 15618, 9447, 7658, 1027, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5680, 16, 6048, 17, 2743, 16, 1930, 27388, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MTEVISTPSGYPILGNVLDVDPEHPHNSLARMVSTYVSGSLQQVRNALHDEIFTAYPGEHNWETAHRTLMPAFGPLSIGDVFWVLMPAQMRRHLSQMIIKWARFGPDMPSDVQDDFMRLTLNSIPLCAMGTRFHSFYHESQHPFVRAMVGVLTESFTRSRRPPLSKILFQTQEKKYREDIEELEAVAKELLNDRRANPRSKKDLLNAMILNKDPKTGESLDNDTIIRNMIIFLIAGHETTAGLLSFLFYELWQNLEVYRKTQEEIDTVGSISARNPSSSPYRTCIHTSGKRRPDS", "metadata": {"id": "A0A2T3YRD7", "cluster": 13550399, "interpro_all": ["IPR001128", "IPR036396"], "interpro_used": ["IPR001128"], "interpro_unused": ["IPR036396"]}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein includes 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. Also, the protein belongs to 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. Also, the protein is included 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. It is derived from Corynebacterium sp. HMSC28B08.\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, 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, 2222, 16, 1920, 2213, 14440, 1942, 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, 2222, 16, 1920, 2213, 1977, 3063, 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, 2176, 1977, 3595, 2037, 2233, 17151, 7972, 2341, 18842, 1989, 2056, 18, 21904, 8054, 1025, 1014, 13895, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MRLRLECDGGSRGNPGVAGAGSSIAKATNNFAEYYGLLNGLALATEVASKKKVKHPDLKPLAAKAQQLGADFAAVNYTWVPRWFQDMTDKSSPSAEPTSSPAPTSSWHGGRRPARFLLLRHGQTQMSQAEQAARFLASRGGVAAIVSSPLQRAKQTLIEMDFGHWEGRRFSEVRDDHPEEQAYRRVSELIDELTGEYAGKNVLLVSHVTPIKSVLRYAMNFYGGAATLVRAVNDTHYLVGVDAASAVRGNKQELAARWEYFGVKPGDVELDVFMDSKLIVEQMSGRWAQNKRADELANRAMDDGEGGEVDGQYSGLSDPELTDMGQWALTAASALGMDEEAVEVDERECFADCTKAPHGGESPEQVAGGEVYRTVHLDLASLSIAE", "metadata": {"id": "A0A1F1ZQM7", "cluster": 16175133, "interpro_all": ["IPR013078", "IPR029033", "IPR050275", "IPR012337", "IPR014636", "IPR002156", "IPR036397"], "interpro_used": ["IPR002156", "IPR013078", "IPR050275"], "interpro_unused": ["IPR012337", "IPR036397", "IPR014636", "IPR029033"]}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein is classified under the UPF0332 putative toxin family, which comprises proteins containing a HEPN domain that function as the toxin component of type VII toxin-antitoxin (TA) systems. These proteins facilitate bacterial survival under stress by inhibiting cell growth when the neutralizing antitoxin degrades. Furthermore, the protein should include a HEPN domain that functions as a predicted nucleotide-binding module found in bacteria, archaea, and the eukaryotic chaperonin sacsin. It forms a five-helix bundle structurally similar to kanamycin nucleotidyltransferases and is often associated with enzymatic domains involved in aminoglycoside antibiotic resistance. It occurs in Omnitrophica bacterium (Omnitrophota bacterium).\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2353, 1038, 12962, 6763, 6770, 9165, 3416, 16, 2154, 12936, 2697, 3165, 43, 3357, 1022, 3418, 1988, 2347, 1966, 1920, 9165, 4594, 1927, 2601, 16852, 9165, 17, 10310, 9754, 12, 4410, 13, 3771, 18, 2144, 2697, 6628, 4543, 3298, 2441, 3071, 2007, 7918, 2024, 2905, 2469, 1920, 12130, 10310, 9754, 28004, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 3357, 1022, 3418, 1988, 4088, 1966, 43, 4396, 5489, 17, 2743, 9059, 2435, 1922, 4802, 16, 21501, 16, 1930, 1920, 10825, 10686, 6655, 10791, 6777, 18, 2176, 4952, 43, 3628, 17, 7864, 14142, 12171, 2551, 1942, 19404, 2797, 4090, 2199, 18580, 1930, 1977, 3868, 2458, 1956, 8145, 4682, 3286, 1922, 23029, 8028, 7267, 3554, 18, 2176, 5110, 1922, 18825, 3032, 24888, 3375, 14061, 12, 18825, 3032, 2102, 7336, 14061, 13, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MCFQSLLCQSTCGSRRILQTGELETEWADILSRELRYRINADYMRMKAYLWSKGISLPDEFQKVFDIVPKSHNALKRLFGKYLIIDFEISEETAESLVHDAERFVE", "metadata": {"id": "A0A3A4PMK5", "cluster": 17781516, "interpro_all": ["IPR007842", "IPR052226"], "interpro_used": ["IPR052226", "IPR007842"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "It is part of 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. Furthermore, the protein incorporates a RNA polymerase Rpb7-like, N-terminal domain that contains an SHS2 motif involved in protein-protein interactions, specifically mediating heterodimer formation with Rpb4-like subunits. Found in eukaryotic and archaeal RNA polymerases, this domain supports interaction with the nascent RNA strand during elongation, contributing to transcription, mRNA transport, and DNA repair. In addition, the protein should feature a RNA polymerase III, subunit Rpc25 domain that acts as a strongly conserved component of RNA polymerase III required for transcription initiation. This subunit is not essential for elongation and shares homology with Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II, and the archaeal RpoE subunit. It is identified in Thelohanellus kitauei (Myxosporean) and is annotated with UniProt keywords DNA-directed RNA polymerase and Nucleus. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 2176, 1977, 3131, 1927, 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, 3677, 16, 1920, 2213, 19683, 43, 3146, 6479, 4822, 29606, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 5461, 1925, 22705, 1028, 5219, 3286, 1922, 2213, 17, 2213, 3719, 16, 4475, 10239, 15672, 3337, 1956, 4822, 16290, 17, 3189, 6991, 18, 2435, 1922, 10825, 1930, 22367, 3146, 20910, 16, 2052, 3418, 7825, 2835, 1956, 1920, 16861, 3146, 5984, 2409, 9971, 16, 8739, 1942, 3213, 16, 3616, 4860, 16, 1930, 2678, 5059, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 3146, 6479, 4337, 16, 5903, 4822, 8054, 1015, 3418, 1988, 8016, 1966, 43, 4937, 5305, 4594, 1927, 3146, 6479, 4337, 3414, 1958, 3213, 6035, 18, 2052, 5903, 1977, 2084, 4415, 1958, 9971, 1930, 16495, 9039, 1956, 16454, 7514, 1922, 3146, 6479, 51, 16, 4822, 29606, 1922, 3146, 6479, 2890, 16, 1930, 1920, 22367, 4822, 6802, 5903, 18, 2176, 1977, 2899, 1922, 1920, 6012, 15409, 1992, 1957, 4712, 6346, 14209, 12, 21464, 9890, 5376, 1022, 13, 1930, 1977, 10633, 1956, 20709, 11569, 2678, 17, 6554, 3146, 6479, 1930, 5607, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MFMLVRLKILVEVKPQNFSEHEDQYIRNSILGRFVDKVVLNVGLFIAIHHIDSVEQPSIFPGSGSYFTHVEFTAVVFRPFIGELIEGRIKCINQNEIRLSIRFFEDIFIELPYSRGPTSSGPSIISGTLIYKDPKEGSNRKLAISEGDKCLVRVLKVKFNDVNLKLSKDKSISPLRVTATISEEGLGLVKSSG", "metadata": {"id": "A0A0C2M837", "cluster": 18511216, "interpro_all": ["IPR012340", "IPR013238", "IPR036898", "IPR045113", "IPR005576"], "interpro_used": ["IPR012340", "IPR005576", "IPR013238"], "interpro_unused": ["IPR036898", "IPR045113"]}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: 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 Bodo saltans (Flagellated protozoan).", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 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, 2176, 2258, 2252, 3330, 1922, 14426, 1037, 7012, 2075, 12, 26538, 2013, 23583, 13642, 1928, 13, 18, 3], "output": "MLSSNSPRIIVAGDYASGKTTFCQRMERPMSVESPTENTDDMERDESSQSSSFVLVDQRQLCTETRDTPMGETRSSTLSSSASPYSDSPSRTRGSSQYFAVLMWKTVVQDEAELCNERGSKFKLPLAVIFTKKYHCGMECRGKEIQADVFAFVSLVEASSEEMKNLQSVAFNDPRAQEQPEKKRTKPCCGSEAEVRLENGAVNRDHYSSLQRMVFRRAVGLIVMVDATTIFSLFPAGGVSWETCLAQLMDVLAKEDEEAVTAFRLALSTCVNRRLSVAPTRQRR", "metadata": {"id": "A0A0S4IK46", "cluster": 21838557, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein features a Serpin conserved site that characterizes the MEROPS inhibitor family I4, typically centered on a Pro-Phe sequence located near the reactive bond. While most members function as serine protease inhibitors, some exhibit cross-class inhibition of cysteine proteases like caspases and cathepsins, or lack protease inhibition capabilities entirely. It is native to Entamoeba invadens IP1.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 4075, 43, 27453, 1921, 5305, 3200, 1988, 26735, 1920, 6902, 4001, 4106, 3416, 51, 1006, 16, 5745, 10841, 1990, 43, 1965, 17, 10422, 3244, 4810, 4931, 1920, 6079, 5403, 18, 2679, 2501, 4678, 2347, 1966, 8468, 7154, 4472, 16, 2673, 5987, 3567, 17, 2921, 3523, 1927, 8666, 12447, 3189, 18535, 1930, 16808, 1036, 16, 2014, 3630, 7154, 3523, 13693, 11668, 18, 2176, 1977, 6196, 1942, 8496, 1976, 6802, 7972, 23122, 3355, 5416, 1009, 18, 3], "output": "MLSNKVCSAAVFSNEYTACCLSYSDTNNQIAFVMPNDIEKFEKAREGEIYEIMRSLSQNFPEKRSVTFPKFSVESSVNMVQQLRKLGLNLPFSCDANFSKMAKGKFYVSDAIHKAVVKVDENGTEATAATAIAATFCCCGPFDEPRPVVIDKPFYFSILGRYKLPLFFGKITNPKY", "metadata": {"id": "A0A0A1U7R8", "cluster": 23670153, "interpro_all": ["IPR023795", "IPR023796", "IPR000215", "IPR036186", "IPR042178", "IPR042185"], "interpro_used": ["IPR023795"], "interpro_unused": ["IPR042178", "IPR000215", "IPR036186", "IPR023796", "IPR042185"]}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is associated with the Myb-like transcription factor family, which binds specific DNA sequences to regulate gene expression as either transcriptional activators or repressors involved in cell proliferation, differentiation, and development. These proteins play critical roles in diverse biological processes, ranging from hematopoietic progenitor cell regulation in animals to secondary cell wall biosynthesis, abiotic stress responses, and reproductive development in plants. In addition, the protein has 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. Additionally, 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. It is found in Coptis chinensis and is associated with UniProt keywords Transcription regulation.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 1977, 2458, 1956, 1920, 16851, 17, 3189, 3213, 2991, 3416, 16, 2154, 6876, 2487, 2678, 3709, 1942, 5741, 2359, 2294, 1966, 3108, 5224, 15497, 2014, 26446, 3286, 1922, 2024, 4031, 16, 4155, 16, 1930, 2740, 18, 2144, 2697, 3918, 4140, 5456, 1922, 6445, 3933, 4028, 16, 6485, 2037, 9960, 9411, 2024, 3640, 1922, 3555, 1942, 4067, 2024, 4821, 8132, 16, 16596, 3071, 3387, 16, 1930, 7986, 2740, 1922, 4793, 18, 1922, 2459, 16, 1920, 2213, 2258, 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, 4950, 16, 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, 2176, 1977, 2435, 1922, 3725, 3600, 6790, 8134, 1930, 1977, 2458, 1956, 20709, 11569, 3213, 3640, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MVNGDRIKGSWSPEEDSMLTKKSCRLRWCNQLSPLVQHRPFTPAEDAIIVKNAIKNHWNSTLRRRLANESSSVSSEPDDESDSYSVHQGEDDDEGEGFLEPVTSLTLSPEKGVKKSGGMRVREEMENEKDKKGRVRNYMDKNLVLLGWTRRPQTRVQFGVCLPRVQYIPMSKTDFLTNLKKQVKLENPIFLVETHGPRNWSVISSGISGRSGAHANHGNKWATIARLLPGRTDRKRQCVRLSSENNPGKTTVVNVAVPASVATAAPGLVRYEDECATEIKEMCLMSIMHRMIAEENFVFGRPQTRFNLESAIVLG", "metadata": {"id": "A0A835HGK2", "cluster": 24054741, "interpro_all": ["IPR009057", "IPR017930", "IPR050560", "IPR001005"], "interpro_used": ["IPR050560", "IPR017930", "IPR001005"], "interpro_unused": ["IPR009057"]}, "task_type": "infilling"} {"instruction": "The protein is categorized in the Protein of unknown function DUF481 family, which comprises several proteins of uncharacterised function. It is present in Thiotrichales bacterium. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 11425, 3416, 16, 2154, 12936, 2980, 2697, 1927, 23229, 3495, 2347, 18, 2176, 1977, 2481, 1922, 15331, 3319, 7289, 1918, 14061, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MRLNISVMAASSHTCCVKPSLPLNVAQQKRAKALSILLSAFLMPTAHAIVNIEEMRGPPQTDGLTGDASLSMSGDAGNTRQSHLSASSQFFWQRGAVTKLIAADYSYGENSRHRNTNKGFVHLRYIKQQTPTRALEVFTQAVRNEFSRLSLRTLIGAGTRLTLHHSRNDAVHLGAGAFYLKESQQARAGLSDDGTEKFWRGNFYLALRYQINEQVRIVSTTYYQPALDNGHDFRLLEEASLKIKLTDALNFKLTLALTHDSEPPQAVEKTDINYKTGIEYRF", "metadata": {"id": "A0A2A4RZG3", "cluster": 25950186, "interpro_all": ["IPR007433"], "interpro_used": ["IPR007433"], "interpro_unused": []}, "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 contains 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 is assigned to 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 contains 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. It is found in Bacteroidetes bacterium ADurb.Bin397 and has UniProt annotations Transcription regulation.", "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, 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, 1977, 6304, 1942, 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, 5461, 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, 2176, 1977, 2435, 1922, 26808, 14061, 2041, 5223, 18, 8768, 28163, 1930, 2258, 20709, 15010, 3213, 3640, 18, 3], "output": "MDIRMPEMDGIEATAHIRKTNQEVKILGLSMMDDRANIVNMFKAGANGYLLKNTNKLELLDAFHSMLAGKNYYAKEVAEVFLLKEFSNSTFLKKKNINNEITTREEDILRLICQQYSTREISEILCLSEKTIEGHRKKLLDKTHSRNIAGLVWYALENGIIKEAKG", "metadata": {"id": "A0A1V5NPC3", "cluster": 28704102, "interpro_all": ["IPR011006", "IPR016032", "IPR001789", "IPR000792", "IPR039420"], "interpro_used": ["IPR001789", "IPR039420", "IPR000792"], "interpro_unused": ["IPR016032", "IPR011006"]}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein is grouped in the Inner Membrane YidH-like family, which comprises conserved inner membrane proteins, including *Escherichia coli* YidH and *Mycobacterium tuberculosis* Rv2272, involved in undefined membrane-associated processes. These proteins are hypothesized to participate in transport or signaling activities. In addition, the protein should feature a DUF202 domain that is characteristically found in bacterial inner membrane proteins and yeast vacuolar transporter chaperones. It is produced by Actinospica durhamensis and has UniProt annotations Cell membrane and Transmembrane helix.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 6671, 3260, 19929, 6018, 17, 3189, 3416, 16, 2154, 12936, 5305, 6671, 3260, 2697, 16, 2710, 14, 10210, 5178, 14, 19929, 6018, 1930, 14, 16389, 8449, 14, 8309, 4460, 10180, 16, 3286, 1922, 26687, 3260, 17, 2458, 4028, 18, 2144, 2697, 2032, 7149, 1942, 7352, 1922, 4860, 2014, 3197, 4209, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 4855, 6680, 11636, 3418, 1988, 1977, 6293, 2169, 2435, 1922, 4543, 6671, 3260, 2697, 1930, 5688, 21582, 9054, 18098, 18, 2176, 1977, 4152, 2007, 4718, 3106, 6102, 2335, 8527, 8134, 1930, 2258, 20709, 15010, 2024, 3260, 1930, 9117, 7864, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MDAEDSARMRDLMANSRTLLFGVETGLQRTSDAIGIVMALIGLVFIVLGTATAAACCAVSCLMLAVYLALTAWIRTSISFAGLGFVVAKYLQYLKTMELEQGPARSPVPLHWP", "metadata": {"id": "A0A941IW57", "cluster": 28881654, "interpro_all": ["IPR003807", "IPR052053"], "interpro_used": ["IPR052053", "IPR003807"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Function:\nThe protein should contain 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 has been characterized in Chlamydiia bacterium and is associated with UniProt keywords ATP-binding.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 3066, 5531, 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, 2258, 2252, 4378, 1922, 14667, 3907, 1019, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MSTSQRILLTGARAPVTLDLARMLSNAVKRSFVVPAPIEGTLSFVIALKDIVCAEQIDCRVFCEAIDRLEPLHNKATFIELLQSFGVFKPVYSRFARDVLICHRSDTERVRCVLPSASDPHTSYPVEHCLGRIGSALAYRNVHHRAALALSLDLIVGPDGVPVPIECNPRATSGLGIPAKTPPEGRHAHVALPLLLMGGKHRFKAWTQGLYFAIKGLKLGMSMTQASTYDIEWNGHDICASVQANGHKVFVADTTQAHVCRFCLIPTCEEVFAIAQHMDVLTKHLPFPQTLKLTSPADVEAALERWERVWVAQQYIEGERLCTYTVAEEGRVLAVAELVNKLDYTGQLHLFRAEDRLDQAFLGRDVIFSSRDPLPALISPLLL", "metadata": {"id": "A0A960T4Z3", "cluster": 250674, "interpro_all": ["IPR011761", "IPR003806"], "interpro_used": ["IPR003806"], "interpro_unused": ["IPR011761"]}, "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 TDU repeat that mediates specific interactions with TEA/ATTS domain-containing transcription factors, such as mammalian TEF proteins and Drosophila Scalloped. This motif is homologous to the Vestigial interaction domain and facilitates the formation of transcriptional complexes that regulate developmental gene expression. It has been characterized in Cylicocyclus nassatus (Nematode worm).", "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, 6888, 1032, 6865, 1988, 10412, 2487, 3719, 1956, 12459, 19, 3099, 1036, 3418, 17, 3165, 3213, 2790, 16, 2427, 1966, 6492, 3602, 1038, 2697, 1930, 8273, 7350, 6012, 7438, 18, 2052, 5219, 1977, 8725, 1942, 1920, 5634, 2677, 2086, 2835, 3418, 1930, 11374, 1920, 3337, 1927, 5224, 5048, 1988, 5741, 5878, 2359, 2294, 18, 2176, 2258, 2252, 4378, 1922, 11768, 5670, 22170, 1957, 7312, 5735, 1031, 1957, 12, 18827, 11055, 13, 18, 3], "output": "MMFAVLSPIQESEMSRVSDTPYQCSSAIPSTANTSHIPVSDLTSSLACSLLSCSIPTATVIAPPPPDMHSSSSVTEADADVVGLSQSTKEVSIQDNSLYSPTTSRPSVIIESPTVRNPPVRRSASSVSATRKIDDEKMRASPITRRTSFNNHGSNCTTQPHFENWQRKRNATSQSSKKLHKMMATPIASLNSLMIYHSINHQHTMRSLFDVDQSDKPLDLSLKSSNEQPDVHEHFRRSLSGKWPRRSVIVSNTGVDIVDHFRRALSEKE", "metadata": {"id": "A0AA36H3B5", "cluster": 406041, "interpro_all": ["IPR006627"], "interpro_used": ["IPR006627"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe 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. Moreover, the protein carries a DEAD/DEAH-box helicase domain that functions as an ATP-dependent nucleic acid-binding module essential for unwinding RNA structures during metabolism. It facilitates diverse cellular processes, including pre-mRNA splicing, ribosome biogenesis, and translation, by coupling ATPase activity with helicase function via the conserved motif III. 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. It has been detected in Phellinidium pouzarii and contains UniProt keyword associations Hydrolase.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 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, 3950, 16, 1920, 2213, 16252, 43, 9535, 19, 30097, 1023, 17, 5758, 15318, 3418, 1988, 4088, 1966, 1925, 4498, 17, 3100, 11079, 2687, 17, 2743, 9059, 4415, 1958, 26801, 3146, 4061, 2409, 4714, 18, 2176, 11374, 6445, 3689, 4028, 16, 2710, 2097, 17, 3616, 8490, 16, 12794, 13008, 16, 1930, 6410, 16, 2007, 7590, 9444, 2455, 1956, 15318, 2347, 3454, 1920, 5305, 5219, 4337, 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, 2176, 2258, 2252, 3330, 1922, 10422, 11560, 11566, 7408, 1989, 28398, 12813, 21094, 1930, 5461, 20709, 11121, 2538, 5253, 20748, 18, 11586, 5655, 3581, 18, 3], "output": "MDDVGFVSGAALHRDQKQPSPTFAESSKQAKLGLDCYRTLTKVFGHESYRGKQKKIVETAILGVDVFXCCSDWEGFLLYLLLNKFLLILESDLQHGVTLVISPLLSPERKMILADLQSGRPTTRLLYITPEMLFNAGFSKVGHDFRSGYRKLGSFRDKYPDVPIMALTASATKTVMLRVMDPFNRENLFYDVRYTACPSSTAQMSPSSGIVYCRMRATCDELSHYLRSNGISATMWEWQEGGDGSGGIDVVCATIAFGMGIDKPDVRYIVHFDLPYSREDALAVKHLVKRSHNLRREKALSMSLFGESEPSPQFGEPIDENDVDVCKYPDKVKRRKETLSSEEWVLSQIEQRGNNIEESALDGHDEDWEDAEFEDENGYPKAQKHAKHSNHRVEMKDGATAKPVVFALSMLKRSSSITSSKPSYASGASSAFKKPFKTPFKVPFKEMPQNSAKIFNSREGSVESSISKCSSFSTTEKVVDRASGSLAIPALPEGGLFDNETEEMDVDVMDARSPITLREQSLSKIKXRTARSFRKRLPLAYFCSAEGSKFEVKRREYASVTTHGQESLLPSSCRGRLMKNQVSKLQDLNVSASAYTSDTLAITRLHQRGEINRLVVDEAHCISEWQEDIINSLHMDQDRDVRQFIANLHQRRGRRPYHRGLSTKELEKKSLEGYYQETGRAGRDGSPARCLLYGTDSFSALVNLAENISLCRHITICKYLRKSAVLGEDEREGVRIPDENNPEIVRSTPGAVVSKRPRIDYCASIAPPLVPAQRIESSISESPAEVISDEDDTEKEVEESPPSPQSGSHEINLDPDAAFSLKI", "metadata": {"id": "A0A4S4LIN9", "cluster": 1306054, "interpro_all": ["IPR011545", "IPR004589", "IPR014001", "IPR001650", "IPR027417"], "interpro_used": ["IPR014001", "IPR011545", "IPR001650"], "interpro_unused": ["IPR027417", "IPR004589"]}, "task_type": "infilling"} {"instruction": "Please generate an amino acid sequence that is capable of: 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 features a Signal recognition particle SRP54 GTPase domain that functions as a P-loop NTPase to regulate the targeting of nascent secretory proteins to the endoplasmic reticulum or plasma membrane. Located within the SRP54 subunit or its prokaryotic homolog Ffh, this domain binds GTP to coordinate the docking of the ribosome-polypeptide complex to the SRP receptor. It is native to Betaproteobacteria bacterium TMED82 and features UniProt keywords GTP-binding.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 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, 4075, 43, 2733, 5708, 7022, 19939, 5651, 14809, 3418, 1988, 4088, 1966, 43, 58, 17, 5881, 29676, 2051, 1942, 5741, 1920, 5133, 1927, 16861, 11518, 2697, 1942, 1920, 13355, 12279, 2014, 3582, 3260, 18, 4810, 2651, 1920, 19939, 5651, 5903, 2014, 2496, 21545, 5928, 10735, 1023, 16, 2052, 3418, 6876, 9319, 1942, 11865, 1920, 10909, 1927, 1920, 12794, 17, 13022, 2796, 1942, 1920, 19939, 3148, 18, 2176, 1977, 6196, 1942, 4666, 9218, 1021, 10296, 14061, 22377, 1007, 11715, 1930, 4075, 20709, 11569, 9319, 17, 2743, 18, 3], "output": "MELKRIIARDLRSATEEAIRIYGPNTLVVSSERHNGKVEVIVAADLTPEPLIYSEKENRIQNNKNEKISLSDELARECFDDILNKSMNNDRVKAKSLKGDFANSEKTREKRKASDSGSKRKSFASFQPSLSQRKKTVEPKINRVEDLNFSQDFKDSTRKSLEIREDKAEQIYSARETEESDSLRAKELVDLVLREVAEMKKEFKLTKKMMVEKSQDDLSESLEALIKSIHDANLPVSLETLLLGDFYSFKDENEALLSIKTQLLNSSGGKTVSSKTELLSGVHIIAGPAGSGKTSAAIKFVSNALKHNVPPEKIAVLSYKDQKIGGWTQLQMATSSLGVETFKVMTEDFFTANAIELSQKELILIDTSRTFLTEKANTLSLNSLNKKVFYHLVLGADAPASVFTKYLSSSDEYWSDVIVSKFDDSIAPWGLLQDVLNGDSPICPICCCGPSAEDWFYFESNIFIEKVLSLIFDLAANQSKKITAVGLKSTNEHYLEKNL", "metadata": {"id": "A0A1Z8Z2D9", "cluster": 1823393, "interpro_all": ["IPR027417", "IPR000897"], "interpro_used": ["IPR027417", "IPR000897"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence for a protein with the following function: 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 present in Hyphodiscus hymeniophilus.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1958, 43, 2213, 1956, 1920, 2894, 2347, 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, 2481, 1922, 2483, 10647, 15783, 6973, 28034, 28131, 18239, 18, 3], "output": "MPPTQRLLAPGIQGFVCRSCLSKLRPSRSQRPLWLSRSTASDNGPRKSRLFRAKEGSHEQPRKDYESVVRVWDETSDGVRTERGTDPGEKALLETLESTIQDMRQEMSAKDETEEIDEDELQDRVLGRHMQDMVQGDGMVDMVVEEMESLMTKLDPEVDKRLEKMDLENISEEERFKIGGEIFASLLKERQKPDPEPFSPSEPTQQGSSSPNQEFPSEFKEQLPVFVDALRSATTLLGQGRLNKPASVEIWNAWNLCRINFMSNPNQVPSEVWEALWNIFADKKTINYGFLKLLGQDMTDAGLPMQNWQRLVHIQATFAMGSCDAAIKMWEESEATLSSDIETSIQYWQVGGKMYTEQCQLDKALGATQALIQSTNDCSHFRGVLPIIRALLSSQEAAKIQKAWALYTRIKLGLGHQMVMKDYDNVAATFFEADQPELALGVFRDMMLGGDATASKDDSTVLNKNAPALQKDLHLMNIDEGEIAWDDPRVVSKIPAKFNNKFFFGKWLKKLIGDGEYNSSVKVFHLMNERGIRPDARYVNGLVGAWLRTGKPKYHELAEDTCWRMIEARLEYFENRDTRPELSFPLRSVNMGVKPGYKSVWHYPRATVETFSILIMDYRRRQRQDRLKDLMKALELARIQPNNFLMNQIMMMDSATVPNFQPWDTYTSLTRTRGVHPDFDTFGYLWHLTKRAVDPNSNPAQFPKVVENVQNLAVPRLMIAEMAFWADKLNRRNKLPRKLYDAIILTFSLAQDHVGTAITLRLLQRHFHMFPNEDTVRTVVLQLARSGLKNEDHPRRRRLAVRKSPVVKDRVVQVTKLLEGFKARRVAELSRQGIVFEELSEVVRLEETLSLMTHLLRHVTQVRVEEGHDVDELFEIAAKDMGVPECVPAVPTEKLGSGK", "metadata": {"id": "A0A9P7AZ15", "cluster": 3561451, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nIt is part of the Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B/E family, which functions as a component of the GatABC or GatDE complexes to generate correctly charged Gln-tRNA(Gln) or Asn-tRNA(Asn). This process occurs via the ATP-dependent transamidation of mis-acylated Glu-tRNA(Gln) or Asp-tRNA(Asn) in organisms or organelles lacking specific tRNA synthetases. In addition, the protein has a Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic domain that enables the formation of correctly charged Gln-tRNA(Gln) through the ATP-dependent transamidation of misacylated Glu-tRNA(Gln). This subunit operates within a heterotrimeric complex in microbes and eukaryotic mitochondria to compensate for the absence of glutaminyl-tRNA synthetase. Furthermore, the protein is included in 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. It is present in Megaselia scalaris (Humpbacked fly) (Phora scalaris) and is associated with UniProt keywords ATP-binding, Ligase, and Protein biosynthesis.\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, 2176, 1977, 3131, 1927, 1920, 12053, 2199, 19, 25345, 17, 10089, 12, 15118, 19, 15236, 13, 28813, 14165, 5903, 44, 19, 47, 3416, 16, 2154, 4088, 1966, 43, 4594, 1927, 1920, 12534, 8284, 2014, 13530, 3695, 5048, 1942, 5655, 10329, 9516, 15236, 17, 10089, 12, 15236, 13, 2014, 15118, 17, 10089, 12, 15118, 13, 18, 2052, 2585, 5110, 3454, 1920, 4498, 17, 3100, 2127, 25238, 1943, 1927, 5682, 17, 11337, 1981, 9258, 17, 10089, 12, 15236, 13, 2014, 4138, 17, 10089, 12, 15118, 13, 1922, 7373, 2014, 14487, 7046, 2487, 10089, 18185, 1036, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 12053, 2199, 19, 25345, 17, 10089, 12, 15236, 13, 28813, 14165, 16, 5903, 44, 19, 47, 16, 6804, 3418, 1988, 10217, 1920, 3337, 1927, 10329, 9516, 15236, 17, 10089, 12, 15236, 13, 2596, 1920, 4498, 17, 3100, 2127, 25238, 1943, 1927, 5682, 14645, 1981, 9258, 17, 10089, 12, 15236, 13, 18, 2052, 5903, 22460, 2651, 43, 27042, 19103, 2796, 1922, 14889, 1930, 10825, 6489, 1942, 14746, 1958, 1920, 3905, 1927, 6298, 1921, 2199, 17, 10089, 18185, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 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, 2176, 1977, 2481, 1922, 20418, 4127, 12191, 1019, 27156, 1937, 12, 2490, 16752, 2401, 1919, 11716, 13, 12, 20175, 5524, 27156, 1937, 13, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 11905, 16, 1930, 2213, 8132, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MLRIISRNYSTKPIIKSSQISFNAPLNSRVSLFDAAIPGTLPRAALGVNKKPYTKEVKLEQLQLEQDEASSLVKELILILKSLGTCSGKMEGEPSITQAVNYEINRQIEIKSEGGEITNETRNWDATLRKMLLVDTEPDDKIRGNFKLKRIVSDLPKLESLLLAYFRKILGSNPKLSPKEWKTVVGLEVHAQIQSNSKLFSGANNGVIKFPVFTPDSGKGIPLMELVFDHTLEDGLGTRTEIKNIGSIRTVAMRDKEIQQDYRFMPEPNLPPAEIRKELVENFGLPEETAIIIVN", "metadata": {"id": "T1H2G2", "cluster": 3747299, "interpro_all": ["IPR017959", "IPR006075", "IPR014746"], "interpro_used": ["IPR017959", "IPR006075", "IPR014746"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein should have a DHHA1 domain that is diagnostic of DHH subfamily 1 members and is predicted to possess RNA-binding activity, as suggested by its presence in alanyl-tRNA synthetases. This approximately 60-residue region contains a conserved GG motif and is typically found adjacent to the DHH domain. Additionally, the protein is categorized in the Bifunctional oligoribonuclease/pAp-phosphatase and c-di-AMP PDE family, which comprises enzymes that degrade short RNA and DNA oligonucleotides and convert 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP, thereby regulating RNA metabolism. Some members additionally exhibit cyclic-di-AMP phosphodiesterase activity, influencing cellular growth, DNA repair, and cell wall homeostasis, potentially in response to heme or nitric oxide levels. Moreover, the protein should contain a DDH domain that functions as a predicted phosphoesterase, typically exhibiting 5'-to-3' exonuclease activity on single-stranded DNA. It plays a key role in DNA repair and recombination pathways by catalyzing the processive degradation of ssDNA, as exemplified by the bacterial RecJ protein. It is identified in Dorea formicigenerans.\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, 6781, 2722, 1009, 3418, 1988, 1977, 4785, 1927, 6781, 1023, 16227, 21, 4678, 1930, 1977, 4396, 1942, 7150, 3146, 17, 2743, 2455, 16, 1966, 3978, 2007, 2496, 2990, 1922, 10527, 16323, 1024, 17, 10089, 18185, 1036, 18, 2052, 3993, 3276, 17, 6181, 3031, 5461, 43, 5305, 12358, 5219, 1930, 1977, 5745, 2435, 6811, 1942, 1920, 6781, 1023, 3418, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 29491, 15039, 3027, 20226, 2626, 2051, 19, 3860, 17, 8167, 1930, 45, 17, 2137, 17, 3681, 13309, 3416, 16, 2154, 12936, 5038, 1988, 17069, 3662, 3146, 1930, 2678, 12545, 1930, 14450, 23, 11, 12, 22, 11, 13, 17, 8078, 10185, 7506, 25, 11, 17, 5413, 12, 3860, 13, 1942, 3681, 16, 6113, 6773, 3146, 4714, 18, 2673, 4678, 4950, 5987, 9821, 17, 2137, 17, 3681, 24821, 2455, 16, 11623, 3689, 2905, 16, 2678, 5059, 16, 1930, 2024, 4821, 7622, 16, 5063, 1922, 2644, 1942, 10954, 2014, 10233, 7491, 2428, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 28549, 3418, 1988, 4088, 1966, 43, 4396, 8078, 8342, 2051, 16, 5745, 12196, 25, 11, 17, 1942, 17, 23, 11, 24966, 2455, 1990, 2957, 17, 10338, 2678, 18, 2176, 5705, 43, 3834, 2770, 1922, 2678, 5059, 1930, 7827, 3873, 2007, 29601, 1920, 2585, 2320, 4877, 1927, 15063, 16, 1966, 22236, 2007, 1920, 4543, 2090, 1013, 2213, 18, 2176, 1977, 2899, 1922, 19638, 5376, 17202, 26176, 17182, 1036, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MNLNKILEPAKTIAIGGHVRPDGDCVGSCMAFYRIKGTDEILHEIDESKHYDLFIVLDCGDTGRLEFSVNICFAQDNYVVPDASSTSELVYNLIDKDKITKEIAEALYLAAAELLETGIDVADLIMDTFYEKSYARMKKVMDFYGVKPKDLDGIVSQLRNTRGVEVAIFMYELDQNVSGVTMTGTPQDILNNLAERIDEQLKGQAMYQYIQNNYPDKEVDVFLEEIPSTPLFVSAGHTLCIDHHVSGIVHDTGVFQYSCAGPSTFRQIFGRALVESFLFMEGKCIVSYIRFKVSLRSGNEVDVSKIAGYFGGGGHEKA", "metadata": {"id": "A0A3E4Q2R3", "cluster": 3827196, "interpro_all": ["IPR001667", "IPR038763", "IPR003156", "IPR051319"], "interpro_used": ["IPR003156", "IPR051319", "IPR001667"], "interpro_unused": ["IPR038763"]}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein carries 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. Additionally, the protein is grouped in 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 produced by Anaerolineae bacterium.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 16252, 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, 4950, 16, 1920, 2213, 1977, 10809, 1922, 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, 4152, 2007, 11381, 8419, 3336, 14061, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MVLPGCVSGFAPAQASESVLVQAPPLMAAAYPEKLSEQVAPCQAGVDLVYAEAVAADALAIVVNPANRVGPLDTESLGSIQVVGWQPGSGAAAALSALILQGGELTPGAIGFLPASELRAGVRVVTVGGVRPELQSQEGQAILGNHYAPRDVIARHATMPPVALHLAVEGEFADLAAESGYADAALVWGPPPTVADPLAQLADIFTGRTQEWSSFGQSTALIAGSSDAVLDSVAARPSRVRRGEYPLMTGVWLVLRKGGAGEQFLAF", "metadata": {"id": "A0A7V4W7Y0", "cluster": 4172285, "interpro_all": ["IPR024370", "IPR050811"], "interpro_used": ["IPR024370", "IPR050811"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein is classified under the The D-tagatose-1,6-bisphosphate aldolase subunit GatZ/KbaZ-like family, which primarily functions as a non-catalytic regulatory subunit required for the stability and full activity of Class II aldolases involved in galactitol and galactosamine catabolism. While typically lacking aldolase activity, some members act as D-tagatose 6-phosphate 4-epimerases, catalyzing the conversion of D-tagatose 6-phosphate to D-fructose 6-phosphate. It is identified in Tunturiibacter lichenicola.\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, 1920, 46, 17, 5218, 8286, 4127, 17, 21, 16, 26, 17, 29443, 11174, 21524, 5903, 13530, 1011, 19, 6633, 3408, 17, 3189, 3416, 16, 2154, 5985, 4088, 1966, 43, 2447, 17, 6804, 4948, 5903, 3414, 1958, 1920, 5057, 1930, 4125, 2455, 1927, 2921, 2890, 11174, 21524, 1036, 3286, 1922, 9479, 8148, 1930, 9479, 17454, 19480, 18, 2679, 5745, 7046, 11174, 21524, 2455, 16, 2673, 4678, 4033, 1966, 46, 17, 5218, 8286, 4127, 26, 17, 5413, 24, 17, 13872, 9213, 2319, 16, 29601, 1920, 7309, 1927, 46, 17, 5218, 8286, 4127, 26, 17, 5413, 1942, 46, 17, 15102, 26, 17, 5413, 18, 2176, 1977, 2899, 1922, 6367, 1031, 18330, 26073, 2341, 1915, 28088, 29902, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MYHSPDQTMLPEPANWKPYYDGTPAEQKPLPIPEAVDTLISNLSAVTTRLRSKQIEVIQCHNDVAQKLRVPRDSHHDSIEKLYSYGDRIRNYCHRSKPESLYSGNLSSQYV", "metadata": {"id": "A0A9X0QEV6", "cluster": 4419660, "interpro_all": ["IPR012062"], "interpro_used": ["IPR012062"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: 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 should contain a Phosphoribulokinase/uridine kinase domain that catalyzes the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in carbon dioxide assimilation within the pentose phosphate pathway of autotrophs. This enzymatic activity is typically regulated by the thioredoxin/ferredoxin system in plants or by NADH in photosynthetic bacteria. It is native to Aureobasidium melanogenum (Aureobasidium pullulans var. melanogenum). 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, 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, 3066, 5531, 43, 3421, 2023, 1944, 18655, 19, 26104, 4016, 3418, 1988, 17097, 1920, 4498, 17, 3100, 4050, 1927, 5216, 8658, 17, 25, 17, 5413, 1942, 5216, 8658, 17, 21, 16, 25, 17, 5413, 16, 43, 3834, 3537, 1922, 5056, 15422, 22317, 2651, 1920, 9412, 2217, 5413, 3374, 1927, 5728, 1997, 2688, 1036, 18, 2052, 8145, 2455, 1977, 5745, 4335, 2007, 1920, 23684, 19, 25304, 22389, 10960, 2433, 1922, 4793, 2014, 2007, 14261, 1922, 16068, 4802, 18, 2176, 1977, 6196, 1942, 8689, 26205, 12924, 7408, 1989, 5313, 2404, 1989, 12, 8689, 26205, 12924, 7408, 1989, 10875, 25341, 4953, 18, 5313, 2404, 1989, 13, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MGHSYYDLATRALACYQALPEPDASRNQSKRLLIALAGPPGSGKGRIASKVAKIVNQSGVSCSVISIDGCSQDSHNDTSSILPKSPSWTFKGAAAVDLVQQIQRQTTEPNDIKSPYTIHVEDVESHKLNVAGDASIVIFEGLYMLCEDLPWARIQDLVNERWFVEVEPEVGRQRVVKRFLDTGFEKDYEAACTRYDENDVFNAEFINRTSKGRDVTVKSIDRRSSSGSSY", "metadata": {"id": "A0A9P8E1L1", "cluster": 5806960, "interpro_all": ["IPR027417", "IPR006083"], "interpro_used": ["IPR027417", "IPR006083"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein is included in the Peptidase C85-like family, which comprises OTU domain-containing deubiquitinases that cleave ubiquitin to regulate pathways such as protein synthesis downstream of mTORC1 and the innate immune response. This group includes mammalian proteins like OTUD5 and OTUD6B, as well as putative viral ubiquitin thioesterases. Additionally, the protein carries a OTU domain that typically functions as a cysteine protease with deubiquitinating activity, regulating cell signaling and chromatin structure. It employs a conserved catalytic triad to hydrolyze peptide bonds, although some structural homologs lack enzymatic activity. This domain is also found in viral replicases and RNA-dependent RNA polymerases. Additionally, the protein is included 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 native to Sistotremastrum niveocremeum HHB9708. 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, 3063, 1922, 1920, 24050, 19189, 1015, 17, 3189, 3416, 16, 2154, 12936, 20392, 3418, 17, 3165, 29436, 2319, 1988, 21252, 6526, 1942, 5741, 3873, 2427, 1966, 2213, 4271, 5863, 1927, 13694, 1930, 1920, 8539, 3743, 2644, 18, 2052, 2210, 5921, 6492, 2697, 3189, 20392, 1007, 1015, 1930, 20392, 1007, 22022, 16, 1966, 2486, 1966, 6770, 4324, 6526, 30215, 2319, 18, 4950, 16, 1920, 2213, 16252, 43, 20392, 3418, 1988, 5745, 4088, 1966, 43, 8666, 7154, 1956, 29436, 2287, 2455, 16, 6773, 2024, 3197, 1930, 6338, 3170, 18, 2176, 22620, 43, 5305, 6804, 21845, 1942, 7222, 6931, 4207, 9031, 16, 2876, 2673, 4346, 14279, 3630, 8145, 2455, 18, 2052, 3418, 1977, 2222, 2435, 1922, 4324, 5825, 2319, 1930, 3146, 17, 3100, 3146, 20910, 18, 4950, 16, 1920, 2213, 1977, 3063, 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, 6196, 1942, 19149, 4575, 4265, 3368, 2156, 24277, 18054, 1021, 10981, 17800, 1989, 9645, 1014, 8528, 13895, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "MGSGKKSVRQARQMQSQSLPTLRPHCHHRENRTDRGFPQRSLDDPASNNALLTSQLRSLGLYAAPTLGDGNCLFRALSDQLFGVPSHHLTLRKEICDWMAARKERYEPFVEDDRGLDVHLRNMREQGTYGGHLELSAFAHLKRRNVKVIQPGLVYVIEWAGGSDPEELRREEKRRKGKGKEVDNESDDEDEDTAVYVAYHDWEHFSSVRNLKGPHQGRPHVVESSPAPLPISKPSRPSPTRTKSGSLRIKLKPSKPSAAATGDPAVSSLQPTAVPLPRSVSPSSDLTTTSGSASASTSSFSQPPATPPDAFSALNPGLSPPPLHPRASRSPKRSFDESEGADSVASSGGGGKRPRGMAHGTEDAGLDNSSNIVDDDELEDSRSDLSSPLTSPGSTPARVRSPSPASHPHPPPLSLPEPLPSFIETPPTPQEVSKSLNQRPLTRRQRKLLGLPKPRPNLVRAAGAHGSSGKIVVPGGKHPKRQGKGWVIVSEDDEPGPVQDAPFQEWVSNGNGRVDVRGFRELKI", "metadata": {"id": "A0A164M8E7", "cluster": 6452585, "interpro_all": ["IPR003323", "IPR038765", "IPR050704"], "interpro_used": ["IPR050704", "IPR003323", "IPR038765"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to these design specifications: The protein should have a DUF4005 domain that is typically found at the C-terminus of plant IQ domain-containing proteins and facilitates cooperative interactions with calmodulins or calmodulin-like proteins. It may also associate with nucleic acids to regulate gene expression at the transcriptional or post-transcriptional level. It is expressed in Acer negundo (Box elder).", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 3066, 2162, 43, 4855, 10432, 24316, 3418, 1988, 1977, 5745, 2435, 2019, 1920, 45, 17, 7822, 1927, 4496, 8338, 3418, 17, 3165, 2697, 1930, 11374, 13350, 3719, 1956, 17537, 1036, 2014, 17537, 17, 3189, 2697, 18, 2176, 2278, 2222, 11774, 1956, 11079, 4576, 1942, 5741, 2359, 2294, 2019, 1920, 5224, 2014, 2753, 17, 5224, 2237, 18, 2176, 1977, 3198, 1922, 8298, 1005, 2922, 2652, 1037, 12, 5758, 7177, 13, 18, 3], "output": "MAEEESSKVNFPQPPPFLEVECKISGKTSRYAAGTKAGFAVNLINKKLDCVRPLALHIEAVKQGEEPVSFGPDALLVDYGDGWKLQIVTQLDFTATWNGEGFGPIPQRIPGAMDSEDGRPIYRISKPGISGGKPVAEIWRLPPWCPTTWSTASTQARLRSRSAPRQREKSGLGSGSAKKRLSFPVPEPGFGDSDIGSHEYSWRSTSYKSIAHGIHPRMEQRSNISSCCNESIEDDEIYPPSTNNLRRWLR", "metadata": {"id": "A0AAD5J6C6", "cluster": 6995609, "interpro_all": ["IPR025064"], "interpro_used": ["IPR025064"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that will have the following function: The protein belongs to the DNA mismatch repair protein MutS, core domain superfamily, which initiates the post-replicative repair of point mutations and small insertion/deletion loops by specifically recognizing mispaired nucleotides. This domain adopts a multi-helical structure that acts as a central lever within the MutS dimer, facilitating the formation of an ATP-dependent clamp that translocates along the DNA. By recruiting partners such as MutL, it ensures genomic fidelity and prevents recombination between partially homologous sequences. It is present in Myxococcales bacterium and corresponds to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 2678, 10265, 5059, 2213, 2446, 1036, 16, 4728, 3418, 13975, 16, 2154, 18637, 1920, 2753, 17, 20604, 5059, 1927, 3575, 3527, 1930, 2858, 7413, 19, 5541, 11109, 2007, 4475, 15667, 5682, 4302, 3030, 9519, 18, 2052, 3418, 24032, 43, 2779, 17, 11514, 3170, 1988, 8016, 1966, 43, 4101, 13732, 2651, 1920, 2446, 1036, 7632, 16, 12440, 1920, 3337, 1927, 1925, 4498, 17, 3100, 10209, 1988, 29102, 4231, 1920, 2678, 18, 2007, 17040, 7228, 2427, 1966, 2446, 1024, 16, 2176, 18705, 4935, 14013, 1930, 10299, 7827, 2192, 6426, 8725, 3709, 18, 2176, 1977, 2481, 1922, 21464, 11748, 1918, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MFTGAPVLDSPAMTSDSHPFAEYRRRAERCRKTLARLERWSLALANTRLTLFLLALALAGLGWWGKLPATALWAALGLGLGFLVAAVAHDRVLSAGERARHRLAINERGLARLEDRWAELPQLGEAYDDPSHPYAHDLDLFGRSSLFQLLDATTTRWGEERLAGWLRQGAPSSEIASRQQAVAELAPLVELREELEAEGRMLAETKPDPARMLAWAESKRPARFARVSRWLPFALPPLTLALYLAGDFGLLPARLWFAGLGAQAAIAFFAS", "metadata": {"id": "A0A3D1QYQ7", "cluster": 8910316, "interpro_all": ["IPR036187"], "interpro_used": ["IPR036187"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein possesses 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. In addition, the protein is included in the Neurokinin receptor family, which constitutes a group of rhodopsin-like G protein-coupled receptors (GPCRs) that recognize tachykinin peptides such as substance P, substance K, and neuromedin K. These integral membrane proteins possess a seven-transmembrane architecture and transduce extracellular signals via G proteins to regulate biological activities including sensory transmission and smooth muscle contraction. It is native to Operophtera brumata (Winter moth) (Phalaena brumata) and is associated with UniProt keywords Transducer, Transmembrane helix, and G-protein coupled receptor.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 14465, 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, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 3366, 21124, 3148, 3416, 16, 2154, 14879, 43, 2210, 1927, 20586, 17, 3189, 49, 2213, 17, 6416, 4086, 12, 17723, 13, 1988, 9967, 12762, 23674, 15020, 5320, 2427, 1966, 7311, 58, 16, 7311, 53, 16, 1930, 11408, 1919, 1921, 53, 18, 2144, 12328, 3260, 2697, 7150, 43, 5260, 17, 9117, 9335, 1930, 30334, 5329, 4771, 3454, 49, 2697, 1942, 5741, 3933, 4209, 2710, 6893, 5303, 1930, 6689, 3760, 8332, 18, 2176, 1977, 6196, 1942, 3641, 2688, 24661, 28171, 3368, 3857, 12, 12028, 6798, 13, 12, 28752, 3336, 2175, 28171, 3368, 3857, 13, 1930, 1977, 2458, 1956, 20709, 11569, 14848, 16, 9117, 7864, 16, 1930, 49, 17, 2213, 6416, 3148, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "VVKMFILVIVIFGICWLPYHTYFAMANAMVNPLIYYWMNAKFRTYFSPPDNSQSGSRSRSGFYSLTIRVSIYTHFHPSILYMKYVQHMYLGFYWLRTAILCRWPICCRRKRPPPD", "metadata": {"id": "A0A0L7KMW3", "cluster": 9195204, "interpro_all": ["IPR000276", "IPR017452", "IPR001681"], "interpro_used": ["IPR017452", "IPR001681"], "interpro_unused": ["IPR000276"]}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein is assigned 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. In addition, the protein has a Thioredoxin-like fold domain that regulates target protein activity through thiol-disulfide exchange reactions within redox signaling pathways such as the ferredoxin/thioredoxin and glutathione/glutaredoxin systems. It features a characteristic three-layer \u03b1/\u03b2/\u03b1 core structure and functions as a hydrogen donor to reduce disulfide bonds in substrate proteins. Moreover, the protein is classified under the Thioredoxin-like, prokaryotic family, which includes small proteins such as ArsE that serve as components of nitroreductase systems capable of reducing nitro groups on aromatic organoarsenicals. While sharing the thioredoxin fold, some members exhibit low intrinsic thioredoxin activity and lack glutathione-disulfide oxidoreductase function. It has been characterized in Margulisiibacteriota 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, 6304, 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, 1922, 2459, 16, 1920, 2213, 2258, 43, 23684, 17, 3189, 3728, 3418, 1988, 7014, 2758, 2213, 2455, 2596, 13914, 17, 11830, 6818, 5298, 2651, 9366, 3197, 3873, 2427, 1966, 1920, 25304, 22389, 10960, 19, 23684, 1930, 9153, 19, 19406, 1919, 9754, 3771, 18, 2176, 4075, 43, 6293, 2559, 17, 4757, 160, 19, 161, 19, 160, 4728, 3170, 1930, 4088, 1966, 43, 6201, 6282, 1942, 4412, 11830, 9031, 1922, 4510, 2697, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 23684, 17, 3189, 16, 21545, 3416, 16, 2154, 5921, 2858, 2697, 2427, 1966, 9896, 1021, 1988, 7120, 1966, 4178, 1927, 8686, 3510, 10410, 3771, 7131, 1927, 5526, 8686, 2671, 1990, 10761, 3090, 12729, 17221, 2046, 1036, 18, 2679, 10763, 1920, 23684, 3728, 16, 2673, 4678, 5987, 2330, 7598, 23684, 2455, 1930, 3630, 9153, 17, 11830, 27388, 2347, 18, 2176, 2258, 2252, 4378, 1922, 6142, 13004, 12924, 26073, 2341, 18842, 7336, 14061, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MIKIEVVGTESEEQQDMLRNVHHAIHELKLNGKLKCQGHIIDVEKIKECLKEVKEAEVDEITDVNEIADRFGMVVTPAIFV", "metadata": {"id": "A0A948DP04", "cluster": 13184531, "interpro_all": ["IPR012336", "IPR036249", "IPR005243"], "interpro_used": ["IPR036249", "IPR012336", "IPR005243"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein possesses 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. Moreover, the protein is classified under 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. 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. It has been detected in Plebeiobacterium sediminum. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 14465, 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, 3950, 16, 1920, 2213, 1977, 5947, 2441, 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, 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, 2176, 2258, 2252, 3330, 1922, 6483, 5873, 3940, 7972, 2341, 18842, 1989, 6276, 1980, 28658, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MKNISVLLADDDHRIRNAIHTILVQNFISIQIVAKTDSLENTIEALNTYKPDIAILDMHLINGTAIEVLKKTTHLSYKVIFMSAYQEYALDDIRFASIDFIYKPLDISDLLITVDNVITELVEEGYKKKMQTFFINTNYENEDKQIIFKTKSQILSVPISAIIYGESHYSLSYFALETGKQIEIKEPLRRYESMLQSYNFFRCHPLFIVNINHILAVDYSTKLLTLTNHLTIPFEKKRLGILTQNWHKNTKSEVRIKSYKSV", "metadata": {"id": "A0AAE3M7S4", "cluster": 14251854, "interpro_all": ["IPR011006", "IPR046947", "IPR007492", "IPR001789"], "interpro_used": ["IPR007492", "IPR046947", "IPR001789"], "interpro_unused": ["IPR011006"]}, "task_type": "autoregressive"} {"instruction": "The protein has 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 native to Elysia marginata and carries UniProt keyword assignments Metal-binding and Zinc-finger. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 2258, 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, 6196, 1942, 2349, 2012, 2126, 9027, 5499, 1930, 16252, 20709, 11121, 2538, 18306, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MKELKFIDLIVFLRERKPSSVGEMKTLAERYRVAHPNKPLAKPCVMENTFIASAYKTNQQAGQYTQNFKHRGPAFAAQEPSFSGQRPQNYKTQSSGSGVPPVDSGSPTGEPTNPRSAYTCYRCGERGHIAKSCENPPLCKKC", "metadata": {"id": "A0AAV4GAC1", "cluster": 15658119, "interpro_all": ["IPR001878", "IPR036875"], "interpro_used": ["IPR001878"], "interpro_unused": ["IPR036875"]}, "task_type": "autoregressive"} {"instruction": "The protein is assigned to the Small ribosomal subunit protein uS4 family, which binds directly to 16S rRNA to initiate small subunit assembly and stabilize the RNA tertiary structure. Members of this family, including the U3 small nucleolar ribonucleoprotein IMP3, are also essential for pre-18S rRNA processing and play a critical role in maintaining translational fidelity. Also, the protein features a RNA-binding S4 domain that mediates binding to RNA and is widely distributed in translation-related proteins. This small structural motif is found in ribosomal subunits, pseudouridine synthases, and tyrosyl-tRNA synthetases, where it facilitates nucleic acid recognition across bacterial and eukaryotic systems. It has been detected in Rhizodiscina lignyota and exhibits UniProt keyword tags Ribosomal protein and rRNA-binding. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 1977, 6304, 1942, 1920, 2858, 11196, 5903, 2213, 2022, 1006, 3416, 16, 2154, 6876, 4103, 1942, 11209, 9067, 1942, 11051, 2858, 5903, 5957, 1930, 13448, 1920, 3146, 10832, 3170, 18, 4678, 1927, 2052, 3416, 16, 2710, 1920, 63, 1010, 2858, 23770, 18347, 6657, 2754, 1010, 16, 2032, 2222, 4415, 1958, 2097, 17, 17659, 9067, 4587, 1930, 3918, 43, 4140, 2770, 1922, 8231, 8414, 14013, 18, 2222, 16, 1920, 2213, 4075, 43, 3146, 17, 2743, 6934, 3418, 1988, 10412, 2743, 1942, 3146, 1930, 1977, 5673, 6533, 1922, 6410, 17, 2712, 2697, 18, 2052, 2858, 4346, 5219, 1977, 2435, 1922, 11196, 6991, 16, 11520, 23864, 8921, 1036, 16, 1930, 6578, 2199, 17, 10089, 18185, 1036, 16, 2597, 2176, 11374, 11079, 2687, 5708, 3436, 4543, 1930, 10825, 3771, 18, 2176, 2258, 2252, 3330, 1922, 13458, 15799, 12709, 4058, 12975, 25749, 3857, 1930, 9826, 20709, 11121, 2538, 14392, 11196, 2213, 1930, 9067, 17, 2743, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "KVRQDWSKWTLYNLSRLTVPRTDRASYFQQKWAAKSITRGYHGEHIREKKWNRIFSRSIPAVVPMDYRDLAKSDGADQAMGRGQGEDVNTDAVTRLPSKQRTPYMQMAFHPLERRLDTAIWRALFASSVRQARMLCTQGHVRVNGKEMRHPSYNLNPGDMFSVTPKWVMQATGATKFYLGTQERTKKIYEKAQELLKDIRTEFSKATQAEEASADQAAAEAEADAEEEAAASEDGLSEEERAAKKTLKDLRKEIMAVLDEKKPDLSNKQKQLLRALRTDIPKMMSKKQFSAEDVAAAQQRFTEANSANLSDTATSATGASDDLSTPEFTETQIASSTSLLTDLRSQIQYLGQPWRPRPYMSAFAFIPRYLEVNQNVCSAVYLRHAVVRPGLAEVPTPFPEGLNQLAFNWYLKRR", "metadata": {"id": "A0A9P4IL00", "cluster": 16238588, "interpro_all": ["IPR022801", "IPR002942", "IPR036986"], "interpro_used": ["IPR022801", "IPR002942"], "interpro_unused": ["IPR036986"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: It is part of the Universal stress protein A family, which facilitates cell survival during growth arrest and stationary phase. These cytoplasmic serine/threonine phosphoproteins are predicted to bind DNA and may be structurally related to MADS-box proteins. Moreover, the protein should have a UspA domain that confers stress endurance and enhances bacterial cell survival during prolonged exposure to adverse conditions. Adopting an \u03b1/\u03b2 fold, this domain is also utilized in regulatory contexts, such as modulating ectoine uptake in the TeaD protein via ATP-dependent oligomerization. It is present in Pseudomonadales bacterium.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 2176, 1977, 3131, 1927, 1920, 10321, 3071, 2213, 43, 3416, 16, 2154, 11374, 2024, 3298, 2409, 2905, 8048, 1930, 12563, 3193, 18, 2144, 6823, 8468, 19, 13143, 8078, 22163, 1036, 2032, 4396, 1942, 4566, 2678, 1930, 2278, 1998, 12171, 2712, 1942, 9133, 1036, 17, 5758, 2697, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 14277, 1019, 3418, 1988, 16556, 3071, 17948, 1930, 9515, 4543, 2024, 3298, 2409, 7171, 3395, 1942, 5246, 2961, 18, 20478, 1925, 160, 19, 161, 3728, 16, 2052, 3418, 1977, 2222, 7079, 1922, 4948, 11144, 16, 2427, 1966, 10871, 7495, 9024, 1021, 5047, 1922, 1920, 12459, 1007, 2213, 3454, 4498, 17, 3100, 17371, 18, 2176, 1977, 2481, 1922, 11520, 3947, 7324, 2612, 14061, 18, 3], "output": "MLSLNRILVAVEQDDTARFVVEDASIHDAADRQQLKTYLMEAEESWLQDFLDGLSLNARDCEANLVVKAAHQPHGLDAVMRTPQDWNLLRHAELHEEQETLNRAILREAAGLTQVLEGELDVVVAHPFVQGEIESEIRTTVNKLADEESVKYRYLHIEEGTTAVAVARDGLKGLVLGNTSETILYHVQSDVVVLRKAAELAQAANAELHIVRVIYDANVVKVIESATIWNKDEYAGILDAIPVMIVKSQAWKASPVVLAAIDVPWIGPNTVPIDFDRVKGHQVDSTGAELLVMGTV", "metadata": {"id": "A0A962L0G3", "cluster": 16323794, "interpro_all": ["IPR006015", "IPR006016"], "interpro_used": ["IPR006015", "IPR006016"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein belongs to 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. In addition, the protein incorporates a BD-FAE-like domain that adopts an \u03b1/\u03b2-hydrolase fold with a Ser-Asp-His catalytic triad to primarily function as a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans. This versatile scaffold also supports diverse hydrolytic activities across organisms, including kynurenine formamidase activity in tryptophan degradation, isoprenylcysteine demethylation in plants, and immunogenic lipase activity in bacterial pathogenesis. It has been detected in Bacteroidota bacterium.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 14440, 1942, 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, 1922, 2459, 16, 1920, 2213, 19683, 43, 5238, 17, 5685, 1021, 17, 3189, 3418, 1988, 24032, 1925, 160, 19, 161, 17, 20748, 3728, 1956, 43, 2375, 17, 4138, 17, 4167, 6804, 21845, 1942, 5985, 2347, 1966, 43, 29491, 4635, 1944, 10921, 1930, 6894, 23665, 26389, 3500, 1990, 2796, 4613, 23665, 1036, 18, 2052, 20425, 7281, 2222, 7825, 6445, 26702, 4209, 3436, 7373, 16, 2710, 23523, 24684, 2053, 2386, 25238, 2051, 2455, 1922, 13489, 4877, 16, 26690, 2199, 23159, 7595, 20254, 1922, 4793, 16, 1930, 18835, 16653, 2455, 1922, 4543, 6559, 18, 2176, 2258, 2252, 3330, 1922, 24323, 7336, 14061, 18, 3], "output": "MQVLRNQVVPGYNNMYSHGFNGFKDWGGMNLIAXNGFVAGDCQAFSQDNFSIGLYDLSMCMNLLTQNANQTAKDARVSALITWASVHECKTRTAQQMPLNYQLAQDFSDHEEGTQDQAVPITAGRLLRSWNPVAACFEVMETMIDFLNRQELMPILWDLFLPETPANTVLLFFKYNASHNGTSPEHPEEFVNLHFQGFKHIVLLGHSKGGGLSILPWGRWNDEQMQLWKQNGVAYYFNAAFDLQSNISRIQQPMLLIHWMEPETDHVFGRKHPESNTALPEL", "metadata": {"id": "A0A7D5N6D7", "cluster": 16504924, "interpro_all": ["IPR029058", "IPR049492"], "interpro_used": ["IPR029058", "IPR049492"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein I want to design has this role: The protein possesses a Cyclic nucleotide-binding conserved site that mediates the interaction with cAMP or cGMP to regulate signal transduction. This domain typically folds into a structure composed of three alpha-helices and a distinctive eight-stranded antiparallel beta-barrel, maintained by invariant glycine residues. It is found in diverse proteins, including prokaryotic catabolite gene activators, cyclic nucleotide-dependent kinases, and vertebrate ion channels. Additionally, the protein is assigned to the RmlC-like jelly roll fold superfamily, which adopts a mainly beta jelly roll topology and functions as a dTDP-sugar isomerase, specifically dTDP-4-dehydrorhamnose 3,5-epimerase. This domain catalyzes a key step in the biosynthesis of L-rhamnose, a saccharide essential for the virulence of certain pathogenic bacteria. It is identified in Rotaria sordida. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 14465, 43, 9821, 5489, 17, 2743, 5305, 3200, 1988, 10412, 1920, 2835, 1956, 6225, 2014, 15958, 1942, 5741, 2733, 8201, 18, 2052, 3418, 5745, 16231, 2460, 43, 3170, 7179, 1927, 2559, 4595, 17, 12789, 1930, 43, 15308, 5066, 17, 10338, 28892, 4666, 17, 19560, 16, 5514, 2007, 17004, 10646, 4248, 18, 2176, 1977, 2435, 1922, 6445, 2697, 16, 2710, 21545, 3115, 3016, 2394, 2359, 15497, 16, 9821, 5489, 17, 3100, 7784, 16, 1930, 13416, 4755, 5628, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 10625, 8293, 17, 3189, 8988, 11560, 1012, 12970, 3728, 13975, 16, 2154, 24032, 43, 4994, 4666, 8988, 11560, 1012, 12970, 13678, 1930, 4088, 1966, 43, 7711, 10274, 17, 9523, 25510, 16, 4475, 7711, 10274, 17, 24, 17, 28936, 5004, 17652, 2217, 23, 16, 25, 17, 13872, 9213, 2051, 18, 2052, 3418, 17097, 43, 3834, 3537, 1922, 1920, 8132, 1927, 54, 17, 23120, 2217, 16, 43, 14175, 2205, 3695, 4415, 1958, 1920, 9304, 1927, 4908, 8070, 4802, 18, 2176, 1977, 2899, 1922, 30029, 3027, 1019, 6548, 7408, 3825, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MALNYGTLIRAASKLPEQRTTTEINDFIVPWLKQSLKKKQGIFQKISDDVIYDICKTIMLERRPAWDVVIRQNDPGDTFYIILQGSVNIYRLDDDNPQSILMDIDTVTEFPQLDDDLDKREELIAQAFGNYIVTLVGGFDFGERALITNEPRSATVMTTMPTDLLVVDREVFSRTLKSAHEKELQEKTEFINRCPLFSSWPARLKRLVSLSLERGRFAYDTVLYKQGTFADAVYFIWSGEVKLTIDPLLHWLQYPHLLPQSDPMKQRAFELFLPMLQLSRPMDTVSRESFAIKRRYMTFAEAEKERSYRNRQVALLNTGDIVGLESYVCDLTTHMNSARCTAPCDLFYILKHNFIRLQKRHGTQGLSERLREIVLLSFQAYPSRILHLPLFKSLMKRQLAPVMNDEQQQYHVKQSWLFHIHNATHSNTRRLGATLAHTSTTNNTSPTRLYRSTPLGSAAAVQYVTNDHVRLSKIEDRLKQWHAQMGDDSKTQIRSLTRFNVACATGSAPTRPSPPDTLESQSDATGITSSTFSDGNEPTVSVEALTEATSSMNEPLSTHPISTSSSSTTHLPQLRIYTKQERYEDLRAYLKQAWKEFLKRPIPTVY", "metadata": {"id": "A0A815IUZ1", "cluster": 17863856, "interpro_all": ["IPR018488", "IPR000595", "IPR018490", "IPR014710"], "interpro_used": ["IPR018488", "IPR014710"], "interpro_unused": ["IPR018490", "IPR000595"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein should feature a Damage-control phosphatase ARMT1-like, metal-binding domain that functions as a metal-dependent hydrolase involved in metabolic damage pre-emption. It coordinates a metal ion, likely magnesium, to limit the accumulation of potentially harmful phosphometabolites in a cellular \"housecleaning\" process. Additionally, it is part of the Damage-control phosphatase PH1575-like family, which comprises metal-dependent phosphatases found in bacteria and archaea that likely perform damage-control functions. These enzymes exhibit phosphatase activity against p-nitrophenyl phosphate and are suggested to hydrolyze oxidatively damaged purine nucleotides or their biosynthetic intermediates. It has been detected in Bacillota bacterium (Firmicutes 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, 3066, 5961, 43, 4293, 17, 2285, 8167, 6011, 6613, 17, 3189, 16, 6048, 17, 2743, 3418, 1988, 4088, 1966, 43, 6048, 17, 3100, 20748, 3286, 1922, 4487, 4293, 2097, 17, 9613, 2001, 18, 2176, 10675, 43, 6048, 4755, 16, 3205, 13148, 16, 1942, 4411, 1920, 4858, 1927, 5063, 13635, 8078, 14578, 3016, 2923, 1922, 43, 3689, 6, 5953, 3283, 15393, 1029, 6, 2585, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 4293, 17, 2285, 8167, 2087, 16151, 1015, 17, 3189, 3416, 16, 2154, 12936, 6048, 17, 3100, 19131, 2435, 1922, 4802, 1930, 21501, 1988, 3205, 2385, 4293, 17, 2285, 4088, 18, 2144, 5038, 5987, 8167, 2455, 3316, 58, 17, 28513, 5413, 1930, 2032, 3978, 1942, 7222, 6931, 5163, 1954, 10756, 19700, 9519, 2014, 2310, 14041, 12386, 18, 2176, 2258, 2252, 3330, 1922, 8175, 22538, 3857, 14061, 12, 24474, 14061, 13, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "MKAKKPCIECSVNQAIRALEQVNYSEELRQEVIRRTREELEGLALDATTPAEVSTIAVKTACRLMGNADPYAAEKERYNLLALEMAPRLEKLVDESGDPLMTAILLSIAGNIIDLGIVSDIDLDETVESVLRRGLAISHYEEFIRHLERAKTLLFLADNAGEIVFDKFLLRKFRDRGIDVTFAVKGGPVANDACVEDAKMVGIDQLARVITTGADRLGIPLERCSEAFLEEFNRADMVISKGQANFESLDELRDRDNLFLLLTAKCDMVAQRLGVEPKSVVLVKCGQI", "metadata": {"id": "A0A7C6PSU4", "cluster": 18189849, "interpro_all": ["IPR036075", "IPR002791", "IPR014444"], "interpro_used": ["IPR002791", "IPR014444"], "interpro_unused": ["IPR036075"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein can be placed in the CoA-transferase III domain-containing protein family, which functions as a coenzyme A (CoA) transferase involved in metabolic pathways such as oxalate catabolism, the methylaspartate cycle, and aromatic compound degradation. These enzymes catalyze the transfer of CoA to carboxylic acid substrates like succinate, mesaconate, and glutarate, playing roles in fatty acid metabolism and the detoxification of plant-derived compounds. Additionally, some members contribute to acid tolerance responses in low pH environments. It is expressed in Acidobacteria bacterium RIFCSPLOWO2_02_FULL_59_13.\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, 10027, 17, 13763, 4337, 3418, 17, 3165, 2213, 3416, 16, 2154, 4088, 1966, 43, 22051, 43, 12, 10027, 13, 13763, 3286, 1922, 4487, 3873, 2427, 1966, 25069, 19480, 16, 1920, 4963, 13432, 5263, 2010, 4048, 16, 1930, 10761, 3547, 4877, 18, 2144, 5038, 18170, 1920, 3856, 1927, 10027, 1942, 18708, 2687, 6249, 3189, 19234, 16, 4438, 26704, 2010, 16, 1930, 19406, 2010, 16, 14797, 5456, 1922, 5934, 2687, 4714, 1930, 1920, 18169, 1927, 4496, 17, 3595, 4300, 18, 4950, 16, 2673, 4678, 4672, 1942, 2687, 6555, 3387, 1922, 2330, 2087, 8114, 18, 2176, 1977, 3198, 1922, 2687, 10296, 14061, 12424, 2792, 2030, 1971, 5265, 41, 5725, 41, 4125, 41, 4777, 41, 2590, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MDVSMQEAVAADLQWTMALYDLKGVAREREGGWEEMVSWMASEGMAGDLEEPRWQNVMERRAGEAHIREAVKRRLAFGPSNTAGELVSDPHLNARDFFVDVEHPEKRAPLRGEHNQEIYVQRLGLSPDEVTKLQKQGAISKLFPCKDGYVRYSAGRNEVLVAFLLTHTKAEIYELGQTFRYPGPPVRLTETPWAV", "metadata": {"id": "A0A1F2T3C2", "cluster": 19186561, "interpro_all": ["IPR050483", "IPR003673", "IPR044855", "IPR023606"], "interpro_used": ["IPR050483"], "interpro_unused": ["IPR003673", "IPR023606", "IPR044855"]}, "task_type": "infilling"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein is categorized in the Protein of unknown function DUF5076 family, which represents a group of uncharacterised bacterial proteins. It occurs in Sphingomonas lutea.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 17968, 14099, 1016, 3416, 16, 2154, 4972, 43, 2210, 1927, 23229, 3495, 4543, 2697, 18, 2176, 5110, 1922, 13502, 10480, 12867, 1019, 18, 3], "output": "MSFGRKPRNQLDLVGNDHHQGPVDTFLDPTLLKEPEAFGLNRIYQGMMKHLTDPEGSAAESRVRILGHERTLDDLTFEVLRVWVTMMATVLHDASRAYAEEYRLDGSVA", "metadata": {"id": "A0A7G9SJH4", "cluster": 19669227, "interpro_all": ["IPR031796"], "interpro_used": ["IPR031796"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We aim to build a protein that does the following:\nThe protein incorporates a Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain that functions as a non-heme iron-dependent catalyst within the cupin superfamily, characterized by a double-stranded $\\beta$-helix core. It coordinates an Fe(2+) ion using histidine and aspartate residues to drive oxidative reactions, such as the cyclization of peptides in beta-lactam antibiotic biosynthesis. This domain is also essential for diverse metabolic processes, including collagen modification in animals and ethylene formation in plants. Additionally, the protein should contain a Non-haem dioxygenase, N-terminal domain that constitutes the highly conserved N-terminal region of enzymes with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity. It is found in a diverse array of proteins, including isopenicillin N synthase, 1-aminocyclopropane-1-carboxylate oxidase, and gibberellin oxidases. Moreover, the protein should have a Oxoglutarate/iron-dependent dioxygenase domain that catalyzes the oxidation of diverse organic substrates using dioxygen, a ferrous iron cofactor, and 2-oxoglutarate as a co-substrate. Structurally characterized by a conserved double-stranded $\\beta$-helix core, this domain functions in a wide array of biological processes, including DNA repair, oxygen sensing via prolyl hydroxylation, and the biosynthesis of antibiotics and plant hormones. It has been characterized in Mycolicibacterium fortuitum (Mycobacterium fortuitum) and contains UniProt keyword associations Metal-binding and Oxidoreductase.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 19683, 43, 10301, 7245, 6806, 56, 8921, 17, 3189, 16, 2650, 12, 22, 15, 13, 22, 2021, 23652, 10465, 2432, 2051, 3418, 1988, 4088, 1966, 43, 2447, 17, 10954, 5680, 17, 3100, 12715, 2651, 1920, 14967, 1921, 13975, 16, 4378, 2007, 43, 4825, 17, 10338, 8, 38, 4666, 8, 17, 7864, 4728, 18, 2176, 10675, 1925, 2650, 12, 22, 15, 13, 4755, 2193, 13873, 1930, 12878, 4248, 1942, 9265, 5163, 5298, 16, 2427, 1966, 1920, 25267, 1927, 5320, 1922, 4666, 17, 15294, 7267, 8132, 18, 2052, 3418, 1977, 2222, 4415, 1958, 6445, 4487, 4028, 16, 2710, 5621, 6295, 1922, 3555, 1930, 13183, 3337, 1922, 4793, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 2447, 17, 7105, 23652, 10465, 2432, 2051, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 3626, 5305, 56, 17, 4262, 3031, 1927, 5038, 1956, 22, 17, 18588, 16542, 17488, 19, 2650, 12, 2890, 13, 17, 3100, 23652, 10465, 2432, 2051, 2455, 18, 2176, 1977, 2435, 1922, 43, 6445, 6472, 1927, 2697, 16, 2710, 10301, 7245, 6806, 56, 8921, 16, 21, 17, 3835, 22170, 27379, 2516, 17, 21, 17, 20877, 10488, 16, 1930, 10122, 2361, 20912, 10488, 1036, 18, 3950, 16, 1920, 2213, 3066, 2162, 43, 18588, 16542, 17488, 19, 5680, 17, 3100, 23652, 10465, 2432, 2051, 3418, 1988, 17097, 1920, 6638, 1927, 6445, 6805, 6249, 2193, 23652, 10465, 2432, 16, 43, 26739, 5680, 15155, 16, 1930, 22, 17, 18588, 16542, 17488, 1966, 43, 2081, 17, 4510, 18, 12171, 4378, 2007, 43, 5305, 4825, 17, 10338, 8, 38, 4666, 8, 17, 7864, 4728, 16, 2052, 3418, 4088, 1922, 43, 4743, 6472, 1927, 3933, 4028, 16, 2710, 2678, 5059, 16, 4612, 9306, 3454, 3192, 2199, 21319, 16, 1930, 1920, 8132, 1927, 7560, 1930, 4496, 10224, 18, 2176, 2258, 2252, 4378, 1922, 5078, 4485, 26073, 2341, 18842, 1989, 17133, 6420, 1989, 12, 16389, 17133, 6420, 1989, 13, 1930, 5461, 20709, 11121, 2538, 5253, 6048, 17, 2743, 1930, 27388, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MTQPEVIVDQVVLRDGFVPLIDISSARNGDSSGFLLLVGHGVPDRVIDDANRALREFFSLFSSAGSLAATNDGADRAAEHESPDHVEKFVYFAGFRTAYQRYYDEMAALATELSRLFAHYPADNQPEGHIRLSPHSDWGNLTILLQDESQSGLQVRIGDLLARWTNDRWVSTVHRVVSTGAPTAERFSPDNPARYEPVVSGPYLLDKFRVAYALNPQQRQRQAVADAIGRCCEPQAVKEQVKADPSDPLARGPLGNPEGVDGPGWTDQRVAVAERWPEVLALGLREDWFDEKIDRHNSNLMANGDRGDWLDVPVVPGSFVINLPFFHQPNFDAVIECIPTCAT", "metadata": {"id": "A0AAE5ADI6", "cluster": 21732179, "interpro_all": ["IPR026992", "IPR044861", "IPR027443", "IPR050231", "IPR005123"], "interpro_used": ["IPR044861", "IPR026992", "IPR005123"], "interpro_unused": ["IPR027443", "IPR050231"]}, "task_type": "infilling"} {"instruction": "I want to make a protein that can have this function: 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 includes a AMP-binding enzyme, C-terminal domain that functions as a dynamic module in ATP-dependent AMP-binding enzymes, such as Acetyl-coenzyme A synthetase, by undergoing a large rotation to permit both catalytic half-reactions. This structure consists of a central \u03b2-sheet core flanked by \u03b1-helices and is found in eukaryotes, bacteria, and archaea. Additionally, the protein includes 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 Planctomycetaceae bacterium. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 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, 5921, 43, 3681, 17, 2743, 4113, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 5760, 9059, 1922, 4498, 17, 3100, 3681, 17, 2743, 5038, 16, 2427, 1966, 6894, 17, 22051, 43, 18185, 16, 2007, 7258, 43, 3103, 8891, 1942, 11832, 2321, 6804, 4768, 17, 5298, 18, 2052, 3170, 7543, 1927, 43, 4101, 161, 17, 11130, 4728, 20185, 2007, 160, 17, 12789, 1930, 1977, 2435, 1922, 15021, 16, 4802, 16, 1930, 21501, 18, 4950, 16, 1920, 2213, 5921, 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, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MTEFQFDKSFIEILEDALQTHAARTCLKFGAHSFSYAQVADLSGRISRGLISRGLKKGMKGAVYSTNSAISFIAALGLLRAGGVWIPINPRNSVRDNIDTLELFDCELLFYQSSFADVATDAAGRLGSDLLIVDIDDGPMAPLKIGDFLSLTGASVPEVRVVGSDMITIPSTGGTTGRPKGVMLTNRNFCALDYGMRQRYGGYDPVVMCAAPMTHVAGRIALTSMSSGARFVILDQVDPQRVLNTIQDEGITDFFLPPTGIYSLLDQPNVREFDYSSLKAIGYGSAPMAPKKIREAIQVFGPVMRGGFGQTECPMFISSLSQKDHFIDGAIAPDSRLLSVGKATCISEIAILNDEGDVLPPNELGEIAVKGPMVSEGYYMNPEETEQIRLNGWHLTGDIGYLTEDGYLYVVDRKKDMIITGGFNVYSSEVEQALMSIPGISVAVVVGVPSERWGEEVKAVIQTDSDCVLTEDEVIAYSKDLIGSVKSPKSVEFTADIPRTSVGKIDKKMIRQKYWASTDRYV", "metadata": {"id": "A0A5Q4GKR2", "cluster": 22787446, "interpro_all": ["IPR025110", "IPR045851", "IPR000873", "IPR042099"], "interpro_used": ["IPR042099", "IPR025110", "IPR000873"], "interpro_unused": ["IPR045851"]}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe 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 has been detected in Candolleomyces eurysporus.\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, 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, 2258, 2252, 3330, 1922, 4954, 2201, 1021, 29249, 18180, 2012, 2074, 1957, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MPTPSQLSRPESDGCISFFVFPRELIDSIVEDIRGLEDNDSTLRSFAIACKALRNDSAVISMVRNVRVEFLQQDFDSTFEHTSRARVFRELSKVWELSLRVPMLSSKALVSLSIVFFSLPSSIFSLCTNLKELNIQMGCIVECPVEPSNHTAQSRWPVPGGSRYTTADDKLAFPDLKKLQHLKAWFPDYVLRSIIDEPENPHKRRGLKKLTVEVLCLERGFSPEQVLPKFIRPLASLKNVERFEFIGVFQSLLVIEGCENALHPVSRDFAHAFLESVGARNTGRQFTNLIQQASRLLSRAGEEAVADIFAAAGIRLSIQYLMLEEELAAADILDICRPFLFEKITITPGRDYTALLSSPQGSRCRFNPEDVNCSLQPIKSLPSGEVERPQLEVLSILKSLHLQVRAHNVDQLETFLSNEMFRSNMGTMLTEFNIKIACKEDVFGPSA", "metadata": {"id": "A0A9W8IWF7", "cluster": 24785684, "interpro_all": ["IPR032675"], "interpro_used": ["IPR032675"], "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 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 is identified in Sphingobacterium humi.\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, 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, 1977, 2899, 1922, 13502, 12022, 2490, 1033, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MMKKLVALIITLTSLHLGGIQDNWFVGVNAGGAIYFGDHDKQMDRFGARLGLGGFQYKGATQDPNYLNVNADFMFNWLNDVNGDHTKKMRVSPSLGILQTFEFGGRNAEGSLAALVGLNFKIWYAETEPKEGEPLLRKPSRAYQFGDLGKRISPKFEVYAGKWFDNLGTGKVWDASQNLQYQKFYSEQRLYSLIPYAGVGLMIGIRLSESLDLNIDVRGNIHGDGFDG", "metadata": {"id": "A0A6N8KV32", "cluster": 26104125, "interpro_all": ["IPR011250"], "interpro_used": ["IPR011250"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me a peptide sequence capable of: The protein is assigned to the The TMEM120A/B family, which comprises transmembrane proteins involved in lipid metabolism and adipocyte differentiation. While originally implicated in mechanosensation as potential ion channels, structural similarities to ELOVL7 and the presence of bound coenzyme A suggest they likely function as lipid-modifying enzymes. It is present in Rotaria sp. Silwood1 and features UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 1977, 6304, 1942, 1920, 1920, 22414, 9363, 1019, 19, 44, 3416, 16, 2154, 12936, 9117, 2697, 3286, 1922, 4486, 4714, 1930, 16219, 4155, 18, 2679, 10398, 6835, 1922, 2665, 6642, 5735, 1929, 1966, 2889, 4755, 5628, 16, 4346, 10857, 1942, 2349, 2579, 1024, 1027, 1930, 1920, 2990, 1927, 4124, 22051, 43, 3220, 2611, 3205, 2347, 1966, 4486, 17, 12691, 5038, 18, 2176, 1977, 2481, 1922, 30029, 3027, 1019, 2056, 18, 4059, 15269, 1009, 1930, 4075, 20709, 11569, 9117, 7864, 18, 3], "output": "GLSFLVPFLLVGYLFQLYNAYTLWELAHVSSTHEWQVMVLAIIFFLLFLGNILTTLSVLREKLREKPPPTLLKEKYQSLKTFLSTNYHRRTRSIHQYGHREDRQRLNKDNNTKITSKED", "metadata": {"id": "A0A821Y8D6", "cluster": 26737588, "interpro_all": ["IPR012926"], "interpro_used": ["IPR012926"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein has 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. Additionally, the protein is included 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 is present in Gemmatimonadetes bacterium 13_1_40CM_4_65_7.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2258, 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, 4950, 16, 1920, 2213, 1977, 3063, 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, 1977, 2481, 1922, 10607, 3368, 2265, 12502, 3695, 14652, 14061, 2590, 41, 21, 41, 3040, 12819, 41, 24, 41, 4459, 41, 27, 18, 3], "output": "MVTGSGALTTSTPVLSDAVLVERIAALGDRAALAELDTRHGMTLYAIAYTLLLNPDAADVAVAATLREAWRRAASFIAREQTVGRWLAQLTRKAAQDQLRRSVMSPGGLLPRRTSVAPPSPRPPAREPSAHRARTSLRLTWVAAALVLPLILLT", "metadata": {"id": "A0A1Q7GK25", "cluster": 27316908, "interpro_all": ["IPR007627", "IPR013325"], "interpro_used": ["IPR007627", "IPR013325"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should have a Formate/nitrite transporter conserved site that mediates the bidirectional transport of formate or nitrite across membranes, primarily in bacteria and archaea. It is characteristic of proteins such as FocA, FocB, and NirC, which facilitate the passage of these anions. Additionally, the protein is included in the Aquaporin-like superfamily, which comprises the Major Intrinsic Protein (MIP) family of transmembrane channels responsible for the energy-independent transport of water and small neutral solutes. These proteins form aqueous pores that function either as specific water channels or as facilitators for glycerol, urea, ammonia, and other carbohydrates. Found ubiquitously across all domains of life, they facilitate passive diffusion to regulate osmotic balance and solute permeability. It is found in Rotaria sp. Silwood1 and is annotated with UniProt keywords Transmembrane helix. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 3066, 2162, 43, 25741, 19, 15988, 9054, 5305, 3200, 1988, 10412, 1920, 18934, 4860, 1927, 25741, 2014, 15988, 3436, 5726, 16, 5985, 1922, 4802, 1930, 21501, 18, 2176, 1977, 6293, 1927, 2697, 2427, 1966, 3438, 1019, 16, 3438, 1014, 16, 1930, 12951, 1030, 16, 2154, 6628, 1920, 11008, 1927, 2144, 20464, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 29180, 1921, 17, 3189, 13975, 16, 2154, 12936, 1920, 3044, 7598, 2213, 12, 15070, 13, 3416, 1927, 9117, 5628, 5061, 1958, 1920, 3844, 17, 3484, 4860, 1927, 3224, 1930, 2858, 5459, 27993, 18, 2144, 2697, 2386, 8052, 14711, 1988, 2347, 3108, 1966, 2487, 3224, 5628, 2014, 1966, 21485, 1958, 9244, 16, 10505, 16, 14880, 16, 1930, 2303, 16282, 18, 2435, 21853, 3436, 2136, 4682, 1927, 3308, 16, 2611, 6628, 9832, 6601, 1942, 5741, 13951, 6766, 1930, 19661, 8828, 18, 2176, 1977, 2435, 1922, 30029, 3027, 1019, 2056, 18, 4059, 15269, 1009, 1930, 1977, 10633, 1956, 20709, 11569, 9117, 7864, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MTTIDARNFYETIEVISVNGVHKTKQRIDHMIIKTLLAGVFLSFGGLLLLTVGAGSTPIVQNLGSSIHKMIQGSVFPIGFVLIVITGADLFTGNTMVLMISTLHRKTTWLDLLISWIVSFFGNLAGCLFFQYIFVYYAGLLSNDPFRSFTVQLAETK", "metadata": {"id": "A0A822ARA6", "cluster": 28859936, "interpro_all": ["IPR023271", "IPR000292", "IPR024002"], "interpro_used": ["IPR024002", "IPR023271"], "interpro_unused": ["IPR000292"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe protein possesses a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. In addition, the protein is grouped in the Phosphoribosylglycinamide formyltransferase family, which catalyzes the third step in de novo purine biosynthesis by transferring a formyl group from formyl tetrahydrofolate to generate 5'-phosphoribosyl-N-formylglycinamide. While found as a standalone enzyme in prokaryotes, this domain typically occupies the C-terminal region of a multifunctional protein in eukaryotes that also exhibits GAR synthetase and AIR synthetase activities. It is native to Pseudanabaenaceae cyanobacterium LEGE 13415.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 14465, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3416, 16, 2154, 17097, 1920, 4563, 3537, 1922, 2028, 9441, 19700, 8132, 2007, 21902, 43, 29285, 2210, 2037, 29285, 21196, 27851, 1942, 5655, 25, 11, 17, 3421, 2023, 11731, 17, 56, 17, 29285, 17038, 3665, 5482, 18, 2679, 2435, 1966, 43, 2924, 20807, 2912, 4113, 1922, 28149, 16, 2052, 3418, 5745, 28646, 1920, 45, 17, 4262, 3031, 1927, 43, 20136, 2213, 1922, 15021, 1988, 2222, 9826, 13139, 18185, 1930, 4433, 18185, 4209, 18, 2176, 1977, 6196, 1942, 6050, 7241, 7972, 11496, 1972, 3336, 26898, 7972, 2341, 18842, 1989, 6703, 1021, 12724, 3962, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MVALISPEFAEFPPHPRIKLGVMASGSGSNFEAIAQSIQDGHLNAEVQVVIREALDQAIVETLKQHSVDWVIMAGWMRIVTPVLIEAFRDRILNIHPSLLPSFKGNRAVDQGKIIIQAAVPVIEGDTVESLQHRIHAQEHRIYPAAIAIAAIHSVTDDERHQSYNNPGAKVVDRANRFNVPSVLLNHREFASALQAGVQITGCTVHLVVPEVDS", "metadata": {"id": "A0A928YZC1", "cluster": 11184017, "interpro_all": ["IPR002376", "IPR036477", "IPR004607"], "interpro_used": ["IPR002376", "IPR004607"], "interpro_unused": ["IPR036477"]}, "task_type": "infilling"} {"instruction": "Generate a protein according to these design specifications: The protein is included in the Lipid A 3-O-deacylase-related family, which comprises outer membrane proteins, such as PagL, that function as lipid A 3-O-deacylases. These enzymes typically adopt an 8-stranded beta-barrel structure. It has been characterized in Hyphomonadaceae bacterium and features UniProt keywords Signal.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 1977, 3063, 1922, 1920, 4486, 43, 23, 17, 57, 17, 30097, 13796, 24605, 1021, 17, 2712, 3416, 16, 2154, 12936, 7642, 3260, 2697, 16, 2427, 1966, 17869, 1024, 16, 1988, 2347, 1966, 4486, 43, 23, 17, 57, 17, 30097, 13796, 24605, 1918, 18, 2144, 5038, 5745, 14103, 1925, 28, 17, 10338, 4666, 17, 19560, 3170, 18, 2176, 2258, 2252, 4378, 1922, 2483, 25808, 12502, 3825, 1972, 3336, 14061, 1930, 4075, 20709, 11569, 2733, 18, 3], "output": "MARFDLTPRFLATGLAIAISSLISLPAQAQISEVRGAIMAHNVETNVSKNAGKEDGPDVQVEVLWNSPDWLKFAFSPRPGIVASLNTQGGTSFAGVGLDWTFPVSKNVTIDPYLGYVIHNGDPLDNPYAPADSVRRAKFNAEELALGSRDLFRLGVAVGYRHSETWTSYLVYEHLSHGHILGGSKNQGLDNVGIRLGRNF", "metadata": {"id": "A0A3D3Z5A1", "cluster": 3105343, "interpro_all": ["IPR018550"], "interpro_used": ["IPR018550"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein is grouped in the Rim-like family, which acts as a presynaptic scaffold at the active zone to regulate synaptic vesicle docking and priming. These proteins interact with partners such as Rab3 and Munc13 to modulate Ca2+ channel density and facilitate neurotransmitter release. In addition, the protein incorporates 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. Also, the protein incorporates a RIM zinc finger domain that specifically binds to the C2A domain of Munc13-1 to facilitate presynaptic scaffolding. Structurally resembling a FYVE zinc finger, this motif is critical for regulating synaptic membrane exocytosis and vesicle docking at the active zone. It is expressed in Diaphorina citri (Asian citrus psyllid) and is annotated with UniProt keywords Synapse. 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, 10809, 1922, 1920, 14764, 17, 3189, 3416, 16, 2154, 8016, 1966, 43, 13111, 7281, 2019, 1920, 3500, 7441, 1942, 5741, 6251, 11502, 10909, 1930, 11794, 18, 2144, 2697, 6310, 1956, 7228, 2427, 1966, 4673, 1010, 1930, 30403, 3633, 1942, 8480, 5497, 15, 4999, 3824, 1930, 6628, 15223, 4012, 18, 1922, 2459, 16, 1920, 2213, 19683, 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, 2222, 16, 1920, 2213, 19683, 43, 14764, 7997, 8497, 3418, 1988, 4475, 6876, 1942, 1920, 8453, 1019, 3418, 1927, 30403, 3633, 17, 21, 1942, 6628, 13111, 22582, 18, 12171, 18994, 43, 27976, 1961, 7997, 8497, 16, 2052, 5219, 1977, 4140, 1958, 6773, 6251, 3260, 18904, 1930, 11502, 10909, 2019, 1920, 3500, 7441, 18, 2176, 1977, 3198, 1922, 13471, 14258, 1019, 9230, 1033, 12, 9686, 24117, 2742, 10196, 1960, 13, 1930, 1977, 10633, 1956, 20709, 11569, 13103, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MCLTEGMVTSMAQTNADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRXAQQKHTTITSCHAAGSEQQKKAGVELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKSSSALSHKKRDRRSGGPSKPGGMTQSQLIQQGSFSSSEDDVRSTSEGTSCEEHDSEKESKRRKKTVRFDGTHNQNHINHQSSTGKDSGIDTFTSSEDSNSAQVGCESEGLVKAQSGVARQGLPYTRQSATPVQIVLACTYLQGFKEFAKTLANTNDPKWNQSFFYPGIRRSDLKLRSIEITVWDYTRYGVNDFLGEVIIELSSSLCTDEPEWFYLTKHFPLSNLSKTLANTNDPKWNQSFFYPGIRRSDLKLRSIEITVWDYTRYGVNDFLGEVIIELSSSLCTDEPEWFYLTKHTGSRGVPQQGRSHSAASASHSPRSRSKSPPHRSLSPPYSEKSKRRTKTLANTNDPNPPPDLDYVSEKRKSRRDISPPDHKRVHPHHAHPHLMSMESVRRVSSVNKSKPMGDLQVNSYLRKNHMELVFPAPLICFLAEFRFLAEFRLDAVRLLHVHVNREEQKNSEVCEEKKKCVDSEVCGNSEEQKISEVCEEKKKCVDSEVCVDLKNQVHEPPGVVLPTYAYIPRFHSRSATATPVSSPKKHRQLPQIPAIKDQALKERVAQDLEERSKYINQKMRQAMYPRSTGGYLSGSSRRHWSGVSDGDLNIYPRRSFSPPPHDSDMDSVVSSAFSTQSERPRGSTHYSMSNLADASSYLDSLFVDSSSDATVKPSIPQLTLDSPTDPNYCSSCSSRKDVTKPYDVLTGGHYLLTTRVDSRCLICNCDLSKKINKLLSNNIIYKENNGIVLGSDGIVISSSGGNDPIRVLERDVDDVIKIDVTNELIGDLDRKVIGESKSLDETVYKETDSELVDKTPTKKSHSFERDYNRVVKVTKENINPVVHAGKVKFPNQVDSPDVSKEKRTRFGLSVQSYDYKTDEPYPTQIGFNDPVHSDSVDSSSLNDISNSDHSSRYKRSKEKRTRFGLSVQSYDYKTDEPYPTQIGFTDPVHSDSVDSSSLNDISNSDHSSRYKRHVFNSFDFPSIEEYPEEMEEDEATQADNFVNNLSFDSTTNNYTANNVNNRYTNTTTAVVVIVTGVGLVTVTSTFTRAGNSSDRGERSDRERERGERSSNLGKKSSSTSQLSATGRRRRLGFGAKGKSSFTVHRSEEILPGGLPATSKPLVKQASSVSSDGDNTAADAERLTRFYILYLTRVFQTRRRKTWEFVYNIYIAIDFPLLCHEIPDTCSFAYLLLLVYFLDHKEEYPEEMEEDEATQADNFVNNLSFDSTTKNVNRYTNNSINKDKLYCSFVNISNNYVTVWGDYGRLEGKKVFMGVAQIMLDQLDLSKMEIGWYKLFGTSALVNPAGLNLSRRSSLASLDSIKL", "metadata": {"id": "A0A3Q0JCR0", "cluster": 3303444, "interpro_all": ["IPR000008", "IPR035892", "IPR039032", "IPR054386", "IPR011011", "IPR013083"], "interpro_used": ["IPR039032", "IPR000008", "IPR054386"], "interpro_unused": ["IPR011011", "IPR035892", "IPR013083"]}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that has the following function: The protein possesses a Fungal-type protein kinase domain that functions as a variant of the standard protein kinase catalytic domain found primarily in Basidiomycota and Ascomycota. This domain is notably present in secreted effectors like CRN8, where it exhibits kinase activity to induce cell death in host plants. Also, it is part 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 has been characterized in Pleurotus ostreatus (Oyster mushroom) (White-rot fungus). Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 8697, 17, 2601, 2213, 4016, 3418, 1988, 4088, 1966, 43, 6031, 1927, 1920, 2970, 2213, 4016, 6804, 3418, 2435, 5985, 1922, 2726, 13756, 13386, 7336, 1930, 7249, 13386, 7336, 18, 2052, 3418, 1977, 7388, 2481, 1922, 8366, 13066, 3189, 2345, 1022, 1025, 16, 2597, 2176, 9826, 4016, 2455, 1942, 4769, 2024, 3539, 1922, 4423, 4793, 18, 2222, 16, 2176, 1977, 3131, 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, 2258, 2252, 4378, 1922, 6483, 18916, 1031, 1957, 17677, 1936, 7482, 12, 57, 11356, 21903, 13, 12, 4511, 17, 5337, 16461, 13, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MPILGDLDGHRTDIVDDLKSNLFIVDSLQTLIEGNLLSPQGFTKILAAQKTGKLGNKIYSHIQEIVTKSQSALRQVSAEYESAQISDHPSYVTFLDGGIFLAASNEERAADCVAEEDDHELKIHDSILAGELNKKNNPKAFFDNVKKAIGAATSTLYNDPCRRHVYAMTLQGKQLPMWYFCRSHIAISLPFNIHKAQDDFLLFLLFLISATKEEPGFDPTVVRVIRRTGTVFRYKVGDVYYETVGDPLNQDAAYHISSRSTCVWKVRKVILDGAGWREDERDKELHVLRDVWLYHGSTMEKDNQDQIFGKFDEGTREKARPHFLTILQDVEVSFKTNDVERKDITPLATGLSFAILDYQGASKISFQPSREAPKARIHVRTVFKECCEPVYDIEDSVTLAKCLDGAIVGLHYLRQAGFVHRDISGGNILWYAPERSEDTTAVKAAGIGKIADLEYCRPYEDSKPNEHITGTPYFLPTEYSTQTYQFFPPENDGPAQKVSFNFYHALESLIWVYVWFLFNHVPTSLLVADKGFQKAAKSLRASASRWFASVDNMARFDVIKGGCHEEWRELREFWAMTGSFPAPFLEEVRPVVIRQSFASAQRELQKQEPDKHTRRWPREFFKDTPYTGFRDYIATHFESLTSLPVMSLSEIIKPESEGGVLRKGSPVPDLSPILDTENEDHEDDGTAAEY", "metadata": {"id": "A0A8H6ZKG5", "cluster": 5555870, "interpro_all": ["IPR011009", "IPR040976"], "interpro_used": ["IPR040976", "IPR011009"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should include 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. It is derived from Rhodospirillaceae bacterium.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 3066, 3951, 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, 2176, 1977, 3595, 2037, 11490, 3106, 23576, 11560, 9914, 14061, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MSNVKAVDCETLKEWIDNNEAIIIDVIPHNPEKKLVFHCKAGIRGGKACEVDTWIAKGYPVETSREVHEYETAHIKDAILIPVGTCSAESCANAMPEKTVYNLEGGL", "metadata": {"id": "A0A3D2ST37", "cluster": 7010778, "interpro_all": ["IPR001763", "IPR036873"], "interpro_used": ["IPR001763"], "interpro_unused": ["IPR036873"]}, "task_type": "infilling"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein belongs to the cAMP-responsive element-binding ATF subfamily, which functions as a group of transcriptional activators involved in the unfolded protein response (UPR) and cellular stress adaptation. These proteins bind to specific DNA sequences, such as the cAMP response element (CRE) and the unfolded protein response element (UPRE), to regulate gene expression governing cell survival, proliferation, inflammation, and lipid metabolism. They are integral to the endoplasmic reticulum stress response and may interact with other transcription factors and histone deacetylases to modulate transcriptional outcomes. Also, the protein should include a Basic-leucine zipper (bZIP) domain that functions as a DNA-binding and dimerization motif in eukaryotic transcription factors. It features a contiguous $\\alpha$-helix containing a basic region for DNA interaction and a leucine zipper that mediates parallel dimerization, forming a flexible fork structure that grips specific DNA sequences. It is native to Acanthoscelides obtectus (Bean weevil) (Bruchus obtectus) and exhibits UniProt keyword tags Coiled coil, Nucleus, and Transcription regulation.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 14440, 1942, 1920, 6225, 17, 8487, 6149, 17, 2743, 28538, 16227, 16, 2154, 4088, 1966, 43, 2210, 1927, 5224, 15497, 3286, 1922, 1920, 17416, 2213, 2644, 12, 13238, 13, 1930, 3689, 3071, 7810, 18, 2144, 2697, 4566, 1942, 2487, 2678, 3709, 16, 2427, 1966, 1920, 6225, 2644, 6149, 12, 3478, 13, 1930, 1920, 17416, 2213, 2644, 6149, 12, 13238, 1021, 13, 16, 1942, 5741, 2359, 2294, 20012, 2024, 3298, 16, 4031, 16, 4531, 16, 1930, 4486, 4714, 18, 2611, 2032, 12328, 1942, 1920, 13355, 12279, 3071, 2644, 1930, 2278, 6310, 1956, 2303, 3213, 2790, 1930, 6632, 19489, 1036, 1942, 8480, 5224, 3685, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 5937, 17, 12624, 27910, 12, 30450, 13, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 1930, 13640, 5219, 1922, 10825, 3213, 2790, 18, 2176, 4075, 43, 20030, 8, 38, 4595, 8, 17, 7864, 3165, 43, 5937, 3031, 1958, 2678, 2835, 1930, 43, 12624, 27910, 1988, 10412, 6110, 13640, 16, 7402, 43, 9964, 15630, 3170, 1988, 17480, 1036, 2487, 2678, 3709, 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, 17524, 9121, 16, 5607, 16, 1930, 3213, 3640, 18, 3], "output": "MDTMDVSLNYDESDLMSSEFFDSVLSLENNMEDGFLSALEDDINLSSDTSSHMDEVLSPQSFYSESDKNSLSSTDYVDLDDSANVHNIDNFDDPLLMSLLESLPETKPEVISVPAPVEKQPTKILIQNPNNKKFIAKPIVDTTQLKTGPLKVKPQILKVQPVLNNGRPVLLPLSLKSIKILNASPVNLTALSNIRKRKIKVVSSGSESEVTSSTNQYPPLILTHEEKKLLEKEGIQLPTHHPLTKNEERELKRIRRKIRNKISAQDSRKRKKEYVDNLEDRVKRGSEENKNLLQRVRALQRQNKTLIAHVNKLQAMIKNSTTTKATPSTCLMVVLLSALLVSLPNMKLFNDKNSLSTEQEQVAVRRSLLSSPQATEDDTVNMEEFLIFKDEDDYNRAKLAEELDIENSTDKEFTKMIEEMEKKYGGLLSENNSSNVGLFGKVVEAVRGFLERDKPEMFVNSDYGGLNKKGFIEPEIDEYLPNEDLPFKRMKYITEDVNESLHSNDRLVSATVDTNTLGMNTKDQ", "metadata": {"id": "A0A9P0PBV8", "cluster": 14075267, "interpro_all": ["IPR004827", "IPR046347", "IPR051381"], "interpro_used": ["IPR051381", "IPR004827"], "interpro_unused": ["IPR046347"]}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: 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 have 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. Additionally, the protein is classified under the Acetyltransferase NSI-like family, which comprises prokaryotic and eukaryotic GCN5-related enzymes that catalyze dual N-alpha and epsilon-lysine acetylation on various substrates, including plastid proteins and histones. These enzymes play a central role in melatonin biosynthesis by converting serotonin to N-acetylserotonin and regulate nuclear export events, such as viral genome transport, via interactions with nuclear shuttle proteins. Bacterial members also function in amino acid metabolism, specifically converting L-glutamate to alpha-N-acetyl-L-glutamate. It is found in Herpetosiphonaceae bacterium. 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, 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, 2162, 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, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 22226, 4246, 1033, 17, 3189, 3416, 16, 2154, 12936, 21545, 1930, 10825, 5469, 19870, 17, 2712, 5038, 1988, 18170, 7064, 56, 17, 4595, 1930, 22206, 17, 9082, 10339, 1990, 3425, 6249, 16, 2710, 19754, 2697, 1930, 15808, 18, 2144, 5038, 3918, 43, 4101, 2770, 1922, 13366, 8132, 2007, 15025, 11153, 1942, 56, 17, 6894, 13545, 11099, 8635, 1022, 1930, 5741, 4254, 12660, 3916, 16, 2427, 1966, 4324, 3843, 4860, 16, 3454, 3719, 1956, 4254, 23814, 2697, 18, 4543, 4678, 2222, 2347, 1922, 3835, 2687, 4714, 16, 4475, 15025, 54, 17, 7627, 1942, 4595, 17, 56, 17, 6894, 17, 54, 17, 7627, 18, 2176, 1977, 2435, 1922, 3656, 9626, 4575, 12924, 2102, 12502, 1972, 3336, 14061, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MITSIDVFVPQRHEPEVRARVRRASVEDVEAMAGLINGYAADGLMLPKTLAQLYNNVRDFVVAEADGQVVGCAGLKVTWRDLSEIVSLAVAPAYQGQGLGRRLVEPLIKEAQTLRIPTVFALTYQVPFFTKLGFLIVPKDTLSQKVWQDCVTCPKQSCCDEIAMVRVLQKEQ", "metadata": {"id": "A0A7W1THC2", "cluster": 15080396, "interpro_all": ["IPR016181", "IPR000182", "IPR045039"], "interpro_used": ["IPR016181", "IPR000182", "IPR045039"], "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 has 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. It has been detected in Carboxylicivirga sediminis and features UniProt keywords Secreted and Signal.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 30, 1920, 2213, 2258, 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, 2176, 2258, 2252, 3330, 1922, 18708, 20614, 4223, 6276, 1980, 15472, 1930, 4075, 20709, 11569, 8366, 1930, 2733, 18, 3], "output": "MKGLTTFLLVMLMAGATTMSAMANKPVKVKVSQDAFVQGGNTANEPMGVTESGELRIMKSGGTDKYSRTSYLQFNLKKVEDFTSVDLNICIKVYESKEDASAEFEMQVYACADNKWNESSLAFNNKPEKGELLATQTMGVNEKNEWVTISLPADKVKQMLKQSKKGKISLVLSNDNFNKTSGVVLSKERLWSNGTPANREAYLQFK", "metadata": {"id": "A0A941FBE2", "cluster": 18019665, "interpro_all": ["IPR055372"], "interpro_used": ["IPR055372"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a polypeptide chain with the following function: It is part of the Sterol biosynthesis ERG24/DHCR-like family, which comprises hydrophobic integral membrane enzymes that catalyze the reduction of double bonds in sterol precursors within the steroid biosynthetic pathway. Members of this family, including 7-dehydrocholesterol reductase and Delta(14)-sterol reductase, typically possess seven or eight transmembrane regions. It is expressed in Caenorhabditis briggsae and corresponds to UniProt keyword Steroid metabolism, Cholesterol biosynthesis, 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, 2176, 1977, 3131, 1927, 1920, 20408, 8132, 11949, 4561, 19, 6781, 2145, 17, 3189, 3416, 16, 2154, 12936, 7919, 12328, 3260, 5038, 1988, 18170, 1920, 3378, 1927, 4825, 9031, 1922, 20408, 10416, 2651, 1920, 9507, 14041, 3374, 18, 4678, 1927, 2052, 3416, 16, 2710, 27, 17, 28936, 22513, 8342, 1945, 11386, 1930, 9649, 12, 2607, 13, 17, 20408, 11386, 16, 5745, 7150, 5260, 2014, 5066, 9117, 3451, 18, 2176, 1977, 3198, 1922, 22418, 2387, 1950, 4874, 3336, 1930, 8852, 1942, 20709, 11121, 2538, 9507, 4714, 16, 5463, 8132, 16, 1930, 9117, 7864, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MHTGLFVPTITALFFRFPFVFQCIPPVWDTVAWKFSIVHCAIQLIFYWVLPHDQALVMSSAGDQMREINSFFSCILTCLLYVLGASAGIYRGDLIYIHFNSIILIFAIFAVTIWAALIVSYHFGTGNSVTTISEFWFGIENHPKVLDIDLKSFIRTRFTFVIWPLFIISALFFHKITYGKISTSLICASSVQLLYIFQFHWNEDLYLNSLDSKRCDCGFYRLWADFVLGPIIYTSPITVLAATNRSVGLISNGLFCLAAVVSIIFTAKCDRQKYEFRKSKGDLKMGGVDAFFISAKYRTDSGDPNANLLLGSGHWGVCRHPNYTSEAVSFLAFSAFQGFPSTLAHFPALLVTLFLIARAFTDENRCLIKYGQYWAQYCAKVKYRFLPGLF", "metadata": {"id": "A0AAE9ADN6", "cluster": 21094682, "interpro_all": ["IPR001171"], "interpro_used": ["IPR001171"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein carries a putative DNA-binding phage zinc finger domain that binds zinc and is predicted to interact with double-stranded DNA. It is found in both phage and bacterial proteins, occurring as a standalone unit in phages or associated with resolvase domains in bacterial site-specific recombinases. It has been detected in Streptomyces sp. SolWspMP-5a-2.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 16252, 43, 6770, 2678, 17, 2743, 10503, 7997, 8497, 3418, 1988, 6876, 7997, 1930, 1977, 4396, 1942, 6310, 1956, 4825, 17, 10338, 2678, 18, 2176, 1977, 2435, 1922, 2321, 10503, 1930, 4543, 2697, 16, 6966, 1966, 43, 2924, 20807, 2912, 5344, 1922, 18273, 2014, 2458, 1956, 24321, 10916, 1021, 4682, 1922, 4543, 3200, 17, 2487, 21366, 1036, 18, 2176, 2258, 2252, 3330, 1922, 22874, 2056, 18, 2638, 8327, 17922, 1034, 17, 6871, 17, 22, 18, 3], "output": "MNTGEQAPMTAWMNRMRDEALRMRRPDVSKIVHVGWAIAVTRAKKVLKAVGALTERRRPNLPSVYVLADVADRLEWEEHLHLYVDTRQERATAPGSEPAVPAPADPGAGPAPTASEQEEGAALTLVPALLLSVPGQQAATDADLRQALETQGVPAAMRLYGRGGPAPAEWAVPCPECQASVDAPCVSGAGRRGVPCPSCPARPGDPCTGPGGTRRHGIHPQRAALGARTRTATDHTSTGTSYIGPDGTAECPLPTIAAIVGSDPETRKKAAKEKSIAAAVAALDEEPRAVRRPDRASRVSAPTQPPPVLQALADSLATIPPTAAVHEARLEVWDTAT", "metadata": {"id": "A0A1C4IW30", "cluster": 22454237, "interpro_all": ["IPR056911"], "interpro_used": ["IPR056911"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein can be placed in the Plasmid conjugal transfer TrbL/VirB6 family, which acts as an essential component of the type IV secretion machinery to facilitate T pilus formation and T-DNA transfer. These proteins localize to the bacterial surface and are necessary for maintaining the stability of the VirB3 and VirB5 subunits. It has been characterized in Sphingomonadales bacterium and has UniProt annotations Membrane, Transmembrane, and Transmembrane helix. 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, 2112, 1998, 5396, 1922, 1920, 5609, 5225, 1923, 3856, 2025, 3450, 19, 2787, 26937, 3416, 16, 2154, 8016, 1966, 1925, 4415, 4594, 1927, 1920, 2601, 4370, 5512, 10853, 1942, 6628, 62, 7547, 1957, 3337, 1930, 62, 17, 2678, 3856, 18, 2144, 2697, 14380, 1942, 1920, 4543, 3154, 1930, 2032, 4680, 1958, 8231, 1920, 5057, 1927, 1920, 2787, 13965, 1930, 2787, 24462, 6991, 18, 2176, 2258, 2252, 4378, 1922, 13502, 20050, 7324, 2612, 14061, 1930, 2258, 20709, 15010, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "VFIVMALFSGTRGLFVGWLRGVVLTGVVPLFVVVGGGMMMELMVPIIANLSDGVAINGRAAIALFLIACIHMALMGIVMKVAATVVSGWQVFGLAGQGERSGASAAQPAPQQVVGVQPAPVTAAPAQVSAMRQQQAMAAVGGAMGTAQGAPPSTTLRESHKTIVAGAPGQSASLPSLPASRARGVGSRFRSSRPTQFREIRK", "metadata": {"id": "A0A4Q3CPE0", "cluster": 22800979, "interpro_all": ["IPR007688"], "interpro_used": ["IPR007688"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein should feature a Sec7 domain that functions as a guanine nucleotide exchange factor (GEF) specific for ADP-ribosylation factors (ARFs). This alpha-helical module activates ARF GTPases to regulate essential vesicular protein trafficking and membrane remodeling processes in eukaryotes. It is native to Arion vulgaris.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 2532, 1027, 3418, 1988, 4088, 1966, 43, 16904, 5489, 6818, 2991, 12, 15022, 13, 2487, 1958, 9828, 17, 29117, 3017, 2790, 12, 13720, 1036, 13, 18, 2052, 4595, 17, 11514, 9059, 9094, 13720, 18390, 1942, 5741, 4415, 16168, 2213, 9604, 1930, 3260, 8378, 4028, 1922, 15021, 18, 2176, 1977, 6196, 1942, 27950, 1916, 22621, 18, 3], "output": "NSLSYQRKLRMSMASEPQTIPRTNDKMRKRLYRIGLNLFNKKPEKGLDFLLDNLFLEGSPKSVARFFITRKGLSKQMIG", "metadata": {"id": "A0A0B6YEN9", "cluster": 23474585, "interpro_all": ["IPR000904", "IPR035999"], "interpro_used": ["IPR000904"], "interpro_unused": ["IPR035999"]}, "task_type": "autoregressive"} {"instruction": "The protein is assigned to the eukaryotic phosphatidylethanolamine-binding protein (PEBP) family, which encompasses structurally conserved proteins with diverse roles ranging from the regulation of floral transitions in plants to the inhibition of kinase signaling cascades in mammals. Notable members include the Raf kinase inhibitory protein (RKIP), which modulates MAP kinase and NF-kappaB pathways, as well as structural components of the mitochondrial large ribosomal subunit like mL38. Despite sharing a common fold, these proteins display varied substrate specificities and oligomerization states. In addition, the protein is grouped in the PEBP-like superfamily, which encompasses highly conserved proteins found across diverse organisms that function in lipid binding, serine protease inhibition, and the regulation of developmental processes such as flowering. These proteins also modulate signal transduction, notably inhibiting the MAP kinase and NF-kappaB pathways through interactions with kinases like Raf-1, MEK, and TAK1. It is present in Hanseniaspora valbyensis NRRL Y-1626 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, 1977, 6304, 1942, 1920, 10825, 10951, 22935, 17, 2743, 2213, 12, 2737, 3846, 13, 3416, 16, 2154, 21569, 12171, 5305, 2697, 1956, 6445, 5456, 6485, 2037, 1920, 3640, 1927, 20741, 10673, 1922, 4793, 1942, 1920, 3523, 1927, 4016, 3197, 15967, 1922, 9902, 18, 11892, 4678, 3951, 1920, 12783, 4016, 5431, 2213, 12, 21179, 2049, 13, 16, 2154, 13112, 4446, 4016, 1930, 4651, 17, 19901, 3873, 16, 1966, 2486, 1966, 4346, 4178, 1927, 1920, 4596, 3103, 11196, 5903, 3189, 2646, 4745, 18, 4281, 10763, 43, 3059, 3728, 16, 2144, 2697, 4434, 6760, 4510, 18764, 1930, 17371, 4376, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2737, 3846, 17, 3189, 13975, 16, 2154, 21569, 3626, 5305, 2697, 2435, 3436, 6445, 7373, 1988, 2347, 1922, 4486, 2743, 16, 8468, 7154, 3523, 16, 1930, 1920, 3640, 1927, 5878, 4028, 2427, 1966, 15346, 18, 2144, 2697, 2222, 8480, 2733, 8201, 16, 7388, 7918, 1920, 4446, 4016, 1930, 4651, 17, 19901, 3873, 2596, 3719, 1956, 7784, 3189, 12783, 17, 21, 16, 12551, 16, 1930, 24950, 18, 2176, 1977, 2481, 1922, 28435, 10657, 21086, 2326, 4864, 8134, 5214, 1005, 1024, 67, 17, 15333, 1016, 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": "MLRNCMFKANLQKISVSKVSYPKFYSSFNKEVEEYFKNATNETKPPSLSYEESLQYKPILRLNDLYKESVSSLEKELAETTDNKLELEFNDSANIYEFENTFPKLHSFKNKSVIDYNRDINRFFLYEKWTMDRSIREQFKTSSEYLKDKVNSFSSPVKRNYKKNGVLNHNSLDPNHKETLITHDDKFFMRDEFAKNEFGYEQDKDLIGGKYKIFQRLEQFGLLPDTVPTIVDLNTIVRFRFPFSDSSFHVYSQAENELVAKKDLKAVEKEVINYNNPMAWIESGEILNNDVLKTVPEFQIFDLRREKITTQPSKLMDVSLPRNLDQLSELENEGQEFVLDTITKEPVSIDQIQNSKYSLLMMTPDVVDYERASYKSKLNYCISNISIKDLNDNFVSEFKEGVEVVKRYEPPMPMKGELKPQRYLILLLEQPKDLDVASMKAYLEQNASSSQENTENTDIVDYEDDHFSIREFIKKFNLQPIGANCFRSKYDSFLPITVDHHTVEEELKYYKVPDNLDPVRQYKIRKNI", "metadata": {"id": "A0A1B7TAZ0", "cluster": 24291414, "interpro_all": ["IPR036610", "IPR035810"], "interpro_used": ["IPR035810", "IPR036610"], "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 include 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. Additionally, the protein carries 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. Additionally, the protein should feature 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 derived from Poribacteria bacterium and is connected to UniProt keyword 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, 3951, 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, 4950, 16, 1920, 2213, 16252, 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, 4950, 16, 1920, 2213, 3066, 5961, 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, 3595, 2037, 4572, 26073, 2341, 18339, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3213, 3640, 18, 3], "output": "MARGINRSLVEQCRNGDISSFEKLFYLLKDDVFVKIWINLKNFKMESSIRTWVYKITVNLCYDFLKLLTEKELREKIERAFKMLSSDNRLILTLREIEGLVDAAKMKAHRARVEFKKIISKYLESTVNYNVAFRVLSNHQDAEDITQEVRRGRIPLAEEPVENFKELPSDENPLLPYKEIAEILDCS", "metadata": {"id": "A0A800DSU3", "cluster": 25067058, "interpro_all": ["IPR000551", "IPR039425", "IPR014284", "IPR007627", "IPR013249", "IPR013325", "IPR013324", "IPR036388"], "interpro_used": ["IPR007627", "IPR014284", "IPR000551"], "interpro_unused": ["IPR036388", "IPR039425", "IPR013249", "IPR013324", "IPR013325"]}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein is included in the Intra-flagellar transport protein 57 family, which functions as a subunit of the intra-flagellar transport (IFT) complex B essential for the assembly and maintenance of eukaryotic cilia and flagella. This protein participates in the bi-directional movement of particles along the organelle but is not required for the association of core complex subunits. In humans, it is known as Huntington-interacting protein-1. It is native to Catenaria anguillulae PL171 and carries UniProt keyword assignments Coiled coil, Cell projection, and Flagellum.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 1977, 3063, 1922, 1920, 5153, 17, 24154, 4860, 2213, 4786, 3416, 16, 2154, 4088, 1966, 43, 5903, 1927, 1920, 5153, 17, 24154, 4860, 12, 22416, 13, 2796, 44, 4415, 1958, 1920, 5957, 1930, 6291, 1927, 10825, 15714, 1930, 26538, 18, 2052, 2213, 17241, 1922, 1920, 2273, 17, 15062, 5829, 1927, 5569, 4231, 1920, 19309, 2308, 1977, 2084, 3414, 1958, 1920, 3279, 1927, 4728, 2796, 6991, 18, 1922, 5209, 16, 2176, 1977, 3171, 1966, 24289, 17, 8615, 2213, 17, 21, 18, 2176, 1977, 6196, 1942, 3115, 11496, 3027, 1019, 3409, 15444, 11560, 16842, 2123, 27077, 1930, 16252, 20709, 11121, 2538, 18306, 17524, 9121, 16, 2024, 11244, 16, 1930, 7030, 10757, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MSTNNLNASSSVLAASAMDALLDRLLFVQPHATNPTFQLNYFYTLLAWLVSLASTANNAAAVLKTAGIPPPSTEADWNPSKLRQFKKPVFDKNEQFEEAQTDDAAEIGNPGFGGHGGGLADVDQDQPHLDADADTNVDSMSPASPQRPATAAARSMPRLAMIKGERVTPRLKVHLKDDHKQWRVHVSAMGEYRALIANEWGWGLTDLDSTLEKLRSRESYVNTQLDALVDLAQDLQRVSYELDQVKSLMDDLGSKQMEVRRGVLEHQLMSGRIRHKTRQFGGPQRKGSRQQQAEEPFAFMFMGSPEMAIRLLNYSTRFCAAKKMKPMDPDTLDGISFQAPSELDDPNVGYGESVLAALTGMADRALKGSGFATSTDTDDIPEDETLVLSGIFRKSAIASSRSQTNLGAGGASNDPEAWRAEVEGSGPTSTSPATSSQASGVGGKAIVTRLAYREVQSRLGALRLEYNTGSEKMGAGMTDSKPLLNIKSTLQRLKAELVVASSGAAGRTAGGGGVG", "metadata": {"id": "A0A1Y2H598", "cluster": 27430212, "interpro_all": ["IPR019530"], "interpro_used": ["IPR019530"], "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 included 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. In addition, the protein should have 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 contains a CS domain that functions as a protein-protein interaction module with a compact antiparallel beta-sandwich fold. It is often associated with co-chaperones like SGT1 and p23, mediating complex assembly in diverse biological contexts such as plant pathogen resistance and nuclear movement. It is present in Desulfuromonadales bacterium.", "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, 3063, 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, 1922, 2459, 16, 1920, 2213, 3066, 2162, 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, 5461, 43, 3752, 3418, 1988, 4088, 1966, 43, 2213, 17, 2213, 2835, 9059, 1956, 43, 13726, 28892, 4666, 17, 18038, 3728, 18, 2176, 1977, 3868, 2458, 1956, 2081, 17, 18098, 3189, 10075, 6613, 1930, 7535, 1010, 16, 10239, 2796, 5957, 1922, 6445, 3933, 11144, 2427, 1966, 4496, 7055, 3554, 1930, 4254, 5829, 18, 2176, 1977, 2481, 1922, 30311, 18916, 3947, 7324, 2612, 14061, 18, 3], "output": "MFDDFIQDWYWPAMLEEGVLSPRTEKNIDVSLERDSIIIRGNKESKKEDEGKSYYRVETVHLPKAHDTARKRKQIEIHDVSETDKEVTVTAEMPGLDRAYSSFYRAIPLPCEIDDKKIKAVYKKGLL", "metadata": {"id": "A0AA43A5N1", "cluster": 27791326, "interpro_all": ["IPR002068", "IPR007052", "IPR008978", "IPR031107"], "interpro_used": ["IPR008978", "IPR002068", "IPR007052"], "interpro_unused": ["IPR031107"]}, "task_type": "infilling"} {"instruction": "Generate a protein sequence for a protein with the following function: The protein includes 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 has been characterized in Amoebophrya sp. A120 and is associated with UniProt keywords tRNA processing.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1958, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 5921, 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, 2258, 2252, 4378, 1922, 27714, 2688, 6907, 1019, 2056, 18, 8080, 3520, 1930, 1977, 2458, 1956, 20709, 11569, 10089, 4587, 18, 3], "output": "MSLHETAVTGEEAIQRKIERGSCKDCWLQHCACDFLEKNLLSQNFPNTKFVLLLDPFELRRSVSANTGKILTIWGAERVIFGHDEQMQLLERWLDDAKYPVCLYPTPEAVSVPKFFADFQHGETTHSENKVLDEHHREALESAEKGTKELSPSAAQLHQTENNTCGSQVDRKFPDLVIIPDGDWTRCKVMMRHPMLRVRLLGKQDLSEAGNNRADQKFRQEEADRVDGLEQFVPHNFAADTILVPTQIEAWKLRDLTTISTLEQQFTSPFGRTKKYYSGPSERLQTAGAFWLMCHETGAFSDILLEKMALQIHYLISCYHKQINRVIVRGSGQRFHVQPGHG", "metadata": {"id": "A0A8J1W7J8", "cluster": 28778556, "interpro_all": ["IPR005636"], "interpro_used": ["IPR005636"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein is categorized in the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. Also, the protein has a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. Also, the protein has 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 originates from Planctomycetota bacterium and is classified with UniProt keywords Glycogen biosynthesis and Glycosyltransferase.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 2222, 16, 1920, 2213, 2258, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 2222, 16, 1920, 2213, 2258, 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, 22970, 2037, 4720, 2341, 13386, 19446, 3857, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 13302, 8132, 1930, 20067, 9961, 18, 3], "output": "MHAVSVSSEMVPLAKSGGLGDVCGTPAYRCALTSGLPIKPTPIAFTIPMGGKFVQPQYFDRVGLYGDAHGEYRDNCERFCFFSRAVVERARYKQFRWMESARSIMTIHNLAYQGQFWHLDMPLTGKTGIVYADKITTVSPTYAREIMTPEQGIVNGVDYSQWDPRCDRHIPHQYGPESWPEGKVDQKGWDLIVPLLERWGGTREIQWIGARLEFSEGLAHRIEAGADMFLMPSRFEPCGLNQLYSVDATPESIAAGTATGFHMAEYSLRGLEQAMERAIDRSAQQYRQVYEDTLAPRDRGRLPSTESLPPALQQVGCQVTCFLACRLLETALPQGQVPVYLIDAIEQLGLTVDIVHCHDWQAGLVPALVLGWEHFHWQGMEFHGHLNLLCGLDPVLRQRRADLYGAACKLALQQELGLATSPGTPLVGIVSRLAILGTGEQRYERKLRELAARHAPHLKYGTVPVVNPTGGLADTVVYTHQKSVWAQIVLRGMQEDWSWG", "metadata": {"id": "A0A3M1MPP6", "cluster": 803028, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR011835", "IPR013534", "IPR001296"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein features a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. In addition, the protein should have a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. It is expressed in Trichococcus collinsii.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 2176, 1977, 3198, 1922, 10477, 8256, 27362, 3907, 18, 3], "output": "MRIAVFASGNGSNFQAIAEAIASGEVDATIAFLFCDKPNAYAIERAKQYNIPVISFTPKGFEDRVAYENEILKHLAEEKVDLVVLAGYMRIVGPTLLKAYADRIVNIHPSLLPDFPGRHGIQDAFEAGVPETGVTVHFVDEGVDTGPIIAQEKVAILSEDTLETLETRIHQVEHRIFPQVIQQLAQKNKG", "metadata": {"id": "A0AB38A344", "cluster": 6411170, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR002376", "IPR001555"], "interpro_unused": ["IPR036477", "IPR004607"]}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein possesses 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 included 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 has been detected in Photinus pyralis (Common eastern firefly) (Lampyris pyralis) and is connected to UniProt keyword Nucleus, Transcription regulation, and Repeat.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 14465, 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, 3063, 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, 2258, 2252, 3330, 1922, 3822, 22214, 6487, 19337, 12, 3059, 11562, 21235, 13, 12, 12503, 3553, 1937, 6487, 19337, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5607, 16, 3213, 3640, 16, 1930, 6865, 18, 3], "output": "MRSHRPREETPSKRKRRRRALAGDTLRAMHERTHTGEKPHVCSFCGRGFSQRTSMVTSKSAVKVHTKKCMKKLLYKCYFCEKSFKLSFYMHLRTHTGEKPFTCQLCGKAY", "metadata": {"id": "A0A1Y1KSS4", "cluster": 1590510, "interpro_all": ["IPR050758", "IPR036236", "IPR013087"], "interpro_used": ["IPR013087", "IPR036236"], "interpro_unused": ["IPR050758"]}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\nThe protein is associated with 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. In addition, the protein can be placed in the Actin family, which consists of ubiquitous ATPase proteins that polymerize into filaments to form the cytoskeleton and interact with myosin to drive muscle contraction and cell motility. Each monomer binds ATP and divalent cations like calcium or magnesium, hydrolyzing ATP during the rapid formation of filaments. This family encompasses diverse isoforms, including muscle-specific alpha-actins and cytoskeletal beta- and gamma-actins, as well as divergent actin-related proteins (ARPs). It is native to Heterosigma akashiwo (Chromophytic alga) (Heterosigma carterae).\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, 2458, 1956, 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, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4718, 3416, 16, 2154, 7543, 1927, 15498, 9444, 2697, 1988, 4593, 2606, 2460, 11855, 1942, 2386, 1920, 11612, 1930, 6310, 1956, 10863, 1942, 9265, 3760, 8332, 1930, 2024, 9254, 18, 2362, 11287, 6876, 4498, 1930, 21610, 16525, 3189, 5016, 2014, 13148, 16, 7222, 9046, 4498, 2409, 1920, 4052, 3337, 1927, 11855, 18, 2052, 3416, 21569, 6445, 7963, 16, 2710, 3760, 17, 2487, 4595, 17, 4718, 1036, 1930, 14787, 4666, 17, 1930, 7034, 17, 4718, 1036, 16, 1966, 2486, 1966, 13609, 4718, 17, 2712, 2697, 12, 2245, 2523, 13, 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, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "TTKVGYAGEDVPASIVDSFVGFQKIGEQTNHILPNDLPRHDDIWEYSIKNNLFVDTKEHPCLLSERSFSPTAQRHKFCEIWFEKYDVPALFISDVGAELATVTPVSDGWAEQKGIIKSLVAGNMVNKYLQHIIEKRGQKALATISSSSSNCDEHKMDTTELEANGDEGEEDLLTYREYRLQKVVANMPRLPYELPDGTQVQLGSERFEAPELLLNTAPLTEAVGAGAPIPLKGFNHEGLVADWDVLEIKDAVLSCFAAGRTTGLVAKIPPQHMSSRESDIKEGMGRVSDTPVDKSDPRF", "metadata": {"id": "A0A7S3UN21", "cluster": 1835844, "interpro_all": ["IPR004000", "IPR043129"], "interpro_used": ["IPR043129", "IPR004000"], "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 categorized in 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. Additionally, the protein should contain 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 present in Marinirhabdus gelatinilytica.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 1977, 10234, 1922, 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, 4950, 16, 1920, 2213, 3066, 5531, 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, 2481, 1922, 13081, 8635, 5004, 13385, 1957, 13200, 2869, 21788, 18, 3], "output": "MNFFMKLRVFPFYFLFILFFYSCATYSPQYRDTEITYTYPSDKSIEQTFYLIGDAGKSPIGGMSDALTAFKNYIKDKDTEGNYAIFLGDNIYPDGLPPENSPDRDRAAYMLDAQVASMVNFKGNIFFIPGNHDWYNNGLEGLLREQEYLKQKMSGTEVLKPSNGCPLESISVSPNIQLIMIDSQWYLEDWNLHPNINENCEIKSREKFFIELELELEKNKNKNIVFAMHHPMFTNGTHGGFFGANKHLYPTQKKIPLPGLSSLVAQIRAQGGVSVQDRYNELSNKFMNRLATVARNFDNLVFASGHEHTLQHIEQGGLVQILSGSGAKAGFAALGKDGLFSYGGQGFAVYDVFTDGSTYVRYFGVGQEKHPKLLFEKQIFKAKDSFNLATLPRQFPETITTPIYKQDSINEALFFKTIWGKKYKDAYATPISAKVANLDSLYGGLTVVRENNTKDYKNLILRDRAGNLYNLRALQKQALKVLDRRDIVKNENPENQDVDEDQNTDFTTPETYGSEFYTASHPYATLAIPTLADSINIFQNRPNLIYVPKQRALKNYNADFGDELYYISVAPSENNEGDRIFQYARDIETTDDILLKLRKANNVKIDEETYIKARLFDMLIGDWDREPDHWRWALYYTKGNDSVYVPIARNRNDAFASLDGDILDVARSIFGSSHQRHIYTENLTDFKWFNAEGIILDRALLQKSNSSQWKFVAEKIQSQLTDEVIDIAFDNVPIATRDESLEETITTLKARRDNLVTIAQAYYKYLNELRTIKGTDGANYFEITRNGDGSTIVKEFDYINTTKGTLQKEVTYYEDQTKQVWVYGLGGDDYFEVNGTGKGHTLVRMVGGHGHDTYTIKNSHRTRVYDHKSKPNTVAEKNGAVVRLTDLYTLNTYDYRKQVGSENNFTATAGYNPDYDARVGLQYTYEINGFSRNPFSKRHRLNANYYFGTTSFDLAYQGEIANLYKTFNLSFGGRVTSPNYVFNYFGYGNETKNPQEALGFDANRVEVQTFSGNIGLLRNSYFGSFFKLQTRLEAITVNSTITGIENPENAALPEDTKYYGTLEGIYSYRSFDNARNPSRGMLFDLNLGITENFEEMERVFGFLHTRLGFYNSLTSNEKLVLRTNVQGQFNFGNRFDFYQAVTLGGSNGLRGFRQDRFAGKSSLVGSADVRYSFGEFRIELFPMQVGVYGGADLGRVWTPSGSSQRWHNSYGGGLWLNGRGGLTFTSSLFHSTEDTRFVFGLNFGF", "metadata": {"id": "A0A370QG21", "cluster": 2974173, "interpro_all": ["IPR004843", "IPR029052"], "interpro_used": ["IPR029052", "IPR004843"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein is included in the Protein of unknown function DUF1280 family, which represents a conserved domain of approximately 200 residues found within uncharacterized proteins. This family appears to be specific to the nematode *Caenorhabditis elegans*. Furthermore, the protein possesses a RAG1 importin-binding domain that is responsible for binding to importin alpha. It has been detected in Strongylocentrotus purpuratus (Purple sea urchin). What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 5739, 4839, 1008, 3416, 16, 2154, 4972, 43, 5305, 3418, 1927, 3993, 2191, 4248, 2435, 2651, 24528, 2697, 18, 2052, 3416, 5107, 1942, 1998, 2487, 1942, 1920, 18827, 14, 22418, 10861, 14, 18, 3677, 16, 1920, 2213, 14465, 43, 13745, 1009, 28235, 17, 2743, 3418, 1988, 1977, 5061, 1958, 2743, 1942, 28235, 4595, 18, 2176, 2258, 2252, 3330, 1922, 3206, 2199, 26907, 6843, 1957, 25945, 9280, 1031, 1957, 12, 14308, 9309, 3674, 28964, 13, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MSGTPTGSARANCAQTNGSTCAGPGGLDLHSQCLQMFCRICGGKFKSNSGGSRTFREKIHPCQGYKDQLKEILGVDVECDHNDINPPSMCQSCYCQIMIHKKKPNIENVKQWAAHPRIGICDICHTQKSGKPGRKKKKPNMGAKNLPKSFTETTSSIKPLIDNTKYTVICKSCSNPIDITNISQHTCTHTDTVDHDHTYVISHNLTSLTNSERERIAKEVVQEKIKESPDGATIILTGGKRTQDICTRKIDLPRKPSSMVKARTKRSRDECMRDVHLLTHMEDQEEQEEQEECSSLYLDNQDISDLKSMMGISWRKLGKLKNWLLQRKVKSAGEKAVRTLHKTILDGKLQAILLPLQHWEDTICQIRPSPFISVQNLPDMVMTLLDEYDELGELTFHDGMLEEIWVKIGGDKGGDTFKLMLQIANLSHPNSLRATNIIGLFPGKDTPFNLDVTLSTLVEQIDVLQKAKWRGKAIRCFFFGDYEYLCRTYGLSGPSGRHCCLYCVATKTEMATPLASRGRLPERTLDTLKESLAKYKHSNVAKESNNAIRPPQFNIPINQVCPPGLHFSLGIYNKHYKSMEMACHELDLKAASLPHTLTTRLEVAACKQKHLQCIAQKEEERQDILDQHMYLSMAYPDSQPAALLLETAEDIQKEITNLKAEVKKLPDLKVGEGPIAQSLDEVLKSISVQRQAFHGKSFVGNHVHKCLKEENIRKITNTIVQTADEVCPALHNEALSIAHRYSECFKLYGSCDHLFNRGDFLTPEHIHMLDDAIREYMTFVRTTFPSESITPKMHLLEDHTVPWFELWGAGLALMGEQGGEGMHAHLNRIREHLRCYSLTDDLQLHLRSVEEQWVHANPKSYHRNKNN", "metadata": {"id": "A0A7M7PIW7", "cluster": 4303055, "interpro_all": ["IPR009689", "IPR035714"], "interpro_used": ["IPR009689", "IPR035714"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein has 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. In addition, 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 is derived from Racocetra fulgida.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 2258, 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, 1922, 2459, 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, 1977, 3595, 2037, 7195, 1994, 21193, 5257, 6121, 3825, 18, 3], "output": "QNNLKNIHSAGLIHKITTHLSGLGLPKRISGLDISEEIFGVVSYVVSDVYSLGVISANVNWKVIIDIIHLGNILQVSNEVNPEVLLGQRYTMA", "metadata": {"id": "A0A9N9AKJ7", "cluster": 5947194, "interpro_all": ["IPR011009", "IPR000719"], "interpro_used": ["IPR000719", "IPR011009"], "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 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. Also, the protein is included in the Alpha-helical ferredoxin superfamily, which coordinates two Fe4-S4 clusters to facilitate electron transfer in various redox reactions. This domain is integral to respiratory complexes like succinate dehydrogenase and fumarate reductase, as well as metabolic enzymes such as dihydropyrimidine dehydrogenase, where it mediates electron transport between donors and acceptors in pathways including respiration and pyrimidine degradation. It is identified in Pseudomonadota bacterium and exhibits UniProt keyword tags Iron-sulfur, Metal-binding, and Oxidoreductase.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 14465, 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, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4595, 17, 11514, 25304, 22389, 10960, 13975, 16, 2154, 10675, 2288, 2650, 1006, 17, 6934, 5859, 1942, 6628, 4995, 3856, 1922, 3425, 9366, 5298, 18, 2052, 3418, 1977, 12328, 1942, 5481, 5048, 3189, 19234, 9294, 1930, 28343, 11386, 16, 1966, 2486, 1966, 4487, 5038, 2427, 1966, 11842, 18425, 29899, 9294, 16, 2597, 2176, 10412, 4995, 4860, 2192, 8276, 1930, 27916, 1922, 3873, 2710, 11695, 1930, 21611, 4877, 18, 2176, 1977, 2899, 1922, 11520, 3947, 12595, 3857, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 5680, 17, 12585, 16, 6048, 17, 2743, 16, 1930, 27388, 18, 3], "output": "MKYQIRLSGDEGRKCYQCGECTAGCPMTPEMDAGPTKNTPWLCASCETCTSRCPNEIDRVFQDVFLKSVHDYGKPRMLFKGKLPLLPHRSANVAQVEEHAHSGHGHGSEGHGLAREVKVRSGVDLAVLRLVQLGMEQELFRLIALVMDVIRQMARLRGLEAPVKEPLYEPGLIAFYNLKSGHLFKDVALGKLREIMAKAKAYEQEAGR", "metadata": {"id": "A0A7C4SQJ9", "cluster": 7409972, "interpro_all": ["IPR017896", "IPR017900", "IPR051460", "IPR009051"], "interpro_used": ["IPR017900", "IPR009051"], "interpro_unused": ["IPR017896", "IPR051460"]}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence be if I wanted a protein that could perform the following function: The protein carries a HTTM domain that contains four transmembrane regions and is characteristically found at the N-terminus of metazoan Vitamin K-dependent gamma-carboxylases. This horizontally transferred module also appears in diverse bacterial protein architectures, serving as a structural membrane component. Furthermore, the protein contains a HTTM-like domain that comprises four transmembrane regions and is associated with vitamin K dependent gamma-carboxylase enzymatic activity. Conserved catalytic sites indicate a shared function for this family across eukaryotes, bacteria, and archaea. Moreover, the protein is categorized in the Sporulation-related signal maturation family, which comprises proteins involved in the maturation of specific signaling peptides, playing a key role in cellular processes such as sporulation. Characterized members are essential for downstream peptide maturation steps, functioning independently of initial signal peptide cleavage, secretion, or disulfide bond formation. It is found in Streptomyces somaliensis (strain ATCC 33201 / DSM 40738 / JCM 12659 / KCTC 9044 / NCTC 11332 / NRRL B-12077 / IP 733) and is described by UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 5136, 1035, 3418, 1988, 5461, 3006, 9117, 3451, 1930, 1977, 6293, 2169, 2435, 2019, 1920, 56, 17, 7822, 1927, 24207, 1928, 6111, 53, 17, 3100, 7034, 17, 29073, 1036, 18, 2052, 26260, 6311, 9059, 2222, 5107, 1922, 6445, 4543, 2213, 23830, 16, 13915, 1966, 43, 4346, 3260, 4594, 18, 3677, 16, 1920, 2213, 5461, 43, 5136, 1035, 17, 3189, 3418, 1988, 12936, 3006, 9117, 3451, 1930, 1977, 2458, 1956, 6111, 53, 3100, 7034, 17, 29073, 8145, 2455, 18, 5305, 6804, 3402, 3579, 43, 7115, 2347, 1958, 2052, 3416, 3436, 15021, 16, 4802, 16, 1930, 21501, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 23647, 17, 2712, 2733, 7655, 3416, 16, 2154, 12936, 2697, 3286, 1922, 1920, 7655, 1927, 2487, 3197, 5320, 16, 14797, 43, 3834, 2770, 1922, 3689, 4028, 2427, 1966, 23647, 18, 4378, 4678, 2032, 4415, 1958, 5863, 4207, 7655, 5983, 16, 7295, 6407, 1927, 3754, 2733, 4207, 6404, 16, 5512, 16, 2014, 11830, 5403, 3337, 18, 2176, 1977, 2435, 1922, 22874, 18078, 12191, 8134, 12, 3943, 11037, 25530, 6924, 19, 10964, 26474, 4745, 19, 14904, 1035, 10483, 7308, 19, 14331, 6916, 3865, 6609, 19, 10409, 1030, 11549, 6763, 19, 5214, 1005, 1024, 44, 17, 6103, 7658, 19, 5416, 5356, 1010, 13, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 7864, 18, 3], "output": "MLLRIGAGLTAITARDPFGNVLGVSRSLLASATFLTLAVNGPDTLFVPPAPGTAGRAQQCGGAPAIGLFCVAPSLEAGRLAALAVLLVVIAGWRPRWTCVPHWYVAFSVQNNATVLDGGDQVCAVVTLLLVPVGLCDGRRWHWTSPVRGDTDDPVLGLSYARRLTALAFLLLIQVQVFVIYFQAGVAKLGVQEWADGTAMYYWLSDPVFGATAWQQWVLRPILVNGFSVTLFTWSVLVGEIALAVGLLVPWRLRRPFLLASLAFHAGIAFFMGITTFSLTMAAVDLLAYRSVYDPLPVPTGALRAVRRKDGTEATGKAGDLPGAPTGAVCTGK", "metadata": {"id": "A0AA44DAS4", "cluster": 7505762, "interpro_all": ["IPR011020", "IPR053934", "IPR023894", "IPR052964"], "interpro_used": ["IPR053934", "IPR011020", "IPR052964"], "interpro_unused": ["IPR023894"]}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein should have a DinB-like domain that adopts a four-helix bundle fold and is typically found in putative metal-dependent hydrolases. This structural motif was originally identified in DNA-damage-induced proteins but is shared by diverse uncharacterized sequences. Moreover, the protein is associated with the DinB/YfiT-like putative metalloenzyme superfamily, which comprises diverse proteins sharing a four-helix bundle fold that typically function as metal-dependent hydrolases or isomerases. This group includes the DNA-damage-induced DinB protein from Gram-positive bacteria and enzymes such as mycothiol-dependent maleylpyruvate isomerase. It is expressed in Chitinophaga oryzae. 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, 3066, 2162, 43, 11687, 1014, 17, 3189, 3418, 1988, 24032, 43, 3006, 17, 7864, 14142, 3728, 1930, 1977, 5745, 2435, 1922, 6770, 6048, 17, 3100, 30337, 18, 2052, 4346, 5219, 1982, 10398, 2899, 1922, 2678, 17, 4293, 17, 2719, 2697, 2308, 1977, 7115, 2007, 6445, 24528, 3709, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 11687, 1014, 19, 29962, 1932, 17, 3189, 6770, 8969, 6802, 1022, 9318, 13975, 16, 2154, 12936, 6445, 2697, 10763, 43, 3006, 17, 7864, 14142, 3728, 1988, 5745, 2347, 1966, 6048, 17, 3100, 30337, 2014, 25510, 1036, 18, 2052, 2210, 5921, 1920, 2678, 17, 4293, 17, 2719, 11687, 1014, 2213, 2037, 8604, 17, 2843, 4802, 1930, 5038, 2427, 1966, 5078, 17809, 1945, 17, 3100, 4005, 2199, 18425, 12631, 2010, 25510, 18, 2176, 1977, 3198, 1922, 16588, 4965, 1019, 27597, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "MTALLKWTDRRFQWGHTADYVPFFMERLRATAPRLDEMTVLVPEDIMEIRDEGKWSVKEHIGHLADIELLHDKRLEDLLAGRTLTAADPENRATVEAHHNQYPISELVYHFRQVRDNFLKQVEHFSAADMEKRAMHPRLGQQMSLADILYFIAEHDNHHLTVIAAFLRKHYA", "metadata": {"id": "A0AAE6ZBQ3", "cluster": 7944141, "interpro_all": ["IPR024775", "IPR034660"], "interpro_used": ["IPR024775", "IPR034660"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein is assigned to the Chlamydia Large Cysteine-rich Periplasmic OmcB family, which maintains the structural integrity of the outer envelope in infectious elementary bodies. These proteins form disulfide cross-links with porins and other cysteine-rich proteins to create the Chlamydia outer membrane complex (COMC), acting as a functional equivalent to peptidoglycan. In addition, the protein has a Large cysteine-rich periplasmic protein OmcB-like, DUF11 domain that adopts an Ig-like fold to maintain the structural integrity of the outer membrane or cell wall surface in bacteria and archaea. This cysteine-rich module is implicated in porin formation and pathogenicity, particularly in organisms lacking a peptidoglycan layer, and may utilize intramolecular isopeptide bonds for added stability. Also, the protein should include 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. It has been characterized in Parcubacteria group bacterium GW2011_GWB1_41_4 and is linked to UniProt keywords Signal.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 21079, 3103, 8666, 17, 5536, 24334, 7254, 18598, 3416, 16, 2154, 16566, 1920, 4346, 7996, 1927, 1920, 7642, 11262, 1922, 7465, 20530, 8322, 18, 2144, 2697, 2386, 11830, 3567, 17, 10069, 1956, 4572, 2925, 1930, 2303, 8666, 17, 5536, 2697, 1942, 7762, 1920, 21079, 7642, 3260, 2796, 12, 2008, 1030, 13, 16, 8290, 1966, 43, 3183, 6582, 1942, 24183, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 3103, 8666, 17, 5536, 24334, 2213, 7254, 18598, 17, 3189, 16, 4855, 5739, 1009, 3418, 1988, 24032, 1925, 7021, 17, 3189, 3728, 1942, 6698, 1920, 4346, 7996, 1927, 1920, 7642, 3260, 2014, 2024, 4821, 3154, 1922, 4802, 1930, 21501, 18, 2052, 8666, 17, 5536, 9059, 1977, 6835, 1922, 4572, 1921, 3337, 1930, 15903, 16, 4443, 1922, 7373, 7046, 43, 24183, 4757, 16, 1930, 2278, 12561, 18083, 10301, 8253, 9031, 1958, 4057, 5057, 18, 2222, 16, 1920, 2213, 3066, 3951, 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, 2176, 2258, 2252, 4378, 1922, 2096, 18021, 7972, 2341, 18339, 2210, 14061, 8997, 23437, 1009, 41, 8997, 5090, 41, 4353, 41, 24, 1930, 1977, 4624, 1942, 20709, 11569, 2733, 18, 3], "output": "RNLLNSAVFVFLALSVFAVGDFSFATAEKCIDFRDFPAEAVVVKYPNTPGAYAAYVGNIIDGNPILDSLKDFADDVFLSDNAERRNACLDNRGGFALKRGDFNTHNARHHSANLLAYDTNGNIVSQDSLSFSTDTDRNPRTGLLHDKPARVSGSDNIVKVVFKGKSVRGQVTQNMLSDTNVAYGVLCFTDFQPPVQLPIVDIKANNSDGPCVGSGAWSGSKAINGSEAKSNMGSGVYTYTITCSNQHGSATDAVRVNVRQPQSYTLSWTSNNASSCSASGAWSGSKNVFGTESSSNVGVGNYTYNQTFQGVLSISKLARDPAITTSSVYYENLYMIPGREVEFSIAITNSGSTSTTIDGVQTSDGITSSGINVGTILAGQSKTVKFRTRLNDNSFFTQSLTLITNTAYARGDNTVDTGADANTLAVLVTGLGSALSLSGLQIGKRVYWKNRIAQARLDGDNDSSIEGPGVIYPGLNIQASGASSKTSDNIYFNFASPISNFRIKIFDWNPHTFGDACSATSTNQPGNYTFIALNDPANYTLLWTSQHAASMPIVDIKANNSDGPINLVSPATITCSNQYGSANDTVTVYVSQINNLYIQDTLPSGLSYISGASQVQDMANVYAIKQGQVLGAA", "metadata": {"id": "A0A0G0Z123", "cluster": 9677423, "interpro_all": ["IPR008966", "IPR051172", "IPR047589", "IPR001434"], "interpro_used": ["IPR051172", "IPR001434", "IPR047589"], "interpro_unused": ["IPR008966"]}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is a member of 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. Additionally, it is part 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. It occurs in Bosea sp. (strain PAMC 26642).\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, 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, 4950, 16, 2176, 1977, 3131, 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, 2176, 5110, 1922, 16159, 5376, 2056, 18, 12, 3943, 11888, 1030, 22253, 6852, 13, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MQESKNVIRNLMDSVQWLKPLGLSVFEFATIWEINPYVLYEIIEMQAQYDYDYVSGNEKNRTFSLRRKRLQPVRHPGAIIQSEGDRPVDMIVAEKLQNAFNIPMSYW", "metadata": {"id": "A0A126P3E2", "cluster": 10080885, "interpro_all": ["IPR010982", "IPR013430"], "interpro_used": ["IPR013430", "IPR010982"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\nThe protein should feature a P domain that serves as an essential scaffold for the folding and thermodynamic stability of the subtilisin-like catalytic module in prohormone-proprotein convertases. It adopts a jelly roll-like fold to regulate calcium and pH dependence and often contains an RGD motif critical for intracellular trafficking and compartmentalization. Moreover, the protein includes a FTP domain that constitutes the propeptide region of bacterial M4 and fungal M36 peptidases, likely acting as an inhibitor to prevent premature activation or as a chaperone to assist in folding. Additionally, the protein is included in the Peptidase M36 (fungalysin) family, which consists of fungal metallopeptidases that function as pathogenicity factors. These enzymes belong to MEROPS family M36 and utilize a conserved HEXXH motif to bind a divalent cation, typically zinc, for catalysis. They are notably produced by species such as *Aspergillus* to degrade host lung cell walls during infection. It is identified in Anatilimnocola aggregata and is annotated with UniProt keywords Metalloprotease, Protease, and Hydrolase.\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, 5961, 43, 58, 3418, 1988, 10634, 1966, 1925, 4415, 7281, 1958, 1920, 10328, 1930, 16919, 5057, 1927, 1920, 14745, 1921, 17, 3189, 6804, 9059, 1922, 1965, 10647, 23745, 2290, 17, 12031, 7229, 1921, 14450, 2319, 18, 2176, 24032, 43, 8988, 11560, 1012, 12970, 17, 3189, 3728, 1942, 5741, 5016, 1930, 2087, 6816, 1930, 3868, 5461, 1925, 18797, 5219, 4140, 1958, 4776, 9604, 1930, 19643, 2466, 18, 3950, 16, 1920, 2213, 5921, 43, 8916, 1034, 3418, 1988, 14879, 1920, 5062, 8253, 3031, 1927, 4543, 21397, 1930, 8697, 12123, 1016, 24050, 1036, 16, 3205, 8290, 1966, 1925, 4106, 1942, 4625, 9839, 2936, 2014, 1966, 43, 14044, 1942, 6589, 1922, 10328, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 24050, 12123, 1016, 12, 8697, 2012, 1921, 13, 3416, 16, 2154, 7543, 1927, 8697, 8969, 24897, 1036, 1988, 2347, 1966, 15903, 2790, 18, 2144, 5038, 6784, 1942, 6902, 4001, 3416, 12123, 1016, 1930, 12561, 43, 5305, 7142, 1039, 1023, 5219, 1942, 4566, 43, 21610, 9976, 16, 5745, 7997, 16, 1958, 15408, 18, 2611, 2032, 7388, 4152, 2007, 3038, 2427, 1966, 14, 17604, 14, 1942, 17069, 4423, 3614, 2024, 12430, 2409, 2909, 18, 2176, 1977, 2899, 1922, 6289, 5912, 18044, 23338, 1019, 5206, 5499, 1930, 1977, 10633, 1956, 20709, 11569, 28629, 2051, 16, 7154, 16, 1930, 20748, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MANRSANRIRRSHAVKRRRLLAEKLEPRMMLHGGDFLSGPKQGAPLQIAVDFLKEHAADLGLNAADLESSLVSDQYTDEHSGVTHIYLQQIFDRGEVIHATSSFVGDVRVVEDLRPRFVISAPQAFLAWNDDFGLSSLTVKDQMLDDVAAKLVYVPTAKGLELAWRLDVHSRDYTSWFDAFVDYSRPVQSPYDGSRSVLTDPHDTLASPFGWHDTNGAPSGGASLGFNFPFEASQDPANYQSAAITNAFYWINNYGRGGLGNDPVIVDIQDGDGGGDGFAALPDGQSPRMTLHRRSNPFRDSAFDTGPANVSALNAKQSRAMGEGWGDWWALMFTQVATDAKFDAYPIGNYAAGYPSSYSAVQSHYAGAIWAATLWDMNWQLIQKHGFSADLLHGNAGNNRDAILAADLALTGGQNQTEIWAAFARRGMGFSASDGGSASATTVAEAFSGNEPGLANWAVYLDKNNNGIADVATTLTFNSTDTPKTIPDGPKTLSTQTVSGITLISPGNTPIILANYLGGSGANYTKTTFDDEAATYISSATAPFTGSFRAVGGNTGTLQSWSLQIAYGNTDPTVVTDTNGNYVPASGLHDAIITGGQPVIGQNFGNRAAALVANVSTEEDTLSPPLYKSDGITAINNGELISVAEGQSGVRFLPSANSNDAGPTIAMVSVTPVGDTPQITSLSTLEDKLSGAIVINRHATLYKSDGVTVIANGTFITVAEGQAGVRFLPSMNINAVGAFHAESSQNGTTVAAQSDSPDLVTQGLQLTLTVHGVSDPDGVDEVLALEFYRDINGDGAVGTASFYLGDHRYLARAWDGELWSPAATATGTVQPQIVPVVGSLSASYGVTAVEFYRDLNANGSLELGTDQLLGIDASGADGWVWTGWGNPATKTSTIKNALPSIASLSDSPDPVILGGTMTLTANTVADTDGNVVLSDDSVTDGWKWTGSTVSFPVGSVKYLSRARDNNNAWSALLHKGDSLTITASGVSDAAPGTVTAVEFYRDATTAADGWFKVLSTSAFPLGTVQVIARAKDNNSAYSPIVSQSLWVNSKVTLTANTVADTDGYVVLVEFYRDLDNDNVIDPTDEFLGSDDSVTDGSATRYTTGLVNLPPALASISVSSNLLHKGDSLTITASGVSDSNGVIDAGDVSLGSDTTAADGWFKVLSTSAFPLGTVQVIARAKDNNSTIGSLTASPTSVVQGANVTLTANTVADTDGSVVAVEMYLDLNGNNWKLVSSTVGLPIGTVRYLARAKDQLGSWSPTKVLTLTVIAPESLDTFYLPPQHRLGGDATNGLEVMSADLSIHVSPQVTSVTSDVSAAAVTLSVAETGESLYTDDRIGHATYNVAGSEFTDTRGNNVLAQEDLNADNTGGSRLLHDIHYQYGFTEAAGNFQVNDILVHEYGHGISERLTGNGPGIRPYPYSFDMTINPLTYNSYNLALQLVMDGLKVQGTNPSFLAGDVPGSISGTVFRDDDASGTQLSGVITDINVSVDITHPRDGELYPFFDLRQLEGRDPNGTWTLRLDDFLGVGNGTHHVREVMQPGFARTSVTISPAIGQGITHYKISDITSGSRFTVELSQDGSTLAAGTSADGMEVTHFKITGITGGNLAAGTIAVTAVNDAPIIALLTEGDLFLGGDTISSDGWSWSGSPTIVTRPAAITLTANGVSASGGSTAGFDVGVNRYFARAQSLPAIVEFYRDLDNDNVIDPTDEFLGTRYTTGLVNLPPALASISVSSNNSNGVIDAGDVSLGSDPTIGSLTASPTSVVQGANWKWTGSTVSFPVGSVKYLSRARDNNNAWAAPGTVTAVEFYRDANAYSPIVSQSLWVNSKPNVIDSETDVFLGNATSTALG", "metadata": {"id": "A0A517YMA1", "cluster": 10532499, "interpro_all": ["IPR011096", "IPR050371", "IPR008979", "IPR002884", "IPR001842", "IPR027268"], "interpro_used": ["IPR002884", "IPR011096", "IPR001842"], "interpro_unused": ["IPR050371", "IPR027268", "IPR008979"]}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein includes a Outer membrane protein, beta-barrel domain that adopts a membrane-bound beta-barrel fold structure found in a diverse range of outer membrane proteins. Furthermore, the protein is a member 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 is derived from Bacteroidota bacterium and is connected to UniProt keyword Signal.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 5921, 43, 7642, 3260, 2213, 16, 4666, 17, 19560, 3418, 1988, 24032, 43, 3260, 17, 4124, 4666, 17, 19560, 3728, 3170, 2435, 1922, 43, 6445, 3109, 1927, 7642, 3260, 2697, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 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, 1977, 3595, 2037, 24323, 7336, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 18, 3], "output": "MKIISILFISLVISGSAFSQIVDKPYNVGLGLVSIKNSTGFIVVLNGEYFINKSISLSPKIGLAFFMLDLTINKSNNALKPYILFGGKYKIPMTGKMNTSKYPPENSRYSYGISNINSHPKINSLYFHSISFIVYFKAGIVHPNLVLNKGSSDTNRGTVIFEKSNGYKENYDLMSVSYDSFAIDVGIGLNKSITKLIVNPEI", "metadata": {"id": "A0A7C5NPP8", "cluster": 12434898, "interpro_all": ["IPR011250", "IPR027385"], "interpro_used": ["IPR027385", "IPR011250"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein can be placed in the Glucose-6-phosphate isomerase/Oxalate decarboxylase family, which comprises enzymes involved in carbohydrate metabolism and oxalate degradation. Members catalyze the reversible conversion of glucose-6-phosphate to fructose-6-phosphate in glycolysis and gluconeogenesis, or the decarboxylation of oxalate into formate and carbon dioxide. Also, the protein should feature 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. Additionally, the protein can be placed 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 occurs in Aureobasidium pullulans EXF-150.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 3817, 17, 26, 17, 5413, 25510, 19, 25069, 23922, 3416, 16, 2154, 12936, 5038, 3286, 1922, 10590, 4714, 1930, 25069, 4877, 18, 4678, 18170, 1920, 10743, 7309, 1927, 3817, 17, 26, 17, 5413, 1942, 15102, 17, 26, 17, 5413, 1922, 13393, 1930, 25680, 16, 2014, 1920, 22429, 1943, 1927, 25069, 2460, 25741, 1930, 5056, 15422, 18, 2222, 16, 1920, 2213, 3066, 5961, 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, 4950, 16, 1920, 2213, 2112, 1998, 5396, 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, 5110, 1922, 8689, 26205, 12924, 7408, 1989, 10875, 25341, 1975, 1038, 17, 5493, 18, 3], "output": "MLYSRFHVVKSTDVQTSSIMLAEPHSASAVHHHGAAVVSEGGKKRQVLKQGDFALIPAYAEPDVVNLEGWGKSGGQTDGMTRKPAITGLASICSSQDTIVYAVRGQGQEHQEVNDGDEEVEWVIVRSG", "metadata": {"id": "A0A074XYF7", "cluster": 12441919, "interpro_all": ["IPR013096", "IPR051610", "IPR014710", "IPR011051"], "interpro_used": ["IPR051610", "IPR013096", "IPR011051"], "interpro_unused": ["IPR014710"]}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein is classified under the Rho GTPase-activating Regulators family, which functions as Rho GTPase-activating proteins (GAPs) to regulate Rho family small GTPases, particularly of the Rac-type. By catalyzing the conversion of active GTP-bound GTPases to their inactive GDP-bound state, these proteins control signaling pathways governing cytoskeletal dynamics, cell morphology, and polar cell growth. Furthermore, the protein can be placed in 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. Moreover, the protein should feature a Ternary complex factor MIP1, leucine-zipper domain that likely mediates interactions with plant MADS-box factors. It is present in MIP1 subunits of the TORC2 complex, which controls cell growth and proliferation, as well as in putative Rho GTPase-activating proteins. It is found in Tetracentron sinense (Spur-leaf) and corresponds to UniProt keyword Coiled coil.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 10585, 14809, 17, 8019, 9098, 3416, 16, 2154, 4088, 1966, 10585, 14809, 17, 8019, 2697, 12, 11349, 13, 1942, 5741, 10585, 3416, 2858, 18390, 16, 4443, 1927, 1920, 7195, 17, 2601, 18, 2007, 29601, 1920, 7309, 1927, 3500, 9319, 17, 4124, 18390, 1942, 2310, 9078, 15217, 17, 4124, 3360, 16, 2144, 2697, 2285, 3197, 3873, 20012, 14787, 5565, 16, 2024, 6076, 16, 1930, 5676, 2024, 2905, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 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, 3950, 16, 1920, 2213, 3066, 5961, 43, 18734, 2796, 2991, 15070, 1009, 16, 12624, 17, 27910, 3418, 1988, 3205, 10412, 3719, 1956, 4496, 9133, 1036, 17, 5758, 2790, 18, 2176, 1977, 2481, 1922, 15070, 1009, 6991, 1927, 1920, 8184, 8054, 2796, 16, 2154, 3562, 2024, 2905, 1930, 4031, 16, 1966, 2486, 1966, 1922, 6770, 10585, 14809, 17, 8019, 2697, 18, 2176, 1977, 2435, 1922, 12470, 3025, 2830, 25736, 3355, 1021, 12, 21132, 17, 6998, 13, 1930, 8852, 1942, 20709, 11121, 2538, 17524, 9121, 18, 3], "output": "MKEDHLNTPKGNKFHGHLSAPQFEEESKETRVVYMLIGKLVGGQVEGSNQPKEIQALLKDFEELVSEELPNGLPPIRSIQHAIDLVPRAKLPNQTAYGMPPNHRTEMRRQVEDLIAKGLARRTPSMESVDSSGEEELAIRRLEITKNDLRNRIAKESKGNAILQASLERRKQALHERRLALEQDVSRLQEQLQAERDLRAALESLMVYTNMKTRAELEEIALAEADVARLKQKVAELHHQLNQQSQNYHGSPSDACNRYQHIQNLLSQHHLDCNCFFSHLNSSIKCHFNGLLQECSSGADWGNIKGQVLPYSSSSKQLSWKQCADSTSLGDSKSTEASTSLSVDELSGVDSATMPSISRPAEGIEYQRHPSTASSSSLVELTTRLDFFKERRSQLMEQLHNLDLNYGTSSSQGFMYKPSSPPGTNCPR", "metadata": {"id": "A0A834Z4Q4", "cluster": 13180476, "interpro_all": ["IPR043502", "IPR025757", "IPR052799"], "interpro_used": ["IPR052799", "IPR043502", "IPR025757"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\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. In addition, the protein should contain a Endonuclease GajA/Old nuclease/RecF-like, AAA domain that functions in DNA metabolism and structural maintenance within RecF, SMC proteins, and the Gabija antiviral system. Characterized by an AAA superfamily P-loop motif, this domain acts as an endonuclease in GajA, nicking dsDNA within the sequence 5'-TNNNCGGGNNA-3' in the absence of nucleotides to confer phage resistance. It is expressed in Planctomycetota bacterium.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 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, 5531, 43, 18697, 4357, 14174, 19, 4156, 16230, 19, 2090, 1038, 17, 3189, 16, 13835, 3418, 1988, 4088, 1922, 2678, 4714, 1930, 4346, 6291, 2651, 2090, 1038, 16, 16312, 2697, 16, 1930, 1920, 6321, 7483, 1019, 10129, 2433, 18, 4378, 2007, 1925, 13835, 13975, 58, 17, 5881, 5219, 16, 2052, 3418, 8016, 1966, 1925, 18697, 1922, 4357, 14174, 16, 12657, 1941, 16397, 2651, 1920, 3244, 25, 11, 17, 7417, 16443, 1030, 3312, 3223, 2175, 17, 23, 11, 1922, 1920, 3905, 1927, 9519, 1942, 7909, 10503, 3554, 18, 2176, 1977, 3198, 1922, 4720, 2341, 13386, 19446, 3857, 14061, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MALTCSQHQGFTGFPRSDNLIRRIRLINFMSHDDTVIDLADRLTVLTGNHVIRHNEKECSVTVDTDDGHTIEWRRTKLSPKYIIDGEVFDRLGRCGTPDILHQGEQKSPLFLLDKPTSQAAQFFAASSDAASLIEMQALHRKRIVDSRRKQKDLQADMSQLEAQYAEFALIDAQCRELAFAISAVQCGHRQVDECELQFAQTQSDQIANECVAVHQLTAPPILDDIEGRRQLLSHITATAGRVDLSQRISFAEQSQLRLETMHVEMSSLVAPPEWIETQDFSRSLRVLEESEFAQSTENLRAWVAENPICATCGGPMDADRLLDLDRSGEGDHSHGPNNCGKSAVVAALQILCHNGPSILRLPKVKVSAGEAFDIHFRSTLLEDEIAGLDPADGIAIWQSRASSFEELVATPSMIDPEPIGRLLQFNSMLSLEEPPEIVNSESIERDIVAQSRLDTTLLAAEHCTS", "metadata": {"id": "A0A3L7N5H1", "cluster": 14825897, "interpro_all": ["IPR041685", "IPR027417"], "interpro_used": ["IPR027417", "IPR041685"], "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 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. Furthermore, the protein should feature a Phytochelatin synthase N-terminal catalytic domain that functions as a glutathione gamma-glutamylcysteinyltransferase to synthesize phytochelatins and homophytochelatins for heavy metal detoxification. Belonging to peptidase family C83 of the papain superfamily, this alpha/beta folded structure contains a cysteine protease-like catalytic triad and oxyanion hole. It houses the active site and conserved cysteine residues essential for processing metals such as cadmium and arsenate. It is native to Hydra vulgaris (Hydra) (Hydra attenuata) and exhibits UniProt keyword tags Metal-binding.", "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, 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, 3677, 16, 1920, 2213, 3066, 5961, 43, 25512, 15404, 5148, 2268, 8921, 56, 17, 4262, 6804, 3418, 1988, 4088, 1966, 43, 9153, 7034, 17, 25345, 23159, 8037, 2199, 9961, 1942, 15541, 25512, 15404, 5148, 21881, 1930, 16350, 25818, 4575, 15404, 5148, 21881, 1958, 7881, 6048, 18169, 18, 10588, 1942, 24050, 3416, 19189, 1010, 1927, 1920, 3860, 2005, 13975, 16, 2052, 4595, 19, 4666, 16318, 3170, 5461, 43, 8666, 7154, 17, 3189, 6804, 21845, 1930, 20004, 8150, 1916, 13356, 18, 2176, 23407, 1920, 3500, 3200, 1930, 5305, 8666, 4248, 4415, 1958, 4587, 11570, 2427, 1966, 17203, 1930, 21290, 2010, 18, 2176, 1977, 6196, 1942, 22420, 22621, 12, 22420, 13, 12, 22420, 5693, 5499, 13, 1930, 9826, 20709, 11121, 2538, 14392, 6048, 17, 2743, 18, 3], "output": "MINFKSTFSFAKRFYKSQIVLYYTTGLYSTLNPNLSSIGPWYLEDKQQTSNFSSEEGKQVFKESLLSGYANIYFPLAEQFRTQAEPAYCGISTLVMILNSLAVDPKRVWVQQNGITLDQFVCLATCNNLDLNVVRTDDNENIKSFRDVVEEICAGQDKVLTCSYSRSVLKDMVLIFDVARFKYPPHWVKLDLLWEAMKALDGVTGLPRGYIVLATNSVSQSSMAKFMRSWRTFLKNESVKISDSLDVTIGQTLAGLNEALKELLEGDSVFNTTEIYQIIHSMVSKFKKNFFQSRSNFISNQCTCIERVGKPFVNEIDTSTHDGRKVLTTKTGSSTLLYSLNNTNDISTYLARHVEKVLLNGDDLLVNEVKQLRHQIQSLLELIKRNPPVFSNEQFYRRKLPACCLAKGPWRWYHEEMLDCCLSLDLNQTGGGHFSPIGAYHPKRKTEEMPLLLFRLSNIFRVTIQFNTHCIDTLPPDHISAVRKILASLENDNSKELVTDSHFITMLILCWP", "metadata": {"id": "A0A8B6XFM4", "cluster": 14877326, "interpro_all": ["IPR038765", "IPR040409", "IPR007719", "IPR038156"], "interpro_used": ["IPR038765", "IPR007719"], "interpro_unused": ["IPR040409", "IPR038156"]}, "task_type": "infilling"} {"instruction": "Here is the protein function: The protein carries a Peptidase C39-like domain that functions as a cysteine protease to specifically cleave 'double-glycine' leader peptides from bacteriocin precursors during their secretion and maturation. This proteolytic activity is often coupled with ABC transporter systems to facilitate the export of these antimicrobial proteins across the bacterial membrane. It is found in Anaerolineales bacterium and is connected to UniProt keyword Signal. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 16252, 43, 24050, 8351, 1026, 17, 3189, 3418, 1988, 4088, 1966, 43, 8666, 7154, 1942, 4475, 21252, 11, 4825, 17, 10646, 11, 17442, 5320, 2037, 14027, 11778, 10416, 2409, 2310, 5512, 1930, 7655, 18, 2052, 12712, 2455, 1977, 3868, 6416, 1956, 7219, 9054, 3771, 1942, 6628, 1920, 12660, 1927, 2144, 8003, 2697, 3436, 1920, 4543, 3260, 18, 2176, 1977, 2435, 1922, 11381, 8419, 3955, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MKTNSRIFIAAILAVAAICVLVFPAIAGCPDNDPACKLIPPESREVRVSTSAGELVFSEIDGSNPLAPIPMPPPALLQPVTPALDSSSLTPEFTTIALPLRYQDPLDISCGVQALGMALEPLEGAAPKSTAIIDFLLRHDYLYDFGTGVEELALAAQEFGYAGSVGFHNWTREDLQAELTAGRPVVIDLGANGPDEPGHFVALTGISPDGKWAAYNDPLLGERVLPLDDFLDLWALQGNSGVAVAEATPTPLSPNYTPWAALAAAMMATLALAPSVLQNQRRLGTGGMLIAQSGSSGSATYIGFEPPYQAPTGMRWVQGEPVYETHTHSEIIYHKVPKRELQKVRVGTTIKKIPYTKRILVDNGHWVTDYKSERYVKGYRRKRILDGYRTKRYVKYYRTRLYRNRWGFSRRRIPVYGYKRVPVYRTLRVPIYGTRKVPNGRHWESKWEYEVYTEYKTVVKPVYEEQWVTVGYQLIPEEKIIEEQVTVGYQWALERSRDPLPKEHEIDIIDEMHDIRAPILHPKIMVTTAPLRVRSSAGPNSHPSPSQ", "metadata": {"id": "A0A523Z987", "cluster": 25521218, "interpro_all": ["IPR039564"], "interpro_used": ["IPR039564"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the polypeptide chain function: The protein should feature a DUF2207 domain that is located at the N-terminus of uncharacterised prokaryotic proteins, including the predicted membrane protein YciQ from *Escherichia coli*. Also, the protein includes a Predicted membrane protein YciQ-like, C-terminal domain that is present in various hypothetical prokaryotic proteins, including Escherichia coli YciQ, yet possesses no known function. It is characteristically located C-terminal to the domain of unknown function DUF2207. It is identified in Bacillus sp. HNG and is connected to UniProt keyword Transmembrane helix. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 3066, 5961, 43, 4855, 6680, 24368, 3418, 1988, 1977, 4810, 2019, 1920, 56, 17, 7822, 1927, 23229, 3495, 21545, 2697, 16, 2710, 1920, 4396, 3260, 2213, 22386, 22570, 2037, 14, 10210, 5178, 14, 18, 2222, 16, 1920, 2213, 5921, 43, 4396, 3260, 2213, 22386, 22570, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 1977, 2481, 1922, 3425, 15148, 21545, 2697, 16, 2710, 10210, 5178, 22386, 22570, 16, 4898, 14465, 2239, 3171, 2347, 18, 2176, 1977, 6293, 2169, 4810, 45, 17, 4262, 1942, 1920, 3418, 1927, 5435, 2347, 4855, 6680, 24368, 18, 2176, 1977, 2899, 1922, 14587, 2056, 18, 9888, 1029, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9117, 7864, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MLVSLKPVSVFIRISRYEGGTDMRAKIGGLIFLVVFIFIFPIQGLAVDYWINDVKMDAFLQDDGTVQVTEAHTYEFDGEFNGITRTVIPKKGSSIKDFSASENGKELRVEKEDDLYKIHRKGKDETITVTLTYTIMSGVEIYKDVAQFYWPFFDNRNESTYENLVITVHPPQSTSDVIAFGYDEAFQTESVQSDGSVVFHFGEVPSETNGDIRVAYDVELFSGANYVTADKPMKEEILNDKNELLIKAQERAETKETLSKVAIVLVPIFALLFIVIIVRNRLEGRAKLAAVKREMAHAGAPPKQVMSLPATIVFTNHNYLPQGQSMAAALLDLVRKKKVRQVSDEKFQLMDQDAALPHEEILMEWLFEKIGQNGVFDFSDLQTYSKNKKNSGKYSSFQMKWGEAVRNEVKEHFLYEDKSKFKLFLGLLSIVLVPFLFLFPMYELFSWFVLTLVLFGGVIIYLIAYRPKNSEGLRILHEWLMFKDSYKALSPDEWKKWSEDDQMRAYIYGLGTGDKGMMKQNEDLIFALNKPYRYESGGFYPYSVYSFGYVGPNASAQFESANDSIGTGSSSSSSSGGGTGGGGGGSGAF", "metadata": {"id": "A0A371S6K6", "cluster": 27334120, "interpro_all": ["IPR018702", "IPR048389"], "interpro_used": ["IPR018702", "IPR048389"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein is grouped in the Histone H4 family, which functions as a highly conserved core component of the nucleosome octamer responsible for wrapping DNA in a left-handed manner. It associates with histones H2A, H2B, and H3 to compact DNA and undergoes various post-translational modifications that regulate transcription, DNA repair, and chromosomal stability. Additionally, the protein contains a CENP-T/Histone H4 histone fold domain that mediates chromatin association and the structural assembly of nucleosomes. This conserved fold, found in the C-terminus of CENP-T and in Histone H4, facilitates the formation of the octameric core complex responsible for wrapping DNA. Furthermore, it is part of the Histone-fold superfamily, which features a three-helix core that facilitates protein heterodimerization essential for DNA organization and transcriptional regulation. This structural element is found in nucleosome core histones, archaeal histones, and transcription factor components such as TAFs and NC2, where it mediates the protein-protein interactions required for chromatin assembly and RNA polymerase II-dependent transcription. It is derived from Dromaius novaehollandiae (Emu) and has UniProt annotations Chromosome and Nucleus.\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, 10809, 1922, 1920, 6632, 11278, 3416, 16, 2154, 4088, 1966, 43, 3626, 5305, 4728, 4594, 1927, 1920, 14914, 5843, 8835, 5061, 1958, 4573, 5041, 2678, 1922, 43, 3506, 17, 17105, 5222, 18, 2176, 14162, 1956, 15808, 18249, 16, 19542, 16, 1930, 8170, 1942, 13726, 2678, 1930, 14928, 3425, 2753, 17, 8414, 6920, 1988, 5741, 3213, 16, 2678, 5059, 16, 1930, 9220, 5057, 18, 4950, 16, 1920, 2213, 5461, 43, 19990, 17, 62, 19, 6632, 11278, 6632, 3728, 3418, 1988, 10412, 6338, 3279, 1930, 1920, 4346, 5957, 1927, 18729, 18, 2052, 5305, 3728, 16, 2435, 1922, 1920, 45, 17, 7822, 1927, 19990, 17, 62, 1930, 1922, 6632, 11278, 16, 11374, 1920, 3337, 1927, 1920, 5843, 17118, 4728, 2796, 5061, 1958, 4573, 5041, 2678, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 6632, 17, 3728, 13975, 16, 2154, 4075, 43, 2559, 17, 7864, 4728, 1988, 11374, 2213, 15672, 2466, 4415, 1958, 2678, 5901, 1930, 5224, 3640, 18, 2052, 4346, 6149, 1977, 2435, 1922, 14914, 4728, 15808, 16, 22367, 15808, 16, 1930, 3213, 2991, 4178, 2427, 1966, 19063, 1036, 1930, 5301, 1028, 16, 2597, 2176, 10412, 1920, 2213, 17, 2213, 3719, 3414, 1958, 6338, 5957, 1930, 3146, 6479, 2890, 17, 3100, 3213, 18, 2176, 1977, 3595, 2037, 8442, 3368, 11519, 6862, 3336, 12074, 4702, 7955, 12, 2391, 1032, 13, 1930, 2258, 20709, 15010, 5597, 1930, 5607, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "PPYTAARRCSRHTRLRQRRRQHVWQRQGREGAAPGSARRXEAHLGAHLRGDARRAEGVPGERDPRRRHLHGLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGGRQGGRQAAPQSVARQHPGHHQAGHPARLKRISGLIYEETRGVLKVF", "metadata": {"id": "A0A8C4J785", "cluster": 28337536, "interpro_all": ["IPR035425", "IPR009072", "IPR001951"], "interpro_used": ["IPR001951", "IPR035425", "IPR009072"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein is assigned to the Peptide antibiotic immunity-related family, which confers immunity to specific peptide antibiotics such as the DNA replication inhibitor microcin B17. These proteins can function independently or in concert with other factors to induce the SOS repair system as a protective mechanism. In addition, the protein should include a Pentapeptide repeat that adopts a right-handed beta-helical structure to function as a DNA mimic, exhibiting size, shape, and electrostatic similarity to B-form DNA. This structural mimicry facilitates interactions with DNA-binding proteins, such as DNA gyrase, often conferring resistance to fluoroquinolones or protecting against microcin B17 toxicity. Additionally, the protein contains a DUF2169 domain that is found in various hypothetical prokaryotic proteins and currently lacks a characterized biological function. It has been detected in Yersinia pseudotuberculosis serotype O:1b (strain IP 31758). Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 6304, 1942, 1920, 4207, 7267, 7611, 17, 2712, 3416, 16, 2154, 16556, 7611, 1942, 2487, 4207, 7560, 2427, 1966, 1920, 2678, 5158, 4106, 10572, 1921, 10360, 1027, 18, 2144, 2697, 2112, 2347, 6407, 2014, 1922, 21799, 1956, 2303, 2790, 1942, 4769, 1920, 17668, 5059, 2433, 1966, 43, 6337, 2856, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 9412, 24010, 6865, 1988, 24032, 43, 3659, 17, 17105, 4666, 17, 11514, 3170, 1942, 2347, 1966, 43, 2678, 10223, 16, 12196, 3081, 16, 5989, 16, 1930, 12452, 6796, 1942, 44, 17, 2386, 2678, 18, 2052, 4346, 10223, 6907, 11374, 3719, 1956, 2678, 17, 2743, 2697, 16, 2427, 1966, 2678, 9430, 2051, 16, 3868, 21510, 3554, 1942, 23619, 24909, 2014, 15145, 3316, 10572, 1921, 10360, 1027, 5532, 18, 4950, 16, 1920, 2213, 5461, 43, 4855, 6680, 22548, 3418, 1988, 1977, 2435, 1922, 3425, 15148, 21545, 2697, 1930, 5077, 13012, 43, 4378, 3933, 2347, 18, 2176, 2258, 2252, 3330, 1922, 29323, 14102, 11520, 1031, 29603, 8071, 15306, 57, 30, 5462, 12, 3943, 5416, 24006, 7532, 13, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MRIIRPQQLVVLKSSYQIGHESHMGISVVAGCYLSKPEHMVTESQIWQAWKAAPLSFRMLDSAEPKPFAEFLLAGHAGIGEEVTSLSAEVSVGSLTRRWCIEGESNKTGLVIKPFLRMSMDHTQSWGGKGCKENPLGRGYNDERKPTIMSLGLDGSAIVRSPLASPSPVPHDFQLRKVHINEVASTMTDPQYLETFYPGLPPQIDRRYFQMAPPGQWLKKSAWPDSVPFKLIGFRPDNEEISGAFPAVSARAFVWDNPSAPPSEVTLLRKTLWLLPDNDMGLMVFTGSVPLTHLFDEPIDTLLVGLDDSHSLRELEYYQQVYKSRSVEGAASFEFLKDPELMPEGMPLNVIRDLADHPDSLRYSASAMSEAESERFYQDVQDAIDRQEQQKSEEQETLGDLNVPAAGKEEAGTQWLESKEDTATNVTFLGTDFSGMTLDNKQFRYCMFTGCHFDKATFKDCTFEHCQFTQSDFENSRWNNVHLSGCLFKQAEWQKAAFTHCKWEKSTFEYGVFKHAQFTDNALDNCLINHSDFSLGTFDHCTLNGCFFSETHCDQTQFNQVIITSCIFEKCDGPKACFTESTIEKTSFISSSWVGGRLSHCYLNSLTTGLNTNLSESHFEQCSLNKMGFLKVNLQSSTFINCSMLESCCDKADFSQATLIACDMTAVRLKDANLVHSHWQNTSLQQSMFYNADLRDATFQRCNLAGANLAMISQNMDTRFEHCLTEKTHWIPRRYTVPA", "metadata": {"id": "A0A0U1R1B1", "cluster": 28954515, "interpro_all": ["IPR001646", "IPR018683", "IPR052949"], "interpro_used": ["IPR052949", "IPR001646", "IPR018683"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a protein with the following function: It is part of the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. Furthermore, the protein possesses a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. Additionally, the protein carries 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 has been characterized in Abditibacteriaceae bacterium and is classified with UniProt keywords Glycogen biosynthesis and Glycosyltransferase. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 3677, 16, 1920, 2213, 14465, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 4950, 16, 1920, 2213, 16252, 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, 2258, 2252, 4378, 1922, 11754, 2078, 7972, 2341, 18339, 1972, 3336, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 13302, 8132, 1930, 20067, 9961, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MADRLKVLMVTAEAVPFIKTGGLADVAGSLPHALAAQDIDVRLVLPHYKTIDATRFRTQDIAQLYIPFDDDVHLTAIQQVTDNKLPPANNQADVPVYFIDAPHYFGEDKPYGYDDDILRFGFFVRACLELPGLLEWQPDIIHCHDWHTGLLPVYLSTRRRQYPALAATKTVFTIHNLAYQGESHSSYLPRLGLDPSLFNYHQLEFYGKINPMKGGLVFADTLTAVSPGYAHEIQTAEYGAGLEGLLQNRAGVLHGILNGIDYSEWNPRHDPHLAQNYGPEDSKGKAQCKRDLLSQMGLAIPGRKKVPVIGMVSRLSAQKGFDLVADALESLVQMGCYFVLLGSGEPQFMQLFQELEQRFPRAVACRLDTFDNALAHKIYAGSDLFLMPSHYEPCGLAQMISLAYGTIPIVRATGGLADTVHEFDATTGIGNGFVFEPYTASALTEVVQRAVTCYKGKAWPQLMQNGFACDFSWNTSARQYAQLYGSMLSS", "metadata": {"id": "A0A951H9Z0", "cluster": 27609252, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR011835", "IPR013534", "IPR001296"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: The protein is classified under the Phosphoribosylglycinamide formyltransferase family, which catalyzes the third step in de novo purine biosynthesis by transferring a formyl group from formyl tetrahydrofolate to generate 5'-phosphoribosyl-N-formylglycinamide. While found as a standalone enzyme in prokaryotes, this domain typically occupies the C-terminal region of a multifunctional protein in eukaryotes that also exhibits GAR synthetase and AIR synthetase activities. Moreover, the protein incorporates a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. It is identified in Cylindrospermopsis sp. CR12. 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, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3416, 16, 2154, 17097, 1920, 4563, 3537, 1922, 2028, 9441, 19700, 8132, 2007, 21902, 43, 29285, 2210, 2037, 29285, 21196, 27851, 1942, 5655, 25, 11, 17, 3421, 2023, 11731, 17, 56, 17, 29285, 17038, 3665, 5482, 18, 2679, 2435, 1966, 43, 2924, 20807, 2912, 4113, 1922, 28149, 16, 2052, 3418, 5745, 28646, 1920, 45, 17, 4262, 3031, 1927, 43, 20136, 2213, 1922, 15021, 1988, 2222, 9826, 13139, 18185, 1930, 4433, 18185, 4209, 18, 3950, 16, 1920, 2213, 19683, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2176, 1977, 2899, 1922, 15460, 5424, 2166, 8369, 2056, 18, 2345, 3112, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MIQSYSMNSTSSLISPDVSGYQSHDIKPVKLGVMASGNGSNFEVVAQAIKSGDLNAQIQVLIYNNPLAKAAERALNHGVEAILLNHRHYQKREDLDREIVSTLRQYQVDLVVMAGWMRLVTQELIDAFPNHIINIHPSLLPSFKGVRAVEQALEAGVKITGCTVHLLRLEMDSGPILMQAAVPVLPNDTAETLHARIQVQEHRILPLAIAQVADKI", "metadata": {"id": "A0A0R0M8P6", "cluster": 2755928, "interpro_all": ["IPR002376", "IPR036477", "IPR004607"], "interpro_used": ["IPR004607", "IPR002376"], "interpro_unused": ["IPR036477"]}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein can be placed in the MshD mycothiol acetyltransferase family, which catalyzes the final step in the biosynthesis of mycothiol by transferring an acetyl group from acetyl-CoA to desacetylmycothiol. This enzymatic activity produces a vital thiol antioxidant that protects certain bacteria from oxidative stress and maintains intracellular redox balance. Additionally, this family includes related N-acetyltransferases involved in ribosomal protein modification, metabolite detoxification, and antibiotic resistance. Also, 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. Moreover, the protein should have 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 occurs in Geobacter sp. SVR and carries UniProt keyword assignments Cytoplasm.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 19864, 1007, 5078, 17809, 1945, 22226, 3416, 16, 2154, 17097, 1920, 3948, 3537, 1922, 1920, 8132, 1927, 5078, 17809, 1945, 2007, 21902, 1925, 6894, 2210, 2037, 6894, 17, 10027, 1942, 2270, 25913, 14930, 4879, 22523, 1945, 18, 2052, 8145, 2455, 9300, 43, 8970, 13914, 7335, 1988, 14576, 4908, 4802, 2037, 5163, 3071, 1930, 16566, 4776, 9366, 6766, 18, 4950, 16, 2052, 3416, 5921, 2712, 56, 17, 22226, 1036, 3286, 1922, 11196, 2213, 6295, 16, 9483, 18169, 16, 1930, 7267, 3554, 18, 2222, 16, 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, 3950, 16, 1920, 2213, 3066, 2162, 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, 5110, 1922, 14136, 7972, 2341, 1915, 2056, 18, 19407, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 18, 3], "output": "MERSDLDAVLAIEQDAYPNAIPFVAVQDQTVIGYLCLMSLTAIRTARERGAELLTLRRGYYEGTEDAILMEKTLLPWKLEHFIQELHSPLFEEAQILNVAVARLQRGKGIARLLMDEVRESNRAAIALYESYGFVRYFV", "metadata": {"id": "A0A6F9WWU6", "cluster": 768811, "interpro_all": ["IPR006464", "IPR016181", "IPR000182", "IPR050276"], "interpro_used": ["IPR050276", "IPR016181", "IPR000182"], "interpro_unused": ["IPR006464"]}, "task_type": "infilling"} {"instruction": "The protein is a member of the General secretion pathway protein G-type pilin family, which functions as a structural pseudopilin within the Type II secretion system (T2SS) of Gram-negative bacteria. These proteins share sequence characteristics with Type IV pilins and assemble to facilitate the export of virulence factors and other exoproteins across the outer membrane. Furthermore, the protein possesses a Prokaryotic N-terminal methylation site, which directs the methylation of a conserved phenylalanine residue. This motif is typically located at the N-terminus of pilins and proteins associated with secretion pathways. Also, the protein is included in the Pilin-like superfamily, which comprises structural proteins such as type IV pilins and secretion system pseudopilins that assemble into filamentous appendages on the bacterial surface. These proteins typically feature a conserved, methylated hydrophobic N-terminus and facilitate critical functions including cell adhesion, twitching motility, and DNA transformation. Some members, such as YadA-like autotransporters, act as pathogenicity factors by extending from the outer membrane to mediate host interactions. It is produced by Litoribrevibacter albus and is associated with UniProt keywords Transmembrane helix.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 1920, 3335, 5512, 3374, 2213, 49, 17, 2601, 7547, 1921, 3416, 16, 2154, 4088, 1966, 43, 4346, 11520, 10984, 7782, 2651, 1920, 2601, 2890, 5512, 2433, 12, 5787, 5590, 13, 1927, 8604, 17, 3136, 4802, 18, 2144, 2697, 7948, 3244, 3779, 1956, 2601, 4370, 7547, 2925, 1930, 17421, 1942, 6628, 1920, 12660, 1927, 9304, 2790, 1930, 2303, 18930, 22163, 1036, 3436, 1920, 7642, 3260, 18, 3677, 16, 1920, 2213, 14465, 43, 21545, 56, 17, 4262, 5547, 3200, 16, 2154, 28351, 1920, 5547, 1927, 43, 5305, 17388, 6181, 18, 2052, 5219, 1977, 5745, 4810, 2019, 1920, 56, 17, 7822, 1927, 7547, 2925, 1930, 2697, 2458, 1956, 5512, 3873, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 7547, 1921, 17, 3189, 13975, 16, 2154, 12936, 4346, 2697, 2427, 1966, 2601, 4370, 7547, 2925, 1930, 5512, 2433, 11520, 10984, 7782, 1036, 1988, 17421, 2460, 18706, 7958, 2662, 1990, 1920, 4543, 3154, 18, 2144, 2697, 5745, 5961, 43, 5305, 16, 11882, 7919, 56, 17, 7822, 1930, 6628, 4140, 4088, 2710, 2024, 6141, 16, 21596, 1941, 9254, 16, 1930, 2678, 7002, 18, 2673, 4678, 16, 2427, 1966, 26169, 3825, 17, 3189, 5728, 5412, 24095, 1036, 16, 4033, 1966, 15903, 2790, 2007, 12140, 2037, 1920, 7642, 3260, 1942, 8265, 4423, 3719, 18, 2176, 1977, 4152, 2007, 4471, 6658, 10026, 7972, 2341, 1915, 5311, 1957, 1930, 1977, 2458, 1956, 20709, 11569, 9117, 7864, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MNKISKGFTIVELMYRQYIIDAETSVARQHLDQLNNNTFVSGTQVGKSGTFETQLGFCYTAKVYKTADTSISASATKKIITVAIIGIISAVAVPSELFLNAYHLKPGDGGDDFTYVVAACSGGSIAD", "metadata": {"id": "A0AA37W9E0", "cluster": 1328392, "interpro_all": ["IPR000983", "IPR012902", "IPR045584", "IPR050470"], "interpro_used": ["IPR000983", "IPR012902", "IPR045584"], "interpro_unused": ["IPR050470"]}, "task_type": "infilling"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein includes a Motility protein B-like, N-terminal domain domain that functions as a periplasmic plug within the MotA/MotB proton-channel complex, utilizing a conserved amphipathic $\\alpha$-helix to prevent premature proton flow in the bacterial flagellar motor. This domain is also found in ZorB, a component of the Zorya type I antiviral defense system that likely assembles with ZorA in the inner membrane. It occurs in Sphingomonas solaris and features UniProt keywords Transmembrane helix, Flagellum, and Cell projection.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 5921, 43, 9254, 2213, 44, 17, 3189, 16, 56, 17, 4262, 3418, 3418, 1988, 4088, 1966, 43, 24334, 15998, 2651, 1920, 12798, 1019, 19, 12798, 1014, 8433, 17, 4999, 2796, 16, 10232, 43, 5305, 26747, 21494, 8, 38, 4595, 8, 17, 7864, 1942, 4625, 9839, 8433, 3426, 1922, 1920, 4543, 24154, 4842, 18, 2052, 3418, 1977, 2222, 2435, 1922, 11906, 16007, 16, 43, 4594, 1927, 1920, 11906, 6907, 1019, 2601, 51, 10129, 9720, 2433, 1988, 3205, 17421, 1036, 1956, 11906, 5524, 1922, 1920, 6671, 3260, 18, 2176, 5110, 1922, 13502, 10480, 14268, 1937, 1930, 4075, 20709, 11569, 9117, 7864, 16, 7030, 10757, 16, 1930, 2024, 11244, 18, 3], "output": "MSAAAAPIRHRAPPRWILSFADLCLLLLCFFVILNAQKGDTDYRAALLFEPGEAVLTAPAARWLGGLGRQAAAAGADVLIVSDGLDPATARLDVTLSIPAMGGGRHRAAQTLRITTAPRGPKRVAQGMRAAFGEPAPAAARGWELAAARVAATGRAVRAGGLSEAH", "metadata": {"id": "A0A558QR89", "cluster": 2644219, "interpro_all": ["IPR025713"], "interpro_used": ["IPR025713"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Give me a peptide sequence capable of: The protein features a PA14 domain that adopts a $\\beta$-barrel structure and functions as a non-catalytic binding module, likely with specificity for carbohydrates. It occurs as an insert in a diverse array of proteins, including bacterial glycosidases, toxins like the anthrax protective antigen, yeast adhesins, and mammalian fibrocystin. Furthermore, the protein should have a PA14/GLEYA domain that functions as a carbohydrate or peptidoglycan binding module within a diverse array of bacterial and eukaryotic proteins, including toxins, glycosidases, and adhesins. This $\\beta$-barrel structure features proximal N and C termini that facilitate its insertion into other domains without structural disruption, and it encompasses the fungal GLEYA variant involved in cellular agglutination. It is derived from Omnitrophica bacterium (Omnitrophota bacterium).", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 4075, 43, 3838, 3745, 3418, 1988, 24032, 43, 8, 38, 4666, 8, 17, 19560, 3170, 1930, 4088, 1966, 43, 2447, 17, 6804, 2743, 9059, 16, 3205, 1956, 4896, 1958, 16282, 18, 2176, 5110, 1966, 1925, 12844, 1922, 43, 6445, 6472, 1927, 2697, 16, 2710, 4543, 7533, 30413, 16, 13599, 3189, 1920, 14228, 3013, 6337, 4730, 16, 5688, 5315, 2925, 16, 1930, 6492, 5094, 23159, 2268, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 3838, 3745, 19, 16543, 9771, 3418, 1988, 4088, 1966, 43, 10590, 2014, 24183, 2743, 9059, 2651, 43, 6445, 6472, 1927, 4543, 1930, 10825, 2697, 16, 2710, 13599, 16, 7533, 30413, 16, 1930, 5315, 2925, 18, 2052, 8, 38, 4666, 8, 17, 19560, 3170, 4075, 6863, 56, 1930, 45, 17345, 1988, 6628, 2496, 7413, 2460, 2303, 4682, 2979, 4346, 7561, 16, 1930, 2176, 21569, 1920, 8697, 16543, 9771, 6031, 3286, 1922, 3689, 20262, 1943, 18, 2176, 1977, 3595, 2037, 18825, 3032, 24888, 3375, 14061, 12, 18825, 3032, 2102, 7336, 14061, 13, 18, 3], "output": "ELKPVSEGVTESVSLDVSPVEMSYGLRFEGYFKAPETGLYCFTLISNDGTRLFIDNELLIDHDVRHMAIPMGNLIPLEQGFHPIVVEYFQSAGRKHLEMFVEGPGLERQIAGPQLLWHKD", "metadata": {"id": "A0A955MTD5", "cluster": 3028608, "interpro_all": ["IPR037524", "IPR011658"], "interpro_used": ["IPR011658", "IPR037524"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is a member of 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 includes 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 native to Pristionchus mayeri and has UniProt annotations Metal-binding and Zinc-finger. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 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, 5921, 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, 6196, 1942, 17618, 2156, 2001, 2072, 1957, 2278, 18842, 1930, 2258, 20709, 15010, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "EGHQALDETFVPKRTSAPAEKLFACSKCDLKLVSQENLRRHMSTTHAGLRAFDLDNVMDKEKFKKAAASVPKAKKKAKRAKAKKFSCSKCGKKFISKGGFEYHMNRHAGCTQIEHRAVRGKEPRSKVNGLPKSKNVVVFTNSSGLSKMRDGTEAKHKVPEQQSYPLFEDPVKEEQMEEEDKVPEQKFFPFFEEAVKKEETDDEEPGPSWELH", "metadata": {"id": "A0AAN5C2S1", "cluster": 3056193, "interpro_all": ["IPR036236", "IPR013087"], "interpro_used": ["IPR036236", "IPR013087"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein incorporates a RecG domain 3 C-terminal domain that forms a structural hook connecting domains 1 and 3, likely facilitating conformational changes driven by ATP binding and hydrolysis. This region supports the function of the RecG helicase in DNA repair and recombination, specifically in catalyzing the branch migration of Holliday junctions and unwinding branched DNA with 3' to 5' polarity. In addition, 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 includes a DEAD/DEAH-box helicase domain that functions as an ATP-dependent nucleic acid-binding module essential for unwinding RNA structures during metabolism. It facilitates diverse cellular processes, including pre-mRNA splicing, ribosome biogenesis, and translation, by coupling ATPase activity with helicase function via the conserved motif III. It occurs in bacterium TMED6 and has UniProt annotations DNA recombination, Isomerase, and DNA damage.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 19683, 43, 2090, 1029, 3418, 23, 45, 17, 4262, 3418, 1988, 4952, 43, 4346, 17185, 15031, 4682, 21, 1930, 23, 16, 3205, 12440, 8523, 2840, 6446, 2007, 4498, 2743, 1930, 9128, 18, 2052, 3031, 7825, 1920, 2347, 1927, 1920, 2090, 1029, 15318, 1922, 2678, 5059, 1930, 7827, 16, 4475, 1922, 29601, 1920, 6089, 5049, 1927, 14451, 27539, 11245, 1930, 26801, 16484, 2678, 1956, 23, 11, 1942, 25, 11, 12432, 18, 1922, 2459, 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, 5921, 43, 9535, 19, 30097, 1023, 17, 5758, 15318, 3418, 1988, 4088, 1966, 1925, 4498, 17, 3100, 11079, 2687, 17, 2743, 9059, 4415, 1958, 26801, 3146, 4061, 2409, 4714, 18, 2176, 11374, 6445, 3689, 4028, 16, 2710, 2097, 17, 3616, 8490, 16, 12794, 13008, 16, 1930, 6410, 16, 2007, 7590, 9444, 2455, 1956, 15318, 2347, 3454, 1920, 5305, 5219, 4337, 18, 2176, 5110, 1922, 14061, 22377, 1007, 1016, 1930, 2258, 20709, 15010, 2678, 7827, 16, 25510, 16, 1930, 2678, 4293, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MKFQNPLYDDITYLKGVGPKRAKQLKSNGINIISDLLDHEQTVVIGKVVSKNMKILGKRRLFQVTISDGTGELQCIWFNGLSWILDKFKIDDQIAVFGKIEFNYNTGQIISQYPSTSDLKSKGLDSRGFRNLIKNIIYNNKYIIDDFLPSNNDDIKKALYRLKFNEHFFIQMLMALKRKNLKNNLGKSYPNRGKYLKNIYENRSDLKSDQVMNRLIQGDVGSGKTIVAVLTSAIVIAKQSIKEHCDEANITCGLITSRRSKKEKDIIINELKSGEIQLIIGTHSLIQDTIKFNDLGLIIIDEPQVLAMTATPIPRTLSITIHGDMDISIIDELPKNRLPIKTKLIYPQCFVVYPLIEESEKLDLEAAQSGYEKLQKIFKDFKLGYINGKMKKDQIDDQMVIMIENAERFGMTQLHQLRGRIGRGIKQXYCFLIQRKKTPNADKRLNIMENTLHGFIKSKVVDFSNDGAIIRRARQQAFELIINDPRIQKIDNQKIKKVFKTKYNHMLEFVKIGIPRKYLDRTNIKTIDQTKIGYNGLKITHPDFDIFDESEPILKQEDLISLKQAFEKIHFPKLNFDLTNAQIKVLREIEKQVALMAPTEILAEQHFQHRFGVEHRKLLIEKGDSKNIDPTYEFMKEEMKDGGNRMNQGEIDCLVATTVIEVGINIPNATDGFLISDEDLKMRGPGDFFGTKQ", "metadata": {"id": "A0A1Z8KUY1", "cluster": 5415002, "interpro_all": ["IPR004609", "IPR011545", "IPR014001", "IPR001650", "IPR012340", "IPR027417", "IPR047112", "IPR045562", "IPR033454"], "interpro_used": ["IPR045562", "IPR014001", "IPR011545"], "interpro_unused": ["IPR004609", "IPR027417", "IPR047112", "IPR033454", "IPR001650", "IPR012340"]}, "task_type": "infilling"} {"instruction": "Here is the polypeptide chain function: The protein incorporates a Novel STAND NTPase 1 domain that functions as a member of the STAND superfamily of AAA ATPases involved in bacterial conflict systems. Also, the protein should feature a Anaphase-promoting complex subunit 4-like, WD40 domain that adopts a $\\beta$-propeller fold to serve as a stable platform for protein-protein interactions and complex assembly. Typically located at the N-terminus of Apc4, it mediates molecular recognition events required for E3 ubiquitin ligase activity and cell cycle regulation. Also, the protein carries a WD40 repeat conserved site that mediates protein-protein or protein-DNA interactions, typically forming a beta-propeller structure that serves as a rigid platform for the assembly of protein complexes. These motifs are widely distributed in eukaryotes and facilitate diverse functions ranging from signal transduction to transcriptional regulation, with interaction specificity often determined by sequences outside the repeats. It is identified in Oscillochloris trichoides DG-6 and is classified with UniProt keywords Transmembrane helix, WD repeat, and Transmembrane. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 19683, 43, 4008, 2924, 29676, 2051, 21, 3418, 1988, 4088, 1966, 43, 7210, 1927, 1920, 2924, 13975, 1927, 13835, 28132, 3286, 1922, 4543, 8917, 3771, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 20826, 17, 7356, 2796, 5903, 24, 17, 3189, 16, 17907, 4241, 3418, 1988, 24032, 43, 8, 38, 4666, 8, 17, 5062, 13728, 3728, 1942, 7120, 1966, 43, 4700, 6631, 1958, 2213, 17, 2213, 3719, 1930, 2796, 5957, 18, 5745, 4810, 2019, 1920, 56, 17, 7822, 1927, 9187, 1006, 16, 2176, 10412, 3272, 5708, 3916, 3414, 1958, 10968, 6526, 11905, 2455, 1930, 2024, 4048, 3640, 18, 2222, 16, 1920, 2213, 16252, 43, 17907, 4241, 6865, 5305, 3200, 1988, 10412, 2213, 17, 2213, 2014, 2213, 17, 2678, 3719, 16, 5745, 7402, 43, 4666, 17, 5062, 13728, 3170, 1988, 10634, 1966, 43, 12383, 6631, 1958, 1920, 5957, 1927, 2213, 5048, 18, 2144, 8277, 2032, 5673, 6533, 1922, 15021, 1930, 6628, 6445, 4088, 6485, 2037, 2733, 8201, 1942, 5224, 3640, 16, 1956, 2835, 4896, 3868, 3180, 2007, 3709, 7008, 1920, 9569, 18, 2176, 1977, 2899, 1922, 7799, 20845, 1937, 10477, 12363, 9665, 17, 26, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 7864, 16, 17907, 6865, 16, 1930, 9117, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MSHTPITPPFRGPRPFQAGERLYGRDYEARALLSMLVAERAVLLHSPSGAGKTSLIQAALLPLLAERDFVVLPTVRVGEEAPPGWVGNRYVRAMLLALEEGQTDADQVSTAEISAISLKQYLTQRIPENQDTVLIIDQFEEVLTRDPTDQGAKSVFFRELGAALQQPRLWVLCVVREEYVAALEPFMRLLPNRLAAHFRLDLLGVEGALEALREPLQGIGVTFPLPQANRLIDDLRRVNVQQADGSIRSELGPSVEPVQLQVVGLRLWERLPTGTTSISAQQIDALGDVGKALGDYYAERAASVAQASGVEERSLRNWFEHELITPQGVRGQVLQGAGSSAGLENSAITQLIDAYLVRAEPRRGATWYELAHDRLIAPIQANNAFWFAANLSTLQRQAQLWEQQGRPEGLLLRGASLLEAESWASQHSKSLTPSERDFLDLCRRARQRAALLRNLSIAVAVVAVIALILALIANVFRVQAEHNARQARSRELAAAAVTNLLVDPQRSLILAHAAYTTSAAAGDPAPPEALEALQQALAASRVRQIIHVSERGLQDLALSPDGRLVATSANDGMIHIIDRAQGQEIQRITANADGLPVFGLAFSPDGTYLAAGSGDQVVLWEITRGQVAYQFDAHPESGAEVASNDILAVAFSPDGSVIASGSADGSARLWDLNQVQPIHSLAVESEVWAIAYSPDGRYLATGDFAGQIMLWDVLSGEQIWSIPAHQDLITGLAISPDGSSIASSSADLSVRLWASSDGTAIDVLRGHATTVESVAFSATGDRLATASADGSAKVWALDSSRMILSLVGHENGLSGATFSPDGNQLLTSSLDGTLRTWDLSLAPADGAYGALFSPAGDTLATYGATQVQIWNQAGDTLLYSTELPMLIATIAYHPQGTEIAVGSIDGTILLIDPQSGTINQRLEGHSDQINRLAFSPDGQRLVSASRDGSLSIWDCTDGSEIINLPTANNDEVTVVAFSPDGSMIASVANGEISLWDAAGQSLGKTWTLRSNEIVQGLTFSHAGRWIAAGNDGGGSGHLGDQHQPRSGSDHNPERLHRPRL", "metadata": {"id": "E1IDH3", "cluster": 5464849, "interpro_all": ["IPR024977", "IPR020472", "IPR049052", "IPR027417", "IPR015943", "IPR019775", "IPR036322", "IPR001680"], "interpro_used": ["IPR049052", "IPR024977", "IPR019775"], "interpro_unused": ["IPR015943", "IPR001680", "IPR027417", "IPR020472", "IPR036322"]}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that can perform the following function: 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. Also, the protein contains 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. Also, the protein is assigned to the Recoverin family, which comprises N-myristoylated calcium-binding proteins containing four EF-hand motifs, such as visinin, hippocalcin, and guanylyl cyclase-activating proteins. These proteins function as calcium sensors, with recoverin specifically inhibiting rhodopsin kinase (GRK-1) in photoreceptor cells to regulate rhodopsin phosphorylation. It is produced by Megaselia scalaris (Humpbacked fly) (Phora scalaris) and is annotated with UniProt keywords Lipoprotein and Myristate.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 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, 2222, 16, 1920, 2213, 5461, 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, 2222, 16, 1920, 2213, 1977, 6304, 1942, 1920, 4309, 1921, 3416, 16, 2154, 12936, 56, 17, 20234, 10921, 1981, 5016, 17, 2743, 2697, 3165, 3006, 8485, 17, 3897, 8277, 16, 2427, 1966, 2895, 15020, 16, 25771, 23327, 1921, 16, 1930, 13504, 25671, 16526, 17, 8019, 2697, 18, 2144, 2697, 2347, 1966, 5016, 9189, 16, 1956, 4309, 1921, 4475, 7918, 20586, 4016, 12, 2398, 1040, 17, 21, 13, 1922, 16383, 2094, 1942, 5741, 20586, 4050, 18, 2176, 1977, 4152, 2007, 20418, 4127, 12191, 1019, 27156, 1937, 12, 2490, 16752, 2401, 1919, 11716, 13, 12, 20175, 5524, 27156, 1937, 13, 1930, 1977, 10633, 1956, 20709, 11569, 9694, 1930, 28874, 18, 3], "output": "MGKKNSKLKQDTIDRLTTDTYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAFRLYDVDNDGYITREEMYNIVDAIYQMVEDESTPEKRTDKIFRQMDRNKDGKLSLEEFIEGAKSDPSIVR", "metadata": {"id": "T1H6E4", "cluster": 10181789, "interpro_all": ["IPR011992", "IPR018247", "IPR002048", "IPR028846"], "interpro_used": ["IPR018247", "IPR002048", "IPR028846"], "interpro_unused": ["IPR011992"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe 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. It is identified in Flavobacterium sp.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 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, 2176, 1977, 2899, 1922, 7732, 12022, 2056, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MLFYDETTWNEQSWEVDAMAEPNSKRHAAYFPQKVYWCLNEEKKQNISDELREHFKAFCPNLKNIVFILITLTKAETVCMRLLSSAPMLLIGTHKIRDFIIGGIWNNKDKTDMVFTPLADAYLKFMVTQLKPFIDV", "metadata": {"id": "A0A924H6C9", "cluster": 10347415, "interpro_all": ["IPR029058"], "interpro_used": ["IPR029058"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that has the following function: The protein belongs to the La domain containing protein family, which functions as a multifaceted RNA-binding factor involved in the maturation of nuclear RNA polymerase III transcripts and the translational control of cytoplasmic mRNAs. These proteins utilize a conserved N-terminal domain, comprising a winged-helix La motif and an RNA recognition motif (RRM), to bind specific targets including the 3' UTRs of nascent transcripts and 5'-terminal oligopyrimidine (5'TOP) motifs. Additionally, the protein is assigned to 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 carries a La-type HTH domain that adopts a winged-helix $\\alpha/\\beta$ fold at the N-terminus of La proteins to mediate specific RNA recognition, often in coordination with an RNA recognition motif. It facilitates the folding and maturation of nascent RNA polymerase III transcripts by binding their 3' UTRs in the nucleus and regulates translation by recognizing 5'-terminal oligopyrimidine motifs in the cytoplasm. It is found in Dimargaris verticillata. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 5114, 3418, 3165, 2213, 3416, 16, 2154, 4088, 1966, 43, 26031, 3146, 17, 2743, 2991, 3286, 1922, 1920, 7655, 1927, 4254, 3146, 6479, 4337, 6247, 1930, 1920, 8414, 2285, 1927, 6823, 8806, 18, 2144, 2697, 12561, 43, 5305, 56, 17, 4262, 3418, 16, 10351, 43, 12920, 1919, 17, 7864, 5114, 5219, 1930, 1925, 3146, 5708, 5219, 12, 5162, 1035, 13, 16, 1942, 4566, 2487, 4845, 2710, 1920, 23, 11, 22690, 1927, 16861, 6247, 1930, 25, 11, 17, 4262, 15039, 18425, 29899, 12, 25, 11, 3700, 13, 8277, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 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, 16252, 43, 5114, 17, 2601, 5334, 1023, 3418, 1988, 24032, 43, 12920, 1919, 17, 7864, 8, 38, 4595, 19, 38, 4666, 8, 3728, 2019, 1920, 56, 17, 7822, 1927, 5114, 2697, 1942, 8265, 2487, 3146, 5708, 16, 3868, 1922, 9478, 1956, 1925, 3146, 5708, 5219, 18, 2176, 11374, 1920, 10328, 1930, 7655, 1927, 16861, 3146, 6479, 4337, 6247, 2007, 2743, 2310, 23, 11, 22690, 1922, 1920, 5607, 1930, 7014, 6410, 2007, 15667, 25, 11, 17, 4262, 15039, 18425, 29899, 8277, 1922, 1920, 5239, 18, 2176, 1977, 2435, 1922, 3363, 2419, 17295, 3566, 2002, 10888, 3857, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MASTSHLLVANSATSAAADSSEQYTVLKDRIRQQVEYYFSPENLAHDSYLCSQMDPQGNVPIIIVAAFKKLRALTRDVSLIIDAMAESSMVAMDDEQKYFRPNFPREHRLLLLSQVPESCTREDIVALCDNLKSVPLIDLYTCNATTWEIRLATEREAQRLLDYIQDQSLGGAPIRASLKAEPLFQGTWCANPQQPLYQDPVAPYADQLCVPSAQPYSFPYIPYYGPNPMLASVAPGYPGGDYYGYYSAPYYAPAYYPQAAQHQSPKRRNRNGRNHRKSGTNKKSAAGAKANGAAGSPRRSNRKNNHKTVADQPCNPLGDKAPVSVHKVSAKSGARSQPFVQPADSVVGAVTPPPSPKEFRASTKASEPADRDAIAVSDISSRPLTPVSEKPQSMTPPNEPTTPWASPGGKKGTKKSSGYRLQTHGRCVDRSSCAKGTARPLVAPSPDLRTHSFPPLPAKPAPTQAQAKAKRSSPKPVNQATLTPMPSSPAKAKTLADIVKGNSTPTLSRSSIQPKPLHDEYPGLMSDGSSGETLDTISVTSSLASSASTMAPAATTLLTASIFTVSTQLSPSAPQHSINMVPIVHSYAQALRQPAIKST", "metadata": {"id": "A0A9W8B6Q9", "cluster": 11145643, "interpro_all": ["IPR045180", "IPR006630", "IPR036388", "IPR036390"], "interpro_used": ["IPR045180", "IPR036388", "IPR006630"], "interpro_unused": ["IPR036390"]}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein includes a SMP-30/Gluconolactonase/LRE-like region domain that characterizes enzymes including senescence marker protein 30 (SMP-30), gluconolactonase, and luciferin-regenerating enzyme (LRE). This region typically functions as a gluconolactonase, hydrolyzing sugar lactones such as gulonolactone, and displays activity against organophosphates like diisopropyl phosphorofluoridate. Furthermore, the protein has a NHL repeat that folds into a rigid, six-bladed beta-propeller structure implicated in protein-protein interactions. Commonly observed in eukaryotic growth regulators and bacterial serine/threonine kinases, this motif often functions as an extracellular sensor domain or supports enzymatic activities such as peptide amidation. Additionally, the protein is included in the Tripartite Motif and NHL Repeat Containing E3 Ligases family, which functions as a group of E3 ubiquitin-protein ligases regulating diverse cellular processes including embryonic stem cell proliferation, neuronal function, and innate immunity. These proteins utilize a RING domain for ligase activity and a six-bladed beta-propeller NHL domain to interact with specific protein substrates and microRNAs, thereby modulating post-transcriptional gene expression and protein degradation. Their activity is essential for neuroprotection, antiviral responses, and cell differentiation. It is produced by Nitrospirota 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, 5921, 43, 2426, 1034, 17, 2627, 19, 3351, 23557, 5148, 2341, 9259, 1021, 19, 7146, 1021, 17, 3189, 3031, 3418, 1988, 26735, 5038, 2710, 10805, 4966, 2213, 2627, 12, 2426, 1034, 17, 2627, 13, 16, 3351, 23557, 5148, 2341, 9259, 1021, 16, 1930, 7174, 1921, 17, 23617, 4113, 12, 7146, 1021, 13, 18, 2052, 3031, 5745, 4088, 1966, 43, 3351, 23557, 5148, 2341, 9259, 1021, 16, 7222, 9046, 9523, 27735, 1036, 2427, 1966, 3194, 6012, 11873, 5148, 2341, 2290, 16, 1930, 10750, 2455, 3316, 3090, 15707, 1036, 3189, 26028, 2204, 20194, 2199, 3421, 4199, 11525, 21550, 18, 3677, 16, 1920, 2213, 2258, 43, 16849, 6865, 1988, 16231, 2460, 43, 12383, 16, 3798, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 6835, 1922, 2213, 17, 2213, 3719, 18, 5384, 2528, 1922, 10825, 2905, 9098, 1930, 4543, 8468, 19, 13143, 7784, 16, 2052, 5219, 3868, 4088, 1966, 1925, 5329, 6443, 3418, 2014, 7825, 8145, 4209, 2427, 1966, 4207, 28813, 1943, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 8027, 24707, 5219, 1930, 16849, 6865, 3165, 10968, 22423, 3416, 16, 2154, 4088, 1966, 43, 2210, 1927, 10968, 6526, 17, 2213, 22423, 6773, 6445, 3689, 4028, 2710, 7231, 4402, 2024, 4031, 16, 5121, 2347, 16, 1930, 8539, 7611, 18, 2144, 2697, 12561, 43, 6335, 3418, 1958, 11905, 2455, 1930, 43, 3798, 17, 22707, 1007, 4666, 17, 5062, 13728, 16849, 3418, 1942, 6310, 1956, 2487, 2213, 6249, 1930, 15182, 16, 6113, 10871, 2753, 17, 5224, 2359, 2294, 1930, 2213, 4877, 18, 2310, 2455, 1977, 4415, 1958, 21128, 16, 10129, 3387, 16, 1930, 2024, 4155, 18, 2176, 1977, 4152, 2007, 16665, 10984, 6843, 1019, 14061, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MITKLRKTLYLLIIMAAFMSISMGPGKNTGEVQKEHIVWPPPPWFQIKKGFFRRVWEFVAGESREGLIKPFGIFADDNGRLYVTDEGVSKKTRLSSPIDVAVDNEGNIYISDSVMPTGIAIDNMSGALYVVDTLASKIFVGYGGGNGEFNRPTFIALGRDGNLYITDTMNIRVQLANPRGIALDSEGHIYITDTLFEAVTILVHSQRFTVHSNEPRIEFLYSITTPDDTADQSVHVFDPKDSKYFVIRRVYVFNKMGKFLREIGSDNVMQRYSLDGKYIKTIGIIDKQGKFVGKFGRRGNAAGD", "metadata": {"id": "A0A931Q3V5", "cluster": 11921847, "interpro_all": ["IPR011042", "IPR001258", "IPR013658", "IPR050952"], "interpro_used": ["IPR013658", "IPR001258", "IPR050952"], "interpro_unused": ["IPR011042"]}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein should contain a Impact, N-terminal domain that acts as a translational regulator to ensure high levels of protein synthesis under amino acid starvation. It functions by interacting with Gcn1 or Gcn1L1 to inhibit Gcn2 protein kinase activation, thereby preventing the downregulation of translation. This domain is evolutionarily conserved across eukaryotes and archaea. Moreover, the protein is classified under 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. It is derived from Hondaea fermentalgiana.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 3066, 5531, 43, 3829, 16, 56, 17, 4262, 3418, 1988, 8016, 1966, 43, 8414, 7888, 1942, 6486, 2149, 2428, 1927, 2213, 4271, 2441, 3835, 2687, 12767, 18, 2176, 4088, 2007, 8615, 1956, 5469, 7301, 2014, 5469, 7301, 8053, 1942, 2875, 5469, 9090, 2213, 4016, 2936, 16, 6113, 8444, 1920, 9894, 1927, 6410, 18, 2052, 3418, 1977, 18584, 5305, 3436, 15021, 1930, 21501, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 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, 2176, 1977, 3595, 2037, 15372, 3825, 5376, 17748, 20394, 15626, 18, 3], "output": "MKAFRLEVRKSLFVAEAARAPHADAARDFVSSVRARERCDDDGEPSGTAGRPIITAIRSHARAYREAALGALAEFGPADEVLVRRAAVIVPFELTHEVFAALRVCGGDTLEVPASAAGLLEATLSHVRDINVQWESRRHATAGHHCWGFVSTAEVAAELGAVVVVARWKRGPNLGRGGLILSDEIPAGDAHAQELGIGLDAATIRVE", "metadata": {"id": "A0A2R5GFJ8", "cluster": 12539589, "interpro_all": ["IPR023582", "IPR001498", "IPR036956", "IPR020568"], "interpro_used": ["IPR001498", "IPR020568"], "interpro_unused": ["IPR023582", "IPR036956"]}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein can be placed in the Group II Intron Splicing and Mobility/Defense family, which promotes group II intron splicing and mobility through reverse transcriptase, maturase, and DNA endonuclease activities. These proteins facilitate intron duplication and site-specific DNA cleavage, with some members conferring antiviral defense via msDNA synthesis or supporting mitochondrial biogenesis in plants. In addition, the protein contains 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 is grouped in 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 occurs in Pelotomaculum propionicicum.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2210, 2890, 10444, 8490, 1930, 8471, 19, 9720, 3416, 16, 2154, 7383, 2210, 2890, 10444, 8490, 1930, 8471, 2596, 5267, 13335, 16, 2888, 9280, 4127, 16, 1930, 2678, 18697, 4209, 18, 2144, 2697, 6628, 10444, 12630, 1930, 3200, 17, 2487, 2678, 6404, 16, 1956, 2673, 4678, 21510, 10129, 9720, 3454, 23421, 2175, 4271, 2014, 6184, 4596, 13008, 1922, 4793, 18, 1922, 2459, 16, 1920, 2213, 5461, 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, 1977, 10809, 1922, 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, 5110, 1922, 7874, 11957, 1948, 7705, 5062, 14207, 27999, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MLDLARKLKNGTYQPQGYREFTIYEPKIKPIFGKTFIYDSYACLEGKGMPYIVKGDIKKYFFSIDHDILFDLVKKKISDDKVLWLTRIILDSANVYLHQLDIFVKHQLRIKNYVRYMDDFILVVENKETNGKTQIFPVKNGVNFCGYKIKSTHLKIRTESKEDIRTVLVSWIGYARKANSYHLINKILSQFTFERLIRAAPYCDRVIHQWYVINFHRATARVQEFLRRMQAKWPAVDNPGVPVGSYTSQFFAWQLLQQIREFLAKNLKLELRRIKRKLRKFKIKFKAGEMCA", "metadata": {"id": "A0A4Y7RC31", "cluster": 15386324, "interpro_all": ["IPR043502", "IPR051083", "IPR000477"], "interpro_used": ["IPR051083", "IPR000477", "IPR043502"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that will have the following function: The protein is a member of 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. Also, the protein is included 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. Moreover, the protein should contain a Squalene epoxidase domain that functions as a key enzyme in the sterol biosynthetic pathway, typically utilizing a putative FAD-binding site. This domain is conserved across diverse eukaryotes and bacteria. It originates from Candidatus Woesearchaeota archaeon and is connected to UniProt keyword Coiled coil.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 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, 2222, 16, 1920, 2213, 1977, 3063, 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, 3950, 16, 1920, 2213, 3066, 5531, 43, 4687, 2603, 2912, 15751, 18068, 3825, 4127, 3418, 1988, 4088, 1966, 43, 3834, 4113, 1922, 1920, 20408, 14041, 3374, 16, 5745, 10232, 43, 6770, 14134, 17, 2743, 3200, 18, 2052, 3418, 1977, 5305, 3436, 6445, 15021, 1930, 4802, 18, 2176, 22970, 2037, 14550, 1031, 1957, 26334, 21406, 3336, 7336, 13470, 1916, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 17524, 9121, 18, 3], "output": "MKINIIGAGPVGCYLAYLLADKFEVEVYEEHSEIGKPVQCAGIITNSINSVIQIPPEVILNKIKNFEISYKDQKLKIKLRNPDIIIDRTKFDTFFYNKAKERGVKFSLGKRINDLAELKGIIIGADGPNSIVSKAIGNKTTSWMGIQTKIKLPDSQIKASLDYGKFGWTIPEGNGTCRVGIMDEKENAKQTFKKFTKGKQNSLQAGLIPKYNPKNKLCKNNLYIVGDAAGMVKATTGGGIIPGLKAAKVLANCLIKRKKYKRKLRKVRKELKTQLIARKVLDHLNDEEIKKLFKLFRKEKNKKILEEIDRDNLKKIAIKLLLRNPTLITYAPKIYK", "metadata": {"id": "A0A8T5DJF4", "cluster": 15690444, "interpro_all": ["IPR036188", "IPR050407", "IPR013698"], "interpro_used": ["IPR050407", "IPR036188", "IPR013698"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein has a Bacterial transcriptional activator domain that functions as a regulator within the DNRI/REDD/AFSR family to control the formation of secondary metabolites. In proteins such as AfsR, this domain works in conjunction with the C-terminal region to direct the production of antibiotics like actinorhodin. Furthermore, 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. Moreover, the protein is included in the AfsR/DnrI/RedD regulatory protein family, which functions as transcriptional regulators controlling biosynthetic pathways for secondary metabolites like antibiotics and molybdopterin. Members bind DNA to activate specific operons, often acting within two-component systems or utilizing ATPase and GTPase activities to modulate responses to environmental stimuli. It is derived from Flexivirga endophytica.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 4543, 5224, 9518, 3418, 1988, 4088, 1966, 43, 7888, 2651, 1920, 5956, 3027, 19, 2312, 1007, 19, 2221, 19025, 3416, 1942, 2285, 1920, 3337, 1927, 4067, 6926, 18, 1922, 2697, 2427, 1966, 2221, 19025, 16, 2052, 3418, 10997, 1922, 11799, 1956, 1920, 45, 17, 4262, 3031, 1942, 3083, 1920, 3372, 1927, 7560, 3189, 4718, 14514, 25435, 18, 3677, 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, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2221, 19025, 19, 5956, 3027, 19, 2312, 1007, 4948, 2213, 3416, 16, 2154, 4088, 1966, 5224, 9098, 7138, 14041, 3873, 1958, 4067, 6926, 3189, 7560, 1930, 2629, 16924, 22389, 2410, 16654, 18, 4678, 4566, 2678, 1942, 6980, 2487, 28748, 16, 3868, 8290, 2651, 2288, 17, 4594, 3771, 2014, 10232, 9444, 1930, 14809, 4209, 1942, 8480, 3387, 1942, 4813, 5458, 18, 2176, 1977, 3595, 2037, 5795, 20614, 4223, 19771, 4274, 1019, 18, 3], "output": "MSGAAQRLVAYLALHEDSPRLVVAAGLWPESSDEHALSNLRTTTSRLRKTAPGLLTPMSQALRLATTVRVDLVDVLAAAETAYEAEDPAALARRLGRVGELLPGWYDDWVLFEREQLQQQLISASETLAERLLSAGDVAAALAAANASIHREPLRESAHRLLVRIHLAAGNRVEAWHAYERFRRRSIAEVGLAPDSSFQALVAELARERQRRRRS", "metadata": {"id": "A0A916TF62", "cluster": 16444629, "interpro_all": ["IPR051677", "IPR005158", "IPR011990"], "interpro_used": ["IPR005158", "IPR011990", "IPR051677"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein should have a Right handed beta helix domain that adopts a parallel \u03b2-helix fold sharing structural similarity with pectate lyases. This architectural motif often serves as a scaffold for carbohydrate binding or enzymatic degradation activities. Additionally, the protein should feature a Parallel beta-helix repeat that forms a structural coil of parallel beta-strands, frequently stabilized by conserved asparagine ladders. This motif typically assembles into a larger helical fold found in enzymes, such as pectate lyases, that degrade polysaccharide substrates. Also, 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 produced by Hymenobacter montanus. 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, 2162, 43, 3659, 17105, 4666, 7864, 3418, 1988, 24032, 43, 6110, 161, 17, 7864, 3728, 10763, 4346, 6796, 1956, 13494, 3857, 2057, 23928, 1036, 18, 2052, 28937, 5219, 3868, 10634, 1966, 43, 7281, 1958, 10590, 2743, 2014, 8145, 4877, 4209, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 6110, 4666, 17, 7864, 6865, 1988, 4952, 43, 4346, 9121, 1927, 6110, 4666, 17, 13214, 16, 5467, 12017, 2007, 5305, 23677, 22798, 1036, 18, 2052, 5219, 5745, 17421, 1036, 2460, 43, 4327, 11514, 3728, 2435, 1922, 5038, 16, 2427, 1966, 13494, 3857, 2057, 23928, 1036, 16, 1988, 17069, 17167, 6249, 18, 2222, 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, 4152, 2007, 28034, 19824, 7972, 2341, 1915, 20191, 19037, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MKIYTSSLFLGIAVTRLGFGQSASSTHSDDTALANGKAFARFGFIVLLILTTFSSYGTKIVLDAQVFNSTDVTTIVRNAINSSADTIVVKNTGSPWIVQPITIFNKSNKTIIFDYGVTLKAKSGAFADTYATLLKLNTCANFKIIGYGATFEMIKSEYLDGEFRHAIDLTDCNNISISGLLVKDSGGDGLILMGWEGGQYFCNNVRITDCVFDNNKRQGCSIISAKNVFIENCTFSNTKGTPPGSGIDIEPDSEDEFVENIQIRKCKFTNNFGPGLSFGFYKLTSASRISVSVDDCYFSYNCDPLAEIYQGAEISYTEPKNENLTGLITFNRCFVDGSYRPAFAASKSAHNMPLIFNDCVFKNVSQSTNLPYNYPIWLEVQDYRDPIQYLGGITFARSTLEYRTNYKFAWINGWNNSPGAKDINIDLTVIHPTLNTVANNSAVFSNVLSQVNVNLNIRYLSSMPSKSLTLTNTDNDTISKRICTKKSISLSSPTASSLPIALNYTVTGTASNRIDYHQLKGFMLLKQNTTQSSDTLQAINPQLNSSNLSAILSPVNNNGNTIATNAQFIAKISPTRCNPTTITNTKVESSQPTEALMLKLHPNPASREVTISLEGFKGESAVQVKMSDMAGKPFLRQQVQPGAPEVTLSVGHLPQGLFIVTVQGSKTAKSAKLVITK", "metadata": {"id": "A0A927BC08", "cluster": 17614830, "interpro_all": ["IPR039448", "IPR006626", "IPR012334", "IPR011050", "IPR026444"], "interpro_used": ["IPR039448", "IPR006626", "IPR026444"], "interpro_unused": ["IPR012334", "IPR011050"]}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein is categorized in the NMT1/THI5 family, which mediates the biosynthesis of the vitamin B1 precursor hydroxymethylpyrimidine (HMP). Members include eukaryotic enzymes that synthesize HMP-phosphate and bacterial homologues that function as substrate-binding components of ABC transporters for vitamins B1 and B2. Moreover, the protein should feature 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 derived from Xanthobacteraceae bacterium.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2943, 6613, 19, 7566, 1015, 3416, 16, 2154, 10412, 1920, 8132, 1927, 1920, 6111, 10360, 7897, 29078, 18425, 29899, 12, 5833, 1034, 13, 18, 4678, 3951, 10825, 5038, 1988, 15541, 5833, 1034, 17, 5413, 1930, 4543, 18541, 1988, 2347, 1966, 4510, 17, 2743, 4178, 1927, 7219, 10538, 1958, 18818, 10360, 1930, 11054, 18, 3950, 16, 1920, 2213, 3066, 5961, 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, 3595, 2037, 15213, 5883, 9914, 14061, 18, 3], "output": "MQQVLGGGGLLSRTGVSDHIRASISSPDKPIRTPKDMAGKTQGVDKASVPRVQAPNTPAGMALIAQGRIDAYAWNTDEFAPIPGQCYIAKRERAVKKSIDDMLADTDLTTTPDILRNEMQFWLTAGRQNILKHVPERWGLYTNEFVDKALASRPGGDALISVGTISQGSPFFVIGVLSVGGATEIVLDCMLVAIVSAGVPVALKAANERHLSVQRDGDLVVRFLLKRIEGFEIAEMRNRAVAQKGYDLMAAAGFTPAGQAD", "metadata": {"id": "A0A6I1J9W9", "cluster": 19030439, "interpro_all": ["IPR027939", "IPR015168"], "interpro_used": ["IPR027939", "IPR015168"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is grouped in the von Willebrand factor A-like domain superfamily, which functions as a versatile protein-interaction module involved in ligand binding and the assembly of multiprotein complexes. Spanning both extracellular proteins like integrins and collagens as well as intracellular machinery, these domains facilitate diverse biological events including cell adhesion, migration, signal transduction, and DNA repair. It has been detected in Trachysalambria curvirostris majanivirus.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 14147, 30067, 2991, 43, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 2213, 17, 2835, 9059, 3286, 1922, 5207, 2743, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 18, 13346, 2321, 5329, 2697, 3189, 15563, 1930, 5621, 1036, 1966, 2486, 1966, 4776, 10853, 16, 2144, 4682, 6628, 6445, 3933, 3916, 2710, 2024, 6141, 16, 5049, 16, 2733, 8201, 16, 1930, 2678, 5059, 18, 2176, 2258, 2252, 3330, 1922, 11168, 2012, 7010, 2377, 2126, 12578, 10602, 2156, 13950, 3035, 8150, 11074, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MKMDDDIHFKVFKAEEYENGIVHTFLQVPTCLPCIQNDDIYNILMVNIRPILKGRTRIYSFATKVKLLESDSLRRQDLIYGGSTNLTSALNIIRHELPDIEIEKMKPPLGKNVNVYLLGVGQDFPVRYSIDIRSRLHNGNSNIPSLFWANVVNELMKGIMANKLSHNGYSLPGLYSKTDVYPGEWIYFSEPPIELKDLSMIVNGKKILINCDSPGRKNEKIPDGIFILMETLFNKCCDDLMKDDNKRDNIGDLKEKYNSLITQNKKIITTSKYDKRNLIIKGRNIAAYDRDIKNFKNIYEQIKPKIMSLPNSTPDELCSITITGIPAYAPIKDASQINPWTMVIKHILVSPYAVLSQQVLEGAAEVDIIIPIIPANAIDTLKPLLKSDLYMMMTTLCILKNPHIIEYNAHLAALGCAWRLDDIARTAKIYLDRPSVKHYIDLLSSEPNQALMTESIKKINGGNTQSLRDILKIILLEFIGRCLSKYKTNECDATSYKDFFYNGDEDIEDKLTINELKCAIKKYVTGRVNRLSKELKSCIKITLNIDKIYKLRQYASCGNISLDQVELYVYHALKYRDSKQRLYYRKILPSNDLHQQIKSKITQELIRNYKNELLSQTKEQIIDAAQKRGIRVYKETFEIVYKRYDPKLMLLREACQSSQCPHFLVPHRNFNQHLEVDREDDIIKKVASGYLLRKRNERLPKPPSLSYLRNRIDEIDNLNKIYKKMKLSDASSSMHYAVPHIVDGWNEVDNCSESNICIFLITDGDHNVGGIFWIEAECVHDVIIREMKNIKIITADHLLNDIFRQWNSIIIQQDRNKFMDEIELAETILKTTVTQTSTVEYLKENDIDFNVRKFDFMKTFPVSTIGKRDKDYQLQTDNDKTVFNIKTLCEFPIKSRPEYASVKTLKCESLIKPMFLLSLVRENKNKHKKETVKQFELDNNATLENFYMWSTIKSWAEEMDIHKDIIHEAFIEKDEIKKWKERYSKIHYPMIMPMKPNFAHCLHKVTSDSINMTT", "metadata": {"id": "A0A9C7BMT3", "cluster": 19271109, "interpro_all": ["IPR036465"], "interpro_used": ["IPR036465"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein should feature a Gcp-like domain that functions in the biosynthesis of N6-threonylcarbamoyl adenosine (t6A), a universal modification found at position 37 of tRNAs reading codons beginning with adenine. Found in proteins such as Kae1, Gcp, and TsaB, this domain contributes to the essential t6A modification machinery rather than acting as a general endopeptidase. Additionally, the protein is included in the tRNA threonylcarbamoyl adenosine modification protein TsaB family, which participates in the biosynthesis of the N6-threonylcarbamoyladenosine (t(6)A) modification in tRNA. It functions in concert with TsaC, TsaD, and TsaE to catalyze this reaction essential for translational accuracy. Moreover, the protein is a member of 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 is native to Saprospira grandis DSM 2844. 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, 5469, 1034, 17, 3189, 3418, 1988, 4088, 1922, 1920, 8132, 1927, 29077, 17, 6841, 12831, 15339, 7972, 12492, 2199, 10125, 12, 20762, 1019, 13, 16, 43, 10321, 6295, 2435, 2019, 3507, 3191, 1927, 20770, 7461, 14500, 7828, 1956, 15643, 18, 2435, 1922, 2697, 2427, 1966, 9580, 12474, 16, 5469, 1034, 16, 1930, 17309, 1014, 16, 2052, 3418, 7624, 1942, 1920, 4415, 20762, 1019, 6295, 10853, 4356, 2254, 8290, 1966, 43, 3335, 16239, 9626, 2410, 9200, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 10089, 6841, 12831, 15339, 7972, 12492, 2199, 10125, 6295, 2213, 17309, 1014, 3416, 16, 2154, 17241, 1922, 1920, 8132, 1927, 1920, 29077, 17, 6841, 12831, 15339, 7972, 12492, 2199, 10185, 7506, 12, 62, 12, 26, 13, 43, 13, 6295, 1922, 10089, 18, 2176, 4088, 1922, 21799, 1956, 17309, 1030, 16, 17309, 1007, 16, 1930, 17309, 1021, 1942, 18170, 2052, 3227, 4415, 1958, 8414, 4923, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 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, 1977, 6196, 1942, 9235, 5424, 11979, 12038, 1937, 10964, 22783, 1006, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MDQLILVLESSSRKTSVALIKNGLCWLVEESTLDTGDPAAELTLFVQKILTRAKLKGEDLAAIALSKGPGSYTGLRIAYSTAKGLAFAWQLPLLALDTLAALAYGAKWNQSLPKNSLLICLEDARRGNAYAAIYNCQLEIIKSPFFVSLKDLNLSIYQQEYSLYLLGSAARSYQELMPESKLELLPLKTASARFFEQLAQNAYEKQEFAELAYSEPFYLRAPQLTKPKKNKFFSKK", "metadata": {"id": "J0P5H9", "cluster": 21720817, "interpro_all": ["IPR043129", "IPR000905", "IPR022496"], "interpro_used": ["IPR000905", "IPR022496", "IPR043129"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to create: The protein should feature a Pecanex C-terminal domain that comprises the C-terminal region of the pecanex protein, a maternal-effect factor essential for neurogenic development in *Drosophila*. Also, the protein is a member of the Protein Pecanex family, which comprises multi-pass transmembrane proteins that act as maternal neurogenic factors involved in Notch signaling in *Drosophila*. While the specific molecular function is not fully characterized, members of this family are also expressed in mammalian spermatocytes, suggesting a potential role in the testes. It is produced by Trichomonas vaginalis (strain ATCC PRA-98 / G3) and is connected to UniProt keyword 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, 3066, 5961, 43, 13494, 2516, 1039, 45, 17, 4262, 3418, 1988, 12936, 1920, 45, 17, 4262, 3031, 1927, 1920, 13494, 2516, 1039, 2213, 16, 43, 5509, 17, 2495, 2991, 4415, 1958, 21113, 2740, 1922, 14, 8273, 14, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2213, 13494, 2516, 1039, 3416, 16, 2154, 12936, 2779, 17, 4675, 9117, 2697, 1988, 4033, 1966, 5509, 21113, 2790, 3286, 1922, 8091, 3197, 1922, 14, 8273, 14, 18, 2679, 1920, 2487, 3272, 2347, 1977, 2084, 5437, 4378, 16, 4678, 1927, 2052, 3416, 2032, 2222, 3198, 1922, 6492, 29604, 16, 3783, 43, 2889, 2770, 1922, 1920, 16880, 18, 2176, 1977, 4152, 2007, 10477, 10480, 10120, 1937, 12, 3943, 11037, 21227, 17, 5613, 19, 15991, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9117, 7864, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MSLARRNQLNTITGGFHFAKTDAFGNKWKTCILVVLFFSNFVFYFDNWKPKLIFSTTFALIILLLKLFSYIINKLYDNATTYNIEGDDVQEVETEGFQLPKGISLQLWEKRQVIWNNLHNLDEAAFILITSGFNPDEVYALIALASNGTINSTTKLAQRRKNPNIRHTIHFCGKEFNLKRGREEFSRIMDRPTNIFEIFICYFVAALTIFAIGTFKTDYYCIGMGVILGFSLFSLIQQPTVEPYGMLMTDSTYKYTRCLFISIFSGINCILVYFKYDLPLMRILIILIPILIVVGAIGHTILTIHYIFETVNLYLFGILGSTSTWRSLLELLINTAIIAIGYVISTKLHVKFLPTILVSIMSIFANLDSMLFSKFSIKKLILSGLFVVFAAIGSIFPILLVTNAYRFFIPGILIVTCMILPYLQSFNQYIFFHCESIVFPDIFWKIESVLRSFLVGMFISYSIKDENTIYAPLLALLLYRIAMTSPQLGSFAIVIACFTVYYKFSAKNTSVGSILAAFIALKILSVIRVVSAMTINSQWIWINPQEGLLESLLYGLFNLFCTYYINPTSFFTTISLVYSMFTGEAQSLIFGASKLFTFSAPRPYCFLESISMSNDEEFHTNETNQRIELPAYISLGSELENVLNDRLKNGQLGFVLPDSFYLFTSNDLLGIVHVISLSIHDIRFDLRCMEFKQTTSCHHNEIAHLNRLVADHQPFGNFLQSYMYRFSAYELKSKKFSLNNFSLSSISLENVNAGCSDEKKLRYQFFSSILAVIQENLEKSQNNSEQIEETSDNSIPLVQIPKQTESQFTEEEIEMINQFSMKYNTQIDKTIVHNVYEDLKYSVANINETIFDDNFNDDKKNIGKATRNYILLLLMDSVGIAPDILDPNTAETEEEKQQILDDIFDFIDSSLDTEAVPVSSNKKLQEITKRGTPIIFLRTTNEGRTLIRYGKSVQDWFVFQMNTGVVRGFWSGLIRELIFGASASEERLSITLDLNRLRNITNQSINPPVGYPVYVTKVLSNN", "metadata": {"id": "A2DQN3", "cluster": 21791962, "interpro_all": ["IPR039797", "IPR007735"], "interpro_used": ["IPR007735", "IPR039797"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: 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. 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. It occurs in Flavobacteriales bacterium and corresponds to UniProt keyword Transmembrane, Membrane, and Transmembrane helix.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 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, 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, 2176, 5110, 1922, 7732, 15229, 1918, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 9117, 16, 3260, 16, 1930, 9117, 7864, 18, 3], "output": "MGRNKRRENKAVTEPVERVEPPVQEPVASGANRLPYYLVFALGFLEFTKKGFDGIGEIWTNDLMTGFFGTKKKLVEGGRYRPLALTTHAIEYQMFCGVILLLVLKRIFGWNEERWWWSLPFVATALYLAHPLHTEVVANIKSRDEIMSFLLVLSGIWFFLSLTSKESAVTFLGVIPLTLIFFPKGNLKDSSMALSSIASLDVAPELMNKPYLQAQGSERLASIFLTMGLYLKLLVWPHPLTHDYYPFHPFKTFEELQVGMRPYWTLVRKIKGSKGSLIGYSLLLYFGTFILFSNLIFDIGAFMNERFLFIPSLGYALIVAYLLTEVIFSGKTVVRNYAWENDFALASSDIETSDGSAKVRMTMGSELLDQAKDATSPQEKTRLLKEAEQYELSSESENYEYSIHYFEQAVKKKPNDDRILGNLEAVAIKANARFRKGEGRSRIYASVGEVYGKGMNDMVNSKKFLNKAIKHNPQNKSLELEPENARVMLNLGILYSQMGDAETGNRYMQEAVRLDPSLAPSKLYANTVPFDYALDDKLYITANGKNPQLSHFINIVLYGLFVLLSFNAVLKYLEHRKMQEAAFTIAYLAIRLTVFGDQGADWSDPMTLISVIAYAAILGYGLSSKFGEKLAMSLVVLILVGLKIYPAYFPPLDILGNIYYEVGLYEAAIKGYKTANASAYQKIGIVFAMTGSADSALYSF", "metadata": {"id": "A0A945WJ97", "cluster": 21810807, "interpro_all": ["IPR052346", "IPR011990", "IPR019734"], "interpro_used": ["IPR011990", "IPR019734"], "interpro_unused": ["IPR052346"]}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein includes a Tetracyclin repressor-like, C-terminal domain that functions as the ligand-binding and dimerization module within TetR family transcriptional regulators. This multi-helical domain interlocks with the N-terminal DNA-binding domain to repress the transcription of genes involved in antibiotic resistance, biosynthesis, and stress responses. It mediates regulatory control by sensing specific small molecules, such as tetracycline, which trigger conformational changes that modulate DNA binding affinity. Also, the protein falls within 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 should include 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. It occurs in Aggregatimonas sangjinii and features UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 12470, 22170, 1921, 14434, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 5207, 17, 2743, 1930, 13640, 9059, 2651, 5575, 3416, 5224, 9098, 18, 2052, 2779, 17, 11514, 3418, 20856, 20131, 1956, 1920, 56, 17, 4262, 2678, 17, 2743, 3418, 1942, 9055, 1920, 3213, 1927, 2628, 3286, 1922, 7267, 3554, 16, 8132, 16, 1930, 3071, 3387, 18, 2176, 10412, 4948, 2285, 2007, 9306, 2487, 2858, 4206, 16, 2427, 1966, 16179, 16, 2154, 6086, 8523, 2840, 1988, 8480, 2678, 2743, 5173, 18, 2222, 16, 1920, 2213, 12182, 2651, 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, 3066, 3951, 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, 2176, 5110, 1922, 5206, 1968, 3947, 1934, 22671, 28298, 3907, 1930, 4075, 20709, 11569, 3213, 3640, 18, 3], "output": "MGYKHNKEDILKVGYEVFRTNGYHNVGINQILKESGIPKGSFYNFFESKEDFAQQVIQQYGENNRCWMEDYFENCDLSPIECLKSFYNFMMNLNEADRYNGGCLVNNMSVEVGHHSDVIGAEANNHFVGWLNVLAMEITKGQDAGEITKDFSALELAEYMHAGFYGVLARTKVTKNRVYMDVWFEMTFKFIST", "metadata": {"id": "A0A5B7SR40", "cluster": 23736146, "interpro_all": ["IPR009057", "IPR001647", "IPR036271", "IPR011075"], "interpro_used": ["IPR011075", "IPR009057", "IPR001647"], "interpro_unused": ["IPR036271"]}, "task_type": "autoregressive"} {"instruction": "The protein is categorized in the tRNA threonylcarbamoyl adenosine modification protein TsaE family, which functions as an ATPase essential for the biosynthesis of the universal t6A tRNA modification. These proteins feature a unique nucleotide-binding fold with a P-loop motif that binds ADP and likely form a complex with TsaB, TsaC, and TsaD to facilitate the modification process. Additionally, 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 present in Alphaproteobacteria bacterium MarineAlpha10_Bin1 and is described by UniProt keywords tRNA processing, Cytoplasm, and Metal-binding. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 10089, 6841, 12831, 15339, 7972, 12492, 2199, 10125, 6295, 2213, 17309, 1021, 3416, 16, 2154, 4088, 1966, 1925, 9444, 4415, 1958, 1920, 8132, 1927, 1920, 10321, 20762, 1019, 10089, 6295, 18, 2144, 2697, 5961, 43, 5008, 5489, 17, 2743, 3728, 1956, 43, 58, 17, 5881, 5219, 1988, 6876, 9828, 1930, 3205, 2386, 43, 2796, 1956, 17309, 1014, 16, 17309, 1030, 16, 1930, 17309, 1007, 1942, 6628, 1920, 6295, 2585, 18, 4950, 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, 2481, 1922, 4595, 9218, 1021, 10296, 14061, 10789, 13276, 2930, 41, 8768, 1009, 1930, 1977, 2910, 2007, 20709, 11569, 10089, 4587, 16, 5239, 16, 1930, 6048, 17, 2743, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MLETESSDETAGVGKKIGIELGAGDVIMLMGDLGVGKTVFAGGVAVGLGVASSVSSPTYTLIAEYRDGRLPFYHVDLFRLQDVDPFQELGIEEYLRSDGVAAIEWPDPIRSRWPGDYLAVRLEHLGGDDRRLTIDGSGARSDGLILRVAPQLAEAGVDG", "metadata": {"id": "A0A2S6R396", "cluster": 23870312, "interpro_all": ["IPR027417", "IPR003442"], "interpro_used": ["IPR003442", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein has 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. Also, the protein is grouped in the Macrolide Exporter MacB family, which consists of non-canonical ABC transporters that typically function as the inner membrane component of tripartite efflux systems like MacAB-TolC. Utilizing ATP hydrolysis, these proteins actively export substrates to confer macrolide resistance, while variants such as PvdT secrete siderophores for iron acquisition. Moreover, the protein possesses a ABC3 transporter permease, C-terminal domain that functions as the transmembrane component of various ATP-binding cassette (ABC) type 3 systems, mediating substrate translocation across the inner membrane. It participates in diverse biological processes, ranging from lipoprotein release via the LolCDE complex and antimicrobial efflux to bacterial cell division as part of the FtsX septal ring component. It has been detected in Desulfobacterales bacterium and contains UniProt keyword associations Cell membrane and Transmembrane helix.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 2258, 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, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 23929, 2261, 12660, 1915, 3433, 1014, 3416, 16, 2154, 7543, 1927, 2447, 17, 9452, 7219, 10538, 1988, 5745, 2347, 1966, 1920, 6671, 3260, 4594, 1927, 8027, 24707, 11247, 3771, 3189, 13421, 1014, 17, 21930, 1030, 18, 10232, 4498, 9128, 16, 2144, 2697, 11182, 12660, 6249, 1942, 7909, 23929, 2261, 3554, 16, 2679, 4936, 2427, 1966, 5774, 18314, 15989, 22940, 14820, 1958, 5680, 6165, 18, 3950, 16, 1920, 2213, 14465, 43, 7219, 1010, 9054, 6191, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 9117, 4594, 1927, 3425, 4498, 17, 2743, 12992, 12, 7219, 13, 2601, 23, 3771, 16, 10239, 4510, 7849, 3436, 1920, 6671, 3260, 18, 2176, 17241, 1922, 6445, 3933, 4028, 16, 6485, 2037, 9694, 4012, 3454, 1920, 3004, 8293, 3695, 2796, 1930, 8003, 11247, 1942, 4543, 2024, 8451, 1966, 3131, 1927, 1920, 17022, 1039, 16458, 6335, 4594, 18, 2176, 2258, 2252, 3330, 1922, 30311, 5883, 3955, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 2024, 3260, 1930, 9117, 7864, 18, 3], "output": "MINSKYLMSELTGRGRRTIANIGLVALVTCVLVCITLLTGALERAFHAPLSDIGANITVQKSTVIASLPGIQSVSRAILFWDFFDDAFQIVVGMQANDPAGPALLRTAITAGRMLNPEDQIGGLPFTIIGLVDASRISRIGTANLYISLAEAQKIVAAAPGVTTVHSFDSKDSNLLFIQADHDKTEDIAAFSLTQRFSGVISGMVFLLALLLIIRNSSAAIRERTKEIGTMKAVGWTGTDIRGQLLAENTLYIVLGTVAIPIPWDMAPKPHFLPGGEEQLFRQVQLQMKPSLQLLILTCMAPVLLGLATVWAASRAITKLQTSEVLRYEAGDVPEQMAGPVLPCSVAPISAAQTSMALVETVWAEQAKLGIGDQVTIKELLGEKITVSTPDSFKKLLGSLSGLILGTLAAWGLSHITI", "metadata": {"id": "A0A7Z9WW36", "cluster": 25272672, "interpro_all": ["IPR003838", "IPR025857", "IPR050250"], "interpro_used": ["IPR025857", "IPR050250", "IPR003838"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein carries a DUF7704 domain that is found in uncharacterized eukaryotic proteins and shares detectable similarity with Tumor protein p53-inducible protein 11 (TP53I11). It is predicted to adopt a structure homologous to TP53I11. It has been characterized in Rhodotorula taiwanensis and is associated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 1920, 2213, 16252, 43, 4855, 1038, 7658, 14743, 3418, 1988, 1977, 2435, 1922, 24528, 10825, 2697, 1930, 16495, 7398, 6796, 1956, 2798, 2213, 5105, 17, 9376, 2213, 2513, 12, 13544, 11819, 1009, 13, 18, 2176, 1977, 4396, 1942, 14103, 43, 3170, 8725, 1942, 13544, 11819, 1009, 18, 2176, 2258, 2252, 4378, 1922, 11490, 4275, 5617, 12760, 8134, 1930, 1977, 2458, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MTAPPAASSRHSDPLPKAYYLFFAVIEPLLTFAGAGRAYFDSARYFVELYPEDLVIAPKLASLHPAALMAVRQLGSCFFLFAMMACVLLPAMRRTLKNQPKELEQLVRAYLFCLAAADLTHIGATLYDLGPEGATRLGSWNVLTWGNVGITVVLFAWRMCWIAGVGRSRLPNSKKAT", "metadata": {"id": "A0A2S5B4B3", "cluster": 25364830, "interpro_all": ["IPR056121"], "interpro_used": ["IPR056121"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein includes 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 originates from Adhaeribacter swui and corresponds to UniProt keyword Membrane, Transmembrane, 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, 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, 22970, 2037, 21918, 29164, 26073, 2341, 1915, 3476, 15444, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTSPAADSLIKNKYFPALTGLRALAAYLVFFHHMVFAGQSGVTIFFVLSGFLISYKYNPVSGRIDYKNLVWQNDANSRHWFLNLTLLKGFFDAYKFTGIGPGWSLTVELLILILSGGTLVVLAKAYYATIFFNSLSFMLGYTFQYYRQASVLSQNKLFTIMGLLLTLAGIGLVGFTSNIVWFTEESYIGILLYGLITENTLFARILATKPAQVLGKSSYAFFLALNGLAIILYYTLEKPLYTQITRSKTYSEPDLAFPANTSSVYWNQYLLKRFARIYPLYMLLTVLIACFYLLAPLLFSLFRLNGLVTFGRCFEFYCGYLVAAVKWSTAINNFCLPVALIHSGLIYEFFYFHLSTSRFLIF", "metadata": {"id": "A0A7G7G2P7", "cluster": 25476961, "interpro_all": ["IPR002656", "IPR050879"], "interpro_used": ["IPR002656"], "interpro_unused": ["IPR050879"]}, "task_type": "infilling"} {"instruction": "The protein belongs to 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. Also, the protein should contain a Low-density lipoprotein (LDL) receptor class A repeat that forms a calcium-dependent, cysteine-rich structure responsible for ligand binding in extracellular and membrane proteins. It utilizes a conserved cluster of negatively charged amino acids to facilitate high-affinity interactions with positively charged sequences in ligands such as LDL, playing a central role in receptor-mediated endocytosis. Also, the protein is assigned to 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. It is present in Pomacea canaliculata (Golden apple snail) and is linked to UniProt keywords Disulfide bond and Signal. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 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, 2222, 16, 1920, 2213, 3066, 5531, 43, 2330, 17, 3824, 9694, 12, 8017, 13, 3148, 2921, 43, 6865, 1988, 4952, 43, 5016, 17, 3100, 16, 8666, 17, 5536, 3170, 5061, 1958, 5207, 2743, 1922, 5329, 1930, 3260, 2697, 18, 2176, 18127, 43, 5305, 4377, 1927, 7191, 9516, 3835, 4576, 1942, 6628, 2149, 17, 5173, 3719, 1956, 6629, 9516, 3709, 1922, 6908, 2427, 1966, 8017, 16, 14797, 43, 4101, 2770, 1922, 3148, 17, 3434, 11914, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 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, 2176, 1977, 2481, 1922, 12586, 22076, 11152, 16058, 5499, 12, 22357, 19663, 15929, 13, 1930, 1977, 4624, 1942, 20709, 11569, 11830, 5403, 1930, 2733, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MVVYNYLFGLTLLLHLAGVWLLTSDPYLQSQSTPRSKSKIITTSYVVNPYGVSSSVSSVPKATGWVATTNNAVYSTAVGKVYGSYQDTTASNFAQTSFVAVTLKNLTKCLNTSHSLKFTTQNAVVDIRTKSSDKLPRLSSCEIQVTAPASMVFYINVLSINVQCPAFLLELADVGTTSRRLINTCDNDIPSELWSFTNVVTTTFVVTLESQIIQLALNFTAVPVTQRPNLEIMFTSPNRGYIQTPNWDGHRKYPVHMDSWVKVDIPEQSAIMVSVPHMDIEGRVPTICPADGLEYDCIGSEDEADCPYTSPRCGMPWPLMTWKEAFDFCLSQGARLASLNTPAEYNNVFSLLRLTEYGNAYVGMLQMFMQRPMYLNALQWTDGTIAYFKTIDGVATMPACGLFYLQDMNGGIKLKKCDEPRISHALCETEAAPGNQLRPEKSNPRITFLDISAWQNDSSKVVCPAGHMTHTFLSCDVASACWMRSSLSSCDAPLSSLPPAFDCDNGFDRVPHTLVCDHRSDCPDGSDEDFCEFASCYTSGKYDCGNHQVITFVVSANNHI", "metadata": {"id": "A0A2T7P3H7", "cluster": 26256596, "interpro_all": ["IPR016186", "IPR016187", "IPR036055", "IPR002172", "IPR035914"], "interpro_used": ["IPR016187", "IPR002172", "IPR035914"], "interpro_unused": ["IPR036055", "IPR016186"]}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein possesses a Methylated-DNA-[protein]-cysteine S-methyltransferase active site that repairs O6-alkylated guanine in DNA by transferring the alkyl group to a catalytic cysteine residue. This transfer functions as a suicide reaction, irreversibly inactivating the enzyme as the methylated protein accumulates. Furthermore, the protein possesses a Methylguanine DNA methyltransferase, ribonuclease-like domain that constitutes the N-terminal region of DNA-[protein]-cysteine S-methyltransferases involved in DNA repair. It facilitates the removal of mutagenic alkyl groups from O6-alkylguanine and O4-methylthymine by transferring them to a cysteine residue, a suicide reaction that irreversibly inactivates the enzyme. Moreover, 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. It is derived from archaeon HR01 and is annotated with UniProt keywords DNA damage.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 14465, 43, 11882, 17, 2678, 17, 37, 2213, 39, 17, 8666, 61, 17, 16478, 3500, 3200, 1988, 5059, 1036, 57, 1016, 17, 13345, 1981, 16904, 1922, 2678, 2007, 21902, 1920, 13345, 2210, 1942, 43, 6804, 8666, 6181, 18, 2052, 3856, 4088, 1966, 43, 10064, 3227, 16, 12801, 5898, 20862, 1920, 4113, 1966, 1920, 11882, 2213, 18804, 18, 3677, 16, 1920, 2213, 14465, 43, 4963, 11056, 7290, 2678, 16478, 16, 18347, 2051, 17, 3189, 3418, 1988, 14879, 1920, 56, 17, 4262, 3031, 1927, 2678, 17, 37, 2213, 39, 17, 8666, 61, 17, 28253, 3286, 1922, 2678, 5059, 18, 2176, 11374, 1920, 6025, 1927, 21977, 13345, 2671, 2037, 57, 1016, 17, 13345, 11056, 7290, 1930, 57, 1006, 17, 4963, 28935, 25157, 2007, 21902, 3581, 1942, 43, 8666, 6181, 16, 43, 10064, 3227, 1988, 12801, 5898, 22331, 1036, 1920, 4113, 18, 3950, 16, 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, 2176, 1977, 3595, 2037, 13470, 1916, 3668, 6924, 1930, 1977, 10633, 1956, 20709, 11569, 2678, 4293, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MTERAGYYIDRSPLGLLADVFLRELVEKGFTPSKVGSGPAKHFTVELDLRGTAFQKKIWREVIKAYRAAGNAVGANPAPLIVPCHREKLLRLEGSYSQLKKKVAASERGIVMVRLQTRGFEAFNQIVEYLQGVRKIPYGKLKTYSEVAAAAGYPVVRSGWIMGGYGGREDIK", "metadata": {"id": "A0A2H5UX87", "cluster": 27529107, "interpro_all": ["IPR001497", "IPR014048", "IPR036217", "IPR008332", "IPR036631", "IPR036388"], "interpro_used": ["IPR001497", "IPR008332", "IPR036388"], "interpro_unused": ["IPR036217", "IPR014048", "IPR036631"]}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein is grouped 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 possesses a Sortilin, N-terminal domain that constitutes the ten-bladed beta-propeller luminal region of Vps10-D family receptors. Activated by propeptide cleavage in the trans-Golgi network, it binds diverse ligands including neurotensin, pro-neurotrophins, and lipoprotein lipase. Additionally, it is part of the Xyloglucan-specific glycosyl hydrolase family, which comprises enzymes belonging to glycoside hydrolase family 74 (GH74) that hydrolyze the plant cell wall polysaccharide xyloglucan. These proteins exhibit xyloglucanase activity with endo-, exo-, or endo-processive modes of action, cleaving glucosidic bonds to generate specific oligosaccharides. It is found in Anaerolineae bacterium and corresponds to UniProt keyword Glycosidase, Signal, and Polysaccharide degradation. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10809, 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, 14465, 43, 17362, 16207, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 5656, 17, 22707, 1007, 4666, 17, 5062, 13728, 11776, 3031, 1927, 14851, 2930, 17, 46, 3416, 4086, 18, 4128, 2007, 5062, 8253, 6404, 1922, 1920, 2127, 17, 10277, 3504, 16, 2176, 6876, 6445, 6908, 2710, 9124, 9261, 16, 1965, 17, 30302, 1036, 16, 1930, 9694, 16653, 18, 4950, 16, 2176, 1977, 3131, 1927, 1920, 9639, 23135, 1928, 17, 2487, 20067, 20748, 3416, 16, 2154, 12936, 5038, 10588, 1942, 7533, 2261, 20748, 3416, 5446, 12, 6101, 10639, 13, 1988, 7222, 6931, 1920, 4496, 2024, 4821, 17167, 9639, 23135, 1928, 18, 2144, 2697, 5987, 9639, 23135, 7241, 4127, 2455, 1956, 16239, 17, 16, 18930, 17, 16, 2014, 16239, 17, 2585, 2320, 9606, 1927, 4615, 16, 28634, 3351, 27545, 7408, 1030, 9031, 1942, 5655, 2487, 22012, 18, 2176, 1977, 2435, 1922, 11381, 8419, 3336, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 7533, 9200, 16, 2733, 16, 1930, 17167, 4877, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MKASRIIPFLVFALLISSVGLACTSSTSNTTPADTAVVIPSAAPAIVTETPTSQPSQPLDFRQAMDVVLVSDPQIPNTLYIQQSKSDTFLYQSSNGGTSWLKLEGADIAGTPPEVLNQFLLRATPSFLRSIFTLDRETLMLTVNPSDPNTLYAVDETGSNLIVSRDRGVTWESAGVLPNPAFPEMSALAHNPLTPDALYLVTGFGLAKSTDNGKTWLEIGTGFPKAGPAPYYYPTLIFDPTSSNTLYFNDPLYGVYKSVDNGENWVELPRPEPQEVVCLSIDPQNPDTLYMVFKYGAGIYQSTDGGKNWTKTALNLPGADVHYLTFDSQTLGTLYAVMGSGDVSGFYKSVDDGSTWSEIVTDLLP", "metadata": {"id": "A0A7C3PNS2", "cluster": 28635136, "interpro_all": ["IPR031778", "IPR015943", "IPR052025"], "interpro_used": ["IPR015943", "IPR031778", "IPR052025"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein is categorized 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 Candidatus Zhuqueibacterota 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, 1977, 10234, 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, 14550, 1031, 1957, 19533, 5089, 26073, 2341, 6506, 3857, 14061, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "PGNIRELEAFVYEAARAAHRMKQEIIQPSHLPEELVNSAASPQNGSPRPSLRLRAGELYAQYLPPEFQDRHFIWAVANDSANGALRAHELHEQLLVAIPPVPGVPLKLATRAVAHAFERNVLLALLRQTQGKQNEAIKLARIDKSAFINKMKRHGINLKKNEFEKGEHE", "metadata": {"id": "A0A7Y5KBX4", "cluster": 2604926, "interpro_all": ["IPR009057"], "interpro_used": ["IPR009057"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein carries a ATPase domain that mediates ATP binding through a conserved P-loop motif. Moreover, 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 Ignavibacteria bacterium and is connected to UniProt keyword ATP-binding. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 16252, 43, 9444, 3418, 1988, 10412, 4498, 2743, 2596, 43, 5305, 58, 17, 5881, 5219, 18, 3950, 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, 12046, 9188, 7972, 2341, 18339, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MKNPFTVTGYAGAKYFCDREEETKKIISAVENGRNIVLYSIRRLGKTQLIKHVFSSLGKNKKYITVYLDIYHTRDLKSFTQSFAEAVFSALTTNPASILEKAAKVLSNLRVALSFDPFSGKTILTFDIKTPQESEATLRKIFEHISAQKKQVVVAIDEFQQVSLYPEDTTEALLRSFMSECTNASFIFSGSVNHLLISMFASANRPFYQSAEMLRLQKIETAVYARFAKRLFNSKGTNLPLSLATECIQWCRNHTYFVQRLFNRLYSLPVEEITGDVIQRTKNELLLEAEPVFNDYVNFYTQFQWKLLSAVAKEDGAQSVYSTEFINKYELGSTSSVRTALQSLIRRDAIYEEDNKYFVADLFFSRWLEMKIR", "metadata": {"id": "A0A952BUC6", "cluster": 3848302, "interpro_all": ["IPR011579", "IPR027417"], "interpro_used": ["IPR011579", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein is classified under the RNA-binding domain superfamily, which utilizes a conserved \u03b2-\u03b1-\u03b2-\u03b2-\u03b1-\u03b2 fold known as the RNA recognition motif (RRM) to bind single-stranded RNA. These domains facilitate diverse post-transcriptional processes, including pre-mRNA splicing, mRNA stability, and translation regulation, by utilizing aromatic side chains to stack with RNA bases for specific recognition. It is produced by Didymella pomorum.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 3146, 17, 2743, 3418, 13975, 16, 2154, 18127, 43, 5305, 161, 17, 160, 17, 161, 17, 161, 17, 160, 17, 161, 3728, 3171, 1966, 1920, 3146, 5708, 5219, 12, 5162, 1035, 13, 1942, 4566, 2957, 17, 10338, 3146, 18, 2144, 4682, 6628, 6445, 2753, 17, 5224, 4028, 16, 2710, 2097, 17, 3616, 8490, 16, 3616, 5057, 16, 1930, 6410, 3640, 16, 2007, 10232, 10761, 4159, 7835, 1942, 10496, 1956, 3146, 11137, 1958, 2487, 5708, 18, 2176, 1977, 4152, 2007, 2811, 2229, 5870, 12586, 17279, 18, 3], "output": "MQDPPLTIPMGDMTNMQYAGPPGMPVQNMDPRRRPSQHYSNGNALYDPYEDTNPAFRNAGYSNGNKYNRSSMHNNNGRPRKPSLPGSRPYHGQYPNARQQVGGHYNSGPKSHMDNDPSITQDPEYGCDVNWIGRSNKIVNELFMKDLPENTQPAELEELFQARLGVKLTSVNIRFSPQAPYLKHAFVGFPSCAVTKQALAIPDPTIHGFSVSITVPKRFFQKTVDVQSRDTVEAGPSAYSRFTSNPNNREGRNRAPSIREGSDVTPSTTATREKTSYSPQDARSDLPKKKNKQTQQAQVTAGSPEARKVKPQEKRPGSPMMEEPVASAANVQTDNLNNNAKVEGLASAPTTIEPIVFMVSEETDQPQVNEKTVSPPTVEKEMDAKPAGTEAVVSEPDSIGLIPKTAPSKVLPAVPAPSIEPTVDPAMTSLPQPPMTTIGTKVPTTASTPPEVQDPTSDDELKNEASFHSAAESKSELEVKGAHNAISGVANHGTDVRFPEASTAESVSTPAPPAPTTHPTQEADNAPTEDVAVTTDTENSHSKQDSKTTTMSSATSEAAEVQAATQQETKTRETMTFVVGQTKERGPQQPEALFPSRKQMDKLAKKEREKQRKAAKRAEGQRKLAKNGKGEDKTASSQAPPADGSVEKAKSASDKTAAPKDETQSAGNVQSLDTTATSPTTTPDAEEISASTKESTATDISQKTADNVHGTSGKGKSKKVVTPAAEELASTEDKNKDHGKQINGTSVTSETGSMTNKEAKVNPEEIVQEMSIKKTAQESARGTDAQSSKQASGGQVSGPAGTGEESPIASAKKKKNKKKQKSTEGETSKQPLAWPKFDFRLKSPNPSWMGPIDMQNDVHNYGKIMDDVCGGPEDSDFSWSDLRTMEDVMNSDKDKAPAGPASGSGPSQNAHTDEAQRIFNALFPKLKKLRPNKALETYARLSEMSTLEEMAKFAALVAKVDAATRPSQRFKDAPDDEFGEYFQSIIAAPAGTSARELVASSNREELVNRGVAALHAQIGKQSSNLLNLLSLTPTAIKGDEVESEDVVLAANGKQHAERSTGQDPSDSITPDAQPPKKKKKANKQNNKKMKKKYGADNGEPSQSGDAVATTAIASTPPKVSLNFVDPSDQVARQLDHVNAVIDLNQNGAAASGSVSLHRGAATPTEEPTLKRAVEAYLREAHPERKSKGRKALQQDLQ", "metadata": {"id": "A0A9W9DAN6", "cluster": 4573513, "interpro_all": ["IPR035979"], "interpro_used": ["IPR035979"], "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 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 Ruegeria sp. A3M17.", "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, 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, 7212, 6541, 18339, 2056, 18, 12021, 8012, 1027, 18, 3], "output": "MPYSPITGQLGVLLFESEVIGRHPAKYFLDESCGYIWVENPTWLEEAYSDAIALTDTGIVARNLSNLRRVSTAMRANGLADARGIDIGGGYGLFVRGLRDIGLNFHWSDPYAENLLARGFEADDGTYAVATAFEVLEHLPDPLSYIKEARTKFDFETLFFSATCFDPKDLPPRDWWYWAFETGQHISFFSEQSLDYMAEQLEMQKVHLRGDLYAFTALDSLTWPSRWQQWRIRKAFRRASLTQQDYEDMKQRVKSMQLKR", "metadata": {"id": "A0A366WUN1", "cluster": 5663747, "interpro_all": ["IPR029063"], "interpro_used": ["IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein is classified under the Arabinogalactan protein 3/12/13/14/21 family, which comprises extracellular glycoproteins implicated in plant growth and development. This group includes specific members found in rice and *Arabidopsis* that function within the extracellular environment. It is found in Escallonia rubra and contains UniProt keyword associations Lipoprotein, Membrane, and GPI-anchor.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 20790, 27395, 1928, 2213, 23, 19, 2369, 19, 2590, 19, 2607, 19, 2900, 3416, 16, 2154, 12936, 5329, 16268, 6835, 1922, 4496, 2905, 1930, 2740, 18, 2052, 2210, 5921, 2487, 4678, 2435, 1922, 8674, 1930, 14, 8900, 14, 1988, 2347, 2651, 1920, 5329, 3515, 18, 2176, 1977, 2435, 1922, 15279, 6012, 10306, 10010, 5524, 1930, 5461, 20709, 11121, 2538, 5253, 9694, 16, 3260, 16, 1930, 17497, 17, 13333, 18, 3], "output": "MEAMRMKLSAVKGVAAAEAPAPSPTSDYNLASPTKFLLRRFAVLAVVMMMAISAVLVPAAVASVSPSWGYRIQQIC", "metadata": {"id": "A0AA88QYH5", "cluster": 6116567, "interpro_all": ["IPR039281"], "interpro_used": ["IPR039281"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that has the following function: The protein should contain 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. In addition, 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. Furthermore, the protein should include 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. It is native to metagenome. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 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, 1922, 2459, 16, 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, 3677, 16, 1920, 2213, 3066, 3951, 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, 2176, 1977, 6196, 1942, 16552, 2225, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MGTATYLFPGGKMSYSRASMRSTIVMAIAVIGVLLSGTVAQAKPPSRPGAVKNLAAVVTKPAGAYSVAVTWSASTNTTSYALRLTNSSGVVLDSERVTATSWTGLGVAAAGSSVTISITPYNGTRKGPQTSISKTLPDITAPQGSFTVSSTALTGTLTQTSLSDDLSPADAITRTVDWGDGSGLASWSTGSVLQHSYPAQGRYLPSVTLVDLAGNAVTIQVNAMVILDTQAPTGTFSTTPASAWMSYTKVAVTQLGLADDLSPAPQITRSVEWGDGNVTPWTSGTTLSHVYTVAGSYSPTVVLVDEAGNTGHVVASGVTVTQDSLAPALRLRVPATKKAYVASWKVIKGTATDTGTGVKQVRLKAIEKRGATYYSYKAATKRWVKAGTTKSAAWRKATFVIAVPAATGAWKANLKGLKLGTLSISVTARDKVNNTSPARTKSQKLTHA", "metadata": {"id": "A0A2P2BZL1", "cluster": 9033686, "interpro_all": ["IPR013783", "IPR022409", "IPR000601", "IPR035986"], "interpro_used": ["IPR000601", "IPR013783", "IPR022409"], "interpro_unused": ["IPR035986"]}, "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 Peptidase C1A, papain C-terminal domain that functions as a proteolytic enzyme within the papain family, hydrolyzing peptide bonds via a catalytic triad consisting of cysteine, histidine, and asparagine or aspartic acid. This domain is part of a papain-like fold typically active in acidic environments such as lysosomes or plant vacuoles and is sensitive to the inhibitor E64. Also, the protein contains a Cysteine peptidase, histidine active site that acts as the general base component of the catalytic triad in thiol proteases, including papain and cathepsins. This residue facilitates peptide bond hydrolysis by activating a nearby cysteine nucleophile, proceeding through a thioester intermediate. Also, the protein falls within the Peptidase C1A family, which comprises papain-like cysteine peptidases that exhibit diverse proteolytic activities, ranging from broad-specificity endopeptidases to dipeptidyl peptidases. These enzymes are typically synthesized as inactive zymogens requiring N-terminal propeptide cleavage for proper folding and activation, often localizing to lysosomes or the extracellular space. The group also includes catalytically inactive homologues that lack essential active site residues. It is expressed in Philasterides dicentrarchi and is connected to UniProt keyword Disulfide bond and Glycoprotein.", "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, 24050, 8817, 1019, 16, 3860, 2005, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 12712, 4113, 2651, 1920, 3860, 2005, 3416, 16, 7222, 9046, 4207, 9031, 3454, 43, 6804, 21845, 7600, 1927, 8666, 16, 13873, 16, 1930, 23677, 2014, 23047, 2687, 18, 2052, 3418, 1977, 3131, 1927, 43, 3860, 2005, 17, 3189, 3728, 5745, 3500, 1922, 9931, 8114, 2427, 1966, 15222, 2014, 4496, 19129, 1930, 1977, 4532, 1942, 1920, 4106, 14826, 1006, 18, 2222, 16, 1920, 2213, 5461, 43, 8666, 24050, 16, 13873, 3500, 3200, 1988, 8016, 1966, 1920, 3335, 5170, 4594, 1927, 1920, 6804, 21845, 1922, 13914, 12447, 16, 2710, 3860, 2005, 1930, 16808, 1036, 18, 2052, 6181, 11374, 4207, 5403, 9128, 2007, 8019, 43, 15485, 8666, 2797, 28335, 16, 18479, 2596, 43, 30215, 6129, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 24050, 8817, 1019, 3416, 16, 2154, 12936, 3860, 2005, 17, 3189, 8666, 24050, 1036, 1988, 5987, 6445, 12712, 4209, 16, 6485, 2037, 4949, 17, 4896, 16239, 9626, 2410, 30413, 1942, 9137, 3173, 2199, 24050, 1036, 18, 2144, 5038, 2032, 5745, 6653, 1966, 9078, 15856, 6847, 8887, 56, 17, 4262, 5062, 8253, 6404, 1958, 3405, 10328, 1930, 2936, 16, 3868, 29507, 1942, 15222, 2014, 1920, 5329, 5230, 18, 1920, 2210, 2222, 5921, 21446, 9078, 18541, 1988, 3630, 4415, 3500, 3200, 4248, 18, 2176, 1977, 3198, 1922, 10894, 7092, 3726, 9192, 2334, 3983, 1033, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 11830, 5403, 1930, 11424, 18, 3], "output": "MPSSASNPLPQLNFNELPQTWEWPHYCGSCWSFGSTSSLSDRIKIKLQGCKGGYALKAYEWIYHNNITDETCNSYQAKSKCMDCDKEEGCKVAKNPKIYAIKAYGKVTRAFYNYTEGIFVDTTGVTSLTHDCAVVGMFKIIRGVNNLGIETDCSWAEPLDTWTNDIRNKKKQPILSNKANCSIEQSKDFSFKKLFIKDGVNYMSWNVNQHVPKYCGSCWAQAALSSIADRVNNCKQGGTCNGGLSYDLYEILALQGVPEMTCQGGKDKKCWPQEKYDRWYLLAYGSVSGPDRMKGVFSQKLEDPVSKINHAIAVVGWGIENGQKMKMYEDNLAIEHDCSFGIPKLVYWNINGTNFLTVVKNQLVRKAKWPDINISPQVLLNCAQSDIWTDNIGPQNCTAVTSGELQMMNEIYQRGPIACGCGTGWGEENGVKYWLGRNSFGSYWGMKTQTDEQLQKERKKIDQQKNKFPHADIYSSRDQLPESWDWRDIMRGNQFPQLALSVQAVLVYLSEDPDITDCSPIQNCKNCQKQQIQRYGPITCRIAATLEFDFYDGEYWIGRNSWGTYWGDFGFF", "metadata": {"id": "A0A481SBB3", "cluster": 10793090, "interpro_all": ["IPR038765", "IPR025661", "IPR025660", "IPR013128", "IPR000668"], "interpro_used": ["IPR000668", "IPR025660", "IPR013128"], "interpro_unused": ["IPR038765", "IPR025661"]}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: 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. Also, it is part of 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. It has been characterized in Candidatus Gallionella acididurans and has UniProt annotations Transmembrane, Membrane, and ANK repeat. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 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, 2222, 16, 2176, 1977, 3131, 1927, 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, 2176, 2258, 2252, 4378, 1922, 14550, 1031, 1957, 9354, 7253, 11560, 1019, 2687, 1960, 20028, 1036, 1930, 2258, 20709, 15010, 9117, 16, 3260, 16, 1930, 9808, 6865, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MDIKAKFKEKKREIFLLSIVTLISLVANLPHKMLADLVDQKLLLIVLAAVVVIALFYYLNLLLFLCVVALAVGANLPDQMADTLGVSPVVMLTFLVLLVVISQMNAVFKKFETLKVEKKHDTDESRKAVLAAVSKGDLTKLHWLLNANVEINFSEDGVTPLILAAEKGYTDVIQSLISHGADLSAMNPAGLTAMEVALANGFNRTAEIMKLATEGDKLGWSK", "metadata": {"id": "A0A139BST2", "cluster": 13905433, "interpro_all": ["IPR002110", "IPR036770"], "interpro_used": ["IPR002110", "IPR036770"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein should contain a Outer membrane protein, beta-barrel domain 2 domain that assumes a membrane-bound beta-barrel fold and is found in a wide range of outer membrane proteins. It is found in Anseongella ginsenosidimutans and is annotated with UniProt keywords Signal.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 7642, 3260, 2213, 16, 4666, 17, 19560, 3418, 22, 3418, 1988, 17227, 43, 3260, 17, 4124, 4666, 17, 19560, 3728, 1930, 1977, 2435, 1922, 43, 4743, 3109, 1927, 7642, 3260, 2697, 18, 2176, 1977, 2435, 1922, 18229, 1021, 18771, 11560, 1019, 27601, 27545, 7408, 13230, 2075, 1930, 1977, 10633, 1956, 20709, 11569, 2733, 18, 3], "output": "MKKLSFLIVGLLLGSSLFAQEAKFGIMGGVNLANLTKSTGTDLYGEEYNDETYGNMVKPGLALGVYANIPFPGNDVVSLNPELFYSQLGARYESDNGDVEFNRNLHFIELPVLLKFNIVPAFHVMAGPSFSYLMGGKDKFEGEGTVFGVDISSESEQDLDMDDFNRASIGGVIGLGFDATENFKVFGKYGLGFTDMYKSDDSEAFNSNIQVGVGYSF", "metadata": {"id": "A0A4R3KMT7", "cluster": 14092355, "interpro_all": ["IPR025665"], "interpro_used": ["IPR025665"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is included in the Left-Right determination factor family, which comprises TGF-beta superfamily members, such as Lefty and EBAF, characterized by a cysteine-knot motif. These proteins function as morphogens to establish lateral left-right asymmetry in developing vertebrate embryos and are associated with endometrial tissue regulation. Also, the protein carries a TGF-beta propeptide domain that forms the Latency Associated Peptide (LAP), a homodimer that non-covalently binds mature TGF-beta to maintain it in an inactive, latent state. This region also typically forms a disulfide bond with the latent TGF-beta binding protein (LTBP) to target the complex to the extracellular matrix. It has been characterized in Mustela putorius furo (European domestic ferret) (Mustela furo).\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 3506, 17, 3659, 7063, 2991, 3416, 16, 2154, 12936, 5525, 17, 4666, 13975, 4678, 16, 2427, 1966, 3506, 1012, 1930, 6560, 2624, 16, 4378, 2007, 43, 8666, 17, 26646, 5219, 18, 2144, 2697, 2347, 1966, 3901, 6847, 1942, 5389, 5347, 3506, 17, 3659, 13337, 1922, 5130, 13416, 6274, 1930, 2032, 2458, 1956, 11634, 2960, 3640, 18, 2222, 16, 1920, 2213, 16252, 43, 5525, 17, 4666, 5062, 8253, 3418, 1988, 4952, 1920, 9393, 2458, 4207, 12, 7448, 13, 16, 43, 21189, 1988, 2447, 17, 16590, 6876, 6665, 5525, 17, 4666, 1942, 6698, 2176, 1922, 1925, 9078, 16, 9903, 3360, 18, 2052, 3031, 2222, 5745, 4952, 43, 11830, 5403, 1956, 1920, 9903, 5525, 17, 4666, 2743, 2213, 12, 3457, 3846, 13, 1942, 2758, 1920, 2796, 1942, 1920, 5329, 4526, 18, 2176, 2258, 2252, 4378, 1922, 4902, 15208, 5366, 6658, 1957, 2498, 1037, 12, 6785, 11070, 25304, 1031, 13, 12, 4902, 15208, 2498, 1037, 13, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MGEDCSEGAGDGDETPGCEDSCISCPTAKVEQLPFYWRGLLTLFLSSEASTHLLVFSMEWWMPPNSNLVWAGRRACVTVEWLQVCEDSSNSTLWXQLSQPCQPLLLQVTVHREHLGPLASGACQGEQQGEPQLELHTLDLGAYGPGRGSLSALSAPLLRPRRPEVAGRWLAAAPLPGVPLCRHEWLXQYSTLVDSRLVSLLESSWKAFDVTEAVTFAHKLVRFAFPGPR", "metadata": {"id": "A0A8U0TFT3", "cluster": 15281502, "interpro_all": ["IPR003942", "IPR001111"], "interpro_used": ["IPR003942", "IPR001111"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want a protein that has the function: The protein is included in the ATPase OSCP/delta subunit family, which forms a critical component of the peripheral stalk in F-type ATP synthases, linking the F0 and F1 complexes to hold the catalytic core stationary against the torque of the central rotor. This family encompasses the delta subunit found in bacteria and chloroplasts as well as the mitochondrial oligomycin sensitivity conferral protein (OSCP). It is derived from Anaerolineae bacterium and is classified with UniProt keywords Cell membrane, Hydrogen ion transport, and Membrane. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 9444, 7579, 1034, 19, 9649, 5903, 3416, 16, 2154, 4952, 43, 4140, 4594, 1927, 1920, 5009, 19447, 1922, 48, 17, 2601, 4498, 8921, 1036, 16, 9486, 1920, 17930, 1930, 9154, 5048, 1942, 9038, 1920, 6804, 4728, 12563, 3316, 1920, 17601, 1927, 1920, 4101, 21787, 18, 2052, 3416, 21569, 1920, 9649, 5903, 2435, 1922, 4802, 1930, 24627, 1966, 2486, 1966, 1920, 4596, 15039, 14930, 3665, 3802, 7909, 7317, 2213, 12, 7579, 1034, 13, 18, 2176, 1977, 3595, 2037, 11381, 8419, 3336, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 2024, 3260, 16, 6201, 4755, 4860, 16, 1930, 3260, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MNNERMSDMKEKQNPAEAWRDDLKAISERLRDRDLVSPEQVRTLEALAGEFERLVEYEPAVALPLMATAFSAIEFERLSRQQAQAAGMMAWVRSAAPLTEEQRGLLKRRLRERFGEEFILRVEIDPSLIGGLVVRVKDQVFDGSVAGRLDALSERLRTAVEEQRSPALELEEAGE", "metadata": {"id": "A0A7C7UDG3", "cluster": 15851360, "interpro_all": ["IPR000711"], "interpro_used": ["IPR000711"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that will have the following function: It is part of the Stress Response Regulator family, which comprises transcription factors that regulate gene expression in response to environmental stresses, such as oxidative stress, and control metabolic processes including secondary metabolite production. These proteins typically utilize a C6 zinc finger domain to bind specific DNA motifs, playing essential roles in thiamine regulation, meiotic conjugation, and hyphal formation. Furthermore, the protein should contain 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 is present in Sarocladium strictum (Black bundle disease fungus) (Acremonium strictum) and is associated with UniProt keywords Nucleus and Transcription regulation.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 3071, 2644, 7888, 3416, 16, 2154, 12936, 3213, 2790, 1988, 5741, 2359, 2294, 1922, 2644, 1942, 4813, 11962, 16, 2427, 1966, 5163, 3071, 16, 1930, 2285, 4487, 4028, 2710, 4067, 9483, 3372, 18, 2144, 2697, 5745, 12561, 43, 12822, 7997, 8497, 3418, 1942, 4566, 2487, 2678, 8277, 16, 14797, 4415, 5456, 1922, 26901, 3640, 16, 16205, 14122, 16, 1930, 27125, 3337, 18, 3677, 16, 1920, 2213, 3066, 5531, 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, 1977, 2481, 1922, 9851, 5406, 21913, 9610, 1989, 12, 5010, 14142, 2573, 16461, 13, 12, 10428, 1987, 15414, 9610, 1989, 13, 1930, 1977, 2458, 1956, 20709, 11569, 5607, 1930, 3213, 3640, 18, 3], "output": "MASEPERRSPLSSSGGVQKHRACDECRSRKLACSKEPDGCSRCRREGLRCHYSVQKPMGRPRKRRNVDEEQQDERQRTSPLRPQKKDRNPQRQQNQYGQHRKPSADAVPFSNGDGLLPQAMPTNSHHITEFPGYDQSTIMSMDPSISFLEHQRPDENINFLDILPPDYAATTLSHDTPPILPTTESISQGSSQFGIDLGGVDLMGGIGFQHQSTLGSAPPRSAATRIMHNSFDRYMAKTWDSQPTDTLTSTTTPSSDAQGSSTTSTYLRPNPNISCGCLSSLYLTLDCLGNLPADIPAAIRTVRNASRVAHSTIRCEFCSSSALVDDATRPVPIQTFQNLMLLAALVPSACNAYAMILERVDQEADRARRNGEDLWFSFRDIGGHWGMEAEDGKDCLVMQSYNERKMPPDMWRAAMREIIRADVDGVSGVNSLDSQDQKGLRDVIKALEERSHRRHARMDAAFAMGHMPHPSVIIPPTSRPVPPEERHCMRVLDAARMALDNLVIA", "metadata": {"id": "A0AA39GU71", "cluster": 16137259, "interpro_all": ["IPR051711", "IPR036864", "IPR001138"], "interpro_used": ["IPR051711", "IPR001138"], "interpro_unused": ["IPR036864"]}, "task_type": "autoregressive"} {"instruction": "Here is the polypeptide chain function: The protein is classified under the Zona pellucida, ZP-C domain superfamily, which constitutes the C-terminal subdomain of the zona pellucida (ZP) polymerization module found in many secreted eukaryotic glycoproteins. While the associated ZP-N domain serves as a structural building block, the ZP-C domain mediates the specificity of interaction between subunits during the assembly of filaments essential for development, hearing, and immunity. These polymerization processes are often regulated by internal and external hydrophobic patches within the protein precursors. Additionally, the protein should include a ZP-N domain that forms the N-terminal structural component of the Zona pellucida module, adopting an immunoglobulin-like \u03b2-sandwich topology to facilitate protein polymerization. This domain is found in secreted eukaryotic glycoproteins, such as sperm receptors and uromodulin, where it drives the assembly of extracellular matrices essential for fertilization, hearing, and immunity. It has been detected in Podarcis muralis (Wall lizard) (Lacerta muralis) and is classified with UniProt keywords Transmembrane, Transmembrane helix, and Signal. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 26533, 1019, 7455, 6817, 1019, 16, 68, 1034, 17, 45, 3418, 13975, 16, 2154, 14879, 1920, 45, 17, 4262, 27517, 1927, 1920, 26533, 1019, 7455, 6817, 1019, 12, 68, 1034, 13, 11486, 9059, 2435, 1922, 3086, 8366, 10825, 16268, 18, 2679, 1920, 2458, 68, 1034, 17, 56, 3418, 10634, 1966, 43, 4346, 9086, 3367, 16, 1920, 68, 1034, 17, 45, 3418, 10412, 1920, 4896, 1927, 2835, 2192, 6991, 2409, 1920, 5957, 1927, 11855, 4415, 1958, 2740, 16, 8512, 16, 1930, 7611, 18, 2144, 11486, 4028, 2032, 3868, 4335, 2007, 4495, 1930, 5771, 7919, 12667, 2651, 1920, 2213, 10416, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 68, 1034, 17, 56, 3418, 1988, 4952, 1920, 56, 17, 4262, 4346, 4594, 1927, 1920, 26533, 1019, 7455, 6817, 1019, 9059, 16, 20478, 1925, 11837, 17, 3189, 161, 17, 18038, 13678, 1942, 6628, 2213, 11486, 18, 2052, 3418, 1977, 2435, 1922, 8366, 10825, 16268, 16, 2427, 1966, 6283, 4086, 1930, 14984, 7993, 3392, 16, 2597, 2176, 15435, 1920, 5957, 1927, 5329, 11618, 4415, 1958, 14493, 16, 8512, 16, 1930, 7611, 18, 2176, 2258, 2252, 3330, 1922, 10181, 5332, 1937, 6185, 19337, 12, 4821, 26932, 2211, 13, 12, 7511, 3062, 1019, 6185, 19337, 13, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 16, 9117, 7864, 16, 1930, 2733, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "METGRCLAVLLLTWSVVTAGASPVDDPGCTLHPVKNDKQVKMRYTTSRVTSGCVGRGPRDTNMEVHILNLKYNISQMPLTRFSVNVSAAKGGRKVVFVVNSNKHTVLNVTTGDHRLAFVTDKHKLTVIGFNKEINKTDLSSSNAEILNWTKTNYGGVSTFVELEDPRKINFQVNREPSTSEKCVPKSYFDAEPYLEAEFDSDNTKSCLDPTVHPGREAHIMWLQQSPPDSGTQAVDLNIKVTCSNGKPAKELTTLLVLKSHERMFWNIDQMPEYVKFMVSGKYSIKKITKEPINGTVLPDSKEGLIKEARDKDFAFIASYTEIPAAKSITLELVRDCGGKKTEVTTAPHSKISEPSKVVQGLMELCRPWKCTENAIEVALPKSLLERSQVDITEMTLEDPACRATDNMTHFVLKSIIEDCSTNLEGGIHAKNQLVLTLASHPDKIMVPFQCDLPEKLFLHLYQTPDFSSPSTTVVEVNKVTYVQVSFQTADGNSPLRLQDCYLQIPDQAAPQMLIRSGMPKSYSVEILNSPNTKTNRFSFIYKAEEQQRSTLSATLFCQVDRENQHGSYNASIKVMLKNPASLSRGLGIGTVLGITFGAFLIGVMLTATLWYIYSHTRPTAKMQPVSANPPASESSSTNHSIGSTQSTPCSTSSMA", "metadata": {"id": "A0A670JM69", "cluster": 18468968, "interpro_all": ["IPR042235", "IPR055356"], "interpro_used": ["IPR042235", "IPR055356"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should include a CdvA-like coiled-coil domain that functions as a structural motif associated with the CdvA cell division machinery. This region forms a coiled-coil structure likely involved in mediating protein-protein interactions or oligomerization essential for cell division. 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 occurs in Desulfurococcaceae archaeon and is annotated with UniProt keywords Coiled coil.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 3066, 3951, 43, 2464, 7302, 17, 3189, 17524, 17, 9121, 3418, 1988, 4088, 1966, 43, 4346, 5219, 2458, 1956, 1920, 2464, 7302, 2024, 8451, 10853, 18, 2052, 3031, 4952, 43, 17524, 17, 9121, 3170, 3205, 3286, 1922, 10239, 2213, 17, 2213, 3719, 2014, 17371, 4415, 1958, 2024, 8451, 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, 5110, 1922, 30311, 18916, 4879, 2437, 9914, 13470, 1916, 1930, 1977, 10633, 1956, 20709, 11569, 17524, 9121, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MVLMVDEVERYIGLEVKDPYGRKVGRIVAVYSEVDGSKINDDGELQIIPEWKAEALSLIKQLDKAKRRIKALVERNLSMLKIKAKEVKQMLKKRTNQLEDTIIQIGELSEKGYKAAIEALRQAKDKAVEEKEDIKKILNRIENLEAPATSETPILVQVLEGVTGVELEVNEDTFTTIPVSRIDDLYSKNEIPRHAYDEFRKKEKAITALKMSYLAEREPVEIKLPSSQSKPVETKPKV", "metadata": {"id": "A0A7J2KAM7", "cluster": 20963719, "interpro_all": ["IPR041461", "IPR011033"], "interpro_used": ["IPR041461", "IPR011033"], "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 classified under the The putative sensory transduction regulator YbjN family, which is found in Proteobacteria and functions as a potential sensory transduction regulator and general protein stabilizer. It acts as a multi-copy suppressor of coenzyme A-associated temperature sensitivity, suggesting a role in assisting CoA-A1 and stabilizing other labile proteins. It is present in Pseudomonadota bacterium and carries UniProt keyword assignments Signal.", "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, 1920, 6770, 6893, 8201, 7888, 21000, 1013, 1022, 3416, 16, 2154, 1977, 2435, 1922, 22266, 1930, 4088, 1966, 43, 2889, 6893, 8201, 7888, 1930, 3335, 2213, 13448, 1005, 18, 2176, 8016, 1966, 43, 2779, 17, 6983, 9241, 1927, 22051, 43, 17, 2458, 3449, 3802, 16, 3783, 43, 2770, 1922, 27840, 10027, 17, 8080, 1930, 14384, 2303, 22001, 2697, 18, 2176, 1977, 2481, 1922, 11520, 3947, 12595, 3857, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 2733, 18, 3], "output": "MGSWRQTLVLTGLFLGGPATAGALENTVQDFLEDDGWSPQTVDDGLYRAQYRGHDDTWTVVFQVLEAEDRVVVYSHLQRMIPPFRQKAIDDYITRANYGLPVGNFEINHETGEVRLKNSIDVEDGTLTRTMLSNLITANVHTMDRYLPGFNRVLFSNADPQLAINEVEEAPAPQDEPEVVQEDTYSDDNEYEWDPEPESEPESKVKVRGRINTGGGVYLNLLKVRSSRTSNQLGVETDVGYNYSFGKGFSGSTTINGHFTWGFNNKAIGTGVGLGSYIGWGLKFLYVSLGPEFWYDGYGDPERSAYYLPYAPGVGGAANLRLGIERFGAFSQFRGGMVFSESRQGEGLAFMDEAEMIFGLSVHLGVTIRAGYMIRWNVAEITRGVVFGTYF", "metadata": {"id": "A0A9E1IIQ7", "cluster": 23003845, "interpro_all": ["IPR019660"], "interpro_used": ["IPR019660"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to make a protein that can have this function: The protein is included in the Nucleotide-binding leucine-rich repeat (NLR)-like family, which is characterized by a multi-domain architecture involved in nucleotide binding and hydrolysis. These proteins typically contain an N-terminal purine nucleoside phosphorylase (PNP) domain that preferentially cleaves the N-glycosidic bond of ATP and dATP, alongside a C-terminal region featuring TRP repeats likely involved in protein-protein interactions. Additionally, the protein features a Nucleoside phosphorylase domain that catalyzes the phosphorolytic cleavage of purine and pyrimidine nucleosides, such as guanosine, inosine, and uridine, into their respective bases and sugar-1-phosphate molecules. This activity is essential for nucleotide salvage pathways and the metabolism of nucleosides as carbon and energy sources in both prokaryotes and eukaryotes. It is identified in Plectosphaerella cucumerina and is classified with UniProt keywords Signal. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 5489, 17, 2743, 12624, 17, 5536, 6865, 12, 10911, 13, 17, 3189, 3416, 16, 2154, 1977, 4378, 2007, 43, 2779, 17, 3418, 9335, 3286, 1922, 5489, 2743, 1930, 9128, 18, 2144, 2697, 5745, 5531, 1925, 56, 17, 4262, 19700, 18015, 12556, 2051, 12, 21623, 13, 3418, 1988, 10662, 23839, 1920, 56, 17, 7533, 12546, 5403, 1927, 4498, 1930, 2181, 1034, 16, 17764, 43, 45, 17, 4262, 3031, 29931, 7259, 9569, 3205, 3286, 1922, 2213, 17, 2213, 3719, 18, 4950, 16, 1920, 2213, 4075, 43, 18015, 12556, 2051, 3418, 1988, 17097, 1920, 3421, 6586, 6404, 1927, 19700, 1930, 21611, 18015, 1036, 16, 2427, 1966, 24870, 16, 10320, 2053, 16, 1930, 26104, 16, 2460, 2310, 7025, 11137, 1930, 9523, 17, 21, 17, 5413, 4206, 18, 2052, 2455, 1977, 4415, 1958, 5489, 17577, 3873, 1930, 1920, 4714, 1927, 18015, 1036, 1966, 5056, 1930, 3844, 5777, 1922, 2321, 28149, 1930, 15021, 18, 2176, 1977, 2899, 1922, 6483, 2341, 2609, 29164, 5870, 18242, 29419, 4058, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MHFNALFLLSALVPTACTFQFLRPDTSKPFNYSEPVVFEWSPDENLQVPHSSMRWLKLHFHSTGVWPISDAIDWRGNITSHVWDAPEWFEYMEDVDQQLFDGKRNFFSANFYSSPNFTFIESAMSIETDKFEIVGYPHLSAGASGASARLSVGVALAIAASALSRLSKFAMTICQFPGRRAFQIGIICALPLEAEAVLAVFDRFWDDRGQVIGKAPGDQNIYTSGRIGHHNVVLVHMPGKGKAYAASSAANLRLSFPNIKLVLVVGICGAVPASVARDEVILGDVMISEGIVQYDLDRQLQGHSQQKAKAPDMDVRATLARLQSEGGHKALLSGTSAYLKGLQKMPHLRAAYPGAQQDRLFQPTYNHRSPNMTCEECGCNGPTVFSRTLYRETSPIPSVHFGLIASGDTVMKSAMHRDAIAKREGVIAFEMEGAGMWDVLFPSVVIKGAADYADSHKSKMWQRYAAATAAACARAFLDNWHPVD", "metadata": {"id": "A0A8K0X6B2", "cluster": 23605458, "interpro_all": ["IPR053137", "IPR000845", "IPR035994"], "interpro_used": ["IPR053137", "IPR000845"], "interpro_unused": ["IPR035994"]}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein is associated with the Predicted HD phosphohydrolase family, which likely functions as a metal-dependent phosphohydrolase mediated by an HDc domain containing the conserved \"HD\" motif. It is expressed in Calditrichota bacterium. 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, 4396, 4515, 8078, 8535, 24605, 1021, 3416, 16, 2154, 3205, 4088, 1966, 43, 6048, 17, 3100, 8078, 8535, 24605, 1021, 3434, 2007, 1925, 4515, 1030, 3418, 3165, 1920, 5305, 6, 4515, 6, 5219, 18, 2176, 1977, 3198, 1922, 2570, 7408, 3319, 10647, 3857, 14061, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MQIDLNERQALLDAWHHLLTPYVPKPAAREKLFGSLAEQYSHPTRHYHDLRHIREMLAFLEPEHDARRVPAAVQFAVWFHDVVYNTLKDDNETKSAEFAGKLLSRIGAGEALIATVKSLILATHEHRPLLGSDDEACFLDADLAILAAPPERYRQYSKEIRQEYYWVPAFMYGRKRIAILEEFLQRERIFLTPRMAGAPEQQARENLRWEIESLEG", "metadata": {"id": "A0A958HUD1", "cluster": 25155873, "interpro_all": ["IPR009218"], "interpro_used": ["IPR009218"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein should include a Cation-transporting P-type ATPase, C-terminal domain that constitutes the conserved C-terminal region of membrane-bound enzymes responsible for the ATP-driven translocation of cations, including H+, Na+, K+, and Ca2+. This domain functions as part of the catalytic alpha chain in P-type ATPases, utilizing the energy of ATP hydrolysis to drive ion transport across cellular membranes. In addition, the protein should include a P-type ATPase, haloacid dehalogenase domain that functions as the catalytic core of membrane-bound transporters, coupling ATP hydrolysis to the active transport of ions and phospholipids. It mediates the characteristic E1-E2 conformational changes required to translocate diverse substrates, including protons, alkali metals, and heavy metals, across bacterial and eukaryotic membranes. In addition, the protein should have 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. It originates from Candidatus Uhrbacteria bacterium RIFCSPLOWO2_02_FULL_48_12 and is classified with UniProt keywords ATP-binding, Translocase, and Transmembrane helix.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 3066, 3951, 43, 9976, 17, 27038, 58, 17, 2601, 9444, 16, 45, 17, 4262, 3418, 1988, 14879, 1920, 5305, 45, 17, 4262, 3031, 1927, 3260, 17, 4124, 5038, 5061, 1958, 1920, 4498, 17, 6446, 7849, 1927, 16525, 16, 2710, 50, 15, 16, 4049, 15, 16, 53, 15, 16, 1930, 5497, 15, 18, 2052, 3418, 4088, 1966, 3131, 1927, 1920, 6804, 4595, 4659, 1922, 58, 17, 2601, 28132, 16, 10232, 1920, 3844, 1927, 4498, 9128, 1942, 9265, 4755, 4860, 3436, 3689, 5726, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 58, 17, 2601, 9444, 16, 23226, 29272, 2028, 7289, 2404, 2051, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 3260, 17, 4124, 10538, 16, 7590, 4498, 9128, 1942, 1920, 3500, 4860, 1927, 6982, 1930, 15619, 18, 2176, 10412, 1920, 6293, 11123, 17, 6602, 8523, 2840, 3414, 1942, 26377, 6445, 6249, 16, 2710, 15948, 16, 25178, 11570, 16, 1930, 7881, 11570, 16, 3436, 4543, 1930, 10825, 5726, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 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, 2176, 22970, 2037, 14550, 1031, 1957, 23476, 16007, 2422, 2126, 14061, 12424, 2792, 2030, 1971, 5265, 41, 5725, 41, 4125, 41, 3427, 41, 2369, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 12930, 2051, 16, 1930, 9117, 7864, 18, 3], "output": "MVVGISAVVIFLIGLFEGLAWIDVFTTAVAVAVSAIPEGLVLKRQGLVRRPIAAETLGSVTVICSDKTGTLTEGALANEAVREDINGEYRIHGEATDRAKLDYALSHGFLPFDSEAKYIAAWHDDVESPGSQKTIHCFVSGRLISESDRREIIKNIEDLAAHGYRLDQALHQLVINLTWQGLVAVRDPIRADVKDTIRLTRRMAIGRELGFRTGTENVVEGLQLDQYSDDDLAKAIRRIDICVREAVAMTGDGVNDAPALKAADIGVAVGSGAIREGRIAFDNIKKVTVLLLSGSFTAFLLIMGNLVENGLPNFALAFEPGESDVMDRRVFGIALLRDFLLIGVFYWYYVRWGGDLAYVSQPIWREDFFDNWYLLFSIGLGFVMMIPAIYLPVMDVCLIEVVKFYYNRRVDTRNAVAVSAALSVVLAVSTQRIMMKVEKFMPDGDEQKALLSLLDLATVNAAYPRRAGAPEILLEKSSQHGDIGLAHKVISGEIDPDNAGVRLIMVTGDHRLTAVNPEHKLRIVKALLKNGATDVTKEAADLVLLNDGLATIVASLVLGLPLPLTAVQILWPISRSAPVLDSAGKWIRTIVFALLSTDSLFYIFSIKTFNRFLGTIPLSARDAAVVIGIALF", "metadata": {"id": "A0A1F7V9Y5", "cluster": 25783563, "interpro_all": ["IPR006068", "IPR023299", "IPR018303", "IPR023298", "IPR036412", "IPR023214", "IPR001757", "IPR044492"], "interpro_used": ["IPR006068", "IPR044492", "IPR018303"], "interpro_unused": ["IPR001757", "IPR023214", "IPR023298", "IPR023299", "IPR036412"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein can be placed in 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. In addition, the protein belongs to 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. It is native to Candidatus Rokuibacteriota bacterium and is associated with UniProt keywords Signal.\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, 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, 1922, 2459, 16, 1920, 2213, 14440, 1942, 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, 2176, 1977, 6196, 1942, 14550, 1031, 1957, 3039, 1040, 15444, 7972, 2341, 18842, 7336, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 2733, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MIRVLRHVGVALMFVAISASPLIAVAQVPAPPPPYGAPIVDSGGHLVSLQRLDNTQYGSIDVAKGKATTAVSFRRPTKALEDLEGGVPIVVDGKIIGGIGVSGVLSSQDAQIARAGADSLKTFDQAQKAMAAAQAEAKKNNWNVVIAIVITGGGAGLRILKLEGATP", "metadata": {"id": "A0A2V6TSD7", "cluster": 26003105, "interpro_all": ["IPR052517", "IPR005624", "IPR038084"], "interpro_used": ["IPR005624", "IPR052517"], "interpro_unused": ["IPR038084"]}, "task_type": "infilling"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein can be placed in the Saposin-like superfamily, which encompasses lipid-binding proteins and domains characterized by a five-helix bundle topology stabilized by three conserved disulfide bridges. Members include lysosomal sphingolipid activators, antimicrobial peptides, and plant proteases, which often utilize lipid-induced conformational changes and oligomerization to facilitate membrane interactions. Furthermore, the protein should include a Saposin B type domain that adopts a four- or five-helix bundle structure stabilized by three conserved disulfide bridges and facilitates interaction with lipids and membranes. It is found in saposin-like proteins (SAPLIPs) where it serves diverse roles, including acting as a cofactor for lysosomal sphingolipid hydrolases, reducing lung surface tension, or functioning as an antimicrobial effector. It is produced by Trichostrongylus colubriformis (Black scour worm) and features UniProt keywords Disulfide bond and Signal.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 9235, 5872, 17, 3189, 13975, 16, 2154, 21569, 4486, 17, 2743, 2697, 1930, 4682, 4378, 2007, 43, 3628, 17, 7864, 14142, 13678, 12017, 2007, 2559, 5305, 11830, 18142, 18, 4678, 3951, 12097, 13502, 16113, 15497, 16, 8003, 5320, 16, 1930, 4496, 12447, 16, 2154, 3868, 12561, 4486, 17, 2719, 8523, 2840, 1930, 17371, 1942, 6628, 3260, 3719, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 9235, 5872, 44, 2601, 3418, 1988, 24032, 43, 3006, 17, 2014, 3628, 17, 7864, 14142, 3170, 12017, 2007, 2559, 5305, 11830, 18142, 1930, 11374, 2835, 1956, 8238, 1930, 5726, 18, 2176, 1977, 2435, 1922, 9235, 5872, 17, 3189, 2697, 12, 9235, 13567, 13, 2597, 2176, 10634, 6445, 5456, 16, 2710, 8290, 1966, 43, 15155, 1958, 12097, 13502, 16113, 30337, 16, 5526, 3614, 3154, 10146, 16, 2014, 7295, 1966, 1925, 8003, 7917, 18, 2176, 1977, 4152, 2007, 10477, 17414, 2188, 2199, 1957, 2503, 2255, 3027, 2231, 1937, 12, 5010, 2160, 2257, 11055, 13, 1930, 4075, 20709, 11569, 11830, 5403, 1930, 2733, 18, 3], "output": "MKLHVLLLLVFCMVINVSAILSVKPFCKMCTMVIKDVHDLVTEGANIETAARQKCKEKTPKLMHSFCKILLSNVSKMEAQIKTESPKEVCSLLHLCKSSSSLALRPPTAEKGTQTDELIDEQTQDTINN", "metadata": {"id": "A0AAN8FC17", "cluster": 27101623, "interpro_all": ["IPR011001", "IPR008139"], "interpro_used": ["IPR011001", "IPR008139"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has this function description: The protein possesses a Prokaryotic N-terminal methylation site, which directs the methylation of a conserved phenylalanine residue. This motif is typically located at the N-terminus of pilins and proteins associated with secretion pathways. It is derived from Vulcanimicrobiota bacterium and is annotated with UniProt keywords Membrane, Transmembrane, and 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, 14465, 43, 21545, 56, 17, 4262, 5547, 3200, 16, 2154, 28351, 1920, 5547, 1927, 43, 5305, 17388, 6181, 18, 2052, 5219, 1977, 5745, 4810, 2019, 1920, 56, 17, 7822, 1927, 7547, 2925, 1930, 2697, 2458, 1956, 5512, 3873, 18, 2176, 1977, 3595, 2037, 7343, 8337, 1980, 1935, 15129, 3940, 3857, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MKRRESGFTLLEVLVAGALGLMLLGLLHQFLVPIIETSSRVTAEEHLTDQGLLVLSRLSSELAESTPGSLSFSGPETNQRRVVGVTRRDGVSAEGRKLWRKEASVYFWDQQSGQVRWRSWPPAPPDFGLIPRVDRPLVFSSDELNTLSNTVGGSKLLASDVIEFQPFVDWPPTYSVTSRIVLEKKVPGERDAHCEWSRVTAFKN", "metadata": {"id": "A0A956SXX6", "cluster": 28160984, "interpro_all": ["IPR012902"], "interpro_used": ["IPR012902"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein possesses a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. Also, the protein possesses a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. It has been detected in Streptomyces sp. NBC_00334.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 14465, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2222, 16, 1920, 2213, 14465, 43, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 2176, 2258, 2252, 3330, 1922, 22874, 2056, 18, 8789, 1030, 41, 10438, 4857, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MAAKPVDRRAKRLVVLVSGSGRDGIEGLARAERAGLTTFVRKVRDYGTRQEWDAALTDGKEFLARFGGRFVNTHPALLPSFPGAHGVRDALQGVVEVRDEDYEDEGAALHERIKVVGRLARNGYRIEGRKVVIQTNLQAILDEIAAAGAEVYGAEVVAVGADAVAAHEPDLVVSAGFMKIVAYGARVTGCTVHFVDDGVDTGPIIAEVERRLLVD", "metadata": {"id": "A0AAU4J263", "cluster": 7312399, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR002376", "IPR001555"], "interpro_unused": ["IPR004607", "IPR036477"]}, "task_type": "infilling"} {"instruction": "What would the protein sequence be if I wanted a protein that could perform the following function: The protein should contain 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 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. In addition, the protein contains 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. It is found in Halanaerobium sp. T82-1.", "tokenized_instruction": [2, 4663, 2962, 1920, 2213, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 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, 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, 1922, 2459, 16, 1920, 2213, 5461, 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, 2176, 1977, 2435, 1922, 4217, 7241, 6506, 3821, 1989, 2056, 18, 30172, 1028, 17, 21, 18, 3], "output": "RADDLSGILNGISYDKFDPETNKNLAVRFSKGEVDKKIANKVHIQQKMGLEVNGDKPLIGFISRLVEQKGLDLVQAVFDEIMATGAQFLILGTGQREYEEFFKAKQLEYPDDLSVNIKYDAQLADQIYAGSDMFLMPSRFEPCGLSQLISFRYGTIPVVRETGGLNDTVVAYNEETGEGTGFSFANYNAHDMLHTIERAVSFYDQKGIWNKLVTRVMNLDYSWHNSAQKYSELYRQLNGDEGQKLLQKGDESEVQIKVYEPDVKPKPEVKPKKTKASKKISINQAAASELAELPGIGDAYAERIVNYREQNGDFTKKSDLIKVKGIGKKKYQKISKLLTL", "metadata": {"id": "A0A139D4Q6", "cluster": 4618306, "interpro_all": ["IPR004509", "IPR001296", "IPR003583", "IPR010994"], "interpro_used": ["IPR003583", "IPR001296", "IPR004509"], "interpro_unused": ["IPR010994"]}, "task_type": "autoregressive"} {"instruction": "I need a polypeptide chain that performs the following role: The protein features a Mur ligase, C-terminal domain that facilitates the sequential addition of amino acids to UDP-N-acetylmuramic acid during bacterial peptidoglycan biosynthesis. Adopting a dihydrofolate reductase-like fold, this domain is responsible for binding the incoming amino acid substrate in enzymes such as MurC, MurD, MurE, and MurF, as well as in folylpolyglutamate synthase and cyanophycin synthetase. Furthermore, the protein is associated with the UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase family, which catalyzes the ATP-dependent addition of meso-diaminopimelate (or L-lysine in some species) to the UDP-N-acetylmuramoyl-L-alanyl-D-glutamate precursor during the biosynthesis of bacterial peptidoglycan. Also known as MurE, these enzymes typically feature a three-domain structure comprising an N-terminal substrate-binding domain, a central ATP-binding domain, and a C-terminal domain responsible for binding the incoming amino acid. Furthermore, the protein has a Mur ligase, central domain that functions as the ATP-binding catalytic module in the MurC, MurD, MurE, and MurF enzymes responsible for the stepwise assembly of the bacterial peptidoglycan stem peptide. This domain shares structural similarity with ATPase domains and is also present in folylpolyglutamate synthetase and cyanophycin synthetase, where it drives ATP-dependent ligation reactions for folate metabolism and cyanophycin storage. It is expressed in Thioalkalivibrio sp and carries UniProt keyword assignments Cell division, Cytoplasm, and Cell cycle. 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, 4075, 43, 6185, 11905, 16, 45, 17, 4262, 3418, 1988, 11374, 1920, 9454, 2459, 1927, 3835, 4576, 1942, 18500, 17, 56, 17, 6894, 23010, 29085, 1935, 2687, 2409, 4543, 24183, 8132, 18, 20478, 43, 11842, 27851, 11386, 17, 3189, 3728, 16, 2052, 3418, 1977, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 4510, 1922, 5038, 2427, 1966, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 16, 1966, 2486, 1966, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 8921, 1930, 26898, 25818, 3665, 18185, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 18500, 17, 56, 17, 6894, 23010, 29085, 10921, 8056, 16323, 1024, 17, 46, 17, 7627, 17, 22, 16, 26, 17, 21121, 2011, 11593, 5148, 2057, 11905, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 2459, 1927, 23577, 17, 21121, 2011, 11593, 5148, 2057, 12, 2014, 54, 17, 9082, 1922, 2673, 3038, 13, 1942, 1920, 18500, 17, 56, 17, 6894, 23010, 29085, 10921, 17, 54, 17, 10527, 16323, 1024, 17, 46, 17, 7627, 7897, 2409, 1920, 8132, 1927, 4543, 24183, 18, 2222, 3171, 1966, 6185, 1021, 16, 2144, 5038, 5745, 5961, 43, 2559, 17, 3418, 3170, 10351, 1925, 56, 17, 4262, 4510, 17, 2743, 3418, 16, 43, 4101, 4498, 17, 2743, 3418, 16, 1930, 43, 45, 17, 4262, 3418, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 18, 3677, 16, 1920, 2213, 2258, 43, 6185, 11905, 16, 4101, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 6804, 9059, 1922, 1920, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 5038, 5061, 1958, 1920, 13846, 5957, 1927, 1920, 4543, 24183, 4402, 4207, 18, 2052, 3418, 16495, 4346, 6796, 1956, 9444, 4682, 1930, 1977, 2222, 2481, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 1930, 26898, 25818, 3665, 18185, 16, 2597, 2176, 15435, 4498, 17, 3100, 11102, 5298, 1958, 13761, 4714, 1930, 26898, 25818, 3665, 7451, 18, 2176, 1977, 3198, 1922, 15331, 5135, 12498, 2165, 2377, 3940, 2056, 1930, 16252, 20709, 11121, 2538, 18306, 2024, 8451, 16, 5239, 16, 1930, 2024, 4048, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MTASALPLSRLLPERQGLPDVAVNDLSMSSLGLVPGAAFVALRGTRAHGLDFASRALEQGAVAVLWDEGNGEPPPDPRFVHVPQLRRRLPELARRLFGAWPEERPLIAITGTDGKTSVSHQLSTALTHLGLRCAVIGTLGVGTPETLSPTGHTTPDVLELHRHLAELARAGFDAVALEASSHALVQGRLEGLRPRVAVLTHLGRDHLDYHGSLAAYADAKALLFRTHGLHAMVLNLDDELGRRLLAEHCTRPGQPGCWTYGQHDAPDLPGARERHIQARNINASVQGLRFEVQVGPFRGQVNTPLFGAFQVANLLATLGTLLALGQPPARAFAALSAVRGVPGRMERFIKAGGPVLVVDYAHTARALESVLLALRPHVVGRLWVVFGCGGNRDRGKRPAMGEVAARLSDEVIVTDDNPRDESPAAIRRAVLDGCAGPAPVREIGDRAQAIRTAMAEAEAGDIVLIAGKGHEAIQIIAGVEHPFSDRELALRLTAGGGQV", "metadata": {"id": "A0A6I7N1A6", "cluster": 12723925, "interpro_all": ["IPR036565", "IPR004101", "IPR036615", "IPR013221", "IPR000713", "IPR035911", "IPR005761"], "interpro_used": ["IPR004101", "IPR005761", "IPR013221"], "interpro_unused": ["IPR035911", "IPR036565", "IPR000713", "IPR036615"]}, "task_type": "autoregressive"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein should contain a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. Also, the protein should include a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. It has been characterized in Syntrophomonas sp. 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, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2176, 2258, 2252, 4378, 1922, 14913, 2789, 10480, 2056, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MIQIHPAGRLKLAILASGRGSNFDAIYQAIQDGRLNADIQVLISDKSQSMALQKARQRDIPAYFLDPGAFARQTDYEKEMVGLLRKHQVEIVVLAGYMRLVGQVMLEEYPHRIVNIHPALLPAFKGLHAQRQALEYGVKFSGCTVHLVDEGMDTGPIIMQKVVPVYDDDDEDRLTERILEQEHQIYWQSLQMLAEGKLYIQGRRIVTKL", "metadata": {"id": "A0A3B8HZL6", "cluster": 27698652, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR001555", "IPR002376"], "interpro_unused": ["IPR004607", "IPR036477"]}, "task_type": "autoregressive"} {"instruction": "What would the protein sequence be if I wanted a protein that could perform the following function: The protein should contain 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. Furthermore, the protein possesses a Methyl-accepting chemotaxis protein (MCP) signalling domain that functions as a highly conserved transduction module within bacterial receptors to mediate chemotaxis. It responds to changes in the concentration of environmental attractants and repellents by transmitting signals to the downstream histidine kinase CheA to regulate swimming behavior. Also, the protein belongs to the Chemotaxis methyl-accepting receptor family, which mediates bacterial chemotaxis by responding to environmental attractants and repellents to modulate swimming behavior. These receptors detect diverse chemical signals, such as amino acids and sugars, to regulate cellular motility in response to concentration gradients. It originates from Clostridium botulinum B str. Osaka05 and is associated with UniProt keywords Transmembrane, Membrane, and 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, 3066, 5531, 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, 3677, 16, 1920, 2213, 14465, 43, 4963, 17, 26170, 16884, 2213, 12, 11942, 13, 8076, 3418, 1988, 4088, 1966, 43, 3626, 5305, 8201, 9059, 2651, 4543, 4086, 1942, 8265, 16884, 18, 2176, 20575, 1942, 2840, 1922, 1920, 3110, 1927, 4813, 24670, 2356, 1930, 3699, 11560, 2039, 2007, 27622, 4771, 1942, 1920, 5863, 13873, 4016, 10003, 1019, 1942, 5741, 15781, 3379, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 16884, 4963, 17, 26170, 3148, 3416, 16, 2154, 10412, 4543, 16884, 2007, 10884, 1942, 4813, 24670, 2356, 1930, 3699, 11560, 2039, 1942, 8480, 15781, 3379, 18, 2144, 4086, 4277, 6445, 4399, 4771, 16, 2427, 1966, 3835, 4576, 1930, 15592, 16, 1942, 5741, 3689, 9254, 1922, 2644, 1942, 3110, 12741, 18, 2176, 22970, 2037, 21156, 27326, 44, 2114, 18, 25154, 15264, 1930, 1977, 2458, 1956, 20709, 11569, 9117, 16, 3260, 16, 1930, 9117, 7864, 18, 3], "output": "MLKNLKIKTTFYILLAIMIMSMIIIGTFCLNSLYSINKQIHTNINSEIIRTKSIDTARSAQVHFKKQVQEWKNLLIRGNDPNKFQKYLSGFNDEEKATHKDLLSLKDLMKQQGLDTSKVDEAIKTHEELGGKYKEALKSYDWKNSNSLHVVDTLVNGIDRAPTDNIDAIVQQIQDYSTETLKYVQDSSEKKFKKELTLAIIAITLITAICLILTITFVKKIINSINILKDKISDLAEKDGDLTVKLPIIGKDELGLVSEKFNIFIDKLRENITNAANCTFLLTDGCNTLTESTSDVNTSMDQITCTVSEIAKGNQQVANEIVSACSNLDEISKHANTTAKDMTEIIKQYEETNESINIGKDALLEQHSHMDEINIIINNVLVAAKTLEEKSNSVNTIVSTIGSIAEQTNLLALNAAIEAARAGEGGKGFAVVAEEVRKLAESSALSTKEVYSNVQAMQDAVKQTIIHINDANDRLEKQEYIVNKTDTSFNEILEQISSIMDHTKQAGERMNEVTDQVGSLNSSIQNISSIAEETAASTEEALASTEEQSSSIDNVNKLAFEFNKLANDLKGVVNSFKYE", "metadata": {"id": "A0A0S6U316", "cluster": 413322, "interpro_all": ["IPR004090", "IPR003660", "IPR004089"], "interpro_used": ["IPR003660", "IPR004089", "IPR004090"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has the following function: The protein is categorized in the Vexin family, which is required for neurogenesis in the neural plate and retina. Members of this family, including *Xenopus* Vexin and human C8orf46, are transiently expressed in differentiating progenitors within the developing central nervous system. It is derived from Pleurodeles waltl (Iberian ribbed newt) and corresponds to UniProt keyword Cell membrane, Membrane, 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, 10234, 1922, 1920, 3428, 10960, 3416, 16, 2154, 1977, 3414, 1958, 13967, 1922, 1920, 5181, 5500, 1930, 9544, 18, 4678, 1927, 2052, 3416, 16, 2710, 14, 14545, 14, 3428, 10960, 1930, 2616, 19189, 12728, 7772, 16, 2032, 12145, 3198, 1922, 14252, 11561, 2651, 1920, 5130, 4101, 7580, 2433, 18, 2176, 1977, 3595, 2037, 6483, 18916, 16878, 1918, 16567, 14598, 12, 6180, 18339, 1022, 5216, 19011, 2814, 1031, 13, 1930, 8852, 1942, 20709, 11121, 2538, 2024, 3260, 16, 3260, 16, 1930, 5607, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MNRIYSRGEDNLEVFTTVMSPKMCRASRGRTHRSPQTLRKSVAAASDVIHFWPDELLPCPSELIDILCRDDEVWRFGRLQNGQKVLFPVKCAAKKRDISETRIAKSRGDHSEGNSAESKAPSAIPDMMTQRTPVQETPQDGPLTEQPVECRHRNTTEEQAQPEGTEASFLLERMPSGTSSILKKMWMRHKKKAGYLGAKNGAFEAD", "metadata": {"id": "A0AAV7UTB7", "cluster": 1926554, "interpro_all": ["IPR040470"], "interpro_used": ["IPR040470"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that can perform the following function: The protein should include a Cold-shock protein Csp, DNA-binding domain that facilitates cellular adaptation to low temperatures by preferentially binding poly-pyrimidine regions of single-stranded RNA and DNA. It regulates ribosomal translation, mRNA degradation, and transcription termination, and may assist in prokaryotic nucleoid organization. In eukaryotes, this domain functions within Y-box proteins to bind promoter sequences and regulate gene expression. Furthermore, the protein contains a Cold-shock domain conserved site that binds single-stranded nucleic acids to act as an RNA chaperone, facilitating post-translational gene regulation and adaptation to low temperatures. This region adopts a five-stranded antiparallel $\\beta$-barrel structure similar to the OB-fold and utilizes conserved RNP-1 and RNP-2 motifs to rescue RNAs from unproductive folding states. Furthermore, the protein belongs to the Cold shock domain-containing protein family, which binds DNA and RNA to regulate gene expression, particularly during cellular responses to cold stress. Members facilitate diverse nucleic acid-processing activities including transcriptional activation, mRNA stabilization, translational repression, and DNA repair. Additionally, these proteins contribute to cell viability at low temperatures, persister cell formation, and the sorting of RNAs into exosomes. It is identified in Kineococcus xinjiangensis and corresponds to UniProt keyword Cytoplasm.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 6685, 17, 7418, 2213, 16369, 16, 2678, 17, 2743, 3418, 1988, 11374, 3689, 7810, 1942, 2330, 7750, 2007, 10662, 2743, 4286, 17, 21611, 3451, 1927, 2957, 17, 10338, 3146, 1930, 2678, 18, 2176, 7014, 11196, 6410, 16, 3616, 4877, 16, 1930, 3213, 12462, 16, 1930, 2278, 6589, 1922, 21545, 2797, 2642, 5901, 18, 1922, 15021, 16, 2052, 3418, 4088, 2651, 67, 17, 5758, 2697, 1942, 4566, 4465, 3709, 1930, 5741, 2359, 2294, 18, 3677, 16, 1920, 2213, 5461, 43, 6685, 17, 7418, 3418, 5305, 3200, 1988, 6876, 2957, 17, 10338, 11079, 4576, 1942, 4033, 1966, 1925, 3146, 14044, 16, 12440, 2753, 17, 8414, 2359, 3640, 1930, 7810, 1942, 2330, 7750, 18, 2052, 3031, 24032, 43, 3628, 17, 10338, 28892, 8, 38, 4666, 8, 17, 19560, 3170, 2551, 1942, 1920, 2384, 17, 3728, 1930, 18127, 5305, 24767, 17, 21, 1930, 24767, 17, 22, 8277, 1942, 10162, 8624, 2037, 7861, 11483, 9292, 10328, 4376, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 6685, 7418, 3418, 17, 3165, 2213, 3416, 16, 2154, 6876, 2678, 1930, 3146, 1942, 5741, 2359, 2294, 16, 4443, 2409, 3689, 3387, 1942, 6685, 3071, 18, 4678, 6628, 6445, 11079, 2687, 17, 4587, 4209, 2710, 5224, 2936, 16, 3616, 10281, 16, 8414, 10084, 16, 1930, 2678, 5059, 18, 4950, 16, 2144, 2697, 4672, 1942, 2024, 6432, 2019, 2330, 7750, 16, 5762, 1915, 2024, 3337, 16, 1930, 1920, 11404, 1927, 8624, 2460, 12466, 18, 2176, 1977, 2899, 1922, 5838, 8256, 28624, 20124, 8134, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 18, 3], "output": "MAQGTVKWFNAEKGFGFITVDDGGTDVFVHWSAIEMDGYRSLDEGQRVQFEVGQGQKGPQAEAVRAV", "metadata": {"id": "A0A2S6ITN7", "cluster": 6136193, "interpro_all": ["IPR012156", "IPR050181", "IPR011129", "IPR019844", "IPR002059", "IPR012340"], "interpro_used": ["IPR002059", "IPR019844", "IPR050181"], "interpro_unused": ["IPR012340", "IPR012156", "IPR011129"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein contains 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. Also, the protein carries a Fucolectin tachylectin-4 pentraxin-1 domain that functions as a carbohydrate-recognition module, specifically binding fucose to support innate immune responses. Found in secretory proteins such as eel fucolectins and frog pentraxins, this domain facilitates the detection of cell surface markers and potential pathogens through hemagglutination activity. Furthermore, the protein should contain a Domain of unknown function DUF1549 domain that is functionally uncharacterized but is typically found associated with cytochrome c-like domains, including the Planctomycete cytochrome c domain. It is native to Planctomycetaceae bacterium and is linked to UniProt keywords Calcium.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 5461, 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, 2222, 16, 1920, 2213, 16252, 43, 15423, 7794, 2268, 12762, 6752, 2341, 1921, 17, 24, 9412, 5524, 10960, 17, 21, 3418, 1988, 4088, 1966, 43, 10590, 17, 5708, 9059, 16, 4475, 2743, 15423, 2217, 1942, 3373, 8539, 3743, 3387, 18, 2435, 1922, 11518, 2697, 2427, 1966, 11150, 1024, 15423, 7794, 21881, 1930, 23707, 9412, 5524, 10960, 1036, 16, 2052, 3418, 11374, 1920, 3805, 1927, 2024, 3154, 4432, 1930, 2889, 7741, 2596, 20751, 1943, 2455, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 3418, 1927, 5435, 2347, 4855, 5739, 10883, 3418, 1988, 1977, 9346, 24528, 2308, 1977, 5745, 2435, 2458, 1956, 9387, 45, 17, 3189, 4682, 16, 2710, 1920, 4720, 2341, 13386, 11555, 9387, 45, 3418, 18, 2176, 1977, 6196, 1942, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 5016, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MNPLLLMFLTTLSGADPVSFSKQIRPVLADRCYACHGPDAAQRKADLRLARLSSDDPEYQMPPPASKLTVSQEEVALIRRWIDQGAQWEQHWPRNEIDRFVLAGLEAAGLQPTRPALKAHWLRRVTLDITGLPPTLAELAGFLSDASAQSREKVVDYGDTDGLFEDHPRSIYPWRDWVVGAFNANLPYDQFITWQLAGDLLPNATVAQRVADYRVKYLVDRVNTTATSMLGLTLECAQCHDHKYDPMTQREYYQFAGFFNGLVGNRRLKRIDSKVPELLETLQSTPPQLATDFEQWLDELKKPVSWKKASLVPGANGSQPIRGRYVRVALPAGATGFLTLSEVEVFSRGVNVARLGNATQSSVGYRAPASKALEVDLGDAFPVDSVAVWNRTDCCPERLDRASIQLLDAARQTVAQRVLSKAGTRNALPQGAVDTVLQWESRHADVIQVVKAHHVQGEKKTELKFQGDGTLKLKGRPMLLALATPLKMADGEYLELRATLPREKEKRLAHYRTLWPGFAPVRKHLKELQGEKKTIESSAALTMVAAEMASPRAPPASIMPFADTLPRNRLGLAQWLTQRKNPLTARVVVNRYWQLLFGTGIVKTSEDFGTQAVDFMDSGWDVKALIGKIVLSATYQQASTQTAEKQRLDPDNRLLGRGPRRRLPAEAIRDHALAANAIGAANAKFTESKGASLYRRSLYTYWKRQIPAANMRILGADGRTKCFVEAARVLAARAMRRGGSRPGEWLAFAFRLATSRQPTEVERQILLSENAYLTQAARDAQPGLDAAQWAACAAVCSLILNLDESISASDQETPIRSVLVAGDADSSELLAFVAPTRAPLPTVEDGAWRLLKSAAYGERMAQEWLDVARTGYIRNNPTSNEGGIIDEGNTKGASAPTLRDYTPLQVGALKVDAGWWLRSMPVASEADGNRDGKFSSCSCTNEERDAWWGAQVENVEFRLQPEPGNLVVIRCGSNAAFRVATSGSAGAVDNRILVRGEYDRPGQTVETGERPSHAALLDWLISGLLVQQLGGPGVNPYQPAELFGRTRRERTNTPLQALVLLNDPQYADRVREFRGNKALA", "metadata": {"id": "A0A2E7L3G0", "cluster": 7892618, "interpro_all": ["IPR036909", "IPR011429", "IPR011444", "IPR022655", "IPR006585", "IPR008979"], "interpro_used": ["IPR011429", "IPR006585", "IPR011444"], "interpro_unused": ["IPR022655", "IPR036909", "IPR008979"]}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein features a Metal-dependent hydrolase HDOD domain that functions as a phosphodiesterase involved in bacterial signal transduction, specifically catalyzing the hydrolysis of cyclic diguanylate (c-di-GMP). Often found associated with regulatory domains such as GGDEF and EAL, it acts as an output module within larger signaling proteins to regulate nucleotide metabolism. Furthermore, it is part of the EAL domain superfamily, which functions as a diguanylate phosphodiesterase responsible for the degradation of the bacterial second messenger cyclic di-GMP. It utilizes conserved acidic residues for metal binding and often cooperates with GGDEF domains to regulate cell surface adhesiveness. In addition, the protein is grouped in the Signal transduction c-di-GMP phosphodiesterase, EAL/HD-GYP domain-containing family, which functions in bacterial signaling cascades to regulate levels of the second messenger cyclic diguanylate (c-di-GMP). Members typically feature a catalytically active EAL domain that hydrolyzes c-di-GMP, paired with a modified, likely inactive HD-GYP domain lacking conserved metal-binding residues. These proteins often act downstream of two-component systems to modulate processes such as extracellular polysaccharide biosynthesis. It is identified in 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, 4075, 43, 6048, 17, 3100, 20748, 4515, 1986, 3418, 1988, 4088, 1966, 43, 24821, 3286, 1922, 4543, 2733, 8201, 16, 4475, 29601, 1920, 9128, 1927, 9821, 4325, 13785, 9075, 12, 45, 17, 2137, 17, 18033, 13, 18, 3868, 2435, 2458, 1956, 4948, 4682, 2427, 1966, 12358, 3695, 1038, 1930, 11377, 1024, 16, 2176, 8016, 1966, 1925, 6647, 9059, 2651, 4327, 3197, 2697, 1942, 5741, 5489, 4714, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 11377, 1024, 3418, 13975, 16, 2154, 4088, 1966, 43, 4325, 13785, 9075, 24821, 5061, 1958, 1920, 4877, 1927, 1920, 4543, 2812, 16716, 9821, 2137, 17, 18033, 18, 2176, 18127, 5305, 9931, 4248, 1958, 6048, 2743, 1930, 3868, 23230, 1036, 1956, 12358, 3695, 1038, 4682, 1942, 5741, 2024, 3154, 13510, 2971, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 2733, 8201, 45, 17, 2137, 17, 18033, 24821, 16, 11377, 1024, 19, 4515, 17, 8415, 1034, 3418, 17, 3165, 3416, 16, 2154, 4088, 1922, 4543, 3197, 15967, 1942, 5741, 2428, 1927, 1920, 2812, 16716, 9821, 4325, 13785, 9075, 12, 45, 17, 2137, 17, 18033, 13, 18, 4678, 5745, 5961, 43, 21446, 3500, 11377, 1024, 3418, 1988, 7222, 20887, 45, 17, 2137, 17, 18033, 16, 7304, 1956, 43, 4795, 16, 3205, 9078, 4515, 17, 8415, 1034, 3418, 7046, 5305, 6048, 17, 2743, 4248, 18, 2144, 2697, 3868, 4033, 5863, 1927, 2288, 17, 4594, 3771, 1942, 8480, 4028, 2427, 1966, 5329, 17167, 8132, 18, 2176, 1977, 2899, 1922, 14061, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MSAHESSGTGQAAVAVARKAIFDQQRHLWGYELFCVGNTDESPTGIPVAEDVPVSVVMVALSEKSVLDDRVYALPPACTTVLINEGTFSRSGVAARLEQLKGDGFAVAVPIGVTVAGRTPAELGTLLAEIGRFGALPMASHVPDSECVVACRDLGFRLFQGPIGSDDPDLGAIATEIQGDATVSFRLLTYLNSASFGLANRVNSISQAVSLLGWRRVRELLRLASQRARFLEVIATRYAFWGFDPESMHLLGLFSLLDAMMGIPMREVVGFLPLDSSLKWAEVDAAARRLNLDAVGVREAFLDAATVAGDLDVMAGAGAASTGVGLQQLIARQLRDFTAHRDCGPLYRQADIFSKEPEIVRLRRVSSGQIARFNLLKLTWLRVVLLSDIGQTAAMSAALCDEPNSEYVPLLQLVKDLEDAR", "metadata": {"id": "A0A935YBG0", "cluster": 8103037, "interpro_all": ["IPR014408", "IPR035919", "IPR013976", "IPR052340"], "interpro_used": ["IPR013976", "IPR035919", "IPR014408"], "interpro_unused": ["IPR052340"]}, "task_type": "infilling"} {"instruction": "The protein should contain a Tubulin/FtsZ, 2-layer sandwich domain that functions as a C-terminal GTPase module involved in polymer formation. This conserved region is found in eukaryotic tubulins, where it supports microtubule assembly, and in prokaryotic FtsZ proteins, where it facilitates the formation of the contractile ring required for cell division. Additionally, the protein should contain a Cell division protein FtsZ, C-terminal domain that is found in the tubulin-like GTPase FtsZ, a protein that polymerizes to form the Z-ring essential for bacterial cell division. This domain contributes to the machinery required for the constriction of the cell membrane and envelope to yield two daughter cells. Moreover, the protein can be placed in the Tubulin-like protein FtsZ/CetZ family, which comprises GTP-hydrolyzing tubulin homologues that assemble into cytoskeletal structures essential for cellular morphogenesis and division. This family includes FtsZ, which forms a contractile ring to orchestrate bacterial cell or plastid division, and the archaeal CetZ, which regulates cell shape to facilitate motility. It is identified in Lentisphaeria bacterium and is associated with UniProt keywords GTP-binding. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 3066, 5531, 43, 9332, 19, 27497, 16, 22, 17, 4757, 18038, 3418, 1988, 4088, 1966, 43, 45, 17, 4262, 14809, 9059, 3286, 1922, 4593, 3337, 18, 2052, 5305, 3031, 1977, 2435, 1922, 10825, 9332, 1036, 16, 2597, 2176, 7825, 10544, 5957, 16, 1930, 1922, 21545, 27497, 2697, 16, 2597, 2176, 11374, 1920, 3337, 1927, 1920, 13750, 6335, 3414, 1958, 2024, 8451, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 2024, 8451, 2213, 27497, 16, 45, 17, 4262, 3418, 1988, 1977, 2435, 1922, 1920, 9332, 17, 3189, 14809, 27497, 16, 43, 2213, 1988, 4593, 4517, 1942, 2386, 1920, 68, 17, 6335, 4415, 1958, 4543, 2024, 8451, 18, 2052, 3418, 7624, 1942, 1920, 10853, 3414, 1958, 1920, 19837, 1927, 1920, 2024, 3260, 1930, 11262, 1942, 4307, 2288, 16229, 2094, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 9332, 17, 3189, 2213, 27497, 19, 14184, 1011, 3416, 16, 2154, 12936, 9319, 17, 7222, 9046, 9332, 18541, 1988, 17421, 2460, 14787, 4061, 4415, 1958, 3689, 15328, 1930, 8451, 18, 2052, 3416, 5921, 27497, 16, 2154, 4952, 43, 13750, 6335, 1942, 21991, 2010, 4543, 2024, 2014, 19754, 8451, 16, 1930, 1920, 22367, 14184, 1011, 16, 2154, 7014, 2024, 5989, 1942, 6628, 9254, 18, 2176, 1977, 2899, 1922, 10226, 3508, 20051, 3027, 1019, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 9319, 17, 2743, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MTAQIINISSLDKSKPPLSDRVKVIGIGNAGLKIVEKLSMIKEASGLEIAGVDTDSASIMKSTITAKYLVGAEWTNGIGTGGDVLKGESAIAHKSNIAVKNFISNGSLLILVGGFGGGTATGGMPIIARFARERNIPVLMLVTLPFSFEGHSKRDAAEAQINNLLRTKSTVITIPNDLLYCVLPDTTPFDKAFSMANEEVAKAVLGIAELLRCDSTISVDLCDLLNVLAKGKTDCGIGIGTASSVETKDRVNDALKNLLSSPLLGGKQRLKISDALIISLTGGSDLTIGEMRFALDTLKSFAGEHTEIVVGANIDELYEKKIQLTVIPITYDKSNAISTVPIEEKELFNIKTTTHTAIIRNVNKLLKHKEEQPELPFTTRSRGIFTPTSQTLYNGEDIDIPTFQRKEIHIDKGR", "metadata": {"id": "A0A355M8N4", "cluster": 9826085, "interpro_all": ["IPR045061", "IPR024757", "IPR008280", "IPR018316", "IPR036525", "IPR003008"], "interpro_used": ["IPR018316", "IPR024757", "IPR045061"], "interpro_unused": ["IPR003008", "IPR036525", "IPR008280"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein is assigned to 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 falls within the Chitin Synthase Regulator family, which functions in the activation and regulation of chitin synthase enzymes, particularly CHS3, to drive chitin biosynthesis in fungal cell walls. These proteins are crucial for maintaining cell wall integrity during septum formation and sporulation, and they facilitate the production of chitosan to support melanin anchoring and host immune evasion. In addition, the protein incorporates a Sel1-like repeat that constitutes tetratricopeptide repeat sequences originally identified as key negative regulators of the Notch pathway in *Caenorhabditis elegans* receptors. These repeats also occur in mammalian pancreatic proteins, though their specific functions in that context remain largely uncharacterized. It originates from Schizosaccharomyces japonicus (strain yFS275 / FY16936) (Fission yeast). 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, 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, 12182, 2651, 1920, 16588, 8921, 7888, 3416, 16, 2154, 4088, 1922, 1920, 2936, 1930, 3640, 1927, 16588, 8921, 5038, 16, 4443, 22387, 1010, 16, 1942, 9265, 16588, 8132, 1922, 8697, 2024, 12430, 18, 2144, 2697, 2032, 6608, 1958, 8231, 2024, 4821, 7996, 2409, 17026, 3337, 1930, 23647, 16, 1930, 2611, 6628, 1920, 3372, 1927, 13945, 1942, 3373, 20850, 20816, 1930, 4423, 3743, 25092, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 2484, 1009, 17, 3189, 6865, 1988, 14879, 12470, 3319, 21305, 6865, 3709, 10398, 2899, 1966, 3834, 3136, 9098, 1927, 1920, 8091, 3374, 1922, 14, 22418, 10861, 14, 4086, 18, 2144, 9569, 2222, 4704, 1922, 6492, 6356, 2697, 16, 4170, 2310, 2487, 4088, 1922, 1988, 4491, 5555, 6318, 24528, 18, 2176, 22970, 2037, 7071, 5360, 2437, 28476, 29249, 18913, 1957, 12, 3943, 29962, 13262, 8245, 19, 27976, 22548, 5677, 13, 12, 16150, 5688, 13, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MTAEKDSTLTVVARSASASTGNLSRKLEMNSLEALNEELEALDLSSPTPSKATSPENMLAPKSVVGLHFPSASMSSTTSSCSSGKVFSDVSSSSSAINRHHLRPESAFDRTATVEPSVALRPRAVSVCIPPSGTCNNSTSTLASTSTAGSQAPAKQHRHHRTFSLRRAKEFVTKRLSIHRRRRSSSPPTICSQCGKRKVRCRCASEVASAVKDDNASFQTASAAMFADLPLEAVQEQFRPLVVRIREQMETEDSADAAANIATAAQREGEYDKAIVFYELAMEKPLKKHNYVPYELALLYYLRNREGERAKCFPLMQLASSLGHAESTLYVADAYVHGREGCRRDIFRGIQYYHLAADRGLAPAMFTLGKLYLTGVTGHLEANPTIAFEYARRAARLHYRPACRLLELMVQKGIVRNARPFSSFSSFTTR", "metadata": {"id": "B6K1C0", "cluster": 9900213, "interpro_all": ["IPR051726", "IPR006597", "IPR011990"], "interpro_used": ["IPR011990", "IPR051726", "IPR006597"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is assigned to 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. Moreover, the protein should feature 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. In addition, the protein should contain a Glycosyl hydrolase family 26 domain that typically functions as an endo-beta-1,4-mannanase involved in the hydrolysis of mannans, though some members exhibit beta-1,3-xylanase or endoglucanase activity against cellulose and beta-D-glucans. This catalytic domain adopts a classical (\u03b2/\u03b1)8-barrel fold and utilizes two glutamate residues to execute a double-displacement reaction mechanism. It is expressed in Phycisphaeraceae bacterium TMED231 and is annotated with UniProt keywords Glycosidase.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 6304, 1942, 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, 3950, 16, 1920, 2213, 3066, 5961, 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, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 20067, 20748, 3416, 3179, 3418, 1988, 5745, 4088, 1966, 1925, 16239, 17, 4666, 17, 21, 16, 24, 17, 7338, 7241, 4127, 3286, 1922, 1920, 9128, 1927, 7338, 2075, 16, 4170, 2673, 4678, 5987, 4666, 17, 21, 16, 23, 17, 23665, 2051, 2014, 16239, 22988, 7241, 4127, 2455, 3316, 12343, 1930, 4666, 17, 46, 17, 18798, 1036, 18, 2052, 6804, 3418, 24032, 43, 8445, 12, 161, 19, 160, 13, 28, 17, 19560, 3728, 1930, 18127, 2288, 7627, 4248, 1942, 29583, 43, 4825, 17, 9514, 3227, 2856, 18, 2176, 1977, 3198, 1922, 25511, 9119, 29164, 9914, 14061, 22377, 9091, 6800, 1930, 1977, 10633, 1956, 20709, 11569, 7533, 9200, 18, 3], "output": "MKRTSRSSGSRLQRPAAIAMITVASMLDAGAPCVAEDAIGELLEETSIGCPGDLDEDGRIGGADLGLMLAGWGDVSDESSADLDGDGRVAGADLGLLLAGRIRALVTADSRFGLDGVEVRAIDLIGAAWDDVIGRIHVTRPSDTSMDIGRTDLPTGSTATSTGTVDFIAGDEAHSNHRTLLRLELDGVNRDYVGDTLWPADEPGVGVAVFEAAIHGYPWVGFVTRLAEDFGTVDLSGPDTMLSFTVAGGVQGPDDAPYLYVVLEDVREQRVTIPLARFQAANPSLDLSRLIHLKFAARDDNIDGASYCQSNAPQRTTAPNCFWSNDVHRSDPASWNPLSVRFLDQPVSAFKYFHGVFGTNPDTMEFWPDDGGNPLDAMLAGGYDVFLDRLFAGLRDLGGRVEITPFHESNGFWYPWSSNGLGAHNVALGYCLISMPGNAASLREGIESVSSTATDFIGLQGFEQGYGWDTVTFNESEFGYNIADPAQYAKGELTLWSLADMLAERMPHPISTFHYFNVAKMEEGVWKDFRIIDETTGDEELGRNAYETGLRRHARTGYRVGGVEGVTTREAVNRGSVVPRPKASVPPAHRRDFGWGDVLAADASSIRRHVEAALSLELAWGDCPPSGDGFTFATADDIHQGILAELGRPEPGLGKYGVAYGISTDEYDVAGIDFDRDVMRLTWNHDDGDGLGNEAHLPIDIGEINEGSVAIIDVEFFREAWNVIGNCGVIRGNGLTPHVEPWKVAAAFERMASIRDGLFAIPADLLPRATGRPLMIFLAEVGPWVEAIEDLASSDGIRT", "metadata": {"id": "A0A1Z9QFG1", "cluster": 10435238, "interpro_all": ["IPR036439", "IPR018247", "IPR022790", "IPR017853"], "interpro_used": ["IPR036439", "IPR018247", "IPR022790"], "interpro_unused": ["IPR017853"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein should contain a Surface-adhesin protein E-like domain that contributes to pathogenesis by facilitating adhesion to host tissues. It binds to various host proteins, including plasminogen, vitronectin, and laminin. It is native to Flavobacterium sp and carries UniProt keyword assignments Signal.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 3066, 5531, 43, 3154, 17, 5315, 1921, 2213, 47, 17, 3189, 3418, 1988, 7624, 1942, 6559, 2007, 12440, 6141, 1942, 4423, 3878, 18, 2176, 6876, 1942, 3425, 4423, 2697, 16, 2710, 17485, 16, 3596, 2912, 2341, 1921, 16, 1930, 15261, 18, 2176, 1977, 6196, 1942, 7732, 12022, 2056, 1930, 16252, 20709, 11121, 2538, 18306, 2733, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MKTLLLLLTICTFSFTQAQDWKFAFENSSEKIEYFPTREIQNPKIADGYELILYKFDCFSNNHLKMEFASHNSLAERLTNVFCTQIGIYYVKANTSDTAWIKIVKSKKIGFVQSTVYSKDGTILNS", "metadata": {"id": "A0A519QRW1", "cluster": 10888735, "interpro_all": ["IPR031939"], "interpro_used": ["IPR031939"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein is associated with the Pseudouridine synthase TruD family, which catalyzes the isomerization of uridine to pseudouridine, specifically modifying uracil-13 in tRNA. This family is distinguished by a catalytic domain containing a natural circular permutation and a specific insertion domain that forms an RNA-binding cleft involved in substrate recognition. Moreover, the protein is included in the Pseudouridine synthase, catalytic domain superfamily, which catalyses the isomerisation of uridine to pseudouridine in various RNA molecules, including tRNA and rRNA. Members share a conserved $\\alpha+\\beta$ fold and a critical active site aspartic acid, often employing a nucleotide-flipping mechanism to access the target base. In addition to modification, these proteins may act as RNA chaperones or assist in ribosomal subunit assembly. It is derived from Anaerolineae bacterium.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 11520, 23864, 8921, 2025, 2009, 3416, 16, 2154, 17097, 1920, 27027, 1927, 26104, 1942, 11520, 23864, 16, 4475, 12691, 22761, 17, 2590, 1922, 10089, 18, 2052, 3416, 1977, 12080, 2007, 43, 6804, 3418, 3165, 43, 4613, 10262, 19110, 1930, 43, 2487, 7413, 3418, 1988, 4952, 1925, 3146, 17, 2743, 14649, 3286, 1922, 4510, 5708, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 11520, 23864, 8921, 16, 6804, 3418, 13975, 16, 2154, 13928, 1918, 1920, 15348, 6284, 1927, 26104, 1942, 11520, 23864, 1922, 3425, 3146, 4206, 16, 2710, 10089, 1930, 9067, 18, 4678, 7948, 43, 5305, 8, 38, 4595, 15, 38, 4666, 8, 3728, 1930, 43, 4140, 3500, 3200, 23047, 2687, 16, 3868, 12003, 43, 5489, 17, 16405, 9219, 2856, 1942, 4065, 1920, 2758, 5170, 18, 1922, 2459, 1942, 6295, 16, 2144, 2697, 2278, 4033, 1966, 3146, 18098, 2014, 6589, 1922, 11196, 5903, 5957, 18, 2176, 1977, 3595, 2037, 11381, 8419, 3336, 14061, 18, 3], "output": "MRYKVQPEDFTVEEWMRLPLAPRGHFAIYRVRKRGVTTLSVQVQMARALEVPQSAILFPALKDKDAVAIQHVAVRGTGPARLTGKGFLAEFLGRSYPTSPPCGIIPPTSQARSIQCASSSLAGLASSAPISVTACWPTATRSSPWTTSAPAAWTTSPTWPGTSASASSSTT", "metadata": {"id": "A0A7C7QBS4", "cluster": 12075578, "interpro_all": ["IPR020103", "IPR001656", "IPR042214"], "interpro_used": ["IPR001656", "IPR020103"], "interpro_unused": ["IPR042214"]}, "task_type": "autoregressive"} {"instruction": "The protein can be placed in the EKC/KEOPS complex, subunit Gon7 family, which functions as a subunit of the EKC/KEOPS complex involved in transcription and telomere maintenance. This component promotes telomere uncapping and elongation and is required for the efficient recruitment of transcriptional coactivators. It has been detected in Paraphoma chrysanthemicola and exhibits UniProt keyword tags Chromosome, Transcription regulation, and Nucleus. 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, 20529, 1030, 19, 3364, 4001, 2796, 16, 5903, 8239, 1027, 3416, 16, 2154, 4088, 1966, 43, 5903, 1927, 1920, 20529, 1030, 19, 3364, 4001, 2796, 3286, 1922, 3213, 1930, 12025, 6291, 18, 2052, 4594, 7383, 12025, 5269, 5041, 1930, 9971, 1930, 1977, 3414, 1958, 1920, 5807, 6067, 1927, 5224, 22706, 1036, 18, 2176, 2258, 2252, 3330, 1922, 22224, 25808, 1019, 21367, 7744, 4197, 10173, 1930, 9826, 20709, 11121, 2538, 14392, 5597, 16, 3213, 3640, 16, 1930, 5607, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MRPVATVCDRQGGGVQLQGQELLQFPIIAMSSLDATYTSPTESTPKVFSSELPALSSPPSTHDRVAYLAALSTSLKNLQGEINTFLTQKMDEDKALGASKADDAKFEETYGEEVVEED", "metadata": {"id": "A0A8K0RBN0", "cluster": 13103757, "interpro_all": ["IPR014849"], "interpro_used": ["IPR014849"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to make a protein that can have this function: The protein should include 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 derived from Variovorax sp. PBL-E5 and is connected to UniProt keyword Signal. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 3066, 3951, 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, 3595, 2037, 2309, 2579, 18897, 2056, 18, 18434, 17, 28332, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MKKTLRAILLGAIVAAAALGTAAQNAPKLGTITYVGYEGAPLNLTEQVAIDRGLFSARGLDLKFVGAANGGQMVSSLIGGSAQIGTLTISATAPLLKQGQCFQYLSAGARTYYNLVAQPDLKLPHAKEPYPKNLIDLKGKKIAINARGTAMEFMMDAILRQAGLTPADVTYIATGGAATAVAAFRNKQVDIALDFPIQEQMLRPGEFQYMAKLAEMATNNPIYHLTQVFSGASCDYVKKNPQVVEAFCSAVGDAYRFVNDPANKEAVVAVVQKSLNIDKPTAESFWQQYRDSWPSGKIDTASWNAQKILLPAGTELPNFNEYVPSACQARM", "metadata": {"id": "A0A6P2EKZ7", "cluster": 14282079, "interpro_all": ["IPR015168"], "interpro_used": ["IPR015168"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nIt is part of the Protein of unknown function DUF4345 family, which is currently uncharacterized. Members of this family contain a single completely conserved glutamate residue that may be functionally significant. It has been characterized in Sandaracinobacter neustonicus 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, 2176, 1977, 3131, 1927, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 27285, 3416, 16, 2154, 1977, 5077, 24528, 18, 4678, 1927, 2052, 3416, 5531, 43, 2957, 5796, 5305, 7627, 6181, 1988, 2278, 1998, 9346, 2228, 18, 2176, 2258, 2252, 4378, 1922, 9622, 9041, 3665, 5883, 2866, 20476, 24375, 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": "MTLIVRLIIGLVGLFNVAVGLMFLLNPAFFLVGGLFALLGAIRTDPSPLKVPLLAVMIALLLLGQWVFARARQSKARRMGPEFALSPLGSQGLATMRADFSALLAIALFGRTLSLILDGTAPTAYPPMLVE", "metadata": {"id": "A0A501XFR5", "cluster": 14916104, "interpro_all": ["IPR025597"], "interpro_used": ["IPR025597"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given this biological function:\nIt is part 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. Moreover, the protein carries 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. Moreover, the protein includes a Redoxin domain that functions as the catalytic core of peroxiredoxin, thioredoxin, and glutaredoxin systems to facilitate antioxidant defense and redox regulation. It utilizes a strictly conserved cysteine residue to reduce substrates such as hydrogen peroxide, peroxinitrite, and hydroperoxides. Additionally, this domain modulates the activity of various proteins, including those involved in photosynthetic carbon assimilation and cadmium sensitivity, via thiol redox mechanisms. It is identified in Frankiales bacterium and is associated with UniProt keywords Redox-active center, Transmembrane, and Signal-anchor.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 2176, 1977, 3131, 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, 3950, 16, 1920, 2213, 16252, 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, 3950, 16, 1920, 2213, 5921, 43, 9366, 1921, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 11456, 3030, 9754, 16, 23684, 16, 1930, 19406, 1919, 9754, 3771, 1942, 6628, 7335, 9720, 1930, 9366, 3640, 18, 2176, 18127, 43, 14470, 5305, 8666, 6181, 1942, 4412, 6249, 2427, 1966, 6201, 12316, 16, 11456, 11566, 1997, 2394, 16, 1930, 25461, 29508, 18, 4950, 16, 2052, 3418, 13112, 1920, 2455, 1927, 3425, 2697, 16, 2710, 2690, 3286, 1922, 16068, 5056, 22317, 1930, 17203, 3802, 16, 3454, 13914, 9366, 3531, 18, 2176, 1977, 2899, 1922, 14542, 2086, 1918, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 9366, 17, 3500, 4102, 16, 9117, 16, 1930, 2733, 17, 13333, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MRARRTRAVALALLAVVALAGAGDGSVVLLPSAERAPAPSLSGTTRGKVVVLNYWASWCSPCREEAGALDRAYQATHGRRFEVPYPSLYDGDQSIVLALSGTLPPDAIPGAVDYSGLRGMIDPVLAEKACSTTTGSTDGSLGFVLDGARLDLASLQGVDFVGVVAGGKDSVENAAAFVSTLVLDRQGRIAARTL", "metadata": {"id": "A0A931L1I8", "cluster": 17157054, "interpro_all": ["IPR013740", "IPR036249", "IPR013766", "IPR050553"], "interpro_used": ["IPR050553", "IPR013766", "IPR013740"], "interpro_unused": ["IPR036249"]}, "task_type": "infilling"} {"instruction": "Function:\nThe protein is assigned to the Bacterial and chloroplast ATP synthase F0 complex subunit b/b' family, which forms the peripheral stalk of F-type ATP synthases to structurally link the catalytic F1 and membrane-embedded F0 sectors. Acting as a stator, this component prevents the rotation of the catalytic core relative to the proton channel during ATP synthesis or hydrolysis. Furthermore, the protein is assigned to the ATP synthase B chain family, which forms the peripheral stalk of the F(0) channel in ATP synthase, connecting the F(1) catalytic core to the membrane component. These subunits are essential for driving ATP production from ADP using proton or sodium gradients, and in some organisms, they facilitate the generation of sodium electrochemical gradients as ATP-driven Na(+) pumps. It has been characterized in Acidobacteriota bacterium and is classified with UniProt keywords Transport, Transmembrane helix, and Cell membrane.\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, 4543, 1930, 17471, 4498, 8921, 17930, 2796, 5903, 44, 19, 44, 11, 3416, 16, 2154, 4952, 1920, 5009, 19447, 1927, 48, 17, 2601, 4498, 8921, 1036, 1942, 12171, 3300, 1920, 6804, 9154, 1930, 3260, 17, 8222, 17930, 17983, 18, 8290, 1966, 43, 3156, 1924, 16, 2052, 4594, 10299, 1920, 8891, 1927, 1920, 6804, 4728, 3338, 1942, 1920, 8433, 4999, 2409, 4498, 4271, 2014, 9128, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 4498, 8921, 44, 4659, 3416, 16, 2154, 4952, 1920, 5009, 19447, 1927, 1920, 48, 12, 20, 13, 4999, 1922, 4498, 8921, 16, 15031, 1920, 48, 12, 21, 13, 6804, 4728, 1942, 1920, 3260, 4594, 18, 2144, 6991, 2032, 4415, 1958, 9228, 4498, 3372, 2037, 9828, 2193, 8433, 2014, 5227, 12741, 16, 1930, 1922, 2673, 7373, 16, 2611, 6628, 1920, 4841, 1927, 5227, 13197, 12741, 1966, 4498, 17, 6446, 4049, 12, 15, 13, 19263, 18, 2176, 2258, 2252, 4378, 1922, 2687, 5883, 3940, 3857, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 4860, 16, 9117, 7864, 16, 1930, 2024, 3260, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MSRPFRQALVAVALGACLGALAPPEEPSQEKKESRELIYKILRKPAAEYLAARSASIRKGIEEGRKAFEESARQDIASEGAARQELQAFAAAEALRLAGLGGTELAIRLEREGRNPTFGLSRPPSAASLAVNFVILVGALGYFALEASEAELRVVEEKLARLEQEIRERFRRETEAEAEKMLEFARARMGAATRELSVHDRLDAPRREHLFARYLA", "metadata": {"id": "A0A2V9LGP2", "cluster": 18598270, "interpro_all": ["IPR002146", "IPR050059"], "interpro_used": ["IPR002146", "IPR050059"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein contains a DUF1707 SHOCT-like domain that is found in various Actinomycetales proteins and is predicted to be membrane-bound or membrane-associated, although its specific biological function remains uncharacterized. It has been characterized in Tessaracoccus sp. T2.5-30.\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, 4855, 5739, 4618, 1027, 8406, 2341, 17, 3189, 3418, 1988, 1977, 2435, 1922, 3425, 4718, 13386, 3949, 1918, 2697, 1930, 1977, 4396, 1942, 1998, 3260, 17, 4124, 2014, 3260, 17, 2458, 16, 2876, 2496, 2487, 3933, 2347, 4497, 24528, 18, 2176, 2258, 2252, 4378, 1922, 2672, 5735, 5524, 4879, 2437, 1957, 2056, 18, 5787, 18, 25, 17, 2627, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MPDELVPRPRMRAGDADRDDALRVLAQYVDDLLPVVADLPEGALLQAGFMTGRDVDLAPGTSLYRNFAWWGGDDIILDRALSAVMAGHDIYVPEGVRVIDESFAILILKGFLFWAGHDVKLSRRQRGQQAHAAGRLSVEELGSRQDAVLAPAVATPSPATTDVGMSVTGPGVLLTLELMAGNDIDRDARGDGSNGT", "metadata": {"id": "A0A807N343", "cluster": 19365049, "interpro_all": ["IPR012551"], "interpro_used": ["IPR012551"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein possesses a ATP-grasp domain, R2K clade family 2 domain that is predicted to catalyze peptide ligation reactions on protein substrates, likely functioning in biological conflicts between bacteriophages and their hosts. This domain represents a specialized subfamily of the R2K clade characterized by the migration of a conserved lysine residue to the RAGYNA domain within the core ATP-grasp module. It is derived from Neisseriaceae bacterium.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 14465, 43, 4498, 17, 22815, 3418, 16, 7261, 1040, 11315, 3416, 22, 3418, 1988, 1977, 4396, 1942, 18170, 4207, 11102, 5298, 1990, 2213, 6249, 16, 3205, 7295, 1922, 3933, 14306, 2192, 24613, 1036, 1930, 2310, 10865, 18, 2052, 3418, 4972, 43, 11021, 16227, 1927, 1920, 7261, 1040, 11315, 4378, 2007, 1920, 5049, 1927, 43, 5305, 9082, 6181, 1942, 1920, 13745, 2304, 1019, 3418, 2651, 1920, 4728, 4498, 17, 22815, 9059, 18, 2176, 1977, 3595, 2037, 28356, 18339, 1972, 3336, 14061, 18, 3], "output": "MKRFCLEMNGSTREKIAIISSARYLNYDYVYSKKALPDCIPIGSVDYCEEILPKGYLIDFFPDFLKEYSFREINYGYLEKIEKPLFLKKANCWKSDFESKVYNPNENITPDFYYYSEPVEFKQEWRYYISEGCVISSGWYKGEDENEQAPNLIIDFPSDFNAAVDFGRLSTGELAIIESHAPFACGWYGDTHFEYAMWQVEAWNGFLKNIRFA", "metadata": {"id": "A0A3S0DTY0", "cluster": 21056875, "interpro_all": ["IPR041261"], "interpro_used": ["IPR041261"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I'm looking for a protein that can perform the following function: The protein can be placed in the Maleate isomerase/Arylmalonate decarboxylase family, which comprises enzymes that catalyze the cis-trans isomerization of maleate to fumarate. This family also includes proteins functioning as arylmalonate decarboxylases. In addition, the protein is associated with the Isomerization and Racemization Enzyme superfamily, which catalyzes diverse isomerization and racemization reactions, including the cis-trans conversion of maleate to fumarate. These enzymes also facilitate the reversible racemization of hydantoins to produce L-amino acids, exhibiting specificity for maleate and various substituted hydantoins while being responsive to modulation by metal ions. It originates from Leucobacter chromiisoli. Give the amino acid chain.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4005, 2010, 25510, 19, 15578, 9578, 8870, 23922, 3416, 16, 2154, 12936, 5038, 1988, 18170, 1920, 5848, 17, 2127, 27027, 1927, 4005, 2010, 1942, 28343, 18, 2052, 3416, 2222, 5921, 2697, 7295, 1966, 15578, 9578, 8870, 23922, 1036, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 27027, 1930, 7442, 7395, 7659, 4113, 13975, 16, 2154, 17097, 6445, 27027, 1930, 7442, 7395, 7659, 5298, 16, 2710, 1920, 5848, 17, 2127, 7309, 1927, 4005, 2010, 1942, 28343, 18, 2144, 5038, 2222, 6628, 1920, 10743, 7442, 7395, 7659, 1927, 2993, 26182, 2925, 1942, 5074, 54, 17, 3835, 4576, 16, 12196, 4896, 1958, 4005, 2010, 1930, 3425, 11798, 2993, 26182, 2925, 2679, 3301, 8487, 1942, 7145, 2007, 6048, 6982, 18, 2176, 22970, 2037, 9906, 5883, 3233, 3907, 2204, 12191, 18, 7031, 1920, 3835, 2687, 4659, 18, 3], "output": "MSKLHHRGGVIVPPANPTVEPEFRELISPELAMHTTRFPVFTGWDQQQRNQGYLDVLPESVADFGSLALDSVFIACTGSHYLLSPQEDVALCADLGEQLGTAVRSATLTITDALTALGATRIVVASPYETWLTELSHRYWEAAGFEVGDVVRVRAQTGYNPYDVTEEALAEQVEAAGVADDAVILFTGTGMPTIGAMTRLSAGTERRVLSSNLCGARWLQRDLPAGASHPLLARLAAQTAEVAA", "metadata": {"id": "A0A934UUR1", "cluster": 23198268, "interpro_all": ["IPR053714", "IPR026286"], "interpro_used": ["IPR026286", "IPR053714"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein possesses a K+ potassium transporter, C-terminal domain that constitutes the conserved non-membrane region of the KUP/HAK/KT family of potassium transporters found in bacteria, yeast, and plants. It is produced by Actinomycetes bacterium and has UniProt annotations Symport.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 14465, 43, 53, 15, 9057, 9054, 16, 45, 17, 4262, 3418, 1988, 14879, 1920, 5305, 2447, 17, 3260, 3031, 1927, 1920, 23774, 19, 2118, 1040, 19, 15569, 3416, 1927, 9057, 10538, 2435, 1922, 4802, 16, 5688, 16, 1930, 4793, 18, 2176, 1977, 4152, 2007, 4718, 25148, 14061, 1930, 2258, 20709, 15010, 29148, 2718, 18, 3], "output": "MAADVVVATVVTESVPFLTRAPLDILRTSVLGEGEADATYYLSERRLHRNSQAPAAYFSLPPERVIPLGTRIDLVEDVMDRVRPVTVYTGYMETADLPFVATDHGMLPAWLERMFAF", "metadata": {"id": "A0A7K0NXH4", "cluster": 25956194, "interpro_all": ["IPR053952"], "interpro_used": ["IPR053952"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein should contain 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. 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. In addition, it is part of the Heme sensor protein HssS/ArlS-like family, which functions as the sensor histidine kinase component of bacterial two-component regulatory systems. These membrane-associated proteins autophosphorylate a conserved histidine residue in response to environmental stimuli, such as heme, and transfer the phosphoryl group to a cognate response regulator to modulate gene expression. This signaling activity regulates diverse cellular processes, including virulence, biofilm formation, adhesion, and heme homeostasis. It is native to Intestinibaculum porci and has UniProt annotations Transferase and Transmembrane helix.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 3066, 5531, 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, 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, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 10954, 6443, 2213, 4193, 5590, 19, 2245, 4668, 17, 3189, 3416, 16, 2154, 4088, 1966, 1920, 6443, 13873, 4016, 4594, 1927, 4543, 2288, 17, 4594, 4948, 3771, 18, 2144, 3260, 17, 2458, 2697, 20369, 9075, 43, 5305, 13873, 6181, 1922, 2644, 1942, 4813, 5458, 16, 2427, 1966, 10954, 16, 1930, 3856, 1920, 12556, 2210, 1942, 43, 15786, 2644, 7888, 1942, 8480, 2359, 2294, 18, 2052, 3197, 2455, 7014, 6445, 3689, 4028, 16, 2710, 9304, 16, 9638, 3337, 16, 6141, 16, 1930, 10954, 7622, 18, 2176, 1977, 6196, 1942, 9279, 11821, 1948, 7705, 4572, 3349, 1930, 2258, 20709, 15010, 13763, 1930, 9117, 7864, 18, 3], "output": "MKKKVIIGIYVVLLVAATVITSVGFCFNATHIDRVELDKSNLRYNIGQLILYEGKQADPHYQYLSFDKSVSKKKRAAYKKTITKIMADYTKNMRSNDDISYVTKNENGDLKEAHVPEQFHHKSLDMTLTYDQKGRISGKKYTSLYDEFDGDYVNLYTSIGYNTTIGSDEITKLTAAIEQGKVSINNPSNMTITIQVPQKITTNYMRYILNLSDQAESFIETAFLLSGLIIILFMIIVPLKISETIEPFKTMKNWYFIANALIIALGVFFSSLIIRQFFAGMIDLYNGQSMSNTFLLGLSMKQPENTALIGFIFALPSLVIYFLVSVFGFGLKYILVHIKTYFKDHTLIGAMIRHVKKQSDVLIRETMDDPHNKAIVKLFALHLGVIIGLTMLLFIFSSVFYMYTMYTLHPYRNLFMIWLIMMVIYGFVVANTIIKKMLSIKQSYQRLVRQAQDLSRGEFVEVADDLGVFNSLRDEMNHVKEGFEKAVEEEVKSTTMKTELISNVSHDLKTPLTCIKNYVILLKDAKTPEDTKEYTTQIENYTNRLSTLIEDLFEVSKVNSGNVTLHETSLDLLALLDQAVVENEEKLESKSLRVIKKADLEKAMCYLDGEKTYRILDNLLGNIAKYAMPQTRVYIDVTHDKEHVSIALKNISEAEMNFTSEEIVERFVRGDKSRHVAGSGLGLAIAKSFTEVQGGTFALAIDGDMFKVTLTFTLEKPATQDE", "metadata": {"id": "A0A3G9JAC9", "cluster": 28044504, "interpro_all": ["IPR050398", "IPR036890", "IPR005467", "IPR003661", "IPR036097"], "interpro_used": ["IPR003661", "IPR005467", "IPR050398"], "interpro_unused": ["IPR036097", "IPR036890"]}, "task_type": "autoregressive"} {"instruction": "I am designing a protein with the following function: The protein belongs to the Leucine-rich repeat domain-containing protein family, which functions in diverse signaling pathways including innate immunity, MAPK activation, and cell volume regulation via the volume-regulated anion channel (VRAC). Members utilize leucine-rich repeat (LRR) domains to mediate protein-protein interactions essential for Toll-like receptor signaling, Ras effector function, and ubiquitination processes. Additionally, the protein features a Disease resistance R13L4/SHOC-2-like, LRR domain that acts as a scaffolding module to mediate protein-protein interactions in diverse signaling pathways, including plant immunity and animal MAPK regulation. In plants, it facilitates the recognition of bacterial effectors in resistance proteins and aids stomatal closure, while in animals, it functions as a core component of the SHOC2-MRAS-PP1c holophosphatase complex. Moreover, the protein should contain 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 originates from Bacteroidales bacterium. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 12624, 17, 5536, 6865, 3418, 17, 3165, 2213, 3416, 16, 2154, 4088, 1922, 6445, 3197, 3873, 2710, 8539, 7611, 16, 7859, 2936, 16, 1930, 2024, 3776, 3640, 3454, 1920, 3776, 17, 4335, 10985, 4999, 12, 12110, 1948, 13, 18, 4678, 12561, 12624, 17, 5536, 6865, 12, 13947, 13, 4682, 1942, 8265, 2213, 17, 2213, 3719, 4415, 1958, 15204, 17, 3189, 3148, 3197, 16, 6520, 7917, 2347, 16, 1930, 11758, 4028, 18, 4950, 16, 1920, 2213, 4075, 43, 2573, 3554, 12041, 1010, 15245, 19, 8406, 1030, 17, 22, 17, 3189, 16, 13947, 3418, 1988, 8016, 1966, 43, 22582, 9059, 1942, 8265, 2213, 17, 2213, 3719, 1922, 6445, 3197, 3873, 16, 2710, 4496, 7611, 1930, 4027, 7859, 3640, 18, 1922, 4793, 16, 2176, 11374, 1920, 5708, 1927, 4543, 13066, 1922, 3554, 2697, 1930, 8494, 23075, 10408, 16, 2679, 1922, 3555, 16, 2176, 4088, 1966, 43, 4728, 4594, 1927, 1920, 8406, 8054, 17, 24564, 1036, 17, 20724, 1030, 20403, 7824, 7234, 2796, 18, 3950, 16, 1920, 2213, 3066, 5531, 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, 22970, 2037, 24323, 3955, 14061, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MNRKSIIAFLAFITVTFNAMAQIPYQALLAKGEKVYESMTVNVTPDKVLILDLSGQELTSVTGISKFINLRFLILTANELTSLPAEISKLTKLEHLEVWENKLIALPEGIGSLMNLKTLNASGNQLKVLPAGMAKLVKLESLDLSRNKLTALPDALTGLITLQELNLEENAIASLPATFGNLVAIEELNLAKNKISTLPESIGRLKKLTNFDLNTNVLTSLPASFCGLSMLEDLNLSQNQLASLPECFGNLAMLTVLSLSTNNLTAFPASFTKLR", "metadata": {"id": "A0A3C1PMW9", "cluster": 28254913, "interpro_all": ["IPR001611", "IPR003591", "IPR032675", "IPR050216", "IPR055414"], "interpro_used": ["IPR050216", "IPR055414", "IPR003591"], "interpro_unused": ["IPR001611", "IPR032675"]}, "task_type": "autoregressive"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein is classified under the YtxH family, which comprises uncharacterised bacterial proteins. Members are typically 100 to 143 amino acids in length and feature a conserved N-terminal region. Additionally, the protein is grouped in the Uncharacterized desiccation-related membrane-associated family, which is predicted to be membrane-associated and potentially involved in the cellular response to desiccation stress. Members of this family share sequence similarity with desiccation-related proteins found in *Craterostigma plantagineum*, suggesting a role in adaptation to water-limiting conditions, though the specific molecular functions remain uncharacterized. It is produced by Acidobacteriota bacterium and is described by 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, 5947, 2441, 1920, 24412, 1039, 1023, 3416, 16, 2154, 12936, 23229, 3495, 4543, 2697, 18, 4678, 2032, 5745, 2813, 1942, 13370, 3835, 4576, 1922, 3471, 1930, 5961, 43, 5305, 56, 17, 4262, 3031, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 24528, 23843, 1943, 17, 2712, 3260, 17, 2458, 3416, 16, 2154, 1977, 4396, 1942, 1998, 3260, 17, 2458, 1930, 5063, 3286, 1922, 1920, 3689, 2644, 1942, 23843, 1943, 3071, 18, 4678, 1927, 2052, 3416, 7948, 3244, 6796, 1956, 23843, 1943, 17, 2712, 2697, 2435, 1922, 14, 24422, 1967, 2259, 29043, 1019, 4496, 29284, 5926, 14, 16, 3783, 43, 2770, 1922, 7810, 1942, 3224, 17, 8051, 2961, 16, 4170, 1920, 2487, 3272, 4088, 5555, 24528, 18, 2176, 1977, 4152, 2007, 2687, 5883, 3940, 3857, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 7864, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MASNGEKFLYFVIGGFVGAAALGEKARQGREAIAEKSREVSSKVSQKQAYDDEKRKQDPAQSAVGLLLAPKSGEETRAFLGSKYRDGTTIEKGRDMLTRQREQMNAAIEAG", "metadata": {"id": "A0A3N5Z8S9", "cluster": 409117, "interpro_all": ["IPR052928", "IPR024623"], "interpro_used": ["IPR024623", "IPR052928"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein is assigned to the SIS domain superfamily, which functions as a phosphosugar-binding module involved in phosphosugar isomerization or transcriptional regulation. Structurally defined by a three-layer $\\alpha$-$\\beta$-$\\alpha$ sandwich fold, it serves either a catalytic role in enzymes or binds phosphorylated sugar substrates to modulate gene expression in transcriptional regulators. It is produced by mine drainage metagenome.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 19149, 3418, 13975, 16, 2154, 4088, 1966, 43, 8078, 20490, 13279, 17, 2743, 9059, 3286, 1922, 8078, 20490, 13279, 27027, 2014, 5224, 3640, 18, 12171, 3608, 2007, 43, 2559, 17, 4757, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 17, 8, 38, 4595, 8, 18038, 3728, 16, 2176, 10634, 3108, 43, 6804, 2770, 1922, 5038, 2014, 6876, 7199, 9523, 6249, 1942, 8480, 2359, 2294, 1922, 5224, 9098, 18, 2176, 1977, 4152, 2007, 24165, 12790, 16552, 2225, 18, 3], "output": "GPPGEGPPGTLPFPPYRPPSLEDGKAPLLEPSGGRRSGVLSTGGSFRGGPDHGTERAPLEPVPQHPRPARGATGRSGPLPASGPKGRRHPDGPTACLCDGDGHQPPRGLGGPVPAPGEGVDAWALTHQDFALYPPPLSRDDALITISHRGNKRYGMASLQRAQAAGMPVVGLTGLDSPMAGP", "metadata": {"id": "T0YGG8", "cluster": 5919792, "interpro_all": ["IPR046348"], "interpro_used": ["IPR046348"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should include a YcxB-like, C-terminal domain that forms the C-terminus of the *Bacillus subtilis* YcxB protein and similar bacterial transmembrane proteins. The specific biological function of this conserved domain is currently uncharacterized. It originates from Clostridium bornimense. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 3066, 3951, 43, 22386, 26128, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 4952, 1920, 45, 17, 7822, 1927, 1920, 14, 14587, 14745, 14, 22386, 26128, 2213, 1930, 2551, 4543, 9117, 2697, 18, 1920, 2487, 3933, 2347, 1927, 2052, 5305, 3418, 1977, 5077, 24528, 18, 2176, 22970, 2037, 21156, 8813, 11593, 3355, 1021, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MRYDYTFNNEEFTIVAVSSGSKSSSIVKYEKLNKVKESKNNILIYITREQFYILDKKQCDENIQEVIKLLKDKVKKYKTI", "metadata": {"id": "W6RXG0", "cluster": 6312841, "interpro_all": ["IPR025588"], "interpro_used": ["IPR025588"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein is a member of the Mitochondrial inheritance protein 9 family, which is involved in the inheritance and distribution of mitochondria during cell division. Conserved across yeast species, members of this family ensure proper mitochondrial segregation, thereby influencing mitochondrial biogenesis and dynamics. Additionally, 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. Furthermore, the protein contains a Aminoglycoside phosphotransferase domain that confers bacterial resistance to various aminoglycoside antibiotics, including kanamycin, neomycin, and streptomycin, by inactivating them via phosphorylation. It has been detected in Dacryopinax primogenitus (strain DJM 731) (Brown rot fungus).", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 4596, 15762, 2213, 29, 3416, 16, 2154, 1977, 3286, 1922, 1920, 15762, 1930, 3282, 1927, 6489, 2409, 2024, 8451, 18, 5305, 3436, 5688, 3038, 16, 4678, 1927, 2052, 3416, 6486, 3405, 4596, 12707, 16, 6113, 11623, 4596, 13008, 1930, 5565, 18, 4950, 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, 3677, 16, 1920, 2213, 5461, 43, 23029, 8028, 8078, 9961, 3418, 1988, 16556, 4543, 3554, 1942, 3425, 23029, 8028, 7560, 16, 2710, 19404, 16, 26269, 16, 1930, 10666, 16, 2007, 20862, 3581, 3454, 4050, 18, 2176, 2258, 2252, 3330, 1922, 22322, 6907, 2011, 4058, 1039, 2610, 2404, 7831, 12, 3943, 17224, 1035, 5356, 1009, 13, 12, 8084, 5337, 16461, 13, 18, 3], "output": "MSVNFAAAKGMVEAAMGTCHGFEKSAEAGFHTVFQVALGKFNAILRFPNASVKNASDVVRSEQATMTFLREAHGFPIPRVYTWSADLEGDGIGSPYIFMEHIPGVPFEDALHEGKVSNCLWRQIAQIQDRLARIPLARIGSIYRREDLPPHLADSPLY", "metadata": {"id": "M5G9W3", "cluster": 12424302, "interpro_all": ["IPR002575", "IPR011009", "IPR051035"], "interpro_used": ["IPR051035", "IPR011009", "IPR002575"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a polypeptide chain with the following function: The protein contains a Small EDRK-rich factor-like, N-terminal domain that functions as a positive regulator of amyloid protein aggregation and proteotoxicity. This domain is found in short proteins rich in aspartate, glutamate, lysine, and arginine, such as human SERF1 and SERF2, where it induces conformational changes in amyloid proteins to drive compact formations preceding aggregation. It is derived from Fusarium oxysporum NRRL 32931. 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, 2858, 3347, 1005, 1040, 17, 5536, 2991, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 43, 2843, 7888, 1927, 8186, 2213, 7883, 1930, 2174, 11930, 18, 2052, 3418, 1977, 2435, 1922, 3662, 2697, 5536, 1922, 12878, 16, 7627, 16, 9082, 16, 1930, 9732, 16, 2427, 1966, 2616, 2375, 5739, 1930, 2375, 6680, 16, 2597, 2176, 6387, 8523, 2840, 1922, 8186, 2697, 1942, 9265, 13726, 3337, 1036, 12141, 7883, 18, 2176, 1977, 3595, 2037, 24470, 20004, 3508, 17279, 5214, 1005, 1024, 25725, 6800, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MARGNQRDLARAKNEKKKQEDAKRKGSNKSGTKMQQEKETAAEIMRRKQAASEARKAAAGKT", "metadata": {"id": "W9HV06", "cluster": 14329719, "interpro_all": ["IPR007513"], "interpro_used": ["IPR007513"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a protein with the following function: The protein is a member 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. In addition, the protein is included in 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. It is produced by Caligus rogercresseyi (Sea louse). Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 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, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 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, 2176, 1977, 4152, 2007, 2570, 7694, 1036, 20443, 3234, 4479, 10676, 1033, 12, 9309, 3004, 2517, 13, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MLNSLSERIYLTGVGVWMSLKEQILDRHKALTAITSNPGQVVVITGGSRGIGFEAAKKLIQNECMVIVGCRKIEEAERKLKEIPNSEGKFKVFPLDLQSLDSVRAFAGSVRETAPDIHVLLNNAGIMMSPHFETKDGFESQSQTNYLSHFLLSSLLLDRIRSRIVNVSSVAHVMAHRSTNWEDLQMKELYTPEGGYSNSKADQIMFTKYLQSKIDESPNYKGKISVFALHPGVIYSDLYVHMPLGSVLKCLSGVLMKSQAQGGDTLIHAALSPELDGLGGSYTENSQVVSASTFVSDPANQKKLWDKTLEILGMDKFAPNLD", "metadata": {"id": "C1BRG7", "cluster": 14920396, "interpro_all": ["IPR036291", "IPR002347"], "interpro_used": ["IPR036291", "IPR002347"], "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 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. Additionally, the protein should include 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. It is identified in Embleya scabrispora.", "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, 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, 4950, 16, 1920, 2213, 3066, 3951, 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, 2176, 1977, 2899, 1922, 5654, 6659, 1019, 17529, 2377, 1937, 21086, 18, 3], "output": "MTLGDQGVGDVKTSGARRVTLSGSAFGDQDGSPPPTARSRTGGGSGSVSGPGWASGGATRLLADGYVRASAAELARITGLSISVDPEPAGCVVPADGGAWRAVTDGSGTPGWSFTAEGKPIARLGEAGMRNHISHELGHTLGLSNGYQDSRAGQYVQQFDVQGLRLGVAGGRPANGTPIRLRDCDGGVLGNGAADGNGIDLFDCNGTAAQKWAVDARGRLNTPGRGRGQLWTVPKWAGGFAAVALIVAGLPETPDPAPPPPGSARIRAAGAYVIRFLDRRAAEWLGPYAYPRSRGEIVVGALAGPCGFHARGVPDTVTGGHAYIDTSFGHADDAPGGCVRGADSGEAPVMCTVALAEAGGAPVPPQGRVTGLGGRCGQSWIVEKDGTLRAMGKCLDDLVHLASGKALDLAAAGSTDDGAVV", "metadata": {"id": "A0A1T3NRM3", "cluster": 16621761, "interpro_all": ["IPR024079", "IPR035992", "IPR000772"], "interpro_used": ["IPR024079", "IPR000772"], "interpro_unused": ["IPR035992"]}, "task_type": "infilling"} {"instruction": "Target Function: The protein falls within 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. Moreover, the protein should include 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. Also, the protein features a AraC-type arabinose-binding/dimerisation domain that serves as a regulatory module in bacterial HTH-type transcription factors by coupling ligand binding to dimerization. Upon binding L-arabinose within a beta-barrel fold, the domain undergoes a conformational change where the N-terminal arm buries the sugar and mediates dimerization through an antiparallel coiled-coil. It is derived from uncultured Eubacterium sp and contains UniProt keyword associations Transcription regulation.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 12182, 2651, 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, 3950, 16, 1920, 2213, 3066, 3951, 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, 2222, 16, 1920, 2213, 4075, 43, 20289, 1030, 17, 2601, 25965, 17, 2743, 19, 7632, 6284, 3418, 1988, 10634, 1966, 43, 4948, 9059, 1922, 4543, 5334, 1023, 17, 2601, 3213, 2790, 2007, 7590, 5207, 2743, 1942, 13640, 18, 4073, 2743, 54, 17, 25965, 2651, 43, 4666, 17, 19560, 3728, 16, 1920, 3418, 14928, 43, 8523, 3185, 2597, 1920, 56, 17, 4262, 6011, 4598, 2062, 1920, 9523, 1930, 10412, 13640, 2596, 1925, 28892, 17524, 17, 9121, 18, 2176, 1977, 3595, 2037, 5269, 21058, 4791, 7972, 2341, 18842, 1989, 2056, 1930, 5461, 20709, 11121, 2538, 5253, 3213, 3640, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MAMSGFKCIPFSYFQNNKVCILILMNNYGIIYINRISIQVLVDVMIEKLFTIGIRNTEQPFHWYDTLELFFVTEDVHALENKTEDLLYIQLSMSMEAFDQYIPDISIVYFKCDSEEDAISEEIKNYIAQMVRMLDMKMRFNYGRYEMENVSEKELEKIDQIRKVVDYLFDNGKNKITLKDAADHIFVGTSTFKKLMKEYGGGSFESITNIAYECGFSAPRYYYSAFEKKYQCSPVEYRERNRKYFIKEKKSNAMCFTCDEEIKISDIIELLRPYSKVDNVLICEEDDVYRLDFTEELALCRKTLGIRKLRIIGSNSRLCANIEKNVSYLGITVSDIWQKGEKKPLYYIYELFNRIEQPFTRLNPNCILHDKGGNLNITAFNIDNGDEKLLYKFDISGLEDDETKKLDREIVKELAKPSIEYNVYKKGIPFIIDVAVENNSFVNIEIIRIRVRGEVDLISNNNTVHMSRGHIQVVNFEYKENEYLKSETEQTLIYYCVEILSKLLSSIRAEMSLKYLLDSNMEFKADSELNRNIINIDISAKRSHKSKFPKEESERNVLLSELFGRHGDDYICIKTEAPKLTEAVKNLIA", "metadata": {"id": "A0A1C5V9G1", "cluster": 17646717, "interpro_all": ["IPR003313", "IPR009057", "IPR037923", "IPR018060", "IPR018062", "IPR014710"], "interpro_used": ["IPR009057", "IPR018062", "IPR003313"], "interpro_unused": ["IPR018060", "IPR037923", "IPR014710"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein should have a Integral membrane bound transporter domain that functions as a probable transmembrane transport component, predominantly within bacterial species. Predicted to adopt an all-\u03b1 configuration, this domain is associated with putative arylamide transporters, such as those found in *Mycobacterium tuberculosis*. It is expressed in Noccaea caerulescens (Alpine penny-cress) (Thlaspi caerulescens) and corresponds to UniProt keyword Cell membrane and Transmembrane helix.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 3066, 2162, 43, 12328, 3260, 4124, 9054, 3418, 1988, 4088, 1966, 43, 12584, 9117, 4860, 4594, 16, 7700, 2651, 4543, 3038, 18, 4396, 1942, 14103, 1925, 2136, 17, 160, 9674, 16, 2052, 3418, 1977, 2458, 1956, 6770, 15578, 5482, 10538, 16, 2427, 1966, 2690, 2435, 1922, 14, 16389, 8449, 14, 18, 2176, 1977, 3198, 1922, 9812, 3375, 5376, 2332, 29755, 12709, 2099, 12, 14089, 2053, 4959, 16323, 17, 18401, 1036, 13, 12, 1913, 24605, 10984, 2332, 29755, 12709, 2099, 13, 1930, 8852, 1942, 20709, 11121, 2538, 2024, 3260, 1930, 9117, 7864, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "AGSLSSAALPVYFFRYCVELFRGDFLSERQFPKRVLDILCVWKARERFVFAIKCSISLGISLVSGRQGTLTVANSRLQGTAMGRFLPLLPWIAITVFMRHSLILGRRNYGAPTDFAIARIVEDSNTEEETRSGNKGLSLAVLFGIMYNKKNGYWSGLTVASVYGLLCCSVFQNLQEFRVYGQPGGVTAAIAAL", "metadata": {"id": "A0A1J3JQ42", "cluster": 21788168, "interpro_all": ["IPR049453"], "interpro_used": ["IPR049453"], "interpro_unused": []}, "task_type": "infilling"} {"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. Furthermore, the protein contains 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 has been characterized in Streptomyces triticiradicis.\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, 3677, 16, 1920, 2213, 5461, 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, 2258, 2252, 4378, 1922, 22874, 5083, 2002, 11979, 7408, 3349, 1036, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MPVDEDAYDDFYRRGVRAVRREEYAEAFYWFSRAHAAGHTEPVALYAEAARAYREFTATEDLDLLDRSVALNRKSVRSAPPGLQRGRLTDLNEALGVAHEALDVLPGGHCARLKALRTAVEGIGIPALKQSGGAPADRVALESSLCGALSSLAWHTNEAPLLDPDVDLVSRNNLAAALIIRGTWRSSLDDLNFAVEVLCAATAAVDAADLMGRAADKRDAEAAEEYLKEALRRMPTGHPNRRVRESAVTHARALAAAGQWSEAVEEARKAAALVTGGRAAVEVNRALGKLLMGAACTETDYVYAEVKTGQAVALLDRFHHGKEVSDRREAVAALRAAAEANGSSIEAGDRADALVAARAAVTLLREFGWAGLDRDDQVRSMQDGKAMPREAAALAIDLGQPELAVGDLADLAAHDPARAAELEEVRATLNEDDRLGGEERLRLARRWQGPPAFGKLAPAAAEGPVVIVNISTIRCDAILVLPGGKTDVVKAAAEPGATFLERDEARHTVHDTLEWLWDHIARPVLDRLKWPTESPLHAAGRYPRAAEDPTEPVGLPYAAVSSYTTTLSALVDARQRAVPVDPTLLAVALELKEILGHRRLTVLAEDEATSAAVRKQLPAHAWAHFADLNLLDIADLRLDTADLAFLSACQTRLGAGQLPDEAVHTAAALRIAGFRHVDGPTSADAARALHHAVGELRARHPTDPTLWVPFVHDGPPEAADLIYQLLHTAGEPGDPFVVWQPAPVRTLMLASLRDVLRDRYHTQLLIALERAQYEAIGDADSKAIGLGRDAVGRTAAGQHASEAATTFMAALRARGEAGVEATRCALEALPPAHVERPFVAARLDEHGIAVRKGEMLDAFTKAAEQDRLFAARCWSGVTMELLEQGRSVLWASTLHLRQLVREVRESKKFAGFLLPDVDVPGIDKVANTYLNALATDPPRLWWCPTASLTVLTDTGRGHAVLPGVAEELRCHGWLDMTAPAGSGLCLRDGVATLWSISDQAASQVAAAFYRRLDSP", "metadata": {"id": "A0A7J5DI32", "cluster": 22704229, "interpro_all": ["IPR024983", "IPR011990"], "interpro_used": ["IPR011990", "IPR024983"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is included in the Cyclic phosphodiesterase superfamily, which contains enzymes featuring a $\\beta$-barrel catalytic domain that process cyclic nucleotide substrates. Specific activities include the hydrolysis of nucleoside 2',3'-cyclic monophosphates to 2'-monophosphates in animals, and 2'-5' RNA ligase activity in bacteria and archaea that forms atypical phosphodiester linkages. In addition, the protein is categorized in the RNA 2',3'-cyclic phosphodiesterase family, which comprises bacterial and archaeal enzymes that hydrolyse RNA 2',3'-cyclic phosphodiesters to yield RNA 2'-phosphomonoesters. In addition to their phosphodiesterase activity, members of this family are capable of ligating half-tRNA molecules in vitro. It is found in Rhodothermaceae bacterium RA and is linked to UniProt keywords Hydrolase.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 9821, 24821, 13975, 16, 2154, 5461, 5038, 29931, 43, 8, 38, 4666, 8, 17, 19560, 6804, 3418, 1988, 2585, 9821, 5489, 6249, 18, 2487, 4209, 3951, 1920, 9128, 1927, 18015, 22, 11, 16, 23, 11, 17, 9821, 21363, 1036, 1942, 22, 11, 17, 21363, 1036, 1922, 3555, 16, 1930, 22, 11, 17, 25, 11, 3146, 11905, 2455, 1922, 4802, 1930, 21501, 1988, 4952, 10834, 20184, 1967, 19949, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 3146, 22, 11, 16, 23, 11, 17, 9821, 24821, 3416, 16, 2154, 12936, 4543, 1930, 22367, 5038, 1988, 21686, 1021, 3146, 22, 11, 16, 23, 11, 17, 9821, 20184, 3341, 1942, 4307, 3146, 22, 11, 17, 8078, 3947, 6802, 2156, 2045, 18, 1922, 2459, 1942, 2310, 24821, 2455, 16, 4678, 1927, 2052, 3416, 2032, 7131, 1927, 3650, 2287, 4768, 17, 10089, 4206, 1922, 3596, 18, 2176, 1977, 2435, 1922, 11490, 2916, 26016, 5376, 1021, 14061, 4313, 1930, 1977, 4624, 1942, 20709, 11569, 20748, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MVDSDGCAEPSRPMPRLFVALDVTDATRQALADAVEAIRTALATVQAAPVVLRGTGLGVFPPALMRLHAAVEAALTRVGLPPDERPFHPHITLPMRIDAFTLYASRLGPDGAQHHPLTTYPLHAAPHAAALRDDTLPARWTPPHQYHLTLRFLGEVPDSLRRPRVLFARIDETARLSRPDARRVRRFRARHADVRIE", "metadata": {"id": "A0A1V0DBY7", "cluster": 22983098, "interpro_all": ["IPR009097", "IPR004175"], "interpro_used": ["IPR009097", "IPR004175"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein features a Domain of unknown function DUF7580 domain that is found in uncharacterised eukaryotic proteins and exhibits detectable sequence similarity to protein kinase domains. Although its specific biological role remains undefined, it is predicted to adopt a structural fold resembling that of protein kinases. It is found in Microdochium bolleyi.\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, 3418, 1927, 5435, 2347, 4855, 1038, 8245, 4476, 3418, 1988, 1977, 2435, 1922, 23229, 3495, 10825, 2697, 1930, 9826, 7398, 3244, 6796, 1942, 2213, 4016, 4682, 18, 2876, 2496, 2487, 3933, 2770, 4497, 26687, 16, 2176, 1977, 4396, 1942, 14103, 43, 4346, 3728, 18994, 1988, 1927, 2213, 7784, 18, 2176, 1977, 2435, 1922, 14320, 2694, 2457, 10608, 6659, 1033, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MDIAGVVLGTIPLILYAIDKHKQRKTSHDVKRIRRRIFKELETHLKKAHPTHSAQFLDIIDRMEEILQQIMNELMIDSNGQPISQSDGSEWSQMKRFVKWNEDLNNLIGKPEMPSPDYNPLVTSRRAHFDSAHCDKSRTNAALVHEAIMTTWQCQWHKGTSTKSDEFVVAISVPERNKDWFESIVEVGTSLDCPPLSNTQTAGAKRAVSRGVRFSSDPTTCKTVRAQEVHAAPLPQISCLCVFTGALQKRDSTIRSISIASALRHVESSRHPCSLSKKHRLSVAAASCWALLYLHGSSIVLADQMPMVFHSFEKLQRAGKSVWPSHNTDELLGQTISDLLFELAQRSKRGSSVARSHRLSDLEIAEHWLYNKIYEDAGRPDRRTFDFSDFRTEFYKGVVAPIQAFHDIFDGNIDEVLRRNLEQRLLEATFISIGLQLGKTTRRHVGNGSRKALIEELRECCEEHHGALKLIKSAWVSDCPPDSTGIIPGTTMRNSFSLDTAPLGQCGTPWISSSEWSGSHSLQLLVRTHGRNKALFALGILLIELYVDTSFDELREQSYGYAIQRCIRCEFPG", "metadata": {"id": "A0A136IVB5", "cluster": 23887342, "interpro_all": ["IPR056002"], "interpro_used": ["IPR056002"], "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 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. Additionally, the protein incorporates a Toll/interleukin-1 receptor homology (TIR) domain that functions as a central signaling module in innate immunity and host defense by mediating homotypic protein-protein interactions. This conserved cytoplasmic region often possesses intrinsic NADase activity, cleaving NAD+ to regulate cell death and disease resistance across animals, plants, and bacteria. Furthermore, the protein features 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 has been characterized in Citrus x changshan-huyou and contains UniProt keyword associations Hydrolase, Leucine-rich repeat, and Plant defense.", "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, 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, 4950, 16, 1920, 2213, 19683, 43, 15204, 19, 9198, 17, 21, 3148, 9039, 12, 16661, 13, 3418, 1988, 4088, 1966, 43, 4101, 3197, 9059, 1922, 8539, 7611, 1930, 4423, 9720, 2007, 10239, 16350, 5518, 1935, 2213, 17, 2213, 3719, 18, 2052, 5305, 6823, 3031, 3868, 14465, 7598, 6577, 2051, 2455, 16, 28634, 6577, 15, 1942, 5741, 2024, 3539, 1930, 2573, 3554, 3436, 3555, 16, 4793, 16, 1930, 4802, 18, 3677, 16, 1920, 2213, 4075, 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, 2258, 2252, 4378, 1922, 24117, 66, 17583, 6150, 1928, 17, 5897, 25749, 1032, 1930, 5461, 20709, 11121, 2538, 5253, 20748, 16, 12624, 17, 5536, 6865, 16, 1930, 4496, 9720, 18, 3], "output": "MKGVLELIHTDLWGPSPTVSRDGYKYYISFVDDYTRYSWIYPLKLKSQAFEVFKLFKTQVENQFDTKIKMLQSDLGGEFRAFTDFLNQNGIIFRHSCPYTHHQNGLVERKHMHIVELGLTLMAQANLPLQFWWEAVHTTVYHINRLPTPVLKFLSPYEKVFKHKPEESFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYAQILIPVFYRVDPSDLRNQTGSFGDSFSKLEERFKENSKKLQTWRKALKEAASLSGFPSQSIRRESELINEVVNHILKRLDEVFRLRDNKNQLVGVESKVEEIESLLGVESKGVYALGIWGIGGIGKTAIARAIFDKISGDFEGSCFLENVREESQRPGGLACLRQKLLSNLLKDKNAIPGIDLNFRRISHMKVLIVFYDVTCFSQLESLIGSLDWLTPVSRIIITTRNKQVLRNWGVRKIYEMKALEYHHAIELFSRHAFKQNHPDVGYEELSSKVMKYAQGVPLALNVLGCFLHKREKEVWESAIDKLQRILHPSILEVLKISYDDLDDKEKSIFLDVACFFQGEHVNPIMKFFNASGFYPEIGISVLVDKSLIAIDSHKKITMHDLLQELGREIVRQESINPKNC", "metadata": {"id": "A0AAP0MBZ1", "cluster": 2426718, "interpro_all": ["IPR042197", "IPR044974", "IPR001584", "IPR002182", "IPR027417", "IPR012337", "IPR036397", "IPR000157", "IPR035897", "IPR036390"], "interpro_used": ["IPR002182", "IPR000157", "IPR001584"], "interpro_unused": ["IPR042197", "IPR036397", "IPR044974", "IPR012337", "IPR027417", "IPR036390", "IPR035897"]}, "task_type": "autoregressive"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein can be placed in the Bax inhibitor 1-related family, which comprises integral membrane proteins, including BI-1 and lifeguard proteins, that act as suppressors of apoptosis and regulators of ER stress. These proteins localize to the endoplasmic reticulum and interact with BCL2, BCL-X, and calmodulin to mediate a pH-dependent calcium leak essential for calcium homeostasis. It has been characterized in Cimex lectularius (Bed bug) (Acanthia lectularia) and contains UniProt keyword associations Transmembrane helix.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 10635, 4106, 21, 17, 2712, 3416, 16, 2154, 12936, 12328, 3260, 2697, 16, 2710, 2273, 17, 21, 1930, 3308, 11056, 2211, 2697, 16, 1988, 4033, 1966, 21664, 1927, 4091, 1930, 9098, 1927, 2668, 3071, 18, 2144, 2697, 14380, 1942, 1920, 13355, 12279, 1930, 6310, 1956, 17582, 16, 6717, 17, 66, 16, 1930, 17537, 1942, 8265, 43, 2087, 17, 3100, 5016, 9186, 4415, 1958, 5016, 7622, 18, 2176, 2258, 2252, 4378, 1922, 20090, 2783, 17533, 2168, 11519, 12, 7497, 25761, 13, 12, 25645, 2126, 17533, 2168, 2126, 13, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 18, 3], "output": "MGQNMSLDPAADEAGYKEDKFATLQLIFSSILIFGLTYDENIREWIFDRPWLCRTAPCNSILLAVMTACYALTAATAALITIVMTLFAKFAPCDITGCGPVFCIVGLAILVLHLLLAGVMVVFLSLYLIFITQLIIGLYVTIIELFMYLLAIIQACFGEDERVRKNFVSKVYGILIIFAVSGIVVYMILACCDSVRAQYELFVVYLAFLSTGFGIVASIVSIFIFAPIGKRESISPDEVILAVII", "metadata": {"id": "A0A8I6SA09", "cluster": 4502050, "interpro_all": ["IPR006214"], "interpro_used": ["IPR006214"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that can perform the following function: 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. In addition, the protein is assigned to the Protein of unknown function DUF4465 family, which comprises secreted or surface-exposed proteins primarily found in human gut *Bacteroides* that likely participate in cell-cell or cell-nutrient interactions. These proteins adopt a galactose-binding (jelly-roll) \u03b2-barrel fold, suggesting a specific role in carbohydrate recognition. It is found in Muribaculum intestinale. Give the amino acid chain.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 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, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 7772, 1015, 3416, 16, 2154, 12936, 8366, 2014, 3154, 17, 4616, 2697, 5985, 2435, 1922, 2616, 7660, 14, 27978, 14, 1988, 3205, 7352, 1922, 2024, 17, 2024, 2014, 2024, 17, 8708, 3719, 18, 2144, 2697, 14103, 43, 15996, 17, 2743, 12, 8988, 11560, 1012, 17, 12970, 13, 161, 17, 19560, 3728, 16, 3783, 43, 2487, 2770, 1922, 10590, 5708, 18, 2176, 1977, 2435, 1922, 6185, 26073, 18021, 5277, 1035, 6139, 1021, 18, 7031, 1920, 3835, 2687, 4659, 18, 3], "output": "MTGIIHYYLIINNMNRIIISIFTLAGALTLNAQSDIVVLDLTKATTTLNFDAENGAWTGTYDDDAESIDSQCFSFVHNSMGDYNTWWGFTASNSANNVRQDDTLKFQFSNMAKGGIVLNEDGTVKTDENDMPVVSAEVPYMVAYASSAFAKHPADMAFNDGKAYEAVGVYVNLNSYPYYCIEYGDSYARAFHNGDKFTLTIHGIAPDESERTVDTELASYTNGDLTINRGWKYVDLSSLGIVNQIYFSLKTTDVGQWGDNTPTYFCLDKLMVKPVSTSGISTVNANDTNISYDRANKTVSIGNASFASVYNTAGQCVMSSENNSFDISSLSAGIYVIKAGNSSLKIVK", "metadata": {"id": "A0A1B1S9T3", "cluster": 9674023, "interpro_all": ["IPR027828", "IPR026444"], "interpro_used": ["IPR026444", "IPR027828"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Target Function: The protein features a DAN domain that functions as an extracellular antagonist of TGF-beta superfamily ligands, particularly Bone Morphogenetic Proteins (BMPs), to regulate developmental signaling. It is characterized by a conserved cysteine-rich motif likely involved in disulfide bond formation and appears in proteins such as Gremlin, Cerberus, and the insect neurohormone Bursicon. In addition, the protein is associated with the Cerberus family, which functions as a cytokine involved in anterior neural induction and somite formation during embryogenesis. These proteins operate via a BMP-inhibitory mechanism to regulate Nodal signaling during gastrulation and primitive streak patterning. Furthermore, the protein can be placed in the Cystine-knot cytokine superfamily, which comprises a disulfide-rich, all-\u03b2 core domain found in diverse signaling proteins such as glycoprotein hormones and members of the TGF-beta, IL-17, and VEGF growth factor families. It is identified in Cladonema pacificum and features UniProt keywords Secreted.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 4075, 43, 11434, 3418, 1988, 4088, 1966, 1925, 5329, 8151, 1927, 5525, 17, 4666, 13975, 6908, 16, 4443, 3622, 23359, 2697, 12, 9809, 1036, 13, 16, 1942, 5741, 5878, 3197, 18, 2176, 1977, 4378, 2007, 43, 5305, 8666, 17, 5536, 5219, 3205, 3286, 1922, 11830, 5403, 3337, 1930, 5107, 1922, 2697, 2427, 1966, 2705, 26922, 1022, 16, 6580, 2361, 1957, 16, 1930, 1920, 11422, 3366, 10647, 23745, 2290, 13579, 8938, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 6580, 2361, 1957, 3416, 16, 2154, 4088, 1966, 43, 6137, 3286, 1922, 5477, 5181, 4408, 1930, 5714, 2394, 3337, 2409, 18453, 18, 2144, 2697, 15336, 3454, 43, 9809, 17, 5431, 2856, 1942, 5741, 13926, 3197, 2409, 14860, 2281, 1930, 18903, 5044, 2220, 16060, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 9446, 2053, 17, 26646, 6137, 13975, 16, 2154, 12936, 43, 11830, 17, 5536, 16, 2136, 17, 161, 4728, 3418, 2435, 1922, 6445, 3197, 2697, 2427, 1966, 11424, 10224, 1930, 4678, 1927, 1920, 5525, 17, 4666, 16, 2614, 17, 2752, 16, 1930, 5785, 2905, 2991, 5767, 18, 2176, 1977, 2899, 1922, 23415, 2290, 3368, 14148, 1989, 1930, 4075, 20709, 11569, 8366, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "CHAVDFVQESTHRKCTTKYTARGELNICMACRPDNNIELVHTCRCKIEIQNKLCTGTCKSVYTTKVQIQLDCPKSRKKRKRIRFR", "metadata": {"id": "A0A0A8KA18", "cluster": 12600199, "interpro_all": ["IPR016860", "IPR029034", "IPR004133"], "interpro_used": ["IPR004133", "IPR016860", "IPR029034"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein possesses a Fis-type DNA-binding HTH domain that regulates bacterial transcription and DNA structural dynamics through a helix-turn-helix motif. It typically functions within a homodimer to bind specific DNA sequences, activating ribosomal RNA promoters, inhibiting DNA replication initiation, or promoting site-specific DNA inversion. This motif is conserved in various transcriptional regulators, including those involved in nitrogen assimilation and virulence in species such as *Escherichia coli*. Furthermore, 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. Additionally, the protein carries a Sigma-54 interaction domain, ATP-binding site 2 binding site that corresponds to the second conserved ATP-binding motif (motif B) within the ATPase domain of bacterial regulatory proteins. It facilitates the ATP hydrolysis required to induce conformational changes necessary for interaction with the alternative sigma-54 factor and subsequent transcriptional activation. It occurs in Peptoclostridium litorale DSM 5388 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, 6255, 17, 2601, 2678, 17, 2743, 5334, 1023, 3418, 1988, 7014, 4543, 3213, 1930, 2678, 4346, 5565, 2596, 43, 7864, 17, 5165, 17, 7864, 5219, 18, 2176, 5745, 4088, 2651, 43, 21189, 1942, 4566, 2487, 2678, 3709, 16, 8019, 11196, 3146, 9026, 16, 7918, 2678, 5158, 6035, 16, 2014, 7356, 3200, 17, 2487, 2678, 14825, 18, 2052, 5219, 1977, 5305, 1922, 3425, 5224, 9098, 16, 2710, 2690, 3286, 1922, 6634, 22317, 1930, 9304, 1922, 3038, 2427, 1966, 14, 10210, 5178, 14, 18, 3677, 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, 4950, 16, 1920, 2213, 16252, 43, 5139, 17, 4584, 2835, 3418, 16, 4498, 17, 2743, 3200, 22, 2743, 3200, 1988, 8852, 1942, 1920, 2812, 5305, 4498, 17, 2743, 5219, 12, 5219, 44, 13, 2651, 1920, 9444, 3418, 1927, 4543, 4948, 2697, 18, 2176, 11374, 1920, 4498, 9128, 3414, 1942, 4769, 8523, 2840, 4680, 1958, 2835, 1956, 1920, 5012, 5139, 17, 4584, 2991, 1930, 4521, 5224, 2936, 18, 2176, 5110, 1922, 23045, 5406, 17414, 9734, 4471, 6277, 1021, 10964, 4522, 7331, 1930, 2258, 20709, 15010, 3213, 3640, 18, 3], "output": "MKRENLTDVDFKAIIEKSHKRCRDMGVDKTMERIKVALPFMKLLYKFLKGSGFIIDIADKNGYILSIVGDDDGTDMSEKSCGTNSIGTGLYEKTEHFIDIYRTWTCSSSPIRGTSGSVIGCLNLTGVYNAVESIENEIRVRRSKEELSQMHQYNNTIVNSEIFSLSEDRIIGKKVDGIVGNWKEVYLNGNRKKRFNLNAYPTKEISSGKNAYYTFEDIVGKSPQINEIIDYSKTIASTPSTNGPFIAINCGGIPKNLIESELFGYEDGAFTGAKKMPIDMQVTLLRVLQEKCITRVGGTRRIPIDVRVLPPLRQRREDIMLLIEHFLEKKSQRLGIESPKISQLENRIENIVVNGKLPMDFYRLSAGSKAPAQNGNISKAARVLNIDRSTLYKKIEKYSISPSVILTGRKLQNILEKNDELVIRLAKDMGMTVCPFQLAELVHPHTLGLVFAIDFGILSIDNKGYVKSANNKCLIFSSIEKDDAYSNIEFGKISGMVVMLKDIENVYELVNKYVLIQGESGTGKEVLAQSIHNSSSRRGGMPGKFELANNGTIFLDEIGEMAATNKNLIDEIKKEHFRQDLYYRLSVIPIYKDYELLISYNWPGNVRETGQKYEYKMCSLSEWEKIAIAQCIQNC", "metadata": {"id": "A0A069RQJ6", "cluster": 15395960, "interpro_all": ["IPR003593", "IPR029016", "IPR009057", "IPR002197", "IPR027417", "IPR000014", "IPR035965", "IPR002078", "IPR025662", "IPR025943", "IPR025944"], "interpro_used": ["IPR002197", "IPR003593", "IPR025943"], "interpro_unused": ["IPR002078", "IPR000014", "IPR009057", "IPR025662", "IPR025944", "IPR029016", "IPR035965", "IPR027417"]}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein carries 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. Moreover, it is part of 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. It is derived from Schistosoma mansoni (Blood fluke) and features UniProt keywords Transducer, G-protein coupled receptor, and Disulfide bond.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 16252, 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, 3950, 16, 2176, 1977, 3131, 1927, 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, 2176, 1977, 3595, 2037, 16587, 20084, 26087, 12, 2877, 2848, 3324, 13, 1930, 4075, 20709, 11569, 14848, 16, 49, 17, 2213, 6416, 3148, 16, 1930, 11830, 5403, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MNNNITATTTTNTTYNTTYFYIINNQSIIYNTLNNTTNHLLHLERRYWCLVVLSVIRERSLRNATNWFIVSLAIADISLAILVMPLATDVFVMFDVLFCTASILNLVAICLDRYLAVTKPIIYAKVSFLIAVPLICGLNINRYNDPTICQSFNALYIIIKQRHKSLRLNQSTKQQSTTLSSFQQSQQLLQQQQEEVPTLQLYDSQCFNDDQTLTIQSSSSTKVLEDPIQHIQLTNDLNHIRNSCISSHTDRLIYAITHTYPLDHFKSTNQIQGINLNEDHNHNNNLILSNSNQASLISPHTNDDDDDDDDGDEEEEEVSGTTFQKEEESLKEQNQITHNSSMILQEEVICNSIKQSNTSRLSIQKLKYHTKNSTLRNLFTLSWIHTCLNNNHSNVYNSSTSNDSNYSWPCLKNYSDQDDNEDDDVDDDDDDDDVVDEDEGNDHEYYTTYQSLNKNGFMKLNNGFNNNNNNNNNKIIKNNQQKNKKINLNLNEKHKFFEFNDQFKQNLQLMIQYLNKFFKLFHINTNRNHYINEKNQNHNHSPKHHIILKNKNILSNKEKKATKTLAIVLGVFLACWLPFFSQLMSSCTWLGYINSALNPIIYTIFNMEFRIAFQKLLHIKLCLMIFSIATLFGNSWLEVVNGYWVFGTMICHNNMRRVQISIALVWICSSLGSFYLPAIILIVVYQRIFALHQQQSNLHDEEEERRRQRESYENSLDLHFEGPRNDIPSPNLNSINNPFNQLSTSETDLNTLKSFESPKHCDHVYNTSPIKHSPFKQSKLSCHHQHHHHHYILFKNMSECYGLSSDEITDHSSCKCCQHSLCQSSFEQSYECSQCHPMIIQKFKKFSRGKPINHINHSILPIDIDISSEKFIKKISCINITLGLCIYLGLDQYNICEYAN", "metadata": {"id": "A0A5K4F477", "cluster": 15510288, "interpro_all": ["IPR000276", "IPR017452"], "interpro_used": ["IPR017452", "IPR000276"], "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 START-like domain superfamily, which features an \u03b1/\u03b2 sandwich structural fold that binds and transfers lipids such as sterols and phosphatidylcholine. This domain often functions as a regulatory sensor in multidomain proteins, modulating the activity of co-occurring domains like Rho-GAPs or homeodomains in response to ligand binding. In addition, the protein is classified under the Carbon monoxide dehydrogenase subunit G family, which functions as a component of the *cox* gene cluster involved in carbon monoxide metabolism. This system is coordinately transcribed to enable the utilization of CO as a carbon and energy source under chemolithoautotrophic conditions. It is derived from Aeromicrobium sp and contains UniProt keyword associations Membrane, Transmembrane, and 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, 3063, 1922, 1920, 6413, 17, 3189, 3418, 13975, 16, 2154, 4075, 1925, 160, 19, 161, 18038, 4346, 3728, 1988, 6876, 1930, 19180, 8238, 2427, 1966, 29991, 1930, 23842, 18, 2052, 3418, 3868, 4088, 1966, 43, 4948, 6443, 1922, 9184, 2954, 1921, 2697, 16, 10871, 1920, 2455, 1927, 2081, 17, 6966, 4682, 3189, 10585, 17, 11349, 2014, 4502, 17166, 1036, 1922, 2644, 1942, 5207, 2743, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 5056, 26662, 9294, 5903, 49, 3416, 16, 2154, 4088, 1966, 43, 4594, 1927, 1920, 14, 6374, 14, 2359, 4377, 3286, 1922, 5056, 26662, 4714, 18, 2052, 2433, 1977, 11865, 1954, 10078, 1942, 8675, 1920, 8422, 1927, 2081, 1966, 43, 5056, 1930, 3844, 4585, 2441, 13534, 12191, 1963, 6952, 1984, 13653, 2961, 18, 2176, 1977, 3595, 2037, 6049, 22980, 3821, 1989, 2056, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MKLSNSFSIDRPSAEVFAAFLDIERVASCMPGSRVTYTGQFKILEVDHDQLRLTMRAKGRELRGAGNADANTELSIRGKVAQFGRGVIGEVTDGIMQTFAETGLPDPSSRDEEEGPAAFDGPPAAATGGDFDVGTVAAAGLAAYLGARIGVGRKDRYRRNGRPEPDTYEGEVKVKVGPLGVAHIIAQLSEQQGRTLVAIASNVEQMLAPGGSSAPWSLIIRPLLQRHMRSM", "metadata": {"id": "A0A924LBM2", "cluster": 16536231, "interpro_all": ["IPR010419", "IPR023393"], "interpro_used": ["IPR023393", "IPR010419"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the protein function: The protein belongs to the YbiA-like superfamily, which functions in the disposal of reactive riboflavin biosynthesis intermediates by catalyzing the hydrolysis of their N-glycosidic bonds. This family includes the *E. coli* swarming motility protein YbiA and acts to neutralize these highly reactive metabolites into innocuous products. It has been characterized in marine sediment metagenome. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 14440, 1942, 1920, 21000, 2126, 17, 3189, 13975, 16, 2154, 4088, 1922, 1920, 23452, 1927, 6079, 28849, 8132, 12386, 2007, 29601, 1920, 9128, 1927, 2310, 56, 17, 7533, 12546, 9031, 18, 2052, 3416, 5921, 1920, 14, 47, 18, 5178, 14, 26149, 1941, 9254, 2213, 21000, 2126, 1930, 8016, 1942, 25885, 2144, 3626, 6079, 6926, 2460, 6078, 1994, 10358, 4461, 18, 2176, 2258, 2252, 4378, 1922, 10789, 10363, 16552, 2225, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MKFRGNYGFLSNFYPCKIIAWGVEYPTAEHVYV", "metadata": {"id": "A0A0F8ZFJ2", "cluster": 17348318, "interpro_all": ["IPR037238"], "interpro_used": ["IPR037238"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein has a HTH-type transcriptional regulator MT1864/Rv1816-like, C-terminal domain that functions as a regulatory module in bacterial transcription factors, particularly within *Mycobacterium tuberculosis*. Located downstream of a DNA-binding helix-turn-helix domain, it participates in controlling the expression of MmpL lipid transporters, potentially by binding fatty acid ligands to trigger a transcriptional response. Also, 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. Additionally, the protein carries 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. It is identified in Nakamurella alba and is linked to UniProt keywords Transcription regulation. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 5334, 1023, 17, 2601, 5224, 7888, 23317, 11617, 1006, 19, 8309, 26675, 1016, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 4948, 9059, 1922, 4543, 3213, 2790, 16, 4443, 2651, 14, 16389, 8449, 14, 18, 4810, 5863, 1927, 43, 2678, 17, 2743, 7864, 17, 5165, 17, 7864, 3418, 16, 2176, 17241, 1922, 7138, 1920, 2294, 1927, 6736, 1024, 4486, 10538, 16, 5063, 2007, 2743, 5934, 2687, 6908, 1942, 6086, 43, 5224, 2644, 18, 2222, 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, 4950, 16, 1920, 2213, 16252, 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, 2176, 1977, 2899, 1922, 14510, 1976, 2027, 11560, 1019, 5311, 1019, 1930, 1977, 4624, 1942, 20709, 11569, 3213, 3640, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MSAAPDPADAGARRYHHGNLAAALVDAGFELARTGGPDAVVLREAARRVGVSAAAAYRHFAGHAALRLAVKERAMQELGAQMAAAASAALPAGAAGDPAAEIGRFAALGRTYLDFALRESGLFGCICAGIGEEHDEGSWTLDSATPAFGVAFDLLGQLVDAGVVPEQFRRSGALVAWAAVHGLAMLTLAGPLADFTDDQREALYDDAVHILLQGLMAR", "metadata": {"id": "A0A7K1FNX9", "cluster": 17650265, "interpro_all": ["IPR009057", "IPR050109", "IPR001647", "IPR025996", "IPR036271"], "interpro_used": ["IPR025996", "IPR050109", "IPR001647"], "interpro_unused": ["IPR036271", "IPR009057"]}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein features 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 classified under the OTU domain-containing deubiquitinase family, which functions as a group of deubiquitinating enzymes that hydrolyze linear and branched polyubiquitin chains with specificity for various linkages, including 'Lys-48' and 'Lys-63'. These proteins utilize an OTU domain, often alongside zinc fingers, to modulate immune responses by terminating NF-kappa-B activity, while also regulating Wnt signaling, autophagy, and programmed cell death. In addition, the protein has a DUF3638 domain that constitutes an uncharacterized region found in eukaryotes, typically spanning approximately 230 amino acids. It is distinguished by the presence of two conserved sequence motifs, LLE and NMG. It is present in Pinguiococcus pyrenoidosus and is linked to UniProt keywords Ubl conjugation pathway, Thiol protease, and Repeat.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 4075, 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, 5947, 2441, 1920, 20392, 3418, 17, 3165, 29436, 2051, 3416, 16, 2154, 4088, 1966, 43, 2210, 1927, 29436, 2287, 5038, 1988, 7222, 6931, 4258, 1930, 16484, 22405, 7835, 1956, 4896, 1958, 3425, 19949, 16, 2710, 11, 3629, 17, 3427, 11, 1930, 11, 3629, 17, 4968, 11, 18, 2144, 2697, 12561, 1925, 20392, 3418, 16, 3868, 17764, 7997, 18233, 16, 1942, 8480, 3743, 3387, 2007, 5475, 2287, 4651, 17, 12093, 17, 44, 2455, 16, 2679, 2222, 6773, 7028, 3197, 16, 6661, 16, 1930, 13839, 2024, 3539, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 4855, 10892, 7576, 1025, 3418, 1988, 14879, 1925, 24528, 3031, 2435, 1922, 15021, 16, 5745, 13346, 3993, 14980, 3835, 4576, 18, 2176, 1977, 12080, 2007, 1920, 2990, 1927, 2288, 5305, 3244, 8277, 16, 10748, 1021, 1930, 2943, 1029, 18, 2176, 1977, 2481, 1922, 8701, 11056, 3940, 4879, 2437, 1957, 26889, 20815, 13650, 1930, 1977, 4624, 1942, 20709, 11569, 4803, 1024, 14122, 3374, 16, 13914, 7154, 16, 1930, 6865, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "GGMGGLDFGRSAAVAAQQAHTASTTINFANANANANAFGASHGFGGGVSQAGSSLLGHLGYQMGPGLGSTSPPKGGRSRGGKGKNRFSNLTERLSSAGLEQKPLKVVWMYRFQDNECFAQLSTSSSHILESAIQDLEASSEVEEPSTLFYRRRLWVYDELHTTSENVQIFRATHIKRQRPDFSDPTLPVPNGADNDQFQVARLEIEAQLEEIQKLSMYTKEPDVRLRFGDVLSILTMLSDRPDNILGTGGQFGFWRLYPLLGERWTKGPNNTWTKSYGGGSSTRSDKFFTSHRLGKLLYQFHRHANSQSTLNSVITNLCQNPHLARRFPKYPRKHSSSGNAYYRTTGSNDGTLKLVNMWEWCNRGLRRLHLLRSPPLPPHPALPPSEPEPEDGIGLRHLGGKDAWLRPDVSDLSSDSIEIRSFADDQIKALSEETRFDLLREAELRGLNLTHFSSEMRDLQSTDSLVVIFFGADWCPECLKTKPLFHSLAQQIGVHTYFYVDVDLCSNAAHDYNIRGIPATCFVRSGQLQGRSLLGGGGAWQGKENYRRYVEENPLAGANSLERPSGTASKRQSDAYLALATDGKDVLNLATVPLRDVASNVEEHPRSTLGLESVQSELPFDVSAHAYSGTKVAQYSEVLNKSSVTLLKGFDFLRIRDSFDDLTRSEDLLDALAALTKDIMQQVRRVMLKDERMVACGLPLLSHAANFVDLESVEDPTPIKLPLFVSSLLSRLQGEDLRRYNPFLTDERIKALSSFVVLLLLRANRVGHGKRCLGAALKLQKLIKSVKVELSTQLIQATRTLSGLITTQRFCVRGISKGQADVLATMDSSQLAKLEAQNSLEVDPRFLVFEFVWNLLLRKKQVEICDDFRRSMAQPLLALILADGEKLVLNMVPKALLEMSRGLLRQTFGSIIVKRVMTLSYDRSSYPYVSLFRKLRQIARNRGIVALTPTTMKSLMLSYVETLRKIHGYNTLERILQMIKGGAMLLDEVDLILHPLKSELNFPVGLKFDLDLSEDGHRWAIPSFLIDAIFYYKTRKCSVLDARGKALKVLPHIILLDLRFYNTELKPEMAQWAYLWLVKQQFTGLNKAEVLRYILNGSASQSAIQERVALLKKEADAASMIYDGAAQLDEALDQSQNQMHEIDTQIASCKKRIAEYEQPPDGSGDNSQILYLDGCETGCSPFKRSRSSSRSGLDGLQGLSRSLLRSGEFRCMVLVGPPYFADTKTKENPGWRVNDEIIRPIDVLQKCIQEGCLDGLQAEMLGIRGRKVDPALSGLRFYKCPKQRIAIYDVKELSEWINSDPAVVDPLPAQEKVFQEFQDVKDAEMSEGVVILDDDDEPPPAPALLQMKSSGTQVLQELRDQLKSLEGAKADQYAALHELMSRLREELEGLDEALRQKCINPAAELLLPDLKERLEKRLLEDRYLDPQALRAITKGFEFATDAIVLSGKVMANVHNFKFRKFLNLMFNQVNTFLPHALAKINRVSFGVLTTKEVQTELRRNRASEFAHPDVIISLTVMAFRYQGLRKTDFTHVMDAVAEDYSKEPGPPTKRRTTHMYNDWVHSSDGFVRGIDPNPFRAQNSGEVGADDIGDQMSKLYKLLRYNPNVISYYLFRHIFPEYTRLQTQKISACGQELGSDILINDKIGFSGTPSDLLPRGLGRCIYELGDDGKMLTTVLNLDLIAKQSVAGRRVNALIDTGALITGYSNEEVARQLLQRGLEWCDGVVFLDDEDRKQIVVRATGRVIPADQCGIPLERRFAFYDQIVFRDYVQGAFRMRGIGQGQCIQILIIPEVLELIKKTMRTCEDGCSAILQATLACEQDTNSNEAYEGQYAATPETDVHVLQGVTAWLILNTHAFRKVAKTADAFRDGTELENEIMPELPSPAESLRVFDEDVRFDLPAEVPDPTPFSVVLENNLEAHRAFVPDEEIDLARSIIAESRISKEVEQRKDQEIEMEQFIEREYNRENEEPKHWRLEKLVKAVPNAVLDDLDSQAHPFRRLSVFKLPHQEPLPFPANLGTSINYFDPSWSGSTVGTNILKELQVDSESDTAENLAKSVKLLSMLAAKGAEVAGPVDQMRILSRLHSNFNMESEEEARDLLQRIVPDSPVQKDRFYIAVSLSEAETLRRVLHVHSGSGAGLERPIFNTTGDNGEEDCVEFALRYSPMSSHGVGSAGDAGLLLDASPGWSPNHREITPQEEALTRACFRFFDGDLTYSKASLHELIRGLSSANLTSRKRFFGNVMARRRRLQKKWQDTKLKRAMTTKTEWEVLKQKCYAFYMRIALQTAGLRGEEIWAALRFLGLKDLVVKDVAEIMEFADVRNRGELDYADFTGLITLDLEEHEQDEEDDPNASVDRMMERENLLPEKLEPYGSDEIRVVLKQRYQEQLAYIDELHTRARRLGSANPDPNPGLPLQSYKALLYHFAAEVPLRTTKVNQVRNSHSVRHNAVMSIRSGSCVSIYVPSWYIDIYNKDALAPPSGNAVEHDELRGSAAALLRFGEIDESPPRRRNIATCYVNCLGDVGPLPALDLDAEDYGDDEWDAEEPVSKTVSSRAPGNPGKRVIRESPFAASLQKGTASSLNPTEAEKEEAEEEQPPEKKPVRRRVKIGQYHSLVVSANRKKCKLDLFIDGEPYRTFTSPEVHPADLQWTERIYLAGSGKQSENGGCWMGKPARRRDNSGGKSSRGGRSGRNLEVPIDLEEFPPARFRVQFDDPTGQTDVSFGYTGWGGGQYPVQSQEHSALYRMLVAIVARFGEQSHTYARVIPNDFSKAAFARLIELSTEAEKDSMLDRMEADVKYTDSTEEAKLMHALKFKCQRIAMPMDTRTARHGESKVRQMIMGAGKTTVVSTDPETEMLETATITGLRESSRILTRISDILEGGIKKKCIQGERAFAPALSSLSEGFAEAAKQVTHHVENKPDRLYKRVSKASHKSFANYPDFLKKLWDLDIHVFTDNLQRHTEENIEKLQAKSQNEASPSGDDEIRGLRSSLVEEIFFYPMVPKTRLKLAVPFIGKDVPSLSVEEYDEREVVQLRHLQRSNHPDIMSYAVMREGWDISQIHTTGMDIKHKVNATALLTLGKDMSIKNEHIQYNMLCKQSLMTVYRSSLRGGSQLDTEQEREQELEQEQRRIRSVIVLLEYSPKAQEENALMTAAAMEAALKSNILTPSATSEEVLRSPTLSVAGATRWEAFRCFDTDDKKLRDEALEMKQMDAYNRRSREEFTVALQFMYLKSLPKLMVSVAAAQQGEAPTPTAEEEDQKDGAEE", "metadata": {"id": "A0A7R9U396", "cluster": 19600837, "interpro_all": ["IPR022099", "IPR022105", "IPR011992", "IPR051346", "IPR036249", "IPR013766"], "interpro_used": ["IPR013766", "IPR051346", "IPR022099"], "interpro_unused": ["IPR011992", "IPR022105", "IPR036249"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein includes 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. Also, the protein is classified under the 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase family, which encompasses enzymes such as ACC deaminase and D-cysteine desulfhydrase that catalyze distinct elimination and ring-opening reactions. Members of this family convert substrates like 1-aminocyclopropane-1-carboxylate (ACC) to ammonia and alpha-ketobutyrate, a function utilized by rhizobacteria to promote plant growth, or degrade D-cysteine into pyruvate, hydrogen sulfide, and ammonia via alpha, beta-elimination. It occurs in Thermotoga petrophila (strain ATCC BAA-489 / DSM 13996 / JCM 10882 / RKU-10) (Thermotoga naphthophila). 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, 5921, 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, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 21, 17, 3835, 22170, 27379, 2516, 17, 21, 17, 20877, 27955, 19, 46, 17, 8666, 30311, 10806, 2051, 3416, 16, 2154, 21569, 5038, 2427, 1966, 2280, 27955, 1930, 46, 17, 8666, 30311, 10806, 2051, 1988, 18170, 4493, 9570, 1930, 6335, 17, 9497, 5298, 18, 4678, 1927, 2052, 3416, 14450, 6249, 3189, 21, 17, 3835, 22170, 27379, 2516, 17, 21, 17, 20877, 12, 2280, 13, 1942, 14880, 1930, 4595, 17, 21471, 16119, 16128, 16, 43, 2347, 7079, 2007, 13458, 10296, 1942, 5527, 4496, 2905, 16, 2014, 17069, 46, 17, 8666, 2460, 11867, 16, 6201, 21135, 16, 1930, 14880, 3454, 4595, 16, 4666, 17, 9570, 18, 2176, 5110, 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, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MRIDLSLKPTPVQFLKRLSEEYGFNIYVKRDDLTELVGSGNKIRKLEYLLWEALKKGATTVFTCGGLQSNHARATAYVSRKHGLKPVLFLRKGEKVLNGNLLLDILLGAEIVEVSQEEYERIDEIFDVHKKMREKKGEKVYVIPEGGSNSLGAFGYFNAVLEMKDQLNLESFDAIVCAVGSGGTIAGLSAGISFLEYHVPVVGVNVTTKNSDYFVGKVKRIISGMEEHGLKINETVFKVVDDYRGPGYAIPSSEDVEILKEVASIESIILDPVYTAKAFRGMIEMFRNSGKNVLFIHTGGIFGLFAQSGRLV", "metadata": {"id": "D2C7L1", "cluster": 19701244, "interpro_all": ["IPR027278", "IPR005966", "IPR001926", "IPR036052"], "interpro_used": ["IPR001926", "IPR027278"], "interpro_unused": ["IPR036052", "IPR005966"]}, "task_type": "autoregressive"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein is a member of the SMN complex subunit Smn1 family, which constitutes a core component of the SMN complex that catalyzes the assembly of small nuclear ribonucleoproteins (snRNPs). These snRNPs serve as the building blocks of the spliceosome, playing a critical role in the splicing of cellular pre-mRNAs in eukaryotes. It originates from Sesamum angolense.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 23506, 2796, 5903, 23506, 1009, 3416, 16, 2154, 14879, 43, 4728, 4594, 1927, 1920, 23506, 2796, 1988, 17097, 1920, 5957, 1927, 2858, 4254, 18347, 14070, 12, 11970, 13983, 13, 18, 2144, 11970, 13983, 7120, 1966, 1920, 9086, 7644, 1927, 1920, 10708, 4283, 16, 14797, 43, 4140, 2770, 1922, 1920, 8490, 1927, 3689, 2097, 17, 8806, 1922, 15021, 18, 2176, 22970, 2037, 9924, 1976, 1989, 3409, 2456, 3355, 1021, 18, 3], "output": "MHGMSGSTTEGKSVSNAEEHSEHVEDVGGTAKLLQVKENSPNGTHGLINEKHAAKSGSPGNSVISSDVQSHELEVSDSRYSSSSINTAIGIINTLFPNRNSMSPQDSDYVKTAMVAAEGHSAESNKSTTDLDVVLNAWYSAGFYTGHAASLCSSASGVVSGKPSLPAAEADNGSNEFGPLELGSSAKCAGSSNIQNQTTWYSNGPEDYSQLLNKYYVHLLLKSGTCIDKSCDAIPEGSQKALSSLKEANGVKEKSVGMEMKYLSEQSLEKKRHSHSLKCWY", "metadata": {"id": "A0AAE1WAT5", "cluster": 20721746, "interpro_all": ["IPR040424"], "interpro_used": ["IPR040424"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that has the following function: The protein carries a Cyclic-di-AMP phosphodiesterase GdpP-like, PAS domain domain that adopts a typical \u03b1/\u03b2-PAS fold formed by distorted \u03b1-helices and a five-stranded antiparallel \u03b2-sheet. It is typically found in the N-terminal region of GdpP stress signaling proteins, where it functions as a regulatory module for phosphodiesterase activity against cyclic-di-AMP. Moreover, the protein incorporates a DHHA1 domain that is diagnostic of DHH subfamily 1 members and is predicted to possess RNA-binding activity, as suggested by its presence in alanyl-tRNA synthetases. This approximately 60-residue region contains a conserved GG motif and is typically found adjacent to the DHH domain. Furthermore, the protein should contain a DDH domain that functions as a predicted phosphoesterase, typically exhibiting 5'-to-3' exonuclease activity on single-stranded DNA. It plays a key role in DNA repair and recombination pathways by catalyzing the processive degradation of ssDNA, as exemplified by the bacterial RecJ protein. It occurs in Culicoidibacter larvae and is described by UniProt keywords Transmembrane, Membrane, and Manganese. 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, 9821, 17, 2137, 17, 3681, 24821, 15217, 1034, 17, 3189, 16, 9233, 3418, 3418, 1988, 24032, 43, 5939, 160, 19, 161, 17, 9233, 3728, 5333, 2007, 22797, 160, 17, 12789, 1930, 43, 3628, 17, 10338, 28892, 161, 17, 11130, 18, 2176, 1977, 5745, 2435, 1922, 1920, 56, 17, 4262, 3031, 1927, 15217, 1034, 3071, 3197, 2697, 16, 2597, 2176, 4088, 1966, 43, 4948, 9059, 1958, 24821, 2455, 3316, 9821, 17, 2137, 17, 3681, 18, 3950, 16, 1920, 2213, 19683, 43, 6781, 2722, 1009, 3418, 1988, 1977, 4785, 1927, 6781, 1023, 16227, 21, 4678, 1930, 1977, 4396, 1942, 7150, 3146, 17, 2743, 2455, 16, 1966, 3978, 2007, 2496, 2990, 1922, 10527, 16323, 1024, 17, 10089, 18185, 1036, 18, 2052, 3993, 3276, 17, 6181, 3031, 5461, 43, 5305, 12358, 5219, 1930, 1977, 5745, 2435, 6811, 1942, 1920, 6781, 1023, 3418, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 28549, 3418, 1988, 4088, 1966, 43, 4396, 8078, 8342, 2051, 16, 5745, 12196, 25, 11, 17, 1942, 17, 23, 11, 24966, 2455, 1990, 2957, 17, 10338, 2678, 18, 2176, 5705, 43, 3834, 2770, 1922, 2678, 5059, 1930, 7827, 3873, 2007, 29601, 1920, 2585, 2320, 4877, 1927, 15063, 16, 1966, 22236, 2007, 1920, 4543, 2090, 1013, 2213, 18, 2176, 5110, 1922, 6710, 5670, 13756, 7972, 2341, 1915, 8784, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 16, 3260, 16, 1930, 19516, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MKRYTPQRIKNIRRIGYIIIAIIGVVLPLIILLFSTSGNPFDEPLGFLKSYLGLLAIVFFVLLIATIGVSFFFMHIVERRYEEYVKGLAADIDNTSFEFINEMNIGVLAYDELKKISWTNNQLNDLLGEVIVDRTLSEVFPHVNLQQSEDNNDGWLTFEQVPVGTKVFKVLHNVQKHIIYLINVTEEYELRTHYENEKTVIGYIFIDNYDTLSSMEDRLGIDIYSHIQRAISVWGQQFNIYLRRYSSYRWIIVGDQETLATILDDKMSILDRVREIGKEFAAQTTVSIGFGNGDARYVDLSRQALEALELAQSRGGDQAVVKDEKNNVQFIGGKTNTIERRSRARARAMANTLHAFIEQAEHVLIMGHRYGDLDSLGASMGVLEIVEAHKKKAKIVIDFETWSEDTVQQCKELLSDHSDIFIAPVDLDFRNYNNDNTLVIVVDVNTPALVEFDRILSYPTIVIDHHRRGAETIEKTLVTYIEPYASSAGELVTELISYQPMHINLRNSTATLLFAGIVLDTQNFIVRTSARTFDAASLLRTYGADGVWVQNIFKEQFDSFFEKYRIIEQAIIFHNHIAIAPCREKDNYTRQFLAEVADRMLSFQGVQMAFAVGELDDGTVGVSARSIGSDNVQIIMEKLGGGGHFNNAAAQIKDTNIDEVIKQIKTIIEE", "metadata": {"id": "A0A5R8QHD8", "cluster": 22342973, "interpro_all": ["IPR001667", "IPR038763", "IPR003156", "IPR049553", "IPR014528", "IPR051319"], "interpro_used": ["IPR049553", "IPR003156", "IPR001667"], "interpro_unused": ["IPR014528", "IPR051319", "IPR038763"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein should contain a Yippee domain that functions as a putative zinc-finger-like metal-binding module found ubiquitously in eukaryotes. It features a conserved arrangement of cysteine pairs that likely form a zinc-binding pocket, and it localizes to the centrosome and mitotic apparatus, suggesting a role in cell division. It is native to Micractinium conductrix.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 43, 19929, 9434, 5182, 3418, 1988, 4088, 1966, 43, 6770, 7997, 17, 8497, 17, 3189, 6048, 17, 2743, 9059, 2435, 21853, 1922, 15021, 18, 2176, 4075, 43, 5305, 13002, 1927, 8666, 5803, 1988, 3205, 2386, 43, 7997, 17, 2743, 10154, 16, 1930, 2176, 18440, 1942, 1920, 19959, 1930, 9566, 11161, 16, 3783, 43, 2770, 1922, 2024, 8451, 18, 2176, 1977, 6196, 1942, 17020, 11686, 2457, 7569, 3027, 1039, 18, 3], "output": "MSALGSGARCGQHSSGDSPHAPATQPCLLVVFEALKHSLVDAVALSSCCRELWGLGVSAAHRDCHRLELPDGDSYAVEATHLQGGCTLGKAQVLFSLVLCGGCGLHLGLRICQLGKLQASSTAGGCISQWREHLGRPPPAAELACYRCTGARSSLLPAGGCGADLFGGGPERAFFINAFRPGAVEARNERQETLSQGEMRVADVHCLENCNQVGRYGVVRSSIRKDKARLPVAAQPCGPAFPLLALPRRRDVCCAACGHKVLHPDQAFASDRAVLGIRGAGDPGFEVTAREKLQVLGTCFLAKRFLRLRRPDGTEESRDILSRQHCWDAATCGACIGWKFVSDLSPA", "metadata": {"id": "A0A2P6VAP1", "cluster": 27018289, "interpro_all": ["IPR034751"], "interpro_used": ["IPR034751"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein carries a Peptidyl-prolyl cis-trans isomerase, PpiC-type domain that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds, typically preferring hydrophobic residues at the P1 position. While usually enzymatic, this domain also functions as a non-catalytic module in proteins like the periplasmic chaperone PpiD. Furthermore, the protein is classified under the Bacterial extracellular foldase PrsA family, which acts as an essential foldase assisting in the post-translocational extracellular folding and stabilization of secreted proteins, including enzymes and toxins. These proteins ensure the production of active extracellular forms, with some members exhibiting peptidyl-prolyl cis-trans isomerase (PPIase) activity. It is native to Carboxylicivirga sp. M1479 and corresponds to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 16252, 43, 3431, 2199, 17, 3192, 2199, 5848, 17, 2127, 25510, 16, 12481, 1030, 17, 2601, 3418, 1988, 23261, 2213, 10328, 2007, 29601, 1920, 5848, 17, 2127, 27027, 1927, 12958, 20697, 1935, 4207, 9031, 16, 5745, 4458, 8641, 7919, 4248, 2019, 1920, 8632, 3507, 18, 2679, 5394, 8145, 16, 2052, 3418, 2222, 4088, 1966, 43, 2447, 17, 6804, 9059, 1922, 2697, 3189, 1920, 24334, 14044, 12481, 1007, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 4543, 5329, 3728, 2051, 20509, 1019, 3416, 16, 2154, 8016, 1966, 1925, 4415, 3728, 2051, 27840, 1922, 1920, 2753, 17, 7849, 1923, 5329, 10328, 1930, 10281, 1927, 8366, 2697, 16, 2710, 5038, 1930, 13599, 18, 2144, 2697, 6486, 1920, 3372, 1927, 3500, 5329, 4952, 16, 1956, 2673, 4678, 12196, 3431, 2199, 17, 3192, 2199, 5848, 17, 2127, 25510, 12, 12481, 2051, 13, 2455, 18, 2176, 1977, 6196, 1942, 18708, 20614, 4223, 2056, 18, 8510, 6106, 1026, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MRRVKNLLKHPLFIFIILGAFMYVIYGAIGRLVDSNDKKIVVSNHIMDEIFYKEAVNMGLDKSDIAVKKRLRQLMEMMLDDYVTVYATEQQLSDYLLANPEKFRKATAVLNELRKGADISKYEHYSLRMLPISFTSETRSNVARHTGKEFAEQVFDLEKLMWHGPIDKVWDLVEREWAAEQKEIRKKEEYALMREQYKVVFEDSKRGVKDNSAQIELLREDYKRTWSRYPTVDEMQNQIYGAESSISFSHLYFDVNEKEASVYGWHLVWVDEVQKGKVPEL", "metadata": {"id": "A0A553GL59", "cluster": 27347756, "interpro_all": ["IPR046357", "IPR000297", "IPR050245"], "interpro_used": ["IPR000297", "IPR050245"], "interpro_unused": ["IPR046357"]}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein has a Polysaccharide pyruvyl transferase domain that catalyzes the transfer of pyruvate groups to polysaccharides involved in peptidoglycan-associated polymer biosynthesis. This domain facilitates the non-covalent anchoring of S-layer homology (SLH) domain proteins to the cell wall and participates in the production of exopolysaccharides like colanic acid and amylovoran. It is native to Cyanobacteria bacterium 13_1_40CM_2_61_4.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 2258, 43, 17167, 6487, 12631, 2199, 13763, 3418, 1988, 17097, 1920, 3856, 1927, 11867, 2671, 1942, 18686, 3286, 1922, 24183, 17, 2458, 4593, 8132, 18, 2052, 3418, 11374, 1920, 2447, 17, 13577, 20816, 1927, 61, 17, 4757, 9039, 12, 2788, 1023, 13, 3418, 2697, 1942, 1920, 2024, 4821, 1930, 17241, 1922, 1920, 3372, 1927, 18930, 13811, 2012, 11926, 3189, 2503, 19510, 2687, 1930, 7061, 2579, 8846, 1022, 18, 2176, 1977, 6196, 1942, 21897, 14061, 2590, 41, 21, 41, 3040, 12819, 41, 22, 41, 5473, 41, 24, 18, 3], "output": "MTRIALLSPSIGNGNLGDEATVAADTRRRHCLPAFPITRHSGKTGAPDSLEIATLKLFPVLYRGLKALRAAPRCVLAFFPGSGVLSDHFGGPLNLPYTIFKWSLLAKATGACGSYRSSRDVTSKQVLGSLGVPGPTPVRPSCPNADGTIVGINPFPHCAPYYWPEIHNKYTVLLFPTQIRADVLVIEDLKKLLVVDDLTSRLAMTHLVVATRFHGILLSLLTDMGQSQYLLDIETFTFESLIERFILLEKQYDILLSGTQVGLARGHLSLGRTRVIQNIRRRCPTATIYAFSPNPERHTETTGSVRQRIDELRFLATSFKCLKGTDLLIILAFLSVGAGPLRSGMSRRLIKHSISLFPDLANSLTIDPTDITKYQRYLMTLASFLSWLERGVQDTNHSLLEFPIQSMHKPVLALSNHHKMSDLMSNRESVRRQIARRVSGYRRDLD", "metadata": {"id": "A0A1Q7UPV3", "cluster": 2226654, "interpro_all": ["IPR007345"], "interpro_used": ["IPR007345"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Function:\nThe protein is associated with 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*. Furthermore, the protein falls within the Bacterial competence-related DNA uptake protein family, which facilitates the uptake of extracellular DNA during natural transformation. These proteins likely function as components of the membrane-bound transformasome pore complex, mediating the binding and translocation of genetic material essential for horizontal gene transfer. In addition, 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. It is found in Edaphobacter sp. 4G125.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 1977, 2458, 1956, 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, 3677, 16, 1920, 2213, 12182, 2651, 1920, 4543, 12939, 17, 2712, 2678, 5047, 2213, 3416, 16, 2154, 11374, 1920, 5047, 1927, 5329, 2678, 2409, 4613, 7002, 18, 2144, 2697, 3205, 2347, 1966, 4178, 1927, 1920, 3260, 17, 4124, 4331, 8431, 8554, 2796, 16, 10239, 1920, 2743, 1930, 7849, 1927, 3299, 3485, 4415, 1958, 8743, 2359, 3856, 18, 1922, 2459, 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, 2176, 1977, 2435, 1922, 3347, 2575, 5883, 2056, 18, 18385, 15174, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MSLAGWCQSPKGVVGATLFVTPASQSLLIDTGWGDNEGRDADRIAAVAHEDHVGGIPQLLDRVKVGAFIDHKEIAANKIKRIIAKPGDVLPIVGGGAVNPFCKDAETRPADTTENSWDKEMELVCPANKLGRMDVYVAIMDNGERKGGSASVLDTEEGGEEHNTEDEYIANLEGQENGNFLELSTPSPSVAPHISAPDVNPKLKVYFVDVEGGQKDAGLKKIDYVLITHFGSNREDAPAAQRGYATYEGMKAVVVSADGELISASLERSLGVQITFGKLRLLDLGDLTIVSHHGWDHSSSPAMVDAISPRIQKSPGLETLWQLHFSISAGDGTFDVFNSRTGKMKRYG", "metadata": {"id": "A0A7G8C0R4", "cluster": 2370711, "interpro_all": ["IPR052159", "IPR001279", "IPR036866"], "interpro_used": ["IPR036866", "IPR052159", "IPR001279"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that folds into a functional protein 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 carries a Domain of unknown function DUF4143 domain that is typically positioned C-terminal to an ATPase core domain. Also, the protein possesses 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 is native to Phaeodactylibacter sp and features UniProt keywords ATP-binding.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 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, 16252, 43, 3418, 1927, 5435, 2347, 4855, 10432, 24428, 3418, 1988, 1977, 5745, 11814, 45, 17, 4262, 1942, 1925, 9444, 4728, 3418, 18, 2222, 16, 1920, 2213, 14465, 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, 1977, 6196, 1942, 18421, 1021, 25033, 2341, 2199, 26073, 2341, 1915, 2056, 1930, 4075, 20709, 11569, 4498, 17, 2743, 18, 3], "output": "MKSRYIKVNLLSKAKSPFGRIIVLTGARQTGKTTLARLAFPQYKYLSIEDPLMRIEYKTLTAAQWNLTFPFAILDEVQKEPTLIESIKSVYDQYPEPRYLLLGSSQLMLLKKVKESLAGRCSIFEIYPLTIPEIRTKSWDEEIKNSLLQDVVLKQKDADDILPFTLWEDFAERKAAFDHYLKLGGYPALVDDTLDDDERYHWLRNYIRTYLERDIRDLADFKSLEPFVKLQKITALLTGQMMNYSLLGKEAGISSATAKRYLQYLELSYQVVLLKPWHRNKLKRLLKTPKIHYLDPGIKRTIVAKTGSLTGHEYESAIIAEIIKQLKNIHFAGDYYHLRTHDGFEVDFLIELEDAYIPI", "metadata": {"id": "A0A9D0XKZ5", "cluster": 3327346, "interpro_all": ["IPR041682", "IPR025420", "IPR027417"], "interpro_used": ["IPR027417", "IPR025420", "IPR041682"], "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 should contain 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 include a PAS fold domain that acts as a versatile signal sensor in signaling proteins across archaea, bacteria, and eukaryotes. It frequently binds cofactors like heme or flavin to detect specific environmental stimuli and undergoes conformational changes, often in conjunction with an associated PAC domain to form a conserved 3D structure. This fold is integral to diverse systems, ranging from circadian rhythm regulation to the gating of voltage-dependent potassium channels. Additionally, 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. It is identified in Flexistipes sinusarabici and is associated with UniProt keywords Transferase, Two-component regulatory system, and Transmembrane.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 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, 3951, 43, 9233, 3728, 3418, 1988, 8016, 1966, 43, 20425, 2733, 6443, 1922, 3197, 2697, 3436, 21501, 16, 4802, 16, 1930, 15021, 18, 2176, 5467, 6876, 21362, 3189, 10954, 2014, 26758, 1942, 4277, 2487, 4813, 5458, 1930, 14928, 8523, 2840, 16, 3868, 1922, 11799, 1956, 1925, 2458, 6866, 3418, 1942, 2386, 43, 5305, 5050, 3170, 18, 2052, 3728, 1977, 12328, 1942, 6445, 3771, 16, 6485, 2037, 10507, 11529, 3640, 1942, 1920, 12568, 1927, 6889, 17, 3100, 9057, 5628, 18, 4950, 16, 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, 2176, 1977, 2899, 1922, 5795, 2184, 29972, 9414, 9041, 3821, 3349, 1930, 1977, 2458, 1956, 20709, 11569, 13763, 16, 2288, 17, 4594, 4948, 2433, 16, 1930, 9117, 18, 3], "output": "MPGQNNMNKQKLSAVCLFILFFCVFSQPSNSTAHALEKNVSIGVLAKRGETIAHDRWDATAKYLSREVKGYNFRIVPLGFDDIFKAAENGSVDFFITNSAYYVALEYDFGAKRIATLTNEYKGKTTEFFAGVVFTKKNREDVNSFKDLKGKSFMAVDPFSFGGWLVAKREFLSAEINPDEDFSKLLFGETHDAVVLAVKNGDVDVGTVRTGTLERMESEGLININNFKIINKQNYENFPFVSSTRFYPEWPISKAAHTDTALAEKVLVVLLNMQPDSKTAKNAHLAGWTIPDNYQSVEDCLKAVMVRPFENWGEITLKDILRQYGVWFFVVVTLPVFVFLLLAIRQRDILKIKNAEISKSEENLRTTLNSIGDAVISTDSRGRIERMNPVAEKLTGWDIADAVKKPLYEIFEIRNAQTGKRIKNPTEKVINIGRVIGLANHTLLVSKDGNEYQIADSAAPIKNKDGEITGVVMVFRDVTEEYNMREALKESREKYKTLYDNAPLSYQSLDEKGYIIDVNPAWLRTFGYSKDEVVGSWIGDFLHPDFRKNFARKFEIFKKRGYAHDVHLKIRHKDGHYIDMLQEGSIGYYEDGSFKQTYCVLKDITDRLKAEEALKKSNRALKTLSACNETMVWAKSEKELLNDICRIIVEEGDYKLAWVGVVQHDEDKTVKPVAHYGFKDDYLENVKISWGDNPKGRGPTGKCIREGVPEICRDILTDPEYKVWRDEALKRGYKSSIALPLKEAGEVFGALNIYAKDPDAFGRDELRLLENLAGDLSYGIRMFRIREERKRARNELFRMQKLESVGTLAAGIAHDFNNLLTALFGNISLAKMKLKADHPAYEALNSAEKAMDRATSLTNQLLTFSKGGEPLKKKVEIDVIVKKTVEFDLSGSNVKAVFEQKENLWPVLADKGQIQQVISNLVINAKQAMPEGGHFYVTMENVDTEKSEIPAVKEGKYVRISFKDEGVGIKKKDIGKIFDPFFTTKEIGSGLGLATAYSIIRKHGGYIDVESTPGMGTTFFVYLPAVSREESDKKTYVRQFKKDKRLRVLLMDDDDLICDSVKIYFENFNFIVDCVPDGETALEEYKNLWKEGKRYDVVIMDLTIPKGMGGEETVCKLLEIDPDAVCMVSSGYTDDPVMAYYEDYGFKGALTKPFHLEELKDLLRKL", "metadata": {"id": "A0A5D0MP22", "cluster": 5808892, "interpro_all": ["IPR011006", "IPR003018", "IPR029016", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR001610", "IPR000014", "IPR000700", "IPR035965", "IPR013767", "IPR004358", "IPR001789"], "interpro_used": ["IPR005467", "IPR013767", "IPR000700"], "interpro_unused": ["IPR001610", "IPR001789", "IPR011006", "IPR036097", "IPR003018", "IPR000014", "IPR003661", "IPR029016", "IPR004358", "IPR036890", "IPR035965"]}, "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 Spermatogenesis-defective protein 39 family, which mediates intracellular membrane trafficking and maturation events, including endosomal and phagosome maturation. Members of this family are essential for membrane reorganization during spermatogenesis in nematodes and for the innate immune response to bacteria in fruit flies. It is present in Thelohanellus kitauei (Myxosporean) and is associated with UniProt keywords Cytoplasmic vesicle and Endosome.", "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, 21814, 17, 9785, 2213, 3886, 3416, 16, 2154, 10412, 4776, 3260, 9604, 1930, 7655, 3916, 16, 2710, 16514, 1930, 8476, 4283, 7655, 18, 4678, 1927, 2052, 3416, 2032, 4415, 1958, 3260, 18062, 2409, 21814, 1922, 19669, 1930, 1958, 1920, 8539, 3743, 2644, 1942, 4802, 1922, 9021, 10130, 18, 2176, 1977, 2481, 1922, 1920, 6012, 15409, 1992, 1957, 4712, 6346, 14209, 12, 21464, 9890, 5376, 1022, 13, 1930, 1977, 2458, 1956, 20709, 11569, 6823, 11502, 1930, 22321, 18, 3], "output": "MRFEQDKSSEKQKNSENQSDEKISDAPRVSPTTRPSKHKRDMSDPDDLSHSSIKSAFQNIIQKSKNLEILKPTNSAIDFQKHDDSAVEMSRIISNQPYTFYQFQSLDQCIIKVILFLKETLKHELFKILLEKYPEASFEIVYSKPTLDHLLYDYLQLISGKLSETIDILKLQLVRKEIDKTQENPQEVTRLTFEHMQRFTHIPTDFKKVFGLSCCKLNLYQTLNRFYLDKKSSNIIAKYLDYVKDKTVQMFIAEDLLYEKIGIIPEIKKQIFDALNNRNIKWKRASNLFDWNDEEEQLSLFSGSLNNFNEKLRLSMPKFPGPLDNVCQMHHVTQQISNIKKTKEKLLISALSTCHTSYNNFLRSLGQLESLKTIENLERLYKKFCNYKTYSDYVHSIKKHNLLPLELKYEKSLVSMKDLQFEYILVKFGGLAPSSATTFDNICYLLKENDAPDEIRLYEFLVKICISHKNREKLEE", "metadata": {"id": "A0A0C2IHD4", "cluster": 7803788, "interpro_all": ["IPR040057"], "interpro_used": ["IPR040057"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein contains 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. In addition, the protein includes a PAC1/LIS1-like, WD-40 repeat that typically folds into a $\\beta$-propeller structure to serve as a rigid scaffold for protein-protein or protein-DNA interactions. Found in diverse eukaryotic proteins including Class B GPCRs and ribosomal components, these repeats facilitate complex assembly in processes ranging from signal transduction to transcriptional regulation. 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 Favolaschia claudopus and features UniProt keywords WD repeat.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 5461, 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, 1922, 2459, 16, 1920, 2213, 5921, 43, 6866, 1009, 19, 19620, 1009, 17, 3189, 16, 17907, 17, 3040, 6865, 1988, 5745, 16231, 2460, 43, 8, 38, 4666, 8, 17, 5062, 13728, 3170, 1942, 7120, 1966, 43, 12383, 7281, 1958, 2213, 17, 2213, 2014, 2213, 17, 2678, 3719, 18, 2435, 1922, 6445, 10825, 2697, 2710, 2921, 44, 17723, 1930, 11196, 4178, 16, 2144, 9569, 6628, 2796, 5957, 1922, 4028, 6485, 2037, 2733, 8201, 1942, 5224, 3640, 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, 5505, 10173, 14920, 2126, 27094, 12337, 1930, 4075, 20709, 11569, 17907, 6865, 18, 3], "output": "MAQPRRRSFLGGLGGLIDKARSRSGSASSSTPPQIQASSSSNVYLTAGGLPAASASDQSLARRAGTKTAAGVLLWICETVDMVLDNRTELEDFQAKLTAILTVVTKYKRDGGISALDLRIKMFCEAIDRQMQAVERNKDVKIVSKALRDMNSICDIFQMDTQLNIEGRVEDIDIRVRTILQASSINRLRYDMKILADLETWALDENSSKLYWLVGIAGTGKSTISQTYCEILQHRNILGASFFCSRGTDQGRNARAITDDPTLAETNYNDTKDQLNKLVLRPLQVSLGQNIKTYKVVVIDALDECSDLKILIASRDEAPIRQIFNTLPTTTFYLHEVETDLVAEDIRKYIEKSLADILELNGATQQSWPSPAIRYINDEDGNYQRRLSALIDPTKQHRSALQTAEIDDLYAQIIENACNPRLNEPQEIAHMKECLASSAFSAIRSLIHVASPVSRESLVTVFHASFPDFITNPTRCSPTRCPLFQALQSSEEHSNLASRKSHNNSLNHVSKIPRALQYACLYWMSHVKEIGDPNWAGLNDLYIFMDRHLLHWIECLLATCFLKFSKADTDYLALLKDFVRYLQLSFQCIKQCCSESYHSGLVWVPHGLPDSWSPTELILEIGAFVNSIAVSQDGTRIACGSNHNIIHIWNAYSGDLHLELRGHMALVNSGTVWIWNALFGHKQQELTGHSQRVNCVAFSPTGKLVVTGSDDKLIRLYDTTSGNLTQQLIAHTHIINTSGEVQFELKSSRSAVTSLAFSPDGTRIASASGNQGIQIWDSHSGMKIMDLKTEREWISSVAWSPDSAMTGDIEVNLKGHTNTVESVVFTPDGQQIVTASADSTIRFWSIASLGGSTHREGHTEADTTICLWNALTGELEQKLTGHTGFVHHVAFASNSTIVISGSTDDTIRVWFTLDHEVEVVDRPSVNPTPTIQKIACLSEDHAWIMSATQDCWIPPEYRDPLSVAVWGEKICFGYHSGRVVIVDMAVYEGLKTVFQGLYDTSDMFLPLKTLQQRSLATRTAISYKTRHSSYGDPSGCMQGTRELIIPSVAYSLAMASPPIKAEILKRRAAALIRTFHNSMSQLPLQELSAFLAQCGKLFIYAATAAVIFAFTPLTVAAISHLLKIDIKCLRLMNNLLQENMCAVSGTSLISILGELQVAVDSLIQDSIVRRMHPRNSSIPRVIIVAFSPNGSQLVSCSDDVAFSPDSTLLVSGANNGVMYRWDIANRVVSGSYDNLVKIWDVIAVAFSLDGNWIASGSRLPNGTKIHRVDPGEFSVEYQ", "metadata": {"id": "A0AAW0ALC9", "cluster": 9015797, "interpro_all": ["IPR020472", "IPR056884", "IPR027417", "IPR015943", "IPR036322", "IPR001680"], "interpro_used": ["IPR056884", "IPR020472", "IPR027417"], "interpro_unused": ["IPR036322", "IPR001680", "IPR015943"]}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein has a Cold-shock protein Csp, DNA-binding domain that facilitates cellular adaptation to low temperatures by preferentially binding poly-pyrimidine regions of single-stranded RNA and DNA. It regulates ribosomal translation, mRNA degradation, and transcription termination, and may assist in prokaryotic nucleoid organization. In eukaryotes, this domain functions within Y-box proteins to bind promoter sequences and regulate gene expression. Moreover, the protein is a member of 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. Furthermore, the protein carries a Cold-shock domain conserved site that binds single-stranded nucleic acids to act as an RNA chaperone, facilitating post-translational gene regulation and adaptation to low temperatures. This region adopts a five-stranded antiparallel $\\beta$-barrel structure similar to the OB-fold and utilizes conserved RNP-1 and RNP-2 motifs to rescue RNAs from unproductive folding states. It is found in Amoebophrya sp. A120.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 2258, 43, 6685, 17, 7418, 2213, 16369, 16, 2678, 17, 2743, 3418, 1988, 11374, 3689, 7810, 1942, 2330, 7750, 2007, 10662, 2743, 4286, 17, 21611, 3451, 1927, 2957, 17, 10338, 3146, 1930, 2678, 18, 2176, 7014, 11196, 6410, 16, 3616, 4877, 16, 1930, 3213, 12462, 16, 1930, 2278, 6589, 1922, 21545, 2797, 2642, 5901, 18, 1922, 15021, 16, 2052, 3418, 4088, 2651, 67, 17, 5758, 2697, 1942, 4566, 4465, 3709, 1930, 5741, 2359, 2294, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 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, 3677, 16, 1920, 2213, 16252, 43, 6685, 17, 7418, 3418, 5305, 3200, 1988, 6876, 2957, 17, 10338, 11079, 4576, 1942, 4033, 1966, 1925, 3146, 14044, 16, 12440, 2753, 17, 8414, 2359, 3640, 1930, 7810, 1942, 2330, 7750, 18, 2052, 3031, 24032, 43, 3628, 17, 10338, 28892, 8, 38, 4666, 8, 17, 19560, 3170, 2551, 1942, 1920, 2384, 17, 3728, 1930, 18127, 5305, 24767, 17, 21, 1930, 24767, 17, 22, 8277, 1942, 10162, 8624, 2037, 7861, 11483, 9292, 10328, 4376, 18, 2176, 1977, 2435, 1922, 27714, 2688, 6907, 1019, 2056, 18, 8080, 3520, 18, 3], "output": "MAQQGTVKFFNSEKGFGFITPDQGGEDVFVHFSAIEAQGYKSLNEGETVNFDTVWDDRKQKSSAANVTGHGNGQPRQKGGKGKGKGFGGDFGGSYW", "metadata": {"id": "A0A8J1Z8L6", "cluster": 9370206, "interpro_all": ["IPR011129", "IPR019844", "IPR002059", "IPR012340"], "interpro_used": ["IPR002059", "IPR012340", "IPR019844"], "interpro_unused": ["IPR011129"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein falls within the CDP-glycerol glycerophosphotransferase family, which catalyzes the polymerization of the main chain of wall-associated teichoic acids in Gram-positive bacteria. These enzymes sequentially transfer glycerol-phosphate units from CDP-glycerol to a linkage unit, forming phosphate-rich polymers covalently attached to the cell wall peptidoglycan. It is expressed in Frankiaceae bacterium and is linked to 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, 12182, 2651, 1920, 26707, 17, 9244, 7757, 8630, 14165, 3416, 16, 2154, 17097, 1920, 11486, 1927, 1920, 2730, 4659, 1927, 4821, 17, 2458, 3602, 2108, 8643, 4576, 1922, 8604, 17, 2843, 4802, 18, 2144, 5038, 14985, 3856, 9244, 17, 5413, 5701, 2037, 26707, 17, 9244, 1942, 43, 8611, 5344, 16, 7402, 5413, 17, 5536, 11039, 16590, 8765, 1942, 1920, 2024, 4821, 24183, 18, 2176, 1977, 3198, 1922, 14542, 19476, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MPTPSLIRDRRARTRALVLIGAALAVTAGVELLTPHLSPFAIGAMRAATTLSHSLFVATAAVGAGIVGLALGAVTRNIDLGDFDVPAPPPALAMDPRGLDALAQAAYVVSALVLAALITAAPVVALAWQLLALYRAKLLYYAATPEETYQVRMWLEPLAKLNRRVVLVLCSPYNGTIASLPLPTRVAALFVTHSGNNLSMIRPFARVYDEIWVAGPLGRRRYVQANIGIRPDPPVVVYAPTWEGWGDDPHHSSLGNIGVELIERLLADRALRAAHQRILQLVGQVPPHEPLTETFNRSTGLVDEFTRRFPSTAGGFVLGPDLDGLDEFVLLRDTLGDPATSQQRFADAITGLLGLLKLSVVVAIVAAAYRNSWITVRVNAGRPARSALQLVPVAMLEAGRVVVTRVRRLPLVLVAAVGVALARDSSNRTHLTEAATTAIEALAPEVVRSQAVFDALSDVSLPVIRPESRTAFIGHGDSDKPDSVNEAAIIEIGRPQITAPIAPPVDGITVRYRAHPLTGRRGDVSSVINEYLPFDRPYAVVDTRGLGHAALRGGTDSSRTRRRE", "metadata": {"id": "A0A9E3CCJ3", "cluster": 11251022, "interpro_all": ["IPR007554", "IPR043148"], "interpro_used": ["IPR007554"], "interpro_unused": ["IPR043148"]}, "task_type": "infilling"} {"instruction": "It is part 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. Also, the protein should include 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 possesses a SH3 domain that mediates protein-protein interactions by binding to proline-rich regions containing a core PXXP motif. It adopts a characteristic beta-barrel fold and is found in diverse intracellular and membrane-associated proteins, where it facilitates the assembly of multiprotein complexes and regulates subcellular localization. It is present in Symbiodinium natans and is classified with UniProt keywords ATP-binding.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 2176, 1977, 3131, 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, 2222, 16, 1920, 2213, 3066, 3951, 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, 14465, 43, 18824, 3418, 1988, 10412, 2213, 17, 2213, 3719, 2007, 2743, 1942, 12958, 17, 5536, 3451, 3165, 43, 4728, 15194, 1039, 1034, 5219, 18, 2176, 24032, 43, 6293, 4666, 17, 19560, 3728, 1930, 1977, 2435, 1922, 6445, 4776, 1930, 3260, 17, 2458, 2697, 16, 2597, 2176, 11374, 1920, 5957, 1927, 20677, 5684, 5048, 1930, 7014, 11309, 5363, 18, 2176, 1977, 2481, 1922, 17246, 25435, 2457, 3898, 2075, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MQCRNHSARRVWNTRTGYCEDCDWSLRLLEQELRLCLDPQQCSGADSICRKCKDIRYKSSVASEGHEDNWPSLAEVGPTVSFERPALADLQKRKVDLQRSLNAERLDACVHVSRNVREAFRSRVVEACAFAERLAGYRAIPVFYKAATMNWAPSRWSDAPRERNSRSGDLACAVEVKGHRFLLAEPRSGCEYSGLQTTKENHMVFKTQKPSHHDQLNCKGCDLLGRCCGASQSKYIARSFCGFNDGGASARLAGTLSLSDPEAGLRWISVYVRNRRDGACEAHVDFDHAELAGITPHFQGGGGGTLYAADLYGADPCDPELQAALEQTVFRAGCECLGWLSISAPHWLQRAMTQLQRFGEWRTFRLILPWQVFTCLHVVDNMRTAAVDEESLQDSAAAFRAHARGLSQMGDFPEQHTTLLRHVHLFGKPTAASQHFQAHRAGTDQDEDSDGSWQDDPSHWEAQSPEAAPEIPTQAQTPQDGPSGSTLKCGRSKAAFDAREYRQGKQGWFPRSFMDAEHDYSTAGLLLQTEVSSQGFAPSFRLAQGGSCDVFAMLDQHQLFAQEVAALRRISHPNIVRMLDAGVASSGAFVILEEFAGLCYIHSQGVLHRDIKSANILVDADAVANVTAAKISDFGLAIGDPECLRGGGYTQQSDVYSFGIVLLDLLTGICGSEADHFSFLDLAKGCVHVLGKRRPTSQAVHQGLQQLQTSPVVNRQRRFFFLCPRRKHGFTSRRGLVVRVDPNVLAPPSPCESEILNELFQRFPEAVQQEMDSAADSFLAGVADIVTRQQADRCVQTLQKFPFRGLVELLVLRGLPGFADRDFVEDILRDVQVLELAKDILRARLEGAERAAESVSDGQQDDSPVPVVRIQKFTLGMPSNWVRWSRATRQVYRNDQFCSELEDDALGSQSATVEPDGSQSSLDNEAEESDDDYLDLQEGVWVMWNPDTDQDGWCWGSSGDVRLCDRRVAAKVLHHQESRSVACSTTLMHCLQGLEWRQRLVTATQVADAVQERALRGTRHSTRVCGTPGYMAATQEDSVVFHSSWHAAGGALQA", "metadata": {"id": "A0A812S3Q3", "cluster": 13083966, "interpro_all": ["IPR011009", "IPR000719", "IPR008271", "IPR036028", "IPR001452"], "interpro_used": ["IPR011009", "IPR008271", "IPR001452"], "interpro_unused": ["IPR000719", "IPR036028"]}, "task_type": "infilling"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein can be placed in the Plasmodium Circumsporozoite Invasion Protein family, which facilitates the malaria parasite's infection of mosquito vectors and vertebrate hosts by mediating sporozoite development, migration, and hepatocyte invasion. These GPI-anchored proteins bind highly sulfated heparan sulfate proteoglycans on liver cells and alternate between adhesive and nonadhesive conformational states to support both host cell entry and motility. It is produced by Menidia menidia (Atlantic silverside).", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 15663, 28868, 2074, 26553, 6254, 2213, 3416, 16, 2154, 11374, 1920, 7505, 8652, 11, 61, 2909, 1927, 9719, 7623, 1930, 13416, 10865, 2007, 10239, 9130, 26553, 2740, 16, 5049, 16, 1930, 14675, 6254, 18, 2144, 17497, 17, 17199, 2697, 4566, 3626, 26649, 22024, 8767, 25185, 1990, 3568, 2094, 1930, 14263, 2192, 13510, 1930, 2447, 24604, 18522, 1961, 8523, 4376, 1942, 3373, 2321, 4423, 2024, 6904, 1930, 9254, 18, 2176, 1977, 4152, 2007, 3925, 14773, 3925, 14773, 12, 17717, 11078, 13305, 13, 18, 3], "output": "MGFEPQTYTGDFELKRAFSLCPRLPQHQPSVHLSIHLSIHPLIHPSINPSTHPSINLSTHPSIHPSIHPFIHPSIHPSIQLSIHPSIHPSTYPSIYPSTNPSIHPSIHPSIHPSIHPSNQSWDPPPIRAPLSGADSSGLKPPTRQKISEEQDLSVQGTELTI", "metadata": {"id": "A0A8S4BI20", "cluster": 13660131, "interpro_all": ["IPR051860"], "interpro_used": ["IPR051860"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein is included in 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. Moreover, the protein belongs to the Uncharacterized sodium-dependent transporter YocR/YhdH-like family, which comprises prokaryotic integral membrane proteins belonging to the sodium:neurotransmitter symporter superfamily. These proteins, exemplified by *Bacillus subtilis* YocR and YhdH, typically contain 11 transmembrane helices and are predicted to mediate sodium-dependent transport. It is present in Helicobacter sp. 15-1451 and carries UniProt keyword assignments Transmembrane helix.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 1977, 3063, 1922, 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, 3950, 16, 1920, 2213, 14440, 1942, 1920, 24528, 5227, 17, 3100, 9054, 7419, 2145, 19, 67, 6518, 1023, 17, 3189, 3416, 16, 2154, 12936, 21545, 12328, 3260, 2697, 10588, 1942, 1920, 5227, 30, 15223, 29148, 2718, 1915, 13975, 18, 2144, 2697, 16, 22236, 2007, 14, 14587, 14745, 14, 7419, 2145, 1930, 67, 6518, 1023, 16, 5745, 5531, 2513, 9117, 12789, 1930, 2032, 4396, 1942, 8265, 5227, 17, 3100, 4860, 18, 2176, 1977, 2481, 1922, 22293, 2056, 18, 2461, 17, 11491, 1009, 1930, 16252, 20709, 11121, 2538, 18306, 9117, 7864, 18, 3], "output": "MVHFSKIGFILSLAGSAIGLGNIWKFPYVAGQNGGGIFVIIAEMILGRESSKNPVSTFEMLAPRHKNLWKYSGYMFISGLLFYIPENGATAQALFDNFGRYELFWQIVCHLAIIAICGFILVRGIFIMLFFYVITLDSFPKAVDFMFDFKWEQVNSGSAYSAAMPRHINFVSSSFYIATLNTILALIAGLVVFSLLFKEGLMGWVGHIVAFIFFLALLFAGVTSAISMAEPAIAYLIERHHLKRPKATYFHSAEYLGGFTVFQWIDLLTSTVFMPLSGVIICLFVGFVISQNELYIRYIAPIVIVVIMLQNFLNKFFEINLIQIIFSWLFILSVIFVLCSVFLILAFYSMILGWITYYMFYLLKKGIEQINLILMPALFIIILEALGQAFFSMSLGVGTIMSPDAGPNLIFVSLPIVFYQFLVITFCFLVGGITILGQTDGMFSGTIPYWFFRVWLIL", "metadata": {"id": "A0A329ZRA8", "cluster": 15978552, "interpro_all": ["IPR000175", "IPR037272", "IPR047218"], "interpro_used": ["IPR000175", "IPR047218"], "interpro_unused": ["IPR037272"]}, "task_type": "infilling"} {"instruction": "The protein I want to design has this role: The protein should include 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 falls within 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 expressed in Jaapia argillacea MUCL 33604. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 3066, 3951, 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, 12182, 2651, 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, 3198, 1922, 13149, 2026, 2126, 4582, 10888, 1972, 1019, 3422, 1024, 25423, 14743, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MIAEGTAPIVSSSNPIPFRRSDIWYEDGSVILVAEATGFKVYKGVLAANSEVFRDMFDLSVPSTGGSVDGCPIVLLSDDALDVKHLLNALLDREFFRPMENPQPFAVAASLLRLGKKYAIRRVYDEALSCLTHEFPSTLEGWERAESTDYSRLQYYVGLEIDVINVVREINLPSLLPILFYLCAASYDSPTQIFRGVERGDGSVAILSRADQEILLTGRHLMVIEAHDLFWVQLSSLFNCNSAPCGQRKALVHRECFRPPGTLRALCGWSEDWYPGLCDPCRLNGPHAHSVYRKYLWESLPSFFELPEWDTLRAQDHTL", "metadata": {"id": "A0A067PP91", "cluster": 16283654, "interpro_all": ["IPR000210", "IPR011333"], "interpro_used": ["IPR000210", "IPR011333"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I'm looking for a protein that has the following function: The protein carries 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. Moreover, the protein falls within the EF-hand domain pair superfamily, which functions as a calcium-binding module composed of two adjacent EF-hand units forming a four-helix bundle. This domain coordinates calcium ions in a pentagonal bipyramidal configuration within a twelve-residue loop, serving as a critical regulatory or structural element in diverse proteins such as calmodulin, troponin C, and S100 family members. In addition, the protein should contain 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 is native to Helobdella robusta (Californian leech). Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 16252, 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, 3950, 16, 1920, 2213, 12182, 2651, 1920, 8485, 17, 3897, 3418, 3715, 13975, 16, 2154, 4088, 1966, 43, 5016, 17, 2743, 9059, 7179, 1927, 2288, 6811, 8485, 17, 3897, 5701, 7402, 43, 3006, 17, 7864, 14142, 18, 2052, 3418, 10675, 5016, 6982, 1922, 43, 9412, 13481, 8446, 3553, 25238, 1923, 9674, 2651, 43, 12367, 17, 6181, 5881, 16, 13915, 1966, 43, 4140, 4948, 2014, 4346, 6149, 1922, 6445, 2697, 2427, 1966, 17537, 16, 18714, 45, 16, 1930, 12678, 3416, 4678, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 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, 1977, 6196, 1942, 3091, 2389, 16878, 5148, 5786, 1019, 12, 10191, 1022, 10798, 2072, 13, 18, 7031, 1920, 3244, 18, 3], "output": "MTWHKFSSHVTNGIKPDKREWRASRKDDKRGGNYGSHYKQTDGRTSSRYLGMSCHCHDPAVVSQVFDELDADKSGKIDKKELFKVFKLLCEHAGQVVDDGVLQAEAQKAIEELDRSGDGMIDKAEFMEFMNRH", "metadata": {"id": "T1FBC3", "cluster": 19563230, "interpro_all": ["IPR011992", "IPR018247", "IPR002048"], "interpro_used": ["IPR002048", "IPR011992", "IPR018247"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein should feature a OmpA-like domain that mediates non-covalent interactions with peptidoglycan in the periplasm of Gram-negative bacteria. Found in the C-terminal region of outer membrane proteins such as OmpA, Pal, and MotB, it plays a critical role in maintaining cell envelope integrity and anchoring the flagellar motor stator to the cell wall. It is derived from Cyclobacteriaceae bacterium and is associated with UniProt keywords Signal.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 3066, 5961, 43, 21921, 1019, 17, 3189, 3418, 1988, 10412, 2447, 17, 13577, 3719, 1956, 24183, 1922, 1920, 20171, 1927, 8604, 17, 3136, 4802, 18, 2435, 1922, 1920, 45, 17, 4262, 3031, 1927, 7642, 3260, 2697, 2427, 1966, 21921, 1019, 16, 5755, 16, 1930, 12798, 1014, 16, 2176, 5705, 43, 4140, 2770, 1922, 8231, 2024, 11262, 7996, 1930, 20816, 1920, 24154, 4842, 3156, 1924, 1942, 1920, 2024, 4821, 18, 2176, 1977, 3595, 2037, 17009, 7972, 2341, 18339, 1972, 3336, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 2733, 18, 11586, 5655, 3581, 18, 3], "output": "MMTLYPKKAFLIFFLVLATAYVQAQDYYVVIKYDARQGVHEKRRLTYIYVLKTTDYEGPLTTAEPVTPVVVEQPKPKEEPVVTPVEEPKPVEELPPAKGKYFKFVVTDINGQQVSTTLHNVDRILLTIVCGIFGFTEEIKVIDFNDPGLTPDAKGDVSVMYNVSFYKDAVIMTPESKEELDELVNMMKLNISTLGNNKNYFAMAGADSKTGNGKELSKLRAEAWGGMEMLVKQGSASAARLNNRIEIEVLEDGAYRVQKYADIFTGYARNARAEASRMTVRLRNDTEFKDAWLPVEEPVEQPEEPEPEPEDEPGRDLARYPSGTYVDVNRPSDPSVPTQDENGAWIIPYKLERMKPNYKIKIHGHNNGNDNNLRTIQLYLIDNGIDKKRTDIY", "metadata": {"id": "A0A952N2U3", "cluster": 19972725, "interpro_all": ["IPR006665", "IPR036737"], "interpro_used": ["IPR006665"], "interpro_unused": ["IPR036737"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein belongs to the RTX toxin and mannuronan C5-epimerase family, which encompasses bacterial proteins characterized by glycine-rich, calcium-binding repeats essential for their structural stability and function. These proteins primarily act as pore-forming exotoxins that disrupt host cell membranes and signaling to promote virulence, or as enzymes involved in the modification of bacterial alginates. Furthermore, 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. Also, 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. It is expressed in Roseivivax jejudonensis.\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, 29839, 9165, 1930, 7338, 10366, 1928, 13441, 17, 13872, 9213, 2051, 3416, 16, 2154, 21569, 4543, 2697, 4378, 2007, 10646, 17, 5536, 16, 5016, 17, 2743, 9569, 4415, 1958, 2310, 4346, 5057, 1930, 2347, 18, 2144, 2697, 5985, 4033, 1966, 8554, 17, 7402, 18930, 4575, 10960, 1036, 1988, 12512, 4423, 2024, 5726, 1930, 3197, 1942, 5527, 9304, 16, 2014, 1966, 5038, 3286, 1922, 1920, 6295, 1927, 4543, 17987, 1036, 18, 3677, 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, 2222, 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, 2176, 1977, 3198, 1922, 13679, 2068, 17370, 1039, 8988, 29985, 2290, 3355, 1937, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MTYTIQTYGPAGGMADARLFGGNVLAPRGAMTGDGSYAEAIDQLGVTDLRYPGGGVTGEVIDFIPLSEFMAFAGANGHAVNIVIPTRDQLSDRRDADGHRVPQIDESELEYWGSGMMSAAEYGRLAAEMATVIDEELARVPGGEAIEIAVQMGTNFNHSNLSAGNGEVNWGLVANRIVMQPFDTAEEISAVDAIVAHVYSKEPAVDGQRDLDLTTIREQSGSSGHFDDRADYGLHQAHEMLNIVEAFMAQGVTAAQVWPLIQNTFFRMMADALPGKTMVDLDPADRGETEAQLGPVHVHAFSDANRIDLSDLLSGPALVHAILLGVADGAEAGHNRSEVQLEELAAASVRAPSEAVDTPTPHAADPREPAMPERSVTGNGDDRVIGGAAGNDLLGGGLGTDTLTGNAGADTIGGGFGDDLIYGNDGADRLAGSYHHDRIIGDDGDDSLGGGTGRDVLHGEAGNDSLGGGAGGGRDDRVWGGAGADTINGGDGDDVLVGGTGADVFVFNDLIAGERLAGRFEALSLHDTPTGAVVEYAGHRIELSGVRAADLGVDDFLFVSLTEFYFDISDPDATRATHRAFVRDVAGGAYGDARVASFEIGNEFHGMAAPDILAALNAAYDLDLGAEVVRTWGADARFEGTGIHVTEWSPNALSSGFEFTALNAPGVETVVYIASDSARTETTYEDGIVTATLAEGEILQLRIFATGNDTIGGKDGNDDIDGGAGGDFLVAGTGNDTVGGEGDDTVIGGDGDDFLDQISDFALGADLIRLSGVENAPGSG", "metadata": {"id": "A0A1X6Y3W2", "cluster": 22277066, "interpro_all": ["IPR017853", "IPR018511", "IPR001343", "IPR050557", "IPR011049"], "interpro_used": ["IPR050557", "IPR018511", "IPR001343"], "interpro_unused": ["IPR011049", "IPR017853"]}, "task_type": "infilling"} {"instruction": "I want a protein that has the function: The 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. Also, the protein has a Fungal ubiquitin-like domain that is predicted to adopt a structural fold resembling ubiquitin. It is found in a range of fungal proteins and likely functions as a structural or interaction module within the protein architecture. In addition, 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 present in Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1) (Wheat head blight fungus) (Fusarium graminearum) and features UniProt keywords ANK repeat. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 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, 2222, 16, 1920, 2213, 2258, 43, 8697, 6526, 17, 3189, 3418, 1988, 1977, 4396, 1942, 14103, 43, 4346, 3728, 18994, 6526, 18, 2176, 1977, 2435, 1922, 43, 3109, 1927, 8697, 2697, 1930, 3205, 4088, 1966, 43, 4346, 2014, 2835, 9059, 2651, 1920, 2213, 9335, 18, 1922, 2459, 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, 2481, 1922, 10122, 2361, 5870, 6116, 3336, 12, 3943, 11037, 3057, 1019, 17, 4182, 3520, 19, 16341, 10900, 5964, 1027, 19, 13320, 12709, 3865, 8245, 19, 5214, 1005, 1024, 17966, 11068, 19, 2087, 17, 21, 13, 12, 10376, 4469, 2266, 2227, 16461, 13, 12, 24470, 8604, 30377, 1989, 13, 1930, 4075, 20709, 11569, 9808, 6865, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MGQESSEGVPAPTLVTLSKKSFAALDQAIAYTTDHTDPDLRVTLEDERGRLRVWASNLGALQQETSKKSLDYRLRDAPLMRTTVALGLENLHASADRALAIINGSVPNRSAVLPSDDGDTKTINELDELLAGVHSAINHLFGISILIRKQQPRGRLLNLDDFTLESSQDITYVADRFPKAKSNLWLARRLGNNISKQRKIIQYRQEHRASLAKESEQPGVGDTATVVATTYHEIDNLELSDQVPKGVSSSGMSAFTSATSFQSLGNEEGMGRPIPDLSDMTLDGVQLEYGEPFECPYCRTIQVAANRRHVFTDLQPYMCTIKDCRSGNKSFSTRSEWFEHESTVHRWQWECSWCNSPNSTFPSSDDFKRHLNKSHPGMVTEAQMPLIVDACERPIRTFNSGSCPLCEDWKPMSANNNAKGFSRHLARHLQQLSLASIPISTPGLEIKMSDDASDVGGRSSMESIDKEDLQKNALARGNSALLFLAAKNGDQDMITSLLKTGVDVNMTDEKGITPLSWAAKNGHSAVVRILLRSGADIGANDAKTFLTLAALEDNGGPIVSAQATSSSTILDDTNRWLKNRLAEVELQPQPYRLHRQTFGQQVEQSEILSQQAERKKTADAVAAEEAAREEAWKELGAMVGEGTKAKRGELERGAEQGKIRFTDAVGRKFMFPFHLCATWQGMEDLIKQAFVQVDVLGPHVMKGHYDLIAPGARLGYYNDNVANG", "metadata": {"id": "I1S3J7", "cluster": 23998500, "interpro_all": ["IPR002110", "IPR036770", "IPR054464", "IPR013087"], "interpro_used": ["IPR013087", "IPR054464", "IPR002110"], "interpro_unused": ["IPR036770"]}, "task_type": "autoregressive"} {"instruction": "I want to generate an amino acid sequence for a protein. The protein should have the function It is part of the IMEF encapsulin system ferritin-like cargo family, which functions as a ferritin-like iron-binding cargo protein within the iron-mineralizing encapsulin-associated Firmicute (IMEF) system. These proteins exhibit ferroxidase activity to drive iron mineralization inside the encapsulin nanocompartment, playing a key role in microbial iron storage and redox metabolism. It is identified in Marinithermofilum abyssi.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 2176, 1977, 3131, 1927, 1920, 2042, 7726, 10771, 3392, 2433, 15552, 17, 3189, 14713, 3416, 16, 2154, 4088, 1966, 43, 15552, 17, 3189, 5680, 17, 2743, 14713, 2213, 2651, 1920, 5680, 17, 8463, 3903, 10771, 3392, 17, 2458, 24232, 2696, 12, 2042, 7726, 13, 2433, 18, 2144, 2697, 5987, 20976, 18068, 3825, 4127, 2455, 1942, 9265, 5680, 17643, 7836, 1920, 10771, 3392, 14100, 4617, 5263, 2017, 16, 14797, 43, 3834, 2770, 1922, 7293, 5680, 7451, 1930, 9366, 4714, 18, 2176, 1977, 2899, 1922, 13081, 8635, 2098, 12492, 6870, 1989, 2186, 2012, 12924, 18, 3], "output": "MDKVFSELHPIFSRTKASIETFVQMLEPVVEQAATEKERLYFHHIIEEEEQRLERLETLLPRLEKLVDSNIPVQHSKLSPWSVGNLRFKGE", "metadata": {"id": "A0A8J2YDN0", "cluster": 24679786, "interpro_all": ["IPR030909"], "interpro_used": ["IPR030909"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein is a member of the YolD-like protein family, which is predicted to be functionally equivalent to the UmuD subunit of DNA polymerase V. Although experimentally uncharacterised, these proteins are thought to perform roles analogous to those of UmuD in Gram-negative bacteria. It occurs in Caldibacillus debilis GB1.\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, 7419, 4184, 17, 3189, 2213, 3416, 16, 2154, 1977, 4396, 1942, 1998, 9346, 6582, 1942, 1920, 8736, 2009, 5903, 1927, 2678, 6479, 64, 18, 2876, 9568, 23229, 3495, 16, 2144, 2697, 2032, 6212, 1942, 2385, 5456, 12464, 1942, 2690, 1927, 8736, 2009, 1922, 8604, 17, 3136, 4802, 18, 2176, 5110, 1922, 2570, 7408, 7972, 10401, 5277, 1036, 26068, 1937, 7436, 1009, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MSIKDRGTKKWTSFFIPQHVEMIRNMILALHYAIHHDREVELEMIGTYRIETITVPMDDIRNVRVLDEDERMRKPELDDQEKEELDGRIRSIDMLERKIRFEDGRS", "metadata": {"id": "A0A420VDR5", "cluster": 25056123, "interpro_all": ["IPR014962"], "interpro_used": ["IPR014962"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein should feature a LIM-type zinc finger domain that functions as a protein-protein interaction interface rather than a DNA-binding motif. It coordinates two zinc ions to maintain a stable structure and is integral to proteins involved in gene expression, cytoskeletal organization, and developmental differentiation. It is found in Hibiscus syriacus (Rose of Sharon) and is associated with UniProt keywords Metal-binding, Cytoskeleton, and LIM domain.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 3066, 5961, 43, 2784, 17, 2601, 7997, 8497, 3418, 1988, 4088, 1966, 43, 2213, 17, 2213, 2835, 6854, 4356, 2254, 43, 2678, 17, 2743, 5219, 18, 2176, 10675, 2288, 7997, 6982, 1942, 6698, 43, 4700, 3170, 1930, 1977, 12328, 1942, 2697, 3286, 1922, 2359, 2294, 16, 14787, 5901, 16, 1930, 5878, 4155, 18, 2176, 1977, 2435, 1922, 26823, 10368, 1957, 11458, 2126, 6973, 12, 13679, 1927, 4980, 1916, 13, 1930, 1977, 2458, 1956, 20709, 11569, 6048, 17, 2743, 16, 11612, 16, 1930, 2784, 3418, 18, 3], "output": "MAFTGTLDKCKACKYLSFPFRMMSTYSWMDGVLYCKTHFEQTFQGIWQFQQEFSIGTQTSVQLATKRCTRWKRLPWKLFMVKGNSTDLTETLATREETADDDEDQSKEASDDDKTVYVVDLMTLEGVPYHKTCFRCSHCKGYFRTPSKLSSMFSYNHVLQAATHRRNSSTS", "metadata": {"id": "A0A6A3A987", "cluster": 3445569, "interpro_all": ["IPR001781"], "interpro_used": ["IPR001781"], "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 OTU domain that typically functions as a cysteine protease with deubiquitinating activity, regulating cell signaling and chromatin structure. It employs a conserved catalytic triad to hydrolyze peptide bonds, although some structural homologs lack enzymatic activity. This domain is also found in viral replicases and RNA-dependent RNA polymerases. Additionally, the protein is grouped in the Peptidase C85-like family, which comprises OTU domain-containing deubiquitinases that cleave ubiquitin to regulate pathways such as protein synthesis downstream of mTORC1 and the innate immune response. This group includes mammalian proteins like OTUD5 and OTUD6B, as well as putative viral ubiquitin thioesterases. Furthermore, the protein is assigned to 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 Tremella mesenterica (Jelly fungus).", "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, 20392, 3418, 1988, 5745, 4088, 1966, 43, 8666, 7154, 1956, 29436, 2287, 2455, 16, 6773, 2024, 3197, 1930, 6338, 3170, 18, 2176, 22620, 43, 5305, 6804, 21845, 1942, 7222, 6931, 4207, 9031, 16, 2876, 2673, 4346, 14279, 3630, 8145, 2455, 18, 2052, 3418, 1977, 2222, 2435, 1922, 4324, 5825, 2319, 1930, 3146, 17, 3100, 3146, 20910, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 24050, 19189, 1015, 17, 3189, 3416, 16, 2154, 12936, 20392, 3418, 17, 3165, 29436, 2319, 1988, 21252, 6526, 1942, 5741, 3873, 2427, 1966, 2213, 4271, 5863, 1927, 13694, 1930, 1920, 8539, 3743, 2644, 18, 2052, 2210, 5921, 6492, 2697, 3189, 20392, 1007, 1015, 1930, 20392, 1007, 22022, 16, 1966, 2486, 1966, 6770, 4324, 6526, 30215, 2319, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 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, 11797, 5870, 16234, 1019, 12, 8988, 11560, 1012, 16461, 13, 18, 3], "output": "MLPLKSSDDNQPKPVSMRGGKTKRRSTLDDVATEKKDVKDEITRLSLSLREIQGDGNCRKLVCDYLQVHEDDMSPFVVLPGGTSKIVTSVRVILSNSSMTMPYEEEEDDTPEEGTNPRRRTRSGTALTQYIPTVRPGRTMLWLALFSKGEHYQSIRRKGDSERGAARRERAELIKTGRITLDGNVLERKVEKGVENIVDDSTDGNMVDDPSQIAESQAIRNIQTASQITLNIKPRTPPIPPDSLNRRRARPEEYTEEDIVVRSRVSHPISVVRPLEASLVSMIRAEPPVTRRTTRSRSDEDDSITISLLFRALADQLWGDQRRHPEVYQDYVKNMRTSRTYGSQPEIVAATRVFRRTHLLSNPPALPLSSPSYASPSEIEDRLAVPHAKDESEGNMGEICRVDRSQDMAFNDAMEQSHPTVELGPKKRRRVIIPTHLDPPISP", "metadata": {"id": "A0A4Q1BN21", "cluster": 5832295, "interpro_all": ["IPR003323", "IPR038765", "IPR050704"], "interpro_used": ["IPR003323", "IPR050704", "IPR038765"], "interpro_unused": []}, "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 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. Additionally, 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 can be placed in the Casein Kinase 1 Ser/Thr Protein Kinase family, which consists of serine/threonine kinases that preferentially phosphorylate acidic substrates to regulate diverse cellular processes including Wnt signaling, DNA repair, and circadian rhythms. These enzymes modulate pathways such as the circadian clock by controlling the stability and nuclear transport of proteins like PER1 and PER2, while some family members act as pseudokinases involved in host defense mechanisms against viral replication. It is found in Elasticomyces elasticus.", "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, 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, 4950, 16, 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, 2112, 1998, 5396, 1922, 1920, 18576, 4016, 21, 2375, 19, 8481, 2213, 4016, 3416, 16, 2154, 7543, 1927, 8468, 19, 13143, 7784, 1988, 10662, 18730, 9931, 6249, 1942, 5741, 6445, 3689, 4028, 2710, 7028, 3197, 16, 2678, 5059, 16, 1930, 10507, 16622, 18, 2144, 5038, 8480, 3873, 2427, 1966, 1920, 10507, 10357, 2007, 7138, 1920, 5057, 1930, 4254, 4860, 1927, 2697, 3189, 2079, 1009, 1930, 2079, 1028, 16, 2679, 2673, 3416, 4678, 4033, 1966, 11520, 25545, 1036, 3286, 1922, 4423, 9720, 3531, 3316, 4324, 5158, 18, 2176, 1977, 2435, 1922, 10159, 29249, 10159, 1957, 18, 3], "output": "MGFLERLQENRINGRFTLIRKLAEGGGGDVYYGADCEQVPTILTPADVQLGRDHELEQDVAVKLEHRHNHLLRDEGIWLATFEGLPGFPTILWSGYHDEVGFLILNLLGPSLEDLFEYCECQFSLKTTIMLADQLIARLKTVHSENKLHRDVKPGNFLMGTGEDGNTVYITDFATATGYRPGSPLDDGEDLTQSDRGLIGTTWFASIRGHTGQSQAPADDLEALGYMLIYFVQGTLPWLELEACNITEKDQDQVVMEMKMTLSVDELCSGLPTTFAEYMTTVKRLKGCETPPYDELRELFKSLAREEGMEYDNVFDWTERMHRQQLALEDSLLNGAMRSEE", "metadata": {"id": "A0AAN7VSU9", "cluster": 9810321, "interpro_all": ["IPR050235", "IPR011009", "IPR000719"], "interpro_used": ["IPR000719", "IPR011009", "IPR050235"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein is included in 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. Also, the protein belongs to 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 native to Entamoeba histolytica.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 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, 2222, 16, 1920, 2213, 14440, 1942, 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, 6196, 1942, 8496, 1976, 6802, 7972, 2968, 26656, 18, 3], "output": "MLRSKYKKNLYALLEEKEFNVAAFNKLHHSVELTPVKLPKVFRILEDYITKNFTNEVNVVKATRTMGELSNNCREHLALMDERIVRVIRQCLGSANPKIKQAGMQLLGYYVKACNETSIRANFDEIKNLPLDLTKSAVNDTKDSEQALGALKDCVLIFQMVSEIDQILGSKTVLRVIFDCLNKNETNEAAKDIVLDIVSSITDKITMTKFMDGIKDYLDSSQKWENKLSQELIVEISGLIKVTMKDVMIQSILDHIPKTESISVKLSQLKLVQKLVDGRNDISADLLRKIHSLFTFSITSYDDLENSEAKEFINEVFDLIQKTLELVNDDLIKSDFCSFVFSESDNSSESKRFLNTVLLIKIVPLIKRDVIQRIDRIPFIKFLSNLVFSNHEIRSNSVKVIREFLFGSDEVITQQTNDIVFSTQIKYDLAESLLQSSTKTDELVQIYDLWRDIILGGELNELVETIPLIGYMSKRIQKLDAKHRNYVHYIILMLLKTISIKYNIEELATYLDERMKGIERYYDVTELNLKINKATKEYEEISQFIVKQSEIVDILKASDISNKIPNINKLSDEITSKDKNKHKATSSKLVSNNKSIGNNDHHNEKVITTNVDFNTLKKACLQDRNESKNETKTEQSFEGLMKEYQEIKKQEDDLIKEIEEMVKGVDDVNTVLDAKELYGEVNWVFEL", "metadata": {"id": "A0A5K1VQ94", "cluster": 10077598, "interpro_all": ["IPR011989", "IPR016024"], "interpro_used": ["IPR011989", "IPR016024"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein can be placed in the Type VI secretion, TssG-like family, which comprises Gram-negative bacterial proteins, including TssG, that form part of the Type VI secretion system (T6SS). These phage tail homologs are required for the proper assembly of the Hcp inner tube, facilitating the injection of toxins and contributing to virulence. It is derived from Candidatus Magnetomorum sp. HK-1.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2601, 3070, 5512, 16, 15835, 1029, 17, 3189, 3416, 16, 2154, 12936, 8604, 17, 3136, 4543, 2697, 16, 2710, 15835, 1029, 16, 1988, 2386, 3131, 1927, 1920, 2601, 3070, 5512, 2433, 12, 20762, 5590, 13, 18, 2144, 10503, 5281, 14279, 2032, 3414, 1958, 1920, 3405, 5957, 1927, 1920, 24519, 6671, 6723, 16, 12440, 1920, 4107, 1927, 13599, 1930, 8739, 1942, 9304, 18, 2176, 1977, 3595, 2037, 14550, 1031, 1957, 14634, 13777, 24277, 2056, 18, 13595, 17, 21, 18, 3], "output": "MADPIRKHKFDLNNYLIDHKHQFSFYQLMRLLRVLSDHSDETLYENTTIDNNEESKPFFSLTTSILGLYGPGSPLPSYYTEDLMDADKDDLVSGRAFIDMLQARLFDTSVLNRLFCMTGFGEKKVREAVFGSNVTDTKSYELIRYMGLFSQFPKSALKPCISQMVDIPEDQLNFLGKNNNTIGENSIIGEKVIDRMGKFRISIGPVKKEALYLFDHFNFDLEIIVHEKNTPICLGDNKTNIVGVWAWLTEDDKKLSDKSTIIQIQSPLDFSFPASPISELKQLLFESSRKYNMMLSINEYNGLQTILRDALETKAVKSSKFLPGNKGYKTIKRLTVC", "metadata": {"id": "A0A0M9E1R3", "cluster": 12499597, "interpro_all": ["IPR010732"], "interpro_used": ["IPR010732"], "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 a member of the Pescadillo family, which plays a critical role in ribosome biogenesis and is essential for embryonic development. Conserved from yeasts to humans, these proteins have also been linked to chromosomal instability and cancer. Also, the protein should feature a BRCT domain that functions as a protein-protein interaction module involved in DNA repair, recombination, and cell cycle control. Often arranged in tandem pairs, it forms a head-to-tail architecture that creates a specific cleft for binding phosphorylated peptides. It occurs in Porphyridium purpureum (Red alga) (Porphyridium cruentum) and has UniProt annotations Nucleus 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, 43, 7210, 1927, 1920, 14901, 3375, 7408, 11560, 1037, 3416, 16, 2154, 5705, 43, 4140, 2770, 1922, 12794, 13008, 1930, 1977, 4415, 1958, 7231, 2740, 18, 5305, 2037, 22486, 1942, 5209, 16, 2144, 2697, 2162, 2222, 2252, 4624, 1942, 9220, 9557, 1930, 2539, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 2387, 2341, 3418, 1988, 4088, 1966, 43, 2213, 17, 2213, 2835, 9059, 3286, 1922, 2678, 5059, 16, 7827, 16, 1930, 2024, 4048, 2285, 18, 3868, 14940, 1922, 10361, 5803, 16, 2176, 4952, 43, 4469, 17, 1942, 17, 5281, 9335, 1988, 15628, 43, 2487, 14649, 1958, 2743, 7199, 5320, 18, 2176, 5110, 1922, 17376, 3553, 9734, 25945, 2027, 1989, 12, 2312, 4326, 1019, 13, 12, 17376, 3553, 9734, 2345, 12044, 1989, 13, 1930, 2258, 20709, 15010, 5607, 1930, 9067, 4587, 18, 3], "output": "MKNKLKKGTRGSATNYITRGKALKPRDPKKKAEGPLKTYYLAKDIQFLAREPLLDIFRYTLDHIVRERYPTFHDALRDLDDPLCMIFLFSSLPAFASVKGMYYEAEVMGVTVIWLEPHKFAQKLPNFKLFLTLGLSYPPPAAVFSKLRSGTAESGLRSKRDRKSLSVSHESVSAAVQAVMAAAARKEGSQEQVDEEELFSGLSFFLGRETPMSVLDFVIRSFGGSPKLRGEKRVDLEYVQPQWIFDSVNAGILLDGYRPAFSEFIERIKAGDTSVLAESAFMRREDGHDHEDDAMPAGEGAKDGAGSSRSSAEEEQEEDEKVLDARAAKLYETIMRGRKRRSAKMQTVVAKRRAIDDAKLQLTLTDFRRLCVLKGIYQIRVQKRKIIRAKSRSEPGTLKQLRESMPKLGHISADRVKNCVHLAREFQLYVQQSHSLRKVRDVDYKVMGTFLEFYECLMRFVVADLKQDAGGEMAKKRELAGAQDGGDELDNEDDSKTLVVCETDCRSVGSVRGKITHWVVDRPVSLYSPGAHLPPHLSPFTKEEELGQAPHVKQGRLELPAADAKSEEKELAKMMMPRKHQ", "metadata": {"id": "A0A5J4YX68", "cluster": 15254498, "interpro_all": ["IPR001357", "IPR036420", "IPR010613"], "interpro_used": ["IPR010613", "IPR001357"], "interpro_unused": ["IPR036420"]}, "task_type": "infilling"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein is categorized in the Glycosyltransferase group 1 family, which catalyzes the transfer of sugar moieties to specific acceptors to form glycosidic bonds involved in diverse biosynthetic pathways. These enzymes mediate the production of essential cell envelope components and protective molecules, including mycothiol, glycolipids, and virulence-associated polysaccharides like lipopolysaccharides and capsular polymers. Also, 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 Oscillospiraceae bacterium.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 1977, 10234, 1922, 1920, 20067, 9961, 2210, 21, 3416, 16, 2154, 17097, 1920, 3856, 1927, 9523, 16706, 1942, 2487, 27916, 1942, 2386, 7533, 12546, 9031, 3286, 1922, 6445, 14041, 3873, 18, 2144, 5038, 8265, 1920, 3372, 1927, 4415, 2024, 11262, 4178, 1930, 6337, 4206, 16, 2710, 5078, 17809, 1945, 16, 14193, 2049, 3753, 16, 1930, 9304, 17, 2458, 18686, 3189, 15614, 1036, 1930, 22590, 11039, 18, 2222, 16, 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, 7799, 3106, 11979, 1972, 3336, 14061, 18, 3], "output": "MHFVFKGENMKIVFVSNFLNHHQIPFCKYLKSLVDEFWFIATDNGNSQGYQTSHHDNYLIDYFTEKTRAEKEILSADAVIFGACPDKLVTLRMKEDKLSFIYSERIFKKGILRCLIPKNFIYLKNRYLRYKTKNLYVLAASAFLPYDLSIFGFPQNKIFKWGYFPSCSAHKTQEKEQNTILYVGRLLKLKHADTVIKTAQFLKQEGVDFKVNIVGDGPEKDNLLKAVHAYKLQDHVHFLGSKTHTEVLKIMNKSQIYMFTSDFNEGWGAVLNEAMASGCAIVASSAIGSVPFLINHGENGLIYKYGNYKNAYNEVKSLLCDTQKAKFLGENAKATIAYYNHEIAAERFVNAVKEFHSVNTITSSDSGIFSSVKIIKNNWFK", "metadata": {"id": "A0A9D5T4P0", "cluster": 15921432, "interpro_all": ["IPR001296", "IPR050194"], "interpro_used": ["IPR050194", "IPR001296"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "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. Moreover, 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. Moreover, the protein is categorized in the C-type lectin and snaclec domain-containing protein family, which utilizes calcium-dependent carbohydrate recognition domains to mediate diverse biological processes including cell-cell adhesion, immune response, and pathogen recognition. Members of this family, particularly snake venom C-type lectins (snaclecs), can also modulate hemostasis by binding to coagulation factors or platelet receptors to inhibit or induce aggregation. It is produced by Chloroflexota 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, 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, 3950, 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, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 45, 17, 2601, 13468, 1930, 10459, 3283, 1030, 3418, 17, 3165, 2213, 3416, 16, 2154, 18127, 5016, 17, 3100, 10590, 5708, 4682, 1942, 8265, 6445, 3933, 4028, 2710, 2024, 17, 2024, 6141, 16, 3743, 2644, 16, 1930, 7055, 5708, 18, 4678, 1927, 2052, 3416, 16, 4443, 24044, 15540, 45, 17, 2601, 25607, 12, 10459, 3283, 2792, 13, 16, 2112, 2222, 8480, 23963, 2007, 2743, 1942, 12441, 2790, 2014, 7163, 4086, 1942, 2875, 2014, 4769, 7883, 18, 2176, 1977, 4152, 2007, 10107, 18222, 7336, 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": "MAQAKSRYAVFVTILGLFFLLAGGCSKIQGVFATPTSAPTSTPTLNPTPISTPTLIPTPTPYKGIQNPDNSHWYLVLPQMDWDNAENYCASRKGHLVTIEDEEENMFVYNLAPYALLGATDRDKEGHWVWVAGQEMSYTNWCQGEPNNCGSREVYGYCISENYLNFHNDPRCLSGQWNDVSISGEESYVCEFEN", "metadata": {"id": "A0A8T7FS63", "cluster": 16367006, "interpro_all": ["IPR001304", "IPR016186", "IPR050111", "IPR016187"], "interpro_used": ["IPR016187", "IPR001304", "IPR050111"], "interpro_unused": ["IPR016186"]}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein has a Sulfotransferase domain that catalyzes the transfer of sulfate groups to diverse substrates, including hormones and xenobiotics, via an SN2-like mechanism. It adopts a central \u03b2-sheet fold flanked by \u03b1-helices and utilizes conserved PAPS-binding and 3' phosphate binding regions, featuring a critical catalytic lysine and serine, to mediate detoxification, hormone regulation, and cell signaling. Moreover, 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 has been characterized in Mesorhizobium wenxiniae.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 2258, 43, 5141, 14165, 3418, 1988, 17097, 1920, 3856, 1927, 8767, 2671, 1942, 6445, 6249, 16, 2710, 10224, 1930, 29821, 1036, 16, 3454, 1925, 3437, 1028, 17, 3189, 2856, 18, 2176, 24032, 43, 4101, 161, 17, 11130, 3728, 20185, 2007, 160, 17, 12789, 1930, 18127, 5305, 3860, 1036, 17, 2743, 1930, 23, 11, 5413, 2743, 3451, 16, 29931, 43, 4140, 6804, 9082, 1930, 8468, 16, 1942, 8265, 18169, 16, 6365, 3640, 16, 1930, 2024, 3197, 18, 3950, 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, 2258, 2252, 4378, 1922, 23577, 5004, 2061, 23156, 2038, 14272, 14102, 1021, 18, 3], "output": "MLDDLGVDAAYTHDGSDHKDLRDIAQISPDKSRYKRQRILFLTRDPRDTAVSGYFQLFNLQWFAAASHMRKIALLRYEDVQRDTNDALRSIGKFLGKSFEESQLADVAVSRSFKRMQQSEVRKGKVGGYLDYLGADDIAFCDNVLARLDYWKRLDEAFQRHGISYADDRAGVNVNKRHGLEAGPMGDCIRSPKHGVEKIAISGELGARYGGRLQPRNPDDPESFK", "metadata": {"id": "A0A271KHC8", "cluster": 18923068, "interpro_all": ["IPR027417", "IPR000863"], "interpro_used": ["IPR000863", "IPR027417"], "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 is a member of the DRAM/TMEM150 Autophagy Modulator family, which modulates macroautophagy to enhance autophagic flux and influence cell survival under stress, often acting as lysosomal modulators implicated in p53-mediated apoptosis. Additionally, members function as components of mechanosensitive cation channels and regulate phosphatidylinositol 4-kinase localization, playing roles in diverse processes ranging from proprioception to photoreceptor cell renewal. In addition, the protein carries a CWH43-like N-terminal domain that functions as a conserved transmembrane region involved in diverse cellular processes, including stress-induced autophagy and phospholipid regulation. It characterizes proteins such as the lysosomal p53-effector DRAM and the plasma membrane protein Sfk1, playing a role in cell survival and the maintenance of phosphatidylinositol 4-phosphate (PI4P) levels. It has been characterized in Triparma laevis f. longispina and is linked to UniProt keywords 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, 1920, 2213, 1977, 43, 7210, 1927, 1920, 7287, 19, 22414, 20091, 6661, 18521, 3416, 16, 2154, 13112, 10133, 19847, 17539, 1942, 4826, 15319, 8220, 1930, 4039, 2024, 3298, 2441, 3071, 16, 3868, 8290, 1966, 12097, 17455, 6835, 1922, 5105, 17, 3434, 4091, 18, 4950, 16, 4678, 2347, 1966, 4178, 1927, 2665, 6642, 12924, 2185, 9976, 5628, 1930, 5741, 16927, 24, 17, 4016, 5363, 16, 14797, 5456, 1922, 6445, 4028, 6485, 2037, 24061, 14132, 1942, 16383, 2024, 14498, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 13198, 20360, 1010, 17, 3189, 56, 17, 4262, 3418, 1988, 4088, 1966, 43, 5305, 9117, 3031, 3286, 1922, 6445, 3689, 4028, 16, 2710, 3071, 17, 2719, 6661, 1930, 14608, 3640, 18, 2176, 26735, 2697, 2427, 1966, 1920, 12097, 5105, 17, 7917, 7287, 1930, 1920, 3582, 3260, 2213, 6347, 4835, 16, 14797, 43, 2770, 1922, 2024, 3298, 1930, 1920, 6291, 1927, 16927, 24, 17, 5413, 12, 4269, 24612, 13, 2428, 18, 2176, 2258, 2252, 4378, 1922, 8027, 21964, 25042, 48, 18, 2815, 1937, 9512, 1019, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 7864, 18, 3], "output": "MTLLTKTRSISIPTLTLSASAICIATFVTCYAISMANGDMEYPYYFLSSSLDFSPASCFGSFGLSPVSFLLPIIGWVRYEQVREVTKSIINRIMVMSSFVSAIGAHGVASFQAHNWMTVHLFFAFLFFGGGSLVVVCAVTTDYYCSSFGTALMRNYRRFAAAVVGCCLTALCTLAVLFIPPGGECDKTCQKFQFINAILEITVMVLMLSFYVSFIPEFQGWKFKVIIEREGGGGVGMGVGGLTEPLKNTV", "metadata": {"id": "A0A9W7KXA7", "cluster": 20871505, "interpro_all": ["IPR050911", "IPR019402"], "interpro_used": ["IPR050911", "IPR019402"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein can be placed in the Ribonuclease H superfamily, which comprises the catalytic domains of diverse polynucleotidyl transferases characterized by a conserved 3-layer $\\alpha/\\beta/\\alpha$ fold. This superfamily includes enzymes such as RNase H, retroviral integrases, transposases, and exonucleases that utilize this domain to catalyze nucleic acid backbone cleavage or transfer during DNA replication, repair, and recombination. Moreover, the protein falls within 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. It is derived from Corchorus olitorius.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 18347, 2051, 50, 13975, 16, 2154, 12936, 1920, 6804, 4682, 1927, 6445, 15176, 2626, 4090, 2199, 13763, 1036, 4378, 2007, 43, 5305, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 18, 2052, 13975, 5921, 5038, 2427, 1966, 9843, 50, 16, 16599, 27252, 1036, 16, 12935, 2319, 16, 1930, 24966, 1036, 1988, 12561, 2052, 3418, 1942, 18170, 11079, 2687, 10787, 6404, 2014, 3856, 2409, 2678, 5158, 16, 5059, 16, 1930, 7827, 18, 3950, 16, 1920, 2213, 12182, 2651, 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, 2176, 1977, 3595, 2037, 2233, 28226, 3176, 1036, 2865, 6733, 11519, 18, 3], "output": "MDFCCMTSPDPMIVICKSQHSIMEIEQVLMELPTPGWVKLNCDGTQDPMKKKVSIGVILIIAKAMAVKEGLQLAKNKVHCGSGINIWQDSWVLGVDHEDHCWKDEGPGDQKDFNRPLQVEKWDDSEGLQLAKNKGINIWQDNWVVSEIIDLEDHCWKDEGPGDQKDFNRCITEELAAAINRPLQVEKWRDDSGMIIRGANREAKAKSAGRLERIGDGVIPLSTPQKVSKIIGMIIRGANRETKTRSAIIVKAMVVKIGIGRLERIEDGDIPLNAPQK", "metadata": {"id": "A0A1R3GBE5", "cluster": 23262151, "interpro_all": ["IPR052929", "IPR012337", "IPR036397"], "interpro_used": ["IPR036397", "IPR052929"], "interpro_unused": ["IPR012337"]}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein has a YjeF N-terminal domain that functions as a bifunctional NAD(P)H-hydrate epimerase in bacteria and archaea, often found fused to the YjeF C-terminal domain. It catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the ADP-dependent dehydration of the S-form of NAD(P)HX. It originates from Gloeomargarita lithophora Alchichica-D10.", "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, 2258, 43, 67, 12518, 1038, 56, 17, 4262, 3418, 1988, 4088, 1966, 43, 29491, 6577, 12, 58, 13, 50, 17, 27864, 13872, 9213, 2051, 1922, 4802, 1930, 21501, 16, 3868, 2435, 10305, 1942, 1920, 67, 12518, 1038, 45, 17, 4262, 3418, 18, 2176, 17097, 1920, 13872, 9213, 2466, 1927, 1920, 61, 17, 1930, 60, 17, 4952, 1927, 6577, 12, 58, 13, 22721, 1930, 1920, 9828, 17, 3100, 16585, 1927, 1920, 61, 17, 2386, 1927, 6577, 12, 58, 13, 22721, 18, 2176, 22970, 2037, 25632, 1021, 2954, 1005, 13279, 9909, 10945, 22575, 1019, 4143, 23733, 23733, 1019, 17, 8524, 1008, 18, 3], "output": "MNEPFCTSTGLPIPTLTPAQVTAGRSGAMLTLGWLGEDWQVGRVVVLVGNGRVWLNPEILDNQFLQNQYNLYQKTGAAVVVVGSDTPLPPEIWCWVAESGAEVLRVLGLPVTETPYGGQLYLADVGVREEGGLDLGAEIATPPDCRWWASVAHAGLSQAVWVETVTGSVVLSAARHLANRCLNVAQRVDLAELTGETGAMLDGTAAATLVPLAVYEQLGLYHRFVFGNQYIIPMYQ", "metadata": {"id": "A0A1J0AA13", "cluster": 26076072, "interpro_all": ["IPR004443", "IPR036652"], "interpro_used": ["IPR004443"], "interpro_unused": ["IPR036652"]}, "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 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 occurs in Candidatus Veblenbacteria bacterium and corresponds to UniProt keyword Cell membrane 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, 12182, 2651, 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, 5110, 1922, 14550, 1031, 1957, 3428, 7272, 17046, 2422, 2126, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 2024, 3260, 1930, 9117, 7864, 18, 3], "output": "MLSPLGHNTLIQLIGKLLATLAGLVVVAFMTRSLGPTGFGHYTTIIVFLQTFAILIDFGLTMTAGRSLGEHKIPSHIFLSNLLSFRVITAAMTFALAPTVALFLPYPGIVKLGITATSLAFFLASLTQSFQAVFQASLKSGYLVAADLAGKLLLLVGTILVAQLNLGLMAFLAVYTVSSAAIAGGTLFYARKLMPFKWELDLLVWKTIWLATWPIAITIGLNLIYLKXRHFDIGRHLASPRCRSLRCGLQSAGGIAGRAGHYRRTGAPASCPLLGLS", "metadata": {"id": "A0A353WDT6", "cluster": 26523392, "interpro_all": ["IPR050833"], "interpro_used": ["IPR050833"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is included in 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. In addition, the protein is associated with the THEM6/lcsJ thioesterase family, which functions as a thioesterase involved in the biosynthesis of bioactive compounds such as oxaleimides and lipopeptide antibiotics. Members of this family hydrolyze thioester bonds to facilitate the release and maturation of secondary metabolites generated by polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) pathways. It is identified in Trichoderma asperellum (Filamentous fungus) and is described by UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 3063, 1922, 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, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 3581, 1016, 19, 22913, 1013, 30215, 2051, 3416, 16, 2154, 4088, 1966, 43, 30215, 2051, 3286, 1922, 1920, 8132, 1927, 13570, 4300, 2427, 1966, 18512, 14209, 16408, 1918, 1930, 3178, 21305, 7560, 18, 4678, 1927, 2052, 3416, 7222, 6931, 30215, 9031, 1942, 6628, 1920, 4012, 1930, 7655, 1927, 4067, 6926, 3999, 2007, 4286, 18540, 2261, 8921, 12, 26137, 13, 1930, 2447, 17, 11196, 4207, 18185, 12, 5214, 2523, 13, 3873, 18, 2176, 1977, 2899, 1922, 10477, 20532, 14176, 10757, 12, 18706, 16461, 13, 1930, 1977, 2910, 2007, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MGLWKWAFGLFLVVNLKLLPFLWHFRFFWALGSGILLNRRARRLLKPHHILLDLDVSRAFLSGVIFGPLITGSGGKRCNLIVGAVSCTFKREIKPYKSYETWTRVASWDELRAGQRVLQSHSSEWADEKPETTSRSEGSRVVFASAVTRFVCKRGRLTVPPAQALEECGLLRVSTSTAAGACLTMLEDVESSRIANLPIVRLQQGWDKVHELFREDIAVLGTYSDMVWPPTISTTRAPLMEIDFNFHKSNSTYFTEKWIYMVTHFVQRGVALSIGETGLQHEEHPNVDSAAKPDV", "metadata": {"id": "A0A6V8R2M3", "cluster": 27605360, "interpro_all": ["IPR029069", "IPR051490"], "interpro_used": ["IPR029069", "IPR051490"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein can be placed in the Protein of unknown function DUF3619 family, which consists of uncharacterized bacterial proteins approximately 140 amino acids in length. Members of this family are defined by the presence of two conserved sequence motifs, AAR and DDLP. It originates from Tropicibacter naphthalenivorans.\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, 2213, 1927, 5435, 2347, 4855, 10892, 9171, 1026, 3416, 16, 2154, 7543, 1927, 24528, 4543, 2697, 3993, 8949, 3835, 4576, 1922, 3471, 18, 4678, 1927, 2052, 3416, 2032, 3608, 2007, 1920, 2990, 1927, 2288, 5305, 3244, 8277, 16, 27907, 1930, 6758, 13857, 18, 2176, 22970, 2037, 29746, 26073, 2341, 1915, 26795, 28131, 15525, 17182, 1036, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MSDTSTTDLEQQVRAERARFAASLSGLAQAADPRKNGGKAARAAKDNPAGLALIGVGLAVLALNPSKKKDIEQDRPSASKMRQALDAGLDKLPPEARERVQAAKDTHQSQPLLTAAIAAGIGGLIGALLPSTERESELAKAGADAVAARLDSAPAERPHADHAMQQMTETGQALARSETPDPRSFDDRVAHADQRMRLKAARLKAIDAQDKLEREAARMTLLGAQRDAFMRDAEAVLRAEMHT", "metadata": {"id": "A0A0P1G1N1", "cluster": 28038248, "interpro_all": ["IPR022064"], "interpro_used": ["IPR022064"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is classified under 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 is classified under the YpeA/RimI acetyltransferase family, which catalyzes the transfer of acetyl groups from acetyl-CoA to diverse substrates, including proteins, polyamines, and antibiotics. This family includes RimI, known to specifically acetylate the N-terminal alanine of ribosomal protein bS18, as well as members that confer resistance to antibiotics such as gentamicin and streptothricin. Furthermore, the protein should have 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 produced by Anaerolineae bacterium.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 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, 1977, 5947, 2441, 1920, 21995, 5376, 19, 14764, 1033, 22226, 3416, 16, 2154, 17097, 1920, 3856, 1927, 6894, 2671, 2037, 6894, 17, 10027, 1942, 6445, 6249, 16, 2710, 2697, 16, 27883, 1036, 16, 1930, 7560, 18, 2052, 3416, 5921, 14764, 1033, 16, 3171, 1942, 4475, 6894, 2010, 1920, 56, 17, 4262, 10504, 1927, 11196, 2213, 8242, 3928, 16, 1966, 2486, 1966, 4678, 1988, 7909, 3554, 1942, 7560, 2427, 1966, 17144, 1930, 8987, 2195, 3133, 1921, 18, 3677, 16, 1920, 2213, 3066, 2162, 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, 4152, 2007, 11381, 8419, 3336, 14061, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MGVRLKNRWAAETTTHDLGAVQVAYYGDAEVASFQMEFFIQSGETYVLNVAHADETPDTTYASLFEVKRPAQAMYVNETHLQHEPMPVHIVVIQSVPNIAYINNLYTLPDFRRLLLIPSEMAKHFYATHGYQPLLYFSVWRPAEAFLKSYTEIFAAIYDAVDAEPSAVLEAIRAYPGYQYQHTYPLYGIEFPAPLDVPKIAVGHPNIRQFFAKIEGQAVGWIQRGVAGALLNRVQQVCAEAGVSH", "metadata": {"id": "A0A6L4AH32", "cluster": 28190768, "interpro_all": ["IPR016181", "IPR000182", "IPR050680"], "interpro_used": ["IPR016181", "IPR050680", "IPR000182"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "\"The protein is grouped in the Lipid A-modifying glycosyltransferase 83 family, which modifies bacterial lipopolysaccharide (LPS) by transferring specific sugar moieties, such as L-Ara4N, to lipid A. This activity confers resistance to cationic antimicrobial peptides like polymyxin, thereby enhancing bacterial survival and virulence. Some members also contribute to LPS inner core assembly by transferring galacturonic acid residues. Moreover, the protein should contain 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 is native to Microlunatus endophyticus and has UniProt annotations Transmembrane, Transmembrane helix, and Cell membrane.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 1977, 10809, 1922, 1920, 4486, 43, 17, 12691, 20067, 9961, 5893, 3416, 16, 2154, 25436, 4543, 15614, 12, 5887, 13, 2007, 21902, 2487, 9523, 16706, 16, 2427, 1966, 54, 17, 20289, 1006, 1022, 16, 1942, 4486, 43, 18, 2052, 2455, 16556, 3554, 1942, 15175, 8003, 5320, 3189, 3491, 28330, 16, 6113, 9221, 4543, 3298, 1930, 9304, 18, 2673, 4678, 2222, 4672, 1942, 5887, 6671, 4728, 5957, 2007, 21902, 9479, 21280, 2687, 4248, 18, 3950, 16, 1920, 2213, 3066, 5531, 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, 1977, 6196, 1942, 16262, 17864, 1031, 1957, 19771, 4274, 1957, 1930, 2258, 20709, 15010, 9117, 16, 9117, 7864, 16, 1930, 2024, 3260, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MSAVDTARTGSGGPGSGGPGSGGAGAGAPATLLTIISALFARVLLPGEYAVLVSFVSAYVGLHKRLFRRGLALGLGIGAVLAALAGPSAVLLALARGRLYGTQSVGGTVATLITEPIGGVVAAGYAALAAASIAARRRPEPLPRLAEDTGRHVACLASANAIFSNRQLGPGEAGVFAAVASGSRDSGRSSLLVAVGVAGAVSLAGVGVVALLPAVVAYVAAMAALGIGRVLIAQLCKTGLARAAAVLSGCGMLLVGSAAVLLREARLQRAMVVVDVVQRVPLGSKIKALWPLWLAMGIGIGLRLPYPDMINTLKNDDVHPPLFHTILWALVHTACIPISFAMAKDLWNRRTAVVAGFVVAVAPVAVWIRILRDIKEGKGYGSLADWAGFTVVHLIFLIAVLKVRKWRFVRNWLLSAVVQASTAPSQTGSDTATTGKPDVYAAVANTIWSVWGYHADSVRDRTNLILATIAVAPPAMLFLVGFERRQATWGRGPLTKLLLPVVTIASLGAGLIDQQANSQPQDVVLYAPNFLRTELEYYQTGMPAIPKQGRRVFVFGSFLEEPQVAGQVYQQLPPSKSDTSKADTDHTKQTKGGKRVRRAGSKQLLTMSGQLVAGVGNMLMHMVGSSVTAAVAIDPSGVLSPLLNLPVPVIILLGARAVIGLLLGSVIGPVGAAVARRARTGDSLYVTVTFLLTIGSAAYFATGTIPMMLRAYAMVLGEHYASVGDYALSVAVQVGVLIPAHSASAVVAATAAPEASRTAVRPSAAPAPAAPPVIVTRSIWVDEAISIQQAQLTGSTAEYIVRLPSLLAGYSQEARMYGLWMLGATILAWCQTAAMIYVQWFTALPIITQLILFAPLVPYMLDQFGNIIAAQGTMVQLGAFWPVAVLMCFAALGRFFELRYFDSTVPMLLLVLARMAINQSNPRVYDFRGAVGWVKPSGLTTLDANSAHPSRAGGVLSDLDRASNTKRLAVHSVANVKVWE", "metadata": {"id": "A0A917S865", "cluster": 28307700, "interpro_all": ["IPR050297", "IPR038731"], "interpro_used": ["IPR050297", "IPR038731"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The desired role of my protein is: The protein should have a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. Also, the protein contains a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. It has been detected in Candidatus Corynebacterium gallistercoris. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 3066, 2162, 43, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 2222, 16, 1920, 2213, 5461, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2176, 2258, 2252, 3330, 1922, 14550, 1031, 1957, 2233, 17151, 7972, 2341, 18842, 1989, 9354, 7263, 4879, 13950, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MKIVILASGTGSLLQAVINQAKKEKIQILSVGSDRPCHALKRAEEAGIPTFTVDYRPGETDRAQWNTQLAETLASYGPDLVVSAGFMRIIGEEVIQQFPQQIINTHPALLPAFPGAHAVEDAINYGVAVTGTTVHVVDAGVDTGPIIDQRAVRVQADDTVDSLHERIKQTERELLVDVLHAIADHGLTIDGRKARINND", "metadata": {"id": "A0A9D1RYM8", "cluster": 22206069, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR001555", "IPR002376"], "interpro_unused": ["IPR004607", "IPR036477"]}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein is a member of 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. It is native to Actinomycetes bacterium.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 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, 2176, 1977, 6196, 1942, 4718, 25148, 14061, 18, 3], "output": "MAELPAQISLSFPGRPEYLRLARLTAALRIAVSELCHVIGGTDSDDRLTLEFTIEPGSLEVRIVAAVVDDHEVDAHSDGSTRFWMVKRSAVPADRDAGSRAGFDYEEIDDGTSAVATSTHDNEFSRA", "metadata": {"id": "A0A537ZHA1", "cluster": 110558, "interpro_all": ["IPR036890"], "interpro_used": ["IPR036890"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein falls within the Invasion protein B family, which functions as a major virulence factor essential for human erythrocyte parasitism, notably in *Bartonella bacilliformis*. These proteins are up-regulated by environmental cues signaling vector-to-host transmission to facilitate bacterial survival under stress-inducing conditions. It is identified in Hyphomicrobiales bacterium.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 12182, 2651, 1920, 6254, 2213, 44, 3416, 16, 2154, 4088, 1966, 43, 3044, 9304, 2991, 4415, 1958, 2616, 15469, 16891, 2421, 16, 7388, 1922, 14, 21959, 2290, 11560, 1019, 25332, 2231, 1937, 14, 18, 2144, 2697, 2032, 2353, 17, 4335, 2007, 4813, 8972, 3197, 4580, 17, 1942, 17, 4423, 5303, 1942, 6628, 4543, 3298, 2441, 3071, 17, 7834, 2961, 18, 2176, 1977, 2899, 1922, 2483, 25808, 1935, 7839, 1918, 14061, 18, 3], "output": "MKLNFAAAGRLAGTAAAALLLAGTLTAGATATNLFISKPTRQRLVGVAVRTEEKQKVKALLVVQVVTCRRDGCHAQFTLGDGMYKELRKAKNLNLIYIAEAFEGPAAKLPPPPMPKKAKATEPGANNWIKQCTKNKAGHKICLLPLGIYITPGFTVKLDEGEGYKGDHKRQKLNVAVPMAGF", "metadata": {"id": "A0A2N6AX19", "cluster": 1282705, "interpro_all": ["IPR038696", "IPR010642"], "interpro_used": ["IPR010642"], "interpro_unused": ["IPR038696"]}, "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 ABC transporter type 1, GsiC-like, N-terminal domain that functions as the transmembrane component of bacterial binding-protein-dependent transport systems. It facilitates the translocation of substrates, such as glutathione and dipeptides, across the cell membrane in permease proteins like GsiC and DppB. Also, the protein should feature 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. In addition, the protein is assigned to 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. It is produced by Anaerolineae bacterium and is linked to UniProt keywords 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, 4075, 43, 7219, 9054, 2601, 21, 16, 5022, 1935, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 9117, 4594, 1927, 4543, 2743, 17, 2213, 17, 3100, 4860, 3771, 18, 2176, 11374, 1920, 7849, 1927, 6249, 16, 2427, 1966, 9153, 1930, 9137, 11536, 16, 3436, 1920, 2024, 3260, 1922, 6191, 2051, 2697, 3189, 5022, 1935, 1930, 16423, 1014, 18, 2222, 16, 1920, 2213, 3066, 5961, 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, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 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, 2176, 1977, 4152, 2007, 11381, 8419, 3336, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 7864, 18, 3], "output": "MITLIVRRLASLPFVIFSITFITFVVGYLAPGDPILTMMLYGLDLPWFQQYGNYMLGLVQGDLGLSFRYQGVPVGLLAALHQNTLVDRASTTFMLALYSIPSFPSLPVAGWGRPEHWIMPVIVLSGASMGYIARLTRSSVAMHIFRNAMLPVITVIGPSIAFLVTGAFVVENLFAIPGIGFLSVVAIAVVLMNLVTDFMYTILDPRVQVEAGARHDPATYERLRHGRPVWELIRTGVPVSFTLGLAALSLSVAVVLIPVLQWLNYQSYFRGGVEVIRQDYVRTAHAKGLTERRVNQAIAQRDYPVIQSTTVI", "metadata": {"id": "A0A9E3W9G4", "cluster": 3431783, "interpro_all": ["IPR045621", "IPR000515", "IPR035906"], "interpro_used": ["IPR045621", "IPR000515", "IPR035906"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a polypeptide chain that performs the following role: The protein falls within the Nuclear hormone receptor-like domain superfamily, which functions as a ligand-responsive transcription regulator involved in embryonic development, cell differentiation, and homeostasis. This feature comprises an all-helical C-terminal ligand-binding domain that acts as a molecular switch, undergoing conformational changes upon binding steroids or hormones to facilitate dimerization and coactivator recruitment for gene regulation. Furthermore, the protein is assigned to the Nuclear hormone receptor family member nhr-150 family, which comprises the orphan nuclear receptor Nhr-150 found in *Caenorhabditis elegans*. As an orphan receptor, its specific ligand and precise biological function have not yet been characterized. In addition, the protein should contain a Nuclear hormone receptor, ligand-binding domain that regulates transcription in metazoans by binding specific small hydrophobic molecules within a conserved $\\alpha$-helical sandwich structure. This binding event induces conformational changes in the ligand-dependent activation function (AF-2) region, facilitating the recruitment of transcriptional coregulators to modulate gene expression. It is found in Caenorhabditis briggsae and has UniProt annotations Transcription regulation. 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, 12182, 2651, 1920, 4254, 6365, 3148, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 5207, 17, 8487, 3213, 7888, 3286, 1922, 7231, 2740, 16, 2024, 4155, 16, 1930, 7622, 18, 2052, 5961, 12936, 1925, 2136, 17, 11514, 45, 17, 4262, 5207, 17, 2743, 3418, 1988, 8016, 1966, 43, 3272, 6195, 16, 7258, 8523, 2840, 4073, 2743, 13039, 2014, 10224, 1942, 6628, 13640, 1930, 22706, 6067, 1958, 2359, 3640, 18, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 4254, 6365, 3148, 3416, 7210, 5331, 1005, 17, 5493, 3416, 16, 2154, 12936, 1920, 21614, 4254, 3148, 5331, 1005, 17, 5493, 2435, 1922, 14, 22418, 10861, 14, 18, 1966, 1925, 21614, 3148, 16, 2496, 2487, 5207, 1930, 8162, 3933, 2347, 2162, 2084, 4898, 2252, 4378, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 4254, 6365, 3148, 16, 5207, 17, 2743, 3418, 1988, 7014, 3213, 1922, 24207, 2075, 2007, 2743, 2487, 2858, 7919, 4206, 2651, 43, 5305, 8, 38, 4595, 8, 17, 11514, 18038, 3170, 18, 2052, 2743, 4817, 6387, 8523, 2840, 1922, 1920, 5207, 17, 3100, 2936, 2347, 12, 2221, 17, 22, 13, 3031, 16, 12440, 1920, 6067, 1927, 5224, 26648, 20219, 1942, 8480, 2359, 2294, 18, 2176, 1977, 2435, 1922, 22418, 2387, 1950, 4874, 3336, 1930, 2258, 20709, 15010, 3213, 3640, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MELMAIIWIIFFDHAYNDISWKSTNLCWSIRKVIHRELRNYLIEKFSGDVEMAENRFLNLLEIPMIVERGEQNFKKKLYFFN", "metadata": {"id": "H8WH84", "cluster": 3503033, "interpro_all": ["IPR042936", "IPR035500", "IPR000536"], "interpro_used": ["IPR035500", "IPR042936", "IPR000536"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein belongs to the Membrane-spanning 4-domains subfamily A (MS4A) family, which comprises proteins characterized by four transmembrane domains that are predominantly expressed in hematopoietic cells and function in immune signaling and regulation. Members include the B-cell antigen CD20 and the high-affinity IgE receptor beta chain, and variants within this cluster have been implicated in Alzheimer's disease. It is present in Acanthocheilonema viteae (Filarial nematode worm) (Dipetalonema viteae) and exhibits UniProt keyword tags Transmembrane helix.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 3260, 17, 13346, 24, 17, 4682, 16227, 43, 12, 3012, 9458, 13, 3416, 16, 2154, 12936, 2697, 4378, 2007, 3006, 9117, 4682, 1988, 2032, 7700, 3198, 1922, 9960, 2094, 1930, 2347, 1922, 3743, 3197, 1930, 3640, 18, 4678, 3951, 1920, 44, 17, 2024, 4730, 16494, 1930, 1920, 2149, 17, 5173, 10777, 3148, 4666, 4659, 16, 1930, 4936, 2651, 2052, 4377, 2162, 2252, 6835, 1922, 9116, 11, 61, 2573, 18, 2176, 1977, 2481, 1922, 25645, 2694, 14209, 6012, 19319, 1019, 5208, 5376, 1021, 12, 3313, 14968, 18827, 11055, 13, 12, 9137, 3949, 2290, 3368, 5208, 5376, 1021, 13, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 7864, 18, 3], "output": "MGMEENDLKPISLVTTSPSSAVRKDFSESMELNVAQVWPCRLCGVILGICHLPLGIVLLIFDVVTNNISETAFAITASLSFIICGIFSFISARRLDRPAQLLLLFFSIFSMAMSITMFIDSAALINYNCDRGKCYEVLSNIHVVLLCFGLVEFTISFTTMIVCFRSLRLAYRVRKASSPYSTLIEGHYDAFYIKPSIMFITSSLPKNMDSECDV", "metadata": {"id": "A0A498SB41", "cluster": 3581153, "interpro_all": ["IPR030417"], "interpro_used": ["IPR030417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein is associated with the The Sel1/AlgK family, which encompasses proteins involved in diverse structural and regulatory functions, including endoplasmic reticulum quality control and exopolysaccharide biosynthesis. Members facilitate the ER-associated degradation (ERAD) of misfolded proteins and Notch signaling, or contribute to biofilm formation by potentially catalyzing mannuronate polymerization. Some variants also provide positional information for organelle localization or bind secretory immunoglobulin A to evade host immune defenses. Additionally, 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. In addition, the protein incorporates a Sel1-like repeat that constitutes tetratricopeptide repeat sequences originally identified as key negative regulators of the Notch pathway in *Caenorhabditis elegans* receptors. These repeats also occur in mammalian pancreatic proteins, though their specific functions in that context remain largely uncharacterized. It has been characterized in Neisseria weixii.", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 1920, 2484, 1009, 19, 4326, 1040, 3416, 16, 2154, 21569, 2697, 3286, 1922, 6445, 4346, 1930, 4948, 4088, 16, 2710, 13355, 12279, 3455, 2285, 1930, 18930, 13811, 2012, 9466, 8132, 18, 4678, 6628, 1920, 2668, 17, 2458, 4877, 12, 14827, 13, 1927, 20303, 2697, 1930, 8091, 3197, 16, 2014, 4672, 1942, 9638, 3337, 2007, 5063, 29601, 7338, 10366, 2010, 11486, 18, 2673, 4936, 2222, 3394, 20172, 2988, 1958, 19309, 5363, 2014, 4566, 11518, 11837, 43, 1942, 28917, 4423, 3743, 24226, 18, 4950, 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, 1922, 2459, 16, 1920, 2213, 19683, 43, 2484, 1009, 17, 3189, 6865, 1988, 14879, 12470, 3319, 21305, 6865, 3709, 10398, 2899, 1966, 3834, 3136, 9098, 1927, 1920, 8091, 3374, 1922, 14, 22418, 10861, 14, 4086, 18, 2144, 9569, 2222, 4704, 1922, 6492, 6356, 2697, 16, 4170, 2310, 2487, 4088, 1922, 1988, 4491, 5555, 6318, 24528, 18, 2176, 2258, 2252, 4378, 1922, 28356, 18339, 24815, 18068, 1033, 18, 3], "output": "MSAATPETLYQQACALLAKSPDSIQGLTLLRQAAEQGHADAAFEISLIMMEAPQPDYPGILSWLDIAAEQKHPYATYNLLRIRESMGASFDRHIQQYAWLAESGLLAAQLSLLEYYADRHETQAVYWAQQVAEQGHPFGQYFLALHHHFSAEPDLAQARELYHQAAEQGLHVAHWQLGKIYRYGLGTNIDNALAAHHLRFAADNGFIAAQTLLADVLAEQNHADALKWYQTAADNGDQQARTALARHYLTGQLTERDPLQAAKHAKIAAAHHHPEALQLMGDIYRYGLGIKADARTAEHYYREAAEHGSLSAYQKLLSDAALHHPEQYGRIKTAALQHQEAEQAHQTALAHHQGRRNQAVNYVEARKLYVQAASQGHAAAAFGLGLIYYHGQGVKADNRQAAYWFEQAAEQGHAEAQYHLARLYYYGQGVVANLPIACTWLQAAIENGYENPQAFQYLLDKWQREAGLTSSK", "metadata": {"id": "A0A3N4MUF1", "cluster": 4346576, "interpro_all": ["IPR006597", "IPR050767", "IPR011990"], "interpro_used": ["IPR050767", "IPR011990", "IPR006597"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein has a McpB, third HAMP domain that acts as a signal transduction module within the aerotaxis transducer Aer2 (McpB) of *Pseudomonas aeruginosa* and related gammaproteobacteria. This domain adopts a parallel four-helix bundle structure composed of two parallel $\\alpha$-helices, facilitating the conformational changes required for chemotactic signaling and bacterial virulence. In addition, the protein features 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. Additionally, the protein includes a Methyl-accepting chemotaxis protein (MCP) signalling domain that functions as a highly conserved transduction module within bacterial receptors to mediate chemotaxis. It responds to changes in the concentration of environmental attractants and repellents by transmitting signals to the downstream histidine kinase CheA to regulate swimming behavior. It is identified in Saccharospirillum sp. MSK14-1 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, 2258, 43, 11942, 1014, 16, 4563, 8616, 1034, 3418, 1988, 8016, 1966, 43, 2733, 8201, 9059, 2651, 1920, 6049, 7336, 18068, 1036, 14848, 6049, 1028, 12, 11942, 1014, 13, 1927, 14, 13461, 10830, 14, 1930, 2712, 7034, 9218, 1021, 10296, 18, 2052, 3418, 24032, 43, 6110, 3006, 17, 7864, 14142, 3170, 7179, 1927, 2288, 6110, 8, 38, 4595, 8, 17, 12789, 16, 12440, 1920, 8523, 2840, 3414, 1958, 20513, 3197, 1930, 4543, 9304, 18, 1922, 2459, 16, 1920, 2213, 4075, 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, 4950, 16, 1920, 2213, 5921, 43, 4963, 17, 26170, 16884, 2213, 12, 11942, 13, 8076, 3418, 1988, 4088, 1966, 43, 3626, 5305, 8201, 9059, 2651, 4543, 4086, 1942, 8265, 16884, 18, 2176, 20575, 1942, 2840, 1922, 1920, 3110, 1927, 4813, 24670, 2356, 1930, 3699, 11560, 2039, 2007, 27622, 4771, 1942, 1920, 5863, 13873, 4016, 10003, 1019, 1942, 5741, 15781, 3379, 18, 2176, 1977, 2899, 1922, 14175, 15742, 3508, 23576, 11560, 1989, 2056, 18, 3012, 4835, 1006, 17, 21, 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": "MFDNLKTRTRLNIGFIIWRFNDQVSRISNEHAPAQGFLLNADRDAFEHQRQAHAENIQQAHDRVLRLEAEWQSSSNALVDALESASSPLARSRLSARSELTILLQHETANAQSSYYLSLAIMLTLSLGGEPKTAAHISRQIAEGNLDIPIDVKDGDDSSILAAHAEGEIDVVIDAKKFGGAQRTALNCIEAFGAGKMDTPLAPFPGEGELNIRADEAVHQGDFRKIVAGLNSVMNAFAEPQSNSYRGRIKDLQTSINATLAQLNTTISLNGTSRRLSQSTLDQAANVEETTASIELTVEAEKGSEAVERTIAAMKKIAEKIGIIDNIAYQTNLVVAAEVRRLAEQSQGASQEIGQAAKHSVELSETAGQLFEVSVASGEQSSATRQINSAMEQMSSITQSMAFFRTQQALPASGILIAGLILIVALSTLLQQALVAERSMLVLEPGSEYASLVRTDISNQLVEQYLALDEVDAQFNTMRDVIDEVGNIMVLCALFLSVRISRSILSELALQVVRSCINELIAEMNRMSKYRTMAESLNQMVQGHIIDQKVFINTTIEKVRSNIKALIEDTNKLVDAAVIDEITVMMQALEKGDLTQTLQEVLLSAAKLGTAASEMSASIDKNAKNAQTTESIAQQLALNATVEATKAGNHGRGFASDIVPTIQKTFELVRNADSAENLTSSADELSEQAEHLRAV", "metadata": {"id": "A0A2T6E3J3", "cluster": 5946774, "interpro_all": ["IPR004090", "IPR003660", "IPR051310", "IPR041395", "IPR004089"], "interpro_used": ["IPR041395", "IPR003660", "IPR004089"], "interpro_unused": ["IPR004090", "IPR051310"]}, "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 Seed Storage and Functional Proteins family, which primarily accumulates as reserves to provide carbon and nitrogen for seedlings post-germination. Some members also contribute to plant defense through lectin-like carbohydrate binding and antimicrobial activities, or function as metalloproteases and alpha-amylase inhibitors. It is identified in Olea europaea subsp. europaea.", "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, 4861, 7451, 1930, 3183, 2697, 3416, 16, 2154, 5985, 18804, 1966, 28227, 1942, 3394, 5056, 1930, 6634, 1958, 12575, 2753, 17, 14609, 18, 2673, 4678, 2222, 4672, 1942, 4496, 9720, 2596, 13468, 17, 3189, 10590, 2743, 1930, 8003, 4209, 16, 2014, 2347, 1966, 28629, 2319, 1930, 4595, 17, 19139, 4472, 18, 2176, 1977, 2899, 1922, 12188, 1019, 5498, 24145, 19615, 18, 5498, 24145, 18, 3], "output": "MSILSGFDPLKLSTAFNSDYWPLGKSDTGIYLVNLSTGSMMAPHINPRVTLKPTSVLGGGKLLLRTIRGPEFANAFRVSEKRLSKILNSQRELISLPSASIAPPDEKGDETKEMEMKKSEMVPYMIRRFGNEMIMGFDQ", "metadata": {"id": "A0A8S0U0J4", "cluster": 7513357, "interpro_all": ["IPR050253"], "interpro_used": ["IPR050253"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: It is part 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. Furthermore, the protein can be placed in the BTB/POZ domain containing protein At1g01640-like family, which consists of plant proteins that likely function as substrate-specific adapters within the CUL3-RBX1-BTB E3 ubiquitin-protein ligase complex. These adapters facilitate the ubiquitination and subsequent proteasomal degradation of specific target proteins. It is produced by Larinioides sclopetarius.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 2176, 1977, 3131, 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, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 29034, 19, 2510, 1011, 3418, 3165, 2213, 20823, 27427, 22934, 1008, 17, 3189, 3416, 16, 2154, 7543, 1927, 4496, 2697, 1988, 3205, 2347, 1966, 4510, 17, 2487, 21054, 1036, 2651, 1920, 6710, 1010, 17, 6160, 7653, 17, 29034, 10968, 6526, 17, 2213, 11905, 2796, 18, 2144, 21054, 1036, 6628, 1920, 11758, 1930, 4521, 19308, 4877, 1927, 2487, 2758, 2697, 18, 2176, 1977, 4152, 2007, 6590, 11566, 12363, 22305, 4907, 3857, 3027, 1957, 18, 3], "output": "MATHLYYAADKYEIGRLKTVCFSFLAEHLSPTNAGELLLLADSDGDLKRVVEDFILMHEEEVFGSKEWEMLMETNSQLTGKTMQLKYKKKKSMK", "metadata": {"id": "A0AAV2BXH9", "cluster": 10086221, "interpro_all": ["IPR044784", "IPR011333"], "interpro_used": ["IPR011333", "IPR044784"], "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 has 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. Furthermore, the protein is assigned to the NMT1/THI5 family, which mediates the biosynthesis of the vitamin B1 precursor hydroxymethylpyrimidine (HMP). Members include eukaryotic enzymes that synthesize HMP-phosphate and bacterial homologues that function as substrate-binding components of ABC transporters for vitamins B1 and B2. It has been detected in Waddliaceae bacterium and is described by UniProt keywords Signal, Thiamine biosynthesis, and Transferase.", "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, 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, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2943, 6613, 19, 7566, 1015, 3416, 16, 2154, 10412, 1920, 8132, 1927, 1920, 6111, 10360, 7897, 29078, 18425, 29899, 12, 5833, 1034, 13, 18, 4678, 3951, 10825, 5038, 1988, 15541, 5833, 1034, 17, 5413, 1930, 4543, 18541, 1988, 2347, 1966, 4510, 17, 2743, 4178, 1927, 7219, 10538, 1958, 18818, 10360, 1930, 11054, 18, 2176, 2258, 2252, 3330, 1922, 4114, 10882, 12191, 9914, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 2733, 16, 26901, 8132, 16, 1930, 13763, 18, 3], "output": "MMKAYFSLIIIMASLLQVVDINVDVADAADTEEIDEEEPEDDAEEELEGDSEYYVALENGIYEEYGLDVEIFYATPLKENDNDNNFVNLAQIVQKSSLMFVAKIWSKDYEAPPRIFIAKNGLDATWYNEYDTIINSGYDPEDILYEEDSDMCDAFVKASLEGWRYAFDNKEIPASRVHQEWMLDRMEEIIKGDGIITNSMEYKEFFKPMIEAQPSPMAPCYADKTDVEYADNTDTEYADEADEEYADESGLISTSLMVQWFPQAQFAGDEFAVDYLVWEEVDFITAWLPTAKESGISTLSDFNGKKMSVDVIMQGTTVNLFLRDGVDIATTTFFFKDYGLDLPEDGIYTRGDEAIDIIMMYMEDEESNEISGELREEDYRRVVDAMKEE", "metadata": {"id": "A0A9E2DBM3", "cluster": 11542215, "interpro_all": ["IPR027939", "IPR015168"], "interpro_used": ["IPR015168", "IPR027939"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein has a HUWE1/REV1, ubiquitin-binding motif conserved site that mediates interactions with ubiquitin within HECT E3 ubiquitin ligases and Y-family translesion polymerases. This structural element is approximately 20 amino acids in length and comprises two predicted helical segments separated by a Leu-Pro motif. Also, the protein includes 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. In addition, the protein should contain a HECT domain that functions as the catalytic core of E3 ubiquitin-protein ligases, accepting ubiquitin from an E2 conjugating enzyme to form a thioester intermediate at a conserved cysteine residue. It subsequently transfers the ubiquitin to specific substrate lysines or growing ubiquitin chains, typically marking target proteins for degradation by the 26S proteasome. It is produced by Trypanosoma congolense (strain IL3000) and is associated with UniProt keywords Zinc-finger, Metal-binding, and Transferase.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 2258, 43, 5897, 2172, 1009, 19, 5197, 1009, 16, 6526, 17, 2743, 5219, 5305, 3200, 1988, 10412, 3719, 1956, 6526, 2651, 28702, 1031, 10968, 6526, 22423, 1930, 67, 17, 3416, 3851, 18522, 1916, 20910, 18, 2052, 4346, 6149, 1977, 3993, 2036, 3835, 4576, 1922, 3471, 1930, 12936, 2288, 4396, 11514, 7492, 6239, 2007, 43, 10632, 17, 1965, 5219, 18, 2222, 16, 1920, 2213, 5921, 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, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 28702, 1031, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1927, 10968, 6526, 17, 2213, 22423, 16, 26170, 6526, 2037, 1925, 6602, 5225, 2287, 4113, 1942, 2386, 43, 30215, 6129, 2019, 43, 5305, 8666, 6181, 18, 2176, 5326, 19180, 1920, 6526, 1942, 2487, 4510, 9082, 1036, 2014, 6552, 6526, 7835, 16, 5745, 23471, 2758, 2697, 1958, 4877, 2007, 1920, 27868, 9993, 18, 2176, 1977, 4152, 2007, 29504, 27450, 15253, 4127, 12, 3943, 2614, 17450, 1008, 13, 1930, 1977, 2458, 1956, 20709, 11569, 7997, 17, 8497, 16, 6048, 17, 2743, 16, 1930, 13763, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MQGRVGHLRNQGSMMFHCGETHVTQSLELMPPMLRYFVGRLRACSVAHQQAPDVFREILYSEEFFRQLDGFFNNKFAELLKAAAGGWWTACMRDVLQKSNRSAERGDLADATQTSTSRGGANEFDGQNAGVAALSSEECKDLRSILQLVVIMCAPYRVVREVGAPAITCTTRVMLCRDPSIIYLGLLMNVVQSNQLEKSIDSTMVHRVLAHGWGSTPTFERRKGSATWGSGETAEGEEGNGDKAEAEADVALLQMPDLPTDPLQTVHERARGAPVAGESRYSADSLSIGVCVLRSIADAAGNPERLLWWCRCRLLSLQLLPAVDREEILAGTACEFFRSAWKGSSSAGYDVSMVPSGATLVGTIADIVRAWHNADSCGGAMGNLIVNHTAQNPLETVNRMVPGHRKFQQDGHRCLAQSWQYKLLIDYHSTYLAVFPHNSSPYSTMHSAMVSQLTEVLHSVALNSGLVDAIVTVTRTHLDEKKPHQDDGGNEADEEHRYGWSYRGAIALHWCFTVLERLSMVSTHETVNPIVFLLSPREDGYELCRDILEKVFYPGGHPILLIAAFRFFAACIHHNVRDVVPALQQRGVMDKPGREPEAPAVTEATLETNQASPDEATAISKTTFGDYVAYYEQALPIACMGILLQAFGVHNSTHTTLDNPTIMRYLVWSLSVPNFDKEDAKSSAVELYSEKVQPQRVTTSIASAAGGDILSLMEAEAAGRSTHLRNVALSLWNIFACLAGIEFRQLSQRSSHRRQRSRQSNYSSDVNDPIVRKFAGCTTEVANALETLLKLASAVPPSDPESLMSNSAVLCTFLFDLPSTMFDCNGSEGATPDEHASTLWSLVATFFMKSNGVSTTVTALKFCRELANAIFDAYIALKMAKDPNTSQEDDLAGSAQAPADVPLPLLAPPSSEAAVTAVDDVPYGLEEFHAWDTAGTSGFIRSFSTTVEGVTSTNTVLGARRATASPTENDPAVSGACNSVDTFLRNTGVLLATSQDYFRGYILERSQHHSGGVLLGSHMSGSPPVILVTPVHVIRHVDSLEGDSQRQAKSLRELRSSVALEAVDLMSLQKAELCMRAAEASLSTSWKLGSGSSEPLQHLCSVIASLWKIVKLVLSQKDQQSIQSPPHAPPADHPSSTPHGDSVARDASVVEAGEGKLKVVIGCMTNILQGLLRCSPDYRPVFDPWLRRLIYLTIVLWRSLGLPISPAMTLSALTRLLELNNDIFKKDRDAAHGASTTGITRSEIGDRSPPPLEPSTQADPENYGQPEEGDLISLGHFQDRSSPQELEPAARASASLAECAIQWVLEVAATMGSSVESGRTLWTRIRRFCCKLCWIYHVHSISVSDNASKGDKEGNQGSDDSAGRVGDHELLLVKMIRLILENPGSRAEREALITQTQLPRALTDRILMEAKRIENETSEGVFQGQQKWATRKAMLGQLFCFLSACTAGTLPEREARPCVHYSNNTEGFCWMGHLCRMPHIRDESDVRPSRARRVRRCVERLLAEFGYEGRITDDKEVARKKFVDVKLDLSSVVGGTSLLPTGMLHECVVLALEYLGDDDNNNNSNDDGNVSGTRHQEARGREKFDNSISSHVGHPTGRLTIKESRDHTDDCTVISHIYRLNETTKKGFVTRAISRLLRDDMATATWGATVLKALIDQSEHTEWVVYLAMVSAVQNCLQAGTTSPLSESDVQEMCAHNAGTSGRKNTIPRTGFIVSLRTVIDKHPKAFCAVFNSSCVVHILSETTTRPAPKPSVWLAPRKSPRTQTASGASTARRAAAERLLNTLLYRFSRRHLSLAFVAKILDCITTLPSVASLVITYHVNVTIPVCTKGVRVDRNTERAYGEVRPRTFTAFVAALLMMEGSPIEGFEPFLFNVAQKAPSRLVQVILQALDAAVTMLAVGKGSGDKPDVAENEEVEGKTNAVDTNLAKFMARSLLRTLRLLLAMPSSSLVWRLCEELCQRDKDAATLILVIRRLHLAHSKCAKLYQQSEQNNTISSHFSTRVVAEQHEEQRQQREDDARNPPTQPGGDEPAISEGNASSTQTTGRQGQLQQTQSVDDSFYVSALVSGGDHEGFLLGLGELLRPNQSVTVFDSHDSEGTRRGDETIVAPSSELNIEPPMSSERLQLLEGISEMMLRHEGDDPDDDIDAEDIERSNHVRNDSEDGYNTSDVDDENSVNDDDDDDDDDDDGDSDGDANILSLNGGFFDNDIDHSLLQYTGNQLLPTGLLRELGMSSATNPSAMRIGINMGNRMPPVGLWEIASSRRDAGLRAGAGGVVVDDSWMPHDISTYHSELFTSRLLNICAVVNAAVANQYDTVQSVRPLLPVLRETSVAPPREEAAPPSAIETDTAISAINEEGDGRAEDNGGGGSQEAHPNPTISALAQVLNDDMQFFHLMGIAVPEEMAEAYVGQPPEENSGEGGDTSVVAARGPTDVVQVPDGDASYLDVNETDPAPHGPRSRAVSPTRNTVAATTTTPTAAATEPQMEQQPWFDVIAPHFLVELPESLRRELLFDHMNLLLGGEERELNGQRTRIFAAFFTQLPPDVQREAVEVELRWRRVTGDVPLRQEILLTCDLRELEGDDDLLREATQLREAREMEAGVEEGNLASHLRQRREGAGATPRGRRNADATQPNAAVARALAVGSLDLSTSTPSSPTVAQEPPVRRDNLRSSLFNRRGNFLFWRSLSVTSSYDDDGNTNSWGILPRSFPHISENQLMTRVRDQQSRSVRDENILPPPVREKGAAGVENSVLALPDAVLKQLVELIWFSESTYPEIDHQMLLSPGLSVAPQLLHLLVTACRNIPAAAKAMTYLMDTVCGRVALQVLYVISQLIKRCRAAGLAFTTLPDSVYAKGIPMSPDEPIEVEGGVIGARLFQKLVELVLRVSSPRMEDAFTRIVQRLNAQLQQLEEPSTAKSQSPREYPYDNGGYICNRCNTSYHTEGVAFHCERCRYDICPLCSFVFLTPEEEASRARCWGYAFVSSKGTIEAALRLLRHPNCTAETARAVMKLFSRGIKESAQRDKGFGVVIELAKEITAEIHACVKKLRAAYPRKAMRSSFLGATPPIGSPRVHGDSDDDDSGVGGGSGNLTTDGSEGPQWTLQEASEALSYMKLNSTSNQTHAFFFPYAESHRILQHTKNRSSILLPPAVLLLLNTFCKFHMAGPRRDASISVASESTGSTTLEKTETERFMLDTTLTPSTVSDAASSAVAKANKRQHQNESSGTTGSSSSRTEGSDPDELIQYDPKLLEGNFKFLKIEPGFVDFNVRLLDFQRQIGYASRGPRISLSITRDQCLRDSFAQLSKLENFHGTISVRFRGEEGADAGGLTREWFQLLAEEMVNDNYALFIHSREGMTYQPNPFSDVNIDVHFTRAMYRHMTGVQPIFSDLKSVDPELHENLNWLLANDVSELGLFFTVSCERFGVVQETELMPNGSQVAVTNANKSQYVRLRCEFHMTQQIEQQLQEFLKGFYTVIPRNEIRVEDLRIHSVYEGYSSTSPQIRWFWEVVAAMSKEDRANLLQFATGASKVPHGGFSNLESASGLPQRFTITRWEDSADLLPQAHTCFNKIVLPEYGSREELRKKLMLAITFGSRGFTMLRSTAGALNEEAPLTRDDVVKCCMRARRRQQVERLFADMLDAANCDDEDEEMVACRYPKYCPIQIMRTLVFTREDTNTLVEIANHRNLIELYNRFPKEEDEEERTLPELQNHFFDVLRETLSTLAVSSRVISFTNSVAALAVESGITDWSLPLMEFLLTGIAKSVEEAVVRRLGDEALKREGSHGNADSSNENCEPQNAEVAQSANAMPSEPDGLDARNYTLLEFLAVLLSQGGEGVVKGSRGDASEQGNDASGDSKVLETPVTHIATTLLAQLLNGEVYRQSIPLDELQGRETSESPATVGEGALDLLCRLAQENYCATRETGSAHNRHRRGRQEEPFARDNGRDHEEEEDDTDDDSDGDGDDTALSQPRSGPVGRLHNSFGGTSSRGSEQATTIPENSTGAVEVEVGSLSSGNESRSSARSMLTDVFATLDRENNNNTASGNDRGTGSRDHHDSLEKIPTPTAHPPQPDAFGVVRDMSSREHPPGSDNIIYYPRHAHPLRWQSLNRPAGDTGSAIVVVEPEPREVSLMWHAAQMYLAEVAHRPTLPRVVRQFVEHNKLTINTPNHLQYFKFAGTVVGMAVAHRVANFSAQELELVICGMPDID", "metadata": {"id": "G0URB6", "cluster": 19146683, "interpro_all": ["IPR046349", "IPR050409", "IPR000569", "IPR035983", "IPR025527", "IPR000571"], "interpro_used": ["IPR025527", "IPR000571", "IPR000569"], "interpro_unused": ["IPR035983", "IPR050409", "IPR046349"]}, "task_type": "infilling"} {"instruction": "Generate a protein sequence for a protein with the following function: 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. Furthermore, 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. In addition, the protein should contain 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 native to Streptomycetaceae bacterium NBC_01309 and corresponds to UniProt keyword Hydrolase.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1958, 43, 2213, 1956, 1920, 2894, 2347, 30, 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, 3677, 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, 1922, 2459, 16, 1920, 2213, 3066, 5531, 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, 6196, 1942, 9718, 2773, 9215, 1972, 3336, 14061, 8789, 1030, 41, 17695, 13192, 1930, 8852, 1942, 20709, 11121, 2538, 20748, 18, 3], "output": "MFALHALWRADRTLAVWGEDGRARAEPAGESRAAHPHACATDLLAELLGGVSPGLEWLVGRARHRWAGLLLPTFADTLPQPSPEIPGEPVRGPRPDLALRPWRVPALVFDADEAAQLLGSLFDPRHAALRTETAADGAVDVPYGASLRWLTAVHDVAWRLAGRGRVLPDLVVEDDAAVARWRPAPTEDDWSLIRAVAAACPPVCRAEVHGDVPAAGRADDSWDGSAVGAMELVADLLDVLVDREVRAVLDGQPSLLPPGRPPRGPETADERWLAALTGPSGRIGPLAPLGRSTSARAAPAEAVATEDVVRLRDALARWQSSEAPPVRPLRTCFRLVEPLGPDPADLFGGTTDDNWRVDILLQAPDEPSLLVEASRVWTAGPVLNVFERKQYQPQNALLADLERAARAWPVLDATLREARPGTVRLDREGALAFLRDAAPALAEAGFGVLLPTWWRNPPRVGLTLSARTRTPGLVSGGSLLDQDAVVAFEWRAALGDAVLTESELRELASTTRPLVRFRGQWTEAALADITAAAAFIARQGTGVMVAGEVVRTAIDPGATVAGLPVFGVDADAWLGELLAGADAVRERPVVLPDAFATTLRPYQQRGLDWLAFLARLGVGAVLADDMGLGKTVQTLALLAAEQHEEAGTAGESGPTLVVCPMSLVGNWAREAERFAPTLRVHIHHGADRRTDEQFQEVARRADIVITTYETALRDTEMLRTVAWRRVVADEAQNIKNIATRQSRSIRALPARHRIALTGTPVENRLAELHSVLDFANPGLFGSAEQFKATYAIAIERNGSEAALAALRRVTTPFVLRRHKTDPAIAADLPAKQEMTVLCSLTPEQAGLYRAVVADMDHRVAHTAGIERQGLILATIGKLKQICNHPAQFLKETGTPVAGRSGKVERLAAILEEAAAEGDKTLCFTQYARFGGLLHEHLADRLGGEVLFLHGGITGRQRDELVERFQDPDGPSVFVLSLKAGGTGLNLTAANQVVHVDRWWNPAVEDQATDRAYRIGQRQHVQVRKFVCVGTVEERVDALIAAKRGLAASVVGGPGAAGGAPGEHWLTDLSAEALRELVALSEEAEA", "metadata": {"id": "A0AAU2WU24", "cluster": 20875213, "interpro_all": ["IPR014001", "IPR001650", "IPR022138", "IPR027417", "IPR038718", "IPR049730", "IPR000330"], "interpro_used": ["IPR014001", "IPR001650", "IPR000330"], "interpro_unused": ["IPR027417", "IPR049730", "IPR022138", "IPR038718"]}, "task_type": "autoregressive"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein is grouped in the Protein of unknown function DUF3224 family, which consists of predominantly bacterial proteins with currently uncharacterized function. In addition, the protein is assigned to the SO1590-like superfamily, which represents a $\\beta$-barrel domain found in bacterial proteins of currently uncharacterized function. While the specific biological role remains unknown, crystal structures have been determined for members from *Shewanella* species. It is found in Actinomycetota bacterium and is annotated with UniProt keywords Signal.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 10892, 27479, 3416, 16, 2154, 7543, 1927, 7700, 4543, 2697, 1956, 5077, 24528, 2347, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2577, 20982, 1008, 17, 3189, 13975, 16, 2154, 4972, 43, 8, 38, 4666, 8, 17, 19560, 3418, 2435, 1922, 4543, 2697, 1927, 5077, 24528, 2347, 18, 2679, 1920, 2487, 3933, 2770, 4497, 5435, 16, 6561, 4061, 2162, 2252, 3180, 1958, 4678, 2037, 14, 4693, 13956, 28690, 1019, 14, 3038, 18, 2176, 1977, 2435, 1922, 4718, 13386, 19446, 3857, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 2733, 18, 3], "output": "MQQARNRFGGSAAIATAIAIAAVTVISTATASSKETAAGTITGTFSGTEVSLVHNVTHPDGSADLTVVSSCSCTVEGRTVRRKIIDATGGLEGLRGRLEVSDLLAAPAQAYTGRYDLDAVTERTLVLSYRDGNDIVRELQVRRTLGTVTFSERATVDLAGVIT", "metadata": {"id": "A0A7W0JJ20", "cluster": 21314690, "interpro_all": ["IPR021607", "IPR023159"], "interpro_used": ["IPR021607", "IPR023159"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein contains a RecD N-terminal domain that forms the principal interface between the RecD 5'-3' helicase and domain 2B of the RecC subunit. This domain mediates a conformational change in RecD that significantly impacts the structural configuration of the RecC subunit within the RecBCD enzyme complex. In addition, the protein is assigned to the Coronaviruses polyprotein 1ab family, which serves as a multifunctional replicase complex essential for the replication and transcription of viral RNA. It encompasses critical enzymatic domains, such as RNA-directed RNA polymerase, helicase, and proteinases, that coordinate to process the polyprotein, synthesize capped viral RNA, and manipulate host membranes. These activities collectively drive the assembly of replication complexes and the evasion of host immune responses. Additionally, the protein features a UvrD-like helicase C-terminal domain that adopts an AAA-like structural fold and is typically found at the C-terminus of a wide variety of helicase enzymes. It occurs in Balneolaceae bacterium and exhibits UniProt keyword tags Nuclease, Exonuclease, and DNA repair.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 5461, 43, 2090, 1007, 56, 17, 4262, 3418, 1988, 4952, 1920, 7944, 6854, 2192, 1920, 2090, 1007, 25, 11, 17, 23, 11, 15318, 1930, 3418, 5751, 1927, 1920, 2090, 1030, 5903, 18, 2052, 3418, 10412, 43, 8523, 3185, 1922, 2090, 1007, 1988, 2567, 9653, 1920, 4346, 9674, 1927, 1920, 2090, 1030, 5903, 2651, 1920, 2090, 8284, 1007, 4113, 2796, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 5548, 26979, 6240, 5684, 5123, 1014, 3416, 16, 2154, 10634, 1966, 43, 20136, 5825, 2051, 2796, 4415, 1958, 1920, 5158, 1930, 3213, 1927, 4324, 3146, 18, 2176, 21569, 4140, 8145, 4682, 16, 2427, 1966, 3146, 17, 6554, 3146, 6479, 16, 15318, 16, 1930, 16172, 1036, 16, 1988, 11865, 1942, 2585, 1920, 6240, 5684, 16, 15541, 22069, 4324, 3146, 16, 1930, 21034, 4423, 5726, 18, 2144, 4209, 10182, 9265, 1920, 5957, 1927, 5158, 5048, 1930, 1920, 25092, 1927, 4423, 3743, 3387, 18, 4950, 16, 1920, 2213, 4075, 43, 5819, 8544, 17, 3189, 15318, 45, 17, 4262, 3418, 1988, 24032, 1925, 13835, 17, 3189, 4346, 3728, 1930, 1977, 5745, 2435, 2019, 1920, 45, 17, 7822, 1927, 43, 4743, 5386, 1927, 15318, 5038, 18, 2176, 5110, 1922, 4641, 2912, 10173, 1972, 3336, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 16230, 16, 24966, 16, 1930, 2678, 5059, 18, 11586, 5655, 3581, 18, 3], "output": "MIAMPVFLDELLHQELISEVEIEYGNAQLNGHICLDVARSFEKGLLASTALHDDCGIPQNVDEGDTKPLILEQGRLYLQKLWRYEYELAQLENKTLFDPINWQSVALTLSFMRDLLFISGGPGDYRIAMAAPTGKASRRLSDSIQKGKKLLGSDYQGSTFKYGEHNKLPYDLIIVDEASMLLVILGDKDQLASVEAGSILGDVCMGENSFSVEAKSYRFDHTSGIKRLAKAINGSNAAGAIVSTQNIQSVIDEYVLHHYEQYSSHNDALGSSNKIKKREGITAGQEWYPERIVMSKRNNPIVKIRNGEIGISKEPAYALTIHKSQGSEFDDIAIVLPNRINPLLSGDEEVIKSTIEASVYRNSGLKQRIWEQMLRFLYSLEGELDPVVLVAGIATLIIARLAESKLVGEAWLNAKSRVIHSISDAEKAIIQSFTGKTHAVLNIITALKTAKGGENPITSQVDIPEEAVTVHDIHMWMRLVRAIAESAKARCLLEVLGMEAPVNENLPVINDNMVFLTELLKSESYADLKLLSGKKILCALRAGPFGVERINALGEKNDGEEYRIYFEGESKVPVSASRLSEYKELLYTAVTRARHSVLVI", "metadata": {"id": "A0A6A8Q7D1", "cluster": 23053178, "interpro_all": ["IPR050534", "IPR027417", "IPR006344", "IPR049550", "IPR041851", "IPR027785"], "interpro_used": ["IPR049550", "IPR050534", "IPR027785"], "interpro_unused": ["IPR027417", "IPR041851", "IPR006344"]}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe 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. Additionally, 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. It is produced by Blomia tropicalis (Mite).\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, 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, 4950, 16, 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, 2176, 1977, 4152, 2007, 16635, 6026, 12862, 1937, 12, 24688, 13, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MTKERSSSNGSGSKKSGSKSAHSSHSKASNSRSSKSDKSSVILGSCVPEMPSNVSGIVSINKMSPLKSTNMDDITKSGYKVGRVVVKLIHINKCTPRYKKNMMKYSLNIERYMCGSDDNKLKCDSYIRVYDMFKIDESIYIFDDDPIDTETARNWTVDLVNGVKKMHEMGVAHRFLKLQHILFDKSHKVKIAGKALLQRKERRSKKNLHLPPECFETNKLIRNALNKVFFIDPNRAPADKISVLETKKSKDPKFVSINDASLHVSKANISSIKGSKSKTKSKIKSVTTKNSSNSNSKGSSTSSSPSSHGSGSASSAKTSKGPSTRSSGCSAKPSASTHGSSCASAKQSSKGPASCPSASTRGSSCASAKQSSKGPASCPSASPSSCPSASSGGSKQSSKNLSTKSSASSRGSGTSSAKPSSKGPASCPSASTRGRGSSCSSAKQSSIGPSSCPSASSGGSSCSSAKKSESSKKSNTKSSMAKSENKSVASSKVSGSGKGSGTKAASGSGSKTSATNTGKSSGSVSSGSVKEASGTGSKTASKTDTGKSSGSVNQSGTKEASGSGSKAAEKGFEEASGTGGSKGSGVAGASGTEGAKGSGVAEASASGENQDGAQPEGNEGGSVVDQMTNEEAAYEAAEGAAPEEQEDQSDPVEAEGSKVKGKLPKTKSKSSKSKSSKHKSKSHSKKSGPVIVEDDCYQFLTGNKDSEMDEVPGKSLYLRIFWSKAVPFWEPNKKRVTPSNFLSLPYFKSKPSSKKSSKVSSKGSASQHPSTSKKSKDPSSASSGGSKQSSKGPASCTRGSSCSSAKQSSIGSSCASAKQSSRGPASCPSASTSKSREGKTVQISKSKVSGKKEASGSGSKANSNADTGKAAGASGTDAEKVSGSVKGSGTGQGGEELDPGVNQAS", "metadata": {"id": "A0A9Q0RRW7", "cluster": 23600966, "interpro_all": ["IPR011009", "IPR000719"], "interpro_used": ["IPR011009", "IPR000719"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein features a Gnk2-homologous domain that mediates plant defense and stress responses, exhibiting antifungal activity and involvement in pathogen-induced signaling. Structurally, it forms a compact $\\alpha+\\beta$-fold stabilized by three intramolecular disulfide bridges within a conserved cysteine-rich motif. This domain is found in proteins ranging from seed storage factors to receptor-like kinases associated with the hypersensitive reaction and programmed cell death. It has been characterized in Eleusine coracana subsp. coracana and is associated with UniProt keywords Membrane, Repeat, and Transmembrane.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 4075, 43, 9005, 6779, 17, 8725, 3418, 1988, 10412, 4496, 9720, 1930, 3071, 3387, 16, 12196, 15216, 2455, 1930, 5668, 1922, 7055, 17, 2719, 3197, 18, 12171, 16, 2176, 4952, 43, 13726, 8, 38, 4595, 15, 38, 4666, 8, 17, 3728, 12017, 2007, 2559, 18083, 11830, 18142, 2651, 43, 5305, 8666, 17, 5536, 5219, 18, 2052, 3418, 1977, 2435, 1922, 2697, 6485, 2037, 4861, 7451, 2790, 1942, 3148, 17, 3189, 7784, 2458, 1956, 1920, 26145, 3227, 1930, 13839, 2024, 3539, 18, 2176, 2258, 2252, 4378, 1922, 3064, 24327, 2912, 2233, 10973, 2175, 19615, 18, 2233, 10973, 2175, 1930, 1977, 2458, 1956, 20709, 11569, 3260, 16, 6865, 16, 1930, 9117, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MVPAAALLVLVPLFTALAAVPADDRRWPAIDDSPLALSPGHICGEHGSYPANVNADSCNCSNGNIAGDSPDRVVASAFCLWRQRQADVVVDGGACSLNFHDYDRREQEVSMAEPRGRDTSFGLVCVVLLLVLEWRSRSRGPGRIAPAEEFSQLPLRRRTAFASVTGHRHALLQSRVSAHTTLPLTPVSKPSRKRRATSHRAWQLRCPTVAAVVLPYFTRQDANAPGSAYEVSLQLLAATVPGANSSDCGACVALAFREAQRLCPYWLENVMVFPDVLLALLFQAVISPPLQCAVPCLRTPVCSPTTPWF", "metadata": {"id": "A0AAV5DMW0", "cluster": 1202312, "interpro_all": ["IPR002902", "IPR038408"], "interpro_used": ["IPR002902"], "interpro_unused": ["IPR038408"]}, "task_type": "infilling"} {"instruction": "Function:\nThe protein has a Prokaryotic N-terminal methylation site, which directs the methylation of a conserved phenylalanine residue. This motif is typically located at the N-terminus of pilins and proteins associated with secretion pathways. In addition, the protein is associated with the Pilin-like superfamily, which comprises structural proteins such as type IV pilins and secretion system pseudopilins that assemble into filamentous appendages on the bacterial surface. These proteins typically feature a conserved, methylated hydrophobic N-terminus and facilitate critical functions including cell adhesion, twitching motility, and DNA transformation. Some members, such as YadA-like autotransporters, act as pathogenicity factors by extending from the outer membrane to mediate host interactions. It is present in Phycisphaerales bacterium and is classified with 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, 2258, 43, 21545, 56, 17, 4262, 5547, 3200, 16, 2154, 28351, 1920, 5547, 1927, 43, 5305, 17388, 6181, 18, 2052, 5219, 1977, 5745, 4810, 2019, 1920, 56, 17, 7822, 1927, 7547, 2925, 1930, 2697, 2458, 1956, 5512, 3873, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 7547, 1921, 17, 3189, 13975, 16, 2154, 12936, 4346, 2697, 2427, 1966, 2601, 4370, 7547, 2925, 1930, 5512, 2433, 11520, 10984, 7782, 1036, 1988, 17421, 2460, 18706, 7958, 2662, 1990, 1920, 4543, 3154, 18, 2144, 2697, 5745, 5961, 43, 5305, 16, 11882, 7919, 56, 17, 7822, 1930, 6628, 4140, 4088, 2710, 2024, 6141, 16, 21596, 1941, 9254, 16, 1930, 2678, 7002, 18, 2673, 4678, 16, 2427, 1966, 26169, 3825, 17, 3189, 5728, 5412, 24095, 1036, 16, 4033, 1966, 15903, 2790, 2007, 12140, 2037, 1920, 7642, 3260, 1942, 8265, 4423, 3719, 18, 2176, 1977, 2481, 1922, 25511, 9119, 29164, 3955, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 7864, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MHTICNKKGFTLIELLVVISIVSLMMHHQIFVMQSSFATDNKDQVPLGVAGSIGTSGIFYCPAESQWLPTDPNPASNYWTNTFQVWGTDADATLQHPWPRWLDWPTDTVLYADTFGTESRIQAKREFQHYYELALPSSTRVHNIFDFLDSYSILLPALSAARKAAHRTGCLSNANYRLKVFDTYTGVAYPVNQGYVKWGRGTYGSREQIDGVVRVHGTGINITHADGSSKWFA", "metadata": {"id": "A0A3C0ES85", "cluster": 2092781, "interpro_all": ["IPR012902", "IPR045584", "IPR050470"], "interpro_used": ["IPR012902", "IPR045584"], "interpro_unused": ["IPR050470"]}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: 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. Moreover, the protein is included 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. Furthermore, 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. It originates from Petrolisthes manimaculis and exhibits UniProt keyword tags Repeat, Transcription regulation, and Metal-binding.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 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, 3950, 16, 1920, 2213, 1977, 3063, 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, 3677, 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, 2176, 22970, 2037, 16901, 23747, 20536, 1036, 2323, 12874, 18021, 12191, 1036, 1930, 9826, 20709, 11121, 2538, 14392, 6865, 16, 3213, 3640, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MNEILRSMNDNAIAQQNVGSREGVLDDESDFKKKSSLECHMRVHSGEKPFTCAHCHTGEMPYACEVCGKKFRQRSNYTLHMKSHTLHVRLHTGEKPFVCDVCGKRFFQKCNLTRHRRLTAHERIHSRKDPLIAKSVGSTYTRKSNCEVCHKMFLKKSHLKHHRFTHTGERPYPCQKCEKKFTNLSVESLKESKLMSSCDCDNANDQSSFVYNSRLCLTVNSVNDGFDEAKPNKVSKLGDASKYPRYPILCDEKSGSPGMLKKTLNEEIENVHRTVMTRQIGMTQIRVSAYVAQVGGGQNLADITRIKGNIKQEIEVKEEEIFGEAYEGRHECEAKTKTTTTTAFTCQECDRPGAKFTHKSTLLAHTRLDKRFKCDVCSKQFSQRVHLTASHASEKNHTCVVCNKKFSCVSYSLGLSERKKTIENECEPGSLKRHSRIHEKNPSRDVMVEKCKNTDQVDTKMIKSESNDATNMLNTTVAYTARSYSKKEEGKSEIYSQKPYTGENKNSGLASEMSLTGQAVAEDGMKT", "metadata": {"id": "A0AAE1TTJ0", "cluster": 3864118, "interpro_all": ["IPR050527", "IPR036236", "IPR013087"], "interpro_used": ["IPR013087", "IPR050527", "IPR036236"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein includes 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 found in Planctomycetota bacterium.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 5921, 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, 2435, 1922, 4720, 2341, 13386, 19446, 3857, 14061, 18, 3], "output": "MTWPLVERRAFPRRNLRIKIQIELPKSFTENPVTQLRRYAFARNIGLGGMLIISSISIPPGIQVRVWIPFYKQGQTLELTGVVTRSVRTMLGHEVALQFVNMNSLAESLIAQYVGAEQDVV", "metadata": {"id": "A0A523TT62", "cluster": 4377300, "interpro_all": ["IPR009875"], "interpro_used": ["IPR009875"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the protein function: The protein is assigned to 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. Additionally, the protein can be placed 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. Moreover, the protein includes a Tryptophan synthase alpha chain active site that catalyses the aldol cleavage of indoleglycerol phosphate to yield indole and glyceraldehyde 3-phosphate. This site relies on conserved acidic residues acting as proton donors and acceptors to facilitate the reaction, supplying the indole intermediate to the beta subunit for the final biosynthesis of tryptophan. It is derived from hydrothermal vent metagenome and features UniProt keywords Amino-acid biosynthesis, Aromatic amino acid biosynthesis, and Lyase. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 1977, 6304, 1942, 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, 4950, 16, 1920, 2213, 2112, 1998, 5396, 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, 3950, 16, 1920, 2213, 5921, 43, 13489, 8921, 4595, 4659, 3500, 3200, 1988, 13928, 1918, 1920, 11174, 1945, 6404, 1927, 18050, 18207, 5413, 1942, 4307, 18050, 1930, 22447, 23, 17, 5413, 18, 2052, 3200, 12850, 1990, 5305, 9931, 4248, 8290, 1966, 8433, 8276, 1930, 27916, 1942, 6628, 1920, 3227, 16, 28314, 1920, 18050, 6129, 1942, 1920, 4666, 5903, 1958, 1920, 3948, 8132, 1927, 13489, 18, 2176, 1977, 3595, 2037, 26959, 14654, 16552, 2225, 1930, 4075, 20709, 11569, 3835, 17, 2687, 8132, 16, 10761, 3835, 2687, 8132, 16, 1930, 23928, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MTRIGKTLKRLKNEKRSALVLFLTAGDPSVKQTVDLVRAAFDAGADIVEIGVPFSDPVADGPVIQESYLRAIDKGTNVKDAMEIARKVRTTHPDSPIVFMLTCNLVLTYGVKKFMKDSAECGVDGLIL", "metadata": {"id": "A0A3B1CSI3", "cluster": 4471847, "interpro_all": ["IPR013785", "IPR011060", "IPR018204", "IPR002028"], "interpro_used": ["IPR011060", "IPR013785", "IPR018204"], "interpro_unused": ["IPR002028"]}, "task_type": "autoregressive"} {"instruction": "The protein contains 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 is classified under the Putative L,D-transpeptidase tautomerase family, which comprises bacterial proteins predicted to function as L,D-transpeptidases. It is present in Novosphingobium mathurense.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 5461, 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, 1977, 5947, 2441, 1920, 6770, 54, 16, 46, 17, 22796, 18877, 7462, 4575, 9213, 2051, 3416, 16, 2154, 12936, 4543, 2697, 4396, 1942, 2347, 1966, 54, 16, 46, 17, 22796, 18877, 1036, 18, 2176, 1977, 2481, 1922, 9441, 3508, 7969, 2029, 23156, 8250, 24684, 4127, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MVKWSSEFNRRNLLFAGATLAAGALISARPRRLPAVAKRSTAGPKFDVNPRLLEKALAALEKERMHFLDIENGKATQILVAHGSGSDPDHTGFVERFSNHGRSQRLIGLDPTNDNALDRAIVVHSAWYANEDFAVGEKHLDDLFSFLGKGRMIYAGRTKRPSPDPVPAIPVATHSKRIRDHGRIALVDFSVSSSVFGSNASSQGAFLTDDYYVGKMIRTHGMLGRSQGC", "metadata": {"id": "A0A1U6HZA1", "cluster": 7465327, "interpro_all": ["IPR006311", "IPR032676"], "interpro_used": ["IPR006311", "IPR032676"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: 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. Additionally, the protein includes 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 Trichomonas vaginalis (strain ATCC PRA-98 / G3) and is connected to UniProt keyword ATP-binding 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, 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, 4950, 16, 1920, 2213, 5921, 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, 10477, 10480, 10120, 1937, 12, 3943, 11037, 21227, 17, 5613, 19, 15991, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 1930, 13763, 18, 3], "output": "MSFSERRKKSGFVVPKLDNDSPGYYKGTSSFESLFSQEYPVVTLADLKFHEQLGHGVQGTVYRCTHIPSGKEFALRHPNVVHLFSAFAQKGSIHILMDLVNGAQMIAGLRFCCKNHIIHRDIKPSNVMLSLDGRIQIADFIGTTCYMSPERIRGQSYGLKSDVWSLGLILYQSCIGRYPFLGPNYSPLLLDFIEKCLVMEQDDRATFEELNAHEDANQKRNIDLDAQRRSHDALFAHENFEAEIIRESADYGELKLRSDGTIVKSIKYQDKSQLQKTVDEIHSLRISLGDYLKYSPIIPEPALHEITVGLARQLRDTGDFAQSVGENKTHFWDLNFETQNDIIVDWITNGSGSKDELVKWIQ", "metadata": {"id": "A2F5W2", "cluster": 8195600, "interpro_all": ["IPR011009", "IPR000719", "IPR008271"], "interpro_used": ["IPR011009", "IPR008271"], "interpro_unused": ["IPR000719"]}, "task_type": "infilling"} {"instruction": "I am designing a protein with the following function: The protein is included in the Mediator complex and homeobox domain-containing protein family, which comprises components of the Mediator complex that function as transcriptional coactivators for RNA polymerase II-dependent genes. These proteins act as a bridge between gene-specific regulatory proteins and the basal transcription machinery to facilitate preinitiation complex assembly. Additionally, they regulate the expression of neural basic helix-loop-helix genes to influence developmental processes such as neuronal differentiation, eye development, and limb morphogenesis. It has been detected in Chlamydomonas incerta. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 11370, 2796, 1930, 27566, 3418, 17, 3165, 2213, 3416, 16, 2154, 12936, 4178, 1927, 1920, 11370, 2796, 1988, 2347, 1966, 5224, 22706, 1036, 1958, 3146, 6479, 2890, 17, 3100, 2628, 18, 2144, 2697, 4033, 1966, 43, 11925, 2192, 2359, 17, 2487, 4948, 2697, 1930, 1920, 5342, 3213, 10853, 1942, 6628, 2097, 11566, 11574, 1929, 2796, 5957, 18, 4950, 16, 2611, 5741, 1920, 2294, 1927, 5181, 5937, 7864, 17, 5881, 17, 7864, 2628, 1942, 4039, 5878, 4028, 2427, 1966, 5121, 4155, 16, 5723, 2740, 16, 1930, 7755, 15328, 18, 2176, 2258, 2252, 3330, 1922, 14667, 10480, 2043, 3062, 1019, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MLTDVYQHSQQLATPVTNAFVEGLQLQISGMNLYPQAAPGMPWAGGPHYEGAYDPAYGAADGGDYGAEWYPDGGVYPGMDYGGEAWYDPHDPYDPHGAAAAAAAAAAAAAAAVGPSGPYYATAAAPTGPSRAANNNYGNAGGAGPSNAAAGGRAPVPAYVGRIRETALVKRAAVEQLAGAAAYWLAYPNYTVSGPAGPALLLTPAGLTAAFNSRRVHGHTLLVGLTAAAAAAVAPAAAAAAARAASGGSAAVPLPADRRALLPPSFLRPLVFCLAAAHAGGAYEAVDTAALDAGAPPAGWCVPGSLFQPAAGGAAAGGGSGRGPVGSWSDAAVDAAVAALLARAPRWCVLTQYGETGRWNCPLNISASQARSRLGAGAAALAACLLGYGEELPANLWIPTSLVLPLGALLQIADSHPGLVYRPPPAADVTFFIEDAARAVVGRPDAAARLDTHLAAAAAGAGGGGGGHAAGAAGAAGQAQQGRGQQGAGAAHAPALDPGAAAFVPPASASASTNTKTNASSSSKAGAAGASWEAGAAGTGAAAADASRPRASANGGRQAAAAAPAGAAEAAAATAAAPEPSPSSSGFAAGPQAAAVAPAPVGSPPNGQPTYAQAAAAAAARAAALRSARQTPSPTPPVQPIPPPQLHYGGGPQPYMPIPMPQPLPVVVQVQTQTQMQQQAAAEQQQQPAPAAPSSSSPGGVLVPIPTPFVRFETAVFKLFQGDHGQHSFSSLWWWLDAGGGGERVLGPYSCEQMILAYIAQLLPHDSRICGTQGTLAPPAAPPASAFSPLGVLLGAVDEGRPYRLLETKPEHPAAQQQQQHLGPAAGLLPPALAAAAAARGGR", "metadata": {"id": "A0A835W1U3", "cluster": 11681575, "interpro_all": ["IPR052145"], "interpro_used": ["IPR052145"], "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 Bacterial-type extracellular solute-binding protein family, which acts as the high-affinity solute-recognition component of ABC transport systems involved in the active uptake of substrates across the cytoplasmic membrane. These proteins function either as soluble periplasmic receptors in Gram-negative bacteria or as membrane-anchored lipoproteins in Gram-positive bacteria and archaea. Also, the protein falls within the Bacterial solute-binding protein 1 family, which comprises periplasmic components of ABC transporter complexes responsible for the high-affinity binding and import of substrates such as sugars, glycerol-3-phosphate, and osmoprotectants. These proteins facilitate nutrient uptake essential for bacterial survival and virulence, while some members additionally exhibit pH-regulated molecular chaperone activity. It is expressed in Elstera cyanobacteriorum and is connected to UniProt keyword Signal.", "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, 4543, 17, 2601, 5329, 19661, 17, 2743, 2213, 3416, 16, 2154, 8016, 1966, 1920, 2149, 17, 5173, 19661, 17, 5708, 4594, 1927, 7219, 4860, 3771, 3286, 1922, 1920, 3500, 5047, 1927, 6249, 3436, 1920, 6823, 3260, 18, 2144, 2697, 2347, 3108, 1966, 6622, 24334, 4086, 1922, 8604, 17, 3136, 4802, 2014, 1966, 3260, 17, 17199, 18393, 1922, 8604, 17, 2843, 4802, 1930, 21501, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 4543, 19661, 17, 2743, 2213, 21, 3416, 16, 2154, 12936, 24334, 4178, 1927, 7219, 9054, 5048, 5061, 1958, 1920, 2149, 17, 5173, 2743, 1930, 2582, 1927, 6249, 2427, 1966, 15592, 16, 9244, 17, 23, 17, 5413, 16, 1930, 9405, 18018, 2341, 2356, 18, 2144, 2697, 6628, 8708, 5047, 4415, 1958, 4543, 3298, 1930, 9304, 16, 2679, 2673, 4678, 4950, 5987, 2087, 17, 4335, 3272, 14044, 2455, 18, 2176, 1977, 3198, 1922, 9614, 24661, 26898, 7972, 2341, 18842, 17279, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 18, 3], "output": "MHRVSFSALVCGAALGLLTISPAWAECGFSGRTGTVNVLANSFPVLDHMASAMQLKEEVEQAFNSGASPFDLAQVGTGSFTTLAANGSLQPITDLVLKYKAKYDIQNLQHLFYRKDLLEQHKIPVPKTYAEVLAAAKKLKEVGAVENPFSAAYKPGWDLANEFEPKFQSPEALKTLATMKDLVSYMSPNALGLATGDVTTAFQQGTTALGILWATRAAAMDDAKVSKVAGKVGFAAATTQFWDAFVMPRSMKGDRETAFLLLMEATKLETMKAAPDLANGFPTEPYFSLALAALGQQVGDYLAGRKTAEQALAEATRAYTQSAKEKGFLKKACAKDGLTVNVKLTSYPMLITIGKEVYGIAFQTTNIYLSEGGKFFADGSAAAPAADIGAPWLRPGISTSDYAKGVQESVAAQAP", "metadata": {"id": "A0A255XZS5", "cluster": 12235133, "interpro_all": ["IPR050490", "IPR006059"], "interpro_used": ["IPR006059", "IPR050490"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The desired role of my protein is: The protein is a member of the Secondary Metabolite Biosynthesis-Associated family, which comprises enzymes involved in the biosynthesis of bioactive secondary metabolites like glycolipid biosurfactants and reduced long-chain polyketides. These proteins catalyze diverse modifications, including fatty acid hydroxylation, glycosylation, and amide bond formation, to produce compounds often exhibiting antimicrobial properties. Moreover, the protein belongs to 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. Also, the protein should feature a Acyl-CoA thioesterase-like, N-terminal HotDog domain that adopts a Hotdog fold and typically functions as an acyl-CoA thioesterase to hydrolyze acyl-CoA thioesters. It generally constitutes the N-terminal portion of a paired HotDog domain architecture found in enzymes like E. coli TesB and human ACOT8. It is found in Microbotryum saponariae. 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, 4067, 9483, 8132, 17, 2458, 3416, 16, 2154, 12936, 5038, 3286, 1922, 1920, 8132, 1927, 13570, 4067, 6926, 3189, 14193, 2049, 1960, 4589, 17680, 21016, 1930, 3028, 2815, 17, 4659, 4286, 18540, 3726, 18, 2144, 2697, 18170, 6445, 6920, 16, 2710, 5934, 2687, 21319, 16, 12082, 16, 1930, 13601, 5403, 3337, 16, 1942, 5074, 4300, 3868, 12196, 8003, 3879, 18, 3950, 16, 1920, 2213, 14440, 1942, 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, 2222, 16, 1920, 2213, 3066, 5961, 43, 11337, 17, 10027, 30215, 2051, 17, 3189, 16, 56, 17, 4262, 9529, 22389, 1029, 3418, 1988, 24032, 43, 9529, 22389, 1029, 3728, 1930, 5745, 4088, 1966, 1925, 11337, 17, 10027, 30215, 2051, 1942, 7222, 6931, 11337, 17, 10027, 30215, 1036, 18, 2176, 4933, 14879, 1920, 56, 17, 4262, 7717, 1927, 43, 7304, 9529, 22389, 1029, 3418, 9335, 2435, 1922, 5038, 3189, 47, 18, 5178, 2672, 1014, 1930, 2616, 2000, 1991, 1025, 18, 2176, 1977, 2435, 1922, 11565, 6286, 1012, 1989, 9235, 12502, 3027, 3336, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MPNLKQALKLERVESSAQEGPFRFKAELSVVWTVGGKPHGGYLLALITSACSLVMKDSTTPDPAQLMTSFLMGCNNGAAEVVVTVVRRGKSWTNLEARIVQDGKTTVVSQALYTSFPSLPTSCPHPPFSTSNQYLLPLTPSPYAKRIPHLTHPSLCDPQAAHARKHDEFGRRWGKNENSAMFMIAEGEMEWVEDEQIKKRREEGDERGRKELEWASWVEFKDLDGEALNMDMMPFFSDIMSSIPELLPPGERVDPHYYPTLTMSIHFHTKLPFPSNSPYLFSPKTVGVYSTGHHIKAGRHEQLTEVWTAPSALGQGDVQQGWRERSMLLITGTQLAVSVDIQKIFGGNFGKM", "metadata": {"id": "A0A2X0KA33", "cluster": 12513209, "interpro_all": ["IPR049450", "IPR042171", "IPR029069", "IPR052389", "IPR049449"], "interpro_used": ["IPR052389", "IPR029069", "IPR049449"], "interpro_unused": ["IPR049450", "IPR042171"]}, "task_type": "autoregressive"} {"instruction": "Here is the intended role of my protein: 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 should include 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. It originates from Acidimicrobiales bacterium. Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 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, 3066, 3951, 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, 2176, 22970, 2037, 2687, 1980, 1935, 7839, 1918, 14061, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "MADHSEHTNRTPTPGDPWPWDERFRDMPWPKDPDPLLVEYCSDLPKGKAVDLGAGTGRNSIFLAGLGYEVTAVDASQVGLDITANRAKSEALVIETVLANLDDFHLEADTYDLVVIANIHMMPPDSKKLFKMAINGLKHGGHLFVVGHDRSNLGVHGPPLPELLYSVDDMQDLFPEDLEIKVLKNEERPVGDSPHGVPDMAVIVLGEKK", "metadata": {"id": "A0A7Y3PLS7", "cluster": 13545374, "interpro_all": ["IPR041698", "IPR029063"], "interpro_used": ["IPR029063", "IPR041698"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein belongs to 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. Also, the protein incorporates a Carboxylesterase type B active site that hydrolyzes carboxylic esters via a catalytic triad composed of a serine, a glutamate or aspartate, and a histidine. This conserved region specifically contains the essential nucleophilic serine residue found in type-B carboxylesterases of higher eukaryotes. Additionally, the protein can be placed in the Type-B Carboxylesterase/Lipase family, which encompasses enzymes with broad hydrolytic activity involved in lipid metabolism, xenobiotic detoxification, and the activation of prodrugs. Members of this family act on diverse substrates, including short- and long-chain fatty acid esters, triglycerides, and pesticides, while also participating in biological processes such as cell adhesion, virulence, and mycotoxin biosynthesis. It is native to Alteromonas lipolytica. 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, 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, 2222, 16, 1920, 2213, 19683, 43, 9943, 8342, 2051, 2601, 44, 3500, 3200, 1988, 7222, 20887, 18708, 16785, 3454, 43, 6804, 21845, 7179, 1927, 43, 8468, 16, 43, 7627, 2014, 12878, 16, 1930, 43, 13873, 18, 2052, 5305, 3031, 4475, 5461, 1920, 4415, 24456, 8468, 6181, 2435, 1922, 2601, 17, 44, 9943, 8342, 2319, 1927, 2580, 15021, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2601, 17, 44, 9943, 8342, 2051, 19, 16653, 3416, 16, 2154, 21569, 5038, 1956, 4949, 26702, 2455, 3286, 1922, 4486, 4714, 16, 29821, 18169, 16, 1930, 1920, 2936, 1927, 21499, 1036, 18, 4678, 1927, 2052, 3416, 4033, 1990, 6445, 6249, 16, 2710, 3662, 17, 1930, 2815, 17, 4659, 5934, 2687, 16785, 16, 13631, 16, 1930, 17937, 16, 2679, 2222, 9505, 1922, 3933, 4028, 2427, 1966, 2024, 6141, 16, 9304, 16, 1930, 5078, 11140, 8132, 18, 2176, 1977, 6196, 1942, 4238, 10480, 3178, 26656, 18, 7031, 1920, 3244, 18, 3], "output": "MPFNRLGKTVRYASRLALAIVASVMMSGCGSEPADPLVVATAQGKVKGSQQNSLRVFKGIPFAKAPVGERRWQAPEPVEAWANVRSATEFAPGCSQTIHPIMSNPGQPVSEDCLYLNVWTPAQKAADNLPVVVWIHGGGFSYGSTAMSLFDGTAIAERDVVFVSIAYRLGPLGFFSHPELSAESEHNASGNYALMDQVAGLKWVQENIAAFGGDPQKVTIMGESAGGMSVSLMAQTPLASGLFRGVISQSGASVVNTGMMASLAEAEQAGVTLMKNAGASSLAELRKLPAEVIVNAATATSGFTRSSSWPTIDGYVITKDPTALYQQGEQNDVALLIGLNEYEGALFNTIKTADEFKAMVNQRYGDKASQVLAAYPAEDDNQAVASAIDYGTDSTFAIQAWSWARLQKRHGDTPVYYYHFNHNPPVRPGVPQGAIHGAELPYMLGTQHTRDIGWTADDKAMSALMISYWTNFIKTLDPNSSKLTSWPEYNEQSEQVLLFENGGSMAVTLPHKTRMTAIDPLQ", "metadata": {"id": "A0A1E8FID0", "cluster": 16861843, "interpro_all": ["IPR029058", "IPR002018", "IPR019826", "IPR019819", "IPR050309"], "interpro_used": ["IPR029058", "IPR019826", "IPR050309"], "interpro_unused": ["IPR019819", "IPR002018"]}, "task_type": "autoregressive"} {"instruction": "I want to make a protein that can have this function: The protein belongs to the Pectin lyase fold superfamily, which encompasses enzymes with a characteristic $\\beta$-helical architecture, including pectin lyases, pectate lyases, polygalacturonases, and iota-carrageenases. These proteins primarily function to degrade cell wall polysaccharides such as methylated or demethylated pectin and carrageenan, often acting as microbial virulence factors. In addition, the protein is grouped in 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. Additionally, the protein contains a Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain that adopts a $\\beta$-helical fold essential for the two-partner secretion (TPS) of large bacterial proteins. Located near the N-terminus, this transport module facilitates the export of diverse virulence factors, including the contact-dependent growth inhibitor CdiA, the adhesin FhaB, and the hemolysin HpmA. It is derived from Myxococcales bacterium. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 14440, 1942, 1920, 22422, 23928, 3728, 13975, 16, 2154, 21569, 5038, 1956, 43, 6293, 8, 38, 4666, 8, 17, 11514, 9335, 16, 2710, 22422, 23928, 1036, 16, 13494, 3857, 2057, 23928, 1036, 16, 16115, 23276, 10366, 2319, 16, 1930, 30360, 1019, 17, 28682, 11496, 4127, 1036, 18, 2144, 2697, 5985, 2347, 1942, 17069, 2024, 4821, 18686, 2427, 1966, 11882, 2014, 21732, 1981, 22422, 1930, 30486, 16, 3868, 8290, 1966, 7293, 9304, 2790, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 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, 4950, 16, 1920, 2213, 5461, 43, 18706, 7105, 17003, 1921, 11912, 1993, 19, 10089, 16230, 19238, 1019, 17, 3189, 16, 21387, 3418, 1988, 24032, 43, 8, 38, 4666, 8, 17, 11514, 3728, 4415, 1958, 1920, 2288, 17, 8240, 5512, 12, 21387, 13, 1927, 3103, 4543, 2697, 18, 4810, 4931, 1920, 56, 17, 7822, 16, 2052, 4860, 9059, 11374, 1920, 12660, 1927, 6445, 9304, 2790, 16, 2710, 1920, 5217, 17, 3100, 2905, 4106, 19238, 1019, 16, 1920, 5315, 1921, 11912, 1993, 16, 1930, 1920, 3243, 23872, 4688, 3368, 18, 2176, 1977, 3595, 2037, 21464, 11748, 1918, 14061, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MNPLVSTPPQSMAQDTPDSGTKNPQRTTSVIAYGPRPAIAIPDSPSLVDIMPVQGQNGPWNFLFPHASLTNPDSPQAEVKAHEPRREYRQVKVAVACALYTKAGAPHIHFTLIMIGDNGPVVAQISIMSSPESDARASLQNASVAGGTRRPMSSLARKLFGPMSVLLSAMLLSGHASGQMAPPPDWSAVETLIRTDGSLGPGGTLTAETEFPGVFVIGEELGTSFGQNLFHSFESFNLGAGDTAKFTASRPFSSVVSRITGSAPSYLNGQIRSDISGADFYFLNPSGVFFGPGASLDVPGAFYASTADDLEFSDGRVFAARPGSDPPLLSMANPAAFGFFGQAPIGRIGVDESNLRMAPGQALTLVGGDIEISGGFLQQGVLRAPGGTVSLLAVASAGKARFDASDPSGGIDSLSFASLGAIELNELAFIDTRNYGSDSNGALEILDFGPSGDVFLTADSVRLLEFSLINTRSYGIGGSGNVNIEAGDYIQDWSDIWTDAQQLGSFRDFGEGNAGNVRILASRSARLVDSGISASIFVLDPDDPPTSSAGTIEIRVGEGPATGSGDAPPAQPDLRLSNTQIQIVNAGSGSGGALELSAEELVIESGSLLGSLSTGTGAAGSVSLLGRRSIALHDSGINAGSLGAGAGGEIRLEAPDIALAGNGLLAASTSGSGSGDRVLLLGERIRLTGGFGITTINSSLGPGAGAGADIEIQASESLLLEDVGLFSATFGDGDAGNITISGNGITNPDVSILGGEIGALAVAESGPTVGNAGNISVRARTLSMDASPNRLTLVNAGTAFAENLGQGGDIVLEIDERIDISSGAHISSGVWGQGEGGAVRVTSPNATMTVEGSIDTSTFGSAPAGIIEIDVKSLEIRDGGFLAAIANSEGAGGDIDIRASKSVEISGRSSLNQPSRITTEASGVGAAGSIFVQTPRLTL", "metadata": {"id": "A0A7C7YF01", "cluster": 18731948, "interpro_all": ["IPR008638", "IPR012334", "IPR011050"], "interpro_used": ["IPR012334", "IPR011050", "IPR008638"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein incorporates 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. Also, the protein should include a Reverse transcriptase, RNase H-like domain that provides the ribonuclease H activity necessary for converting single-stranded retroviral RNA into double-stranded DNA during infection. This domain is typically found within enzymatic polyproteins of retroviruses and animal retrotransposon-like elements, where it complements DNA polymerase activity to enable genomic integration. Also, the protein has 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 has been detected in Peltaster fructicola and exhibits UniProt keyword tags Aspartyl protease, Nucleotidyltransferase, and Transposable element. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 19683, 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, 2222, 16, 1920, 2213, 3066, 3951, 43, 5267, 13335, 16, 9843, 50, 17, 3189, 3418, 1988, 4558, 1920, 18347, 2051, 50, 2455, 4680, 1958, 15025, 2957, 17, 10338, 16599, 3146, 2460, 4825, 17, 10338, 2678, 2409, 2909, 18, 2052, 3418, 1977, 5745, 2435, 2651, 8145, 6240, 10355, 1927, 26371, 1930, 4027, 27181, 1916, 17, 3189, 5362, 16, 2597, 2176, 30405, 2678, 6479, 2455, 1942, 8675, 4935, 7122, 18, 2222, 16, 1920, 2213, 2258, 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, 2258, 2252, 3330, 1922, 7874, 3857, 2156, 1915, 13478, 29902, 1930, 9826, 20709, 11121, 2538, 14392, 12053, 2199, 7154, 16, 2797, 4090, 2199, 9961, 16, 1930, 12935, 2115, 6149, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MSLTSEQTLHLRQLAALLRVETATVPPTIRAPLTAFASLHERLDEFPDDWANDEQARARAIELGTRYLNQINSQHRELRSPSRQQNQNDDEPSPPRHQRRRRTTRDNLEALNNRRVRQPNLSPVRTIESDQGQAGTSSGGGSGHTESIPRDTPANPNMSEPPNPFSREQIDALSALIAQSVAAALRSNAARPNPAPNDPLDVERDQSMREPLVPSIDRRAPSWRDDEVGYFWPDHPDSEDTFTNNNGQVIMRDVHLFIDRVKDATACRGEPFMRERIPALLRGTAAQWYTTALPSLVKEGLRHASIDQWYTTLLEQFKRPLLESLGSLQRMRYTLTDARDRKPIATYVYTIVRHARDAGMDTPVQQLTYAYQGIDVMLRDSNLRNAVKTGHNSPIDSSELTPTTRQNEFAARTYPALQNRPALPASQNRLAITPAGEPAARPYVNERYDRPGYRPTLRPFTAKVNFVDAQPADEDEVMQEYDEQDYAEQGEEYEELGCESLEGVETNDAVHVDAHFLNTESTAVTPKDMHEPVRNPKIMAARSTKQMDPPINHPRYHYATVHLSLKHDAPLQPVCIDSGTSTTLVGTNFLEQQGTSLVHLVPAYLKWVRGVGGATSRVLGAMTLSLYFQNNLTSHCFAHVVENLRPNLLLGTDWLVTTSATLDFRSCQLALPQGDVSMFVDKPFGSRAQSDIPVRARTRTVLQPNKITAIPIVTGPDVQGLHLFTPTHQHLLHQILNTENNTIYAVNESNLTTEIPQGFPLGHLSTSFDGLTATEAYSWQDAKADNISPSWSYNTEPVVYQDTSNNPEGLPTRTGPFGATIYGDDDTALRISELVALFQDLFTDDGKIATIPEQEWMTVPLAGEWNTADAKLAHKVYPMGPKDRELLDATHDKLHRQGRMEWTKTPTPFGFPVFVVWRLVDGVRKGRVVVDVRGLNKITIPDSYPLPLQTDITSAVAGCSYLSTVDCTKFFHQLPVAKEDRHKFTVVTHRGQEQYNVALMGYKNAPPYAQRQIDRLLRESGIAFAKAFIDDIIVFSKSLQEHLGHLHYLFSVLQDYKITLSGDKSNLGFPSLNLLGQRVDAYGLRTTSDKLAAIKNLSFPSTLKDLETYIGMTGWLRHYVLHYATIVEPLQTYKTKRLKSAPQSKQARTHFTNAARIEATPELLDAFNALQDAFSDPKTLVHYARARPLHIFTDSAKQRGFGVIVAHLLGDPQPPKGLTADNKLPASTKIQPILYLSKTLSGAERRYWPTELEVAALVWAIKRVRWMIEGSEHVTTIYTDHEAIVGLSKQTSLNSSATDKLNNRLTRASQYMSQFNLNVIVVQGRLHLFADALSRLPARQTTPVDDHDDVLDDLVFAHLLTTENGTSTTILEIQPDFKKELQKAYDSDKHFSRIKARAESMDDSESLGFAWRDGLLWKDGRLCIPKALDGDIFEIAHDQQFHPGFHRLYARIRDQYYIRKLEKRLRLYIMHCDECKQLQTRRHKPFGDLHPILSPAIPFHTIAMDFIVGLPEYDEYNCLLTVTCKFSKRTILIPGHDQLDATAWAHKLLDELFSCDWGLPSAIISDRDPKFTSKLWSTMFDRLGIKLLRSTAYHPQTDGQSERTNQTVEIALRYYLAKNPDHALGWAYVLPQLRFMLNNSVSRGTGVSPNELCYGFRPREATDVSVALPDEHKVRHQEAEDSIAYAQAAMKIRYDTQHTPWSPQVGDRVYLKLDNYRIPGFKNDKLSQKYAGPFAIANAVGRHAYKLLLPSTWKMHPVVSVTELEPAATGDDPYERRRHDDRRQLKKSLKLRELEDNQLLPERLLDRRTRTLRGKQVEEFRVRHATTTAEHDKWVNRQNLPVQLLREYLRNHPHYNYFFITSALQQASSTTTTMDTEQNNDAASMQPANTEQHNEAPSMPKEVPRVTFFPEEFLDTLYGKKIYGPRTKAQQDTMDFLADPETAKIPLNLGNKDMKNKKDKKDNNDDGVDKAVTKNTLDTPKDDEDDYDGFVFNLDTDTLNKLTSNAEDKANKSKNKHNDLDDIPASTRALKNKRAAARQRRTLTSRLIERHQLILNNMAVLPRDATQDYRPENVDYQRAFKLQDQVLSAVQGNQRLVKSLQKNAPKWNEDNVGEYTVSIATFAGSIGLRTTQSSSAAADDVGPVLAPATIVPSAATQALDALLTGYTPSSATFAAPVLRRPPPPVMVDKMSSPIPEPEATSAPPPDYAVLAVTLAGVIIGVLLSLLFLFIIWMIPTKHEVALIDGTDD", "metadata": {"id": "A0A6H0Y070", "cluster": 20418137, "interpro_all": ["IPR043502", "IPR001584", "IPR041588", "IPR021109", "IPR050951", "IPR043128", "IPR012337", "IPR036397", "IPR000477", "IPR041373", "IPR056924"], "interpro_used": ["IPR000477", "IPR041373", "IPR001584"], "interpro_unused": ["IPR012337", "IPR036397", "IPR056924", "IPR041588", "IPR043128", "IPR043502", "IPR021109", "IPR050951"]}, "task_type": "autoregressive"} {"instruction": "Design a protein's amino acid sequence that will have the following function: It is part of 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 is categorized in the Bacterial competence-related DNA uptake protein family, which facilitates the uptake of extracellular DNA during natural transformation. These proteins likely function as components of the membrane-bound transformasome pore complex, mediating the binding and translocation of genetic material essential for horizontal gene transfer. In addition, the protein should include 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. It is expressed in Chloroflexota bacterium.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 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, 1977, 10234, 1922, 1920, 4543, 12939, 17, 2712, 2678, 5047, 2213, 3416, 16, 2154, 11374, 1920, 5047, 1927, 5329, 2678, 2409, 4613, 7002, 18, 2144, 2697, 3205, 2347, 1966, 4178, 1927, 1920, 3260, 17, 4124, 4331, 8431, 8554, 2796, 16, 10239, 1920, 2743, 1930, 7849, 1927, 3299, 3485, 4415, 1958, 8743, 2359, 3856, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 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, 2176, 1977, 3198, 1922, 10107, 18222, 7336, 14061, 18, 3], "output": "MSEPPHADVQLRFACTEHSVGGQKGAVMYLRISEDRARKARPRKRRRASLLASHLEVRTFNVGHGEAVLVTFDNGRAWLMDCGSNSVPRNERLGNHIIDYLGVNGVVLDTIVASHPHFDHAGAIETILGSASPNVASPVTIYRTDIAEWISSSGWRQRYADAVAARGADVDEILLLSAHREVTISDHASAHIYVGARDGVYTSLFVHLRYRESRLLFTGDAYCGYEVELLNAFGSADFRADVLKITHHGSSSGTAATIVNEVRPGLAIASTGDHGGHRLERDTLDRLGGRPGPRAIFETVVDGDIILRTDGMSYGGGILYEAEFESPGRFAESLGGEILRLAYVDSTRTVSDHPNCV", "metadata": {"id": "A0A9E4XPH2", "cluster": 22269913, "interpro_all": ["IPR052159", "IPR001279", "IPR036866"], "interpro_used": ["IPR036866", "IPR052159", "IPR001279"], "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 can be placed in the Phage virion morphogenesis protein family, which comprises proteins involved in the structural assembly of bacteriophage particles. Members of this family, such as the S protein from phage P2, are thought to mediate late-stage maturation events including tail completion and the stable joining of the head to the tail. It occurs in BD1-7 clade bacterium.", "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, 10503, 19230, 15328, 2213, 3416, 16, 2154, 12936, 2697, 3286, 1922, 1920, 4346, 5957, 1927, 24613, 5569, 18, 4678, 1927, 2052, 3416, 16, 2427, 1966, 1920, 61, 2213, 2037, 10503, 7535, 16, 2032, 6212, 1942, 8265, 5058, 17, 3587, 7655, 3916, 2710, 5281, 9297, 1930, 1920, 4700, 15836, 1927, 1920, 4469, 1942, 1920, 5281, 18, 2176, 5110, 1922, 5238, 1009, 17, 27, 11315, 14061, 18, 3], "output": "MTGVRLEIDSSSIERLQDRLAGFSGLPLNDLRHAIGSEVEHQTRRRLQDEKTTPDGDAWQALDEGYAARKALKSSGGILERDGDLIDSIAYAVDGDEIEIGSPLVYAAIQHFGGDEVGIPIVSRQFLGLSQDNENDLLALVDQWLDQQVGGQSHAI", "metadata": {"id": "A0A5S9Q4A3", "cluster": 26614217, "interpro_all": ["IPR006522"], "interpro_used": ["IPR006522"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein is a member of the Protein of unknown function DUF2203 family, which represents a conserved group of proteins with no currently defined biological function or structural role. It has been detected in Sulfuricaulis limicola.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2213, 1927, 5435, 2347, 4855, 6680, 24640, 3416, 16, 2154, 4972, 43, 5305, 2210, 1927, 2697, 1956, 2239, 5077, 3608, 3933, 2347, 2014, 4346, 2770, 18, 2176, 2258, 2252, 3330, 1922, 12585, 6102, 13004, 1036, 2784, 29902, 18, 3], "output": "MTSAAQIYQISACNNPRVFTLSEAEELFPLMWKITEEAYRELEPVRRTLEAMVPSNPQVRKVEKQYEAIVRRWMGKMERLGLVVKGLWLADFDTGDGYLCWKFPELRIGHYHGYHEGFGGRRPLQDIIEELDPDWAHL", "metadata": {"id": "A0A1B4XEK2", "cluster": 28721272, "interpro_all": ["IPR018699"], "interpro_used": ["IPR018699"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: The protein possesses a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. In addition, the protein features a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. It is identified in Dadabacteria 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, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 2176, 1977, 2899, 1922, 23053, 20013, 2341, 18339, 14061, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MSDKFRIGVFSSGNGSNFEAIVKADIPNVEVSFLLCNIEDAYVLERAKNFSIDSILLPHKNFESRKDFEKEIISRIQDYDVDLIILAGFKRILSPFFINYFEKKIINLHPSLLPSFPGLRAPKQALEYGVKFTGCTVHFVDDGVDTGPIILQGLIEILDSDDEESLMKKIHEKEHEILPVAIELISEGKVKTTEGRRVFIDN", "metadata": {"id": "A0A836QV14", "cluster": 12747794, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR002376", "IPR001555"], "interpro_unused": ["IPR004607", "IPR036477"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to create: The protein contains a Cytidyltransferase-like domain that mediates nucleotidyl transfer reactions, typically utilizing CTP or ATP to activate substrates and release pyrophosphate. It functions as the catalytic core in diverse enzymes such as glycerol-3-phosphate cytidyltransferase and phosphocholine cytidylyltransferase, contributing to lipid biosynthesis and coenzyme production. Also, the protein is associated with the Archaeal FAD synthase family, which catalyzes the transfer of the AMP moiety from ATP to flavin mononucleotide (FMN) to produce the essential redox coenzyme FAD. These enzymes are vital for archaeal metabolism and energy production, and while primarily specific to ATP, some members can utilize nucleotides such as CTP or GTP to form modified coenzymes. Additionally, the protein features a RfaE domain II domain that catalyzes the transfer of ADP to D-glycero-D-manno-heptose 1-phosphate to yield ADP-D-glycero-D-manno-heptose. This enzymatic activity is a critical step in the biosynthetic pathway of the lipopolysaccharide (LPS) inner core. It has been characterized in Armatimonadota bacterium and is annotated with UniProt keywords ATP-binding, Carbohydrate metabolism, and Nucleotidyltransferase. 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, 2702, 19743, 9961, 17, 3189, 3418, 1988, 10412, 2797, 4090, 2199, 3856, 5298, 16, 5745, 10232, 25639, 2014, 4498, 1942, 6980, 6249, 1930, 4012, 24937, 18, 2176, 4088, 1966, 1920, 6804, 4728, 1922, 6445, 5038, 2427, 1966, 9244, 17, 23, 17, 5413, 2702, 19743, 9961, 1930, 8078, 11603, 2702, 19743, 2199, 9961, 16, 8739, 1942, 4486, 8132, 1930, 22051, 3372, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 22367, 14134, 8921, 3416, 16, 2154, 17097, 1920, 3856, 1927, 1920, 3681, 11804, 2037, 4498, 1942, 26758, 29932, 4749, 12, 29599, 13, 1942, 5074, 1920, 4415, 9366, 22051, 14134, 18, 2144, 5038, 2032, 8970, 1958, 22367, 4714, 1930, 3844, 3372, 16, 1930, 2679, 5985, 2487, 1942, 4498, 16, 2673, 4678, 2112, 12561, 9519, 2427, 1966, 25639, 2014, 9319, 1942, 2386, 4795, 22051, 1036, 18, 4950, 16, 1920, 2213, 4075, 43, 22465, 1021, 3418, 2890, 3418, 1988, 17097, 1920, 3856, 1927, 9828, 1942, 46, 17, 7757, 1037, 17, 46, 17, 7338, 1037, 17, 20662, 2217, 21, 17, 5413, 1942, 4307, 9828, 17, 46, 17, 7757, 1037, 17, 46, 17, 7338, 1037, 17, 20662, 2217, 18, 2052, 8145, 2455, 1977, 43, 4140, 3537, 1922, 1920, 14041, 3374, 1927, 1920, 15614, 12, 5887, 13, 6671, 4728, 18, 2176, 2258, 2252, 4378, 1922, 6011, 1968, 3947, 12595, 3857, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 16, 10590, 4714, 16, 1930, 2797, 4090, 2199, 9961, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MIEEKIVSRENARETLRAWQEAGKKVVFTNGCFDLIHAGHVRYLEKARALGDKLIVAVNDDDSVRQLKGPDRPIQPVTDRAMIIAALASVDLVVVFPELTTDNLLNLLRPDVLAKGGDYTMETLVASERDFVKSYGGEVIIIRRLDSTSTSGLVERIRGKDS", "metadata": {"id": "A0A9E5TCA6", "cluster": 17649963, "interpro_all": ["IPR050385", "IPR004821", "IPR011914", "IPR014729"], "interpro_used": ["IPR004821", "IPR050385", "IPR011914"], "interpro_unused": ["IPR014729"]}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein has 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. In addition, 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 identified in Armatimonadota bacterium.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 2258, 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, 1922, 2459, 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, 2899, 1922, 6011, 1968, 3947, 12595, 3857, 14061, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MPPDSTLPSRPPASDPGTPLIHTRLGVSRSSLSRVLSGQRGPSFSFAWKVTQAVERLDPCELFSLDGSYPTPAARRWEQQQAGHGHSGPGTGKGGAEGVMLHINWYLSSGRARLAAEARRLTRLWKGTGREGTVCALCGCPGCRVGRTWEQEQ", "metadata": {"id": "A0A9E3CDG8", "cluster": 942201, "interpro_all": ["IPR001387", "IPR010982"], "interpro_used": ["IPR001387", "IPR010982"], "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 Asparagine Synthetase/Amidase family, which primarily catalyzes the synthesis of asparagine from aspartate using glutamine as a nitrogen donor. These enzymes typically operate via a two-step mechanism involving the hydrolysis of glutamine to release ammonia, which is subsequently transferred to the aspartate substrate. Additionally, some members function in the biosynthesis of secondary metabolites, such as chrysogine, by facilitating similar amidation reactions. In addition, the protein should have a Glutamine amidotransferase type 2 domain that catalyzes the transfer of an ammonia group from glutamine to a specific substrate, playing a key role in the biosynthesis of purines, amino sugars, and amino acids. Structurally classified as an N-terminal nucleophile (Ntn) hydrolase, it features a four-layer \u03b1/\u03b2/\u03b2/\u03b1 fold and utilizes a conserved N-terminal cysteine to initiate nucleophilic attack. Also, the protein should include a Asparagine synthase domain that catalyzes the ATP-dependent conversion of aspartate to asparagine, typically utilizing glutamine as a nitrogen donor. This domain shares structural similarities with GMP synthetase and is found in proteins such as ASND1, which is associated with degenerative myopathy. It originates from Planctomycetota bacterium and corresponds to UniProt keyword Amino-acid biosynthesis, Ligase, and Asparagine biosynthesis.", "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, 23677, 18185, 19, 28813, 2051, 3416, 16, 2154, 5985, 17097, 1920, 4271, 1927, 23677, 2037, 12878, 2193, 9959, 1966, 43, 6634, 6282, 18, 2144, 5038, 5745, 15336, 3454, 43, 2288, 17, 3537, 2856, 5884, 1920, 9128, 1927, 9959, 1942, 4012, 14880, 16, 2154, 1977, 5326, 6311, 1942, 1920, 12878, 4510, 18, 4950, 16, 2673, 4678, 2347, 1922, 1920, 8132, 1927, 4067, 6926, 16, 2427, 1966, 21367, 2021, 2053, 16, 2007, 12440, 2551, 28813, 1943, 5298, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 9959, 28813, 14165, 2601, 22, 3418, 1988, 17097, 1920, 3856, 1927, 1925, 14880, 2210, 2037, 9959, 1942, 43, 2487, 4510, 16, 14797, 43, 3834, 2770, 1922, 1920, 8132, 1927, 19700, 1036, 16, 3835, 15592, 16, 1930, 3835, 4576, 18, 12171, 5947, 1966, 1925, 56, 17, 4262, 2797, 28335, 12, 5891, 1022, 13, 20748, 16, 2176, 4075, 43, 3006, 17, 4757, 160, 19, 161, 19, 161, 19, 160, 3728, 1930, 18127, 43, 5305, 56, 17, 4262, 8666, 1942, 11051, 24456, 8926, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 23677, 8921, 3418, 1988, 17097, 1920, 4498, 17, 3100, 7309, 1927, 12878, 1942, 23677, 16, 5745, 10232, 9959, 1966, 43, 6634, 6282, 18, 2052, 3418, 16495, 4346, 10857, 1956, 18033, 18185, 1930, 1977, 2435, 1922, 2697, 2427, 1966, 15118, 7240, 16, 2154, 1977, 2458, 1956, 15676, 25017, 18, 2176, 22970, 2037, 4720, 2341, 13386, 19446, 3857, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 3835, 17, 2687, 8132, 16, 11905, 16, 1930, 23677, 8132, 18, 3], "output": "MCGIAGILGHGAIEHENAVHKMIDAMAHRGPDGQGIYVSDSNFVLVYNGECYNFRELRDRLSNDGLGFVSSGDTEVVLKLLQKEGVDALPKLNAMFALYFTRIGKLLLFASEVRTLLASGLVPRKADLAAIHSYLAYGAVQEPNTIVSGVSRYSKREKKLSSQELRDSFLSAVHRHLISDAPLGLFLSGGIDSSSIVAAATRRSNTRIKTLSVIEHFQIPVTGQQMLQMLPEALDAMDQPTGDAINTYLISQAASQTLFRDVPKMLAMRRFLSLIRKPAAHLLGKCNLFALKPAKLADFFDAPANILNYYLVRLVKPEWDSALDSEYFQDLLTLIDGSKIHDAVGRLEMRAYMGQTLLRDSDPESRIPQNTPKARFVEAMGNWLPEGIANRSKQGFTLPLKNWMQQELKKNVLLDLWEQFCSRPERIGWFRPWSLFVLGRYLQTHKLGLGTCVLGHRRLAILDLSEAASQPMISRDGALWDERKQTLLIAHDRYGQKPLVLKPAGYMLCKPDGTKSYDIYWFPEQPDESEAEYAGKMAEWAGTGLKAVLSGVGGDELFGGYHRRIFSWRQIREIAPEVMGMAHGLEIRLPFLDSEFSIGSLNLENEITEGISSLQRNCNVMK", "metadata": {"id": "A0A9E3I3U4", "cluster": 2132874, "interpro_all": ["IPR006426", "IPR001962", "IPR051786", "IPR033738", "IPR017932", "IPR029055", "IPR014729"], "interpro_used": ["IPR051786", "IPR017932", "IPR001962"], "interpro_unused": ["IPR006426", "IPR033738", "IPR014729", "IPR029055"]}, "task_type": "infilling"} {"instruction": "Function:\nThe protein contains a PGG domain that is distinguished by a highly conserved sequence motif at the start of the domain, although its specific biological function is currently unknown. Also, it is part of 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 originates from Tripterygium wilfordii (Thunder God vine) and corresponds to UniProt keyword ANK repeat.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 5461, 43, 5306, 1029, 3418, 1988, 1977, 12080, 2007, 43, 3626, 5305, 3244, 5219, 2019, 1920, 6413, 1927, 1920, 3418, 16, 2876, 2496, 2487, 3933, 2347, 1977, 5077, 5435, 18, 2222, 16, 2176, 1977, 3131, 1927, 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, 22970, 2037, 8027, 1967, 4121, 2457, 8534, 8331, 3907, 12, 1913, 2652, 1915, 21100, 11132, 1021, 13, 1930, 8852, 1942, 20709, 11121, 2538, 9808, 6865, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MDIQRLFEAARCGNVEVLRKSLQENSLILTEVVLTTSSKDTLLHVYRPMDIAAVVGNVEIVAELNKNNRGTCRLKGKDQRTPLHHAAIHGRIEVINELVSKNHQVDAFDVLVELLKSFNKEKVINWCATNGNTVLHLAIKGLTAMDILDIVMEDVNDVQLKKILEHAGAKGAQEISTMKPASTSNEAKEKKFQKHRDSAGDARNALLVIAALIVSVTFQAGLQLPTSLEQLEQKDSSSTTSSNSGDPAPSESRNPAIVGLSLAQLSISEVTIFLIGNSLALSWGILIIEYLTEGFPTTAIKFTLLTTSLALPSIIRYGPFCGRKLINKLKRSSSATQASQPLPISRGATKAKQLSFVRELLEQMPDLAHELDKDGKSPESLEDVTAYNETVLHLAVSRKQKESVELLLGNFGALEVNAINSYQTPHEEHSRDNFESVLKYFPATVVKYSYSSLASTTSLPFRRELVGSVYALMITYGFAVGSNDK", "metadata": {"id": "A0A7J7DD45", "cluster": 2553001, "interpro_all": ["IPR002110", "IPR036770", "IPR026961"], "interpro_used": ["IPR026961", "IPR036770", "IPR002110"], "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 PDZ domain that mediates protein-protein interactions by binding to specific carboxyl-terminal or internal peptide sequences within cytoplasmic signaling proteins. Frequently associated with the plasma membrane, this domain facilitates complex assembly and can, in specific subsets, directly interact with phosphatidylinositol 4,5-bisphosphate (PIP2). It is native to Myxococcales bacterium and is annotated with UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 5961, 43, 17755, 3418, 1988, 10412, 2213, 17, 2213, 3719, 2007, 2743, 1942, 2487, 9943, 17, 4262, 2014, 4495, 4207, 3709, 2651, 6823, 3197, 2697, 18, 5467, 2458, 1956, 1920, 3582, 3260, 16, 2052, 3418, 11374, 2796, 5957, 1930, 2112, 16, 1922, 2487, 9524, 16, 4103, 6310, 1956, 16927, 24, 16, 25, 17, 29443, 12, 21753, 13, 18, 2176, 1977, 6196, 1942, 21464, 11748, 1918, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 9117, 7864, 18, 3], "output": "MLEATIPEELVRAFCGRDDAAHATFRGDVTAAFAPRKSHETEDNRALATQEGHRFAGFLGVTVSADGTGPVRIQKVEPQGRRVGDVSDLVPPPRARTARLGLHRGSQSAAAVMAVDVASALLLLLLALSPLGRFSTWLALAVSARSGGGGRKPHEQWLSVARGLSGALSVPLVARELDLPILLLAAGSAAIVAGALSQVAQRGRFTPVSGVLSVGSLRADDFAAAQAGMPWRFLAFASPIHFMALLLGVLALVPEATLALAAVEWTHLVICSGLLSVMLLGGFAVPWLSELDRVSSAGRMAVGAVSVEQCGSALLRGALPAALLLPVAAKLWSVGALALFVATALACLLVIRRLGQNLRLQRGEASINPWLSGAPPVAGSLQGVVLDIAPAAQVGLAAGDVIEELSGVEFKPGTLSDLTPALALVGALPSGAAAYFGVALGSAAIALGALRRAFWVVIAQLPLVSALLVPSSPSQSLPRAADRRLPLLVVKSFGLVLLVAALRWALGRVAEGLVLSAYRGVI", "metadata": {"id": "A0A4Q5WZL3", "cluster": 3886272, "interpro_all": ["IPR001478", "IPR036034"], "interpro_used": ["IPR001478"], "interpro_unused": ["IPR036034"]}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe 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 is identified in Armatimonadota bacterium and is described by UniProt keywords Signal.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 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, 1977, 2899, 1922, 6011, 1968, 3947, 12595, 3857, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 2733, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MLRNVFKWACVLGLLILTLPSWLGAQETPTADTDSGKHYKLLGRVSRPAKSPFTFSVALGQSLIVCPVRSSASKTSKKIQTNLPKSHPLFHDFLPPENTHLFLQLTPKEVTKEVVAKECVKLTEAYQAEAVERAKANDPIVYVTYSIDGDQVAAQNTEPFSYDWDTKNRQGNLITRARVLVVVTNTHETYRLRIENYTFGKVEISMVDRSANVAGSILRSTHEFGGTASAPPTSAIGFTDKIPETFTLGEEDTFIFTVSLGKTQVVSGMLALQPKLPLGEPQVSNGEHLVEIRAL", "metadata": {"id": "A0A4P5TJL6", "cluster": 5637115, "interpro_all": ["IPR013783"], "interpro_used": ["IPR013783"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein carries a Helix-turn-helix motif conserved site that mediates specific DNA binding to regulate gene expression. It consists of two $\\alpha$-helices joined by a short turn, where the second helix interacts with the DNA major groove while the first helix stabilizes the structure. Furthermore, the protein should have a Homeodomain domain that functions as a conserved DNA-binding module involved in transcriptional regulation, often directing developmental processes such as body axis formation. It folds into a globular structure of three $\\alpha$-helices, utilizing a helix-turn-helix motif to establish specific hydrogen bonds and hydrophobic interactions within the major groove of the DNA target. Also, the protein is associated with the Paired homeobox Bicoid family, which comprises transcription factors characterized by a homeobox domain that bind DNA to regulate gene expression. Members of this family are implicated in growth regulation and morphogenesis, including skeletal patterning, heart development, and the formation of somatosensory neural systems. It is present in Chrysochromulina tobinii and contains UniProt keyword associations Nucleus. 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, 16252, 43, 7864, 17, 5165, 17, 7864, 5219, 5305, 3200, 1988, 10412, 2487, 2678, 2743, 1942, 5741, 2359, 2294, 18, 2176, 7543, 1927, 2288, 8, 38, 4595, 8, 17, 12789, 23186, 2007, 43, 3662, 5165, 16, 2597, 1920, 2812, 7864, 9034, 1956, 1920, 2678, 3044, 15920, 2679, 1920, 2561, 7864, 19658, 1920, 3170, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 4502, 17166, 3418, 1988, 4088, 1966, 43, 5305, 2678, 17, 2743, 9059, 3286, 1922, 5224, 3640, 16, 3868, 23258, 5878, 4028, 2427, 1966, 3362, 5432, 3337, 18, 2176, 16231, 2460, 43, 20975, 3170, 1927, 2559, 8, 38, 4595, 8, 17, 12789, 16, 10232, 43, 7864, 17, 5165, 17, 7864, 5219, 1942, 5389, 2487, 6201, 9031, 1930, 7919, 3719, 2651, 1920, 3044, 15920, 1927, 1920, 2678, 2758, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 7304, 27566, 8876, 2642, 3416, 16, 2154, 12936, 3213, 2790, 4378, 2007, 43, 27566, 3418, 1988, 4566, 2678, 1942, 5741, 2359, 2294, 18, 4678, 1927, 2052, 3416, 2032, 6835, 1922, 2905, 3640, 1930, 15328, 16, 2710, 7345, 16060, 16, 4003, 2740, 16, 1930, 1920, 3337, 1927, 17562, 5181, 3771, 18, 2176, 1977, 2481, 1922, 21367, 10086, 3392, 1019, 7551, 11566, 1033, 1930, 5461, 20709, 11121, 2538, 5253, 5607, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "MASRADPAVEVAAVVTDESDTLIHDVVDDDTALVVVPATMDDAAATSESNQRKKVNQRWVLSDEAKRALEAVYNERRFPTLAMREELAQELGGSLRQVQVWFQNRRQRDHRPDDEATLSTGASPPIGSSAVSGTRAPAPASTGAVSGAPSAPVQPFDPLPSVAPSSSALPTLPALPTLGTALGTAAGALASGAVSGMDHLAGAPALTPSVLRRIS", "metadata": {"id": "A0A0M0JUL2", "cluster": 10213850, "interpro_all": ["IPR001356", "IPR009057", "IPR000047", "IPR052631"], "interpro_used": ["IPR000047", "IPR001356", "IPR052631"], "interpro_unused": ["IPR009057"]}, "task_type": "autoregressive"} {"instruction": "The protein includes a Pyruvate/ketoisovalerate oxidoreductase, catalytic domain that catalyzes the thiamine-dependent oxidative decarboxylation of pyruvate to acetyl-CoA, a key step in anaerobic carbohydrate fermentation. This domain interacts with electron carriers like ferredoxin or flavodoxin and includes variants required for nitrogen fixation in cyanobacteria under iron-limited conditions. Also, the protein belongs to the Pyruvate-flavodoxin oxidoreductase, central domain superfamily, which encompasses prokaryotic domains found in enzymes that catalyze the thiamine-dependent oxidative decarboxylation of pyruvate to acetyl-CoA. This reaction serves as the final step in anaerobic carbohydrate fermentation and is required for cyanobacterial growth on molecular nitrogen when iron is limited. Additionally, the protein falls within the Indolepyruvate oxidoreductase subunit IorB-like family, which facilitates the ferredoxin-dependent oxidative decarboxylation of arylpyruvates. These enzymes play a key role in the catabolism of aromatic compounds, contributing to their breakdown for energy production and biosynthesis. It is present in Candidatus Bathyarchaeota archaeon. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 5921, 43, 11867, 19, 21471, 23854, 28144, 5524, 2057, 27388, 16, 6804, 3418, 1988, 17097, 1920, 26901, 17, 3100, 5163, 22429, 1943, 1927, 11867, 1942, 6894, 17, 10027, 16, 43, 3834, 3537, 1922, 12554, 10590, 12670, 18, 2052, 3418, 9034, 1956, 4995, 8974, 3189, 25304, 22389, 10960, 2014, 7732, 1986, 9754, 1930, 5921, 4936, 3414, 1958, 6634, 7938, 1922, 21897, 2441, 5680, 17, 3892, 2961, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 11867, 17, 7732, 1986, 9754, 27388, 16, 4101, 3418, 13975, 16, 2154, 21569, 21545, 4682, 2435, 1922, 5038, 1988, 18170, 1920, 26901, 17, 3100, 5163, 22429, 1943, 1927, 11867, 1942, 6894, 17, 10027, 18, 2052, 3227, 10634, 1966, 1920, 3948, 3537, 1922, 12554, 10590, 12670, 1930, 1977, 3414, 1958, 21897, 1024, 2905, 1990, 3272, 6634, 2469, 5680, 1977, 3892, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 18050, 18425, 12631, 2010, 27388, 5903, 21509, 16007, 17, 3189, 3416, 16, 2154, 11374, 1920, 25304, 22389, 10960, 17, 3100, 5163, 22429, 1943, 1927, 15578, 18425, 12631, 2209, 18, 2144, 5038, 3918, 43, 3834, 2770, 1922, 1920, 19480, 1927, 10761, 4300, 16, 8739, 1942, 2310, 13630, 1958, 3844, 3372, 1930, 8132, 18, 2176, 1977, 2481, 1922, 14550, 1031, 1957, 10481, 9771, 15618, 20051, 7336, 13470, 1916, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MKLDLVFAGIGGQGIVVLSDIFCEAALLDGFDVAKAEVHGMAQRGGSIVAYARIGEKVEAPLIERGKADVILGFEILETARVLPMLKKDGTVVVNTKYIPPNLAVQGSNKLTKPQDLIGLLRKKAAKVHEVDGAGIAEKVGNPIVVNTVLLGALSALPENPIKKETLEKAICSRLKPMFQGINLQAFQLGRESLSLG", "metadata": {"id": "A0A550GTN2", "cluster": 11428817, "interpro_all": ["IPR052198", "IPR019752", "IPR002869"], "interpro_used": ["IPR019752", "IPR002869", "IPR052198"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein is included in 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. Furthermore, the protein features 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. It is found in Artemia franciscana (Brine shrimp) (Artemia sanfranciscana) and is associated with UniProt keywords Transposable element.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 1977, 3063, 1922, 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, 3677, 16, 1920, 2213, 4075, 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, 2176, 1977, 2435, 1922, 20897, 6026, 28740, 8337, 1019, 12, 29221, 25184, 13, 12, 20897, 6026, 6867, 7134, 2412, 10368, 7241, 13, 1930, 1977, 2458, 1956, 20709, 11569, 12935, 2115, 6149, 18, 11586, 5655, 3581, 18, 3], "output": "MQVNPHASVSSCQGQGHFSPVSGGITNIEWNEDFPPLPSSENSEEEMRTVNPLEAEGVISENLKRKLNEVQSSINQNPTMLNKKSVDMPYSDLLSISINFLNKLDFRVPASRVYSTVKSLISGSREDGVPDPLSDCEIEVKAKDKRFSKSHRSVAYNQPFLTQEIEFPQFVKALPKNWVAALLNIINELWNEGQFPKIWKDGVYRTITLLPVLGKVYERLVKQRMNQVIELNRGYALENKKVLLMAFLDVVSAFDLEGREVKIKAQVNSSKKKTMNLLSHFPNVKNYSVPTSNRFQSLQTNIDNPTKTGMKRRDVSPVSEYLNQPQNRAAEFKKTVIAAKRVSWQTNPPITYKNSTLLEYQIIKVINHLPLTAPGEDMIVVLIPKVGKDKSKLENLKNIQCGFRRNRNTEDVMLMFMNDAVSMVHRHILEAIMAAAVKGQLLEFSDSF", "metadata": {"id": "A0AA88KT87", "cluster": 13279513, "interpro_all": ["IPR043502", "IPR000477"], "interpro_used": ["IPR043502", "IPR000477"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should contain a Putative sensor domain that functions in stimulus sensing and is typically found at the N-terminus of two-component system histidine kinases. This domain detects environmental signals to regulate downstream signal transduction. It is found in Halorubrum ezzemoulense (Halorubrum chaoviator) and contains UniProt keyword associations Transmembrane helix, Transmembrane, and Transferase. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 3066, 5531, 43, 6770, 6443, 3418, 1988, 4088, 1922, 5794, 9306, 1930, 1977, 5745, 2435, 2019, 1920, 56, 17, 7822, 1927, 2288, 17, 4594, 2433, 13873, 7784, 18, 2052, 3418, 19998, 4813, 4771, 1942, 5741, 5863, 2733, 8201, 18, 2176, 1977, 2435, 1922, 23226, 3176, 2377, 1989, 11650, 6931, 12492, 3466, 3355, 1021, 12, 23226, 3176, 2377, 1989, 13297, 25210, 3061, 13, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 16, 9117, 16, 1930, 13763, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MALSDALSDPPANRRVAEAVLSAPFRIRTYAAAAYLALSFPLGIAYFVCTVVGLSLGVSLSVLLVGVPILAATLGGVVLVSIGERVLARRLLGADIADPSWKVTEASGIADRALAAATDLAVWGALLFVLSKLIIGVAGFTLLTVVLSVGASLLAAPLYYDAPGASVGLILPEPIRRELSLVVPWEQFEVGVSFIVRLTSWEVSTLPGALLMSLFGVLAALVGLNVVSAAGWLCARWAEFALGAGTSPVSDD", "metadata": {"id": "A0A256JT90", "cluster": 13945363, "interpro_all": ["IPR025828"], "interpro_used": ["IPR025828"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein belongs to the DNA repair protein Rad4-like family, which plays a central role in initiating global-genome nucleotide excision repair (NER) by recognizing diverse DNA lesions and recruiting downstream factors. These proteins specifically detect chemically and structurally varied damage on a single DNA strand, such as that caused by ultraviolet radiation or genotoxic chemicals. Additionally, the protein features a Rad4 beta-hairpin domain 2 domain that binds to DNA and is found in the Rad4 protein. Furthermore, the protein should have a Rad4/PNGase transglutaminase-like fold domain that adopts an ancient transglutaminase structure shared by peptide-N-glycanases (PNGases) and RAD4/Xp-C proteins. In PNGases, it retains the catalytic triad to facilitate glycan removal from glycoproteins, whereas in RAD4/Xp-C proteins, the domain is catalytically inactive and functions as an interaction module in DNA repair. It occurs in Latimeria chalumnae (Coelacanth) and has UniProt annotations DNA damage and Nucleus.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 2678, 5059, 2213, 4226, 1006, 17, 3189, 3416, 16, 2154, 5705, 43, 4101, 2770, 1922, 12410, 4906, 17, 3843, 5489, 10940, 5059, 12, 4919, 13, 2007, 15667, 6445, 2678, 4518, 1930, 17040, 5863, 2790, 18, 2144, 2697, 4475, 4277, 13944, 1930, 12171, 6760, 4293, 1990, 43, 2957, 2678, 5984, 16, 2427, 1966, 1988, 4189, 2007, 17077, 5442, 2014, 20558, 10164, 18, 4950, 16, 1920, 2213, 4075, 43, 4226, 1006, 4666, 17, 14565, 3418, 22, 3418, 1988, 6876, 1942, 2678, 1930, 1977, 2435, 1922, 1920, 4226, 1006, 2213, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 4226, 1006, 19, 25990, 2051, 2127, 16542, 15848, 17, 3189, 3728, 3418, 1988, 24032, 1925, 17364, 2127, 16542, 15848, 3170, 7115, 2007, 4207, 17, 56, 17, 15060, 2319, 12, 25990, 2319, 13, 1930, 4226, 1006, 19, 15930, 17, 45, 2697, 18, 1922, 25990, 2319, 16, 2176, 21645, 1920, 6804, 21845, 1942, 6628, 15060, 6025, 2037, 16268, 16, 3417, 1922, 4226, 1006, 19, 15930, 17, 45, 2697, 16, 1920, 3418, 1977, 21446, 9078, 1930, 4088, 1966, 1925, 2835, 9059, 1922, 2678, 5059, 18, 2176, 5110, 1922, 4144, 5770, 2126, 29343, 22008, 3336, 12, 29295, 10973, 4905, 1023, 13, 1930, 2258, 20709, 15010, 2678, 4293, 1930, 5607, 18, 3], "output": "MKRRSKGFEGNENEKPLVGGRRSKGFGGKVKSGQAAQTAAGGAAKGKKTRGKKSEEKVAVKQEEEEDVGKSVVSDLAFHREHGDSEEDSGEDTAVKKSEGDDDDDDESDEEWEEVEELSEPVPEGLAAAAVLEPGVPTKPVEIEIETPEQAKKRERREKRKAEFETYLRRMVNRFNKELRVETHKVGDLRMGEGGLHHLRVGEGGLHQSQSGGGWTAPTSEWGRVEKKKQHFVFRFIAAFSLNPNLSVDEGNNLQSALERSFGNYSIRDEEEMVHVFLIILRALKLMCRLVLSLHPVPLKEESPGQSNKAKSASRKSAPSKKRAARMPEKGLSDDSDKEDEEPGEELRKQAPSGAKRPSTEKAEPRKSVKRRKATGDHVVKLESTVEGPQRPKNNRRRRVASKVSYKEDSKSDENSDSDFELPGGGDSDFSDDGSGTTWKDKRRASGLQKTTTQEKTKAARSSGVKNLKREEESEEECDQGSKTSKKGSVRDDAEAAKEASGGSGGCDQWLEVYLEKMERWVCVDPVRGSVNQAKLCYKHASKPVYYIVGVDNNGYVKDVTRRYDAAWMTITRKQRIDSDWWEETLEPYQNPFVEKESKEEMETKNFKANFFHPPIPSVSELNDDHDYTKLHRLVVMFIIVLYFKSQALAVCRRILVVFRDCVHILHSRDTWLKEARVVRLGEVPYKMVKGHSNRARKARVAEPENREKNDLGLFGSWQTEEYQPPVAVDGKVPRNDYGNVYLFKPCMLPVGCVHLHVPSLHKVARKLDIDCVPAVTGFDFHSGYSHPVVDGYIVCEEYQDLLLAAWDKDQAEMEQKKREVRGWRTVAAVLGGREGVKKKIAPNDKVTALGQAGGSGFSSDEAEEDGPGSQKPAGDLSCSWPQNRQTTQQEGKIVRRSKREKRGEEKHLFPFEKK", "metadata": {"id": "H3APK5", "cluster": 16147635, "interpro_all": ["IPR018327", "IPR004583", "IPR018026", "IPR038765", "IPR018325", "IPR018328", "IPR042488", "IPR036985"], "interpro_used": ["IPR018026", "IPR018327", "IPR018325"], "interpro_unused": ["IPR036985", "IPR042488", "IPR038765", "IPR018328", "IPR004583"]}, "task_type": "autoregressive"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein is classified under the tRNA intron endonuclease, catalytic domain-like superfamily, which functions as the catalytic core responsible for removing introns from pre-tRNA by cleaving at 5'- and 3'-splice sites. This three-layer \u03b1/\u03b2/\u03b1 domain recognizes pseudosymmetric substrates to generate tRNA half-molecules with 2',3' cyclic phosphate and 5'-hydroxyl termini, typically operating within homodimeric or homotetrameric assemblies. Furthermore, the protein is a member of the tRNA endonuclease-like domain superfamily, which adopts a 3-layer \u03b1/\u03b2/\u03b1 topology to facilitate endonucleolytic cleavage in diverse genetic systems. This domain functions as the catalytic component in the Tn7 transposase TnsA for 5' DNA breakage, the archaeal Hjc resolvase for processing Holliday junctions during recombination, and tRNA-intron endonucleases for RNA splicing. Additionally, the protein should have a tRNA-splicing endonuclease subunit Sen15 domain that functions as a structural component of the heterotetrameric tRNA intron-splicing endonuclease. It associates with the catalytic subunit Sen34 to form an alpha2-beta2 tetramer required for the cleavage of introns from precursor tRNA. It originates from Polysphondylium violaceum and is classified with UniProt keywords tRNA processing.", "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, 10089, 10444, 18697, 16, 6804, 3418, 17, 3189, 13975, 16, 2154, 4088, 1966, 1920, 6804, 4728, 5061, 1958, 11340, 15778, 2037, 2097, 17, 10089, 2007, 28634, 2019, 25, 11, 17, 1930, 23, 11, 17, 10708, 3402, 18, 2052, 2559, 17, 4757, 160, 19, 161, 19, 160, 3418, 16197, 11520, 18801, 7445, 5287, 6249, 1942, 5655, 10089, 4768, 17, 4206, 1956, 22, 11, 16, 23, 11, 9821, 5413, 1930, 25, 11, 17, 9420, 17345, 16, 5745, 8654, 2651, 21189, 1935, 2014, 16350, 28959, 17118, 16137, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 10089, 18697, 17, 3189, 3418, 13975, 16, 2154, 24032, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 13678, 1942, 6628, 16239, 1022, 2626, 6586, 6404, 1922, 6445, 3299, 3771, 18, 2052, 3418, 4088, 1966, 1920, 6804, 4594, 1922, 1920, 7417, 1027, 12935, 2051, 7417, 5735, 1958, 25, 11, 2678, 25816, 16, 1920, 22367, 23941, 1030, 24321, 10916, 1021, 1958, 4587, 14451, 27539, 11245, 2409, 7827, 16, 1930, 10089, 17, 10444, 18697, 1036, 1958, 3146, 8490, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 10089, 17, 8490, 18697, 5903, 6964, 3962, 3418, 1988, 4088, 1966, 43, 4346, 4594, 1927, 1920, 19732, 28959, 17118, 10089, 10444, 17, 8490, 18697, 18, 2176, 14162, 1956, 1920, 6804, 5903, 6964, 4857, 1942, 2386, 1925, 4595, 1028, 17, 4666, 1028, 16798, 3414, 1958, 1920, 6404, 1927, 15778, 2037, 7897, 10089, 18, 2176, 22970, 2037, 9548, 2102, 17843, 2457, 7088, 8565, 1035, 1930, 1977, 5947, 1956, 20709, 11569, 10089, 4587, 18, 3], "output": "MMIINNDIINQGLEGQSKILESIKNHFKDLKKWYGVQVKSGRKTNDSNEKQEHQQTSEDEKLKKCQYVVPTKSASLWSLCTIKKYKELRKFTTAIQDGDGSVTYYQLSKPLMDCTLDQIHLCFQLIIDLMIQQSSTPFLYLKAFEFEIFGKDSDEDGGG", "metadata": {"id": "A0A8J4Q5F5", "cluster": 20475862, "interpro_all": ["IPR018593", "IPR011856", "IPR036167"], "interpro_used": ["IPR036167", "IPR011856", "IPR018593"], "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: It is part of the Flagellar basal body-associated protein FliL family, which controls the rotational direction of the flagella during chemotaxis. It functions as a cytoplasmic membrane protein associated with the basal body. It has been detected in Mucispirillum schaedleri ASF457 and corresponds to UniProt keyword Cell membrane, Flagellar rotation, 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, 24154, 5342, 3362, 17, 2458, 2213, 2300, 1970, 3416, 16, 2154, 3562, 1920, 16577, 4924, 1927, 1920, 26538, 2409, 16884, 18, 2176, 4088, 1966, 43, 6823, 3260, 2213, 2458, 1956, 1920, 5342, 3362, 18, 2176, 2258, 2252, 3330, 1922, 3422, 1937, 10984, 3027, 11560, 1989, 26121, 1919, 3823, 1033, 1966, 10432, 5071, 1930, 8852, 1942, 20709, 11121, 2538, 2024, 3260, 16, 24154, 8891, 16, 1930, 9117, 7864, 18, 3], "output": "MSKERKDTTYKKLVKLVIWLLVLTAAALIIWKLYGRVDLKRTNFSKAVVKKQEPAIYDMYRVRSEKKNNKLYYVRIKNIYCDAYKIRETDTPRYFKIDIVFEAHNKKDAKAIENITAQTVNEIRNIMKNYPVTDIDRPSIMAYIKRDLKAKMNNVLKTDAVVTIYFESFLCG", "metadata": {"id": "V2Q0L7", "cluster": 20987926, "interpro_all": ["IPR005503"], "interpro_used": ["IPR005503"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a polypeptide chain with the following function: The protein falls within the S-2-haloalkanoic acid dehalogenase family, which catalyzes the hydrolytic dehalogenation of short-chain (S)-2-haloalkanoic acids to yield the corresponding (R)-2-hydroxyalkanoic acids with inversion of configuration. As members of the HAD-like hydrolase superfamily, these enzymes specifically target C2-C4 substrates, such as 2-chloropropionic acid, to facilitate the metabolism of halogenated compounds. Additionally, the protein is associated with 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. Also, the protein is associated with 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 originates from Fictibacillus phosphorivorans. 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, 12182, 2651, 1920, 61, 17, 22, 17, 23226, 5135, 29860, 2687, 2028, 7289, 2404, 2051, 3416, 16, 2154, 17097, 1920, 26702, 2028, 7289, 2404, 1943, 1927, 3662, 17, 4659, 12, 61, 13, 17, 22, 17, 23226, 5135, 29860, 4576, 1942, 4307, 1920, 3980, 12, 60, 13, 17, 22, 17, 8275, 5135, 29860, 4576, 1956, 14825, 1927, 9674, 18, 1966, 4678, 1927, 1920, 2430, 17, 3189, 20748, 13975, 16, 2144, 5038, 4475, 2758, 8453, 17, 10872, 6249, 16, 2427, 1966, 22, 17, 10107, 20194, 14207, 2687, 16, 1942, 6628, 1920, 4714, 1927, 24778, 1981, 4300, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 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, 2222, 16, 1920, 2213, 1977, 2458, 1956, 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, 22970, 2037, 17662, 4397, 13707, 5277, 1036, 3421, 2068, 8846, 3355, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MKAYVYDAYGTLFDVHSVTEKAELHFRGHGKAISEEWRKKQVEYFMLHQLTRTYLPFSEITRNALSYTLKKFSLQCNEEALDSLMDSYLELQVYEEVPKTLHKLQQNKVKQVIFSNGTYNMLKPLVKKRELTNVIDLLSIEDIEQFKPAPAAYQYVHETLAVNREEVLFMSSNFWDITGAAAYGFKTAWVNRGNLPLDVLGIIPHYIFSSLRDLLNERELRS", "metadata": {"id": "A0A161IJV3", "cluster": 21054978, "interpro_all": ["IPR006328", "IPR036412", "IPR006439", "IPR023214", "IPR023198", "IPR051540"], "interpro_used": ["IPR051540", "IPR006439", "IPR023214"], "interpro_unused": ["IPR006328", "IPR023198", "IPR036412"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein includes a Recombinase conserved site that catalyzes site-specific DNA rearrangements, such as inversion, cointegration, or excision, in prokaryotic organisms. It functions through a strand exchange mechanism where a catalytic residue forms a transient phospho-protein linkage to cleave and re-ligate the backbone without requiring high-energy cofactors. This site is characteristic of the resolvase family, which typically couples this catalytic domain with a C-terminal helix-turn-helix DNA-binding region. Also, the protein possesses a Resolvase, N-terminal catalytic domain that mediates site-specific recombination in prokaryotes through a strand exchange mechanism. This domain functions as a dimerization interface and contains a conserved active site serine that forms a transient covalent phosphoprotein linkage during DNA cleavage and re-ligation. Moreover, the protein features a DNA-binding recombinase domain that functions as a structural module within the C-terminal region of large serine recombinases (LSRs) to coordinate DNA binding and rearrangement activities. This moderately conserved domain adopts a mixed \u03b1/\u03b2 fold consisting of a four-stranded \u03b2-sheet embedded in a core four-helix bundle. It is produced by Arenibacter troitsensis and is linked to UniProt keywords DNA integration and DNA recombination.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 5921, 43, 21366, 5305, 3200, 1988, 17097, 3200, 17, 2487, 2678, 13955, 16, 2427, 1966, 14825, 16, 24073, 4905, 6541, 5524, 1929, 16, 2014, 10940, 16, 1922, 21545, 7373, 18, 2176, 4088, 2596, 43, 5984, 6818, 2856, 2597, 43, 6804, 6181, 4952, 43, 6809, 8078, 17, 2213, 8611, 1942, 21252, 1930, 1964, 17, 3650, 2010, 1920, 10787, 2979, 8887, 2149, 17, 3844, 21362, 18, 2052, 3200, 1977, 6293, 1927, 1920, 24321, 10916, 1021, 3416, 16, 2154, 5745, 14002, 2052, 6804, 3418, 1956, 43, 45, 17, 4262, 7864, 17, 5165, 17, 7864, 2678, 17, 2743, 3031, 18, 2222, 16, 1920, 2213, 14465, 43, 24321, 10916, 1021, 16, 56, 17, 4262, 6804, 3418, 1988, 10412, 3200, 17, 2487, 7827, 1922, 28149, 2596, 43, 5984, 6818, 2856, 18, 2052, 3418, 4088, 1966, 43, 13640, 6854, 1930, 5461, 43, 5305, 3500, 3200, 8468, 1988, 4952, 43, 6809, 13577, 8078, 22163, 8611, 2409, 2678, 6404, 1930, 1964, 17, 11102, 18, 3950, 16, 1920, 2213, 4075, 43, 2678, 17, 2743, 21366, 3418, 1988, 4088, 1966, 43, 4346, 9059, 2651, 1920, 45, 17, 4262, 3031, 1927, 3103, 8468, 21366, 1036, 12, 6639, 5675, 13, 1942, 11865, 2678, 2743, 1930, 14154, 4209, 18, 2052, 11224, 5305, 3418, 24032, 43, 4985, 160, 19, 161, 3728, 7600, 1927, 43, 3006, 17, 10338, 161, 17, 11130, 8222, 1922, 43, 4728, 3006, 17, 7864, 14142, 18, 2176, 1977, 4152, 2007, 28225, 26073, 2341, 1915, 12730, 2664, 8134, 1930, 1977, 4624, 1942, 20709, 11569, 2678, 7122, 1930, 2678, 7827, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MKTVAYLRVSTEDQSLERQYEDIEKFATTNADDREGFSKLERYLELNEDIKHILVLEISRLGRKNNDIQNIVSTLDKDGKRSATSDIMISVMGAMAAGESRLLKIIGYKKADDGTPMIDEDEAPIIRRIFELSADGLMHMSTLGGIIRNTFHKGERKYNDLILPVEPINKFGSRTKVNTNIVEGRIKCHCGEPMYQKVVPSGRMDSFVCKDLSCERHAKKSRDAKYRKDIGLKMSSHQAQINGDLSDDDYKYQLQVIKQNLLKINVDNIQLNEDINLLGKDIVKYVEIDKDSVIINVFGRWGYDLFKPNIEDEVIEIMADTYGDENYDDKLDDYMNELDNRKNLQLVKIFEDKVSGSKERYNEKGICIHFDDLSISARVKSGKMSRARKNQAFGSGMRGISAIIESEFNRRVSMEIWQKANDSMDSRKNSVNRPWLFRMVKKVVLNNREEEKLNARKWKFQDAWGDNDLNSEIKHFSDDLELFKNEISVKLGWEARKPESERYLNEKLPLRHP", "metadata": {"id": "A0A1X7J9G6", "cluster": 24482956, "interpro_all": ["IPR038109", "IPR011109", "IPR006118", "IPR006119", "IPR036162", "IPR050639"], "interpro_used": ["IPR006118", "IPR006119", "IPR011109"], "interpro_unused": ["IPR036162", "IPR050639", "IPR038109"]}, "task_type": "infilling"} {"instruction": "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. Additionally, the protein is associated with the Multifunctional Ankyrin Repeat Domain-Containing Protein family, which comprises proteins with diverse roles in translational fidelity, neurotransmitter release, ubiquitination, and membrane stabilization. These members function through various mechanisms, including preventing amino acid misactivation, forming membrane pores, regulating the ubiquitin-proteasome system, and acting as regulatory subunits for protein phosphatases. Moreover, the protein is classified under 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. It originates from Neocallimastix californiae and exhibits UniProt keyword tags ANK repeat.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 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, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 20136, 28336, 6865, 3418, 17, 3165, 2213, 3416, 16, 2154, 12936, 2697, 1956, 6445, 5456, 1922, 8414, 14013, 16, 15223, 4012, 16, 11758, 16, 1930, 3260, 10281, 18, 2144, 4678, 2347, 2596, 3425, 3531, 16, 2710, 8444, 3835, 2687, 5682, 6042, 16, 7402, 3260, 14711, 16, 6773, 1920, 6526, 17, 9993, 2433, 16, 1930, 8290, 1966, 4948, 6991, 1958, 2213, 19131, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 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, 2176, 22970, 2037, 11724, 5657, 7265, 2197, 2416, 10191, 1021, 1930, 9826, 20709, 11121, 2538, 14392, 9808, 6865, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MKEYFDNILFDLECFGIIFEISKSRSYQDFENKIKAFEKQFKCYKYRYYLFELCLRHGFNINASFDENFEASKFSNINPKVRSNLLFSLFNCRSKGLFTEPDFSMNFHSDNTVDELSVIEVIILDSILRVESFFKSNIYQTIINEKRREKYKKRKKYIIFEEIQKKHYYGLKTLLASDNFNINIKNEALETPLMYAIRYCIENRGTTLLHIACQYNNYRIIPKIVTDKAINFKDRNGLAKVLLSNTKFDINTNLEGNNDGERPLIYMLSKEIDNSPIYEVKNSSFLKVIMKNGINVFKSKKNIPIKQILIFSIEHDLFELTDALLNLLVKSGKINFNVTDCGGTTPLIYAMKNVEVLPEIVDILLDHNEDKDQYKNNKYIPKLITEKNVNMTDNNNKNTPLMMAIKKGNFDGAMELLSNEIKSNVNLEEERLFQFLLKNGAFIDQTYFTSEWISKIIDNESLINAILKEGFYLSHDDNHDDHNNLINLARCLLEHCHILNEKGKNGKPCIFYVIEQVDDENFFNLLLNSSKINKLLLFHYVNTYEKEKYRQRIKKIIDFGFDRLIQSLSQCDVFDYLTIKGKSGTRNDTGKEKPTKNDSVKKHQTEVKSNNEKESREYKEEHVNPMDNVKNEIKESETLITPDISMNYEKEAKEEEETDESNNTNYEIMTSEEDKIKKEMITSFKIKKVSITLDENNLKNDNIIYEEENNINNENNETLLNLEEGSLRNIPEDYKISAIPINASSNEYTILGMACIIGNIQILKSLIRLNIYDINRGNGADPNIKDSYDNTPLVYMLKYSIVNEEIYRLLIRHNSYIDKVRFFIQKKVLINEGIMGKIRPNIIKEPLLFAIDLRNTPLLFAIENNNVEIVKLLIEKGANIFQCNCKGIYPLNLAQNNNNQEILSLLQIHSQNEFNYDYGNDYRNDYRNDYRNDYGNEYGNEYENEYGNEYGNEYGNENEYGNEYGNEYVNEYGNEYGNEFGNNYGDDYNYMEYVYKEVLKDIKIQEHLKKPNIDLNQTCGKYQFSPLMTLVFEEDFTNAKLLIERGANVNGNKEFYTLLLNNGAFVDKDLFRIPKFLAQIYNNFDFIQLILKDRFTIYDKEENTFFAILLIKNHANLDEEDDSHNTPIFYAIKYNNAEIVKSLIIHHADLNKRNALGQDDILKKGNEIIDQRTNYNDLIFQCIDNSSPKDALELINRHKINLNYESPSGLTISHCVDIHSVNRNGLSPLKYAQQKGNKEILKTLLEQSLPYNEHREQSIATLKDNIERINAKPTLSNIPQNLIVNHKLFDEINEENKKYEGMNVMTNKNIFNNSYNTNVLYDRVFIEFFLQKYFVIKLKKEDPPKQINQPLHFIIDQEEEQSLVHYVIIEKKDSKALSILLAYRDDLFKRDDKGRTPLILGVKSKNFHINEKDSQGETALFYAVRNKDLEMIKFLIEKGINVETKNNKEENVSNSENYTLLDYAIQKKHKKIIQLLKSHEITDSHRDKGSSIIYHAVEFNLPYNRIEYFLEERVQFLITNGIDVNFRYKANKQPNFKQCLSKLDKIRSISDQESPEIQDLLLDSSSEKDWITPLMIAIKNGHYECLLIKHGAYIKYNEFKQKSLLLSMEYYDQIDEVDENNTPCLFYAINSKKLDYLITDTDHDGFTALHMACSDKNNDTPLLYMIKNGVDVHEIIYVNTPFIFSIEFEECDAHGKYPLKYSIELHKKDMTIAPIYRDFKKESNSNQNEVIHEEIIDFKPNNRNNTNNIDNENKEKMIISDENGNNTYTNTYYDDNNNNLIITSEKHNITLGERQLTPLMLSIIHEKYECAKFLIFDPQFMEKIINNPCFIQLLEFIKSLIQGGVNINEYFSNIDVNNSSNVDPIVFNNDYYGNEYGNKYGNEYRNKYGNEYGEDTNKSILHSACIINNIDTRTTFIRDYFNNTPLIYLLKYNRKIMKIKYPLIFAIENNFVYEYALNHSTKIYPLLYAIYKKNIKFVDFLDSEYGQLLSHEINLEHFFTAIYIVNYLVIHSDVYDRNFFEFLINNGAYFNLKKYKYLKHLLSTNDYKDKIKEIVGQLLEKGLFPAIKSGKVFILDYLLGKVEDKTT", "metadata": {"id": "A0A1Y2AET3", "cluster": 26330033, "interpro_all": ["IPR002110", "IPR036770", "IPR051165"], "interpro_used": ["IPR002110", "IPR051165", "IPR036770"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein belongs to 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. In addition, the protein should have 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. It is expressed in Oesophagostomum dentatum (Nodular worm).", "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, 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, 1922, 2459, 16, 1920, 2213, 3066, 2162, 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, 2176, 1977, 3198, 1922, 29521, 28009, 1989, 12547, 9576, 12, 21106, 11055, 13, 18, 3], "output": "YCTETLELDVKKDCQWGFELVLPDGNLQLQCPSKDEMSKWMRLVNEALNSQGDDDAAACMVMVTEAELVVAQEGEKCYTDGFIRTLVSFPLSDIREGWILRTDTHMVLVLHVDAMHHWFFFRSEAELDRIAKTLSVYPISLVEIDQHCQEKAMAFLLNQCRPYARFMA", "metadata": {"id": "A0A0B1RQZ6", "cluster": 28250963, "interpro_all": ["IPR011993", "IPR001849"], "interpro_used": ["IPR011993", "IPR001849"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to this functional description: The protein includes a GntR C-terminal domain that serves as the effector-binding and oligomerization module in bacterial transcriptional regulators. It binds diverse ligand molecules to modulate the activity of the N-terminal DNA-binding domain, thereby controlling the expression of genes involved in processes such as sugar biosynthesis. Also, the protein is assigned to 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 contains 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. It is found in Leptolyngbya sp and is connected to UniProt keyword Transcription regulation.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 5921, 43, 9005, 1997, 45, 17, 4262, 3418, 1988, 10634, 1966, 1920, 7917, 17, 2743, 1930, 17371, 9059, 1922, 4543, 5224, 9098, 18, 2176, 6876, 6445, 5207, 4206, 1942, 8480, 1920, 2455, 1927, 1920, 56, 17, 4262, 2678, 17, 2743, 3418, 16, 6113, 7138, 1920, 2294, 1927, 2628, 3286, 1922, 4028, 2427, 1966, 9523, 8132, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 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, 5461, 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, 2176, 1977, 2435, 1922, 16976, 26558, 2029, 4864, 1019, 2056, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3213, 3640, 18, 3], "output": "MALSSQPLQRNQSLHEQTYQALRTAILSGDLAAGSRLVETQLADLLEVSRTPVRESIRQLQRENLITTDATGAVRVAMLSVVDAMQLYDCRIALEQLSVSEACRNVTNEQLERLDQAIVQAEKAFGQVPNQLTSFQLLHMDYQFHRLLAESSENAWLVQILDQVFDKMALLRLRTMQHNPGVLEIRGEHRRIYEAVRDRNPIAATQAIQYHLISSKERVIQEIKALEPRSLDSADSS", "metadata": {"id": "A0A2W7AHB4", "cluster": 2929156, "interpro_all": ["IPR011711", "IPR008920", "IPR000524", "IPR036388", "IPR036390"], "interpro_used": ["IPR011711", "IPR036388", "IPR000524"], "interpro_unused": ["IPR036390", "IPR008920"]}, "task_type": "autoregressive"} {"instruction": "The protein falls within the SOSS complex subunit B family, which functions as a sensor of single-stranded DNA, particularly polypyrimidines, within the SOSS complex to promote the DNA damage response. Members of this family are essential for homologous recombination-dependent repair of double-strand breaks, ATM-dependent signaling, and activation of the G2/M checkpoint to maintain genomic stability. Furthermore, the protein is assigned 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. In addition, the protein should have a Single-stranded DNA binding protein Ssb-like, OB fold domain that recognizes and binds single-stranded DNA via a conserved OB fold structure, typically coupled to a flexible C-terminal tail. Present in archaeal Ssb proteins and eukaryotic homologues like the SOSS complex subunits, it utilizes aromatic base-stacking interactions to facilitate specific DNA recognition. It has been characterized in Candidatus Methanomethylophilaceae archaeon.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 17668, 1036, 2796, 5903, 44, 3416, 16, 2154, 4088, 1966, 43, 6443, 1927, 2957, 17, 10338, 2678, 16, 4443, 6240, 3553, 29899, 1036, 16, 2651, 1920, 17668, 1036, 2796, 1942, 5527, 1920, 2678, 4293, 2644, 18, 4678, 1927, 2052, 3416, 2032, 4415, 1958, 8725, 7827, 17, 3100, 5059, 1927, 4825, 17, 5984, 13065, 16, 7513, 17, 3100, 3197, 16, 1930, 2936, 1927, 1920, 9616, 19, 55, 11714, 1942, 6698, 4935, 5057, 18, 3677, 16, 1920, 2213, 1977, 6304, 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, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 2957, 17, 10338, 2678, 2743, 2213, 22228, 17, 3189, 16, 2384, 3728, 3418, 1988, 16197, 1930, 6876, 2957, 17, 10338, 2678, 3454, 43, 5305, 2384, 3728, 3170, 16, 5745, 6416, 1942, 43, 9964, 45, 17, 4262, 5281, 18, 2481, 1922, 22367, 22228, 2697, 1930, 10825, 18541, 3189, 1920, 17668, 1036, 2796, 6991, 16, 2176, 18127, 10761, 5170, 17, 19058, 3719, 1942, 6628, 2487, 2678, 5708, 18, 2176, 2258, 2252, 4378, 1922, 14550, 1031, 1957, 17348, 18403, 7766, 1972, 3336, 13470, 1916, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MNEEQLTPIVEELTKVLDGKASREEIEEQVNTYANVYKMGPTIDTSFVTADHVSKKIAELRGNENRVDILAKVVFAENRTATIDGENCSLEKGSVYRFRNAYTKLWNDKVQINIGNNPGSAPAGNGPANGMKMKIADLKGSEPNVDLEVKAIAAERRTTGTAQFTVWEARGANVEEGKSYTFLSAYTKLWNDQVQVNIGNKGAVEPVEDPRRIKEAILRKHGKGSQRKLVSGILGDETGTASFTVWGTIAKEDVQIDVVNIRGETKEIISGTIGDE", "metadata": {"id": "A0A843IU40", "cluster": 3277115, "interpro_all": ["IPR012340", "IPR051231", "IPR048970"], "interpro_used": ["IPR051231", "IPR012340", "IPR048970"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: The protein should feature a Large cysteine-rich periplasmic protein OmcB-like, DUF11 domain that adopts an Ig-like fold to maintain the structural integrity of the outer membrane or cell wall surface in bacteria and archaea. This cysteine-rich module is implicated in porin formation and pathogenicity, particularly in organisms lacking a peptidoglycan layer, and may utilize intramolecular isopeptide bonds for added stability. Additionally, the protein incorporates a Domain of unknown function DUF6701 domain that represents an uncharacterised region found in a wide range of bacterial cell surface proteins. It is present in Massilia sp. CCM 9029 and is described by UniProt keywords Signal.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 30, 1920, 2213, 3066, 5961, 43, 3103, 8666, 17, 5536, 24334, 2213, 7254, 18598, 17, 3189, 16, 4855, 5739, 1009, 3418, 1988, 24032, 1925, 7021, 17, 3189, 3728, 1942, 6698, 1920, 4346, 7996, 1927, 1920, 7642, 3260, 2014, 2024, 4821, 3154, 1922, 4802, 1930, 21501, 18, 2052, 8666, 17, 5536, 9059, 1977, 6835, 1922, 4572, 1921, 3337, 1930, 15903, 16, 4443, 1922, 7373, 7046, 43, 24183, 4757, 16, 1930, 2278, 12561, 18083, 10301, 8253, 9031, 1958, 4057, 5057, 18, 4950, 16, 1920, 2213, 19683, 43, 3418, 1927, 5435, 2347, 4855, 17136, 4618, 1009, 3418, 1988, 4972, 1925, 23229, 3495, 3031, 2435, 1922, 43, 4743, 3109, 1927, 4543, 2024, 3154, 2697, 18, 2176, 1977, 2481, 1922, 3411, 25600, 2056, 18, 25993, 3865, 4539, 1930, 1977, 2910, 2007, 20709, 11569, 2733, 18, 3], "output": "MTQRIDRFWRAALAVGCGAGLLLASLPARADTPIALFKSYAGRLNFTGTQKTMRTGANGSAPCAITNNPLVARLAGIPATAKIVSAHLYWAGSSSTPDYGVSMDGVALSAPANRRFTTATIGYNYFSGAVDVTAQVTAKRNGDYTFSNLTITNGTPYCAVEGVVGGFSLVAIYSDPNEAFRVLNLYEGFQYIRTFGTDNIKVSLNLSNFRTPSPLGSATGRIAHVTWEGDSSLSGGGENLKFNGAEMVDGANPTGNQFNSTSNIGGTVDNASYGIDFDSYLLASPKLFAGQTTATMLYESGQDMVLLNAEIVSVPNVDVADLSLAIALTGTPARGNNVNLVHTVTNQGPLPDAGPITVKHTLANGLTYLSSSGTGWSCGASGQVVTCTSAKSLEVGESAPALSITARIDLTAPNSMTSSATASGLQFDNDMGNNSASNTITFSSARYVFTDNPCEVGVAFGPPGKCNLLSVPTLQAGVQSPVYVTFVDNNFKPAVPPSTTPTLQFSFRCVNPTTGAGGVARLKGVALKACISSTALQSATQWQGIAMAFATGSPSSALMQFVYGDVGMIELFLSETATALALTSTSGQFVVRPYKFALSTPLSNPAGTVAADDMTADIGRFWKAGAGFTLNVVAQAADSTPTPNFGKETTPQEVELLTTATIDSTNYAIPGDTNSETLPFAEMQTGPGDPVRKVEGSFGTFGAGAATGNNFTFAEVGIVNVNVHMKNSNYLGVEDVASDGVALGRFYPDHFRTTVPIVITCAAPHPLNCQNIGLHYSKQPIQTIVTAYNAAGEITRFYQGKFVKSPKLLPYTALGGLTQSPSGTLTPSPIANAATVFVQGSGTAWPSFDFAAASMAPVDIYLRASDADLVTSGRSGLSVEGATKIVRGRLLIENAFGSELLALPVVMRAQYWTGTSATDGRWADSRTDSISIVATPVPASGVVTFPHSVTAAQLTLSYSQCLKSMAACSAATPFPDPKTTLASSSMVNGLVKFKFAATNKTGSVNVSVGQPVWLPPAAGKLTFGVYKSTPLIYIREVF", "metadata": {"id": "A0AA90Q8S0", "cluster": 8197123, "interpro_all": ["IPR046524", "IPR001434"], "interpro_used": ["IPR001434", "IPR046524"], "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 falls within the Undecaprenyl-diphosphatase UppP family, which comprises small, highly hydrophobic proteins that function as undecaprenyl pyrophosphate phosphatases (EC 3.6.1.27). Originally identified as BacA, this enzyme confers resistance to bacitracin, particularly when over-expressed in *Escherichia coli*. It has been characterized in Gammaproteobacteria bacterium and is annotated with UniProt keywords Cell wall biogenesis/degradation, Transmembrane, 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, 12182, 2651, 1920, 3075, 19384, 20367, 2199, 17, 11791, 2609, 7234, 2353, 9434, 3416, 16, 2154, 12936, 2858, 16, 3626, 7919, 2697, 1988, 2347, 1966, 3075, 19384, 20367, 2199, 24937, 19131, 12, 3270, 23, 18, 26, 18, 21, 18, 3225, 13, 18, 10398, 2899, 1966, 8175, 1019, 16, 2052, 4113, 16556, 3554, 1942, 8175, 4250, 9151, 16, 4443, 2469, 2338, 17, 3198, 1922, 14, 10210, 5178, 14, 18, 2176, 2258, 2252, 4378, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 2024, 4821, 13008, 19, 4877, 16, 9117, 16, 1930, 20748, 18, 3], "output": "MSVLHIFVLAVIQGITEFLPISSSGHLALVPWFVNWPDQGLVFDIAVHVGTLMAVMIYFWXDLXSIIGDMLGVRNNTNSYGSXLAKRILLTLPPVFIAGGIIAWLNPNFIRSIEIIAITTPLFGVFLWMSDKYNVSSKRIEKLPFGEVIFIGLAQAVAVIPGTSRSGITISTARMMGVERTDAARFSMLISIPVIIGAASVAGYKLGNSEYTFSIAEAGLAVGISFITALLSIAVLMKXVKXIHFGPFAIYRIILGAILLXWIYVYDSVGLELSP", "metadata": {"id": "A0A2E4GGD3", "cluster": 10785181, "interpro_all": ["IPR003824"], "interpro_used": ["IPR003824"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein belongs to the Two-component response regulator ARR-like family, which functions as a class of MYB-type transcription factors central to the transcriptional activation of cytokinin-responsive genes in plants. These proteins act as terminal effectors in a phosphorelay cascade involving histidine kinase receptors and phosphotransfer proteins to modulate developmental processes such as shoot organogenesis and leaf senescence. Members are categorized into type-A or type-B groups, characterized by a conserved receiver domain and, in type-B variants, a C-terminal DNA-binding domain. Also, 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. Furthermore, the protein incorporates a Plant Myb domain that functions as a DNA-binding module restricted to plant proteins. It is frequently found in association with response regulator domains and is related to the Myb-like DNA-binding domain. It is present in Buddleja alternifolia and exhibits UniProt keyword tags Nucleus, Transcription regulation, and Two-component regulatory system.\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, 14440, 1942, 1920, 2288, 17, 4594, 2644, 7888, 3853, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 2921, 1927, 16851, 17, 2601, 3213, 2790, 4101, 1942, 1920, 5224, 2936, 1927, 4192, 15020, 17, 8487, 2628, 1922, 4793, 18, 2144, 2697, 4033, 1966, 4262, 13066, 1922, 43, 3421, 15208, 1012, 9861, 5884, 13873, 4016, 4086, 1930, 8078, 17204, 2697, 1942, 8480, 5878, 4028, 2427, 1966, 16652, 3090, 3761, 1930, 6998, 10805, 18, 4678, 2032, 10234, 2460, 2601, 17, 43, 2014, 2601, 17, 44, 2671, 16, 4378, 2007, 43, 5305, 12608, 3418, 1930, 16, 1922, 2601, 17, 44, 4936, 16, 43, 45, 17, 4262, 2678, 17, 2743, 3418, 18, 2222, 16, 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, 3677, 16, 1920, 2213, 19683, 43, 4496, 16851, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 9059, 6715, 1942, 4496, 2697, 18, 2176, 1977, 5467, 2435, 1922, 3279, 1956, 2644, 7888, 4682, 1930, 1977, 2712, 1942, 1920, 16851, 17, 3189, 2678, 17, 2743, 3418, 18, 2176, 1977, 2481, 1922, 8344, 5395, 14174, 4070, 27325, 1930, 9826, 20709, 11121, 2538, 14392, 5607, 16, 3213, 3640, 16, 1930, 2288, 17, 4594, 4948, 2433, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MSVEEIRGENENNEQFPAGLRVLAVDDDLICLKVLEKMLRNCHYNVTTDMFDLVISEVHMPDVDGFRLLELVGLEMDLPVILLSANSDTNNVMKAVTHGACDYLPKKFNDQGHAHQACGEGRGSPEPGNTDHNGKFNRKRKDEEDESEDNGNESDPGTQLGIEKAVPKRILDLMNDDRLTRESKYRLYLKRNSSVAATPQANMIVSPFMRMGSLVGLSPFTTGGMLGRLNSPANVNLRNLTPSALVQPNRPQNLTNSIPALGKVHLQQNKGVSGIPNFNTMDDSRMFITPATQKKPLVVWSVELHKKFVAAVNQLGIEKAENVASHLQAINSPSLHKYLLYLKRISSVAATQQANMVASPFMDTSSLDGLGDFRTLAGVGRLGILNDKAEDLRNSVGSPIQETRNTNPKKYVVSRHENKAGCAWNNPLGSWYLALCSSFRFIQELIEGTGSCGGVQSDGVDMDRELVVYDRAPYFVSDLLLRDVSVSLLTSQARTALKMLRENKVKPVRLEVLRNIWQHVLRRKKFDPKNQKKPRVVWSIELHRKFVAAVNDGLGDFQTLAGSGQLRNPLFSPTSQNPSLFQGMPLGLELDQVPKTILHLMNDDRLTQNVALSPFTTDGILSKLNSPAKTVEKGKNLTLPGFRAHQLQYFQPPFIRR", "metadata": {"id": "A0AAV6WBM4", "cluster": 10976714, "interpro_all": ["IPR045279", "IPR011006", "IPR009057", "IPR006447", "IPR001789"], "interpro_used": ["IPR045279", "IPR001789", "IPR006447"], "interpro_unused": ["IPR009057", "IPR011006"]}, "task_type": "infilling"} {"instruction": "The protein is included in the Major facilitator, sugar transporter-like family, which comprises a subfamily of the major facilitator superfamily responsible for the binding and transport of various carbohydrates, organic alcohols, and acids. Found in a wide range of prokaryotic and eukaryotic organisms, most members of this family specifically catalyze the transport of sugars across the cell membrane. Additionally, the protein is included in 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. In addition, the protein includes a Major facilitator superfamily domain that functions as a secondary active transporter, utilizing a twelve-transmembrane helix topology to move small solutes across membranes via uniport, symport, or antiport mechanisms. Driven by chemiosmotic ion gradients rather than ATP hydrolysis, this domain mediates the uptake or efflux of a diverse array of substrates, including sugars, drugs, metabolites, and ions. It is present in Stylonychia lemnae (Ciliate). Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 3044, 29543, 16, 9523, 9054, 17, 3189, 3416, 16, 2154, 12936, 43, 16227, 1927, 1920, 3044, 29543, 13975, 5061, 1958, 1920, 2743, 1930, 4860, 1927, 3425, 16282, 16, 6805, 21773, 16, 1930, 4576, 18, 2435, 1922, 43, 4743, 3109, 1927, 21545, 1930, 10825, 7373, 16, 2501, 4678, 1927, 2052, 3416, 4475, 18170, 1920, 4860, 1927, 15592, 3436, 1920, 2024, 3260, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 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, 1922, 2459, 16, 1920, 2213, 5921, 43, 3044, 29543, 13975, 3418, 1988, 4088, 1966, 43, 4067, 3500, 9054, 16, 10232, 43, 12367, 17, 9117, 7864, 13678, 1942, 6532, 2858, 27993, 3436, 5726, 3454, 15943, 2718, 16, 29148, 2718, 16, 2014, 2246, 2272, 3531, 18, 6446, 2007, 2975, 14356, 12492, 2002, 4755, 12741, 4356, 2254, 4498, 9128, 16, 2052, 3418, 10412, 1920, 5047, 2014, 11247, 1927, 43, 6445, 6472, 1927, 6249, 16, 2710, 15592, 16, 4195, 16, 6926, 16, 1930, 6982, 18, 2176, 1977, 2481, 1922, 26435, 14186, 19519, 1019, 15551, 26243, 12, 15714, 2057, 13, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MKDGNEDRNATIDSDRNDTRQQCLDDFDNLTRGLTLEQAYAKIGGFTYFHYWASSLFVWGFTTGGLFFFALSMLEKTPRYLCFNDDGTTYECQADKTFCKDQSIKYKIDWDNDSSLHNWVETLDLTCESSAKIGLIGSIYFVGWAVAAIFLPRLSDLFGRKWVYFYSMLFHGLVYLGLILSHNLNLTIVLMGFFGFCSLGRASVGYLYMQELTPIKQQTIIGTILSITGGLVTVFIALYFLYVSKHWEGFQIFGCATNFLIVVSIPFLPESPKYLISKNRYEDARDSLKVIAYFNRHSGEVNFKFDTEVHNELFNSKIDLNYSVDASIASPGKLTQDSHERVKFVQSSILSSNAGCNQLQGQSVIDDKLQPHIHKGELVKEEQQLNGSLKDLIKIRRHMINLLIMVIIWIASSFSYYLINFQLKYIKGDFFVNTITASLTEVPAYILSGILYEKLGIRIVLVSCFIISLVGGIFLLIFSNNTNVIPVFILLARFGVSATFNICYLANATIFPTIFAGTAFGICNVFAKMATIISPMLAEVDAPVPMTVFCIVSGVATVLSLFIQTAPKKLQIHQRLYKGKITVNQKIVKQKIECHSNCS", "metadata": {"id": "A0A077ZUM3", "cluster": 11096588, "interpro_all": ["IPR020846", "IPR005828", "IPR036259"], "interpro_used": ["IPR005828", "IPR036259", "IPR020846"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein is grouped in the Kelch-type beta-propeller superfamily, which adopts a six-bladed beta-propeller fold composed of four-stranded antiparallel beta-sheets. This structural scaffold supports diverse biological roles, ranging from cytoskeletal actin cross-linking to enzymatic oxidoreductase activity against substrates like D-galactose. It occurs in Blepharisma stoltei.\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, 16080, 2072, 17, 2601, 4666, 17, 5062, 13728, 13975, 16, 2154, 24032, 43, 3798, 17, 22707, 1007, 4666, 17, 5062, 13728, 3728, 7179, 1927, 3006, 17, 10338, 28892, 4666, 17, 14685, 18, 2052, 4346, 7281, 7825, 6445, 3933, 5456, 16, 6485, 2037, 14787, 4718, 3567, 17, 9486, 1942, 8145, 27388, 2455, 3316, 6249, 3189, 46, 17, 15996, 18, 2176, 5110, 1922, 6189, 4151, 13950, 3368, 13046, 19174, 14209, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MCSNHLTPHCLSSYGHNLIVIKNPEPPKLDESSKRIIVNKIGVLIAKTTKHINEMKTNMGLLIEENRISTEKYREIVNFICRQSDCRDLMQNTNFPFYDSVYQEIKKFENFIGNTEQREPSYIEKIPQLSMKTELGSEQLKQENKKLLEKIRQLEERINRKSSDINELHRDLAVFKMKFRDFGIHKEKEDKRLNEEIEKLQKEVYLKDKDNQSLKEKLGKIEEELKLRNSKHIDKYKKSVDTKSWDKEVVEPPRKSNKANTTDSWDESNEKIKKLTIPQLAGDATESWDGKDENSKQPKDLKKAEDPWSEADDSKRHSHSRSKEKSHVTEIRDAWNEAEASRHSHSRSKEKSHTTLSWDRKYESPKKPKSHTTSSWDRKYETPKKPMDPKAAEDAWNEAEASQKHSSSRENPNELKDSKRDSHSRSREKSHTTDSWGSKNEEAKKPTNSRWTRDTDVEIPKKHSDLNSNNEWKCKSIFPGTKTAYFREKSKILRTKNLNELKETEIVTTIFCYGNLYNGHATGITFIIEKDFSLIMRDYGRPCFHTSVCYYKGSVYAFGGSNDDGKTKEVSNFCTTLAYEDKIYIAGPSLSKIYIYDPHHDTYDIVKEFLEREKPKLWNRARNTTELFSKNPSSFRTIYRTNIYFTCGDARYYKFNSNGELGHAFDWIHLASINTEISASSVFPEHYQQLNIDLLSNTNKNRLENNLIEKSPDDSIHTPDAQKEIDQKTHEKNYILDQFESDKDIFKKNAEEKPKDESAQENREWKEIKTPQKHSNQTFNEKSQTDRKNESSKKPIDPKVAEIDPKAAEDAWNEAEASQKHSHSHSKEKKSHTTESWDSWAENASKSSNKYDHYDSPRKIPKYEDHELSGLPELISTYIAMCQTSSEVASRFSFNSNTWKPIADLPELLSLYNKIYLLQSEGDLLVYDGK", "metadata": {"id": "A0AAU9J1U2", "cluster": 11328538, "interpro_all": ["IPR015915"], "interpro_used": ["IPR015915"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein is included in the Glutamic endopeptidase family, which preferentially cleaves peptide bonds on the C-terminal side of proline residues, and to a lesser extent, alanine residues. These enzymes are capable of degrading proteins of various sizes and are implicated in the digestion of prey. Furthermore, the protein contains a Neprosin activation peptide domain that constitutes the N-terminal activation region of neprosin, a digestive glutamic endopeptidase found in pitcher plants. This enzyme preferentially cleaves peptide bonds on the C-terminal side of proline residues and is notable for its ability to effectively degrade proteins of any size. It has been characterized in Microthlaspi erraticum and is linked to UniProt keywords Signal. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 18626, 16239, 9626, 2410, 9200, 3416, 16, 2154, 10662, 23839, 4207, 9031, 1990, 1920, 45, 17, 4262, 4159, 1927, 12958, 4248, 16, 1930, 1942, 43, 11318, 5064, 16, 10504, 4248, 18, 2144, 5038, 2032, 7131, 1927, 18192, 2697, 1927, 3425, 6562, 1930, 2032, 6835, 1922, 1920, 9379, 1927, 14071, 18, 3677, 16, 1920, 2213, 5461, 43, 26046, 2263, 1921, 2936, 4207, 3418, 1988, 14879, 1920, 56, 17, 4262, 2936, 3031, 1927, 26046, 2263, 1921, 16, 43, 15486, 18626, 16239, 9626, 2410, 9200, 2435, 1922, 14665, 1915, 4793, 18, 2052, 4113, 10662, 23839, 4207, 9031, 1990, 1920, 45, 17, 4262, 4159, 1927, 12958, 4248, 1930, 1977, 11892, 1958, 2496, 3682, 1942, 7098, 17069, 2697, 1927, 2967, 3081, 18, 2176, 2258, 2252, 4378, 1922, 7666, 7806, 13432, 1033, 3781, 2479, 1989, 1930, 1977, 4624, 1942, 20709, 11569, 2733, 18, 7031, 1920, 3244, 18, 3], "output": "MISRVMASFVFSILIITVVVTGSKFSDTEIDQLLKKLNKPAIKSIKSPDGDIIDCVHINKQPAFDNPLLRNHTIMMRPSVYPEGWNKVSEKQSNMVTQLWTTKGRCPDNTVPIRRTRREDILRAESIERFGKRNPNMIYDPSKAANPTAQNALNGTHSYAILAAMNGRFHGAKADINLWKPYLQKRQEFSLSQIWVNAGTHGVDLNTIEAGWQINHIMIPGAVLNPTSIYGGQQRDFIVYMWKDFHSGAWWLGINNNIVVGYWPATCFTHLQNGATGVMWGGEVIDEKTGDQHTTTQMGSGHFPQEGHTKASYFKNVQVLDETNNLRPVPAQHQTSVTEAHCYNIKLGQDSSWGSYFFYGGPGRNRMCP", "metadata": {"id": "A0A6D2J0Q3", "cluster": 13673733, "interpro_all": ["IPR053168", "IPR004314", "IPR025521"], "interpro_used": ["IPR053168", "IPR025521"], "interpro_unused": ["IPR004314"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein contains a Glycosyltransferase subfamily 4-like, N-terminal domain that constitutes the N-terminal Rossmann-fold structure of GT-B family enzymes, including MshA and family 1 subfamily 4 members, and participates in glycosyltransferase activity. It originates from Flavobacteriaceae bacterium and carries UniProt keyword assignments Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 5461, 43, 20067, 9961, 16227, 24, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 18215, 8890, 17, 3728, 3170, 1927, 4637, 17, 44, 3416, 5038, 16, 2710, 19864, 1019, 1930, 3416, 21, 16227, 24, 4678, 16, 1930, 17241, 1922, 20067, 9961, 2455, 18, 2176, 22970, 2037, 7732, 10296, 1972, 3336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MKSKTIIHQVTFAAVGGIQSSFISLFSLLKNKSEFNHKIYGMHEVDTYYIQILISKNYIIHLYNNLSSKRIYYLLRFLRCSNIIYHERGTSWNASASKIILTKRFKVDKNKIKVIYNGVLSESFKNGNFKKYSDHFSIGFIGRKEIKFFIAGDGVLEKDLKIRANGYENINFMGRSNPIEFISKMDVIVVPSIRKPVIASKVDGIPEIITNNKNGILLNPKNEITFKSKQKNIDQKDLIKAIYKLKNDDKLRLKLSKNLNQTVKKKFSLESYFYNIHEIYRMFKKYYTNFSKSLYEMIKFLFFKKDIKIIKKNAENADVIVANSELDTPKGVHILIDVAKKMEPLGNVIIESGFCSAVPVPDYVVNFETKELVKPKE", "metadata": {"id": "A0A2E1GR26", "cluster": 14708796, "interpro_all": ["IPR028098"], "interpro_used": ["IPR028098"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein can be placed in the RmlC-like jelly roll fold superfamily, which adopts a mainly beta jelly roll topology and functions as a dTDP-sugar isomerase, specifically dTDP-4-dehydrorhamnose 3,5-epimerase. This domain catalyzes a key step in the biosynthesis of L-rhamnose, a saccharide essential for the virulence of certain pathogenic bacteria. In addition, the protein possesses 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. In addition, the protein falls within the cAMP-dependent protein kinase regulatory subunit-like family, which primarily modulates cAMP signaling by inhibiting protein kinase A (PKA) catalytic subunits until cAMP binding induces dissociation and kinase activation. This diverse group influences metabolic pathways and cell growth, and also encompasses enzymes such as cAMP-stimulated phosphodiesterases and the acetyltransferase Pat, which inactivates acetyl-CoA synthetase to aid in environmental adaptation. It is native to Desulfuromonadales bacterium.", "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, 10625, 8293, 17, 3189, 8988, 11560, 1012, 12970, 3728, 13975, 16, 2154, 24032, 43, 4994, 4666, 8988, 11560, 1012, 12970, 13678, 1930, 4088, 1966, 43, 7711, 10274, 17, 9523, 25510, 16, 4475, 7711, 10274, 17, 24, 17, 28936, 5004, 17652, 2217, 23, 16, 25, 17, 13872, 9213, 2051, 18, 2052, 3418, 17097, 43, 3834, 3537, 1922, 1920, 8132, 1927, 54, 17, 23120, 2217, 16, 43, 14175, 2205, 3695, 4415, 1958, 1920, 9304, 1927, 4908, 8070, 4802, 18, 1922, 2459, 16, 1920, 2213, 14465, 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, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 6225, 17, 3100, 2213, 4016, 4948, 5903, 17, 3189, 3416, 16, 2154, 5985, 13112, 6225, 3197, 2007, 7918, 2213, 4016, 43, 12, 10110, 13, 6804, 6991, 4801, 6225, 2743, 6387, 9182, 1930, 4016, 2936, 18, 2052, 6445, 2210, 8061, 4487, 3873, 1930, 2024, 2905, 16, 1930, 2222, 21569, 5038, 2427, 1966, 6225, 17, 5449, 24821, 1036, 1930, 1920, 22226, 2917, 16, 2154, 22331, 1036, 6894, 17, 10027, 18185, 1942, 8379, 1922, 4813, 7810, 18, 2176, 1977, 6196, 1942, 30311, 18916, 3947, 7324, 2612, 14061, 18, 3], "output": "MPLFRNIDPKQLRVVAMMGESLTYRAGERLFEAEQSVATLGQGEIFGELAVLCDQQGDDGDAAFIVLDGEVEVLVRSDG", "metadata": {"id": "A0A967ID20", "cluster": 15065786, "interpro_all": ["IPR050503", "IPR000595", "IPR018490", "IPR014710"], "interpro_used": ["IPR014710", "IPR000595", "IPR050503"], "interpro_unused": ["IPR018490"]}, "task_type": "infilling"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein is associated with the Tetracycline regulation of excision, RteC family, which is essential for the self-transfer of tetracycline resistance (Tcr) conjugative transposons found in human colonic *Bacteroides* species. This protein facilitates the mobilization of these genetic elements, a process that is upregulated in the presence of tetracycline. It is native to Aureibaculum algae.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 16179, 3640, 1927, 10940, 16, 4341, 1940, 3416, 16, 2154, 1977, 4415, 1958, 1920, 3543, 17, 3856, 1927, 16179, 3554, 12, 8367, 13, 5225, 2178, 18808, 1036, 2435, 1922, 2616, 12401, 14, 27978, 14, 3038, 18, 2052, 2213, 11374, 1920, 14586, 1927, 2144, 3299, 5362, 16, 43, 2585, 1988, 1977, 7675, 1922, 1920, 2990, 1927, 16179, 18, 2176, 1977, 6196, 1942, 8689, 26073, 18021, 5277, 1035, 17721, 18, 3], "output": "MNEKEYITIVNNFKQYMKVIEQVEFMDFNYIHKAIVLCRKTLSKLKFKNYKNLVLKNLIYYSELRLIQSQFPELSINSQRDYILRQEHKIKKFFKKHDSLVQYINLYTDTSFYTHHDFLIAKIKAYDQLLEYLKSKFKSIDDFMRYGKPMHHNKTLHWTGTLESIFNIKLNDIYKIYSEIKNRQKSRTKFLEEMIEGLMSEINKSYRKYTVLYQFDSMEEEIGFELINLDELFFTIRPIKESYSCVLQPGKTQLTELIYALHAAKTINNGKTDIVEIQRE", "metadata": {"id": "A0A5B7TQ41", "cluster": 17008797, "interpro_all": ["IPR018534"], "interpro_used": ["IPR018534"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to create: The protein is a member of the Protein-L-isoaspartate(D-aspartate) O-methyltransferase family, which catalyzes the transfer of a methyl group from S-adenosylmethionine to D-aspartyl or L-isoaspartyl residues within peptides and proteins. This enzyme specifically targets these abnormal residues, formed by spontaneous deamidation or isomerization, to facilitate the repair or degradation of damaged proteins. 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 occurs in Caenorhabditis tropicalis. 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, 43, 7210, 1927, 1920, 2213, 17, 54, 17, 4911, 13432, 5263, 2010, 12, 46, 17, 12878, 13, 57, 17, 16478, 3416, 16, 2154, 17097, 1920, 3856, 1927, 43, 4963, 2210, 2037, 61, 17, 29283, 23568, 11215, 1942, 46, 17, 12053, 2199, 2014, 54, 17, 4911, 13432, 5263, 2199, 4248, 2651, 5320, 1930, 2697, 18, 2052, 4113, 4475, 4845, 2144, 4552, 4248, 16, 5333, 2007, 6242, 30097, 16408, 1943, 2014, 27027, 16, 1942, 6628, 1920, 5059, 2014, 4877, 1927, 10756, 2697, 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, 5110, 1922, 22418, 12862, 1937, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MGNSESRTTDSMVDYLITAKHITQRNTERAFRLVERTRFLPESHRRYPHLPEQIRDRPGGQFYPGPLLVSSVGIYAQVAEYLKVKRGHAFLNVGTGSGYFSTLIGILLGDFGINHGIELYQNLIDYSETMINQWTETTGASSVGWSRPVIQLGDVFDPNFTGTHVERYDRIYIGFVIRDRATICRVIRMLRIGGILVIPSLSNLCRYTRTGAGTANIEILGTCTFSRAVVFEESERPVAPLFETFPTLITLARQAVRRKCRKEAYNDRVMKIINKSWKIPKGGIETPRRRDSDSEREQRLRIYRRETHPLPLFERRAGNLGARRDDLAHRTGPPSLSDVLGQFLNRNNENDERPRAFGGEAGTSNQRRTSPGRPAIGIERYRTRSPLRSGPRRTYLLPPHDPESTEQRPETSEGSGNNQIESQIRNGGDEPYVGNRAIRNPTFRRPYPPTYRSATRVRTPPLTPPLMPTPFYQAPLNIEMDDEEMQDLLSPLFPIRTTETGGTSEANLNERSDQTSSSSTSSSATSASSTSTSSDTDSLLIQDTTDEESSSEDSATTHFTEFLNLRGQDPTAPHEPPPGTTGRSIYFRRRLFPSELSDSRSQNSVPTVPILSTVLSSSSSSTTTQNRSQFPNSNDNPNIGSQTLGQGSSEGRMNPEMESMAAIHRRSLQNMLRASRTRQAIEGIVRRRNERNRTRNNHPIRRDADEDLYWRGPNDRDWETFNLYNNNNNNNNNDNRIDEQTRARFVADLELFDQNRMDYTLQLLAVNGNNRGENDFGVVLGMEADEDLDDPSIQIEFTINNRIILEEVDGDLTGDDDSDDDIDPNEPSTSTAPPPSRQRSVDERPYIGPPMSFREMRRRGRVNSNTAVQSYIEQTSSDNLNAAISDEQINYLRVDRNLEINFSNIDYQRRIDNLPLPQKLKRFIKSEGNGV", "metadata": {"id": "A0A1I7T820", "cluster": 17354280, "interpro_all": ["IPR000682", "IPR029063"], "interpro_used": ["IPR000682", "IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein incorporates a Alpha/beta hydrolase fold-1 domain that constitutes the structural core of a diverse superfamily of hydrolytic enzymes, featuring an alpha/beta-sheet arrangement that scaffolds a catalytic triad. This domain typically contains a conserved nucleophile elbow to drive hydrolysis, although some members lack catalytic residues and participate in surface recognition. Additionally, the protein is included in the AB hydrolase superfamily, which encompasses a diverse range of serine hydrolases, lipases, esterases, and peptidases that catalyze the cleavage of C-C, C-O, and C-N bonds. These enzymes participate in lipid metabolism, pyrimidine catabolism, and biotin biosynthesis by acting on substrates such as monoacylglycerols and esters, while some bacterial members contribute to environmental adaptation by degrading pollutants. In addition, it is part of 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 present in Diacronema lutheri (Unicellular marine alga) (Monochrysis lutheri) and carries UniProt keyword assignments 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, 19683, 43, 4595, 19, 4666, 20748, 3728, 17, 21, 3418, 1988, 14879, 1920, 4346, 4728, 1927, 43, 6445, 13975, 1927, 26702, 5038, 16, 29931, 1925, 4595, 19, 4666, 17, 11130, 13002, 1988, 10603, 43, 6804, 21845, 18, 2052, 3418, 5745, 5461, 43, 5305, 2797, 28335, 17621, 1942, 9265, 9128, 16, 2876, 2673, 4678, 3630, 6804, 4248, 1930, 7352, 1922, 3154, 5708, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2186, 20748, 13975, 16, 2154, 21569, 43, 6445, 3109, 1927, 8468, 30337, 16, 16653, 1036, 16, 26389, 1036, 16, 1930, 24050, 1036, 1988, 18170, 1920, 6404, 1927, 45, 17, 45, 16, 45, 17, 57, 16, 1930, 45, 17, 56, 9031, 18, 2144, 5038, 7352, 1922, 4486, 4714, 16, 21611, 19480, 16, 1930, 8622, 8132, 2007, 8290, 1990, 6249, 2427, 1966, 8914, 21295, 1036, 1930, 16785, 16, 2679, 2673, 4543, 4678, 4672, 1942, 4813, 7810, 2007, 18192, 16826, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 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, 2481, 1922, 25141, 2145, 2290, 3368, 10908, 2098, 1033, 12, 24797, 3386, 10789, 4326, 1019, 13, 12, 18688, 6570, 4662, 10908, 2098, 1033, 13, 1930, 16252, 20709, 11121, 2538, 18306, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MLSHAANELVWLALYLALSAVLGIFALPVCLALMALAFFVAWAWLLAGRLSTRSHDGLVLSYAVSRPRAPDGAPAAAAAGVEPRKCVLLCEPLGQSGPLVFAPLISISAHADDAATVLRAAGFSRASICVGHSLGVQVALELTLLWQPVVRLPLIGTATREFVRALQRRPERFYAAQPLLAPLLRHVISPVAFWRDYMAGLDASRGPHNLEHFLLSFLEIDAHSAAHLLDKIDQPALVISGMRCDPLSTHSTLLESPEWALHHIHRFLARTSSLDLDVASQMQRKSLLDAPRLREPAIPEFEQRTCTLATLGPEYVFVTWDYRGFFKSALPQRKRRPERVERLVLLNGCAGQAFQTAFFCALFGSPLLRRVLGPNYLYLDLLVPALVSAEMVARMRRAEH", "metadata": {"id": "A0A8J5XA80", "cluster": 17751209, "interpro_all": ["IPR000073", "IPR029058", "IPR050266"], "interpro_used": ["IPR000073", "IPR050266", "IPR029058"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein has a Clp1 P-loop domain that binds ATP and serves as the central nucleotide-binding region of the polyribonucleotide 5-hydroxyl-kinase Clp1. It functions within the cleavage factor IA (CF IA) complex to facilitate pre-mRNA 3'-end formation and participates in tRNA splicing. Furthermore, the protein belongs to the Clp1/Grc3 family, which functions as polynucleotide 5'-hydroxyl-kinases involved in pre-mRNA 3'-end maturation, tRNA splicing, and rRNA processing. Members such as Clp1 operate within the cleavage factor IA (CF IA) complex, while Grc3/NOL9 proteins specifically target ribosomal RNA. These enzymes typically utilize a central ATP-binding domain and an N-terminal $\\beta$-sandwich domain to bind and phosphorylate single- or double-stranded nucleic acid substrates. 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 is produced by Quillaja saponaria (Soap bark tree) and contains UniProt keyword associations 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, 2258, 43, 18017, 1009, 58, 17, 5881, 3418, 1988, 6876, 4498, 1930, 10634, 1966, 1920, 4101, 5489, 17, 2743, 3031, 1927, 1920, 4286, 3027, 20226, 15274, 25, 17, 9420, 17, 4016, 18017, 1009, 18, 2176, 4088, 2651, 1920, 6404, 2991, 11640, 12, 4920, 11640, 13, 2796, 1942, 6628, 2097, 17, 3616, 23, 11, 17, 2482, 3337, 1930, 17241, 1922, 10089, 8490, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 18017, 1009, 19, 2398, 12981, 3416, 16, 2154, 4088, 1966, 15176, 15274, 25, 11, 17, 9420, 17, 7784, 3286, 1922, 2097, 17, 3616, 23, 11, 17, 2482, 7655, 16, 10089, 8490, 16, 1930, 9067, 4587, 18, 4678, 2427, 1966, 18017, 1009, 15336, 2651, 1920, 6404, 2991, 11640, 12, 4920, 11640, 13, 2796, 16, 2679, 2398, 12981, 19, 2239, 1024, 1026, 2697, 4475, 2758, 11196, 3146, 18, 2144, 5038, 5745, 12561, 43, 4101, 4498, 17, 2743, 3418, 1930, 1925, 56, 17, 4262, 8, 38, 4666, 8, 17, 18038, 3418, 1942, 4566, 1930, 18730, 2957, 17, 2014, 4825, 17, 10338, 11079, 2687, 6249, 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, 1977, 4152, 2007, 2571, 10888, 14174, 9235, 12502, 3027, 1019, 12, 2577, 2026, 18399, 6694, 13, 1930, 5461, 20709, 11121, 2538, 5253, 13763, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MASGPENPSPNIFIPREWSEAAAKNSGKTTFSRHLLNVLLQRYKKVAYLDTDVTPDLTIPCLKTPERCFFFGDNTSKTDPEAYLNYIYAIYDYKGVGYDALVHMLNYIDPTHVVKIRISAINSARQDSFNRSVLVQKDARLMRDFRLEVSISSVKVRHLYCQVPSTEKFYSLNATIVGLWSVGLGIVRGIDTFKGVLFVLTPVPQSSLEQGCISPYMSGNTLPTSESIAYDSITSPPPVVLICGGQPEFTPPGLLSLTVVDKVYKKEYYVSDEGEDPSKTGLPLVVNTPGWVESKNLPAGQFWLDEEYNETVNLIEMAYFRQCFPSSRNITTIKELAHALASHPPFAVESEDSENLPKVNLLLQGLIQIPTCLLQV", "metadata": {"id": "A0AAD7KU93", "cluster": 21195007, "interpro_all": ["IPR045116", "IPR032319", "IPR027417"], "interpro_used": ["IPR032319", "IPR045116", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein is classified under the Putative pre-16S rRNA nuclease family, which comprises predicted nucleases involved in the 5'-end processing of pre-16S rRNA during ribosome maturation. Typified by *Escherichia coli* YqgF, members of this family adopt an RNase H structural fold. In addition, the protein should contain a YqgF/RNase H-like domain that is predicted to function as a ribonuclease or Holliday junction resolvase similar to RuvC, particularly in bacteria. In eukaryotic orthologs like Spt6 and bacterial Tex proteins, it often lacks catalytic activity and instead plays a structural role in chromatin maintenance and toxin expression. Also, the protein is assigned to 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. It is expressed in Chlamydiota bacterium and is connected to UniProt keyword Cytoplasm, Hydrolase, and Ribosome biogenesis.\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, 5947, 2441, 1920, 6770, 2097, 17, 11209, 9067, 16230, 3416, 16, 2154, 12936, 4396, 29305, 3286, 1922, 1920, 25, 11, 17, 2482, 4587, 1927, 2097, 17, 11209, 9067, 2409, 12794, 7655, 18, 2357, 2828, 2007, 14, 10210, 5178, 14, 67, 1055, 2818, 16, 4678, 1927, 2052, 3416, 14103, 1925, 9843, 50, 4346, 3728, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 67, 1055, 2818, 19, 9843, 50, 17, 3189, 3418, 1988, 1977, 4396, 1942, 2347, 1966, 43, 18347, 2051, 2014, 14451, 27539, 6910, 24321, 10916, 1021, 2551, 1942, 7212, 27881, 16, 4443, 1922, 4802, 18, 1922, 10825, 16634, 3189, 19375, 1016, 1930, 4543, 4708, 2697, 16, 2176, 3868, 13012, 6804, 2455, 1930, 5974, 5705, 43, 4346, 2770, 1922, 6338, 6291, 1930, 9165, 2294, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 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, 2176, 1977, 3198, 1922, 14667, 3940, 3857, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 5239, 16, 20748, 16, 1930, 12794, 13008, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MRILGVDIGTVRLGMIEGGSAKKVSKSILSLVLEHLNGTESDMSKMAKECVRLLKEYFKQNFTREIDIILQDRVAAQLILQNYLDIKKVLIAVSDPMGMTAQPLPTYEKTNSEKQKIKTVVIGNPIDERLTSVAAEKVLLSADLSRKKRKEIK", "metadata": {"id": "A0A661WWB1", "cluster": 24443836, "interpro_all": ["IPR012337", "IPR005227", "IPR006641", "IPR037027"], "interpro_used": ["IPR005227", "IPR006641", "IPR012337"], "interpro_unused": ["IPR037027"]}, "task_type": "infilling"} {"instruction": "The protein contains 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 should contain a OmpR/PhoB-type DNA-binding domain that functions as a transcriptional regulator within bacterial two-component signal transduction systems. Adopting a winged helix-turn-helix fold, this C-terminal effector binds to specific DNA tandem repeats and interacts with RNA polymerase subunits to modulate gene expression in response to environmental stimuli. Also, the protein is a member of the O-mannosyl-transferase TMTC family, which mediates the post-translational O-mannosylation of proteins by transferring mannosyl residues to serine or threonine hydroxyl groups. Members of this family specifically modify the cadherin superfamily by adding O-linked mannose glycans, while also displaying broader specificity towards substrates like PDIA3. It has been detected in Pseudoalteromonas phenolica and is annotated with UniProt keywords Transmembrane, Transmembrane helix, and Membrane.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 5461, 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, 3066, 5531, 43, 21921, 1005, 19, 20175, 1014, 17, 2601, 2678, 17, 2743, 3418, 1988, 4088, 1966, 43, 5224, 7888, 2651, 4543, 2288, 17, 4594, 2733, 8201, 3771, 18, 20478, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 3728, 16, 2052, 45, 17, 4262, 7917, 6876, 1942, 2487, 2678, 10361, 9569, 1930, 9034, 1956, 3146, 6479, 6991, 1942, 8480, 2359, 2294, 1922, 2644, 1942, 4813, 5458, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 57, 17, 7338, 11731, 17, 13763, 24958, 1030, 3416, 16, 2154, 10412, 1920, 2753, 17, 8414, 57, 17, 7338, 21385, 1927, 2697, 2007, 21902, 7338, 11731, 4248, 1942, 8468, 2014, 13143, 9420, 2671, 18, 4678, 1927, 2052, 3416, 4475, 11675, 1920, 8875, 13975, 2007, 8013, 57, 17, 4624, 17936, 15509, 16, 2679, 2222, 13867, 11462, 4896, 5681, 6249, 3189, 20506, 12779, 18, 2176, 2258, 2252, 3330, 1922, 11520, 1923, 1967, 10480, 14223, 1019, 1930, 1977, 10633, 1956, 20709, 11569, 9117, 16, 9117, 7864, 16, 1930, 3260, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MEKIAASFKLANWYVEPHLNKLTLAEQSLECSLPPKVMALLVLLTRHQNTPLVVTDSSIYQAVAQLRKTLHQDKTITEAIEQISGKGYRLSPNIELRFEREEQYSLTKGSSKKQALQIVFWFMNNGSIKEDLKAQLKNQPNEQAYFEDLTLADHLVKQREVSAINQASKLYKTILNESPNNANALFGLCNSDYQQKAIEIEPHHINAIALLGALQQQKGDLKTAKTYFEQGLLLEQKSSLFHSLKTAFKLSPNDPEVLIKLAYAYLVKRDRKKAQQYFERARLIAPNLRNAPLYALDFYTLTNNKFAHFQLQHVLFLLSTNQLKNAEALFKQTDKQYIHSDFVWYVEAALAAKDGRLIPYIHGLMTNNDNQMAFNLFTKHFAEFASLTAPVEQNLGLYLTYTQILQGLEKLTQDLALWRELNGEFSGFNEVQWHVIKQDGENVKLAATKLLNSDWLPDYNDNMFTETLLHRYLKEHKHESLDFIAKEIWPARQTLAEKITKKHKLTAFAVCILVFAVLLVYGQHSQTKTYASCLPLLLFYGDFLLSQQQTTEALTKPIAADYEAWYEQYSYDNENSEYIVAFEKLKQRYQLAPELNRYVMGNSVHENSETSQTLA", "metadata": {"id": "A0A5R9Q3M0", "cluster": 25763207, "interpro_all": ["IPR001867", "IPR016032", "IPR052384", "IPR011990", "IPR019734", "IPR036388"], "interpro_used": ["IPR019734", "IPR001867", "IPR052384"], "interpro_unused": ["IPR011990", "IPR016032", "IPR036388"]}, "task_type": "infilling"} {"instruction": "The desired role of my protein is: The protein is assigned 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 is derived from Castor canadensis (American beaver). 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, 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, 1977, 3595, 2037, 12273, 1924, 2112, 10185, 8362, 12, 5339, 1998, 14666, 13, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MPRPTGEWLAEGFLASPRPDSSCHRPLLCCRLLQNMSKSLKKLVEESREKNQPEVDMSDRGISNMLDVSGLFSLAHITQLVLSHNKLTSLCSYHSQAVPATQKRKVGGSRVRSPPGQKKLCHQT", "metadata": {"id": "A0A8C0XRN7", "cluster": 27274885, "interpro_all": ["IPR032675"], "interpro_used": ["IPR032675"], "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 Serpentine receptor class v (Srv) family, which comprises seven-transmembrane G-protein-coupled receptors (GPCRs) belonging to the Srg superfamily. Primarily found in nematodes such as *Caenorhabditis elegans*, these receptors mediate chemoreception, enabling the detection of specific environmental chemical stimuli. Additionally, the protein has 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 found in Steinernema hermaphroditum and is connected to UniProt keyword Transmembrane helix.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 27453, 9830, 1021, 3148, 2921, 64, 12, 4581, 1020, 13, 3416, 16, 2154, 12936, 5260, 17, 9117, 49, 17, 2213, 17, 6416, 4086, 12, 17723, 13, 10588, 1942, 1920, 4581, 1029, 13975, 18, 5985, 2435, 1922, 19669, 2427, 1966, 14, 22418, 10861, 14, 16, 2144, 4086, 8265, 13534, 5943, 15577, 16, 12180, 1920, 3805, 1927, 2487, 4813, 4399, 5458, 18, 4950, 16, 1920, 2213, 2258, 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, 2435, 1922, 21557, 1915, 19319, 1019, 19432, 2575, 11483, 13378, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9117, 7864, 18, 3], "output": "MMEPNSPEGIVLGSISALTSIIYIYVLVIIAKNRDLRHAPFYMLNLAMGIVDIGNIWTTYVFQRIPAVGFLNDEVYLLFGHRSILATMCTQGFGFFNSTQKYYLIAIGFNRFTAVVTPSFHKTVWTKKHTLIVIVIAAAVNFVQNAVLEIISPSYWEDYRSEDSNDGLHCRMPSESIYKGGLQYSIYLSLAAAIVMCLLYGVIIFALFSNRHKLKTASSSTRKTYNVEMKLTLSVLLHTVLLTADGCTATLIFLAKQRYLMPYSYVIQDLLSGCNPYLLLFFSSELRKKVFWWTKVFQSPNASSIQPIQSMLERNSPRNRQ", "metadata": {"id": "A0AA39H8K5", "cluster": 27334941, "interpro_all": ["IPR019426", "IPR017452"], "interpro_used": ["IPR019426", "IPR017452"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein is grouped 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. In addition, the protein features a Reelin, subrepeat B repeat that adopts a $\\beta$-jelly roll fold containing a signature Asp-box motif as a structural component of the extracellular matrix protein Reelin. It contributes to the binding of lipoprotein receptors VLDLR and LRP8, thereby playing a critical role in regulating neuronal migration and cortical layering. In addition, the protein should have a **Peptidase C25, Ig-like** domain that is found in MEROPS family C25 proteases from the periodontal pathogen *Porphyromonas gingivalis*. This domain functions as a virulence factor by supporting the proteolytic metabolism of peptides and facilitating erythrocyte agglutination. It is present in candidate division TA06 bacterium SM1_40.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 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, 1922, 2459, 16, 1920, 2213, 4075, 43, 21747, 7782, 16, 2316, 20483, 5376, 1031, 44, 6865, 1988, 24032, 43, 8, 38, 4666, 8, 17, 8988, 11560, 1012, 12970, 3728, 3165, 43, 9983, 4138, 17, 5758, 5219, 1966, 43, 4346, 4594, 1927, 1920, 5329, 4526, 2213, 21747, 7782, 18, 2176, 7624, 1942, 1920, 2743, 1927, 9694, 4086, 21288, 1005, 1930, 17883, 1025, 16, 6113, 14797, 43, 4140, 2770, 1922, 6773, 5121, 5049, 1930, 5586, 4757, 1941, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 14, 14, 24050, 8453, 1015, 16, 7021, 17, 3189, 14, 14, 3418, 1988, 1977, 2435, 1922, 6902, 4001, 3416, 8453, 1015, 12447, 2037, 1920, 12928, 7055, 14, 17376, 5134, 3947, 1934, 22118, 14, 18, 2052, 3418, 4088, 1966, 43, 9304, 2991, 2007, 6184, 1920, 12712, 4714, 1927, 5320, 1930, 12440, 15469, 20262, 1943, 18, 2176, 1977, 2481, 1922, 6610, 8451, 4410, 14265, 14061, 2426, 1009, 41, 3040, 18, 3], "output": "MYLWLGDPETDVWTAVPQDMTVSYPAAIPIGTQPVTVSVSMGGSSVEDALVCLLKPGEVYEAGYTDAAGQVTLTVSPTVPGQMAVTVTAHNGLPYTGTIQVIQPEGPYIILDEYLIDDSVGGNNDGQVDIGEPIRLPAALKNVGVEAAQDVDAVLATDDPYMTISDNYEYYGDINPDQVVWCPDDYDFEAKAVCPDGHTAGFSITAEDIYDSTWTSAFNIPVHAPVLAFESYIIDDTGGGNGNGRLEPGETAELTVTLANEGSGFAASVEATLSTIDPYVTVVSGSASYGNIAAGGTGVGSPAYVVEAAATAPEGRQAQLDLTAEAQAGYVRYDACWVTVGGIFDDMEQGPAGWTHEVVTPGYYDQWHQSTELNHTPGGSVSWKCGDTGPGNYADSLDAGLMTVELILPENPVLTFWHWMDAEASSMYPDSAYDGGLVEISIDGGLNWTQIMPEEGDTHAIRPGSDNPLPGGTMVYSGSFGWTQAMFDLAAYSGQTVQFRFRFASDWGVNREGWYIDDVLIAGQPAVTVMVEPDAYEVPRGGTLGYTATVQNLSSSAQSFYGLIEAWLPNGSPYSGNPLVGPRPVTLAPGGSQSVHLEHPVPAVAPLGEYLLRVKVGNPPADLLDQDFFHFRVVP", "metadata": {"id": "A0A0S8JM17", "cluster": 88190, "interpro_all": ["IPR013783", "IPR005536", "IPR049419"], "interpro_used": ["IPR013783", "IPR049419", "IPR005536"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "\"The protein is assigned to the YegP-like superfamily, which represents an uncharacterised domain often found as tandem repeats or in the C-terminal region of putative tryptophan--tRNA ligases. The structure comprises two subunits of \u03b2(3)-\u03b1-\u03b2 motifs that assemble into a single \u03b2-sheet via C-terminal strand swapping. It is native to Actinomycetes bacterium.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 1977, 6304, 1942, 1920, 5293, 19874, 17, 3189, 13975, 16, 2154, 4972, 1925, 23229, 3495, 3418, 3868, 2435, 1966, 10361, 9569, 2014, 1922, 1920, 45, 17, 4262, 3031, 1927, 6770, 13489, 17, 17, 10089, 22423, 18, 1920, 3170, 12936, 2288, 6991, 1927, 161, 12, 23, 13, 17, 160, 17, 161, 8277, 1988, 17421, 2460, 43, 2957, 161, 17, 11130, 3454, 45, 17, 4262, 5984, 3476, 5041, 18, 2176, 1977, 6196, 1942, 4718, 25148, 14061, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MRILIDRDSNGHYRWERSCQDAAGLVGRASWQWAISGPDGERLRRASNGARTGRLVRRTPHGADVLARGVRGYPDGEAMLIVQRSDGHAESPAIFTDAAACGRALEDL", "metadata": {"id": "A0A538N6S0", "cluster": 973975, "interpro_all": ["IPR036913"], "interpro_used": ["IPR036913"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is grouped in the Protein of unknown function DUF1642 family, which consists of phage and prophage proteins with uncharacterized function. It is produced by Streptococcus phage phiBHN167.\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, 2213, 1927, 5435, 2347, 4855, 5739, 8760, 1028, 3416, 16, 2154, 7543, 1927, 10503, 1930, 8839, 2170, 2697, 1956, 24528, 2347, 18, 2176, 1977, 4152, 2007, 15746, 10503, 17971, 12937, 7301, 6038, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MNKQELIKKLEERRTIIRNFQAPRYVKNILARLRELPLHDREVWLKAIMEGMVEREKVIVPQCVADWIEEARKAGKWFMQELPFDLAARAWLDGYEVEEEKRYTVVTKATKQPEEAGVGWVFDCPGIEIEEVEYDTNAGYAVWWKDVKEIFEQLDEPEIGHADESEFEQDFSHAKWREGYEQGKICKDVVDFFEFNFTNDEVLYYNAMDKKLFFSMGGLATKFTRKQL", "metadata": {"id": "U4KJ89", "cluster": 1060632, "interpro_all": ["IPR012865"], "interpro_used": ["IPR012865"], "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 uS15/NS1, RNA-binding domain superfamily, which adopts a three-helix structural fold to facilitate RNA recognition and binding. This domain is essential for the assembly of the bacterial 30S ribosomal subunit through uS15 binding to 16S rRNA, and is also utilized by the influenza virus NS1 protein and glutamyl-prolyl-tRNA synthase. Additionally, the protein can be placed in the Small ribosomal subunit protein uS15 family, which comprises bacterial, chloroplast, and mitochondrial proteins that serve as structural components of the small ribosomal subunit. These proteins decorate the rRNA core to organize and stabilize its tertiary structure, thereby facilitating mRNA-directed protein synthesis. It originates from Bacteroidetes bacterium QH_1_64_81 and is classified with UniProt keywords Ribonucleoprotein, Ribosomal protein, and rRNA-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, 6304, 1942, 1920, 2022, 3962, 19, 19082, 16, 3146, 17, 2743, 3418, 13975, 16, 2154, 24032, 43, 2559, 17, 7864, 4346, 3728, 1942, 6628, 3146, 5708, 1930, 2743, 18, 2052, 3418, 1977, 4415, 1958, 1920, 5957, 1927, 1920, 4543, 27755, 11196, 5903, 2596, 2022, 3962, 2743, 1942, 11209, 9067, 16, 1930, 1977, 2222, 7079, 2007, 1920, 7108, 3413, 19082, 2213, 1930, 25345, 17, 3192, 2199, 17, 10089, 8921, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2858, 11196, 5903, 2213, 2022, 3962, 3416, 16, 2154, 12936, 4543, 16, 17471, 16, 1930, 4596, 2697, 1988, 7120, 1966, 4346, 4178, 1927, 1920, 2858, 11196, 5903, 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, 22970, 2037, 26808, 14061, 59, 1023, 41, 21, 41, 4723, 41, 6206, 1930, 1977, 5947, 1956, 20709, 11569, 18347, 6657, 16, 11196, 2213, 16, 1930, 9067, 17, 2743, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MITKEEKQEIIDRFGNGPHDTGTPEVQIAIFTKRIQRLTEHLEEHPNDNSTRHGLLDLVGKRQRLLNYLEENEIERYRTIRDELELRT", "metadata": {"id": "A0A2T2SV75", "cluster": 1609609, "interpro_all": ["IPR000589", "IPR005290", "IPR009068"], "interpro_used": ["IPR009068", "IPR005290"], "interpro_unused": ["IPR000589"]}, "task_type": "autoregressive"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein falls within 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. Moreover, the protein belongs to the Divergent polysaccharide deacetylase family, which comprises bacterial proteins structurally related to the 7-stranded barrel catalytic domain of polysaccharide deacetylases (DACs) within the carbohydrate esterase 4 (CE4) superfamily. These proteins are predicted to function in the removal of N-linked acetyl groups from cell wall polysaccharides. It is derived from Vannielia litorea. 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, 12182, 2651, 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, 3950, 16, 1920, 2213, 14440, 1942, 1920, 13609, 17167, 19489, 3416, 16, 2154, 12936, 4543, 2697, 12171, 2712, 1942, 1920, 27, 17, 10338, 19560, 6804, 3418, 1927, 17167, 19489, 1036, 12, 22322, 1036, 13, 2651, 1920, 10590, 26389, 24, 12, 5827, 1006, 13, 13975, 18, 2144, 2697, 2032, 4396, 1942, 2347, 1922, 1920, 6025, 1927, 56, 17, 4624, 6894, 2671, 2037, 2024, 4821, 18686, 18, 2176, 1977, 3595, 2037, 7409, 8635, 14007, 4471, 2073, 1019, 18, 7031, 1920, 3244, 18, 3], "output": "MGKGLLSGVAWGALVSVLGLGGASVLAPLPEDVAAVSAPGGLEAPRADAAPEAPEPAPSDTTGTTAESELTPPPGSEFARAGEDTEPAAPGAEAEPISPAAPEQPDVEVAEAPVPDTTPPAVPETAPEAVAAPVAPVVEETAPVIGGGDAAKVVAEAPGTAAQPEAGRTPETATVAPEVPRSTPEVVSAEAATAAPAESETVGAAPGAAAPVAAAEVAPGETAERTAPVQAAGAGERAPKVEAVAPSTGGEVAAVAEVEAAGRTEAPEVAAAPEAEVVTGTEPVAESAAVPESAESAVPEQVASVEPEAPRAEAPDVVEIVEPNPQAAPQPSPEAEAPVAETPSVPATEATGDAPEPTQPDRESPSMAAETPAAPEAERAEVERETELPADPSSPPSSVPITERQPRTGTGNGLPRRIVTAGESGGGFGKRVVPLTERNKPESRLPVIGASAEAEAEAPRLSALAANAAPFENAEGRPLVSVILFDVGDQGLDRAALTAINFPVTFAVDATDPGAAETAQRYRDAGFEVLIVPSGLPRGATPQDMETTLQSYIGQFPGAAGLLETGEEGISDDPALSRQLLAIAADTGHGLVFVDSGLNSAQRGAESAGLPSALVWKVIDAGGEDGAAIGRTLDRAAFRSGQEGAVVVMGHSFSQTVTGLLNWAAGPKGQSVALAPVSAVLMR", "metadata": {"id": "A0A1N6FPZ3", "cluster": 2197080, "interpro_all": ["IPR006837", "IPR011330"], "interpro_used": ["IPR011330", "IPR006837"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that has the following function: The protein is a member of the Heterokaryon Regulation/Transcriptional Modulator family, which regulates fungal growth and non-self-recognition by restricting heterokaryon formation to maintain organismal integrity. These proteins indirectly influence gene expression through protein-protein interactions, modulating the suppression of mutations in promoters induced by transposable elements. It is found in Lophiotrema nucula. 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, 19732, 15292, 1916, 3640, 19, 5224, 18521, 3416, 16, 2154, 7014, 8697, 2905, 1930, 2447, 17, 3543, 17, 5708, 2007, 20571, 19732, 15292, 1916, 3337, 1942, 6698, 9669, 1923, 7996, 18, 2144, 2697, 10818, 4039, 2359, 2294, 2596, 2213, 17, 2213, 3719, 16, 10871, 1920, 6412, 1927, 3527, 1922, 9026, 2719, 2007, 12935, 2115, 5362, 18, 2176, 1977, 2435, 1922, 3004, 24888, 6286, 6666, 25020, 5617, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MSGSDAVPWENVNIRLRSDGVYGLNSLADGAPLLVHDGAVIQGSYNFPDTEFRILESMQTAWQNEARSVWQPIISESGAMGKVAMSVYMSTTDVPPLRLRDVPDLIFGQTSKILKSYGERYKAIRSQIYRACANRAMFVTSKGYLGLAPGNAQEGDIVCVLLGGCTPYLLRPIAGSKQFTFVGEAYVYGIMGGELLGHEMGHARMRDFEIV", "metadata": {"id": "A0A6A5YF50", "cluster": 2640460, "interpro_all": ["IPR052895"], "interpro_used": ["IPR052895"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: It is part of 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. Furthermore, the protein contains 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. It is native to Bacteroidota bacterium.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 2176, 1977, 3131, 1927, 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, 3677, 16, 1920, 2213, 5461, 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, 2176, 1977, 6196, 1942, 24323, 7336, 14061, 18, 3], "output": "MDMALIKFTPRFTPALPDLFGDFFNQEAGRNWSDVNTFAKVNVMEKNDAFQIEVAAPGLKKEDFQLQVDKDILSIRVQKENKQEESGEKYMRREFSFESFERRFQLPESVDQGKIEAKYENGVLYVLLPKKAEEVQKERMIEIA", "metadata": {"id": "A0A3M1TJC8", "cluster": 4595478, "interpro_all": ["IPR002068", "IPR008978", "IPR031107"], "interpro_used": ["IPR008978", "IPR002068"], "interpro_unused": ["IPR031107"]}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein possesses a Cds6 C-terminal domain that contributes to cell shape determination in *Helicobacter pylori* through peptidoglycan modification and deglycosylation of the flagellar protein FlaA. This NTF2-like domain contains a putative binding pocket for pseudaminic acid, suggesting it functions as a pseudaminase. Furthermore, the protein is classified under the NTF2-like domain superfamily, which constitutes a versatile structural fold characterized by a \u03b2-\u03b1(2)-\u03b2 insertion. This domain scaffolds diverse functional roles, ranging from facilitating nuclear protein transport in NTF2 to supporting enzymatic activity in dioxygenases and structural roles in type IV secretion systems. It is found in Rickettsiales 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, 14465, 43, 14963, 1016, 45, 17, 4262, 3418, 1988, 7624, 1942, 2024, 5989, 7063, 1922, 14, 22293, 10665, 14, 2596, 24183, 6295, 1930, 3744, 19602, 21385, 1927, 1920, 24154, 2213, 2300, 5025, 18, 2052, 5891, 6680, 17, 3189, 3418, 5461, 43, 6770, 2743, 10154, 1958, 6050, 3717, 1935, 2687, 16, 3783, 2176, 4088, 1966, 43, 6050, 15848, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 5891, 6680, 17, 3189, 3418, 13975, 16, 2154, 14879, 43, 20425, 4346, 3728, 4378, 2007, 43, 161, 17, 160, 12, 22, 13, 17, 161, 7413, 18, 2052, 3418, 10603, 6445, 3183, 5456, 16, 6485, 2037, 12440, 4254, 2213, 4860, 1922, 5891, 6680, 1942, 6184, 8145, 2455, 1922, 23652, 10465, 2432, 2319, 1930, 4346, 5456, 1922, 2601, 4370, 5512, 3771, 18, 2176, 1977, 2435, 1922, 24479, 2086, 1918, 14061, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MWYSTKILSKNRKDSLSNCSYENTDGETDMTEKNEEKETRKISKTKLIIFLTALTIFIASGQHINVGAFETKNEKLIIDNERKSFENFSRNKIARSLVLLDLEDWRKNWSARNLEGFMGYYHPDFIFKKNRFIKISLKNISSRVEGDRTEFGWKILEENIINPNVAKRGKKDKRNESKEQLFSKSFDLDNSQKSIHEINLFASNLDFFSNLLKSQSQGPRKKSAPHAKFSKDIKVFRNNKKRYIITEFTQIYKSKNYNDSATKELIWA", "metadata": {"id": "A0A2D7DWL0", "cluster": 8662989, "interpro_all": ["IPR056203", "IPR032710"], "interpro_used": ["IPR056203", "IPR032710"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein should feature a Aldehyde dehydrogenase domain that oxidizes a wide variety of aliphatic and aromatic aldehydes using NADP as a cofactor. This catalytic region relies on conserved cysteine and glutamic acid residues and is found in dimeric or tetrameric enzymes across bacteria, fungi, and mammals. Furthermore, the protein is included in the The Aldehyde/histidinol dehydrogenase superfamily, which encompasses NAD(P)-dependent oxidoreductases that catalyze the conversion of various aldehydes and alcohols, such as L-histidinol, into their corresponding carboxylic acids. These enzymes, characterized by a conserved 3-layer $\\alpha/\\beta/\\alpha$ structural domain and a catalytic cysteine, include aldehyde dehydrogenases that oxidize diverse aliphatic and aromatic substrates as well as histidinol dehydrogenases essential for the final step of histidine biosynthesis. It is native to Schistosoma japonicum (Blood fluke).\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 3066, 5961, 43, 18727, 9294, 3418, 1988, 3618, 4517, 43, 4743, 5386, 1927, 22234, 1930, 10761, 25075, 2193, 24221, 1966, 43, 15155, 18, 2052, 6804, 3031, 12850, 1990, 5305, 8666, 1930, 18626, 2687, 4248, 1930, 1977, 2435, 1922, 18150, 2014, 30442, 5038, 3436, 4802, 16, 10520, 16, 1930, 9902, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 1920, 18727, 19, 27507, 22816, 1945, 9294, 13975, 16, 2154, 21569, 6577, 12, 58, 13, 17, 3100, 27388, 1036, 1988, 18170, 1920, 7309, 1927, 3425, 25075, 1930, 21773, 16, 2427, 1966, 54, 17, 27507, 22816, 1945, 16, 2460, 2310, 3980, 18708, 4576, 18, 2144, 5038, 16, 4378, 2007, 43, 5305, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 4346, 3418, 1930, 43, 6804, 8666, 16, 3951, 18727, 9294, 1036, 1988, 3618, 2606, 6445, 22234, 1930, 10761, 6249, 1966, 2486, 1966, 27507, 22816, 1945, 9294, 1036, 4415, 1958, 1920, 3948, 3537, 1927, 13873, 8132, 18, 2176, 1977, 6196, 1942, 16587, 20084, 18913, 1989, 12, 2877, 2848, 3324, 13, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "KLDELANYESVLCVASVTRYYAEYLMRVDDMVGLLITSESYSFLSCISKVVPCLCTGYTIMLKEAAVTDFRRYSGILYVSIMYRLKCTCSSLRLFTTLRKATGVVAFPVLRTLSFSIFLMRLI", "metadata": {"id": "A0A4Z2D7F2", "cluster": 9282444, "interpro_all": ["IPR016161", "IPR016162", "IPR015590"], "interpro_used": ["IPR015590", "IPR016161"], "interpro_unused": ["IPR016162"]}, "task_type": "infilling"} {"instruction": "The protein possesses 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. Also, it is part of the Winged helix DNA-binding domain superfamily, which features a winged helix-turn-helix motif responsible for sequence-specific DNA binding. This domain anchors to the DNA major groove via a recognition helix and interacts with the minor groove or backbone through beta-sheet loops, while frequently facilitating protein-protein interactions via an exposed hydrophobic surface. Furthermore, the protein features 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 is derived from Hyphomicrobiales bacterium and carries UniProt keyword assignments Transcription regulation.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 14465, 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, 2222, 16, 2176, 1977, 3131, 1927, 1920, 12920, 1919, 7864, 2678, 17, 2743, 3418, 13975, 16, 2154, 4075, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 5219, 5061, 1958, 3244, 17, 2487, 2678, 2743, 18, 2052, 3418, 27127, 1942, 1920, 2678, 3044, 15920, 3454, 43, 5708, 7864, 1930, 9034, 1956, 1920, 5857, 15920, 2014, 10787, 2596, 4666, 17, 11130, 11109, 16, 2679, 5467, 12440, 2213, 17, 2213, 3719, 3454, 1925, 4616, 7919, 3154, 18, 3677, 16, 1920, 2213, 4075, 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, 1977, 3595, 2037, 2483, 25808, 1935, 7839, 1918, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 3213, 3640, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MLNRLNHPVAGQGLHPSDCRLNVTGLSPLKEIISFERGQGAVAQSAILDDGRRQIINYFTPQSTLTWVSMQSLTSSPTMAPNAISELSSEEKICHFLSEITHRIGAICNRKDIADYLALNTSTKTIIVHHFECIHESPIRRICGDNKCNFKHDVPRVSIGRDINRDDHILIVVEGDVIFSIGDLTADDYRVETLSQYLIQTQLERSNRNQVSLGFYKGGFRIHLPMVIKALRDMQKYGMITFVSP", "metadata": {"id": "A0A2N6AU30", "cluster": 9764154, "interpro_all": ["IPR000595", "IPR018490", "IPR012318", "IPR014710", "IPR036390"], "interpro_used": ["IPR012318", "IPR036390", "IPR000595"], "interpro_unused": ["IPR014710", "IPR018490"]}, "task_type": "infilling"} {"instruction": "The protein incorporates a Coagulation factor 5/8 C-terminal domain that mediates binding to anionic phospholipids, particularly phosphatidylserine, on cell membranes such as platelets and endothelial cells. Found in blood coagulation factors and adhesion proteins, it typically utilizes an amphipathic alpha-helix to facilitate membrane interaction and is stabilized by a conserved disulfide bond connecting the domain extremities. Additionally, the protein should have 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. Additionally, the protein carries 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 is present in Actinia tenebrosa (Australian red waratah sea anemone). 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, 19683, 43, 12441, 2991, 25, 19, 28, 45, 17, 4262, 3418, 1988, 10412, 2743, 1942, 19696, 15619, 16, 4443, 28563, 16, 1990, 2024, 5726, 2427, 1966, 10097, 1930, 5003, 2094, 18, 2435, 1922, 2877, 12441, 2790, 1930, 6141, 2697, 16, 2176, 5745, 18127, 1925, 26747, 21494, 4595, 17, 7864, 1942, 6628, 3260, 2835, 1930, 1977, 12017, 2007, 43, 5305, 11830, 5403, 15031, 1920, 3418, 18884, 18, 4950, 16, 1920, 2213, 3066, 2162, 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, 4950, 16, 1920, 2213, 16252, 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, 1977, 2481, 1922, 4718, 2126, 5656, 13495, 2263, 1019, 12, 13078, 2312, 8200, 5499, 1023, 9309, 9860, 3947, 1021, 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": "MAAACMALANQVCSTQPKIRGRYGLSGVLNTPGYPSKYKQAETQIWNITVPIDNSIRLQFIHFQLQQVDCKNLYIEIRYDNQNTALCSYNSSLPLTFQTSGRHLIIELFNPDGLENRFLAYYKAVARDEPIVPCAYPLVHEYEGVCYGFQNNLAGQDPYNTCKEVKSTPASLITDKENVYAVGLLHQHGYSEALIGLKHSPTNNSYLWMDGSTLVLTRWSQGDPPVPPDQGLVYCAALNSDSKWHQKLCFIQSPVLCKRKVLPRSLSSDTCSSPLGIQDKRIENSLISASTSNFQKGASEARLYHSNWWQSNKNDNEQWIEVKSPSGKFNITGVAIQGSPNGQNFVKNFWIYYSNHGSELILYNKGHNKNAWVFRGNIGKGVQFVLLRPSVVGWRIRIHPRQWEGSIALRMELYGCYLKEQNNCTLPIGMQDMEIKDEDINASSSTLPMNPRLHWDLLSSSEHSGWRAGVLNSMQWLQIQLKNHYKITAIATQGLASDYAWEWVTKYRLSYSHHDNVFFYYEEANEIKVFEGNSDRNSVVKHFLNIDQANHVRILPKTWNGHISLRAELYGCKVEKTKGGCDIALGLETGAIPDGNFKSSSNYNAYHDAKGARLNFLGKPGTTSGWSAGKNDQNPWIMVKLVDLTLVTGVATQGRDDWPQWVTRYQLRYSDNGQQFIMYTENGNVKTFVGNYDQSTIIKQYLQNPVRMHYLRLYPVDRFGWISMRMEIYGCNFTFSESDLCSHPMGMGSTYIPIQAISASSKMNDERSPNASRLIPETNDGNKGWRPIYSTPNEWLQVYFGTRSKITGIATKGIKDQSSWVTWYHVLYGMDGNAFQPYFNYSSLSTPMGNVNGYGIKKHYLKPAIEAIYIRIAPKEWYGGIALKVEFYGCGNSYTANAMKTTCNASIGLEDGAFLSPAFQASSVKPSRAYSPSYARLNNMSAWTAGHSNEKQWIQLYFKDVHIITAIATQGIADKQEWVKSYRIAFSNSYEENTFKVYNSSTMTAKVFKGNLNNSDIVKNEFNPSFTAKYIRLLPVTWNIRISLRMELYGHTDPTLSIPGVPLGLENGAVKDAAINSSSYLHSYYYPWQGRIRWENTTHSFWSPSNNDLKQWLQVDLGKITNLTGVATQGANNEQWWVTSYVLKFASFSATNGFEYYIENKNPRIPMRRGIY", "metadata": {"id": "A0A6P8IEE3", "cluster": 11736932, "interpro_all": ["IPR001304", "IPR016186", "IPR016187", "IPR000859", "IPR000421", "IPR008979", "IPR035914"], "interpro_used": ["IPR000421", "IPR001304", "IPR000859"], "interpro_unused": ["IPR016187", "IPR035914", "IPR016186", "IPR008979"]}, "task_type": "autoregressive"} {"instruction": "Function:\nThe protein contains 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. Additionally, the protein should have a Retrovirus-related Pol polyprotein from transposon TNT 1-94-like, beta-barrel domain that is predicted to adopt a \u03b2-barrel fold with significant structural similarity to retroviral acid proteases. It is typically found in retrovirus-related Pol polyproteins from transposons across eukaryotes, including plants, fungi, and arthropods. It is identified in Pisum sativum (Garden pea) (Lathyrus oleraceus) and is described by 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, 5461, 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, 4950, 16, 1920, 2213, 3066, 2162, 43, 23987, 17, 2712, 2492, 6240, 5684, 2037, 18808, 24185, 21, 17, 5650, 17, 3189, 16, 4666, 17, 19560, 3418, 1988, 1977, 4396, 1942, 14103, 43, 161, 17, 19560, 3728, 1956, 2228, 4346, 6796, 1942, 16599, 2687, 12447, 18, 2176, 1977, 5745, 2435, 1922, 23987, 17, 2712, 2492, 6240, 10355, 2037, 18808, 1036, 3436, 15021, 16, 2710, 4793, 16, 10520, 16, 1930, 21680, 13816, 18, 2176, 1977, 2899, 1922, 17850, 1989, 15036, 1020, 1989, 12, 26981, 20384, 13, 12, 4144, 30338, 3176, 1036, 12188, 5524, 1972, 1957, 13, 1930, 1977, 2910, 2007, 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": "MARVECYHCHKHGHYQYECPVKEKETKVHFSETEEEFLLMAYSGNMSWFYDLDERFRETVKLGNNSCISVMGKGDIKFHVKNNIIHTIIIIIQQSKCQIPHPEKGLIAEAEMTSNQNTWDWDSESQLQLPTKSLGEILPNPSSTVSTPNEDKDKDNLLCNTWYLDSGCSNHMCSSAFYVPDLKSNLIIMGQPQEKCYRSTEKQQMLIDGEEVGETSQ", "metadata": {"id": "A0A9D4WYR7", "cluster": 17341910, "interpro_all": ["IPR054722", "IPR001878", "IPR036875"], "interpro_used": ["IPR001878", "IPR054722"], "interpro_unused": ["IPR036875"]}, "task_type": "infilling"} {"instruction": "Output the amino acid sequence for a protein 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. It has been characterized in Arthrobacter sp. Soil736.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 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, 2176, 2258, 2252, 4378, 1922, 9273, 15129, 2422, 2056, 18, 6072, 8966, 1016, 18, 3], "output": "MATDKESIREFPPMSARINGDNTGVLMIGTNEQLVSGESTNDVRRALIGMVQKEAELAGQTLRVTTSDDEGIEVLLVHPDGTLRLDDKRPADPVEAPQPEVQAEPVIVRREAPATAVAVKDRAPAVTRERASRPAPVIAPEPVSVETDGMVESAAAASRRWNPEFVNASTVTTVAEREKDDSLFYVLGHGYDLDDFLQDGPAEQGFNGWLNKATGGSSKLAPGLSETAARREQAELLCCERIIRQATWQRGSVAFTVANKKGNSAKTPATVSVSGILASIRGGSVAMMEVSDDPGQLAGRSEGEQRSGIGELVLNAAYVTTKAQLEGYALPQTSFAHTFGSSPTRRAPLDRESIETVSALIDQFYTIRAMDSGNVYTSSAFAGAMATSDALLVPMMNASDSMGEAVELFHFLESHDDPHFRELAKRAIVVRVSDGRPEYKVERLVKDFMHQTGVAADRMFTVPYDAHLAERGAITLDKLAPATRAALVRISAALVVQLQDAVANPTTLTTTGRRGQTTQAH", "metadata": {"id": "A0A0Q9M6P3", "cluster": 18954783, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Give me a peptide sequence capable of: The protein should feature 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. In addition, the protein is grouped 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. It is found in Pseudomonas sp. Leaf58.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 3066, 5961, 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, 1922, 2459, 16, 1920, 2213, 1977, 10809, 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, 2176, 1977, 2435, 1922, 13461, 2056, 18, 6998, 7532, 18, 3], "output": "MVAVVKAKTPSKRATSDLADFATRVRQARKLLGLSQQGLSDASKIPASTLKNYELGHSSPSAENLQKMFRVGINPMWVLLGHKPVLVETFTSPTTRHSRALAAAARRDAAALSTGRPQPRAPSKPPIASKRAITTIKRENAPSPTSSTPEVDND", "metadata": {"id": "A0A0Q4MZS2", "cluster": 19090560, "interpro_all": ["IPR001387", "IPR010982"], "interpro_used": ["IPR001387", "IPR010982"], "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 classified under 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. It is native to Methanobacteriota archaeon and contains UniProt keyword associations Membrane, Transmembrane, and Transmembrane helix.", "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, 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, 2176, 1977, 6196, 1942, 17348, 5883, 3940, 3857, 13470, 1916, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTNPGANTKISGTSVTHSASGGTSWTFDWIPPAVGSGDVTVQLAVVWSKTLFIIAELEEKDSDGDGFTDSNDAFPNDPEFPNDPSETSDSDGDGVGDNSDWAPNDPAESADTDASETTDSDGDGVGDNSDWAPNDSTESADTDGDGVGDNADEFPDDASETTDAPNDPAETADTDGDGVGDNGDAFPDDASETLDTDGDGVGDNSDWAPTDATAFPEDPAETQDSDADGVGDNTDAFPNPNDASESADTDSDGVGDNADAFPNDATETQDSDLDGVGDNGDNADAFDDDPTETTDSDGDGTGDNSDVFPDDATETEDTDEDGGDGVGDNSDWAPNDAAETADTDGDGVGDNADAIAEAEAARQKAADEKRRNSIIIGIVAVVVIIAAIAVFLRYVHNQLQILNQWKDQSGYTWRKMSDGSFHYWDGEQWIKHSMNANLASGNNGDNEWEDSDNDGVGDNADGDGVGDNADEFPNDSDGDGVGDNADWESADTDGDGVGDNGDDATETVDSDLDGVGDNSDWAADAFPNDAAEVSDTDGDGVVGNNADAFDNDPTETADSDAFPEDATETLDTDGDGVGDNAQKPNNNGKDSVTKDYSQTQTSGPAP", "metadata": {"id": "A0A8S8XNY4", "cluster": 20000656, "interpro_all": ["IPR028974"], "interpro_used": ["IPR028974"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein incorporates a Beta-ketoacyl synthase active site that catalyzes the condensation of malonyl-ACP with a growing fatty acid or polyketide chain. Utilizing a conserved cysteine residue, it mediates a two-step reaction where an acyl primer is condensed with a malonyl donor, resulting in chain elongation and carbon dioxide release. 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. Moreover, the protein should include 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. It is produced by Rhexocercosporidium sp. MPI-PUGE-AT-0058 and has UniProt annotations Multifunctional enzyme and Transferase.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 4666, 17, 21471, 14645, 8921, 3500, 3200, 1988, 17097, 1920, 16112, 1927, 3054, 12831, 17, 18543, 1956, 43, 6552, 5934, 2687, 2014, 4286, 18540, 2261, 4659, 18, 10232, 43, 5305, 8666, 6181, 16, 2176, 10412, 43, 2288, 17, 3537, 3227, 2597, 1925, 11337, 6194, 1977, 20481, 1956, 43, 3054, 12831, 6282, 16, 3864, 1922, 4659, 9971, 1930, 5056, 15422, 4012, 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, 3950, 16, 1920, 2213, 3066, 3951, 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, 2176, 1977, 4152, 2007, 8472, 1039, 1994, 3234, 9890, 9734, 2056, 18, 26586, 17, 6612, 2106, 17, 2019, 17, 9163, 1025, 1930, 2258, 20709, 15010, 20136, 4113, 1930, 13763, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MERNYGDALEPIAVVGMACRFAGEASSVDKLWEMMKGAISTKRGFFLKEDVSLFDAPFFSMAANEVVGMDPMQRQLLELAYESFENAGMSLQDLIGSSASDTYHLPLNSASGTGRAMLSNRLSWFFDLRGPSLTLDTACSSSLYALGVNLILHPSLMSQLSSMHMISVDGISHSFDVSANGYGRGEGVGGIVIKPLSAALADGDTIRAVIRGSGVADLISATYLAAGLTFEDTSYFEAHGTGTALGDPVEMRAVAATIGKARKHHSTPLYILCLEKGVLTPVVGFKTLNPKLHFSDWHMALPLETMAWPTPGLRRGSVNSFGFGGSNAHVILDDALCPSGPANPPAALSNGHFSHEQLFVFSSSDKAGLHRVAEAYKGSFLPETVRLDFLSYTDYRSFVVADSQPSLMRALARGLPSFPRRSGLGMPALVFTGQGAQWVGMGRELISNAIYRESVLKSQHALSSFDRPSISQPICTILQIALVDMLFAWGLVPGAVVGHSSGEIVAAYAAGAISQHDAMKVAYYRMMAAGISEEEACSYLKHEVVNNEVVIGCVNSPFSVTLSGERKAIERLELILQRDHSPQMQVVAADFLESIGEITTAPSFRYPMFSSVTTKRVPHPQDLGPSYWVRNMLGSVKFAGAVWAVLLEVGPAKTLKGPLDQILAALDPSFSEKISYTSILQYQKSAVTTAFEAMGHLWCSNNVLANVLKPQALTMLPSYPWNHKTRFWHEPEANRSARHKRWPRTDLLGMPYENQNPFEPQWYPGAGILIMVLEAACQMADPQSIAGVDFEDVFFERGLVIPAEDSAVEVSLNIKPKGAGWTKHAHGMFLLRLPPANENDLVASQSEWAFLKSQHADLTQLPSKPVDAANFYQELKAAVSFDGVRSASGRVLVPDTRSSMPSEFEFPHYIHPATLDAMFHLVYVALSGGARMAEAAGAKYTGFSHATSTKDGGCADLLFSDEQWTGPKVHFQGIRLQSVSSEKSNHSKATPTQGPLAAARIKEEAYTAHTKCLGVGAKYTTEACVAWLRRLCHKHADLSVLVAMGVAGGQEILKSCTVFNSSERNLDILKKSLVERNITCRYSRSLASEVLDSYDLVICDVDTVERENGCLGQRSSLGSPVEKKLLSTGFNGLSLQIQDDKDAFIVTRLDEKHNDTPHIAEVYLLQPTIVSSMEITTRVICLDQVSDLKDKTVISLLEIEQPFVLTWTGNELEHFRTLVSSAECVLWVSRGGFLSPDIQLPHLDLSRDLGSEHAASVICKLLQSTSASPLKNNETEYIELAGHLHIPRLTKSSYLDRFLADLGPSADIDTFDSIEDDEVVICSSFTTPNTLGPQVSAPALFDTLVGKVSKVRHAQVCPLPSSFNAAFGAYISLGMASAWHVLFHVTRLKRGDHVLIHVKSKQLSRFLALIAHHLGAVIFLVVDSSSILQQHVLRATGSVGVHFLITTCHGLPLNRLASCITEDGHLVDLGLKSATLCKLFTEASQHLDIGLFHRLPKPVVKDITELDVFLQDAHGGPEGNASVFSSTSTGMLNPQGTYILSGGLGALGLAIADDLINYGARHLVFLSRSGPTSLVQKATLQSFRARGCMLCKDNNWRVTGVLQCAMVLRDAIFENMTIESWRQAIDPKIKGSWNLHLHAPAAHLEFFIIYEDALAHYRQSLGLPATTLNVGLVTDASHFHSDYTIEDYLKKFGHLAPISVDIHELLSCLAIIMTRPAHRDLSYVWPNDRKFDHRVQDADEHDERRELDIETSLKESKSAAQALSVVENFLRRRVAASITALPNWIQSELKCGISVFDIMSPMSLTELALQMAAKSPFTPANLVPEVISLTASMNGRHAASDIPEDRFNADAWYHPSPERHTAVYSGVMTNDYELIHLACQALRQGEASQALVTNQDGKTPGITMPSEQAQVGSVKTNIGHTEGMAGLAGVIKTHYLHSRGLSGNHITAADRLSSRRTHFRSFGCDWDVLDMLSGSRVGIHSEEIPRRLKHLEGAGKFARRLRVDVAYKNMICSPASRGNGGKRNEHGCSIDLVKVNNRNVLGIRENPWLKDHIITETCLPHESIPSRYCFAVYSMAGLEYGPLFTNLDEAIPVQIDRAFISTSLPSGSERERPSRTAQIQWLEDVDFFQRYAPDQKNNSSETFRFWLDTLRLLLRKSGSLALIQDLMSNLQEQLKLSLQFAPTTGLLRTIRVEHSSTTMPPNSKQLDSRHGDDPRKELVIGLMVLDLQLGQNVIVFGPKAVKGHIKVEDEDFWQAMGDVAPTTILDSEQNIQAADFPRTFFQRNITFSSVDLMKFEEPAISTPDSLTPKIDSLKCDISNAEEVERAMLSSMSAVIGNSAQANYCAGNSVVVQPLPPQLLIGVSDQIPREDIDVGRPLFSFGFDSLKAMETR", "metadata": {"id": "A0A9P9MNN8", "cluster": 21941073, "interpro_all": ["IPR001227", "IPR036736", "IPR014043", "IPR016035", "IPR018201", "IPR014031", "IPR014030", "IPR016036", "IPR036291", "IPR056501", "IPR032821", "IPR020841", "IPR042104", "IPR020807", "IPR049551", "IPR049552", "IPR020843", "IPR013968", "IPR049900", "IPR050091", "IPR020806", "IPR009081", "IPR006162", "IPR016039"], "interpro_used": ["IPR018201", "IPR006162", "IPR020806"], "interpro_unused": ["IPR001227", "IPR016035", "IPR013968", "IPR056501", "IPR042104", "IPR016039", "IPR049551", "IPR020807", "IPR009081", "IPR014043", "IPR049900", "IPR014031", "IPR020841", "IPR014030", "IPR036736", "IPR032821", "IPR016036", "IPR049552", "IPR050091", "IPR020843", "IPR036291"]}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: It is part 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. Additionally, the protein falls within the Diverse Retrotransposon and Effector-Associated Protein family, which encompasses proteins involved in the replication and mobilization of retrotransposable elements, as well as secreted oomycete RxLR effectors that mediate host-pathogen interactions. This diverse group includes retrovirus-related pol polyproteins and uncharacterized mitochondrial proteins associated with mobile genetic elements. Additionally, the protein includes 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. It occurs in Acer negundo (Box elder).", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 2176, 1977, 3131, 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, 4950, 16, 1920, 2213, 12182, 2651, 1920, 6445, 27181, 1916, 1930, 7917, 17, 2458, 2213, 3416, 16, 2154, 21569, 2697, 3286, 1922, 1920, 5158, 1930, 14586, 1927, 27181, 2115, 5362, 16, 1966, 2486, 1966, 8366, 57, 13386, 11555, 21159, 4844, 13066, 1988, 8265, 4423, 17, 7055, 3719, 18, 2052, 6445, 2210, 5921, 23987, 17, 2712, 2492, 6240, 10355, 1930, 24528, 4596, 2697, 2458, 1956, 8785, 3299, 5362, 18, 4950, 16, 1920, 2213, 5921, 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, 2176, 5110, 1922, 8298, 1005, 2922, 2652, 1037, 12, 5758, 7177, 13, 18, 3], "output": "MENIIQSFFVNLFKSSSPSQEDIESPFLGEEDVITACLKCLNEGAALGNMNDVGFECLHRLKRRKRKFGSMALGFFRLWVNWIIRCISSVSYSFVLNLFLFCAEGFSSLVNVVLVNEHPKLSPAMSRVLDTLLVLIPKRFIPRRRISDNTIIKLDMSKAFDRVEWIFIEKMMLKGEICEICGFVKPSRGLRQGDPLSPY", "metadata": {"id": "A0AAD5J0G6", "cluster": 22036985, "interpro_all": ["IPR043502", "IPR052343", "IPR000477"], "interpro_used": ["IPR043502", "IPR052343", "IPR000477"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein has a Sterol-sensing domain that confers sensitivity to sterol levels through a conserved cluster of five membrane-spanning segments. It functions in cholesterol metabolism, transport, and signaling by undergoing conformational changes upon sterol binding to modulate protein activity. This domain is found in both metabolic moderators and transmembrane transporters, including bacterial multidrug-resistance proteins. Also, the protein includes a Protein export membrane protein SecD/SecF, C-terminal domain that forms the C-terminal region of prokaryotic SecD and SecF subunits within the multimeric Sec protein export complex. It functions in concert with SecA, SecE, SecG, SecY, and YajC to facilitate protein secretion and is essential for maintaining the proton motive force. Furthermore, the protein possesses a Membrane transport protein MMPL domain that functions as a component of transmembrane export systems for complex cell envelope lipids and siderophores. Often occurring in tandem copies, it is required for the biosynthesis and secretion of polyacyltrehalose and diacyltrehalose in mycobacteria. It is identified in Alphaproteobacteria bacterium and carries UniProt keyword assignments 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, 2258, 43, 20408, 17, 9306, 3418, 1988, 16556, 3802, 1942, 20408, 2428, 2596, 43, 5305, 4377, 1927, 3628, 3260, 17, 13346, 7492, 18, 2176, 4088, 1922, 5463, 4714, 16, 4860, 16, 1930, 3197, 2007, 7258, 8523, 2840, 4073, 20408, 2743, 1942, 8480, 2213, 2455, 18, 2052, 3418, 1977, 2435, 1922, 2321, 4487, 27665, 1036, 1930, 9117, 10538, 16, 2710, 4543, 16398, 17, 3554, 2697, 18, 2222, 16, 1920, 2213, 5921, 43, 2213, 12660, 3260, 2213, 2532, 1007, 19, 2532, 1038, 16, 45, 17, 4262, 3418, 1988, 4952, 1920, 45, 17, 4262, 3031, 1927, 21545, 2532, 1007, 1930, 2532, 1038, 6991, 2651, 1920, 11129, 3383, 2532, 2213, 12660, 2796, 18, 2176, 4088, 1922, 21799, 1956, 2532, 1019, 16, 2532, 1021, 16, 2532, 1029, 16, 2532, 1012, 16, 1930, 26169, 30271, 1942, 6628, 2213, 5512, 1930, 1977, 4415, 1958, 8231, 1920, 8433, 7038, 1021, 5495, 18, 3677, 16, 1920, 2213, 14465, 43, 3260, 4860, 2213, 6736, 1024, 3418, 1988, 4088, 1966, 43, 4594, 1927, 9117, 12660, 3771, 1958, 2796, 2024, 11262, 8238, 1930, 22940, 14820, 18, 3868, 6966, 1922, 10361, 9425, 16, 2176, 1977, 3414, 1958, 1920, 8132, 1930, 5512, 1927, 4286, 14645, 4265, 7289, 2217, 1930, 25141, 13796, 19174, 5920, 20807, 4127, 1922, 23446, 18, 2176, 1977, 2899, 1922, 4595, 9218, 1021, 10296, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 2024, 3260, 1930, 9117, 7864, 18, 3], "output": "MKYIVKLILQTSVARPIISMVVIGLLAILAAVGVLRIQYEDGLKTLFSSEFTQNETNIAVLVETKNGFNSASLTELQDFILEVQFVDGITAIRSIFSLRRFDEANESFSPLLPMISNDLKQTVVILSISPKMSEIGGTAKILHNLRQLTDEFAQSARFDSGGLKFGITGLLSVRASIIKGVSLIAFRSFWVAAVNTITPVAALLFSLGAFGWLGMPINVLTNALPVLLGEGELEAIKNTMREMASPSILTSLTTILAFSSLFYSQSPIIRDLALAGASGVFIALVVVLPGKTVNIGGIFHAIIRHSRSISVIGALLSAGALWVLLPLQTSYRFLENIDTTTPAAVVLDKVDPSVNQDLAAIHRALEQVQEVRSVLSVFNLLERATAGTSTTGARDLSRVLALFPDRVQGSRAVARLVKRADRALAGLDLKALKPARPTGFLVMSSTLSDSMIRQLTISFLIAALALAAVIPNILPIAFVGGLLTLTGQGIQLTSALALTIAFGIALDDSIHVFNRLDLIDTAILSAGIMATQVSVMPMIRLFGLLCIATFALALLCDLVLLPAIISWLKRPFRRVSPAFQDYKTQAKSSDLNDKKALGAALKSASGAGSTAPALKTDQMRINLLGAVLGFIILVLASSDSIHITYEIRRRLGFLHPLVFVIAMRVPIIRRSLPKAPKEKVAGPISSINIPLRLNVGVNLSSVLISKDQRELQVLLMVPDNSCPILIGLWFRRVDFRDKTKVTPDQDIWLGMVHISPVLVTT", "metadata": {"id": "A0A9E6BKJ0", "cluster": 23037679, "interpro_all": ["IPR004869", "IPR050545", "IPR048634", "IPR000731"], "interpro_used": ["IPR000731", "IPR048634", "IPR004869"], "interpro_unused": ["IPR050545"]}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nThe protein should contain 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. In addition, the protein contains a Methyl-accepting chemotaxis protein (MCP) signalling domain that functions as a highly conserved transduction module within bacterial receptors to mediate chemotaxis. It responds to changes in the concentration of environmental attractants and repellents by transmitting signals to the downstream histidine kinase CheA to regulate swimming behavior. Furthermore, the protein should contain 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. It is derived from Desulfobaculum xiamenense and exhibits UniProt keyword tags Transmembrane helix, Membrane, and Transmembrane.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 3066, 5531, 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, 1922, 2459, 16, 1920, 2213, 5461, 43, 4963, 17, 26170, 16884, 2213, 12, 11942, 13, 8076, 3418, 1988, 4088, 1966, 43, 3626, 5305, 8201, 9059, 2651, 4543, 4086, 1942, 8265, 16884, 18, 2176, 20575, 1942, 2840, 1922, 1920, 3110, 1927, 4813, 24670, 2356, 1930, 3699, 11560, 2039, 2007, 27622, 4771, 1942, 1920, 5863, 13873, 4016, 10003, 1019, 1942, 5741, 15781, 3379, 18, 3677, 16, 1920, 2213, 3066, 5531, 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, 2176, 1977, 3595, 2037, 30311, 14357, 7705, 27645, 19047, 4480, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 7864, 16, 3260, 16, 1930, 9117, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MRFRSMATGFMLTVVLVIITSVAAIVFMATLTGSIVTQLDDFIDKGSDVVTGLAMQSAVQNALVRNSSFGIVVSGLNANGSDLRGMDVSGFSFVQGIANGDAAFIDRNLVRELVGGVVASVDWEKFTQKVVTPVTIGTSGYAYMYDQNMREDFETTIRERQTGTLFYEYEGEGKVAVFSHHPGTGVLLGIGAVAVFVLAVLVMLLFRRRVITPLGRVGAFAEAEFRYEIADLARHIATMTGELKSKLAFAQGVAAMVEAVGREGSSDDYLGRTTADFAFGDASRTDFVTHKGEKRVFSVVATPLYDLDGKVFGALTMWLIEDVAHKASTVSDQVASASEELSAQVEQSSRGADQQNASVLEVARNASAAAEIAERTRSTARKGVDVVGEVIHGFDEDIADQTNLLALNAAIEAARAGEAGRGFAVVADDSTGRTMQDMSESGAIMKTLSGQTEEAVSSLRDILAMVQISQSAGDINRIADETADAMTQSASAVTSLARLAGDLQELIGTMRFYANRAVYQLEVDTNTEDQQLQNMIRNNKAFEAVFMFNMNGKSPVSKHLTFCIAAPVSRGGVIAHPDSKIILLDAPLWIVVLTATERDLAAGATQVRNVASGDLKAELSGLGGIAMPCAVADAEERLTFLNTVLAKAIREKRQVTQEIFDLTEVRMQQTAIEQKNARGMAAEAATAIEQMRVHSGFLQVDESMKGLGTQAEGISTIVQVIEVRKLAEKTMTATKEVGRAVHAIQEETSAQVQSIASAAEEQSAASE", "metadata": {"id": "A0A846QM78", "cluster": 23393660, "interpro_all": ["IPR033479", "IPR003660", "IPR004089", "IPR000700", "IPR035965", "IPR013656"], "interpro_used": ["IPR003660", "IPR004089", "IPR000700"], "interpro_unused": ["IPR033479", "IPR013656", "IPR035965"]}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein is associated with the Splicing factor, RBM39-like family, which comprises proteins such as mammalian RBM39 and fungal Pad1 that function as RNA splicing factors. Members of this family typically contain an N-terminal arginine-rich low complexity domain followed by two or three RNA recognition domains, sharing structural similarity with the U2AF splicing factor family. Also, the protein is categorized in the Bromo adjacent homology (BAH) domain superfamily, which functions as a protein-protein interaction module in chromatin-associated proteins to facilitate gene silencing. This domain links DNA methylation, replication, and transcriptional regulation, often by binding to partners such as silent information regulators. Also, the protein should contain a Agenet-like domain that adopts a bent beta-sheet fold and functions as a reader module for methylated lysine residues, specifically recognizing trimethylated peptides or histone H3K9 methylation marks. It is commonly found in proteins involved in chromatin regulation and RNA metabolism, such as the neuronal FMRP family and plant transcriptional silencers. It has been detected in Protea cynaroides.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 1977, 2458, 1956, 1920, 8490, 2991, 16, 26543, 6021, 17, 3189, 3416, 16, 2154, 12936, 2697, 2427, 1966, 6492, 26543, 6021, 1930, 8697, 9941, 1009, 1988, 2347, 1966, 3146, 8490, 2790, 18, 4678, 1927, 2052, 3416, 5745, 5531, 1925, 56, 17, 4262, 9732, 17, 5536, 2330, 7778, 3418, 3489, 2007, 2288, 2014, 2559, 3146, 5708, 4682, 16, 10763, 4346, 6796, 1956, 1920, 15823, 2624, 8490, 2991, 3416, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 21392, 6811, 9039, 12, 24891, 13, 3418, 13975, 16, 2154, 4088, 1966, 43, 2213, 17, 2213, 2835, 9059, 1922, 6338, 17, 2458, 2697, 1942, 6628, 2359, 8343, 18, 2052, 3418, 10069, 2678, 5547, 16, 5158, 16, 1930, 5224, 3640, 16, 3868, 2007, 2743, 1942, 7228, 2427, 1966, 15381, 2988, 9098, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 2632, 14278, 17, 3189, 3418, 1988, 24032, 43, 13847, 4666, 17, 11130, 3728, 1930, 4088, 1966, 43, 10571, 9059, 1958, 11882, 9082, 4248, 16, 4475, 15667, 21849, 1981, 5320, 2014, 6632, 16149, 5547, 13387, 18, 2176, 1977, 5384, 2435, 1922, 2697, 3286, 1922, 6338, 3640, 1930, 3146, 4714, 16, 2427, 1966, 1920, 5121, 27884, 3416, 1930, 4496, 5224, 24974, 5675, 18, 2176, 2258, 2252, 3330, 1922, 2174, 1019, 23836, 15742, 3726, 18, 3], "output": "MFVLNRSVATFLGPGNQIAPYQPASQTLKFRLSGRMPTTARQDSGTRGCWFRCTLLRASQKQLKFQYNDLQNEDGCGNLEEWIPAFKLSAPDQWTFLLRKELKWMHGGVVHAGLIPVVRVLEDPSTEKKEEAEPEADDVYEFFSWAGKGRIARKLKGCGTDIVWSGAAWACGKQLKHYPAREENHYLAYLEDMYEDNKGQKKVISAESVDGATTILTLSAMRNASLLFPIIPQLYLGPHAWLTTPFKVHEKIELLCKLGQYTLVASQFGHALLSIPERDQRTVFAYQICLKADEKSCRNGTTIASHSFVFIMA", "metadata": {"id": "A0A9Q0L3E6", "cluster": 23636399, "interpro_all": ["IPR008395", "IPR043151", "IPR006509"], "interpro_used": ["IPR006509", "IPR043151", "IPR008395"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein should have a YtkA-like domain that is typically found in the C-terminal region of the copper transport protein YcnJ. It is involved in the uptake of extracellular oxidized copper under copper-limiting conditions in organisms like *Bacillus subtilis*. It is native to Alteribacter lacisalsi and is classified with UniProt keywords Signal.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 3066, 2162, 43, 24412, 7640, 17, 3189, 3418, 1988, 1977, 5745, 2435, 1922, 1920, 45, 17, 4262, 3031, 1927, 1920, 9541, 4860, 2213, 22386, 1022, 1013, 18, 2176, 1977, 3286, 1922, 1920, 5047, 1927, 5329, 11339, 9541, 2441, 9541, 17, 8051, 2961, 1922, 7373, 3189, 14, 14587, 14745, 14, 18, 2176, 1977, 6196, 1942, 4238, 26073, 2341, 1915, 7511, 16516, 12924, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MLRKAMLLAIIVIAASLSAGCLNPLLIRVTQGGEPLDTAEEVMFEVWMYESMYHFEEDNYYYVQPRVKNGRNPDQVPDLPSEMFVSFGLQEGVAAGEADVRFEITNTEGHTSSVEAYSVIIYMEKDDVSEQLSDVVKIESDEGEERENTAEEREPPIDIQVLYESRQDAETEVRHGQSTEAAVLEAEALGDGDRSTTLVSEIIVGRFTVNEPSVVKLQVNWEDEPWEEETAPGEYHGEHTFEALGE", "metadata": {"id": "A0A2W0H4Z1", "cluster": 24010867, "interpro_all": ["IPR032693"], "interpro_used": ["IPR032693"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein contains a PTS system mannose/sorbose-specific IIA subunit domain that functions as a cytoplasmic component of the bacterial phosphotransferase system (PTS) to facilitate carbohydrate uptake. It accepts a phosphoryl group from the phosphocarrier protein HPr and transfers it to a specific IIB subunit, thereby driving the transport and phosphorylation of sugars such as mannose or sorbose. Furthermore, the protein falls within the Bacterial PTS system sugar-specific components family, which mediates the simultaneous transport and phosphorylation of carbohydrates via the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). These proteins facilitate the transfer of a phosphoryl group to specific sugars, such as mannose, fructose, and N-acetylgalactosamine, during uptake and may also participate in bacterial chemotaxis or phage infection. It is produced by Tetragenococcus osmophilus and features UniProt keywords Kinase and Sugar transport.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 5461, 43, 8618, 2433, 17936, 19, 20029, 2217, 17, 2487, 17433, 5903, 3418, 1988, 4088, 1966, 43, 6823, 4594, 1927, 1920, 4543, 8078, 9961, 2433, 12, 8618, 13, 1942, 6628, 10590, 5047, 18, 2176, 5861, 1036, 43, 12556, 2210, 2037, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 19180, 2176, 1942, 43, 2487, 19795, 5903, 16, 6113, 9228, 1920, 4860, 1930, 4050, 1927, 15592, 2427, 1966, 17936, 2014, 20029, 2217, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 4543, 8618, 2433, 9523, 17, 2487, 4178, 3416, 16, 2154, 10412, 1920, 5710, 4860, 1930, 4050, 1927, 16282, 3454, 1920, 8078, 9356, 18425, 12631, 2010, 17, 3100, 9523, 8078, 9961, 2433, 12, 8618, 13, 18, 2144, 2697, 6628, 1920, 3856, 1927, 43, 12556, 2210, 1942, 2487, 15592, 16, 2427, 1966, 17936, 16, 15102, 16, 1930, 56, 17, 6894, 5411, 2131, 17454, 16, 2409, 5047, 1930, 2278, 2222, 7352, 1922, 4543, 16884, 2014, 10503, 2909, 18, 2176, 1977, 4152, 2007, 12470, 2432, 8256, 9405, 18239, 1930, 4075, 20709, 11569, 4016, 1930, 9523, 4860, 18, 3], "output": "MIDFLIVTHGSLAAGLLDSTKKEEIEFSISNGRQLLVFTGENVEAIVGVNLSMLLEGLMAGLDGIKDLKEAFELLIVGDASNISVLGFDHGDDPEELEQTIDLFGGTPSNRVVLTIKQLAKSVQQRGDVRTIKGKCLQ", "metadata": {"id": "A0AA37XL25", "cluster": 25082641, "interpro_all": ["IPR051471", "IPR004701", "IPR036662", "IPR033887"], "interpro_used": ["IPR033887", "IPR051471"], "interpro_unused": ["IPR004701", "IPR036662"]}, "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 associated with the PROPPIN family, which comprises conserved $\\beta$-propeller proteins that function as sensors for phosphatidylinositol 3-phosphate (PI(3)P). These proteins utilize an essential FRRG motif to bind phosphoinositides and play a critical role in autophagosome biogenesis during autophagy. It is found in Tuber aestivum (summer truffle) and is linked to UniProt keywords WD 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, 1977, 2458, 1956, 1920, 5062, 9512, 3416, 16, 2154, 12936, 5305, 8, 38, 4666, 8, 17, 5062, 13728, 2697, 1988, 2347, 1966, 9189, 1958, 16927, 23, 17, 5413, 12, 4269, 12, 23, 13, 58, 13, 18, 2144, 2697, 12561, 1925, 4415, 2415, 1005, 1029, 5219, 1942, 4566, 23546, 1036, 1930, 3918, 43, 4140, 2770, 1922, 21631, 13008, 2409, 6661, 18, 2176, 1977, 2435, 1922, 19594, 12893, 2113, 1989, 12, 12495, 2025, 15937, 1952, 13, 1930, 1977, 4624, 1942, 20709, 11569, 17907, 6865, 18, 3], "output": "MKLLHTIETIPNPTAICALSSSLKKCYIAYPRPTNSSASSFSPHSHTPPGVNAPPTASGDVILFGAIKLEAADVIEVHKALLVILSLNSEGSLLATSSDKGTIIRAFFYSRFPETLGSFRRGRYPSRIFTISSKLISTVLCGSSATETVHTLRRDGLNPQESLSRSFRATDLDAGGPLTGSLTSPPNQAGAAGGGFDHYVVSKRRSGSGMFGSIVGRSSQKIGRTIAGAAGGYLPHDVTEMLESARDFAFAKLPNAGLKSVVALSSTSPHTIVVTNDGCFIAHDADVERGGECMLTKQYSLTLIWLTTSRAGICLLDSSKKMGQSLMYD", "metadata": {"id": "A0A292PHH9", "cluster": 25807400, "interpro_all": ["IPR048720"], "interpro_used": ["IPR048720"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a polypeptide chain that performs the following role: The protein is grouped in the YdjM inner membrane family, which comprises putative metal-dependent hydrolases predicted to act as membrane-bound phospholipases. These proteins are regulated by LexA and function within the SOS network to rescue cells from DNA damage. It originates from Candidatus Heimdallarchaeota archaeon and features UniProt keywords Transmembrane helix. 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, 67, 1007, 1013, 1035, 6671, 3260, 3416, 16, 2154, 12936, 6770, 6048, 17, 3100, 30337, 4396, 1942, 4033, 1966, 3260, 17, 4124, 17570, 1036, 18, 2144, 2697, 2032, 4335, 2007, 14596, 1019, 1930, 2347, 2651, 1920, 17668, 3504, 1942, 10162, 2094, 2037, 2678, 4293, 18, 2176, 22970, 2037, 14550, 1031, 1957, 2234, 1980, 3825, 11560, 3983, 3336, 7336, 13470, 1916, 1930, 4075, 20709, 11569, 9117, 7864, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MPDWVTHIITTWLIYQLLARFKILKKNRYNEIILLFGAILPDINRLALIGEVLQPLLLFYTNEQTYYFFLVIHTPIGSLLIAGIIAQIFEKRKETFLYLVGGITSHLMLDMLLTSINKGVYFLFPFSFQPFQLKLLNSMDMSYMIITITIFLCTLFYQKAKNKIVIVNNFNY", "metadata": {"id": "A0A842RB16", "cluster": 982515, "interpro_all": ["IPR007404"], "interpro_used": ["IPR007404"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein can be placed in the DinB/YfiT-like putative metalloenzyme superfamily, which comprises diverse proteins sharing a four-helix bundle fold that typically function as metal-dependent hydrolases or isomerases. This group includes the DNA-damage-induced DinB protein from Gram-positive bacteria and enzymes such as mycothiol-dependent maleylpyruvate isomerase. Also, the protein is classified under the Protein of unknown function DUF1706 family, which comprises hypothetical proteins primarily found in bacteria and yeast, including the budding yeast protein Irc4 (Increased Recombination Centres 4). It originates from Chloroflexi bacterium RBG_13_48_10.\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, 11687, 1014, 19, 29962, 1932, 17, 3189, 6770, 8969, 6802, 1022, 9318, 13975, 16, 2154, 12936, 6445, 2697, 10763, 43, 3006, 17, 7864, 14142, 3728, 1988, 5745, 2347, 1966, 6048, 17, 3100, 30337, 2014, 25510, 1036, 18, 2052, 2210, 5921, 1920, 2678, 17, 4293, 17, 2719, 11687, 1014, 2213, 2037, 8604, 17, 2843, 4802, 1930, 5038, 2427, 1966, 5078, 17809, 1945, 17, 3100, 4005, 2199, 18425, 12631, 2010, 25510, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2213, 1927, 5435, 2347, 4855, 5739, 4618, 1016, 3416, 16, 2154, 12936, 15148, 2697, 5985, 2435, 1922, 4802, 1930, 5688, 16, 2710, 1920, 15909, 5688, 2213, 3166, 17875, 12, 2502, 7827, 13152, 24, 13, 18, 2176, 22970, 2037, 10107, 18222, 1033, 14061, 6160, 1029, 41, 2590, 41, 3427, 41, 2119, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MPGGKIIPEADMRRPTSKVNLIESISAERGLLERKIAGLTPEELVGKRGETVVTPEPGYNWRQMNLLNEKYRLKSKDRPLSEVLAHFSASYMQIMDVIGKYPLMVWIAANTCDHYKWAVQMIHPIAIRRKMKSGKRDNSEYPGTMGEWSVKDILQHLVDWEQRWIGWYEAYKVLEEEMLEPGYYPWT", "metadata": {"id": "A0A1F8LVB4", "cluster": 1895094, "interpro_all": ["IPR034660", "IPR012550"], "interpro_used": ["IPR034660", "IPR012550"], "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 is a member of 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. It is produced by Trifolium pratense (Red clover).", "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, 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, 2176, 1977, 4152, 2007, 13453, 30438, 21227, 2777, 4127, 12, 2312, 12596, 2004, 13, 18, 3], "output": "DGWHLEFDLEDKAPPRVRNLLWRICRRCVPTHVNLRSRGVNCTTQARPGVMRQRMTTEIKWKKSANERVKCNIDASFSSLNNRVGIGVCIRDEKDAFVVAKLDQFSPICDVRV", "metadata": {"id": "A0A2K3KEC9", "cluster": 2689973, "interpro_all": ["IPR052929"], "interpro_used": ["IPR052929"], "interpro_unused": []}, "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 Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. Additionally, the protein has a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. It originates from Poribacteria bacterium.", "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, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 4950, 16, 1920, 2213, 2258, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2176, 22970, 2037, 4572, 26073, 2341, 18339, 14061, 18, 3], "output": "MKIAVLVSGSGTNLQTLIEQLHQEPNSGIDIAVVISDRTGAYALTRAEHVGIPTRVVKPQNFKNRVDFDAAISREIERARAELIVLAGFMRLFQPPFVRKYRNRILNVHPTLLPAFPGAHPVADTLAYGVKVTGVTVHFVDEGVDSGPIIAQTAVPVFDTDDEASLHARIQIEEHQLYPQVIQWYAQGKLRIEGRKVIVTAT", "metadata": {"id": "A0A496AQ06", "cluster": 3350898, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR001555", "IPR002376"], "interpro_unused": ["IPR004607", "IPR036477"]}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein is included in the Ribbon-helix-helix superfamily, which encompasses bacterial and phage transcription repressors, such as MetJ, CopG, Arc, and Mnt, that typically function as obligate dimers to regulate gene expression. These proteins share a core topology of four helices arranged in an open array of two hairpins, with specific members like MetJ binding S-adenosylmethionine to repress methionine synthesis. It is derived from Gammaproteobacteria 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, 3063, 1922, 1920, 25149, 17, 7864, 17, 7864, 13975, 16, 2154, 21569, 4543, 1930, 10503, 3213, 26446, 16, 2427, 1966, 2130, 1013, 16, 3725, 1029, 16, 9952, 16, 1930, 5890, 1031, 16, 1988, 5745, 2347, 1966, 25554, 13351, 1942, 5741, 2359, 2294, 18, 2144, 2697, 7948, 43, 4728, 13678, 1927, 3006, 12789, 14940, 1922, 1925, 4437, 6472, 1927, 2288, 14565, 1036, 16, 1956, 2487, 4678, 3189, 2130, 1013, 2743, 61, 17, 29283, 23568, 11215, 1942, 9055, 12417, 4271, 18, 2176, 1977, 3595, 2037, 7034, 9218, 1021, 10296, 14061, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MSAIYNKPKNKSFCARAIKKNLTNLTIDENLLKRAKVASFLTKKSISQMVRESADDEQELSRILSDDEFITDKKFSHKFDLNLSYVLLYITTSLHKKLYMHRLLSDYLTNNKKVADKTSLVLN", "metadata": {"id": "A0A661EBG5", "cluster": 4557552, "interpro_all": ["IPR010985"], "interpro_used": ["IPR010985"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein should have a Mitochondrial carrier protein, transmembrane region repeat that forms the structural core of transporters found in the inner mitochondrial membrane or peroxisomes. Typically present in three tandem copies, these repeats assemble into a six-helix channel-like structure that mediates the translocation of substrates, such as ADP/ATP and phosphate, through a conformational shift. In addition, the protein carries a SAP domain that functions as a putative DNA-binding motif, predicted to form two $\\alpha$-helices separated by a turn, which targets proteins to specific chromosomal sites such as AT-rich regions. It is utilized by diverse nuclear proteins to coordinate transcription, DNA repair, RNA processing, and apoptotic chromatin degradation. Additionally, the protein incorporates a B-box-type zinc finger domain that mediates protein-protein interactions and contributes to substrate recognition, particularly within ubiquitination pathways and transcriptional regulation. Frequently found in tripartite motif (TRIM) E3 ligases, this zinc-coordinating module adopts a \u03b2/\u03b2/\u03b1 cross-brace structure to facilitate the assembly of macromolecular complexes such as ribonucleoproteins. It is derived from Stylophora pistillata (Smooth cauliflower coral) and features UniProt keywords Coiled coil, Metal-binding, and Zinc-finger.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 3066, 2162, 43, 4596, 9685, 2213, 16, 9117, 3031, 6865, 1988, 4952, 1920, 4346, 4728, 1927, 10538, 2435, 1922, 1920, 6671, 4596, 3260, 2014, 28990, 18, 5745, 2481, 1922, 2559, 10361, 9425, 16, 2144, 9569, 17421, 2460, 43, 3798, 17, 7864, 4999, 17, 3189, 3170, 1988, 10412, 1920, 7849, 1927, 6249, 16, 2427, 1966, 9828, 19, 4498, 1930, 5413, 16, 2596, 43, 8523, 5950, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 9235, 3418, 1988, 4088, 1966, 43, 6770, 2678, 17, 2743, 5219, 16, 4396, 1942, 2386, 2288, 8, 38, 4595, 8, 17, 12789, 6239, 2007, 43, 5165, 16, 2154, 4845, 2697, 1942, 2487, 9220, 3402, 2427, 1966, 2019, 17, 5536, 3451, 18, 2176, 1977, 7079, 2007, 6445, 4254, 2697, 1942, 11865, 3213, 16, 2678, 5059, 16, 3146, 4587, 16, 1930, 6353, 6338, 4877, 18, 4950, 16, 1920, 2213, 19683, 43, 44, 17, 5758, 17, 2601, 7997, 8497, 3418, 1988, 10412, 2213, 17, 2213, 3719, 1930, 7624, 1942, 4510, 5708, 16, 4443, 2651, 11758, 3873, 1930, 5224, 3640, 18, 5467, 2435, 1922, 8027, 24707, 5219, 12, 7103, 13, 10968, 22423, 16, 2052, 7997, 17, 19355, 9059, 24032, 43, 161, 19, 161, 19, 160, 3567, 17, 18303, 1972, 3170, 1942, 6628, 1920, 5957, 1927, 21815, 5048, 2427, 1966, 18347, 14070, 18, 2176, 1977, 3595, 2037, 26435, 22575, 1019, 17850, 3839, 5499, 12, 6689, 20200, 12191, 9893, 1915, 17358, 13, 1930, 4075, 20709, 11569, 17524, 9121, 16, 6048, 17, 2743, 16, 1930, 7997, 17, 8497, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MHGLFGWTEIKMASIANDSKLSETKEEGFILTEDDIAKTSGKKSALVSRLKHYVENGLDKKYLRDPDNGANIMLDKREPQTNGKFPKEEEFMLKYKIAVALHEGSKRRVSQLPCCYFDREEIQQSSGGERKYKGPLNCLRDVPSIGVYFCSYEWILNKLTLEGESRENLNPLRIFVAGGLVRQIGDGRSITCSQCRKNNSRMHYCFDCGLFFKAEDYELLLRRQPFCSQQFHEKEIMRFFCVPCQSCITESIKEKIKELNADIRQLEETTSVMESNVSKAKRTSIETTRAKRLERIDSAKQDILSLLKQLNQAVDFADNIVKRSSSTEVPKHGDIVYVKFTPASLANLTFGSVQKTKKADVKESTICDMKSKQIEFLVEPADAASKTSVNENEEGTFQLGEKLAICPITVLVKECELAVVGELDLNFFPGDKLQGYVFDSERTCLRKLGPFKHPFDVAFVDDEEIYNTRTGEYIKRLGRPGTGKGEFTNPIGLFMDDKEQIVICDYGNNRIQVLTKHKGRFFVSDNCCIKVFDQTGQFLYKFGSKGMVNGQFGRPGRFIGKCTTPGLTNLNGVAEMPDGRILVTSTNAAKVHIITTKPGAVLQNRNVEACSVVQLKRWLICRGKKKADLGLLVTVSFRESCPNPTQPTLPILLIYQQPVAKQLYKEKGIRSLYRGTFATLTGMICWASIIPVDVLKSRYQTMCPDILNAHEVLKTSFEGHKVISVKECHICIVTDHRNHEVVVLDKAAQDEKHNIITGEVMEAAEQMITKIRACEREVIDIMQNKGTLKERFEELSAIYHLQGIDQPLRASVEADFSLCPKTSSGEKFTPKVPGEYSLEVKINPFGIALNKEGTIVVVDYSGYSVLVSDYGNHRIYQDGVNIFTFGDTGPEKLSRPLSCISSGLHIDRQDCLLVCDQNSGRFQKFSLD", "metadata": {"id": "A0A2B4S111", "cluster": 4836340, "interpro_all": ["IPR011042", "IPR017868", "IPR001298", "IPR013783", "IPR014756", "IPR018108", "IPR023395", "IPR001258", "IPR003034", "IPR036361", "IPR047153", "IPR000315"], "interpro_used": ["IPR018108", "IPR003034", "IPR000315"], "interpro_unused": ["IPR017868", "IPR013783", "IPR001298", "IPR047153", "IPR011042", "IPR001258", "IPR023395", "IPR036361", "IPR014756"]}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: The protein is categorized in the AB hydrolase superfamily, which encompasses a diverse range of serine hydrolases, lipases, esterases, and peptidases that catalyze the cleavage of C-C, C-O, and C-N bonds. These enzymes participate in lipid metabolism, pyrimidine catabolism, and biotin biosynthesis by acting on substrates such as monoacylglycerols and esters, while some bacterial members contribute to environmental adaptation by degrading pollutants. In addition, it is part of 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. Also, the protein incorporates a Alpha/beta hydrolase fold-1 domain that constitutes the structural core of a diverse superfamily of hydrolytic enzymes, featuring an alpha/beta-sheet arrangement that scaffolds a catalytic triad. This domain typically contains a conserved nucleophile elbow to drive hydrolysis, although some members lack catalytic residues and participate in surface recognition. It has been characterized in Candidatus Rokubacteria bacterium 13_1_40CM_2_68_8.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2186, 20748, 13975, 16, 2154, 21569, 43, 6445, 3109, 1927, 8468, 30337, 16, 16653, 1036, 16, 26389, 1036, 16, 1930, 24050, 1036, 1988, 18170, 1920, 6404, 1927, 45, 17, 45, 16, 45, 17, 57, 16, 1930, 45, 17, 56, 9031, 18, 2144, 5038, 7352, 1922, 4486, 4714, 16, 21611, 19480, 16, 1930, 8622, 8132, 2007, 8290, 1990, 6249, 2427, 1966, 8914, 21295, 1036, 1930, 16785, 16, 2679, 2673, 4543, 4678, 4672, 1942, 4813, 7810, 2007, 18192, 16826, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 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, 2222, 16, 1920, 2213, 19683, 43, 4595, 19, 4666, 20748, 3728, 17, 21, 3418, 1988, 14879, 1920, 4346, 4728, 1927, 43, 6445, 13975, 1927, 26702, 5038, 16, 29931, 1925, 4595, 19, 4666, 17, 11130, 13002, 1988, 10603, 43, 6804, 21845, 18, 2052, 3418, 5745, 5461, 43, 5305, 2797, 28335, 17621, 1942, 9265, 9128, 16, 2876, 2673, 4678, 3630, 6804, 4248, 1930, 7352, 1922, 3154, 5708, 18, 2176, 2258, 2252, 4378, 1922, 14550, 1031, 1957, 3039, 1040, 26605, 2341, 18339, 14061, 2590, 41, 21, 41, 3040, 12819, 41, 22, 41, 5117, 41, 28, 18, 3], "output": "MTTAEAACAEDLVEVAGVRIQLRRGGSGAPLLILHSGQSARPDWIVSVRDLAAWVTWFVRDLKLSLPLPQVFTKMVLVGAAGLPPAEGHVWDYFIHSHQEALTQAWRPEDERQAEQNREMAARLLWKPYMRSHTLAALLRGVATPTLVGATAKVLERCGHLPEMEQPDAFVKMVLDFLAPGTELGVPGWLRAYEQLARHFTVYVPSLPGFAIGFSLGGWVAAEIATMNAAFYDPAKAPEYAQYFGRIWGREDAIIPLDACQRYQHAIP", "metadata": {"id": "A0A1Q7PDG5", "cluster": 5534860, "interpro_all": ["IPR000073", "IPR029058", "IPR050266"], "interpro_used": ["IPR050266", "IPR029058", "IPR000073"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: 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. Moreover, the protein is classified under 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 Tilletia indica and features UniProt keywords TPR repeat.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 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, 3950, 16, 1920, 2213, 1977, 5947, 2441, 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, 15983, 4988, 1019, 29338, 1930, 4075, 20709, 11569, 22288, 6865, 18, 3], "output": "MEAPTTPESRAVLTHDRLIGLANRFLTGTSPDARTAASKIPTLPTPDYITAAFFSLLALARFPNSIPASTSAGCPSPVTAGPGLLTGGISSAAAHAALSLLQSGPAGVYDALSWTVDHTTGFRSRLASMNAKGKAPAGLAGLGIVQGMVPPIGTAALLASLTPPTPDPSTSNTHSSSSSSQPIKIFVSLAEAASSFESALDADRWNWAAWAGLCDVARVGSRRGAIDGGNLPENMDDWEALLVRLVAQEAEAEGKWRLLGGGAGAAATTGNAGLPTYARAGSRTTTGARTAAGNPGSNKRFVPTFTGPSMENRNVGGVGGGAPSRSGVSSSASARTLTTEPMLVDEMMPAAESGAALVEGKQNLPVDTAPVVQAPVGGAAARTRVGAGTGAVAGVGGGGNVAGRRVGGATVGAGARRAAPNSSSTMMSSTALSRTQGTSAQGRGIPGHASSLSKSSSSTDSGYGTGSVSSLALPARAGMAAGKGAALSAAAAELESVRAQRVEVETRISDAKMAAVEVAKLWSDVDVELRSVDEVARASLGTAAATEEQQVELAFNRAVYGTTPFSLGHDSAKYAEAERHFDAARRSTTQPTGSRSSAVVPTRHMDIYSLLDSNAAETHIASGNAFALQREHGQAMRAFKRAALIAPDMRHWNAWAGLGQIFLKIGKMDWAEAHYREALGRWKEALDEYDAALAMSPKLAMTRLKRAELLSHMEKYEDAHEENGQFADPNYGSTSTHGGGDKSTSMAAQDPIAPNEYHEAIAAMGEGARAALKGARRPIDASAMDSTVDSTAFSGATRVTDEPMADSPFPGEEDEEEEEDSDDDEEEDDEDEDGDSDDEDHDAENDANAVGQHEAHDDSESENIEPRPAAVGEDSENSYRGRPSRHAHNVQQQQQQQVPTPLSVSSTASLAAAGMSASTGDGSMAMSEEQSMELDSITSPSGSSTASSSSSSRRLLAACILAGADPFPFAPEDVGCATLFAQASSALSAFSEAHAGGSQMREEQNQGEENEPRHTSLDLAQQSQTLTSLGHLAAKGNRFHDTLERWSYTELGLHRLEEFATGAPSQSASQGQPSSQPKGTTNGAGARRSGADASVASSTRSAATRSARTNVGVPSTRQPPHPESEVPSAVGGTTEDGVVREFEKGGGPVRRSTRTNTGTGAGVGAGSGTAGRMGGAASALARAGARAPTRRVGVAAGVTNGTTGTSNAAAILSTVRQLAEAYRTVRLYEGRKTAYLIPDAVLNTEPVRCLLGRAALVLFHLNREVKLSALAQDLGGCAYAYTLAGYEAIELSQLERAVGFFRSAIRVVNPHHAVLKDLLGWTYESQGLLRVADLVPDESRVHILLAKSYMRLGFHLAAAIDLDPKNVRIVKSSMYPVEQSGEVFEDGPEELDDDDEDDEDVSDAESEDDGGGAVAGARGTTMTASSRRTGAAGRIAQAAAVAAAEAAVAATTAD", "metadata": {"id": "A0A177TIT2", "cluster": 7106605, "interpro_all": ["IPR011990", "IPR019734"], "interpro_used": ["IPR019734", "IPR011990"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein carries a DEAD-box helicase, OB fold domain that regulates helicase activity through the binding of RNA substrates and G-patch domain proteins. This C-terminal module features an OB-fold positioned at the entrance of the nucleic acid cavity, serving as a critical site for modulating enzymatic function and substrate interaction. It is present in Limosa lapponica baueri and corresponds to UniProt keyword Membrane, Transmembrane helix, and Transmembrane.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 16252, 43, 9535, 17, 5758, 15318, 16, 2384, 3728, 3418, 1988, 7014, 15318, 2455, 2596, 1920, 2743, 1927, 3146, 6249, 1930, 49, 17, 7504, 3418, 2697, 18, 2052, 45, 17, 4262, 9059, 4075, 1925, 2384, 17, 3728, 11814, 2019, 1920, 21539, 1927, 1920, 11079, 2687, 8568, 16, 13915, 1966, 43, 4140, 3200, 1958, 10871, 8145, 2347, 1930, 4510, 2835, 18, 2176, 1977, 2481, 1922, 2784, 5360, 7448, 21851, 6102, 6813, 21726, 1033, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 7864, 16, 1930, 9117, 18, 3], "output": "MWPGNTESLLWKKVIISLCLMFMKPLCCRTGTDLRPRGIATTSLMMLLAHGILVVYESAWLLELAPHFYQQGTHLSLKAKRAKVDDHPLSNLFAAGGSSIAGAFGNTDSGLKSLFGNEVIQTAKYYMRDVTAV", "metadata": {"id": "A0A2I0T5G5", "cluster": 7406488, "interpro_all": ["IPR011709"], "interpro_used": ["IPR011709"], "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 should include a Resolvase, N-terminal catalytic domain that mediates site-specific recombination in prokaryotes through a strand exchange mechanism. This domain functions as a dimerization interface and contains a conserved active site serine that forms a transient covalent phosphoprotein linkage during DNA cleavage and re-ligation. In addition, it is part of the Site-specific recombinase resolvase family, which catalyzes the inversion of DNA segments to regulate gene expression and the resolution of cointegrated replicons during transposition. These enzymes execute strand exchange through coordinated cleavage and religation steps, playing critical roles in viral host specificity, plasmid stability, and bacterial phase variation. Additionally, the protein should contain a DNA-binding recombinase domain that functions as a structural module within the C-terminal region of large serine recombinases (LSRs) to coordinate DNA binding and rearrangement activities. This moderately conserved domain adopts a mixed \u03b1/\u03b2 fold consisting of a four-stranded \u03b2-sheet embedded in a core four-helix bundle. It is identified in Catenuloplanes atrovinosus and contains UniProt keyword associations DNA recombination.", "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, 3066, 3951, 43, 24321, 10916, 1021, 16, 56, 17, 4262, 6804, 3418, 1988, 10412, 3200, 17, 2487, 7827, 1922, 28149, 2596, 43, 5984, 6818, 2856, 18, 2052, 3418, 4088, 1966, 43, 13640, 6854, 1930, 5461, 43, 5305, 3500, 3200, 8468, 1988, 4952, 43, 6809, 13577, 8078, 22163, 8611, 2409, 2678, 6404, 1930, 1964, 17, 11102, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 3200, 17, 2487, 21366, 24321, 10916, 1021, 3416, 16, 2154, 17097, 1920, 14825, 1927, 2678, 7492, 1942, 5741, 2359, 2294, 1930, 1920, 4885, 1927, 24073, 4905, 6541, 5524, 2013, 27255, 1036, 2409, 22596, 18, 2144, 5038, 29583, 5984, 6818, 2596, 11651, 6404, 1930, 12055, 1943, 5983, 16, 14797, 4140, 5456, 1922, 4324, 4423, 4896, 16, 5609, 5057, 16, 1930, 4543, 3193, 4516, 18, 4950, 16, 1920, 2213, 3066, 5531, 43, 2678, 17, 2743, 21366, 3418, 1988, 4088, 1966, 43, 4346, 9059, 2651, 1920, 45, 17, 4262, 3031, 1927, 3103, 8468, 21366, 1036, 12, 6639, 5675, 13, 1942, 11865, 2678, 2743, 1930, 14154, 4209, 18, 2052, 11224, 5305, 3418, 24032, 43, 4985, 160, 19, 161, 3728, 7600, 1927, 43, 3006, 17, 10338, 161, 17, 11130, 8222, 1922, 43, 4728, 3006, 17, 7864, 14142, 18, 2176, 1977, 2899, 1922, 3115, 1917, 1944, 3513, 4484, 6204, 25210, 11873, 20490, 1036, 1930, 5461, 20709, 11121, 2538, 5253, 2678, 7827, 18, 3], "output": "MNITARMALLRGESPMPSEKQGVGYIRVSKVGDRGDDLISPELQQHAIETWSVNHGVRITKWIIELDESGRSFARRKVAEIVADIKAGRYQYVVLWKWSRWGRNMRESQIYLGQAEEVGGIVRAATEDFDPTTTMGRFSRDQMLLVAQLQSDMLSDSWKEVHERRRRLGLPHTGMKHWGYIYENKSYRPDPDFSPILANAYERYVAGESLGKLHREWNAAGLRTTRGNLWYQSTLGSMLDTGFAAGLLREKQNTKRSGRGNLAIQSWDSWRIGSHQPIIPMSLWDGYVARRLQQAAMPPRSRVAAYSLSALLRCGWENCNSPMTIRHSNQTRRLPDGTSERVKYRNWACRAAWERKSHAPNYISHTRAEAQVLAWLVKQSSPNVEITREARRAAAARQVQGETESLDAELARLKVKRARLVDLYTDSAIDRSDYDRARHDVESLISELSTRLATAHARRKSTGPELVRDFGSLLDEWPRLAPHNRREALSRVVSKFIVLPRGLTEADERVQPVPLWE", "metadata": {"id": "A0AAE3YSE8", "cluster": 11507905, "interpro_all": ["IPR038109", "IPR011109", "IPR006119", "IPR036162", "IPR050639"], "interpro_used": ["IPR006119", "IPR050639", "IPR011109"], "interpro_unused": ["IPR036162", "IPR038109"]}, "task_type": "autoregressive"} {"instruction": "The protein can be placed in the Cytochrome P450, E-class, group I family, which comprises heme-containing mono-oxygenases that typically function within a two-component system requiring an NADPH-dependent reductase. These enzymes catalyze the oxidation of diverse substrates, facilitating essential processes such as xenobiotic detoxification and steroid metabolism in vertebrates, as well as alkaloid biosynthesis in plants. In addition, the protein is categorized in the Cholesterol 24-hydroxylase family, which functions as a neuronal-specific, rate-limiting enzyme responsible for converting cholesterol to 24S-hydroxycholesterol (24S-OHC). This activity regulates brain cholesterol metabolism and provides neuroprotective effects, notably in the context of Huntington's disease. Furthermore, it is part of the Cytochrome P450 superfamily, which comprises diverse heme-thiolate mono-oxygenases found in all kingdoms of life that share a conserved four-helical bundle core. Relying on electron transfer from redox partners, these enzymes oxidize a vast array of substrates to drive essential processes such as steroid and fatty acid metabolism, hormone synthesis, and the detoxification of xenobiotics. It is produced by Crenichthys baileyi (White River springfish) and features UniProt keywords Transmembrane, Metal-binding, and Endoplasmic reticulum.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 9387, 12088, 16, 47, 17, 2921, 16, 2210, 51, 3416, 16, 2154, 12936, 10954, 17, 3165, 8914, 17, 25298, 1036, 1988, 5745, 2347, 2651, 43, 2288, 17, 4594, 2433, 8887, 1925, 11908, 17, 3100, 11386, 18, 2144, 5038, 18170, 1920, 6638, 1927, 6445, 6249, 16, 12440, 4415, 4028, 2427, 1966, 29821, 18169, 1930, 9507, 4714, 1922, 14976, 16, 1966, 2486, 1966, 29951, 8132, 1922, 4793, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 5463, 2686, 17, 16324, 3416, 16, 2154, 4088, 1966, 43, 5121, 17, 2487, 16, 2769, 17, 8051, 4113, 5061, 1958, 15025, 5463, 1942, 2686, 1036, 17, 8275, 22513, 8342, 1945, 12, 2686, 1036, 17, 5622, 1030, 13, 18, 2052, 2455, 7014, 3068, 5463, 4714, 1930, 4558, 14345, 2564, 16, 7388, 1922, 1920, 4491, 1927, 24289, 11, 61, 2573, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 9387, 12088, 13975, 16, 2154, 12936, 6445, 10954, 17, 13914, 2010, 8914, 17, 25298, 1036, 2435, 1922, 2136, 13543, 1036, 1927, 3308, 1988, 7948, 43, 5305, 3006, 17, 11514, 14142, 4728, 18, 21119, 1990, 4995, 3856, 2037, 9366, 7228, 16, 2144, 5038, 3618, 2606, 43, 10983, 6472, 1927, 6249, 1942, 9265, 4415, 4028, 2427, 1966, 9507, 1930, 5934, 2687, 4714, 16, 6365, 4271, 16, 1930, 1920, 18169, 1927, 29821, 1036, 18, 2176, 1977, 4152, 2007, 3478, 19730, 19253, 30338, 1036, 26451, 6659, 1033, 12, 4511, 10423, 11858, 14422, 13, 1930, 4075, 20709, 11569, 9117, 16, 6048, 17, 2743, 16, 1930, 13355, 12279, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MEPARLGHRLRIILKMASEPRMDVMSGSDVEITQELSIVSQHCRLVDIEVFAVLFSVGATALTWLCVILLIAFLGYCFYIKYIHMKYDHIPGPPRDSFFLGHIYGPVYRINILHYIILGVTCPEATKEILMSPKYPKDRFLYKGLFNLFGQRFLGNGLVTARDRAEKLMEKLSEIADKNTEANILQLVNCVTLDVIAKVAFGVDLDLLSKGMVYQIRDSLFQFNPKNWPFITEVREACRLLRTTGAQLNDILTQIIKTAATEENMTEEDEEFMLDNFVTFFIAGQETTANQLAFCIMELARIYLSQVLKETLRIYPTAPGTSRDISGDMTIDGIHLPGGFTCLFSSYVTGRMEKLGPRSCLGQNFSQMEAKVVMAKLLQRFDFSLVPGQTFDIQDTGTLRPKSGVICTIKHRKYKNRSLTLPVLDAACTIMSPTFVRIMKKDGIVHNKFLEWAEHELWYKQRRIMDPAFSSLYLRGLMGTFNENNSPFPKAIEVCLWIHERKTSMQNGEDVHPEILDKVMKEVDDVIGMKQEMSYDDLGKLFFKEPLKFDPDRFHPDSPKPYYCYFPFA", "metadata": {"id": "A0AAV9RG25", "cluster": 11511412, "interpro_all": ["IPR039983", "IPR001128", "IPR002401", "IPR036396"], "interpro_used": ["IPR002401", "IPR039983", "IPR036396"], "interpro_unused": ["IPR001128"]}, "task_type": "infilling"} {"instruction": "The protein contains 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. In addition, the protein possesses 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. It originates from Sphingobacteriales bacterium BACL12 MAG-120813-bin55. 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, 5461, 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, 1922, 2459, 16, 1920, 2213, 14465, 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, 2176, 22970, 2037, 13502, 15229, 1918, 14061, 30491, 3112, 9624, 17, 6103, 11425, 1010, 17, 8768, 7054, 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": "MTANQEIQFEAMRKYMLERYAAELSDKLYYHGVHHVLDVEASVMRIAASLSLTDRELLLLRTAAIFHDYGFIESPHQHEERSCSVAGTLLPDYGYSPSDIATICGMIMATELPQQPQSMLEMIIADADLDYLGRDDYPEIADSLYRELHHQGRVSDRREWLHMQIDFLQRHVYHTTWSQQHRAPTKEARRLLLLQELD", "metadata": {"id": "A0A0R2VNR9", "cluster": 12340002, "interpro_all": ["IPR003607", "IPR006674"], "interpro_used": ["IPR003607", "IPR006674"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein is classified under the Glycosyltransferase family 6 family, which comprises enzymes such as alpha-1,3-galactosyltransferase and alpha-1,3-N-acetylgalactosaminyltransferase that catalyze the formation of glycosidic bonds. These proteins facilitate the biosynthesis of disaccharides, oligosaccharides, and polysaccharides by transferring sugar moieties from activated donor molecules to specific acceptor molecules. It has been characterized in Petromyzon marinus (Sea lamprey) and is annotated with UniProt keywords Manganese and Metal-binding.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 5947, 2441, 1920, 20067, 9961, 3416, 26, 3416, 16, 2154, 12936, 5038, 2427, 1966, 4595, 17, 21, 16, 23, 17, 9479, 25566, 1930, 4595, 17, 21, 16, 23, 17, 56, 17, 6894, 5411, 2131, 5360, 8547, 2199, 9961, 1988, 18170, 1920, 3337, 1927, 7533, 12546, 9031, 18, 2144, 2697, 6628, 1920, 8132, 1927, 2054, 11926, 16, 22012, 16, 1930, 18686, 2007, 21902, 9523, 16706, 2037, 4128, 6282, 4206, 1942, 2487, 12641, 4206, 18, 2176, 2258, 2252, 4378, 1922, 16901, 3542, 13642, 1022, 13081, 1022, 1957, 12, 9309, 12503, 19916, 13, 1930, 1977, 10633, 1956, 20709, 11569, 19516, 1930, 6048, 17, 2743, 18, 3], "output": "MPRRRVLTLVVIAAALLFYFFKFLHVRLHVGGARALGVGGLGAPRAQPAVSRGDDDDDVVASVGLVAFAVGGYVEHLSHFLESAERFFMRGHAITYYVLTDNARAVPRMSLLAGVVQELVAGEERFVFCADVDLVFVDEVGPEVLGSLVATLAARVGRHEGDFYFTSELFGGRCRDVFALAQACAASIAHDSLSDLDARHLDELSPEYCWPIGRERSSEMPMKRILSLRIDSPPTVSAIDIDPLNATWWGAPVVWSAGGGGAAFVPAPGRRLKALFVAERPEGRHLRRAHPGFFTKPRRLFPYERRSASSHLNKYLVLNKPTKI", "metadata": {"id": "A0AAJ7TWT9", "cluster": 21685581, "interpro_all": ["IPR005076", "IPR029044"], "interpro_used": ["IPR005076"], "interpro_unused": ["IPR029044"]}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: 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 native to Clostridium cylindrosporum DSM 605.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 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, 6196, 1942, 21156, 15460, 28988, 1989, 10964, 3276, 1015, 18, 3], "output": "MSKKIYLLLTRTGTRFSSMIYRATGYEYTHASIALDKDLKELYSFGRRNMMLPFIAGFVREDLNSGVYKKYDNTKCVIYELDVTEETYENIKKLINVFEEHKHTYKYNFIGLPLILFNIPYKRERHFVCSQFVAYVLLESGAAELDKEFTMVKPRDFLNIVNKRLIYNGFLRQYTYPVL", "metadata": {"id": "A0A0J8G5M6", "cluster": 287318, "interpro_all": ["IPR038765"], "interpro_used": ["IPR038765"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein falls within the Carboxypeptidase-like, regulatory domain superfamily, which constitutes a regulatory $\\beta$-sandwich module found in eukaryotic M14B metallopeptidases, such as carboxypeptidase D and E, and teneurin signal transducers. This domain adopts a Greek-key topology and shares structural homology with bacterial outer membrane proteins involved in nutrient binding. It has been detected in Candidatus Dojkabacteria bacterium and contains UniProt keyword associations Transmembrane helix.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 12182, 2651, 1920, 15750, 9626, 2410, 9200, 17, 3189, 16, 4948, 3418, 13975, 16, 2154, 14879, 43, 4948, 8, 38, 4666, 8, 17, 18038, 9059, 2435, 1922, 10825, 8510, 14919, 8969, 24897, 1036, 16, 2427, 1966, 15750, 9626, 2410, 9200, 46, 1930, 47, 16, 1930, 5656, 3708, 5572, 2733, 26307, 18, 2052, 3418, 24032, 43, 27568, 17, 3834, 13678, 1930, 16495, 4346, 9039, 1956, 4543, 7642, 3260, 2697, 3286, 1922, 8708, 2743, 18, 2176, 2258, 2252, 3330, 1922, 14550, 1031, 1957, 2608, 29431, 20013, 2341, 18339, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "VGGFTQENAVILKASLFDPDPNISPSNTRRLRAEFEVVLVGESFTGTGTGLIKGQDYKWRVRAENVDDGIFSEWVEFGNNSTSAADFRISTLTVDARDGSNLIDPSYRGTVNFTSTAGAVILPANYAYSAGDAVTATDLLDSALSDTTVDITVNPPATPPSPTDTPVPSVSSPVPTTPGDPTCQEDPLQLKCLVPVEIYNVRVDVADTNDQAVICWDTTDSTDVETAYKVTDHCQTLTNLMEDSAYIFKITATAPTSLYDIYENPNSYVLNDQNTVELPFTTAGEANCTVFYGSNADQLDYTYAEEGQSLSHNLIMDLDNVQGVIPLFKLPETGEVDSEVGIPWWLALLPATGVGLVNLISYPRWILYAIAKKNTPVIFASVKLYQGNKFIKEVITGREGKYGFVANQGQYKIIVDHPDYDTYNVNKKQVDKNWREKLRENLSKLNSILVVVGFTLSVIIFIILFLLSLRNKRHWGYVYNVATKGRIPGAFVRVFSPEENRQLDVQMSDKEDMKNVVSKDGNNFLHTQIKKGQSMNNPIGLEPNSNSTGAVESTSSSNNQPRAFTQNVRRGPVEIFDGSAPIITQINATAEDLSIATNKTNVDIGETIGTHDFTNELIFLEAGTFTPTSGPTPTTGPSPTPGPTSVVSNIETIGYIDYGLNDPGIYSAFSTGKEIIDIIPVACIEVGTDLVYKIECSVLIGDSEEDYTSCEANWIKDRKKEQAWGVIYDAIEDVTIEKEEGMAARDIALRSRQAETIISPSLYNFIVILFYVAQGRYGFLLEEGEYDVSASKMGYQFTGR", "metadata": {"id": "A0A955L6N4", "cluster": 384896, "interpro_all": ["IPR008969"], "interpro_used": ["IPR008969"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein I want to design has this role: The protein is assigned to the Outer dynein arm-docking/coiled-coil domain-containing protein family, which comprises components of the outer dynein arm-docking complex (ODA-DC) essential for anchoring outer dynein arms to doublet microtubules. Members facilitate the assembly of these axonemal structures to ensure proper ciliary function and contribute to spermiogenesis through flagellar elongation and sperm head formation. It is identified in Eimeria acervulina (Coccidian parasite) and carries UniProt keyword assignments Coiled coil. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 1977, 6304, 1942, 1920, 7642, 18188, 6011, 17, 10909, 19, 17524, 17, 9121, 3418, 17, 3165, 2213, 3416, 16, 2154, 12936, 4178, 1927, 1920, 7642, 18188, 6011, 17, 10909, 2796, 12, 4426, 1019, 17, 5330, 13, 4415, 1958, 20816, 7642, 18188, 9715, 1942, 25750, 12444, 18, 4678, 6628, 1920, 5957, 1927, 2144, 9980, 30426, 4061, 1942, 6486, 3405, 17542, 2347, 1930, 4672, 1942, 6283, 3940, 13349, 2596, 24154, 9971, 1930, 6283, 4469, 3337, 18, 2176, 1977, 2899, 1922, 16101, 9213, 2126, 8298, 24895, 3392, 1019, 12, 28014, 24942, 8652, 13, 1930, 16252, 20709, 11121, 2538, 18306, 17524, 9121, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MIGEDPDTAAAGSAARAGRAKAARTTAAAAAAAAAGSRCCAPELLQRDAEVSAAQFAIQKHTRLLELEKRRLRDLSDASLRAQAEYEDKRSRYAFNKPNIRKEFHQAEQQIHLLEDRVAFAASKHNTEISFAAELRLAIDKQRKERLSLEQAHLLLTKEAAAQQSELHAIKQQIAELQQQEQQALQTKRKLYQERDKERAEFKQTLEKKQQVLKQHEQRLKEMLQQASKDNQKLQAQIRSSACAAADGEQQEAAKEKLIKDIFKATLLNAAHRRSIRLYKKQIQIFDKAMESIKKSTGISGVYK", "metadata": {"id": "U6GPD2", "cluster": 1449428, "interpro_all": ["IPR051876"], "interpro_used": ["IPR051876"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the polypeptide chain function: The protein is categorized in the Peptidyl-prolyl cis-trans isomerase FKBP4/5/8-like family, which comprises immunophilins characterized by TPR repeats and FKBP-type domains that exhibit peptidyl-prolyl cis-trans isomerase (PPIase) and co-chaperone activities. These proteins regulate diverse signaling pathways, including the intracellular trafficking of steroid hormone receptors, Akt activation, and NF-kappaB signaling, while also influencing microtubule dynamics and plant development. In addition, 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. Also, the protein belongs to 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 present in Aureoumbra lagunensis. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 3431, 2199, 17, 3192, 2199, 5848, 17, 2127, 25510, 19890, 1006, 19, 25, 19, 28, 17, 3189, 3416, 16, 2154, 12936, 6595, 24888, 7782, 1036, 4378, 2007, 22288, 9569, 1930, 19890, 17, 2601, 4682, 1988, 5987, 3431, 2199, 17, 3192, 2199, 5848, 17, 2127, 25510, 12, 12481, 2051, 13, 1930, 2081, 17, 14044, 4209, 18, 2144, 2697, 5741, 6445, 3197, 3873, 16, 2710, 1920, 4776, 9604, 1927, 9507, 6365, 4086, 16, 5496, 2936, 16, 1930, 4651, 17, 19901, 3197, 16, 2679, 2222, 11623, 10544, 5565, 1930, 4496, 2740, 18, 1922, 2459, 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, 2222, 16, 1920, 2213, 14440, 1942, 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, 2481, 1922, 8689, 4468, 17010, 5524, 9333, 17014, 3355, 1937, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MAATSFEEDEARRQKEVIEQTSFDLDNLNQDGIVEMMIDEKEEIRRTPAMDLAAQIVASAESIKSVGSDYVKKNLWREAIAEYDKALELLSKEKSKISADYESELLAEKCELACRNNKALCALKLMDWSLAKLFCAEGLQVQERAKVPDASSKAKLLFRRGQAQLGNGEARNAVDSMAQALEIEEQLLGVSSKDATIKSTNSDKQRVTTIAAIKRELQKARKLAKAEDQRTKENFKGARGFLQGGKGVPKLTDTKTERKEILEEAMNNVLKSLFEDKDLEIQKACIMRQISSLSKLSKPNDLNGQTKYYFVRGFMEFLAGETMNENQNVPNEHYQKAASHLDMCWARRSEMATARFGVRNDEEEDPLFVHLDLDEDSECFFPIGKICAIETTGHSMLRANQYDPARAYLIAFAQLATANPIAALHNLPDGFLLEKGLPKMDDKQRRAHRWKYRSHEKRAIFDAYVAIASASRRIDDRDMALDAALKALNIAETHEHKRAAHNNLAFLYGSKWSQYGEPTSQDQDLALLHSSLSQCFQALHEEEQRKKDEPPPGASDLPETDDAIQDEAVLDPQDNDVPMPDISF", "metadata": {"id": "A0A7S3JNW6", "cluster": 2269439, "interpro_all": ["IPR050754", "IPR011990", "IPR019734"], "interpro_used": ["IPR050754", "IPR019734", "IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein features a Late nodulin domain that is expressed in plants during the late stages of root nodule formation. This region is homologous to the *Pisum sativum* ENOD3 protein and contains two pairs of C-terminal cysteine residues implicated in potential metal binding. It is expressed in Lupinus albus (White lupine) (Lupinus termis) and contains UniProt keyword associations Signal.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 4075, 43, 5058, 3889, 3392, 3418, 1988, 1977, 3198, 1922, 4793, 2409, 1920, 5058, 5143, 1927, 5904, 17149, 3337, 18, 2052, 3031, 1977, 8725, 1942, 1920, 14, 17850, 1989, 15036, 1020, 1989, 14, 2066, 1986, 1010, 2213, 1930, 5461, 2288, 5803, 1927, 45, 17, 4262, 8666, 4248, 6835, 1922, 2889, 6048, 2743, 18, 2176, 1977, 3198, 1922, 12555, 22214, 5311, 1957, 12, 4511, 12555, 2053, 13, 12, 12555, 22214, 2576, 1937, 13, 1930, 5461, 20709, 11121, 2538, 5253, 2733, 18, 3], "output": "MAKTHLELFYNPLFQVCRRYWCRFLMVLLFSLFILMIMEQIPCQIDADC", "metadata": {"id": "A0A6A4QDV9", "cluster": 2918897, "interpro_all": ["IPR009810"], "interpro_used": ["IPR009810"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "\"The protein includes a Basic-leucine zipper (bZIP) domain that functions as a DNA-binding and dimerization motif in eukaryotic transcription factors. It features a contiguous $\\alpha$-helix containing a basic region for DNA interaction and a leucine zipper that mediates parallel dimerization, forming a flexible fork structure that grips specific DNA sequences. In addition, the protein belongs to the Nuclear Factor Erythroid-derived 2-like family, which comprises Cap'n'Collar (CNC) bZIP transcription factors that regulate developmental processes and cellular stress responses. These proteins control genes involved in erythroid and megakaryocytic differentiation, as well as inflammation and homeostasis, with members like Nrf2 serving as master regulators of the antioxidant defense pathway via the antioxidant response element (ARE). Additionally, the protein should feature a Maf-type basic leucine zipper domain that mediates dimerisation and DNA binding, typically utilizing a conserved bZIP structure. This domain also encompasses the Skn-1 DNA-binding region, which lacks the leucine zipper and binds DNA as a monomer. It originates from Astyanax mexicanus (Blind cave fish) (Astyanax fasciatus mexicanus) and is classified with UniProt keywords Activator, Coiled coil, and Transcription regulation.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 5921, 43, 5937, 17, 12624, 27910, 12, 30450, 13, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 1930, 13640, 5219, 1922, 10825, 3213, 2790, 18, 2176, 4075, 43, 20030, 8, 38, 4595, 8, 17, 7864, 3165, 43, 5937, 3031, 1958, 2678, 2835, 1930, 43, 12624, 27910, 1988, 10412, 6110, 13640, 16, 7402, 43, 9964, 15630, 3170, 1988, 17480, 1036, 2487, 2678, 3709, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 4254, 2991, 17226, 17, 3595, 22, 17, 3189, 3416, 16, 2154, 12936, 2853, 11, 56, 11, 27621, 12, 29898, 13, 30450, 3213, 2790, 1988, 5741, 5878, 4028, 1930, 3689, 3071, 3387, 18, 2144, 2697, 2285, 2628, 3286, 1922, 17226, 1930, 22695, 8316, 4155, 16, 1966, 2486, 1966, 4531, 1930, 7622, 16, 1956, 4678, 3189, 10933, 13915, 1966, 9880, 9098, 1927, 1920, 7335, 9720, 3374, 3454, 1920, 7335, 2644, 6149, 12, 2032, 13, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 16466, 17, 2601, 5937, 12624, 27910, 3418, 1988, 10412, 7632, 6284, 1930, 2678, 2743, 16, 5745, 10232, 43, 5305, 30450, 3170, 18, 2052, 3418, 2222, 21569, 1920, 3097, 1022, 17, 21, 2678, 17, 2743, 3031, 16, 2154, 13012, 1920, 12624, 27910, 1930, 6876, 2678, 1966, 43, 11287, 18, 2176, 22970, 2037, 5988, 12947, 3013, 17165, 1957, 12, 7109, 12207, 5724, 13, 12, 5988, 12947, 3013, 24248, 1031, 1957, 17165, 1957, 13, 1930, 1977, 5947, 1956, 20709, 11569, 9518, 16, 17524, 9121, 16, 1930, 3213, 3640, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MEESGVLRSEQEISLIDILWRQDIDLGVEREAFDVHFQERELDAELEERVMLALRKMDKETGEILPQNVQGDDSTSFNPGFELMTEAFLSGQPPDKEKASIELLALPDLQHYLDALEAHVPESQPELLEKEDNTVLETVSGPHVLAHIHSGCAEIMETPEYAVSHSGKTTQPLPQIIPEMSTNPPENLYQRSFQLSSDLNTQEELFPELENIIEPEHSLCQHVSFSEPIDLDPSLYADDAFITVQPEAEEVRRSQSDQIELFDLSVLSDVVDLQPSEDSLSVHSEDLFETEATTSSLCEITTSSQSPQGHRSWSVCRDEERARTLLLPLSVDDELNEGQLSLMRDIRRRGKNKMAAQSCRKRKLDSLVDLEAEVEELREEREQVMLEKESNRDEHGNPYSTKEYTLQYSTDGRFFILPRSPHASKHTQRARVQEEERKKRESGSPITQNPLLSALLLSEKPIMDNSYGHQLHEPPAPEIEQPFLDTEDFTESFLDTISVQKDSSGSTCDMTLFSLETSSQHLTQVGTLLHTIITMSVDAFNEAISTYAKALRETRGKLSKLYSEVFSQL", "metadata": {"id": "A0A8B9LMK5", "cluster": 3563979, "interpro_all": ["IPR004827", "IPR004826", "IPR047167", "IPR008917"], "interpro_used": ["IPR004827", "IPR047167", "IPR004826"], "interpro_unused": ["IPR008917"]}, "task_type": "infilling"} {"instruction": "Here is the polypeptide chain function: The protein should contain 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. In addition, the protein is grouped in the Golvesin-related Golgi apparatus protein family, which functions as a membrane component involved in the biogenesis and structural maintenance of the Golgi apparatus. Members of this family facilitate intracellular protein transport, sorting, and vesicle trafficking between Golgi compartments, potentially regulating stack assembly. It is found in Lolium multiflorum (Italian ryegrass) (Lolium perenne subsp. multiflorum) and exhibits UniProt keyword tags Metal-binding and Zinc-finger. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 3066, 5531, 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, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 9173, 2940, 1921, 17, 2712, 10277, 11161, 2213, 3416, 16, 2154, 4088, 1966, 43, 3260, 4594, 3286, 1922, 1920, 13008, 1930, 4346, 6291, 1927, 1920, 10277, 11161, 18, 4678, 1927, 2052, 3416, 6628, 4776, 2213, 4860, 16, 11404, 16, 1930, 11502, 9604, 2192, 10277, 10436, 16, 5063, 6773, 10496, 5957, 18, 2176, 1977, 2435, 1922, 3004, 12191, 1989, 15453, 4051, 1989, 12, 15922, 18650, 6541, 29375, 1036, 13, 12, 3004, 12191, 1989, 20095, 16443, 1021, 19615, 18, 15453, 4051, 1989, 13, 1930, 9826, 20709, 11121, 2538, 14392, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MSPQIALAGAAAACCTFPCHLGKSPSRCALDLAGAPQVFVSVSPPLREDARRQIIPNRKKLQSYREEQLASNKIRMMNQSGPSNIPRYRPGSSGGFAPRNNKPPAQTYRPNYTNNNGGHPKPGGNNNNNNDNNHSNNNNHNNNNNHSNNNNNNNNNNNNNNNNNNNNNNNNHNNHNNNNNNNHNGNNNNPNTAPRTGSNATPITPKDKSTVTCYECEVVGHYSNECPKKLAKTAPIPLHLPINSAALQLEGTRTTATVVSTT", "metadata": {"id": "A0AAD8QWQ0", "cluster": 3950977, "interpro_all": ["IPR053259", "IPR001878", "IPR036875"], "interpro_used": ["IPR001878", "IPR053259"], "interpro_unused": ["IPR036875"]}, "task_type": "autoregressive"} {"instruction": "The protein is a member of 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. Also, the protein carries 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 is native to Rhodocytophaga rosea and is connected to UniProt keyword Transmembrane, Transmembrane helix, and Membrane.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 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, 2222, 16, 1920, 2213, 16252, 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, 1977, 6196, 1942, 11490, 3107, 4965, 1019, 13679, 1019, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9117, 16, 9117, 7864, 16, 1930, 3260, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "MFSEGILQILTILNLLGAAQGLFMALLVLSMKSANRKASILLATFPHLIRVGDPFVLLLGPLFYLYARSLARYPLRPKELLHFVPSAGIIVIVVLRLVFLLAYSVITYRFLQTYTARLLVIVCSVGMYVLILFSKLSFLESNYINAFLVSLVIYAVSTAIPVSIEPAETKPATKYENSTLSQEKSSRYLQKLLHSDKLSIPPHYLSQVINEQLGQNFFDFVNTYRVEEVKSNSKSAFNLAFKSITGFTPSQFRTQHKLLFCFSMSIGGATLGVSGYYLRFLVYVLSLIPFFAGTATEKIAFVQQMQESRIKENFSNIDKLNLDWLIAVSKLLGFLGVRQSRVFAAAPLPVMQQDKLYLDSELSLQTLARLTDPKNQHLTILAIAFDAGF", "metadata": {"id": "A0A6C0GKR1", "cluster": 5449579, "interpro_all": ["IPR009057", "IPR018060", "IPR018062"], "interpro_used": ["IPR009057", "IPR018062"], "interpro_unused": ["IPR018060"]}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein should include a Low-density lipoprotein (LDL) receptor class A repeat that forms a calcium-dependent, cysteine-rich structure responsible for ligand binding in extracellular and membrane proteins. It utilizes a conserved cluster of negatively charged amino acids to facilitate high-affinity interactions with positively charged sequences in ligands such as LDL, playing a central role in receptor-mediated endocytosis. Moreover, the protein is assigned to the LDL receptor-like superfamily, which mediates receptor-mediated endocytosis to regulate cholesterol homeostasis, lipid metabolism, and neurodevelopment. These multi-domain transmembrane proteins utilize calcium-coordinated, cysteine-rich Class A repeats for high-affinity ligand binding and Class B $\\beta$-propeller domains to facilitate pH-dependent ligand release and receptor recycling. It originates from Sipha flava (yellow sugarcane aphid) and is annotated with UniProt keywords Disulfide bond.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 2330, 17, 3824, 9694, 12, 8017, 13, 3148, 2921, 43, 6865, 1988, 4952, 43, 5016, 17, 3100, 16, 8666, 17, 5536, 3170, 5061, 1958, 5207, 2743, 1922, 5329, 1930, 3260, 2697, 18, 2176, 18127, 43, 5305, 4377, 1927, 7191, 9516, 3835, 4576, 1942, 6628, 2149, 17, 5173, 3719, 1956, 6629, 9516, 3709, 1922, 6908, 2427, 1966, 8017, 16, 14797, 43, 4101, 2770, 1922, 3148, 17, 3434, 11914, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 8017, 3148, 17, 3189, 13975, 16, 2154, 10412, 3148, 17, 3434, 11914, 1942, 5741, 5463, 7622, 16, 4486, 4714, 16, 1930, 16597, 2017, 18, 2144, 2779, 17, 3418, 9117, 2697, 12561, 5016, 17, 11651, 16, 8666, 17, 5536, 2921, 43, 9569, 1958, 2149, 17, 5173, 5207, 2743, 1930, 2921, 44, 8, 38, 4666, 8, 17, 5062, 13728, 4682, 1942, 6628, 2087, 17, 3100, 5207, 4012, 1930, 3148, 13977, 18, 2176, 22970, 2037, 20978, 2722, 7732, 1019, 12, 7463, 9523, 8337, 1021, 27040, 13, 1930, 1977, 10633, 1956, 20709, 11569, 11830, 5403, 18, 3], "output": "MVFNVIKYIKRFYTSEIKSHNCVNRYIEHFNTVIKQIIFVGVEYHCVNDVRIVQLSVTSKPFSEPRKALPNLKTDEPVCPKDQLQCGNGECMNRDLFCNDRADCKDE", "metadata": {"id": "A0A2S2R983", "cluster": 5917983, "interpro_all": ["IPR036055", "IPR002172"], "interpro_used": ["IPR002172", "IPR036055"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein includes a SNF2/RAD5-like, C-terminal helicase domain that acts as a superfamily 2 (SF2) DEAD-like helicase to facilitate ATP-dependent DNA or RNA unwinding. Commonly found in chromatin-remodeling factors and recombination proteins, this domain contributes to a RecA-like core structure critical for DNA repair. Additionally, 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. In addition, the protein contains 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 expressed in Sphaerotilus sulfidivorans and is connected to UniProt keyword ATP-binding and Hydrolase.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 5921, 43, 22280, 1028, 19, 4226, 1015, 17, 3189, 16, 45, 17, 4262, 15318, 3418, 1988, 8016, 1966, 43, 13975, 22, 12, 6347, 1028, 13, 9535, 17, 3189, 15318, 1942, 6628, 4498, 17, 3100, 2678, 2014, 3146, 26801, 18, 5384, 2435, 1922, 6338, 17, 8378, 2790, 1930, 7827, 2697, 16, 2052, 3418, 7624, 1942, 43, 21534, 17, 3189, 4728, 3170, 4140, 1958, 2678, 5059, 18, 4950, 16, 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, 1922, 2459, 16, 1920, 2213, 5461, 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, 3198, 1922, 9445, 29164, 13323, 5277, 1036, 5141, 13756, 15525, 17182, 1036, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4498, 17, 2743, 1930, 20748, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MTASEPVAVAAEPTAAVPAKPARKRAAPRRKAAASEPAVIEPVEAPVAPAPTPAKPARKRAAPRARKTAAQAEVTPAVAAEPAVAPAPEPVPEPVATPRKRAPRRRAAPEAAVEGAAEPTAEPVVEPVVEAAAEPVTEPAAEPAVAPVAEADALPPAPEPETEPEPEPQPLAPPFSQVVLEAQGPVRRLAWTPGRDCPAELLALAAQLDQPTAAAPLVNDLAAPARDMRERVHLLETRMPEGPASPLLTALVTLPLRTYQGEGALYAACAGRSVLADDAGLGRTVQAVAALRLLAHWAEQWQTLTGLTALQAGSVAEIGAAAQAEASPQAPLLLLADAALAVQDDVVDESDDANLSPWLDTAFAAALATLDGPFALAIARTPVEVRPRALRALEALAEAPVAERLEALGPWLLRRTKTLVLRQLPETVEAICPVELDAAERPLHDARLAYLSDADQRRLLSTLHALRLGCNAGKIGTTIEGIETLLAEPDMRVVVFSQWTDSLEALSAALSERGIAHPQQRVLLCCDDSPGGQLGLRHAATAILHLDRPWNPALLAQRFSRVHRADRVRQVERLVQAQDDAASREHFVGLIDGAQAEAFLGGARLERFMAALAVLAGLPAEPIAEPVAEAEPPAPEAPVEETSVEAVAAAAPEPAAKVDNSCGQAVDNIDDPMPQPDPEKELLEMVRIARERRHALRVDEAVWLWLAQFGAERALVLAPAERLATLAALQAFAPDSVMLEWIDAPRLGAIGRQIVRAVQRWQRSRLALPVDAAGEARRALVSAFQQDPVCHLVASHTLE", "metadata": {"id": "A0A5C1Q4A6", "cluster": 12485811, "interpro_all": ["IPR001650", "IPR027417", "IPR038718", "IPR049730", "IPR000330"], "interpro_used": ["IPR049730", "IPR001650", "IPR000330"], "interpro_unused": ["IPR027417", "IPR038718"]}, "task_type": "infilling"} {"instruction": "The protein carries 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. Additionally, the protein carries 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. Moreover, the protein should feature a 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain that hydrolyzes the phosphodiester bond in the second messengers cAMP and cGMP to regulate the duration and amplitude of intracellular signaling. This compact \u03b1-helical structure coordinates divalent metal ions, typically zinc and magnesium, within a deep active site to catalyze the conversion of cyclic nucleotides to their corresponding 5' monophosphates. It is derived from Chlamydomonas schloesseri and corresponds to UniProt keyword Metal-binding and Transmembrane helix.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 16252, 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, 4950, 16, 1920, 2213, 16252, 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, 3950, 16, 1920, 2213, 3066, 5961, 43, 23, 11, 25, 11, 17, 9821, 5489, 24821, 16, 6804, 3418, 1988, 7222, 20887, 1920, 20184, 1967, 5403, 1922, 1920, 2812, 16716, 1036, 6225, 1930, 15958, 1942, 5741, 1920, 4392, 1930, 6531, 1927, 4776, 3197, 18, 2052, 13726, 160, 17, 11514, 3170, 10675, 21610, 6048, 6982, 16, 5745, 7997, 1930, 13148, 16, 2651, 43, 6515, 3500, 3200, 1942, 18170, 1920, 7309, 1927, 9821, 9519, 1942, 2310, 3980, 25, 11, 21363, 1036, 18, 2176, 1977, 3595, 2037, 14667, 10480, 2966, 6012, 1979, 18842, 1930, 8852, 1942, 20709, 11121, 2538, 6048, 17, 2743, 1930, 9117, 7864, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MAESKHSVVFVEPPTESRGRHSEASTGHTGWRERLKASSLGVWRIVVQHPVNESASSYADTAKVRAYSLAQDTAAYYQREMVGSVVAPVLVPTLLAQTSNKYAGGVELQLLPFGVVAATYPAANSSSSRGGTPLGSDIFASPERDMAIKMVRARPIFITGVPENTTFNNPYPLNPACGEACAYNATTRTAFWGFATAKVWLDIFGSEDTRFGLLVRLASNTEGALPGDSVEVTVQLPNTQWVLRVHPTSGWTPTWYAGLLAGIIVLAVVVAVLAFAVLVSTMEARILQADTPADMLLMVLGELLEGRTPDLRDVVFIRTVLMRNQDVYAPLNLRGHLRGSSLGSGRIAEEEADHSDGGGGGRGGGGGHDSDSGGYGASGGGSGGTEGGYPKHDLSLILNVQPYHAVRSVAGEVGGGLSGCGGPVLNMQHSGDSELRSPVVGAFDVEPSGASSAETRSRWRGGGKKTPLKLSSNGRPGLPCGPPQPLLQPVAIPPTIIEDSEKVLRLVDSWSVLGFYLMQRAGLVSRFRLKPVVLARLLRAIESGYLDNPYHSAYLDALGLLASYYAAIVHDFAHPGLTGDFLIATSDPLAIRYNDRELDALAPLSQSERSSFRKQVIELVLATDMKQHFSILSHFNTVHRLTSYSQQQAAAALQPSPSLARPRQPLSLLQAPQPVDDTERLLSLQIALKCADIGHLGESLEVHKKWLANLEEEFFRQGDKESKSQVGFYDFVGLPLVHALSSAFPGSQQLMRCFLTNYNHWRQVDGQPPVEPPRARTLAAAAAAAARLDRARPPPLTVPAAPGAEDKAGMASVQLTLAGGKGARVSTLLPPLLLLGLILGLGIWGTSAMVHYNPNYQDVGSLFQGLASLTLAGPMDFMRGGFGVIITMERGYNYEVLVPDGAGGQARRQHQTLLEAVLPKEVIRELRKEDNAVDADVVRALMRQLGSGHDFESTSMYPFSGQPAGSVEGAGGAITGVLVAASLGSVVEGAAAVAASEFDTWALQEATQGHALIHAADVLQTLHVIIHSAQLHVHRSPLENHHCAASFGLLRRAVSLRPNGSGDRNGGIPPPSRELGIPISPLFDRSKQGVSGQGSGRQLIASVSNRLLSAAPSTPRGN", "metadata": {"id": "A0A835WIF8", "cluster": 13789472, "interpro_all": ["IPR006189", "IPR003607", "IPR023088", "IPR002073", "IPR036971"], "interpro_used": ["IPR003607", "IPR006189", "IPR002073"], "interpro_unused": ["IPR036971", "IPR023088"]}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this 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. Additionally, the protein is categorized 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. Additionally, the protein is included in the Binding-protein-dependent ABC transporter permease family, which forms the integral membrane component of ABC transporter complexes to facilitate the translocation of sugars and oligosaccharides across the cellular membrane. These permeases mediate the specific uptake of substrates such as maltose, maltodextrin, and trehalose, playing a critical role in bacterial nutrient acquisition and virulence. It is expressed in uncultured Pleomorphomonas sp and is linked to UniProt keywords Sugar transport and Transmembrane helix.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 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, 4950, 16, 1920, 2213, 1977, 10234, 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, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2743, 17, 2213, 17, 3100, 7219, 9054, 6191, 2051, 3416, 16, 2154, 4952, 1920, 12328, 3260, 4594, 1927, 7219, 9054, 5048, 1942, 6628, 1920, 7849, 1927, 15592, 1930, 22012, 3436, 1920, 3689, 3260, 18, 2144, 6191, 2319, 8265, 1920, 2487, 5047, 1927, 6249, 2427, 1966, 25902, 16, 15505, 24359, 16, 1930, 23995, 16, 14797, 43, 4140, 2770, 1922, 4543, 8708, 6165, 1930, 9304, 18, 2176, 1977, 3198, 1922, 5269, 21058, 6483, 10728, 10480, 2056, 1930, 1977, 4624, 1942, 20709, 11569, 9523, 4860, 1930, 9117, 7864, 18, 3], "output": "MILLQRLEKLLLAVCIVVASPPQILFTPTLEHYIALFSFVNSIVVTAVSMLLTIAIACPAAYALSVVPLFRFLQPLGLNDTYPRELEEAAMIDGCGRLGAFFTGLLAWNDLVFSLPLTTTRAVTMPVIIVPVILLTFFVQRHIVSGIASGAVKGVVAVAVTPLAWMILTSLKPSLIAVGGDAGSTLGLARLRPAGTASLTVFIIGVRMLPPIVLLALLVPYVGLSIPLAVWMLIGFFQNLWHVILPLAAPGMAATSIAARMRVEEGVLWGQLGAVSTIM", "metadata": {"id": "A0A212LCK9", "cluster": 14290495, "interpro_all": ["IPR050901", "IPR000515", "IPR035906"], "interpro_used": ["IPR000515", "IPR035906", "IPR050901"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein includes 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. Furthermore, 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. Additionally, the protein should have a HTH-type transcriptional repressor KstR2, C-terminal domain that functions as the multi-helical dimerization and regulatory module of TetR family transcriptional regulators. It interlocks with the N-terminal DNA-binding domain to form a functional homodimer, controlling pathways such as cholesterol catabolism in *Mycobacterium smegmatis* and multidrug efflux. It occurs in Pseudomonadota bacterium and is described by UniProt keywords Transcription regulation.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 5921, 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, 3677, 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, 4950, 16, 1920, 2213, 3066, 2162, 43, 5334, 1023, 17, 2601, 5224, 14434, 11626, 1997, 1028, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 2779, 17, 11514, 13640, 1930, 4948, 9059, 1927, 5575, 3416, 5224, 9098, 18, 2176, 20856, 20131, 1956, 1920, 56, 17, 4262, 2678, 17, 2743, 3418, 1942, 2386, 43, 3183, 21189, 16, 7138, 3873, 2427, 1966, 5463, 19480, 1922, 14, 16389, 2426, 6541, 19808, 14, 1930, 16398, 11247, 18, 2176, 5110, 1922, 11520, 3947, 12595, 3857, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 3213, 3640, 18, 11586, 5655, 3581, 18, 3], "output": "MKRPIVDIPTSVKDPELVKKRRGQIIRAIRTKEEVVVLNQDLFLESAGARLRQCIENVENLLFLTRERHYLTEKYGSLTLQLERTRLSIFDEVLEECIATGHMIDSWVMKGWDLREHADIAEMEATIVEILWNGLPGKAHPGRLPAAEAFQAMVAFLVSKGARPTVYACNSDAESRSAPHPPEPFPNIRVYSSRDYGPLDANHDLGIGNTRADPGPDEMAEAGRRLEANLKSVQETAECLLEFASTVKGAVVALTRMMAGELTRTSANVHCIVPGYIRVTNALIFLASDASKFLTGQVLEVSREAGCSEPGLKRTIHATRLFAQKGFHKTTIRDIAEKSGLSMGAIYEYPLEKLRRLIHTELHMMDRHADYIPLCNVRLVTQLIKVLEGKSVFVANGGTLLGRLFKRIMSDMKELDVYLRSSARCIYLAPWSWDRHANPIRYEASEGSSGIGGAFSDELIEKIPFDCLCNLSD", "metadata": {"id": "A0A9E2N601", "cluster": 15383129, "interpro_all": ["IPR009057", "IPR050109", "IPR001647", "IPR041490", "IPR036291", "IPR002347", "IPR036271"], "interpro_used": ["IPR001647", "IPR050109", "IPR041490"], "interpro_unused": ["IPR036291", "IPR002347", "IPR036271", "IPR009057"]}, "task_type": "infilling"} {"instruction": "\"The protein is classified under the Thiopurine S-methyltransferase, Se/Te detoxification family, which mediates the methylation of selenium and tellurium as a mechanism for cellular detoxification. Members of this lineage function as thiopurine S-methyltransferases specifically adapted to process and neutralize these toxic metalloids. 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. In addition, the protein is assigned to the Thiopurine S-methyltransferase family, which comprises cytosolic enzymes found in both prokaryotes and eukaryotes that catalyze the S-methylation of aromatic and heterocyclic sulphydryl compounds. These proteins are notably responsible for metabolizing thiopurine drugs, thereby modulating the therapeutic efficacy and toxicity of these anticancer and immunosuppressive agents. It is produced by Salinisphaeraceae bacterium and carries UniProt keyword assignments Cytoplasm.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 1977, 5947, 2441, 1920, 15331, 1034, 17687, 61, 17, 16478, 16, 2058, 19, 3602, 18169, 3416, 16, 2154, 10412, 1920, 5547, 1927, 17277, 1930, 17812, 15709, 1966, 43, 2856, 1958, 3689, 18169, 18, 4678, 1927, 2052, 7924, 2347, 1966, 15331, 1034, 17687, 61, 17, 28253, 4475, 8461, 1942, 2585, 1930, 25885, 2144, 6161, 8969, 4929, 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, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 15331, 1034, 17687, 61, 17, 16478, 3416, 16, 2154, 12936, 9410, 5038, 2435, 1922, 2321, 28149, 1930, 15021, 1988, 18170, 1920, 61, 17, 5547, 1927, 10761, 1930, 27804, 13153, 13528, 2584, 6907, 1024, 4300, 18, 2144, 2697, 2032, 7388, 5061, 1958, 27044, 15331, 1034, 17687, 4195, 16, 6113, 10871, 1920, 4272, 4348, 1930, 5532, 1927, 2144, 11515, 1930, 12910, 4820, 18, 2176, 1977, 4152, 2007, 30128, 9119, 29164, 9914, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MPAFGGLRHDFASPLARTFFFDSLLLSAVVNPAPPIRVGHDPREVGVGRQTGWHEADGNALLRQHWSTLGIPQAAAVLVPLCGKARDMAWLAAQGHPVLGVDLQRFAGSGIQIIAGDFLSLPADRLGSVTGFFDRAALIALPPEDRVADMSGPPFSVDDAEVRGLFGRHFGIELLTERDALAGNDHLRERGVTALVERAYRLERTSDAMNVNNSFWLDRWSAGSDRAARAFFEENDLDYTVEADAAGRYAAHLADGLRPGCRGLLITLAYPQ", "metadata": {"id": "A0A2D4SGW7", "cluster": 15561627, "interpro_all": ["IPR029063", "IPR022474", "IPR025835", "IPR008854"], "interpro_used": ["IPR022474", "IPR029063", "IPR025835"], "interpro_unused": ["IPR008854"]}, "task_type": "infilling"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein incorporates a Surface glycan-binding protein B (SGBP-B) xyloglucan-binding domain that mediates the specific recognition and binding of xyloglucan at the cell surface, typically in *Bacteroides ovatus*. This C-terminal module adopts a $\\beta$-sandwich fold structurally similar to the C-terminal domain of glycoside hydrolase family 13 enzymes. In addition, the protein is assigned to the Galactose-binding-like domain superfamily, which functions as a versatile ligand-binding module characterized by a $\\beta$-sandwich structure with a jelly roll fold. Found in both eukaryotes and prokaryotes, this domain interacts with diverse targets ranging from cell-surface carbohydrates and phospholipids to membrane-anchored proteins and DNA complexes. In addition, it is part of 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 found in Candidatus Alistipes intestinigallinarum and is classified with UniProt keywords Signal.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 19683, 43, 3154, 15060, 17, 2743, 2213, 44, 12, 10075, 3846, 17, 44, 13, 9639, 23135, 1928, 17, 2743, 3418, 1988, 10412, 1920, 2487, 5708, 1930, 2743, 1927, 9639, 23135, 1928, 2019, 1920, 2024, 3154, 16, 5745, 1922, 14, 27978, 12329, 1031, 1957, 14, 18, 2052, 45, 17, 4262, 9059, 24032, 43, 8, 38, 4666, 8, 17, 18038, 3728, 12171, 2551, 1942, 1920, 45, 17, 4262, 3418, 1927, 7533, 2261, 20748, 3416, 2590, 5038, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 15996, 17, 2743, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 5207, 17, 2743, 9059, 4378, 2007, 43, 8, 38, 4666, 8, 17, 18038, 3170, 1956, 43, 8988, 11560, 1012, 12970, 3728, 18, 2435, 1922, 2321, 15021, 1930, 28149, 16, 2052, 3418, 9034, 1956, 6445, 4845, 6485, 2037, 2024, 17, 3154, 16282, 1930, 15619, 1942, 3260, 17, 17199, 2697, 1930, 2678, 5048, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 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, 2435, 1922, 14550, 1031, 1957, 15356, 2156, 29972, 9279, 2268, 1950, 2214, 4058, 24277, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 3], "output": "MKAIYLWISILLFAATGCADENYDYGVTVGQAVQFVGDNLGSVHKISINGVEVARSESYVMTLENDFGSTEVALSIEFPPFQITGIFGVSKLMFGDKAALVTEVSETYVKAVVPEGVGNKTVIENLEDKSTTRYPDWVVPNDDYPIANYNLVIPESYFTTDADNYVLRLAIALNQSMNWYAFGPSSLTTDPALMISTGVGSHPSGNSYDFCIDNVRLQPINWEDKGAPKIDYAIDPVAMARLDVIGSTTRLTHSLYLTIPRLTNEWTPPGQELKLLGESMDLYAKVITFLADDASEGVKCPVRYRDDTFIAPLDPAPTEGSQYTRIVTEVGKTGLVNMKFELCTIKPIAYGEWQTFTIPMDTWKNKGGTKNMRIW", "metadata": {"id": "A0A9D1Z263", "cluster": 15928592, "interpro_all": ["IPR008979", "IPR013783", "IPR040475"], "interpro_used": ["IPR040475", "IPR008979", "IPR013783"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Function:\nThe protein is classified under 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. Furthermore, 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. Additionally, the protein carries 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. It occurs in Pseudobdellovibrionaceae bacterium.\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, 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, 3677, 16, 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, 4950, 16, 1920, 2213, 16252, 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, 2176, 5110, 1922, 11520, 13602, 20783, 2165, 2377, 2001, 9914, 14061, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "PFRPKTREEFTPAVIKSKYPRVQVSVFKTWAEYISAHSGFYQNKSVSAKADGVLLWLAENLTYSRRWLSPGAGWSPRPIGEIVKTKTGDCKDFAYVSLVRSEDPSSILKGPINEKAPIVSDYFNHVVVRYLDGDTWRVIEPGLGESAGTLYRISLPKSDYAYAKFHSNISPKLDGNFMVRTSVELTGEFSNFFKDIYFGMGNEAAKQPISRARGALLVDLEYTLKSRTDKIIKEGFSYSPHFLPFFAWEHQNRPVPKYDCLVRGPFGDIDRRVTNIKEGVQITDFIRFWTPNYFPEDSDDKKLQALHIDSIRECMGSNIPFEKSIDIAKPYQAPESVTGIGLEARLTEIRKLDAYLDARLADPDLLWRKANKEHLEEAKKILLSAIEKNPSYPTNFGVLGKHHLLSGESAEALRAFNRGYALSKQDSNVLHALAANFAKTNDERLTQHERQAEILCYFQNKCEEGARVYEEKILKGKPHRWKLHNAALMYQSMKNYKRVISESRLSLIEAKIESMGRMNQKTDFGPINKELAEMYKEDRHHAGILAMLVRINSEGARNAIEHLKTAMSLVRSAPKFGGRTPAAASAPDELGQKGDKRKTLPLELAGVVKKLNAEKSVATLVLLKELGIRAEPVRGLGDSSRPAYFLKDAWALNAFENALKGLANTDAGINVQFPFIPGESKETVLVKGMFTFKEMALVTLDGKDKTQHVRSLGYHSGKLYIALGAEISKANKNLDIALRYAIELERKALEDGPWGMAQQIAAMVGQSEDNLALANQYAEELKVVAHENP", "metadata": {"id": "A0A968VUF7", "cluster": 18821597, "interpro_all": ["IPR038765", "IPR011990", "IPR002931"], "interpro_used": ["IPR038765", "IPR011990", "IPR002931"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein includes 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 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 has been characterized in Peptoanaerobacter stomatis.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 5921, 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, 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, 2258, 2252, 4378, 1922, 23045, 6952, 26243, 15129, 2422, 9347, 2807, 18, 3], "output": "MAHLPGSIGELIGDLRRNKSTLSHIESGITKQVDATAIRTPKHIDIMKLGLSEDVARGWSQKELAKRSGVTELGKIAFALDTSTDYLLGLSK", "metadata": {"id": "J4W2I2", "cluster": 19194119, "interpro_all": ["IPR001387", "IPR010982"], "interpro_used": ["IPR001387", "IPR010982"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\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 features a DNA2/NAM7 helicase-like, C-terminal domain that functions as an ATP-dependent Superfamily 1 (SF1) helicase responsible for unwinding DNA or RNA substrates. Characterized by a P-loop motif within a RecA-like fold, this module supports diverse activities ranging from DNA replication and repair to nonsense-mediated mRNA decay. Additionally, the protein should include a Helicase MOV-10-like, beta-barrel domain that forms a predicted OB-fold-like structure located N-terminal to the catalytic region in MOV-10 family proteins. These proteins function as 5'-3' RNA helicases within the RNA-induced silencing complex (RISC), playing key roles in mRNA metabolism, viral defense, and the regulation of translational repression. It is identified in Monosiga brevicollis (Choanoflagellate) and is linked to UniProt keywords ATP-binding, Cytoplasm, and RNA-mediated gene silencing.\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, 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, 2678, 1028, 19, 5400, 1027, 15318, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1925, 4498, 17, 3100, 13975, 21, 12, 6347, 1009, 13, 15318, 5061, 1958, 26801, 2678, 2014, 3146, 6249, 18, 4378, 2007, 43, 58, 17, 5881, 5219, 2651, 43, 21534, 17, 3189, 3728, 16, 2052, 9059, 7825, 6445, 4209, 6485, 2037, 2678, 5158, 1930, 5059, 1942, 19605, 17, 3434, 3616, 9310, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 15318, 8007, 17, 2119, 17, 3189, 16, 4666, 17, 19560, 3418, 1988, 4952, 43, 4396, 2384, 17, 3728, 17, 3189, 3170, 4810, 56, 17, 4262, 1942, 1920, 6804, 3031, 1922, 8007, 17, 2119, 3416, 2697, 18, 2144, 2697, 2347, 1966, 25, 11, 17, 23, 11, 3146, 29919, 2651, 1920, 3146, 17, 2719, 8343, 2796, 12, 2511, 1030, 13, 16, 14797, 3834, 5456, 1922, 3616, 4714, 16, 4324, 9720, 16, 1930, 1920, 3640, 1927, 8414, 10084, 18, 2176, 1977, 2899, 1922, 18491, 1950, 1019, 3022, 9833, 2201, 1937, 12, 4551, 9286, 20631, 19606, 13, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 16, 5239, 16, 1930, 3146, 17, 3434, 2359, 8343, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MGAPDFSLLTMKVFKNQGPPPATHVPALVQALAELSIAVTHDQRSPAYIRELTRLLEPFDGVSDDEDHALNAPRTFARREPLPEPADFERLVKWQWEAQGRPTGSVAQQLYQAICVLLRHRPEHELFVRHGLNDIEKLGLKLDLRQMYRTADDAQIAAVDEAPDFKWLRADQYKELGLPGRKAAGPLIKAFAAHEVNSKTKVVMDFRAVSDFVALYLEPINKLMDYHEPLDMSIFAPQRTYNPRSVPRNRGEKPVWIVLDPSIGLAPGKRVSVEFDLKKQLGDVDGLEVPLRCHPDCRFPIPLQREAATPVPFVVASDLKHDHATPYALILTFLDPDLAQMRRERIPYQPPDRPIHKEYAHKTSGTRMISGHEMPKPKLDDHPLQTPDDYTRARFHGLLYLEEIKSALHMQRYNQRDVLLTLEEQYLRLEIPGLSEKRPSLQPNDCISLIADEIEHKGYIHKKYVVKFNLSRLPFMRKHTALDLLHECPAAVQLLLPKYFPASAAYMRQADGGDVHFIEERVKIVARTEKSAEQLPPFCIFGPPGTGKTTTLLEAILQVLAVKKTPKVLVCTSSNAAADLISRRLRRTLDTVEPEVREYGIWNADRSMHGIRCLHDVQVVVCTASMAPVVMHEELRFGSPSHLFIDEATAAYHEKLDLVLCGDPRQLGPVVTSDLALQGGLNISTMERLMERPPYLRTDSSSKHSFYDGELVPERPLADLDMAEWKHLPNPGFPIIFHGVVGTHLRDNRSPSWYNLEEINCIRDHVVELRASGRRVRYSDMASSRLAEDPDGSTVNDIMIGTAEKLQGNERRIVLVSTVRSLKTIDSRTLLQTLRADMRHHLGFVVVGNPRVLWVDERWRFLISYAHQHNGYIGCKFNVHEEGLSELARLEQSLAADLFEDDSSVTSDIRNTYRVEVDVAPLEHFLKHNDQDIRRFDILKRDIEQHHNVIVSLAKLKLMSLPLESRTVTALIADEVPTYVEKLDDTPRVLQFDKGVRSRVTTILSLSILSRPANVNAMDLKDYVVMEADAVQLCVHNICLNQWNPNSIHFRNERLNPEQRLAIASGPACKTNGWTLFRANAVGFMDEAELVMTVPWFLVKLIRNYRSHPHILHVYNELIVTPYHQQAERIRFALRQGEKSRFNVAVSRARELLI", "metadata": {"id": "A9V6R3", "cluster": 19395685, "interpro_all": ["IPR041679", "IPR041677", "IPR049080", "IPR027417", "IPR047187"], "interpro_used": ["IPR027417", "IPR041679", "IPR049080"], "interpro_unused": ["IPR047187", "IPR041677"]}, "task_type": "infilling"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein should include a Plasmid pRiA4b, Orf3-like domain that is homologous to the ORF-3 protein encoded by the *Agrobacterium rhizogenes* pRiA4 plasmid. While its specific biological role is not fully defined, members of this family are frequently annotated as putative TnpR resolvases or LexA repressors, suggesting potential involvement in DNA binding or recombination events. Additionally, the protein is included in the MM3350-like superfamily, which comprises uncharacterised proteins of unknown function. This domain is structurally characterized by an arrangement of five alpha-helices and a beta-roll. It is expressed in Desulfofustis sp. PB-SRB1.", "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, 3951, 43, 5609, 17618, 16010, 1014, 16, 11234, 1010, 17, 3189, 3418, 1988, 1977, 8725, 1942, 1920, 11234, 17, 23, 2213, 7905, 2007, 1920, 14, 26896, 13458, 10864, 14, 17618, 16010, 5609, 18, 2679, 2496, 2487, 3933, 2770, 1977, 2084, 5437, 3608, 16, 4678, 1927, 2052, 3416, 2032, 5467, 10633, 1966, 6770, 7417, 2047, 24321, 10916, 1918, 2014, 14596, 1019, 26446, 16, 3783, 2889, 5668, 1922, 2678, 2743, 2014, 7827, 3916, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 14226, 5798, 1008, 17, 3189, 13975, 16, 2154, 12936, 23229, 3495, 2697, 1927, 5435, 2347, 18, 2052, 3418, 1977, 12171, 4378, 2007, 1925, 13002, 1927, 3628, 4595, 17, 12789, 1930, 43, 4666, 17, 12970, 18, 2176, 1977, 3198, 1922, 30311, 4199, 2892, 1937, 2056, 18, 5242, 17, 4581, 5090, 18, 3], "output": "MAKVVHADFTRKTRRDVDKRIVVAGQTSLARFHHIIQACMGWHDEDKEMQERDADYDEARFSLHDLEEAMGFIFTYLYDFPDDYELPRLVDGERAAPPEAAGDILTFNPAAFDHDGCGRRLAEAAGMSSDKPISAYQFKISLPFSDPLIWRTHQFMVGKIFYQSGFGIGGDGWEVEITLEEILPPHRYQALVHDSRGSITIDD", "metadata": {"id": "V4JL71", "cluster": 20724792, "interpro_all": ["IPR024047", "IPR012912"], "interpro_used": ["IPR012912", "IPR024047"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is associated with the Calycin superfamily, which is defined by a shared \u03b2-barrel structural fold typically used to bind and transport hydrophobic molecules. Members of this diverse group, including lipocalins and fatty acid-binding proteins, function in extracellular transport, receptor recognition, and the formation of macromolecular complexes. Furthermore, the protein includes a Biogenesis factor required for ATP synthase 1-like (DUF3598) domain that promotes the assembly of the CF1 subcomplex of the chloroplast ATP synthase by specifically interacting with the gamma and beta subunits. Found primarily in cyanobacteria and plants, it features a structure composed of two distinct $\\beta$-barrels that resembles the lipocalin superfamily. It occurs in Okeania sp. KiyG1. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 2570, 4636, 13975, 16, 2154, 1977, 3608, 2007, 43, 7115, 161, 17, 19560, 4346, 3728, 5745, 2251, 1942, 4566, 1930, 4860, 7919, 4206, 18, 4678, 1927, 2052, 6445, 2210, 16, 2710, 3178, 5000, 2925, 1930, 5934, 2687, 17, 2743, 2697, 16, 2347, 1922, 5329, 4860, 16, 3148, 5708, 16, 1930, 1920, 3337, 1927, 21815, 5048, 18, 3677, 16, 1920, 2213, 5921, 43, 13008, 2991, 3414, 1958, 4498, 8921, 21, 17, 3189, 12, 4855, 10892, 7308, 1025, 13, 3418, 1988, 7383, 1920, 5957, 1927, 1920, 4920, 1009, 5736, 19667, 1927, 1920, 17471, 4498, 8921, 2007, 4475, 8615, 1956, 1920, 7034, 1930, 4666, 6991, 18, 2435, 5985, 1922, 21897, 1930, 4793, 16, 2176, 4075, 43, 3170, 7179, 1927, 2288, 4493, 8, 38, 4666, 8, 17, 19560, 1036, 1988, 17602, 1920, 3178, 5000, 1921, 13975, 18, 2176, 5110, 1922, 12167, 5376, 10306, 2056, 18, 8191, 4121, 1009, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MNQISKFKVLPKLVGTWEGNWIALDPTGKERYQFTSILKQKIANNQWVQTNENTYSDGRQETLHFFGKAVGENTLLLESPDIHYYDFLMLVSELGENLIIINVTHKITGIQLTAETINLVSPNERIRTLQQFNTSDGKLRGFTLVIEKK", "metadata": {"id": "A0A916R0E1", "cluster": 22308008, "interpro_all": ["IPR022017", "IPR012674"], "interpro_used": ["IPR012674", "IPR022017"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein contains a ApeA, N-terminal domain that adopts a structure composed primarily of $\\beta$-strands and is typically found fused to the HEPN domain. This region is characterized by the presence of several conserved aromatic residues. Also, the protein should include a Apea-like HEPN domain that exhibits nuclease activity. In epsilonproteobacteria, it is typically embedded within Restriction-Modification (R-M) operons, suggesting a role in bacterial defense mechanisms. It is produced by Armatimonadota 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, 2100, 5376, 16, 56, 17, 4262, 3418, 1988, 24032, 43, 3170, 7179, 5985, 1927, 8, 38, 4666, 8, 17, 13214, 1930, 1977, 5745, 2435, 10305, 1942, 1920, 3357, 1022, 3418, 18, 2052, 3031, 1977, 4378, 2007, 1920, 2990, 1927, 2980, 5305, 10761, 4248, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 2100, 5376, 17, 3189, 3357, 1022, 3418, 1988, 9826, 16230, 2455, 18, 1922, 22206, 9218, 1021, 10296, 16, 2176, 1977, 5745, 8222, 2651, 7587, 17, 6295, 12, 60, 17, 55, 13, 28748, 16, 3783, 43, 2770, 1922, 4543, 9720, 3531, 18, 2176, 1977, 4152, 2007, 6011, 1968, 3947, 12595, 3857, 14061, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MAPGAFAFGEGSGRFPVIHGVAEAKEQEIHVGQLLIGVLLDAPEAKAFSGLTGSRWSVEVDQAEPLTVTVDDLTIETASYFRITSSEPKSLDEWDDIAKVFQDLLTFAMDSPCAVLAQHIVIGDPEAPSVETRKALFTLATEGVDFKTLIILGLLYVQSGYLQTELIIAVSAAEALHEGIGVPEQHKTWLREKLGHNTRTLRAKLLDLAAIPDTKKERDPVAHGGKNISSDVKLLSAIVKMTTFAVYDNPTLASAMRLAGQHWPGDDGGALLGGKPVTLLDCLITRSKRVMFSPIELENLTVWDRREDVMLRIERHPDLPGLRRRYVEPSGDAQRHGIDTSTFVSESLTPSEALRNDQAAQVGSAITSPRWWKIRSQFNVTFDMFDPPMSKSEFKALKKSLLEHAEAMSRLLPNPEAWADAAVVYMNLLHQLGIPKERLL", "metadata": {"id": "A0A7C5BUR4", "cluster": 24834416, "interpro_all": ["IPR041223", "IPR041229"], "interpro_used": ["IPR041223", "IPR041229"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein falls within the Uncharacterized protein YheV family, which comprises small proteins found in proteobacteria that are approximately 70 residues in length. These proteins feature a basic N-terminal triplet and a conserved CPXCX(18)CXXC motif, suggesting probable metal-binding capabilities. It is identified in Pseudomonadales bacterium.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 12182, 2651, 1920, 24528, 2213, 67, 4116, 1020, 3416, 16, 2154, 12936, 2858, 2697, 2435, 1922, 22266, 1988, 2032, 3993, 3895, 4248, 1922, 3471, 18, 2144, 2697, 5961, 43, 5937, 56, 17, 4262, 17011, 1930, 43, 5305, 4244, 21487, 1039, 12, 2654, 13, 5639, 21487, 5219, 16, 3783, 12584, 6048, 17, 2743, 13693, 18, 2176, 1977, 2899, 1922, 11520, 3947, 7324, 2612, 14061, 18, 3], "output": "MTKRFIAGAVCPGCRNEDTTYIETTRVSTLGDDVPESEVVVSEWQPVRLGSEKPEVSPEKVAQTRRCTRCDFSD", "metadata": {"id": "A0A962IUK4", "cluster": 26806432, "interpro_all": ["IPR012658"], "interpro_used": ["IPR012658"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: The protein should have a TonB-dependent outer membrane protein SusC/RagA conserved site that acts as a generalized nutrient receptor for the import of large protein or carbohydrate oligomers. Found abundantly in Bacteroidetes species of the human gut microbiome, this feature distinguishes these transporters from typical siderophore-associated receptors. Also, the protein features a TonB-dependent receptor, plug domain that acts as an independently folding channel gate within bacterial outer membrane receptors, blocking the pore until ligand binding induces conformational changes to open the pathway. It facilitates the high-affinity, energy-dependent uptake of specific substrates into the periplasmic space by coupling with the TonB-ExbBD complex. In addition, the protein should contain a TonB-dependent receptor-like, beta-barrel domain that forms a bacterial outer membrane channel enclosing a gating plug domain. It facilitates the high-affinity active transport of scarce substrates, such as iron-siderophores and vitamin B12, by interacting with the TonB complex to transduce energy for pore opening. It originates from bacterium A37T11 and is described by UniProt keywords Cell outer membrane, TonB box, and Transmembrane beta strand. 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, 16501, 1014, 17, 3100, 7642, 3260, 2213, 3447, 1030, 19, 13745, 1019, 5305, 3200, 1988, 8016, 1966, 43, 9612, 8708, 3148, 1958, 1920, 2582, 1927, 3103, 2213, 2014, 10590, 14160, 18, 2435, 23849, 1922, 26808, 3038, 1927, 1920, 2616, 7660, 13665, 16, 2052, 5961, 27502, 2144, 10538, 2037, 5939, 22940, 11082, 17, 2458, 4086, 18, 2222, 16, 1920, 2213, 4075, 43, 16501, 1014, 17, 3100, 3148, 16, 15998, 3418, 1988, 8016, 1966, 1925, 6407, 10328, 4999, 11898, 2651, 4543, 7642, 3260, 4086, 16, 7472, 1920, 8554, 4801, 5207, 2743, 6387, 8523, 2840, 1942, 4437, 1920, 3374, 18, 2176, 11374, 1920, 2149, 17, 5173, 16, 3844, 17, 3100, 5047, 1927, 2487, 6249, 2460, 1920, 24334, 5230, 2007, 7590, 1956, 1920, 16501, 1014, 17, 1975, 6936, 1007, 2796, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 16501, 1014, 17, 3100, 3148, 17, 3189, 16, 4666, 17, 19560, 3418, 1988, 4952, 43, 4543, 7642, 3260, 4999, 17439, 11934, 43, 12568, 15998, 3418, 18, 2176, 11374, 1920, 2149, 17, 5173, 3500, 4860, 1927, 16937, 6249, 16, 2427, 1966, 5680, 17, 22940, 14820, 1930, 6111, 17492, 16, 2007, 8615, 1956, 1920, 16501, 1014, 2796, 1942, 30334, 3844, 1958, 8554, 9497, 18, 2176, 22970, 2037, 14061, 12021, 1027, 6613, 1009, 1930, 1977, 2910, 2007, 20709, 11569, 2024, 7642, 3260, 16, 16501, 1014, 5758, 16, 1930, 9117, 4666, 5984, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MNRNLYLKVVTIFFAATTYICSAQTRQISGKVIDSISSTPLMGVTIQNGTQKTVSDANGLFSIALREDVAVIFTILGYHRKIVVLSASDPFPVIDLQPAANLLDEVEVANTGYQKIPLERVTGSFSVINQKLLDRVVSTNVLNRIENVVPGLLFNKGDAAQTDPFLIRGRSTITADAQPLIVVDDFPYDGDIRNLNPNDFEQVSILKDAAAASIWGARAANGVIVITTKRGQFGAPTWTFTANTSLQGRPDLNNVSIMSSADRVEWERMLFEQGYYNNAKNPTTLLNKVSPIPGAVELMIKNPADLEERLSELKKQDVRDDLKKYFYQTSLKQQYNLSISGRGKDLSYLLSGGYDRNSTNLNGEQYERVSIRSQNNYQLTGKINIFAGMAYTESFQQTGENPGLNLSPTRGLSPYVRLIGNQGEALPYYGDYRKGFLDTAGSGLLQDWVWRPYDEITLRENKSHVRDMTLNTGLEYQVLPGLDLILKYQYENQLEAGKDLHSENSYYARDMVNRFAQVSAESGSVAYPLPMGGILQENNSDLGAHQGRLQFNFMHHWGVRHEISGLAGYEIRNKVTQTSNYLLYGYRAESAAINSSVDFQHNYPSNINGNTTKIPNSQGIGKQTDHFISYFANAAYTYLKRYTLSASLRKDEANLFGVAANQKGTPLWSSGIAWRIDEEKFYSVSFLPRLKLRATYGINGNISRRSSANTTVIFLSGGDSHSFTAAQILNPPNKNLRWEKVKNWNVGIDFSSALNRVSGTIELYRKNAVDLLAEAPTDPTMGFTSIYANVGGMKGSGMDILLESQNIKGWFSWRSNLIFSIAKTEVTKYLMPVSSNGFTYAASGMSVMPVVGKSLYSIYSYSWAGLDPQDGDPQFFLNNSRSKDYPTIYSLPLEDMQYNGPVQPTHFGALRNTFSLQNMELSFNISFKAGNFFRVNSIYNSGIINGSTGHGDFGKRWLKPGDELKTTVPSMIYPADPIRDQLYQYASSLVAHADEIRFDDLNISYAIDKKNLGKIRVHQARVFIYLSQLGMIWASNKAGIDPDFNNVPKEAPTFSLGLNIKF", "metadata": {"id": "A0A1H7WZP8", "cluster": 28342244, "interpro_all": ["IPR008969", "IPR012910", "IPR037066", "IPR023996", "IPR023997", "IPR039426", "IPR000531", "IPR036942"], "interpro_used": ["IPR023997", "IPR012910", "IPR000531"], "interpro_unused": ["IPR039426", "IPR023996", "IPR037066", "IPR008969", "IPR036942"]}, "task_type": "autoregressive"} {"instruction": "Here is the polypeptide chain function: The protein includes a Hyaluronan/mRNA-binding protein domain that exhibits dual binding affinity for hyaluronan and RNA, often functioning in the regulation of mRNA stability. Found in proteins such as HABP4 and PAI-RBP1, this domain is also implicated in nuclear processes including chromatin remodeling and transcriptional regulation. It is identified in Apophysomyces sp. BC1034. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 5921, 43, 29614, 19, 3616, 17, 2743, 2213, 3418, 1988, 9826, 7064, 2743, 5173, 1958, 29614, 1930, 3146, 16, 3868, 7295, 1922, 1920, 3640, 1927, 3616, 5057, 18, 2435, 1922, 2697, 2427, 1966, 6192, 12425, 1930, 15885, 17, 18246, 1009, 16, 2052, 3418, 1977, 2222, 6835, 1922, 4254, 4028, 2710, 6338, 8378, 1930, 5224, 3640, 18, 2176, 1977, 2899, 1922, 11466, 25818, 2204, 14930, 3707, 2056, 18, 6452, 14726, 1006, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MTRSKETTWAGKHERHVSRNGQTDIRCPVKKSGAGFANWGLPGGELADMEDVATQQAASDPVAKKLQLVDHKTFEDLRQSDQRVGITA", "metadata": {"id": "A0A9P6PBF1", "cluster": 28615143, "interpro_all": ["IPR006861"], "interpro_used": ["IPR006861"], "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 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 is derived from Nitrosarchaeum sp.", "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, 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, 16665, 3983, 3336, 1989, 2056, 18, 3], "output": "MKQTLALLLAALLLLPAAVVAQQTTLVGQGTSLTAELLRYEPNPAEPGDLVTVNVVLTNEGGEVARGVELELVDSYPFSAADPNEAAKQITSIPGQQSTVTSFLVLVDKDAPEGTAFLKVRYKPTNSAGWKESLLSLDITTN", "metadata": {"id": "A0A846SNN8", "cluster": 28686996, "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 is a member of the Nucleotide-diphospho-sugar transferase superfamily, which catalyzes the transfer of sugar moieties from activated donor molecules, such as nucleotide diphospho-sugars, to specific acceptor molecules to form glycosidic bonds. These enzymes play a critical role in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides. It is derived from Paracoccus alcaliphilus.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 5489, 17, 11791, 2609, 1037, 17, 9523, 13763, 13975, 16, 2154, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 6282, 4206, 16, 2427, 1966, 5489, 11791, 2609, 1037, 17, 15592, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2144, 5038, 3918, 43, 4140, 2770, 1922, 1920, 8132, 1927, 2054, 11926, 16, 22012, 16, 1930, 18686, 18, 2176, 1977, 3595, 2037, 13344, 15648, 1957, 4143, 12498, 24888, 5277, 1036, 18, 3], "output": "MIVNGGNQDVAGRLSAEGRGFNPDNSEFLALDNRNGNQFDGIVFTHDDVEFHRDGAAELEARLGELSALIDDPHQLGMRVEAPVLVETLDENFFCRISEIMGGRAYVIPFLLRHHSGGKIDESFLFGLREGWNETPQSRWDYLKRNVYASDTVRNVSKGVRYLTEPVDHDILFSFVTLVANQDSYDRFLEYDAMRRTVVEAKGRYDPDWTIAGNSGGIRYRRGKNYLTQHIIRRDRPVLNSYDLRGFHLYASDLLPCRERFARKYRRYFIGRNLQATVTEFRFG", "metadata": {"id": "A0A1H8N9Z9", "cluster": 28850373, "interpro_all": ["IPR029044"], "interpro_used": ["IPR029044"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein should contain a Mur ligase, central domain that functions as the ATP-binding catalytic module in the MurC, MurD, MurE, and MurF enzymes responsible for the stepwise assembly of the bacterial peptidoglycan stem peptide. This domain shares structural similarity with ATPase domains and is also present in folylpolyglutamate synthetase and cyanophycin synthetase, where it drives ATP-dependent ligation reactions for folate metabolism and cyanophycin storage. In addition, the protein features a Mur ligase, C-terminal domain that facilitates the sequential addition of amino acids to UDP-N-acetylmuramic acid during bacterial peptidoglycan biosynthesis. Adopting a dihydrofolate reductase-like fold, this domain is responsible for binding the incoming amino acid substrate in enzymes such as MurC, MurD, MurE, and MurF, as well as in folylpolyglutamate synthase and cyanophycin synthetase. Furthermore, the protein should include a Folylpolyglutamate synthetase conserved site that belongs to the ATP-dependent enzyme responsible for adding polyglutamate tails to folate and its derivatives, thereby aiding in the retention of the intracellular folate pool. This site is situated within the active site in a large interdomain cleft adjacent to an ATP-binding P-loop motif. It has been detected in Lachnospiraceae bacterium and is described by UniProt keywords Cell shape, Magnesium, and Peptidoglycan synthesis.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 3066, 5531, 43, 6185, 11905, 16, 4101, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 6804, 9059, 1922, 1920, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 5038, 5061, 1958, 1920, 13846, 5957, 1927, 1920, 4543, 24183, 4402, 4207, 18, 2052, 3418, 16495, 4346, 6796, 1956, 9444, 4682, 1930, 1977, 2222, 2481, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 1930, 26898, 25818, 3665, 18185, 16, 2597, 2176, 15435, 4498, 17, 3100, 11102, 5298, 1958, 13761, 4714, 1930, 26898, 25818, 3665, 7451, 18, 1922, 2459, 16, 1920, 2213, 4075, 43, 6185, 11905, 16, 45, 17, 4262, 3418, 1988, 11374, 1920, 9454, 2459, 1927, 3835, 4576, 1942, 18500, 17, 56, 17, 6894, 23010, 29085, 1935, 2687, 2409, 4543, 24183, 8132, 18, 20478, 43, 11842, 27851, 11386, 17, 3189, 3728, 16, 2052, 3418, 1977, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 4510, 1922, 5038, 2427, 1966, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 16, 1966, 2486, 1966, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 8921, 1930, 26898, 25818, 3665, 18185, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 5305, 3200, 1988, 14440, 1942, 1920, 4498, 17, 3100, 4113, 5061, 1958, 8013, 16115, 26697, 21084, 18103, 1942, 13761, 1930, 2496, 8383, 16, 6113, 8379, 1941, 1922, 1920, 7521, 1927, 1920, 4776, 13761, 5562, 18, 2052, 3200, 1977, 18287, 2651, 1920, 3500, 3200, 1922, 43, 3103, 13633, 2954, 1921, 14649, 6811, 1942, 1925, 4498, 17, 2743, 58, 17, 5881, 5219, 18, 2176, 2258, 2252, 3330, 1922, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 2024, 5989, 16, 13148, 16, 1930, 24183, 4271, 18, 3], "output": "MKLEELFKEISYEIVNGGDDKGVSAMQTEVKELVNDSRKLQEGCLFLCIRGSNFDGHTKAFEAFARKAAAIVVEEEVEIPKNTQTVVIRVKDTRYAMAFIAAAFYSHPAKELTTIGITGTKGKTTTTYLVKNMLENAGIQTGLIGTIEMIIGEEHFPASNTTPESLSLQRDFRRMVDAGMKAVVMEVSSQALMMHRTQGFLFDMGIFTNIEPDHIGPNEHKDFAEYMHCKGLLFQQCKHGIVNADDEHLPQILEGHTCDLTTFGLGDGADLKAEALAYMHKPGELGVYFDTKGIVNMHAEIAMPGKFSVYNALCAIAVAHRMGCRVEEMEEALKKVRVRGRIEMVKVSDEYTLMIDYAHNAMALHSLLTTLRYYRPNRLICLFGCGGNRSRERRFEMGEVSGKLADLTIITSDNPRFEDPMEIIRDIETGIQKTDGHYVEIPDRKEAIRYAMAQGERGDIIILAGKGHEDYQEIRGVKYPMDERVLIHEILQENQQAQQKQ", "metadata": {"id": "A0A929XX66", "cluster": 13023970, "interpro_all": ["IPR018109", "IPR036565", "IPR004101", "IPR036615", "IPR013221", "IPR000713", "IPR035911", "IPR005761"], "interpro_used": ["IPR013221", "IPR004101", "IPR018109"], "interpro_unused": ["IPR036615", "IPR005761", "IPR036565", "IPR035911", "IPR000713"]}, "task_type": "autoregressive"} {"instruction": "Function:\nThe protein carries a Membrane transport protein MMPL domain that functions as a component of transmembrane export systems for complex cell envelope lipids and siderophores. Often occurring in tandem copies, it is required for the biosynthesis and secretion of polyacyltrehalose and diacyltrehalose in mycobacteria. Moreover, the protein carries a Sterol-sensing domain that confers sensitivity to sterol levels through a conserved cluster of five membrane-spanning segments. It functions in cholesterol metabolism, transport, and signaling by undergoing conformational changes upon sterol binding to modulate protein activity. This domain is found in both metabolic moderators and transmembrane transporters, including bacterial multidrug-resistance proteins. In addition, the protein is grouped in the Mycobacterial membrane protein Large (MmpL) family, which transports diverse substrates across the bacterial inner membrane, including cell wall lipids essential for virulence and envelope integrity. Additionally, members facilitate iron acquisition via siderophore export and contribute to antibiotic resistance through the efflux of toxic compounds. It is derived from Desulfuromonas sp and contains UniProt keyword associations Cell membrane and Transmembrane helix.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 16252, 43, 3260, 4860, 2213, 6736, 1024, 3418, 1988, 4088, 1966, 43, 4594, 1927, 9117, 12660, 3771, 1958, 2796, 2024, 11262, 8238, 1930, 22940, 14820, 18, 3868, 6966, 1922, 10361, 9425, 16, 2176, 1977, 3414, 1958, 1920, 8132, 1930, 5512, 1927, 4286, 14645, 4265, 7289, 2217, 1930, 25141, 13796, 19174, 5920, 20807, 4127, 1922, 23446, 18, 3950, 16, 1920, 2213, 16252, 43, 20408, 17, 9306, 3418, 1988, 16556, 3802, 1942, 20408, 2428, 2596, 43, 5305, 4377, 1927, 3628, 3260, 17, 13346, 7492, 18, 2176, 4088, 1922, 5463, 4714, 16, 4860, 16, 1930, 3197, 2007, 7258, 8523, 2840, 4073, 20408, 2743, 1942, 8480, 2213, 2455, 18, 2052, 3418, 1977, 2435, 1922, 2321, 4487, 27665, 1036, 1930, 9117, 10538, 16, 2710, 4543, 16398, 17, 3554, 2697, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 21424, 3260, 2213, 3103, 12, 6736, 1024, 13, 3416, 16, 2154, 4860, 1036, 6445, 6249, 3436, 1920, 4543, 6671, 3260, 16, 2710, 2024, 4821, 8238, 4415, 1958, 9304, 1930, 11262, 7996, 18, 4950, 16, 4678, 6628, 5680, 6165, 3454, 22940, 11082, 12660, 1930, 4672, 1942, 7267, 3554, 2596, 1920, 11247, 1927, 6161, 4300, 18, 2176, 1977, 3595, 2037, 30311, 18916, 3947, 1934, 2056, 1930, 5461, 20709, 11121, 2538, 5253, 2024, 3260, 1930, 9117, 7864, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MQNISIIFVWLLTRGRPMVMGLLIPVEQDTRSMTSRNPEQVALYDKFRQLFGNDEDLLLSTRQISEFEGVVRVFSLSNARQLVAGPYGRIEAVLQANPHYQGLLISPDRKTAGLIIEISRVRNLIGLYSDRARMHLTGVGVQLVALVLAVMLAGIFRRPSGVILPMLTELNTITALLSPVVMVLAVSNSVHLYNGWLNLQLSLTISSVPAVRQFGLFAAVGVMLSFLVALTVLILHRTARLTIRHASKIMGQNNTNLIGFLHADAPLAVDTRYILPLDRVEDYRRIEQFAKLTTLPDNNDDLRYELELMANDAEQSLRQRFIAADRKTARVIENFQQQGQQIFGADYRLQPTGSYYRMIDDSNLLRSPWLTLLSMIPNVIPILWTVGVMIGLAVDDTIHYLVNYRRVFTGSVLVLALGFWVGCFGSFKPTILVLGDTGRKVRPAVSTLFFSVFAARLVTHPQLLEPNQLSLLAELAEARPLLPEGEPGEDSGNLEDRSDDADLRRSLQSDVASFIQRDQQVILPTGISLIWTMGLYSLSGFGQPHQRIELLAGKVNELFIPCFFTALTTALGLPVGLSFLPLPGRRHRTGTGLLRWIAVILLVVALFGLPRLDRHLAGVNVLDFMIVRSDGGEAAVAGHFSILTLLKPLHRAESGATELASIRLHDIGSREAAGLRLVADMIKSFSLSLLLVTLSILLGYCKIDLSTGTAMIGAVVRRAVTITTTRVGRALMIASYFSLLVGGTLIGALICDLLVLPAC", "metadata": {"id": "A0A2N6F874", "cluster": 3002414, "interpro_all": ["IPR004869", "IPR050545", "IPR000731"], "interpro_used": ["IPR004869", "IPR000731", "IPR050545"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a protein with the following function: The protein should contain 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. Moreover, the protein contains 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. Additionally, the protein falls within the Heme chaperone HemW-like family, which functions as a heme chaperone catalyzing the insertion of heme into hemoproteins. Members of this family, such as HemW, are closely related to the oxygen-independent coproporphyrinogen III oxidase HemN but lack specific N-terminal motifs and are often present in species that do not synthesize heme *de novo*. It is produced by Fusobacterium sp. FSA-380-WT-2B and contains UniProt keyword associations Cytoplasm, Metal-binding, and S-adenosyl-L-methionine. 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, 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, 3950, 16, 1920, 2213, 5461, 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, 4950, 16, 1920, 2213, 12182, 2651, 1920, 10954, 14044, 3243, 1018, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 10954, 14044, 29601, 1920, 7413, 1927, 10954, 2460, 3243, 14070, 18, 4678, 1927, 2052, 3416, 16, 2427, 1966, 3243, 1018, 16, 2032, 6538, 2712, 1942, 1920, 4612, 17, 3484, 3725, 17351, 11119, 30338, 5572, 2404, 4337, 10488, 3243, 1022, 2308, 3630, 2487, 56, 17, 4262, 8277, 1930, 2032, 3868, 2481, 1922, 3038, 1988, 2608, 2084, 15541, 10954, 14, 2028, 9441, 14, 18, 2176, 1977, 4152, 2007, 10630, 12022, 2056, 18, 8612, 1019, 17, 19275, 17, 3751, 17, 5751, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 16, 6048, 17, 2743, 16, 1930, 61, 17, 29283, 17, 54, 17, 12417, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MLDGIYIHIPFCMNKCNYCDFLSFKSNEEERKKYVDYILKEIDLYPKYEYDTVYLGGGTPSLLNCEDVERIIKKLNIKAGAEITLEVNPKTVNLEKLKGFKKAGINRVSIGIQTFDEKMLQVLGRMHNSNEGIETYYQAREAGFDNISLDLMFSLPNQSIEKVKQDLERLLELRPEHFSIYSLIWEEETAFFKKLEEEVYRETDNDLEAQMFEYIIDRATEAGYIHYEISNFCLPSKEARHNSKYWENREYLGIGLGASGYIGVKRYKNQVQFSKYYDNIERGILPILEEEIVTAETKEEYKYMLGFRLLNKGVIPSGKYLEKCISLEEQGFLKRNGEAYILTRKGIMLANDVLDEFI", "metadata": {"id": "A0A6N7VM34", "cluster": 3162841, "interpro_all": ["IPR013785", "IPR034505", "IPR006638", "IPR004559", "IPR007197"], "interpro_used": ["IPR006638", "IPR007197", "IPR004559"], "interpro_unused": ["IPR013785", "IPR034505"]}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein incorporates a RES domain that is widely distributed in bacteria and features a conserved arginine, glutamate, and serine motif presumed to form an enzymatic active site. It has been detected in Pandoraea terrae.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 19683, 43, 1995, 3418, 1988, 1977, 5673, 6533, 1922, 4802, 1930, 4075, 43, 5305, 9732, 16, 7627, 16, 1930, 8468, 5219, 15326, 1942, 2386, 1925, 8145, 3500, 3200, 18, 2176, 2258, 2252, 3330, 1922, 14548, 8846, 5376, 11420, 3336, 18, 3], "output": "MPTGEDDVLHRVQCGILRPGDYWHVFPAFHSMFYAGDTPAAALWETALRNAGVRQGYVYTDPVHLKPLLDLRTPYRRELVDANSALDAMWDHALKAAGYPDGAALRWHSRQAGSDSAFLFFEPPMTSAWWTYEDAHQGLTWRGAPGGTEFEPDLHECKVYSPTASNPNSKARLAWRDGGMSLARLSLTVEVRSDYEATHDITQQLMAQLMSDIFPLDELSGQEQIRQAL", "metadata": {"id": "A0A5E4RDF5", "cluster": 3364967, "interpro_all": ["IPR014914"], "interpro_used": ["IPR014914"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe 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. 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. Moreover, the protein is associated with 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 occurs in Ktedonobacter sp and exhibits UniProt keyword tags Transcription regulation.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 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, 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, 3950, 16, 1920, 2213, 1977, 2458, 1956, 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, 5110, 1922, 15569, 1919, 23557, 7972, 2341, 1915, 2056, 1930, 9826, 20709, 11121, 2538, 14392, 3213, 3640, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MHIDLPINQQQKSRERILEAAKAIFAHKGFSETKMSDIATKALQGALGTHAARASNLGPPGIACTGEYMSPRTEETNARIREEQKAANVSYGLAYHHFANKEAIFTSLLQ", "metadata": {"id": "A0A3B9YAG0", "cluster": 7649754, "interpro_all": ["IPR009057", "IPR050109", "IPR001647"], "interpro_used": ["IPR050109", "IPR001647", "IPR009057"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: It is part 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 can be placed 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 found in Planctomycetota bacterium.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 2176, 1977, 3131, 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, 2112, 1998, 5396, 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, 2435, 1922, 4720, 2341, 13386, 19446, 3857, 14061, 18, 3], "output": "MKDPIAGILDMLEAGTPEQKVVKALRTITIEGEGFFKPYAVEALGMIGNNAGERAEKVLDAEYEKADSTTQAAILEILAQLKRVLSGLEEEEDKEPFRKTFAQALKLELLAEIPSQELRPLFLSNITKTQPPEVRFLKEDDFLNVVGPSLEILEDFKPTGSSQAGMLGKLLLQVEDPKVRAEVSQSLGHNPEAIPGLLKTLAAKNLNRNQLKKILTRFVQLIEAGDPVQEYNEAHKLKQARKHVLALQVLMTVPTRDGRIPDDIRYEKLLNSGYGIMAKLKKEKALQPKAALYLGTRLIETDPESKEAIQASQKLKIEGLAGAAIQVLSWLKPKEDRVSLSALIPILHQEGPIRTHVIRALSKASHGKIAIRRLLEVLKHPPSSFMAETVVGYKVPKSAAPDYKRHLRAALRGLRTLKLTPKQEGQIFGTHPHVDVRLFAIRQMGNYKTASSAKQLLPFILFQGRDLEEASRPLQALYRQILQDSDPNIIAPLLSIAINTLLAREEHPSLIEGDPVMGHLTIEGLPAQKDLGRQILEWL", "metadata": {"id": "A0A7C5PWU3", "cluster": 8093935, "interpro_all": ["IPR011989", "IPR016024"], "interpro_used": ["IPR011989", "IPR016024"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is classified under the Snf8/Vps36 family, which functions as a component of the endosomal sorting complex required for transport II (ESCRT-II) to mediate Golgi-to-endosome trafficking. Members of this family are essential for multivesicular body (MVB) formation and the sorting of endosomal cargo proteins into MVBs. Additionally, 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. In addition, the protein is a member of the The Vacuolar protein sorting protein 36 (Vps36) family, which functions as a core subunit of the ESCRT-II complex to drive the sorting of ubiquitinated cargo from endosomes to lysosomes. It facilitates pathway progression by bridging ESCRT-I and ESCRT-II via interaction with Vps28 and coordinates multivesicular body formation by binding phosphatidylinositol 3-phosphate and ubiquitin. It has been detected in Polytomella parva and is associated with UniProt keywords Cytoplasm and Protein transport.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 1920, 22280, 1025, 19, 14851, 5677, 3416, 16, 2154, 4088, 1966, 43, 4594, 1927, 1920, 16514, 11404, 2796, 3414, 1958, 4860, 2890, 12, 27678, 17, 2890, 13, 1942, 8265, 10277, 17, 1942, 17, 22321, 9604, 18, 4678, 1927, 2052, 3416, 2032, 4415, 1958, 5738, 18522, 18021, 5148, 1005, 3362, 12, 5963, 1014, 13, 3337, 1930, 1920, 11404, 1927, 16514, 14713, 2697, 2460, 5963, 2083, 18, 4950, 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, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 1920, 21582, 2213, 11404, 2213, 3480, 12, 14851, 5677, 13, 3416, 16, 2154, 4088, 1966, 43, 4728, 5903, 1927, 1920, 27678, 17, 2890, 2796, 1942, 9265, 1920, 11404, 1927, 20895, 14713, 2037, 14978, 1942, 15222, 18, 2176, 11374, 3374, 4380, 2007, 17908, 27678, 17, 51, 1930, 27678, 17, 2890, 3454, 2835, 1956, 14851, 4839, 1930, 10675, 5738, 18522, 18021, 5148, 1005, 3362, 3337, 2007, 2743, 16927, 23, 17, 5413, 1930, 6526, 18, 2176, 2258, 2252, 3330, 1922, 25276, 2225, 11560, 1019, 19995, 1019, 1930, 1977, 2458, 1956, 20709, 11569, 5239, 1930, 2213, 4860, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "GGGGGGGGGGKKGDIKEKEGNAQPFDSRSYPNPQSSNDVYCLFNRARGTELVSPEDLLLACRHFAKARVPLTLRTFPSGVLIRQLVDPNFDQENGNTEKGSKEKGSKERDKNIGSSAGKQTVDLALTLGTAISAYLLAAEAAGVLCRDDGPEGLRFFRNFFKDVSVPQSSNPQSATPPPLLHSLGGILSLPAIQDETCLSDRVVFDRSDVAAVLRVGTTLAAE", "metadata": {"id": "A0A7S0V6M6", "cluster": 8297179, "interpro_all": ["IPR040608", "IPR037855", "IPR036388", "IPR036390"], "interpro_used": ["IPR040608", "IPR036388", "IPR037855"], "interpro_unused": ["IPR036390"]}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\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. Furthermore, the protein is associated with the Immunoglobulin E-set superfamily, which adopts an Ig-like beta-sandwich fold typically utilized for protein-protein interactions and structural scaffolding. This diverse group encompasses domains involved in transcriptional regulation, enzymatic catalysis, immune signaling, viral membrane fusion, and ligand recognition. Additionally, the protein should feature 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 originates from Myxococcales 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, 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, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 11837, 47, 17, 2735, 13975, 16, 2154, 24032, 1925, 7021, 17, 3189, 4666, 17, 18038, 3728, 5745, 7079, 1958, 2213, 17, 2213, 3719, 1930, 4346, 22582, 18, 2052, 6445, 2210, 21569, 4682, 3286, 1922, 5224, 3640, 16, 8145, 15408, 16, 3743, 3197, 16, 4324, 3260, 5289, 16, 1930, 5207, 5708, 18, 4950, 16, 1920, 2213, 3066, 5961, 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, 22970, 2037, 21464, 11748, 1918, 14061, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "DGDGLLDSEDEDDDNDGCIDEFDDFPQDPAFCVLDAEEVSEGADGWVTSPLDPDTDGDQVNDRDDVCPTVPDDQPVITRFSPAEAGAGAALEILGRNLDDPIYGGASIQLQFGRLLFTVPPNASTGRLILRSHGLTTTSSDTFTFRPDTDGDGLANEVDDDDDGDGLADSDGDGRGDACPPEVSSSTDYPAYPANDGAIAVPTEVAAG", "metadata": {"id": "A0A955XGY4", "cluster": 11705325, "interpro_all": ["IPR018247", "IPR013783", "IPR014756", "IPR028974"], "interpro_used": ["IPR013783", "IPR014756", "IPR018247"], "interpro_unused": ["IPR028974"]}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nIt is part of 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. It is derived from Halobacteriales archaeon QS_1_68_17.\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, 2176, 1977, 3131, 1927, 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, 2176, 1977, 3595, 2037, 23226, 7972, 2341, 18339, 2612, 13470, 1916, 15178, 41, 21, 41, 5117, 41, 2752, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "METLAAVVGRERRSDRPAVETGDGRPRYNGLVAGRTLGVADVPAVQPLVAAFGAALLGAAVVGDYDLPPGGQRFAFGGVPDDPEVEQFERGIWSENPLVTDRSAYTHAAVLAATEDVIAEYAIDRTDVVALRPSLRRPGTVDSTGTLAVGDARVPEETAISPEAVSLYSYRTFCTETWKAANLFRFDPPADTDVRAVLAPVDRTVPPREVEPDATAVAGVVAPLVAGASILLPDGDDPT", "metadata": {"id": "A0A2R6H429", "cluster": 11797326, "interpro_all": ["IPR042099"], "interpro_used": ["IPR042099"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should contain 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 is found in Jimgerdemannia flammicorona.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 3066, 5531, 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, 1977, 2435, 1922, 28599, 4938, 3695, 8890, 2126, 2300, 2595, 5670, 2830, 1019, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MANLYIRTYLHLSICHKSPQSLDSGKLGSSLLPTGQTKECMDCRWKKKCCLHASLRVTHAPKRTKPGGACAQCKKLKKKTRANMLFVDSKKPYARVAKVGGTTAQDESLPAASPNTNQGLLPHQPLAAYSLSRVAIESTTTATIGRQGQCCKKFGEKSAPATHARLQRLANIDRLDDAASILQPYCGSTSFLLAPGGSALPEVIVDLKDDHELCANTAIRGALWTAASEASSIRDKRLIGDLFQRIFVAIDNKDDIIHNIIELFAHIEKSFSIVCCDNCSKKLYCICLLLDWYQLVSLQDNLCMKYAHSIDMSNLISKVKDIVGIVFCPIDVSKPTSNTTVFLPIQCDGFPCSRCKNLGIDCQRQIVQTVQDKEVEIHADSDGNRARRQDCPYSRYGVPCTVCKDTAQIKIRSNIRLILELICERRFTTCDDTEALKTICQLGMLKTLIRSTLPDFGDDLEGHSYSSMI", "metadata": {"id": "A0A433QVH6", "cluster": 12938277, "interpro_all": ["IPR036864", "IPR001138"], "interpro_used": ["IPR001138"], "interpro_unused": ["IPR036864"]}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein should contain 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 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 has been characterized in Cadophora sp. M221.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 5531, 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, 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, 2258, 2252, 4378, 1922, 5643, 22575, 1019, 2056, 18, 6056, 4716, 18, 3], "output": "MEPSLVLTEAILLSPAAYHPPLDSLDIISNPTWDIDGAEPDGRQIWAIPDLADPSNPSLAILKSGSLQLCSRKAACESLLCRHVLRERFGDFEEEYMALPFGSQIAISSVEVELWDMEITFLDEDALPPSIDVGELRFQKQLYDSIGLMEIYHELKVLLTMPPHPNASPPPLYLSGARLAQSLLLQWAKQLTEAMIHVRDGGALQLVLIDHDQRTPGYTRRHLARIARPYLGAIRSVGAVFKGIQSVAGFTAGADEWEGVQQPFVIRGSRIYARKFEIDRARGSSASERQPPVVYPASNTNAITEPEWSHSFLNPRNRIRFARNKHPRRIDVYIGALEFWSERPVYGLEQQWLFVKSLQEIWGLAGKEGELLVLKTISLDTKALITKKVRFGGKRGVCGLLMMYYPLGTVDQLRRSPARFYSDLNPRNIALSSRPKSNTSLPLKPWRAPKSLIALSRKDSCRLLAGCPTFPNFDKTPKELKSVIRDRDLETGELSDSVTALQESTRSWW", "metadata": {"id": "A0A8H7XDS1", "cluster": 14082099, "interpro_all": ["IPR011009", "IPR000719"], "interpro_used": ["IPR000719", "IPR011009"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a protein with 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. 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. Furthermore, the protein is grouped in the Energy-coupling factor transporter ATP-binding protein family, which constitutes the energy-coupling ATPase component of ECF ABC-transporter complexes. These proteins utilize energy derived from ATP hydrolysis to drive the specific uptake of micronutrients, including vitamins such as biotin, thiamine, and riboflavin, across the cell membrane. It originates from Candidatus Zhuqueibacterota bacterium. Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 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, 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, 3677, 16, 1920, 2213, 1977, 10809, 1922, 1920, 3844, 17, 7590, 2991, 9054, 4498, 17, 2743, 2213, 3416, 16, 2154, 14879, 1920, 3844, 17, 7590, 9444, 4594, 1927, 3270, 1038, 7219, 17, 9054, 5048, 18, 2144, 2697, 12561, 3844, 3595, 2037, 4498, 9128, 1942, 9265, 1920, 2487, 5047, 1927, 22522, 2039, 16, 2710, 18818, 2427, 1966, 8622, 16, 26901, 16, 1930, 28849, 16, 3436, 1920, 2024, 3260, 18, 2176, 22970, 2037, 14550, 1031, 1957, 19533, 5089, 26073, 2341, 6506, 3857, 14061, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "YSYEDMHEIVDAALDKFGLLKYRLQSPHYLSGGEKQRLALAAVMAMQPRYLILDEPTSLLDPRSRREILALVQELHTGGARDITTMLITQFPDEALMADRLLVFDHGRIIMDAPPKAIFADEQALHEIGLEPPLVFKVDKLLAQLDAC", "metadata": {"id": "A0A661WPN2", "cluster": 15259527, "interpro_all": ["IPR003439", "IPR050095", "IPR027417"], "interpro_used": ["IPR027417", "IPR003439", "IPR050095"], "interpro_unused": []}, "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 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. Also, the protein falls within the Ran GTPase-activating protein family, which functions as a GTPase activator for the nuclear Ras-related regulatory protein Ran, converting it to the inactive GDP-bound state. By antagonizing the guanine nucleotide exchange factor RCC1, members of this family control Ran-dependent transport between the nucleus and the cytoplasm. It is found in Odontella aurita and contains UniProt keyword associations GTPase activation.", "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, 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, 2222, 16, 1920, 2213, 12182, 2651, 1920, 2845, 14809, 17, 8019, 2213, 3416, 16, 2154, 4088, 1966, 43, 14809, 9518, 1958, 1920, 4254, 6520, 17, 2712, 4948, 2213, 2845, 16, 15025, 2176, 1942, 1920, 9078, 15217, 17, 4124, 3360, 18, 2007, 5605, 3903, 1920, 16904, 5489, 6818, 2991, 13253, 1009, 16, 4678, 1927, 2052, 3416, 2285, 2845, 17, 3100, 4860, 2192, 1920, 5607, 1930, 1920, 5239, 18, 2176, 1977, 2435, 1922, 21422, 5870, 11826, 9909, 1930, 5461, 20709, 11121, 2538, 5253, 14809, 2936, 18, 3], "output": "NNFGPEGAAALGDALRRNASLSFVTIAGNELGDDGATALARGVCLKRPSLPSSSSSSSSSSSLRGLSLVNCSVGDRGAVAFAVSLRRTNNCSLRCLCLSGNLIADRGAMALATTLRYDRRLEDLSLDDNPFGGRGLRELAWALMLNTTLRRGRFRPTTVAFRGVVGTRDDDAEEGRAFLRTAARHVCDDGNSSSLGVDRVHRFARSLFEGSLSAPPTSADIAVAARNLEDDDFDDDALLTIDGVFERRPWVGQ", "metadata": {"id": "A0A7S4K7L3", "cluster": 17087521, "interpro_all": ["IPR001611", "IPR032675", "IPR027038"], "interpro_used": ["IPR001611", "IPR027038"], "interpro_unused": ["IPR032675"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein is associated with the Glycosyl hydrolase, five-bladed beta-propeller domain superfamily, which constitutes a catalytic domain with a five-bladed \u03b2-propeller fold found in glycosyl hydrolase families such as GH32, GH43, GH62, and GH68. These enzymes typically exhibit beta-xylosidase, alpha-L-arabinanase, or bifunctional beta-xylosidase/alpha-L-arabinofuranosidase activities. It is produced by Synechococcus sp. BIOS-U3-1.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 20067, 20748, 16, 3628, 17, 22707, 1007, 4666, 17, 5062, 13728, 3418, 13975, 16, 2154, 14879, 43, 6804, 3418, 1956, 43, 3628, 17, 22707, 1007, 161, 17, 5062, 13728, 3728, 2435, 1922, 20067, 20748, 5767, 2427, 1966, 6101, 6763, 16, 6101, 7514, 16, 6101, 8166, 16, 1930, 6101, 6735, 18, 2144, 5038, 5745, 5987, 4666, 17, 9639, 12224, 16, 4595, 17, 54, 17, 20790, 7241, 4127, 16, 2014, 29491, 4666, 17, 9639, 12224, 19, 4595, 17, 54, 17, 20790, 4199, 20028, 12224, 4209, 18, 2176, 1977, 4152, 2007, 26734, 8256, 2056, 18, 4589, 17, 63, 1010, 17, 21, 18, 3], "output": "MKFKLADKPIVSREIVKNKFDTDIQHFMLPVVESIQNSVIAVLFADRDAKNRSFIRRIHIDMEPFPHISGKSVETVFQPGELGCFDDNGVSPSSVVSSENITKLLYYIGWKPRSTVRFGLFGGLAIQIAGNKYTRVSRAPIFTLSDSEPFHVLTAPWVLFDKKSSIFRMWYVSGTGWKSPDTPCYNIKYAESSDGKHWDQNICVCLDNTEEITSLARPSVIKTKNGFHMWYSKKSPKTEYSIHHVYSVDGKNWGPMENSSELSLHSNFNCEWASEMVCYSYPFVYNNNLYIFHNGNGYGSTGFGITSIPLKKLI", "metadata": {"id": "A0A7G8DJD1", "cluster": 20767816, "interpro_all": ["IPR023296"], "interpro_used": ["IPR023296"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want a protein that has the function: The protein is categorized in the DNA-directed RNA polymerase III subunit Rpc5 family, which functions as a peripheral component of the RNA polymerase III complex responsible for synthesizing small RNAs such as tRNAs and 5S rRNA. By forming a subcomplex with RPC4 near the active center, it facilitates open promoter complex formation, transcription termination, and reinitiation. This subunit is also implicated in innate immune responses, helping to sense intracellular pathogens and induce type I interferon signaling. It has been detected in Rhizophlyctis rosea. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2678, 17, 6554, 3146, 6479, 4337, 5903, 4822, 26542, 3416, 16, 2154, 4088, 1966, 43, 5009, 4594, 1927, 1920, 3146, 6479, 4337, 2796, 5061, 1958, 25292, 2858, 8624, 2427, 1966, 20770, 1930, 23131, 9067, 18, 2007, 7402, 43, 5736, 19667, 1956, 4822, 17875, 4931, 1920, 3500, 4102, 16, 2176, 11374, 4437, 4465, 2796, 3337, 16, 3213, 12462, 16, 1930, 13604, 2078, 1943, 18, 2052, 5903, 1977, 2222, 6835, 1922, 8539, 3743, 3387, 16, 16235, 1942, 7534, 4776, 7741, 1930, 4769, 2601, 51, 10001, 3197, 18, 2176, 2258, 2252, 3330, 1922, 13458, 2688, 19602, 3600, 13679, 1019, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MSASDGDEDMEQYDGDVGYDEEDIYVRDEVEENDGGMDYDQEDGENIADVEPIAVEERTPAAKVPSPRKIIPKGKGPSLFADSDEDEEDEEFDGGDSGGPSATDIPESNGATHTKAPTDPSPHTNGTHAPTEMDIDEPEDPTYQSDEEDEIIKEVDVFFSRKLAESLYIFQYPTRPHAFTDDYHPVAGRFKSRAQQVELDIPLQTRGPHYSRKKGEEFGEGTHDRPIATATEMRRDDPGDAILTKQTLSSSLLPSHAKYMVGMFTEGELHLTPVKAALQLRPSLQYIDKINEKHKATSQRANAELKKEEDPSYEDEGKLLQVTMRSAEDKEGARKAAQAELMRKMEEEPWTPMDIQGVESEESRNMAFELLSDTRDALDSKTDGDQYLDDIHPKIVTAQNKKDEKITVRRGIPVGDMGVLPLVDQLKALLLNAHIASFKAMTELLHVGHNEEDIIAKLPSVGVLVNGAWVVRSEIMYTGRALEARRHLLSMFHEQQTVSRWDFAEYVKLSPEMCKNMLNEIAYLGADKRWNLKVEADHEFMSSYPDVVDAQVKMVLEEAASARDALEAVKREVKQENTGPLTSRGPVNGGPSNGRPSSAKSAAAKKAAAKGASPEEQLKSFIEDLFKENAVCSWKFVNSRIAARIAEKDKDNLITADTASARKVENIIEGMCIKITDVYALTAVGDTTTDKYRPAVCELFRTKKTVKKADVMKACKDKTGEEPGLGPYKKLMSGLATNQGYSWTLKESP", "metadata": {"id": "A0AAD5X0E9", "cluster": 21502055, "interpro_all": ["IPR006886"], "interpro_used": ["IPR006886"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein should feature a Core Histone H2A/H2B/H3 domain that utilizes a conserved histone fold to mediate DNA wrapping in the nucleosome core or facilitate protein-protein interactions in transcription factors. This structural motif is essential for chromatin compaction and acts as a dimerization interface in regulatory proteins. Furthermore, the protein is associated with the Histone-fold superfamily, which features a three-helix core that facilitates protein heterodimerization essential for DNA organization and transcriptional regulation. This structural element is found in nucleosome core histones, archaeal histones, and transcription factor components such as TAFs and NC2, where it mediates the protein-protein interactions required for chromatin assembly and RNA polymerase II-dependent transcription. Additionally, the protein belongs to the Histone H3/CENP-A family, which comprises the core histone H3 and its centromere-specific variant CENP-A that assemble with histones H2A, H2B, and H4 to form the nucleosome octamer. These proteins wrap DNA to structure chromatin and regulate genomic processes through post-translational modifications, with CENP-A specifically serving as a scaffold for kinetochore assembly at the centromere. It is identified in Tetranychus urticae (Two-spotted spider mite) and is described by UniProt keywords Chromosome and Nucleus.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 3066, 5961, 43, 4728, 6632, 18249, 19, 19542, 19, 8170, 3418, 1988, 18127, 43, 5305, 6632, 3728, 1942, 8265, 2678, 4573, 5041, 1922, 1920, 14914, 4728, 2014, 6628, 2213, 17, 2213, 3719, 1922, 3213, 2790, 18, 2052, 4346, 5219, 1977, 4415, 1958, 6338, 26580, 1930, 8016, 1966, 43, 13640, 6854, 1922, 4948, 2697, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 6632, 17, 3728, 13975, 16, 2154, 4075, 43, 2559, 17, 7864, 4728, 1988, 11374, 2213, 15672, 2466, 4415, 1958, 2678, 5901, 1930, 5224, 3640, 18, 2052, 4346, 6149, 1977, 2435, 1922, 14914, 4728, 15808, 16, 22367, 15808, 16, 1930, 3213, 2991, 4178, 2427, 1966, 19063, 1036, 1930, 5301, 1028, 16, 2597, 2176, 10412, 1920, 2213, 17, 2213, 3719, 3414, 1958, 6338, 5957, 1930, 3146, 6479, 2890, 17, 3100, 3213, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 6632, 8170, 19, 19990, 17, 43, 3416, 16, 2154, 12936, 1920, 4728, 6632, 8170, 1930, 2496, 22242, 17, 2487, 6031, 19990, 17, 43, 1988, 17421, 1956, 15808, 18249, 16, 19542, 16, 1930, 11278, 1942, 2386, 1920, 14914, 5843, 8835, 18, 2144, 2697, 4573, 2026, 2678, 1942, 3170, 6338, 1930, 5741, 4935, 4028, 2596, 2753, 17, 8414, 6920, 16, 1956, 19990, 17, 43, 4475, 13915, 1966, 43, 7281, 1958, 21563, 5957, 2019, 1920, 22242, 18, 2176, 1977, 2899, 1922, 12470, 16323, 2072, 1957, 27986, 3336, 12, 2288, 17, 21268, 26376, 24688, 13, 1930, 1977, 2910, 2007, 20709, 11569, 5597, 1930, 5607, 18, 3], "output": "MARTVQQVNKKKQKKLLPIKFYQASTNLLLRKRPFMRLVREVQLTALEALQEAAETYLTHVQFILRIKEDDLKFTKKTTKRTKPGVRSLRETQKLSLQAHFWLFEHSNLAAIHAKRITVFPKD", "metadata": {"id": "T1JTZ6", "cluster": 25022464, "interpro_all": ["IPR009072", "IPR007125", "IPR000164"], "interpro_used": ["IPR007125", "IPR009072", "IPR000164"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe 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. Furthermore, the protein includes 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. Moreover, the protein incorporates 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 originates from Kiloniellaceae bacterium and is connected to UniProt keyword Two-component regulatory system, Membrane, and Transmembrane.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 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, 3677, 16, 1920, 2213, 5921, 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, 3950, 16, 1920, 2213, 19683, 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, 22970, 2037, 13829, 13339, 5870, 1972, 3336, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2288, 17, 4594, 4948, 2433, 16, 3260, 16, 1930, 9117, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MAGELPTYSRLTILFVSSRIDKYVPFIANVGLLALLAWSAKVSLGLLFGVTSAGLMFVPIEVEPGTTTMAALTRLSIGGAGVFSGLVYVISLGAIGPAPDAKQLVLLAAAASVATLPVVLLLPGREIQRLKWEVALVHSEQRFRDFAKSASSERYSQITGFDGATIMGRTRHQVTMEELRTAEGGIITIAINGVPIFDSAGAFANRAKSAFLANMSHELRTKSGLAALMDTLWDAIARGVSALARSPFALHAKQTKTIFGDGRGAPLLLAGVVGGPLAAAILVYHYFTRRRATPEKQLAALMTIWPKLTIANIVGVGVLGSLLDWYWETNAELKFTYVTDNEKWTQHLEDLHQHRPFKEFSYKMGYRGIGTDITQRVAAEQAILRAKDKAEE", "metadata": {"id": "A0A7C7KJD0", "cluster": 27577754, "interpro_all": ["IPR003661", "IPR036097", "IPR001610", "IPR000014", "IPR000700", "IPR035965", "IPR050736", "IPR011620"], "interpro_used": ["IPR003661", "IPR000700", "IPR000014"], "interpro_unused": ["IPR036097", "IPR050736", "IPR011620", "IPR035965", "IPR001610"]}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is classified under the Protein of unknown function DUF3422 family, which consists of functionally uncharacterised proteins found in bacteria, archaea, and eukaryotes. Members of this family are typically between 426 and 444 amino acids in length. It is expressed in Steroidobacteraceae bacterium.\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, 2213, 1927, 5435, 2347, 4855, 10892, 6852, 1028, 3416, 16, 2154, 7543, 1927, 9346, 23229, 3495, 2697, 2435, 1922, 4802, 16, 21501, 16, 1930, 15021, 18, 4678, 1927, 2052, 3416, 2032, 5745, 2192, 3858, 1016, 1930, 4044, 1006, 3835, 4576, 1922, 3471, 18, 2176, 1977, 3198, 1922, 9507, 5883, 9914, 14061, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MPHALAGFLTHKNHAPMRMTQLVMYTGEQQVSEARSHAEMSLGELHLVWEHHTEFSTYSFIKKGALRATQVALTARSQPEPSDELLARIWSDFKLHEDGMGRLLIRDQTLHGLGLPMAQSLTPPLRTALIDEMHVRRFPAFTALCARYNVVPPKGKYFSTDDPFASPVLLELPHDWVESLPGQVSSFSAADLMSCEVQNSEAGGDTARLVQRLQELGNYRNMAL", "metadata": {"id": "A0A925MVT8", "cluster": 1503984, "interpro_all": ["IPR021830"], "interpro_used": ["IPR021830"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein features a TadE-like domain that contributes to the assembly or export of Flp pili, which are essential for bacterial surface adherence. Associated with the *tad* locus, this domain features hydrophobic regions indicative of a transmembrane role within the secretion system. It is present in Mesorhizobium sp. L103C119B0 and is associated with UniProt keywords Transmembrane helix. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 4075, 43, 17857, 1021, 17, 3189, 3418, 1988, 7624, 1942, 1920, 5957, 2014, 12660, 1927, 25714, 7547, 1033, 16, 2154, 2032, 4415, 1958, 4543, 3154, 7015, 18, 2458, 1956, 1920, 14, 17857, 14, 6730, 16, 2052, 3418, 4075, 7919, 3451, 10779, 1927, 43, 9117, 2770, 2651, 1920, 5512, 2433, 18, 2176, 1977, 2481, 1922, 23577, 5004, 2061, 23156, 2056, 18, 7554, 12962, 5800, 4136, 1014, 1008, 1930, 1977, 2458, 1956, 20709, 11569, 9117, 7864, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MSAERIGSRWRRDCSGAAGLEFALIAPFLVMLLFGIFAFGWAMNAVSTVRYTLARELLKRLGQRRRDVALGWEDADPSTVAVSAFQADVLRSAFRRLLRETGAPECQWRDLAKAPWCAI", "metadata": {"id": "X6JE70", "cluster": 4142966, "interpro_all": ["IPR012495"], "interpro_used": ["IPR012495"], "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 Sortase family, which functions as a transpeptidase and protease to covalently anchor surface proteins to the cell wall, primarily in Gram-positive bacteria. These enzymes recognize and cleave a specific C-terminal LPXTG motif to catalyze the assembly of pili and the attachment of various substrates to the peptidoglycan layer. It is found in Gallintestinimicrobium propionicum.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 14440, 1942, 1920, 17362, 2051, 3416, 16, 2154, 4088, 1966, 43, 22796, 18877, 1930, 7154, 1942, 16590, 13333, 3154, 2697, 1942, 1920, 2024, 4821, 16, 5985, 1922, 8604, 17, 2843, 4802, 18, 2144, 5038, 9967, 1930, 21252, 43, 2487, 45, 17, 4262, 8182, 3306, 1029, 5219, 1942, 18170, 1920, 5957, 1927, 7547, 1033, 1930, 1920, 8576, 1927, 3425, 6249, 1942, 1920, 24183, 4757, 18, 2176, 1977, 2435, 1922, 9354, 2879, 2158, 11566, 4913, 15129, 2457, 5062, 14207, 1989, 18, 3], "output": "MKKRKPAACNGLLRGILTGICVFQSSPAEETSIEEAEAAVDAAQVEAVLQDAYAWLEIPGTGISQPILQSGAIYTETANDIDFSDGNTVIYGHNTLDRFEKLHEYQDRAAYPYDDRHLIAAYDFSDPIIFRNVTEDDKLITLETGVSGEPDQRYLVQAVLVEGQGVTLSGCSSSNPETADMAGAETITSDAEIPLKLNELCALNASIDDEYYLTHNAAKEEAEDTFFDENREVRIYLPEKMLVYRIFYLEEVFSIRQIDAFIDDTMD", "metadata": {"id": "A0AAE3AR34", "cluster": 4522884, "interpro_all": ["IPR005754", "IPR023365", "IPR009835"], "interpro_used": ["IPR005754"], "interpro_unused": ["IPR023365", "IPR009835"]}, "task_type": "infilling"} {"instruction": "Here is the polypeptide chain function: The protein belongs to the Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily, which forms the homodimeric four-helical bundle responsible for histidine autophosphorylation and phosphotransfer in two-component systems. It facilitates the transfer of a phosphoryl group from ATP to a specific histidine residue and subsequently to an aspartate on a response regulator, thereby controlling processes such as osmoregulation and development in microorganisms. Furthermore, 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. Furthermore, the protein includes 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 originates from Botrytis paeoniae. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 14440, 1942, 1920, 2733, 8201, 13873, 4016, 16, 7632, 6284, 19, 8078, 22790, 1924, 3418, 13975, 16, 2154, 4952, 1920, 21189, 1935, 3006, 17, 11514, 14142, 5061, 1958, 13873, 22009, 1930, 8078, 17204, 1922, 2288, 17, 4594, 3771, 18, 2176, 11374, 1920, 3856, 1927, 43, 12556, 2210, 2037, 4498, 1942, 43, 2487, 13873, 6181, 1930, 5326, 1942, 1925, 12878, 1990, 43, 2644, 7888, 16, 6113, 7138, 4028, 2427, 1966, 9405, 14424, 2281, 1930, 2740, 1922, 11679, 18, 3677, 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, 3677, 16, 1920, 2213, 5921, 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, 22970, 2037, 12499, 6907, 3600, 25726, 6114, 1021, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MSLQCGSGHSLGVEHVGINTRHKNNEETTGTDLVLAELGAVDLLRQDSRPSFIVDMSIENEICELPVVFTNDAFKTYAKFKNIASWLSGNSCQGGNAFIKWIHTRPSKAVNQYWFRHQRWSKVLLGDRWCVVSGHEMAFSKSVQDTDVIHCKHLQSKHTQYRFPPTKIRSQNSNSHCENHYSIMRSPGSHNSAVAAHLYFTPSLSFETPFAKFFCSKDWSSTTVESISEQLLDMTSLISNFSQLSPIAMFIIDAKDGSLLFANEAWTRITGGTVEEHSNLRWLDCLIDEDREFVAEQWYLVLTEKCPVHFEGRSKTLWRPQFPDPALFGEDEVYYTWAECSAVPRLNDKGEVEHVVGCLSDVTHIKWAARIQERRLNEALKEKKEREEFMNMTSHELMNPLSAAVQAAHTMISSLDEINKALSHTQDNVLHDGNSKSYGEIKTSVRRNIEIAKIIISCGEHQRKLMEDARMMSKLDINLFSISPTRTEPIRVVDTAMSMLSGETSKLDISIRLEVDPSMEALSSQWLCFDPSRFLQLLLNLLKNANKYTKSFKTRNVLVRLGATTGSPYHKEIGREIQYIPLRIARNDPTLKDASGTGEIVYLHCSITDTGKGLSETERQTLFKKFSQTSLSTLTQYGDSSLGLFICRELAELQGGAIGIGYADSQATGSTFAFYIKTRRSEFKPAGLPLETSAESSQLDGQSSMGDFDV", "metadata": {"id": "A0A4Z1FE60", "cluster": 9263790, "interpro_all": ["IPR036890", "IPR005467", "IPR036097", "IPR000014", "IPR035965", "IPR004358"], "interpro_used": ["IPR036097", "IPR000014", "IPR005467"], "interpro_unused": ["IPR035965", "IPR004358", "IPR036890"]}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein features a Pre-mRNA polyadenylation factor Fip1 domain that facilitates the specific polyadenylation of cleaved mRNA precursors by mediating interactions within the polyadenylation factor complex. This motif is required for binding to the Yth1 subunit and directly interacting with poly(A) polymerase. It is present in Ichthyophthirius multifiliis (White spot disease agent) (Ich) and features UniProt keywords mRNA processing and Nucleus.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 4075, 43, 2097, 17, 3616, 24544, 2991, 14856, 5113, 3418, 1988, 11374, 1920, 2487, 24544, 1927, 10246, 3616, 10416, 2007, 10239, 3719, 2651, 1920, 24544, 2991, 2796, 18, 2052, 5219, 1977, 3414, 1958, 2743, 1942, 1920, 24412, 8600, 5903, 1930, 4103, 8615, 1956, 4286, 12, 43, 13, 6479, 18, 2176, 1977, 2481, 1922, 14910, 28935, 2688, 22523, 3027, 1957, 15453, 5912, 1937, 12, 4511, 9177, 2573, 5899, 13, 12, 14910, 13, 1930, 4075, 20709, 11569, 3616, 4587, 1930, 5607, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MSTQLPTKPPIQIKKDKKEVMKLLIPQIFYTKFTKDTDRCEETFRAYTNQVRACRGNFSINDTYKENEYNLNKMVSKFVRRFEEENDEEENQNEDFEEEDENIIRIVYTQYWIKRRKNLQRTHFQNILYKPWLQSNQDLTDYFNYGFNDKTPLEYGGFSHPFDKNFNCIQEEENFENYKEYNKKKTKNNRLCG", "metadata": {"id": "G0QZ97", "cluster": 12250199, "interpro_all": ["IPR007854"], "interpro_used": ["IPR007854"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein contains a Aminotransferase, class I/classII, large domain that forms the catalytic core of pyridoxal-phosphate (PLP) dependent enzymes, featuring a 3-layer \u03b1/\u03b2/\u03b1 sandwich topology. It facilitates the covalent binding of the PLP cofactor to a conserved lysine residue to drive transamination reactions in enzymes such as LL-diaminopimelate aminotransferase and histidinol-phosphate aminotransferase. Additionally, the protein is categorized in 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. Furthermore, the protein is included in the Histidinol-phosphate aminotransferase family, which comprises class I pyridoxal-5'-phosphate (PLP)-dependent enzymes that catalyze a critical step in L-histidine biosynthesis. These proteins are typically highly specific for imidazoleacetol phosphate, although a subgroup exhibits broader specificity towards aromatic amino acids. It has been detected in Candidatus Gottesmanbacteria bacterium and features UniProt keywords Amino-acid biosynthesis. 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, 15817, 16, 2921, 51, 19, 2921, 3907, 16, 3103, 3418, 1988, 4952, 1920, 6804, 4728, 1927, 24828, 23859, 17, 5413, 12, 21453, 13, 3100, 5038, 16, 29931, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 18038, 13678, 18, 2176, 11374, 1920, 13577, 2743, 1927, 1920, 21453, 15155, 1942, 43, 5305, 9082, 6181, 1942, 9265, 2127, 8732, 5298, 1922, 5038, 2427, 1966, 10748, 17, 21121, 2011, 11593, 5148, 2057, 15817, 1930, 27507, 22816, 1945, 17, 5413, 15817, 18, 4950, 16, 1920, 2213, 1977, 10234, 1922, 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, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 27507, 22816, 1945, 17, 5413, 15817, 3416, 16, 2154, 12936, 2921, 51, 24828, 23859, 17, 25, 11, 17, 5413, 12, 21453, 13, 17, 3100, 5038, 1988, 18170, 43, 4140, 3537, 1922, 54, 17, 13873, 8132, 18, 2144, 2697, 2032, 5745, 3626, 2487, 1958, 16045, 7681, 1945, 5413, 16, 2876, 43, 6200, 9826, 11462, 4896, 5681, 10761, 3835, 4576, 18, 2176, 2258, 2252, 3330, 1922, 14550, 1031, 1957, 14643, 14652, 3862, 7972, 2341, 18339, 14061, 1930, 4075, 20709, 11569, 3835, 17, 2687, 8132, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MDITKLIRKNVQTFQTYKPSLTLEQISKEINIERENILKLDSGENPYVETLQDKALASGVNFYTYPDPLCIQLREELSDYVRIDKEWILCGNGSDELINLLTCAFVSKGEEIIICPPTFPMYEFYGKLSEAKIIPILRRSNFSLDIEKIQNSISIKTKIVFIDSPGNPSSVVVPQRDIEVLLEEDAIIVSDEAYFEYCGKSALPLLKKYSNLVILRTFSKWAGLAGLRIGYLIARPEVTDILLSIKSPYNVNSVAQKAAEYVLGNRKEFLQIVDRLVAVRKALIEKLQKFPQLSVFPSEGAYILFKPKKSAQHLQSFLKKNGILVKVVNQPLLENCIRINIMMDDDAQKLTMLLRRYYENEVI", "metadata": {"id": "A0A9D6ESM3", "cluster": 14456361, "interpro_all": ["IPR004839", "IPR005861", "IPR015424", "IPR015421", "IPR015422"], "interpro_used": ["IPR004839", "IPR015421", "IPR005861"], "interpro_unused": ["IPR015424", "IPR015422"]}, "task_type": "autoregressive"} {"instruction": "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 is expressed in Cytospora mali (Apple Valsa canker fungus) (Valsa mali).\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 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, 1977, 3198, 1922, 5521, 21086, 3054, 1033, 12, 19663, 2326, 5735, 2112, 13548, 16461, 13, 12, 2326, 5735, 3054, 1033, 13, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MDLSCILNHFEPSSVADSAPSSGADDDVIAYMLSPGSPCKPCIVLRASKLPRSDFHFAIIPSAKDMLQLTDIGGTTVTYDGWETHSCFHRVIAGEHVVSKLAIKIILPNVSFEFVVPYDPPSHERYLKNLSTATVASSLETQERPSGRQDGAESVFRISRIFRDHLNIINVTSYNGSIVVLEHLPLGQLEFLHRHDITHSAISLESIYIRQLKPFTVVLGGITGVVAHQDDTGRGSRHKAEDIKDLGTVIQADPNQRPTASKCVLVVIAKVMGVELEASRRGKSVPGPETRWKTGQPKKYARLQPRSQERLARLSMGCPYKGFTFGTSRRSSCRIPGKRIRTFYNSMMLKARSLVTIPHKLGSVFLDLAGVLDQVGERDRLQAVEQLTRADLLGVLEPTNRLELLTESMQQ", "metadata": {"id": "A0A194VJV4", "cluster": 14997526, "interpro_all": ["IPR011009"], "interpro_used": ["IPR011009"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein can be placed in the NUDIX hydrolase-like domain superfamily, which hydrolyzes nucleoside diphosphates linked to other moieties to regulate cellular metabolism and sanitize the nucleotide pool. Members of this diverse family, found in prokaryotes, viruses, and eukaryotes, degrade a wide range of substrates including ADP-ribose, NADH, sugar nucleotides, and mutagenic oxidized nucleotides like 8-oxo-dGTP. It is expressed in Planctomycetota bacterium.\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, 28416, 2416, 20748, 17, 3189, 3418, 13975, 16, 2154, 7222, 20887, 18015, 23266, 1036, 4624, 1942, 2303, 16706, 1942, 5741, 3689, 4714, 1930, 6867, 2078, 6931, 1920, 5489, 5562, 18, 4678, 1927, 2052, 6445, 3416, 16, 2435, 1922, 28149, 16, 6241, 16, 1930, 15021, 16, 17069, 43, 4743, 3109, 1927, 6249, 2710, 9828, 17, 17870, 16, 14261, 16, 9523, 9519, 16, 1930, 21977, 11339, 9519, 3189, 28, 17, 18588, 17, 9665, 17475, 18, 2176, 1977, 3198, 1922, 4720, 2341, 13386, 19446, 3857, 14061, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MNFSDYEKQFQQACENVEPKSWPYTHREPSLTLLVRSDPVPLSSLIYLPGGIRCTPYGYLGLYPLHNLEFDAHIYLGTVPSPEKWDIDPNYFDLKRPEFHLHVDEEVFTVSIASDLGYGKRLPFLSRAGAFLLPIVDDLSPQSTMYENVEKDIGLQPKDIRLDTVDQIYKVPLETLMDEFRASDATAAILCLLLRRI", "metadata": {"id": "A0A3M1B2R8", "cluster": 15630409, "interpro_all": ["IPR015797"], "interpro_used": ["IPR015797"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein possesses a Dynein heavy chain, C-terminal domain that serves as a distinctively flat structural component spreading over the AAA1, AAA5, and AAA6 domains of the dynein motor complex. This architecture comprises six $\\alpha$-helices and an incomplete six-stranded antiparallel $\\beta$-barrel. Furthermore, the protein should contain a Dynein heavy chain AAA lid domain that is located near the C-terminal region of the dynein heavy chain. It contributes to the structural integrity of the AAA+ ring assembly, facilitating the ATP-dependent mechanochemical cycles required for microtubule-based motility. Furthermore, the protein should include a Dynein heavy chain region D6 P-loop domain that constitutes the sixth AAA module (D6) within the dynein motor unit, contributing to the hexameric ring architecture essential for microtubule-based transport. Although this C-terminal module has evolutionarily lost the P-loop signature, it retains the general structural fold of an ATP-binding site to support the mechanical function of the AAA+ ATPase motor. It occurs in Piptocephalis cylindrospora.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 14465, 43, 18188, 7881, 4659, 16, 45, 17, 4262, 3418, 1988, 10634, 1966, 43, 15308, 1954, 9778, 4346, 4594, 13405, 2338, 1920, 13835, 1009, 16, 13835, 1015, 16, 1930, 13835, 1016, 4682, 1927, 1920, 18188, 4842, 2796, 18, 2052, 9335, 12936, 3798, 8, 38, 4595, 8, 17, 12789, 1930, 1925, 9876, 3798, 17, 10338, 28892, 8, 38, 4666, 8, 17, 19560, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 18188, 7881, 4659, 13835, 13096, 3418, 1988, 1977, 4810, 4931, 1920, 45, 17, 4262, 3031, 1927, 1920, 18188, 7881, 4659, 18, 2176, 7624, 1942, 1920, 4346, 7996, 1927, 1920, 13835, 15, 6335, 5957, 16, 12440, 1920, 4498, 17, 3100, 2665, 4829, 6355, 3414, 1958, 10544, 17, 2454, 9254, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 18188, 7881, 4659, 3031, 15304, 58, 17, 5881, 3418, 1988, 14879, 1920, 17961, 13835, 9059, 12, 15304, 13, 2651, 1920, 18188, 4842, 5344, 16, 8739, 1942, 1920, 25602, 1935, 6335, 9335, 4415, 1958, 10544, 17, 2454, 4860, 18, 2876, 2052, 45, 17, 4262, 9059, 2258, 18584, 7621, 1920, 58, 17, 5881, 9983, 16, 2176, 21645, 1920, 3335, 4346, 3728, 1927, 1925, 4498, 17, 2743, 3200, 1942, 3373, 1920, 5821, 2347, 1927, 1920, 13835, 15, 9444, 4842, 18, 2176, 5110, 1922, 6556, 4575, 9175, 1937, 15460, 28988, 1019, 18, 3], "output": "MEAPEGTLYAFRALLLIRCLRSDRLVSSVEGFVRRVFQQENFLTQASTTELQLGELVDKEVASATPVALCSVPGHDASNRVEQLAAERTARCVAVALGSAEGFTLADAAITSAAKTGTWVLLKNVHLAPQWLGQLEKRLHALRPHASFRLFLTMETHPKVPVNLLRRARVLMFEPAPGVRAHLQQLLRGIPTARVAKAPAERARLYFLLAWLHAVVVERLRYVPLGWSKGYEFGEADHESALATIDRWLDSSAIGEEEGAAKTHISPEKIPWAAIRTLLTESVYGGRIDNEYDQRVLESFVGTLFTPKSYDYNFALVKREEGSSGSGEVDESPEEEEGASKRKISASIHKDLCIPDATRMEQFLTWVDALPDREPPTWLGLPADAERVILTARGQTLLSRARKMQSVASDESGEADGGGDAVELSGGLGGMGGADGGEGGSTAANQQQQPAWMRTLGTHVAQWLDLLPNVSTPPQVPSDLLKDPLVRVFVREAQLGRSLLARVVGDLQEVAEVCAGTAPQTNHRRMLLSSLSRGLIPDHWRKFKVPRNRSLAQWIVNLGTRLKQATDAEAKSLAGAGGASLGEGAVWLGGLFNPGAFITATRQAVAQRHAWSLEELTLRLDLSSGEEDEGAEGGGMKHEEDRFAVSGLRLEGARWEGGKDGRLALCAPGDGGFTRLGQCGIRWVKGDSEADASSESKGAVTLLPVYLNGDREDLLFGVDISIRDEDKAAVLQRGLAITTD", "metadata": {"id": "A0A4P9Y1F2", "cluster": 17978333, "interpro_all": ["IPR041658", "IPR042219", "IPR026983", "IPR041228", "IPR043160", "IPR004273", "IPR027417"], "interpro_used": ["IPR041228", "IPR041658", "IPR004273"], "interpro_unused": ["IPR042219", "IPR043160", "IPR026983", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein belongs to the Type I restriction modification DNA specificity domain superfamily, which functions as the target recognition domain (TRD) within bacterial Type I restriction-modification (R-M) systems. As the specificity subunit of a heteromeric complex, it directs the methylation of protected host sequences and the endonucleolytic cleavage of unmodified foreign DNA. It originates from uncultured Rubrobacteraceae bacterium and exhibits UniProt keyword tags Restriction system.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14440, 1942, 1920, 2601, 51, 7587, 6295, 2678, 4896, 3418, 13975, 16, 2154, 4088, 1966, 1920, 2758, 5708, 3418, 12, 2025, 1007, 13, 2651, 4543, 2601, 51, 7587, 17, 6295, 12, 60, 17, 55, 13, 3771, 18, 1966, 1920, 4896, 5903, 1927, 43, 19732, 9213, 1935, 2796, 16, 2176, 28351, 1920, 5547, 1927, 9713, 4423, 3709, 1930, 1920, 16239, 1022, 2626, 6586, 6404, 1927, 18602, 12400, 2678, 18, 2176, 22970, 2037, 5269, 21058, 10010, 15129, 2422, 9914, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 7587, 2433, 18, 3], "output": "MQVDDLLLSERGPEHGSVLVERADVRGTLQRGTLATTVSLMQGVMTRIAVERLREIPVPLVSISTFEDLDSVETELRAKADELTRLGSMLSTSIESSGQLQFQISNAYPYPIAYGYRLLNSYAGPWERYLEQLAAGIDIGKLWEGGVAFGSWKRVIEKCAGVFESYRNHPLASALAGLDIAFAEVAIRRASNEAQERLHRCMEALAFLIAFPIYQVQDMDLLEQRIVVSPRAEKKNRLFIDLGGATGLRQQRPKLRLKDGRLSPEYLMEYLNSATARTLVAALSTLRRSLFEARDARAFREQLGERVAENMLAFLASLSLSILQKEDLASGKRGFGADVNALISARNNLGHGREANDDGIRLDLKCLLYRGDHPG", "metadata": {"id": "A0A6J4NMH3", "cluster": 19495821, "interpro_all": ["IPR044946"], "interpro_used": ["IPR044946"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein carries a ORC1/DEAH AAA+ ATPase domain that functions as an ATP-dependent motor involved in diverse genomic processes such as DNA replication, DNA transposition, and mRNA splicing. This domain is found in Origin Recognition Complex (ORC) subunits, transposon proteins like TnsC, and pre-mRNA-splicing factor RNA helicases. In addition, the protein is assigned to the ExeA/AAA ATPase DNA-binding & secretion family, which includes regulators of general secretion pathways and ATP-dependent DNA activators involved in transposition. These proteins polymerize into helical filaments around DNA to select target sites, recruit recombinases, and ensure target immunity. They are structurally characterized by a central ATPase module flanked by N-terminal and C-terminal DNA-binding domains. 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 occurs in Desulfobulbaceae bacterium.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 2014, 5800, 19, 30097, 1023, 13835, 15, 9444, 3418, 1988, 4088, 1966, 1925, 4498, 17, 3100, 4842, 3286, 1922, 6445, 4935, 4028, 2427, 1966, 2678, 5158, 16, 2678, 22596, 16, 1930, 3616, 8490, 18, 2052, 3418, 1977, 2435, 1922, 4853, 5708, 2796, 12, 2014, 1030, 13, 6991, 16, 18808, 2697, 3189, 7417, 12709, 16, 1930, 2097, 17, 3616, 17, 8490, 2991, 3146, 29919, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 1975, 5376, 19, 13835, 9444, 2678, 17, 2743, 10, 5512, 3416, 16, 2154, 5921, 9098, 1927, 3335, 5512, 3873, 1930, 4498, 17, 3100, 2678, 15497, 3286, 1922, 22596, 18, 2144, 2697, 4593, 2606, 2460, 11514, 11855, 4760, 2678, 1942, 8702, 2758, 3402, 16, 5608, 21366, 1036, 16, 1930, 6486, 2758, 7611, 18, 2611, 2032, 12171, 4378, 2007, 43, 4101, 9444, 9059, 20185, 2007, 56, 17, 4262, 1930, 45, 17, 4262, 2678, 17, 2743, 4682, 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, 5110, 1922, 30311, 2389, 1944, 7972, 1972, 3336, 14061, 18, 3], "output": "MNYQKSLQCMTEPVTTPSGAEIFLSQAVRDACEKLSHNIRIGVGLQLVIGDDGSGKTTLFNQLAQRFSTDNNTVVLLLNNPQFRDLQQFLVTVAAVFKTIKTPSDFDDSLLQSAFNSFFYKLCLQEKKTVLLLIDNGQNLPDFCLNALNSFYDHHMDCRSLLQVVICCEPSLVRKINANDSLNSRVAFAAVLKPLGFKDTRKFILFHLERTTADHSFPPALFSIPAQWAIYHMTQGHPKEIIELYHFIVLTLAIENRKKVGWFMTLRCAKQLIPPRAKKLQIIQASSLASLVVLILLLGLWSVQTKTLSVPQPEYLPEVTTPQRIPPPEQQPLESVKVPQKILSPAILTEGQVEVAAPAENSAAFPVQPEDKAASVQVPVLESATVTPAIKESRQVMLGDTFLGMIQQVYGPDYVNTQYIDQVIAANPHLRDFDNLKVGDKVFFPVLVQEAAKPFLAATASKSQPAPGVVSQPQPDDSADSIGKRVEPPEYLGDIITASGETFGDMVRRIYGPWSFNPENVKTVMAANPDLKSPELLSVGYKVRFPTIPVALTSKAEEVWWARITTFDNIQSAYRFLRKYSKASSPLLIIPSRDNSGQILMNILLEEYFVDKKSAQKAIHALSDEISAQAQALHGLSPATFYYQLTPND", "metadata": {"id": "A0A2N6BU78", "cluster": 21494354, "interpro_all": ["IPR049945", "IPR052026", "IPR027417"], "interpro_used": ["IPR049945", "IPR052026", "IPR027417"], "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 grouped in the Unsaturated glycosaminoglycan hydrolase family, which catalyzes the hydrolysis of unsaturated glycosaminoglycans, including hyaluronate, chondroitin, and heparin disaccharides, to facilitate extracellular matrix degradation during tissue remodeling and cell invasion. These enzymes preferentially target sulfated substrates or ulvan to release unsaturated monosaccharides, and their activity is often partially inhibited by divalent metal ions. Moreover, the protein can be placed in 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 identified in Saccharolobus sp. E5-1-F.", "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, 10809, 1922, 1920, 19172, 25982, 15391, 20748, 3416, 16, 2154, 17097, 1920, 9128, 1927, 19172, 25982, 19900, 16, 2710, 22825, 2010, 16, 26437, 16, 1930, 9962, 2054, 11926, 16, 1942, 6628, 5329, 4526, 4877, 2409, 2960, 8378, 1930, 2024, 6254, 18, 2144, 5038, 10662, 2758, 26649, 6249, 2014, 3570, 25777, 1942, 4012, 19172, 18491, 11926, 16, 1930, 2310, 2455, 1977, 3868, 6426, 5069, 2007, 21610, 6048, 6982, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 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, 2899, 1922, 14175, 15742, 6012, 26835, 2056, 18, 28332, 17, 21, 17, 48, 18, 3], "output": "MKFQEALEKIKEKILRLIDISGSKFPIYKDYNSKEWVFADGKHWISPFWCGILWNIGSYFSDEKIIESAIKCSFLLTAEEDIDTHDRGFKYFYSTVKGWELTNYTKFKEISLRGANDLANMFNPSLGFIPLGSDVRFPGEPPEVSNYEFIIDTMTASLPLLLWAYKVTSEPKFYYISIIHAHRTFDLLIRKDWSTYHAVRILPSNGEVYRHTHQGYSNESCWSRGQAWAIYGFTKLYEETHLRFFLVIAEKLLEYFIKNLPINKIPFYDFTDPLIPNVRLDTSASAIVSSAMLDLYKLTGNNYYIINAIDMIRALLRNEVFVDGGLQHSRYRQGEAEDAEIMFGDYYLSEALIKALYLGFQS", "metadata": {"id": "A0A5Q0SP32", "cluster": 22520498, "interpro_all": ["IPR008928", "IPR012341", "IPR052369"], "interpro_used": ["IPR052369", "IPR008928"], "interpro_unused": ["IPR012341"]}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe 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. In addition, the protein has a 3-beta hydroxysteroid dehydrogenase/isomerase domain that catalyzes the oxidation and isomerization of 5-ene-3-beta-hydroxysteroid precursors into 4-ene-ketosteroids. This enzymatic activity is essential for the biosynthesis of all classes of steroid hormones. It has been detected in Amblyomma americanum (Lone star tick).\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, 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, 1922, 2459, 16, 1920, 2213, 2258, 43, 23, 17, 4666, 8275, 2156, 6506, 1960, 9294, 19, 25510, 3418, 1988, 17097, 1920, 6638, 1930, 27027, 1927, 25, 17, 2066, 1021, 17, 23, 17, 4666, 17, 8275, 2156, 6506, 1960, 10416, 2460, 24, 17, 2066, 1021, 17, 21471, 2156, 6506, 3753, 18, 2052, 8145, 2455, 1977, 4415, 1958, 1920, 8132, 1927, 2136, 7190, 1927, 9507, 10224, 18, 2176, 2258, 2252, 3330, 1922, 26441, 1947, 3368, 5339, 1989, 12, 10969, 1021, 3632, 12085, 13, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MDTRISTSHKTDAQAAMLEADSTIGDQRPIRVVLVTGSSVQEVRLFDTRPFENTLGELLHFDKTRGHPMIKKTADAVIHCAALVPTTAAEDEAAFERINVQDALYENRAAAFLGPLIEGHGIRIFPRPVPYLPMLLLASCTQCIVGVLGHRYMYGGAFFDDAETRKALAWRPKYSPQEAARMSRSFYDTLGMLGHHVLRELQDHPSREVVASVCDIQALREAVRGSGRCLVACDDTPVDIVLFPGIRRGQVLKPSTI", "metadata": {"id": "A0AAQ4DXY8", "cluster": 24049972, "interpro_all": ["IPR002225", "IPR036291"], "interpro_used": ["IPR036291", "IPR002225"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein is associated with the ATP-dependent Clp protease ATP-binding subunit CLPT1/2 family, which comprises plant accessory proteins that regulate the assembly of the plastidial Clp protease system. Structurally homologous to bacterial ClpA/C chaperone N-domains, these subunits facilitate the sequential binding of the P-ring to the R-ring during proteolytic core formation. Moreover, the protein includes a Clp repeat (R) N-terminal domain that regulates substrate specificity and recruitment within Clp/Hsp100 chaperone ATPases by binding to adaptor proteins. Structurally consisting of two four-helix bundles, this domain modulates target recognition to facilitate protein disaggregation and degradation. It is found in subfamilies such as ClpA, ClpB, and ClpC, and mediates specific interactions with partners like the VipA/VipB complex in ClpV. It is native to Candidatus Curtissbacteria bacterium GW2011_GWA1_41_11.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 4498, 17, 3100, 18017, 7154, 4498, 17, 2743, 5903, 18017, 6613, 19, 22, 3416, 16, 2154, 12936, 4496, 15954, 2697, 1988, 5741, 1920, 5957, 1927, 1920, 19754, 2086, 18017, 7154, 2433, 18, 12171, 8725, 1942, 4543, 18017, 1019, 19, 45, 14044, 56, 17, 4682, 16, 2144, 6991, 6628, 1920, 9454, 2743, 1927, 1920, 58, 17, 6335, 1942, 1920, 60, 17, 6335, 2409, 12712, 4728, 3337, 18, 3950, 16, 1920, 2213, 5921, 43, 18017, 6865, 12, 60, 13, 56, 17, 4262, 3418, 1988, 7014, 4510, 4896, 1930, 6067, 2651, 18017, 19, 6418, 9029, 14044, 28132, 2007, 2743, 1942, 15077, 2697, 18, 12171, 7600, 1927, 2288, 3006, 17, 7864, 16073, 16, 2052, 3418, 13112, 2758, 5708, 1942, 6628, 2213, 29512, 1943, 1930, 4877, 18, 2176, 1977, 2435, 1922, 24167, 2427, 1966, 18017, 1019, 16, 18017, 1014, 16, 1930, 18017, 1030, 16, 1930, 10412, 2487, 3719, 1956, 7228, 3189, 1920, 16107, 1019, 19, 16107, 1014, 2796, 1922, 18017, 1020, 18, 2176, 1977, 6196, 1942, 14550, 1031, 1957, 3580, 3600, 1036, 7972, 2341, 18339, 14061, 8997, 23437, 1009, 41, 8997, 4904, 41, 4353, 41, 2513, 18, 3], "output": "MSTPETVPARTLVFSPEGQRILDLANEEAKKLNHNYVGTEHILLGLAQLEDNEVALLLHNMGADASKIRSAIEFIVGKGDETQTTEPQQTPRAKKVLEFAHAEANKDGTDTISPVHLLSGLIGEGEGIGASVLESMGVSYYELYTGLLNLRFPEIQKTFPAVRELIAVFHDSSVDDRTKNQLAVLISSAIHIIKGNETGSL", "metadata": {"id": "A0A0G0XH08", "cluster": 24856490, "interpro_all": ["IPR036628", "IPR004176", "IPR044217"], "interpro_used": ["IPR044217", "IPR004176"], "interpro_unused": ["IPR036628"]}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: It is part of 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. In addition, the protein is included in the Pectinacetylesterase/NOTUM family, which includes the animal extracellular carboxylesterase Notum, responsible for removing the essential palmitoleate moiety from Wnt proteins, and plant pectinacetylesterases (PAEs) that catalyze the deacetylation of pectin in primary cell walls. It is expressed in Acidobacteriota bacterium.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 2176, 1977, 3131, 1927, 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, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 22422, 25913, 8342, 2051, 19, 2084, 1989, 3416, 16, 2154, 5921, 1920, 4027, 5329, 9943, 8342, 2051, 2084, 1989, 16, 5061, 1958, 11340, 1920, 4415, 13615, 2456, 2010, 11804, 2037, 7028, 2697, 16, 1930, 4496, 22422, 25913, 8342, 2319, 12, 25726, 1036, 13, 1988, 18170, 1920, 23764, 1927, 22422, 1922, 3065, 2024, 12430, 18, 2176, 1977, 3198, 1922, 2687, 5883, 3940, 3857, 14061, 18, 3], "output": "MRAWMVPLVIALGAARLDAQWQAVVPGGDTLGACWDDATCATSIYTRNVTLDPAAVERHVYVPYCTGDLHWGANDRTYAGFTGPYVVVPAPRQLFVAGCSAGGYGALLWSAQVMGHYSIPLANWGVAAAWPSFIPSLSLDRLDASRVTMADVYGGDATQVFFYILTKGALAPPEEWAAQMQASMVSIEAANGGVRLVDWLRKLSDTRAPGSVPCADGSPYRFFVYPGDPGKLLLEFEGGSGQLVGIYDRTNPDNPFRDWMHHRGAVNAAAAVSWAYENGAAAAQFSDSAAGVVPPGFFVVAGFYPLSAFSQFNRLAPNFFGYIAPGSDHCVINSAALYTTQV", "metadata": {"id": "A0A2V7XKF1", "cluster": 26544198, "interpro_all": ["IPR029058", "IPR004963"], "interpro_used": ["IPR029058", "IPR004963"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein contains a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. Moreover, the protein has a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. It occurs in Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / CCUG 9996 / CIP 106432 / VR4).\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 5461, 43, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 3950, 16, 1920, 2213, 2258, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2176, 5110, 1922, 2687, 19143, 4879, 2437, 1957, 17748, 2075, 12, 3943, 11037, 6330, 10025, 19, 10964, 18063, 6800, 19, 4928, 2215, 23598, 1016, 19, 12998, 7758, 7514, 1028, 19, 12110, 1006, 13, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MTKRKIGVLVSGRGSNFQAVAVISDSPEAYALERAEKMGIPHYAIARQDLVVLAGFMRILSGDFVNSWYHRIINIHPALLPAGCTVHFVDAGMDTGPIIMQAAVPVLDEDKLWAEDRLTVNGRKVKIRKDKIKKENLPIEIAVYVDKPSFEAAIDKTLREAGVESFTGLDAQGQALNYGVKITHDTLAARILVQEHTILPEVV", "metadata": {"id": "D2RKN7", "cluster": 7085612, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR001555", "IPR002376"], "interpro_unused": ["IPR036477", "IPR004607"]}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein is categorized in the Histone H1-like Hc1 family, which functions analogously to eukaryotic histone H1 to mediate chromatin condensation. These proteins are primarily expressed during the late stages of the chlamydial life cycle to facilitate the reorganization of reticulate bodies into elementary bodies. It has been detected in Chryseobacterium sp. T16E-39.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 6632, 9169, 17, 3189, 4387, 1009, 3416, 16, 2154, 4088, 12464, 1954, 1942, 10825, 6632, 9169, 1942, 8265, 6338, 16112, 18, 2144, 2697, 2032, 5985, 3198, 2409, 1920, 5058, 5143, 1927, 1920, 21079, 1024, 3308, 4048, 1942, 6628, 1920, 18062, 1927, 18905, 2010, 8322, 2460, 20530, 8322, 18, 2176, 2258, 2252, 3330, 1922, 21367, 1021, 12022, 2056, 18, 6197, 1016, 1021, 17, 3886, 18, 3], "output": "MKELIEKINAEFEAFATEANQQAEKGNKAAGTRARKSALELSKLFKDFRKVSVEESKK", "metadata": {"id": "A0A220S872", "cluster": 780386, "interpro_all": ["IPR010886"], "interpro_used": ["IPR010886"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein is included in the Insulin-like superfamily, which represents a diverse group of disulfide-rich $\\alpha$-helical proteins, including insulin, relaxin, and insulin-like growth factors, that share a conserved fold of two polypeptide chains linked by interchain disulfide bonds. These signaling molecules exert their effects by binding to specific cell-surface receptors to regulate essential physiological processes such as glucose homeostasis, metabolism, and cell growth. It has been characterized in Lysmata vittata and is described by UniProt keywords Cleavage on pair of basic residues. 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, 4122, 17, 3189, 13975, 16, 2154, 4972, 43, 6445, 2210, 1927, 11830, 17, 5536, 8, 38, 4595, 8, 17, 11514, 2697, 16, 2710, 4122, 16, 7327, 1921, 16, 1930, 4122, 17, 3189, 2905, 2790, 16, 1988, 7948, 43, 5305, 3728, 1927, 2288, 13022, 7835, 4624, 2007, 8590, 29559, 1022, 11830, 9031, 18, 2144, 3197, 4206, 10788, 2310, 2564, 2007, 2743, 1942, 2487, 2024, 17, 3154, 4086, 1942, 5741, 4415, 5005, 4028, 2427, 1966, 3817, 7622, 16, 4714, 16, 1930, 2024, 2905, 18, 2176, 2258, 2252, 4378, 1922, 3629, 3368, 3857, 5208, 3857, 3857, 1930, 1977, 2910, 2007, 20709, 11569, 6404, 1990, 3715, 1927, 5937, 4248, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MGPAYLSMVLLLSSSTYLTLLPQETSGYNITCLAFDFDCGQLADTMSLLCKVYRSHIDERRRRSVNQSQPSPLRNFQGIRTLPFKMYEELTQETTNTSLNIRGGRFRRNTRRNTTNVYNECCQQPNCTYNDLREYCEILQDGIYTC", "metadata": {"id": "A0A7L7YYA2", "cluster": 1837463, "interpro_all": ["IPR036438"], "interpro_used": ["IPR036438"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein incorporates a RpiR-like SIS domain that functions as a phosphosugar-binding module commonly found in sugar isomerases and transcriptional regulators. This domain typically binds phosphosugar ligands to modulate the activity of transcription factors involved in sugar metabolism, such as the negative regulation of the *rpiB* gene by RpiR. Furthermore, the protein includes 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 has a Helix-turn-helix protein RpiR domain that functions as a regulator of genes involved in phosphosugar metabolism. This domain contains a DNA-binding helix-turn-helix motif and is typically found N-terminal to a SIS domain. It originates from Grylomicrobium aquisgranensis and is annotated with UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 19683, 43, 4822, 1996, 17, 3189, 19149, 3418, 1988, 4088, 1966, 43, 8078, 20490, 13279, 17, 2743, 9059, 5384, 2435, 1922, 9523, 25510, 1036, 1930, 5224, 9098, 18, 2052, 3418, 5745, 6876, 8078, 20490, 13279, 6908, 1942, 8480, 1920, 2455, 1927, 3213, 2790, 3286, 1922, 9523, 4714, 16, 2427, 1966, 1920, 3136, 3640, 1927, 1920, 14, 4822, 2023, 14, 2359, 2007, 4822, 1996, 18, 3677, 16, 1920, 2213, 5921, 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, 2258, 43, 7864, 17, 5165, 17, 7864, 2213, 4822, 1996, 3418, 1988, 4088, 1966, 43, 7888, 1927, 2628, 3286, 1922, 8078, 20490, 13279, 4714, 18, 2052, 3418, 5461, 43, 2678, 17, 2743, 7864, 17, 5165, 17, 7864, 5219, 1930, 1977, 5745, 2435, 56, 17, 4262, 1942, 43, 19149, 3418, 18, 2176, 22970, 2037, 2398, 2199, 22980, 3821, 1989, 10059, 1937, 18218, 8134, 1930, 1977, 10633, 1956, 20709, 11569, 3213, 3640, 18, 3], "output": "MLFGYTQIISLNENESGVFKYVIEHPAQAVQMNIREFLSRIQAYEQQMPDQNTCAGYMVSALQVTVMGCGNCGALAMYAARYLSNAGFYATAVTDVFYPPQEMVQQAMLNQKYGSHILVMTGNPDSTLASLATSGVSMLYGVEYLGQELLRYNDRIKKTDPKIHVDAGKALAQETGTSTATVARMYKKLGCASYPVTTIDLIQKNNDAWQKAVKMICESDALGNTEKHLILILSESGENREAVLPIVMQRYLLPQTYDL", "metadata": {"id": "A0AB35U3R7", "cluster": 2253666, "interpro_all": ["IPR009057", "IPR000281", "IPR047640", "IPR035472", "IPR001347", "IPR046348", "IPR036388"], "interpro_used": ["IPR035472", "IPR001347", "IPR000281"], "interpro_unused": ["IPR046348", "IPR036388", "IPR009057", "IPR047640"]}, "task_type": "infilling"} {"instruction": "The protein is included in 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. Moreover, the protein can be placed in the Phosphoesterase MJ0037 family, which comprises archaeal proteins that share a conserved motif with phosphoesterases such as the nucleases SbcD and Mre11. These proteins likely exhibit nuclease activity similar to the SbcCD complex, which cleaves DNA hairpins to unblock stalled DNA replication. Moreover, the protein includes 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 has been characterized in Candidatus Woesearchaeota archaeon. 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, 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, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8078, 8342, 2051, 15697, 23820, 1027, 3416, 16, 2154, 12936, 22367, 2697, 1988, 7948, 43, 5305, 5219, 1956, 8078, 8342, 2319, 2427, 1966, 1920, 29305, 7760, 9547, 1930, 26460, 18, 2144, 2697, 3205, 5987, 16230, 2455, 2551, 1942, 1920, 7760, 2437, 1007, 2796, 16, 2154, 23839, 2678, 14565, 1036, 1942, 2067, 3450, 2602, 27084, 2678, 5158, 18, 3950, 16, 1920, 2213, 5921, 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, 2258, 2252, 4378, 1922, 14550, 1031, 1957, 26334, 21406, 3336, 7336, 13470, 1916, 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": "MELLPGFRTIGCALLFRKTLVLSDLHLGYEKALGAGTGFISRFQFDELIRELDWVFRVAGKLDAIVLNGDIKHEFGTIEEREWRYVLRFLDYLQKHAKRIILIKGNHDTLLKPIAEKRSYPLEPFVLLHDVLITHGDEITNEFKKAAKKAKTIVIGHEHPAVTLRKGSRSETFKCFLAGKWKRNKMIVLPSANPLTQGTDILSSGRLSPFLGSLSSFRAFLVGEEGVYDFGKVSNLARAQRW", "metadata": {"id": "A0A8T4PYP7", "cluster": 2461740, "interpro_all": ["IPR004843", "IPR029052", "IPR004376", "IPR024173"], "interpro_used": ["IPR029052", "IPR004376", "IPR004843"], "interpro_unused": ["IPR024173"]}, "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 associated with the UDP-D-xylose:L-fucose alpha-1,3-D-xylosyltransferase family, which catalyzes the transfer of D-xylose from UDP-alpha-D-xylose to L-fucose, a reaction likely involved in the biosynthesis of the complex pectic polysaccharide rhamnogalacturonan II (RG-II). Essential for cell wall integrity in rapidly growing plant tissues, these proteins rely on a conserved DXD motif for their enzymatic activity. Also, the protein possesses a Nucleotide-diphospho-sugar transferase domain that catalyzes the transfer of sugar moieties from activated nucleotide diphospho-sugar donors to specific acceptor molecules, forming glycosidic bonds. This domain constitutes the catalytic core of various glycosyltransferases, including arabinosyltransferases and xylosyltransferases, which mediate the biosynthesis of disaccharides, oligosaccharides, and polysaccharides. It is native to Edaphochlamys debaryana and is linked to UniProt keywords Transmembrane, Signal-anchor, and Golgi apparatus.", "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, 2458, 1956, 1920, 18500, 17, 46, 17, 21055, 30, 54, 17, 15423, 2217, 4595, 17, 21, 16, 23, 17, 46, 17, 9639, 25566, 3416, 16, 2154, 17097, 1920, 3856, 1927, 46, 17, 21055, 2037, 18500, 17, 4595, 17, 46, 17, 21055, 1942, 54, 17, 15423, 2217, 16, 43, 3227, 3205, 3286, 1922, 1920, 8132, 1927, 1920, 2796, 13494, 2002, 17167, 23120, 27395, 10366, 1928, 2890, 12, 9372, 17, 2890, 13, 18, 4415, 1958, 2024, 4821, 7996, 1922, 6221, 6552, 4496, 3878, 16, 2144, 2697, 11396, 1990, 43, 5305, 14852, 1007, 5219, 1958, 2310, 8145, 2455, 18, 2222, 16, 1920, 2213, 14465, 43, 5489, 17, 11791, 2609, 1037, 17, 9523, 13763, 3418, 1988, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 5489, 11791, 2609, 1037, 17, 9523, 8276, 1942, 2487, 12641, 4206, 16, 7402, 7533, 12546, 9031, 18, 2052, 3418, 14879, 1920, 6804, 4728, 1927, 3425, 20067, 18580, 16, 2710, 20790, 25566, 1036, 1930, 9639, 25566, 1036, 16, 2154, 8265, 1920, 8132, 1927, 2054, 11926, 16, 22012, 16, 1930, 18686, 18, 2176, 1977, 6196, 1942, 3347, 2575, 2694, 10082, 2012, 8911, 2141, 7241, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 16, 2733, 17, 13333, 16, 1930, 10277, 11161, 18, 3], "output": "MVEAKTNQIAKFSKSHFTTHGARLPTPEFVAAVGAAAIDITHLSCRKSMVMIGMANEEALAHTVPLFLRSLRRASLSGGRQRGASLDRHLVLVAWSEQALADCRALQGKGNRPNGEGREGEGKGKGEGRQGKGEGREEEGEEKGEGKEVGEGYGHQCVRDAEHSAGTGSFGFHDAGFNSLGFAKIKYILNGLSLGHDVVFLDTDIVVLRDPVPYFLSRRADLFGSMEKCMIYNDTHAFHSPEFLRMKKRPPPINIGVLYFKATAGVTRCVYNWMWDMHSEVQGRPRIWDQDIYGKVMIKCTATHSLRFQVLDPRLFQSACFPFCGCTYDDDVITRENIGRFSKGQRGDDFGRCGPQHWGGWLMRHFPCAGMTRTKAELMQNLLEGYYDNKTAQINRQ", "metadata": {"id": "A0A835YF64", "cluster": 2920231, "interpro_all": ["IPR005069", "IPR029044", "IPR052636"], "interpro_used": ["IPR052636", "IPR005069"], "interpro_unused": ["IPR029044"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein should feature 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. Furthermore, the protein should include 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. Furthermore, the protein has 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 derived from Pirellulales bacterium and is annotated with UniProt keywords Transferase, Transmembrane, and Membrane.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 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, 3677, 16, 1920, 2213, 3066, 3951, 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, 3677, 16, 1920, 2213, 2258, 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, 3595, 2037, 13774, 1992, 5617, 2612, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 13763, 16, 9117, 16, 1930, 3260, 18, 3], "output": "MQIKHDLRTLSRAVEQTTASIVITRVDGTIEYVNSGFVKATGYTPEEVLGQNPRILKSGLQPLSFYEDLWRTILEGREWRGQFHNRRKDGSLYWEQATISSVTDENGAITHFVAVKEDITDRKLAKEQLETSERNFRTCFESIGDMIFVVAVDGRVLYGNAASLKNLGYGAEELTGRCVLDLHPPDTHREASEIFAAMIRGERETCPLPLVRKNRETVPVETRAWRGTWNGLDCIFAICKDLTAEQEAKQRFERMFRSNPALMAVSSMQDRVFLDVNEVFLAALGYSREEVIGKTSAELGLFAAPEDHAAAADRLQTCGSITNVELQIRRKDGTLLDGLFSGERIRHQGREQFLTVMIDITERKQVERDLKQAVAALERAGALAESATRAKSEFLANMSHEIRTPMTAILGFSEVLLAEPGLDHAPPARVEALKTIQRNGRYLLELINDILDLSKIEAGKLDIERVECDLMHLVREVVRLMQVRADAKGIDLSLEGAGPVPERITTDPTRLRQILINLTGNAIKFTATGGVRLIVRTAVNGGGLPSVRFDVVDTGIGMTPDQQNRLFRPFTQGETSTNRKYGGTGLGLAISKRLAAMLGGDIAVCSTAGKGSTFTVTIDPGPLQSARMLDDPAPNTVRQDEDRCRPPKQHAGPDCRVLLAEDTPDIRRLIAALLKLSGAEVVTAENGEDAVREALAAQQDGHPFDLILMDMQMPVVDGYGATRQLRLAGYAGRIVALTAHAMNGDREKCLEAGCDGYLAKPVDRDRLAALVQESGSTRQSKIEGDSNAALLSPAPAVTDWAGAASAVR", "metadata": {"id": "A0A7Y5W7X3", "cluster": 3699635, "interpro_all": ["IPR011006", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR001610", "IPR000014", "IPR000700", "IPR035965", "IPR013656", "IPR004358", "IPR001789"], "interpro_used": ["IPR000014", "IPR000700", "IPR005467"], "interpro_unused": ["IPR036097", "IPR036890", "IPR001789", "IPR011006", "IPR001610", "IPR035965", "IPR003661", "IPR004358", "IPR013656"]}, "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 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 Sphingobium subterraneum.", "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, 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, 13502, 23156, 13329, 5385, 2516, 1989, 18, 3], "output": "MKTIFLHAGAHKTGSSSIQTNLAENAKLLSTAGIFYPTGWDEDFTFLHEGFKSSPSGTAPETQRTFDSLFSRIENNDCVILSHEDLVASSECFLYHFKTACGQHVRQLRYSGDLEPLVTRSLEHPDWYQKIRRFENVFGSNNIKVKLFDKRIALSEKKVNFGSDVSDYVLLSYIFRQTIDSLQLRRLEEYVVGNSKTNFRIQMPRTTAYFNETDQKRFHRSMQAFDEVDDLTGLALQRMMEIFCHWIEDAEKPIPGNANPLAYAMHGDDVAGWTLEPVIFIRDQMSWHISNFSRGILKMFFSAIDIKIANLKLHIIQQYYNDGNHSIAER", "metadata": {"id": "A0A841IYR1", "cluster": 4577370, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "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 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 has 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. It is native to Bacteroidota bacterium and carries UniProt keyword assignments Coiled coil.\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, 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, 2258, 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, 2176, 1977, 6196, 1942, 24323, 7336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 17524, 9121, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MLTNQKFFDAVSDSYDNKYLKEFISSEIQSAADLGCGTGVDSIALYKLGINVKEKAEINFINKSITEIEHENYDKYDFIISLNGSVVIQILNYIPVLEKKERIINITKEDYLQFNILKYSIQNPKDNQIIYGGLDKSSFSESTSKDLVIHAEVMILFNEAVEKKKTAFDISKGMIDKAKQNAEGNSLGNLDEQQLNLSVSIIKNMLRKSDGNFNFVRFYDFSTKIYPHKYNYINNLFKQSGFRKINM", "metadata": {"id": "A0A9E2J8H9", "cluster": 4709815, "interpro_all": ["IPR041698", "IPR029063"], "interpro_used": ["IPR029063", "IPR041698"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein features 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 occurs in Gomphosphaeria aponina SAG 52.96 = DSM 107014 and is annotated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 4075, 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, 5110, 1922, 3611, 6588, 10647, 3508, 20051, 3027, 1019, 11466, 8635, 2175, 11001, 4764, 18, 4746, 33, 10964, 9176, 6924, 1006, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MTNTNPPEPPSRKKKLDSDELIAIAIAFLTIGGILFGVLTNKNKFGLDTTTLFGQTSNVEQTAESNIADRLLADSEPTTEYQPSQESPPPAEIRKPIEKTEKSTAVIPTIPVPVPVPVPTPTPTPTPTPTPTPTPTPEVETTPPTPTPEVEATPPTPTPEVAIAGFKDVPEDFWAYPFIEGLRKEGVFPEEELGETFAPDQPITRGDMAALIKKAFQEPPTESPKEFEDVSESDPVASDVDAAITRGFMKGYSEGEFRPEETIPRYQVLVALATGLKLLPSKEPNEILAYYTDSDQLPDWAVEQVAAATESDLVVNYPELTSLHPEQPATRAEVAAMIYQALHNLGRVEAVSSEYIVSEQETMPSEETTSEEETMEDETTSEEETMEDETTSEEETMEDETTSEEETMEEETTSEEETMEEETTSEEETMEDETTSEEETMEDEIIPEIEIMPEGEIMPEGEIMPEGEIMPEGEIMPQDDTNSEVEKRMETETIPETENTPPAEQ", "metadata": {"id": "A0A941GRT7", "cluster": 7528474, "interpro_all": ["IPR001119"], "interpro_used": ["IPR001119"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein is grouped in the Elongation factor Tu GTPase family, which catalyzes the GTP-dependent delivery of aminoacyl-tRNA to the ribosome A-site during protein synthesis to ensure accurate translation. These enzymes hydrolyze GTP upon codon recognition to release the tRNA, and in mitochondrial contexts, they can regulate autophagy and innate immunity by recruiting ATG5-ATG12 and NLRX1. It has been characterized in Sanghuangporus baumii (Phellinus baumii).", "tokenized_instruction": [2, 7031, 2142, 1925, 3835, 2687, 3244, 1988, 2112, 3728, 2460, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 9971, 2991, 9037, 14809, 3416, 16, 2154, 17097, 1920, 9319, 17, 3100, 4868, 1927, 3835, 14645, 17, 10089, 1942, 1920, 12794, 43, 17, 3200, 2409, 2213, 4271, 1942, 6486, 6305, 6410, 18, 2144, 5038, 7222, 6931, 9319, 4073, 8905, 5708, 1942, 4012, 1920, 10089, 16, 1930, 1922, 4596, 11144, 16, 2611, 2112, 5741, 6661, 1930, 8539, 7611, 2007, 17040, 23289, 17, 9353, 3112, 1930, 10911, 7653, 18, 2176, 2258, 2252, 4378, 1922, 22671, 24315, 2657, 2074, 1957, 6813, 28851, 1033, 12, 10422, 11560, 22214, 6813, 28851, 1033, 13, 18, 3], "output": "MFGESESESPRTGSPWDGFLSKSDPASPAVEPTRSPRVVPKLVPEVEEGNVEYKLRLLNPSTERFTRLVTQLKWRLLEGGGQAYYELGVADSGQLVGLSRTHLEQSLQTLEEMAGEIGASVIVVKEIELPPTLVEAVKNSEKSGKIADGAMRMHKVRVSDYVETPPSSAGGDEESEFSAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDVAERAPAE", "metadata": {"id": "A0A9Q5HTP3", "cluster": 8294170, "interpro_all": ["IPR050055"], "interpro_used": ["IPR050055"], "interpro_unused": []}, "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 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 derived from Pseudogymnoascus sp. VKM F-4518 (FW-2643). 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, 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, 3595, 2037, 11520, 26983, 18044, 6952, 12709, 1957, 2056, 18, 26855, 1035, 48, 17, 26401, 1025, 12, 16451, 17, 16710, 1010, 13, 18, 7031, 1920, 3244, 18, 3], "output": "MESDQQQRFFLASFKCIRIPKALFARTARRNYEWGNNGELERIPEDHYSQSLYSHLFGESNDVGKFMQDIEAYGIASLGGKSWSEWFIVQESWRKRTLKYSSPDIAKKNQFTILGLVISVFPDAWSEIAWEEIEAQLWEVVETTCVPFLSVLTTADIEDCLAYSSRQGIFLSLVTILGEKTSPNFRFLIREGICLLRTSGSKALEDVSYLELLQSTVYILSTNNNQPWAARKELMALKTNLSKRSNATIGFALASLPLSWATSRTVVQWFPNEVPSTMEIIAYALLAGTSSIADVLTPSLQNLSLESRVLIAFCEAKRKSFSPAYLLLRESFTELTNSYGWSSMEYLLAGTALVSCFEVEFPQQTFPMIAVADCLLGQSKFNEAREILIRILEYPLVDFNLSNIAICTELRLLKMGRRQRKEPSDFEDWERLRHVFSQFDMATDPIKYECIEELVSFLSVLKPRDKPPQIFEIVKVLNNYHVKEYKGSADSKENLISNIESLQQYKNELNLFTVLGPQLHYCRKMRDRFPHATVDFIERIGAANWHRFQRIKGLIEPVDRMEVTMDTAESKFQDSGLGSSLGSKLSGNQVLDVPQDARSMVSIRSFMETEQGATTLQSMPPEDSAGNRICYICQKALKDVHNESQWKRHAFSDLRPYVCIVEDCKANSIQFASRSEFAAHLTEHQSYKTWRCTKCDTSSQNFDFIQDHVAHSHLPSMSAEQDCQIQELSHVRDLSTQRCPFCNDIPGKANFVGHICHHLEETSLSAIPREEEEFDGDYGEVMSWEGASLGRADKKEMGATAAGEILEESEPEPVTNPGNDEDDWGSAVTIVIPGQDKEIKDVEETEPAPKSVPDPKKTTEDGFSAENDNDGFHSESYRRRPAPMAAFEAEAANAAIGGQYHRDTGEDREVDRRENKLANDTDEIRRSKYPRGGEDAEAATQDYIRRDASRDREEDSRGNKTPKARLETYFVPGTGIDRDVITTDICRYLGNDAIVRPGRHKNAEGEPVQGYFITAYRVLTTENLADIKADSAKWQAERQKYQQSETRHQASEYSHTTQGPKLQKDRYPTYALPWERLNGFLVKRFPGYTFKEMTLREFYIFDVPEPLTMEDHNAIAMLRIY", "metadata": {"id": "A0A094ES91", "cluster": 9695649, "interpro_all": ["IPR013087"], "interpro_used": ["IPR013087"], "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 Protein of unknown function DUF3425 family, which comprises a functionally uncharacterised domain found in eukaryotes. This domain is typically between 120 to 143 amino acids in length. It is derived from Stachybotrys elegans.", "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, 2213, 1927, 5435, 2347, 4855, 10892, 6852, 1015, 3416, 16, 2154, 12936, 43, 9346, 23229, 3495, 3418, 2435, 1922, 15021, 18, 2052, 3418, 1977, 5745, 2192, 6103, 1942, 13370, 3835, 4576, 1922, 3471, 18, 2176, 1977, 3595, 2037, 23891, 2072, 16924, 6286, 2012, 10861, 18, 3], "output": "MHETPGALQALPSRPKKKVNRKDPAKRREQNRRSQKLYREKQKQRIEELERCAANAAVAGGACGAGIANFQTGALDLDLTSGSEFGLDVIDLPYQQSSFAQSPYSVPACSDLGPHAPSPDYQQWLNDSFACFSADSTTFSCMPGFHQPGCPVLLMPAISLKPRPSLLPDPLINNLLFNPQCVFMALKENCLHLGISNNDFCTDLGMSPFFRPEFESASESDSKALLSLSRQSYTNVKFDLRPVEGQLVINHHPYIDVIPFRDLRRNLLRMLDEIDEDDFFRDCLESWTCWGPSAGIPSGRPWDPRSWEASEAFLGKWSHVIGGDEGELARQSRWWQSIRGDRITEIL", "metadata": {"id": "A0A8K0T2V0", "cluster": 10470548, "interpro_all": ["IPR021833"], "interpro_used": ["IPR021833"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein is categorized in the Cytochrome c biogenesis protein Ccs1/CcsB/ResB family, which plays an essential role in the biogenesis of c-type cytochromes in bacteria and chloroplasts by facilitating the heme attachment step. Also, the protein features a ResB-like domain that functions as a predicted transmembrane component involved in cytochrome c biogenesis. It is found in proteins such as ResB and is considered essential for cell growth. It has been characterized in Marinilabiliales bacterium and carries UniProt keyword assignments Cytochrome c-type biogenesis 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, 1977, 10234, 1922, 1920, 9387, 45, 13008, 2213, 17267, 1009, 19, 17267, 1014, 19, 1995, 1014, 3416, 16, 2154, 5705, 1925, 4415, 2770, 1922, 1920, 13008, 1927, 45, 17, 2601, 9387, 1036, 1922, 4802, 1930, 24627, 2007, 12440, 1920, 10954, 8576, 3537, 18, 2222, 16, 1920, 2213, 4075, 43, 1995, 1014, 17, 3189, 3418, 1988, 4088, 1966, 43, 4396, 9117, 4594, 3286, 1922, 9387, 45, 13008, 18, 2176, 1977, 2435, 1922, 2697, 2427, 1966, 1995, 1014, 1930, 1977, 3311, 4415, 1958, 2024, 2905, 18, 2176, 2258, 2252, 4378, 1922, 13081, 8635, 11792, 25600, 2612, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 9387, 45, 17, 2601, 13008, 1930, 9117, 7864, 18, 7031, 1920, 3244, 18, 3], "output": "MKKKKKMWREPWDYKEGFTIAIVLVVLGFIMELIIGNNSVRLPSWPTNFIILIFFIAYLVYTANFVKHHIIRFFSTTAAAISSTVVFTALILIMGFVPQDETRIPDFVARLGIGSIKSSYAYLFSSLYLITVLGFTIVKRLKNFNLRNIAFFLNHAGLWIILATASLGSSDMVRLRMQIDEGQTAMVAMDQYSNQYQLPFGIQLLDFKLTEYPPNLILYSSKDGKPVYEKEKGLEEVEEGKSFNVEGWTVTIDEFLPMAKMKEDLFYKDTTLGATHAAYITAIKDTDTVKGWISPGNAFFKIIYLPLGDQYDITMTYPMAKEYESEVKIFIMPEGEVRKEKISVNKPIKVKGYKIYQSGYDDVMGRWSFISGFELIRDPWLPVVYTGFFMVLLGALYLLWTGKKQS", "metadata": {"id": "A0A2J6HTT6", "cluster": 12161700, "interpro_all": ["IPR023494", "IPR007816"], "interpro_used": ["IPR023494", "IPR007816"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein belongs to the Dehydrodolichyl diphosphate synthase complex subunit Nus1 family, which functions as a critical subunit of cis-prenyltransferase involved in synthesizing dolichol for protein glycosylation. It plays an essential role in vascular development and angiogenesis by binding the Nogo-B ligand to activate Akt signaling and stimulate endothelial cell chemotaxis. Additionally, this subunit modulates Ras signaling pathways to influence cell growth in developmental and pathological contexts. In addition, the protein is associated with the Decaprenyl diphosphate synthase-like superfamily, which functions as a group of cis-isoprenyl diphosphate synthases to catalyze the condensation of isopentenyl pyrophosphate into long-chain polyprenyl diphosphates. Members include the bacterial undecaprenyl diphosphate synthase essential for peptidoglycan biosynthesis and the eukaryotic dehydrodolichyl diphosphate synthase involved in carrier lipid formation. These Mg2+-dependent enzymes typically form homodimers and adopt a three-layered \u03b1/\u03b2/\u03b1 fold with a central six-stranded parallel \u03b2-sheet. It is produced by Spizellomyces sp. 'palustris' and is associated with UniProt keywords Transmembrane, Endoplasmic reticulum, and Membrane.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 28936, 22389, 24250, 2199, 23266, 8921, 2796, 5903, 13232, 12030, 3416, 16, 2154, 4088, 1966, 43, 4140, 5903, 1927, 5848, 17, 9972, 2199, 9961, 3286, 1922, 25292, 17837, 2108, 1945, 1958, 2213, 12082, 18, 2176, 5705, 1925, 4415, 2770, 1922, 4541, 2740, 1930, 8244, 2007, 2743, 1920, 29181, 17, 44, 5207, 1942, 6980, 5496, 3197, 1930, 9084, 5003, 2024, 16884, 18, 4950, 16, 2052, 5903, 13112, 6520, 3197, 3873, 1942, 4039, 2024, 2905, 1922, 5878, 1930, 6598, 11144, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 2344, 21358, 8033, 23266, 8921, 17, 3189, 13975, 16, 2154, 4088, 1966, 43, 2210, 1927, 5848, 17, 26690, 2199, 23266, 8921, 1036, 1942, 18170, 1920, 16112, 1927, 10301, 30340, 16323, 1024, 24937, 2460, 2815, 17, 4659, 6240, 2825, 2199, 23266, 1036, 18, 4678, 3951, 1920, 4543, 3075, 19384, 20367, 2199, 23266, 8921, 4415, 1958, 24183, 8132, 1930, 1920, 10825, 28936, 22389, 24250, 2199, 23266, 8921, 3286, 1922, 9685, 4486, 3337, 18, 2144, 14756, 15, 17, 3100, 5038, 5745, 2386, 29227, 1930, 14103, 43, 2559, 17, 19445, 160, 19, 161, 19, 160, 3728, 1956, 43, 4101, 3798, 17, 10338, 6110, 161, 17, 11130, 18, 2176, 1977, 4152, 2007, 15776, 22996, 6012, 14930, 3707, 2056, 18, 11, 5755, 3894, 1937, 11, 1930, 1977, 2458, 1956, 20709, 11569, 9117, 16, 13355, 12279, 16, 1930, 3260, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MTIPPVTSQALQRPSGGSQLVSAFPSRFWGRKKHVDQDIELSGKCPRHLAVVFRGHQNWMNAVGNIVEWCISDGVACLTVFIVDKLDLCRESADPPVQVKASIQLLVSGSPVDRTQREPSTSSNKSSESDRHVDLWVNLISASDGRNSLVHADNRAHLTTNVDLVDKLIKADSPDLNQFPEPELIYPRIVLSPDSLSDAVRCKVNCHLWGIEEAFIYLRLLAIVLWLRTVWVAPLQHSLSSAYDEDGRFDEKGLLKSHAARLAQRTILDEGIDLDPHGVRRPTNERVARTLGRQALAASVVGCQSNFLEIGNLCPWNIRLSEFWFVDNIRI", "metadata": {"id": "A0A507E3A9", "cluster": 12803002, "interpro_all": ["IPR038887", "IPR036424"], "interpro_used": ["IPR038887", "IPR036424"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein includes a Metal-dependent hydrolase HDOD domain that functions as a phosphodiesterase involved in bacterial signal transduction, specifically catalyzing the hydrolysis of cyclic diguanylate (c-di-GMP). Often found associated with regulatory domains such as GGDEF and EAL, it acts as an output module within larger signaling proteins to regulate nucleotide metabolism. Also, the protein is associated with the Signal transduction c-di-GMP phosphodiesterase, EAL/HD-GYP domain-containing family, which functions in bacterial signaling cascades to regulate levels of the second messenger cyclic diguanylate (c-di-GMP). Members typically feature a catalytically active EAL domain that hydrolyzes c-di-GMP, paired with a modified, likely inactive HD-GYP domain lacking conserved metal-binding residues. These proteins often act downstream of two-component systems to modulate processes such as extracellular polysaccharide biosynthesis. Furthermore, it is part of the EAL domain superfamily, which functions as a diguanylate phosphodiesterase responsible for the degradation of the bacterial second messenger cyclic di-GMP. It utilizes conserved acidic residues for metal binding and often cooperates with GGDEF domains to regulate cell surface adhesiveness. It occurs in Oceanirhabdus seepicola. 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, 5921, 43, 6048, 17, 3100, 20748, 4515, 1986, 3418, 1988, 4088, 1966, 43, 24821, 3286, 1922, 4543, 2733, 8201, 16, 4475, 29601, 1920, 9128, 1927, 9821, 4325, 13785, 9075, 12, 45, 17, 2137, 17, 18033, 13, 18, 3868, 2435, 2458, 1956, 4948, 4682, 2427, 1966, 12358, 3695, 1038, 1930, 11377, 1024, 16, 2176, 8016, 1966, 1925, 6647, 9059, 2651, 4327, 3197, 2697, 1942, 5741, 5489, 4714, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 2733, 8201, 45, 17, 2137, 17, 18033, 24821, 16, 11377, 1024, 19, 4515, 17, 8415, 1034, 3418, 17, 3165, 3416, 16, 2154, 4088, 1922, 4543, 3197, 15967, 1942, 5741, 2428, 1927, 1920, 2812, 16716, 9821, 4325, 13785, 9075, 12, 45, 17, 2137, 17, 18033, 13, 18, 4678, 5745, 5961, 43, 21446, 3500, 11377, 1024, 3418, 1988, 7222, 20887, 45, 17, 2137, 17, 18033, 16, 7304, 1956, 43, 4795, 16, 3205, 9078, 4515, 17, 8415, 1034, 3418, 7046, 5305, 6048, 17, 2743, 4248, 18, 2144, 2697, 3868, 4033, 5863, 1927, 2288, 17, 4594, 3771, 1942, 8480, 4028, 2427, 1966, 5329, 17167, 8132, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 11377, 1024, 3418, 13975, 16, 2154, 4088, 1966, 43, 4325, 13785, 9075, 24821, 5061, 1958, 1920, 4877, 1927, 1920, 4543, 2812, 16716, 9821, 2137, 17, 18033, 18, 2176, 18127, 5305, 9931, 4248, 1958, 6048, 2743, 1930, 3868, 23230, 1036, 1956, 12358, 3695, 1038, 4682, 1942, 5741, 2024, 3154, 13510, 2971, 18, 2176, 5110, 1922, 13563, 1996, 2722, 13602, 1957, 3365, 19232, 10173, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MDIFIARQPIYDKKDNVFAYELLYRGSEENFCNCQDLDKATISVLLNAFVDIGIDKITHGKKAFVKFTENLLFSNIFDFLPSNKVVIAISSDINPSRELLDRCLELRRMGFSLAFDNFVFKENLIDLLKITHYIKIDFSSTDIKYQGLLVNKLSSKNIKFIASKLETISDHSVSRDLGYSFFQGYYFSKPSIIKSKKIPMSTLTKIDLLGKISSEFLTLDELEDIIKKDVSLSYNILKIINSAKYALRSEIKTIKHAICMLGEAELKKWLYYLIIQSEATNCPPELFKLSIIRGKFSELIAKETDNKEISFDAFIMGVLSLMDRLFNVSLDTIIENLFVSEDVKSALFETSNNNLFKILNVVKAYENAHWEEVEQYAHELNIDPKYLGDAYLEALDWVDLA", "metadata": {"id": "A0A9J6P0B1", "cluster": 13706970, "interpro_all": ["IPR014408", "IPR035919", "IPR013976", "IPR052340"], "interpro_used": ["IPR013976", "IPR014408", "IPR035919"], "interpro_unused": ["IPR052340"]}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein should include a Thioredoxin-like fold domain that regulates target protein activity through thiol-disulfide exchange reactions within redox signaling pathways such as the ferredoxin/thioredoxin and glutathione/glutaredoxin systems. It features a characteristic three-layer \u03b1/\u03b2/\u03b1 core structure and functions as a hydrogen donor to reduce disulfide bonds in substrate proteins. 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 Candidatus Nitrobium versatile.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 3066, 3951, 43, 23684, 17, 3189, 3728, 3418, 1988, 7014, 2758, 2213, 2455, 2596, 13914, 17, 11830, 6818, 5298, 2651, 9366, 3197, 3873, 2427, 1966, 1920, 25304, 22389, 10960, 19, 23684, 1930, 9153, 19, 19406, 1919, 9754, 3771, 18, 2176, 4075, 43, 6293, 2559, 17, 4757, 160, 19, 161, 19, 160, 4728, 3170, 1930, 4088, 1966, 43, 6201, 6282, 1942, 4412, 11830, 9031, 1922, 4510, 2697, 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, 14550, 1031, 1957, 8686, 3821, 1989, 20425, 18, 3], "output": "MRRVGKGVLGAALLLSFVSSGHALDLGCGVNYFNGWCDGQKKEEGKEPSAVKESTPKGDKKKELDPYEWMPKDTPPVMADLFRSPTEENAEKALKWKEERMQRINEVAKLLQKRAAGTSAGNGQGNADASSGLAGQKAQRVLFNKAVYFFQEGCPACQKMTPLLAEVQGTGKIVAVGIGLSDSGAAQYLARHGVSVSAGGDPLKQLARNYKVPNTPALILLSPSGDIVRRYEGLLDRATIMSIFTEGNQ", "metadata": {"id": "A0A953JD81", "cluster": 14308576, "interpro_all": ["IPR012336", "IPR036249"], "interpro_used": ["IPR012336", "IPR036249"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein is categorized in the Stretch-activated cation channel MID1/Yam8 family, which functions as a plasma membrane calcium transporter essential for pheromone-induced calcium influx during the mating process in yeast. Members of this family contain four hydrophobic regions involved in membrane localization and C-terminal cysteine-rich motifs thought to facilitate oligomerization through disulfide bond formation. It is present in Wickerhamomyces ciferrii (strain ATCC 14091 / BCRC 22168 / CBS 111 / JCM 3599 / NBRC 0793 / NRRL Y-1031 F-60-10) (Yeast) (Pichia ciferrii) and carries UniProt keyword assignments Signal.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 9064, 17, 4128, 9976, 4999, 3953, 1009, 19, 16523, 1025, 3416, 16, 2154, 4088, 1966, 43, 3582, 3260, 5016, 9054, 4415, 1958, 21567, 17, 2719, 5016, 12403, 2409, 1920, 11786, 2585, 1922, 5688, 18, 4678, 1927, 2052, 3416, 5531, 3006, 7919, 3451, 3286, 1922, 3260, 5363, 1930, 45, 17, 4262, 8666, 17, 5536, 8277, 6212, 1942, 6628, 17371, 2596, 11830, 5403, 3337, 18, 2176, 1977, 2481, 1922, 11980, 12940, 1915, 8527, 29249, 3371, 2070, 21094, 12, 3943, 11037, 8949, 12118, 19, 10915, 1030, 17043, 6735, 19, 16341, 10118, 19, 14904, 1035, 27204, 1026, 19, 8789, 15618, 6627, 11436, 19, 5214, 1005, 1024, 67, 17, 9373, 1009, 48, 17, 3276, 17, 2119, 13, 12, 5688, 13, 12, 7271, 7969, 1019, 3371, 2070, 21094, 13, 1930, 16252, 20709, 11121, 2538, 18306, 2733, 18, 3], "output": "MLRLNCMVFVLFMVLCIGVHAISIDCSEIKDPEERAECLGKVDDLLDSDPHQVYDWRPVSINIEPGQALQYRFEINYITGNLCNHPIGLSNPNDYLTLFYGLNDTKSEGFENGYLQATSYTTVKTNGTYYLLGVSQDDLLFQWDNRTWINLVDSDDTTALFITIHVFHDEQSNYFSNMYRSWCSIVNSVPLVPQIYVRGLQPSTDYIAYVTQDFSNKDDGGVVFDTFCDNVAYSVPRSSNLEIGSDFANLGRLYDDQRYSPIVTCDDCRTSYKNWLCGVTIPRCTPSEYFEVLPCINMCYAMVRDCPADFSFSCPRDNIHDVVMNKGILFVSLMFIGFVLGIQDKFEGNIIQNSLDEFSKFDDWSLLDKRDISQLTGSTTHPYNQVFYQVLVGIFENTTSEDLHESHDMLLVADDVPDFNGSFTVQTGNLTTKYNNATDILSASSNYYPENITYSFTQRGGGIKERISFRTKDPDICQLVFNLEYAEEAFGNFSKALDQIPCDAENTENQTHYKHRPLGESRMDFINDSIDPASLVKSYYYKDDDYSYDTCNYVGIIPKTSGA", "metadata": {"id": "K0KUL7", "cluster": 15543209, "interpro_all": ["IPR024338"], "interpro_used": ["IPR024338"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is a member of the LURP-one-related family, which plays a role in plant defense against pathogens. Members of this family display structural similarity to the C-terminal domain of the Tubby protein, featuring a 12-stranded beta-barrel with a central C-terminal alpha-helix that is predicted to function as a transmembrane anchor. Furthermore, the protein is associated with the Tubby-like, C-terminal superfamily, which constitutes a unique family of bipartite transcription factors essential for nervous system function and development. This conserved domain forms a 12-stranded, anti-parallel closed \u03b2-barrel surrounding a central \u03b1-helix and is implicated in metabolic regulation, with defects often associated with obesity and sensory deficits. It has been characterized in Petromyces alliaceus (Aspergillus alliaceus). Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 1920, 10908, 11119, 17, 2340, 17, 2712, 3416, 16, 2154, 5705, 43, 2770, 1922, 4496, 9720, 3316, 7741, 18, 4678, 1927, 2052, 3416, 4434, 4346, 6796, 1942, 1920, 45, 17, 4262, 3418, 1927, 1920, 3710, 4864, 2213, 16, 29931, 43, 2369, 17, 10338, 4666, 17, 19560, 1956, 43, 4101, 45, 17, 4262, 4595, 17, 7864, 1988, 1977, 4396, 1942, 2347, 1966, 43, 9117, 13333, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 3710, 4864, 17, 3189, 16, 45, 17, 4262, 13975, 16, 2154, 14879, 43, 5008, 3416, 1927, 8446, 24707, 3213, 2790, 4415, 1958, 7580, 2433, 2347, 1930, 2740, 18, 2052, 5305, 3418, 4952, 43, 2369, 17, 10338, 16, 2246, 17, 6110, 8047, 161, 17, 19560, 7510, 43, 4101, 160, 17, 7864, 1930, 1977, 6835, 1922, 4487, 3640, 16, 1956, 6007, 3868, 2458, 1956, 5379, 1930, 6893, 7961, 18, 2176, 2258, 2252, 4378, 1922, 16901, 29249, 2136, 2126, 1972, 1957, 12, 17604, 2136, 2126, 1972, 1957, 13, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MASNLPPLKQPIAIRPDHIATGPTTLQVKHHTYSISQGDFTVSYSPDRTNTHATKLFSVNGHALSWRQRRDFCDASGLPLFELHRKGAGGTWFVQLPGSISSSDPIITLAPRWSWTKDKVDVYFRNAMGGEEVVLEVRGQDTWKRRTNVYRDGVLVMTIRVVDLLRVSSTRKPERVVEIAEGMDLALASVVTVLVAEKFAGNVCLKSTFSPSGGGGGGDVDETKNLEYVRDYIQAETLKPSLPSMTLDQYIRNLSSLPKTLKIVNLWVKVMHGLESTQESAAFFMEYCRHNTGLLAVRADEGTGGNYLRFLDGNIPPRSPSHHPT", "metadata": {"id": "A0A5N7CA73", "cluster": 17990725, "interpro_all": ["IPR007612", "IPR038595", "IPR025659"], "interpro_used": ["IPR007612", "IPR025659"], "interpro_unused": ["IPR038595"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein is included in the WD40-repeat-containing domain superfamily, which folds into a characteristic $\\beta$-propeller structure comprised of multiple short repeating motifs to serve as a stable scaffold for protein-protein or protein-DNA interactions. These domains facilitate the assembly of multi-protein complexes involved in diverse eukaryotic processes, ranging from signal transduction and transcriptional regulation to cell cycle control. Additionally, the protein should include a Histone-binding protein RBBP4-like, N-terminal domain that forms an alpha-helical structure upstream of a WD40 beta-propeller to create a binding groove for histone H4. As a component of the chromatin assembly factor 1 (CAF-1) complex, it facilitates the deposition of histones H3 and H4 onto newly synthesized DNA during replication or repair. Moreover, it is part of the The Glutamate-rich WD repeat-containing family, which regulates chromatin dynamics and ribosome biogenesis by functioning as histone-binding proteins and facilitating 60S subunit assembly. These proteins facilitate the loading of MCM complexes at replication origins and act as substrate receptors for CRL4 E3 ligase complexes to modulate processes such as thermotolerance. It originates from Cystoisospora suis.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 17907, 4241, 17, 6865, 17, 3165, 3418, 13975, 16, 2154, 16231, 2460, 43, 6293, 8, 38, 4666, 8, 17, 5062, 13728, 3170, 8842, 1927, 3137, 3662, 21763, 8277, 1942, 7120, 1966, 43, 4700, 7281, 1958, 2213, 17, 2213, 2014, 2213, 17, 2678, 3719, 18, 2144, 4682, 6628, 1920, 5957, 1927, 2779, 17, 2213, 5048, 3286, 1922, 6445, 10825, 4028, 16, 6485, 2037, 2733, 8201, 1930, 5224, 3640, 1942, 2024, 4048, 2285, 18, 4950, 16, 1920, 2213, 3066, 3951, 43, 6632, 17, 2743, 2213, 6160, 3846, 1006, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 4952, 1925, 4595, 17, 11514, 3170, 7671, 1927, 43, 17907, 4241, 4666, 17, 5062, 13728, 1942, 7762, 43, 2743, 15920, 1958, 6632, 11278, 18, 1966, 43, 4594, 1927, 1920, 6338, 5957, 2991, 21, 12, 20250, 17, 21, 13, 2796, 16, 2176, 11374, 1920, 7860, 1927, 15808, 8170, 1930, 11278, 6131, 7471, 6653, 2678, 2409, 5158, 2014, 5059, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 1920, 7627, 17, 5536, 17907, 6865, 17, 3165, 3416, 16, 2154, 7014, 6338, 5565, 1930, 12794, 13008, 2007, 7295, 1966, 6632, 17, 2743, 2697, 1930, 12440, 3276, 1036, 5903, 5957, 18, 2144, 2697, 6628, 1920, 6693, 1927, 15379, 5048, 2019, 5158, 13538, 1930, 4033, 1966, 4510, 4086, 1958, 21460, 1006, 10968, 11905, 5048, 1942, 8480, 4028, 2427, 1966, 7967, 4575, 3823, 2152, 18, 2176, 22970, 2037, 9446, 13082, 9890, 1019, 2020, 1937, 18, 3], "output": "MAKGEDEERKHEQASSCSSGGYAQGEEEEAIMRDKLSPEKGSCSSSLSMKKKKNKKSENEEVTSHRRKRQAEEDEEGKSRQCRGEGREGGEEEEEQLDFEDPFDDEFDEEDTHGLEAYGQGNSSEEEEDEEEEEMKEKDEESQEVNGEGSSSSSAKTKSVRAWRPGIDELSPDEELDYDSSAYEMLHRATMEWPCLSFDILTQLAGGAGEATACQAMVSCKPPYTAYVVGGTQAEKSSGNRLFVMKWSDLHKTNKDARDSDEDEDSDGDDDDDDSVEGSEEEPKFDFRIRAHQGTVNRLRCCPQMNRLVATWSDRGEVNVYDIQQQILRLDDPGAPGIRPHTHTQAPHSRSSRRRRRRSSRSPSSISNSSTCPNTITTTSSSRSSTNSSGSPKSSA", "metadata": {"id": "A0A2C6KS32", "cluster": 20005285, "interpro_all": ["IPR051972", "IPR022052", "IPR015943", "IPR036322"], "interpro_used": ["IPR036322", "IPR022052", "IPR051972"], "interpro_unused": ["IPR015943"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has this function description: The protein should include a Right handed beta helix domain that adopts a parallel \u03b2-helix fold sharing structural similarity with pectate lyases. This architectural motif often serves as a scaffold for carbohydrate binding or enzymatic degradation activities. Also, the protein is assigned to 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. Additionally, the protein falls within the SCF Complex Subunits and Alginate Epimerases family, which comprises components of SCF E3 ubiquitin ligase complexes that mediate the ubiquitination and proteasomal degradation of specific substrates involved in cell cycle regulation and immune responses, as well as bacterial enzymes responsible for polysaccharide epimerization during alginate synthesis. It is present in Atribacteria bacterium and contains UniProt keyword associations Membrane, Transmembrane, and 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, 3951, 43, 3659, 17105, 4666, 7864, 3418, 1988, 24032, 43, 6110, 161, 17, 7864, 3728, 10763, 4346, 6796, 1956, 13494, 3857, 2057, 23928, 1036, 18, 2052, 28937, 5219, 3868, 10634, 1966, 43, 7281, 1958, 10590, 2743, 2014, 8145, 4877, 4209, 18, 2222, 16, 1920, 2213, 1977, 6304, 1942, 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, 4950, 16, 1920, 2213, 12182, 2651, 1920, 12437, 2796, 6991, 1930, 17987, 13872, 9213, 2319, 3416, 16, 2154, 12936, 4178, 1927, 12437, 10968, 6526, 11905, 5048, 1988, 8265, 1920, 11758, 1930, 19308, 4877, 1927, 2487, 6249, 3286, 1922, 2024, 4048, 3640, 1930, 3743, 3387, 16, 1966, 2486, 1966, 4543, 5038, 5061, 1958, 17167, 13872, 9213, 2466, 2409, 17987, 4271, 18, 2176, 1977, 2481, 1922, 26500, 7972, 2341, 18339, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MVNHLKKDVYYLFFGILFIAFFIGCSPVPPIMPTPENQTLPVNNSTQGTSFSTIQAAIDASVPGDIIIVYPGTYYENIDFKGKNITIQSTDPLNSTILLNTIIDGQLKGSVVTFKSGETKNAVLKGFTIQNGSGSKVGNWSKYGGGIYCVQSSPTISNNFILNNNADNGGGIYCSFSSPIIRQNKIGLNSAKGGGGIFCGDSSSPAISQNTISENSSTHNSHGGGILCYNSSPNIVSNEISWNDATNGGGIYILDSMPVIYGNDIHKNTATQYGGGIFVSKQSIVKDSHGDSWLRLNDPPHNETNNLYSGNTHQGTLNTDGVNVYFEMNVFSIRILGLGLDS", "metadata": {"id": "A0A7X8H9Y9", "cluster": 20713388, "interpro_all": ["IPR039448", "IPR012334", "IPR011050", "IPR051550"], "interpro_used": ["IPR039448", "IPR011050", "IPR051550"], "interpro_unused": ["IPR012334"]}, "task_type": "autoregressive"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein is categorized 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 is produced by viral metagenome.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 1977, 10234, 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, 1977, 4152, 2007, 4324, 16552, 2225, 18, 3], "output": "MKKKLLVLGLAWDANVETNLAGYKVYYNTRGPGVGNIVEFYFNSIDFRAVTTKGLIPLPPGGCVLRIPTKLALGIFLAVGVYAAPANKLAPYDGIGQVEGDSPIDKDFWFVVTAYNTEGFESGYSNE", "metadata": {"id": "A0A6H1ZCM0", "cluster": 21107478, "interpro_all": ["IPR013783"], "interpro_used": ["IPR013783"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe 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 derived from Prevotella sp.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 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, 3595, 2037, 2817, 7229, 11560, 1019, 2056, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MKNLSSEVLIPALQRGLVWSTKKALENVSIYTLWQIASWTSDEKPRQVELLWDSILRGFPFGSFIL", "metadata": {"id": "A0A3B9U5Q3", "cluster": 21264849, "interpro_all": ["IPR004919"], "interpro_used": ["IPR004919"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein is classified under the Ribbon-helix-helix superfamily, which encompasses bacterial and phage transcription repressors, such as MetJ, CopG, Arc, and Mnt, that typically function as obligate dimers to regulate gene expression. These proteins share a core topology of four helices arranged in an open array of two hairpins, with specific members like MetJ binding S-adenosylmethionine to repress methionine synthesis. Also, the protein is grouped in 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. In addition, the protein is classified under the DNA partition complex, ParG family, which acts as an essential component of the plasmid partition system found in the multi-drug resistance plasmid TP228. Members of this family adopt a ribbon-helix-helix fold with a core of four alpha-helices to facilitate DNA segregation. It is expressed in Tolypothrix sp. PCC 7601. 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, 25149, 17, 7864, 17, 7864, 13975, 16, 2154, 21569, 4543, 1930, 10503, 3213, 26446, 16, 2427, 1966, 2130, 1013, 16, 3725, 1029, 16, 9952, 16, 1930, 5890, 1031, 16, 1988, 5745, 2347, 1966, 25554, 13351, 1942, 5741, 2359, 2294, 18, 2144, 2697, 7948, 43, 4728, 13678, 1927, 3006, 12789, 14940, 1922, 1925, 4437, 6472, 1927, 2288, 14565, 1036, 16, 1956, 2487, 4678, 3189, 2130, 1013, 2743, 61, 17, 29283, 23568, 11215, 1942, 9055, 12417, 4271, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 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, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2678, 11334, 2796, 16, 2096, 1029, 3416, 16, 2154, 8016, 1966, 1925, 4415, 4594, 1927, 1920, 5609, 11334, 2433, 2435, 1922, 1920, 2779, 17, 2838, 3554, 5609, 6213, 24894, 18, 4678, 1927, 2052, 3416, 14103, 43, 25149, 17, 7864, 17, 7864, 3728, 1956, 43, 4728, 1927, 3006, 4595, 17, 12789, 1942, 6628, 2678, 12707, 18, 2176, 1977, 3198, 1922, 21930, 2085, 2195, 3027, 1039, 2056, 18, 16003, 29854, 1009, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MEEKKKPGRPSTNKDDPVYVRARVPRELHKSFKLACTEDDLVMEDVVRDLIKDWLTRRGKKNSA", "metadata": {"id": "A0A0D6KFG1", "cluster": 23172057, "interpro_all": ["IPR013321", "IPR015354", "IPR010985"], "interpro_used": ["IPR010985", "IPR013321", "IPR015354"], "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 Dihydroxy-acid dehydratase family, which utilizes a catalytically essential [4Fe-4S] cluster to catalyze the dehydration of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid, representing the fourth step in isoleucine and valine biosynthesis. This family is evolutionarily related to 6-phosphogluconate dehydratases, which perform a similar dehydration reaction in the Entner-Doudoroff pathway. Additionally, the protein contains a Dihydroxy-acid/6-phosphogluconate dehydratase conserved site that characterizes enzymes such as dihydroxy-acid dehydratase and 6-phosphogluconate dehydratase, which catalyze dehydration reactions in isoleucine/valine biosynthesis and the Entner-Doudoroff pathway. This site contains a conserved cysteine residue involved in binding a 2Fe-2S iron-sulphur cluster. It occurs in Psychroflexus torquis (strain ATCC 700755 / CIP 106069 / ACAM 623) and features UniProt keywords Amino-acid biosynthesis, Magnesium, and Metal-binding.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 20684, 17, 2687, 11725, 7234, 3416, 16, 2154, 18127, 43, 21446, 4415, 37, 15338, 1021, 17, 26814, 39, 4377, 1942, 18170, 1920, 16585, 1927, 22, 16, 23, 17, 20684, 17, 4911, 28144, 1935, 2687, 2460, 4595, 17, 21471, 23854, 28144, 3133, 2687, 16, 7479, 1920, 8776, 3537, 1922, 25398, 1930, 21884, 8132, 18, 2052, 3416, 1977, 18584, 2712, 1942, 26, 17, 8078, 22988, 8870, 11725, 18135, 16, 2154, 2385, 43, 2551, 16585, 3227, 1922, 1920, 8496, 3239, 17, 2608, 2009, 30232, 2040, 3374, 18, 4950, 16, 1920, 2213, 5461, 43, 20684, 17, 2687, 19, 26, 17, 8078, 22988, 8870, 11725, 7234, 5305, 3200, 1988, 26735, 5038, 2427, 1966, 20684, 17, 2687, 11725, 7234, 1930, 26, 17, 8078, 22988, 8870, 11725, 7234, 16, 2154, 18170, 16585, 5298, 1922, 25398, 19, 21884, 8132, 1930, 1920, 8496, 3239, 17, 2608, 2009, 30232, 2040, 3374, 18, 2052, 3200, 5461, 43, 5305, 8666, 6181, 3286, 1922, 2743, 43, 13775, 1021, 17, 20759, 5680, 17, 13528, 1949, 4377, 18, 2176, 5110, 1922, 3463, 28716, 2592, 1957, 8184, 2048, 1937, 12, 3943, 11037, 11851, 8245, 1015, 19, 12998, 7758, 14265, 1026, 19, 18699, 1035, 5374, 1010, 13, 1930, 4075, 20709, 11569, 3835, 17, 2687, 8132, 16, 13148, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MIFENETDTMELNKYSKTVTQDPTQPAAQAMLHAIGLTKEDFFKPIIGIASTGYEGNPCNMHLNDLAKLAKQGTANEDIIGLIFNTIGVSDGISMGTPGMRYSLPSRDIIADSMETVVQAMSYDGLITVVGCDKNMPGALIAMIRLDRPCIMIYGGTIDSGCHNGKKLDVVSAFEAWGSKVAGTMQEEEYQSIVEKACPGAGACGGMYTANTMASSIEALGMTLPYNSSNPALSPEKKQESIKAGEALRVLLEKDIKPSDIITRKSLENAIRLITILGGSTNAVLHFLAIARAAEIDFTLTDFQTISDNTPFLADLKPSGKYLMEDLHEVGGIPAVLKYLLKKGLIYGDCLTVTGKTLAENLRDVEDLKEGQEVIKPIESPIKISGHLRMLFGNLAEEGSVAKITGKEGLKFRGKAKVFEGEYKANDGIRDGKVQKGDVVVIRYEGPKGGPGMPEMLKPTAAIMGAGLGKDVALITDGRFSGGTHGFVVGHITPEAQEGGTIALVEEGDYITIDAETNSINLEVSDEELIKRKKNWKAPNLKFKRGVLYKYARMVNSASKGCVTDEF", "metadata": {"id": "K4IDF7", "cluster": 24969964, "interpro_all": ["IPR050165", "IPR042096", "IPR004404", "IPR020558", "IPR056740", "IPR000581", "IPR037237"], "interpro_used": ["IPR004404", "IPR020558"], "interpro_unused": ["IPR042096", "IPR050165", "IPR037237", "IPR056740", "IPR000581"]}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is categorized in the Nucleotide-diphospho-sugar transferase superfamily, which catalyzes the transfer of sugar moieties from activated donor molecules, such as nucleotide diphospho-sugars, to specific acceptor molecules to form glycosidic bonds. These enzymes play a critical role in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides. Also, the protein should contain a Glycosyltransferase, DXD sugar-binding motif conserved site that mediates carbohydrate binding within enzymes using nucleoside diphosphate sugars as donors. It requires divalent cations, typically manganese, to facilitate the transfer of sugars to substrates such as proteins, phosphates, or other sugars. It is found in Littorina saxatilis and is associated with UniProt keywords Signal.\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, 5489, 17, 11791, 2609, 1037, 17, 9523, 13763, 13975, 16, 2154, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 6282, 4206, 16, 2427, 1966, 5489, 11791, 2609, 1037, 17, 15592, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2144, 5038, 3918, 43, 4140, 2770, 1922, 1920, 8132, 1927, 2054, 11926, 16, 22012, 16, 1930, 18686, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 20067, 9961, 16, 14852, 1007, 9523, 17, 2743, 5219, 5305, 3200, 1988, 10412, 10590, 2743, 2651, 5038, 2193, 18015, 23266, 15592, 1966, 8276, 18, 2176, 5474, 21610, 16525, 16, 5745, 19516, 16, 1942, 6628, 1920, 3856, 1927, 15592, 1942, 6249, 2427, 1966, 2697, 16, 26473, 16, 2014, 2303, 15592, 18, 2176, 1977, 2435, 1922, 4471, 2684, 4058, 18585, 18554, 1937, 1930, 1977, 2458, 1956, 20709, 11569, 2733, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MRSPCRKQKGVLLALLFVLSLLLWFVNIGQQVCQQFQIHDTDPPSGVTIVHYVWSGRKRKFVFRDCLSLLSVVRVLQPLKIIFHKSSIPGLEFKQANFGSSDLMDIAFEILPPEGGVASDPSQGIVFASKSLKELPASDLNKAKSASKKQCVHVDAYDSDLRLKTPSAELAQWIFYGRRALQVAKQDFRNPIPRISHYVIGGFERVYLHAETAPRGHWWEELAGENVTVVKADRPYGGAYQDFDVTWTKRVPDWLLAYPTVIDLEVEYNKAPWLRHFLESMRDYRDDDWAYNSLRMSYRTFEHYPDTVYIDKYSAPFPLRQEARSFHLGRPRPQASLASLDSVKHPHDVFADIGRMVLEKSGRKNLLGQPFTASRSTRDLLWQEPWPERYSTMPQTDSYHSWLLELVIGNGAVLSRPPPHPAVTPISLFSATFVSHAHCVIMASDVLPRDIYAELDGGKDVSSELRFPHFLNILSALYVRSVYQTEVKVIQHVSDVLRAEILYKSSDWPDIFNNGVILSRRHALQVMCGETVCHPSWGVSYDTKVLPL", "metadata": {"id": "A0AAN9BH48", "cluster": 26911596, "interpro_all": ["IPR007577", "IPR029044"], "interpro_used": ["IPR029044", "IPR007577"], "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 include a MYND-type zinc finger domain that functions primarily as a protein-protein interaction interface, particularly for the recruitment of transcriptional co-repressors like N-CoR and SMRT. This motif consists of a cluster of conserved cysteine and histidine residues arranged to form a stable zinc-binding structure that mediates complex assembly and transcriptional repression. It has been detected in Chlamydomonas schloesseri and is described by UniProt keywords Metal-binding and Zinc-finger.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 3066, 3951, 43, 3057, 10249, 17, 2601, 7997, 8497, 3418, 1988, 4088, 5985, 1966, 43, 2213, 17, 2213, 2835, 6854, 16, 4443, 1958, 1920, 6067, 1927, 5224, 2081, 17, 26446, 3189, 56, 17, 2233, 1930, 28018, 1031, 18, 2052, 5219, 7543, 1927, 43, 4377, 1927, 5305, 8666, 1930, 13873, 4248, 14940, 1942, 2386, 43, 4700, 7997, 17, 2743, 3170, 1988, 10412, 2796, 5957, 1930, 5224, 10084, 18, 2176, 2258, 2252, 3330, 1922, 14667, 10480, 2966, 6012, 1979, 18842, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 3], "output": "MGLKLMYALHLTCGWTTMEARFTARLFFFAQPPAGVAAGATGGHMPGGPGAGSGQQRRPPYPATVTIQGCSPRAFLTITAAVPTAWRISYNIWAYVAVRERVRAELGVWASACVSGLSAAVRSGLADPAHGSYNQALVAYALQPVWLAVMEHGQLPQIVSFSEAMARRGEAEGCDPALVIGQSTGPYGRSPYPLGELRAMYGRARGAQRRLARKRCLATLAAEPDSALVRLPAKEQQQPPGSASSTNTTNTTNTTTTTGSRSDGADKSSSSDDDGAGPPCGGGAVVTSILAPGERLCDGCERGSLQDCQAKHWRAGHKTECKRLAAEAAAGAAAGACAGWQAARHVEALAETHASAVVEVPMEEAVAAWEGQRWSADDFVLLLVALFSCTNVAQLPQLAARSAGRPWALSVEAMERYGCDRLVALAPALSPLLLRLVLKGSLRGSPWNMAAGALKNMCGEAMDIAKGSKTGKKKGATTTGAAAAATAAAATAAAPANGVTRKCGQCRQRRYCS", "metadata": {"id": "A0A835TCL5", "cluster": 27038895, "interpro_all": ["IPR002893"], "interpro_used": ["IPR002893"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein according to this functional description: The protein contains 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. Also, the protein contains 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. Moreover, the protein belongs to the GTPase Obg family, which comprises proteins thought to function as GTPases capable of binding both GTP and GDP. While the family is largely uncharacterised, this nucleotide-binding activity is exemplified by the Obg protein from the spirochaete bacterium *Brachyspira hyodysenteriae*. It is found in Candidatus Bathyarchaeota archaeon and features UniProt keywords Metal-binding and S-adenosyl-L-methionine.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 5461, 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, 2222, 16, 1920, 2213, 5461, 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, 3950, 16, 1920, 2213, 14440, 1942, 1920, 14809, 2384, 1029, 3416, 16, 2154, 12936, 2697, 6212, 1942, 2347, 1966, 18390, 7131, 1927, 2743, 2321, 9319, 1930, 15217, 18, 2679, 1920, 3416, 1977, 6318, 23229, 3495, 16, 2052, 5489, 17, 2743, 2455, 1977, 22236, 2007, 1920, 2384, 1029, 2213, 2037, 1920, 22075, 25588, 11555, 14061, 14, 20372, 3508, 11979, 4527, 26812, 9583, 7955, 14, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 10481, 9771, 15618, 20051, 7336, 13470, 1916, 1930, 4075, 20709, 11569, 6048, 17, 2743, 1930, 61, 17, 29283, 17, 54, 17, 12417, 18, 3], "output": "MRSRPSIPTARRATGSRSSSKPLGYSTVYGPVPSWRLGLSLGIDPIGPPKTCTFNCVYCQLGPTVRQVSSPLDLRDSVRAARIVGDLGRALRRIDLRRISFVTFSGSGEPTLNLHLGGMIDGVKEVVGDVPVAVLTNSSLMYRPDVRAALSKADLVVAKLDSADESTFRGINRPALTIGLDRVIDGIRSFKEEGSAFLAIQVMFIDSDRDAVPVNFKGRPLRRLLEVISDIGPDQVQINTPTRPPSEPYIRRVGRRGLGEIYDEVAGIVGKEKVLLVTSPRVIGEPSVSLADDLIEGEVIRLLERRPCSAHDISLSLDLPPQRVRRVLRDLSRRGLILSRKYARRVFFYSSGRSTLTGPMRGRPRKLSSTRVHGGVMRVDAKMAPDSCYSG", "metadata": {"id": "A0A7J4FA86", "cluster": 28317266, "interpro_all": ["IPR013785", "IPR011991", "IPR040084", "IPR007197", "IPR036388", "IPR036390"], "interpro_used": ["IPR007197", "IPR011991", "IPR040084"], "interpro_unused": ["IPR036388", "IPR036390", "IPR013785"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein carries 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. Also, the protein should contain a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. Additionally, the protein is grouped in the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. It is expressed in Priestia koreensis and is described by UniProt keywords Glycogen biosynthesis and Glycosyltransferase.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 16252, 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, 2222, 16, 1920, 2213, 3066, 5531, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 2176, 1977, 3198, 1922, 17618, 2158, 2126, 8233, 8134, 1930, 1977, 2910, 2007, 20709, 11569, 13302, 8132, 1930, 20067, 9961, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MNVLFVVSECVPFIKTGGLADVAGAYGLIPEKFKEKMVLKKVLYVQVGWRRQYCGLEVLEDDAERFTFFCRAVIDALPHLDQLPDIIHCHDWHTGMVPFLLNLQFQGIFPKGILYELLNLDDYYFTTSQLEFKDEIQMPYYGEQLDGLLRRRNQDLVGIINGIDDTIYNELQKSLGLNVDEKIPVMSMITRLTKQKGLSGEKEFEHFFQEMERQYPEKIRCVVGFNEEQLIALKYGTIPVVRETGGLNDTVEPYNEYEKTGNGFSFFYQKEDAWQAIIEEAMNRDYTWAKSAFIYNQLYADLISTLPKELAQLGTNVTVMMPKQDGVQYIFVDNEYYFNRDSLYGHYRADYAYYSSIQTVFTIHYGNVSFMKAALVSADKITTVSPTYPTEDTYIAQKYSVKSLTKKTVNKTDLVRHVFHEIMSHDIQLIILGLAHTIYAGSDLFLMPSQFEPCGLGTNFNAHDMLHTIERALM", "metadata": {"id": "A0A0M0L7U7", "cluster": 24554678, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR001296", "IPR013534", "IPR011835"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein carries a BEN domain that functions as an intrinsic sequence-specific DNA-binding module involved in transcriptional regulation and the higher-order structuring of chromatin. This domain adopts an all-\u03b1 fold with four conserved helices and acts as an adaptor to recruit chromatin-modifying factors. In addition, the protein is a member of the BEN domain-containing protein 6-like family, which functions as a transcriptional co-repressor that antagonizes Notch signaling to regulate cell fate. These proteins bind CSL transcription factors via their BEN domain or recognize CCAATTGG palindromes to repress target genes and promote neurogenesis. It occurs in Parnassius apollo (Apollo butterfly) (Papilio apollo) and is linked to UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 16252, 43, 7129, 3418, 1988, 4088, 1966, 1925, 7598, 3244, 17, 2487, 2678, 17, 2743, 9059, 3286, 1922, 5224, 3640, 1930, 1920, 2580, 17, 3238, 2581, 4729, 1927, 6338, 18, 2052, 3418, 24032, 1925, 2136, 17, 160, 3728, 1956, 3006, 5305, 12789, 1930, 8016, 1966, 1925, 15077, 1942, 5608, 6338, 17, 12691, 2790, 18, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 7129, 3418, 17, 3165, 2213, 26, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 5224, 2081, 17, 14434, 1988, 28104, 1036, 8091, 3197, 1942, 5741, 2024, 11211, 18, 2144, 2697, 4566, 3752, 1024, 3213, 2790, 3454, 2310, 7129, 3418, 2014, 9967, 13980, 8788, 3312, 29716, 4191, 1036, 1942, 9055, 2758, 2628, 1930, 5527, 13967, 18, 2176, 5110, 1922, 2096, 3676, 12924, 1957, 11466, 11560, 1037, 12, 11466, 11560, 1037, 20883, 15972, 13, 12, 3860, 5912, 1037, 11466, 11560, 1037, 13, 1930, 1977, 4624, 1942, 20709, 11569, 3213, 3640, 18, 3], "output": "MESIIKDLCAKIETLESKLKMKSSVSFYALKTRTSSSKRKRYTICADSDWVPIGDGHAFVPSRLLKNMDWSATHSLTGKPSPAFPNKPAKKRLDPALVNTKCADESKIFRSCLRKANSSAQEEVESSATAVLFLNSLFLKRRYLKSNSQYGSSRFTTRLEPPCKKRLLQKKKTTGQAAKSIVLATHSLLVNDIVQTVVDNCCVPESVVRTIITTKCADESAKIDQENIPPLVCKSGESDESYLSTGRNNVKSKSCNLNSSDSGDENVAVTHTYATRKLLRAVFPRSVLDIVQTVVDNCCVPESVVRASITSNLKSTRPGPSVQKTSPSTPTGKPSPAFPNKPAKKRLDPAKMFRSRLRKSKSNS", "metadata": {"id": "A0A8S3WFP4", "cluster": 350885, "interpro_all": ["IPR018379", "IPR037496"], "interpro_used": ["IPR018379", "IPR037496"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein is grouped in 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. Moreover, the protein falls within 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 Oligoflexia 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, 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, 3950, 16, 1920, 2213, 12182, 2651, 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, 15039, 18222, 2126, 14061, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MKPRSLFFEDARKVPAFLLAQKLLSGGAQVMICSRPPVLKEFVSGNHRWFRRVCTAPAVVITGGTRGLRSVDLESALAKLGGAIAV", "metadata": {"id": "A0A924PCX7", "cluster": 380703, "interpro_all": ["IPR036291", "IPR002347"], "interpro_used": ["IPR002347", "IPR036291"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is associated with the PLP-binding barrel superfamily, which constitutes an N-terminal eight-stranded \u03b1/\u03b2 barrel domain responsible for covalently binding the cofactor pyridoxal 5'-phosphate (PLP). This domain is characteristic of alanine racemases and class-II ornithine, lysine, and arginine decarboxylases, where it anchors the cofactor via an aldimine linkage to a lysine residue to facilitate catalysis. Furthermore, the protein belongs to the Pyridoxal phosphate homeostasis protein family, which binds pyridoxal 5'-phosphate (PLP) to regulate the homeostasis of this essential vitamin B6 cofactor. These proteins supply PLP to apoenzymes while minimizing the toxic side reactions associated with the free molecule. It is produced by Sphenodon punctatus (Tuatara) (Hatteria punctata).\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 21453, 17, 2743, 19560, 13975, 16, 2154, 14879, 1925, 56, 17, 4262, 5066, 17, 10338, 160, 19, 161, 19560, 3418, 5061, 1958, 16590, 2743, 1920, 15155, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 18, 2052, 3418, 1977, 6293, 1927, 10504, 7442, 3368, 4127, 1036, 1930, 2921, 17, 2890, 26918, 16, 9082, 16, 1930, 9732, 23922, 1036, 16, 2597, 2176, 27127, 1920, 15155, 3454, 1925, 11174, 24906, 8611, 1942, 43, 9082, 6181, 1942, 6628, 15408, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 24828, 23859, 5413, 7622, 2213, 3416, 16, 2154, 6876, 24828, 23859, 25, 11, 17, 5413, 12, 21453, 13, 1942, 5741, 1920, 7622, 1927, 2052, 4415, 6111, 11750, 15155, 18, 2144, 2697, 9042, 21453, 1942, 10290, 1022, 16367, 2679, 16362, 1920, 6161, 4159, 5298, 2458, 1956, 1920, 3294, 5388, 18, 2176, 1977, 4152, 2007, 9445, 19824, 28615, 18636, 1031, 1957, 12, 9037, 28999, 1019, 13, 12, 16133, 1967, 2126, 18636, 3857, 13, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "SWEDISWTAQLGIAVTILYMLETADSVKLADKVNSTWQEDRKWLYGASFTLQERGLSVCNNIHYNINKLKKGPSQRLKIMVQINTSG", "metadata": {"id": "A0A8D0HLK1", "cluster": 408959, "interpro_all": ["IPR029066", "IPR011078"], "interpro_used": ["IPR029066", "IPR011078"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is included 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. Moreover, the protein possesses a Glutaredoxin domain that functions as a glutathione-dependent thioltransferase to reduce protein disulfide bonds using a redox-active CXXC motif within a thioredoxin fold. It facilitates electron transfer from NADPH and glutathione to target substrates, playing a critical role in DNA synthesis, signal transduction, and defense against oxidative stress. It is native to Mesorhabditis spiculigera and is associated with UniProt keywords Electron transport, Redox-active center, and Transport.\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, 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, 3950, 16, 1920, 2213, 14465, 43, 19406, 1919, 9754, 3418, 1988, 4088, 1966, 43, 9153, 17, 3100, 13914, 9961, 1942, 4412, 2213, 11830, 9031, 2193, 43, 9366, 17, 3500, 5639, 21487, 5219, 2651, 43, 23684, 3728, 18, 2176, 11374, 4995, 3856, 2037, 11908, 1930, 9153, 1942, 2758, 6249, 16, 14797, 43, 4140, 2770, 1922, 2678, 4271, 16, 2733, 8201, 16, 1930, 9720, 3316, 5163, 3071, 18, 2176, 1977, 6196, 1942, 23577, 5004, 13385, 3678, 15776, 18021, 12191, 4938, 1019, 1930, 1977, 2458, 1956, 20709, 11569, 4995, 4860, 16, 9366, 17, 3500, 4102, 16, 1930, 4860, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MSASDSRAPKQGYPRFLEPIIQDTDQNVLKSEKINFVEKNVDTLTKEDAKKVYPQLFVCGDLVGDLAELEAAKKSVLDPLPVVLYTKDKCEESKKARGGKDYALGLRVITQSREKTKTSLKEMVSQCAGIRKKRKE", "metadata": {"id": "A0AA36G6M2", "cluster": 684941, "interpro_all": ["IPR002109", "IPR036249"], "interpro_used": ["IPR036249", "IPR002109"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein according to these design specifications: The protein contains a Carboxyltransferase domain, subdomain A and B domain that constitutes the N-terminal portion of the carboxyltransferase component in biotin-dependent enzymes like urea carboxylase and urea amidolyase. It interacts with subdomains C and D to facilitate the ATP-dependent carboxylation of urea, although variants such as *Bacillus subtilis* KipA lack catalytic residues and function primarily as structural binding partners. In addition, the protein is categorized 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. Furthermore, the protein is assigned to the 5-oxoprolinase subunit C family, which catalyzes the ATP-dependent cleavage of 5-oxoproline to L-glutamate as part of the glutathione degradation pathway. In *Bacillus subtilis*, this protein also regulates sporulation by binding the inhibitor PxpB (KipI) to prevent its suppression of kinase A. It is present in Clostridia bacterium and is associated with UniProt keywords ATP-binding and Hydrolase.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 5461, 43, 9943, 9961, 3418, 16, 27517, 43, 1930, 44, 3418, 1988, 14879, 1920, 56, 17, 4262, 7717, 1927, 1920, 9943, 9961, 4594, 1922, 8622, 17, 3100, 5038, 3189, 10505, 29073, 1930, 10505, 28813, 26558, 2051, 18, 2176, 9034, 1956, 30103, 45, 1930, 46, 1942, 6628, 1920, 4498, 17, 3100, 9943, 1943, 1927, 10505, 16, 2876, 4936, 2427, 1966, 14, 14587, 14745, 14, 8191, 4302, 3630, 6804, 4248, 1930, 2347, 5985, 1966, 4346, 2743, 7228, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 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, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 25, 17, 18588, 15743, 11413, 5903, 45, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 6404, 1927, 25, 17, 18588, 15743, 2053, 1942, 54, 17, 7627, 1966, 3131, 1927, 1920, 9153, 4877, 3374, 18, 1922, 14, 14587, 14745, 14, 16, 2052, 2213, 2222, 7014, 23647, 2007, 2743, 1920, 4106, 15194, 16752, 12, 8191, 10984, 13, 1942, 4625, 2496, 6412, 1927, 4016, 43, 18, 2176, 1977, 2481, 1922, 17938, 14773, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 1930, 20748, 18, 3], "output": "MIRITDGGSYTLPVTARRHFLEPMGMPTGGPMDRVRALLANRLIDAPDDAALLEAAFALPGMVFTSPAAIAVTGGAEAVKLIRKGKEISFPCGETIYVEAGDELVSAPIERGMRAYIAFSGGLELDGVRQKPVKKGDSLSCGEARLPSPKKLAYDPLPYPEGRAVLRVIEGVQSDHFSREGVGAFFGGEYAYTPQSDRMGIRLSGPSVGFGEGRDGNIISEGMMPGDIQIPPNGQPIIMTADCQTTGGYAKIAHVIEADLPLAAQLRPGDKLMFRRVLVADAHIAMRKLLMKIDGAVENEKTV", "metadata": {"id": "A0A939UTD2", "cluster": 4569849, "interpro_all": ["IPR003778", "IPR029000", "IPR052708"], "interpro_used": ["IPR003778", "IPR029000", "IPR052708"], "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 included in the Protein of unknown function DUF4299 family, which is currently functionally uncharacterised. This family is defined by two conserved sequence motifs, RGF and DAY, along with invariant proline and aspartic acid residues that may be critical for its structure or function. It is produced by Fusobacterium nucleatum 13_3C.", "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, 3063, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 29702, 3416, 16, 2154, 1977, 5077, 9346, 23229, 3495, 18, 2052, 3416, 1977, 3608, 2007, 2288, 5305, 3244, 8277, 16, 9372, 1038, 1930, 3007, 16, 4231, 1956, 17004, 12958, 1930, 23047, 2687, 4248, 1988, 2278, 1998, 4140, 1958, 2496, 3170, 2014, 2347, 18, 2176, 1977, 4152, 2007, 10630, 12022, 2797, 9576, 2590, 41, 7550, 18, 3], "output": "MNNSSYVENCFFIKNKKKFFSYEKVITVKEAIELCKDKKLSIYNFDFGLEGESSRGFEFFYDNKNKNYIVRILTPSTKEDWLLALEYSKVLAEDYKNDTIRTLKEFKNILSDPNDQPRTIMLNGIHRTVIFNEKICDDILNEIDPVQAFDEQNITILTNEKTGKDTLLGIYILGTGMKVILPYSKIPVLEDESLLTNEILEKIEWGIYADFITNLPKDKYKKLDGAYMLLDELTVDEMFDIYKKSERVNLCGDENFDEEKFLNLKINSYDCFKLKMKADIIYEKKEIYTVDTIKKFSFLKPLQYIEEAINLFLDFVSDKSKKDLSMLIK", "metadata": {"id": "X7S316", "cluster": 4735629, "interpro_all": ["IPR025387"], "interpro_used": ["IPR025387"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: It is part of the Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase family, which functions as a holo-citrate lyase synthase (CitX) responsible for activating the citrate lyase system. This enzyme transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein, and may occur as a fusion with CitG in genera such as *Haemophilus*. It is produced by Pisciglobus halotolerans.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 11466, 17, 11599, 23928, 3421, 2023, 11731, 17, 2554, 10647, 3508, 10647, 17, 10027, 13763, 3416, 16, 2154, 4088, 1966, 43, 20403, 17, 11599, 23928, 8921, 12, 12366, 1039, 13, 5061, 1958, 8019, 1920, 11599, 23928, 2433, 18, 2052, 4113, 19180, 1920, 19019, 2210, 22, 11, 17, 12, 25, 11, 11, 17, 14051, 2609, 6658, 29258, 2199, 13, 17, 23, 11, 17, 2554, 10647, 3508, 10647, 17, 10027, 1942, 1920, 11599, 23928, 7034, 4659, 16, 1925, 11337, 9685, 2213, 16, 1930, 2278, 4704, 1966, 43, 5289, 1956, 12366, 1029, 1922, 12774, 2427, 1966, 14, 7105, 18239, 14, 18, 2176, 1977, 4152, 2007, 24641, 17780, 2389, 1957, 23226, 4575, 3823, 2075, 18, 3], "output": "MDLFNSGKHVSLEEVLENREKRAFFQQKLLERYSGSLVSFNCNIPGPIKNNPMIKQIFDVGKSALMIKLRENKVNVLMSKEWDNVTGPELFLVADIRPSKLKKLTVQIEETTLGRLFDMDVLFKETTEQIRSVNRQELGLPVRKCFVCEDEAKNCGRSRKHSLEEIFHSINKMLEQEETVLY", "metadata": {"id": "A0A1I3BP05", "cluster": 5470224, "interpro_all": ["IPR005551"], "interpro_used": ["IPR005551"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein is associated with the 5'-nucleotidase/apyrase family, which encompasses enzymes including 5'-nucleotidases, UDP-sugar hydrolases, and apyrases that catalyze the hydrolysis of phosphate esters in nucleotides and nucleotide sugars. These metalloenzymes, often requiring zinc or cobalt cofactors, facilitate processes ranging from bacterial nutrient scavenging and host platelet inhibition to the regulation of adenosine-mediated signaling by GPI-anchored members like CD73. In addition, the protein should feature a 5'-Nucleotidase, C-terminal domain that catalyzes the hydrolysis of phosphate from the 5' position of ribose and deoxyribose in nucleotide molecules, converting them into their corresponding nucleosides. This activity regulates adenosine availability for cell signaling, such as in T-cell activation, and supports nutritional nucleotide degradation in bacteria. The domain is often found in membrane-bound enzymes, including GPI-anchored proteins like CD73, and typically requires metal ions such as zinc or cobalt for catalytic function. It has been detected in Myxococcales 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, 1977, 2458, 1956, 1920, 25, 11, 17, 2797, 4090, 2051, 19, 2100, 3553, 2051, 3416, 16, 2154, 21569, 5038, 2710, 25, 11, 17, 2797, 4090, 2319, 16, 18500, 17, 9523, 30337, 16, 1930, 2100, 3553, 2319, 1988, 18170, 1920, 9128, 1927, 5413, 16785, 1922, 9519, 1930, 5489, 15592, 18, 2144, 8969, 6802, 1022, 16367, 16, 3868, 8887, 7997, 2014, 20773, 21362, 16, 6628, 4028, 6485, 2037, 4543, 8708, 15561, 1930, 4423, 7163, 3523, 1942, 1920, 3640, 1927, 10125, 17, 3434, 3197, 2007, 17497, 17, 17199, 4678, 3189, 29018, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 25, 11, 17, 2797, 4090, 2051, 16, 45, 17, 4262, 3418, 1988, 17097, 1920, 9128, 1927, 5413, 2037, 1920, 25, 11, 3507, 1927, 17870, 1930, 26405, 2217, 1922, 5489, 4206, 16, 15025, 3581, 2460, 2310, 3980, 18015, 1036, 18, 2052, 2455, 7014, 10125, 6855, 1958, 2024, 3197, 16, 2427, 1966, 1922, 62, 17, 2024, 2936, 16, 1930, 7825, 9369, 5489, 4877, 1922, 4802, 18, 1920, 3418, 1977, 3868, 2435, 1922, 3260, 17, 4124, 5038, 16, 2710, 17497, 17, 17199, 2697, 3189, 29018, 16, 1930, 5745, 5474, 6048, 6982, 2427, 1966, 7997, 2014, 20773, 1958, 6804, 2347, 18, 2176, 2258, 2252, 3330, 1922, 21464, 11748, 1918, 14061, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "EICPGEGDSCELPVYEGRQVEPDQDVASAMAPFLPKSREEETALGNLLADLMREARDGDVAIMNGGGVFPFDNRFAVANISGEQLYQIVGDVLEGSGSIISLSGITAVAEDEVRLIVSDFIAMGGDGLLEEVLAAGVEDGSGDLDPAQYLDTQSPRISYPGSRPICQARTEEVRNRELGVSVVALFIRADLLPGALTYGAFYTCGDQGMSLTLLRTDGTPVAPEEPEIESGRPIRDVLVDLM", "metadata": {"id": "A0A955XZQ4", "cluster": 5752517, "interpro_all": ["IPR008334", "IPR036907", "IPR006179"], "interpro_used": ["IPR006179", "IPR008334"], "interpro_unused": ["IPR036907"]}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein incorporates a SMP-30/Gluconolactonase/LRE-like region domain that characterizes enzymes including senescence marker protein 30 (SMP-30), gluconolactonase, and luciferin-regenerating enzyme (LRE). This region typically functions as a gluconolactonase, hydrolyzing sugar lactones such as gulonolactone, and displays activity against organophosphates like diisopropyl phosphorofluoridate. Additionally, the protein is associated with the SMP-30/CGR1 family, which exhibits lactonase activity involved in maintaining membrane homeostasis and contributing to bacitracin resistance. These metal-dependent enzymes are capable of degrading various lactones and organophosphorus compounds, including nerve agents, although their specific natural substrates often remain unidentified. Furthermore, the protein is associated with the Six-bladed beta-propeller, TolB-like superfamily, which forms a structural domain consisting of six 4-stranded beta-sheet motifs that serves as a scaffold for diverse biological activities ranging from enzymatic catalysis to transport. Members of this family include enzymes like quinoprotein glucose dehydrogenase, signaling components such as the LDL receptor, and the periplasmic TolB protein, where the domain mediates protein-protein interactions within the Tol-dependent translocation system. It has been characterized in Aspergillus violaceofuscus (strain CBS 115571) and is described by UniProt keywords Hydrolase.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 19683, 43, 2426, 1034, 17, 2627, 19, 3351, 23557, 5148, 2341, 9259, 1021, 19, 7146, 1021, 17, 3189, 3031, 3418, 1988, 26735, 5038, 2710, 10805, 4966, 2213, 2627, 12, 2426, 1034, 17, 2627, 13, 16, 3351, 23557, 5148, 2341, 9259, 1021, 16, 1930, 7174, 1921, 17, 23617, 4113, 12, 7146, 1021, 13, 18, 2052, 3031, 5745, 4088, 1966, 43, 3351, 23557, 5148, 2341, 9259, 1021, 16, 7222, 9046, 9523, 27735, 1036, 2427, 1966, 3194, 6012, 11873, 5148, 2341, 2290, 16, 1930, 10750, 2455, 3316, 3090, 15707, 1036, 3189, 26028, 2204, 20194, 2199, 3421, 4199, 11525, 21550, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 2426, 1034, 17, 2627, 19, 7294, 7011, 3416, 16, 2154, 9826, 5641, 9259, 1021, 2455, 3286, 1922, 8231, 3260, 7622, 1930, 8739, 1942, 8175, 4250, 9151, 3554, 18, 2144, 6048, 17, 3100, 5038, 2032, 7131, 1927, 18192, 3425, 27735, 1036, 1930, 3090, 16847, 1957, 4300, 16, 2710, 5507, 4820, 16, 2876, 2310, 2487, 4613, 6249, 3868, 5555, 18788, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 3798, 17, 22707, 1007, 4666, 17, 5062, 13728, 16, 21930, 1014, 17, 3189, 13975, 16, 2154, 4952, 43, 4346, 3418, 7600, 1927, 3798, 24, 17, 10338, 4666, 17, 11130, 8277, 1988, 10634, 1966, 43, 7281, 1958, 6445, 3933, 4209, 6485, 2037, 8145, 15408, 1942, 4860, 18, 4678, 1927, 2052, 3416, 3951, 5038, 3189, 9012, 6657, 3817, 9294, 16, 3197, 4178, 2427, 1966, 1920, 8017, 3148, 16, 1930, 1920, 24334, 21930, 1014, 2213, 16, 2597, 1920, 3418, 10412, 2213, 17, 2213, 3719, 2651, 1920, 21930, 17, 3100, 7849, 2433, 18, 2176, 2258, 2252, 4378, 1922, 17604, 7088, 2431, 4199, 7801, 1957, 12, 3943, 16341, 10709, 5071, 1009, 13, 1930, 1977, 2910, 2007, 20709, 11569, 20748, 18, 3], "output": "MEPQGVLLFDPATNKIGPFLDLYFTDQDQTGLSDPTGCVYRLTPGGRLDGGDHTRECAVATCAADGGDAPRRNLERFNSPNDLTISSKGCLIANGVSPNGLALSPDERFRR", "metadata": {"id": "A0A2V5H5W2", "cluster": 6646320, "interpro_all": ["IPR011042", "IPR013658", "IPR051262"], "interpro_used": ["IPR013658", "IPR051262", "IPR011042"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: It is part of the Anthrone oxygenase family, which comprises bacterial and fungal enzymes that function as oxygenases in the biosynthesis of secondary metabolites. These proteins contribute to the production of diverse compounds, including geodin, endocrocin, and monodictyphenone. It is native to Leptotrichia hongkongensis and is linked to UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 14228, 2290, 25298, 3416, 16, 2154, 12936, 4543, 1930, 8697, 5038, 1988, 2347, 1966, 25298, 1036, 1922, 1920, 8132, 1927, 4067, 6926, 18, 2144, 2697, 4672, 1942, 1920, 3372, 1927, 6445, 4300, 16, 2710, 14136, 22816, 16, 13573, 4104, 1921, 16, 1930, 27939, 5847, 11397, 18615, 18, 2176, 1977, 6196, 1942, 16976, 18935, 19519, 1019, 15908, 8323, 2029, 8134, 1930, 1977, 4624, 1942, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MKKMIVLLLLYLLTVALSAGIYFVFSNTIIKSLSDFPSELATKTMQKINQVIQNPFFLTIFFGPLLLGSTLSWHYLTVKEARGRLWILLSFLTYFLGVFLITIIFNVPMNNKLDNNTDGSYWPYYMIHWTRFNTLRFLCCLLTIIFLFLGLIA", "metadata": {"id": "A0A510L8P3", "cluster": 8388941, "interpro_all": ["IPR013901"], "interpro_used": ["IPR013901"], "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 belongs to the Protein trafficking Pga2 family, which comprises single-pass membrane proteins involved in protein trafficking and the processing of glycosylated proteins. It is expressed in Penicillium bovifimosum.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 2213, 9604, 25546, 1028, 3416, 16, 2154, 12936, 2957, 17, 4675, 3260, 2697, 3286, 1922, 2213, 9604, 1930, 1920, 4587, 1927, 17514, 2697, 18, 2176, 1977, 3198, 1922, 25142, 2457, 6643, 1974, 1980, 14740, 18, 3], "output": "MSTPSPDLSEAASAAAEDFFVQIYEFFELIITRFFKNGYASIAQMSGKRWTKVIGSVVFYLIIRPYIEKLFKWMHDRDRRKEKEKRDKERAQFGKVKMTANSLRPGADDKGKVLGEVENTDDELEDEEDIMAAASGVPEWNKMARRRQKNYIKSVKKDQRAEDLSRDQIMELLDWSEDEVVDEKTKKEL", "metadata": {"id": "A0A9W9GJ89", "cluster": 15092229, "interpro_all": ["IPR011431"], "interpro_used": ["IPR011431"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein possesses a KaiC-like domain that adopts a P-loop NTPase fold typically involved in ATP binding and hydrolysis. This domain functions as a core component of the cyanobacterial circadian clock oscillator KaiC, where it enables autophosphorylation, and is also essential for assembly of the archaeal motility machinery in FlaH and DNA repair in RadA. Additionally, the protein includes a KaiC domain that functions as a central oscillator in the circadian clock system, primarily in cyanobacteria, where it generates rhythms through autophosphorylation and acts as a transcriptional repressor. This domain often appears in multiple copies and facilitates circadian timing through direct protein-protein associations within the KaiABC complex. Also, the protein is included in the Circadian clock protein kinase KaiC family, which functions as the central component of the cyanobacterial circadian clock by forming the hexameric KaiABC oscillator complex. This protein undergoes temperature-compensated, rhythmic cycles of autophosphorylation and dephosphorylation modulated by interactions with KaiA and KaiB to maintain timing, even in the absence of transcription. Additionally, it regulates downstream signaling through interactions with SasA and CikA to drive circadian gene expression. It is derived from Armatimonadota bacterium and is associated with UniProt keywords Hydrolase, Transferase, and ATP-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, 14465, 43, 9580, 1935, 17, 3189, 3418, 1988, 24032, 43, 58, 17, 5881, 29676, 2051, 3728, 5745, 3286, 1922, 4498, 2743, 1930, 9128, 18, 2052, 3418, 4088, 1966, 43, 4728, 4594, 1927, 1920, 21897, 1024, 10507, 10357, 25539, 9580, 1935, 16, 2597, 2176, 10217, 22009, 16, 1930, 1977, 2222, 4415, 1958, 5957, 1927, 1920, 22367, 9254, 10853, 1922, 2300, 5945, 1930, 2678, 5059, 1922, 4226, 1019, 18, 4950, 16, 1920, 2213, 5921, 43, 9580, 1935, 3418, 1988, 4088, 1966, 43, 4101, 25539, 1922, 1920, 10507, 10357, 2433, 16, 5985, 1922, 21897, 16, 2597, 2176, 12399, 16622, 2596, 22009, 1930, 8016, 1966, 43, 5224, 14434, 18, 2052, 3418, 3868, 5107, 1922, 3137, 9425, 1930, 11374, 10507, 8035, 2596, 3083, 2213, 17, 2213, 5253, 2651, 1920, 9580, 14461, 1030, 2796, 18, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 10507, 10357, 2213, 4016, 9580, 1935, 3416, 16, 2154, 4088, 1966, 1920, 4101, 4594, 1927, 1920, 21897, 1024, 10507, 10357, 2007, 7402, 1920, 25602, 1935, 9580, 14461, 1030, 25539, 2796, 18, 2052, 2213, 14928, 3449, 17, 17566, 16, 20275, 6355, 1927, 22009, 1930, 16881, 9985, 2007, 3719, 1956, 9580, 2126, 1930, 9580, 2023, 1942, 6698, 8035, 16, 3385, 1922, 1920, 3905, 1927, 3213, 18, 4950, 16, 2176, 7014, 5863, 3197, 2596, 3719, 1956, 9767, 1019, 1930, 3371, 7640, 1942, 9265, 10507, 2359, 2294, 18, 2176, 1977, 3595, 2037, 6011, 1968, 3947, 12595, 3857, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 20748, 16, 13763, 16, 1930, 4498, 17, 2743, 18, 7031, 1920, 3244, 18, 3], "output": "LHGGIPQGFTVLVQGEPGTGKTTLGLQFVYHGATVEDQAGLVVTFEQPPERMCRDAANLGWDLRRAMEEGKLRIMATSPQAFVQQLKEAGSPFHRAIMEMGVQRLVIDSVSHFSRITQDPVQLREIVDLLINALRRYELTTILTSEVYGVPGAVTLEEYAADAVIRLSYEPVDELSRRRFLEVVKVRGHPFMTGKHGMSIGEGGIKVYPAPHPARPKRVEVGPEVRKVTTGIEGLDIMLGGGLIEGFSALIAGTPGTGRTAFGIHFLAEGAKNGEMGLLVSLEETPDKAFKCAKSIGIDLEGFVKEGKIIFIHRSPVVLDPLEIFDTIRRIVEKHPIRRVLIDPLTDIKTSIRDVAQFRDYLYALVDLFSSRGITSIFTAEVPPDTPETEVGDPNMAAIVDTIISLRFRRVEDQIRRTICLVKVRGSAHDTGVRWFKITDEGVQVAAAFIGVQEVPKVVLDL", "metadata": {"id": "A0A7Z9ZXH0", "cluster": 16920026, "interpro_all": ["IPR030665", "IPR014774", "IPR010624", "IPR027417"], "interpro_used": ["IPR014774", "IPR010624", "IPR030665"], "interpro_unused": ["IPR027417"]}, "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 included in 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. In addition, the protein should include a Glucosamine/galactosamine-6-phosphate isomerase domain that serves as the catalytic core for enzymes involved in carbohydrate metabolism, including 6-phosphogluconolactonase and glucosamine-6-phosphate isomerase. It facilitates critical reactions such as the hydrolysis of 6-phosphogluconolactone in the pentose phosphate pathway or the conversion of D-glucosamine 6-phosphate to D-fructose 6-phosphate during N-acetylglucosamine utilization. It is native to Phycisphaerales bacterium.", "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, 3063, 1922, 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, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 28627, 19, 9479, 17454, 17, 26, 17, 5413, 25510, 3418, 1988, 10634, 1966, 1920, 6804, 4728, 1958, 5038, 3286, 1922, 10590, 4714, 16, 2710, 26, 17, 8078, 22988, 23557, 5148, 2341, 9259, 1021, 1930, 28627, 17, 26, 17, 5413, 25510, 18, 2176, 11374, 4140, 5298, 2427, 1966, 1920, 9128, 1927, 26, 17, 8078, 22988, 23557, 5148, 2341, 2290, 1922, 1920, 9412, 2217, 5413, 3374, 2014, 1920, 7309, 1927, 46, 17, 28627, 26, 17, 5413, 1942, 46, 17, 15102, 26, 17, 5413, 2409, 56, 17, 6894, 22988, 17454, 8422, 18, 2176, 1977, 6196, 1942, 25511, 9119, 29164, 3955, 14061, 18, 3], "output": "MSVNFQREYDQGMVYDLSDPIPELPNDFRHQADCCVRAFGDFHVALPGDVCFGALYRRLLVDPLFRMLPWRHDHTDLPREQWHPFRDNDPEAFDRELRENFAFRGADIDAPGVVNTSVGLALGFGALVRARMQAVACFGSVRPNPQEGVRLFYVDASAFEEASSTELPGQVEVCPDADVAAERLLKTHLWMLDAYGDGEPAADLIGGWLEAGQDRLDFVLLPVREDGALPDHIAPVLNRVGGGEALAL", "metadata": {"id": "A0A3D1ENK8", "cluster": 19152610, "interpro_all": ["IPR006148", "IPR037171"], "interpro_used": ["IPR037171", "IPR006148"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: 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 originates from Candidatus Bathyarchaeota archaeon.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 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, 2176, 22970, 2037, 14550, 1031, 1957, 10481, 9771, 15618, 20051, 7336, 13470, 1916, 18, 3], "output": "MLDGAKRRIQETYRQTAKIYDIGVSERLGDSKWGIESLTCLLLRDIEFQENPVVLDLACGTGLSTFQLIE", "metadata": {"id": "A0A842YHX4", "cluster": 21083258, "interpro_all": ["IPR029063"], "interpro_used": ["IPR029063"], "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. It originates from Candidatus Izimaplasma bacterium HR2 and is described by UniProt keywords Kinase, Nucleotidyltransferase, and Transferase.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 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, 14550, 1031, 1957, 25455, 12874, 15403, 1019, 14061, 3668, 1028, 1930, 1977, 2910, 2007, 20709, 11569, 4016, 16, 2797, 4090, 2199, 9961, 16, 1930, 13763, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MEFYIGGKYNGKLEYVLNKYKKNEYFDISKDSNIDDVVLFLLQKDEDPIKYLKKLSFDNKIIIKYLVSVSDSTYNIIYGIEVKLKVDAILDYDIINGNIITNGVVPINKLHRELRDDVGSLY", "metadata": {"id": "A0A094IG82", "cluster": 22916031, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein should feature a Prokaryotic N-terminal methylation site, which directs the methylation of a conserved phenylalanine residue. This motif is typically located at the N-terminus of pilins and proteins associated with secretion pathways. Also, the protein is a member of the Pilin-like superfamily, which comprises structural proteins such as type IV pilins and secretion system pseudopilins that assemble into filamentous appendages on the bacterial surface. These proteins typically feature a conserved, methylated hydrophobic N-terminus and facilitate critical functions including cell adhesion, twitching motility, and DNA transformation. Some members, such as YadA-like autotransporters, act as pathogenicity factors by extending from the outer membrane to mediate host interactions. It occurs in Victivallis lenta and is annotated with UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 3066, 5961, 43, 21545, 56, 17, 4262, 5547, 3200, 16, 2154, 28351, 1920, 5547, 1927, 43, 5305, 17388, 6181, 18, 2052, 5219, 1977, 5745, 4810, 2019, 1920, 56, 17, 7822, 1927, 7547, 2925, 1930, 2697, 2458, 1956, 5512, 3873, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 7547, 1921, 17, 3189, 13975, 16, 2154, 12936, 4346, 2697, 2427, 1966, 2601, 4370, 7547, 2925, 1930, 5512, 2433, 11520, 10984, 7782, 1036, 1988, 17421, 2460, 18706, 7958, 2662, 1990, 1920, 4543, 3154, 18, 2144, 2697, 5745, 5961, 43, 5305, 16, 11882, 7919, 56, 17, 7822, 1930, 6628, 4140, 4088, 2710, 2024, 6141, 16, 21596, 1941, 9254, 16, 1930, 2678, 7002, 18, 2673, 4678, 16, 2427, 1966, 26169, 3825, 17, 3189, 5728, 5412, 24095, 1036, 16, 4033, 1966, 15903, 2790, 2007, 12140, 2037, 1920, 7642, 3260, 1942, 8265, 4423, 3719, 18, 2176, 5110, 1922, 8159, 2113, 2214, 1937, 24589, 3857, 1930, 1977, 10633, 1956, 20709, 11569, 9117, 7864, 18, 3], "output": "MRNTFTLIELLVVIAIIAILASMLLPALNQARSRAHAVKCAGNLKQFGMAEAIYSTAYDDFVVPLLLNNSWDNAMRWCNNAGFLQALGASMKSTYDDGNVNLNTGFFCPAKPADRNANNYTGHWYAKNMHYPGVAASDSFPSGTDASRQSFKITSLARPSLRMNIVDGVGTFVRYNDPKYMIPEKGDSSGYWMAFRHHNYTLNALLWDGHVETLNRRQLHDGNWTQQPGCPIFDRWILSAR", "metadata": {"id": "A0A844G3I9", "cluster": 23942780, "interpro_all": ["IPR012902", "IPR045584", "IPR050470"], "interpro_used": ["IPR012902", "IPR045584"], "interpro_unused": ["IPR050470"]}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein carries a VPLPA-CTERM sorting domain that acts as a probable protein export signal recognized by the putative transpeptidase exosortase D. Characterized by a conserved VPLPA motif, this variant is primarily found in members of the Rhodobacterales. It has been characterized in Paucidesulfovibrio gracilis DSM 16080 and is described by UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 16252, 43, 9314, 13857, 1019, 17, 29486, 23745, 11404, 3418, 1988, 8016, 1966, 43, 12584, 2213, 12660, 2733, 6783, 2007, 1920, 6770, 22796, 18877, 24602, 2718, 2051, 46, 18, 4378, 2007, 43, 5305, 9314, 13857, 1019, 5219, 16, 2052, 6031, 1977, 5985, 2435, 1922, 4678, 1927, 1920, 11490, 5883, 3955, 18, 2176, 2258, 2252, 4378, 1922, 18424, 3726, 4042, 25210, 2377, 3940, 24689, 10401, 1937, 10964, 9608, 4476, 1930, 1977, 2910, 2007, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTRNIFTNFIMALAVVLFAGSAMALRIDPNNALVYDPAGDDQSGNYNFTINGAGADLQVFETSWGGGTDNWAAYPETAYAQQDGSFDFDGLITGTSAILVRDVSRDFGFLPAGIWLLGGGLIGLIGLRHRRRGAVMPVGFSSYSPVGVSDASLGFGGSIVLNFANPIEVWAFQGNYSGQAYGDPGWVRLGTGSGDGFDLDGVVANYATP", "metadata": {"id": "A0A1T4XLP5", "cluster": 24709948, "interpro_all": ["IPR022472"], "interpro_used": ["IPR022472"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to make a protein that can have this function: The protein possesses a DUF4815 domain that is found in viral and bacterial proteins, though its specific molecular function remains uncharacterized. It is identified in uncultured Caudovirales phage. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 14465, 43, 4855, 10432, 11425, 1015, 3418, 1988, 1977, 2435, 1922, 4324, 1930, 4543, 2697, 16, 4170, 2496, 2487, 3272, 2347, 4497, 24528, 18, 2176, 1977, 2899, 1922, 5269, 21058, 10268, 20165, 1918, 10503, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MAINFNTDPYYDDYSEDKNFHRILFKPGVAVQARELNQLQTILQNQVSRFGNHVFKPGSMVIPGNTFFDKNFNYVKLEATYNSVDIDTANYLDRELIGQTSGIRAKVIKVEAATTTEPPTLFVKYLDSGTSRTATAFTTAEVIQTNDTGTVYYATVGATAPTGKCIGVSINTGVYFIRDAFVRVAADTLILDKYLSNSSYKVGLEVTESTVNSDDDETLLDPAIGTYNYFAPGADRYKIALTLAKRDINDASSADSFIELVRVKDGELVDIVTKPGYNVLADELARRTYDESGDYTVNPFNLKFIEHLKDTTNTDGYLITGDGGDSTKAIAVLSPGKSYVKGYEVATTSNRYLVFNKPRDTANVTNAIVRTPIGNYVSVSNAYSIPNFTSDLITVNLYNKYTATKGSAAGTLVGNARIRGVETTTSNVMSNASTFSTFLFDVKMRSGYTFDRDVKQLYHAAVSDTGYVSAAFTGDIVATDVVTSGSVNLTNGSNSVVGVNTLFTTDLKAGDYVQFTSDTSNSYLVDNVISNTAFYIGRTYPLANVSGANFTRDAATIVDSDKATYLFPFPNTTIKDLADITVRTRRALYGTLSAGVVTFSTAVGTTFASRSDTNYYAVGVSGGAAGKLYAITSGKFAFTDAPTNRNISIDLSGYGLTTEDVIVYATVIKASPTAKTKTSTSGQTSYTAATDCQAPVISLGYADAYAIANVKMSSNVFGTAYSDGNAVDVTSNYTLDTNQTPTYYGVSRIKLKPGAPAPTGPIQINFTYYAHGAGDYFCATSYPDYEDIPKFTDQGIVYDLRDCLDFRPRISNAATNFKDTGASRNEFLDYTNDFQTDYEYYLPRTDKIFLTTDKEIVYKEGVSSLTPAEPSTPVDAMPLYVIEHPAYGFDINRDSTFTSVDQKRYTMKDIGKLENRIKNLEYYTTLSLLELDTAVFSVKDSFGLDRYKNGFIVDSFRGHGVGDIRNSDYNISMDFEEGKLKPAYYQKNIKVSEVNTSDAQRTANGYVLVNNNTVMLEYTDEEYINVNVASGTESITPFDNFTFTGKMTLAPSGDTWFDDTTKPLVYKDDNGTYDTLIPDSVGEKTYGTVWNSWKQFWFSSDNKDKVKAIEGGAVVTDAGVTGDSTSVVFPYVRANSIAFNASRLKPNTHYYAFFDEYNVTNYCTSGNTTSNVFGFDANTTNFANIITDYTGTVNGVFNFDPVTSGLKVPSGKVTFRLTDSSTNSSNKESFADAFFVSNGTLIQAIPPRINYTADAPLSSGSALSTASPGLVAHAVAFITGNKDPNSITAEQAAAYEKYFKTTGGAGVAFNEALFQSLAPSGTNIYNVRSLITSNSYNFVSGNGTNATTSTGTDLNSYLTATNILEATNTVTGKTFVQEAYDRIQADLGYNAIAQVVEPVYQGVRGVAADVVAKSAGNYDSLPKDMKDFWEAGLANGSFTESAEGVAKALDNYAAAITVGYLDRSSSSSQAAASAAASNGLV", "metadata": {"id": "A0A6J7X3S3", "cluster": 25683422, "interpro_all": ["IPR032096"], "interpro_used": ["IPR032096"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein falls within the Protein of unknown function DUF503 family, which comprises conserved hypothetical bacterial proteins characterized by a ferredoxin-like \u03b1+\u03b2-sandwich fold. It occurs in Bacillota bacterium (Firmicutes bacterium).", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 12182, 2651, 1920, 2213, 1927, 5435, 2347, 4855, 17968, 12962, 3416, 16, 2154, 12936, 5305, 15148, 4543, 2697, 4378, 2007, 43, 25304, 22389, 10960, 17, 3189, 160, 15, 161, 17, 18038, 3728, 18, 2176, 5110, 1922, 8175, 22538, 3857, 14061, 12, 24474, 14061, 13, 18, 3], "output": "MIIGTLTIRLYAPWVHSLKEKRMEVKSVSIAEIEGMDTHQIIVLGTNTEAEVVTVDMEIFLIDKTKNKFNIGCVSNDTKYVNSVLDEVINFIE", "metadata": {"id": "A0A7C6YY02", "cluster": 26443138, "interpro_all": ["IPR007546", "IPR036746"], "interpro_used": ["IPR007546"], "interpro_unused": ["IPR036746"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein can be placed in the Serine/threonine-protein kinase family, which acts as a regulatory link between membrane-associated GTPases and downstream MAPK cascades to drive cell fate decisions such as proliferation, differentiation, and survival. These proteins phosphorylate diverse substrates, including MAP kinase kinases, integrins, and histones, to modulate pathways ranging from JNK signaling to inflammatory responses. The family comprises both catalytically active enzymes involved in stress and apoptotic signaling and predicted pseudokinases with regulatory functions. Also, it is part 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. Additionally, 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. It is expressed in Candidatus Methylumidiphilus alinenensis.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 8468, 19, 13143, 17, 2213, 4016, 3416, 16, 2154, 8016, 1966, 43, 4948, 3300, 2192, 3260, 17, 2458, 18390, 1930, 5863, 7859, 15967, 1942, 9265, 2024, 11211, 8693, 2427, 1966, 4031, 16, 4155, 16, 1930, 3298, 18, 2144, 2697, 18730, 6445, 6249, 16, 2710, 4446, 4016, 7784, 16, 15563, 16, 1930, 15808, 16, 1942, 8480, 3873, 6485, 2037, 10063, 3197, 1942, 3769, 3387, 18, 1920, 3416, 12936, 2321, 21446, 3500, 5038, 3286, 1922, 3071, 1930, 6353, 3197, 1930, 4396, 11520, 25545, 1036, 1956, 4948, 4088, 18, 2222, 16, 2176, 1977, 3131, 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, 4950, 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, 2176, 1977, 3198, 1922, 14550, 1031, 1957, 4963, 28851, 7408, 24888, 5277, 1036, 15356, 2912, 2912, 3355, 1937, 18, 3], "output": "MMVFTASQQEIEIEPMPFAKGGEQKIEYMVGNPPPGLNSRVYMVCWPSDVVFDTDNPTETSPASKPWLSTKFDRKTSLGQESRLKKHYVFVDMKPQNILLTADAKIAIVDLDSIQIADKKKAIQLEKDCVPEHWDQFSLAVVFYQVLFGLHPYMASPPPHQAFEGLDAKLKSLFKRAFDIGFRHPKLRPFLAPHTQALLEHRIRNIQSILKHGVDSLGAVHKILSPGTLQSFCVKLYYDKYRTAERRKKFLGFLMPAAWQDNTLLYGLCLPLIVNIASAVHSIHASVLFGAKVLTPEYMPPEASFKGGYADIATPREAIKHGLFVHGSKRHHIHALSAAEWGETIHGLLVPMGKRRNSES", "metadata": {"id": "A0A2W4QRK2", "cluster": 28349825, "interpro_all": ["IPR011009", "IPR000719", "IPR050167"], "interpro_used": ["IPR050167", "IPR011009", "IPR000719"], "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 categorized in the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. Also, the protein should feature a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. Furthermore, the protein should have 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 occurs in Methylomusa anaerophila and carries UniProt keyword assignments Glycogen biosynthesis and Glycosyltransferase.", "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, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 3677, 16, 1920, 2213, 3066, 2162, 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, 5110, 1922, 4963, 1947, 28553, 11381, 7766, 1930, 16252, 20709, 11121, 2538, 18306, 13302, 8132, 1930, 20067, 9961, 18, 3], "output": "MKPVLFLATESFPFVKSGGMGDVIGSLPRELRRQGVEARVILPSFDVKLGWRKQPCRLWRLEYDGVIFYFVDNDYYFNRQGLYGWPEALPHLDFAPHILHCHDWHTAILPLLLKAGYAGLASYTYYFTSDRLEFYGTVSYLKAGIVFADALTTVSPSYAWEITTPEGGRGLDGILRGGDPLIDTPYTWQSVQHKQQNKTKLQELSGLPVQPDIPLMQWVIMSTGEERYETLLRAIAHQYPDRLYVQTYFDEGMAHRIYSVPLVRATGGLKDTVIPFNEATGAGTGFVFDSANETWHSLVKNAMKSDHSWRRSVDGYLAVYRRLQSKFSAIPPSLAQAMTPLSDDAERFAYFCRAVLSRLKTVLTIHNIEYQGCFDRSVLTDLLELDNERQADLTGIVNGIDYDTYNPSMVSRLVPAKGLDILLESLPVMMDYNAAGSDLYLQPSLSEPCGTSQLVAMRYGSREFLAALRQAVILYHHR", "metadata": {"id": "A0A348AHX0", "cluster": 1606264, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR011835", "IPR013534", "IPR001296"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: The protein falls within the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. In addition, the protein carries 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. Also, the protein carries a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. It has been characterized in Clostridiaceae bacterium and features UniProt keywords Glycogen biosynthesis and Glycosyltransferase.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 12182, 2651, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 1922, 2459, 16, 1920, 2213, 16252, 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, 2222, 16, 1920, 2213, 16252, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 2176, 2258, 2252, 4378, 1922, 17938, 14773, 1972, 3336, 14061, 1930, 4075, 20709, 11569, 13302, 8132, 1930, 20067, 9961, 18, 3], "output": "MTQVLFVTAECAPFIKAGGLGDVAASLPGAITEFAFHASFVVDFEGGRRRVRVYRAERSGVEHYFLQAPDYFTCFACALMAALPALGYRPDILHLNDWHTGPLAAMIAYRRRHDPFYANMRTYMQYCTRLPDEVFDTGGMAWYDRTANPMRCGLYYADRFGEGMDGLLRERSAVVSGIVNGLDYEVFSPEADTYLTRGHYGPADVREAASISRLTDQKGIDLIVAAAGQLVSRGAQIIITGDGDDRHTRMVNELASRFEPCGLSQLIAMRYGTVPIVRRTGGLRDTVTPCEGGAGLGFVFDGYDALIQRDMRADFSWDASAVRYEALYDGLRDEALGASRVKGCEVRVVLPYYSCMNDEEKPYDGDCGVETRRFAFIFTIHNLRYQGVCDRDVTTVSERYAEEIQQPEGKWRYKEQLQREFGLRIDRDAFLKRFPGQIAAYPVFNEAFSRILYAAADALLMPTPGEFDAAFAAAERLYHGDRRAW", "metadata": {"id": "A0A6N9P7D8", "cluster": 24118758, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR011835", "IPR001296", "IPR013534"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein carries a Alpha/beta hydrolase fold-1 domain that constitutes the structural core of a diverse superfamily of hydrolytic enzymes, featuring an alpha/beta-sheet arrangement that scaffolds a catalytic triad. This domain typically contains a conserved nucleophile elbow to drive hydrolysis, although some members lack catalytic residues and participate in surface recognition. Also, 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. Moreover, the protein belongs to the AB hydrolase superfamily, which encompasses a diverse range of serine hydrolases, lipases, esterases, and peptidases that catalyze the cleavage of C-C, C-O, and C-N bonds. These enzymes participate in lipid metabolism, pyrimidine catabolism, and biotin biosynthesis by acting on substrates such as monoacylglycerols and esters, while some bacterial members contribute to environmental adaptation by degrading pollutants. It is found in Candidatus Gottesmanbacteria bacterium GW2011_GWA2_47_9.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 16252, 43, 4595, 19, 4666, 20748, 3728, 17, 21, 3418, 1988, 14879, 1920, 4346, 4728, 1927, 43, 6445, 13975, 1927, 26702, 5038, 16, 29931, 1925, 4595, 19, 4666, 17, 11130, 13002, 1988, 10603, 43, 6804, 21845, 18, 2052, 3418, 5745, 5461, 43, 5305, 2797, 28335, 17621, 1942, 9265, 9128, 16, 2876, 2673, 4678, 3630, 6804, 4248, 1930, 7352, 1922, 3154, 5708, 18, 2222, 16, 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, 3950, 16, 1920, 2213, 14440, 1942, 1920, 2186, 20748, 13975, 16, 2154, 21569, 43, 6445, 3109, 1927, 8468, 30337, 16, 16653, 1036, 16, 26389, 1036, 16, 1930, 24050, 1036, 1988, 18170, 1920, 6404, 1927, 45, 17, 45, 16, 45, 17, 57, 16, 1930, 45, 17, 56, 9031, 18, 2144, 5038, 7352, 1922, 4486, 4714, 16, 21611, 19480, 16, 1930, 8622, 8132, 2007, 8290, 1990, 6249, 2427, 1966, 8914, 21295, 1036, 1930, 16785, 16, 2679, 2673, 4543, 4678, 4672, 1942, 4813, 7810, 2007, 18192, 16826, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 14643, 14652, 3862, 7972, 2341, 18339, 14061, 8997, 23437, 1009, 41, 8997, 8398, 41, 4261, 41, 29, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MPYQISDGVRTYYQLIGKGPLLVLGFGKSDEPQSEGWTTQDYAHWLSGFLSGGKIGAVFCVSPHTKDQKPKRLILIGPSGIPNAMTKKNVVLSGVIGETDYAYATPFQQKTLRKVLPEDITTELKNITIIPKSTLLIVKQAGHFPHIEQTEAVLEYVQSWMKILHGWANRWEAWSPLIPPDLPEFTKNKTYTLIGHSFITKAVPGVVKKVLPHAFVRKFYEKPTLIIWGDHDTSAQVAHAEVFHKT", "metadata": {"id": "A0A0G1TVT5", "cluster": 1950016, "interpro_all": ["IPR000073", "IPR029058", "IPR050266"], "interpro_used": ["IPR000073", "IPR029058", "IPR050266"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein is associated with the Golgin subfamily A member 6-like family, which comprises coiled-coil proteins localized to the Golgi stack that play roles in membrane traffic and the maintenance of Golgi structure. These proteins may interact with small GTPases to regulate Golgi organization. It is native to Xenopus laevis (African clawed frog). Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 1920, 10277, 1022, 16227, 43, 7210, 26, 17, 3189, 3416, 16, 2154, 12936, 17524, 17, 9121, 2697, 6579, 1942, 1920, 10277, 10496, 1988, 3918, 5456, 1922, 3260, 12368, 1930, 1920, 6291, 1927, 10277, 3170, 18, 2144, 2697, 2278, 6310, 1956, 2858, 18390, 1942, 5741, 10277, 5901, 18, 2176, 1977, 6196, 1942, 14545, 25042, 12, 7050, 6958, 2172, 1007, 23707, 13, 18, 7031, 1920, 3244, 18, 3], "output": "MGSKSERIGSRKDGMQAVLDRKQEVKDRKQEVKDRKQKEKDRKQEVKDRKQEVKDRKQEEKDRKQEVKDRKQEVKDRKQAVLDRKQEEKYRKQEVKDRKQEEKDRKQEVKDRKQEEKDRKQEVKDRKQAVLDRKQEEKDRKQEVKDRKQEKKDRKQEVKDRKQKVKDRKQ", "metadata": {"id": "A0A974HU79", "cluster": 2740494, "interpro_all": ["IPR026737"], "interpro_used": ["IPR026737"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein incorporates a Serpentine receptor class x (Srx) domain that functions as a G protein-coupled chemoreceptor in nematodes, mediating the detection of specific environmental chemical stimuli. As a member of the Srg superfamily, it features a characteristic seven-transmembrane topology distinct from other serpentine receptors. It is identified in Rhabditophanes sp. KR3021 and is classified with UniProt keywords Transmembrane helix. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 27453, 9830, 1021, 3148, 2921, 66, 12, 4581, 1039, 13, 3418, 1988, 4088, 1966, 43, 49, 2213, 17, 6416, 13534, 5943, 7344, 1924, 1922, 19669, 16, 10239, 1920, 3805, 1927, 2487, 4813, 4399, 5458, 18, 1966, 43, 7210, 1927, 1920, 4581, 1029, 13975, 16, 2176, 4075, 43, 6293, 5260, 17, 9117, 13678, 4493, 2037, 2303, 27453, 9830, 1021, 4086, 18, 2176, 1977, 2899, 1922, 20637, 8752, 18547, 1918, 2056, 18, 6203, 29906, 1009, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 7864, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MSVFDKTIYIVLIIFDYVIHAICIYSIIKLKAFKNCFGYICFIISITECFLILISAFYIFYDADIEPKSKISIFRRLTGVMQMYLWTALAIGHLYQCLNRMVAVIWSTFYYLKFNTKVSLVCATSIWFLSIFFILPYIDDRCQYYYDPLNKKWEYLDTAFMRIIIKKSKKVVKTDHTIKNNSQITKNHISTKEKMFAFQCFFLTLSLLINSMVYMVLFNIKGFQFDLNFAINIFPLIWRTCVPMTFNENLVLGLFTSIIENSSDDCTGQPCNLGEQTVLQR", "metadata": {"id": "A0A1I8CQW9", "cluster": 3346908, "interpro_all": ["IPR019430"], "interpro_used": ["IPR019430"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein includes a Domain of unknown function DUF1592 domain that characterizes a conserved region within predicted secreted cytochrome-like proteins found in *Rhodopirellula baltica*. In addition, the protein has 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 has been characterized in Planctomycetales bacterium.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 5921, 43, 3418, 1927, 5435, 2347, 4855, 5739, 7308, 1028, 3418, 1988, 26735, 43, 5305, 3031, 2651, 4396, 8366, 9387, 17, 3189, 2697, 2435, 1922, 14, 11490, 2011, 2952, 11560, 5617, 4641, 21788, 14, 18, 1922, 2459, 16, 1920, 2213, 2258, 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, 2258, 2252, 4378, 1922, 4720, 2341, 13386, 3949, 1918, 14061, 18, 3], "output": "MTVRTEYIESLSNRIITGRWLQTNWRGLLPRFSARCIFGRSHVLGQDAEPQIVRAVKDHCLDCHDHASFALWVKVYNRVQRREMPPADSVTTANARRQRSEGRTQYRRLSRTQYLPEDTPSDGFDNIGSALNLSEIQIARYLTRLIASQNGRFRQVLGKQQEAVNVDGAVEPPVDGYYRIRMKTFGFHWDAGTVRPPLDVPASRGADAIEFEGFLRVGDQIQYRAPGVAVEWLEVHGPISPAGLPASYVSLLLQPPIPIITEGVGKRAVEDARSLLHQFAQRAFRRPVEPIEIEDIQEAMRIGYQAILCSPEFLFLDESPGKLSDHALASQSNLTRPEVLRNQVDRLIDYDVKRCNAITVATRIILIVAAHIFSQSAESGLDLAALKYDPNDTIEPAVRQSFLDSLARDLAENSMRRLLALPELSVADMDAADHALDQAIVLTDRPEILTGLLRQPNTAQAPWFWSKFNQNHVVTFHAVQGSTKRALTSIWFETLDDRNKPGRLPITDFGDLPVEPYHLDSGRVPAKPKRVQFMRVVPRDPTLRLVQTKIDQRHCFASRLSFFLWNEMPDEKLLEL", "metadata": {"id": "A0A954TMS6", "cluster": 3376272, "interpro_all": ["IPR011429", "IPR013036", "IPR013042", "IPR013043"], "interpro_used": ["IPR013042", "IPR011429"], "interpro_unused": ["IPR013036", "IPR013043"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that has the following function: It is part of the RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta superfamily, which represents an \u03b1/\u03b2 structural domain shared by enzymes essential for RNA modification and bacterial cell wall synthesis. Members include RNA cyclases that catalyze the ATP-dependent formation of terminal 2',3'-cyclic phosphodiesters, and enolpyruvate transferases that transfer enolpyruvate from phosphoenolpyruvate to UDP-N-acetyl-glucosamine during the first step of peptidoglycan biosynthesis. In addition, the protein should have a RNA 3'-terminal phosphate cyclase domain that catalyzes the ATP-dependent conversion of an RNA 3'-terminal phosphate to a 2',3'-cyclic phosphodiester, a process potentially involved in tRNA splicing or U6 snRNA processing. While the active site typically utilizes a conserved histidine as an adenylate acceptor, a specific eukaryotic subfamily lacks cyclase activity and instead functions in nucleolar ribosomal modification. It is produced by Chaetomium sp. MPI-SDFR-AT-0129 and corresponds to UniProt keyword Membrane, Transmembrane, and Transmembrane helix. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 3146, 23, 11, 17, 4262, 5413, 16526, 19, 2066, 1945, 18425, 12631, 2010, 13763, 16, 4595, 19, 4666, 13975, 16, 2154, 4972, 1925, 160, 19, 161, 4346, 3418, 7115, 2007, 5038, 4415, 1958, 3146, 6295, 1930, 4543, 2024, 4821, 4271, 18, 4678, 3951, 3146, 16526, 1036, 1988, 18170, 1920, 4498, 17, 3100, 3337, 1927, 4262, 22, 11, 16, 23, 11, 17, 9821, 20184, 3341, 16, 1930, 2066, 1945, 18425, 12631, 2010, 13763, 1036, 1988, 3856, 2066, 1945, 18425, 12631, 2010, 2037, 8078, 9356, 18425, 12631, 2010, 1942, 18500, 17, 56, 17, 6894, 17, 28627, 2409, 1920, 2561, 3537, 1927, 24183, 8132, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 3146, 23, 11, 17, 4262, 5413, 16526, 3418, 1988, 17097, 1920, 4498, 17, 3100, 7309, 1927, 1925, 3146, 23, 11, 17, 4262, 5413, 1942, 43, 22, 11, 16, 23, 11, 17, 9821, 20184, 1967, 16, 43, 2585, 5063, 3286, 1922, 10089, 8490, 2014, 22275, 11970, 2175, 4587, 18, 2679, 1920, 3500, 3200, 5745, 18127, 43, 5305, 13873, 1966, 1925, 23052, 12641, 16, 43, 2487, 10825, 16227, 13012, 16526, 2455, 1930, 5974, 4088, 1922, 23770, 11196, 6295, 18, 2176, 1977, 4152, 2007, 13297, 23345, 2457, 2056, 18, 26586, 17, 18876, 1005, 17, 2019, 17, 14632, 1026, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MSAPSRTKTTTESIVIDGTAYEGGGGLIRYALAFACILNRPVHIHSIRAGRPGVGGLRSEHTVAVSTMAQLTSAAVIGNQTASRELIFTPYASLDADADGNGDALSPQPVLQQQKLDIKLEGSAGIFLVAMLPYLLFSRLASKTHHTPPTATPDEFELTIRAGTLCVKAPSIFYLQQVFLPTMALIGIGSNHLNILPDHYEQGWHTDTNKLPGKMTARIKPLLTPLLAFVLDRRGRVQTVRATAHAPPQLLDKFKQTLEAELADAISRDAGVDIAVDMFPSLVDHQYHLLLVAEATAPAAFLGYEEVYPQRDVFPSDLEGDTDRIIRHLVRACIRGLWEELRRGHAVDENLEDMLALYQSLAVGFSSVITPQGNGCLVPEFNIETPAIRRLPVPFFYMHTYVFCLVYCVTVYMNTKVGRRLLLTRCCGANVQGTSTTR", "metadata": {"id": "A0A8K0LLU5", "cluster": 4992206, "interpro_all": ["IPR023797", "IPR037136", "IPR000228", "IPR013792", "IPR036553"], "interpro_used": ["IPR013792", "IPR023797"], "interpro_unused": ["IPR000228", "IPR037136", "IPR036553"]}, "task_type": "autoregressive"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein should feature 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. In addition, 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. Additionally, the protein features 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 is identified in Tissierellia bacterium.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 3066, 5961, 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, 1922, 2459, 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, 4950, 16, 1920, 2213, 4075, 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, 1977, 2899, 1922, 2660, 3453, 16025, 1019, 14061, 18, 3], "output": "MIEVVKLNKSFGKHHVLKGKSTTMKCLVNLIFALIEAPGLYPNLTGLDNLKLFGELKKVKKEYKKVREYSMGMKQRLALGIILLPQGVFDLRKVLLSLAEAGHGLMVSSHQIKSGEIVHREALSNSSSLIIENDYILKYELEDHLHLFHIPVVKLLMPIDDIESLYQSIYSDISFKVSKGEIVGFIGPNGSPDIGKITIDEYDLLNKRKEALSLVNRIEQVMEIIQLDKEISKPKYLILDEPFNGLDLLELEKITTRNIFYKILFEDGILPSENFIKELDKNISDLLKKLLDNHLN", "metadata": {"id": "A0A7X6WCE9", "cluster": 5293324, "interpro_all": ["IPR003593", "IPR003439", "IPR027417"], "interpro_used": ["IPR003439", "IPR027417", "IPR003593"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a polypeptide chain with function: 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 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. Furthermore, the protein should have a PAS fold domain that acts as a versatile signal sensor in signaling proteins across archaea, bacteria, and eukaryotes. It frequently binds cofactors like heme or flavin to detect specific environmental stimuli and undergoes conformational changes, often in conjunction with an associated PAC domain to form a conserved 3D structure. This fold is integral to diverse systems, ranging from circadian rhythm regulation to the gating of voltage-dependent potassium channels. It is native to anaerobic digester metagenome and is annotated with UniProt keywords Transferase and Two-component regulatory system.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1956, 2347, 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, 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, 3677, 16, 1920, 2213, 3066, 2162, 43, 9233, 3728, 3418, 1988, 8016, 1966, 43, 20425, 2733, 6443, 1922, 3197, 2697, 3436, 21501, 16, 4802, 16, 1930, 15021, 18, 2176, 5467, 6876, 21362, 3189, 10954, 2014, 26758, 1942, 4277, 2487, 4813, 5458, 1930, 14928, 8523, 2840, 16, 3868, 1922, 11799, 1956, 1925, 2458, 6866, 3418, 1942, 2386, 43, 5305, 5050, 3170, 18, 2052, 3728, 1977, 12328, 1942, 6445, 3771, 16, 6485, 2037, 10507, 11529, 3640, 1942, 1920, 12568, 1927, 6889, 17, 3100, 9057, 5628, 18, 2176, 1977, 6196, 1942, 12554, 20808, 1915, 16552, 2225, 1930, 1977, 10633, 1956, 20709, 11569, 13763, 1930, 2288, 17, 4594, 4948, 2433, 18, 3], "output": "MKKGRENKQKPVKPDVKKKKTRTRTGTLSAGKPGLRPADPRRGGGSVNKDIHRDVFDGVMDAWYFHDLEGRFLETNAAFRRMLGYPENQPLPENFRIEDLLSEDMKHLVSGYIETIMRDRKSEGLMRVSCPDGSEKFIEYKNAMVFDGNGKAIGVRGMGRDITERYLARKEMKEIEQRYRDIFDNVTDLLFFHDLDGNFDLKQCNPAVRQQLVGGNPEIETVNIREFMPEAYRAGFDEYLERIKKNGRDEGLFTIINFAGRESVMEYRNSLVSDKNGPIGVRGSARDITDRIIYERALRMSEEKYRTILESIEHGYYEVDTAGDITFFNDSFCRIFDIPKDELIGKNYKTFIDEETAKKVYDVFHTVYSTGRDMMWTEWEFITRKGRKISFEASISCIMTRSGKCRGFRGIVRDVTERVATEQALKESESKYRNILEGIEEGYYETDLKGRYTFMNDSMCRITGFSREEMTGMSYKNCMDEENARRVFEAFRHVFTSGEPMKGFGWDFTRKDGSKVQVESSILLIQDPQGRPAGFKGILQDVSERKKAQEQTRLLEERLKNAQKMEALGTLAGGVAHDLNNILSGIVSYPEMLLMKIDKDDPLRGPLEKIQKSGQKAAAVVQDLLTLARRGVAVKQVVNLNGLIREYLESSEFGRPQSLHPNVRVDFRHDDSLMNIIGSPAHLSKAIMNLISNAAEAMPKGGTITIETCNLQHRDLGECEGNIKEEGRWVSLSVTDTGKGIPAEDIPRIFEPFYTKKKMGYSGTGLGLAVVWGAVQDHDGSVAVTSREGKTTFTLNFPATSEQITEAKAKQLMKDYQGKGEHILVVDDSKEQREIAAEILMMLGYRVDTVSSGESAIEYMKGHSADLILLDMIMEQGIDGLETYERILELHPGQKVIIASGYSETDRVKQAQTLGAGRYIKKPYLIEDLAMAVMQELRKDRA", "metadata": {"id": "A0A485M4T7", "cluster": 6676177, "interpro_all": ["IPR011006", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR001610", "IPR000014", "IPR000700", "IPR035965", "IPR013656", "IPR013767", "IPR004358", "IPR001789"], "interpro_used": ["IPR000700", "IPR005467", "IPR013767"], "interpro_unused": ["IPR000014", "IPR011006", "IPR035965", "IPR013656", "IPR001789", "IPR003661", "IPR036097", "IPR001610", "IPR036890", "IPR004358"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence for a protein with the following function: The protein possesses a Very large inducible GTPase (VLIG)-type guanine nucleotide-binding (G) domain that functions as a molecular switch by binding and hydrolyzing GTP to regulate interferon-mediated immune responses and cell cycle progression. This P-loop GTPase module is essential for the activity of proteins like GVINP1 and URGCP, contributing to pathogen resistance and cell proliferation control through conserved G1 and G3 motifs. 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. In addition, the protein is a member of the Interferon-induced very large GTPase family, which belongs to the TRAFAC class dynamin-like GTPase superfamily and plays a key role in the antiviral immune response. These proteins exhibit GTPase activity to facilitate cellular membrane remodeling and regulate signaling pathways following interferon induction. It is expressed in Gopherus agassizii (Agassiz's desert tortoise) and carries UniProt keyword assignments Coiled coil.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1958, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 3345, 3103, 9376, 14809, 12, 9920, 1950, 13, 17, 2601, 16904, 5489, 17, 2743, 12, 49, 13, 3418, 1988, 4088, 1966, 43, 3272, 6195, 2007, 2743, 1930, 7222, 9046, 9319, 1942, 5741, 10001, 17, 3434, 3743, 3387, 1930, 2024, 4048, 4380, 18, 2052, 58, 17, 5881, 14809, 9059, 1977, 4415, 1958, 1920, 2455, 1927, 2697, 3189, 12042, 1921, 5113, 1930, 11460, 10020, 16, 8739, 1942, 7055, 3554, 1930, 2024, 4031, 2285, 2596, 5305, 8533, 1930, 15991, 8277, 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, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 10001, 17, 2719, 3345, 3103, 14809, 3416, 16, 2154, 14440, 1942, 1920, 14803, 1948, 2921, 22653, 17, 3189, 14809, 13975, 1930, 5705, 43, 3834, 2770, 1922, 1920, 10129, 3743, 2644, 18, 2144, 2697, 5987, 14809, 2455, 1942, 6628, 3689, 3260, 8378, 1930, 5741, 3197, 3873, 2894, 10001, 4408, 18, 2176, 1977, 3198, 1922, 3611, 2102, 25822, 8770, 5590, 2061, 3907, 12, 8770, 5590, 2061, 11, 61, 28333, 23832, 13082, 1021, 13, 1930, 16252, 20709, 11121, 2538, 18306, 17524, 9121, 18, 3], "output": "MPASFKKRRRTFQGILFKMKLKKYRSRKLTLRDLQKISPESLKNWSAQTLGDLPWHFLRKVMALNGMTRNTSLGHGELEDEAVSEDEEELDIEDDFFSLNDTCTTDSLHPLDILGAVLLCSDSFLQQEILSRMSMCQFALPLLLPALDTPRCALMLWAMRDIVRKWRPHSLAESRGFREESLVLTAMPTISFVRLGSCSFSKSKLLNEVLSPSQQYHDFFIHRDMECGNVPREIADGLVEISWYFPAGRENSDLFSESIAVTNLHGDIESHQLQFSFLMKVSTLLIIFVERLTEREYTLLLSLKEAGTKLYFMLSSEAEKSKDTLGFLKKLVLDLKLSKSHLLFKQSTTNQAQLVKKLRSTIGRITKFPHRHVTMEDMAETARELGIQVDEDCEECQSASKCVKEITAEIKDVAKYKREMLRLQGDLGKTVAKVEKELCRMRKRRTAHLEKYESELKEKLLALHKEKNQWDLTDGLVQFISGIACLSQVERCYFLKWMHLSLDHITRGNLASLQAEYKEKVKTSESDPQELAELGKLISARSLGSEHFMRELAQFYEAEHSRVKQSKLTESQRQFIHLPGIAADLMLEGFPMELIDGDASNIPLQWVTDVLTQLHAKLGGRSRMLVLTVLGGQSTGKSTLLNTMFGLQFAVSSGRCTRGAFMSLIQVAENFQQELGCDFILVIDTEGLKAPELAMLEDSYEHDNELATLVVGLSDITIVNMAVENATEMKDVLQIVVHAFLRMEEIGHKPNCQFVHQNVSDVSAHEQNMGNRKHLLEQLDEMSKAAAKMETQIKEMAILDIMDYDPEKHNWYIPGLWHGVPPIAPVNIGYSERVCELKNYLFEFTKSCSANRSLKDIPQFIERLRSLWNIIKHEDFGVSFKSSLVDEVYNQLSMNYAEWEWGFRKEMHLWVSEKETFILNQSAADLNFSVFKNIALEKLQYGDQKIMDCLQQYFARKASDLHLVEKYKEDFIRCIKTLKNDLKTHVFRKCEEAILTQIGRLKSHNIQINYMKIIEGEIDQLLANCRRSTQQLDDKKLESKFEAVCHETSLCPLQNCQVAGDMEAQLRNDLMNQRSAITEMLQGAGSLKDYRMNSFKMKSKYLEKWLIQRAGLHKDSYLQKAKDIAKSLMDQCQDYIQEKVISKTDYDKTYCRELLRMINERLQEADVRKCYTNAFFEVDLKLHILGEAAHEFQKMHEVFIQEHNPQKHLEKFKPQYLSRFKDLYLEKDSCQKRAWDFCEHCLKPALIDYVNKRIATEIVDDFLSSGQAIKYGCKIFFQFTVEKKLLEDGNFNNYLNYINSYEEFVQSWIHRHLLDYYNKTNGLEVLEREILSTIVNKVRGVLEHAKDIKPNSVSAFLDDFCKALEQDLVISKDSLVGILFRNTAMAHQFSADIQTFLTDLEKQILSEFKELELESKLSNLPLKPQDEMFKQVSGFAEASIP", "metadata": {"id": "A0A452ISR6", "cluster": 8221028, "interpro_all": ["IPR030383", "IPR027417", "IPR052986"], "interpro_used": ["IPR030383", "IPR027417", "IPR052986"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is classified under 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. Also, it is part of the Glycosyl hydrolase 39 family, which encompasses enzymes involved in the hydrolysis of xylo-oligosaccharides and the degradation of glycosaminoglycans. Members include beta-xylosidases that break down xylan for plant biomass utilization, and lysosomal alpha-L-iduronidases essential for metabolizing heparan sulfate and dermatan sulfate to maintain cellular function. It is present in Thermoleophilaceae bacterium.\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, 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, 2222, 16, 2176, 1977, 3131, 1927, 1920, 20067, 20748, 3886, 3416, 16, 2154, 21569, 5038, 3286, 1922, 1920, 9128, 1927, 9639, 1037, 17, 22012, 1930, 1920, 4877, 1927, 25982, 19900, 18, 4678, 3951, 4666, 17, 9639, 12224, 1036, 1988, 6017, 3292, 23665, 1958, 4496, 9397, 8422, 16, 1930, 12097, 4595, 17, 54, 17, 2313, 10366, 30413, 4415, 1958, 27044, 22024, 8767, 1930, 13467, 1928, 8767, 1942, 6698, 3689, 2347, 18, 2176, 1977, 2481, 1922, 7967, 1952, 7766, 1972, 3336, 14061, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "GWATARAGDPQGVERPDPREFGRFVRARVDFWSIWNEPNHPQFLLPLGSRGGAVGSLRATGHGPDTILFGEILPIGRRAGAAARARGCQRFRRVSGVSGLAYHPYTRPLDRVARTLDRAAALGRLDRRGLPIYNTPPDPFQTRVGRIPAFLNEAEWIQARGAERFGLFQAGLRYGDGREKRGVYEIWGAARPGGSGDLWIEQRRAGGRFLEAPATRSFRLRYSDAGKTSYSRIATPVAEGGSAGTRYDGSHSDAAGVPLPVPLAPHAYRGLVTAIGPRYTIKPLVFLRELFCLDARSRPFREGPRAAEPTQDDATIRSEFGYQSRSYRNRRVASWSQYGLLDDPLLADAYRLPIFARLRGTREVGGRVSARNGQGYFRRRLRLGQA", "metadata": {"id": "A0A7V9S0X6", "cluster": 8540104, "interpro_all": ["IPR017853", "IPR051923"], "interpro_used": ["IPR017853", "IPR051923"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein according to this functional description: The protein carries a Major facilitator superfamily domain that functions as a secondary active transporter, utilizing a twelve-transmembrane helix topology to move small solutes across membranes via uniport, symport, or antiport mechanisms. Driven by chemiosmotic ion gradients rather than ATP hydrolysis, this domain mediates the uptake or efflux of a diverse array of substrates, including sugars, drugs, metabolites, and ions. Furthermore, the protein is categorized in 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 Bacillota bacterium (Firmicutes bacterium).", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 16252, 43, 3044, 29543, 13975, 3418, 1988, 4088, 1966, 43, 4067, 3500, 9054, 16, 10232, 43, 12367, 17, 9117, 7864, 13678, 1942, 6532, 2858, 27993, 3436, 5726, 3454, 15943, 2718, 16, 29148, 2718, 16, 2014, 2246, 2272, 3531, 18, 6446, 2007, 2975, 14356, 12492, 2002, 4755, 12741, 4356, 2254, 4498, 9128, 16, 2052, 3418, 10412, 1920, 5047, 2014, 11247, 1927, 43, 6445, 6472, 1927, 6249, 16, 2710, 15592, 16, 4195, 16, 6926, 16, 1930, 6982, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 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, 8175, 22538, 3857, 14061, 12, 24474, 14061, 13, 18, 3], "output": "MPYLLLLLLSLGHGIVDVCGSSLPMLLPVLKSQYHLTYTALGQVVFIFNLSSSLIQPVFGVASDRRSCRWLMPLGCILAAAIALVGLIPNYGWIIICVLLCGIGVAAYHPEGAKQSFLISGEHQAAAQSIYTIGGNLGAGLGPIVATLLLAMSGMKGIIWLIIPNMLVAVLIMYQLPVLSQLGRERESQCRQIERKSVGSSTWSIVTILVLICTIRSIIYTCVTTFIPLYMMNDLGESRFLTGLCLSGFLLTGVLGSAIAGPLADRWGRNKILFFSFLVAIPPLLLLPYTKGILSLIMACWSGFAIIASFGITVVIAQELIPGQVGLASGLILGFASAVAALGVLMFGAIADARGVGFVLKLVSILPVIPLALTFALPKE", "metadata": {"id": "A0A353C139", "cluster": 8605267, "interpro_all": ["IPR011701", "IPR020846", "IPR036259"], "interpro_used": ["IPR020846", "IPR036259"], "interpro_unused": ["IPR011701"]}, "task_type": "autoregressive"} {"instruction": "The protein is assigned 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. Also, the protein should feature 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 Porphyromonadaceae bacterium COT-184 OH4590. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 1977, 6304, 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, 2222, 16, 1920, 2213, 3066, 5961, 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, 17376, 5134, 3947, 7324, 1972, 3336, 14061, 17150, 17, 16053, 5622, 6803, 5124, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MKKLFFTITIVLLAAVWGASLKAQEVNMDVYITITVKQKAQVKFDLMGLSTTEVKVVNGSKEEIFTINRGWTGDKKYIAETSVITIYGDVAGFDCGFNYDNLTAINVSHNTLLSYLAFQTTQVKSIDVSKNINLEYISTGNAPLTSLDVSKNIKLKKMHCHGNKFNAQAFDDLYCSLPNRTNQSEGIIQVIWGRDSENHNEVLNSNATNANNKNWRVQYCEDDKDIPTTGKYICPTSNLEKIDAVRMDIYPNPVEDILYVQSDSEVHIICIYDIYGKEVARATNSQQIDVSHLPSGLYMANINTLNGTAVRRIIKR", "metadata": {"id": "A0A0A2EY21", "cluster": 14906466, "interpro_all": ["IPR032675", "IPR026444"], "interpro_used": ["IPR032675", "IPR026444"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein has 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. In addition, it is part of the Peptidase M48 family, which functions as a putative metallopeptidase homologous to the HtpX protease (MEROPS subfamily M48B). These enzymes typically utilize a divalent cation, such as zinc, coordinated by a conserved HEXXH motif to activate a water molecule for catalysis. Furthermore, the protein is associated with the Membrane-localized HtpX protease family, which comprises ATP-independent metalloproteases involved in the quality control of integral membrane proteins. These enzymes endoproteolytically degrade misfolded or overproduced membrane proteins, such as SecY, at specific cytoplasmic sites to maintain cellular homeostasis. It has been detected in Phycisphaerales bacterium and is described by UniProt keywords Cell membrane, Hydrolase, and Metal-binding.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 2258, 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, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 24050, 21397, 1025, 3416, 16, 2154, 4088, 1966, 43, 6770, 8969, 24897, 8725, 1942, 1920, 5334, 1034, 1039, 7154, 12, 6902, 4001, 16227, 21397, 1025, 1014, 13, 18, 2144, 5038, 5745, 12561, 43, 21610, 9976, 16, 2427, 1966, 7997, 16, 11651, 2007, 43, 5305, 7142, 1039, 1023, 5219, 1942, 6980, 43, 3224, 5388, 1958, 15408, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 3260, 17, 6579, 5334, 1034, 1039, 7154, 3416, 16, 2154, 12936, 4498, 17, 3484, 28629, 2319, 3286, 1922, 1920, 3455, 2285, 1927, 12328, 3260, 2697, 18, 2144, 5038, 16239, 9218, 1021, 26656, 11560, 1012, 17069, 20303, 2014, 22922, 23323, 3260, 2697, 16, 2427, 1966, 2532, 1012, 16, 2019, 2487, 6823, 3402, 1942, 6698, 3689, 7622, 18, 2176, 2258, 2252, 3330, 1922, 25511, 9119, 29164, 3955, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 2024, 3260, 16, 20748, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MTAFVNNIKTVVLLGALTGLLVAVGGMIGREFMLPFLIMALVMNFVAWFFSDKLAIAAMRGKELDENTGGDLYRMLVRLSERAGLPRVPRLYISPHDAPNAFATGRSPSKAAVCFTQGALDLMNPSEIEGVMAHELAHIKNRDTLISTVSAVVAGVLAFIAQWGLLLGMGRGGHGNPLVMFLVIIIAAVGAAVLKSMISRAREYVADADGAKIAGSPYGLISALERLDSYSKRIPLRQPNPAQNNLFIVEPLTGDAVGRLFATHPPVADRVRKLRELG", "metadata": {"id": "A0A6N2EKH9", "cluster": 15412972, "interpro_all": ["IPR050083", "IPR022919", "IPR001915"], "interpro_used": ["IPR001915", "IPR022919", "IPR050083"], "interpro_unused": []}, "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 possesses a Hydantoinase/oxoprolinase, N-terminal domain that forms the N-terminal structural component of enzymes involved in the hydrolysis of cyclic amides, such as hydantoins and 5-oxoproline. Also, the protein should include a Hydantoinase B/oxoprolinase domain that functions as the catalytic module in enzymes such as 5-oxoprolinase, which converts 5-oxo-L-proline to L-glutamate within the gamma-glutamyl cycle for glutathione metabolism. Additionally, this domain is present in N-methylhydantoinase B, where it catalyzes the hydrolysis of hydantoin to N-carbamyl-amino acids. Also, 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. It is expressed in Acidobacteriota bacterium.", "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, 14465, 43, 2993, 26182, 11413, 19, 18588, 15743, 11413, 16, 56, 17, 4262, 3418, 1988, 4952, 1920, 56, 17, 4262, 4346, 4594, 1927, 5038, 3286, 1922, 1920, 9128, 1927, 9821, 13601, 1036, 16, 2427, 1966, 2993, 26182, 2925, 1930, 25, 17, 18588, 15743, 2053, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 2993, 26182, 11413, 44, 19, 18588, 15743, 11413, 3418, 1988, 4088, 1966, 1920, 6804, 9059, 1922, 5038, 2427, 1966, 25, 17, 18588, 15743, 11413, 16, 2154, 21420, 25, 17, 18588, 17, 54, 17, 12958, 1942, 54, 17, 7627, 2651, 1920, 7034, 17, 25345, 4048, 1958, 9153, 4714, 18, 4950, 16, 2052, 3418, 1977, 2481, 1922, 56, 17, 4963, 3963, 26182, 11413, 44, 16, 2597, 2176, 17097, 1920, 9128, 1927, 2993, 26182, 1921, 1942, 56, 17, 17742, 2199, 17, 3835, 4576, 18, 2222, 16, 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, 2176, 1977, 3198, 1922, 2687, 5883, 3940, 3857, 14061, 18, 3], "output": "MDRGWWFWIDQGGTFTDVVAMDPQGGIHLEKLPSRSLAGKDPITRAVQQLAGEAPVTGLKIGTTVGTNALLERRGERVLFLTTSGFADALLIGTQHRTDLFDLNIQRTQPLYDSVVEARERMDAQGRVIDPLDEPSLQASLTAALEKGYTVLAIGFVNAYANPSHERRAAEIAMNLGFKWVTCSTDVSRMVKWLPRSDTAVLNAYLSNKLMEFVRRTQQAIGKGRAWAMTSRGELTSLSRFLPHESLLSGPAGGVAGTAAVARRHGIRGFVSLDMGGTSTDVAAFADRFEIRLETDIDGVRVHSPTLMIHTIAAGGGSLLKTTNGRMVVGPQSAGADPGPACYGRGGPAALTDCQVVLGFLDAQHFPACFGPNADQPLNEKAARVALAELLTDLNEDYSLERLAFGYVQIAVHQMASAIRRVTLARGQDARQLVLLGFGGAAGQYATMIADEMDMDRVMVPAHASLLSAVGMSEAEISATRQRTFCTPLTQASLKSISGWCDQIEGDLDRELEIAADDSRRKEVMLGLRVDGMDDVVEVPFSAEATLRHEFERGYEQRYGLESEHRPLVIEYARLSHYARIGHLIPAIRIEGSAPNSSHRSVYYNGHTYEYRVVWTAGLASGAVIDGPALLVDTHTTVSVHPGWQAQLLSDGSIDLHRVSARKGTNTQTAIDPVLLEVYRNGFQEVAESMGVVLKQTAMSVNIKERLDFSCAIFDSVGRLIANAPHMPVHIGSMDMCVKALIERETPFSDGDCYAVNDPAMGGTHLPDITVVTAVFVAGDLAFFVASRGHHADIGGTVPGSMPSASKTLEEEGVVFSGFLIKSQGRFLSDEVREHLSSHRYPARNPSVNLSDLKAQIAANMRGRRDLLAWAERVGWASLLAYMTHIRNHAAASIRRALCGIRPSRWSLAMDNGAVISVDISRRTDGLWTIDFEGTSAQTDDNMNAPLAITRAAVLYVLRTLISEAIPLNAGCMEPVRLRVPAGSVLNPGPGAAVAAGNVETSQHIVDLLLAAFGTCAASQGTMNNFSFGDGTLQYYETICGGTGAGPGFHGADAIHSHMTNSRLTDPEILERVFPVRLLQFGIRRGSGGLGRFCGGDGAVRELMFLRPMTCSLLTTRRKTRPFGIMGGSDGLPGQNSWRPKDGTWQPLQGCDEVDVQEGDRILIKTPGGGGFGEKDGSNESD", "metadata": {"id": "A0A960PXT7", "cluster": 18024381, "interpro_all": ["IPR008040", "IPR002821", "IPR003692", "IPR045079"], "interpro_used": ["IPR008040", "IPR003692", "IPR002821"], "interpro_unused": ["IPR045079"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein contains 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. Also, the protein can be placed in the Transcriptional regulatory protein family, which regulates gene expression governing cell state transitions, sexual development, and secondary metabolite biosynthesis. These proteins maintain phenotypic stability, such as fungal white-opaque switching essential for mating and virulence, participate in calcium homeostasis, and control the production of bioactive compounds with antimicrobial and antitumor properties. It occurs in Blumeria graminis f. sp. triticale and contains UniProt keyword associations Metal-binding, Nucleus, and Transcription regulation.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 5461, 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, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 5224, 4948, 2213, 3416, 16, 2154, 7014, 2359, 2294, 20012, 2024, 3360, 10673, 16, 5702, 2740, 16, 1930, 4067, 9483, 8132, 18, 2144, 2697, 6698, 8189, 5057, 16, 2427, 1966, 8697, 4511, 17, 24646, 10880, 4415, 1958, 11786, 1930, 9304, 16, 7352, 1922, 5016, 7622, 16, 1930, 2285, 1920, 3372, 1927, 13570, 4300, 1956, 8003, 1930, 11775, 3879, 18, 2176, 5110, 1922, 2266, 29419, 2126, 8604, 15472, 48, 18, 2056, 18, 5083, 2506, 1021, 1930, 5461, 20709, 11121, 2538, 5253, 6048, 17, 2743, 16, 5607, 16, 1930, 3213, 3640, 18, 3], "output": "MAPAETKDKIGHVPGGARRIAHSKVKTGCITCRARRVKTNRGASPRNNFRTIRVRALVPKPPYPSNGGPLFQFPTVGLFQSNLEQRYFTILQACMSHPSIRCAAIAIGALGKTNEIARLCKRPVTGELILMEHHQHALEFYGKAINGMRREMKGFYQDIRVSLIICIIISCFEGIHENFHSQVKSSPILHPKGYSSPCPDVVDDFLVQSFGRIDIIAAMPKIIRSIEEARIYHDLITRRIMHFNSSIHTPRSRPVGSGDANHNPIPWVDLKISLEEIDSTISSTKLKNEKDMLSRELRSWVEASHRIAALSNEISLGAAFSITESAYDIFLPHFRLIVQHASQVLALQQEHFAGLIPSLYIVLIKCRHGPTRRQALALLRKYPHREGVWDTASSSGLGSWNYYAAQTCTFIPAAVHSMESCKDGEANHSTSTMAAPVTEQARMRFDLLERRAVLFGVQMDLNSGAYIEKTGIYEWCDEGKPKCLRCHKYGTECGGYQSDIFSTRIARQLCPYFDAERWTLDVKHVVGSGTIDTKKMINQANGNHRSAAAQLQAGLAIVQSMSVFDPRPVEVHSTLKCEGKETQKPWPTLQLLPQGINPLLLQARMKMKSQDTIPAHILRFHCHSGAPGPVDIHFSFEIVMELEEEGARTSDPDSLSIPEVVRVR", "metadata": {"id": "A0A9W4GHN4", "cluster": 18063099, "interpro_all": ["IPR052360", "IPR001138"], "interpro_used": ["IPR001138", "IPR052360"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The 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 present in Gammaproteobacteria bacterium.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 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, 2481, 1922, 7034, 9218, 1021, 10296, 14061, 18, 3], "output": "MTTIRGKLKVGTEVEANRSCSPGISIVIPCHNDGEYLTRSAKSVLEQEDANTQSILQEISLLDDRVRILHRKTAGGVASARNYGDADDEWLPTALQDRWALVARYPDAEWIGADHVLFWDNQPVVLKRPVVEFLETMPAWTGTVFVKKSVFELVGGFDSHFKQAEDNRYRQRNGSLTSTSDSSYFWDYKMLLDLKKQAQFSDYKSNIRSLIACCVAPLRPKSYRLFLSTFLAGMTKMFHGTEANGLPGFELLIIDDGSVENAVGTWVAFLGEMEDEGFLASRERPRQCLKEAFEKGHLWLRLAAYTDYIFLPKVIAQRILSDLKNDVWFQRGIKKWSKALRS", "metadata": {"id": "A0A7C3HDH6", "cluster": 18267879, "interpro_all": ["IPR001173", "IPR050834", "IPR029044"], "interpro_used": ["IPR001173"], "interpro_unused": ["IPR050834", "IPR029044"]}, "task_type": "infilling"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein is associated with 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 belongs to 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 has been detected in Euzebyaceae bacterium and exhibits UniProt keyword tags Transmembrane helix.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 1977, 2458, 1956, 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, 14440, 1942, 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, 2258, 2252, 3330, 1922, 4791, 6931, 4864, 9914, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 7864, 18, 3], "output": "MWASAAATNAADGVRLAALPLLATALTRDPRLIAGLTVAGTLPWARAVVLGVVTLAVAGGHVTLPLLYLAAFLLGAGEVVFDNVAQTLVPSLVGIAGPGLGGLLYAAAAAAPFALGTACYAGAAALVLRLDGTFRPARGAGPGISATAEMVLAWIAGAVMLLNSAATAVLVLFAKQDLGLGDAGYGALLSATMGGFLLGGAVAVIAVAATSQFAVGLTSRPVATAAALACGTAAFGTASILLVGVRQTLVPDRPIGAALGGVLASAHGVRAPFLLGGAAMLVVAAAAARLPRGALLLSIPAGVLVDRVDRRSALLFTAAAGALDRANARLHVSEVAGNDEGVRWLRHQPVLRRAPRLRRHLPLNRALALLGRVNGLYRFCGLGAV", "metadata": {"id": "A0A838HQB3", "cluster": 18767354, "interpro_all": ["IPR036259", "IPR010290"], "interpro_used": ["IPR036259", "IPR010290"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein should include a Na-Ca exchanger/integrin-beta4 domain that comprises a self-contained beta-sheet motif, known as Calx-beta, utilized for calcium binding, signal transduction, or extracellular matrix organization. It is found in the cytoplasmic regions of sodium-calcium exchangers and integrin-beta4, as well as in Fras1/Frem proteins required for proper organogenesis. In addition, the protein possesses a Lamin tail domain that adopts a globular immunoglobulin-like fold and functions as a structural module at the C-terminus of nuclear lamins and invertebrate intermediate filaments. It facilitates interactions with DNA and chromatin-binding proteins within the nuclear lamina, while prokaryotic homologs likely assist in tethering proteins to membrane structures. Furthermore, the protein has 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 identified in Crocinitomicaceae bacterium and exhibits UniProt keyword tags Repeat.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 3066, 3951, 43, 4049, 17, 2332, 27419, 19, 8920, 17, 4666, 1006, 3418, 1988, 12936, 43, 3543, 17, 5543, 4666, 17, 11130, 5219, 16, 3171, 1966, 2570, 1039, 17, 4666, 16, 7079, 1958, 5016, 2743, 16, 2733, 8201, 16, 2014, 5329, 4526, 5901, 18, 2176, 1977, 2435, 1922, 1920, 6823, 3451, 1927, 5227, 17, 5016, 27419, 1036, 1930, 8920, 17, 4666, 1006, 16, 1966, 2486, 1966, 1922, 23228, 12030, 19, 2805, 1035, 2697, 3414, 1958, 3405, 3090, 3761, 18, 1922, 2459, 16, 1920, 2213, 14465, 43, 7962, 5281, 3418, 1988, 24032, 43, 20975, 11837, 17, 3189, 3728, 1930, 4088, 1966, 43, 4346, 9059, 2019, 1920, 45, 17, 7822, 1927, 4254, 7962, 1036, 1930, 26381, 6129, 11855, 18, 2176, 11374, 3719, 1956, 2678, 1930, 6338, 17, 2743, 2697, 2651, 1920, 4254, 14310, 16, 2679, 21545, 14279, 3205, 6589, 1922, 23991, 2697, 1942, 3260, 4061, 18, 3677, 16, 1920, 2213, 2258, 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, 2899, 1922, 9442, 3665, 8752, 4913, 9914, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 6865, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MKKSILLIFGGVISFSTSIFSQAIDLSDYKLQLFSSNSSTVSQEVQLPAIIAQADLQSSSVINYNGDDAIALAYDPTGNDPGTNWPVGSGGTAGSTVNNTLIRSATEWEAQGNDNFSFLGSHTMTSITITVNIAGENANPTSADIVLLGSGTVTFPASSATAQTINIPIIDNMLLDGDLTFVLELQNLTNTISQIDDLDGAGVAVSDGVECQLSGYVYGVNMRATGSNLGYTVTEGDSVDVTGVIDQFNGYLQIVTALDESTESELVQINDVTIINLADWNPAGAGFEVDLFSMMAPDGTFDLVGIGSQFDNSTPFDAGYQLDQTICPGDSLTVDYSNVTYLWNGTNATTQTVVADTAGTYAVATDLPDAGFTASAVSVCDNVDITITDTSINANSISIDFPNTYTVSLAATSSFGCVDSATVLAQFTTNVQGAYDLKIMDLTGQVIKTIKYFIRLSSQKESQTIKFVKRCTDLFISEYIEGSSFNKAVEIYNPTSSSGTLNPGAVFVACHASADSSATVIDAIGSMDGSINQGQTNWVVGAPCTPPSNPEVQFSVATANVNENAGTAVEGTDFTYASTASATTGTNSQITVTIVDDEIPYYVQFTIHDGTGGIGVINFSVVTEINMHSQGHTLPVPTVNADVTDGVNTYTMRIDALPRYNNDIHIKPMIIGGVTYGTVTAMATSVVTITGDGNSTTTSPAMHQYTTQITVNDCASIDENEAIEMKLFPNPSNGTSNQVVQLDLTEQPAGI", "metadata": {"id": "A0A958ZFM7", "cluster": 19042891, "interpro_all": ["IPR038081", "IPR003644", "IPR013783", "IPR001322", "IPR012340", "IPR022409", "IPR000601", "IPR035986", "IPR026444"], "interpro_used": ["IPR003644", "IPR001322", "IPR000601"], "interpro_unused": ["IPR013783", "IPR026444", "IPR012340", "IPR035986", "IPR022409", "IPR038081"]}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\nThe protein is included in 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. Additionally, the protein contains a Membrane attack complex component/perforin (MACPF) domain that mediates transmembrane pore formation and cell lysis through oligomerization and conformational change. Found in contexts ranging from vertebrate immunity to pathogen invasion, this domain assembles into ring-like complexes to breach lipid bilayers, a process structurally supported by a central kinked four-stranded antiparallel beta-sheet. In addition, the protein incorporates a Polymorphic outer membrane protein repeat that constitutes the N-terminal domain of *Chlamydia* polymorphic membrane proteins, typically adopting a $\\beta$-helical structure. It is expressed in Tieghemostelium lacteum (Slime mold) (Dictyostelium lacteum) and is connected to UniProt keyword Signal, Secreted, and Cytolysis.\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, 3063, 1922, 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, 4950, 16, 1920, 2213, 5461, 43, 3260, 8926, 2796, 4594, 19, 28039, 12, 3433, 1034, 1038, 13, 3418, 1988, 10412, 9117, 8554, 3337, 1930, 2024, 8502, 2596, 17371, 1930, 8523, 3185, 18, 2435, 1922, 11144, 6485, 2037, 13416, 7611, 1942, 7055, 6254, 16, 2052, 3418, 17421, 1036, 2460, 6335, 17, 3189, 5048, 1942, 3022, 2155, 4486, 21992, 16, 43, 2585, 12171, 4427, 2007, 43, 4101, 30322, 1919, 3006, 17, 10338, 28892, 4666, 17, 11130, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 14240, 7642, 3260, 2213, 6865, 1988, 14879, 1920, 56, 17, 4262, 3418, 1927, 14, 21079, 14, 14240, 3260, 2697, 16, 5745, 20478, 43, 8, 38, 4666, 8, 17, 11514, 3170, 18, 2176, 1977, 3198, 1922, 19108, 2509, 1987, 18092, 12191, 1989, 5641, 3708, 1035, 12, 2788, 11593, 20459, 13, 12, 29060, 18092, 12191, 1989, 5641, 3708, 1035, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 16, 8366, 16, 1930, 22953, 27004, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MIFYYAALKGNIYSVEAASPCISNCIGNDGFQTFQAALTYLRNNQITSAILLVEVQIKSRTGINTVIDCQGIGNAFNVVNNSMFSVSGITFQNCNSNYGGAIKIQSSNVQISSCTFTSNTALERGGAIYSVDSKFKILSSTLSCNRRLLSGTSTYTRSDIYGTFCGDNTIIFTSLDSNSLCQSTPTQCSGMVVKQPNTTSVCGNNICEIEYKCLYSNVGCQVYSSSPLVGNSISDLMKGIDGPVSAILTGYFRVVKPEVYKFKFLFENIGAQVKINQYIVDGFTNYFQLSLKSFTKSNKGARSVSFFIQGPDDLEFQPFDWVFYSLNNCGDGVYDAAELTCLDDRSNGIDDPNSCIQDCYTYLTPYCSPVSVRDGSITPGSALERDTLGVLINNQMVWHLPGISHFMFGYCKDKENRIIEDVYRANFYQLPSEVEAVPLPICTFDVQTSEFADASEYQSSMSSSIKHEAGGSIGGGIGAIHAEASAIENQVQCSTSNVRLREFPFHPSFVKAISKLNTDTDFINFFGQYGTHFYREGTLGGKLKQVSVSVSAPVFTASASFSQNQGNSFSTESLNKFSKSSSRSSVITYGGAAGSYGPSRNGPSTFGSWAQIIPKAWKTPDGNSTFERWVQAEVLFYQGTLLSQSDLNRSNMIGRWFSKTFISEVNSIAYSSLKLLKYQCPFYRDVYHYYDGPNNTVLNYTTPEYKCSFDNALKFQFKQSTKRENIAWKIIVGLSKSTYFFYTLSNSTNTLVKMDSISFVILPPIRFETEISITLGAFDGDLFTIWPYPDTLRDISPVISITANSITQIHDMPFSVTILSRCAVRGFDSFFNFLTGPILDIPQNFQFTSINSNNYQSQLFALQTDSTFNLDVEITLPTAKIQAFSLFNAGNYIGINNKLLNFISSFLNNIGSIGGAIHSYNSQVQIKSSTKSTIELDSSTSTTNSPSFSSETCLNCPSDCKSCYFNGLKLVRTHIESQFFSTSESTFSTVQMIQSGNSSCGDGICQEIGVNVIDMSPANLPIFNFAYSSEKSTNSAKELNQERTGSLTKMDSSMSSEFSSDEVSDMSSYSFTIDLLPVPINFTLQAIRDFEKNDLYQSESIFVNNANGASTQGNDYLHMIGSIFMFQDTVTIDSSKVGRTSNYQCEINDGKYLITTLKPSFIDPT", "metadata": {"id": "A0A151ZBZ6", "cluster": 22907843, "interpro_all": ["IPR020864", "IPR011050", "IPR003368"], "interpro_used": ["IPR011050", "IPR020864", "IPR003368"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein should feature 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 includes a Oligopeptide transport permease C-like, N-terminal domain that constitutes the first transmembrane region of the OppC component within bacterial oligopeptide permease (Opp) systems. It functions as part of the integral membrane channel in this ABC transporter complex, facilitating the translocation of peptides across the membrane. Additionally, the protein belongs to 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. It is produced by Candidatus Bathyarchaeota archaeon and features UniProt keywords Cell membrane and Transmembrane helix.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 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, 5921, 43, 15039, 9626, 2410, 2261, 4860, 6191, 2051, 45, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 2561, 9117, 3031, 1927, 1920, 2494, 7693, 4594, 2651, 4543, 15039, 9626, 2410, 2261, 6191, 2051, 12, 2494, 1034, 13, 3771, 18, 2176, 4088, 1966, 3131, 1927, 1920, 12328, 3260, 4999, 1922, 2052, 7219, 9054, 2796, 16, 12440, 1920, 7849, 1927, 5320, 3436, 1920, 3260, 18, 4950, 16, 1920, 2213, 14440, 1942, 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, 2176, 1977, 4152, 2007, 14550, 1031, 1957, 10481, 9771, 15618, 20051, 7336, 13470, 1916, 1930, 4075, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 3], "output": "MNMANVKYTLKRLSINIRNIKENSYILAGLCLLISIVLFAFIGILITPYDPVKIGSVPSDLPPSFNHLLGTDSLGRDLFTQLCFGTLTSLQIGFLAGIIGFFIALIVAFVGGYYGGTLDSILTILTEVFLTTPTLVILIIIASVVERVEIPIMATIIAAFAWAWPSKTIRAQVLSLKERGFIYLSKLSGLSGLEIIFKHMIPNILPFLGSYFAVVVSAAMLSEVGLEVLGLGPRHTITLGMMLHWAMMHAAVTRNLIWWWLPPCIMLFLIFLSLFLIQRGLDIIANPRLKGE", "metadata": {"id": "A0A7C4DUY5", "cluster": 26164959, "interpro_all": ["IPR000515", "IPR035906", "IPR025966"], "interpro_used": ["IPR000515", "IPR025966", "IPR035906"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein includes a TonB-dependent receptor-like, beta-barrel domain that forms a bacterial outer membrane channel enclosing a gating plug domain. It facilitates the high-affinity active transport of scarce substrates, such as iron-siderophores and vitamin B12, by interacting with the TonB complex to transduce energy for pore opening. Furthermore, the protein should include a TonB-dependent receptor, plug domain that acts as an independently folding channel gate within bacterial outer membrane receptors, blocking the pore until ligand binding induces conformational changes to open the pathway. It facilitates the high-affinity, energy-dependent uptake of specific substrates into the periplasmic space by coupling with the TonB-ExbBD complex. It occurs in Desulfobacca acetoxidans (strain ATCC 700848 / DSM 11109 / ASRB2) and corresponds to UniProt keyword TonB box, Signal, and Cell outer membrane.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 5921, 43, 16501, 1014, 17, 3100, 3148, 17, 3189, 16, 4666, 17, 19560, 3418, 1988, 4952, 43, 4543, 7642, 3260, 4999, 17439, 11934, 43, 12568, 15998, 3418, 18, 2176, 11374, 1920, 2149, 17, 5173, 3500, 4860, 1927, 16937, 6249, 16, 2427, 1966, 5680, 17, 22940, 14820, 1930, 6111, 17492, 16, 2007, 8615, 1956, 1920, 16501, 1014, 2796, 1942, 30334, 3844, 1958, 8554, 9497, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 16501, 1014, 17, 3100, 3148, 16, 15998, 3418, 1988, 8016, 1966, 1925, 6407, 10328, 4999, 11898, 2651, 4543, 7642, 3260, 4086, 16, 7472, 1920, 8554, 4801, 5207, 2743, 6387, 8523, 2840, 1942, 4437, 1920, 3374, 18, 2176, 11374, 1920, 2149, 17, 5173, 16, 3844, 17, 3100, 5047, 1927, 2487, 6249, 2460, 1920, 24334, 5230, 2007, 7590, 1956, 1920, 16501, 1014, 17, 1975, 6936, 1007, 2796, 18, 2176, 5110, 1922, 30311, 14357, 3375, 4118, 4811, 2075, 12, 3943, 11037, 11851, 11068, 1025, 19, 10964, 10118, 13192, 19, 1966, 16007, 1028, 13, 1930, 8852, 1942, 20709, 11121, 2538, 16501, 1014, 5758, 16, 2733, 16, 1930, 2024, 7642, 3260, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MKRILFLLICLVLHPGIGLAQETASSEGVNPEETTNVAALGQSTSTSEDVSVSSTVITAPEIEKRQVTRVEEMLRSVPGVVVNQTGSQGGNTSLFMRGGNTVDNVERIEVVRGPMSSLYGADAMTGVTNLITKKGVGPPTFTYSGAWGAHSEKGQSIGFSRIDDQGILPINNRFGSNVLNGRFDLDPTEKLSFTFSTLFIDRTDLLFGLTTKYSPYSWWENELTLSTYHRDWSYDDAFDPVDIFGGSVFHPIEDRSSLDYRSNLKQSYESFGVWPYSSETRAHRRSVDFYFQEQISFWERLAFRITETDTTLRAAGGRAIKAPTFSEQYYQSTTAVGVDQYALNDRLKFGLTYFENHFTDLIAYITRAWPATSFYGNISDARVRGLETSLTAKPLPYLTVLSTGGEDLGLNYEVGKPLVRRPKHTVSFTINYDHKPFNVNLNGLYVGKRDDFYYITYLLFNLAATYDIAENLRYAKKMQLQARIGNLFDQNYQETYNYSSPGFNFVTGLRFVFQKVDEIIITATGTEEQLKKTSNMSQVLLNGIRLNNAGGTYDWANLFISENRFSLMGSAKDRFGYTYFGYPTEYGDRVDPAPDPNQNQTRFNFSDRIGTTTTIGLAAFTERLFLTAGMRLEDNTAFDGTEFSPRASAGNPNLKPEKNTSWEVLSASYTYLLSQDPFFVTHTGRVFNPS", "metadata": {"id": "F2NG62", "cluster": 26688370, "interpro_all": ["IPR012910", "IPR037066", "IPR039426", "IPR000531", "IPR036942"], "interpro_used": ["IPR000531", "IPR012910"], "interpro_unused": ["IPR037066", "IPR036942", "IPR039426"]}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein belongs to the Nonsense-mediated mRNA decay protein 3 family, which comprises Upf3 and its homologues that function in the nonsense-mediated mRNA decay (NMD) pathway. These proteins act as components of the exon-junction complex (EJC) to promote NMD and regulate translation efficiency. Also, the protein has a UPF3 domain that functions as an essential component of the nonsense-mediated mRNA decay (NMD) pathway in eukaryotes by forming a complex with UPF2. It utilizes a modified ribonucleoprotein (RNP) domain to mediate this protein-protein interaction rather than bind RNA, aiding in the detection and degradation of transcripts containing premature termination codons. Also, the protein is classified under the RNA-binding domain superfamily, which utilizes a conserved \u03b2-\u03b1-\u03b2-\u03b2-\u03b1-\u03b2 fold known as the RNA recognition motif (RRM) to bind single-stranded RNA. These domains facilitate diverse post-transcriptional processes, including pre-mRNA splicing, mRNA stability, and translation regulation, by utilizing aromatic side chains to stack with RNA bases for specific recognition. It has been detected in Lepeophtheirus salmonis (Salmon louse) (Caligus salmonis).\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 14440, 1942, 1920, 19605, 17, 3434, 3616, 9310, 2213, 23, 3416, 16, 2154, 12936, 2353, 10892, 1930, 2496, 18541, 1988, 2347, 1922, 1920, 19605, 17, 3434, 3616, 9310, 12, 12557, 13, 3374, 18, 2144, 2697, 4033, 1966, 4178, 1927, 1920, 7049, 17, 6910, 2796, 12, 16004, 1030, 13, 1942, 5527, 12557, 1930, 5741, 6410, 5034, 18, 2222, 16, 1920, 2213, 2258, 43, 2353, 10892, 3418, 1988, 4088, 1966, 1925, 4415, 4594, 1927, 1920, 19605, 17, 3434, 3616, 9310, 12, 12557, 13, 3374, 1922, 15021, 2007, 7402, 43, 2796, 1956, 2353, 6680, 18, 2176, 18127, 43, 4795, 18347, 6657, 12, 24767, 13, 3418, 1942, 8265, 2052, 2213, 17, 2213, 2835, 4356, 2254, 4566, 3146, 16, 8379, 1941, 1922, 1920, 3805, 1930, 4877, 1927, 6247, 3165, 9839, 12462, 14500, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 3146, 17, 2743, 3418, 13975, 16, 2154, 18127, 43, 5305, 161, 17, 160, 17, 161, 17, 161, 17, 160, 17, 161, 3728, 3171, 1966, 1920, 3146, 5708, 5219, 12, 5162, 1035, 13, 1942, 4566, 2957, 17, 10338, 3146, 18, 2144, 4682, 6628, 6445, 2753, 17, 5224, 4028, 16, 2710, 2097, 17, 3616, 8490, 16, 3616, 5057, 16, 1930, 6410, 3640, 16, 2007, 10232, 10761, 4159, 7835, 1942, 10496, 1956, 3146, 11137, 1958, 2487, 5708, 18, 2176, 2258, 2252, 3330, 1922, 8530, 1021, 2688, 20536, 5811, 9590, 1937, 12, 9590, 3004, 2517, 13, 12, 2570, 7694, 1036, 9590, 1937, 13, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MWRTDQEPDPLKKNHFQQKSYVDDCLQRWTKPTFLDLVSPLKQEDVFNFTERFDGYVFLDKQGNEYPAIVEFAPYQKVSKVKTDQRPDAKCNTLDTENREKIKETSTPLLEFLALKKINKKGKFREKKSRRQRMGDAGHKHEKKKRNDDERRSRRNREDKKHASDSKDDSSRKNYTEDSGHGERTRRHNRDENKESDRRKEEVVSSKRYSDRRHDDRGRWGERSRNKYKDNDAGYSSKDNENDSGGNTKSKNSKRSNTERIKNKERPAIQIYREPQDSGNKSSKSFKKYSHKQYYAGGGARFSSSYREKREQPEYNYFRFEKPNNEDGNISFCRAYFNFLDKEYLAFVEAYENKENENIAHPTPEQYLEEIGWRGKNDSKESNEPGEEPVKNGSESKEEPSRKKNTDDQPITVLQKDDFPAINSGPGMGKFSSQTIKSDSAKEDEGGKCD", "metadata": {"id": "A0A7R8CSM4", "cluster": 27105042, "interpro_all": ["IPR012677", "IPR035979", "IPR039722", "IPR005120"], "interpro_used": ["IPR039722", "IPR005120", "IPR035979"], "interpro_unused": ["IPR012677"]}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that can perform the following function: The protein includes 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 is categorized in the The RTX toxin determinant A family, which comprises the structural component of cytolytic Type I secretion system exotoxins in Gram-negative bacteria. These pore-forming virulence factors contain hydrophobic transmembrane helices and calcium-binding glycine-rich repeats, functioning as either broad-spectrum hemolysins or specific leukotoxins. Full biological activity requires calcium binding and post-translational acylation of internal lysine residues. Furthermore, the protein carries 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 originates from Neogemmobacter tilapiae. 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, 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, 1977, 10234, 1922, 1920, 1920, 29839, 9165, 12483, 43, 3416, 16, 2154, 12936, 1920, 4346, 4594, 1927, 29198, 2601, 51, 5512, 2433, 18930, 4575, 10960, 1036, 1922, 8604, 17, 3136, 4802, 18, 2144, 8554, 17, 7402, 9304, 2790, 5531, 7919, 9117, 12789, 1930, 5016, 17, 2743, 10646, 17, 5536, 9569, 16, 7295, 1966, 3108, 4949, 17, 5648, 3243, 23872, 1036, 2014, 2487, 5104, 20223, 18, 4125, 3933, 2455, 5474, 5016, 2743, 1930, 2753, 17, 8414, 11337, 1943, 1927, 4495, 9082, 4248, 18, 3677, 16, 1920, 2213, 16252, 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, 22970, 2037, 11724, 2106, 7445, 5883, 10935, 2026, 7955, 18, 7031, 1920, 3835, 2687, 4659, 18, 3], "output": "MEIEMAYIEGSISNDSLVGTNDADTFYGYLGDDTIQGLDGADYVIAGSGADSVLGGAGNDYVNGDEGNDTLYGEDGDDSLYGGADHDLIDGGAGNDEIYSSDGNDTLTGGDGVDTLSSGAGDDLQYGGEGDDKVFSAEGADSLYGGNGHDELRSGNDNDLIDGGSGNDLIYGELGDDTISAGDGNDNVVADNVNTTGGNDSIDGGAGNDTLRGMYGDDTILGGEGDDVLEGDYPVSSELDGRDLIYGGDGQDTLKGFSANDTLYGGDDNDSLEGDEGNDSLFGDDGDDALYGGDGWDTLYGGAGNDSLYGGAGINILNGGDGDDLLQVGSDISQLTGEAGNDTLIGGSGDDILSGGADNDSLNGQSGNDLITAGEGDDSVHAGFGDDSLYGGNGNDELDGQGGNDSMTGDGGADDLFGGAGQDTMSGGDGADSLHGGDGHDLMSGDQGDDTLFGASGNDTLNSGGGVDYMDGGDGDDSLLGEGGPATLVGGSGDDTVQGGGFNDFVSGNDGSDLLFGGNGDDGVYGGTGQDSLSGDNGFDTLDGHDGDDTLYGGAGNDLIYGGNDHDSLYGGEGADSLRGDDGNDALDGGDGNDTLEGGDGADTLVGQAGADTLDSGNDADLLYGGTDNDTLNAGDGDDSLFGGDGDDRLDGGSGNDQMDGGNGADSYVVDSADDAVSDSGTDGARDTIETAISINLADHVGVEDVRLLGSGNVSAVGDEQSNQLYGNLGNHTLDGGAGDDLLLGGAGRATLLGGDGKDVIEGQGLADRLDGGNSNDSLTAGAGDDVLLGGAGRDTLKGGADDDRLTGGLGADLQSGGAGEDVFLFASSAEAKGDHITDFKHGTDTINLRAFMKGGEFIGASAFSKDQDQVRYVKATGLLQGDVNGDGKVDWTITIDNNVKLTADDFLF", "metadata": {"id": "A0A918TG98", "cluster": 27595465, "interpro_all": ["IPR018511", "IPR001343", "IPR050557", "IPR003995", "IPR011049"], "interpro_used": ["IPR018511", "IPR003995", "IPR001343"], "interpro_unused": ["IPR011049", "IPR050557"]}, "task_type": "autoregressive"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein should include a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. Moreover, the protein can be placed in the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. Additionally, the protein incorporates 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 occurs in Candidatus Scybalocola faecigallinarum and is associated with UniProt keywords Glycogen biosynthesis and Glycosyltransferase. 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, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 4950, 16, 1920, 2213, 19683, 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, 5110, 1922, 14550, 1031, 1957, 2160, 16924, 20807, 4879, 5148, 5685, 1940, 1950, 2214, 4058, 24277, 1930, 1977, 2458, 1956, 20709, 11569, 13302, 8132, 1930, 20067, 9961, 18, 7031, 1920, 3244, 18, 3], "output": "MKNILFVSSEAVPFIKTGGLADVAGSLPKAFNKDEFDVRVIIPKYRIIPDHFKQQMQYCTHFYMDLGWQNQYVGILEMQLDGVTFYFVDNEHYFSGDQAYESGLWDLEKFAFFSKAALSCLPAIGFHPDIIHCHDWQTGLVPVYLKNVFNNNDFYWNIKTIMTIHNLKFQGTWDPKTIMGMTGLPAYLFTPDKLEAYKDANYLKGGIVYADYVTTVSDTYAGEIQMPFYGERLDGLMRARNNCLMGIVNGIDYDEWNPETDPMIPYHYNAITFRKEKYKNKCAFQEELGLEVNADKFMIGLVSRLTDQKGLDLVDYVMDQICADDVQFVVLGTGEAKYENMFRYFAWKYPGRVSANIFYSNERSHKIYAACDAFLMPSLFEPCGLSQLMSLRYGTVPIVRETGGLKDTVEPYNEYESTGTGFSFANYNAHEMLNTINYAKHVFYNNKREWHKIIDRGMAKDFSWGSSARRYEDLYRML", "metadata": {"id": "A0A9D1F4T1", "cluster": 12085279, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR013534", "IPR011835", "IPR001296"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein is classified under 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. It is produced by Paraphaeosphaeria minitans and is connected to UniProt keyword Coiled coil.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 1977, 5947, 2441, 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, 2176, 1977, 4152, 2007, 22224, 20051, 2609, 29164, 2126, 9696, 3285, 1036, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 17524, 9121, 18, 3], "output": "MSGPVKLAGTEDGFCDKEECLDNVMKIFHLQKHGEELGARVDDLLEKNTELEKQIESITRYDGKLASAEQRHEECQSILEAEKRSRAEEQADLKVKIENLATTEQRHEECQSMLEAEKRSRAEEKADFKVKRSIAGETKSSELACVQPMFEEPEEKQAAVSPLSPCLENLLDDEMRQQRSLKEELWSVGISETEFGDQASPTAQGFQSPHRTNTDTAGESTASEHPDIRATDQAVVMLEHDFAKAQQPITQAGARMISSDVELCSRDEGYRQPSSTPTISNSQREEPGVIAGTLASFGSHSRVSPRVTLKLDDQMVCCPTSSTERYPTTPESHHSGRRVLAPPAERISIGDRRHREDVAQEHKSDRHFQAYSSTHVKLNALRSYAGGRRISLKDESRTGAPSVEAIIYESHCSELSKTRMGYCVLLKNFAVRFDVQGRPCLKSRGSSAWCVWDQSGGQHGADYMLSTPYISYTEDYLRSMESDLPISSIFPNATEATSASPGHETRLFDLERHTPSQAYCFFIHIMVSAHPIQADEPFFSSLPRWIGSPERSPMPSVSWTGYAATRDEPCPDWIHDHGSLGANEHAWFGGSVDGGSSERTSIQSVGAQMVSLVSADLLVRNEEIDGPRRKVKVANKKVVSRQDKGRVSKSNQMLTGNVEQDGCGNTKSRLTSGDKLQSKKLPRYQVSTSNKHILIIHLTYGSRCFPEPLRASSRAFNGASHDLHEHAHCNYLGGSLPWRDTNGLRRTYREAFVLALECYQPPEQANLLSVSAPVSTRSSLGSKQLSPVYVCALPAAVLHPAANDIAGLGQWHRKLHTHMGAFYPSVWRLQHDFFNKDKNIEELKKYIENLKEINEQLLRSLAGRRESNDLAPLCDEIIAQNDMASLATPSTADDGRVRGEDKNANHPFAENTSKRRRKRAKGRNSRSIPRQISVDIMAIVTADIHQGEDEIPVHEHQIPICKAELEVVQRLLKWWESEQTHQGVSLHSAQDITLPALCAPPDALDPIFASQGEFSECSLRAEGKITPLSKEIAPPLRVRGSLALAGELVYINAYTCIRQHCAAKENENIARQAGIARGLYSIATIATT", "metadata": {"id": "A0A9P6G3Q5", "cluster": 1911266, "interpro_all": ["IPR012340"], "interpro_used": ["IPR012340"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein incorporates a Outer membrane protein, beta-barrel domain that adopts a membrane-bound beta-barrel fold structure found in a diverse range of outer membrane proteins. Additionally, the protein falls within the Outer Membrane Porin-like family, which comprises major bacterial outer membrane components associated with peptidoglycans that function as porins to allow the passive diffusion of small molecules. These proteins form channels across the outer membrane and share a conserved domain, with some variants displaying a C-terminal deletion that may influence structural properties. Furthermore, the protein is associated with 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 is identified in Hyphomicrobiales bacterium and is described by UniProt keywords Cell outer membrane and Signal.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 19683, 43, 7642, 3260, 2213, 16, 4666, 17, 19560, 3418, 1988, 24032, 43, 3260, 17, 4124, 4666, 17, 19560, 3728, 3170, 2435, 1922, 43, 6445, 3109, 1927, 7642, 3260, 2697, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 7642, 3260, 4572, 1921, 17, 3189, 3416, 16, 2154, 12936, 3044, 4543, 7642, 3260, 4178, 2458, 1956, 24183, 1036, 1988, 2347, 1966, 4572, 2925, 1942, 3235, 1920, 9832, 6601, 1927, 2858, 4206, 18, 2144, 2697, 2386, 5628, 3436, 1920, 7642, 3260, 1930, 7948, 43, 5305, 3418, 16, 1956, 2673, 4936, 13867, 43, 45, 17, 4262, 5541, 1988, 2278, 4039, 4346, 3879, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 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, 1977, 2899, 1922, 2483, 25808, 1935, 7839, 1918, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 2024, 7642, 3260, 1930, 2733, 18, 3], "output": "MKPRLSAVFVLLGLATSVAARAADLPAPAVAPAPAVYDWTGFYLGVNAGYGWNTGDGPLTCVGPTGVSFATGCGLIPFAGLKPAGPLGGGQAGYNWQAGQYLVGLESDFQWSDIQGSTRTNGPWPHVNTLAISPATSFFTASHKIDWFGTTRLRIGYAGFDRTLIYATGGLIYARVDEQTAVVHQETGISYPVSESVNRAGWTAGAGIEYAMTRNVTAKLEGLYYDLGEDTISSHSVPLVNGFTRGMTFETRGAIVRAGLNYKFDWGGPVVARY", "metadata": {"id": "A0A950JCJ0", "cluster": 2974375, "interpro_all": ["IPR051692", "IPR011250", "IPR027385"], "interpro_used": ["IPR027385", "IPR051692", "IPR011250"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nIt is part of the The Chemotaxis phosphatase, CheZ family, which functions as a bacterial phosphatase that dephosphorylates CheY to maintain a continuous chemotactic response to environmental changes. These proteins form a dimer characterized by a long four-helix bundle and utilize a conserved glutamine residue to orient a water molecule for nucleophilic attack at the CheY active site. It is found in Thermomonas haemolytica and is classified with UniProt keywords Protein phosphatase, Cytoplasm, and Flagellar rotation.\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, 1920, 16884, 8167, 16, 10003, 1011, 3416, 16, 2154, 4088, 1966, 43, 4543, 8167, 1988, 13517, 9075, 1036, 10003, 1012, 1942, 6698, 43, 4798, 20513, 2644, 1942, 4813, 2840, 18, 2144, 2697, 2386, 43, 7632, 4378, 2007, 43, 2815, 3006, 17, 7864, 14142, 1930, 12561, 43, 5305, 9959, 6181, 1942, 5567, 43, 3224, 5388, 1958, 24456, 8926, 2019, 1920, 10003, 1012, 3500, 3200, 18, 2176, 1977, 2435, 1922, 7967, 3947, 1934, 7105, 26656, 1930, 1977, 5947, 1956, 20709, 11569, 2213, 8167, 16, 5239, 16, 1930, 24154, 8891, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MSMPARPPAIPADQADVIGRLHAAMSALEAGDAEARELDELERTIDARMPAAAQANASGSLPDACSRLEHVVKMTEPEHAATVEAIRTRLSAMVEAQSFQDLTGQIIQRVIHLIREQGHGPAVAGVDAPAATQDEANDLLAALGIWRHHLDSLLEWRRQPVVESLVKLAEASMRTLDLADECRGLLATFGSLQTGLGDIQAMHTSD", "metadata": {"id": "A0A4R3N4S5", "cluster": 5003015, "interpro_all": ["IPR007439"], "interpro_used": ["IPR007439"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein should include a Sugar transporter conserved site that identifies a superfamily of integral membrane proteins responsible for the binding and transport of carbohydrates, organic alcohols, and acids. These transporters typically comprise twelve transmembrane domains and are evolutionarily conserved across prokaryotic and eukaryotic organisms. Moreover, the protein contains a Major facilitator superfamily domain that functions as a secondary active transporter, utilizing a twelve-transmembrane helix topology to move small solutes across membranes via uniport, symport, or antiport mechanisms. Driven by chemiosmotic ion gradients rather than ATP hydrolysis, this domain mediates the uptake or efflux of a diverse array of substrates, including sugars, drugs, metabolites, and ions. Also, the protein is classified under the Major Facilitator Superfamily Sugar Transporter family, which mediates the transport of sugars across cellular membranes, functions through mechanisms including facilitative glucose diffusion and proton-coupled symport. Members of this family facilitate the uptake of substrates such as glucose, D-xylose, galactose, and myo-inositol, playing essential roles in metabolic distribution and cardiovascular system development. It has been characterized in Actinomycetota bacterium. 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, 9523, 9054, 5305, 3200, 1988, 14133, 43, 13975, 1927, 12328, 3260, 2697, 5061, 1958, 1920, 2743, 1930, 4860, 1927, 16282, 16, 6805, 21773, 16, 1930, 4576, 18, 2144, 10538, 5745, 13817, 12367, 9117, 4682, 1930, 2032, 18584, 5305, 3436, 21545, 1930, 10825, 7373, 18, 3950, 16, 1920, 2213, 5461, 43, 3044, 29543, 13975, 3418, 1988, 4088, 1966, 43, 4067, 3500, 9054, 16, 10232, 43, 12367, 17, 9117, 7864, 13678, 1942, 6532, 2858, 27993, 3436, 5726, 3454, 15943, 2718, 16, 29148, 2718, 16, 2014, 2246, 2272, 3531, 18, 6446, 2007, 2975, 14356, 12492, 2002, 4755, 12741, 4356, 2254, 4498, 9128, 16, 2052, 3418, 10412, 1920, 5047, 2014, 11247, 1927, 43, 6445, 6472, 1927, 6249, 16, 2710, 15592, 16, 4195, 16, 6926, 16, 1930, 6982, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 3044, 29543, 13975, 9523, 9054, 3416, 16, 2154, 10412, 1920, 4860, 1927, 15592, 3436, 3689, 5726, 16, 4088, 2596, 3531, 2710, 4753, 2178, 3817, 6601, 1930, 8433, 17, 6416, 29148, 2718, 18, 4678, 1927, 2052, 3416, 6628, 1920, 5047, 1927, 6249, 2427, 1966, 3817, 16, 46, 17, 21055, 16, 15996, 16, 1930, 15924, 17, 16246, 16, 14797, 4415, 5456, 1922, 4487, 3282, 1930, 5321, 2433, 2740, 18, 2176, 2258, 2252, 4378, 1922, 4718, 13386, 19446, 3857, 14061, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MGGSSIRAGIFAGTLFGYGTGIIAGALIPLTNQYGFDPLSAGLITATALLGALLGALFAGPVADRVGRLNALSIGAVLFGIGSVLSAITLFGIMPLLITGRLIVGLGIGFVSAVAPMYLSEVAPAARRGLGVGLYQSLVASSMVVAYLVGFALQGSENGWRVMFALGLVLALGQLLCNRAGLESPVYLRAQGELEHAEGNTRALGLELESISAGQASRPWSAFLHRPGRHFLILAATLAGAQILTGINVLLYYAPTMFINAGITDSSGAFVAVIIIGVVNAIGTFIGLAVIERFNRRTLLVVGAAGMTLSMAGVALIAAFGAATSLATVMVGLLMAFVLFFEISIGPVAWLMISELMPAELRGKGVSFAVMVNWALNTALTLGALSLISGLGLGVTFAIFATFNLALLAFAVFALPETRGRRLDDVHAELGWVSGPEAMAEAQSRGGQPRQ", "metadata": {"id": "A0A960BMJ6", "cluster": 5567162, "interpro_all": ["IPR020846", "IPR005828", "IPR050820", "IPR036259", "IPR003663", "IPR005829"], "interpro_used": ["IPR005829", "IPR020846", "IPR050820"], "interpro_unused": ["IPR003663", "IPR036259", "IPR005828"]}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence be if I wanted a polypeptide chain capable of the following function: It is part of the Galactose-binding-like domain superfamily, which functions as a versatile ligand-binding module characterized by a $\\beta$-sandwich structure with a jelly roll fold. Found in both eukaryotes and prokaryotes, this domain interacts with diverse targets ranging from cell-surface carbohydrates and phospholipids to membrane-anchored proteins and DNA complexes. It is found in Sphingomonas lutea and exhibits UniProt keyword tags Signal.", "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, 15996, 17, 2743, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 5207, 17, 2743, 9059, 4378, 2007, 43, 8, 38, 4666, 8, 17, 18038, 3170, 1956, 43, 8988, 11560, 1012, 12970, 3728, 18, 2435, 1922, 2321, 15021, 1930, 28149, 16, 2052, 3418, 9034, 1956, 6445, 4845, 6485, 2037, 2024, 17, 3154, 16282, 1930, 15619, 1942, 3260, 17, 17199, 2697, 1930, 2678, 5048, 18, 2176, 1977, 2435, 1922, 13502, 10480, 12867, 1019, 1930, 9826, 20709, 11121, 2538, 14392, 2733, 18, 3], "output": "MLKRSLPIIASLAVLCATPTSAAIIIDEDFEAGYGVFAPDGQVARTTATGGYQTCCLAFGSPGAMANYFIAFGGGNQPSGNILSTTFNTALNVMYSLTFDYAALGAGSENLYLEVAGETFTVTPNANPNMDSNWATKTFNFAGIGGSTTLKVYSGGIDNVDAIFDNVLVASIPEPEVWAMLLLGFLGIGWQMRRRQELQPVTA", "metadata": {"id": "A0A7G9SGZ5", "cluster": 9472799, "interpro_all": ["IPR008979"], "interpro_used": ["IPR008979"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want a protein that has the function: The protein is grouped in the Torsin-1A-interacting protein 1/2 family, which comprises inner nuclear membrane proteins (also known as LAP1) that interact with and activate the AAA+ ATPase Torsin A. These proteins possess an atypical AAA+ fold and form a heterohexameric ring with Torsin A, providing a critical arginine finger to stimulate its ATPase activity and target it to the nuclear envelope. It has been detected in Aphidius gifuensis (Parasitoid wasp) and is classified with UniProt keywords Transmembrane helix. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 14823, 1921, 17, 5123, 17, 8615, 2213, 21, 19, 22, 3416, 16, 2154, 12936, 6671, 4254, 3260, 2697, 12, 2222, 3171, 1966, 7448, 1009, 13, 1988, 6310, 1956, 1930, 6980, 1920, 13835, 15, 9444, 14823, 1921, 43, 18, 2144, 2697, 7150, 1925, 10834, 13835, 15, 3728, 1930, 2386, 43, 19732, 17797, 17118, 6335, 1956, 14823, 1921, 43, 16, 5453, 43, 4140, 9732, 8497, 1942, 9084, 2496, 9444, 2455, 1930, 2758, 2176, 1942, 1920, 4254, 11262, 18, 2176, 2258, 2252, 3330, 1922, 27040, 11519, 23320, 2182, 3355, 1937, 12, 16891, 2642, 21830, 13, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 7864, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MDIKKNQNLIAVVPRARPPLPRMQTKTYRSTRTLPKCYDEDIDDDDDSNDDSDDEDKSQEEIRSEGFHRMSKEHLLDSLSPISGSPEKSIRRKNRHDPDDNDADDDDDDDYDGRKSSKTQVDSSRKKKKPLIQQIRKSEPVKHNFFQWLFFIGLVIIFIAIIPYLSVALNAQNVESSVNKTNKEDVKLIMNNFRKNINDIRLIFKNQDDTIWNDIEGRIYEIIVNPKRPTVIFLFANDDQPMFCLARLLGNASRTVLNCEEDLLLTADDSILGDDYGMVIENLKDKIIQQRVVIFENILNINPEAMRAFHNLCDSENPLVRNAIYILTMVNNKNDNNYYKKTMNTRESMKFIEHQLTQKLTGNIDPDKLQPLVTRMTDAVIINVQSEPEFQSCPLRY", "metadata": {"id": "A0A834XSQ7", "cluster": 11506574, "interpro_all": ["IPR038599", "IPR008662"], "interpro_used": ["IPR008662"], "interpro_unused": ["IPR038599"]}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein falls within the Intracellular Trafficking Regulator family, which regulates intracellular trafficking and endosome-to-lysosome pathways. Members interact with motor proteins like kinesin to facilitate the axonal transport of cargos such as mitochondria and receptors, thereby supporting neuronal outgrowth, synaptic function, and autophagy. Furthermore, the protein should feature a HAP1 N-terminal domain that mediates intracellular trafficking and motor protein interactions in Huntingtin-associated protein 1 (HAP1) and TRAK/Milton family proteins. It facilitates binding to huntingtin, kinesin-1, and dynein/dynactin complexes, thereby regulating axonal outgrowth, dendritic development, and amyloid precursor protein sorting. It is present in Caenorhabditis nigoni and is described by UniProt keywords Coiled coil and Mitochondrion. 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, 4776, 9604, 7888, 3416, 16, 2154, 7014, 4776, 9604, 1930, 22321, 17, 1942, 17, 19171, 3873, 18, 4678, 6310, 1956, 4842, 2697, 3189, 19378, 1942, 6628, 1920, 10623, 4860, 1927, 14713, 1036, 2427, 1966, 6489, 1930, 4086, 16, 6113, 6184, 5121, 15040, 16, 6251, 2347, 16, 1930, 6661, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 13466, 1009, 56, 17, 4262, 3418, 1988, 10412, 4776, 9604, 1930, 4842, 2213, 3719, 1922, 16426, 2268, 17, 2458, 2213, 21, 12, 13466, 1009, 13, 1930, 3390, 1040, 19, 5142, 5405, 3416, 2697, 18, 2176, 11374, 2743, 1942, 16426, 2268, 16, 19378, 17, 21, 16, 1930, 18188, 19, 11165, 11686, 5048, 16, 6113, 6773, 10623, 15040, 16, 8104, 2740, 16, 1930, 8186, 7897, 2213, 11404, 18, 2176, 1977, 2481, 1922, 22418, 19000, 13339, 1930, 1977, 2910, 2007, 20709, 11569, 17524, 9121, 1930, 30017, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MSPSPSRNSTPFDPSCALNEQLDCNELMVILEKKDRDLELAAKIGQSLLDQNKDLQTKNEFLEESVNKNLDTIVQLKHELNQRIELLRVYSHLDDEGVPRSNSDETLRERLKSTKSENERLRQECDQLRQETAIFTAQKNNTYQLEKQLDYANDKVMGLQKMIEQKTSELCQQYENTGRLMSELADKDKKEKMISMEKDEMGAILIEMIQRHDTMQSELKEMQDQYAELMANFAETESELTKLRSSGNLRMSFDSLYDSLASEMENSEFSPAGRSTQLTVLTGRDSYANDSGIDAGPMSLAAEIEHSEKHFITFSNPQMLLPSIHEPIFSTSAKLAALCDASTSCTDIFRESSLPHEDVATTPSVSGVNIIDEETKNPSFPSEEAVSTPIVARKYIPCSSPSKSNLSKLQRLHIGNRPHAHSVDMPSMSTKQPIEDNSSYAEPKLGQPGMPGTRDLDISLKIIKAREEVQKEFAAFCQRKGIDQQQFFGSSQNRRQSHDTSWTDFSVAYGVRMIQNLKTSPGDHQPLALGLRQGVLTRAELLTSPSSSPQHRSLSLSLSPGTSDGGLTKIGAIHGVLSRR", "metadata": {"id": "A0A2G5VMJ5", "cluster": 15161589, "interpro_all": ["IPR006933", "IPR051946"], "interpro_used": ["IPR051946", "IPR006933"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is associated with the Zinc-containing alcohol dehydrogenase family, which catalyzes the NAD(+)-dependent oxidation of diverse substrates, including sugars and amino acids. Members of this family, such as L-threonine 3-dehydrogenase and glucose 1-dehydrogenase, play essential roles in various metabolic pathways ranging from nutrient catabolism to antibiotic biosynthesis. Also, the protein carries a Alcohol dehydrogenase-like, C-terminal domain that forms a classical Rossmann fold to reversibly bind NAD(H) or NADP cofactors. It serves as the cofactor-binding module in diverse enzymes, including zinc-containing alcohol dehydrogenases, quinone oxidoreductases like the structural eye lens protein zeta-crystallin, and synaptic vesicle proteins. Additionally, the protein contains a Alcohol dehydrogenase-like, N-terminal domain that functions as the catalytic core for a diverse family of oxidoreductases, including zinc-dependent alcohol dehydrogenases and quinone oxidoreductases. It typically adopts a GroES-like fold to catalyze the reversible oxidation of alcohols to aldehydes or ketones using NAD or NADP cofactors, often utilizing coordinated zinc ions for activity. In addition to enzymatic roles, it can perform structural functions, such as in the mammalian lens protein zeta-crystallin. It is native to Archaeoglobi archaeon.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 1977, 2458, 1956, 1920, 7997, 17, 3165, 4284, 9294, 3416, 16, 2154, 17097, 1920, 6577, 12, 15, 13, 17, 3100, 6638, 1927, 6445, 6249, 16, 2710, 15592, 1930, 3835, 4576, 18, 4678, 1927, 2052, 3416, 16, 2427, 1966, 54, 17, 13143, 23, 17, 9294, 1930, 3817, 21, 17, 9294, 16, 3918, 4415, 5456, 1922, 3425, 4487, 3873, 6485, 2037, 8708, 19480, 1942, 7267, 8132, 18, 2222, 16, 1920, 2213, 16252, 43, 4284, 9294, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 4952, 43, 8445, 18215, 8890, 3728, 1942, 26778, 4566, 6577, 12, 50, 13, 2014, 24221, 21362, 18, 2176, 10634, 1966, 1920, 15155, 17, 2743, 9059, 1922, 6445, 5038, 16, 2710, 7997, 17, 3165, 4284, 9294, 1036, 16, 25093, 27388, 1036, 3189, 1920, 4346, 5723, 8540, 2213, 18943, 17, 24572, 16, 1930, 6251, 11502, 2697, 18, 4950, 16, 1920, 2213, 5461, 43, 4284, 9294, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 43, 6445, 3416, 1927, 27388, 1036, 16, 2710, 7997, 17, 3100, 4284, 9294, 1036, 1930, 25093, 27388, 1036, 18, 2176, 5745, 24032, 43, 8947, 1918, 17, 3189, 3728, 1942, 18170, 1920, 10743, 6638, 1927, 21773, 1942, 25075, 2014, 21876, 1036, 2193, 6577, 2014, 24221, 21362, 16, 3868, 10232, 11651, 7997, 6982, 1958, 2455, 18, 1922, 2459, 1942, 8145, 5456, 16, 2176, 2112, 2385, 4346, 4088, 16, 2427, 1966, 1922, 1920, 6492, 8540, 2213, 18943, 17, 24572, 18, 2176, 1977, 6196, 1942, 13470, 6292, 1033, 13470, 1916, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MRAIVLELNFLKVGLTMFLSKFSKSAYYGPLSILKTRICGICGSDVRLITLSESTYLYPMTSFPLIPGHEIVATVEETGKNPCRVRGFEECEFCRMGRFAICKNTDRGTLSPGIFVGICRDVPGGWAEYTVGIHTALRAFPEEDDIVAVVGCGMIGLATIAAIERNERLSEIAKNFGASRVIVGDPISEIAELTGGRVYRPPMDGLDTCLRIAKPLGKVVVAGTVSKVPIDLAPIFAKELEVLGVFGASYEKHTFPLEEYRKALWTVLNKRKSGAIKVAFRPVKYRRDYPEPKLPSEDWVKVGDFQRGDRVVVVPALIAHHDALVSVPDEIPDENAVFAEPLTLRHLGFRGEIWGKVLVGGGVDIAYECVGTAESVGGEIKNPFEMAFDMMRERDFSSLLT", "metadata": {"id": "A0A523AAC7", "cluster": 16378801, "interpro_all": ["IPR013149", "IPR013154", "IPR011032", "IPR036291", "IPR050129"], "interpro_used": ["IPR050129", "IPR013149", "IPR013154"], "interpro_unused": ["IPR011032", "IPR036291"]}, "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 ADP-ribosylglycohydrolase family, which regulates cellular processes such as the DNA damage response by hydrolyzing ADP-ribose from proteins, specifically targeting alpha-O-linkages on serine or threonine residues. While many members function to reverse ADP-ribosylation or degrade free poly(ADP-ribose) to prevent cell death, others are catalytically inactive and participate in structural roles like cardiac myofibril assembly. Moreover, the protein is categorized in the The ADP-ribosylation/Crystallin J1 family, which primarily functions as enzymes that hydrolyse ADP-ribosyl bonds to reverse protein modifications or degrade free ADP-ribose derivatives. These proteins participate in diverse contexts, including the regulation of nitrogen fixation, bacterial contact-dependent immunity, and animal cellular signaling, though the family also includes jellyfish crystallins that lack active sites and serve structural roles. It originates from Neolewinella aquimaris and is connected to UniProt keyword Magnesium and 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, 6304, 1942, 1920, 9828, 17, 29117, 2199, 17038, 4879, 8535, 24605, 1021, 3416, 16, 2154, 7014, 3689, 4028, 2427, 1966, 1920, 2678, 4293, 2644, 2007, 7222, 9046, 9828, 17, 17870, 2037, 2697, 16, 4475, 5133, 4595, 17, 57, 17, 19949, 1990, 8468, 2014, 13143, 4248, 18, 2679, 3086, 4678, 2347, 1942, 5267, 9828, 17, 29117, 3017, 2014, 17069, 3294, 4286, 12, 9828, 17, 17870, 13, 1942, 4625, 2024, 3539, 16, 4991, 2032, 21446, 9078, 1930, 7352, 1922, 4346, 5456, 3189, 4435, 26565, 1970, 5957, 18, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 1920, 9828, 17, 29117, 3017, 19, 24572, 52, 1009, 3416, 16, 2154, 5985, 4088, 1966, 5038, 1988, 21686, 1021, 9828, 17, 29117, 2199, 9031, 1942, 5267, 2213, 6920, 2014, 17069, 3294, 9828, 17, 17870, 8383, 18, 2144, 2697, 7352, 1922, 6445, 11144, 16, 2710, 1920, 3640, 1927, 6634, 7938, 16, 4543, 5217, 17, 3100, 7611, 16, 1930, 4027, 3689, 3197, 16, 4170, 1920, 3416, 2222, 5921, 8988, 11560, 1012, 14422, 24572, 1036, 1988, 3630, 3500, 3402, 1930, 7120, 4346, 5456, 18, 2176, 22970, 2037, 11724, 1952, 17860, 5870, 10059, 12874, 13950, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 13148, 1930, 6048, 17, 2743, 18, 3], "output": "MASTYPHSDRIGYCIIVALLPFACAENDSPAITPTDTNHSVAAHDEANYQDLSLSDSVLYDKVLGSLVGSAIGDAMGAPTEMWTQGDITDEYGHVDSLDLVLREPSPEGPWNYNLPPGAGTDDTRWKSLMVEFMVEEHAQRAPNGPLLPGAGRFSKFINGRYSASVDDLKATEGLDPEPLEDAMRRLTWLQEWAKVTRAYAARDLDGYRNALSRFYGGEMSCAGMLFSPVLGAAFPGRPEKAYRAAYDLALFDLGYARDIAGLTAALTSAAFTPGAGPGTFVDVMREVDPEGFFRSRLIGRIAYQQFRQARSIVRTARRLTQEEVRAMKFRMPDTYPYDSLTYGRMLKAYELLDRAKQDVPFHAGEIHLINLTALLFSGYEFGPAMEFVINYGRDNDTVAAVTGAILGALHGYGGLPVDQREMVVRVNREVLDIDLEARAADLTAAILARRNQVE", "metadata": {"id": "A0A840DZ95", "cluster": 16809227, "interpro_all": ["IPR050792", "IPR005502", "IPR036705"], "interpro_used": ["IPR050792", "IPR005502"], "interpro_unused": ["IPR036705"]}, "task_type": "autoregressive"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: 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. 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 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 produced by Actinobacteria bacterium HGW-Actinobacteria-4 and features UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 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, 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, 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, 4152, 2007, 29130, 14061, 7175, 1018, 17, 29130, 17, 24, 1930, 4075, 20709, 11569, 9117, 7864, 18, 3], "output": "MRVRSVMATSLTAERRAAVDSVAMTSEGVTRAASAGKSPLERLEFSFEFRKYQRLILTHLGERIDTPQVSEKFHIVSPPGSGKTILGIELIRRLGERAVVFAPTSTIQRQWHDKVSMFAQSPDHHDQVAGMDPHALRPITIFTYQLLTAAGDSRALLAEAALEQWIDQLVTADRSLTPEYARARIDTMRANNPDSHRKELARRTTSIRRSLLRERDPDVGRFLHPNARALIDRLVDSGVKTVVLDECHHLLDYWAVVLAYFIARIDTPRVIGLTATLPSPEDQNEYENYTGLLGEVDYEVPTPAVVKEGDLAPYRDLVAFVEPTDAEAEYLTQAHTAFDAAVESVTHDPRFVTWLQDASFAAGESAPQRWLEMMRNDTPLAVAAIRHLRALDLPDPPDLPIPLETGAEPEFGDKLAVVGRYALDVLKVSPDATDHAQLKALRQSLTKVGFTLTETGLRQQRTPGDLILAYSDAKAHMTGAILGLEAEAMGDRLRAVVVTDFERTGAAATSADRHAQAGSARKVFLDLVHHRRSHDLDPVLVTGRTLWLDADHGQELIDTFNTWLADRNLRATCVGEPGPYPGVIEVHGEGPQWSSGTYVSMVTYLFETGRLRCLVGTRGLFAEGWDTLTLNTLVDLTTATTATTAQQLRGRSIRIDPAWPRKVAHNWDVIAVHKGAEKGDRDIRRLRTKHQRVWGVTPDYPGVMPEVHGHVVRGLRHLDPELKQDMATRKFRDWRLDEATERSMQQVTRRDASYQLWDVGAAYSNFSYRATTLHARDLTIRTVHSVQQTLKRYMAEFRFALVMIAIEGALIAAHLSSTRVRSIPGGWRVVMALVGLVAVATVIRAAVVGWRAAKHVLKADHADAALLDIGRAVMAALKDAGLVSTNLQPEFVRVVEQPDLSYSVQLDYASTSDAAIFIDAYRQVFAPVLNQRYLVSRNESALPAIWLRPLWAVLRRVVRTMRGTEVTYHPVPDVLASHKRRAEAFAKRWHQYVGSGDLTYTRTPAGWRILIQARAKPQPTAPSDAYDVWR", "metadata": {"id": "A0A2N3FXT7", "cluster": 17704973, "interpro_all": ["IPR003593", "IPR006935", "IPR014001", "IPR050742", "IPR027417"], "interpro_used": ["IPR014001", "IPR003593", "IPR006935"], "interpro_unused": ["IPR027417", "IPR050742"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe protein is associated with the Proteobacterial nitrogen fixation protein FixH family, which functions as a component of a putative membrane-bound complex involved in nitrogen fixation. Along with FixG, FixI, and FixS, it is thought to help couple the FixI cation pump with a redox process catalyzed by FixG. Also, 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 derived from Rhodoblastus acidophilus (Rhodopseudomonas acidophila) and is associated with UniProt keywords 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, 2458, 1956, 1920, 22266, 1024, 6634, 7938, 2213, 4011, 1023, 3416, 16, 2154, 4088, 1966, 43, 4594, 1927, 43, 6770, 3260, 17, 4124, 2796, 3286, 1922, 6634, 7938, 18, 4231, 1956, 4011, 1029, 16, 4011, 1033, 16, 1930, 4011, 1036, 16, 2176, 1977, 6212, 1942, 4087, 15116, 1920, 4011, 1033, 9976, 8912, 1956, 43, 9366, 2585, 12139, 2007, 4011, 1029, 18, 2222, 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, 3595, 2037, 11490, 7439, 1957, 2687, 18239, 12, 11490, 4001, 3708, 5081, 9259, 2687, 7766, 13, 1930, 1977, 2458, 1956, 20709, 11569, 9117, 7864, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MTEDSDYQPKGRPLTGRKVLVMLLGFDAGVAYNKEIAAARAQDALGWSVGLTRAKGLEAALHFDHPSSSRLDVDVAAPWQVEIEFKRAGEIVFRSKNTLNVEFGVMAAVNFYMAREAIATHPGLDHKNPYNGAATEVTASVKDKAGQPVTAKAAGVYAGAADLPPGH", "metadata": {"id": "A0A6N8DH19", "cluster": 17878366, "interpro_all": ["IPR008620", "IPR018037", "IPR013783"], "interpro_used": ["IPR018037", "IPR013783"], "interpro_unused": ["IPR008620"]}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will be able to perform the following function: The protein incorporates a G-protein beta subunit-like, WD40 repeats domain that adopts a barrel-shaped $\\beta$-propeller structure to mediate protein interactions, most notably forming a stable dimer with G-protein gamma subunits. This complex regulates downstream effectors in GPCR signaling pathways upon dissociation from the alpha subunit, and the fold is also conserved in nuclear proteins such as Chromatin assembly factor 1. Moreover, the protein includes a WD40 repeat conserved site that mediates protein-protein or protein-DNA interactions, typically forming a beta-propeller structure that serves as a rigid platform for the assembly of protein complexes. These motifs are widely distributed in eukaryotes and facilitate diverse functions ranging from signal transduction to transcriptional regulation, with interaction specificity often determined by sequences outside the repeats. Furthermore, it is part of the WD40-repeat-containing domain superfamily, which folds into a characteristic $\\beta$-propeller structure comprised of multiple short repeating motifs to serve as a stable scaffold for protein-protein or protein-DNA interactions. These domains facilitate the assembly of multi-protein complexes involved in diverse eukaryotic processes, ranging from signal transduction and transcriptional regulation to cell cycle control. It occurs in Phaeodactylibacter sp and is described by UniProt keywords WD repeat.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 19683, 43, 49, 17, 2213, 4666, 5903, 17, 3189, 16, 17907, 4241, 9569, 3418, 1988, 24032, 43, 19560, 17, 9132, 8, 38, 4666, 8, 17, 5062, 13728, 3170, 1942, 8265, 2213, 3719, 16, 2501, 7388, 7402, 43, 4700, 7632, 1956, 49, 17, 2213, 7034, 6991, 18, 2052, 2796, 7014, 5863, 13066, 1922, 12542, 3197, 3873, 4073, 9182, 2037, 1920, 4595, 5903, 16, 1930, 1920, 3728, 1977, 2222, 5305, 1922, 4254, 2697, 2427, 1966, 6338, 5957, 2991, 21, 18, 3950, 16, 1920, 2213, 5921, 43, 17907, 4241, 6865, 5305, 3200, 1988, 10412, 2213, 17, 2213, 2014, 2213, 17, 2678, 3719, 16, 5745, 7402, 43, 4666, 17, 5062, 13728, 3170, 1988, 10634, 1966, 43, 12383, 6631, 1958, 1920, 5957, 1927, 2213, 5048, 18, 2144, 8277, 2032, 5673, 6533, 1922, 15021, 1930, 6628, 6445, 4088, 6485, 2037, 2733, 8201, 1942, 5224, 3640, 16, 1956, 2835, 4896, 3868, 3180, 2007, 3709, 7008, 1920, 9569, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 17907, 4241, 17, 6865, 17, 3165, 3418, 13975, 16, 2154, 16231, 2460, 43, 6293, 8, 38, 4666, 8, 17, 5062, 13728, 3170, 8842, 1927, 3137, 3662, 21763, 8277, 1942, 7120, 1966, 43, 4700, 7281, 1958, 2213, 17, 2213, 2014, 2213, 17, 2678, 3719, 18, 2144, 4682, 6628, 1920, 5957, 1927, 2779, 17, 2213, 5048, 3286, 1922, 6445, 10825, 4028, 16, 6485, 2037, 2733, 8201, 1930, 5224, 3640, 1942, 2024, 4048, 2285, 18, 2176, 5110, 1922, 18421, 1021, 25033, 2341, 2199, 26073, 2341, 1915, 2056, 1930, 1977, 2910, 2007, 20709, 11569, 17907, 6865, 18, 3], "output": "MDKPKDTRTKNKLLPDLPGYDPGSADGVRVGESPIPGLTLKRILRGHTKAIYRIAWSPDGRFLASPSYDGTIRIWELESGECKTKLEGDKSGVFCVSWSPDGCRLASSSSDNTINIWETETWKTVGAATGHNALIYRVAWSPDGQKLASGGSDGTIRIWDVETWQTSYELKDKASGGVQSLAWSPQGHLLAFGDTAGTIMQFDA", "metadata": {"id": "A0A959CQT9", "cluster": 18079157, "interpro_all": ["IPR020472", "IPR001632", "IPR015943", "IPR019775", "IPR036322", "IPR001680"], "interpro_used": ["IPR001632", "IPR019775", "IPR036322"], "interpro_unused": ["IPR020472", "IPR015943", "IPR001680"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe protein is included in the Primosome PriB/single-strand DNA-binding family, which comprises proteins such as the single-strand binding protein (SSB) and Primosomal replication protein N (PriB) that bind tightly to single-stranded DNA (ssDNA). These proteins typically function as oligomers to stabilize ssDNA intermediates during DNA replication, recombination, and repair, or to facilitate primosome assembly on the lagging strand template. Moreover, the protein is classified under 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. In addition, the protein is classified under the Single-stranded DNA-binding protein family, which plays a central role in DNA replication, recombination, and repair. It binds to single-stranded DNA (ssDNA) and interacts with an array of partner proteins to recruit them to their sites of action during DNA metabolism. It is present in Lipomyces tetrasporus and has UniProt annotations Mitochondrion.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 1977, 3063, 1922, 1920, 2610, 4283, 17618, 1014, 19, 2957, 17, 5984, 2678, 17, 2743, 3416, 16, 2154, 12936, 2697, 2427, 1966, 1920, 2957, 17, 5984, 2743, 2213, 12, 22228, 13, 1930, 2610, 4969, 5158, 2213, 56, 12, 17618, 1014, 13, 1988, 4566, 12129, 1942, 2957, 17, 10338, 2678, 12, 15063, 13, 18, 2144, 2697, 5745, 2347, 1966, 14160, 1942, 13448, 15063, 12386, 2409, 2678, 5158, 16, 7827, 16, 1930, 5059, 16, 2014, 1942, 6628, 2610, 4283, 5957, 1990, 1920, 9333, 6066, 5984, 7662, 18, 3950, 16, 1920, 2213, 1977, 5947, 2441, 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, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2957, 17, 10338, 2678, 17, 2743, 2213, 3416, 16, 2154, 5705, 43, 4101, 2770, 1922, 2678, 5158, 16, 7827, 16, 1930, 5059, 18, 2176, 6876, 1942, 2957, 17, 10338, 2678, 12, 15063, 13, 1930, 9034, 1956, 1925, 6472, 1927, 8240, 2697, 1942, 5608, 3581, 1942, 2310, 3402, 1927, 4615, 2409, 2678, 4714, 18, 2176, 1977, 2481, 1922, 3178, 29249, 27346, 2074, 1957, 1930, 2258, 20709, 15010, 30017, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MIWSLFSRSALRSTATSARSFSSTSAEKATSANGRDYARYSVAVRLNNFAKGNLVYVEASASLQPFERLSAPRKEEQAESAQTEAEVENAKDLARVTLIGRLGANPQGRDTEPSWYHVVSFDQHLDYLTADGRRVGSLQLVQRSIQ", "metadata": {"id": "A0AAD7QZ85", "cluster": 19384583, "interpro_all": ["IPR012340", "IPR000424", "IPR011344"], "interpro_used": ["IPR000424", "IPR012340", "IPR011344"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein is associated with the UBX domain-containing protein family, which functions as ubiquitin-binding adapters or tethering factors that recruit the segregase VCP/p97 to specific protein complexes. Members of this family regulate diverse cellular processes, including endoplasmic reticulum-associated degradation (ERAD) and ciliogenesis, by mediating the turnover of misfolded proteins and controlling signaling pathways. These proteins utilize the UBX domain for VCP/p97 interaction and may employ additional domains, such as UBA or UIM, to bind ubiquitinated substrates or NEDD8 modifications. Moreover, the protein features a UAS domain that is characteristically found in FAS-associated factor 1 (FAF1) proteins as well as other proteins of uncharacterized function. Despite its recurrence in these sequences, the specific molecular role or mechanism of this domain remains unknown. Additionally, the protein contains a UBX domain that is found in ubiquitin-regulatory proteins of the ubiquitination pathway, including FAS-associated factor 1 (FAF-1) and Rep-8. This domain is associated with the induction of apoptosis, although its precise molecular function is not fully characterized. It has been characterized in Zingiber officinale (Ginger) (Amomum zingiber) and exhibits UniProt keyword tags Ubl conjugation pathway. 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, 2458, 1956, 1920, 4803, 1039, 3418, 17, 3165, 2213, 3416, 16, 2154, 4088, 1966, 6526, 17, 2743, 21054, 1036, 2014, 23991, 2790, 1988, 5608, 1920, 9762, 2051, 11025, 1034, 19, 58, 8528, 1942, 2487, 2213, 5048, 18, 4678, 1927, 2052, 3416, 5741, 6445, 3689, 4028, 16, 2710, 13355, 12279, 17, 2458, 4877, 12, 14827, 13, 1930, 19692, 3761, 16, 2007, 10239, 1920, 9781, 1927, 20303, 2697, 1930, 7138, 3197, 3873, 18, 2144, 2697, 12561, 1920, 4803, 1039, 3418, 1958, 11025, 1034, 19, 58, 8528, 2835, 1930, 2278, 4417, 3281, 4682, 16, 2427, 1966, 4803, 1019, 2014, 20487, 1035, 16, 1942, 4566, 20895, 6249, 2014, 20210, 1025, 6920, 18, 3950, 16, 1920, 2213, 4075, 43, 15124, 3418, 1988, 1977, 6293, 2169, 2435, 1922, 4557, 17, 2458, 2991, 21, 12, 5685, 5739, 13, 2697, 1966, 2486, 1966, 2303, 2697, 1927, 24528, 2347, 18, 4281, 2496, 6339, 1922, 2144, 3709, 16, 1920, 2487, 3272, 2770, 2014, 2856, 1927, 2052, 3418, 4497, 5435, 18, 4950, 16, 1920, 2213, 5461, 43, 4803, 1039, 3418, 1988, 1977, 2435, 1922, 6526, 17, 4948, 2697, 1927, 1920, 11758, 3374, 16, 2710, 4557, 17, 2458, 2991, 21, 12, 5685, 1038, 17, 21, 13, 1930, 3073, 17, 28, 18, 2052, 3418, 1977, 2458, 1956, 1920, 4408, 1927, 4091, 16, 2876, 2496, 8162, 3272, 2347, 1977, 2084, 5437, 4378, 18, 2176, 2258, 2252, 4378, 1922, 28666, 2029, 14965, 15857, 2526, 1021, 12, 12485, 1915, 13, 12, 2150, 1947, 1989, 28666, 2029, 14965, 13, 1930, 9826, 20709, 11121, 2538, 14392, 4803, 1024, 14122, 3374, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MRNAWNGMSRVKFLVYNVLDHTTTSCLGAYHGGGSNFSSDISWRQGNAGEMKSYEGTEEGSGLDFGGNNQDVRKGKSAKKNVARSSLLYNVRTFPGISLFASFPVPITLSTSPIAYLVQTSRSGWSMETLPSAAERQQLVSFFLEVAAGQTADIAARFLEAAAWKFDEAVQLFYFSNESGGVESSFLPPQTNGITSVENMLASGSSVQGALEDEVRAPLPVVRDILNEDPAFFRSQPSLDVPFGISRHSAIWESSESVLSTSNGTHDNLASLYTPPFSLMFQGRFDQAKVEASRRGKWLLLNLQSHEEFSSHMLNRDTWANQAVAEIIHSNFIFWQVYHDNIEGKKVCTYYNLFKLPAVLLIDPITGQKMNAWTGMVHPERLLEGLLPFLDKGPKEHHAFLLQKQKQRAAHDSAVINVAGKEAVKDDVEMVQAIATSLENTRGPRPLVTDEESRPEKSHATNSNEKLTYPPLLEEPQGSKGLCRVAIRLPDGCRLQRKFLLTDSIKLLWSFCSSKLEDGLKRPFHFIQFYLGASRSLEYEKDLTFDAAGLSNSLISLVWD", "metadata": {"id": "A0A8J5IKS7", "cluster": 19440388, "interpro_all": ["IPR036249", "IPR006577", "IPR029071", "IPR001012", "IPR050730"], "interpro_used": ["IPR050730", "IPR006577", "IPR001012"], "interpro_unused": ["IPR036249", "IPR029071"]}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein is grouped in the Protein of unknown function DUF6913 family, which comprises uncharacterised bacterial proteins exhibiting remote similarity to the UDP-glycosyltransferase superfamily. Unlike typical members of that superfamily, these proteins are predicted to consist of a single standalone domain. It is found in Saprospiraceae bacterium.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 17136, 12118, 1010, 3416, 16, 2154, 12936, 23229, 3495, 4543, 2697, 12196, 12597, 6796, 1942, 1920, 18500, 17, 20067, 9961, 13975, 18, 7945, 5939, 4678, 1927, 1988, 13975, 16, 2144, 2697, 2032, 4396, 1942, 3149, 1927, 43, 2957, 2924, 20807, 2912, 3418, 18, 2176, 1977, 2435, 1922, 9235, 5424, 11979, 1972, 3336, 14061, 18, 3], "output": "MIAKIKEWFFYRDFTVKDNMPESIRANINKEQNLNGNGTGNRNIKSLAFIDNALPLDNVDYAEEFINLPSDILIVLCKNMLPHFEYIVAHSSTDFNMDSLEKLSQSIIKGIDKIAVKICILYDGTNETDRKSLHRFKKLAYNHKNIKWHGVPFGEKVIVGPFLKKSEKYFNLIVETE", "metadata": {"id": "A0A9D7Y693", "cluster": 23301088, "interpro_all": ["IPR054207"], "interpro_used": ["IPR054207"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: 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. Moreover, 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. Moreover, the protein features 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. It has been detected in Arthrobacter sp. ZBG10 and has UniProt annotations Transmembrane helix, Two-component regulatory system, and Transferase. 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, 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, 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, 3950, 16, 1920, 2213, 4075, 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, 2176, 2258, 2252, 3330, 1922, 9273, 15129, 2422, 2056, 18, 68, 19966, 2930, 1930, 2258, 20709, 15010, 9117, 7864, 16, 2288, 17, 4594, 4948, 2433, 16, 1930, 13763, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MRRLSLRWALVLALTTTAVLVSVLVTVVLVGITRDATYASRQEALLADFRESTAPFSRAVTLAAPDAEWDLYGEVLPGRTVIFDLQGTRSAGDLGRADIPAPFLGALGPETTDLQFRRGTLNGDEVFFVGGVLPARGEDQQPRLAVVTAYSLEPERRQLLQLVGAGVAIGGIAVALAIVLGLFLGTALTRPLRRLARMAQQVGDGAVPEPARSAFPDIDKVAGTLAESSRSLSVSMAQLARREQEARRLVGDVAHELRTPLASMAAVSEILADFRQATPEEQAAAVRITTDGTRRLSVLVAEVLELSRMEAGAARISVSRGRLLAALQEAVLDADPERSGSVALSCPRSLVLVTDFARVRTVVSNLLTNALRYGAAPIRVSAAERGGGIIITVQDHGPGIPADRREHIFERFTVLDPARRRPDSSGLGLAIARENARLLGGTLALAGTETGATFVLALPAAPASWTVDAAMV", "metadata": {"id": "A0A0L1LX33", "cluster": 23372903, "interpro_all": ["IPR003660", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR004358", "IPR050428"], "interpro_used": ["IPR005467", "IPR003661", "IPR003660"], "interpro_unused": ["IPR036097", "IPR004358", "IPR050428", "IPR036890"]}, "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 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. It is derived from Hexamita inflata and is connected to UniProt keyword Metal-binding and Zinc-finger.", "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, 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, 2176, 1977, 3595, 2037, 7142, 14981, 3857, 2552, 5499, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 3], "output": "MWCNFAKAHGKSQGSISKSTKNTCTRHLRCKEILGSIFKTNGMPDNRAITGIIVDNGVQSDIINIEDDQNYFYINIFGEHQNDGLGKCASNRKLIAMRYKFSEQEIQIISENLLSHGGTNGIRQLWDTQRGKTLNCSYRQLQRKVQSLTKILFNDSVQMAKYAEENDLYYQPNIENGVLISFGIANKKHIELFNQCPNCIIADFTFSKLQNINYQILNFCSLLDSKMVFLIASYVFCNVEEHSGESKLKTDESLVFLRNCQVNMKAVRVFASDGANCFRNEEFLKQFSQHTQNIQCSYHIFSKHFRGKFPGTSPEILQQIRYNFFNAIRSGTREDYEYRLLQFKKALYKAEGTKTNKDDKFKVLTENIDYMCYYCRNLNQNAVTDIIATSAIESANWWDCKGRLLSNARLIDLFKQLSGTHFFAEHHAKEHARINDTTFNRNGLEGFVLSVENQLKIEITNSKTYIITEENNQVIVSVQLQENGQNYLGQCQIFNKTKLIEKQISCKCAVFLLTNIACGHMIAALQYISDQQAIQNNLPCKKLQYSDLRNFIDSKYSVKTMYKRLKVLKIPGLQQECSFNTNEFVKNTTTINTNDQTITNESQNQQITINDCEPNQLSVSDEFDPCQKLQNETIKLIRTIQDEVALKEIQYYINNSIKKLSFKIDNKFGNTKGSKIRKRPLNERKRGVQNKYRKVQQVINSKKQNKQ", "metadata": {"id": "A0AA86TB86", "cluster": 25995652, "interpro_all": ["IPR007527"], "interpro_used": ["IPR007527"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein possesses a DUF4219 domain that is typically found at the N-terminus of Gag-pol polyproteins in retrotransposons and related sequences. This short region is characterized by a highly conserved YxxWxxxM sequence motif. Moreover, the protein should feature 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. Also, 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. It is derived from Dillenia turbinata.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 14465, 43, 4855, 10432, 4716, 1026, 3418, 1988, 1977, 5745, 2435, 2019, 1920, 56, 17, 7822, 1927, 9819, 17, 2492, 6240, 10355, 1922, 27181, 2101, 1930, 2712, 3709, 18, 2052, 3662, 3031, 1977, 4378, 2007, 43, 3626, 5305, 67, 14710, 1018, 14710, 1039, 1035, 3244, 5219, 18, 3950, 16, 1920, 2213, 3066, 5961, 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, 2222, 16, 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, 2176, 1977, 3595, 2037, 4333, 15253, 2126, 13840, 4058, 3857, 18, 3], "output": "MEAIWLHRFPVDDNSTIKLVVDVWFYYSTCMESEVIAEVFQTKAFVQESYLTGEDLWDVVISCGFDLRQRIDINEFKSAQTAWNQLYSHFVCTRPPVNPESLGLWDVVDKEIHEHSKIWEQKNAKALHHIQISCGQNTVDPYLPLYHDLKKAGNPMIRQLLESKTVPDELRRCITPYRVVKDLVKKLTPEDLKQKDDMDDTALLLAARVGNEKIADIPLVVAAHFGHKSTVRYLYSVTPEEHLEFFDIALDLAKRFPKLASGREKSGWIYSCMPVELPHAASKASRGDPETGHEGQTTNQDMIARESNSSPVPTCREPEKANYLPGKENSQEKDAKALEVIKSPPVLEDDNYENWSKSMQEYLLHQILDLNSAKAAWEKLASIQRQTIFHIATMQQQKNRYIIESCPELVTIGNAVGNPDHPRYDPRHPHGTRLLVSCINDVEALQKLASKPLAFQSGKERVFWKQ", "metadata": {"id": "A0AAN8ZQY6", "cluster": 27269478, "interpro_all": ["IPR002110", "IPR036770", "IPR025314"], "interpro_used": ["IPR025314", "IPR002110", "IPR036770"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein should contain a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. Moreover, the protein possesses a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. It is produced by Spiroplasma tabanidicola.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 3066, 5531, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 3950, 16, 1920, 2213, 14465, 43, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 2176, 1977, 4152, 2007, 22075, 15403, 1019, 8514, 8150, 7408, 4879, 5148, 18, 3], "output": "MTNIAIMASGNGSNFQAIIDAYNEAIKRAQQNNIKNYNFFLKDYPSKEEYEKDIRKIINTHPSLLPSFKGKDAIQDALDYKVYLAGFTIHYVNIYKDDTHDTLQKRIQEQEHIYYWQIINKVIKGEKIKKLEVDKIILITNKKNCFLKVLKEENIDYVILAGYMTMISNTLLSHYEEMDAGEIIFQKEVRV", "metadata": {"id": "A0A6I6CDS0", "cluster": 3405106, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR002376", "IPR001555"], "interpro_unused": ["IPR036477", "IPR004607"]}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein is assigned to 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. Moreover, the protein is categorized in the Divergent polysaccharide deacetylase family, which comprises bacterial proteins structurally related to the 7-stranded barrel catalytic domain of polysaccharide deacetylases (DACs) within the carbohydrate esterase 4 (CE4) superfamily. These proteins are predicted to function in the removal of N-linked acetyl groups from cell wall polysaccharides. It is derived from Gammaproteobacteria bacterium and is connected to UniProt keyword Signal.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 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, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 13609, 17167, 19489, 3416, 16, 2154, 12936, 4543, 2697, 12171, 2712, 1942, 1920, 27, 17, 10338, 19560, 6804, 3418, 1927, 17167, 19489, 1036, 12, 22322, 1036, 13, 2651, 1920, 10590, 26389, 24, 12, 5827, 1006, 13, 13975, 18, 2144, 2697, 2032, 4396, 1942, 2347, 1922, 1920, 6025, 1927, 56, 17, 4624, 6894, 2671, 2037, 2024, 4821, 18686, 18, 2176, 1977, 3595, 2037, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 18, 3], "output": "MFFLRVFLSALILLALPAAAEQVTLPRVAVIIDDLGYALAAGERAINLPGPVACAILPGTPRAIRLAEQAHASGKEVLLHLPLQAENDYDLGDAAEPGSLHLDMSQAEFAHTFIEDIEAVPHVIGVNSHRGSLLTRHPGHMNWLMEEIRDRGDLFFVDSYTTAASVALQLARETGVPAAKRDVFLDPDQSPETVAREFARLKKLAQQNGFALGIGHPYPATLAFLEKELPKLRNEGFELISISELIALTNATQNNNAGHAVAAPAGQ", "metadata": {"id": "A0A661GC46", "cluster": 1154440, "interpro_all": ["IPR006837", "IPR011330"], "interpro_used": ["IPR011330", "IPR006837"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is categorized in 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. Also, the protein falls within 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 Short-chain dehydrogenase/reductase conserved site that characterizes the catalytic core of NAD- or NADP-dependent oxidoreductases. This region features two perfectly conserved residues, a lysine and a tyrosine, with the tyrosine directly participating in the catalytic mechanism. It has been detected in Nanoarchaeota archaeon.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 10234, 1922, 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, 2222, 16, 1920, 2213, 12182, 2651, 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, 3662, 17, 4659, 9294, 19, 11386, 5305, 3200, 1988, 26735, 1920, 6804, 4728, 1927, 6577, 17, 2014, 24221, 17, 3100, 27388, 1036, 18, 2052, 3031, 4075, 2288, 19981, 5305, 4248, 16, 43, 9082, 1930, 43, 6941, 16, 1956, 1920, 6941, 4103, 9505, 1922, 1920, 6804, 2856, 18, 2176, 2258, 2252, 3330, 1922, 9788, 3983, 3336, 7336, 13470, 1916, 18, 3], "output": "MEESVLITGANGLIGYNIALKFLERGDQVFLSDYYNKNNRIDVKKMMETIETKCSGIDVLINNAGIVKDKTFIKMTYDEWNDVIQTNLYGYGSIVSIASIVGKNGAYGQTNYAASKAALIGFTKSLAKEVSKYNIRVNAKIVASLPAGRMAKPEEMAEAVFNLANEKDTTGEVRDICQELCKKYPTQAHKIEADIRNAEDTMFITKGVLQKMIDKKVTPGYVETDMTAKIPEDVKA", "metadata": {"id": "A0A8T5MWH8", "cluster": 1513704, "interpro_all": ["IPR036291", "IPR020904", "IPR050259", "IPR002347"], "interpro_used": ["IPR050259", "IPR036291", "IPR020904"], "interpro_unused": ["IPR002347"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to create: The 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. Moreover, 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. It is expressed in Undibacterium fentianense and contains UniProt keyword associations Signal and TPR repeat. 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, 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, 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, 2176, 1977, 3198, 1922, 3075, 26073, 2341, 18842, 1989, 17232, 3122, 4480, 1930, 5461, 20709, 11121, 2538, 5253, 2733, 1930, 22288, 6865, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MRLVWFLSLLCSLLALPCVAQAQKLAEPSDSLIQYLKTFPKAYDLFAGANYVEAQQALENELASHENEANYFNVLGVLQLKQQNYLGAAASFERAVLIDPSNAGSWMDLAIATLETGNLGSASSYFDYIEVTFKPSKDIQQVIDGYKRFIQKAKEPKKKLRYTAEFGVGRDSNANSGLQSAYIPITFGSDRVNLPLDPSYQARSDQYVAAALQARYDSPFDVPGLEMNASVKRRGYQRERDFSTTELSGNVGWQRPSPLGLVGVTAFTDVSWLGDKGLLRDFRLSGSIERSWRDCFYGASLENEWRRYMGLHSQDADLRWAQLAGACKMPIAGKALQATIVARYGNDLPTRQRAGGKTRRKEVVAQLGAVFRPQWRFDLSWNAAFALDSEGYSPLLENNARRQVTRRTARIQLTKTLNADLDLFFRVDDSSIASNILLFSQKAKSFNLGLQRRF", "metadata": {"id": "A0A941E854", "cluster": 1629752, "interpro_all": ["IPR011990", "IPR019734"], "interpro_used": ["IPR019734", "IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe 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. Also, the protein should include 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 is produced by Polarella glacialis (Dinoflagellate).\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, 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, 3066, 3951, 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, 1977, 4152, 2007, 5676, 5870, 27424, 1937, 12, 11687, 4199, 5148, 20178, 5148, 2057, 13, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "CFGSGPPVFRPLGEAMSAMSPWLFAQKSVGSLARTGRRGVSVGSLSTHDALGSSSSGGSSSSSSSSPDSFHSSDINAMLKQSEDCYTPPTRPFPVPRAAPKAAGEAGAANHGAFGGSLTVALQSKRHWADYVEQQPVRFVDRLVQCPPTELLPMPNVTTAMNTILRSWQRREAASVRVASETGAEIDEVPLHFPLGPEGLTPALQELERHLSADAICRRVAPNALVIVDGAHSLGQVDLALCGTELSAALDLRMGALRNGNASSTSSSYGRGFGIFGEKARAHFRLDENSSQTLFLELFSQAAHITRRLAKRGGAPGSPRRFVLFSTTYGSTKILLRQTALVVIDSIPSNTPVAFPVEEAV", "metadata": {"id": "A0A813JVR9", "cluster": 1826108, "interpro_all": ["IPR000192", "IPR015424", "IPR015421"], "interpro_used": ["IPR015421", "IPR000192"], "interpro_unused": ["IPR015424"]}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein is classified under 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. In addition, the protein incorporates 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 is present in Cladophialophora immunda and is linked to UniProt keywords Nucleus and Transcription regulation.\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, 5947, 2441, 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, 1922, 2459, 16, 1920, 2213, 19683, 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, 1977, 2481, 1922, 23415, 2688, 2086, 22575, 1019, 2519, 3825, 1930, 1977, 4624, 1942, 20709, 11569, 5607, 1930, 3213, 3640, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MEIQRSRRGCAACRMRHLKCDEAKPACFRCQAAGRQCEKGPLFSQWREPKTRRKQGAYVHRVTDSTIEEILSQHSPKQQDGEPTTGASKDSSPIFSAGEVTSISQLLSNDPTRSTTFQCTVTEVSTTDSDTGIACETRSLEARSGQLVDRHSLIKDRTEAHLLRHYCQNLAPWFDVLHLSRVSSLDPSIAESYHSRCNSQLIPLLNDRHCAANVNLLATVVILRKYEELSVTGQDHPDCPFNDGLAQAAFWQFVRQDIYMSLPRRRPPRTSILIQPPLTNDRTMPDCHWANRMVWGTLAIMALCFRDERPDFTPMYRRERSVVDGRYFPEIWLSDPWHATAWQYYHLSKILLALYNPHLQRPAADLKYDFATTRFTLSAIMLTCGGWFKDPQEQEAIIDLLSATSKESGWPTKSVIEALRESWAVEEPRKERRWVEIPSTLTFSMDMTFTELSSIDFMDMGDFTDSNRHFQLEVPRRASTCDVLLNAIFALSAGHHLAGVSALFSSIATYENHSQRVKDWHDTKPTSQRDHNQLERDVLEHARFACGIASSN", "metadata": {"id": "A0A0D2C0X8", "cluster": 2497696, "interpro_all": ["IPR021858", "IPR036864", "IPR001138"], "interpro_used": ["IPR021858", "IPR001138"], "interpro_unused": ["IPR036864"]}, "task_type": "infilling"} {"instruction": "The protein features 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. Moreover, the protein should feature 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. Additionally, the protein should include a 4Fe4S-binding SPASM domain that binds auxiliary [4Fe-4S] clusters to support complex post-translational modifications within radical SAM enzymes. Characterized by a conserved cysteine-rich motif, this domain facilitates diverse reactions including anaerobic sulphatase maturation, cofactor biogenesis, and thioether bond formation in bacteriocins. It originates from Theionarchaea archaeon and is linked to UniProt keywords Metal-binding and S-adenosyl-L-methionine. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 4075, 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, 3950, 16, 1920, 2213, 3066, 5961, 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, 4950, 16, 1920, 2213, 3066, 3951, 43, 15338, 1021, 1006, 1036, 17, 2743, 24431, 3418, 1988, 6876, 21549, 37, 15338, 1021, 17, 26814, 39, 5859, 1942, 3373, 2796, 2753, 17, 8414, 6920, 2651, 6917, 2235, 5038, 18, 4378, 2007, 43, 5305, 8666, 17, 5536, 5219, 16, 2052, 3418, 11374, 6445, 5298, 2710, 12554, 13528, 7234, 7655, 16, 15155, 13008, 16, 1930, 15331, 2682, 5403, 3337, 1922, 14027, 11778, 1036, 18, 2176, 22970, 2037, 1920, 2001, 3983, 24145, 13470, 1916, 1930, 1977, 4624, 1942, 20709, 11569, 6048, 17, 2743, 1930, 61, 17, 29283, 17, 54, 17, 12417, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MNEKLRVQQRPARRRKVHGRYPFIMQFGITSRCNLRCSHCYDDTEEHIHMPFDQCIAVLDKFFSFCNHWNRFPHIWLTGGEPIIHPRFWDILDYIDDHSKDSDTGFHVSVLSNGFKFDGALLKKLERYPVVHAVQISVDGARAESHDAIRGKGSFDRAIRALNLLVPSRLETHMHFVVFKDNYEDAFEMTDLAKKLGIDILTITRLVPWGRGGELRESMLNTDQVQILFKKLSDDYDVILQTDSRKPTIGRNRCDWPVIYPDPSTPDAFAKNGYRCGVAYSYINVMENGDVYPCRRMPIIVGNLLEEDLMHIWQHPLMWKLREKQRFVQGKCRNCFFLKEAPDICSGGASCIAYAVHGDPFQPDPQCPYNPPEGS", "metadata": {"id": "A0A8J8BY43", "cluster": 4438305, "interpro_all": ["IPR023885", "IPR013785", "IPR034391", "IPR006638", "IPR017200", "IPR050377", "IPR007197"], "interpro_used": ["IPR007197", "IPR006638", "IPR023885"], "interpro_unused": ["IPR034391", "IPR017200", "IPR013785", "IPR050377"]}, "task_type": "autoregressive"} {"instruction": "The protein falls within the TIP41-like protein family, which regulates the activity of type 2A protein phosphatases to control cellular signaling. In mammals, these proteins interact with PP2A, PP4, or PP6 catalytic subunits to inhibit phosphatase activity, thereby facilitating H2AX phosphorylation and the subsequent DNA damage response. In addition, the protein belongs to the Phosphatase regulators and Met sulfoxide reductases family, which comprises regulators of serine/threonine-protein phosphatases, such as PP2A and PP4, as well as free methionine-R-sulfoxide reductases. Members acting as phosphatase regulators modulate catalytic activity in pathways including the DNA damage response and TOR signaling, while reductase members catalyze the reduction of methionine sulfoxide to methionine to protect against oxidative stress. It is derived from Bugula neritina (Brown bryozoan) (Sertularia neritina).\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 7933, 8099, 17, 3189, 2213, 3416, 16, 2154, 7014, 1920, 2455, 1927, 2601, 5251, 2213, 19131, 1942, 2285, 3689, 3197, 18, 1922, 9902, 16, 2144, 2697, 6310, 1956, 17772, 16, 4108, 1006, 16, 2014, 4108, 1016, 6804, 6991, 1942, 2875, 8167, 2455, 16, 6113, 12440, 19741, 4050, 1930, 1920, 4521, 2678, 4293, 2644, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 8167, 9098, 1930, 2130, 20139, 11386, 1036, 3416, 16, 2154, 12936, 9098, 1927, 8468, 19, 13143, 17, 2213, 19131, 16, 2427, 1966, 17772, 1930, 4108, 1006, 16, 1966, 2486, 1966, 3294, 12417, 17, 60, 17, 20139, 11386, 1036, 18, 4678, 8290, 1966, 8167, 9098, 8480, 6804, 2455, 1922, 3873, 2710, 1920, 2678, 4293, 2644, 1930, 8184, 3197, 16, 2679, 11386, 4678, 18170, 1920, 3378, 1927, 12417, 20139, 1942, 12417, 1942, 9145, 3316, 5163, 3071, 18, 2176, 1977, 3595, 2037, 25761, 5617, 4919, 4823, 1019, 12, 8084, 26949, 28071, 13, 12, 17498, 2168, 2126, 4919, 4823, 1019, 13, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MATAKHGLFSFGNWDFNITESHILKSDGTYDQNILRVTHTEGFGVEFSALDALKLVNAEKDLMKFSTTYSGTLINEGEQAFTGQFHKVNKTVPDREAFEKILSPLPQTPEMVAVSEAWKSSRDESQHIHEVFKPFDWT", "metadata": {"id": "A0A7J7JY16", "cluster": 10989790, "interpro_all": ["IPR051330", "IPR007303"], "interpro_used": ["IPR007303", "IPR051330"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein possesses a Alpha-D-phosphohexomutase, C-terminal domain that forms the C-terminal region of enzymes in the alpha-D-phosphohexomutase superfamily, which catalyze phosphoryl transfer on sugar substrates. These enzymes, such as phosphoglucomutase and phosphomannomutase, participate in glucose metabolism and the biosynthesis of carbohydrates including lipopolysaccharides, alginate, and UDP-N-acetylglucosamine. Furthermore, the protein has a Alpha-D-phosphohexomutase, alpha/beta/alpha domain I domain that adopts a three-layer $\\alpha/\\beta/\\alpha$ topology and serves as a core component of enzymes catalyzing phosphoryl transfer on sugar substrates. This domain is integral to the alpha-D-phosphohexomutase superfamily, including phosphoglucomutases and phosphomannomutases involved in glucose metabolism, as well as bacterial enzymes driving lipopolysaccharide and alginate biosynthesis. It originates from Clostridiales bacterium and is classified with UniProt keywords Isomerase, Magnesium, and Metal-binding. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 4595, 17, 46, 17, 8078, 17797, 1947, 26455, 4127, 16, 45, 17, 4262, 3418, 1988, 4952, 1920, 45, 17, 4262, 3031, 1927, 5038, 1922, 1920, 4595, 17, 46, 17, 8078, 17797, 1947, 26455, 4127, 13975, 16, 2154, 18170, 12556, 3856, 1990, 9523, 6249, 18, 2144, 5038, 16, 2427, 1966, 8078, 22988, 1947, 26455, 4127, 1930, 8078, 8890, 1947, 26455, 4127, 16, 7352, 1922, 3817, 4714, 1930, 1920, 8132, 1927, 16282, 2710, 15614, 1036, 16, 17987, 16, 1930, 18500, 17, 56, 17, 6894, 22988, 17454, 18, 3677, 16, 1920, 2213, 2258, 43, 4595, 17, 46, 17, 8078, 17797, 1947, 26455, 4127, 16, 4595, 19, 4666, 19, 4595, 3418, 51, 3418, 1988, 24032, 43, 2559, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 13678, 1930, 10634, 1966, 43, 4728, 4594, 1927, 5038, 29601, 12556, 3856, 1990, 9523, 6249, 18, 2052, 3418, 1977, 12328, 1942, 1920, 4595, 17, 46, 17, 8078, 17797, 1947, 26455, 4127, 13975, 16, 2710, 8078, 22988, 1947, 26455, 4127, 1036, 1930, 8078, 8890, 1947, 26455, 4127, 1036, 3286, 1922, 3817, 4714, 16, 1966, 2486, 1966, 4543, 5038, 9228, 15614, 1930, 17987, 8132, 18, 2176, 22970, 2037, 17938, 26890, 1918, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 25510, 16, 13148, 16, 1930, 6048, 17, 2743, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MTYLDRYNEWLNSPYIDDDIKDELREISENKEEIKDRFYKDLEFGTGGMRGVIGAGTNRINKHIVARAIQGLANFINKSEHNLKSCVIAHDSRHKSEDFSVMAARVLAASGVKTYLFNGIRSTPELSFAVRELGCTAGIVFTASHNPPEYNGFKVYWDYGCQMLPEMAEELIGMIEQVSFNAINTISYEEALKQGNIVLIGQELDDMFISNVKAMRLRVNLDKDIKIVYTPLNGTGNVPVRRVLRECGYEKIYLVEEQLEPDPDFTTARYPNPEDEKAFELAYKKAREVDADLVIANDPDSDRLGLSVKTKSGEYKLLGGNQVGPLFINYILSTLKDKNAIPANPLVIKTIVTSELGRKVAEEFGAECLDTLTGFKYIGEKMELFAKNGEKDFIMGYEESIGYTMGPFVRDKDAVTMTLIACEMAAYYNMLDSDLMNELQNLYNRHGYFVDSLKSLTMEGKEGGEKIIQIMEYFRNTNIDKICECNVETISDYQTGVTKNLIQNSITSTGLPESNVLKFILDNGSWFVLRPSGTEPKIKIYFSVVGKDHDTAENFSNSLINEVMDTISQI", "metadata": {"id": "A0A3B9I8G8", "cluster": 12535956, "interpro_all": ["IPR005844", "IPR016055", "IPR005845", "IPR005846", "IPR005843", "IPR036900", "IPR005841"], "interpro_used": ["IPR005843", "IPR005844"], "interpro_unused": ["IPR005845", "IPR005846", "IPR036900", "IPR005841", "IPR016055"]}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein can be placed in the SAP domain superfamily, which comprises nuclear proteins containing a conserved 35-residue motif predicted to form a helix-turn-helix structure essential for DNA binding and chromosomal organization. This domain functions in diverse processes such as transcription, RNA processing, DNA repair, and apoptosis, often by targeting AT-rich chromosomal regions or mediating specific protein-protein interactions. It has been characterized in Bondarzewia mesenterica.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 9235, 3418, 13975, 16, 2154, 12936, 4254, 2697, 3165, 43, 5305, 3259, 17, 6181, 5219, 4396, 1942, 2386, 43, 7864, 17, 5165, 17, 7864, 3170, 4415, 1958, 2678, 2743, 1930, 9220, 5901, 18, 2052, 3418, 4088, 1922, 6445, 4028, 2427, 1966, 3213, 16, 3146, 4587, 16, 2678, 5059, 16, 1930, 4091, 16, 3868, 2007, 5133, 2019, 17, 5536, 9220, 3451, 2014, 10239, 2487, 2213, 17, 2213, 3719, 18, 2176, 2258, 2252, 4378, 1922, 5403, 1933, 6931, 17045, 1019, 16234, 1019, 18, 3], "output": "MASTPAPADLDLSKLTVPRLKALCKGRGITGYSKLGKAALIERLRGESLISDGTLSGGNTTHSEVSSNVLVPPVIFANVLSSTSLYAPSSSSAGLXXGXPCSSSQSTXRQKTXSSVSTPXVGLVAKSSLSATXPLTSSRTGNSSXRPSXAFSGFKXPAVPKLKLGAPLLKSNLQIQTXNVASLTISKPVSKRPEESENVRRSCLSSGPATXYPGXSXIYLXFPXXSXXVSLRPISGLSEKEXXQCVLVSRIPXHEKQLTVALRFLMTRLWFTISIGSSRQDPDEIWMXTVQSIPEAAXXGLKTESYYVLETTCEVIGRPHXRAXWSQYXXHRXSSSEENXSSPHASLFEHLKWADHGEYESGISRHWLGRMESKGEESTQMAQEFAGLSERAPNTKQKXXHMSMFLPAHHHVESMHLTGIGNVPLHPAEEDGVAPVWRDIIGCDERGLFVGPGTMSLAQLNEYVWTRMDESMAPLNPSFAAQPKPPPSVPSRYPPPTLGAPTGASATLSKRATAXTDKTSTAESSPPKKQKLSAXYTXASTSSSVLLXTXPAVPTNPGKRFKPTLPPSLSQRKHVHRWSIILLVWLRSVVVDAQEVVKSSMQPSGAAPVDDEXPVGVALRTIAERYVFACVVGNSVSGSWMSIAIAQTPGREYFILKDNGMQVGC", "metadata": {"id": "A0A4S4L7F4", "cluster": 15223514, "interpro_all": ["IPR036361"], "interpro_used": ["IPR036361"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein features a Heat shock protein 70 conserved site that represents the Hsp70 family of chaperones, which facilitate protein folding through ATP-dependent cycles of substrate binding and release. These proteins contain an N-terminal ATPase domain and a C-terminal substrate-binding region, operating in various cellular compartments under both normal and stress conditions. Moreover, the protein belongs to 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 characterized in Bicosoecida sp. CB-2014.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 4075, 43, 5631, 7418, 2213, 3895, 5305, 3200, 1988, 4972, 1920, 12886, 3416, 1927, 18098, 16, 2154, 6628, 2213, 10328, 2596, 4498, 17, 3100, 6355, 1927, 4510, 2743, 1930, 4012, 18, 2144, 2697, 5531, 1925, 56, 17, 4262, 9444, 3418, 1930, 43, 45, 17, 4262, 4510, 17, 2743, 3031, 16, 8654, 1922, 3425, 3689, 10436, 2441, 2321, 2791, 1930, 3071, 2961, 18, 3950, 16, 1920, 2213, 14440, 1942, 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, 4378, 1922, 8876, 1951, 6802, 3349, 3825, 2056, 18, 5529, 17, 4037, 18, 3], "output": "GGAAGGAGGKAVKGPVEAADSTAVIGLHLGATAGAVAVWADSGSGRPTVIANADGARTTSSVAVWVHAAAAGGEARSGTTVMAARLARAAAGAAEARAAAKAATWPWEVEWPESEEAEPVIVMTVPPPMVVRVTPTSVIALMLGKLKGEAEAYLGMPARAVLAARATSTPVAVIPTHIAAAIAYGFDDPAQPPPASSPLVATAVVSASPGGVLRTLATAVDHTVGGDAFDRCLFDHCAREFARKARGAKAGKRALSKSASTAIAIDSLWEGIDFHTSVSEALAAAGLTQADVTDVVLVGGASQMPRLQATVAAYVGGGAMLHTNVPHGAGAGGDGGDGGGGDAAKAIAFRHPATTVALADASFDDDAGAAPLADEAELSALRAAAAEAGVALAPRTVLVYDAGGSSVEAISGARATTRLLAACERQRFEDACAPLYGACVKPIA", "metadata": {"id": "A0A7S1G617", "cluster": 15411815, "interpro_all": ["IPR043129", "IPR018181", "IPR013126"], "interpro_used": ["IPR018181", "IPR043129"], "interpro_unused": ["IPR013126"]}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein features a Mur ligase, C-terminal domain that facilitates the sequential addition of amino acids to UDP-N-acetylmuramic acid during bacterial peptidoglycan biosynthesis. Adopting a dihydrofolate reductase-like fold, this domain is responsible for binding the incoming amino acid substrate in enzymes such as MurC, MurD, MurE, and MurF, as well as in folylpolyglutamate synthase and cyanophycin synthetase. Furthermore, the protein is classified under the Folylpolyglutamate synthetase family, which functions as an ATP-dependent enzyme responsible for the addition of polyglutamate tails to folate and folate derivatives to ensure their intracellular retention. In some bacteria, this enzyme serves a dual role by also catalyzing dihydrofolate synthetase activity. Structurally, members of this family typically adopt a modular two-domain architecture, with the active site located in an interdomain cleft adjacent to an ATP-binding P-loop. Furthermore, the protein carries a Mur ligase, central domain that functions as the ATP-binding catalytic module in the MurC, MurD, MurE, and MurF enzymes responsible for the stepwise assembly of the bacterial peptidoglycan stem peptide. This domain shares structural similarity with ATPase domains and is also present in folylpolyglutamate synthetase and cyanophycin synthetase, where it drives ATP-dependent ligation reactions for folate metabolism and cyanophycin storage. It is native to Rhodanobacter sp. C03 and carries UniProt keyword assignments Folate biosynthesis, Magnesium, and Metal-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, 4075, 43, 6185, 11905, 16, 45, 17, 4262, 3418, 1988, 11374, 1920, 9454, 2459, 1927, 3835, 4576, 1942, 18500, 17, 56, 17, 6894, 23010, 29085, 1935, 2687, 2409, 4543, 24183, 8132, 18, 20478, 43, 11842, 27851, 11386, 17, 3189, 3728, 16, 2052, 3418, 1977, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 4510, 1922, 5038, 2427, 1966, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 16, 1966, 2486, 1966, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 8921, 1930, 26898, 25818, 3665, 18185, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 3416, 16, 2154, 4088, 1966, 1925, 4498, 17, 3100, 4113, 5061, 1958, 1920, 2459, 1927, 16115, 26697, 21084, 18103, 1942, 13761, 1930, 13761, 8383, 1942, 6486, 2310, 4776, 7521, 18, 1922, 2673, 4802, 16, 2052, 4113, 10634, 43, 7064, 2770, 2007, 2222, 29601, 11842, 27851, 18185, 2455, 18, 12171, 16, 4678, 1927, 2052, 3416, 5745, 14103, 43, 16078, 2288, 17, 3418, 9335, 16, 1956, 1920, 3500, 3200, 4810, 1922, 1925, 13633, 2954, 1921, 14649, 6811, 1942, 1925, 4498, 17, 2743, 58, 17, 5881, 18, 3677, 16, 1920, 2213, 16252, 43, 6185, 11905, 16, 4101, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 6804, 9059, 1922, 1920, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 5038, 5061, 1958, 1920, 13846, 5957, 1927, 1920, 4543, 24183, 4402, 4207, 18, 2052, 3418, 16495, 4346, 6796, 1956, 9444, 4682, 1930, 1977, 2222, 2481, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 1930, 26898, 25818, 3665, 18185, 16, 2597, 2176, 15435, 4498, 17, 3100, 11102, 5298, 1958, 13761, 4714, 1930, 26898, 25818, 3665, 7451, 18, 2176, 1977, 6196, 1942, 11490, 9286, 7972, 2341, 1915, 2056, 18, 24948, 1010, 1930, 16252, 20709, 11121, 2538, 18306, 13761, 8132, 16, 13148, 16, 1930, 6048, 17, 2743, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MTRTLAEWLAYQEHVNVRSIELGLDRVREVWQRMGAPAPAHRVITVGGTNGKGSTVALLEAMLRAAGLRVGAFTSPHLLDYNERVRIDGANVDDAALTASFERIDAARGAIPLTYFEFGTLAALDLFARAGLDVAVLEVGLGGRLDAVNIIDAAVAIVTTVDLDHMDWLGPDRDSIGREKAGIARAGRPVIVGELDPPAGLLDALAACGARVERAGLDFHFERHADGWRWQHRDGSAMELPDPALAAPVQFANAAAAIAALHVLWAGDVSFAPKDVFAAVSAGLHEVRVPARLQSLGGDPLLIVDVGHNPQAARALAEWLDARPAGRVHAVYGALADKDVAGVIGALGARIDHWHLAGLDHATLRGLAVDALAGILRQTLPQPAFDTHADVAAALAAARAAARPGECILAFGSFFVASAVIAEAVG", "metadata": {"id": "A0A1V3Q066", "cluster": 15776537, "interpro_all": ["IPR001645", "IPR036565", "IPR004101", "IPR036615", "IPR013221"], "interpro_used": ["IPR004101", "IPR001645", "IPR013221"], "interpro_unused": ["IPR036615", "IPR036565"]}, "task_type": "autoregressive"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein includes 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 includes a Orc1-like, AAA ATPase domain that contains a P-loop motif characteristic of the AAA superfamily and functions in ATP binding and hydrolysis. This domain is typically found in Origin Recognition Complex (ORC) subunits involved in DNA replication initiation and in serine/threonine-protein kinases such as PknK. Moreover, 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 native to Acidimicrobiia bacterium and is associated with UniProt keywords TPR repeat.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 5921, 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, 5921, 43, 2014, 5800, 17, 3189, 16, 13835, 9444, 3418, 1988, 5461, 43, 58, 17, 5881, 5219, 6293, 1927, 1920, 13835, 13975, 1930, 4088, 1922, 4498, 2743, 1930, 9128, 18, 2052, 3418, 1977, 5745, 2435, 1922, 4853, 5708, 2796, 12, 2014, 1030, 13, 6991, 3286, 1922, 2678, 5158, 6035, 1930, 1922, 8468, 19, 13143, 17, 2213, 7784, 2427, 1966, 4652, 1022, 1040, 18, 3950, 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, 6196, 1942, 2687, 1980, 1935, 15129, 3907, 1019, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 22288, 6865, 18, 3], "output": "MSDEVSRLREAIAVLEDQRALPQLEKALATAEDQEHQRKQVTVLFADVSGDRIIVEHGGRVDKHIGDAVMALWGAPVAREPLQMRIGLNTGAVLVGTVGSTEEYTAIGHSHDTFALVSGLFNVVALEPITVKGVTEPVEEELAVLTSALAPDLSSGSPTRLVTVMGEAGVGQERGTYLFRGRATADDEHDAYALLRDVVYFRYEIADSDSPGEAKSKIGIDYSDDPAISGLLEEPRLILERAERHLDIHWADNESLDLFERLADEATSYPFLMVANARPIAWRRTVRLEALPASEADALFDSIFSRMAVVPPELRTLIDDGAIAAGEEWIADESRLENLSIPRTLLQDASVIGRVFWQDALVSIGQRRELVYQQQASDFADTREYKLRRVYHAAIAAWLERRSAGRQGEFLVVAAHQARQSYAPEAAIRDYQQALQTLLDTLEGLGDALSTRGRYEEAAAAFHGLAVALAYKGDFRAGLEAAEAGATACLLRLGELAQAEETVSSVVTASQALGNEAQLAKFEEAAATFRAMSSDESVMPILNNLGVLDERDGEMVYSSNLGMAKLGMGSTDETHRGLAEALLKRGEIEEARLAALEALRLAVEAIGDTLEVTSAGIGDTFDAEACFSKAVALAEEEEDESELARSLELFESLGVGGELDRWRTAGETARSSAVLGDDVVDSAVANLRFTRMSETMDHEDVAEKMNAIWASLNDPERAVTAALAMQDALADFSPPGTDYTVNLASRLESAAPAGGVLISTYHVRERKPREFRVGARGVAGVITPTVGRKSRLLYEFFNWLDVLRSGLVAAAGEKAAQWAPFIGHVRQAIIAGADDRYIVMLIELATRRPEWVKNEDMVVERSEGNPFYLEELVKMTGVLQARVDAMPRNERKALAIDMNPPPGPGDVAAWMASIFKHAILHDVVYESVTRASRIAEHYARAGHDGERARWDLWNAEPDGAPDPEELLRLAGADDDRAAEARGRARTLDDEMLFVRCRWMQSWAQNLSGVLQYTKGNYDAATAAARGHYESAVGRYAEALDIAKSVGSEAESLFRNVIAMATSGLNVLSEAPDDEAGAWRLLGLVSGSAAWGGWAARADLVDRAG", "metadata": {"id": "A0A7Y1UYH0", "cluster": 16166635, "interpro_all": ["IPR001054", "IPR041664", "IPR029787", "IPR027417", "IPR011990", "IPR019734"], "interpro_used": ["IPR019734", "IPR041664", "IPR001054"], "interpro_unused": ["IPR011990", "IPR029787", "IPR027417"]}, "task_type": "infilling"} {"instruction": "The protein should feature 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 originates from Ambrosiozyma monospora (Yeast) (Endomycopsis monosporus). Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 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, 22970, 2037, 6168, 2263, 3940, 3105, 1019, 18491, 21086, 12, 5688, 13, 12, 16239, 14930, 2972, 8362, 18491, 2074, 1957, 13, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MDLFSIQQQNTNSQFQIHEDSIIEQLKVEPIWDGIPVSKPLGPKTLREREQIRQLENETSNVINSKPQENTSQEQLNGGVYTMQLWKLYSNSLMPTETGNRNGDGYDELDTHFTRLVLFIGSQCRLQLLVDRFNYVNMKSRTLSIIDGDFNDFENDERITLNFVRINLLADEWALEVLGPAQLQNVTLLFEKVCNVTVIDLFGKISVVLSDTQTLGNNVKKNSLFHANIPGNLFTILETTFKYLNVETLIEKSTQARKAFAESFSCYKPPSSTTSIVMKENPETNYDPEREKRSVYHTKYEHGNYRKIIKVKHKHVRFLLGNKGARITRIRKRTKVHIKIMDDDKENGFQGNININGWPVDDTIDSYQSICLTGEEKEVNIVEKMLLTEIKSGFQLYI", "metadata": {"id": "A0A9W6YT29", "cluster": 17352618, "interpro_all": ["IPR004087", "IPR004088", "IPR036612"], "interpro_used": ["IPR004087"], "interpro_unused": ["IPR036612", "IPR004088"]}, "task_type": "autoregressive"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein is categorized in the Lipoprotein localisation LolA/LolB/LppX superfamily, which facilitates the translocation of lipoproteins and complex lipids to the bacterial outer membrane. Members of this family, including LppX, LolA, and LolB, share a U-shaped $\\beta$-half-barrel fold with a large hydrophobic cavity that accommodates lipid substrates during transport in Gram-negative bacteria and Mycobacteria. Moreover, the protein can be placed in the Outer membrane lipoprotein carrier protein LolA-like family, which functions as a periplasmic molecular chaperone essential for the sorting and transport of lipoproteins to the outer membrane. These proteins accept lipoproteins released by the inner membrane ABC transporter LolCDE, forming a water-soluble complex that traverses the periplasm. Subsequently, they interact with the receptor LolB to transfer and anchor the lipoprotein to the outer membrane. It is produced by Pelagibacteraceae bacterium TMED233 and has UniProt annotations Signal.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 9694, 22376, 3004, 5148, 19, 3004, 1024, 1014, 19, 8182, 1034, 1039, 13975, 16, 2154, 11374, 1920, 7849, 1927, 18393, 1930, 2796, 8238, 1942, 1920, 4543, 7642, 3260, 18, 4678, 1927, 2052, 3416, 16, 2710, 8182, 1034, 1039, 16, 3004, 5148, 16, 1930, 3004, 1024, 1014, 16, 7948, 43, 63, 17, 9132, 8, 38, 4666, 8, 17, 4768, 17, 19560, 3728, 1956, 43, 3103, 7919, 8568, 1988, 16848, 1036, 4486, 6249, 2409, 4860, 1922, 8604, 17, 3136, 4802, 1930, 23446, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 7642, 3260, 9694, 9685, 2213, 3004, 5148, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 24334, 3272, 14044, 4415, 1958, 1920, 11404, 1930, 4860, 1927, 18393, 1942, 1920, 7642, 3260, 18, 2144, 2697, 5861, 18393, 6988, 2007, 1920, 6671, 3260, 7219, 9054, 3004, 8293, 3695, 16, 7402, 43, 3224, 17, 6622, 2796, 1988, 27480, 1918, 1920, 20171, 18, 5326, 16, 2611, 6310, 1956, 1920, 3148, 3004, 1024, 1014, 1942, 3856, 1930, 13333, 1920, 9694, 1942, 1920, 7642, 3260, 18, 2176, 1977, 4152, 2007, 7874, 29284, 7972, 2341, 7124, 1972, 3336, 14061, 22377, 9091, 6498, 1930, 2258, 20709, 15010, 2733, 18, 3], "output": "MKRNLLFILVLYIFFCTEVFATQKKNIISNLSKIKNITFDFEQTIDEEKEKGKCVIKYPKLINCSYEGIKGKKMISNGNSLVIKITNSDISYIYPLESTPLNYILDKNYIISEIKKLEPKFIEDKYIYFTMLNENQKLNIFFDNKDFHIIGWQTEDIYQNLVITFISKIKINQKIDDNLFKLPKLN", "metadata": {"id": "A0A3R7SZG5", "cluster": 19611020, "interpro_all": ["IPR029046", "IPR004564"], "interpro_used": ["IPR029046", "IPR004564"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is categorized in the Ubiquitin-like modifier Hub1/Ubl5 family, which functions as a modulator of spliceosome performance and facilitator of alternative splicing. Lacking the C-terminal glycine necessary for covalent attachment, members bind non-covalently to the HIND element of spliceosomal proteins such as Snu66 and Prp38. Additionally, they interact with the DEAD-box helicase Prp5 to mediate enhanced, though error-prone, splicing. Moreover, the protein is grouped in 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. It is identified in Castor canadensis (American beaver) and is classified with UniProt keywords Ubl conjugation pathway.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 6526, 17, 3189, 22883, 13988, 1009, 19, 4803, 1024, 1015, 3416, 16, 2154, 4088, 1966, 43, 18521, 1927, 10708, 4283, 3604, 1930, 29543, 1927, 5012, 8490, 18, 7046, 1920, 45, 17, 4262, 10646, 4680, 1958, 13577, 8576, 16, 4678, 4566, 2447, 17, 16590, 1942, 1920, 8858, 6149, 1927, 10708, 4969, 2697, 2427, 1966, 3437, 1032, 7283, 1930, 11533, 4745, 18, 4950, 16, 2611, 6310, 1956, 1920, 9535, 17, 5758, 15318, 11533, 1015, 1942, 8265, 4256, 16, 4170, 4622, 17, 10424, 16, 8490, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 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, 2176, 1977, 2899, 1922, 12273, 1924, 2112, 10185, 8362, 12, 5339, 1998, 14666, 13, 1930, 1977, 5947, 1956, 20709, 11569, 4803, 1024, 14122, 3374, 18, 3], "output": "MTEVVCKDCTGDKLITAKTSTHKNKIVRFYYQLGEKVKFQTNDTTGDLEKVLKKSQIVLKDHMSLGDCEIHDGMIL", "metadata": {"id": "A0A8C0ZNP0", "cluster": 20138872, "interpro_all": ["IPR039732", "IPR029071"], "interpro_used": ["IPR039732", "IPR029071"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein is included in the Large ribosomal RNA subunit accumulation protein YceD family, which facilitates the accumulation of the large ribosomal subunit and is essential for maintaining 23S rRNA levels. These proteins are universally conserved in bacteria and plants, where they localize to the chloroplast. It has been detected in Alphaproteobacteria bacterium.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 1977, 3063, 1922, 1920, 3103, 11196, 3146, 5903, 4858, 2213, 22386, 1919, 3416, 16, 2154, 11374, 1920, 4858, 1927, 1920, 3103, 11196, 5903, 1930, 1977, 4415, 1958, 8231, 3020, 1036, 9067, 2428, 18, 2144, 2697, 2032, 22809, 5305, 1922, 4802, 1930, 4793, 16, 2597, 2611, 14380, 1942, 1920, 17471, 18, 2176, 2258, 2252, 3330, 1922, 4595, 9218, 1021, 10296, 14061, 18, 11586, 5655, 3581, 18, 3], "output": "MSPARNSAPLLDAGVRLDALPLAGLSVDRLEAELLARPIKGGIEVGGSLDAEVTQECVVSFVSGEPEHNAGAEVFVDLDGADPPDYFEGPEPRKPGAEIDPDYRDGEDDKDSPFKALKDLKPTKPRRLAVAATKEQCAAIAERLGIEPVPERIAEKPFRLFLSGADLSEWLIETLALALNPY", "metadata": {"id": "A0A947WQY9", "cluster": 21086883, "interpro_all": ["IPR003772"], "interpro_used": ["IPR003772"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: 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. Additionally, the protein should include a Sel1-like repeat that constitutes tetratricopeptide repeat sequences originally identified as key negative regulators of the Notch pathway in *Caenorhabditis elegans* receptors. These repeats also occur in mammalian pancreatic proteins, though their specific functions in that context remain largely uncharacterized. Additionally, the protein falls within the The Sel1/AlgK family, which encompasses proteins involved in diverse structural and regulatory functions, including endoplasmic reticulum quality control and exopolysaccharide biosynthesis. Members facilitate the ER-associated degradation (ERAD) of misfolded proteins and Notch signaling, or contribute to biofilm formation by potentially catalyzing mannuronate polymerization. Some variants also provide positional information for organelle localization or bind secretory immunoglobulin A to evade host immune defenses. It has been characterized in Gammaproteobacteria bacterium and is linked to UniProt keywords Coiled coil and TPR repeat. 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, 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, 4950, 16, 1920, 2213, 3066, 3951, 43, 2484, 1009, 17, 3189, 6865, 1988, 14879, 12470, 3319, 21305, 6865, 3709, 10398, 2899, 1966, 3834, 3136, 9098, 1927, 1920, 8091, 3374, 1922, 14, 22418, 10861, 14, 4086, 18, 2144, 9569, 2222, 4704, 1922, 6492, 6356, 2697, 16, 4170, 2310, 2487, 4088, 1922, 1988, 4491, 5555, 6318, 24528, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 1920, 2484, 1009, 19, 4326, 1040, 3416, 16, 2154, 21569, 2697, 3286, 1922, 6445, 4346, 1930, 4948, 4088, 16, 2710, 13355, 12279, 3455, 2285, 1930, 18930, 13811, 2012, 9466, 8132, 18, 4678, 6628, 1920, 2668, 17, 2458, 4877, 12, 14827, 13, 1927, 20303, 2697, 1930, 8091, 3197, 16, 2014, 4672, 1942, 9638, 3337, 2007, 5063, 29601, 7338, 10366, 2010, 11486, 18, 2673, 4936, 2222, 3394, 20172, 2988, 1958, 19309, 5363, 2014, 4566, 11518, 11837, 43, 1942, 28917, 4423, 3743, 24226, 18, 2176, 2258, 2252, 4378, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 17524, 9121, 1930, 22288, 6865, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MINFEKILQASLQGETGATRLLRSRIDKGKLSLQELSRCIECFDEEIANKNSHAMYLRACMHETGQGGEVNYAAADSLFFQAQELGNSDAICRIACSYYTEGNYRTAFDLFKQVINKDPTNRAALYFMAWMHHKGEGCSQNTELAIPLFDKAIELGHAEAMNAAGCIARDTRKYPKAIALFDRAIKLKNVSAMINRAGMHEENEKWLEAVKLYRRAYFQSSDRKVTDYAARRIQYINRFKISSLEIQYTASLVGANDSYLNTHPNKFLNLLASEDASLHPVGLNFFVKNFPSNGFDRINQANIDFIASWYLTSANQELQKRNIAGALSLYSKVPSNSGSRGAACYGMGIHIYQNTLQKNNDEINALEKAKQYLEEGSKLGDLNCIEFYTKALQSIINPDMKEDSTDDLLLESLKLDYEALVDLRYTSMLKTFTDEHKLTHLNFWADKAGWFEGTDVTFNDKKITVPKGIAVIYDIINDPIKTSFEKITALSTAVSLNDSWFALVKPKYITKDCYMAASNLLSLITSTPLSKVNNLEGADQQQEAPVVIIQDKPARQTSRSNSVILLTPKKKIAEQVVTLPIKLSVGSASSSIRLSQNRARINFGSDDKNKNEEQLPSNEEQLSSNEEDERVVLKSKY", "metadata": {"id": "A0A8T3Q5N5", "cluster": 23294450, "interpro_all": ["IPR006597", "IPR050767", "IPR011990", "IPR019734"], "interpro_used": ["IPR019734", "IPR006597", "IPR050767"], "interpro_unused": ["IPR011990"]}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein carries a Organic solvent tolerance-like, N-terminal domain that contributes to bacterial cell envelope stability and organic solvent tolerance by assisting in the transport of lipopolysaccharides and lipoproteins to the outer membrane. It is typically found in export system proteins, such as LptD and LptH, which are essential for outer membrane biogenesis. Moreover, the protein falls within the Lipopolysaccharide export system LptA family, which facilitates the transport of lipopolysaccharide (LPS) across the bacterial periplasm to the outer membrane. Members of this family adopt a beta-jellyroll structure to bind LPS directly and interact with LptC and LptD to form a structural bridge essential for cell envelope integrity and viability. It has been characterized in Candidatus Aminicenantes bacterium 4484_214 and contains UniProt keyword associations Transmembrane helix.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 16252, 43, 6805, 7596, 6555, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 7624, 1942, 4543, 2024, 11262, 5057, 1930, 6805, 7596, 6555, 2007, 27840, 1922, 1920, 4860, 1927, 15614, 1036, 1930, 18393, 1942, 1920, 7642, 3260, 18, 2176, 1977, 5745, 2435, 1922, 12660, 2433, 2697, 16, 2427, 1966, 8182, 1031, 1007, 1930, 8182, 1963, 16, 2154, 2032, 4415, 1958, 7642, 3260, 13008, 18, 3950, 16, 1920, 2213, 12182, 2651, 1920, 15614, 12660, 2433, 8182, 3857, 3416, 16, 2154, 11374, 1920, 4860, 1927, 15614, 12, 5887, 13, 3436, 1920, 4543, 20171, 1942, 1920, 7642, 3260, 18, 4678, 1927, 2052, 3416, 14103, 43, 4666, 17, 8988, 11560, 5134, 11560, 3170, 1942, 4566, 5887, 4103, 1930, 6310, 1956, 8182, 6916, 1930, 8182, 1031, 1007, 1942, 2386, 43, 4346, 11925, 4415, 1958, 2024, 11262, 7996, 1930, 6432, 18, 2176, 2258, 2252, 4378, 1922, 14550, 1031, 1957, 8584, 2927, 24254, 14652, 14061, 29877, 1006, 41, 16708, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MNIPPVLKVISTLRRLSIILLVTLVVLLGLDIIFSLSHGGKSPDRLDLDSSFFVEKKEHYLGEKGLFHLEGNVEIVFPQRQKGEDVIIRAESLLYDQEFNHFWSTRPEKVFEGKGKVKVRSGQWTLEADFFQFNLRSRKMVSQGRVAFAGSGEVTLQHGASQGKAGEVTFKLGAEEGFIKWLNLKNGVEAQLQDEEIKADSIDIEIFAQTKTLKKIEIRGGARLAFFSEASDYSQLQAEKIKAFWTQNRSIKKVIKLEIWGPKQMISVSPGPQENAFFKSPTLEFKAGKIEIKTQEGDLRGRDGVEQKTCFLTCQEMRRKAEGRRLIVSGKVKIWQGDRVLKAEKVILNPISSQLFRIQGESMRFDPGASLLEFEQDIALEMGEVAIKCLRLLVFLDPETRYQFTQQVLIMSGQPLLEDPSRGKIRGDKLTFHLPDDRIVIENEGEERSILLIKSKIQFQELREGQKEHLRVRAEKPAQVEWGEMKIEAERVDYYAQLTSFLGGSKSLILKTQRFTYDRRTKIGWEKGQSLLQSGLSAWFYLFSQAEESVSFIRKGGETQDLFIGGEATLERALEQAESSPPPGFFDPEAKGQVEVNMVEVKPSQGDQHQLVKFEALDQVQVSYQKVTAAAQKAE", "metadata": {"id": "A0A1W9P9G7", "cluster": 23627709, "interpro_all": ["IPR052037", "IPR005653"], "interpro_used": ["IPR005653", "IPR052037"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein has a RNase H-like domain that confers ribonuclease H activity to reverse transcriptases, enabling the conversion of single-stranded retroviral RNA genomes into double-stranded DNA for integration into the host chromosome. This catalytic module is also found in animal retrotransposon-like proteins. Additionally, 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. It originates from Peronospora belbahrii. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 9843, 50, 17, 3189, 3418, 1988, 16556, 18347, 2051, 50, 2455, 1942, 5267, 13335, 1036, 16, 12180, 1920, 7309, 1927, 2957, 17, 10338, 16599, 3146, 7313, 2460, 4825, 17, 10338, 2678, 1958, 7122, 2460, 1920, 4423, 5597, 18, 2052, 6804, 9059, 1977, 2222, 2435, 1922, 4027, 27181, 1916, 17, 3189, 2697, 18, 4950, 16, 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, 2176, 22970, 2037, 2079, 23557, 3508, 8846, 3262, 7972, 6570, 3907, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MIDDASTSDDSDGEMSSASDNVFSVITHGPPSTRAYQNEEKMLRARRALSDPDCPFSVVCDASDFAIGSALLQVDSEGQERIIALESRQLRAADMNYPVHDKELLAMNDKVASSLAENGSLALLFAEHNFEVKYKPGKQNVLADALLRRPDYKLAHLTVVSSSVTDRIRKAYARDEACVAILQALGSADFENSKVKLPPRNRARLHRYALTDGLLYYNTGSDDQPRVVVPHDEDLKYQILYEAHDTPRGSHLGREKTYTRVKPSPNTAALLASLPVPSGL", "metadata": {"id": "A0AAU9L9Z4", "cluster": 25318985, "interpro_all": ["IPR043502", "IPR041577"], "interpro_used": ["IPR041577", "IPR043502"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to make a polypeptide chain that will have the following function description: The protein has a Domain of unknown function DUF2007 domain that is found in a variety of bacterial sequences. As a DUF, it currently lacks a characterized biological role, enzymatic activity, or specific binding partner. It has been detected in Gemmatimonadota 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, 2258, 43, 3418, 1927, 5435, 2347, 4855, 6680, 21982, 3418, 1988, 1977, 2435, 1922, 43, 5386, 1927, 4543, 3709, 18, 1966, 43, 4855, 1038, 16, 2176, 5077, 13012, 43, 4378, 3933, 2770, 16, 8145, 2455, 16, 2014, 2487, 2743, 8240, 18, 2176, 2258, 2252, 3330, 1922, 10607, 3368, 2265, 12502, 22389, 3857, 14061, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MARWETFATAPDQLTAEMWRDLVRQAGVECEIRPGDTVRFLGLSPYPVRLIARDGDLDRARAALDAALGRGEEADPI", "metadata": {"id": "A0A938KY71", "cluster": 25797776, "interpro_all": ["IPR018551"], "interpro_used": ["IPR018551"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "\"The protein is included 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. Furthermore, the protein contains a RING finger protein 37 N-terminal domain that serves as a variable regulatory region in the U-box-containing protein RNF37. Moreover, the protein should feature a XPG N-terminal domain that constitutes a conserved catalytic region within the XPG/RAD2 family of structure-specific DNA endonucleases. This magnesium-dependent domain participates in nucleotide excision repair by facilitating the cleavage of DNA strands at the junction between duplex and single-stranded regions. It originates from Rhipicephalus sanguineus (Brown dog tick) (Ixodes sanguineus).\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 1977, 3063, 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, 3677, 16, 1920, 2213, 5461, 43, 6335, 8497, 2213, 3191, 56, 17, 4262, 3418, 1988, 10634, 1966, 43, 4650, 4948, 3031, 1922, 1920, 63, 17, 5758, 17, 3165, 2213, 20077, 5494, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 15930, 1029, 56, 17, 4262, 3418, 1988, 14879, 43, 5305, 6804, 3031, 2651, 1920, 15930, 1029, 19, 4226, 1028, 3416, 1927, 3170, 17, 2487, 2678, 18697, 1036, 18, 2052, 13148, 17, 3100, 3418, 17241, 1922, 5489, 10940, 5059, 2007, 12440, 1920, 6404, 1927, 2678, 13214, 2019, 1920, 6910, 2192, 12450, 1930, 2957, 17, 10338, 3451, 18, 2176, 22970, 2037, 3617, 2049, 2927, 6256, 1957, 22671, 19616, 1957, 12, 8084, 6567, 12085, 13, 12, 13848, 7019, 22671, 19616, 1957, 13, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MGVKDLWEVLAPVARKVQLEDLRGKRLAVDLSGWIVILLVPSKRTSTVRHYSNRHQHHVVQLSETLTPDVMAIDDVGNLISADRRRNGFMAEYFIKPPVSILLTLPCPTELSCVVVGLTATRDDFVLIGRKFGATDEEVVRLRNRCYVPRGPFASLMRDGGSPSFAYESRLKVRLICAMGSASIGLGSLQVWGQPMTSLCSLAAQEDLIRTDQCRSPPAPTVPESLQAKSGGLLQEGAGLATEFHIPTDFQDAESEQMRAKMRQPTIRFCNKNVGTLIECDQICAEGYRGPVKLTGFEIWVSQTGVGDTTTSGTGETLKTAYCKHVCRKFLATTDFNREHSA", "metadata": {"id": "A0A9D4PAM2", "cluster": 25904668, "interpro_all": ["IPR029060", "IPR039847", "IPR045696", "IPR006085"], "interpro_used": ["IPR029060", "IPR045696", "IPR006085"], "interpro_unused": ["IPR039847"]}, "task_type": "infilling"} {"instruction": "I need a polypeptide chain that performs the following role: The protein belongs to 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 is derived from uncultured Geobacillus sp. 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, 14440, 1942, 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, 1977, 3595, 2037, 5269, 21058, 14136, 7972, 10401, 5277, 1036, 2056, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MDFQTVDDSNPRGSYNWGYDPLLYFAPEGSYSSDPDDAYKRITELRHLVHVFHENGLRIVMDVVFNHVFDALTNPLEVLCPGYYFPPQRRWDSFQRQLLRQ", "metadata": {"id": "A0A060CI14", "cluster": 28237089, "interpro_all": ["IPR017853"], "interpro_used": ["IPR017853"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Give me an amino acid sequence that can fold into a protein with the following function: The protein carries a HAUS augmin-like complex subunit 6, N-terminal domain that contributes to mitotic spindle assembly, maintenance of centrosome integrity, and the completion of cytokinesis. This domain functions by interacting with the NEDD1-gamma-tubulin complex and recruiting it to the spindle to promote microtubule polymerization. It is present in Leucosporidium creatinivorum and features 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, 16252, 43, 2118, 1957, 6725, 8547, 17, 3189, 2796, 5903, 26, 16, 56, 17, 4262, 3418, 1988, 7624, 1942, 9566, 10716, 5957, 16, 6291, 1927, 19959, 7996, 16, 1930, 1920, 9297, 1927, 20825, 18, 2052, 3418, 4088, 2007, 8615, 1956, 1920, 20210, 1009, 17, 7034, 17, 9332, 2796, 1930, 17040, 2176, 1942, 1920, 10716, 1942, 5527, 10544, 11486, 18, 2176, 1977, 2481, 1922, 9906, 9890, 9734, 9340, 2068, 17279, 1930, 4075, 20709, 11569, 2733, 18, 3], "output": "MSWINSIQLLIIPNTFLLIGPYSPSTLSQLSPCSFQSTSPLTHRLRHADLILYSLLTHITPSLVSQLPLWPPLDHQAAVKLRAELSKQVEKVLKAEKDTWQEQLTWRRSFLDEAKGEKWERVLDALAAVALRTALERRELQDRLADLGPLPSLSLPASNIAESTSRALELYLTESSLASSLVLQRSSELAHLRQQGRELLDTRASLAKDGKVKKEHSGLDLLHLKALRDQRAQKLRAGMWELLKKGDPRAIVGEERDAQSAKTSNSRPNTRTPSATPSSAPQPTPASHLALLASLSTLSNPPPPIPLPSHTDISTTSAPSQTSAPPSSWSAALALDRERLRGLPTPVPPPAPHTAATGAAPSSAFNFSPPPSSSPSSSSRLLRPRPSSSSAPADDDSLELRISRILDSLDPSSPPPTSPASAPSTEQTELAGAKAPRRSRLPERVKIQSRVEVPEKGKGERVVVQGERERGKEPLKEVQPQPVSRQRDRASEREREEAPTPKALGLGKDAKRVLESMLDGDLSMSDEGEVGQVSY", "metadata": {"id": "A0A1Y2FPR2", "cluster": 447106, "interpro_all": ["IPR028163"], "interpro_used": ["IPR028163"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has the following function: The protein is a member of the BolA protein family, which functions as a stress-responsive morpho-protein involved in regulating cell shape and the switch between elongation and septation during division. These proteins are typically induced during the transition to the stationary phase or under stress conditions, suggesting a general role in cellular adaptation. Some members may also induce the transcription of penicillin-binding proteins. In addition, the protein falls within the BolA/IbaG family, which comprises transcriptional regulators and stress response proteins that modulate cell morphology, growth, and biofilm development. These proteins contribute to general and acid stress resistance, while eukaryotic members specifically act as mitochondrial iron-sulfur cluster assembly factors involved in oxidative stress protection. It originates from Deltaproteobacteria bacterium. 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, 10608, 1019, 2213, 3416, 16, 2154, 4088, 1966, 43, 3071, 17, 8487, 3901, 1037, 17, 2213, 3286, 1922, 6773, 2024, 5989, 1930, 1920, 6195, 2192, 9971, 1930, 8394, 1943, 2409, 8451, 18, 2144, 2697, 2032, 5745, 2719, 2409, 1920, 4832, 1942, 1920, 12563, 3193, 2014, 2441, 3071, 2961, 16, 3783, 43, 3335, 2770, 1922, 3689, 7810, 18, 2673, 4678, 2278, 2222, 4769, 1920, 3213, 1927, 9957, 17, 2743, 2697, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 10608, 1019, 19, 27931, 1029, 3416, 16, 2154, 12936, 5224, 9098, 1930, 3071, 2644, 2697, 1988, 8480, 2024, 6076, 16, 2905, 16, 1930, 9638, 2740, 18, 2144, 2697, 4672, 1942, 3335, 1930, 2687, 3071, 3554, 16, 2679, 10825, 4678, 4475, 4033, 1966, 4596, 5680, 17, 12585, 4377, 5957, 2790, 3286, 1922, 5163, 3071, 6202, 18, 2176, 22970, 2037, 9649, 9218, 1021, 10296, 14061, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MRRELLLARIQESLEPTFIELVDESYKHSAGPDAGTHWRCVVVSAAFDGKRLLQRHRLVYGALGDAMNTFVHAFSPKTLTPTEYSASGQAVQHDTPDCMGGAKAH", "metadata": {"id": "A0A2E7UWC4", "cluster": 563276, "interpro_all": ["IPR002634", "IPR036065", "IPR050961"], "interpro_used": ["IPR002634", "IPR050961"], "interpro_unused": ["IPR036065"]}, "task_type": "autoregressive"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein incorporates a HAT C-terminal dimerisation domain that mediates the formation of extremely stable dimers at the C-terminus of transposases belonging to the Activator (hAT) superfamily. It occurs in Rhizophagus irregularis (strain DAOM 181602 / DAOM 197198 / MUCL 43194) (Arbuscular mycorrhizal fungus) (Glomus intraradices).", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 19683, 43, 16133, 45, 17, 4262, 7632, 6284, 3418, 1988, 10412, 1920, 3337, 1927, 8113, 4700, 13351, 2019, 1920, 45, 17, 7822, 1927, 12935, 2319, 10588, 1942, 1920, 9518, 12, 16133, 13, 13975, 18, 2176, 5110, 1922, 13458, 4965, 1957, 11499, 1937, 12, 3943, 3692, 1947, 16997, 5127, 1028, 19, 3692, 1947, 21307, 8364, 19, 3422, 1024, 29672, 11226, 13, 12, 9859, 10742, 5078, 24062, 1923, 16461, 13, 12, 25632, 23084, 5153, 26208, 3590, 13, 18, 3], "output": "MVPNWSLKSPSKPTSILSFRAVKSVKKFCLSIKKFVLFSREYGAPNLAEFACRLFSIPPNSATSERVWSLMEKSFINKSKKTKGSLNIYNELNDDINDDDVSDEDNMDVDELITYE", "metadata": {"id": "U9T3P9", "cluster": 1750744, "interpro_all": ["IPR008906"], "interpro_used": ["IPR008906"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein incorporates a SAM-dependent methyltransferase RsmB-F/NOP2-type domain that functions as the conserved catalytic core for class I-like enzymes responsible for methylating specific cytosine residues in ribosomal RNA. Found across all cellular organisms, this domain utilizes S-adenosylmethionine to modify targets such as 16S or 25S rRNA, thereby playing a critical role in ribosome biogenesis. Also, the protein is associated with the RNA (C5-cytosine) methyltransferase family, which catalyzes the S-adenosyl-L-methionine (SAM)-dependent methylation of the C5 position of cytosine bases in RNA sequences to produce C5-methylcytosine. The catalytic core adopts a Rossmann fold to accommodate the cofactor and employs a mechanism involving a covalent intermediate formed by a conserved cysteine residue. These enzymes are widely distributed across archaea, bacteria, and eukaryotes, often localizing to the nucleus or nucleolus to modify substrates such as ribosomal RNA. 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. It is found in Thermoplasmatales archaeon SM1-50. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 19683, 43, 2235, 17, 3100, 16478, 4366, 17010, 17, 48, 19, 30272, 1028, 17, 2601, 3418, 1988, 4088, 1966, 1920, 5305, 6804, 4728, 1958, 2921, 51, 17, 3189, 5038, 5061, 1958, 4963, 2287, 2487, 19032, 4248, 1922, 11196, 3146, 18, 2435, 3436, 2136, 3689, 7373, 16, 2052, 3418, 18127, 61, 17, 29283, 23568, 11215, 1942, 11675, 4845, 2427, 1966, 11209, 2014, 2637, 1036, 9067, 16, 6113, 14797, 43, 4140, 2770, 1922, 12794, 13008, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 3146, 12, 13441, 17, 19032, 13, 16478, 3416, 16, 2154, 17097, 1920, 61, 17, 29283, 17, 54, 17, 12417, 12, 2235, 13, 17, 3100, 5547, 1927, 1920, 13441, 3507, 1927, 19032, 11137, 1922, 3146, 3709, 1942, 5074, 13441, 17, 4963, 27932, 7506, 18, 1920, 6804, 4728, 24032, 43, 18215, 8890, 3728, 1942, 16848, 1920, 15155, 1930, 22620, 43, 2856, 5884, 43, 13577, 6129, 5333, 2007, 43, 5305, 8666, 6181, 18, 2144, 5038, 2032, 5673, 6533, 3436, 21501, 16, 4802, 16, 1930, 15021, 16, 3868, 29507, 1942, 1920, 5607, 2014, 27542, 1942, 11675, 6249, 2427, 1966, 11196, 3146, 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, 2176, 1977, 2435, 1922, 7967, 15403, 4607, 1918, 13470, 1916, 2426, 1009, 17, 2761, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MEKKVAVRIVSKYLKKGNMARCLRDILPAAGLSKKQRQEISEIVHDVVRWKRLYEHILDNRGLSLSAENFVNLARDGAQADAYSYAFEYRYSCSSYVADILKDHAEWADFLNEMPPTTLCINFNKTTIDKVLTLLQQETLPSERGVLPSAVLTTSVGKYSKVIQQCFAHVQDESSQFVSFLASILGDSIYDMCAGNGGKTLALASITRNQKKLSAYDLNATKRATLKRRCEKYNAIVTVEQYASEKTYDLVLVDAPCSGLGAARRNPEAKYINGVDNLPKTQISLLCQAAQNVRKNGMLFYAVCTITPEETTRVIETFLKNERFTVSYFEQQPYQTFLLRNSFGAFTMLPRGDLFFLSVLKKE", "metadata": {"id": "A0A151DXE9", "cluster": 3861636, "interpro_all": ["IPR049560", "IPR001678", "IPR023267", "IPR029063"], "interpro_used": ["IPR001678", "IPR023267", "IPR029063"], "interpro_unused": ["IPR049560"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein should have 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 has been characterized in Streptosporangium sandarakinum. 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, 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, 2258, 2252, 4378, 1922, 8987, 9890, 9506, 1989, 9622, 9041, 6856, 1989, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MEQGTRAPSDGVLDAIAAALGIDPSRLLGEATHLDGRVHDTIPLLRQVIAAYDLPEDGPVRPAHQLRAAVTEAVQWRLDAQYIRLSSTLPALMAELIRALNGSSDSNQVTISGIGHRGVEIQGGFCPLGVRPPPWWPFPLDRRAAHDAGTVHLHDPHVTEGIATLPREVINARPPTRQAVRLHPLAAGEDHGGHRIVVSRSRRTHHQHDGHLHSRASPQAPPPYAPPILAIGLFNNGITSADLSASWPAASM", "metadata": {"id": "A0A852UX16", "cluster": 4501029, "interpro_all": ["IPR001387"], "interpro_used": ["IPR001387"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to this functional description: The protein is assigned to the Double-strand break repair protein AddB family, which constitutes the alphaproteobacterial AddB component of the AddAB complex. It functions in the repair of double-stranded DNA breaks, serving as a functional analog to the RecBCD system for genomic maintenance. 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. Additionally, the protein features a PD-(D/E)XK endonuclease-like, AddAB-type domain that functions as a catalytic nuclease involved in the initiation of DNA recombinational repair. Found at the C-terminus of subunits in bacterial helicase-nuclease complexes like AddAB and RecBCD, it shares a common core fold characteristic of the diverse PD-(D/E)XK superfamily. It is produced by Paracoccus alkenifer and is annotated with UniProt keywords ATP-binding.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 1977, 6304, 1942, 1920, 4825, 17, 5984, 6017, 5059, 2213, 3019, 1014, 3416, 16, 2154, 14879, 1920, 4595, 9218, 1021, 15229, 3019, 1014, 4594, 1927, 1920, 3019, 1993, 2796, 18, 2176, 4088, 1922, 1920, 5059, 1927, 4825, 17, 10338, 2678, 13065, 16, 13915, 1966, 43, 3183, 5729, 1942, 1920, 2090, 8284, 1007, 2433, 1958, 4935, 6291, 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, 4950, 16, 1920, 2213, 4075, 43, 3203, 17, 12, 46, 19, 47, 13, 66, 1040, 18697, 17, 3189, 16, 3019, 1993, 17, 2601, 3418, 1988, 4088, 1966, 43, 6804, 16230, 3286, 1922, 1920, 6035, 1927, 2678, 7827, 1923, 5059, 18, 2435, 2019, 1920, 45, 17, 7822, 1927, 6991, 1922, 4543, 15318, 17, 16230, 5048, 3189, 3019, 1993, 1930, 2090, 8284, 1007, 16, 2176, 16495, 43, 3059, 4728, 3728, 6293, 1927, 1920, 6445, 3203, 17, 12, 46, 19, 47, 13, 66, 1040, 13975, 18, 2176, 1977, 4152, 2007, 13344, 15648, 1957, 5638, 28131, 2070, 1930, 1977, 10633, 1956, 20709, 11569, 4498, 17, 2743, 18, 3], "output": "MMPAPIHGLYALPPGANFAAGFVRGLLARMQPRPPEALAATTVWCNSGHTLRAIDTALRVSGPLLLPRLRLIAELGSGAGFAPPAPPLARQLDLAQLVARALTGDATGQSVPVLAASLSALMAEMQAEGLGPEALDRIDAGAHAAHWQQALAFLRIAAGFHLDGPQVDREAQQRAAAERLAADWQQGLNLPEGPVIVAGSTGSHGATRLFMQAVAALPQGAVVLPGYTPMPRGAAAAMHEDHPQARFAPLVAACGEPAPWDDTPAPDPARNALMALALRPAPVTDQWVAEGPSLGDLPLATDRMTLIEADSPAAEANALAALIRGAVHENRPVTLIAADRSLTRRVAATLDRWGIIPDDSAGVPLPLTAAGLFLRHVAELPGQPFGIDSLLVLLKHPLTATGAGDEARRAHLLHSRELELHLRRHGPAFPDGAALRAWGARPARGSGEASPERAAWAEVIGAVLDATLPLIADPGPLPLAERAGRHRRIAEAWAAGAGTAEASKLYAEAAGEKARAVLDHLALHAPRGPAMTARDFARLLADQLQAQAVRMDVAAHPLVRIRGPREARTEATGLVILGGLNEGGWPQALDPDPWLSRPMRAEAGLTLPERRIGLAAHDFQIAIAAPQVVLSRARRSDEAETIPSRWLNRLVNLLGGLPAQGGPQALALMRARGQVWLARARAIEAPADTDLAPPAPRPSPRPPAPALRELSVTAVQTLIRDPYAIYARQVLGLSPLDPLRPEPDAAERGNVLHAIIQRFLTPPPSPQDSPQALQDRLLAAADEVLAAQVPWPTSRLFWRARIGGIAAQLCRDEHARLQQGAPLAVETRHRLAVAGLDFTLTAKPDRIDRLHDGAAVIYDYKSGTPATRPQILQFDKQLPLTAAMAERGAFGEPMSVADLRHIRLGGEGETRSHGWDDEMQATWDQFVALISAYLRGEYGFTARRAMERVTHGSDYDHLSRLGEWSESDPPQPQEVGHG", "metadata": {"id": "A0A1H6MGW9", "cluster": 6394508, "interpro_all": ["IPR014153", "IPR027417", "IPR011604", "IPR038726"], "interpro_used": ["IPR014153", "IPR027417", "IPR038726"], "interpro_unused": ["IPR011604"]}, "task_type": "autoregressive"} {"instruction": "The protein carries a Putative zinc-finger domain that is conserved in fungi and likely coordinates a zinc ion through a characteristic C-x8-C-x5-C-x3-H motif containing three cysteines and one histidine. Also, the protein is categorized in the NURS complex subunit red1 family, which mediates the targeted degradation of specific mRNA transcripts via the nuclear RNA silencing (NURS) or poly(A) tail exosome targeting (PAXT) complexes. Characterized by a conserved C3H1-type zinc finger, these proteins recognize degradation signals to direct RNAs, such as meiosis-specific or polyadenylated transcripts, to the exosome for elimination. In addition, 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 derived from Polychaeton citri CBS 116435 and contains UniProt keyword associations Metal-binding.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 16252, 43, 6770, 7997, 17, 8497, 3418, 1988, 1977, 5305, 1922, 10520, 1930, 3205, 10675, 43, 7997, 4755, 2596, 43, 6293, 45, 17, 66, 1025, 17, 45, 17, 66, 1015, 17, 45, 17, 66, 1010, 17, 50, 5219, 3165, 2559, 22446, 1930, 2340, 13873, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 5871, 2796, 5903, 2312, 1009, 3416, 16, 2154, 10412, 1920, 5154, 4877, 1927, 2487, 3616, 6247, 3454, 1920, 4254, 3146, 8343, 12, 5871, 13, 2014, 4286, 12, 43, 13, 5281, 20235, 5133, 12, 10532, 1031, 13, 5048, 18, 4378, 2007, 43, 5305, 22056, 1009, 17, 2601, 7997, 8497, 16, 2144, 2697, 9967, 4877, 4771, 1942, 3083, 8624, 16, 2427, 1966, 17979, 17, 2487, 2014, 20920, 4336, 6247, 16, 1942, 1920, 20235, 1958, 9570, 18, 1922, 2459, 16, 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, 3595, 2037, 25754, 3336, 5405, 9230, 1033, 16341, 10922, 7514, 1015, 1930, 5461, 20709, 11121, 2538, 5253, 6048, 17, 2743, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MLDHISAPSLYDPNKIVADIDLALELQDKPTKVRYTAYHSPLEQFKDFRYHPNYASIPDTPLCPYEASGGRCNDPNCNFQHFANMGFNRGLAAIVNELKASSLSRDVNAIAQRILDFEWWDKKYGSKQEEEVAQLDDNQLYPIRSHPPVPGGFKSLTYNHKINFTDNELIRILGTEYGNHHEEIRNEVNFRRGFLGDPSRV", "metadata": {"id": "A0A9P4QI86", "cluster": 7457907, "interpro_all": ["IPR019607", "IPR039278", "IPR000571"], "interpro_used": ["IPR019607", "IPR039278", "IPR000571"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein should include a AMP-binding enzyme, C-terminal domain that functions as a dynamic module in ATP-dependent AMP-binding enzymes, such as Acetyl-coenzyme A synthetase, by undergoing a large rotation to permit both catalytic half-reactions. This structure consists of a central \u03b2-sheet core flanked by \u03b1-helices and is found in eukaryotes, bacteria, and archaea. Moreover, the protein should contain 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. Furthermore, the protein features 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 found in Rhodospirillaceae bacterium.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 3066, 3951, 43, 3681, 17, 2743, 4113, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 43, 5760, 9059, 1922, 4498, 17, 3100, 3681, 17, 2743, 5038, 16, 2427, 1966, 6894, 17, 22051, 43, 18185, 16, 2007, 7258, 43, 3103, 8891, 1942, 11832, 2321, 6804, 4768, 17, 5298, 18, 2052, 3170, 7543, 1927, 43, 4101, 161, 17, 11130, 4728, 20185, 2007, 160, 17, 12789, 1930, 1977, 2435, 1922, 15021, 16, 4802, 16, 1930, 21501, 18, 3950, 16, 1920, 2213, 3066, 5531, 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, 3677, 16, 1920, 2213, 4075, 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, 2435, 1922, 11490, 3106, 23576, 11560, 9914, 14061, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MIQTVYEQFSAAAKESPELTFLCYPPSDDRGYLSSGAEFSYGNSLDLIDSLATRYIEAGFVAGASVVPLNPAYLDHELEYAIKFANCALVVTTADRVGDLNKVCLSMSPKVSVFCINAKEDREALIIYTSGTTGRPKGCIISNTSCLAAGESYGEAGGLINFEAGKDRLYIPLPAFHMNVSVYTLNTTTRLRNCIVLQPLLIKSERSRHENSHKIKFGQGAGVDPVVREEFEARFGFPLIEAWGMTETSRAIQNCRLPRDPAGRAFGYPRLPLEVLVVDESDRPVPFNTQPEETEKAWRLGWFHTGDVVTQREDGMLSFVDRKKNIIRRSGENIAAAEVEEALIEDSKIKSVAILAAKDSRLITYKLPGWISFVDKIPVTGTQKIRKDAIFPKDFNLKQDANSFDMRGFKRKRVGHRVALLLGNLPDHFWHLLALNSIDTIPRPTCNAETIPSAKGDRFRASTWWSDIYYTKATCLHYMGIIPPGELLVRCAGDNPRHGFFSGYLKEFHDEEIHACIVLMPNSDASELTAKSIFDFGR", "metadata": {"id": "A0A945V4S5", "cluster": 7573323, "interpro_all": ["IPR025110", "IPR045851", "IPR020845", "IPR000873", "IPR042099"], "interpro_used": ["IPR025110", "IPR020845", "IPR000873"], "interpro_unused": ["IPR042099", "IPR045851"]}, "task_type": "infilling"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein is classified under 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. Also, the protein is classified under 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. It is present in Ignavibacteria bacterium and has UniProt annotations Cell membrane and Transmembrane helix.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 1920, 2213, 1977, 5947, 2441, 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, 2222, 16, 1920, 2213, 1977, 5947, 2441, 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, 2176, 1977, 2481, 1922, 12046, 9188, 7972, 2341, 18339, 14061, 1930, 2258, 20709, 15010, 2024, 3260, 1930, 9117, 7864, 18, 3], "output": "MASFEKPSSVFKHTFFYSAGNLLSRGGIYSVIISAVTILSTVINLGFPSIFNIFLLILSISVISFLIVLIFIKPFLSILIYNFSYYTASIYITQEASRKYVRTGINGIFISQILSSVVLIYLSKDGLTILSLPLFFSGLFSILVEVIDRIFIVKILLSFKSSWIPHFMRLKNLDEDERSKHFKFKIFGVNIISTQYQASSEIILIVMLGYFHFLFADMIAALTNIGLNFILIKTYGIIGAAYSSSRVVKVKYEIKKLILVFLISVIIYLIGKNFGKNFLNVNQNNKFLNFLLLPFYSHFITTNDFIKNLSEAETDEERKRIFSLSKFLIGNENYQLEVFLGSKTAISAVLNFVLNLIFIGYLENYFEFMLDRALTKQLDESSAGIYSFGYRIALIYNLFIIGRIFTKLIYISALIILMISLFIDELFSLMMTFYSPAPYLTNQTITLIAFFFGSVYLFVYVNNLFTELTLIVFLILVGLRLNL", "metadata": {"id": "A0A7V3PLT3", "cluster": 9191918, "interpro_all": ["IPR050833", "IPR002797"], "interpro_used": ["IPR050833", "IPR002797"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the polypeptide chain function: The protein is categorized in the Bacterial Cell Wall Glycosylation GtrA family, which facilitates the translocation of bactoprenol-linked glucose across the cytoplasmic membrane to support O-antigen modification and cell wall teichoic acid decoration. Members of this family also serve as anchor proteins that recruit arabinosyl transferases essential for the biosynthesis of arabinogalactan and the maintenance of bacterial cell envelope integrity. Additionally, the protein should have 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 has been characterized in Ruminococcus sp and contains UniProt keyword associations Transmembrane helix. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 4543, 2024, 4821, 12082, 30441, 1019, 3416, 16, 2154, 11374, 1920, 7849, 1927, 17170, 15370, 11873, 1024, 17, 4624, 3817, 3436, 1920, 6823, 3260, 1942, 3373, 57, 17, 4730, 6295, 1930, 2024, 4821, 3602, 2108, 8643, 2687, 23038, 1943, 18, 4678, 1927, 2052, 3416, 2222, 7120, 1966, 13333, 2697, 1988, 5608, 20790, 11731, 13763, 1036, 4415, 1958, 1920, 8132, 1927, 20790, 27395, 1928, 1930, 1920, 6291, 1927, 4543, 2024, 11262, 7996, 18, 4950, 16, 1920, 2213, 3066, 2162, 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, 2258, 2252, 4378, 1922, 22631, 8256, 2056, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MLEALLQFALKLMPKPIKNLFYKYENGLRYCYYGAWTTLLSIITKLVGEWLFSLGGYTMEMDIPNMVNTAVSWVICATFAFVVNKKYVFMSKTDTTADLLREMRGFYGARLVSFFMELFIMWLTVTRFKWNFALMTVLVQVIILVSNYLFSKLVVFRKKSDPQKEADPS", "metadata": {"id": "A0A928QB54", "cluster": 9773751, "interpro_all": ["IPR051401", "IPR007267"], "interpro_used": ["IPR051401", "IPR007267"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein incorporates a Quinone oxidoreductase/zeta-crystallin conserved site that contains a histidine residue serving as the second ligand for the catalytic zinc atom essential for NADP-dependent quinone oxidoreductase activity. This domain is characteristic of the zinc-containing alcohol dehydrogenase family, functioning structurally as zeta-crystallin in the mammalian eye lens or enzymatically in bacteria and yeast. Additionally, the protein should contain 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 features 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 is produced by Streptosporangium sp. NBC_01469 and is described by UniProt keywords Multifunctional enzyme 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, 25093, 27388, 19, 18943, 17, 24572, 5305, 3200, 1988, 5461, 43, 13873, 6181, 13915, 1966, 1920, 2812, 5207, 1958, 1920, 6804, 7997, 6761, 4415, 1958, 24221, 17, 3100, 25093, 27388, 2455, 18, 2052, 3418, 1977, 6293, 1927, 1920, 7997, 17, 3165, 4284, 9294, 3416, 16, 7295, 12171, 1966, 18943, 17, 24572, 1922, 1920, 6492, 5723, 8540, 2014, 23958, 1922, 4802, 1930, 5688, 18, 4950, 16, 1920, 2213, 3066, 5531, 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, 4075, 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, 1977, 4152, 2007, 8987, 9890, 9506, 1989, 2056, 18, 8789, 1030, 41, 17763, 7093, 1930, 1977, 2910, 2007, 20709, 11569, 20136, 4113, 1930, 13763, 18, 3], "output": "MSSNDQQVSRPIAVIGTACRLPGAPDPRAFWRLLDEGRGAVREIPGHRDSSAVLAGIARDNPGVRYGGYLDDIGGFDAGFFGVSPREAAAMDPQQRLVLELAWEALEDAFVGSIADEYAALSRASAIGRHTLTGTTRGIIANRVSYALGLRGPSIAVDTAQSSSLVAVHLAVESLRRGETRLALAGGVNLIVDPAGTAAVARFGGLSPDGRCHTFDRRANGYVRGEGAGLVGSAVNNDGTTDGLTVPSAEAQAEVIRRAWAAAEVSPSDVQYVELHGTGTRVGDPVEARALDLARNGGPVLHVGSVKTNIGHLEGAAGIAGLLKTVLSVGERRLPASLNYSEPNPDIDLDAWRLAVTNCHIVVAEAPEPYERPETPESPREPDARAPRTPLVLSARTEPALREQAARLRDLIAEHGEIPPGLPRSLATTRTAFEWRAAVTGDAPAGLDALAGGRPAAGVVTGRSGTAPVAVLFPGQGSQRLGMGRRLPRPIKDVVWAEPDSAEARLLDRTAFTQPAIFAVEVATFRLLASLGVEPSFLAGHSIGEVAAAHVSGILDLSSAAELIVARGRLMESLPAGGGMLAVGAGEADVAELVARAGGTAVIAAVNGPESVVVHRLSVSHAFHSPLMDPVLDDFREVLAGIPFGRSRIPFVSTVTGELVESTDPEYWVEHARRPVRFADGLARLRELGAGILVEAGPGAALSGLGREAEGGAATFVPVLGRHDEVEVAVGRLFTAGVPLDWDAVFPPGGPAAVENPAPGRGSVPAVPAVPAVPAGTAGTAGTADVERRVLDEVAAVLGFSDPARVDQDATFKDLGLDSLGLVELRDRVGAALDVDLPAATLFGHPTTAALVRHLTGGTAPDVPDAPAATGGHGADPVVIVGMGCRFPGGVADLETLYDPDPERPGTSYTRHGGFLREAGGFDAGFFGMSPREALATDPQQRLLLQVAWEALERAGIDPLSLKESDTGVFVGATASDYTPRLHEGDGASDGYLLTGGSISVASGRIAYVLGLRGPALTVDTACSLALAGGVAVMASPGMFVEFSRQRGLSADGRCRAFGAGADGTGWAEGVGVVAVERLSRARVLGHRVLAVVAGSAVNQDGASNGLTAPNGRAQEEVIARALADAGVGPGEVDVVEAHGTGTRLGDPIEAQALIAAYGRGREVPGVIKMVMALRRGVLPRTLHVGEVSPLVGWDGSGVELLRDSVGWPERGGVRRAGVSSFGVSGTNAHVILEQAPVDPELGDVPDGGGQVPLVLSAKTATALRAQAGALHDALTSGTAPELRDIGFTLARRPRFEHRAVVDADAANPRVEDGRALPDQRLAFLFSGQGTQRTGMGAELLETSTPYAEAFDEISASMEPLLHVGLRELVTGDPDPLRRTQHAQPALFALEVALYRLAESHGLRPDFLIGHSVGELAAAHVAGVLGLADACALVAARGRLMQSAREGGTAVNGPVATVLSGDADEIDRLVGRWRDAGRKAARLKVGHAFHSAHMDGVLDEFRRVVSGLSFHAPRVPVISTVTGALAGEREMSAPDYWVAQLRGTVRFADAVRAAHRSGVTRFAELGPDGSRPGRPEAATFRTALGRLHAAGVPVDFGPLLSGGRLVDLPTYPFETRHYWLLPAEDDGRPATYGLDASPHPLLTASTELPDGARLFTGALSARRQPWLAEHRVDGRVLVPAAALAELALAIGASAGRPALGDFVMHAPLRGRAAGAGWTSHVTAVLTDGEVTPSRTALPLGRGTRLDAGGPEAAYRLLAEHGYEYGPAFQGLGAAWLDGTDLYAEAELPAPLRGEATRYGLHPALLDAVLHTISLHGIDGPRRVPYALDGVRLHAAHATVGDDGQAVLTVERLRLRPLPSAAGLYRLRWEAVAPPAPAAGDFTVAGSLPERLAGTVLLALTADGDDPYAEVEAARRAVRRWLAEAEGGRLVFLTRGLAVDDGETARPSTAALWGLVRAARAEHPGRFALLDLGDDDAADPALLAAIPELEPEPGAKTEPGAEVQVEPEPEPESAPEPGAEVEPGAGAVTGGAAWPRSAAGGTVLITGGLGALGRRIARHLVTRHGVRDLLLVSRRGEGHPDAARAEAELTGLGARVAIRACDPSDRGALAALLAALDTPLTGVVHAAGVIEDGNLDEATRDAGLDAFVLFGSVAGVVGTAGQGGYCAANAALEAITHRRRLSGGHGVTVHWGLWDIGAGMGAELTDRDVARLGRAGIKPMSEADGTALFDRVLRLDTAAVVAARLDPRAADRAPVTPAPNTSHLVLDAVAAVLGHAGGAEVDPERSFSDLGFDSLTAVELRNRLSDELGVRLPGTIVFDHPNPVALVRFLDEATGAGTRDEPREPAAPVAAAADDPREYGGYLGTGSAGSVASGRVDTACSSSLVALHLAEQALRGGECDLALVGGATLMATPATFVEFSRQRGLSPDGRCRAFADAADGTGFSEGVGLLLVERLSDARRNGHPVLAVVKGSAVNQDGASNGLTAPNGPSQERVIEEALRAAGLSPADVDAVPVEAQALLATYGAARGDRPPLRLGSLKSNIGHTQAAAGVGGIIKMVLALEHGTLPRTLHVDRPSRHVDWDRGGVALLTENTPWLAGDRPRRFGVSAFGMSGTNAHVVIEEPPAPEIAPAPEPEPFEGPVPLVLSARSARAADVAAALVTTRAEFGHRAVVVAGDREEALAALADVADGAPSASAVTGHARDPRVPVLLYPGQGTQWEGMARALLAESPVFARRVGECAAALDPVTGWPLLDALRGGADLGRVDVVQPVLWAVMTGLTALWESFGVRPAAVIGHSQGEAAAVVALRSRAIRTIAGGGAMLSVAASRERVRAVLEALGVSGDAGDAGDAGDTVSVAALNGPASTVVAGEVGAVHRVRRELEERGVRVRPVDVDYASHSPQVEALEAELLEILPRPAPGRTFTVGVFSTVTGARIEPGDGTQAAVEAAAAAGHEVFVEVSPHPVVGMGVQEILEAVPGVERPAVLGTLRRDDGGMARVLTSVAEAWVNGVRVDWPGHLGERRGRVPVLPTYAFDRHRYWLDAAAAGRAPAGTPAGTRPVAHPLLGQPWLGDHVVDGAVLVPGAVLVELAGHAGELAGAARVDELTLRRPLVLDGSGAVEIQVTVGPAERDGFRPVGIHARPADTGDPLGAPWTVHAVGSLAPLPGPAARPVPAVWPPPGAVPVDVGGLYGEDVLAEVFLEGPPGYRVAPTLLDAALHAVGLAGLFPDDGAVRLPFAWRGFTRYADAPAAVRVRVRRTGDDTVAVDLATAEGDPVAGVEAVTFRVADPADLTAAGAEDPLYELAWEPVRPGAGVPRERVRILGATGVTGDAEPAPEVLVVPAGGEAGPVPEAVRAALLRVLSTLRRGLADGRLAGTLFVVRTRHAVEAVPGERAGALDGAGVWGLVRSVQAEEPGRVVVVDTETASTPLSEVLDAVASGEPQAANWRLEAAESGVADDLAYRPVEDRLLGAGEVRVAVRVAGLNFRDAMLALGMYPGAADLGTEGAGVVLAVGDDVTGIEPGDRVMGLIPGGIGPEAVTDHRLLVPIPTGMSFAQAATVPAVFLTAYYALRDLAGARPGEHWGLTVFGTASPAKWPALEGAGLPPGRIAGSRDLSFADAVRAATGGRGVDVVLNSLAREFVDASLELLAPGGRFVEMGKTDVRDPDEVRARHGVHYRAFDLAEAGPDRIGRMLAELAGLFEGGILHLGLARHVGKVALRIPRPIRADGTVLVTGATGGVGRLVALHLAGEHGARHLLLLSRRGARAEGAGRLREELEGLGAKVTIAAADVADAGALARVLADVPDEHPLTAVVHAAGVLDDATLANLVPERLDAVLRPKVDGAWNLHELYAAANVFLDALAAARTREGLPATSIAWGLWRSESAMTGSLSAVDRARMARSGLLPLSPGRGLALLDAAMAAAEPSLAAVRLDLARLAEIPDPAPPLRALVRGRALPAKAGDDPSGAGPALPRMLADTEFQYVEAVLGRAPGDAGDAGDAGDAAEEGRSFKELGFDSLTAVELRNRLGKATGLRLPATVVFDHPTPAALADHLLGRLAPGDPGPGDPGPGDPGPGGQAAEEVPATAEELFRFIDSELRSGLVPATLSGSATGVLLKPLDAAVEDGDRVYAVLLRDRGGAWPRENERLVAGVSSFGMGGAHRDFPVWRSAFDEVAAALDDRAGETRTLGEVAALGAARGYRTGPRVGLPTYPFQREHHWLDVGPVQSPEELWELVSSGTDAIGEFPADRGWCSSSLVALDLAVRSVRSGELWLGSLKSNIGHAQAAAGVGAATALAALRDGGRHMAAFAATEAEAVELAATSDGRVEIALAAMARESAGGVLAVPLLLELDGTAETQLQVSVSAAGELTRVRAHLTPAAPTDPDTYRVDLGTELPEAALRDGVPRVPRLSAPIERLSAGALRRMIEAKAVAAHRGPAAVRRAPAPDTTDIAYTYGLQGPAITEAHGTGTTLGDLRGEARRLRAYLERYPEAALEIAAALTAGALSLEGFGSPGYWYRNLRRPVLLTTVVRAASEDGLLLFGRLSLDEDLAARGYHYGPAFRGLRGAWRSGDTEEELGAVLAALDAGLAIRDGGPLVPRLRLRRRDPVPSGWLLVHSAAGGVGGAAIQLARTPLPVTSWDAGRAPDAVRTRDLDLAAFVLFSSAAGIVGSAGQSAPARRAELMTATV", "metadata": {"id": "A0AAU6DXW8", "cluster": 10168948, "interpro_all": ["IPR001227", "IPR036736", "IPR014043", "IPR016035", "IPR013154", "IPR011032", "IPR018201", "IPR014031", "IPR014030", "IPR016036", "IPR036291", "IPR032821", "IPR020841", "IPR042104", "IPR020807", "IPR049551", "IPR049552", "IPR020843", "IPR013968", "IPR049900", "IPR050091", "IPR020806", "IPR009081", "IPR006162", "IPR002364", "IPR055123", "IPR016039"], "interpro_used": ["IPR002364", "IPR020806", "IPR006162"], "interpro_unused": ["IPR016036", "IPR016039", "IPR050091", "IPR055123", "IPR036736", "IPR013154", "IPR014031", "IPR013968", "IPR016035", "IPR042104", "IPR020841", "IPR009081", "IPR014030", "IPR049551", "IPR020843", "IPR018201", "IPR049900", "IPR001227", "IPR014043", "IPR036291", "IPR032821", "IPR020807", "IPR011032", "IPR049552"]}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein is classified under 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 identified in Penicillium daleae and is classified with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 5947, 2441, 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, 2899, 1922, 25142, 2457, 15880, 5376, 1021, 1930, 1977, 5947, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MALQFRPSQIGGENLPLPYTASPISLLWDDFRLSALDELRLTPKNRTILVTHGALIIGQLGGVILVNFAICSYLNGWNRLLTSRETVIPPSIDRLAQAFGRKVVGVHNPTWGIVFDLALLEDKYKKVVLVLHSQGPQDLLDQLEVYTFASAANHFNNPYTQAKVIRYIEHYANSDDFVSRFGVLNFAYVRNRYMGRGRTLDENDFMDSEVRFPIEHLGERGNEEGVISKVKDLSRLWLYRNGMSPPAEQILRSLVYVPGIFLPLRPLRSFIISLPFCIMLPIMSFIVYFMAPQDEYWVFINGVAAGHLWLQDNIQCLVERDFTYPVQDVRDAYPVIKQGIEGGLIIDWLLDEVSHLKSAHTQGGSSRNSLFVQDASGHMLNQHYLDTMFASDADTIRCSHGRSEDDIRDNYGCDKRPI", "metadata": {"id": "A0AAD6G6H7", "cluster": 10817737, "interpro_all": ["IPR029058"], "interpro_used": ["IPR029058"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein falls within the Glycosyltransferase group 1 family, which catalyzes the transfer of sugar moieties to specific acceptors to form glycosidic bonds involved in diverse biosynthetic pathways. These enzymes mediate the production of essential cell envelope components and protective molecules, including mycothiol, glycolipids, and virulence-associated polysaccharides like lipopolysaccharides and capsular polymers. Also, the protein possesses 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. Furthermore, the protein should feature a Glycosyltransferase subfamily 4-like, N-terminal domain that constitutes the N-terminal Rossmann-fold structure of GT-B family enzymes, including MshA and family 1 subfamily 4 members, and participates in glycosyltransferase activity. It is native to Actinomycetes 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, 12182, 2651, 1920, 20067, 9961, 2210, 21, 3416, 16, 2154, 17097, 1920, 3856, 1927, 9523, 16706, 1942, 2487, 27916, 1942, 2386, 7533, 12546, 9031, 3286, 1922, 6445, 14041, 3873, 18, 2144, 5038, 8265, 1920, 3372, 1927, 4415, 2024, 11262, 4178, 1930, 6337, 4206, 16, 2710, 5078, 17809, 1945, 16, 14193, 2049, 3753, 16, 1930, 9304, 17, 2458, 18686, 3189, 15614, 1036, 1930, 22590, 11039, 18, 2222, 16, 1920, 2213, 14465, 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, 3677, 16, 1920, 2213, 3066, 5961, 43, 20067, 9961, 16227, 24, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 18215, 8890, 17, 3728, 3170, 1927, 4637, 17, 44, 3416, 5038, 16, 2710, 19864, 1019, 1930, 3416, 21, 16227, 24, 4678, 16, 1930, 17241, 1922, 20067, 9961, 2455, 18, 2176, 1977, 6196, 1942, 4718, 25148, 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": "MLSLPAHRISNLGRAISPAKDFRAYLELKKLIQELKPDVVHSHTYKAGLIARLIRGNFKRVHTFHGHLFEDQSFTSLEKFVILLSEKFLSKRTDQFISVGARVGVELRALGIGAAKKWISIPPGVKKLKLISKIEARSKLNLPPTGLIVGWMARVTSVKNPKMAVEIAKHFPEIQFAIAGGGDLLPEIKQSAGSNVNVIGWVDAALMWSAVDIVLSTSDNEGMPIALIEAQLAGLPVVATDVGSTSEVILNSETGFVVSKDIGEVTNSLSRLIKDDELRGRLSAAAILHAEKEFTLEKMASEHAHIYINV", "metadata": {"id": "A0A7K0Z2Q4", "cluster": 11457964, "interpro_all": ["IPR001296", "IPR028098", "IPR050194"], "interpro_used": ["IPR050194", "IPR001296", "IPR028098"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein should have a Palmitoyltransferase DHHC domain that functions as a protein acyltransferase to catalyze the S-acylation of target proteins by transferring a palmitoyl group from palmitoyl-CoA to cysteine residues. This activity relies on a conserved Asp-His-His-Cys (DHHC) motif which forms a stable acyl-intermediate to mediate post-translational modifications essential for regulating protein stability, trafficking, and function. Also, the protein is grouped in the Palmitoyltransferase PFA4/ZDHHC16/ZDHHC20/ERF2-like family, which functions as a palmitoyl acyltransferase that catalyzes the reversible addition of palmitate to substrates such as Ras proteins, EGFR, and chitin synthase. This modification regulates the membrane localization, intracellular trafficking, and stability of target proteins, thereby modulating signaling pathways involved in processes ranging from fungal development to neural stem cell proliferation. It is identified in Trichoplax adhaerens (Trichoplax reptans) and carries UniProt keyword assignments Transmembrane helix.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 3066, 2162, 43, 25997, 9961, 6781, 7727, 3418, 1988, 4088, 1966, 43, 2213, 11337, 9961, 1942, 18170, 1920, 61, 17, 11337, 1943, 1927, 2758, 2697, 2007, 21902, 43, 25997, 2210, 2037, 25997, 17, 10027, 1942, 8666, 4248, 18, 2052, 2455, 12850, 1990, 43, 5305, 4138, 17, 4167, 17, 4167, 17, 4998, 12, 6781, 7727, 13, 5219, 2154, 4952, 43, 4700, 11337, 17, 6129, 1942, 8265, 2753, 17, 8414, 6920, 4415, 1958, 6773, 2213, 5057, 16, 9604, 16, 1930, 2347, 18, 2222, 16, 1920, 2213, 1977, 10809, 1922, 1920, 25997, 9961, 17340, 1006, 19, 68, 6018, 7727, 3672, 19, 68, 6018, 7727, 3520, 19, 2668, 6680, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 25997, 11337, 9961, 1988, 17097, 1920, 10743, 2459, 1927, 22047, 1942, 6249, 2427, 1966, 6520, 2697, 16, 5775, 16, 1930, 16588, 8921, 18, 2052, 6295, 7014, 1920, 3260, 5363, 16, 4776, 9604, 16, 1930, 5057, 1927, 2758, 2697, 16, 6113, 10871, 3197, 3873, 3286, 1922, 4028, 6485, 2037, 8697, 2740, 1942, 5181, 4402, 2024, 4031, 18, 2176, 1977, 2899, 1922, 10477, 3513, 3013, 21918, 29164, 2099, 12, 10477, 3513, 3013, 3073, 3285, 1036, 13, 1930, 16252, 20709, 11121, 2538, 18306, 9117, 7864, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MDIIIIIIIAVGILQLPLLVDVIRNLFPRLNIERITQDFSAYLYVKAENPYATINGWIHIFLASYFCIVSFFHYTYASFHDPGTAPLATLGSVCQRCICMMDHHCPFTVNCVGLNNFYYFVSFLGYAWLGMSFAIYMTFTAFNAIVLVPIVTLWLALGTLLAFQIICLLCNVSTLQENSRMQVLYFSRRNYFWQHFLPLPIQDLPCCYYASYLLFSLVVTVYSGFMYLFHTDYPVCTKCDRIKVGATRHCKMGCMIGQTSYRNALPASICFNLGKLDFSLLFRQTKSLRKMWYQFRNMEF", "metadata": {"id": "B3S507", "cluster": 11518178, "interpro_all": ["IPR001594", "IPR039859"], "interpro_used": ["IPR001594", "IPR039859"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe protein should include a DUF6440 domain that is functionally uncharacterised and primarily found in proteins from Firmicutes and viruses. It features three conserved motifs: RF, TGxxY, and TPLLD. It has been detected in Clostridiales bacterium and carries UniProt keyword assignments Signal.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 3066, 3951, 43, 4855, 17136, 6609, 1008, 3418, 1988, 1977, 9346, 23229, 3495, 1930, 5985, 2435, 1922, 2697, 2037, 24474, 1930, 6241, 18, 2176, 4075, 2559, 5305, 8277, 30, 7751, 16, 6030, 14710, 1012, 16, 1930, 6213, 11560, 1007, 18, 2176, 2258, 2252, 3330, 1922, 17938, 26890, 1918, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 2733, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MRRNAMIIALAMSDENFNTNLDQYILYDPETMVIYNSDGTPKVYSPELLCACGPAKEDNGSYKGRFIVVGKVMYIFVKSYKSGGLS", "metadata": {"id": "A0A9D5WBX9", "cluster": 11870708, "interpro_all": ["IPR045515"], "interpro_used": ["IPR045515"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The desired role of my protein is: The protein features a SCP2 sterol-binding domain that facilitates the binding and transport of sterols. It is characterized structurally by a 3-layer \u03b1/\u03b2/\u03b1 fold and is typically found in proteins such as Sterol Carrier Protein 2. It is found in Oceanobacillus sp. E9. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 4075, 43, 29980, 1028, 20408, 17, 2743, 3418, 1988, 11374, 1920, 2743, 1930, 4860, 1927, 29991, 18, 2176, 1977, 4378, 12171, 2007, 43, 23, 17, 4757, 160, 19, 161, 19, 160, 3728, 1930, 1977, 5745, 2435, 1922, 2697, 2427, 1966, 20408, 9685, 2213, 22, 18, 2176, 1977, 2435, 1922, 13563, 14357, 8898, 2056, 18, 27520, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MGEIEKLVEELENQLKINPEIVNEIESVVKVSLKDTKEEYILFLKGKNPYVTQEKINNVDCLIQIDTKDFIKLANNKLNTTMAYMTGKLKVKGNIAIALKLQEILQKYNAY", "metadata": {"id": "A0A1E5K4I7", "cluster": 24823753, "interpro_all": ["IPR003033", "IPR036527"], "interpro_used": ["IPR003033"], "interpro_unused": ["IPR036527"]}, "task_type": "autoregressive"} {"instruction": "The protein possesses a DivIVA domain that facilitates membrane binding and self-assembly into filamentous structures involved in cell division initiation. It forms a parallel coiled-coil capped with crossed loops that expose hydrophobic and positively charged residues essential for lipid interaction. It occurs in Ignavibacteriales bacterium CG07_land_8_20_14_0_80_59_12 and corresponds to UniProt keyword Cell cycle, Coiled coil, and Cytoplasm.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 14465, 43, 6421, 17370, 3418, 1988, 11374, 3260, 2743, 1930, 3543, 17, 5957, 2460, 18706, 4061, 3286, 1922, 2024, 8451, 6035, 18, 2176, 4952, 43, 6110, 17524, 17, 9121, 22069, 1956, 14925, 11109, 1988, 21369, 7919, 1930, 6629, 9516, 4248, 4415, 1958, 4486, 2835, 18, 2176, 5110, 1922, 12046, 9188, 7972, 2341, 18339, 2612, 14061, 7294, 14099, 41, 7559, 41, 28, 41, 2036, 41, 2607, 41, 20, 41, 3729, 41, 4777, 41, 2369, 1930, 8852, 1942, 20709, 11121, 2538, 2024, 4048, 16, 17524, 9121, 16, 1930, 5239, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MKLTPLEIRKAQFHKRFRGFDRQEVETTLELISTRLETQLTDFRQIERSLQNTLRQAEEMSASVQAQAQKQAEIVIRDAESKAQQIVEKARMDELELLRALRLDAEADLREHLSQGTGKEIIDLQEVVKSVTETGTPQTTNGAPLDTEELLKQNREMHDKIVLLRLQTEIGMLRGKREMLQAQLATLLGS", "metadata": {"id": "A0A2M6YXG6", "cluster": 2169368, "interpro_all": ["IPR019933", "IPR007793"], "interpro_used": ["IPR019933"], "interpro_unused": ["IPR007793"]}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein contains a Pentapeptide repeat that adopts a right-handed beta-helical structure to function as a DNA mimic, exhibiting size, shape, and electrostatic similarity to B-form DNA. This structural mimicry facilitates interactions with DNA-binding proteins, such as DNA gyrase, often conferring resistance to fluoroquinolones or protecting against microcin B17 toxicity. In addition, the protein is included in the Pentapeptide repeat and BTB/POZ domain-containing protein family, which encompasses proteins with diverse roles ranging from fluoroquinolone resistance via DNA gyrase inhibition to substrate recognition in E3 ubiquitin-protein ligase complexes. Some members also contribute to bacterial virulence by reorganizing host endosomal compartments and recruiting kinesin-1 to facilitate intracellular survival. In addition, the protein carries a Toll/interleukin-1 receptor homology (TIR) domain that functions as a central signaling module in innate immunity and host defense by mediating homotypic protein-protein interactions. This conserved cytoplasmic region often possesses intrinsic NADase activity, cleaving NAD+ to regulate cell death and disease resistance across animals, plants, and bacteria. It is identified in Phototrophicus methaneseepsis and carries UniProt keyword assignments Coiled coil.\nInfill the correct amino acids.", "tokenized_instruction": [2, 43, 13022, 4659, 2258, 17476, 3709, 1930, 1920, 2347, 1977, 4378, 2007, 2052, 30, 1920, 2213, 5461, 43, 9412, 24010, 6865, 1988, 24032, 43, 3659, 17, 17105, 4666, 17, 11514, 3170, 1942, 2347, 1966, 43, 2678, 10223, 16, 12196, 3081, 16, 5989, 16, 1930, 12452, 6796, 1942, 44, 17, 2386, 2678, 18, 2052, 4346, 10223, 6907, 11374, 3719, 1956, 2678, 17, 2743, 2697, 16, 2427, 1966, 2678, 9430, 2051, 16, 3868, 21510, 3554, 1942, 23619, 24909, 2014, 15145, 3316, 10572, 1921, 10360, 1027, 5532, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 9412, 24010, 6865, 1930, 29034, 19, 2510, 1011, 3418, 17, 3165, 2213, 3416, 16, 2154, 21569, 2697, 1956, 6445, 5456, 6485, 2037, 23619, 13048, 3554, 3454, 2678, 9430, 2051, 3523, 1942, 4510, 5708, 1922, 10968, 6526, 17, 2213, 11905, 5048, 18, 2673, 4678, 2222, 4672, 1942, 4543, 9304, 2007, 1964, 7023, 3903, 4423, 16514, 10436, 1930, 17040, 19378, 17, 21, 1942, 6628, 4776, 3298, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 15204, 19, 9198, 17, 21, 3148, 9039, 12, 16661, 13, 3418, 1988, 4088, 1966, 43, 4101, 3197, 9059, 1922, 8539, 7611, 1930, 4423, 9720, 2007, 10239, 16350, 5518, 1935, 2213, 17, 2213, 3719, 18, 2052, 5305, 6823, 3031, 3868, 14465, 7598, 6577, 2051, 2455, 16, 28634, 6577, 15, 1942, 5741, 2024, 3539, 1930, 2573, 3554, 3436, 3555, 16, 4793, 16, 1930, 4802, 18, 2176, 1977, 2899, 1922, 10066, 1997, 2688, 24375, 18863, 4127, 9431, 1937, 1930, 16252, 20709, 11121, 2538, 18306, 17524, 9121, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MPPQNDEERAELDRLITQMREGKTDGAQYRAELRRAEKRWTDLIGADLRWTDLRGANLGNAWADLSEADLQEADLSEADLRMADLSGADLNGATIGGTILTDMDLSGCIGLEKMNHLRPSYIDYTTLPSLVSKGIELFSTFISYSYDSRNPNDPGCWLDKHQVNAGDFVLESIDEGIKVWDKLVFCCNERAMNSKLGKRLPIIIPLNMDDYLFSEACKKHPYRLELVERNAVDFVDLRALRLDGGKPPAPEPKIFPLDDDNRDFENEKNDEVVQAITLLRERGWFDLSGTNLSDAHLIRAHLSGAHLSSADLRHLSGAHLSGADLSGAHLNGAHLQGAFYKSGPLSEAFLKGCGVPENLITFNIFAQKVHDWLQKQGVREWVRKELRRAIEKENETEKWEVDEDKFQHGMELV", "metadata": {"id": "A0A7S8E963", "cluster": 3624760, "interpro_all": ["IPR001646", "IPR051082", "IPR000157", "IPR035897"], "interpro_used": ["IPR001646", "IPR051082", "IPR000157"], "interpro_unused": ["IPR035897"]}, "task_type": "infilling"} {"instruction": "Generate a protein according to the following functional description: The protein is classified under the CorA, cytoplasmic domain superfamily, which constitutes the N-terminal region of magnesium and zinc transporter proteins involved in divalent cation efflux. These domains assemble to form the large opening of a funnel-shaped homopentameric channel, containing regulatory metal-binding sites and an aspartate ring for ion discrimination at the pore entrance. Furthermore, the protein belongs to the Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB family, which mediates the transport of divalent cations, primarily magnesium and zinc, across cellular and organellar membranes. These proteins typically form pentameric channels characterized by a conserved GMN motif within their transmembrane domains and possess cytoplasmic metal-binding sites that regulate ion selectivity and flux. It is present in marine sediment metagenome and is associated with UniProt keywords Cell membrane, Ion transport, and Transmembrane helix.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2233, 1019, 16, 6823, 3418, 13975, 16, 2154, 14879, 1920, 56, 17, 4262, 3031, 1927, 13148, 1930, 7997, 9054, 2697, 3286, 1922, 21610, 9976, 11247, 18, 2144, 4682, 17421, 1942, 2386, 1920, 3103, 9497, 1927, 43, 20914, 17, 9132, 16350, 17125, 3857, 9213, 1935, 4999, 16, 3165, 4948, 6048, 17, 2743, 3402, 1930, 1925, 12878, 6335, 1958, 4755, 8638, 2019, 1920, 8554, 21539, 18, 3677, 16, 1920, 2213, 14440, 1942, 1920, 14756, 15, 9054, 2213, 16, 2233, 1019, 17, 3189, 19, 7997, 4860, 2213, 7230, 27414, 3416, 16, 2154, 10412, 1920, 4860, 1927, 21610, 16525, 16, 5985, 13148, 1930, 7997, 16, 3436, 3689, 1930, 3090, 7852, 5726, 18, 2144, 2697, 5745, 2386, 9412, 17118, 5628, 4378, 2007, 43, 5305, 5711, 1022, 5219, 2651, 2310, 9117, 4682, 1930, 7150, 6823, 6048, 17, 2743, 3402, 1988, 5741, 4755, 9008, 1930, 8220, 18, 2176, 1977, 2481, 1922, 10789, 10363, 16552, 2225, 1930, 1977, 2458, 1956, 20709, 11569, 2024, 3260, 16, 4755, 4860, 16, 1930, 9117, 7864, 18, 3], "output": "MIFLRKSVWPLREVISGLERTESSLIEESTGIYLRDVYNHSIQVIDTIETFRDMISGMLDIYLSSISNKMNEVMKVLTIIATIFIPLTFIAGIYGMNFVYIPELQLRWGYFAALFIMAVIGIIMLIYFRRKK", "metadata": {"id": "X0U693", "cluster": 5899684, "interpro_all": ["IPR045861", "IPR045863", "IPR002523"], "interpro_used": ["IPR045861", "IPR002523"], "interpro_unused": ["IPR045863"]}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein can be placed in the MutL C-terminal regulatory subdomain superfamily, which forms the regulatory component of the MutL C-terminal domain essential for DNA mismatch repair. This subdomain connects to the dimerization region via a helical lever spanning the conserved endonuclease motif, helping to coordinate strand removal signals following mismatch recognition by MutS. In addition, the protein has a MutL C-terminal dimerization domain that mediates the homodimerization of MutL, a critical step in the DNA mismatch repair pathway. This domain facilitates the formation of a signaling complex with MutS to identify and correct replication errors such as mispaired or unpaired bases. Additionally, the protein falls within the DNA mismatch repair protein MutL/Mlh/Pms-like family, which ensures the fidelity of DNA replication by correcting mismatched base pairs that escape polymerase proofreading. This family encompasses bacterial MutL homodimers and eukaryotic heterodimers, such as those formed by Mlh1 with Pms1, Pms2, or Mlh3, all of which share a conserved ATP binding site. It has been detected in Pseudomonadota bacterium.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2446, 1024, 45, 17, 4262, 4948, 27517, 13975, 16, 2154, 4952, 1920, 4948, 4594, 1927, 1920, 2446, 1024, 45, 17, 4262, 3418, 4415, 1958, 2678, 10265, 5059, 18, 2052, 27517, 26414, 1942, 1920, 13640, 3031, 3454, 43, 11514, 13732, 13346, 1920, 5305, 18697, 5219, 16, 16235, 1942, 11865, 5984, 6025, 4771, 2894, 10265, 5708, 2007, 2446, 1036, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 2446, 1024, 45, 17, 4262, 13640, 3418, 1988, 10412, 1920, 21189, 2466, 1927, 2446, 1024, 16, 43, 4140, 3537, 1922, 1920, 2678, 10265, 5059, 3374, 18, 2052, 3418, 11374, 1920, 3337, 1927, 43, 3197, 2796, 1956, 2446, 1036, 1942, 3512, 1930, 5550, 5158, 6109, 2427, 1966, 5682, 4302, 3030, 2014, 12352, 11137, 18, 4950, 16, 1920, 2213, 12182, 2651, 1920, 2678, 10265, 5059, 2213, 2446, 1024, 19, 2646, 1023, 19, 13673, 17, 3189, 3416, 16, 2154, 18705, 1920, 14013, 1927, 2678, 5158, 2007, 21042, 24963, 5170, 5803, 1988, 11781, 6479, 10034, 4406, 1941, 18, 2052, 3416, 21569, 4543, 2446, 1024, 29227, 1930, 10825, 21523, 16, 2427, 1966, 2690, 5333, 2007, 25265, 1956, 13673, 1009, 16, 13673, 1028, 16, 2014, 2646, 18649, 16, 2136, 1927, 2154, 7948, 43, 5305, 4498, 2743, 3200, 18, 2176, 2258, 2252, 3330, 1922, 11520, 3947, 12595, 3857, 14061, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "VPPSLKTVYCLRKLHKKKIFTPPPAPRPLSEPVLVDKPVTAPPEKPQISLGTALAQLRNTYILAQNEQGLIIVDDPAHFLATQPLLIPITVNLNRQELLVWEKHQQELLQAGLITESFHDVLADLTVDQRSARINHTIHEILGNIACKHAVQANEHGRPTWKQITWPEIDKFFLRGRPQVTPRQVAMAFSIQIHAAHERLSYEKMKQCGPETILIREIPVLLHKADIKQLRLSLPQMDALLRQMEQTPNSSFCN", "metadata": {"id": "A0A941PIZ3", "cluster": 11181492, "interpro_all": ["IPR038973", "IPR014790", "IPR042120", "IPR042121", "IPR037198"], "interpro_used": ["IPR042121", "IPR014790", "IPR038973"], "interpro_unused": ["IPR042120", "IPR037198"]}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein incorporates a RanBP2-type zinc finger domain that mediates specific binding to RanGDP, serving as a protein-interaction module rather than a nucleic acid binder. This motif is central to the function of nucleoporins like RanBP2, facilitating the regulation of receptor-mediated transport across the nuclear pore complex. It is expressed in Enterocloster bolteae and exhibits UniProt keyword tags Membrane, Transmembrane helix, and Transmembrane.\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, 2845, 19109, 17, 2601, 7997, 8497, 3418, 1988, 10412, 2487, 2743, 1942, 4840, 10274, 16, 13915, 1966, 43, 2213, 17, 2835, 9059, 4356, 2254, 43, 11079, 2687, 26748, 18, 2052, 5219, 1977, 4101, 1942, 1920, 2347, 1927, 2797, 7540, 5572, 1036, 3189, 2845, 19109, 16, 12440, 1920, 3640, 1927, 3148, 17, 3434, 4860, 3436, 1920, 4254, 8554, 2796, 18, 2176, 1977, 3198, 1922, 5553, 5406, 5171, 10608, 2057, 3336, 1930, 9826, 20709, 11121, 2538, 14392, 3260, 16, 9117, 7864, 16, 1930, 9117, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MKSISKTFGGVILFLGIIGSIFLFLSCALPSIVLSIILYALSEVLERQEAIFKALNISMKSTNEKASISYDDMVKAKTAKSSWQCPTCGHINDVSQSTCSSCKITRPSSTLIANFFGKVMDYHSLEFERDWGMTIINSSLETHSGIKDIS", "metadata": {"id": "A0A412ZBZ6", "cluster": 14355061, "interpro_all": ["IPR001876", "IPR036443"], "interpro_used": ["IPR001876"], "interpro_unused": ["IPR036443"]}, "task_type": "infilling"} {"instruction": "It is part of the Carboxypeptidase-like, regulatory domain superfamily, which constitutes a regulatory $\\beta$-sandwich module found in eukaryotic M14B metallopeptidases, such as carboxypeptidase D and E, and teneurin signal transducers. This domain adopts a Greek-key topology and shares structural homology with bacterial outer membrane proteins involved in nutrient binding. Additionally, the protein should feature a Domain of unknown function DUF2341 domain that is found in various prokaryotic proteins, including MotA, TolQ, and ExbB proton channels and other transport proteins. It is expressed in Archaeoglobales archaeon. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 2176, 1977, 3131, 1927, 1920, 15750, 9626, 2410, 9200, 17, 3189, 16, 4948, 3418, 13975, 16, 2154, 14879, 43, 4948, 8, 38, 4666, 8, 17, 18038, 9059, 2435, 1922, 10825, 8510, 14919, 8969, 24897, 1036, 16, 2427, 1966, 15750, 9626, 2410, 9200, 46, 1930, 47, 16, 1930, 5656, 3708, 5572, 2733, 26307, 18, 2052, 3418, 24032, 43, 27568, 17, 3834, 13678, 1930, 16495, 4346, 9039, 1956, 4543, 7642, 3260, 2697, 3286, 1922, 8708, 2743, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 3418, 1927, 5435, 2347, 4855, 6680, 4857, 1009, 3418, 1988, 1977, 2435, 1922, 3425, 21545, 2697, 16, 2710, 12798, 1019, 16, 21930, 1055, 16, 1930, 1975, 6936, 8433, 5628, 1930, 2303, 4860, 2697, 18, 2176, 1977, 3198, 1922, 13470, 6292, 3955, 13470, 1916, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MYIYYGKSDATYAGDGEATFLFFDDFSEAELDPDKWWIYGHTEISDGILTFYGGSGYHGSGNRIQSKTSFSPGVAWRFKAKYDLTTYYTIRSGLTDGSNPSKRFGSDPDNTFLDVTPENGNERLINRVDASGVSANLQSISENVWRTWELRWLSNKTVLVCFETGNSVSLTDKVPSVDLYPGFDAEGTGQSKWYIDIVFLRKYVDPEPSHGTWYAEEEQKVTLSGKVQLPDGTAVANATIIVIDEETNEILATTTSASDGTWSVEISPGKTVTVVAIPQESDYGGDAKPHIQAS", "metadata": {"id": "A0A497RUC5", "cluster": 16941944, "interpro_all": ["IPR008969", "IPR018765"], "interpro_used": ["IPR008969", "IPR018765"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein incorporates a Reverse transcriptase, RNA-dependent DNA polymerase domain that catalyzes the synthesis of DNA from an RNA template. It is typically associated with mobile genetic elements, such as retrotransposons, retroviruses, and group II introns, where it facilitates replication and transposition. It originates from Symbiodinium pilosum (Dinoflagellate).", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 19683, 43, 5267, 13335, 16, 3146, 17, 3100, 2678, 6479, 3418, 1988, 17097, 1920, 4271, 1927, 2678, 2037, 1925, 3146, 7662, 18, 2176, 1977, 5745, 2458, 1956, 8785, 3299, 5362, 16, 2427, 1966, 27181, 2101, 16, 26371, 16, 1930, 2210, 2890, 15778, 16, 2597, 2176, 11374, 5158, 1930, 22596, 18, 2176, 22970, 2037, 17246, 25435, 2457, 7547, 14740, 12, 11687, 4199, 5148, 20178, 5148, 2057, 13, 18, 3], "output": "MILIKQGSAAGADPRNRTEESDDGNEPDDRSNAGLWLATTKHLARDDTWMDSPQNGQLLLKMMDTKELYGEDEREEMLQGQKDVKEWVRIHETDLDLKNKANGSKKPSDAVHYLDNDEDIEVLLNAVQDLDDRVPTETTDDENGVFDEGEARLVRRLELSLSLSVAAATSAIGSSGNHSVNFLELGASEVNFMLPANKRSRADDPKDTGTWLESWRRMVLHFMVICAYKNCQDMIKQLSVAELKHLSSLVSQTLEVREIGATAPIHRCYCGQPVVVLVTRKEVGSSEPVISKEHAESTNCEPEDSSFDNKFVVFLEFQKFQNMRRGQGSLRKLNGNGLSWSTIIGDKRRSAAAAQVYPNRFLKHELDEIEVNLAVPERSLHQEILVNEEALDQPGPETYGISEEMIAKDGWSLVDNKVWLNSLENSREIPNPEPDHPAFNFPWRLALPDPARRVAPPKEETHINERAPTQRGLTERAGGVFKNILYMTRNRLLLRAGYSPIQRGYSPRLPGGLLSGGEKAAAVAFHEADCDQALRAAALGGPRRFQNFEIGQAVYCWRRGAGTHPNAVWISFNGTIVKAAPERVRHATPEEDLTISGAVNEPAGPPEKRSRVQLLEIYHMHLQALSKQRARKEAKFAYQLLSPKESRDIRNNKPEKIMESRYVFTKKPIEPCETAARHVMKGYSEESALDVEFTTPQVNRDSVIFVLQVGDEINRELYCFQPKEGIPGAHPEQILKLLKTCYGLTDGPFAWYQADPCVFMLHDRECPDGPRLEGIMGIATDDLVHGEYKLGKNQTGEGRFTGKHVKLELDGSITANQDFYVKEKQLRSSLGALSWLAKETRCDLAGRVSLLQQAFPEPKVMPIPWQDLRISVVTDAAWGNTKETPWIEDNPADHWQELPDRWIRHHVQARRLIDKYTATDQSLRHEQIEDEWSDQQGIRVLQEFPWTSLVQLQNLSSQGGQIVIYHHKSLSETERPAMTTVALQAGIGSVHWHRLLSSSRPSTACCRQVTGELLHVGSHFWRPPPPSWDGTTSFRDYLVRARSLVTEVKLLMNYTQGRLYVEGEDLDPNDHDEPEVLATMIKEHSKRRTFSAVNTAKKARNLARGLGFDEFKAIKEAVMSANLITHAGRQAFMNYLMIRGPDGQIENMNAGSFIVLEPPLKEKDEEQLPPRTPKLGTTTPEYAALVDAILEAYARSDQERDKRYGQDRPNEAEPALIRDLLSSCVKENGSWRLLEDEVRWSGKSMMDYGCQSRGEWLELVDIACNDHMAADLIRIGDRDAVRAMKMRKKTRDSYWHGPGRVLMTDLEDAEIRGEVGEVISGSGVKREGGEDQASDFKGRDAVKLQNAIRKEIDNNLRTKAARIDGVLLEDEPGEACKAKIASMGWVPGFLDFTQAFHSHLARRLQEDFGYRPSQGSEKHWANVAQIARVHDIPLTRKRKQQRYSRCTAQEVESDLVEANRIASEARKFSHLGIKIRRTTFHPGAAPGGPDLHEIASGQSIFFKQDAKEAKPSKIHSSWKSYRLKRKTVDTLAAEGQA", "metadata": {"id": "A0A812IT36", "cluster": 17206397, "interpro_all": ["IPR013103"], "interpro_used": ["IPR013103"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein is classified under 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 is derived from Rhizorhabdus dicambivorans and is described by UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 1977, 5947, 2441, 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, 1977, 3595, 2037, 13458, 20846, 1957, 9192, 6739, 2068, 8846, 3355, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 7864, 18, 3], "output": "WGFLFKPTGPILNRCLARFYPGVDTAGIRYYIVLLAASVPLAGLTFSVHSPLVFLGLLGILQIVALPFMLVMSASVISILPNALRGQLTATFGFVMSVVGTAASPVLVGALTDYVFGDDQKIGLSLAIITSIGCAGSLIAFWCSLRPLVELTIRKDGGAA", "metadata": {"id": "A0A2A4FQ30", "cluster": 18525995, "interpro_all": ["IPR036259"], "interpro_used": ["IPR036259"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein possesses 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 Hwanghaeella grinnelliae and is classified with UniProt keywords Membrane, Transmembrane, 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, 14465, 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, 18515, 2657, 20051, 5870, 2398, 1921, 28690, 7955, 1930, 1977, 5947, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MPANSRTIIVLATAALLLTLGIFGFTEVDLAVQDRLFDAATGSWIWDKHEPVARMLFYTGPKLALVALAAACLLTLLASGHWDFARKRRQGLAVLLISLIIVPAAAGALKTATNVACPARSDRYGGNVPTISLFERYPDDARPADRQRCFPAGHASGGFALFALVFMFKGRAARRVAVVIALTVGGAMAAYKMAIGDHFLSHTLVTMELAAILVALIASAAVQVERHFGRLP", "metadata": {"id": "A0A437QX31", "cluster": 19379448, "interpro_all": ["IPR036938", "IPR000326"], "interpro_used": ["IPR000326"], "interpro_unused": ["IPR036938"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein contains a TusA-like domain domain that adopts a conserved \u03b1/\u03b2 sandwich fold comprising a mixed four-stranded \u03b2-sheet stacked against two \u03b1-helices. This structural motif is characteristic of small bacterial proteins, including TusA and members of the UPF0033 family such as YedF. It is produced by Candidatus Brocadia sp. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 5461, 43, 9037, 5735, 17, 3189, 3418, 3418, 1988, 24032, 43, 5305, 160, 19, 161, 18038, 3728, 10351, 43, 4985, 3006, 17, 10338, 161, 17, 11130, 24669, 3316, 2288, 160, 17, 12789, 18, 2052, 4346, 5219, 1977, 6293, 1927, 2858, 4543, 2697, 16, 2710, 9037, 5735, 1930, 4678, 1927, 1920, 2353, 1038, 23820, 1010, 3416, 2427, 1966, 5293, 12324, 18, 2176, 1977, 4152, 2007, 14550, 1031, 1957, 4188, 3375, 7408, 1019, 2056, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MNLKATVCSDNYAKAKLTLAAMKHGQGLKVVVDYEVAVTDLTKAVRSEEYKVLKQTRNNRNKLIL", "metadata": {"id": "A0A399WFH8", "cluster": 21955282, "interpro_all": ["IPR001455", "IPR036868"], "interpro_used": ["IPR001455"], "interpro_unused": ["IPR036868"]}, "task_type": "autoregressive"} {"instruction": "I want to make a protein that can have this function: The protein is a member of 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 derived from Lacihabitans soyangensis. 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, 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, 3595, 2037, 7511, 4442, 28808, 3285, 1036, 11205, 5285, 3355, 1937, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MTQAHTTYRIAINDANLLFDLFDVDLIDAFFQLNLEFHTTSLIIGELDIEQKAKIQTHIDSNRLKIREIELSEIETFKGLTVQTKKLSIPDLSLYFYAKELKEFMILTGDNKLRKEAEKLGFEVHGVLRVFEEMVNQKILQKQLAVQKLEELMKVNLWLPVRECEKLIGVWI", "metadata": {"id": "A0AAE3KRF6", "cluster": 26691873, "interpro_all": ["IPR029060"], "interpro_used": ["IPR029060"], "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 classified under the Protein of unknown function DUF1759 family, which comprises a small group of proteins with currently uncharacterized biological roles. It is identified in Caerostris extrusa (Bark spider) (Caerostris bankana).", "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, 2213, 1927, 5435, 2347, 4855, 5739, 8245, 1026, 3416, 16, 2154, 12936, 43, 2858, 2210, 1927, 2697, 1956, 5077, 24528, 3933, 5456, 18, 2176, 1977, 2899, 1922, 2332, 6506, 2156, 13950, 2821, 28553, 12, 18399, 26376, 13, 12, 2332, 6506, 2156, 13950, 10596, 7241, 13, 18, 3], "output": "MSLLIDILHTLTYLFKVLFCFLHAEAAAKILSLFEKIGSDEGPGSKAARVVESLPMTAANYDLLVQIYVRTVGNGHEKCYLWDDFKRDLSIAIRDSTLPAEDKSQYLAQSLVPKAMELLKERFGRE", "metadata": {"id": "A0AAV4XUT8", "cluster": 3006252, "interpro_all": ["IPR005312"], "interpro_used": ["IPR005312"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein includes a MacB-like, ATP-binding domain that functions as the catalytic component of ABC transporter systems, including MacB macrolide exporters and the LolCDE lipoprotein release complex. It binds and hydrolyzes ATP via conserved Walker A and B motifs to energize the transmembrane transport of substrates such as antibiotics or lipoproteins. Additionally, the protein should include 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. 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. It is identified in Nitrospinota bacterium.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 5921, 43, 3433, 1014, 17, 3189, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4594, 1927, 7219, 9054, 3771, 16, 2710, 3433, 1014, 23929, 2261, 12660, 2045, 1930, 1920, 3004, 8293, 3695, 9694, 4012, 2796, 18, 2176, 6876, 1930, 7222, 20887, 4498, 3454, 5305, 20138, 43, 1930, 44, 8277, 1942, 2066, 2693, 2606, 1920, 9117, 4860, 1927, 6249, 2427, 1966, 7560, 2014, 18393, 18, 4950, 16, 1920, 2213, 3066, 3951, 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, 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, 2176, 1977, 2899, 1922, 16665, 9512, 7336, 14061, 18, 3], "output": "MEFFLIVTLEKITKEYTQGTFRFNAVENLNLIGCIDSPTSGEIIINGKNIANFHDFFNLMPTMSALENVSLPLVLAGGNKKEIELSGGEMQRVAIARAFINSPSLLLADEPTGNLDTVLMVSHDPMALFSASRRVEIRDGMLGEEVSINLKVDKGEFLAISGPSGSGKSTLRELSEMRREEIGFVHQEKSGNLLSKVGLENRMNFLPQQSNRGKEILELISTLSKEDNV", "metadata": {"id": "A0A2E4HLX1", "cluster": 3500540, "interpro_all": ["IPR003593", "IPR003439", "IPR017871", "IPR017911", "IPR027417"], "interpro_used": ["IPR017911", "IPR017871", "IPR003593"], "interpro_unused": ["IPR027417", "IPR003439"]}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\nThe protein is categorized in the Transglycosylase-associated protein family, which consists of bacterial integral membrane proteins predicted to function in association with transglycosylases. These proteins likely participate in cell wall maintenance, although their specific activity lacks direct experimental confirmation. It is present in Dokdonella koreensis DS-123 and is described by UniProt keywords Cell membrane 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, 1977, 10234, 1922, 1920, 2127, 17038, 4879, 18801, 24605, 1021, 17, 2458, 2213, 3416, 16, 2154, 7543, 1927, 4543, 12328, 3260, 2697, 4396, 1942, 2347, 1922, 3279, 1956, 2127, 17038, 4879, 18801, 24605, 1918, 18, 2144, 2697, 3205, 7352, 1922, 2024, 4821, 6291, 16, 2876, 2310, 2487, 2455, 13012, 3083, 3599, 12398, 18, 2176, 1977, 2481, 1922, 2608, 16200, 2290, 11560, 1019, 8233, 8134, 4473, 17, 10900, 1930, 1977, 2910, 2007, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MEVFGGTYGIIFLKPGKDPGGFIITTLIGGFIGSVIGAIVLLILYGLITRKRMTIVIGLVVGIVAKIAGSFLATFLGKTLGWYQPGQTA", "metadata": {"id": "A0A160DWP6", "cluster": 5039382, "interpro_all": ["IPR007341"], "interpro_used": ["IPR007341"], "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 have a Isochorismatase-like domain that exhibits hydrolase activity in enzymes such as isochorismatase, nicotinamidase, and ureidoacrylate amidohydrolase. It typically catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, adopting a helix-sheet-helix sandwich structure composed of a central six-stranded parallel beta-sheet flanked by alpha-helices. Moreover, the protein can be placed in the Isochorismatase-like hydrolase family, which catalyzes the hydrolysis of substrates such as ureidoacrylate to release ammonia and carbon dioxide within nitrogen metabolism pathways. These enzymes facilitate the biosynthesis of secondary metabolites, including siderophores and antibiotics, and participate in herbicide degradation. Furthermore, members of this family are implicated in bacterial virulence and the regulation of plant immunity and germination. It has been detected in Chloroflexota 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, 2162, 43, 24179, 10647, 13950, 3368, 3857, 4127, 17, 3189, 3418, 1988, 9826, 20748, 2455, 1922, 5038, 2427, 1966, 24179, 10647, 13950, 3368, 3857, 4127, 16, 14518, 25238, 2051, 16, 1930, 6794, 15072, 19627, 28813, 8601, 21524, 18, 2176, 5745, 17097, 1920, 7309, 1927, 24179, 10647, 13950, 23874, 1942, 22, 16, 23, 17, 20684, 13058, 25120, 1930, 11867, 16, 20478, 43, 7864, 17, 11130, 17, 7864, 18038, 3170, 7179, 1927, 43, 4101, 3798, 17, 10338, 6110, 4666, 17, 11130, 20185, 2007, 4595, 17, 12789, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24179, 10647, 13950, 3368, 3857, 4127, 17, 3189, 20748, 3416, 16, 2154, 17097, 1920, 9128, 1927, 6249, 2427, 1966, 6794, 15072, 19627, 1942, 4012, 14880, 1930, 5056, 15422, 2651, 6634, 4714, 3873, 18, 2144, 5038, 6628, 1920, 8132, 1927, 4067, 6926, 16, 2710, 22940, 14820, 1930, 7560, 16, 1930, 7352, 1922, 23725, 2261, 4877, 18, 3677, 16, 4678, 1927, 2052, 3416, 2032, 6835, 1922, 4543, 9304, 1930, 1920, 3640, 1927, 4496, 7611, 1930, 14609, 18, 2176, 2258, 2252, 3330, 1922, 10107, 18222, 7336, 14061, 18, 7031, 1920, 3244, 18, 3], "output": "MAKALNVKTRFYQLFPADGYLGYGYEDYEAEYGRSAFLVVDVYGLGLHPDDPKPSYMQDEHLDGARPALAWLGSADHEERIARNALLPALEAARAIKMPIIYLNNSAPKIGLRYSEFGKLLKRQLNTDMELMFAEDEIDPKEYHYGESDHVKISKLLAPRENEYFIRKHVYSGFVGTRLDLLLRYLDIKNLFTVGYSADACLMTTVIDALWYNYKVILLRDCTLGNDYPEEQAELLGTQRLVKMMESLYCTTITSKEFIEAAQAYSGEVGEPQVPEAAAV", "metadata": {"id": "A0A3N5R8J0", "cluster": 5226435, "interpro_all": ["IPR000868", "IPR050272", "IPR036380"], "interpro_used": ["IPR000868", "IPR050272"], "interpro_unused": ["IPR036380"]}, "task_type": "autoregressive"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: 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. Furthermore, the protein has a BspA-type LRR region repeat that forms an \u03b1/\u03b2 horseshoe fold to facilitate protein-protein interactions. This motif is notably present in BspA-like surface antigens of *Trichomonas vaginalis*. Moreover, the protein should include a Dockerin domain that facilitates the assembly of the bacterial cellulosome complex by binding with high affinity to cohesin modules on scaffoldin subunits. This domain features a structure composed of three $\\alpha$-helices and duplicated calcium-binding loops resembling EF-hand motifs, which coordinate Ca$^{2+}$ ions to support the enzymatic degradation of plant cell wall polysaccharides. It is expressed in Ruminococcus callidus ATCC 27760 and is connected to UniProt keyword Membrane, Transmembrane, 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, 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, 3677, 16, 1920, 2213, 2258, 43, 28915, 1019, 17, 2601, 13947, 3031, 6865, 1988, 4952, 1925, 160, 19, 161, 15638, 10647, 1021, 3728, 1942, 6628, 2213, 17, 2213, 3719, 18, 2052, 5219, 1977, 7388, 2481, 1922, 28915, 1019, 17, 3189, 3154, 7769, 1927, 14, 10477, 10480, 10120, 1937, 14, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 9170, 16654, 3418, 1988, 11374, 1920, 5957, 1927, 1920, 4543, 18485, 4283, 2796, 2007, 2743, 1956, 2149, 5173, 1942, 22822, 10803, 1990, 7281, 1921, 6991, 18, 2052, 3418, 4075, 43, 3170, 7179, 1927, 2559, 8, 38, 4595, 8, 17, 12789, 1930, 19479, 5016, 17, 2743, 11109, 18994, 8485, 17, 3897, 8277, 16, 2154, 11865, 2332, 8, 40, 69, 22, 15, 71, 8, 6982, 1942, 3373, 1920, 8145, 4877, 1927, 4496, 2024, 4821, 18686, 18, 2176, 1977, 3198, 1922, 22631, 8256, 4567, 22291, 11037, 21711, 5127, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 7031, 1920, 3244, 18, 3], "output": "MKNCKFRRKHCKFRRLLAQVLFLWYHKYNFNEEEVFMKKKVLSLLTAAMMSGTCFFVGAEQICAAEYPSFTLRLNQHTGNAEFMEDETDKKVVFTATCLKYSGSDVELVDAKTNEVVAKMLDDGNFDVSGDDLENDRTWSAVLSFENAAVGSYSYYARLTDADGTVSTTKTFSVVIYDAVSDADAERMAEIAQKVGALSSDTTFQNADQETRKQMADALFDQLIAEGYVKENSVNYDAEKHWYAYQCEGVGGFSDVTCYLDIAVKDPDQVSTGIATATSAFTYVNHGDSIEITGFDNSISDVVIPSEIEGLPVTAISVGAFYLSAITSIEIPNTVTSIGEMAFLGCTSLKSVKLSTGVAKIDKNAFGSCSALQEIQVAKDNPNFSSLNGVLYSKKQDTLIIYPAAKTDAAYIIPSGVTSVAMYAFSENPYLETLTIPNSLIKVGDSAFYNCKNLRAVSYNGTEEEWNQITIGLLNEKLTGATIQYQERIIGDVNADGAFTISDVVLLQKWLLSVPDTQLADWKAADFNGDQTLNVFDLCQMRYNLLKQEEDSKR", "metadata": {"id": "U2KYV1", "cluster": 5911489, "interpro_all": ["IPR002105", "IPR016134", "IPR036439", "IPR018247", "IPR026906", "IPR032675", "IPR053139"], "interpro_used": ["IPR018247", "IPR026906", "IPR016134"], "interpro_unused": ["IPR053139", "IPR036439", "IPR002105", "IPR032675"]}, "task_type": "autoregressive"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein is assigned to the Plant developmental regulator family, which comprises probable transcriptional regulators that control cell proliferation, floral organ development, and meristem determinacy. These proteins typically act by repressing genes associated with cell division and growth, and may interact with DNA to mediate responses to plant hormones. In addition, 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. Also, 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. It is present in Apostasia shenzhenica and is linked to UniProt keywords Metal-binding, Transcription regulation, and Zinc-finger.", "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, 4496, 5878, 7888, 3416, 16, 2154, 12936, 12584, 5224, 9098, 1988, 2285, 2024, 4031, 16, 20741, 3090, 2740, 16, 1930, 29842, 8894, 3217, 18, 2144, 2697, 5745, 4033, 2007, 26047, 2628, 2458, 1956, 2024, 8451, 1930, 2905, 16, 1930, 2278, 6310, 1956, 2678, 1942, 8265, 3387, 1942, 4496, 10224, 18, 1922, 2459, 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, 2222, 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, 2176, 1977, 2481, 1922, 11466, 2156, 6646, 22239, 1011, 22467, 6102, 1930, 1977, 4624, 1942, 20709, 11569, 6048, 17, 2743, 16, 3213, 3640, 16, 1930, 7997, 17, 8497, 18, 3], "output": "MEGEEKKELKASSDDAESPHPAGDDKRGFSTAQALGGHMNIHRRERTKIRPAGSFPPAPAGRGSSSSMGSREWRSVESEQQEVQSSRPPELENEEKKVEADLDLELRLGHGGNQKAGASSEAGTGGGRFYDCIFCAEGYHPYSREQRRGQFPAVGPSAASYVVYFPAAGEELQLGLAGGGFGRGGRPP", "metadata": {"id": "A0A2I0ATC2", "cluster": 8817156, "interpro_all": ["IPR052426", "IPR036236", "IPR013087"], "interpro_used": ["IPR052426", "IPR013087", "IPR036236"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: It is part of the Phosphatidic acid phosphatase type 2/haloperoxidase superfamily, which comprises enzymes with a five-helical bundle core that function as lipid phosphatases or vanadium-dependent haloperoxidases. These proteins regulate phospholipid synthesis and signaling by dephosphorylating phosphatidate to diacylglycerol, or catalyze halide oxidation via a conserved histidine-mediated mechanism. It originates from Verrucomicrobiota bacterium.", "tokenized_instruction": [2, 3036, 1920, 6814, 3451, 1958, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 2766, 8525, 1935, 2687, 8167, 2601, 22, 19, 24980, 19883, 13975, 16, 2154, 12936, 5038, 1956, 43, 3628, 17, 11514, 14142, 4728, 1988, 2347, 1966, 4486, 19131, 2014, 7409, 21913, 17, 3100, 24980, 19883, 1036, 18, 2144, 2697, 5741, 14608, 4271, 1930, 3197, 2007, 13517, 2199, 2287, 2766, 8525, 2010, 1942, 29527, 16, 2014, 18170, 4217, 2261, 6638, 3454, 43, 5305, 13873, 17, 3434, 2856, 18, 2176, 22970, 2037, 3566, 3176, 13055, 1935, 15129, 3940, 3857, 14061, 18, 3], "output": "MKKSSILVFLVALSVFGRGQSNSLHDTFGLLYQTDSVRRWNEIAMDCGAIDHGTLRQQLGPGLNAVLAQYESYTGVQAPKGAVSLDVAVSQAAHKNKNASRSWSSPTASFEFRRHRLDPQVAAGPRHGPRKELRLSRALAIVHIAIFDADTLAALYSGQAASLDSYLAEDLAAI", "metadata": {"id": "A0A2V5NKU9", "cluster": 8970463, "interpro_all": ["IPR036938"], "interpro_used": ["IPR036938"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would the protein sequence be if I wanted a protein that could perform the following function: The protein should feature a MarR-type HTH domain that functions as a winged helix-turn-helix (wHTH) DNA-binding module found in bacterial and archaeal transcriptional regulators. It typically facilitates homodimerization and interaction with the DNA major groove to control genes involved in antibiotic resistance, oxidative stress, and virulence, often in response to aromatic compounds. Furthermore, the 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. It is native to Acidobacteriota bacterium and is associated with UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 4663, 2962, 1920, 2213, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 3684, 1005, 17, 2601, 5334, 1023, 3418, 1988, 4088, 1966, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 12, 2003, 1963, 13, 2678, 17, 2743, 9059, 2435, 1922, 4543, 1930, 22367, 5224, 9098, 18, 2176, 5745, 11374, 21189, 2466, 1930, 2835, 1956, 1920, 2678, 3044, 15920, 1942, 2285, 2628, 3286, 1922, 7267, 3554, 16, 5163, 3071, 16, 1930, 9304, 16, 3868, 1922, 2644, 1942, 10761, 4300, 18, 3677, 16, 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, 2176, 1977, 6196, 1942, 2687, 5883, 3940, 3857, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 3213, 3640, 18, 3], "output": "MPGKTDTSGIHLWLVLMKAHQSLERYAWHSIGQTGLGFSDFAVLETLLHMGPSPVNILGAGIPLTSGSMTAAIDRLERRHLVRRGVDSADRRARIVHLTAEGRRLIETAFHDHQAAMEIAAESVTPAERAILIRLLKKWGKATLEKLDSSPQKGEPHVWTTGKHRSR", "metadata": {"id": "A0A2V9V0Y2", "cluster": 11396981, "interpro_all": ["IPR000835", "IPR036388", "IPR036390"], "interpro_used": ["IPR000835", "IPR036388"], "interpro_unused": ["IPR036390"]}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein can be placed in the Serralysin-like metalloprotease, C-terminal superfamily, which forms a calcium-binding parallel $\\beta$-roll structure required for the secretion of bacterial zinc-endopeptidases. This domain enables the export of these virulence factors without a traditional signal peptide and stabilizes the protein through tandem repeat motifs. In addition, the protein incorporates a xxxLxxG heptad repeat that facilitates the extended zippering of alpha-helices through a specific periodicity of alternating leucine and glycine residues. This arrangement creates an alpha-helical structure with alternating bulky and small side chains on one face, functioning analogously to leucine zippers to mediate protein dimerization. It originates from Arthrobacter jiangjiafuii 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, 2112, 1998, 5396, 1922, 1920, 20835, 29872, 1921, 17, 3189, 28629, 2051, 16, 45, 17, 4262, 13975, 16, 2154, 4952, 43, 5016, 17, 2743, 6110, 8, 38, 4666, 8, 17, 12970, 3170, 3414, 1958, 1920, 5512, 1927, 4543, 7997, 17, 16239, 9626, 2410, 30413, 18, 2052, 3418, 10217, 1920, 12660, 1927, 2144, 9304, 2790, 2979, 43, 6378, 2733, 4207, 1930, 19658, 1920, 2213, 2596, 10361, 6865, 8277, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 22995, 19776, 14710, 1029, 20662, 2015, 6865, 1988, 11374, 1920, 6091, 27910, 1941, 1927, 4595, 17, 12789, 2596, 43, 2487, 27909, 1927, 17403, 12624, 1930, 10646, 4248, 18, 2052, 13002, 15628, 1925, 4595, 17, 11514, 3170, 1956, 17403, 22605, 1930, 2858, 4159, 7835, 1990, 2340, 6171, 16, 7295, 12464, 1954, 1942, 12624, 27910, 1036, 1942, 8265, 2213, 13640, 18, 2176, 22970, 2037, 9273, 15129, 2422, 16684, 11801, 2624, 15444, 1033, 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": "MTSSPSGQATSRPHTLLTALLALFLVLLLAFFVLFTNQVANLEAGATKAKEGADKVAAGSEKVDTGLKEGATTLDEGALKLLTGAEAANTGANKLAAGATTANNLAAGATNARVGSDTLAAGANKLYTEMKPLAEGAGIQKVNGGINGIQDGQTESVATQIRKDLSVYGPTGESAGSALKAAAKLEGLERLIASIDLGLQGIDPVTGASYTGLMDGSQQLSAGEQLYAGAGTLSAGATELNTGLKTLEVGAGTLAASTLEAGAYSLADGNYKIYDGTISLAEGTNKLATADLKKGASELADGNTKLADGSTTLASGNGEISAGADSMMERTSAMTLLVPIAMLLSGRARRNQHGATQLSEGAQRASTGAGDANTLAKGIASAKTGVVSGAGQLVTGANSAAEGANQPGLAAGAQKVASGIAVAAPGAAALSGELELLAEYQSPLIPGAREGILAALNDPAAAPTLAAGAQTAAAGIGNNKLATGAGSLASGITGAGTLDEGVVKLDDGGKTLTAGPGEIMTSPKVLAVLIPLIL", "metadata": {"id": "A0A975QZF5", "cluster": 13324034, "interpro_all": ["IPR011049", "IPR023908"], "interpro_used": ["IPR011049", "IPR023908"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein is assigned to the NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 4 family, which facilitates the assembly of the mitochondrial NADH:ubiquinone oxidoreductase complex (complex I). Members of this family may also be involved in cell proliferation and the survival of hormone-dependent tumor cells. It has been detected in Chironomus riparius.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 14261, 9294, 37, 5582, 22123, 39, 21, 4595, 5736, 19667, 5957, 2991, 24, 3416, 16, 2154, 11374, 1920, 5957, 1927, 1920, 4596, 14261, 30, 5582, 22123, 27388, 2796, 12, 2796, 51, 13, 18, 4678, 1927, 2052, 3416, 2278, 2222, 1998, 3286, 1922, 2024, 4031, 1930, 1920, 3298, 1927, 6365, 17, 3100, 2798, 2094, 18, 2176, 2258, 2252, 3330, 1922, 30251, 11873, 23084, 18970, 3027, 1957, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MGKAMSVITSPFKYYNKFKDTIKDLERVLKDHPEIIEQAGKKDAGLDNRLDRPLPTNKHFAGFFELGYQEPEFLTPGKVTLKIALEYKLKLEDVKMMLEYYKLFALYVPEKDKITFLPDENQRKPSNKEYPTRSDYKEIESRAHKVISQSKPVVAPKQVFVTSSHEIDQKRVINPKQILQFLGDYRLHPDEWTAEGDEKKRKLLKQQETKNFNQLLKQST", "metadata": {"id": "A0A9N9WZG0", "cluster": 18990692, "interpro_all": ["IPR009622"], "interpro_used": ["IPR009622"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein should contain 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. 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 derived from Neisseria musculi.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 3066, 5531, 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, 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, 3595, 2037, 28356, 18339, 25795, 1033, 18, 3], "output": "MTELSDLSFIEKHENAVLTGPGRMAGIKIRFVTAADLMLQPAAYNRGKRKLPFEREANLFFNVAAKRYGRGSMILTLRHCHVVRISGEIYRLKDKKKIGITIKLPVPVLKWLVFESAGETDLAVSLAYPAVSYLQGSVMGPRLPVIDETGCADLPFGRRAGAFANDTALTAAMSDRLAPVIKEIYPPRGVS", "metadata": {"id": "A0A7H1MA40", "cluster": 19382146, "interpro_all": ["IPR002611", "IPR027417"], "interpro_used": ["IPR002611", "IPR027417"], "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 incorporates 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. Furthermore, the protein should feature 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. Furthermore, the 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. It is expressed in Ignavibacteriae bacterium HGW-Ignavibacteriae-1 and is described by UniProt keywords Transcription regulation.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 19683, 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, 3677, 16, 1920, 2213, 3066, 5961, 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, 3677, 16, 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, 2176, 1977, 3198, 1922, 12046, 9188, 7972, 2341, 18339, 1021, 14061, 7175, 1018, 17, 12046, 9188, 7972, 2341, 18339, 1021, 17, 21, 1930, 1977, 2910, 2007, 20709, 11569, 3213, 3640, 18, 3], "output": "MLEKFAHKTDEELFVYLKSKDRTVSRQAFDEIYSRYANKIYTYCRKVLNSSNMSEDIFQDIFIKFYESVQKIDEMSNVQGYLIRIARNLCLNEKTRGKVVKVPFDESHYEYNDTKIENNEIADILHTSLDALPEDFREVIVMKEFMDMSYKDIAFALDVTVSVVRIRIFRGKQKLREIMTPYIDDIQNEN", "metadata": {"id": "A0A2N1VKA1", "cluster": 19565467, "interpro_all": ["IPR039425", "IPR014284", "IPR007627", "IPR013249", "IPR013325", "IPR013324", "IPR036388"], "interpro_used": ["IPR007627", "IPR014284", "IPR036388"], "interpro_unused": ["IPR039425", "IPR013324", "IPR013325", "IPR013249"]}, "task_type": "autoregressive"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein should feature 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. Furthermore, the protein incorporates a MYND-type zinc finger domain that functions primarily as a protein-protein interaction interface, particularly for the recruitment of transcriptional co-repressors like N-CoR and SMRT. This motif consists of a cluster of conserved cysteine and histidine residues arranged to form a stable zinc-binding structure that mediates complex assembly and transcriptional repression. Moreover, 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. It is expressed in Phallusia mammillata and is classified with UniProt keywords ANK repeat, Metal-binding, and Zinc-finger.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 3066, 5961, 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, 3677, 16, 1920, 2213, 19683, 43, 3057, 10249, 17, 2601, 7997, 8497, 3418, 1988, 4088, 5985, 1966, 43, 2213, 17, 2213, 2835, 6854, 16, 4443, 1958, 1920, 6067, 1927, 5224, 2081, 17, 26446, 3189, 56, 17, 2233, 1930, 28018, 1031, 18, 2052, 5219, 7543, 1927, 43, 4377, 1927, 5305, 8666, 1930, 13873, 4248, 14940, 1942, 2386, 43, 4700, 7997, 17, 2743, 3170, 1988, 10412, 2796, 5957, 1930, 5224, 10084, 18, 3950, 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, 2176, 1977, 3198, 1922, 19938, 24327, 1019, 4632, 10888, 3857, 1930, 1977, 5947, 1956, 20709, 11569, 9808, 6865, 16, 6048, 17, 2743, 16, 1930, 7997, 17, 8497, 18, 3], "output": "MNKFFHDKVKDVSGLERLQAIQVMKDELNKLENDEKRKQVLAAKDETGNTLFHTAAACGLDHVCQFMYEYGVDLETTNNAGHTPLFTALGVNQDIKLGKWLLDHGADPTVSIIDEKSTWTVFHVGFVLDNEQVMRLLVKYGANPTIPFKDGTVPLMYAKIDEKRELLCELSRRYNRRVEKLGAYCSWCGKQPNTLKRCKSCYVVFYCDVDCQQYDWKFTHSKSCRKPIICGKRLAETMAKAKRKDYVKTEPYIYLKDATLEQELSVWKSYKKALRKAVGKHFVVALQVYEHKYQTIIVYNQDHSIHTKVFYNCDHFDWLRHLLFETSKKQVLFLWATPCDPDNGTLFVYPGKPAPQQPWNDPVIEIRPFDKGEAPVFKF", "metadata": {"id": "A0A6F9DHD4", "cluster": 23299220, "interpro_all": ["IPR002110", "IPR036770", "IPR002893"], "interpro_used": ["IPR002110", "IPR002893", "IPR036770"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein can be placed 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. Also, the protein should feature 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. It is produced by Clostridiaceae 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, 2112, 1998, 5396, 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, 2222, 16, 1920, 2213, 3066, 5961, 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, 2176, 1977, 4152, 2007, 17938, 14773, 1972, 3336, 14061, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MKRKQDGRSCGTIYESLTFNSKGGSTISPIENVEHGSKITAPQAPTRLGYSFVGWY", "metadata": {"id": "A0A7V6U959", "cluster": 25349515, "interpro_all": ["IPR013378", "IPR042229"], "interpro_used": ["IPR042229", "IPR013378"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein belongs to the MlaA lipoprotein family, which acts as a lipid-anchored outer membrane component of the Mla ABC transport system responsible for maintaining membrane asymmetry through phospholipid transport. Also known as VacJ, this protein is required for the intercellular spreading of *Shigella flexneri*. It has been detected in Ketobacter sp and carries UniProt keyword assignments Signal.\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, 2646, 5025, 9694, 3416, 16, 2154, 8016, 1966, 43, 4486, 17, 17199, 7642, 3260, 4594, 1927, 1920, 2646, 1019, 7219, 4860, 2433, 5061, 1958, 8231, 3260, 13337, 2596, 14608, 4860, 18, 2222, 3171, 1966, 7017, 1013, 16, 2052, 2213, 1977, 3414, 1958, 1920, 15685, 13405, 1927, 14, 25698, 5795, 3239, 1033, 14, 18, 2176, 2258, 2252, 3330, 1922, 21471, 7972, 2341, 1915, 2056, 1930, 16252, 20709, 11121, 2538, 18306, 2733, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MTSWTLGYVFWVAMAFGAAGTAWAFNDTLDFYVLKPVAKGEIKTIFNGLLQLKFKQAGLDTTRFLVNTTVGDEDFGQTLGYWGVGSGPYVVLPLLGPHDLTRYSIRALQVVDLRAGLLEAESLIAGFLEDDDLFEDFDDDEGWDEGNLEDSEEPLTETEGEGHPRDPWEGFNRAMFGYDKAMPDPLQDGVSNFFNNIGVFGFIDIGSRIGLEQHNTVRDSIGMIPDDYISPYQTVDDRYSFFRDAYLQRRDFLVNDGQMADD", "metadata": {"id": "A0A3L8C7V5", "cluster": 25748001, "interpro_all": ["IPR007428"], "interpro_used": ["IPR007428"], "interpro_unused": []}, "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 should contain 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. Furthermore, the protein is included 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*. In addition, the protein is included in the Ribonuclease Z/BN family, which functions in the maturation of tRNA by endonucleolytically removing 3'-trailer sequences from precursor molecules. These enzymes typically cleave directly after the discriminator nucleotide, with activity often inhibited by the presence of the mature CCA motif to prevent degradation of functional tRNAs. It is expressed in Symbiochloris irregularis and contains UniProt keyword associations Endonuclease, Metal-binding, and tRNA processing.", "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, 3066, 5531, 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, 3677, 16, 1920, 2213, 1977, 3063, 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, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 18347, 2051, 68, 19, 11006, 3416, 16, 2154, 4088, 1922, 1920, 7655, 1927, 10089, 2007, 16239, 1022, 2626, 26656, 11560, 1012, 11340, 23, 11, 17, 11558, 1915, 3709, 2037, 7897, 4206, 18, 2144, 5038, 5745, 21252, 4103, 2256, 1920, 15964, 3061, 5489, 16, 1956, 2455, 3868, 5069, 2007, 1920, 2990, 1927, 1920, 6665, 13980, 5219, 1942, 4625, 4877, 1927, 3183, 20770, 18, 2176, 1977, 3198, 1922, 17246, 20845, 1937, 11499, 1937, 1930, 5461, 20709, 11121, 2538, 5253, 18697, 16, 6048, 17, 2743, 16, 1930, 10089, 4587, 18, 3], "output": "MQPHRLLWSRLCALRSLQPALRGEQGQQACLHSQSGFTNCQSLWHAQRAFTGSIRLRATAERELITELLSRKRKWGTASKMIHLRAELERRGMNADGKKVVLLDKIRKADEREAAEEAAKQLQATSSPEPSTLQSPPEPPAEAPAMPAASAVESPLAETHTMSSGEADPAAAATGLAVTWLGTSSGAPTHRRTVSSICLRTPSHAFLVDCGEGTFKQLQAAAVPAQRINRIFITHLHGDHCFGLVGVLSAISAGRVESGLASQQEPLHVFGPPGLHSLIQTAFAFGPKDLAMPLVVFELAVQPSRSFPPRQVEGLSQGLKFACLGPDRTPKAQAVLKQLNAKGGDKWSSRRTDQNAMHEVPVVPGLVWTLPCPKGITVTAAQLKHRVPCWGYVFQEASSAGGAPGRKVVLLGDTCNSEAIAEVGMDADLLSHEATFSTEMYRKARVAQHSTARDAGNFARHIRARSLVLTHFSNRYSFEGSRPAGGTLLDASSGDIMQLCREASQAYGSSQNPSYLQNADRRQRRAQQFSVIGPDGQEMNEGFQRQYTPERYNGRRPSPEGFQRQHSPQQYDRRQSVDRSWSDRNTRQYDGNEHFWRWRVAKACDEVQGQWRQEDGGRKASQKQRREARVRGTVQHVGQRWAAPLSLAFCTFSR", "metadata": {"id": "A0AAW1NSU3", "cluster": 25936964, "interpro_all": ["IPR001279", "IPR036866", "IPR013471"], "interpro_used": ["IPR001279", "IPR036866", "IPR013471"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein has a Thioesterase TesA-like domain that functions within non-ribosomal peptide synthetases to catalyze the addition of the final amino acid and the cyclization of the peptide antibiotic product. This domain is often integrated into peptide synthetase complexes and shares similarity with type II fatty acid thioesterases. Additionally, the protein is assigned to the Thioesterase type II family, which comprises stand-alone $\\alpha/\\beta$ hydrolase enzymes that function as editing factors in non-ribosomal peptide and polyketide biosynthesis or as chain-terminating enzymes in vertebrate fatty acid synthesis. These proteins maintain biosynthetic efficiency by regenerating mis-acylated carrier proteins or interact with fatty acid synthase complexes to facilitate the premature release of medium-chain fatty acids. Additionally, the protein possesses a Thioesterase domain that catalyzes the termination and release of peptide or polyketide intermediates from non-ribosomal peptide synthetases and polyketide synthases. It facilitates the final step of synthesis, often forming cyclic antibiotics or other bioactive compounds via mechanisms such as intramolecular C-C bond formation, macrolactone closure, or hydrolysis. It is native to Streptomyces malaysiensis.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 2258, 43, 30215, 2051, 2672, 1019, 17, 3189, 3418, 1988, 4088, 2651, 2447, 17, 11196, 4207, 18185, 1036, 1942, 18170, 1920, 2459, 1927, 1920, 3948, 3835, 2687, 1930, 1920, 25267, 1927, 1920, 4207, 7267, 4863, 18, 2052, 3418, 1977, 3868, 6714, 2460, 4207, 18185, 5048, 1930, 16495, 6796, 1956, 2601, 2890, 5934, 2687, 30215, 2319, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 30215, 2051, 2601, 2890, 3416, 16, 2154, 12936, 2924, 17, 4298, 8, 38, 4595, 19, 38, 4666, 8, 20748, 5038, 1988, 2347, 1966, 10454, 2790, 1922, 2447, 17, 11196, 4207, 1930, 4286, 18540, 2261, 8132, 2014, 1966, 4659, 17, 5475, 2287, 5038, 1922, 13416, 5934, 2687, 4271, 18, 2144, 2697, 6698, 14041, 5034, 2007, 23617, 5682, 17, 11337, 1981, 9685, 2697, 2014, 6310, 1956, 5934, 2687, 8921, 5048, 1942, 6628, 1920, 9839, 4012, 1927, 3649, 17, 4659, 5934, 4576, 18, 4950, 16, 1920, 2213, 14465, 43, 30215, 2051, 3418, 1988, 17097, 1920, 12462, 1930, 4012, 1927, 4207, 2014, 4286, 18540, 2261, 12386, 2037, 2447, 17, 11196, 4207, 18185, 1036, 1930, 4286, 18540, 2261, 8921, 1036, 18, 2176, 11374, 1920, 3948, 3537, 1927, 4271, 16, 3868, 7402, 9821, 7560, 2014, 2303, 13570, 4300, 3454, 3531, 2427, 1966, 18083, 45, 17, 45, 5403, 3337, 16, 23929, 20023, 10408, 16, 2014, 9128, 18, 2176, 1977, 6196, 1942, 22874, 18704, 24222, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MAPPVTPASPWFRRFHPRPDAEVALVLSGRLSASADVLAVQYPGRQDRLHEPCLDLVAGRPFALFGHSMGAAVAFELALLRRREGRGIRFLDDDGLIAEVRRLAGTDALVLDDTYDAGPGAVVHCDIVALTGDGDDHVGIADAEDWRDHTTGAFDLRAEIVGTALRSAERPRPGTRGPGARGKEDDRARSIRDAGCLPHAGGSASSYFSSVRDLARGVAADLERARAPHTLFLSGRGAPPCGTDPDLVELALPSLRADYTAAEVFSGGHFFLGEHEPRI", "metadata": {"id": "A0A2J7YRC6", "cluster": 26952354, "interpro_all": ["IPR029058", "IPR020802", "IPR012223", "IPR001031"], "interpro_used": ["IPR020802", "IPR012223", "IPR001031"], "interpro_unused": ["IPR029058"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein carries 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. In addition, the protein contains a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. In addition, it is part of the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. It is found in Lachnospiraceae bacterium and carries UniProt keyword assignments Glycogen biosynthesis and Glycosyltransferase.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 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, 1922, 2459, 16, 1920, 2213, 5461, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 2176, 1977, 2435, 1922, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 13302, 8132, 1930, 20067, 9961, 18, 3], "output": "MKKVAYIASECVPFIKTGGLADVVGTLPRIFDKKEYMRYITHFHMDIGWKQQYVGVMYLEYEGVPVYFIDNEYYFNGFNAILPSIGFQPDIVHCHDWQAGLVPVYLKTLFAGNPFYSGMKSIMTIHNLQFQGPDKLEMHKDAAMLKGGLVYADKITTVSNTYAWNQSLWGIVNGIDYNDYNAATDKKIYKNYTIKNFRKNKVMNKTALQRQLGLPEDPNMNNICTDGTQFVVLGTGDRRYEDMFKYYQGIHPAKVSANIYEPCGLTQLMALRYGTLPIVRETGGLKDTVQPYNEFEGTGTGFSKENWESMQERAMQQNYSWVASAEIYQRLYEQVDVRVIIPNYMCLPAKFKEKIYGDVKWDIEKFCYFSKAALRWDIKTIQEYSGLPDYLFTEIQTPQYGEGLDGLLSARAYMIGIISRLTDQKGLDLVDRIYSDDLSHKMYAACDAMLVPSRFFANYSAQELLDTINYSKKVFFDY", "metadata": {"id": "A0A927V949", "cluster": 8977529, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR001296", "IPR013534", "IPR011835"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein contains 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. Also, the protein can be placed in the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. In addition, the protein incorporates a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. It occurs in Clostridiales bacterium and has UniProt annotations Glycogen biosynthesis and Glycosyltransferase.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 5461, 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, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 2176, 5110, 1922, 17938, 26890, 1918, 14061, 1930, 2258, 20709, 15010, 13302, 8132, 1930, 20067, 9961, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MKILFAASECVPFIKTGGLADVIGALAPVLAKMGHDVRVIIPKYSAIPDEHVNQMQHVVDGVTYYFVDNRYYFGRNYIYGLAGDEYERFAFFSRSVLNSLPLIGFMPDYAHLPDYANIKTVMTIHNLRYQGVFGVKEVQDVLGLGDSLFTDDKLVSPSYSEEIQTAYYGERLDGLLRAKKDHLHGILNGLDIVDYDPEHDKLGLEVREDAPIIAMVSRLSNQKGLDLVDYVIADIMRQDVQLVCLGMGDSRMDHALAHQVYAGADIFLMPSQFEPCGLSQMIALRYGTLPIVRETGGSFFNYNAHDMLHTIERALDYYWHKPEIWAKIQERGMSTDFSWDRSANAYIDKASEKATGKPSKTETKPTVQEKPVKAKAAAKKSVATKAVETEAEEAKAPAKKKAVTKEAEIAEEPKRKVSAKKVSKPKAAADKPKKASKDFEVELGWRKQYCGIEQLQKVLHAHDWQAGMIPALLRIQEFFGAANFLKAGIVYADEVTTYIAATYSAGNLEGKKACKKALQEQYVNLFSWAEQNYPGRVAARFVLRDTVLSYNEFTGEGNGFLYSKLIGSRKEKPVPPVVEEKPSTQKPVAKKTVA", "metadata": {"id": "A0A7C6BMP2", "cluster": 11944639, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR001296", "IPR011835", "IPR013534"], "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 should have a Folylpolyglutamate synthetase conserved site that belongs to the ATP-dependent enzyme responsible for adding polyglutamate tails to folate and its derivatives, thereby aiding in the retention of the intracellular folate pool. This site is situated within the active site in a large interdomain cleft adjacent to an ATP-binding P-loop motif. Furthermore, the protein should feature a Mur ligase, central domain that functions as the ATP-binding catalytic module in the MurC, MurD, MurE, and MurF enzymes responsible for the stepwise assembly of the bacterial peptidoglycan stem peptide. This domain shares structural similarity with ATPase domains and is also present in folylpolyglutamate synthetase and cyanophycin synthetase, where it drives ATP-dependent ligation reactions for folate metabolism and cyanophycin storage. Furthermore, the protein includes a Mur ligase, C-terminal domain that facilitates the sequential addition of amino acids to UDP-N-acetylmuramic acid during bacterial peptidoglycan biosynthesis. Adopting a dihydrofolate reductase-like fold, this domain is responsible for binding the incoming amino acid substrate in enzymes such as MurC, MurD, MurE, and MurF, as well as in folylpolyglutamate synthase and cyanophycin synthetase. It is present in Lachnospira eligens and carries UniProt keyword assignments Cytoplasm, Peptidoglycan synthesis, and Cell shape.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 5305, 3200, 1988, 14440, 1942, 1920, 4498, 17, 3100, 4113, 5061, 1958, 8013, 16115, 26697, 21084, 18103, 1942, 13761, 1930, 2496, 8383, 16, 6113, 8379, 1941, 1922, 1920, 7521, 1927, 1920, 4776, 13761, 5562, 18, 2052, 3200, 1977, 18287, 2651, 1920, 3500, 3200, 1922, 43, 3103, 13633, 2954, 1921, 14649, 6811, 1942, 1925, 4498, 17, 2743, 58, 17, 5881, 5219, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 6185, 11905, 16, 4101, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 6804, 9059, 1922, 1920, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 5038, 5061, 1958, 1920, 13846, 5957, 1927, 1920, 4543, 24183, 4402, 4207, 18, 2052, 3418, 16495, 4346, 6796, 1956, 9444, 4682, 1930, 1977, 2222, 2481, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 1930, 26898, 25818, 3665, 18185, 16, 2597, 2176, 15435, 4498, 17, 3100, 11102, 5298, 1958, 13761, 4714, 1930, 26898, 25818, 3665, 7451, 18, 3677, 16, 1920, 2213, 5921, 43, 6185, 11905, 16, 45, 17, 4262, 3418, 1988, 11374, 1920, 9454, 2459, 1927, 3835, 4576, 1942, 18500, 17, 56, 17, 6894, 23010, 29085, 1935, 2687, 2409, 4543, 24183, 8132, 18, 20478, 43, 11842, 27851, 11386, 17, 3189, 3728, 16, 2052, 3418, 1977, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 4510, 1922, 5038, 2427, 1966, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 16, 1966, 2486, 1966, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 8921, 1930, 26898, 25818, 3665, 18185, 18, 2176, 1977, 2481, 1922, 7511, 11619, 3106, 11979, 29188, 7470, 1930, 16252, 20709, 11121, 2538, 18306, 5239, 16, 24183, 4271, 16, 1930, 2024, 5989, 18, 3], "output": "MKLSEILKICSENETADFRYSVVCGSTESQVTGITSDSRKMQDGYAFVCIKGAVSDGHKYIDQIKDKASVIVVLDGEYEAKDCKAAVVSTDNTRLALALMSAAIYGNPDKKLFTIGITGTKGKTTTTYMVKNVLEACGIKTGLIGTIETIIGDKAIPAHNTTPESIEIHQSFAKMVDAGCKAVVMEVSSQGLKLDRTAGIMFDIGVFTNLEPDHIGPNEHESFEDYLNCKAKLFKQCKVGIVNADDKHTKDILRGAICKVESYGIGDNADIKAENIELLHEPGKIGLTYDCTGLVNMKVELNLPGKFSVYNSLCAIAITRHFDVDEEALKETLKHVRVKGRIELVKVSDDFTLMIDYAHNAMALESILTTLKEYHPHRLVCLFGCGGNRSKERRYEMGEVSGKLADLTIITSDNPRFEEPEAIIEDIKTGIAKTTGKHVDITDRKEAIKYAIEHGEPGDIIVLAGKGHEDYQEIKGVKYPMDERVLIKEVLEELKGN", "metadata": {"id": "A0A174ZDV6", "cluster": 3034933, "interpro_all": ["IPR018109", "IPR036565", "IPR004101", "IPR036615", "IPR013221", "IPR000713", "IPR035911", "IPR005761"], "interpro_used": ["IPR018109", "IPR013221", "IPR004101"], "interpro_unused": ["IPR036615", "IPR005761", "IPR035911", "IPR000713", "IPR036565"]}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein should include 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 originates from Passalora fulva (Tomato leaf mold) (Cladosporium fulvum) and is described by UniProt keywords Nucleus. 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, 3951, 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, 22970, 2037, 4675, 20807, 5524, 5257, 7302, 12, 13920, 6998, 20459, 13, 12, 23415, 9890, 2457, 5257, 1020, 1989, 13, 1930, 1977, 2910, 2007, 20709, 11569, 5607, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MPAVHVSSRRAERRRIPPTLRTKSGCLTCRSRRKKCDEASPICHRCSKSSRECTWAHVAYPPGAAHPHVPSSAQSAPRCTIAAGIAACNNAVMLRDVEPAIVQHFVRRYFALIINPESHQLFYRDWMTIIQQALSCHGGVRYSVLSNAASNIFFRDGSASMQDLALKYYSRSMSSTREVVAVVKDTPEHLRTTLTSIIFLYLHGCMGLGTFNDIPAHLNAAIFIVDSQWFDTHDRPILPGPFDRLVVESVMYQIFVVTVDLWSSDGSTQSHFDPDFWERCTRFLTATTPFPEQLNTRNSPVLGVDVDMFRLMISIRKHWSMRHVRHAAAFELRTEELRGWEKYAHLLGNEGEICEGTSTRMLRSITDDATCLYMLCASMLIDQLLRHAGKEQAAVGGQIQEESWQIPIIMAILCRRRQDANWLGCYIGNWPVYTAGIFANSSREVEVINHEMNERWESMRLYQVRRYWDDLKMIWASKGIDP", "metadata": {"id": "A0A9Q8P9U8", "cluster": 2437078, "interpro_all": ["IPR036864", "IPR001138"], "interpro_used": ["IPR001138"], "interpro_unused": ["IPR036864"]}, "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 Prokaryotic N-terminal methylation site, which directs the methylation of a conserved phenylalanine residue. This motif is typically located at the N-terminus of pilins and proteins associated with secretion pathways. Moreover, the protein is associated with the Pilin-like superfamily, which comprises structural proteins such as type IV pilins and secretion system pseudopilins that assemble into filamentous appendages on the bacterial surface. These proteins typically feature a conserved, methylated hydrophobic N-terminus and facilitate critical functions including cell adhesion, twitching motility, and DNA transformation. Some members, such as YadA-like autotransporters, act as pathogenicity factors by extending from the outer membrane to mediate host interactions. It occurs in Phycisphaeraceae bacterium and is described by UniProt keywords 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, 21545, 56, 17, 4262, 5547, 3200, 16, 2154, 28351, 1920, 5547, 1927, 43, 5305, 17388, 6181, 18, 2052, 5219, 1977, 5745, 4810, 2019, 1920, 56, 17, 7822, 1927, 7547, 2925, 1930, 2697, 2458, 1956, 5512, 3873, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 7547, 1921, 17, 3189, 13975, 16, 2154, 12936, 4346, 2697, 2427, 1966, 2601, 4370, 7547, 2925, 1930, 5512, 2433, 11520, 10984, 7782, 1036, 1988, 17421, 2460, 18706, 7958, 2662, 1990, 1920, 4543, 3154, 18, 2144, 2697, 5745, 5961, 43, 5305, 16, 11882, 7919, 56, 17, 7822, 1930, 6628, 4140, 4088, 2710, 2024, 6141, 16, 21596, 1941, 9254, 16, 1930, 2678, 7002, 18, 2673, 4678, 16, 2427, 1966, 26169, 3825, 17, 3189, 5728, 5412, 24095, 1036, 16, 4033, 1966, 15903, 2790, 2007, 12140, 2037, 1920, 7642, 3260, 1942, 8265, 4423, 3719, 18, 2176, 5110, 1922, 25511, 9119, 29164, 9914, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 7864, 18, 3], "output": "MIDRLLHTPPTPTPTSIPSRCPGKGFTLIEVLVVVAIVAALISLAVVGLRGARKASAANDQKGWLPFFADPKSTPAFRNAGMGFQYNQQVLYWFKRGRREERLAHYTRSFILFSDYELTLTAAYDPRFLAEAAYPARKGLFVEPRPAHRGETMGRHESPSLYYHAGRRGPFDRLTPGHTRPGDTALDLPVHGTPSGVLGDDLKGRTPTPTPTPSSRTTRSSRSVPATLSRDHPLRCRAHALACRAHIRNAAQITHAYTIPLQGYLSQPRVAPEQFCPSSELYLDVFTPAGDTPPSPARAVAHVAFFDAHAEEVDF", "metadata": {"id": "A0A7L9BR03", "cluster": 3127916, "interpro_all": ["IPR012902", "IPR045584", "IPR050470"], "interpro_used": ["IPR012902", "IPR045584"], "interpro_unused": ["IPR050470"]}, "task_type": "infilling"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein is grouped in the Lysozyme-like domain superfamily, which encompasses a structural fold found in glycosyl hydrolases and transglycosylases. These enzymes catalyze the hydrolysis or remodeling of glycosidic bonds in carbohydrate polymers, playing critical roles in processes such as cell wall degradation and biosynthesis. Also, it is part of the Membrane-bound lytic murein transglycosylase B-like family, which degrades bacterial peptidoglycan by cleaving the beta-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues. These enzymes, including the membrane-anchored *E. coli* MltB, facilitate murein turnover by forming a specific 1,6-anhydrobond in the muramic acid product. Also, the protein should include a Transglycosylase SLT domain 2 domain that functions as a bacterial lytic transglycosylase to degrade murein by cleaving beta-1,4-glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine residues in peptidoglycan. This catalytic process results in the concomitant formation of a 1,6-anhydrobond in the muramic acid residue and is observed in proteins such as the membrane-bound MltB. It is present in Hippea maritima (strain ATCC 700847 / DSM 10411 / MH2).", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 18581, 17, 3189, 3418, 13975, 16, 2154, 21569, 43, 4346, 3728, 2435, 1922, 20067, 30337, 1930, 2127, 17038, 4879, 18801, 24605, 1918, 18, 2144, 5038, 18170, 1920, 9128, 2014, 8378, 1927, 7533, 12546, 9031, 1922, 10590, 11039, 16, 14797, 4140, 5456, 1922, 4028, 2427, 1966, 2024, 4821, 4877, 1930, 8132, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 3260, 17, 4124, 17033, 6185, 14818, 2127, 17038, 4879, 18801, 24605, 1021, 44, 17, 3189, 3416, 16, 2154, 28004, 4543, 24183, 2007, 28634, 1920, 4666, 17, 21, 16, 24, 17, 7533, 12546, 5403, 2192, 56, 17, 6894, 23010, 29085, 1935, 2687, 1930, 56, 17, 6894, 22988, 17454, 4248, 18, 2144, 5038, 16, 2710, 1920, 3260, 17, 17199, 14, 47, 18, 5178, 14, 2646, 27414, 16, 6628, 6185, 14818, 9781, 2007, 7402, 43, 2487, 21, 16, 26, 17, 21999, 20226, 1007, 1922, 1920, 6185, 13514, 2687, 4863, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 2127, 17038, 4879, 18801, 24605, 1021, 2788, 1031, 3418, 22, 3418, 1988, 4088, 1966, 43, 4543, 17033, 2127, 17038, 4879, 18801, 24605, 1021, 1942, 17069, 6185, 14818, 2007, 28634, 4666, 17, 21, 16, 24, 17, 7533, 12546, 9031, 2192, 56, 17, 6894, 23010, 29085, 1935, 2687, 1930, 56, 17, 6894, 22988, 17454, 4248, 1922, 24183, 18, 2052, 6804, 2585, 2274, 1922, 1920, 8537, 3337, 1927, 43, 21, 16, 26, 17, 21999, 20226, 1007, 1922, 1920, 6185, 13514, 2687, 6181, 1930, 1977, 2528, 1922, 2697, 2427, 1966, 1920, 3260, 17, 4124, 2646, 27414, 18, 2176, 1977, 2481, 1922, 5266, 5376, 13081, 2265, 1019, 12, 3943, 11037, 11851, 11068, 1027, 19, 10964, 8824, 3242, 19, 5146, 1028, 13, 18, 3], "output": "MRFILVTLIIVLSYPVYGFNIDEIAVKLNARYNVPVEYTHYVLSKAKVVDNVRSFVERVANSPEKTFVFGDFVKFFVNKRRIKEGVEFYKSHRKLLNRVYQEFGVDPCVVVAILSIETNFGRIKLTTNALDALYTLSLYSKRKRYFLSELESFIVYTFRHRVNPFSVKGSITGALGIPQFMPSNIDRYGVDFNGNGLNLNEVDDATASIANYLLKHGWKKDKPVVKFLSNDSKLCRRLNAKNLNGGKVITFNYGSGVRCFVAYDNFWALKKYNGTKNYAMAVYELSEEICKKIR", "metadata": {"id": "F2LW89", "cluster": 3200898, "interpro_all": ["IPR023346", "IPR043426", "IPR031304"], "interpro_used": ["IPR023346", "IPR043426", "IPR031304"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein incorporates 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. It is present in Clydaea vesicula and features UniProt keywords Transmembrane helix.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 19683, 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, 2176, 1977, 2481, 1922, 2111, 2584, 24145, 5634, 16058, 1019, 1930, 4075, 20709, 11569, 9117, 7864, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MLENSSNKKNNSNIFGKTKSIDSSEYSNQTKYFWIFQLLISNVELYHNIIYFYNKSSIARYAFTFFLFCLVLVDIVLDCSTPSLYLVEDTDDEEEQLAPPHYEDSKPPTTFLVISSFSVLILGRVVNVYAPVYYKKIVDDFSTVQNKEQLSLPWVDIFLFVFVGQATTKNISLKMFSHLHSLSLRYHLNRKTGEILRIQEFAITFVKIIKYGGMEGRVHPAIQYEFAQIAMVYSRFLTNLLSNLTSQLELKKNFILLTCQRVATPSWNMISALRQFLYVIVNEYKNTQLFRSPLDCAGQSLVLRSTLLINAKEAVKEKSACIKKFIKILSFELENLCGKYVYGRLNIDLRESVNEGSNRHEFYFIFRIGFDVKFVLEPLIDFNTIGLREYFGSNSKEVSVYVSGNLFTFGSEFFKHFKKLIPFVWPSGKENWFLQFLRFLAGNSGFLSGFEDYLWIPKTVSSHSHDVDFAHNMLKVSAKNAILRDISNEDEFLILEAIKDKHEEDFKKLCCFGLMCGGLNSARC", "metadata": {"id": "A0AAD5U1B9", "cluster": 3464301, "interpro_all": ["IPR011527", "IPR036640"], "interpro_used": ["IPR011527"], "interpro_unused": ["IPR036640"]}, "task_type": "infilling"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: The protein incorporates a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. It has been detected in Diacronema lutheri (Unicellular marine alga) (Monochrysis lutheri) and corresponds to UniProt keyword Plastid, Amyloplast, 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, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 2176, 2258, 2252, 3330, 1922, 25141, 2145, 2290, 3368, 10908, 2098, 1033, 12, 24797, 3386, 10789, 4326, 1019, 13, 12, 18688, 6570, 4662, 10908, 2098, 1033, 13, 1930, 8852, 1942, 20709, 11121, 2538, 19754, 16, 7061, 9574, 16, 1930, 13763, 18, 3], "output": "MYLELSPALVAVLHVDGACSRAQWAAQTVRALARGLHAPGEGAHTSASGECGGMLDASVRTGLRARLHVADVDQLLADGPDADDGGEAERVTCGSVLRVPLAADADASAMVCAAVWAALDARAVSAARASRDGGWAPEDGQGAARQLLVWCAYVERHAFTVERYHATAAQLVEGSGCSDVGLCALENGLVSAQLSGDDGVASAARRLLGVLRDCTSWQLESALPVTVCKVGDRLTVRLPADSRSADGIRAARVRRSQQDDRNSRSSSASSACSSSSSFSSAARSLAPRGAWRAGADDDVDEDAARGVWRGRWHVQVAEPHALRCAGAAAERMRGALLCRRVTTHSVNLRARSGAYDWRLVRVLPDGSALAPAGGVGAACGRIVAFAPDVRAGLTAQVVAFGGTESGVAPAPLGRVPAPVRMRGHGGERCGESESPESPRDAPARPACPAGGRGECADECTTRSDGACMRDITLAPFAPHASTARDAWHAPPGESPADERTFGALERSLVALARGGVRLLVLEDATTPGCGSTPRAELGGASALASLCATARGEHGGATLRAVDQRTGHVAPLLSHCVHTSSRDGVGAPHARLARNMRDSAVWAQIVDNACDLVSSCGLHRLDRYEPDGGRQRPAVDTLRSPVVLACAHAPRRTQGGCAGAGASCAFAAPLANAIAAQLGARCRGALGCVPVLDVDALLHACATRAHACGAACAARRSGAPRAGGCAPDEWPAQPSHASFCCARLGCAIGEHAERGALVDAAAARGGATDGAAQCEERKSLAQARWQLTLGRARPALRCGANVACHASRCALAAPAAPPRRRSSAQPAVEAGAATTRGQPGSGRWSTRSGYAHLEMAANPPSDNDTALSWPAALAAFCARGARADAAAAFALALPQWRARWQADAPSSAQATTAEQPPSADTATAAAAGPRAVRRSQLAPLAALARARAERAELFDAPLSAIVAHGWRVRGGGLTALIALCDGRPWASRVSLQIGPALLPARRSGGAAANRVLVTPVALELLAGQLWFEVPAGARGCTLCVELSAARARHAGTHAGRHAGTHAGRHAGTHAGRHAGTHAGRHAGTHAGTERASNHRLARLPFALCTRGNAVGALLADGFARQRVADADAAGRAEPRSAPLAAGVRCGDAGGDGAERTGAPTDALRAALATAHACERALSDRRLVELLGCARGEAPRALCASSPLVLALVSPEYARLAGSALGGLGVFVPHLAEALAARAGVTVHVVTPLWARRAGGERVDVRRAHASGASPVVSSLHSARVHGVHVHLVACAGHFEGEPYEGFALRSAAVFALASVRALEVCAVCPDVVVSNDWTTAAGLAERAAALAISRARLLHLIHNLEHGYDGFLLSTAAEVALVEAAGIPASLMVATGGGGGWGGIVPSAPRACCADLGGARLFSDASLAGSCSASSPSSVDASAFGAARAARAARVAPASTKPAASAQPPLAREQLPPPPPSIAGASAPVAVSLTRAALLCSDRWATVGHAYAARLGESARLGESARLGESARLGESARLGESARLVAPASVPVALHRAQIAQLGMSRADAKAAVQLRCFGRAAMLPRRPLIAFVGRVCRQKGVHLLLDAFPALLERYASACAAQMSDLRARFPERFWARPAEFCNDGPLVNLAADLCVMPSLFEPGGLVQHEFLAAGTPVVASDADGLRDTLVLERALTAYHAPDGASWAALQANAVRAARDVGDSARVWHVELQRMCRELPTAAGGEDEPAPPARQAALVLYAHMLVANQACLARALTPLVMRALALAARARGALDTGAEVALGRLEVLLVACTGHRAQAEDDGDGDGDGDGDDDGLHAEARPAAAGARAAFTLPGVAGVAVTRADRAGAQPQQPQARPATAPARSEAGGRSREGAGVGVRVLLALRLDACAVCTEGVYLPCSMASLELPHADAAVLARCASSRDAWRVCAARGMLPRGVLLAVHCAPGVALFSASARARPAGASAAVHAAAATAGLCALCDDDGESAGSRPMWVRRVRARVLSGCSSAAAPGTAPRSNALLLGAHGGADMEGGAWLFCADRHGAADDGEGALLATALARARAARADERRGPLLACLARLPMAPPSELALASPPAALGDAAGELRVARFTVDVGLLPAAIRAARGARTASPAGWASGETHAAPPLAPAARAPWPDVPQSSVGASARARAAPLRAGESARLAPLLRARGPPLCGGDAQLIVCGRAAAGDRDVSERPCAGCAFVFRAGNHAALLAA", "metadata": {"id": "A0A8J5XVV3", "cluster": 6532260, "interpro_all": ["IPR013534"], "interpro_used": ["IPR013534"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein should feature a Aminoglycoside phosphotransferase domain that confers bacterial resistance to various aminoglycoside antibiotics, including kanamycin, neomycin, and streptomycin, by inactivating them via phosphorylation. Moreover, 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 derived from Sporothrix schenckii 1099-18.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5961, 43, 23029, 8028, 8078, 9961, 3418, 1988, 16556, 4543, 3554, 1942, 3425, 23029, 8028, 7560, 16, 2710, 19404, 16, 26269, 16, 1930, 10666, 16, 2007, 20862, 3581, 3454, 4050, 18, 3950, 16, 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, 3595, 2037, 9130, 2195, 3027, 1039, 25762, 15895, 13800, 9359, 1026, 17, 2654, 18, 3], "output": "MPNLEGVQYAVTFDELFNEDNDKEYMAWLDALLEPASIEFLKRFVASKLGGDRGSVHYVDMARGSFNVVLQFRIDDDRAPARLALRIPQRGFTAEAVTAERLENEVHWMQYIEEQSTVPVPHIYSWAASGDAVDPRIGPYMLMDYVEGQSLHSCLATWEASDNETDAVEKRTAVFEQLADILLQLRSHHVDKIGSITRVDGGGWAVTRRPLTIDMHIQLVTMPGFSTDDWPTSPLLHAKNYVSLATALRNHQMLCLRNINIPGAWNKDGFYDFQEGDAIDMQRALKTARGRVLARRAMGLPATAAHLVDGDGNDGGEHDKKPFVLFHPDLNASNILVDLDTARITALIDFEYTNAVPAALADDPPVWLSHINFVHCLTFGFFAEWQARYKYRLDAFLAVLERVEQKQKQQQQQQSPLPVSERPPLSAKMRASWEKKTYLINHALQRAELADTIYHGQPALFPAVVEAIDGTDDWTQEVYMYEEYTRWQIDLYEADRKARLRKKQPAGT", "metadata": {"id": "A0A0F2MI16", "cluster": 9742282, "interpro_all": ["IPR051678", "IPR002575", "IPR011009"], "interpro_used": ["IPR002575", "IPR011009"], "interpro_unused": ["IPR051678"]}, "task_type": "autoregressive"} {"instruction": "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 belongs 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. In addition, the protein is grouped in the Ankyrin repeat domain-containing protein 49 family, which regulates diverse cellular processes including spermatogenesis, autophagy promotion via the NF-kappaB pathway, and planar cell polarity establishment. Additionally, members serve as chaperones during 26S proteasome assembly and participate in signal transduction, such as EGF-induced AKT activation, to impact tumorigenesis and apoptosis. It is identified in mine drainage metagenome and features UniProt keywords ANK repeat. 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, 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, 14440, 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, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 28336, 6865, 3418, 17, 3165, 2213, 4343, 3416, 16, 2154, 7014, 6445, 3689, 4028, 2710, 21814, 16, 6661, 10693, 3454, 1920, 4651, 17, 19901, 3374, 16, 1930, 14334, 2024, 12432, 11108, 18, 4950, 16, 4678, 7120, 1966, 18098, 2409, 27868, 9993, 5957, 1930, 7352, 1922, 2733, 8201, 16, 2427, 1966, 4451, 17, 2719, 5496, 2936, 16, 1942, 3829, 11472, 1930, 4091, 18, 2176, 1977, 2899, 1922, 24165, 12790, 16552, 2225, 1930, 4075, 20709, 11569, 9808, 6865, 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": "MDARDLGYIAGSIKPQLRNPSLWPIVKDVLYGNTAALENALDSGLNPNVVVEKGNGNVESLLDMAISAGQRGTIKALIAHGAAVNLNQYDLGKYGTGTQDATYVEPLVEAATAGEDDVVKYLLENGANINQGNNLIGDTQTALTAAAAGGNVSTVYLLLANGADINTALDANGYVPQNLIQAAKRKPVYAAVVKLLVNYGARVPPGS", "metadata": {"id": "T1CPJ1", "cluster": 9754374, "interpro_all": ["IPR051637", "IPR002110", "IPR036770"], "interpro_used": ["IPR002110", "IPR036770", "IPR051637"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein is associated with the Pectin lyase fold superfamily, which encompasses enzymes with a characteristic $\\beta$-helical architecture, including pectin lyases, pectate lyases, polygalacturonases, and iota-carrageenases. These proteins primarily function to degrade cell wall polysaccharides such as methylated or demethylated pectin and carrageenan, often acting as microbial virulence factors. Furthermore, it is part 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 produced by Microbacterium faecale.", "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, 2458, 1956, 1920, 22422, 23928, 3728, 13975, 16, 2154, 21569, 5038, 1956, 43, 6293, 8, 38, 4666, 8, 17, 11514, 9335, 16, 2710, 22422, 23928, 1036, 16, 13494, 3857, 2057, 23928, 1036, 16, 16115, 23276, 10366, 2319, 16, 1930, 30360, 1019, 17, 28682, 11496, 4127, 1036, 18, 2144, 2697, 5985, 2347, 1942, 17069, 2024, 4821, 18686, 2427, 1966, 11882, 2014, 21732, 1981, 22422, 1930, 30486, 16, 3868, 8290, 1966, 7293, 9304, 2790, 18, 3677, 16, 2176, 1977, 3131, 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, 4152, 2007, 11565, 18417, 15380, 1021, 18, 3], "output": "MDSMSVRFIPLANINGKDGAQGPQGPAGTFTSASGHTLPAGSPGLNAVPTDEAMAVLVGAMDTLTGNALENRFVPKNSLVFNAADHGVVGDGTADDTATMQALIWSVKGRTLDIDLSNAHLVKTDPDNEIFRAEGSFDAPVSVNAGDIVKVFSNDEIRDSRPRNETEKSWQGEFAVVANIDGTEVHVSPPLLDTSFRFGTADYDGNPGTEFTRRMFRYSALNGSYIAGHVVRGPGTAFSDAADGYGVTCGGSSWGDYRIVANRLRHAFTDDTAGRAATGQTDPAVFGRAMYGYGHHFYDITATGTDARWLFRIRGRAHTLSDCIAIGAESYQHRFVNCATYRVGQPFNVAKDTLDDPAFDSVVIEGMVDPVLVFTEGPYEYDGIAFFNIVNGRLRGSCTLDATKGTNQIDVDVKLNLSDSARHQMQAVVQWNSMDGQVRAHLLGNHSMLPWASGGSMIQMRSGDAVVTCRLNSSGSVTTAGIEPGAFSGQRGGDVTLQARESMSLVWDSVSAIWLQLSQATVETSGSPTAKHLEIGVPRGLDQVPDGSTIVAPPGAVYRSAGGGVITNQRYSRLVVADTDGFYSTNIRVARIQNHRVHSCVYTVADLRVENLPCKITGSSARATAVPWDTHHGSGFGVMAEAGLGGQGTGYFEFFRQGPVIEYGYVRLGPDEAPNFVFRGSTGPAWNLTRDASRQSVILTNSLGPGTAPTTAFRSITRLDLYAVGGSVTIPSGGAANTSL", "metadata": {"id": "A0A916Y7Z5", "cluster": 12876734, "interpro_all": ["IPR012334", "IPR011050"], "interpro_used": ["IPR012334", "IPR011050"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: 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. In addition, the protein incorporates a Saccharopine dehydrogenase, NADP binding domain that binds the cofactor NADPH to catalyze the reductive condensation of L-alpha-aminoadipate-delta-semialdehyde and L-glutamate to form saccharopine. This catalytic unit is integral to lysine metabolism and frequently occurs as part of a bifunctional enzyme alongside lysine ketoglutarate reductase. It is derived from Prescottella agglutinans.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 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, 1922, 2459, 16, 1920, 2213, 19683, 43, 14175, 15742, 12184, 9294, 16, 24221, 2743, 3418, 1988, 6876, 1920, 15155, 11908, 1942, 18170, 1920, 23335, 16112, 1927, 54, 17, 4595, 17, 3835, 2713, 4302, 2057, 17, 9649, 17, 8762, 8790, 1930, 54, 17, 7627, 1942, 2386, 14175, 15742, 12184, 18, 2052, 6804, 5344, 1977, 12328, 1942, 9082, 4714, 1930, 5467, 5110, 1966, 3131, 1927, 43, 29491, 4113, 17764, 9082, 21471, 16542, 17488, 11386, 18, 2176, 1977, 3595, 2037, 2244, 4879, 3519, 5870, 20262, 2075, 18, 3], "output": "MKLVILSAGSIASSVARILAPTGSYDELVIADIDLDKATAVASELGGKAERFDGMPIIRAAIECGVNYVDVCDEFDVAEQLVSAADLDEAAKAAGVSVIFGMGYAPGITSLIGRWAVESLDSGATINEHMLHSMSGDVVQYIDGSMKRVPAWGDPKPFSFSAPFDTTAYAGYMGHPEGITLLFEKLGLTNPNKLGDLPMSPRQYLAHYMSTEEGERGLAVERAGQPGTAMQIIADGAGADPTPHAAAAAVREMLEGRITRTGVMSPEACIDPEPFVTRVLDATGVRLSKRVTTTTTIRATDPASIKSVITGADVVFNAVGPFYRFAHSVDVAMAIPYMVDMGTYLPGLRNATVRYTWFEQAGNDLWQIDGEPARVVFETQILYTEAS", "metadata": {"id": "A0A438BE68", "cluster": 15144101, "interpro_all": ["IPR036291", "IPR005097"], "interpro_used": ["IPR036291", "IPR005097"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein includes a YSIRK Gram-positive signal peptide domain that functions as a specialized signal sequence for surface proteins in *Streptococcus*, *Staphylococcus*, and related lineages. It contains a conserved [YF]SIRKxxxGxxS[VIA] motif at the start of the transmembrane region, suggesting a specific role in protein secretion or anchoring. Moreover, the protein should contain a LPXTG cell wall anchor domain that mediates the covalent attachment of surface proteins to the peptidoglycan cell wall in Gram-positive bacteria. It comprises a conserved LPxTG motif, a hydrophobic stretch, and a positively charged tail that are recognized by sortase enzymes to facilitate the tethering of the protein to the cell surface. It originates from Carnobacteriaceae bacterium zg-84 and features UniProt keywords Peptidoglycan-anchor, Secreted, and Transmembrane helix. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 24018, 1996, 1040, 8604, 17, 2843, 2733, 4207, 3418, 1988, 4088, 1966, 43, 11021, 2733, 3244, 1958, 3154, 2697, 1922, 14, 15746, 14, 16, 14, 13452, 14, 16, 1930, 2712, 10439, 18, 2176, 5461, 43, 5305, 37, 29962, 39, 4520, 1040, 14710, 1039, 1029, 14710, 1036, 37, 3454, 39, 5219, 2019, 1920, 6413, 1927, 1920, 9117, 3031, 16, 3783, 43, 2487, 2770, 1922, 2213, 5512, 2014, 20816, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 8182, 3306, 1029, 2024, 4821, 13333, 3418, 1988, 10412, 1920, 13577, 8576, 1927, 3154, 2697, 1942, 1920, 24183, 2024, 4821, 1922, 8604, 17, 2843, 4802, 18, 2176, 12936, 43, 5305, 8182, 3306, 1029, 5219, 16, 43, 7919, 9064, 16, 1930, 43, 6629, 9516, 5281, 1988, 2032, 6783, 2007, 17362, 2051, 5038, 1942, 6628, 1920, 23991, 1927, 1920, 2213, 1942, 1920, 2024, 3154, 18, 2176, 22970, 2037, 14933, 10296, 1972, 3336, 14061, 68, 1029, 17, 5686, 1930, 4075, 20709, 11569, 24183, 17, 13333, 16, 8366, 16, 1930, 9117, 7864, 18, 7031, 1920, 3244, 18, 3], "output": "MFRQKKYRYYNVSQTKQRFTIKKFKFGVTSVLLGLTFLGVGGYQVLANESDSKVEATQSNTSPNTTSVNSEELLSTTSMTEERKQETDQESVLNTEKINSSLTTYSTIGSEEYNPRLLLLSNGVPSDNVHSLGGGVDVTPLEAKNLGDGFVEYSYQVSVQAIVSSDHIQTSGTVHVALPGFGQDVKFTQIGTYDGELLKDNAEFSPFELLHARMTASKNVEVPLGITHSIEAFNKTQEERHAQREANNYDYITGSSLAFNEEIELRKAKGMLDLPNAVIFTGYTQSGFNPAVDVFDDKDSSNPAKTIEENIAKYENLPNTIKNYVFSTYSGGHPMAVKVSFKVKEEQALKTPNLPLWSALAWRAFNEGGIASYKTEAQNLYDFDNGAKAAAFVANPETIKDNQFDKHGLYGADTGVTAYTGDWRLIGTDITKANFNYVSNFNLTSNLAVTYFAPRTEDVRDIAVVRYETKPDTQPQDIQPNPDSVSPVESQPTDNIHTLGGGVDVTPLEARDLGDGFVEYSYQISVQAVQSSDHIQTANTLHVALPGIGQDVTFTQIGTYNKDDLGIDEYDKDKLRERRLKASKDVEVPLGVTTSMAEFEKTQEERLALLKANNKENYFQYTSLAWNEEIELRKARGLDTLPNAIVFAGLSKNEYNAEADSPRDYDNILELGTIEEQIEKYGDRPNMIKNYLLSAEGIGHPLALRISFKVSKEQALKIRNLPLWASIAWRSFAEGYIGSYDNGSQSLYDYPGGRMSAQFISYPEHIHKEQFDKNGLYGTTAGVTRYTGDWRFIGNDVSQSSFNYAAIYNLRSNLAVTYFAPIDEDLRDIAVVRFEEQSETTEEPNEKVEKPTEDQTETPTPNETPNEPVKPGEKIEQPKNPTGKTTSSEALPPKQPMEQKVAQLLPKTGETENRFFSVAMLAIVSSISLLFGTKKKQN", "metadata": {"id": "A0A7D7C2A4", "cluster": 16680037, "interpro_all": ["IPR019931", "IPR005877"], "interpro_used": ["IPR005877", "IPR019931"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I need a polypeptide chain that performs the following role: It is part of the Protein of unknown function DUF4389 family, which is functionally uncharacterised. This family is distinguished by a single completely conserved arginine residue that may be important for its function. It is produced by Chloroflexota bacterium and exhibits UniProt keyword tags Membrane, Transmembrane, and Transmembrane helix. Please generate this polypeptide chain's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 13022, 4659, 1988, 17436, 1920, 2894, 2770, 30, 2176, 1977, 3131, 1927, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 29367, 3416, 16, 2154, 1977, 9346, 23229, 3495, 18, 2052, 3416, 1977, 12080, 2007, 43, 2957, 5796, 5305, 9732, 6181, 1988, 2278, 1998, 2715, 1958, 2496, 2347, 18, 2176, 1977, 4152, 2007, 10107, 18222, 7336, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 2052, 13022, 4659, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MTGYPITVGVEYTERLSRLTTFFRIFMVIPHSICLYFLGIAAGVVVFIAWWAILFTARYPKWAFDFVSGYLRWSTRVGGYYYLLTDRYPPFSLD", "metadata": {"id": "A0A661V7G2", "cluster": 17197204, "interpro_all": ["IPR025498"], "interpro_used": ["IPR025498"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein includes a TGS domain that adopts a \u03b2-grasp fold with nucleic acid-binding affinity, serving as a regulatory module in enzymes such as threonyl-tRNA synthetases and OBG-family GTPases. Within bacterial stringent response proteins like SpoT, it facilitates the transcription of survival and virulence genes during environmental stress. Additionally, the protein should have a ACT domain that functions as a conserved regulatory binding fold involved in the allosteric control of enzymes within amino acid and purine metabolism. It typically adopts a ferredoxin-like topology, where pairs of domains form an eight-stranded antiparallel sheet to bind ligands, such as serine, at the interface. This module is found in a variety of proteins, including 3-phosphoglycerate dehydrogenase and chorismate mutases, across archaea, bacteria, and plants. Moreover, the protein features a RelA/SpoT domain that functions as the catalytic core for the synthesis and hydrolysis of the alarmone (p)ppGpp, regulating cellular responses to stresses such as amino acid starvation and carbon limitation. Belonging to the Pol beta-like nucleotidyltransferase superfamily, this domain utilizes a conserved two-metal ion mechanism to catalyze the production of (p)ppGpp from ATP and GTP/GDP or its degradation. It is derived from Thiomicrospira sp. CG2_30_44_34 and contains UniProt keyword associations Kinase. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 5921, 43, 29977, 3418, 1988, 24032, 43, 161, 17, 22815, 3728, 1956, 11079, 2687, 17, 2743, 5173, 16, 13915, 1966, 43, 4948, 9059, 1922, 5038, 2427, 1966, 6841, 12831, 17, 10089, 18185, 1036, 1930, 2384, 1029, 17, 3416, 18390, 18, 2651, 4543, 16801, 2644, 2697, 3189, 9177, 16, 2176, 11374, 1920, 3213, 1927, 3298, 1930, 9304, 2628, 2409, 4813, 3071, 18, 4950, 16, 1920, 2213, 3066, 2162, 43, 4033, 3418, 1988, 4088, 1966, 43, 5305, 4948, 2743, 3728, 3286, 1922, 1920, 14772, 2285, 1927, 5038, 2651, 3835, 2687, 1930, 19700, 4714, 18, 2176, 5745, 24032, 43, 25304, 22389, 10960, 17, 3189, 13678, 16, 2597, 5803, 1927, 4682, 2386, 1925, 5066, 17, 10338, 28892, 11130, 1942, 4566, 6908, 16, 2427, 1966, 8468, 16, 2019, 1920, 6854, 18, 2052, 9059, 1977, 2435, 1922, 43, 5386, 1927, 2697, 16, 2710, 23, 17, 8078, 14966, 2010, 9294, 1930, 25952, 18538, 2010, 2446, 2319, 16, 3436, 21501, 16, 4802, 16, 1930, 4793, 18, 3950, 16, 1920, 2213, 4075, 43, 22247, 19, 9177, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 1920, 4271, 1930, 9128, 1927, 1920, 19065, 2290, 12, 58, 13, 23166, 9434, 16, 6773, 3689, 3387, 1942, 11962, 2427, 1966, 3835, 2687, 12767, 1930, 5056, 7789, 18, 10588, 1942, 1920, 2492, 4666, 17, 3189, 2797, 4090, 2199, 9961, 13975, 16, 2052, 3418, 18127, 43, 5305, 2288, 17, 6048, 4755, 2856, 1942, 18170, 1920, 3372, 1927, 12, 58, 13, 23166, 9434, 2037, 4498, 1930, 9319, 19, 15217, 2014, 2496, 4877, 18, 2176, 1977, 3595, 2037, 15331, 4913, 5424, 11979, 2056, 18, 7294, 1028, 41, 2627, 41, 4044, 41, 3540, 1930, 5461, 20709, 11121, 2538, 5253, 4016, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MDSVQSVYAKIFSTHPQDALALKACEIAFEVSHKPYERFVKSIDVAIILADLKLDRDTLIATLLSDMALEPHYSIDDLNSQFGNNIAELVIGIRRLNHFKDFQSNRISNETQTERMRQMLLAMVSDIRIMIVKLAYRVARLRSLKHEPEEVRHQVAYETQLIFAPLANRLGIAQLKWELEDLSFRYLEPDTYQDVARQLDANRKGREAYIEKVIHGLKEMMQANHIDFHISGRPKHIYSIWKKMNRKKVPIDELYDLRAVRIYVDTVQQCYEVLGLIHSRWSYIREEFDDYIASPKENGYQSIHTVIVGTEDKPVEVQIRTYEMHHHAEFGVAAHWRYKEDGKKLDPSLENSINLVRQMLEYNDNPDLLNEISTELLSEHIYVMTPNSDIVTLSQGATPLDFAYQIHTELGHRCRGAKINGKIMPLTTPLKTGDKVEILAVKSGSPNRNWLNPNLKYLGNSRSRTKVRHWFNQQNKESNIEAGETLFNKESKRLHVKDIPLQLLLERFKCDSDKAFYEALGKGKINERQLTDAIQNWINPRSKLTKPLSAPPQIAGERSSAADGTPFVVGSPQLKTQLAPCCEPALGDEIVGYVTRGRGVTIHKQDCANILNLTDEEQRRLIEVAWTQRFDNKKDFSEAEAYEATLNLLAFDRKGLLRDVMTVLTEWDINLNHCDTNTNKSDGSVSMIMEIEVLPNSNIGAFLDQLEQVKNIVSTSINLNQKTATH", "metadata": {"id": "A0A1J5ITR7", "cluster": 21880456, "interpro_all": ["IPR045865", "IPR002912", "IPR012675", "IPR043519", "IPR004811", "IPR007685", "IPR004095", "IPR012676", "IPR033655"], "interpro_used": ["IPR004095", "IPR002912", "IPR007685"], "interpro_unused": ["IPR043519", "IPR012675", "IPR004811", "IPR012676", "IPR045865", "IPR033655"]}, "task_type": "autoregressive"} {"instruction": "Here is the polypeptide chain function: The protein includes a ZMYM2-like/QRICH1, C-terminal domain that constitutes the C-terminal region of Zinc finger MYM-type proteins and QRICH1, which are key regulators of chromatin remodeling, transcriptional repression, and DNA repair. Although the specific mechanism of this domain is uncharacterized, the associated proteins function as scaffolds in gene silencing, facilitate BRCA1 recruitment to damaged chromatin, and mediate the integrated stress response. Moreover, the protein is associated with the Uncharacterized protein KIAA1958 family, which consists of proteins whose specific biological function and cellular role have not yet been characterized. It is found in Mytilus galloprovincialis (Mediterranean mussel). Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 5921, 43, 21748, 2229, 1028, 17, 3189, 19, 30313, 2108, 1009, 16, 45, 17, 4262, 3418, 1988, 14879, 1920, 45, 17, 4262, 3031, 1927, 7997, 8497, 3057, 1035, 17, 2601, 2697, 1930, 30313, 2108, 1009, 16, 2154, 2032, 3834, 9098, 1927, 6338, 8378, 16, 5224, 10084, 16, 1930, 2678, 5059, 18, 2876, 1920, 2487, 2856, 1927, 2052, 3418, 1977, 24528, 16, 1920, 2458, 2697, 2347, 1966, 10603, 1922, 2359, 8343, 16, 6628, 11779, 6067, 1942, 10756, 6338, 16, 1930, 8265, 1920, 6714, 3071, 2644, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24528, 2213, 8191, 5025, 24853, 1025, 3416, 16, 2154, 7543, 1927, 2697, 6098, 2487, 3933, 2347, 1930, 3689, 2770, 2162, 2084, 4898, 2252, 4378, 18, 2176, 1977, 2435, 1922, 3057, 2583, 1957, 9354, 12964, 11800, 3349, 19337, 12, 16825, 26874, 1938, 13, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MMETNMNQHPLKGMLCSFDRYLRHHNYGYQISKSAEFSKVKDVLTAKQVELKKLGKGNGHKKAETLCDEDIEKLFQSGEIGDDNPTTLLHTVWFFNTIYFGLRGVTEHHQMTWGDVKIVRDTSSGLEYLQMNERNTKTRTGKSLRDQRDIPQMAWANLENKLKCPVHAYKLYKSKRPLKYSNPSDPFYIQENINREKTGLWYKSQPIGINKLGKFMKKMATAADIWTQKYPEYFHLFQAKFKETSGNFEDHLGG", "metadata": {"id": "A0A8B6FY89", "cluster": 23030335, "interpro_all": ["IPR021893", "IPR042838"], "interpro_used": ["IPR021893", "IPR042838"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein incorporates 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 native to Operophtera brumata (Winter moth) (Phalaena brumata) and corresponds to UniProt keyword Transmembrane helix.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 19683, 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, 6196, 1942, 3641, 2688, 24661, 28171, 3368, 3857, 12, 12028, 6798, 13, 12, 28752, 3336, 2175, 28171, 3368, 3857, 13, 1930, 8852, 1942, 20709, 11121, 2538, 9117, 7864, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MLYAWDKVKKIVMVVKTEFWYMGIVALAAYKGGAAKVWMFPEGTRTLAVDAQVPIIPIVFSPHYFINDKKHIFYNNGKVIMRLHQIMWDAFFYGSRNVILNKVRFHLRISKIGEGSELGSQFAPRGTRNTGNTVKLLPFKKGAFRCLEPVPTEGLTPEDIPELQE", "metadata": {"id": "A0A0L7KZD6", "cluster": 24181161, "interpro_all": ["IPR002123"], "interpro_used": ["IPR002123"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein includes a Heavy metal-associated (HMA) domain that mediates heavy metal transport and detoxification in organisms ranging from bacteria to mammals. It adopts a ferredoxin-like $\\alpha$-$\\beta$ sandwich fold containing two conserved cysteine residues responsible for binding metals such as copper, cadmium, and lead. Also, the protein can be placed in the P-type ATPase family, which utilizes ATP hydrolysis to transport a diverse range of cations and phospholipids across cellular membranes in both prokaryotes and eukaryotes. Also known as E1-E2 ATPases, these integral membrane proteins cycle between two conformational states to pump substrates, including H+, Na+, K+, Ca2+, and heavy metals, against electrochemical gradients. Additionally, the protein is included in 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. It has been characterized in Acidimicrobiia bacterium and contains UniProt keyword associations Cell membrane, ATP-binding, and Transmembrane helix. 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, 5921, 43, 7881, 6048, 17, 2458, 12, 5833, 1019, 13, 3418, 1988, 10412, 7881, 6048, 4860, 1930, 18169, 1922, 7373, 6485, 2037, 4802, 1942, 9902, 18, 2176, 24032, 43, 25304, 22389, 10960, 17, 3189, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 18038, 3728, 3165, 2288, 5305, 8666, 4248, 5061, 1958, 2743, 11570, 2427, 1966, 9541, 16, 17203, 16, 1930, 2949, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 58, 17, 2601, 9444, 3416, 16, 2154, 18127, 4498, 9128, 1942, 4860, 43, 6445, 3109, 1927, 16525, 1930, 15619, 3436, 3689, 5726, 1922, 2321, 28149, 1930, 15021, 18, 2222, 3171, 1966, 11123, 17, 6602, 28132, 16, 2144, 12328, 3260, 2697, 4048, 2192, 2288, 8523, 4376, 1942, 8912, 6249, 16, 2710, 50, 15, 16, 4049, 15, 16, 53, 15, 16, 5497, 15, 16, 1930, 7881, 11570, 16, 3316, 13197, 12741, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 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, 2176, 2258, 2252, 4378, 1922, 2687, 1980, 1935, 15129, 3907, 1019, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 2024, 3260, 16, 4498, 17, 2743, 16, 1930, 9117, 7864, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "MQLNNSVVDEPVDLQVIGLHCAEEVGALRRALDRQAGVSDVHIDQVRSRVSFRLAAPATLPLVSAAVTRAGLRLVQPEEAVLELAVEPRVWWLSILSASSLAVAVATQFIESGGAWLSLVADVEADGPAWVSTTAYALAALTASVIILPKALTSARAGRFDMHVLVVIAIAGAAWLGEVSEAAAVASLFAGSQLLEAWSAARARRSVGALMQGTAGHACCCIDGHEHDVAVHDIEPGMVLRVKPGERIPVDADVISGSSSVDESATTGEPTPVLKRVGNLVTAGSVNGSGALEIRARGRADESSLARMHRAVEHARQGRTEAERWVERFAGVYTPVVVVLALGVWLVPPLLGFGVWEEWFRRGLVVTLVACPCALVISTPVTIVAAISAAARHGVLVKGGEHLERFATLRAVAFDKTGVVTTGRPKIVSLRLLGARTEREVLEHIVALETRSEHPLAHALVTFAASRGVAERAARVRDVQAVPGRGVVGQAWGHKFWIGSAQFLGEHAQVGDEAAAEIARLHAAGLTVVACGSGAELWAVLGAHDTTRADAITAAQLLRARGVRQLVILSGDHAAAVQATAQAMHVSEVRGECTPTDKAAAIAELGMRGPVAMVGDGINDVPALVAATLGVAAGPRATDAALDAADVVLVHNDLRYLPWLVEHARRTLRVIQQNLWFAVGIKVAFLVAAALGEATLWMAVLADTGATLAVTMNGLRLLRMQAPPVSHHHHHHDGEGGHTYQAAQSH", "metadata": {"id": "A0A9D8F514", "cluster": 27763597, "interpro_all": ["IPR023299", "IPR023298", "IPR008250", "IPR051014", "IPR036412", "IPR023214", "IPR006121", "IPR036163", "IPR027256", "IPR001757"], "interpro_used": ["IPR006121", "IPR001757", "IPR051014"], "interpro_unused": ["IPR008250", "IPR023299", "IPR036163", "IPR027256", "IPR036412", "IPR023298", "IPR023214"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe protein should contain 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. Moreover, the protein is associated with 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 Bacterial competence-related DNA uptake protein family, which facilitates the uptake of extracellular DNA during natural transformation. These proteins likely function as components of the membrane-bound transformasome pore complex, mediating the binding and translocation of genetic material essential for horizontal gene transfer. It has been detected in Peptococcaceae bacterium.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 3066, 5531, 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, 3950, 16, 1920, 2213, 1977, 2458, 1956, 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, 4543, 12939, 17, 2712, 2678, 5047, 2213, 3416, 16, 2154, 11374, 1920, 5047, 1927, 5329, 2678, 2409, 4613, 7002, 18, 2144, 2697, 3205, 2347, 1966, 4178, 1927, 1920, 3260, 17, 4124, 4331, 8431, 8554, 2796, 16, 10239, 1920, 2743, 1930, 7849, 1927, 3299, 3485, 4415, 1958, 8743, 2359, 3856, 18, 2176, 2258, 2252, 3330, 1922, 23045, 26941, 9914, 14061, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MPQQHIECEFCFHNVGQGLFYTGHVDDLKFIYDCGSQKEACAEKAVVSYCSLKALLAHTTVEVAVLPYLTPWERLLLACVVPDYLQWYLDILKDPVGFLSEYKVGKVVLDSSHRSGPDLIGDTPVDMRELADLNEDDLHKIFQKEEENGNDWRKLYRDGKLMVKTCIEAFKNCVSQLPAPADYDKFPLTLLLKEKNFIKELRKCYCEDLMRDRDDLNFTSLVLWDGIYRTKFALEACAIGVGCSFVVDLFRKPALGQLLTGDMNLNNNYEAFKGHLGTRLESTCKIWVISAGRENHYYHPHKEVLQDLLQRGKALCVVHENLCLIINAIQGKSSGKVSLLVLSHLHYDHISGIAHGRPKEPNDRGGSHDGVFRLRNLWEFALYNQPVADDHGPINPDWWPKLQWGHCPCYASAVCLVPHHGSGHSWNNKIIEDLPW", "metadata": {"id": "A0A357VF42", "cluster": 27789571, "interpro_all": ["IPR052159", "IPR001279", "IPR036866"], "interpro_used": ["IPR001279", "IPR036866", "IPR052159"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that has this function description: The protein is a member of the Lipid II flippase MurJ/MviN family, which functions as a transporter essential for bacterial peptidoglycan biosynthesis by flipping lipid-linked precursors across the cytoplasmic membrane. This translocation from the inner to the outer leaflet supports cell wall assembly, maintaining cell shape and providing rigidity against osmotic pressure. Furthermore, the protein is a member of the Peptidoglycan biosynthesis protein MurJ family, which functions as a lipid II flippase essential for bacterial cell wall synthesis. These proteins translocate the peptidoglycan precursor lipid II from the cytosolic face of the membrane to the extracellular side, enabling the incorporation of its glycopeptide moiety into the growing cell wall mesh. It is produced by Aquificales bacterium and carries UniProt keyword assignments Cell membrane, Peptidoglycan synthesis, and 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, 1977, 43, 7210, 1927, 1920, 4486, 2890, 16405, 5506, 6185, 1013, 19, 5963, 1921, 3416, 16, 2154, 4088, 1966, 43, 9054, 4415, 1958, 4543, 24183, 8132, 2007, 16405, 9219, 4486, 17, 4624, 10416, 3436, 1920, 6823, 3260, 18, 2052, 7849, 2037, 1920, 6671, 1942, 1920, 7642, 20097, 7825, 2024, 4821, 5957, 16, 8231, 2024, 5989, 1930, 5453, 20471, 3316, 13951, 3772, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 24183, 8132, 2213, 6185, 1013, 3416, 16, 2154, 4088, 1966, 43, 4486, 2890, 16405, 5506, 4415, 1958, 4543, 2024, 4821, 4271, 18, 2144, 2697, 26377, 1920, 24183, 7897, 4486, 2890, 2037, 1920, 9410, 6171, 1927, 1920, 3260, 1942, 1920, 5329, 4159, 16, 12180, 1920, 8629, 1927, 2496, 8821, 8253, 11804, 2460, 1920, 6552, 2024, 4821, 10238, 18, 2176, 1977, 4152, 2007, 10059, 2077, 3955, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 2024, 3260, 16, 24183, 4271, 16, 1930, 9117, 7864, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MGLKSFLTPSKETVLQAIFRSSFLNLLSRVFGYLKQVTIAVLIGFNINTDAFFLAMGLLGLFLTFVDVFDSLGVPNLVRARQKSFKEFRNLAAVLLTFTTALAVTITLLALLLSPIVVNIAFGYNEGEKQLLKEYFMLLTPYLFFSFFFHHFGAIYRSLRHFTVYFFGEFLFAFFSFLFTFLGLLFTKNPKVLPIAVSLSQFLATFYILFVSKPYWEIKFYLDKTVKSMLKQFIQLLGVYAVFHIYTLVDRTFASYLPHKSISALTYGWMVAMIPRGLFKFEHIVITSLSEVNAKWEKIKFYTLRISLFTLPFVVFIFVFAPYIVKLLFGYGTFSVLDIKLTTTATKFYVLSLPFVFLWAIFYRIFQIKEKIYWVVPIIGLTSILNGLLNYFFIFKFNLALEGICIATLIAYLVLTFLSFTLLKFLINKEGNYG", "metadata": {"id": "A0A7Z9Z8H0", "cluster": 27830453, "interpro_all": ["IPR051050", "IPR004268"], "interpro_used": ["IPR051050", "IPR004268"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: It is part of the Pectin lyase fold superfamily, which encompasses enzymes with a characteristic $\\beta$-helical architecture, including pectin lyases, pectate lyases, polygalacturonases, and iota-carrageenases. These proteins primarily function to degrade cell wall polysaccharides such as methylated or demethylated pectin and carrageenan, often acting as microbial virulence factors. Furthermore, the protein is grouped in 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. Also, the protein features a Right handed beta helix domain that adopts a parallel \u03b2-helix fold sharing structural similarity with pectate lyases. This architectural motif often serves as a scaffold for carbohydrate binding or enzymatic degradation activities. It has been characterized in Cryptomonas curvata. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 2176, 1977, 3131, 1927, 1920, 22422, 23928, 3728, 13975, 16, 2154, 21569, 5038, 1956, 43, 6293, 8, 38, 4666, 8, 17, 11514, 9335, 16, 2710, 22422, 23928, 1036, 16, 13494, 3857, 2057, 23928, 1036, 16, 16115, 23276, 10366, 2319, 16, 1930, 30360, 1019, 17, 28682, 11496, 4127, 1036, 18, 2144, 2697, 5985, 2347, 1942, 17069, 2024, 4821, 18686, 2427, 1966, 11882, 2014, 21732, 1981, 22422, 1930, 30486, 16, 3868, 8290, 1966, 7293, 9304, 2790, 18, 3677, 16, 1920, 2213, 1977, 10809, 1922, 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, 2222, 16, 1920, 2213, 4075, 43, 3659, 17105, 4666, 7864, 3418, 1988, 24032, 43, 6110, 161, 17, 7864, 3728, 10763, 4346, 6796, 1956, 13494, 3857, 2057, 23928, 1036, 18, 2052, 28937, 5219, 3868, 10634, 1966, 43, 7281, 1958, 10590, 2743, 2014, 8145, 4877, 4209, 18, 2176, 2258, 2252, 4378, 1922, 11829, 10480, 12578, 5499, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "LIKGNYDRHLIIPSNIANLTIDGENSAFLRSIRCESNGLLLRNIFLKRCASASDADQEAAITVVSGATLTAIKCSVDGWNGNGVKVEEGGCVKFEDCQIVNCVQYGILNHGQVDALRLSITKNKKTGILSRGAGAKVCGEVVNTNENDGNGMGCDEGGVIEVKSSQMNSNKQVGLCVGALGSALVRSSCMVRNCMHGASMSGGYLVMHDCDVRDNGKLGVMLRGGPPGPAGPCSAELVGTTVRGSGNHGVFMDR", "metadata": {"id": "A0A7S0QK10", "cluster": 27897832, "interpro_all": ["IPR039448", "IPR012334", "IPR011050"], "interpro_used": ["IPR012334", "IPR011050", "IPR039448"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein is categorized in the WD40-repeat-containing domain superfamily, which folds into a characteristic $\\beta$-propeller structure comprised of multiple short repeating motifs to serve as a stable scaffold for protein-protein or protein-DNA interactions. These domains facilitate the assembly of multi-protein complexes involved in diverse eukaryotic processes, ranging from signal transduction and transcriptional regulation to cell cycle control. Furthermore, the protein incorporates a WD40 repeat conserved site that mediates protein-protein or protein-DNA interactions, typically forming a beta-propeller structure that serves as a rigid platform for the assembly of protein complexes. These motifs are widely distributed in eukaryotes and facilitate diverse functions ranging from signal transduction to transcriptional regulation, with interaction specificity often determined by sequences outside the repeats. Additionally, the protein is associated with 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 Planctomycetaceae bacterium and is classified with UniProt keywords WD repeat.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 1977, 10234, 1922, 1920, 17907, 4241, 17, 6865, 17, 3165, 3418, 13975, 16, 2154, 16231, 2460, 43, 6293, 8, 38, 4666, 8, 17, 5062, 13728, 3170, 8842, 1927, 3137, 3662, 21763, 8277, 1942, 7120, 1966, 43, 4700, 7281, 1958, 2213, 17, 2213, 2014, 2213, 17, 2678, 3719, 18, 2144, 4682, 6628, 1920, 5957, 1927, 2779, 17, 2213, 5048, 3286, 1922, 6445, 10825, 4028, 16, 6485, 2037, 2733, 8201, 1930, 5224, 3640, 1942, 2024, 4048, 2285, 18, 3677, 16, 1920, 2213, 19683, 43, 17907, 4241, 6865, 5305, 3200, 1988, 10412, 2213, 17, 2213, 2014, 2213, 17, 2678, 3719, 16, 5745, 7402, 43, 4666, 17, 5062, 13728, 3170, 1988, 10634, 1966, 43, 12383, 6631, 1958, 1920, 5957, 1927, 2213, 5048, 18, 2144, 8277, 2032, 5673, 6533, 1922, 15021, 1930, 6628, 6445, 4088, 6485, 2037, 2733, 8201, 1942, 5224, 3640, 16, 1956, 2835, 4896, 3868, 3180, 2007, 3709, 7008, 1920, 9569, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 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, 4720, 2341, 13386, 9215, 1972, 3336, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 17907, 6865, 18, 3], "output": "MVKRFQLALAFLLFCSTGVFGQAAEDPLAIKYLEGHTGPIRSVGCTADGQTFVSVGLDGKICYWDRPRGLLRVALSPDGQTAAVGDVDGSVQFAGVPTRHPIRGLSSSLPGNPTSIAVSKDGQFVITGDQSKYVRMWSNAGHVIGASIDGTVKSWNLADAKVLTTNYYAPSNSMDFHEASKKAVLAGNDGYARVINWPPVLPTKYEGNSGGDEKKVHLYKVGETKPTKTLTGELASIRGLAFDAAGQHVAVGDSGGKVNIFKLDDGSITQLATCGDDGKIKIWTLGGEEEPIESKHPSGSVTSLKLIANGQQVITCGADKMAYLWNVSDGRQLARFVGATATVNCVPQGDIQPVKKFEGPSAVRSVAFDKQSILAAGDSGRVHVWDVDSELLIERMIAHGSRISVIQAIGKISEHPLRCVRFAPDGKSFVTASDSGAVRQWTLDIQPGHTFVGPTGKLRTISISVDGRWIAAAGEAFGKRGEKLVVATHDQILRVFAVNPKDGGGFVVEPFQELKGHPQFASHSQPTAAICFAEDNNTLLSAHQSAVFGLQFSSKGEWLATCGADRQAAVWQLSSLEKRWSQQGPGTLFDVAFDGTDERVLAPPPAEATESADSSDEEATEEAGPVKLTMETPSRLLSVAFTKDRSSLLSVGTGKQWHLWLLSDQSLTRDLDGHLCVWNVSDGNLLYHRRLPVTAAYDVCYTSGGTEVVVASRDHRLIRFQLPSNARETNALLHTMVALTNAHARDFGGSTQALVDVFFDNETAQITAMALSKDGKWLVQTITAHSGQVRCVEFFEATRAVSADGQWLAACGDDKFTRIWPLKNVNSDGSVFSASTDKMIQHQIRSVATPKVWAWSLADAKALATIDVPVAVNSLVGFERTLRRWYVSSPRIEKSVQIAVVGEGGFAQVSNIKDSGQGNNSAVYRLLVSPSGARFVTI", "metadata": {"id": "A0A2E7CYF4", "cluster": 1344238, "interpro_all": ["IPR015943", "IPR019775", "IPR036322", "IPR001680"], "interpro_used": ["IPR036322", "IPR019775", "IPR015943"], "interpro_unused": ["IPR001680"]}, "task_type": "infilling"} {"instruction": "I want a protein that has the function: The protein is categorized in 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. In addition, the protein contains 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. It is present in Haptolina brevifila. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 1977, 10234, 1922, 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, 1922, 2459, 16, 1920, 2213, 5461, 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, 2176, 1977, 2481, 1922, 29683, 8261, 1019, 3022, 2165, 6870, 1019, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "GALTGNLTISKTGSMAFGLATGEASDASRTMHGSATDATRASIVPVDRLDNLFTAERLGFAHLDVEGSEADVLRGAATILVRDRPVLTVEVHGHTMAAKALGVSLIGTLDSYGYQSWLIHEVCGLIPSCRNIISV", "metadata": {"id": "A0A7S2FZ44", "cluster": 3898580, "interpro_all": ["IPR006342", "IPR052514", "IPR029063"], "interpro_used": ["IPR052514", "IPR006342"], "interpro_unused": ["IPR029063"]}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein is associated with the FNIP repeat-containing protein family, which utilizes FNIP repeats to mediate protein-protein interactions and complex formation. Members of this family participate in diverse cellular processes, including signal transduction, cell adhesion, and the regulation of transcription and translation. Additionally, the protein incorporates a FNIP repeat that is predominantly found in proteins from mimivirus and lower eukaryotes, including the calmodulin-binding protein CmbB. This motif appears to be related to leucine-rich repeats and consists of tandem repeats named after a conserved pattern of residues. It has been detected in Dictyostelium discoideum (Social amoeba).\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, 9945, 2049, 6865, 17, 3165, 2213, 3416, 16, 2154, 18127, 9945, 2049, 9569, 1942, 8265, 2213, 17, 2213, 3719, 1930, 2796, 3337, 18, 4678, 1927, 2052, 3416, 7352, 1922, 6445, 3689, 4028, 16, 2710, 2733, 8201, 16, 2024, 6141, 16, 1930, 1920, 3640, 1927, 3213, 1930, 6410, 18, 4950, 16, 1920, 2213, 19683, 43, 9945, 2049, 6865, 1988, 1977, 7700, 2435, 1922, 2697, 2037, 6571, 19913, 1930, 2826, 15021, 16, 2710, 1920, 17537, 17, 2743, 2213, 3195, 6936, 18, 2052, 5219, 5107, 1942, 1998, 2712, 1942, 12624, 17, 5536, 9569, 1930, 7543, 1927, 10361, 9569, 10314, 2256, 43, 5305, 3114, 1927, 4248, 18, 2176, 2258, 2252, 3330, 1922, 29060, 18092, 12191, 1989, 2863, 2642, 3708, 1035, 12, 3686, 27714, 1019, 13, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MTQIEPGIITNTVESLYMIGYNHNALTIGSLPNTLKELNLSTMQPVSKPSKYIYPFFPNIIPNTFTFLMTVFKYCLSLTTGTNKTSANSQNSVLLIGSIPNSVRKIKLSHGFSHDLPIGIIPHSVEDLDLFEKQNSYVPGIIPDGLEELQISGKLELYVPPTTAPPTNKDQENQDQTPLSADKM", "metadata": {"id": "Q54PC0", "cluster": 7207816, "interpro_all": ["IPR008615", "IPR052697"], "interpro_used": ["IPR052697", "IPR008615"], "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 associated with 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. Moreover, the protein features 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 is found in Blastocatellia bacterium.", "tokenized_instruction": [2, 51, 12914, 1942, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 18, 1920, 2213, 3066, 2162, 1920, 2347, 1920, 2213, 1977, 2458, 1956, 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, 3950, 16, 1920, 2213, 4075, 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, 1977, 2435, 1922, 7851, 21259, 2057, 11560, 2126, 14061, 18, 3], "output": "MSQPEFVIEYLDPATLTPHEQNFRRHPAIQAAALESSLSDYGWLAAPIVNRRTGNRILDGHARVEIALQRGEATIPVRLVDVTEADEKRILASFDKIGEMRERDDQALALLLAELAETEDGLPAGWSDDDLAALLAGMTTPDFQPVGEDEQGQLDQKAKVTCPECGHQFSPAA", "metadata": {"id": "A0A7V9R4D9", "cluster": 9370994, "interpro_all": ["IPR003115", "IPR036086"], "interpro_used": ["IPR036086", "IPR003115"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: 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. Furthermore, the protein should have a RNA polymerase sigma-70 ECF-like, HTH domain that functions as a C-terminal DNA-binding module in sigma factors to regulate extracytoplasmic functions (ECF). It enables bacteria to respond to external environmental stimuli and is typically controlled by interactions with anti-sigma and anti-anti-sigma factors. Furthermore, the protein should contain 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 has been characterized in Rhodanobacter denitrificans.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 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, 3677, 16, 1920, 2213, 3066, 2162, 43, 3146, 6479, 5139, 17, 3895, 3270, 1038, 17, 3189, 16, 5334, 1023, 3418, 1988, 4088, 1966, 43, 45, 17, 4262, 2678, 17, 2743, 9059, 1922, 5139, 2790, 1942, 5741, 3439, 2355, 11302, 4088, 12, 3270, 1038, 13, 18, 2176, 10217, 4802, 1942, 4409, 1942, 5771, 4813, 5458, 1930, 1977, 5745, 4642, 2007, 3719, 1956, 2246, 17, 5139, 1930, 2246, 17, 2246, 17, 5139, 2790, 18, 3677, 16, 1920, 2213, 3066, 5531, 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, 2258, 2252, 4378, 1922, 11490, 9286, 7972, 2341, 1915, 26319, 2077, 2075, 18, 3], "output": "MSDAGAITVLLRRLSAGEREAHAALLPLVYLVHEAWLRLSTETALAPEDRRAFFAGERAEVTLSGLADDGGDRIDILALDQALERDIADLLGVSRATAQRDWEVARAFLLDALAADLRRIAARHLAGERAGHTLSPTAIAARRMRQILVDHARRRDAAKRGGLEAADPRKAQVVELRYFAGIEMT", "metadata": {"id": "A0A2W5JXJ4", "cluster": 10376114, "interpro_all": ["IPR053812", "IPR014284", "IPR011517", "IPR013324", "IPR036388"], "interpro_used": ["IPR036388", "IPR053812", "IPR014284"], "interpro_unused": ["IPR011517", "IPR013324"]}, "task_type": "infilling"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein falls within the ClpP/crotonase-like domain superfamily, which comprises a diverse group of enzymes sharing a repeated \u03b2/\u03b2/\u03b1 structural unit, including Clp and tail-specific proteases involved in protein degradation, as well as crotonases and biotin-dependent carboxyltransferases. In addition, the protein is assigned to the Clp protease proteolytic subunit and translocation-enhancing protein TepA family, which comprises ATP-dependent proteases like ClpP that cleave protein substrates such as casein and albumin. These proteins typically function as the catalytic subunit in a heterodimer with an ATP-binding regulatory partner, a complex found across bacteria, metazoa, and plant chloroplasts. Notably, the family also includes non-peptidase homologues that lack the residues essential for catalytic activity. It is produced by Cyanobacteria bacterium REEB67 and has UniProt annotations Hydrolase.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 12182, 2651, 1920, 18017, 1034, 19, 9442, 5405, 2051, 17, 3189, 3418, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 5038, 10763, 43, 5116, 161, 19, 161, 19, 160, 4346, 5344, 16, 2710, 18017, 1930, 5281, 17, 2487, 12447, 3286, 1922, 2213, 4877, 16, 1966, 2486, 1966, 9442, 5405, 2319, 1930, 8622, 17, 3100, 9943, 18580, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 1942, 1920, 18017, 7154, 12712, 5903, 1930, 7849, 17, 9221, 2213, 27120, 1019, 3416, 16, 2154, 12936, 4498, 17, 3100, 12447, 3189, 18017, 1034, 1988, 21252, 2213, 6249, 2427, 1966, 18576, 1930, 7712, 18, 2144, 2697, 5745, 2347, 1966, 1920, 6804, 5903, 1922, 43, 15672, 1956, 1925, 4498, 17, 2743, 4948, 8240, 16, 43, 2796, 2435, 3436, 4802, 16, 24207, 1019, 16, 1930, 4496, 24627, 18, 7388, 16, 1920, 3416, 2222, 5921, 2447, 17, 24050, 18541, 1988, 3630, 1920, 4248, 4415, 1958, 6804, 2455, 18, 2176, 1977, 4152, 2007, 21897, 14061, 21747, 26937, 1027, 1930, 2258, 20709, 15010, 20748, 18, 3], "output": "MNTTPALHRTAFVFNGSFDKSIDSFTDYVTKFIEINRGNNRPLLIRISSSGGVPEVVFAFCGLLRQVQVEGHEVWVHVLSQLCNFTYMIAEVADKVYMEPSASFQFGQMTARVSGNIIKIADKKKHQQQLFDQLCDSIVKRSKGKLKKEEVSAWRAKHISAQEALALGLCDEVAPDPEPQEKPTNKSEWVMRVSGSFANQADIYNLQIALNIFLEDSANTGRPIRVYLTSQGGTVAYALALYGLLLEAQRLGHHVTVHVIGQAYSCALWFATCALKAGTVLIDSYAMLMFHAPWIDEIAADLDDIDDLVAVQLAVYKQTRALLKQIPGFTEALISEWEVGEDRFMNAAEAVSLGLGRLSTDKPVAA", "metadata": {"id": "A0A949ITB2", "cluster": 10543281, "interpro_all": ["IPR029045", "IPR023562"], "interpro_used": ["IPR029045", "IPR023562"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein is assigned to the 2-oxoglutarate dehydrogenase E1 component family, which constitutes the E1 subunit of the 2-oxoglutarate dehydrogenase complex, a key regulator of metabolic flux through the TCA cycle. It catalyzes the thiamine pyrophosphate-dependent decarboxylation of 2-oxoglutarate and transfers the resulting succinyl group to the lipoyl moiety of the E2 subunit. It is native to Selaginella moellendorffii (Spikemoss) and carries UniProt keyword assignments Oxidoreductase.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 22, 17, 18588, 16542, 17488, 9294, 11123, 4594, 3416, 16, 2154, 14879, 1920, 11123, 5903, 1927, 1920, 22, 17, 18588, 16542, 17488, 9294, 2796, 16, 43, 3834, 7888, 1927, 4487, 8220, 2596, 1920, 13828, 4048, 18, 2176, 17097, 1920, 26901, 24937, 17, 3100, 22429, 1943, 1927, 22, 17, 18588, 16542, 17488, 1930, 19180, 1920, 3864, 13791, 2199, 2210, 1942, 1920, 3178, 10921, 11804, 1927, 1920, 6602, 5903, 18, 2176, 1977, 6196, 1942, 2484, 29284, 28690, 1019, 2661, 12339, 10249, 12728, 19894, 1033, 12, 10429, 12492, 5590, 13, 1930, 16252, 20709, 11121, 2538, 18306, 27388, 18, 3], "output": "MAPPRPAALFTISIYWVRVCHYAGSRLEVNRPFTSHLVALCDVDDVGNTIVLSARAISTSPLKRSLQFHHCTACHYLQGSYLNDIENLMTVMTYVQQCLPLELHRPFPRAKRHEECPTKLSCLATGRKKKEKKKELNHVTRKLYDEVYFESLMATNEPNTENEDEKNAWTMEFGHIVQTSLEGISSDVEPLVKVELGKLVGERRAAFQKDVAFFRASKAVQERNKKSADEDLAEAKQKALEESTSIPSEEAHCHHPIKGSEGEELALGNVVGSLCGKYLASLLEGRGWGYSGSGDVKYHLGTSYNRPTRTGKHIHLSLVVNPSHLEAVDPVVATTTRGRRTWRFCFMEIASLAKVKKKLVESGLILDGLHGSGAVVTVKKHRCQTRGWQENRRIERSRGCVSIEAGDGVDWATAEALAFTMRHASSLGVSGQTIHDSRPCTRWSSSKHKKFCNQVKVDKGAPPAQAKFLDLPDDLSEGWWSAGKPNRKLLVRSCYDPIFDLVWEHNEVEAESLDVPNRGRRNIIIKLPTTDDYVFVTWENDQLKVDKHSEVPNTLNGGGEGVPWPSLQRLATCVRMLLDPVWTEDELLALNEHNFGHDPEEVRKRFLKWGGTPRYVLEKVWPEAQAEISRAIGLVRDFDKIIMLQALPDDPARKAFHTIVDESTFTSSRLAPAYVEEQLLSNLPLPGLKRFLSVEQPDGIRDIQAKLLESFVCNVLVPRGGKLQFKEELDMRLSFRN", "metadata": {"id": "D8S543", "cluster": 14522216, "interpro_all": ["IPR011603"], "interpro_used": ["IPR011603"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Functionally defined as:\nThe protein incorporates 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. Additionally, the protein is categorized in the Invasin/intimin cell-adhesion fragments superfamily, which mediates the intimate attachment of pathogenic bacteria, such as *E. coli* and *Yersinia*, to host intestinal epithelial cells. This outer membrane module functions by binding to the translocated intimin receptor (Tir) to trigger cytoskeletal reorganization and the formation of actin pedestals beneath the bound bacteria. Furthermore, the protein carries a Coagulation factor 5/8 C-terminal domain that mediates binding to anionic phospholipids, particularly phosphatidylserine, on cell membranes such as platelets and endothelial cells. Found in blood coagulation factors and adhesion proteins, it typically utilizes an amphipathic alpha-helix to facilitate membrane interaction and is stabilized by a conserved disulfide bond connecting the domain extremities. It has been characterized in Sphingobacterium corticibacterium and is linked to UniProt keywords Signal.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 19683, 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, 4950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 4390, 1921, 19, 11757, 1921, 2024, 17, 6141, 6535, 13975, 16, 2154, 10412, 1920, 20252, 8576, 1927, 8070, 4802, 16, 2427, 1966, 14, 47, 18, 5178, 14, 1930, 14, 29323, 14102, 14, 16, 1942, 4423, 6139, 4944, 2094, 18, 2052, 7642, 3260, 9059, 4088, 2007, 2743, 1942, 1920, 22198, 11757, 1921, 3148, 12, 16661, 13, 1942, 6086, 14787, 18062, 1930, 1920, 3337, 1927, 4718, 5296, 2158, 2472, 22419, 1920, 4124, 4802, 18, 3677, 16, 1920, 2213, 16252, 43, 12441, 2991, 25, 19, 28, 45, 17, 4262, 3418, 1988, 10412, 2743, 1942, 19696, 15619, 16, 4443, 28563, 16, 1990, 2024, 5726, 2427, 1966, 10097, 1930, 5003, 2094, 18, 2435, 1922, 2877, 12441, 2790, 1930, 6141, 2697, 16, 2176, 5745, 18127, 1925, 26747, 21494, 4595, 17, 7864, 1942, 6628, 3260, 2835, 1930, 1977, 12017, 2007, 43, 5305, 11830, 5403, 15031, 1920, 3418, 18884, 18, 2176, 2258, 2252, 4378, 1922, 13502, 12022, 8106, 26073, 2341, 18842, 1989, 1930, 1977, 4624, 1942, 20709, 11569, 2733, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MKNFKPVLCWMSIALCMMLFVNCKDENVEPTSIRVQDAINIADQVTILPENAANKRIIFSSSNKKIATVDEEGLVTVHNAGTAIITVPPVLTNEIAISDPEVELQEGTTVDIADRITVLPVGVITAVSQGTTTITISSVQVPEITNTINVTVTEADHIGDYDIDGDINSRFILVRPSKTNQFGVTVPSKENQKQQKVSYFRLRHVPGLNQLRYYMIETISGSNDGENWTVIAIPSSNYRYIRFWCQKDECWKSMSQGATAQLTEIYLGNQSVTISESLKQGVTLQVGSIVDGQTDQFTITADPKDAANKVVTFSSADPNIATVNQGRAGWVVSASQDPLPNTPEDNKVGNAGGSISFTIDMASDVEVTDAPDGSIVESPNI", "metadata": {"id": "A0A4Q6XTV1", "cluster": 15785143, "interpro_all": ["IPR003343", "IPR000421", "IPR008979", "IPR008964"], "interpro_used": ["IPR003343", "IPR008964", "IPR000421"], "interpro_unused": ["IPR008979"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that has the following function: The protein should include a Cytochrome c oxidase, subunit IV, bacterial aa3 type domain that acts as a structural component of the bacterial cytochrome c oxidase complex. It consists of a single transmembrane helix that maintains its position through indirect contacts via phospholipid molecules, though its specific functional role remains unknown. It occurs in Limimonas halophila. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 9387, 45, 10488, 16, 5903, 4370, 16, 4543, 6440, 1010, 2601, 3418, 1988, 8016, 1966, 43, 4346, 4594, 1927, 1920, 4543, 9387, 45, 10488, 2796, 18, 2176, 7543, 1927, 43, 2957, 9117, 7864, 1988, 16566, 2496, 3507, 2596, 6354, 9070, 3454, 14608, 4206, 16, 4170, 2496, 2487, 3183, 2770, 4497, 5435, 18, 2176, 5110, 1922, 2784, 1980, 9259, 23226, 24888, 5148, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MTDPNRANENTEHGPMASETTEFKELERERKTTFGGVMKLLAYSSAAIAIVLALMFIFLT", "metadata": {"id": "A0A1G7P8T0", "cluster": 16073939, "interpro_all": ["IPR012422"], "interpro_used": ["IPR012422"], "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: It is part of the Type II pantothenate kinase family, which catalyzes the ATP-dependent phosphorylation of pantothenate (vitamin B5) as the first and rate-limiting step in the universal coenzyme A biosynthetic pathway. Primarily found in eukaryotes and some Gram-positive bacteria, this enzyme is biochemically distinct from type I and III forms, exhibiting specific regulatory properties including inhibition by acetyl-CoA. In addition, the protein belongs to 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 is native to Babesia caballi and corresponds to UniProt keyword Coenzyme A biosynthesis.", "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, 2601, 2890, 23942, 2195, 11496, 2057, 4016, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 4050, 1927, 23942, 2195, 11496, 2057, 12, 6111, 24365, 13, 1966, 1920, 2561, 1930, 2769, 17, 8051, 3537, 1922, 1920, 10321, 22051, 43, 14041, 3374, 18, 5985, 2435, 1922, 15021, 1930, 2673, 8604, 17, 2843, 4802, 16, 2052, 4113, 1977, 25839, 4493, 2037, 2601, 51, 1930, 4337, 4952, 16, 12196, 2487, 4948, 3879, 2710, 3523, 2007, 6894, 17, 10027, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 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, 1977, 6196, 1942, 9560, 7156, 11026, 2214, 1033, 1930, 8852, 1942, 20709, 11121, 2538, 22051, 43, 8132, 18, 3], "output": "MLDDVIRCVQQSQRALLALFNGAPAAWSNTSVLQESALKLIHSYDSLIQCIDPLIKSGPNGLLPVSPTRRLHDDHMNDDPQGFSEEVVQLLNEVASTACSLKATVFKHLMNVEIDVTPLLDGSAFSPLANLPLLGAPNEDGSPSGPPRRIAFDIGGTLIKLAYCCESSDCDALYTIYWAQRAVHDTVRCLERHCQVDLLSGCSLGRNLRRLAPAMIRLGKSTVIRFQKFPVDSLSSVLNDLTANKVVAGGTVINLTGGGAYKFAHVFEERLPHCEFRKIPEMACVVTGTEAMHGVNSCFASYDLRNGHAEPTTAKKSYPYLTVNIGSGISILKVSSETSFERVTGTSLGGGTMHGLTNILLGLNGHDELPMLYDNGTNCMDTFIPEASESRPPPYGLKASRENAARSTSDMISYNIGLIAFLVAKTHGVKRVIFTGSYTVNAPMTMDVAAAGVAYMAQCYQEETMDTMVPVFGAYAGVLGCLLTP", "metadata": {"id": "A0AAV4LZ48", "cluster": 16918146, "interpro_all": ["IPR043129", "IPR004567"], "interpro_used": ["IPR004567", "IPR043129"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein falls within the Gibberellin regulated protein family, which consists of cysteine-rich proteins stabilized by up to six disulfide bonds that function in plant development and antimicrobial defense. These proteins are up-regulated by the hormone gibberellin, and several members found in fruits and pollens are identified as allergens. It is native to Oldenlandia corymbosa var. corymbosa and carries UniProt keyword assignments Signal.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 12182, 2651, 1920, 10122, 2361, 20912, 4335, 2213, 3416, 16, 2154, 7543, 1927, 8666, 17, 5536, 2697, 12017, 2007, 2353, 1942, 3798, 11830, 9031, 1988, 2347, 1922, 4496, 2740, 1930, 8003, 9720, 18, 2144, 2697, 2032, 2353, 17, 4335, 2007, 1920, 6365, 10122, 2361, 20912, 16, 1930, 2980, 4678, 2435, 1922, 12953, 1930, 12206, 1036, 2032, 2899, 1966, 19226, 18, 2176, 1977, 6196, 1942, 4156, 1917, 4702, 2126, 2233, 19077, 5360, 4953, 18, 2233, 19077, 5360, 1930, 16252, 20709, 11121, 2538, 18306, 2733, 18, 3], "output": "MNPRVVLVVAILMICIYQISSDAETEEKLQEQSMVVVRGRCGLHSRPNLCKRACGTCCFRCKCVPPGTSGNRELCGTCYTDAVEKSIPFPTNTSGAVVWSASPFSSHIQLLYKSLPPSTPGCFRFYNGKSAPFFANRRLLPLMDCGGLCSVMTTHGNRTKMVPRRAQPKYIKLSAG", "metadata": {"id": "A0AAV1CDU4", "cluster": 17085634, "interpro_all": ["IPR003854"], "interpro_used": ["IPR003854"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein falls within the Protein of unknown function DUF2141 family, which consists of conserved hypothetical proteins with no currently known function. It is found in Litorilituus sediminis and is associated with UniProt keywords Signal. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 2213, 1927, 5435, 2347, 4855, 6680, 27311, 3416, 16, 2154, 7543, 1927, 5305, 15148, 2697, 1956, 2239, 5077, 3171, 2347, 18, 2176, 1977, 2435, 1922, 4471, 6658, 12191, 1031, 25901, 1036, 6276, 1980, 15472, 1930, 1977, 2458, 1956, 20709, 11569, 2733, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MKFLYVTLLFLNMFHQAALASTEEEKVTQQALMQVQIDRIKNVSGQLHYQLFACPDDDMHGWNELTLLSQGQVAITDNTVDLPLAAVASSEVIFRAYQDLNNNGQLDYASNGVPKEPTAFANNPNLMLGMPKPLDACVNWQNISTVKVKMNNKRQRRKRD", "metadata": {"id": "A0A4P6P660", "cluster": 18239080, "interpro_all": ["IPR018673"], "interpro_used": ["IPR018673"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the precise sequence of amino acids to fill the masked gaps, targeting this function: It is part of 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. In addition, it is part of 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 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. It is present in Ignavibacteriales bacterium CG18_big_fil_WC_8_21_14_2_50_31_20.", "tokenized_instruction": [2, 5655, 1920, 8162, 3244, 1927, 3835, 4576, 1942, 11928, 1920, 17476, 11349, 16, 5133, 2052, 2347, 30, 2176, 1977, 3131, 1927, 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, 1922, 2459, 16, 2176, 1977, 3131, 1927, 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, 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, 2176, 1977, 2481, 1922, 12046, 9188, 7972, 2341, 18339, 2612, 14061, 7294, 3928, 41, 9769, 41, 3313, 41, 14888, 41, 28, 41, 2900, 41, 2607, 41, 22, 41, 2761, 41, 3470, 41, 2036, 18, 3], "output": "MKKKIIIMEDDLFLREFYTFEKLNANKYNLILMDLSLKNTYLKSIPIILVTAHSVDYHSKHLRQFLEKIDAVMEKYNFVFNKIGYDADILEDGDVFNNQKVDGVTISRLVKGNELFFYESLADEYIIKPISDV", "metadata": {"id": "A0A2H0FTJ2", "cluster": 20040541, "interpro_all": ["IPR050595", "IPR011006", "IPR001789"], "interpro_used": ["IPR050595", "IPR011006", "IPR001789"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein should have 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. Furthermore, the protein belongs to the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. Additionally, the protein carries a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. It is expressed in Omnitrophica bacterium (Omnitrophota bacterium) and features UniProt keywords Glycogen biosynthesis, Glycosyltransferase, and Nucleotidyltransferase.\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, 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, 3677, 16, 1920, 2213, 14440, 1942, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 4950, 16, 1920, 2213, 16252, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 2176, 1977, 3198, 1922, 18825, 3032, 24888, 3375, 14061, 12, 18825, 3032, 2102, 7336, 14061, 13, 1930, 4075, 20709, 11569, 13302, 8132, 16, 20067, 9961, 16, 1930, 2797, 4090, 2199, 9961, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MEPLIGSLNRIGVPAVEALVKIGDKRAIEPIIEYMKYTSDPDLVISALNKLSATKEQIERALEGCEYDTEAEAMDAIRLIGVENSFTVKAVSYHTTGWDDGGGSYVFEPGVVPDWFVRGQIDDVESIKYKIVRKSPITGALRNYQGVDNTMQDIMAGLVQKVITLEGESDEIKAKIETLLGNKTQRKELLNNKTIRIVQDNDRLMHFSEAPDMITNRAVSSRAPPTAEQRTQEEAEITAQEVELFLLFTQDAQTRILEALKADNDLDDQKFYKVLEAYVRLRPDAARFTGVQASIYDTSVTFGFPMQIADSAAIADIQKTLRETIPNEGVLYIQPKELLHSTMEVIGGVGPFEVDFTGVNITSRGDIILQGYAKDDAVDNLRAKLRGVFGIKQYYPVDIIHVSIGRILKPLDKATFAKLMRTRDNLGEDKDELVVQYLVNRKLLDDAAKTFNLDEGNKEYFRQMWIKYLKRIQGAPGSQALTIITDPGMLTRADYNPENDPNFIEDVQKLIGTVQYLDLVTDANNKDKAKSVVVTVNGLDGGIGENVGRLKFLKQVATLRGKNPENVKLGEAKIMQLVLAANAGKFAKIQFQPVVNYESKISYDELLDQVCIEDRFDTAKERAEPKKTYKELKPGTQRTYFPGIKQLTKTTGDVYTDKDEDEEITKQYVQHGGHGNCGFLLLLKTLRDELPADGKTHIRVFVNGDNVNSRINEDTKGGKDGLRVVKRADGTFLYVPDQMEVADARTADNKNPGQLTAFYKSGQDPAKPTQPFNTNIFYINTSVLHGILKINKILKKIEKGLHAGDSFMALEGAIGTAMHNLNSYFMESADLRVQNILKERGLDRVLFFVDVPGKYFGALNAVEPWSLYDSEAVKVNKKEPPEFDIAPAGKKDYWDDVQVFIDALGKDADVTELVSLKIRGKVTLPDAKLILKDQQKYPDFFIDDKLVLGNKIIIIDEKGVLGWKSSEKFETFTDSSGADWSMWEYGGKDGADLDGLIRRDGSSEFARRSAWRSRDIVTANVDGRDVDFRLLFQKTGFWLADRADKTGGTILITQTRTPPPSLTHNDYNYGFREDLETERIAKEGIVPLRNIGYSGIKTVFEHKSSATLNSPENGYPVTSMTTNYQWAKDAYFPILPGDKIGVIPTIRTGDPSEPYFSGKDMGEYHTEDPISYDHALLLTSKDEYERIRAAKPKSREGALILLGRRLGLPVNPEDISGVEINPLYKLLVGYRARSQIEEGMLFHLRAPPGAKVMLTGEFNNWADSEASGAMKLEEIEKGFIVEKDGKREYENGLYGNADDIYKNSIITISGNETYFSKERASARLKAIQDKSGILYVATEAEPFIKIGGLGDFMIEDTGIAFNVPIGNKTERIVLQRARSNGVTIYLIESEHYFKNPYEDTDSIYGLREAVLLSRASLEIAVRLGITLYREALPNVYTVLGLHNLGYQGLYPMAWFLQTGIPMTEIDSGRPVWARKLGLLKYGLVTADKIHVIIGILDGIDLKKWNPETDSAIYERYNSTSSEKKSINKVKLQEAYGLKIDPEAPLIGIISRAEDILNTTNAQIIVLGKGEEKYEKAFAELGAKYHGRVIIQKVYNDDLSRKIYAGSDIFLMPSLYEPCGISQQIAMDTVTSDRGFMFTEFDSKSMMAALKAAMEVFNNDKPRWKEMMRKAMEADLGWETKESQFESMYNSRGINLVMRAGVTEGRYDIATAKVVNGTLRDYQGVDNSMKDIMAGLVQKVITLEGESDAVKAKIEALLGNETQRRENDRLMHFSEAPDMITFDIDALKYTELLFMEFIHELLHANRAVSSIGPPTDEQRIQEEKEVTTQEVELFLDDREFYTILEKVRTQGANSITDNIRKYVIGLTAITPSMSADAAREAYLEALAHKTFPEFIIALPNVNELKGIINIEFVRDVNAFNTRVAAGNVNGIFLDTSMLEMSADTELQNVLNEVTIDASAILVSSRTRVELERILKEIGLQQKLAGQISALKTALIARKEAVSATYNSMPMADKVALAGKSYALATTEKVAFSNMFTIDNMFKAEAMGVVNCFIYGEMIDNIRFVDKRGLSYEEIVSAISARTGVTAQNNIGIACAKDELGAVTAITGEKLLEMKEMDMGGVKPEDLLNKMIADGQLPPGVTYDSVKRIFIYLPKAMPINYGREIETYRNAIRAIRTAAKEIWKKEKQAKSKAIRGGTLEGRHDLATAEVKDLDIDALKHTELLFMEFIHELLHAYYDSIFEKTKESGLEITTPPDEATISERIRRVSGVLGEIDIESMRFTHIGTEKVNALKFSYHLDAMAQDILAGKNLSPAKGTDLGFIIKDYMGQPEVFISIARQLMEESEIEVLPMMDAPDHIAGAMAKEGWPIVKLTTKATLIDLEAVIGRERLYEIISPSLRTEFFTPVKKTFDLWFLSHGNVVIINKSNEVVDQGTYPSGKFDIVSLEAIVPIKPVPEMIFKLTVFDSTRHIAVYGEYRGIKVQYKYGPYVFAMEDQAEYENRVYEESLGNIYAIVVPKNRIKQGTYKFKGELPGVMSQHKNSITVVIPRYKSMDDASLSGIDVIHCNDWQTALVPAYIKPSITYAAEIITPEQGMGLEHILRERAADLFAQKGLELVIRERYGSLPVVRATGGLVFLSPKAPDQDLVLRQTPQPSLILLKSKNMRIAQGLLFPQDVQDKILEILKTDNDAVDRKNEQIVKKAIEGAPAAATLDEIGRFDIDKAVQLRLGIGHRDLKTEDEARAFVTASGYEGNVVASINYYQTLLQMVTT", "metadata": {"id": "A0A947JHV1", "cluster": 21592599, "interpro_all": ["IPR001296", "IPR011835", "IPR013783", "IPR014756", "IPR029044", "IPR013534", "IPR002618"], "interpro_used": ["IPR001296", "IPR011835", "IPR013534"], "interpro_unused": ["IPR013783", "IPR002618", "IPR014756", "IPR029044"]}, "task_type": "infilling"} {"instruction": "Here is the intended role of my protein: The protein includes a BAG domain that modulates chaperone activity by binding to the ATPase domain of Hsp70/Hsc70 proteins and promoting substrate release. Comprising three anti-parallel $\\alpha$-helices, it functions as a molecular switch by mediating mutually exclusive interactions with Hsp70 or the kinase Raf-1 to regulate cell growth and apoptosis. It is present in Hibiscus syriacus (Rose of Sharon). Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 30, 1920, 2213, 5921, 43, 12570, 3418, 1988, 13112, 14044, 2455, 2007, 2743, 1942, 1920, 9444, 3418, 1927, 12886, 19, 30183, 2697, 1930, 7356, 4510, 4012, 18, 10351, 2559, 2246, 17, 6110, 8, 38, 4595, 8, 17, 12789, 16, 2176, 4088, 1966, 43, 3272, 6195, 2007, 10239, 16632, 13132, 3719, 1956, 12886, 2014, 1920, 4016, 12783, 17, 21, 1942, 5741, 2024, 2905, 1930, 4091, 18, 2176, 1977, 2481, 1922, 26823, 10368, 1957, 11458, 2126, 6973, 12, 13679, 1927, 4980, 1916, 13, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "MMPFSGYMDSNPLRNQTPYPQHYFPGFEAVQPYFKADPSQSSMMYESWPCSSSCSRSLKIEEQENDAKEKEDGSVANSTKKFPISNCVDSTRGEGEKQSQNQQKQDQKMQMPLPSFGYRILIGSRKQMKTEINKGLQTASYNSKQAPFSVEYVPVEHSVSDAKIDNHNWSWRALRTRMLLKQRGRGKQAEVKDVSVKRDEDAPKVDLGKTVMVVQGLLASKGQSEDILTKASITPDKKKKLQSEENKVGETTSANQDQVSGSLSITSVEVSGQPTVERTKIESHESKRGNKSKFEEVVGAEKEVGSDNAANTVEMAHGQCKAEKKECQMLKQPSSSNLPSVDSSVREARKSLVKELVTLQEKLDALASKWAEEKIKDLGSAESADSSGRASGIVSMEEESGNASAAFEDTSENVNIIKESDQDCLNVKDGKDEETTKIPGVEQGLDEKVDNNTVEVSIEHHTVPRIEVDVPPNLEQVTHMSSVPELKFEADELVE", "metadata": {"id": "A0A6A2Y413", "cluster": 21610160, "interpro_all": ["IPR003103"], "interpro_used": ["IPR003103"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Functionally defined as:\nThe protein can be placed in 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. Moreover, the protein should include 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. It is present in Jiangella rhizosphaerae.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 1920, 2213, 2112, 1998, 5396, 1922, 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, 3950, 16, 1920, 2213, 3066, 3951, 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, 2176, 1977, 2481, 1922, 16684, 5870, 13458, 2609, 29164, 3336, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MTTSDAFGFSGEAVRTAHDIRADWARTGLRGALYARNVDTGEDLGFDVHVPYALASLVPGQSTPGPTGAALFRHPSRIALEDLLLLMLSVSDNAAADAVFALVPPERVTATLQGAAAAVAPDDPVLALELAVRATTDGGGHVLPTLDVAAATSGTAAGLVSLVERITSELAGDSVTVASKTGTFLNLRHEAGMVTTSAGDRIAVAALTASTVAARSQPEADRAIGRAARAAVDVLRLVSKLPLALVVLDLIAAGELDPAQPVDWGCEGIVVRHPMRLLYEWTDDVSVPAATARLRELLGYQVNRNRM", "metadata": {"id": "A0A418KVS3", "cluster": 21817557, "interpro_all": ["IPR012338", "IPR045155", "IPR000871"], "interpro_used": ["IPR012338", "IPR045155"], "interpro_unused": ["IPR000871"]}, "task_type": "infilling"} {"instruction": "The protein is a member of the 6-pyruvoyl tetrahydropterin synthase/QueD family, which comprises zinc-dependent, hexameric enzymes that catalyze the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin in tetrahydrobiopterin biosynthesis or to 6-carboxy-5,6,7,8-tetrahydropterin (CPH4). It is present in Promethearchaeota archaeon and is connected to UniProt keyword Lyase and Metal-binding. 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, 26, 17, 6487, 12631, 10921, 21196, 2410, 16654, 8921, 19, 10730, 1007, 3416, 16, 2154, 12936, 7997, 17, 3100, 16, 25602, 1935, 5038, 1988, 18170, 1920, 7309, 1927, 11842, 2912, 13798, 1921, 17978, 1942, 26, 17, 6487, 12631, 10921, 21196, 2410, 16654, 1922, 21196, 15193, 2410, 16654, 8132, 2014, 1942, 26, 17, 15750, 17, 25, 16, 26, 16, 27, 16, 28, 17, 21196, 2410, 16654, 12, 4244, 20360, 13, 18, 2176, 1977, 2481, 1922, 2720, 3184, 2656, 3336, 7336, 13470, 1916, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 23928, 1930, 6048, 17, 2743, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MFERKVINLSYKIVINETKLGFTASHFLTNHPTCGTIHGHNYGVTVSIEVKEGFLDNNYMVIDFHDLKKIILNIIEKLDHKLMIPENSNELEIGKKKDIVEVKVKPSDKTYIFPSRDIVFLPISATTAECLARFIFKEIQKELQIKEYNMIVRIHENRGCYSEYSE", "metadata": {"id": "A0A8T6RNP2", "cluster": 22029011, "interpro_all": ["IPR007115", "IPR038418"], "interpro_used": ["IPR007115"], "interpro_unused": ["IPR038418"]}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein is grouped in the Nucleotide-diphospho-sugar transferase superfamily, which catalyzes the transfer of sugar moieties from activated donor molecules, such as nucleotide diphospho-sugars, to specific acceptor molecules to form glycosidic bonds. These enzymes play a critical role in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides. In addition, the protein is included in the **Acylneuraminate cytidylyltransferase** family, which catalyzes the synthesis of CMP-N-acetylneuraminic acid (CMP-NeuAc) from CTP and N-acetylneuraminic acid, generating the essential donor substrate for sialyltransferases. These enzymes are critical for modifying outer membrane lipooligosaccharides, a process often linked to microbial pathogenesis. The family also encompasses related cytidylyltransferases involved in lipopolysaccharide biosynthesis and outer cell membrane development. It is derived from Mesonia sp. HuA40.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 5489, 17, 11791, 2609, 1037, 17, 9523, 13763, 13975, 16, 2154, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 6282, 4206, 16, 2427, 1966, 5489, 11791, 2609, 1037, 17, 15592, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2144, 5038, 3918, 43, 4140, 2770, 1922, 1920, 8132, 1927, 2054, 11926, 16, 22012, 16, 1930, 18686, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 14, 14, 11337, 2912, 9280, 8547, 2010, 2702, 19743, 2199, 9961, 14, 14, 3416, 16, 2154, 17097, 1920, 4271, 1927, 28738, 17, 56, 17, 6894, 2912, 9280, 8547, 1935, 2687, 12, 28738, 17, 2866, 1948, 13, 2037, 25639, 1930, 56, 17, 6894, 2912, 9280, 8547, 1935, 2687, 16, 9155, 1920, 4415, 6282, 4510, 1958, 12952, 2199, 18580, 18, 2144, 5038, 2032, 4140, 1958, 12691, 7642, 3260, 3178, 4545, 21592, 5735, 2437, 28476, 3726, 16, 43, 2585, 3868, 4624, 1942, 7293, 6559, 18, 1920, 3416, 2222, 21569, 2712, 2702, 19743, 2199, 18580, 3286, 1922, 15614, 8132, 1930, 7642, 2024, 3260, 2740, 18, 2176, 1977, 3595, 2037, 23577, 10306, 2056, 18, 5897, 16010, 1008, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MRKKCGFIIQARLSILQLIMYRIKREFPDYPVKFAVNNNFKYYRGSEENVLSRDMFYLQKLLNRLKISYTDYDYKKHFGFFGEIVKVKALKTKNFKLNLAVIPNYISDKEKKLICYINSKDNIIRDMRNNIKKYSKGSTRLPGKVLKPFHNDKAIIATSNNPIDDEIFLDIARIYQLEFVIRICADNPFIYSFVDVDNVPVITAQKTSKSIYLEHVTNYIYENYLRLTVDDDVDFKNLKTLYREYENYNFDL", "metadata": {"id": "A0A5C8LAJ7", "cluster": 23798835, "interpro_all": ["IPR003329", "IPR029044"], "interpro_used": ["IPR029044", "IPR003329"], "interpro_unused": []}, "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 possesses a Ciliogenesis-associated TTC17-interacting protein, N-terminal domain that plays a role in primary ciliogenesis by modulating actin polymerisation. This region is predicted to adopt a structural fold consisting mainly of $\\beta$-sheets. It is produced by Hucho hucho (huchen) and corresponds to UniProt keyword Cytoplasm, Nucleus, and Cilium biogenesis/degradation.", "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, 14465, 43, 19692, 3761, 17, 2458, 19914, 3952, 17, 8615, 2213, 16, 56, 17, 4262, 3418, 1988, 5705, 43, 2770, 1922, 3065, 19692, 3761, 2007, 10871, 4718, 4593, 6284, 18, 2052, 3031, 1977, 4396, 1942, 14103, 43, 4346, 3728, 7600, 4994, 1927, 8, 38, 4666, 8, 17, 14685, 18, 2176, 1977, 4152, 2007, 25558, 10647, 25558, 10647, 12, 25558, 22467, 13, 1930, 8852, 1942, 20709, 11121, 2538, 5239, 16, 5607, 16, 1930, 28997, 13008, 19, 4877, 18, 3], "output": "MQNYNPLQNLTSYTCSVEKNIHRHGASAAERPLPTDTSDQMPWWANTSNCGQRELGCRHQTVEVFGVERTVGSVEDIPATWQCWHCYFLPDGHLASRMQEELKAEHVSNLRQHQELRAMMADFLQFLYQRKPRNVFMFASKDFSPVASCRPPWGTFNTSLS", "metadata": {"id": "A0A4W5PS85", "cluster": 24845891, "interpro_all": ["IPR048777"], "interpro_used": ["IPR048777"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein features a Acylphosphatase conserved site that specifically catalyzes the hydrolysis of the carboxyl-phosphate bond in acylphosphates, such as 1,3-diphosphoglycerate and carbamyl phosphate. Located within a domain characterized by a mainly beta-sheet structure with short alpha-helices, this site is present in both tissue-specific isozymes and prokaryotic hydrogenase maturation HypF proteins. It is thought to play a regulatory role in the glycolytic pathway and pyrimidine biosynthesis. It occurs in Bacteroidota bacterium and exhibits UniProt keyword tags Hydrolase.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 11337, 7824, 7234, 5305, 3200, 1988, 4475, 17097, 1920, 9128, 1927, 1920, 9943, 17, 5413, 5403, 1922, 11337, 25324, 1036, 16, 2427, 1966, 21, 16, 23, 17, 11791, 2609, 13572, 13108, 1930, 17742, 2199, 5413, 18, 4810, 2651, 43, 3418, 4378, 2007, 43, 4994, 4666, 17, 11130, 3170, 1956, 3662, 4595, 17, 12789, 16, 2052, 3200, 1977, 2481, 1922, 2321, 2960, 17, 2487, 4911, 16367, 1930, 21545, 6201, 2051, 7655, 2483, 1038, 2697, 18, 2176, 1977, 6212, 1942, 3918, 43, 4948, 2770, 1922, 1920, 17580, 3374, 1930, 21611, 8132, 18, 2176, 5110, 1922, 24323, 7336, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 20748, 18, 3], "output": "MLNVTGRVQGVFYRATANEIAIELGLKGYVMNMNDGSVFIEAEGTIEQLTKFIEWCKRGPSRAIVTDVNIQEGMVKEFTDFKIRH", "metadata": {"id": "A0A4P5TSB1", "cluster": 27018604, "interpro_all": ["IPR020456", "IPR001792", "IPR036046", "IPR017968"], "interpro_used": ["IPR017968"], "interpro_unused": ["IPR001792", "IPR020456", "IPR036046"]}, "task_type": "autoregressive"} {"instruction": "Function:\nThe 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. In addition, the protein carries 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 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. It is found in Prasinoderma coloniale and is associated with UniProt keywords ATP-binding, Serine/threonine-protein kinase, and Transferase.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 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, 1922, 2459, 16, 1920, 2213, 16252, 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, 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, 2176, 1977, 2435, 1922, 29033, 3522, 2179, 3368, 4120, 2086, 1021, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 8468, 19, 13143, 17, 2213, 4016, 16, 1930, 13763, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "ARGHAAMSGAALAALFGCCDFARPRGGAWASFPPPGNEGKAEHSRQRESTPGARVESGAGHAATEAPAAAALPTRTKETWVLYTKIRALGQGSYGKVVLYEDERGGVVAVTALTDAMREVAIMKQLHCDQVVRLIEVIDDLREEKLYLRREKAMRESDAARQVVADAASGTAYRAKLGDMGVSQAFSGENDSLLRSPGTPAFFSPECCVFGSYPFIGNTEAATYAAIQRSELVLPRGTSAELESLLRCHPWLGAHAKRDAYALGAAGGPSDDGSRPVAQGAAGGGKESGGGDGGGGDASMARAGGSYVRVPSDNKSRDEASGRKRINQKVLARAKLRKAVVSGHVMEFAQGGVAMEPVLHARGVCHLDIKPENLLMFSGGGGEYSGRAADCWALGVTIYCLVGLLHPDPGKRMCAADAA", "metadata": {"id": "A0A7R9XWX4", "cluster": 28109951, "interpro_all": ["IPR011009", "IPR000719", "IPR017441", "IPR008271"], "interpro_used": ["IPR000719", "IPR017441", "IPR011009"], "interpro_unused": ["IPR008271"]}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe protein features a Solute-binding protein family 3/N-terminal domain of MltF domain that functions as a high-affinity receptor for amino acids and other polar solutes, facilitating their active transport via bacterial ABC systems. This domain also appears in the N-terminus of the murein-degrading enzyme MltF and in eukaryotic glutamate receptors, where it mediates specific ligand recognition and binding. It is identified in Monoraphidium neglectum and exhibits UniProt keyword tags Signal.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 4075, 43, 19661, 17, 2743, 2213, 3416, 23, 19, 56, 17, 4262, 3418, 1927, 2646, 27807, 3418, 1988, 4088, 1966, 43, 2149, 17, 5173, 3148, 1958, 3835, 4576, 1930, 2303, 5676, 27993, 16, 12440, 2310, 3500, 4860, 3454, 4543, 7219, 3771, 18, 2052, 3418, 2222, 5107, 1922, 1920, 56, 17, 7822, 1927, 1920, 6185, 14818, 17, 18192, 4113, 2646, 27807, 1930, 1922, 10825, 7627, 4086, 16, 2597, 2176, 10412, 2487, 5207, 5708, 1930, 2743, 18, 2176, 1977, 2899, 1922, 8914, 5524, 24888, 7408, 1989, 18256, 1989, 1930, 9826, 20709, 11121, 2538, 14392, 2733, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MSRAMVAILVVLPLLALSAHANGTPRGASLPRSALLSARRAGFPPAAILFPNGTWGGEEVQHLTSFAKAHNLALTVVEVPSFKGIWLELGTRASFSTHYRADARALAVRSVTASGAPRKVVINGPKDLAGNSEDKAGADVAAGTVLKGSKEPVFAYATGAEGALALANKLKGRVAAATPTTSNKRDTSLLDALNAYVVNTKGGPQGKWPSDFIKCPPAQNGTRRFWLLAKVQPRLTTLEPGKLKVCLYQPGLGNCDLAAGGISITPSRVTRVILVTNGSTAETDLKARLKAAGVTATLHYTWVHCLMLADGTEVPEHLGYVAR", "metadata": {"id": "A0A0D2LNC2", "cluster": 28159533, "interpro_all": ["IPR001638"], "interpro_used": ["IPR001638"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe 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. It is expressed in Bdellovibrionales 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, 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, 2176, 1977, 3198, 1922, 5238, 20783, 2165, 2377, 12778, 1918, 14061, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MNSKRIQNESSLSPTARRVFAALELRARDSYTHVHRGKDEGFISEMTAIFDPTALESERRWFKRAEKCKGVMVLEIAKRTKLSEQLVKYGYTLYIVYLRFSGASS", "metadata": {"id": "A0A958K0U0", "cluster": 28855639, "interpro_all": ["IPR036388", "IPR036390"], "interpro_used": ["IPR036388"], "interpro_unused": ["IPR036390"]}, "task_type": "infilling"} {"instruction": "I want to design a protein that can perform the following function: The protein carries 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. Furthermore, the protein is included in the plant Myb transcription factor family, which functions as a transcriptional regulator governing diverse developmental processes and stress responses. Members are essential for pollen development and anther function, while also regulating the biosynthesis of defensive aliphatic glucosinolates. Furthermore, they mediate adaptation to abiotic challenges such as salt and osmotic stress, potentially through the control of cell wall modification and suberin deposition. Also, 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. It originates from Nelumbo nucifera (Sacred lotus) and has UniProt annotations Transmembrane, Transmembrane helix, and Nucleus.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 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, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4496, 16851, 3213, 2991, 3416, 16, 2154, 4088, 1966, 43, 5224, 7888, 20012, 6445, 5878, 4028, 1930, 3071, 3387, 18, 4678, 2032, 4415, 1958, 12206, 2740, 1930, 8795, 1915, 2347, 16, 2679, 2222, 6773, 1920, 8132, 1927, 25427, 22234, 3351, 5872, 8649, 1036, 18, 3677, 16, 2611, 8265, 7810, 1942, 16596, 7321, 2427, 1966, 7012, 1930, 13951, 3071, 16, 5063, 2596, 1920, 2285, 1927, 2024, 4821, 6295, 1930, 2316, 16654, 7860, 18, 2222, 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, 2176, 22970, 2037, 2069, 5277, 17010, 1037, 25020, 19582, 12, 9854, 1919, 12026, 1957, 13, 1930, 2258, 20709, 15010, 9117, 16, 9117, 7864, 16, 1930, 5607, 18, 3], "output": "MCRKTEVCCLISILSNVSASMLLAIGMLLNFQGAWPIWIAPLTIPLWILGVLFDVCIEETSQGSKLEFTEDEETLIARMYNLLGDRWSLIAGRIPGRTAEEIEKYWTSRYSTSE", "metadata": {"id": "A0A822YWM0", "cluster": 829336, "interpro_all": ["IPR009057", "IPR017930", "IPR015495", "IPR001005"], "interpro_used": ["IPR001005", "IPR015495", "IPR017930"], "interpro_unused": ["IPR009057"]}, "task_type": "autoregressive"} {"instruction": "Target Function: The protein possesses 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. Moreover, the protein is associated with 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*. In addition, it is part of the Exodeoxyribonuclease WalJ/YycJ-like family, which functions as a prokaryotic 5'->3' double-stranded DNA exonuclease involved in the WalK/WalR signal transduction pathway. These proteins utilize a metallo-beta-lactamase domain to facilitate mutation mismatch repair and cell wall metabolism, ensuring the coordination of cell division with DNA replication. It is produced by Clostridiaceae bacterium.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 14465, 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, 3950, 16, 1920, 2213, 1977, 2458, 1956, 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, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 18930, 3695, 7221, 3027, 20226, 2626, 2051, 16567, 1013, 19, 67, 2773, 1013, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 21545, 25, 11, 17, 34, 23, 11, 4825, 17, 10338, 2678, 24966, 3286, 1922, 1920, 6846, 19, 16567, 1005, 2733, 8201, 3374, 18, 2144, 2697, 12561, 43, 8969, 1037, 17, 4666, 17, 23023, 3418, 1942, 6628, 3979, 10265, 5059, 1930, 2024, 4821, 4714, 16, 14435, 1920, 9478, 1927, 2024, 8451, 1956, 2678, 5158, 18, 2176, 1977, 4152, 2007, 17938, 14773, 1972, 3336, 14061, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MIGGISLRSGSSGNCTLIRNGEKRIIVDCGLNGKNFTNSLAEIGETPANIDGIVTEKTFEAIQPRLGKFENSLINFILPEGKFTINDQQIESFLVPHDAPETLAYRFITSEVLTKIKKSRLVFLESNYDLEMLTNGPYPYYLKERIKNGGGHLSNGQCPALAELTSVQALEEIEAEQNKDYLLQVAKRNQVSNWMQIITHEHSDHVSGLGVILRRYKIPVYLNGDISVCTDIGAVTPGDTLCHLVNSGTEQITLAHLSAQNNI", "metadata": {"id": "A0A7X8E2Q3", "cluster": 1761118, "interpro_all": ["IPR001279", "IPR036866", "IPR052533"], "interpro_used": ["IPR001279", "IPR036866", "IPR052533"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: 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. Moreover, the protein has a Peptidase family A1 domain that functions as an aspartyl protease, utilizing a catalytic Asp dyad within a bilobed $\\alpha/\\beta$ structure to hydrolyze peptide bonds. This domain specifically targets peptides with hydrophobic residues via an active site groove enclosed by a structural flap, and typically undergoes autocatalytic activation at acidic pH. It is present in Acer negundo (Box elder).", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 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, 3950, 16, 1920, 2213, 2258, 43, 24050, 3416, 8080, 3418, 1988, 4088, 1966, 1925, 12053, 2199, 7154, 16, 10232, 43, 6804, 4138, 28679, 2651, 43, 5088, 16248, 1007, 8, 38, 4595, 19, 38, 4666, 8, 3170, 1942, 7222, 6931, 4207, 9031, 18, 2052, 3418, 4475, 4845, 5320, 1956, 7919, 4248, 3454, 1925, 3500, 3200, 15920, 24360, 2007, 43, 4346, 11924, 16, 1930, 5745, 14928, 22658, 18914, 2936, 2019, 9931, 2087, 18, 2176, 1977, 2481, 1922, 8298, 1005, 2922, 2652, 1037, 12, 5758, 7177, 13, 18, 3], "output": "MRRTVQEGYCSGVVALFTTAAPPPEAAIASSNRARKKFKPIIFTFSSNRAKNALDISSGRACVSSQSGSAAVREELPSMQTQNTNGETEPGLLIFSPGVQELGQRWFRNGQSDYLIKVGIGSPKQEVYVVMDTGSNISGHNASPAWPVLTATPPPEGTEANFPLTNAIKSQQISCDHHHFHFVNRESASKAISIPTDAGSVV", "metadata": {"id": "A0AAD5ICT0", "cluster": 2117308, "interpro_all": ["IPR033121", "IPR021109"], "interpro_used": ["IPR021109", "IPR033121"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Target Function: The protein carries 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. Also, the protein is classified under the rRNA (guanine-N(2)-)-methyltransferase RsmC/RlmG family, which comprises S-adenosyl-L-methionine (AdoMet)-dependent enzymes responsible for the N2-methylation of specific guanine residues in ribosomal RNA. Members of this family typically feature a bipartite structure with an N-terminal substrate-recognition domain and a C-terminal catalytic domain that binds AdoMet. Notable representatives include RsmC, which modifies position 1207 of the 16S rRNA, and RlmG, which targets position 1835 of the 23S rRNA. Furthermore, the protein incorporates 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. It is found in Thalassotalea sp. PP2-459 and contains UniProt keyword associations Cytoplasm and rRNA processing.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 16252, 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, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 9067, 12, 16904, 17, 56, 12, 22, 13, 17, 13, 17, 16478, 4366, 7112, 19, 11929, 9759, 3416, 16, 2154, 12936, 61, 17, 29283, 17, 54, 17, 12417, 12, 2041, 14080, 13, 17, 3100, 5038, 5061, 1958, 1920, 9585, 17, 5547, 1927, 2487, 16904, 4248, 1922, 11196, 3146, 18, 4678, 1927, 2052, 3416, 5745, 5961, 43, 8446, 24707, 3170, 1956, 1925, 56, 17, 4262, 4510, 17, 5708, 3418, 1930, 43, 45, 17, 4262, 6804, 3418, 1988, 6876, 2041, 14080, 18, 11892, 18315, 3951, 4366, 7112, 16, 2154, 25436, 3507, 6103, 1027, 1927, 1920, 11209, 9067, 16, 1930, 11929, 9759, 16, 2154, 4845, 3507, 16228, 1015, 1927, 1920, 3020, 1036, 9067, 18, 3677, 16, 1920, 2213, 19683, 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, 2176, 1977, 2435, 1922, 20338, 10868, 5376, 2056, 18, 27537, 17, 3607, 1026, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 1930, 9067, 4587, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MFLTNLSQVLARHDDLLIASSPLLVNMPQDNFYDAYLFRDNTVKSNAIFHSQYQSKTLHDLMENARILIVGENKSGIKSISKLTQGYHNTLDKIDSARFQYYDLTINGEQCVIAALPGVFSQGGLDKGTSVLFEHLPNTGAGVIATYLAKTNQHITIELADVSALALASAEKTLKYDHVVTNPPFHQGIKTHYAATESFLSGIHVSTAATKHGFTVYSARKANHLQQISSADEITFYDTQIMTFPKSKKELTFTLAMLSANLSHCVLYELTLNKLPTFNLEDWNLSGHVLDFGINKLSGNLIATNSLSSIKAQKYIKPNGTLTVVANSFLKYQPIMASYFKK", "metadata": {"id": "A0A1Q6CI55", "cluster": 2295257, "interpro_all": ["IPR002052", "IPR013675", "IPR023543", "IPR046977", "IPR029063", "IPR007848"], "interpro_used": ["IPR007848", "IPR046977", "IPR002052"], "interpro_unused": ["IPR029063", "IPR013675", "IPR023543"]}, "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 a member of the Chaperonin Cpn60/GroEL/TCP-1 family, which comprises molecular chaperones essential for the correct folding and assembly of polypeptides into oligomeric structures. These proteins, including bacterial GroEL, mitochondrial Hsp60, and cytosolic TCP-1, typically form ATP-dependent stacked-ring complexes that stabilize unfolded proteins and prevent aggregation, often in cooperation with co-chaperonins such as Cpn10 or GroES. Furthermore, the protein includes a Retrotransposon gag domain that functions as a structural component in eukaryotic retrotransposons, analogous to retroviral capsid proteins. It binds its own mRNA and self-assembles into virion-like capsids, facilitating the packaging of genetic material. Additionally, the protein belongs to the GroEL-like equatorial domain superfamily, which forms the ATPase-active base of chaperonin monomers essential for assisting protein folding. This domain powers the cylindrical complex, enabling it to sequester partially folded polypeptides in a protected environment. It is derived from Kingdonia uniflora and corresponds to UniProt keyword Membrane, ATP-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, 43, 7210, 1927, 1920, 10686, 6655, 4244, 1022, 5127, 19, 8947, 1938, 19, 19940, 17, 21, 3416, 16, 2154, 12936, 3272, 18098, 4415, 1958, 1920, 5550, 10328, 1930, 5957, 1927, 18633, 2460, 19206, 4061, 18, 2144, 2697, 16, 2710, 4543, 8947, 1938, 16, 4596, 6418, 5127, 16, 1930, 9410, 19940, 17, 21, 16, 5745, 2386, 4498, 17, 3100, 24669, 17, 6335, 5048, 1988, 13448, 17416, 2697, 1930, 4625, 7883, 16, 3868, 1922, 13830, 1956, 2081, 17, 10686, 28756, 2427, 1966, 4244, 7301, 1008, 2014, 8947, 1918, 18, 3677, 16, 1920, 2213, 5921, 43, 27181, 1916, 9819, 3418, 1988, 4088, 1966, 43, 4346, 4594, 1922, 10825, 27181, 2101, 16, 12464, 1942, 16599, 14681, 2697, 18, 2176, 6876, 2496, 6614, 3616, 1930, 3543, 17, 17421, 1036, 2460, 19230, 17, 3189, 28550, 16, 12440, 1920, 15627, 1927, 3299, 3485, 18, 4950, 16, 1920, 2213, 14440, 1942, 1920, 8947, 1938, 17, 3189, 29089, 3418, 13975, 16, 2154, 4952, 1920, 9444, 17, 3500, 5170, 1927, 10686, 6655, 13256, 4415, 1958, 27840, 2213, 10328, 18, 2052, 3418, 24234, 1920, 18677, 2796, 16, 12180, 2176, 1942, 23504, 6426, 16318, 18633, 1922, 43, 9713, 3515, 18, 2176, 1977, 3595, 2037, 10721, 28615, 2126, 24386, 29404, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 4498, 17, 2743, 16, 1930, 9117, 7864, 18, 3], "output": "MFYAQFINLGVYWFSLSPKLDSIILCYLNVVGKGKIESDIGKEVTGKGDLEKKGDGDDVFKEVGDGKDSMEEDGDEHEEYEDKVMSVLACANIGVETDTTKNVATTPDEAVPHLKNLWVADGGNTNVKDQQIGNLERSVLIHLKKHHGKHIIDGLECWNVLIIYRYDLNDKEITSIQIKLLKPSLGVGFDGGGVVWVVAMAVVLQLGYRVVTLTVLMILKANRAYSLFQVLVAAVVIFGELRWWPILQLLLLGLLRREVLELDSFLMARGGSGRGRARTHGGIYEGLRSGVVAEAAGVGVGILPGVQIHQGTLPTPVIPEQAGILPVTAAPILWASFRDRFFDQYFPKSYRHACISEFYMLEQGDMSISRYDQGFNELSRYFRRFLITSGANTYREVLFKALALEQNDVEDRKSKDLRGQQRQDQRLDKGKVVQTQYDSLGLKLNFLGMFQSIEEAEWSLHDAIMMIRRALKNSTVVAGGGAIDMEISQYLRQHARTIVGKFQLFTNAYARALEVIPRQQLPSSEGALYGVDVHTSGIAYFFVNIIWEPSVVKINTLNAAAEVTCLVLGMDETVKSPKVCSSGFTLESKKGEEDEIGDGELLTTCPPTEAGSPLPNFPTTVDCGVYPCSVIRVACPRDSVVGASGLFAAFLVFQWLLGGGGFVLCSGTLGWSGVSAKMKQFMEGTIVKTYVMFIINDEEQRKMKFLKGLHPKRQREFLCCSRIFDLYMAILKRCDNVVYDATDVLNQLRQKHAL", "metadata": {"id": "A0A7J7LUN3", "cluster": 4439030, "interpro_all": ["IPR017998", "IPR002423", "IPR027413", "IPR005162"], "interpro_used": ["IPR002423", "IPR005162", "IPR027413"], "interpro_unused": ["IPR017998"]}, "task_type": "infilling"} {"instruction": "Here is the polypeptide chain function: The protein contains a Mor transcription activator domain that functions as a sequence-specific DNA-binding protein to mediate transcription activation. It contains an N-terminal dimerization region and a C-terminal helix-turn-helix motif, facilitating activation through interactions with the alpha and sigma subunits of bacterial RNA polymerase. Furthermore, the protein belongs 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. It is derived from Halomonas saccharevitans. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 13022, 4659, 2347, 30, 1920, 2213, 5461, 43, 2803, 3213, 9518, 3418, 1988, 4088, 1966, 43, 3244, 17, 2487, 2678, 17, 2743, 2213, 1942, 8265, 3213, 2936, 18, 2176, 5461, 1925, 56, 17, 4262, 13640, 3031, 1930, 43, 45, 17, 4262, 7864, 17, 5165, 17, 7864, 5219, 16, 12440, 2936, 2596, 3719, 1956, 1920, 4595, 1930, 5139, 6991, 1927, 4543, 3146, 6479, 18, 3677, 16, 1920, 2213, 14440, 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, 2176, 1977, 3595, 2037, 23226, 3947, 1934, 14175, 2768, 2165, 3285, 1036, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MEQSLDEISIADAYLEGVITDDDLLAESGENFGALVVACGEMAARLVDAYGGTRLYVPCRLDPGGQLAQALGEQSAQTLIDLCEREDVGVPRLMSLRRTIRNQKIVALRETGAAPAKLALHFNLTERQIHSIVRQHRIQAKA", "metadata": {"id": "A0A1I7CKY0", "cluster": 5105789, "interpro_all": ["IPR009057", "IPR014875"], "interpro_used": ["IPR014875", "IPR009057"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein falls within the Uncharacterized protein AN11006-like family, which comprises proteins of unknown function found primarily in fungi. It is native to Trematosphaeria pertusa.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 12182, 2651, 1920, 24528, 2213, 1925, 24307, 14265, 17, 3189, 3416, 16, 2154, 12936, 2697, 1927, 5435, 2347, 2435, 5985, 1922, 10520, 18, 2176, 1977, 6196, 1942, 11797, 8286, 3508, 20051, 3027, 1019, 7548, 28553, 18, 3], "output": "MQAQAGSRFLRLPGEVRNKICEHVLTGSSPIPGSPAEGINQMKFVCRQLRHETARLLLGPCRYLVFPERCTAQQIDALEVVEVQEQVTRNVRSFYKKLFDLECFTSPLTCTCLSTIAGIVQLASRKRYTAPFYHYGFDRVMAAPFPQNIKFYPAYNFETGDGWKFYNARPFQGIYCFKSETDEVAFNFFRSSDFACATEASAAATCTLFLQAMGVLVEFARTHNHLTFNVILLTVDTLGRMSRKWSGYG", "metadata": {"id": "A0A6A6I2K9", "cluster": 5467118, "interpro_all": ["IPR038883"], "interpro_used": ["IPR038883"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should include a Cyclin, N-terminal domain that regulates cyclin-dependent kinases (CDKs) to control nuclear cell division cycles. This all-alpha fold domain binds catalytic partners, such as p34(cdc2) or cdk2, to form complexes like the Maturation Promoting Factor (MPF) essential for G1/S and G2/M transitions. Moreover, the protein is assigned to the Cyclin-like superfamily, which comprises proteins sharing a core structural fold essential for cell cycle progression and transcriptional regulation. This domain, characterized by a duplication of a five-helix bundle, is found in cyclins, transcription factor IIB (TFIIB), and the retinoblastoma tumor suppressor. It is present in Musa troglodytarum.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 3066, 3951, 43, 8180, 16, 56, 17, 4262, 3418, 1988, 7014, 8180, 17, 3100, 7784, 12, 9727, 1036, 13, 1942, 2285, 4254, 2024, 8451, 6355, 18, 2052, 2136, 17, 4595, 3728, 3418, 6876, 6804, 7228, 16, 2427, 1966, 9234, 1006, 12, 28190, 13, 2014, 18664, 16, 1942, 2386, 5048, 3189, 1920, 7655, 7356, 2991, 12, 5438, 1038, 13, 4415, 1958, 8533, 19, 61, 1930, 9616, 19, 55, 10673, 18, 3950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 8180, 17, 3189, 13975, 16, 2154, 12936, 2697, 10763, 43, 4728, 4346, 3728, 4415, 1958, 2024, 4048, 4380, 1930, 5224, 3640, 18, 2052, 3418, 16, 4378, 2007, 43, 12630, 1927, 43, 3628, 17, 7864, 14142, 16, 1977, 2435, 1922, 29201, 16, 3213, 2991, 19795, 12, 27935, 1014, 13, 16, 1930, 1920, 25526, 2798, 9241, 18, 2176, 1977, 2481, 1922, 3177, 1019, 12730, 4365, 2756, 3857, 24277, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MADKKNAPPRLTQMVANRAGDGLRGSVHSFHPLDGSHPCLGRPLHLRRPVYPASGDFDGLVVRKIWRNNITAYQKKKRNCHHRRLSLLILLHESRATSKERWEISHPRKGEASLPDDPQTCTHYATDIYAYLRSLEEVHSMWSRRLRIFKPVVSVSRKLPQFTLVVSCNLARWRLTWRHRGRTSIGKLSDTDRSRRWQRNQEARKQGKAAPDRRSSSAAGYIQGAPTAGDLPSTAAGRVQGASGIRLPRKTWPCRRTSVLRPRHGVPSRPSLQRRELPSSAADCIQGASGSHCGHKKDGTGPPDIPGTSLAEPAPSISAKKDNARPSDLPDASQAATAPLDLCGLNPRSVGRSVFQENRFQMCIPDVSDIKCLVDWMAQVVECFRLRSDILCLAVSRFTQAGRDDGKVSVCLFVLLLGCNPFPNSYITQMRSGREIQAGLGCAVPHTCGIAIALAGTFPVDTTTSIEVDSKIDQSVGFGISEAIPKILGESACEEPTLMDQSLKKDVPRSPDSHAASQSTSKERRGFSLPRRRWRSRTTPSRRDCNQGASGDQSSYGYLKSREVKLRPLANYLEAVKIGITATMR", "metadata": {"id": "A0A9E7ICY7", "cluster": 5963788, "interpro_all": ["IPR036915", "IPR006671"], "interpro_used": ["IPR006671", "IPR036915"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein is a member of the Translation protein SH3-like domain superfamily, which comprises domains with a partly opened beta-barrel topology found in proteins associated with the translation machinery. This group includes the RNA-binding domain of ribosomal protein L2, involved in 23S rRNA assembly and peptidyl transferase activity, as well as the eukaryotic translation elongation factor 5A (eIF5A), which plays a role in translation elongation and acts as a cofactor for viral proteins. Furthermore, the protein is categorized in the NusG-like family, which comprises bacterial transcription elongation factors involved in the regulation of transcription termination and antitermination. Members such as NusG and its paralogue RfaH interact with RNA polymerase and the termination factor Rho to suppress pausing and bypass termination signals, facilitating the complete synthesis of long RNA chains. This activity is essential for the expression of operons encoding extracytoplasmic components, including lipopolysaccharides and virulence factors. Moreover, the protein carries a NusG-like, N-terminal domain that facilitates transcription elongation, termination, and antitermination processes. It constitutes the N-terminal region of key transcriptional regulators, including NusG, the antitermination protein RfaH, and the elongation factor Spt5. It is identified in Clostridiaceae bacterium and contains UniProt keyword associations Transcription antitermination and Transcription regulation.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 6410, 2213, 18824, 17, 3189, 3418, 13975, 16, 2154, 12936, 4682, 1956, 43, 10028, 16645, 4666, 17, 19560, 13678, 2435, 1922, 2697, 2458, 1956, 1920, 6410, 10853, 18, 2052, 2210, 5921, 1920, 3146, 17, 2743, 3418, 1927, 11196, 2213, 12051, 16, 3286, 1922, 3020, 1036, 9067, 5957, 1930, 3431, 2199, 13763, 2455, 16, 1966, 2486, 1966, 1920, 10825, 6410, 9971, 2991, 6871, 12, 9493, 9422, 13, 16, 2154, 5705, 43, 2770, 1922, 6410, 9971, 1930, 8016, 1966, 43, 15155, 1958, 4324, 2697, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 13232, 18073, 17, 3189, 3416, 16, 2154, 12936, 4543, 3213, 9971, 2790, 3286, 1922, 1920, 3640, 1927, 3213, 12462, 1930, 10310, 2166, 2636, 18, 4678, 2427, 1966, 13232, 18073, 1930, 2496, 16188, 2182, 22465, 1023, 6310, 1956, 3146, 6479, 1930, 1920, 12462, 2991, 10585, 1942, 4400, 3838, 16435, 1930, 10344, 12462, 4771, 16, 12440, 1920, 4080, 4271, 1927, 2815, 3146, 7835, 18, 2052, 2455, 1977, 4415, 1958, 1920, 2294, 1927, 28748, 5797, 3439, 2355, 11302, 4178, 16, 2710, 15614, 1036, 1930, 9304, 2790, 18, 3950, 16, 1920, 2213, 16252, 43, 13232, 18073, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 11374, 3213, 9971, 16, 12462, 16, 1930, 10310, 2166, 2636, 4028, 18, 2176, 14879, 1920, 56, 17, 4262, 3031, 1927, 3834, 5224, 9098, 16, 2710, 13232, 18073, 16, 1920, 10310, 2166, 2636, 2213, 22465, 1023, 16, 1930, 1920, 9971, 2991, 19375, 1015, 18, 2176, 1977, 2899, 1922, 17938, 14773, 1972, 3336, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 3213, 10310, 2166, 2636, 1930, 3213, 3640, 18, 3], "output": "MWYVIQTLGGEEEHTADMIRQWNKVEEILFPAYIFVATKVLGREEGYFVALSEEEESLVRNIRVIEGPLKDYAGDVVKVETELRLGIEMVREDKRALKARRVPSYYIEECFIPKRERMKKFYGDRPGELYQELRRVPRLTLGGHMHRAGLSKVVVGEGKKNLHKREVVVRVGFMGR", "metadata": {"id": "A0A6N9NUM8", "cluster": 6225237, "interpro_all": ["IPR006645", "IPR036735", "IPR043425", "IPR014722", "IPR047663", "IPR001062", "IPR008991"], "interpro_used": ["IPR008991", "IPR043425", "IPR006645"], "interpro_unused": ["IPR014722", "IPR036735", "IPR001062", "IPR047663"]}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein possesses a RNA-binding S4 domain that mediates binding to RNA and is widely distributed in translation-related proteins. This small structural motif is found in ribosomal subunits, pseudouridine synthases, and tyrosyl-tRNA synthetases, where it facilitates nucleic acid recognition across bacterial and eukaryotic systems. In addition, the protein carries a RsuA/RluA-like pseudouridine synthase domain that catalyzes the isomerization of uridine to pseudouridine in 16S and 23S ribosomal RNAs during ribosome assembly. This domain acts on specific sites within the small and large ribosomal subunits and may function as an RNA chaperone, often utilizing a conserved catalytic core structurally linked to an S4 RNA-binding domain. In addition, the protein belongs to the Ribosomal RNA Pseudouridine Synthase RsuA family, which catalyzes the isomerization of specific uracil residues to pseudouridine in ribosomal RNA, a modification critical for ribosome structure and translational fidelity. Members specifically target residues in 16S and 23S rRNA, while some exhibit dual specificity by also modifying the anticodon region of tRNA. It is native to Arcella intermedia and is associated with UniProt keywords Isomerase.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 14465, 43, 3146, 17, 2743, 6934, 3418, 1988, 10412, 2743, 1942, 3146, 1930, 1977, 5673, 6533, 1922, 6410, 17, 2712, 2697, 18, 2052, 2858, 4346, 5219, 1977, 2435, 1922, 11196, 6991, 16, 11520, 23864, 8921, 1036, 16, 1930, 6578, 2199, 17, 10089, 18185, 1036, 16, 2597, 2176, 11374, 11079, 2687, 5708, 3436, 4543, 1930, 10825, 3771, 18, 1922, 2459, 16, 1920, 2213, 16252, 43, 4366, 12169, 19, 11929, 12169, 17, 3189, 11520, 23864, 8921, 3418, 1988, 17097, 1920, 27027, 1927, 26104, 1942, 11520, 23864, 1922, 11209, 1930, 3020, 1036, 11196, 8624, 2409, 12794, 5957, 18, 2052, 3418, 8016, 1990, 2487, 3402, 2651, 1920, 2858, 1930, 3103, 11196, 6991, 1930, 2278, 2347, 1966, 1925, 3146, 14044, 16, 3868, 10232, 43, 5305, 6804, 4728, 12171, 4624, 1942, 1925, 6934, 3146, 17, 2743, 3418, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 11196, 3146, 11520, 23864, 8921, 4366, 12169, 3416, 16, 2154, 17097, 1920, 27027, 1927, 2487, 22761, 4248, 1942, 11520, 23864, 1922, 11196, 3146, 16, 43, 6295, 4140, 1958, 12794, 3170, 1930, 8414, 14013, 18, 4678, 4475, 2758, 4248, 1922, 11209, 1930, 3020, 1036, 9067, 16, 2679, 2673, 5987, 7064, 4896, 2007, 2222, 12691, 1920, 11693, 28615, 3031, 1927, 10089, 18, 2176, 1977, 6196, 1942, 9952, 5870, 11213, 1019, 1930, 1977, 2458, 1956, 20709, 11569, 25510, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MDRILSNMGFCTRSKVRSFIDKNHVLVNNQKMKASEYVFPEDITINGTPISFPYPLYQRRPSLACAGRLDKWASGLVVMTQDGDCNFNITSPKKKSGVLGKVYELELQNPLTDKEAKLVRITLYEGKYHQLRRMLAATGNRAVSIKRVATGPLLLGGRPYLESDKGKGTGGVDVDEAAIGVGELFAEEEEDENEDAEEPPFERDEEEEEPELIVLHKPRGYVCSAKREQKDGKIVYDLLPETWIGDEPKLFSSGQLQLKSEQKPCRPAKFEIILPVGHWRELSREEVLSLGVESDR", "metadata": {"id": "A0A6B2LC90", "cluster": 7721545, "interpro_all": ["IPR042092", "IPR020103", "IPR006145", "IPR050343", "IPR002942", "IPR036986", "IPR020094"], "interpro_used": ["IPR002942", "IPR006145", "IPR050343"], "interpro_unused": ["IPR036986", "IPR020094", "IPR042092", "IPR020103"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein is a member of the Autophagy-related protein 2 (ATG2) family, which acts as a lipid transfer protein essential for autophagosome completion and peroxisome degradation. Belonging to the RBG superfamily, these proteins utilize a long hydrophobic groove to transport lipids, regulating lipid droplet morphology and mediating diverse autophagic processes in conjunction with the Atg1-Atg13 complex. It originates from Acrasis kona and features UniProt keywords Endoplasmic reticulum and Lipid transport. 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, 43, 7210, 1927, 1920, 6661, 17, 2712, 2213, 22, 12, 9353, 1028, 13, 3416, 16, 2154, 8016, 1966, 43, 4486, 3856, 2213, 4415, 1958, 21631, 9297, 1930, 19531, 4877, 18, 10588, 1942, 1920, 6160, 1029, 13975, 16, 2144, 2697, 12561, 43, 2815, 7919, 15920, 1942, 4860, 8238, 16, 6773, 4486, 10622, 6076, 1930, 10239, 6445, 15319, 4028, 1922, 11799, 1956, 1920, 9353, 1009, 17, 9353, 3633, 2796, 18, 2176, 22970, 2037, 10428, 3932, 21947, 1019, 1930, 4075, 20709, 11569, 13355, 12279, 1930, 4486, 4860, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "LYTLNSVQINAKNINDLLKDTPISLKSGYIESINVALPNLFKLFEDSMKIDINGIELVFQIKDAVYMDSNHSRNVLSSLLAESLIGDFGDPNVMTSSILVGDVRRSDLDEFESDVSSPTGSYMRSNDKKSSSSSANNDDGDEIGEAEGYIAQLIERIVSNIKASITNVTLRFEFPTPTTAVNSPLHDVHKNVFLMHFPRMDYADETPMPSASATWQPSIFKYKFTFKGFFVQVFDEHQEPSSSTTMMSASLFGQ", "metadata": {"id": "A0AAW2YIK3", "cluster": 8569470, "interpro_all": ["IPR026849"], "interpro_used": ["IPR026849"], "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 can be placed in the Frataxin/CyaY family, which plays a central role in mitochondrial iron homeostasis and iron-sulphur cluster biosynthesis. This family includes the bacterial CyaY protein, which functions as part of the ISC system, and the eukaryotic Frataxin, a mitochondrial protein whose deficiency causes the neurodegenerative disorder Friedreich's ataxia. 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 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 present in Coleofasciculus chthonoplastes PCC 7420 and is described by UniProt keywords Coiled coil and TPR repeat.", "tokenized_instruction": [2, 4663, 2962, 1920, 2213, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 23228, 3857, 10960, 19, 6002, 2050, 3416, 16, 2154, 5705, 43, 4101, 2770, 1922, 4596, 5680, 7622, 1930, 5680, 17, 13528, 1949, 4377, 8132, 18, 2052, 3416, 5921, 1920, 4543, 6002, 2050, 2213, 16, 2154, 4088, 1966, 3131, 1927, 1920, 23924, 2433, 16, 1930, 1920, 10825, 23228, 3857, 10960, 16, 43, 4596, 2213, 6098, 6179, 5092, 1920, 11128, 4770, 16624, 1936, 2108, 11, 61, 17698, 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, 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, 2481, 1922, 21481, 4199, 2976, 21206, 2016, 1963, 23557, 2030, 2197, 1918, 16003, 5446, 3520, 1930, 1977, 2910, 2007, 20709, 11569, 17524, 9121, 1930, 22288, 6865, 18, 3], "output": "MDESRRQDYRNLIQMLLNCPSGDEPIILRANSNLIDAGLVQTMLQIAAGLIVTGKLDASDFLMNVTGYLLGVYSTPIKRLSSKDAPIAVGIGNSFAVIPEPEKYASFLGELMQAILDHRRNLEGVYPFLKANLDKLDDTFAQVLHDWATSLLLKLEPADAENLAVDIGNFGFLLQQFPLGSKASNLEIAITAYQFTVTVLSREGFPKEWANTHNNLGQAYRNRIRGDKPQNLEKAIAAFQNALQVYTQKDFLQRWAMIKNNLGLVYREQGWIEQAVAAHEDALKGYSYQEFPEEWGVSKFCALALLRGAETLAMSLLWVMFIPKLDTPEEWADTQTYLGNVYSDKGEVDKAIAAYKKALKVRISGTYKWAETQNNLAAQYREIGQIAQAIAIYKDNLQVYTHKEFPERWATTHYNLARAYSKAGQIKQAIKAYQSALKVYTPAAFPIECLHCGNNLGHLAFDAERLEEAIEAYGVAIEAVEESWAWASTDARRQEIQTEAIGVYIGIVKSYVKTKQWKTAIEYAERSKARNLVQLLANRDLYPKGASESDCNQLKYLRREIAAKQRQLETTQINFSTGIEENKQLLDQTYSEQLRQELDKLQQQLNDLLEQIKTLDPNFSFTQRVEPISFERIQALLPNDKTVLIEWYVLGDTFLTFIVTRQSPGITVWQSSPEDAQALFDWLREDFSDDEQPSKENWKNQLEFKLHHLAQILHLEEILSHVPETCDRVILIPHFLLHLLPLHALPVTSTDTSPVEEDRSPLAKKRESDADPARQKCLLDRFPEGVSYAPSCGLLQLTQNSQHSEFSYFFGIQNPTQDLNYADLEVETIRQDFHPNDKVFAREAATKQAIYNQQLHLAHCIHFSCHGYFDSEAPLRSALLLADATPTQTETSQMTNPERYIHLREGSTVNQGKCLTLGEIFGLELSQCRLVTLSACETGITSPKGLIDEYIGIPSGFLIAGSPSVVSSLWRVNDLSTALLMIKFYQNLKSGSTVAVALNTAQTWLRDATKEQLQQWASQLPLDDEQELQLDAFFYNLQPSSKPFESPYHWAAFCAIGQ", "metadata": {"id": "B4VI04", "cluster": 11693279, "interpro_all": ["IPR024983", "IPR002908", "IPR011990", "IPR019734"], "interpro_used": ["IPR002908", "IPR019734", "IPR024983"], "interpro_unused": ["IPR011990"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: 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. Moreover, the protein incorporates a RNA polymerase sigma factor 70, region 4 type 2 domain that mediates specific binding to the conserved -35 promoter element via a helix-turn-helix motif. This interaction directs the RNA polymerase holoenzyme to gene start sites, enabling transcription initiation in bacteria and plant plastids. Additionally, it 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 is identified in Filimonas lacunae and is associated with UniProt keywords DNA-directed RNA polymerase.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 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, 3950, 16, 1920, 2213, 19683, 43, 3146, 6479, 5139, 2991, 3895, 16, 3031, 24, 2601, 22, 3418, 1988, 10412, 2487, 2743, 1942, 1920, 5305, 17, 3259, 4465, 6149, 3454, 43, 7864, 17, 5165, 17, 7864, 5219, 18, 2052, 2835, 28351, 1920, 3146, 6479, 20403, 14896, 1942, 2359, 6413, 3402, 16, 12180, 3213, 6035, 1922, 4802, 1930, 4496, 19754, 1036, 18, 4950, 16, 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, 1977, 2899, 1922, 3313, 1980, 9259, 27152, 3336, 1930, 1977, 2458, 1956, 20709, 11569, 2678, 17, 6554, 3146, 6479, 18, 3], "output": "MSQEDIVLHDYFTSIAAGDVSAFDQFSHLYKHKIMGKAFQETQCWNAAEEITKGFFDNIWKSRTLLTAVENGDHYISTTLDHITKQYLLLKKNSTLLGELIKKFTSGLFTGPCLPMTEEQLKTFVPIAINTLPQQMKQVFELRYYYQEPYEDIARDLGITKGIAQQYFFDSMIQIRNYIDEHLLPG", "metadata": {"id": "A0A173MKZ1", "cluster": 13468647, "interpro_all": ["IPR013249", "IPR013324", "IPR036388"], "interpro_used": ["IPR036388", "IPR013249", "IPR013324"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein is assigned 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 categorized in the Multi-functional host-pathogen interaction and enzymatic activity protein family, which encompasses diverse roles ranging from modulating host immune responses via dendritic cell activation and cytokine regulation to catalyzing heme biosynthesis and substrate oxidation. Members may also facilitate bacterial spread by interacting with host proteins or contribute to the stability of cellular transport complexes. In addition, the protein belongs to 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 Vulcanimicrobiota 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, 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, 10234, 1922, 1920, 2779, 17, 3183, 4423, 17, 7055, 2835, 1930, 8145, 2455, 2213, 3416, 16, 2154, 21569, 6445, 5456, 6485, 2037, 10871, 4423, 3743, 3387, 3454, 8104, 2024, 2936, 1930, 6137, 3640, 1942, 29601, 10954, 8132, 1930, 4510, 6638, 18, 4678, 2278, 2222, 6628, 4543, 6441, 2007, 8615, 1956, 4423, 2697, 2014, 4672, 1942, 1920, 5057, 1927, 3689, 4860, 5048, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 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, 7343, 8337, 1980, 1935, 15129, 3940, 3857, 14061, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MHFVPVTPPALVESARGFDYVTADSAARRIYAAGVAVDPQTGHVYTGNGLARSVSEVDPVSVLHRVYADEDDGTHVYVVDTKTMKQIAAVPIPDVYQNIDNLGEVAVIGASALKVTRTFPTPAIQKNHPLQQGKLLGTVSIQPSVDQCSYNPTTRQIACAGSGKVTVVSVSHTGSNALLVVNADNGKVVGQVEVGTMHLNVLRTANVDGQVDAIAYDPGHKPEYLAVDPQTHYDSQNHILLIGGKNGVLASYTT", "metadata": {"id": "A0A950DRZ6", "cluster": 16577274, "interpro_all": ["IPR051200", "IPR011044", "IPR015943"], "interpro_used": ["IPR015943", "IPR051200", "IPR011044"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want a protein that has the function: The protein contains a ABC-type transport auxiliary lipoprotein component domain that acts as an auxiliary subunit in the gamma-hexachlorocyclohexane (Lindane) uptake permease system. It facilitates the import of this insecticide to serve as a carbon source in bacteria such as *Sphingobium japonicum*. It is derived from Alphaproteobacteria bacterium RIFOXYD12_FULL_60_8 and corresponds to UniProt keyword Signal. Output the protein sequence.", "tokenized_instruction": [2, 51, 12914, 43, 2213, 1988, 2258, 1920, 2347, 30, 1920, 2213, 5461, 43, 7219, 17, 2601, 4860, 21549, 9694, 4594, 3418, 1988, 8016, 1966, 1925, 21549, 5903, 1922, 1920, 7034, 17, 7142, 22918, 20446, 23834, 2516, 12, 16401, 2516, 13, 5047, 6191, 2051, 2433, 18, 2176, 11374, 1920, 2582, 1927, 2052, 21578, 1942, 7120, 1966, 43, 5056, 4585, 1922, 4802, 2427, 1966, 14, 13502, 23156, 18913, 1989, 14, 18, 2176, 1977, 3595, 2037, 4595, 9218, 1021, 10296, 14061, 12424, 7221, 7240, 1028, 41, 4125, 41, 3276, 41, 28, 1930, 8852, 1942, 20709, 11121, 2538, 2733, 18, 6647, 1920, 2213, 3244, 18, 3], "output": "MTLTRSLAALALLALIASCGGGPQPPRDQFYRLDIAPPSVVLDKPVLNGGVEIDRFQADGVTIERAIAYSEDKSQLTQYAYHYWVDTPVLMLRDILVEQMRAAHVAPLVTTPENRAASDFSVLGKVKRFEHRRDNGASAALLEIELTVLDARNGTVLLLKDYAVEEAAADASVPAAVDAMNRAVFSLSAKFLTDLSHLTP", "metadata": {"id": "A0A1F3B2J0", "cluster": 17334451, "interpro_all": ["IPR005586"], "interpro_used": ["IPR005586"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: 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. Also, the protein should have 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. Additionally, the protein should feature 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 has been characterized in Streptomyces sp. WAC07149.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 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, 2222, 16, 1920, 2213, 3066, 2162, 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, 4950, 16, 1920, 2213, 3066, 5961, 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, 2258, 2252, 4378, 1922, 22874, 2056, 18, 4114, 1030, 14099, 22987, 18, 3], "output": "MAFRVLDRVTAPEGCGLEVSRHSRPMGVLAALLVSPGQQASRGDLKRWIWGDSPKEYALTKVLSRLRSALPGEIATVKNGKICSIDVASESVDYLRFRHSLAIARDRSTSDTDRLVALRLGMREWSPREILGGLTGEWAAQARSRLRIEQKHAAVELVRVTQALGDLEAAIAEAEQFLMLWPTDEQMIKLLLDCITAAHNVRAAEEWLDDWYAEHPDGSQRLRAHIRGLATPGGSQRVLGRAAHLVVPREVPSAGPPLRGRESTLDELVSAIAAPARNCGVFVITGMPGVGKTALVRRLANLVKHLFPDGALYLDLQGFTSADTAPLAPEVALSHCLTAFGLKDTPSSLADKAALFRSILAERSVLVVLDNARNSEQIRSLIGSNKRCATLITSRNRLSDLTADEEVQVTEIRPLADTAAKSLLLDAMHGEVDDEADLLLDQLVQWCSGVPLALQLVAARLRNQPAAALGDFVSSMGENRATVLDDRNRLAVWPAYRCSYQTLSPDAGRLLWQLTLYPGADISWGALSDIARAGAVKDVHRAAGELVTGNLLECSEGAYRMHDLIRAYATELAEADDTGLGEQTRQRVFEHLLQNVWACDQVLAPDRGLPIHPCAAVEPIRPKDENAAMAWLEQAYGPVTAAIRLAREAGQHRTMWLLSLAVMTYQWRLNLHAAAEENLSAALHLTHDITTPEERSTLHRMLAGCCFNQGRLAEGVAHLHRAIALVEGSNAATDRLSLGRSLHTLGLVRKTEKHEAEAMEHLHHALDVLRPLDDHPTIGAALECLAEIHCDRGEYDRALDLCFKAQAAFQLSRDRNGRASVQRTFGTIHQARSEPGPAQAAFRQALSIYKELRYDRNIGRTLCALADLHLESGAVQQAREALEEAHTAFTRAGDGFAESVRHRLDTM", "metadata": {"id": "A0A429T0X6", "cluster": 17369028, "interpro_all": ["IPR002182", "IPR027417", "IPR016032", "IPR011990", "IPR019734", "IPR036388"], "interpro_used": ["IPR027417", "IPR002182", "IPR019734"], "interpro_unused": ["IPR036388", "IPR011990", "IPR016032"]}, "task_type": "autoregressive"} {"instruction": "The protein includes 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 identified in Leptotrichiaceae bacterium. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 5921, 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, 2899, 1922, 16976, 18935, 19519, 9914, 14061, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MKFYIVSTMLHVAMLFMLIVSPIVKKEENNTTNQKIKINLETSILEVNNSDGLLNNNEINNGDSNENNKSENNNKKPKENNQILKKEENVVQEKYNSKKIEKNEKIIENKNNLSENNNRNITSSREHSSSNEKGNNQSTGNTSNSSSDGNGKKSIGGNSTNSGNSGSKDSFSGGNVCREGTDFVVTYNPVLPYPISMQRIGKKGTVVVQVKFNFNSNGSISVISLSGGESVFQSEARKAASKIKVSIKNSETLKCTITKSFKFTLN", "metadata": {"id": "A0A9D9ZI33", "cluster": 18056233, "interpro_all": ["IPR037682"], "interpro_used": ["IPR037682"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein should include a TPM domain that adopts a Rossmann-like fold and functions as a thylakoid acid phosphatase involved in photosystem II maintenance in the plant thylakoid lumen. In nematodes, it acts as an auxiliary subunit that positively modulates the gating of levamisole-sensitive acetylcholine receptors. It has been characterized in Candidatus Woesebacteria bacterium RIFOXYB1_FULL_38_16 and is connected to UniProt keyword Transmembrane helix, Signal, and Membrane.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 3066, 3951, 43, 29136, 3418, 1988, 24032, 43, 18215, 8890, 17, 3189, 3728, 1930, 4088, 1966, 43, 30193, 14288, 1960, 2687, 8167, 3286, 1922, 8811, 2405, 2890, 6291, 1922, 1920, 4496, 30193, 14288, 1960, 11223, 18, 1922, 19669, 16, 2176, 8016, 1966, 1925, 21549, 5903, 1988, 6629, 13112, 1920, 12568, 1927, 10157, 14981, 2204, 1952, 17, 4532, 14561, 4086, 18, 2176, 2258, 2252, 4378, 1922, 14550, 1031, 1957, 26334, 2124, 7972, 2341, 18339, 14061, 12424, 7221, 5090, 41, 4125, 41, 3738, 41, 2641, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 9117, 7864, 16, 2733, 16, 1930, 3260, 18, 3], "output": "MLKRKKSTVFLLVILVLAVAGTLTVEAQPPTPQGYVSDFAGVCSVDQLQTLENQLVSIEAETTVEIAKADIDNGLLILSCVSQRELQQEVGYGLEGVLPDLRTSKAADEYFVPQAQAGNICQGLIDLTAYYKIFGIWLFGGVAIAVLVGPDAAVDWWIMWLRFGAILLSSSSKGGHKFGGGRSGGGGSRTRLVVTLDDCGEDPFELRVEIFNQWGVGTLLVKEDEVKSNEEKDNTAGIIAFGV", "metadata": {"id": "A0A1F8CW00", "cluster": 19269818, "interpro_all": ["IPR007621"], "interpro_used": ["IPR007621"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein should include a DUF1595 domain that is a conserved region characteristic of predicted secreted cytochrome-like proteins in *Rhodopirellula baltica*. Additionally, the protein features a Domain of unknown function DUF1585 domain that constitutes a conserved C-terminal region within a family of bacterial cytochrome-like proteins. It is typically observed in species such as *Rhodopirellula baltica* and *Solibacter usitatus* alongside other conserved domains. Additionally, the protein features 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 Planctomycetota bacterium and has UniProt annotations Signal. 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, 3066, 3951, 43, 4855, 5739, 7308, 1015, 3418, 1988, 1977, 43, 5305, 3031, 6293, 1927, 4396, 8366, 9387, 17, 3189, 2697, 1922, 14, 11490, 2011, 2952, 11560, 5617, 4641, 21788, 14, 18, 4950, 16, 1920, 2213, 4075, 43, 3418, 1927, 5435, 2347, 4855, 5739, 7532, 1015, 3418, 1988, 14879, 43, 5305, 45, 17, 4262, 3031, 2651, 43, 3416, 1927, 4543, 9387, 17, 3189, 2697, 18, 2176, 1977, 5745, 2528, 1922, 3038, 2427, 1966, 14, 11490, 2011, 2952, 11560, 5617, 4641, 21788, 14, 1930, 14, 2638, 26073, 2341, 1915, 2022, 9909, 1031, 1957, 14, 17764, 2303, 5305, 4682, 18, 4950, 16, 1920, 2213, 4075, 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, 4720, 2341, 13386, 19446, 3857, 14061, 1930, 2258, 20709, 15010, 2733, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "MRGVARLVVLACLTVSSALAGEVPTATRTLIKQHCAECHDAETKKGDLDLTALSFALTDRSVLESWLKVVEQVESGDMPPAKKQERPSATAVTSALTPLRAALKGQLGQAGVSRVRRLNRVEYEQTLRDLLALPALRIKELLPEDGQRHGYDKVAGALDISHIQMSRYLEAAEVALALAASQPLNVVEKKTWRESAAAQGTALSAIATVQAVPLLGGKLADGYSHKVVGEGANSYRACQFNGTADAVVILKGDLGPHQSQGVQIDRFRPAVAGLYRVRFSAWAMLWDKTEVKSPKEALHVVRASLGDVRLGFFDAPAMKPTVSEFTTWLEPNDRVSFHAMSITDGGPKNWPSVEGIFAYSGSGVAFDWFEVEGPLTDPAASSGVSSGVSASRRLLFGDSGKPDVATVTTVMRTFAERAFRRTVAAVEVKPYVDIAEQLMKQGRSLESALLSAYQAILCAPDFLFLGLEDGLAEAAKPKLGPFALAARLSFMLTNGPPDDELLKLAANGSLSRPKILRAQAERLLASPGSQRFVTHFLDQWLDLRKIDFTTPDKGLYPSYDTWLHDASLAETRGFFRTLLTDDLGVSNLVGSSFVVIDQRLARHYGIDGVQGAALRRVPLPAGSARGGFLTQAAVLKITANGTVTSPVLRGVWVSEHLLGIPHRPPPPNIPAAEPDASGATTIRQIIERHRADSACAGCHAKIDPPGMALETFDAIGAQRTHYLMPDRKQGLAIDSSGKLKGGGAFSGIGELRALLVKDNLGLARSLARQFLIYGTGSNVGFLELEALDAIVATAKPTAYGVRSLLLAVVVSDLFQSK", "metadata": {"id": "A0A7W1IXF3", "cluster": 20769479, "interpro_all": ["IPR011429", "IPR011478", "IPR013036", "IPR013039", "IPR013042", "IPR013043"], "interpro_used": ["IPR013043", "IPR011478", "IPR011429"], "interpro_unused": ["IPR013042", "IPR013039", "IPR013036"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe protein falls within the Protein of unknown function DUF169 family, which comprises uncharacterized proteins found in prokaryotes, including the representative member MJ0308. It occurs in Desulfobacterales bacterium.\nPredict the amino acids that belong in the masked placeholders.", "tokenized_instruction": [2, 1920, 2758, 2213, 4902, 2385, 2052, 2770, 30, 1920, 2213, 12182, 2651, 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, 2176, 5110, 1922, 30311, 5883, 3955, 14061, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MIDTLTLLNDVEFAKVMLDKKELSGAKFFYSEDELSNFKKSENYKIALHPFLGCSNAKYVFRWKEFDEGEITKKRLPINLLAFATAPLHKATFKPDVIHGISKDIHPFEMSMTMNSSACHGSTAVFITNWIWPGQDIEPTIRWTLERMCKLCPFLVWRNPISTRPDIVFILRNLLRMKYYPVAITFCHYLSASRQKGDILLGTAKEKSHIKYAKDREQAERFVKDVLQAYHIANDWCTANKPNITPMCGGSYTSGKTEQGEITVRDGGVSYPRTGETYPGFN", "metadata": {"id": "A0A9D5VRY1", "cluster": 22929694, "interpro_all": ["IPR003748"], "interpro_used": ["IPR003748"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that can perform the following function: The protein contains a Cullin N-terminal domain that functions as the adaptor-binding module of cullin proteins, which serve as scaffolds for Cullin-RING E3 ubiquitin ligase (CRL) complexes. This variable region recruits specific adaptor proteins to target substrates for ubiquitin-mediated destruction, thereby regulating diverse eukaryotic cellular processes ranging from DNA replication to circadian rhythms. In addition, the protein contains a Cullin homology domain that acts as a structural scaffold within multi-subunit E3 ubiquitin ligases, binding RING finger proteins to constitute the catalytic core of complexes such as Cullin-RING ligases (CRLs) and the anaphase-promoting complex. This assembly recruits ubiquitin-conjugating enzymes (E2s) to facilitate the ubiquitin-mediated degradation of substrates involved in diverse eukaryotic processes. It is expressed in archaeon.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 22859, 1921, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 15077, 17, 2743, 9059, 1927, 22859, 1921, 2697, 16, 2154, 7120, 1966, 10603, 1958, 22859, 1921, 17, 6335, 10968, 6526, 11905, 12, 21460, 13, 5048, 18, 2052, 4650, 3031, 18855, 2487, 15077, 2697, 1942, 2758, 6249, 1958, 6526, 17, 3434, 12102, 16, 6113, 6773, 6445, 10825, 3689, 4028, 6485, 2037, 2678, 5158, 1942, 10507, 16622, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 22859, 1921, 9039, 3418, 1988, 8016, 1966, 43, 4346, 7281, 2651, 2779, 17, 5903, 10968, 6526, 22423, 16, 2743, 6335, 8497, 2697, 1942, 11480, 1920, 6804, 4728, 1927, 5048, 2427, 1966, 22859, 1921, 17, 6335, 22423, 12, 21460, 1036, 13, 1930, 1920, 20826, 17, 7356, 2796, 18, 2052, 5957, 18855, 6526, 17, 5225, 2287, 5038, 12, 6602, 1036, 13, 1942, 6628, 1920, 6526, 17, 3434, 4877, 1927, 6249, 3286, 1922, 6445, 10825, 4028, 18, 2176, 1977, 3198, 1922, 13470, 1916, 18, 3], "output": "MQALVRVLNWQEPGRLAAAGPNRAPESLSLYVDERMKGEFKDMEAARLEASLDDVIALFRCLSAKDVFEEHYKNATARRLLSGRMPSEDVERLMISKLKAECGAAFTSKLEGMFMDLSKSAIFMEQYHTARGSSGSSGGAAVHDRRHMADFDATVLTSSNWAGSIQAGPVAQLPPPVSAALADFEAYYGERFNGRRLTWCYNKGTAEMRAWIGATSRPYELLVSTYQMIILYSFNSATEVSYKYVRARTGTRACGHARVHG", "metadata": {"id": "A0A482RKA6", "cluster": 23966831, "interpro_all": ["IPR045093", "IPR016158", "IPR036317", "IPR001373"], "interpro_used": ["IPR001373", "IPR016158"], "interpro_unused": ["IPR036317", "IPR045093"]}, "task_type": "autoregressive"} {"instruction": "The protein is grouped in 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. Furthermore, the protein is classified under the Cyclic phosphodiesterase superfamily, which contains enzymes featuring a $\\beta$-barrel catalytic domain that process cyclic nucleotide substrates. Specific activities include the hydrolysis of nucleoside 2',3'-cyclic monophosphates to 2'-monophosphates in animals, and 2'-5' RNA ligase activity in bacteria and archaea that forms atypical phosphodiester linkages. It originates from Coemansia asiatica and contains UniProt keyword associations Nucleus, Hydrolase, and Lyase. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 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, 3677, 16, 1920, 2213, 1977, 5947, 2441, 1920, 9821, 24821, 13975, 16, 2154, 5461, 5038, 29931, 43, 8, 38, 4666, 8, 17, 19560, 6804, 3418, 1988, 2585, 9821, 5489, 6249, 18, 2487, 4209, 3951, 1920, 9128, 1927, 18015, 22, 11, 16, 23, 11, 17, 9821, 21363, 1036, 1942, 22, 11, 17, 21363, 1036, 1922, 3555, 16, 1930, 22, 11, 17, 25, 11, 3146, 11905, 2455, 1922, 4802, 1930, 21501, 1988, 4952, 10834, 20184, 1967, 19949, 18, 2176, 22970, 2037, 4815, 3862, 12924, 1019, 11624, 21788, 1930, 5461, 20709, 11121, 2538, 5253, 5607, 16, 20748, 16, 1930, 23928, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MSSRLVDYPSSDESSSDHGHHSESSSNNKQDYCEESEPKEPETGPSRDISAERQEDERNDVGHVQGGWAGRVFLEVDAGQQLEQFGRQCMDKLRLEARSKRSCAEALQIIGSQEMHSSEELHISLTRPFYAQEHQIPAFVEALQTSLVGYGRFAVGFERVSTYVNERGNRGFIALDVGAGRTGLAGLLDRVDRVMGRMGKRRFYSRPRFHISLAWMRVNGEQQIKALEMAGEWLGTAMQEEILYLAATQIDTVVCVFGNKQFSISLG", "metadata": {"id": "A0A9W8CJ97", "cluster": 24738272, "interpro_all": ["IPR009097", "IPR027521"], "interpro_used": ["IPR027521", "IPR009097"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein should contain 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. Additionally, the protein is categorized 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 occurs in Hymenobacter lutimineralis and is annotated with UniProt keywords Cell membrane, Protein transport, and Cell inner membrane.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 3066, 5531, 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, 4950, 16, 1920, 2213, 1977, 10234, 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, 5110, 1922, 28034, 19824, 7972, 2341, 1915, 10908, 2265, 21486, 1937, 1930, 1977, 10633, 1956, 20709, 11569, 2024, 3260, 16, 2213, 4860, 16, 1930, 2024, 6671, 3260, 18, 3], "output": "MLMYRVLRLLLPLLLLGVSLVGCKLLSAKSREAKILTGLSEHVRKNLRYPPLYLRSHIEGSSLVGFTIDSTGQVLPGTWQPAQRAGKAVGAECQIPVSFSIRHDVRFTPLAGEAALDSNPVYAGGSNHRIVKPFLQACDEEALRVIKL", "metadata": {"id": "A0A5D6VCG8", "cluster": 26387626, "interpro_all": ["IPR051045", "IPR006260", "IPR037682"], "interpro_used": ["IPR037682", "IPR051045"], "interpro_unused": ["IPR006260"]}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein possesses a Hydantoinase/oxoprolinase, N-terminal domain that forms the N-terminal structural component of enzymes involved in the hydrolysis of cyclic amides, such as hydantoins and 5-oxoproline. Moreover, the protein should contain 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. Furthermore, the protein is assigned to the The Oxoprolinase-like family, which encompasses a diverse group of enzymes including oxoprolinases, hydantoinases, and caprolactamases that primarily catalyse the hydrolysis of cyclic amides and imides, often in an ATP-dependent manner. These proteins participate in various metabolic pathways, such as the biosynthesis of methanofuran and the degradation of compounds like caprolactam and hydantoin derivatives through ring-opening reactions. It is present in marine metagenome.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 14465, 43, 2993, 26182, 11413, 19, 18588, 15743, 11413, 16, 56, 17, 4262, 3418, 1988, 4952, 1920, 56, 17, 4262, 4346, 4594, 1927, 5038, 3286, 1922, 1920, 9128, 1927, 9821, 13601, 1036, 16, 2427, 1966, 2993, 26182, 2925, 1930, 25, 17, 18588, 15743, 2053, 18, 3950, 16, 1920, 2213, 3066, 5531, 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, 3677, 16, 1920, 2213, 1977, 6304, 1942, 1920, 1920, 18588, 15743, 11413, 17, 3189, 3416, 16, 2154, 21569, 43, 6445, 2210, 1927, 5038, 2710, 18588, 15743, 11413, 1036, 16, 2993, 26182, 11413, 1036, 16, 1930, 2853, 2226, 26659, 2319, 1988, 5985, 13928, 1021, 1920, 9128, 1927, 9821, 13601, 1036, 1930, 20697, 1918, 16, 3868, 1922, 1925, 4498, 17, 3100, 5222, 18, 2144, 2697, 7352, 1922, 3425, 4487, 3873, 16, 2427, 1966, 1920, 8132, 1927, 17348, 4199, 20028, 1930, 1920, 4877, 1927, 4300, 3189, 2853, 2226, 26659, 1930, 2993, 26182, 1921, 8383, 2596, 6335, 17, 9497, 5298, 18, 2176, 1977, 2481, 1922, 10789, 16552, 2225, 18, 3], "output": "TFTDIIGIDSHKKIHTNKILSQSPAYADKIERIRIGTTIATNALLERKGAPTALLITSGFKDLLEIGNKPEQLYASVVEVDERLNSNGEVVVGLDIAKLENPIHESICFDIAKEIGFTNISISSQIMPLINIVSRGQTTVMQSSGGLIDSESLTGKDSVLSGPAGSVVEGIRQVLGLKDNEMIPSEQARPSLFDLSIVNDLNSLYNYGYRSLAIVLMHSWKVDSYLYPVLSDYILSLKKELGEIPLEF", "metadata": {"id": "A0A383B590", "cluster": 26754872, "interpro_all": ["IPR008040", "IPR002821", "IPR045079"], "interpro_used": ["IPR008040", "IPR002821", "IPR045079"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein has a Phytase-like domain that likely incorporates PLC-like phosphodiesterase enzymatic activity. This repeated domain features highly conserved glutamate and aspartate residues that are predicted to facilitate this catalytic function. It has been detected in Acidobacteria bacterium RIFCSPLOWO2_12_FULL_66_21 and is described by UniProt keywords Signal.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 2258, 43, 9321, 2051, 17, 3189, 3418, 1988, 3205, 19683, 12897, 17, 3189, 24821, 8145, 2455, 18, 2052, 5116, 3418, 4075, 3626, 5305, 7627, 1930, 12878, 4248, 1988, 2032, 4396, 1942, 6628, 2052, 6804, 2347, 18, 2176, 2258, 2252, 3330, 1922, 2687, 10296, 14061, 12424, 2792, 2030, 1971, 5265, 41, 2369, 41, 4125, 41, 4970, 41, 2900, 1930, 1977, 2910, 2007, 20709, 11569, 2733, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MRKPAASICIFLLVAAAGSCAIPPLTTLDGLKPARFGGISRQDSRIFVFRARPPLSPFRVELRSYFPLPSGAGEIFVASEGIQNHEPRVPPAIVEYSNRVDNASLESLTLTPDGQHLYTAAEAALAFEQVGGTFEPRREFAYPVDRLPKPGDSEFLSMERGYAEEPGGTGRSKNWLRIFTPVRKTLLLDLSTVKGLSPQLANLDNFEGMQVSDDNFSARQRTAFLLFRIREPRRGPSLPSRPAPAPIAGLDLVGEFDGLAVDPTTKEFLGICDDPGAPEGLDPEGIAISSYVRRLTIPSKFIPPATGPITQGVRDQDGELADWKQGTIARILEDFTPGFFINGLVELVALRISLEGASEISKLDSIAGARVFGPVLPDGARTLLV", "metadata": {"id": "A0A1F2U5D7", "cluster": 3612340, "interpro_all": ["IPR027372"], "interpro_used": ["IPR027372"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is a member of the Endonuclease/exonuclease/phosphatase superfamily, which comprises magnesium-dependent enzymes involved in intracellular signaling, DNA repair, and lipid metabolism. Representative members include DNase I, AP endonucleases, and sphingomyelinases, which share a structural core consisting of a beta-sandwich fold and a duplicated alpha+beta motif. It is derived from Nocardioidaceae bacterium and features UniProt keywords Membrane, Transmembrane, and Transmembrane helix.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 1920, 18697, 19, 24966, 19, 8167, 13975, 16, 2154, 12936, 13148, 17, 3100, 5038, 3286, 1922, 4776, 3197, 16, 2678, 5059, 16, 1930, 4486, 4714, 18, 5051, 4678, 3951, 12861, 51, 16, 2100, 18697, 1036, 16, 1930, 28057, 2319, 16, 2154, 7948, 43, 4346, 4728, 7600, 1927, 43, 4666, 17, 18038, 3728, 1930, 43, 19479, 4595, 15, 4666, 5219, 18, 2176, 1977, 3595, 2037, 9812, 3082, 2642, 9914, 14061, 1930, 4075, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MGKHTGRRVDPDARQGKLPFVYALSPRLLVAAVTLTALVGGGLAITQHDDVDQTQWENAKGVPMAEEVKLAGPDKVKLRHRPKPLDTPALRERVETLGQKLANTYANGATRTRAAAAKIKALGISVIGLQEYEPENHSAGIKGVRNSIAWNPSVWQLVESHTSTFPYFRGQPVPLPYVLLEHQVKQRGQNQHWRDVATAKEASLMRSLHAQTGYPVFLTGDFNEGIDWIFGTSDVSFSGYVRDDSTRGRISDHPLVYATATLDAIDNARAVTDLSGAVEPGSGETAGPTEFRIATLNVLGASHSDGGNAAKFVGATGWGVFPGMTMTGQRIWVMSVHNPVSNREEALHGVTRGGGVVAAGVS", "metadata": {"id": "A0A960AZ87", "cluster": 3709638, "interpro_all": ["IPR036691"], "interpro_used": ["IPR036691"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: It is part of the Glutathionylspermidine Synthetase/Amidase family, which comprises enzymes that catalyze the ATP-dependent formation of glutathionylspermidine from glutathione and spermidine, as well as its subsequent hydrolysis. These proteins play a crucial role in maintaining intracellular thiol redox balance and defending against oxidative stress, often functioning as bifunctional enzymes containing a characteristic C-terminal preATP-grasp domain. Additionally, some members participate in the synthesis of trypanothione, a vital antioxidant compound in specific parasitic organisms. Furthermore, the protein should contain 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. Also, the protein incorporates 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. It is present in Candidatus Levybacteria bacterium CG2_30_37_29 and contains UniProt keyword associations Magnesium 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, 2176, 1977, 3131, 1927, 1920, 8889, 2001, 2199, 3508, 2166, 5802, 18185, 19, 28813, 2051, 3416, 16, 2154, 12936, 5038, 1988, 18170, 1920, 4498, 17, 3100, 3337, 1927, 8889, 2001, 2199, 3508, 2166, 5802, 2037, 9153, 1930, 6283, 5802, 16, 1966, 2486, 1966, 2496, 4521, 9128, 18, 2144, 2697, 3918, 43, 6608, 2770, 1922, 8231, 4776, 13914, 9366, 6766, 1930, 30178, 10249, 1941, 3316, 5163, 3071, 16, 3868, 7295, 1966, 29491, 5038, 3165, 43, 6293, 45, 17, 4262, 2097, 24623, 17, 22815, 3418, 18, 4950, 16, 2673, 4678, 7352, 1922, 1920, 4271, 1927, 13479, 17809, 2290, 16, 43, 8970, 7335, 3547, 1922, 2487, 16445, 7373, 18, 3677, 16, 1920, 2213, 3066, 5531, 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, 2222, 16, 1920, 2213, 19683, 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, 2176, 1977, 2481, 1922, 14550, 1031, 1957, 10157, 16924, 2422, 2126, 14061, 7294, 1028, 41, 2627, 41, 3191, 41, 3230, 1930, 5461, 20709, 11121, 2538, 5253, 13148, 1930, 2733, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MAILLFVNFFLFASVTLAEQPPGFGKVLGEYNGEQVHYNGPSTYVDSGSSGYGITWQCVEFVQRFWAKKGWGPNRWGVNAFQMFDSKPSNATSFENGAGTAPVPGDVLVFSQAKFWSYGHVALVTGVSNGFVSFVQQNLGEKWTDKLPISAQNKIDSQGRYPLVRGWIHSQKNSAQNGKTPQPIPTSTAAAAATAKPSSGQATATATKIPNQQPIPGATPKQPTATSTRVPPTATATQTTRPTATATFTPQPTPTQRSSWPPVVTTNAATSVASTSAVLNSTINPNGASTNVNYAYGTSNVACASLPYTLSGPSGLTGSSSLSGASTQAMLSSLAPNTTYYFCVYATNASGTSYDSVLSFTTIAPRPPASVTIRTDKTSYRPGDRVLFCYTVSRPAPIVITDILADGRQQTILSGNDDGTGDCIEATATPPYGVETLRIDMYDGSVVVATANTSFTIIQDAVCSTVPPPPPNMRYIGGDTWTWDISPSSGPCKPFDWIVIISSGQTFTTSGQNRIVIHQGSDCVSLFAINSVGQSSNGGFCDPQ", "metadata": {"id": "A0A1J5FMX6", "cluster": 8185044, "interpro_all": ["IPR007921", "IPR003961", "IPR036116", "IPR051705", "IPR013783", "IPR038765"], "interpro_used": ["IPR051705", "IPR003961", "IPR007921"], "interpro_unused": ["IPR036116", "IPR013783", "IPR038765"]}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein belongs to the HTH-type transcriptional regulator with aminotransferase domain family, which regulates operons involved in amino acid metabolism, such as taurine and GABA, as well as vitamin B6 salvage and biosynthesis. These proteins typically combine a DNA-binding helix-turn-helix motif with a C-terminal class-I pyridoxal-phosphate-dependent aminotransferase domain, allowing them to act as dual-function transcriptional activators or repressors with potential enzymatic activity. Moreover, the protein should feature 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 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. It is present in Sinorhizobium alkalisoli and is connected to UniProt keyword Pyridoxal phosphate and Transcription regulation. 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, 14440, 1942, 1920, 5334, 1023, 17, 2601, 5224, 7888, 1956, 15817, 3418, 3416, 16, 2154, 7014, 28748, 3286, 1922, 3835, 2687, 4714, 16, 2427, 1966, 22769, 1930, 7992, 16, 1966, 2486, 1966, 6111, 11750, 17577, 1930, 8132, 18, 2144, 2697, 5745, 14003, 43, 2678, 17, 2743, 7864, 17, 5165, 17, 7864, 5219, 1956, 43, 45, 17, 4262, 2921, 17, 51, 24828, 23859, 17, 5413, 17, 3100, 15817, 3418, 16, 7201, 3581, 1942, 4033, 1966, 7064, 17, 2347, 5224, 15497, 2014, 26446, 1956, 2889, 8145, 2455, 18, 3950, 16, 1920, 2213, 3066, 5961, 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, 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, 2176, 1977, 2481, 1922, 3132, 14514, 2061, 23156, 25178, 2204, 12191, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 24828, 23859, 5413, 1930, 3213, 3640, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "MDLFSATNFVEMPSTATAVGQRSEHGRNKRCDDHGSRYKGMVDAGPQCTSIVSPLLWPRLASYWPVRNIQFGGKKVVQSEKQVATGRAPKMGARRTYEAIKHQILRRVYEAGSQLPSSRSLANGLHVSRTTVTVVYEQLAAEGASWNCTRARVHAVTA", "metadata": {"id": "A0A1E3VDU0", "cluster": 9196521, "interpro_all": ["IPR051446", "IPR000524", "IPR036388", "IPR036390"], "interpro_used": ["IPR051446", "IPR000524", "IPR036388"], "interpro_unused": ["IPR036390"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: 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 expressed in Pyricularia oryzae (strain P131) (Rice blast fungus) (Magnaporthe oryzae). 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, 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, 3198, 1922, 6487, 4588, 2126, 27597, 12, 3943, 8632, 6800, 13, 12, 8674, 7851, 16461, 13, 12, 3679, 10552, 20536, 27597, 13, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MLGSTTVKSSSASHNRLDLVECRQTQCLLRGGKTILLYTKRPAADFTLFDERQIPKGLDQSLGIKIALPPSDWPQLILNLHAQITSKLGSTGCLEWLGLSATGSLARGRLLDYAAGHSLVTEALVHHFTAAVGIDVSEAMVDQYRAEELSPIPVVKKKAQLFCVIATKK", "metadata": {"id": "L7J0X5", "cluster": 9455140, "interpro_all": ["IPR029063"], "interpro_used": ["IPR029063"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to make a polypeptide chain that will have the following function description: The protein is classified under the RloB-like protein family, which participates in diverse bacterial antiviral defense mechanisms, including restriction-modification and abortive infection systems. This family encompasses proteins such as RloB and the plasmid-encoded AbiLii, the latter of which is required for phage resistance, while other members are annotated as CRISPR-associated Csm2 proteins. It occurs in Phocaeicola coprophilus. 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, 5947, 2441, 1920, 11929, 2389, 17, 3189, 2213, 3416, 16, 2154, 17241, 1922, 6445, 4543, 10129, 9720, 3531, 16, 2710, 7587, 17, 6295, 1930, 11380, 2185, 2909, 3771, 18, 2052, 3416, 21569, 2697, 2427, 1966, 11929, 2389, 1930, 1920, 5609, 17, 7905, 13127, 12191, 1033, 16, 1920, 6296, 1927, 2154, 1977, 3414, 1958, 10503, 3554, 16, 2679, 2303, 4678, 2032, 10633, 1966, 12509, 17, 2458, 30141, 1028, 2697, 18, 2176, 5110, 1922, 20175, 3375, 14209, 4879, 5148, 3725, 2789, 1970, 1957, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MTKREGMEQIRPLEYTIKIYGEGFTEWFYFDGLRTNNRFRFSMVPEVPKNSRSSYKQNLKLIDKELKKKPQERADALFLVIDTDTLVNNKEQYNLYLATKEKYKKQGVIFIESHPCIELWFLYHLADRFARTNYETYEALRPAVEKVLPGYDKTARYYQKNQFFRENILMDTTKRAQAIDYAIRSCKYTPVANEIANYSEIFKAIHFFRLLQKFVEIRTMLAEHLRRPIYLSHEIEQHKQLHVYWEEKDNKQLCCTLKYKEAKLFCFFADGTVFEMNDREPLTHAPEIISRIELTINQL", "metadata": {"id": "A0A413SXX6", "cluster": 10393239, "interpro_all": ["IPR025591"], "interpro_used": ["IPR025591"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein belongs to the Carboxypeptidase-like, regulatory domain superfamily, which constitutes a regulatory $\\beta$-sandwich module found in eukaryotic M14B metallopeptidases, such as carboxypeptidase D and E, and teneurin signal transducers. This domain adopts a Greek-key topology and shares structural homology with bacterial outer membrane proteins involved in nutrient binding. Additionally, the protein is a member of the TonB-dependent receptor-like family, which facilitates the high-affinity, energy-dependent uptake of scarce nutrients such as iron-siderophore complexes and vitamin B12 across the bacterial outer membrane. These proteins feature a C-terminal $\\beta$-barrel and an N-terminal plug domain that acts as a gate, interacting with the inner membrane TonB complex to energize the active translocation of substrates into the periplasm. It originates from Acidobacteriota bacterium and is linked to UniProt keywords Cell outer membrane, Transmembrane beta strand, and Transport.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 14440, 1942, 1920, 15750, 9626, 2410, 9200, 17, 3189, 16, 4948, 3418, 13975, 16, 2154, 14879, 43, 4948, 8, 38, 4666, 8, 17, 18038, 9059, 2435, 1922, 10825, 8510, 14919, 8969, 24897, 1036, 16, 2427, 1966, 15750, 9626, 2410, 9200, 46, 1930, 47, 16, 1930, 5656, 3708, 5572, 2733, 26307, 18, 2052, 3418, 24032, 43, 27568, 17, 3834, 13678, 1930, 16495, 4346, 9039, 1956, 4543, 7642, 3260, 2697, 3286, 1922, 8708, 2743, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 16501, 1014, 17, 3100, 3148, 17, 3189, 3416, 16, 2154, 11374, 1920, 2149, 17, 5173, 16, 3844, 17, 3100, 5047, 1927, 16937, 11312, 2427, 1966, 5680, 17, 22940, 11082, 5048, 1930, 6111, 17492, 3436, 1920, 4543, 7642, 3260, 18, 2144, 2697, 5961, 43, 45, 17, 4262, 8, 38, 4666, 8, 17, 19560, 1930, 1925, 56, 17, 4262, 15998, 3418, 1988, 8016, 1966, 43, 11898, 16, 8615, 1956, 1920, 6671, 3260, 16501, 1014, 2796, 1942, 2066, 2693, 2606, 1920, 3500, 7849, 1927, 6249, 2460, 1920, 20171, 18, 2176, 22970, 2037, 2687, 5883, 3940, 3857, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 2024, 7642, 3260, 16, 9117, 4666, 5984, 16, 1930, 4860, 18, 3], "output": "MVQHSAGTSKAVECRVPTGFDRHRVSALILLPRVLSPPKRSRIRAFQFSVVGIGHGQQGGPVKNARLREISGFVLLCCTASLGQTNSGRILGTIRDQTGAVVAGATIVITDLERGASRRVTSNEVGEYVAADLPPGLYKVSVQAPNFKRAERPSTRLEVARDVHLDLQLHPGAPNEVVEVTDEAPLVETTNDTLGGTFTNKAINDLPLNGRDFQNLVVLRPGVQRYPGGGFLSISSNGNLPEDNNVIIDGVDNNDPYYASTVINAEGVQGTPATHLPIDAIQEFNAQENPSAEYGWKPGATINIGLKSGTNSLHGSTYYFGRNSALDARNWFNQRPDPQHPLRTHQFGATIGGPLVPNRAFYFLAYEGVRAVIGNSEILATPVTSSLGAVPSARFDSIPDAMASLSSHGVPINSISSTLVALFPQNNSSSTDIPLGFPNQTREDNGLAKLDFHLGERHVLTARYLVGDSLQTERDIPVLRPEWQSQAVTRAQLAGGTWTWTPASRWANEAKFGFNRFWQTILTVDHGRDPQTYGINTGITDPINFGMPQISIFGFTPLGGNPNWPLETIPSQTLQGSDNVSYIRGRHTLRFGGEIRHGSTSNLRDRYGKGRIRFIGGNAWRSPEMETQSSPLEDFLAGLPDTGRIFVGDSRRHVSLKSFGAYVQDDLRMSSRFVMNLGLRYELSSTIRERENLLGNFDPNRGLVQVARDVSTPYNIDPNNFAPRVSFAWDPTGKSNTVIRAGAGIAYAIPPISTFIGPKSLTTNAATEGLNVVPTGAAGVTPGGGNIVAAATNVDLDLSAQTWGPSNPVFNVTNIDCSASPCDILGVRRNLETPYVASWNFNIQQRLANNMSLQVAYVGNKGTKLYSVYDINQVDPARDTGDEQSGRPLTYNCPTPVVVGPGCFPFLRFVNFLSNGYESKYHALQATLTERSWRGLYFLAGYTWSHALDQASLNRPRQPQDSLHPEREYGNSDFDLRQRFTLSLTYELPSREGWGQLLEGWQINSIVVMQTGLPWGVIDGYLGGNDVSATGEFSDRWNFTGNPADFKPSPFGPIAYVSPADFGFNKITNQVTTTDPNGQRCIDSAGSPAAADALARFGCYVQGSGILTPPARGTFGTMRRNIFRGPAYRNWDFSIVKNWRIGDRIIAQVRGEFFNILNHPNFSNPYGVGGQLGNVDPSVPSFFGFASATPDVAAANPVMGSGGPRAIQIGLKLRF", "metadata": {"id": "A0A2V9Z2U2", "cluster": 10954936, "interpro_all": ["IPR008969", "IPR039426", "IPR036942"], "interpro_used": ["IPR008969", "IPR039426"], "interpro_unused": ["IPR036942"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein is included in the Type IV secretion system pilin family, which constitutes the structural subunits of the Type IV secretion system (T4SS) pilus. These proteins assemble to form the extracellular filament or channel required for the translocation of DNA or virulence factors across the cell envelope. It is produced by Candidatus Colwellbacteria bacterium RIFCSPLOWO2_02_FULL_44_20b and is connected to UniProt keyword 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, 1977, 3063, 1922, 1920, 2601, 4370, 5512, 2433, 7547, 1921, 3416, 16, 2154, 14879, 1920, 4346, 6991, 1927, 1920, 2601, 4370, 5512, 2433, 12, 10773, 5590, 13, 7547, 1957, 18, 2144, 2697, 17421, 1942, 2386, 1920, 5329, 10797, 2014, 4999, 3414, 1958, 1920, 7849, 1927, 2678, 2014, 9304, 2790, 3436, 1920, 2024, 11262, 18, 2176, 1977, 4152, 2007, 14550, 1031, 1957, 2503, 11324, 7972, 2341, 18339, 14061, 12424, 2792, 2030, 1971, 5265, 41, 5725, 41, 4125, 41, 4044, 41, 2036, 1014, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MIFSPFVKTAYAQIASTDTKLDIMRVINEVICSFKLANIFTYAIGLGGLIALAIMIWAWGLLLLFGGWMILYTINPGIVGRCKINLPGLTFSGGGEGFLYITSATNPSKATESKEWMKAAI", "metadata": {"id": "A0A1G1Z6H0", "cluster": 11393570, "interpro_all": ["IPR043993"], "interpro_used": ["IPR043993"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein features a RelA/SpoT domain that functions as the catalytic core for the synthesis and hydrolysis of the alarmone (p)ppGpp, regulating cellular responses to stresses such as amino acid starvation and carbon limitation. Belonging to the Pol beta-like nucleotidyltransferase superfamily, this domain utilizes a conserved two-metal ion mechanism to catalyze the production of (p)ppGpp from ATP and GTP/GDP or its degradation. 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. It is found in Aliarcobacter butzleri L352. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 4075, 43, 22247, 19, 9177, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 1920, 4271, 1930, 9128, 1927, 1920, 19065, 2290, 12, 58, 13, 23166, 9434, 16, 6773, 3689, 3387, 1942, 11962, 2427, 1966, 3835, 2687, 12767, 1930, 5056, 7789, 18, 10588, 1942, 1920, 2492, 4666, 17, 3189, 2797, 4090, 2199, 9961, 13975, 16, 2052, 3418, 18127, 43, 5305, 2288, 17, 6048, 4755, 2856, 1942, 18170, 1920, 3372, 1927, 12, 58, 13, 23166, 9434, 2037, 4498, 1930, 9319, 19, 15217, 2014, 2496, 4877, 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, 2176, 1977, 2435, 1922, 15356, 5332, 5883, 2308, 26262, 18842, 15859, 8982, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MTEIEFRQKYESEKHIFQAWGNFVSEKIINTLANEGIDSSKFLKINVSTRIKEADSLIAKAFYRSKNYKNPYDDITDKVGARFVALLDDDVRKLCSIIENISEWTYSKDRDYETERADEPLSFNYQSMHYVVKSKNSIFFQDVTIPVNIPCEIQVRTLLQHAYSELTHDRVYKTSFDPTSEVKRAVAKSMAFLETTDEYFQKVSNLMLDLPIFKLYDGLRERFSTIYPQFKDGSKVNIHILHAYYNFINSHNFSDFTIFNDLDEIVKFNIDKTYLNNQPVIYFIYYMCLHQKNILKKNWIYTNEELHPYFTHLGISFD", "metadata": {"id": "A0A837JCW0", "cluster": 11782461, "interpro_all": ["IPR043519", "IPR007685"], "interpro_used": ["IPR007685", "IPR043519"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein incorporates 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. Also, the protein falls within the Type I restriction system S subunit family, which functions as the specificity determinant for type I restriction-modification complexes by recognizing distinct DNA sequences. These proteins direct the complex to target sites, facilitating either ATP-dependent DNA cleavage or protective methylation in concert with restriction and modification subunits. It has been characterized in Bacteroides xylanisolvens XB1A and corresponds to UniProt keyword Endonuclease, Hydrolase, and Nuclease.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 19683, 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, 2222, 16, 1920, 2213, 12182, 2651, 1920, 2601, 51, 7587, 2433, 61, 5903, 3416, 16, 2154, 4088, 1966, 1920, 4896, 12483, 1958, 2601, 51, 7587, 17, 6295, 5048, 2007, 15667, 4493, 2678, 3709, 18, 2144, 2697, 3083, 1920, 2796, 1942, 2758, 3402, 16, 12440, 3108, 4498, 17, 3100, 2678, 6404, 2014, 6337, 5547, 1922, 21799, 1956, 7587, 1930, 6295, 6991, 18, 2176, 2258, 2252, 4378, 1922, 27978, 23665, 23854, 14937, 2099, 20584, 6146, 1930, 8852, 1942, 20709, 11121, 2538, 18697, 16, 20748, 16, 1930, 16230, 18, 3], "output": "MELKKYKKKRITPQGWKEITLAEVFNTSSGATPLSTEASYYENGTIPWINSGELASPYIYDTTNFISQAGFENSSTEIYPIDTVLVAMYGATAGKASLLKMEACTNQAICAILPNKDYSSTFLKYSIDTLYDHLVGLSSGSARDNLSQAELKKLKLIMPPTKNEQNKLVSILASIDRKIELNQAINQNLEAMAKQLYDYWFVQFDFPNEEGKPYKSSGGEMVWNEELKREIPALWETKEVADIANVYNGATPSTVDELNYGGDIVWITPKDLSDQKQKFIYQGERNISQVGYDSCSTHLLPSNTILMSSRAPIGLLAIAKNELCTNQGFKSFVPKYRNIAIYLYYYLQYHLRQIEQLGAGTTFKEVSREDIIKFPVLKPSDNILDLWEERVSAFNDKQLEIQKENENLTKQRDELLPLLMNGQVSVNSDLSDD", "metadata": {"id": "D6D2H3", "cluster": 14687916, "interpro_all": ["IPR000055", "IPR044946", "IPR052021"], "interpro_used": ["IPR000055", "IPR052021"], "interpro_unused": ["IPR044946"]}, "task_type": "autoregressive"} {"instruction": "The desired role of my protein is: The protein is grouped in the Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase superfamily, which comprises metalloenzymes utilizing a \u03b2-\u03b1-\u03b2(3) motif to coordinate metal ions for various catalytic processes. These enzymes perform diverse functions ranging from isomerizations and epimerizations to the oxidative cleavage of C-C bonds and antibiotic resistance-associated nucleophilic substitutions. It is present in Mesorhabditis spiculigera. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 1977, 10809, 1922, 1920, 3376, 23859, 2051, 19, 23004, 3554, 2213, 19, 20684, 3821, 17616, 2199, 23652, 10465, 2432, 2051, 13975, 16, 2154, 12936, 8969, 6802, 1022, 16367, 10232, 43, 161, 17, 160, 17, 161, 12, 23, 13, 5219, 1942, 11865, 6048, 6982, 1958, 3425, 6804, 4028, 18, 2144, 5038, 2385, 6445, 4088, 6485, 2037, 27027, 1036, 1930, 13872, 9213, 7180, 1942, 1920, 5163, 6404, 1927, 45, 17, 45, 9031, 1930, 7267, 3554, 17, 2458, 24456, 10682, 18, 2176, 1977, 2481, 1922, 23577, 5004, 13385, 3678, 15776, 18021, 12191, 4938, 1019, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MRFARRSEWQEQGSLAGPLRRGRLGQGYHGREAISKFYDMTIAIADKLGASDRRFTGRAATVPGHRPGPLSSYSNQPVVLGTENPEMVSGCQRRVSHDGLRQAWRRRTVQGVTRRPFLFNHTIIAAKDRQESAWFFTHMFGLPGPVEAGYFLGVELESIGHYAFLVSEDDFDGIYQRIQALKLDHWARSAPVEYRLPTPTTVGVGSTSSTRRDISRKRDHHASYGG", "metadata": {"id": "A0AA36C308", "cluster": 17360913, "interpro_all": ["IPR029068"], "interpro_used": ["IPR029068"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Give me a peptide sequence capable of: 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. It has been detected in Xylella fastidiosa subsp. sandyi Ann-1.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 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, 2176, 2258, 2252, 3330, 1922, 26130, 11560, 1019, 5867, 13756, 5360, 19615, 18, 9622, 16582, 5112, 17, 21, 18, 3], "output": "MQTTYLLQRSNPPRLLARLPLGGKPCVAGCGDTVGVGAGPTVTTELPASVQELADVIGRKQALTLIGQLPRTYPKGRRSGKVILYVPKALSPHHRLVSILGWEDAQKLVDVFGGEILQPANCNYIARHARDCAVVELLRSGVPFDVIAKIFGISVRHVRNFAAGISSHPPRKTCHRTYAQDTRRMSGNECLRGLSCRPLVKKALH", "metadata": {"id": "A0A060H6I6", "cluster": 17441799, "interpro_all": ["IPR009057"], "interpro_used": ["IPR009057"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Function:\nIt is part of the Protein of unknown function DUF2971 family, which comprises bacterial proteins with no currently known function. It has been characterized in Pseudomonas savastanoi pv. phaseolicola (Pseudomonas syringae pv. phaseolicola).\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 2176, 1977, 3131, 1927, 1920, 2213, 1927, 5435, 2347, 4855, 6680, 8528, 1009, 3416, 16, 2154, 12936, 4543, 2697, 1956, 2239, 5077, 3171, 2347, 18, 2176, 2258, 2252, 4378, 1922, 13461, 13243, 2197, 9286, 1033, 5774, 18, 3193, 4485, 10173, 12, 13461, 19468, 3336, 5774, 18, 3193, 4485, 10173, 13, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MRKFIYRYKYLPDMMGIEGVIASGLKAKNPTMYSVIGGEIQHPVDRLKATLLSDASVLSLSKVPDSILMWSHYAKHFETYYNLLPFDVKYSKARPTMEYSADPTDIFEYNRKHLNAVIIGAKNNELKQIHKTYSIKIPKFRKKKDSEKGTIKFTHPANFNDPFDCMPRSKFGDYSRSLRMLAQKVVKGEMVTDYHTGAVVEFKIPIDIGYERAETIVDTLFMTKSDVWAYEQESRVIKNYGGEGAMVKKASTEIGQEVGFFRAGFCD", "metadata": {"id": "A0A7Z6Y7E7", "cluster": 18519052, "interpro_all": ["IPR021352"], "interpro_used": ["IPR021352"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should contain a Dynamin GTPase domain that functions as the catalytic core for membrane remodeling proteins involved in vesicle scission, organelle division, and cytokinesis. This domain contains conserved motifs responsible for guanine-nucleotide binding and hydrolysis, with catalytic activity typically stimulated by oligomerization. Furthermore, the protein possesses a Dynamin stalk domain that serves as the central structural module between the GTPase and PH domains, mediating cross-like dimerization to orient the catalytic domains in opposite directions. This assembly enables the mechanical force generation required for endocytic membrane fission. Additionally, the protein includes a Dynamin, N-terminal domain that functions as the catalytic GTPase component of the dynamin superfamily, driving membrane remodeling events such as vesicle scission and organelle division. It hydrolyzes GTP to power mechanical constriction during processes including endocytosis, cytokinesis, and pathogen resistance in eukaryotic cells. It has been detected in Clonostachys byssicola. 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, 22653, 14809, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 3260, 8378, 2697, 3286, 1922, 11502, 30198, 2001, 16, 19309, 8451, 16, 1930, 20825, 18, 2052, 3418, 5461, 5305, 8277, 5061, 1958, 16904, 17, 5489, 2743, 1930, 9128, 16, 1956, 6804, 2455, 5745, 5449, 2007, 17371, 18, 3677, 16, 1920, 2213, 14465, 43, 22653, 19447, 3418, 1988, 10634, 1966, 1920, 4101, 4346, 9059, 2192, 1920, 14809, 1930, 2087, 4682, 16, 10239, 3567, 17, 3189, 13640, 1942, 5567, 1920, 6804, 4682, 1922, 8179, 10252, 18, 2052, 5957, 10217, 1920, 5821, 5495, 4841, 3414, 1958, 17674, 3260, 16150, 18, 4950, 16, 1920, 2213, 5921, 43, 22653, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 14809, 4594, 1927, 1920, 22653, 13975, 16, 9228, 3260, 8378, 3916, 2427, 1966, 11502, 30198, 2001, 1930, 19309, 8451, 18, 2176, 7222, 20887, 9319, 1942, 4215, 5821, 19837, 2409, 4028, 2710, 11914, 16, 20825, 16, 1930, 7055, 3554, 1922, 10825, 2094, 18, 2176, 2258, 2252, 3330, 1922, 6138, 2259, 2155, 2012, 2007, 5590, 29902, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MSPSDLQSKEHRDLLDIIDQLRSQGINRYVDLPEIIVCGDQSAGKSSVLEAISGMSFPTKDRLCTRFATELILRRDTDTSVKISISPGPDRHPEDRDHLSSWQPEADIEVDGLRVVIEEAKARMGLQGTKVFSSDILRIELCGPTQPHLTMVDLPGLFRSGNKEQSEDNVALVKALVTRYMSRPRSIILAVVSAKTEYVLQEVTALARSADPQGVRTIGLITKPDTLDNGSESQRSWVNLALNKDVELNLGWHVLKNRNYEERDYSSLQRDISEDEFFSTGIWTSIDPKHYGVKSLKSRLSSVLKDQILQQLPGLIKDVDHGIDDCNVKLSRLGAGRKSSREQLKYLSQLSHQFTSLMTSAVSGTYADTFFGSKNDLNEQRKRLRSVVQNRLELFAQDMRLTGESQLIVDDNEACYDDRQITRSQYVDDVRMRMMKSRGSELPGLFNPAIVSDLFAEQCQPWKGIVSSLTEDIVDAVYRTTRSIVEHIAANEVIREILILLNSEIDQLKVSMNDKVRELLQAQFALHSITYNPQLSENVQKVQWARKKRQLEKRIQEKFGFKSADEPGEKLIIDAPQMVELFLDETELDMIRFGSSMAVDYMQAYYQLARDRFIDDISVMAVERCLMSKLPGILTPIKAVELEDDELLRLVGESEESIDERLRLTEKLEILRNGLRDINRLYTDRGDEAPEVQAVQSTPASTIIQVQRSASVPSELGKDEEEVHSPPPSSAGSSRGEFVG", "metadata": {"id": "A0A9N9U2S7", "cluster": 18799529, "interpro_all": ["IPR022812", "IPR001401", "IPR045063", "IPR000375", "IPR030381", "IPR020850", "IPR027417"], "interpro_used": ["IPR001401", "IPR000375", "IPR045063"], "interpro_unused": ["IPR027417", "IPR022812", "IPR030381", "IPR020850"]}, "task_type": "autoregressive"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein features 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. Additionally, the protein is included in 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. It is present in Thermovibrio ammonificans (strain DSM 15698 / JCM 12110 / HB-1).", "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, 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, 4950, 16, 1920, 2213, 1977, 3063, 1922, 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, 2176, 1977, 2481, 1922, 7967, 2165, 2377, 3940, 9278, 2077, 2075, 12, 3943, 10964, 14198, 8364, 19, 14904, 1035, 11844, 2930, 19, 4873, 17, 21, 13, 18, 3], "output": "MVNEKLLLKNYNPKLFRRLKELGCEFEDVALVDPAEIVVDQGIYPRSKGDQFPPLIVTKKEGKLLLVDGNHRYFAHLKAGVKVVATICNVLGRGRAGKDLTGSEKKRGIIYAFSEGINTVMQKLAEDFETMKKRARELKEQGLSSRQIAERLSEEFGERIPDATVRTWLLSPTDTPTVRSTLDDPERLIQEEEEELLAVDAVAEEADGELSLKEKVEEEVIMELAELFYGKTTIGRLKAQEASAAIRKEQNGQKQPKLKSKEDIYKEVETLLQQWKDGSYTKDPFYRRGRAVYEVEYRRSTDTDRVEMYKEDLLPAEIWRIPGHEIRYTVSYVRKVLSQAGLIRDRKEEKNYPGKNSTLESTIGESVTQVRNAKRLVREEGLVPAEAYEKAGLPEDWERKDLDTINVQLARWESIAGREAVIELL", "metadata": {"id": "E8T2T2", "cluster": 22278771, "interpro_all": ["IPR003115", "IPR036086"], "interpro_used": ["IPR003115", "IPR036086"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What would the amino acid sequence be if I wanted a protein that could perform the following function: 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 present in Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58)) and contains UniProt keyword associations Plasmid.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 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, 2481, 1922, 26896, 6914, 24277, 12, 3943, 13441, 1025, 19, 11037, 24317, 4618, 13, 12, 26896, 30258, 25018, 12, 3943, 13441, 1025, 13, 13, 1930, 5461, 20709, 11121, 2538, 5253, 5609, 18, 3], "output": "MVAELVEITNVVSFLFLPKTRYLTGSVIDVNGGLY", "metadata": {"id": "Q8U5T1", "cluster": 26353646, "interpro_all": ["IPR036291"], "interpro_used": ["IPR036291"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein features 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. Also, the protein contains a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. In addition, the protein is classified under the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. It is present in Lachnospiraceae bacterium and is annotated with UniProt keywords Glycogen biosynthesis and Glycosyltransferase.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 4075, 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, 2222, 16, 1920, 2213, 5461, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 2176, 1977, 2481, 1922, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 13302, 8132, 1930, 20067, 9961, 18, 3], "output": "MKNILFVASECVPFIKTGGLADVVGALPYREKFQYVHHFYMDLGQRFENVHVGIMTYIRFDIEKFTFFSKAALAILPVINFKPDVIHCHDWQAGTIMTIHNLKFQGVWDVKTFKYISGLPDYVFTPDRMEFYKDGIQTPEYGEGLDDLLRFHNQKLCGIVNGIDYDVYNVRSYKKGKATNKMELQKELGLPVDENKMEGIVDPYVQFVVIGTGEAKYENMFKHYQWVYSDRVSANIFYSLRYGTVPIVRETGGLKDTVIPYNEYEGTGTGFSYDHRDEWNRMVVRDMKEDFSWDKSAVKYMQLYDKVLGYKMFPKDQYDVRVVLPNYTCIPWEELDGITYYFIDNEYYFSGWAPYGTLVPVYLHTLYEGNSFFSGTKNMLKAGMVYSDYITTVSDTYAGEDPNTDGKIFKNYYMIAIISRLTDQKGLDLIDWVDERAHKLYAAADAMLMPSRFEPCGLTQLISFTNYNADEMLKIINYSKEVY", "metadata": {"id": "A0A3D2KHP9", "cluster": 6894681, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR001296", "IPR013534", "IPR011835"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the protein function: The protein is assigned to the Phosphoribosylglycinamide formyltransferase family, which catalyzes the third step in de novo purine biosynthesis by transferring a formyl group from formyl tetrahydrofolate to generate 5'-phosphoribosyl-N-formylglycinamide. While found as a standalone enzyme in prokaryotes, this domain typically occupies the C-terminal region of a multifunctional protein in eukaryotes that also exhibits GAR synthetase and AIR synthetase activities. Also, the protein possesses a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. It is produced by bacterium. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3416, 16, 2154, 17097, 1920, 4563, 3537, 1922, 2028, 9441, 19700, 8132, 2007, 21902, 43, 29285, 2210, 2037, 29285, 21196, 27851, 1942, 5655, 25, 11, 17, 3421, 2023, 11731, 17, 56, 17, 29285, 17038, 3665, 5482, 18, 2679, 2435, 1966, 43, 2924, 20807, 2912, 4113, 1922, 28149, 16, 2052, 3418, 5745, 28646, 1920, 45, 17, 4262, 3031, 1927, 43, 20136, 2213, 1922, 15021, 1988, 2222, 9826, 13139, 18185, 1930, 4433, 18185, 4209, 18, 2222, 16, 1920, 2213, 14465, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2176, 1977, 4152, 2007, 14061, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MKIGIFISGTGTNMAAICRNFAEKKLKGIDEISFVLSDKRNAPGLEKAESFGIKTIVLPKKKDEPKEDYETRLLEAVQPFGTGLIVLAGFMKVLGHTFLSGYDGKIINIHPSLLPSFKGVDAQGQAFDYGVKVSGCTVHFVDETLDGGPIILQQPVFRLSDDTKETFKARILEQEHILLSRAISIVANGEYSISGRQVLLSNKEEL", "metadata": {"id": "A0A939WX50", "cluster": 13255604, "interpro_all": ["IPR002376", "IPR036477", "IPR004607"], "interpro_used": ["IPR004607", "IPR002376"], "interpro_unused": ["IPR036477"]}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe 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. In addition, the protein is grouped 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. It is derived from Desulfotignum balticum and is annotated with UniProt keywords Transferase and Two-component regulatory system.\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, 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, 1922, 2459, 16, 1920, 2213, 1977, 10809, 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, 2176, 1977, 3595, 2037, 30311, 13323, 3223, 1989, 4641, 2002, 1989, 1930, 1977, 10633, 1956, 20709, 11569, 13763, 1930, 2288, 17, 4594, 4948, 2433, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "SETAGKTHIDAARVLEACLYFLKPVWGDENQLQQMFINLLLNAVESMNGEGTLRKIEDSGKGVPKELRTQIFDPFFTRGKTQHDSRLGGAALTVTLPSTSRKTTKKENHAFTDRRLKKITVIQDLTLEIHWVSGTTVTDTVSDRHCIGVGLGLFVAQRIAAQHGGTICV", "metadata": {"id": "A0A931CWF1", "cluster": 1687561, "interpro_all": ["IPR036890", "IPR005467", "IPR004358"], "interpro_used": ["IPR005467", "IPR036890"], "interpro_unused": ["IPR004358"]}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein carries a Potassium channel domain that facilitates the selective transport of potassium ions across cell membranes. It is a conserved feature found in a variety of ion channel proteins, including bacterial two-transmembrane helix types, where it forms the essential pore structure for ion conduction. Additionally, the protein incorporates a Coiled-coil domain-containing protein 124/Oxs1, C-terminal domain that mediates conserved stress responses and cell cycle progression. It functions as a transcriptional corepressor by binding bZIP transcription factors, such as Pap1 and cJun, to regulate disulfide stress tolerance, while also serving as a centrosomal component involved in cytokinesis in animals. Moreover, 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 Pseudocohnilembus persalinus (Ciliate). 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, 16252, 43, 9057, 4999, 3418, 1988, 11374, 1920, 5328, 4860, 1927, 9057, 6982, 3436, 2024, 5726, 18, 2176, 1977, 43, 5305, 5961, 2435, 1922, 43, 5386, 1927, 4755, 4999, 2697, 16, 2710, 4543, 2288, 17, 9117, 7864, 3584, 16, 2597, 2176, 4952, 1920, 4415, 8554, 3170, 1958, 4755, 12382, 18, 4950, 16, 1920, 2213, 19683, 43, 17524, 17, 9121, 3418, 17, 3165, 2213, 10955, 19, 2833, 12030, 16, 45, 17, 4262, 3418, 1988, 10412, 5305, 3071, 3387, 1930, 2024, 4048, 4380, 18, 2176, 4088, 1966, 43, 5224, 4728, 29079, 2007, 2743, 30450, 3213, 2790, 16, 2427, 1966, 3860, 1009, 1930, 19090, 1983, 16, 1942, 5741, 11830, 3071, 6555, 16, 2679, 2222, 13915, 1966, 43, 14783, 4229, 4594, 3286, 1922, 20825, 1922, 3555, 18, 3950, 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, 11520, 4879, 11619, 2383, 17010, 1957, 3096, 18130, 1957, 12, 15714, 2057, 13, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MNLSINQDPNKSQTYLLQNPNTKQGHIMKKHFNPQIDNNLKEMHYKLSNQNLEISIDQSIQNLKLEQGQDQFQDKSIEEENSETSIYNLDNPKTNKSKKNTYLQKQTTINSTRTHKKLNYTSTKLKSKSKLENFLTKKNSIFNLKKQKTQKINSPDDLNRYLYEYPDSFLEKPGQKFLKFRLIEFLQKQINNYNQLTQTPNKTFYTKQNYNNSLINPDQQKTINFAKNQSKQYSQVLNSPFRLQTQNKLYSIRHRSSKKGLNIVWQAKGILILSSIIKFISILKGMSIEHRSVQILKNIEHISDTLSLKKKHRAIFDLIKLTIIILLIAHLCGCIFVYVALVQKQQNIKETWIEVAVVESNILIDLNSWFDIYIASFYFSVITMITVGYGELYPINNLERFITILITILSCGVFAYSVNEIGTIFKLMKQQKEEFKEEQAILVNHMKRKGLSKDLQNRVTKYYEYIYNENLQEKQIGDRLIQNLPYSLAQSIKFEFNYQIFSEQKLLLNNFSEAFVKKLANTAKENRFGPEHEIIKEGHEVSDLFFITSGSVDLFQQVGKKQIYVKTIHKQDGIGNYFFISQQYSTLTAKTKNVVGLISVSKQDFLNCLKEFPPDFEHYSMMRDNIIFYKSNRQIHEKCKICDISDHIDIKQCPFISFVPNKYQIINKSLNIGLYQERISFNKRREGRYENYKAQFQLLKESVYFFMISNYPEVELHHIFKQNVEYLNRDLSRKFSRNYSKNYSYSINGTNTVSGRPQFNLHNIPHSHNGLTSQLSNNLQATNLIQQNDLIKSSSKQQMAQSQTQSPRSQYGSQRQSQEDYDPASNNNLYEPLQQQMYQSFNLEQVELQNNKYNSLGRERSFEQDVQSQFHRKTRKNLTTEIATKFNNSFIQEYDQSSQYTDNNKSTFYKNLKQDTNYQSYVDTSSYYQGGLQQQQTQQTMHDTSYMKQNTLQNMHTNFFNNINQQIVNISEDDKLLLKFLKFKNKESIIGFDTMKIFNYYYTRGNLDRILEFLDEKRAVEKQEREKEQKQKKQREEEERKTQEFWRDDDKQLQKKQQRKEEKQEKQLEQLVKKQENKLLYEKDMAEIQGNKKSKVKETPKQEALRKQREALKQTLLAQIQQQKEQEKKNKLQVQKEEEKEFREEHGHIVDSDSDSSENEYKLKLEENLNRLQIQDDEDDKAQQETINRPEKKRKAAFRDFVDKRMPELRQENPKAKRSQLLEMIHKEFEKSPENPMNQQ", "metadata": {"id": "A0A0V0QIP6", "cluster": 1807810, "interpro_all": ["IPR054414", "IPR000595", "IPR018490", "IPR013099", "IPR050818", "IPR014710"], "interpro_used": ["IPR013099", "IPR054414", "IPR000595"], "interpro_unused": ["IPR018490", "IPR050818", "IPR014710"]}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein possesses 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. It is found in Hydrogenoanaerobacterium saccharovorans and is connected to UniProt keyword Membrane, Zinc-finger, and Metal-binding.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 14465, 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, 2176, 1977, 2435, 1922, 6201, 6952, 26243, 15129, 18417, 14175, 15742, 15525, 17182, 1036, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 7997, 17, 8497, 16, 1930, 6048, 17, 2743, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MKILFMSKRSKWGIVLILLSLILFISLLFPSITSELSLPIFDYIYCLLPIESLWKRWEITNNSEDQKRRMLRALLDKLTLIKIDKKTLNGCTCMDFLKRRVPCKHMYKLAIELGAFEPSDDLKIAAQRIADSGDYYEDFYKSTLVLLIVGVALIIPEISFRYAKYAGSTGGTYIT", "metadata": {"id": "A0A1H7YGK0", "cluster": 4418929, "interpro_all": ["IPR007527"], "interpro_used": ["IPR007527"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is a member of the ABC transporter, BtuC-like superfamily, which constitutes the transmembrane permease domain of ABC transporters involved in the import of substrates such as vitamin B12 and ferric dicitrate. These proteins feature a complex multihelical architecture that forms a gated translocation pathway and interact with cytoplasmic ATP-binding subunits to drive transport. Also, the protein is a member of the Cellular Amino Acid Transporter family, which mediates the transmembrane transport or exchange of diverse substrates, including large neutral and cationic amino acids, thyroid hormones, and L-DOPA. Often functioning as heterodimers with SLC3A2, these proteins play critical roles in nutrient absorption, mTORC1 signaling regulation, and neurotransmission. They belong to the L-type amino acid transporter (LAT) lineage within the amino acid-polyamine-organocation (APC) superfamily. Furthermore, the protein falls within 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. It is found in Acidobacteriota bacterium and is classified with UniProt keywords Cell membrane and Transmembrane helix.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 43, 7210, 1927, 1920, 7219, 9054, 16, 8626, 1978, 17, 3189, 13975, 16, 2154, 14879, 1920, 9117, 6191, 2051, 3418, 1927, 7219, 10538, 3286, 1922, 1920, 2582, 1927, 6249, 2427, 1966, 6111, 17492, 1930, 20247, 9192, 26813, 18, 2144, 2697, 5961, 43, 2796, 2779, 23285, 2046, 9335, 1988, 4952, 43, 12336, 7849, 3374, 1930, 6310, 1956, 6823, 4498, 17, 2743, 6991, 1942, 9265, 4860, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 3689, 3835, 2687, 9054, 3416, 16, 2154, 10412, 1920, 9117, 4860, 2014, 6818, 1927, 6445, 6249, 16, 2710, 3103, 5459, 1930, 15175, 3835, 4576, 16, 6918, 10224, 16, 1930, 54, 17, 19428, 18, 3868, 7295, 1966, 21523, 1956, 12150, 6675, 1028, 16, 2144, 2697, 3918, 4140, 5456, 1922, 8708, 6726, 16, 13694, 3197, 3640, 16, 1930, 20221, 18, 2611, 6784, 1942, 1920, 54, 17, 2601, 3835, 2687, 9054, 12, 4144, 13, 7924, 2651, 1920, 3835, 2687, 17, 27883, 17, 3090, 5980, 12, 9187, 13, 13975, 18, 3677, 16, 1920, 2213, 12182, 2651, 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, 2176, 1977, 2435, 1922, 2687, 5883, 3940, 3857, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MSIESTGAERRRLAWRVAVIGLCALLLAAAFVIALGSGSQSIAAVRLPRALVGALVGVNLAVSGTLLQGVVRSPLGDPYILGVSAGGGLAAAITSLELSGYAVAWDGSGVTTTRLALAGVALTAMIGAFTTTIVVMYTASWPEYELIRPYSAIGLELAGAKTRSLLDVAEEAVAFGRRNLPLSLMLGTTAVVLIYVSVNAIYIRALGSLGDTFVTAAIAISTFGFLDLGILAPTRVYYAMAADGVLTGRYEQLLNYVVFAAWLFFRLTLETILGDVIEALRDRESVRRSIAVIIHEFPREYVPITAFVGSLVGALIVNVQGGGQIFFQWLVGGLAALVPILFAYGGWQNANYVAEEIENPLEGLAATTTPASKAAEMMFGFIPALAKLHPTYGTPWLAIAIQSTWTCVLA", "metadata": {"id": "A0A3N5GCR1", "cluster": 4922010, "interpro_all": ["IPR002293", "IPR037294", "IPR000522", "IPR050598"], "interpro_used": ["IPR037294", "IPR050598", "IPR002293"], "interpro_unused": ["IPR000522"]}, "task_type": "infilling"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein has a Cation/H+ exchanger transmembrane domain that mediates the counter-transport of protons and cations, such as sodium or potassium, across lipid bilayers to regulate intracellular pH, cell volume, and sodium concentration. This region contains conserved membrane-spanning segments responsible for ion translocation, effectively removing excess acid from metabolically active cells. It plays diverse roles ranging from conferring salt tolerance in microorganisms to facilitating NaCl reabsorption in mammalian epithelia. Also, the protein can be placed in the Sodium/solute symporter superfamily, which comprises proteins characterized by a Na+/H+ antiporter-like structural fold. These members typically function as symporters, facilitating the co-transport of sodium ions and various solutes across cellular membranes. It is present in Gammaproteobacteria bacterium and is linked to UniProt keywords Ion transport and Transmembrane helix. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 2258, 43, 9976, 19, 50, 15, 27419, 9117, 3418, 1988, 10412, 1920, 5836, 17, 4860, 1927, 15948, 1930, 16525, 16, 2427, 1966, 5227, 2014, 9057, 16, 3436, 4486, 21992, 1942, 5741, 4776, 2087, 16, 2024, 3776, 16, 1930, 5227, 3110, 18, 2052, 3031, 5461, 5305, 3260, 17, 13346, 7492, 5061, 1958, 4755, 7849, 16, 7098, 11340, 5799, 2687, 2037, 21220, 3500, 2094, 18, 2176, 5705, 6445, 5456, 6485, 2037, 21510, 7012, 6555, 1922, 11679, 1942, 12440, 6392, 26287, 1922, 6492, 18546, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 5227, 19, 19661, 29148, 2718, 1915, 13975, 16, 2154, 12936, 2697, 4378, 2007, 43, 4049, 15, 19, 50, 15, 2246, 24095, 17, 3189, 4346, 3728, 18, 2144, 4678, 5745, 2347, 1966, 29148, 2718, 2045, 16, 12440, 1920, 2081, 17, 4860, 1927, 5227, 6982, 1930, 3425, 27993, 3436, 3689, 5726, 18, 2176, 1977, 2481, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 4755, 4860, 1930, 9117, 7864, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "KFSPERMRAWGRVALITSLVQAILTAAVTTLGLVLLGIEPAVALLLGGVACATAPAATFDVVREERAAGPLTDTLLGVVAFDDAWALLIFSLAAAAVAVMTGMGEGNGFLFHALREVGGAVLLGGVLGLVAGWLTQRIRPGEPTLLEALGIVLLTAGLATLWNLSFILAAITLGAVMTNVARHHERAFHEIEHIEWPFLLLFFVLAGASLHVDVLLGVGALGVAYVLLRVVGKIAGGVLGVALAGGDATLRRWLGPALLPQAGIALGLALIIEQRFPDIDGYLLSIIIAATVVFEIFGPPCTRLALRRSGEAGRARPDGDDETPYSP", "metadata": {"id": "A0A964X7R4", "cluster": 4952863, "interpro_all": ["IPR006153", "IPR038770"], "interpro_used": ["IPR006153", "IPR038770"], "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 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 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. Additionally, the protein includes 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 is derived from Sphingomonadaceae bacterium and has UniProt annotations Transcription regulation.", "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, 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, 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, 4950, 16, 1920, 2213, 5921, 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, 1977, 3595, 2037, 13502, 20050, 7324, 1972, 3336, 14061, 1930, 2258, 20709, 15010, 3213, 3640, 18, 3], "output": "MRTQIHNILAETGWSGSLPADVQGHEAIRQGSPFAGLLCVIEGEMQVVGTARRGDELLIGIRAARDSRIVRLGASATRRIFEQGLDRFKLLLRPYRPPMQRLAERMMGLGRWPYSIVDGEMTKCLRQMASHGLVRLGYKSVEVLDPVRVGMIANGEITLESEVIASVQSERVTRLRPGDWTGFLAALDQGEYAFSVELAVSRKNYSYFVETALEELSQADLANAARLSRQTTNT", "metadata": {"id": "A0A963SLQ9", "cluster": 7585223, "interpro_all": ["IPR000595", "IPR018490", "IPR012318", "IPR014710", "IPR036388", "IPR036390"], "interpro_used": ["IPR036388", "IPR012318", "IPR000595"], "interpro_unused": ["IPR018490", "IPR036390", "IPR014710"]}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein is a member of the Ion-translocating oxidoreductase complex subunit B family, which functions as an essential iron-sulfur component of a membrane-bound complex to couple electron transfer with ion translocation. Characterized by a 4Fe4S bacterial-type ferredoxin domain, this subunit facilitates electron transport and contributes to cellular energy metabolism and homeostasis. Additionally, the protein contains 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. It is produced by candidate division Zixibacteria bacterium RBG_16_53_22 and contains UniProt keyword associations Metal-binding.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 4755, 17, 12930, 2287, 27388, 2796, 5903, 44, 3416, 16, 2154, 4088, 1966, 1925, 4415, 5680, 17, 12585, 4594, 1927, 43, 3260, 17, 4124, 2796, 1942, 15116, 4995, 3856, 1956, 4755, 7849, 18, 4378, 2007, 43, 15338, 1021, 1006, 1036, 4543, 17, 2601, 25304, 22389, 10960, 3418, 16, 2052, 5903, 11374, 4995, 4860, 1930, 7624, 1942, 3689, 3844, 4714, 1930, 7622, 18, 4950, 16, 1920, 2213, 5461, 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, 2176, 1977, 4152, 2007, 6610, 8451, 28666, 18068, 7972, 2341, 18339, 14061, 6160, 1029, 41, 2641, 41, 4522, 41, 2950, 1930, 5461, 20709, 11121, 2538, 5253, 6048, 17, 2743, 18, 3], "output": "MSIKRIRVSPGKCSGCASLKIEAHFPQPGLYKPKVCSQCGKCLGECIPVCKPGVIFQHRDVIFTRPVRESARLCMQICAISHYDEINPKKEVCPEGAIYRRDDGAYIVIKAKCTNCDYVIICDNCFKCTELCNTGAIT", "metadata": {"id": "A0A1F4YMI9", "cluster": 8946738, "interpro_all": ["IPR017896", "IPR017900", "IPR050294"], "interpro_used": ["IPR050294", "IPR017900"], "interpro_unused": ["IPR017896"]}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein is a member of the Xylose isomerase-like superfamily, which comprises enzymes such as xylose isomerase and L-rhamnose isomerase that adopt a \u03b2/\u03b1 TIM barrel fold containing metal-binding sites. These proteins typically feature additional \u03b1-helical domains involved in tetramer formation. Moreover, the protein should feature a Xylose isomerase-like, TIM barrel domain that adopts a \u03b2/\u03b1 fold to serve as the metal-binding catalytic core for enzymes including xylose isomerase, L-rhamnose isomerase, and Endonuclease IV. This structural motif supports diverse biological activities, ranging from the isomerization of sugars like D-xylose and L-rhamnose to the cleavage of the DNA backbone during repair synthesis. It has been characterized in Rubrivirga marina. 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, 21055, 25510, 17, 3189, 13975, 16, 2154, 12936, 5038, 2427, 1966, 21055, 25510, 1930, 54, 17, 23120, 2217, 25510, 1988, 14103, 43, 161, 19, 160, 2267, 19560, 3728, 3165, 6048, 17, 2743, 3402, 18, 2144, 2697, 5745, 5961, 3281, 160, 17, 11514, 4682, 3286, 1922, 16798, 3337, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 21055, 25510, 17, 3189, 16, 2267, 19560, 3418, 1988, 24032, 43, 161, 19, 160, 3728, 1942, 7120, 1966, 1920, 6048, 17, 2743, 6804, 4728, 1958, 5038, 2710, 21055, 25510, 16, 54, 17, 23120, 2217, 25510, 16, 1930, 18697, 4370, 18, 2052, 4346, 5219, 7825, 6445, 3933, 4209, 16, 6485, 2037, 1920, 27027, 1927, 15592, 3189, 46, 17, 21055, 1930, 54, 17, 23120, 2217, 1942, 1920, 6404, 1927, 1920, 2678, 10787, 2409, 5059, 4271, 18, 2176, 2258, 2252, 4378, 1922, 10010, 3027, 3026, 4223, 13081, 2175, 18, 7031, 1920, 3244, 18, 3], "output": "MPFRDLRCQASRCPDASPLAPGFSVGAWYLGEADGRFHGTPLEADEVEARLEAAVSLAGYGGRGVVGVEASYPNEIHEGNLDLWRRALDGTGVRLAAVHPHLADDLGGALAHADDSVRQAAINRTAGALRLAREAEADLVAVWAGADGYVVPFGTDVVERRRRFVDGLAEAMDAAPGVRVALDAEPFEPRWRPLFGPAGGVVLARDVEASLGADENCQRLAEGHALVTMNPELGDGMEDEGDLPGTLAWSLAEGRLAHVHWSRWPLGRYLVAPGLDAPTPMEVGLYALRRGGYRGLIGLDVHPAGAPPVVALKVAMDAIRAACDRVNGLDLTALAEANDGRGRVGD", "metadata": {"id": "A0A271IY34", "cluster": 11266724, "interpro_all": ["IPR036237", "IPR013022"], "interpro_used": ["IPR036237", "IPR013022"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is included in 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 has been characterized in Rasamsonia emersonii CBS 393.64.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 3063, 1922, 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, 2258, 2252, 4378, 1922, 6520, 4645, 6114, 21672, 5810, 3907, 16341, 28179, 18, 4723, 18, 3], "output": "MEGSGGLHVQLCGYARKQEMAWISKSWVSSQIGRLQGLGSRARAQASTYINTASSYKLPEADIPVPRTKDLYADPSVNRSITMANPNTAFAVWDKSKDYKQPSQPFSTLPSQPTQPAAPAPSKNDTQTASDEPSNKKAMLKGAWKEGEDLRRDGSVQIYEEGWDPEAIAIVDYYKCIEVIEPFSERWIDQLKGRLASTPELRSIVLLASKHNRGPLQTLGLPIPEAVIDEIEHDLVDKIRTGKHKTYACSKNIECDSILLGALISYAETAKKVSKIRSPEWCTNNGHRCQTHSCSLFLPEDEEDDVSLFSEECQETSYLLNYQLNDFWSHCILADATSFARAPRSCPGSLEADALREFDPDGDVILVLKANSSTQSANPSSTQKTEEIQMKVSSHHLTLASPYFKLTIVMNIIHCHFRKVPRQVSHDMLAKIWVWISWMLRLKEDFKIATLEQRQQFIERLLDSLKEMDARHLSPRPCAPFLGLQSIILSNNIIESYNSVKRLELDD", "metadata": {"id": "A0A0F4Z1B2", "cluster": 11440459, "interpro_all": ["IPR011333"], "interpro_used": ["IPR011333"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that can perform the following function: 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. In addition, the protein belongs to the UDP-2,3-diacylglucosamine hydrolase LpxH-like family, which functions as a hydrolase to catalyze the fourth step of lipid A biosynthesis, converting UDP-2,3-diacylglucosamine into 2,3-diacylglucosamine 1-phosphate and UMP. Members of this family belong to the metallophosphatase (MPP) superfamily and possess a conserved active site featuring a binuclear metal center coordinated by histidine, aspartate, and asparagine residues. Moreover, the protein is associated with 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. It has been detected in hydrothermal vent metagenome and has UniProt annotations Cell inner membrane, Metal-binding, and Lipid biosynthesis.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 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, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 18500, 17, 22, 16, 23, 17, 25141, 13796, 1024, 22988, 17454, 20748, 8182, 1039, 1023, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 20748, 1942, 18170, 1920, 8776, 3537, 1927, 4486, 43, 8132, 16, 15025, 18500, 17, 22, 16, 23, 17, 25141, 13796, 1024, 22988, 17454, 2460, 22, 16, 23, 17, 25141, 13796, 1024, 22988, 17454, 21, 17, 5413, 1930, 8736, 1034, 18, 4678, 1927, 2052, 3416, 6784, 1942, 1920, 8969, 8630, 7234, 12, 23602, 13, 13975, 1930, 7150, 43, 5305, 3500, 3200, 29931, 43, 8768, 13821, 6048, 4102, 11651, 2007, 13873, 16, 12878, 16, 1930, 23677, 4248, 18, 3950, 16, 1920, 2213, 1977, 2458, 1956, 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, 2176, 2258, 2252, 3330, 1922, 26959, 14654, 16552, 2225, 1930, 2258, 20709, 15010, 2024, 6671, 3260, 16, 6048, 17, 2743, 16, 1930, 4486, 8132, 18, 3], "output": "MNTLIISDLHLSSDEDKKTLLLIDFLNQQQNTIQQLFILGDLFNVWLGDDISIQLFPKLIHTFKNSSFPIYIIRGNRDFLLDKKFAKLSNTTLIKEPYVFEDFVLLHGDSFCTDDIKYQQFKKIIQSPITKKIFLSLPKIIRQKIAVFLREKSTISNQKKPTFIMDINQQSVNKFMSKYPNKTLIHGHTHKQKIHKNPSFKRIVLGDWNNTKGNALILNDEIKFIEIS", "metadata": {"id": "A0A1W1CHJ1", "cluster": 11493455, "interpro_all": ["IPR004843", "IPR043461", "IPR029052", "IPR010138"], "interpro_used": ["IPR004843", "IPR043461", "IPR029052"], "interpro_unused": ["IPR010138"]}, "task_type": "autoregressive"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein is assigned to 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. It is identified in Arcobacter nitrofigilis (strain ATCC 33309 / DSM 7299 / CCUG 15893 / LMG 7604 / NCTC 12251 / CI) (Campylobacter nitrofigilis). 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, 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, 2176, 1977, 2899, 1922, 9952, 5883, 8686, 9344, 15291, 12, 3943, 11037, 23142, 13192, 19, 10964, 4395, 6576, 19, 4928, 2215, 14340, 11436, 19, 7735, 1029, 29854, 1006, 19, 10409, 1030, 11191, 7912, 19, 3371, 13, 12, 22657, 8686, 9344, 15291, 13, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MYIKSIYKQVNENKSAKEYRKDLKEISSLNFRRNSKLNVMAVYGALKALENIKYKDNLSIYLASEYGCIEDLLKVLNQINSKESFVMPFDFLNVNTNNTGFLISQALQTIGNNINVSSEDLSFEKAFELAYFDFHFKKVDEILVGGVDESLDNVSNHNSFINNLDNLDSKDGSSWLYINNDKTNSLTEIKHFEFFTNLEELNKYLKTIDYKIVGLNQFAKKYVSELQIDKNLIYKSKNNFCGTYSVPDIIDLLKEKEESSVYISLDSKKRAYLFFFKCD", "metadata": {"id": "D5V102", "cluster": 13964767, "interpro_all": ["IPR016039"], "interpro_used": ["IPR016039"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein includes a MYND-type zinc finger domain that functions primarily as a protein-protein interaction interface, particularly for the recruitment of transcriptional co-repressors like N-CoR and SMRT. This motif consists of a cluster of conserved cysteine and histidine residues arranged to form a stable zinc-binding structure that mediates complex assembly and transcriptional repression. It is found in Micractinium conductrix and is associated with UniProt keywords Metal-binding and Zinc-finger.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 5921, 43, 3057, 10249, 17, 2601, 7997, 8497, 3418, 1988, 4088, 5985, 1966, 43, 2213, 17, 2213, 2835, 6854, 16, 4443, 1958, 1920, 6067, 1927, 5224, 2081, 17, 26446, 3189, 56, 17, 2233, 1930, 28018, 1031, 18, 2052, 5219, 7543, 1927, 43, 4377, 1927, 5305, 8666, 1930, 13873, 4248, 14940, 1942, 2386, 43, 4700, 7997, 17, 2743, 3170, 1988, 10412, 2796, 5957, 1930, 5224, 10084, 18, 2176, 1977, 2435, 1922, 17020, 11686, 2457, 7569, 3027, 1039, 1930, 1977, 2458, 1956, 20709, 11569, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 3], "output": "MAPAANPVQQLQAQQSILQRQARLELAQAAQEGASRCSGCRVVWYCDTAQAAGQAASGSGLLARQLADTLQAWWETPDQALRGCAYLACPNAGAGGALTAGAACSHADWAAGHRRVCKHLGAARAA", "metadata": {"id": "A0A2P6V0E0", "cluster": 14552340, "interpro_all": ["IPR002893"], "interpro_used": ["IPR002893"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: 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. In addition, the protein contains a Topoisomerase 6 subunit A/Spo11, TOPRIM domain that functions as a nucleotidyl transferase/hydrolase to generate transient double-strand DNA breaks essential for topological changes or recombination. Found in type II topoisomerase VIA and Spo11, it utilizes conserved glutamate and DxD motifs to coordinate Mg2+ and catalyze strand cleavage and joining, facilitating supercoil relaxation, decatenation, or the initiation of meiotic homologous recombination. Furthermore, the protein should feature a Spo11/DNA topoisomerase VI, subunit A, N-terminal domain that represents the structurally homologous N-terminal region found in the eukaryotic meiotic recombination protein Spo11 and the A subunit of archaeal type IIB topoisomerase VI. It serves as a core structural component supporting the DNA cleavage and topological modification activities of these enzymes. It is produced by Malassezia japonica and is annotated with UniProt keywords Magnesium 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, 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, 1922, 2459, 16, 1920, 2213, 5461, 43, 20294, 26, 5903, 43, 19, 18055, 3242, 16, 3700, 3027, 1035, 3418, 1988, 4088, 1966, 43, 2797, 4090, 2199, 13763, 19, 20748, 1942, 5655, 6809, 4825, 17, 5984, 2678, 13065, 4415, 1958, 16365, 2840, 2014, 7827, 18, 2435, 1922, 2601, 2890, 20294, 3454, 1930, 18055, 3242, 16, 2176, 18127, 5305, 7627, 1930, 14852, 1007, 8277, 1942, 11865, 14756, 15, 1930, 18170, 5984, 6404, 1930, 15836, 16, 12440, 26936, 1970, 9157, 16, 2344, 20058, 1943, 16, 2014, 1920, 6035, 1927, 16205, 8725, 7827, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 18055, 3242, 19, 2678, 20294, 3070, 16, 5903, 43, 16, 56, 17, 4262, 3418, 1988, 4972, 1920, 12171, 8725, 56, 17, 4262, 3031, 2435, 1922, 1920, 10825, 16205, 7827, 2213, 18055, 3242, 1930, 1920, 43, 5903, 1927, 22367, 2601, 19795, 20294, 3070, 18, 2176, 10634, 1966, 43, 4728, 4346, 4594, 6184, 1920, 2678, 6404, 1930, 16365, 6295, 4209, 1927, 2144, 5038, 18, 2176, 1977, 4152, 2007, 3054, 2331, 11788, 2126, 27096, 1930, 1977, 10633, 1956, 20709, 11569, 13148, 1930, 6048, 17, 2743, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MRRIEHFIAHFVRNAQSRSPRSMTLGAPRSRMRGASVQWPFPARHADRVQHWAQFLRVLSYMHTAVRSDAILSKREIYYRDPSLFGSQRTVDSMIARACMTLNLSRAALSVCATPRSVVWGPIGFGGQAQLAEQTIPDPAHVSSLVSSAEWIVIVEKHAVYQTLRTIDFLGQVGGHLPPGAVVTGKGYPDHATRWMLGELARHASSTHLLFLVDSDPHGVDIFRTYQDALPSSAQVHWSGLRARQWLRLQMAHAIPTMPLTRADRAKAKSML", "metadata": {"id": "A0AAF0F618", "cluster": 18303565, "interpro_all": ["IPR002815", "IPR013049", "IPR036078", "IPR034136", "IPR036388"], "interpro_used": ["IPR036388", "IPR034136", "IPR013049"], "interpro_unused": ["IPR036078", "IPR002815"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein incorporates 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. Moreover, 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. Furthermore, the protein can be placed in 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 is present in Flavobacterium microcysteis and exhibits UniProt keyword tags Transcription regulation.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 19683, 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, 3950, 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, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 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, 1977, 2481, 1922, 7732, 12022, 10572, 2298, 14209, 1036, 1930, 9826, 20709, 11121, 2538, 14392, 3213, 3640, 18, 3], "output": "MQNSNSKHSEEASHTAYMEIAKAFDQLTYKSNRTSEEIIGMGEQLFSTFIKAEDHSIVNQANQAGYTLAYNFHLVDESQNTLLVNHRLTPLLLTNKGKIWKILGMISLALKYDIETDQWICHSKIALSEREIQILRFYAQGLTINDTIKFHRRNLLLKMEVNTINKALAYATAYKLIIYIFDSIQKKIEYISNHRFFLHSAFYATLPESERKSTSNLPGNITLTKDGDTTIEIASVLNLSA", "metadata": {"id": "A0A501QLP7", "cluster": 22091209, "interpro_all": ["IPR016032", "IPR000792", "IPR036388"], "interpro_used": ["IPR000792", "IPR036388", "IPR016032"], "interpro_unused": []}, "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 possesses a DUF4220 domain that is functionally uncharacterised. Also, the protein is a member of the Protein of unknown function DUF594 family, which comprises uncharacterised proteins with currently undefined biological functions. It is expressed in Citrus clementina (Clementine) (Citrus deliciosa x Citrus sinensis) and is annotated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "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, 14465, 43, 4855, 10432, 4460, 1008, 3418, 1988, 1977, 9346, 23229, 3495, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2213, 1927, 5435, 2347, 4855, 17968, 11226, 3416, 16, 2154, 12936, 23229, 3495, 2697, 1956, 5077, 26687, 3933, 4088, 18, 2176, 1977, 3198, 1922, 24117, 2965, 2017, 4058, 12, 2965, 2017, 2053, 13, 12, 24117, 2723, 2478, 5360, 66, 24117, 27613, 13, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MQSFPEEAITFWNQWQIRLLVLLSLTFQTVLSIFGSRRKFTATFWIRALVWSSYLSADWVATVALGNLARSDSAREDKFLKANGEIQLQAFWAPFLLIHLGGPDTITAYALQDNELWLRHLLSLVVQVGVAIYVYVRFWSTSVLTYLATPIFIVGAFKYGERVFVLYSSTKERLKKFNLLQVIHRKWIGEIRETSRRLLEVCTLIENCARLFTGQVLEYGDRQNDRMILLGEEGIKEKSAEEIFKITAIELGFMYDLLYTKAKMIYSGFGISARCFSLLFSVTALVFFSIFIHSPAHPLADIIITYLLLICTIFTDLYGFILHLFSDWTKFYLSKRRNGSHPDSSTYDATFFSHPLLGNHKRWCRSMGQLNLLSYCIKDKITTPSAAVGKLLAINKTLENQWYVTRADVNDDLEKLIFGELKEKITSNTEPEEQLGSTATGQRTMAGRGYYVLEHRYNKSWLLKCTASRSYDFNLLVWHIATDLCYRDDLHKLCNGNANALHRSCKISKRLSDYMLYLLLVCPSLMPEDNLLETIYMETCRQMEHFSGLLEEPPTVMTPEEMQEWTKKIASAKRPGLWLSYHLQSLQSNQDWNNGRKWEMISEVWVDMLAYAASYGTWNEHGQHLRKGGELLTHVRLLVAHLGLIPEYEYLPQ", "metadata": {"id": "V4UAN0", "cluster": 22551864, "interpro_all": ["IPR025315", "IPR007658"], "interpro_used": ["IPR025315", "IPR007658"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: 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. Additionally, the protein should include 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. Furthermore, the protein belongs to 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. It has been characterized in Coemansia sp. RSA 1813. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 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, 4950, 16, 1920, 2213, 3066, 3951, 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, 3677, 16, 1920, 2213, 14440, 1942, 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, 2176, 2258, 2252, 4378, 1922, 4815, 3862, 12924, 1019, 2056, 18, 23788, 16997, 1010, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MAEPQTQAQPQVHPTPHPHLHSHVHGHHHHHHHYRNYHPNRGHHHHNSNAHYHHNHNHHHHNHPAHHHQHHSQNLKAYIVPNSARPGYSSILRHPYYRHGKFSDEFDNVLTLYDLFQRSLGMFPSTPFLGTRHFSNGKHSFGEYRWKTVRDVAETIDYFGSGLDVIYEKHASGGGPSGYAQLPLGIYSKNRAEWIIAEFSAFRSRRYTVALYDTADSDTIEHIIGHAQINVLVCSIDKVPALLTHKSAMPNLRVIISMDTLDGKGKTPWASAFSIGTTRVLHKHAEAQGVVLLDMASVVALGRNNVTAPRPPSPNDVCTISYTSGTTGRPKGVVSTHSNYVYSAKSMYHAVPLYHSTYLSFFTLAHCFERNIVYTGMLGGMHIGFFSGDVERIFEDTQALKPTVMAGVPHLFNEIYHRVSAETTNTSGWSGTLARTAIRQKMQRLDSGKGGVKHGFWDRFVCNRIAQLFGGRLKLVISGGDPIDAHVLNFLRVAISCPLLETYGLSESCAVGTACLISDRSSGHVGVPLPGIDVCLRDVPEIGFLTSNQPCARGELLLRGPNVFMGYYRDDARTHVATDGEWLATGDLAQLNDDGNIEIIDRKENIVRIAEPFNTFVALEHLETVYTRHPLVHDIFIYSIPDRSELVAVVVPVPGSFFPLARNITGNRTASVDTLANDDQVRSAILIVLYQHGKKAHLRSCEMIADVFCETVPFDIEGNGLLTSTYKLRRKIAAKYYKSQIDEMYVRIAKQP", "metadata": {"id": "A0A9W8FL95", "cluster": 22630218, "interpro_all": ["IPR020845", "IPR000873", "IPR042099"], "interpro_used": ["IPR020845", "IPR000873", "IPR042099"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a polypeptide chain with the following function: 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 has been detected in Bacteroidales bacterium and has UniProt annotations 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, 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, 2258, 2252, 3330, 1922, 24323, 3955, 14061, 1930, 2258, 20709, 15010, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MDTLNIITLGIVTFLILRLCVLVYNYLTKPLLTEAPGTSDKLVSILIPARNEEQNIGLLLSDLVNQDYLKTEILVYDDLSEDATATIVEEYANRDSRIRLLRGTRLPEGWLGKNHACYRLAIEARGQYFLFIDADVRLHRSAISSALSYTEKRALHALSVFPTQIMLTRGERALVPLMLWVLLTLLPLRMVEKSRYSSLAAANGQFFLHEAAQYLKFQWHKRYRNHRVEDVAIARALKSEGLRMATLLGNTLVNCRMYKSYTDALQGFSKNFRFFFGNNLVLMYVFILVSTFGWLLPLVSWSWYFSVPFIGVLVLQRCMLAKLTNGNCKQTLLDTPLQQAALIHLALRIGLTSSRGGLQWKGRHLTEY", "metadata": {"id": "A0A7X7UJR1", "cluster": 22951324, "interpro_all": ["IPR001173", "IPR029044"], "interpro_used": ["IPR001173"], "interpro_unused": ["IPR029044"]}, "task_type": "autoregressive"} {"instruction": "The protein contains a Transcription factor MYC/MYB N-terminal domain that functions as the N-terminal region of plant MYB and MYC transcription factors which regulate phenylpropanoid biosynthesis. This domain is distinct from and located upstream of the DNA-binding HLH domain. Moreover, the protein contains a PB1 domain that functions as a protein-binding module facilitating heterodimerization or homo-oligomerization. This conserved domain comprises approximately 80 residues and mediates specific protein-protein interactions across animals, fungi, and plants. Furthermore, the protein carries a PB1-like domain that functions as a protein binding module to facilitate heterodimerization or homo-oligomerization through conserved acidic and basic interfaces. Adopting an ubiquitin-like \u03b2-grasp fold, it mediates specific protein-protein interactions in diverse signaling pathways, including those governing cell polarization, NADPH oxidase assembly, and auxin response. It occurs in Helianthus annuus (Common sunflower) and corresponds to UniProt keyword Homeobox, Nucleus, and Transcription regulation.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 5461, 43, 3213, 2991, 5078, 19, 16851, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 3031, 1927, 4496, 16851, 1930, 5078, 3213, 2790, 2154, 5741, 7971, 20194, 9286, 1960, 8132, 18, 2052, 3418, 1977, 4493, 2037, 1930, 4810, 7671, 1927, 1920, 2678, 17, 2743, 29013, 3418, 18, 3950, 16, 1920, 2213, 5461, 43, 28419, 3418, 1988, 4088, 1966, 43, 2213, 17, 2743, 9059, 12440, 15672, 2466, 2014, 16350, 17, 17371, 18, 2052, 5305, 3418, 12936, 3993, 3729, 4248, 1930, 10412, 2487, 2213, 17, 2213, 3719, 3436, 3555, 16, 10520, 16, 1930, 4793, 18, 3677, 16, 1920, 2213, 16252, 43, 28419, 17, 3189, 3418, 1988, 4088, 1966, 43, 2213, 2743, 9059, 1942, 6628, 15672, 2466, 2014, 16350, 17, 17371, 2596, 5305, 9931, 1930, 5937, 14857, 18, 20478, 1925, 6526, 17, 3189, 161, 17, 22815, 3728, 16, 2176, 10412, 2487, 2213, 17, 2213, 3719, 1922, 6445, 3197, 3873, 16, 2710, 2690, 20012, 2024, 10839, 16, 11908, 10488, 5957, 16, 1930, 16243, 2644, 18, 2176, 5110, 1922, 3091, 19196, 24315, 1036, 5112, 25901, 1036, 12, 3059, 8147, 9893, 1915, 13, 1930, 8852, 1942, 20709, 11121, 2538, 27566, 16, 5607, 16, 1930, 3213, 3640, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MNLLNTGDDPIMLSDMLSTPISSPTFALIDNSRQPWTYAIFWQSSSIVDYSNKSVMVLGAEQEHRKRVIRELDSMISGSELETDAIDEPSQATLSNQPGWITGQKQVLASRCEHVCIPFRRGVVELGSTELIFQSSGVMNQVRVLTARGDTGLSKAKCNTTAISSSQQLVDKQVENQSGNYMKEAAKCKTTEILLPLEVVEKQFGLGIPEWQGPNFVKRKANDSSVCQSNTAKENNGAIQNDMIKFCLPNSQATFMIVQQEIGKKFKLIIGTDEEMIHCIESSTKLDRIVVRLRVVPSPSVDDLLEIFGSSEPYNKYTFQQHLHDWGDGYYRGEFRKPKTTSSSVTSFVTDTEWFFLISMTQSFFNGNGLARQGLAFRLQKMFDITNTQPDLAPIIADQSGNTMKEAAICKTTETSFPQEVKTMKEAAKNLDVSESTLKRKLRKDPSIVNINNSLITIKAEYAYNLKYLDEDGDWICLTS", "metadata": {"id": "A0A251TWX2", "cluster": 26217160, "interpro_all": ["IPR045084", "IPR025610", "IPR053793", "IPR000270", "IPR003035"], "interpro_used": ["IPR025610", "IPR000270", "IPR053793"], "interpro_unused": ["IPR045084", "IPR003035"]}, "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 possesses 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. In addition, the protein contains 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. It is native to Tanacetum cinerariifolium (Dalmatian daisy) (Chrysanthemum cinerariifolium) and is described by UniProt keywords Metal-binding and Zinc-finger.", "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, 14465, 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, 1922, 2459, 16, 1920, 2213, 5461, 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, 2176, 1977, 6196, 1942, 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, 2910, 2007, 20709, 11569, 6048, 17, 2743, 1930, 7997, 17, 8497, 18, 3], "output": "MAMLNMYEKEKEITIYATKNNDSGTTNIQHSGQDEAIGEPHVQDEATGKPHDQDEATHDPHSEKPFDDSDYCKDNEESYQSLHNTDNEDELFNYEVETYSFNKKDPTTQVVAFTFFLMLVISKNAESWTWFLENLRKAIGTPNGLVISSDMQKGLNPGEYEVCRSSQNRSEVKCKGERWEVILDDRQCTCRVWQVMGLPCVHAAAFIAFIRDANWEKYVDPYYTIKKFKEAYALEIAPLPDKDERVRLCGSWTSLNTTKAPAGQHVAPEILAAHNAWIKGSKKIADLMLMTMKPEIQRNLEPLHAHEMLRELKTLFAQQAEQELLQTTRDFHSCRQEEGQSVSSYVLKMKGYIDN", "metadata": {"id": "A0A699IBJ0", "cluster": 27371449, "interpro_all": ["IPR006564", "IPR007527"], "interpro_used": ["IPR006564", "IPR007527"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein can be placed 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. Also, the protein possesses 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. It is native to Paralvinella palmiformis and is annotated with UniProt keywords Cytoplasm, Transport, and Golgi apparatus.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 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, 2222, 16, 1920, 2213, 14465, 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, 2176, 1977, 6196, 1942, 11271, 23551, 11560, 1019, 29686, 2231, 1937, 1930, 1977, 10633, 1956, 20709, 11569, 5239, 16, 4860, 16, 1930, 10277, 11161, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MASPRTRRVLKDLKADTENNGIWICLECSGKHRSLGVHLSFVRSITLEKQDDWDETLPLQQKYGKPWSIETSSARNYRPTTVQPTLTSSQSYPRFNAVHIGTGDSDTNTYQQGKYWGFGNTEEKPKKDDDSKLAAQASEKATKLAVQAGKKTKELSHSHKVKDGTLVNDVSSSVTGLASKMQNVTVKSWKEGSSLLTSDNSIKSYSDSARDERSPERQDSWSGWGDDWSPLGHGDEWNTQNWNADGWSSESSAKVKPSKTSGWDDGWAELESSAAKTKPLHTAKSSKADRCFECGGHNPQWVSVTYMDKWKDLELEKMKIGGNKKARQWNTRAAALYRDKITTEAQSSSGGGGGMSSATYSYTSDTTSMEEAMYWGSLSTGWSSFASGAVNEKVAEAKIIDNVTSGLSSITNMSSMFSEGPKKNQYEELNAEEATTPTNDAHHGTNAKNEVNTGLLIDLQDNDGAANEGWDN", "metadata": {"id": "A0AAD9JY66", "cluster": 27761370, "interpro_all": ["IPR037278", "IPR001164", "IPR038508"], "interpro_used": ["IPR037278", "IPR001164"], "interpro_unused": ["IPR038508"]}, "task_type": "infilling"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein incorporates 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 originates from Thermoleophilia bacterium and contains UniProt keyword associations 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, 19683, 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, 22970, 2037, 7967, 1952, 19740, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MSTDDLNHDEDSSEPGTIGVGRFSPRQRTRKRSRSAAAPAAAPSPGKKNGFPWIGSGSDSSSKSTTDSDLPVITNSRPDTTTQPAVVDDGSIPSAGGTGGTGEEIPSLTDPSTVPTIEPGSSSGTSGTSTVTVDQNGDASTTDASGSSTDTAAASGDWPAGQDAADVQEDGFSDSGVLLSSDFQSLCPGIYVVFSGTAGMYVREVKRNGTRPSGCTTANMGGSCPNCRAPVDLGQEFCLECGAPIPFLVVLALVGAGFALTLVDNGTESSTITTTLQDCDPTRPLDGGGTADDGSSAFGSDNLCDDTATDGSTSTSPIGGWTVIVAGYDTETRAQQRFQSESEANSRLKQLQAKPDY", "metadata": {"id": "A0A9E3XSA2", "cluster": 28219817, "interpro_all": ["IPR007730", "IPR036680"], "interpro_used": ["IPR007730"], "interpro_unused": ["IPR036680"]}, "task_type": "infilling"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein should feature 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 belongs to the HTH-type LysR transcriptional regulators family, which comprises bacterial DNA-binding proteins that utilize a helix-turn-helix motif to act as transcriptional activators or repressors. These regulators modulate diverse cellular processes, including nitrogen metabolism, sulfur response, and the catabolism of specific compounds, often by sensing environmental cues or co-inducers. In addition, the protein should include 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 is identified in Rhodospirillaceae bacterium TMED23 and corresponds to UniProt keyword Transcription regulation.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 3066, 5961, 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, 14440, 1942, 1920, 5334, 1023, 17, 2601, 3629, 1005, 5224, 9098, 3416, 16, 2154, 12936, 4543, 2678, 17, 2743, 2697, 1988, 12561, 43, 7864, 17, 5165, 17, 7864, 5219, 1942, 4033, 1966, 5224, 15497, 2014, 26446, 18, 2144, 9098, 8480, 6445, 3689, 4028, 16, 2710, 6634, 4714, 16, 12585, 2644, 16, 1930, 1920, 19480, 1927, 2487, 4300, 16, 3868, 2007, 9306, 4813, 8972, 2014, 2081, 17, 23329, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 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, 1977, 2899, 1922, 11490, 3106, 23576, 11560, 9914, 14061, 22377, 9091, 1010, 1930, 8852, 1942, 20709, 11121, 2538, 3213, 3640, 18, 3], "output": "MDVRQLRYFVGVVNSGSFSDASLYMHVAQSALSRHIKSLEHTVGGELLERHPKGITPTKLGWHLYEQAKRIVTEVEELPSKIRDKNYKIKGQVTLGAPNSVARDLFPLVADLVMPTYPGISLSFVEGNAISLGSGLDTGEIDIAIMVDPDRRLEFHYEPLFSEQMYLFGKCKDPEFPVNNIKITDLPKYPLVLPSRRNGPRRIIDRALFKSNVALNIKFEVSGSGIVSSFIQRGIAMGVLTHSMLLSGEQKKDLKVAAIDKLVLTYHLVSNRGLSDTPHTRTIMNIVRENIGILLKTDRFFDAKPVLI", "metadata": {"id": "A0A1Z8NY03", "cluster": 28562107, "interpro_all": ["IPR050950", "IPR005119", "IPR000847", "IPR036388", "IPR036390"], "interpro_used": ["IPR005119", "IPR050950", "IPR000847"], "interpro_unused": ["IPR036388", "IPR036390"]}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein contains 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. Moreover, the protein includes a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. Additionally, the protein is classified under the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. It is found in Ignavibacteriaceae bacterium and is connected to UniProt keyword Glycogen biosynthesis and Glycosyltransferase.\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, 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, 3950, 16, 1920, 2213, 5921, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 2176, 1977, 2435, 1922, 12046, 9188, 7972, 2341, 18339, 1972, 3336, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 13302, 8132, 1930, 20067, 9961, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MAAKKYKILFVTSEVVPFVKTGGLADVSAALPIVVPKYGAVDDRKFKIHEVVRLKDLQINIGKKEVIFSLKSCFEYFGSRNSLYTDPMSGKDYSDNDERFILLNRSVFELINDWQCGLIPAYLKTVYKDEENFDKFKTLFTIHNLAKGIINKNKFNFTKSGLLQADVINTVSKTYADEIRMDNSIGNPEKDKHLPKKYSAKNLQFKMMNKQALAERFGFEFQEETPQLMKMDIQMIVLGTGEKKYHTFFDEMARKHPDKFACYLYSLKYGTVPIVRETGGLADTVIKFNEKKKEGTGFVFKKYWEKIVKAGMKSDFSWHSSAKKYIELYKTILSNNQMLAELGHEVRLPGQRVRVQIYFLDNQLKLGWIPDIIHCAYQGEFPKSSFKKTGLPDELNSAGLKEVLAKRKNDLYGIINGIDTKVWVIGLISRLFDSKGIDLVQKILPGFNDDLAHLIEGGADIFFMPSKYEPCGLNQMDAKEFLAEIKRALKVYEDKET", "metadata": {"id": "A0A7Y2TFE1", "cluster": 10309559, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR001296", "IPR013534", "IPR011835"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should feature 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 should contain 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. Furthermore, 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 has been detected in Rhodoferax sp and is described by UniProt keywords Cytochrome c-type biogenesis and Redox-active center.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 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, 3066, 5531, 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, 3677, 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, 2258, 2252, 3330, 1922, 11490, 28079, 3013, 2056, 1930, 1977, 2910, 2007, 20709, 11569, 9387, 45, 17, 2601, 13008, 1930, 9366, 17, 3500, 4102, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MSVISGFGLASCRQSQSKSALDQSRHSSQDYMADLETLHRALAPRGMVLIAILSDPGQRWAGSALKAPGLPTSRAWADSNIQAAVAAQLALREGGRPGRDDHFPEFSLAMGRPLLFNLWATWCAPCRNESIDQDIQLAREFTRRQGLTFTVYLVGADFVIKDVMVGP", "metadata": {"id": "A0A935L983", "cluster": 97620, "interpro_all": ["IPR000866", "IPR036249", "IPR013766", "IPR050553"], "interpro_used": ["IPR000866", "IPR013766", "IPR050553"], "interpro_unused": ["IPR036249"]}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein can be placed in the Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein family, which comprises membrane-bound enzymes involved in the biosynthesis of inflammatory lipid mediators and glutathione metabolism. Members such as leukotriene C4 synthase, prostaglandin E synthase, and 5-lipoxygenase activating protein (FLAP) catalyze the production of leukotrienes and prostaglandins or activate associated enzymes. These proteins contribute to cellular resistance against lipid peroxidation and oxidative stress, often sharing structural similarities in their active sites that allow for substrate modulation. It is derived from Tateyamaria omphalii and exhibits UniProt keyword tags Transmembrane helix.\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, 3260, 17, 2458, 16, 20948, 11201, 2642, 19, 9153, 4714, 12, 4446, 6541, 13, 2213, 3416, 16, 2154, 12936, 3260, 17, 4124, 5038, 3286, 1922, 1920, 8132, 1927, 3769, 4486, 9744, 1930, 9153, 4714, 18, 4678, 2427, 1966, 26045, 2880, 10872, 8921, 16, 15900, 47, 8921, 16, 1930, 25, 17, 3178, 13966, 8019, 2213, 12, 11924, 13, 18170, 1920, 3372, 1927, 26045, 11219, 1930, 25674, 2014, 6980, 2458, 5038, 18, 2144, 2697, 4672, 1942, 3689, 3554, 3316, 4486, 14214, 1930, 5163, 3071, 16, 3868, 10763, 4346, 10857, 1922, 2310, 3500, 3402, 1988, 3235, 1958, 4510, 7145, 18, 2176, 1977, 3595, 2037, 10687, 10676, 10671, 3027, 1019, 21921, 7289, 3907, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 7864, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MATELVILGLLALMGASLWIPYIIGVNTAPQGSIPYRAHLNLLEQSVPFAILVLLVDRVDGFSALARFPGRPLIFTGGWVCCLLMGWALFAAADAPDGFVIPPDPTLQRPWVRRATLWASVAFLVLRIAHAVGYITAT", "metadata": {"id": "A0A1P8MSP4", "cluster": 6341292, "interpro_all": ["IPR023352", "IPR001129"], "interpro_used": ["IPR001129"], "interpro_unused": ["IPR023352"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The 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 is included in the Six-bladed beta-propeller, TolB-like superfamily, which forms a structural domain consisting of six 4-stranded beta-sheet motifs that serves as a scaffold for diverse biological activities ranging from enzymatic catalysis to transport. Members of this family include enzymes like quinoprotein glucose dehydrogenase, signaling components such as the LDL receptor, and the periplasmic TolB protein, where the domain mediates protein-protein interactions within the Tol-dependent translocation system. Moreover, the protein carries a Thioredoxin-like fold domain that regulates target protein activity through thiol-disulfide exchange reactions within redox signaling pathways such as the ferredoxin/thioredoxin and glutathione/glutaredoxin systems. It features a characteristic three-layer \u03b1/\u03b2/\u03b1 core structure and functions as a hydrogen donor to reduce disulfide bonds in substrate proteins. It has been characterized in Alphaproteobacteria 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, 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, 1977, 3063, 1922, 1920, 3798, 17, 22707, 1007, 4666, 17, 5062, 13728, 16, 21930, 1014, 17, 3189, 13975, 16, 2154, 4952, 43, 4346, 3418, 7600, 1927, 3798, 24, 17, 10338, 4666, 17, 11130, 8277, 1988, 10634, 1966, 43, 7281, 1958, 6445, 3933, 4209, 6485, 2037, 8145, 15408, 1942, 4860, 18, 4678, 1927, 2052, 3416, 3951, 5038, 3189, 9012, 6657, 3817, 9294, 16, 3197, 4178, 2427, 1966, 1920, 8017, 3148, 16, 1930, 1920, 24334, 21930, 1014, 2213, 16, 2597, 1920, 3418, 10412, 2213, 17, 2213, 3719, 2651, 1920, 21930, 17, 3100, 7849, 2433, 18, 3950, 16, 1920, 2213, 16252, 43, 23684, 17, 3189, 3728, 3418, 1988, 7014, 2758, 2213, 2455, 2596, 13914, 17, 11830, 6818, 5298, 2651, 9366, 3197, 3873, 2427, 1966, 1920, 25304, 22389, 10960, 19, 23684, 1930, 9153, 19, 19406, 1919, 9754, 3771, 18, 2176, 4075, 43, 6293, 2559, 17, 4757, 160, 19, 161, 19, 160, 4728, 3170, 1930, 4088, 1966, 43, 6201, 6282, 1942, 4412, 11830, 9031, 1922, 4510, 2697, 18, 2176, 2258, 2252, 4378, 1922, 4595, 9218, 1021, 10296, 14061, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MSKKLALILGFAITVVAILWLTFFSRMTFSADRYENLAHHDTWLNTSRKLTKDDLKNRIILLDFWTYCCINCMHVIPDLSYLEKAFGSQITVIGVHSAKFKNEFDTANIRNAIVRYGIEHPVINDFDFSTWNAFNIKSWPTLVLINPRGSIEAVYNGEGHRATIEADIRRLLATSSANLTTTPLPLKLEKNKILPTVLSFPGKIYPSPQGLFVADTGHHRILNISTKGTILTTIGNGMEGFQDGEFSQAQFKRPQGILFSDNKLYIADTGNHALRLADLKTSKVTTLAGTGEVGHVRSGKHIPARIMLLSSPWDLTFFPDNKHIVIAMAGTHQLWSYAIDSHTFSLIAGDGKEDLDDGSLPYNSLAQPSGLSAQGDTLWFVDSESSSLRSLKGNDVETSIGKGLFNFGYQEGNRSKALLQHPIGLLATPHYIYIADTYNHAIERYDPQTKTLHHFIGSGEAGNFDGNIHDALFNEPSDIKQIGNRLYIADTNNNAIRTVDLRSFHVATLPISPSVLPPSQQRFPFSTIFPNLQHIPVPTIPANQPITITLGLKSDWKINEQAPNFIALYHHRKLVEGFEYKDLKNLTLHLNPLKSDEEYQLQATLYYCENKATSQCMIKSFNTPLSIKEGHKPSIAFMLNH", "metadata": {"id": "A0A936Y811", "cluster": 6370631, "interpro_all": ["IPR011042", "IPR012336", "IPR036249", "IPR013766"], "interpro_used": ["IPR013766", "IPR011042", "IPR012336"], "interpro_unused": ["IPR036249"]}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein falls within the Protein of unknown function DUF4315 family, which is currently functionally uncharacterised. It occurs in Pseudoflavonifractor sp. An187 and contains UniProt keyword associations Coiled coil.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 12182, 2651, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 6800, 1015, 3416, 16, 2154, 1977, 5077, 9346, 23229, 3495, 18, 2176, 5110, 1922, 11520, 14794, 13339, 7134, 13804, 2056, 18, 1925, 19544, 1930, 5461, 20709, 11121, 2538, 5253, 17524, 9121, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MNPKIDKLARDIEKTEKKIADLQKKFLKAHRAGTFTVPEAAPPAGEQEVGHEELELFKEEKTRLENEDYGDIGRDFHLTPKELAE", "metadata": {"id": "A0A1Y4KQS0", "cluster": 6374745, "interpro_all": ["IPR025464"], "interpro_used": ["IPR025464"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein should have a Pyruvate:ferredoxin oxidoreductase, core domain II domain that functions as a structural component of the anaerobic enzyme pyruvate:ferredoxin oxidoreductase. It is necessary for establishing inter-subunit contacts in conjunction with domains I and IV. Furthermore, the protein should contain a Pyruvate/ketoisovalerate oxidoreductase, catalytic domain that catalyzes the thiamine-dependent oxidative decarboxylation of pyruvate to acetyl-CoA, a key step in anaerobic carbohydrate fermentation. This domain interacts with electron carriers like ferredoxin or flavodoxin and includes variants required for nitrogen fixation in cyanobacteria under iron-limited conditions. Furthermore, the protein should contain a Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain that binds the aminopyrimidine ring of the thiamine diphosphate (TPP) cofactor and facilitates inter-subunit contacts. This N-terminal domain is essential for the oxidative decarboxylation of pyruvate to acetyl-CoA in anaerobic metabolism. It is found in Planctomycetales bacterium.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 3066, 2162, 43, 11867, 30, 25304, 22389, 10960, 27388, 16, 4728, 3418, 2890, 3418, 1988, 4088, 1966, 43, 4346, 4594, 1927, 1920, 12554, 4113, 11867, 30, 25304, 22389, 10960, 27388, 18, 2176, 1977, 4680, 1958, 11810, 2107, 17, 5903, 9070, 1922, 11799, 1956, 4682, 51, 1930, 4370, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 11867, 19, 21471, 23854, 28144, 5524, 2057, 27388, 16, 6804, 3418, 1988, 17097, 1920, 26901, 17, 3100, 5163, 22429, 1943, 1927, 11867, 1942, 6894, 17, 10027, 16, 43, 3834, 3537, 1922, 12554, 10590, 12670, 18, 2052, 3418, 9034, 1956, 4995, 8974, 3189, 25304, 22389, 10960, 2014, 7732, 1986, 9754, 1930, 5921, 4936, 3414, 1958, 6634, 7938, 1922, 21897, 2441, 5680, 17, 3892, 2961, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 11867, 7732, 1986, 9754, 19, 25304, 22389, 10960, 27388, 16, 21611, 2743, 3418, 1988, 6876, 1920, 3835, 18425, 29899, 6335, 1927, 1920, 26901, 23266, 12, 25282, 13, 15155, 1930, 11374, 2107, 17, 5903, 9070, 18, 2052, 56, 17, 4262, 3418, 1977, 4415, 1958, 1920, 5163, 22429, 1943, 1927, 11867, 1942, 6894, 17, 10027, 1922, 12554, 4714, 18, 2176, 1977, 2435, 1922, 4720, 2341, 13386, 3949, 1918, 14061, 18, 3], "output": "MSPSGSPSQLSIGVVGSGGDGVVLLGELLARSAVLAGLHCYMDKVFGPQIRGGESSVSLRISQSQVLRSADELDVLLVLQWSDLARFHDVLSIAPDALVICSSEDDGDPQACGLPIGHRGPLLSLPLKQLALDHGRSKQARNMVLLGAASGLLDWYPQQLRAILERRMQRYDERSRENNLAAVAAGRDAVASWQGSGIPALPTSNGNADLELASGNELLSRAAIASGCRFMAGYPITPASEILEYMTRRLPQLGGTCIQAEDEIAAACLTIGAALGGVRSMSATSGPGMTLKSESIALSGMAGLPMVVVDVQRCGPSTGIPTRTEQADLNLALYGAHGDSPRIVLAAAHQADCADLATQAFELAGEASAPVILLSEQQIAQGLATVPRDLVPEPNGSVPGWPDTAIGADRQVQLTGLEHDDSGRPLSDAASHQANSLLRNARVNRALSRVPALYEGAAEGELGLLCFGSSYSICREAIELAGSRGVTAGMMCIRMLSPLDQAELRDWLRGYRHVVIVEMNYSGQLHDYLRSRLQLPELTMSLRRSGGRPWRLAEVEDFLVRHGLLPAGPPELQP", "metadata": {"id": "A0A9E7CT39", "cluster": 6720464, "interpro_all": ["IPR033412", "IPR050722", "IPR019752", "IPR002880", "IPR002869", "IPR029061", "IPR009014"], "interpro_used": ["IPR033412", "IPR019752", "IPR002880"], "interpro_unused": ["IPR009014", "IPR029061", "IPR050722", "IPR002869"]}, "task_type": "autoregressive"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein includes 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. Moreover, the protein should contain a HemN, C-terminal domain that constitutes the C-terminal region of oxygen-independent coproporphyrinogen-III oxidases involved in heme biosynthesis. Based on comparisons with other radical SAM proteins, it is predicted to function as a substrate binding domain during the conversion of coproporphyrinogen-III to protoporphyrinogen-IX. In addition, the protein should contain 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. It originates from Acanthamoeba castellanii (strain ATCC 30010 / Neff).", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 2052, 2347, 30, 1920, 2213, 5921, 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, 3950, 16, 1920, 2213, 3066, 5531, 43, 3243, 1022, 16, 45, 17, 4262, 3418, 1988, 14879, 1920, 45, 17, 4262, 3031, 1927, 4612, 17, 3484, 3725, 17351, 11119, 30338, 5572, 2404, 17, 4337, 10488, 1036, 3286, 1922, 10954, 8132, 18, 2454, 1990, 5768, 1956, 2303, 6917, 2235, 2697, 16, 2176, 1977, 4396, 1942, 2347, 1966, 43, 4510, 2743, 3418, 2409, 1920, 7309, 1927, 3725, 17351, 11119, 30338, 5572, 2404, 17, 4337, 1942, 23583, 2074, 25818, 5572, 2404, 17, 13848, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 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, 2176, 22970, 2037, 25645, 1976, 6802, 7972, 12273, 5870, 8635, 1033, 12, 3943, 11037, 5255, 2930, 19, 18301, 1038, 13, 18, 3], "output": "MGSGSIINDATTGREQEEEKEPGLGVYVHWPYCSRICPYCDFNRYLAEKGGSGIDHRRMTQSYKTELAAFRRFLDSDGDPAVFATTSTQTPEPTTTTTTTTTTTTKLRPPARRRRVRSVFFGGGTPSLAKPEVMEEVLAFIDAQWGFEPDAEITMEANPTSVEVGKLRDFRRAGVNRLSIGVQSLNADDLKFLGRAHSPEEALRAIELGKEIFPRVSFDLIYARHRNQTVEEWRKELQAALALASGHISLYTLTLEPGTAFFRRAFQPASPNDALPYPDDERVADLYEATVSTAAQAGYHQYEISNYAQPGHESRHNLIYWRSEDWIGIGPGAHGRLTTHRDGHQRHAFAQGVYQIKLPSKWMDAVENNGHGVQEMKLINPTERMEEALLNGLRVREGISPLRFRMHAGQSIEEALDMDKVAELQAEGFLVYEPQAGLRPTPRGMALLDALLPLLPRRPSTT", "metadata": {"id": "L8GIS9", "cluster": 6769032, "interpro_all": ["IPR034505", "IPR006638", "IPR010723", "IPR004559", "IPR007197"], "interpro_used": ["IPR007197", "IPR010723", "IPR006638"], "interpro_unused": ["IPR004559", "IPR034505"]}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein should include 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. It is native to Candidatus Competibacteraceae bacterium.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 3066, 3951, 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, 2176, 1977, 6196, 1942, 14550, 1031, 1957, 6869, 7972, 2341, 7124, 1972, 3336, 14061, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MAYQEISDAFWRRVEPLLEPEFRRILNGIFYLLKTGCQWEHLSPATVPRVKNGRGLHGNGKPWMGRFKRRKSGGSPPVRFTSTSRSGCMPGYLPKFSVWQLKPI", "metadata": {"id": "A0A962ULG5", "cluster": 6820385, "interpro_all": ["IPR025161"], "interpro_used": ["IPR025161"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nThe protein should feature 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. In addition, the protein should contain 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 should have 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 present in Cloacimonadota bacterium and is connected to UniProt keyword Membrane, Transmembrane, 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, 3066, 5961, 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, 1922, 2459, 16, 1920, 2213, 3066, 5531, 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, 3066, 2162, 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, 2481, 1922, 12596, 28278, 3947, 12595, 3857, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "WKLDGTEVSTTYSYNFTTNYTSAGSYTVTLDVTDNYSDNSILIPAPGPITIYELESIAFSIDAYDPDGNSLSYTWYFDAEIVSNQEYYQYTDNFGSDNTLNFNWDITVIDIDRPIIVVELTPESGLITMNEGETTDFNIDADGTIVSSNADYAFITDYNSAGSYILTLDVTDNFVSDNLLNFIWDIDVIIFIQEGETIDFSIDAYDPDGNTLEYNWVLDGTTVSTTEFFEFITNMSSAGSIQFDWDITVLDAGSNIIVTNVDPAPGGVELFENDEINFIIEAYAFNGGDYVLTLDVEDEQAAETILNFVWNITVFESDQPIVVDDIQPLEYSWQLDGEEVSTIDVYDFITDINSGGIYLVTLDITDGFSENAIESIQPEPGDVTTFENEVIEFVINAYDPDGNPLEYSWQLDGTQVSTTASYDFLVSFSWNVTVIDVDQEIVVVELIPDATTVALNEGESVNFSIVSTTHFYEFVAATGSSGFYTLSLIVDDNYTDSSLEFTWDITVLDPIAETDTINFFINAYAQNGDELTYNWMLDDVSVSTETSYAFLTDFNSAGEYIVTLTIEDPIVIISLEPEPGFVTMLEMEVLNLSIDAYDPDYTSAGEYLITLYVTDNFSDNSLEFEWDITVEDINPNIIIEANNPYGDIYYSWTLDEDEVSTVSNFLFDTNEYTLGNYNETIQFNWGISVINSHLPPIADAGEDQYVNSCVLVQLDGSGSYDPEGEDLTYHWINFTWDVTVNDVDQYIVVIDVSNYNSAGLHTIMLEVYDPDGNDLEYSWELDVDQEIIVNEILPEPGNTYYMELFVTDNYSDSGDDLTYGWQLDGTLVSTTNTYLFTTDFTSTPGEVTISETETINFLIDAYDPDGNSLYYEWDVTVLETDQDIIPDYNSAGQYEITLDITDNFMADNSEAYDPDGNDLTYSWSLDGSQSGNIFINEILPAPGNLTEVPPETLLEFTWNITVTDVDQGNELEYIWELDGTEVSTTDSYDFITTTIEPTPGFLNITLGDSLNFFIILQLIVSTDAITR", "metadata": {"id": "A0A661UML7", "cluster": 9242782, "interpro_all": ["IPR002126", "IPR013783", "IPR022409", "IPR000601", "IPR035986"], "interpro_used": ["IPR000601", "IPR022409", "IPR002126"], "interpro_unused": ["IPR013783", "IPR035986"]}, "task_type": "infilling"} {"instruction": "I need the missing amino acid sequences for a protein described below:\nThe protein is included 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 Pleurodeles waltl (Iberian ribbed newt) and has UniProt annotations Coiled coil.\nPlease generate them.", "tokenized_instruction": [2, 51, 2942, 1920, 6814, 3835, 2687, 3709, 1958, 43, 2213, 2910, 4535, 30, 1920, 2213, 1977, 3063, 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, 6483, 18916, 16878, 1918, 16567, 14598, 12, 6180, 18339, 1022, 5216, 19011, 2814, 1031, 13, 1930, 2258, 20709, 15010, 17524, 9121, 18, 11586, 5655, 3581, 18, 3], "output": "MRSSTDRWGRSAAFWWPPQGLWPRRQALSPSAITPPFPGNISWYVGCVGCPDGAERNEKRHPVPGLKKHSNPHVKGGLHKITRLKQRSTEKAACDSEFKVPGVNDEQVPVASTSLEVVTPGRWWFPPPMGCEKLSEQEPKESDQGPQESNPEKCEVQPCSAQVQRGKQAKPANIDQGPFDTAESFFSLDSDIESSSAASISVSNYSTCRRKSGEQTDMQWDYTATQQALSKSDSACSTLVSPSMGGPAEPPSMKAAKRQLQLSIKKVVKSCQDIGVRIATMETQQISDIQWKLEDAENRQRRNNLRILGIAEDLEGQKEIQRAHRFPLMRKKQALTSTGRDQSYPRLLPEGPAGRCERGARPRSALLFVKQDPSLPTSTTEPRSRDMEKDARYSVPTMFTSMMICDAGGGSHPVERLPVQVQEIAALSCKLNSQQAEGMAKSLTIYETIPSDQSRDSDLDKEIPLTSRGSSGAKLRRDLLKPQEEDGELDLIYRTMVQNHEQAQRESRKRTEELEIEVKAATAQTTTQGDTRAYIASLFKKAFPDLIGWDWE", "metadata": {"id": "A0AAV7PI45", "cluster": 9818075, "interpro_all": ["IPR004244"], "interpro_used": ["IPR004244"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The desired role of my protein is: 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 present in Marinilabiliales bacterium. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 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, 2481, 1922, 13081, 8635, 11792, 25600, 2612, 14061, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MGFNKTINNQFYYGWIEVEVQSTIKIVLKELAIKDYTLSTSLSIENPNYKFYPNPARDKLHIICDPSFSDVEIKIFNQIGKLLHIEKLHVNEIDISKYRPGIYFIEISQDSKPYRHILIIQ", "metadata": {"id": "A0A2J6ID62", "cluster": 12099632, "interpro_all": ["IPR026444"], "interpro_used": ["IPR026444"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein is assigned to 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 derived from Starkeya nomas and exhibits UniProt keyword tags Signal.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 6304, 1942, 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, 3595, 2037, 26052, 10676, 1019, 9684, 1934, 1930, 9826, 20709, 11121, 2538, 14392, 2733, 18, 3], "output": "MKTTVKLVVALAATLFVAPAFAQDKITLDEVVKRTNGKVEWKYFPDDTMVKQAFVPSAITTLDNWIGRVPQVAITASPLWTLTMEQAQAELQPDKLLSLFDIGAPALFSKFDARDPAALKGRTLRDVYSALQRGAIDGALGGLQGAYGLKHYEVTKYVMNRRSFERLPDDVKKAVLEATQVALDTTNKEIAQSAAWEAALKDYREEIKDEFPAETVALVTSVRSLATWGASSHPQVKTYAKVFMPGGQVDISLKPLFQHFEKLLAKQNTAYSKGASQSLQALGAAPVTMGVAYALGTGGVLGALINGYQQYLADTRKHGLEVSELKPGTPER", "metadata": {"id": "A0A5S9Q6F4", "cluster": 12200241, "interpro_all": ["IPR018389", "IPR038404"], "interpro_used": ["IPR018389"], "interpro_unused": ["IPR038404"]}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein can be placed in the Protein of unknown function DUF6952 family, which comprises uncharacterised bacterial proteins distinguished by highly conserved acidic residues and a C-terminal G[S/A]ID motif. It has been detected in Bacteroidia bacterium.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 17136, 8803, 1028, 3416, 16, 2154, 12936, 23229, 3495, 4543, 2697, 12080, 2007, 3626, 5305, 9931, 4248, 1930, 43, 45, 17, 4262, 49, 37, 61, 19, 43, 39, 2313, 5219, 18, 2176, 2258, 2252, 3330, 1922, 24323, 2126, 14061, 18, 3], "output": "MKLAVIGNSIKFDVPGEDEGEQLTKDFFKRVRNSISKDLVENKTLPELIEAETQLLNHILAAIEILKQVENDNIDLRTAI", "metadata": {"id": "A0A923TU38", "cluster": 12952878, "interpro_all": ["IPR053810"], "interpro_used": ["IPR053810"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is categorized in the Carboxypeptidase-like, regulatory domain superfamily, which constitutes a regulatory $\\beta$-sandwich module found in eukaryotic M14B metallopeptidases, such as carboxypeptidase D and E, and teneurin signal transducers. This domain adopts a Greek-key topology and shares structural homology with bacterial outer membrane proteins involved in nutrient binding. Furthermore, the protein is associated with the Histidine phosphatase superfamily, which encompasses a diverse group of enzymes, including acid phosphatases, phytases, and cofactor-dependent phosphoglycerate mutases, that catalyze the hydrolysis of phosphate esters or the transfer of phosphoryl groups. These proteins share a conserved catalytic core centered on a histidine residue that becomes transiently phosphorylated during the reaction, with members functioning in pathways ranging from glycolysis to phytate degradation. It is identified in Desulfotomaculum sp. Give me the amino acid sequence considering the above function.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 15750, 9626, 2410, 9200, 17, 3189, 16, 4948, 3418, 13975, 16, 2154, 14879, 43, 4948, 8, 38, 4666, 8, 17, 18038, 9059, 2435, 1922, 10825, 8510, 14919, 8969, 24897, 1036, 16, 2427, 1966, 15750, 9626, 2410, 9200, 46, 1930, 47, 16, 1930, 5656, 3708, 5572, 2733, 26307, 18, 2052, 3418, 24032, 43, 27568, 17, 3834, 13678, 1930, 16495, 4346, 9039, 1956, 4543, 7642, 3260, 2697, 3286, 1922, 8708, 2743, 18, 3677, 16, 1920, 2213, 1977, 2458, 1956, 1920, 13873, 8167, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 5038, 16, 2710, 2687, 19131, 16, 9321, 2319, 16, 1930, 15155, 17, 3100, 8078, 14966, 2010, 2446, 2319, 16, 1988, 18170, 1920, 9128, 1927, 5413, 16785, 2014, 1920, 3856, 1927, 12556, 2671, 18, 2144, 2697, 7948, 43, 5305, 6804, 4728, 10841, 1990, 43, 13873, 6181, 1988, 8272, 12145, 7199, 2409, 1920, 3227, 16, 1956, 4678, 7295, 1922, 3873, 6485, 2037, 13393, 1942, 9321, 2010, 4877, 18, 2176, 1977, 2899, 1922, 30311, 11957, 1948, 7705, 2056, 18, 7031, 2142, 1920, 3835, 2687, 3244, 6300, 1920, 3538, 2347, 18, 3], "output": "MMYERKPDGGIGPKIPGVKITFVRENGSATKTVTTNKDGFYRISLKKGRYIVSATHSDYEEYTSSPGFIVVTGSGYQTGNIFMKKILMTTVLLIRHAEKSNDSLSSAGMLRADELVHVAKKAGVEAIFATNTNRSQETVQPLATELGLILNIYQQYDEIQEISNKVLTKYAGKVVLVAGHSDTLHTIIEAFGGDPNKCCINGDEFDNLCVITIYGPGKYMDGSRDFDPMCAELL", "metadata": {"id": "A0A356UJN2", "cluster": 14076783, "interpro_all": ["IPR008969", "IPR029033"], "interpro_used": ["IPR008969", "IPR029033"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is associated with the Recombination endonuclease VII family, which includes bacteriophage T4 endonuclease VII and recognizes a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. These proteins form elongated, intertwined molecular dimers characterized by extreme domain swapping and a novel 'four-helix cross' motif. In addition, the protein falls within the His-Me finger superfamily, which comprises diverse endonuclease proteins found in all forms of life that are involved in efficient, nonspecific DNA cleavage. Also known as HNH nucleases, these proteins feature a structural core consisting of a $\\beta$-hairpin and an $\\alpha$-helix that coordinates a single catalytic metal ion essential for enzymatic activity. It has been detected in Leptolyngbyaceae cyanobacterium RM2_2_4.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 1977, 2458, 1956, 1920, 7827, 18697, 16852, 3416, 16, 2154, 5921, 24613, 10773, 18697, 16852, 1930, 16197, 43, 4949, 5648, 1927, 2678, 6249, 6485, 2037, 16484, 20207, 1942, 2957, 5170, 20987, 18, 2144, 2697, 2386, 16158, 16, 27332, 17860, 1919, 3272, 13351, 4378, 2007, 9848, 3418, 3476, 5041, 1930, 43, 4008, 11, 3006, 17, 7864, 3567, 11, 5219, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 4167, 17, 2142, 8497, 13975, 16, 2154, 12936, 6445, 18697, 2697, 2435, 1922, 2136, 4952, 1927, 3308, 1988, 2032, 3286, 1922, 5807, 16, 12720, 2678, 6404, 18, 2222, 3171, 1966, 9888, 1023, 29305, 16, 2144, 2697, 5961, 43, 4346, 4728, 7600, 1927, 43, 8, 38, 4666, 8, 17, 14565, 1930, 1925, 8, 38, 4595, 8, 17, 7864, 1988, 10675, 43, 2957, 6804, 6048, 4755, 4415, 1958, 8145, 2455, 18, 2176, 2258, 2252, 3330, 1922, 16976, 26558, 2029, 4864, 9914, 26898, 7972, 2341, 18842, 1989, 10625, 1028, 41, 22, 41, 24, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MSIQSTNWAKNNREKARLIEQRIRQQNKCLICDKHKSMNKNGGIGIFRDNPSLILKAAEYLKSNGTRAKHPFTRVNAKFKARYGITLAEYEKMSKLFVDHCHSTMKVRGLLCDDCNK", "metadata": {"id": "A0A9E5RD94", "cluster": 15625164, "interpro_all": ["IPR004211", "IPR038563", "IPR044925"], "interpro_used": ["IPR004211", "IPR044925"], "interpro_unused": ["IPR038563"]}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein belongs to the AGC serine/threonine-protein kinase family, which phosphorylates diverse substrates to regulate essential cellular processes including proliferation, apoptosis, migration, and cell cycle progression. These kinases mediate signaling pathways involved in transcription regulation, organ size control, and cellular responses to stress and external stimuli. Moreover, the protein incorporates 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 includes 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 identified in Lymnaea stagnalis (Great pond snail) (Helix stagnalis) and is linked to UniProt keywords ATP-binding and Transferase.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 1920, 21879, 8468, 19, 13143, 17, 2213, 4016, 3416, 16, 2154, 18360, 6445, 6249, 1942, 5741, 4415, 3689, 4028, 2710, 4031, 16, 4091, 16, 5049, 16, 1930, 2024, 4048, 4380, 18, 2144, 7784, 8265, 3197, 3873, 3286, 1922, 3213, 3640, 16, 3090, 3081, 2285, 16, 1930, 3689, 3387, 1942, 3071, 1930, 5771, 5458, 18, 3950, 16, 1920, 2213, 19683, 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, 5921, 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, 2899, 1922, 24494, 26243, 1019, 23891, 3223, 19337, 12, 4733, 15065, 1007, 15929, 13, 12, 7864, 23891, 3223, 19337, 13, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 1930, 13763, 18, 3], "output": "MEESPTSASDSLQDLDIKNKRLANIVQKGTATLASTGKFNLSNEYNPFQFGPKEQSFVVKKVDANKRFEEINAVFKLIEDARDSKTPRGLVLNPEKVSTKLEFEDHVDQIKNLTVLGKGAYSEVILVKDKQTGNNIALKTIMLIQFHRDQILAWIHLGAENLAPELYSFQMENNSVVMKMEVIKGLSLADVLDKGYIKNLDDSVCLSMFVLEGLLNAYESLRSQNFVHQDMHPGNVMIDNKLSVKLLDFDQARRLLSDPSRDIESIKNDIVGIIRIFCLAYSGYDFNDVFEAKKFLEAKNLEELSSSIEHIPEEQRKELYKIMYMLFESVRHPRQENFGDTKHVSNYVKDYFNRESTNMKKKLAVILFPEKFQEREEPDSGYKFECDSDDYSVWDDPDMDGFVQKVTDEDLRKLGVFSLF", "metadata": {"id": "A0AAV2ILD0", "cluster": 16022011, "interpro_all": ["IPR011009", "IPR000719", "IPR017441", "IPR050236"], "interpro_used": ["IPR050236", "IPR017441", "IPR000719"], "interpro_unused": ["IPR011009"]}, "task_type": "autoregressive"} {"instruction": "I want to make a protein that can have this function: The protein should include a Membrane attack complex component/perforin (MACPF) domain that mediates transmembrane pore formation and cell lysis through oligomerization and conformational change. Found in contexts ranging from vertebrate immunity to pathogen invasion, this domain assembles into ring-like complexes to breach lipid bilayers, a process structurally supported by a central kinked four-stranded antiparallel beta-sheet. It is produced by Fusarium oxysporum f. sp. radicis-cucumerinum. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 3066, 3951, 43, 3260, 8926, 2796, 4594, 19, 28039, 12, 3433, 1034, 1038, 13, 3418, 1988, 10412, 9117, 8554, 3337, 1930, 2024, 8502, 2596, 17371, 1930, 8523, 3185, 18, 2435, 1922, 11144, 6485, 2037, 13416, 7611, 1942, 7055, 6254, 16, 2052, 3418, 17421, 1036, 2460, 6335, 17, 3189, 5048, 1942, 3022, 2155, 4486, 21992, 16, 43, 2585, 12171, 4427, 2007, 43, 4101, 30322, 1919, 3006, 17, 10338, 28892, 4666, 17, 11130, 18, 2176, 1977, 4152, 2007, 24470, 20004, 3508, 17279, 48, 18, 2056, 18, 3271, 3349, 1036, 17, 18242, 29419, 28658, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MAKEISTQKQDGNRSEDERPSVKASKKQFSFDEEFDVFLKELAKASDGKEDVSVVSSRLITFHDLKNKGAKDGYSLRTLPLSKLSSRFRNGFFCLRSMDMARVDSSMSLKDYKDRESQSDNGEKRHPSMNVYWTRGFQGDLKKTLKDISEPEKLPKDDEKPIEPDTLSDYQSALTTEQSIGMEKLKEKYSLYGLSRDDWSHVIEGNQLLYAFQVDVDLANRLQALSLQDFLEAEPKKAAPASNNEPQANDPNQPVDPRTISPNFSIMSTVNPVVPISRSTRPVFIINPDSGIGSSEKDEPESTKVHAGLFWSSPNILSSTKIMKVEDTLQQWSLQSGMSSKSFEAGLSIPIGKASVGTKFGFEREQSNRDERENKVKGSSLTALHLITTAQVNINETTVLLSPDAQTDIKRLRQKRRFSDLYTFLVKYGTQVYQTVTLGGQLYHAQSLSSTDTQHEQEQTNTVKKSMNASLGIPDLVEVTTGYSQQDSNKMVEGNREVHTTENLAWSGIGGNPTLIVDPPKWRESLNEYTNWRPIRYETPVRIDTFIGRIQGYSDVPVLFAEILSTGVLNRSIIALPPTGLKNGETTFQYSAPTPGMIINATTGTTLPILTTLSTIPEEVTPGGYSWAVYTEERRVQQEIRASLQSTLNLVVNINYHAPYLKGLHADTNSFSIVLKWTSSSVRESWKLDVQPDTEESTKVKDDLKDSVPKLEEVKKRQNDATTAWEQTKLNLEKEKTSWPTWKKGTPEEKQKAEEQEKALKDAEEKRAIEKSEIDQDLAQHTEKVTYAKVLGLVTADETDSKQFVLRNISSEAWIMGLWTICRKPSNAAPSNSSGNNKLKPLSTEDFEDLKSAFVQRFSGPQDIEGGCDFISDVLRNQLDVDVKFSMFASDGVARQETEVHSNIDPKYAFDFIDRRISLSSIHYLAVTGEIVPATGCQLLPAGYSSEAILLQYQEALARLIFLETRYKKDEVYKNIEDLKKKLEDIDTKQVGEAQTSLTDLFKEIYKLEV", "metadata": {"id": "A0A2H3GLL3", "cluster": 18583681, "interpro_all": ["IPR020864"], "interpro_used": ["IPR020864"], "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 carries a MarR-type HTH domain that functions as a winged helix-turn-helix (wHTH) DNA-binding module found in bacterial and archaeal transcriptional regulators. It typically facilitates homodimerization and interaction with the DNA major groove to control genes involved in antibiotic resistance, oxidative stress, and virulence, often in response to aromatic compounds. Moreover, 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. It has been detected in Peptococcaceae bacterium BRH_c8a.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 30, 1920, 2213, 16252, 43, 3684, 1005, 17, 2601, 5334, 1023, 3418, 1988, 4088, 1966, 43, 12920, 1919, 7864, 17, 5165, 17, 7864, 12, 2003, 1963, 13, 2678, 17, 2743, 9059, 2435, 1922, 4543, 1930, 22367, 5224, 9098, 18, 2176, 5745, 11374, 21189, 2466, 1930, 2835, 1956, 1920, 2678, 3044, 15920, 1942, 2285, 2628, 3286, 1922, 7267, 3554, 16, 5163, 3071, 16, 1930, 9304, 16, 3868, 1922, 2644, 1942, 10761, 4300, 18, 3950, 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, 2176, 2258, 2252, 3330, 1922, 23045, 26941, 9914, 14061, 2387, 1023, 41, 19189, 1019, 18, 3], "output": "MMPHMVRRMHQEMTQALADGITGNQFFVMKMMADRGRMTVSEVAEGFNVSLSAVTSLVDRLCKVEMIQRRRSEDDRRVVWLELTEQGRDMVFTCQASRRRVMQRYLGQLEEGELKFMIAIYEKIISMMLREEQGQVSEER", "metadata": {"id": "A0A0F2PCU1", "cluster": 20176671, "interpro_all": ["IPR000835", "IPR039422", "IPR036388", "IPR036390"], "interpro_used": ["IPR000835", "IPR036388"], "interpro_unused": ["IPR036390", "IPR039422"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein is included in the Fido-like domain superfamily, which comprises globular $\\alpha$-helical domains found in diverse proteins across all kingdoms, including bacterial virulence factors and animal homologues. These domains typically function as enzymes that catalyze AMPylation, a post-translational modification involving the covalent attachment of AMP to substrates such as Rho GTPases to regulate signaling events. This enzymatic activity relies on a conserved central motif containing a critical catalytic histidine residue. It originates from Sphagnurus paluster.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 22394, 1037, 17, 3189, 3418, 13975, 16, 2154, 12936, 20975, 8, 38, 4595, 8, 17, 11514, 4682, 2435, 1922, 6445, 2697, 3436, 2136, 13543, 1036, 16, 2710, 4543, 9304, 2790, 1930, 4027, 18541, 18, 2144, 4682, 5745, 2347, 1966, 5038, 1988, 18170, 3681, 3017, 16, 43, 2753, 17, 8414, 6295, 5884, 1920, 13577, 8576, 1927, 3681, 1942, 6249, 2427, 1966, 10585, 18390, 1942, 5741, 3197, 3916, 18, 2052, 8145, 2455, 12850, 1990, 43, 5305, 4101, 5219, 3165, 43, 4140, 6804, 13873, 6181, 18, 2176, 22970, 2037, 9445, 2531, 19756, 5755, 25078, 18, 3], "output": "MVPHFGHGLNTATGVSNPARVPTPAIGALDLTLQHCESDNTIKFPDFVHDCERVISLILREPENYRKVSESTVQPTLVLAFLRAEAVYKSHWKQDPRIAYLFSDLLVRLDAFEYALEVLHELFAQLAEPGPLVAEAIAYVEKLRLERVEQSKRSNFDQSSTPLFSPFNFVTVLQLAINSSQSRISWLYEPNKIAPIPLLEELSVPILQFTSFPNYCLTPAELSRLVRAIAVHTSIVEGVVTLTSNLTEALVSLGFEFQTFEGIDMDPETKAFTQQVLIDAQEATSMALDSTGDATRLFDAQHMGEIHAMFTRTACIVSSTTGGQRISSFIGRGCYKTLSNHVLTQSGKYHVYCPPEYVDSEIIQLFVMLQGANGRLARALTSSVLRFYGLLPMLVSMHDRPDYILALMQVQTPRLPMPAFLLTLLDMLLVDLQADAGNLKPLAHFIARQQLQAYLIAKSCLAGPDTPVIYAPVRATRIEAAHSFIFKCMNELAPRYWRKVDLHETAPLRPLCNITIHDLHTIKVVPVISASTSSEQSRNQFHLLYGSLWPLETDVFVVYLTTESPVEQELGFYPIRALTGLVYADDAQVWEARLRSFLLDDVAGVMASEPVLHEIYCALRKQLASGPEDFAEVDCRGLAFVKNHQTLHNGQHTLLITLSDFVP", "metadata": {"id": "A0A9P7K4C9", "cluster": 22457512, "interpro_all": ["IPR036597"], "interpro_used": ["IPR036597"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I'm looking for an amino acid sequence that when folded into a protein achieves the following function: The protein belongs to the Global Transcriptional Regulators in Environmental Response family, which functions as a global regulatory system involved in cellular adaptation to environmental changes such as oxygen levels and alternative electron acceptors. Members act as activators or repressors, often modulated by allosteric effectors like cAMP or c-di-GMP, to control genes governing anaerobic respiration, nitrogen fixation, virulence factors, and carbon catabolite repression. Moreover, the protein contains 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. Furthermore, the protein should have 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. It is produced by Omnitrophica bacterium (Omnitrophota bacterium) and is associated with UniProt keywords Transcription regulation. 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, 4906, 5224, 9098, 1922, 4813, 2644, 3416, 16, 2154, 4088, 1966, 43, 4906, 4948, 2433, 3286, 1922, 3689, 7810, 1942, 4813, 2840, 2427, 1966, 4612, 2428, 1930, 5012, 4995, 27916, 18, 4678, 4033, 1966, 15497, 2014, 26446, 16, 3868, 9985, 2007, 14772, 13066, 3189, 6225, 2014, 45, 17, 2137, 17, 18033, 16, 1942, 2285, 2628, 20012, 12554, 11695, 16, 6634, 7938, 16, 9304, 2790, 16, 1930, 5056, 3115, 3016, 2394, 10084, 18, 3950, 16, 1920, 2213, 5461, 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, 3677, 16, 1920, 2213, 3066, 2162, 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, 2176, 1977, 4152, 2007, 18825, 3032, 24888, 3375, 14061, 12, 18825, 3032, 2102, 7336, 14061, 13, 1930, 1977, 2458, 1956, 20709, 11569, 3213, 3640, 18, 7031, 1920, 3244, 18, 3], "output": "IATDKLWYLKRINLFKAMNADEMLDLAQRTTMKNYRKKEIIYLPGQPGQHIYLLKKGVVKISRLTPEGRELTLALLKPGEIFGELEVLGEKGGGTQAEAHSDVMICILNRKDLIGLMQSKPELGIRLSKIIGFRRQVIENRMENLIFRNVSQRLSSLFIELKDDFGEEQNGKLKINIPLTHEDVANLIGAARATVSETITEFRNNGLIETSGKYFLIKDIDSLKRNLA", "metadata": {"id": "A0A955RYN2", "cluster": 22743138, "interpro_all": ["IPR000595", "IPR018490", "IPR050397", "IPR012318", "IPR014710", "IPR036388", "IPR036390"], "interpro_used": ["IPR050397", "IPR000595", "IPR012318"], "interpro_unused": ["IPR018490", "IPR036390", "IPR036388", "IPR014710"]}, "task_type": "autoregressive"} {"instruction": "The protein includes 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. Also, the protein has 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. Also, 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 produced by Trypanosoma vivax (strain Y486) and is classified with UniProt keywords ATP-binding, Transmembrane, and Membrane. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 5921, 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, 2222, 16, 1920, 2213, 2258, 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, 2222, 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, 4152, 2007, 29504, 20236, 12, 3943, 67, 28839, 13, 1930, 1977, 5947, 1956, 20709, 11569, 4498, 17, 2743, 16, 9117, 16, 1930, 3260, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "FAVACAHFTVLLGHYNKLSTVVIALALVWFLTPLVCLVVIAVLYRWECPERDECCSFVARASGGAVPCCGSTELGRAGVGATIAQPRCIAVPPFVSVANMDREPCGEPKVTRGLPSSLSGEAGLSPQDTHKLRACEGDVFFSDNLCPPFLLVSVSGGCVVGASDSFAKCIGFTVGELVGEKFEHLLAALNVECGAELLGIMQSLVAEAVPPTRGYNEVICSQENASHEVGGAVSERRASNSASPLHCSRGVGVALGECGECADRAEELCDPRTGGCIWHRVLLRGCKLRRSPKATRAFGDTGLLSACDCGVANSFRSDRDEVNDQSAPAGSAQEVVLSGSSFSFVVDVWVDRTLRSGEGCVVIRQPLLYWLVDHVPLPCFLVHPETGCVLHWTGAAEECTGQTAYNMVGSPVCVTSPTASAEGRLVERVGGDAECEELLNHCGTGFSALLHVPQDCQPFVVTLRQVHGKYTEVESRLPAGNVVGLVWPPRLPSCTAGVHFRGGRMAPVSEVGSSSTVRRGLEGTATLPCVPSTDGKETCMDGRASKSNCPVGWLSGLLNIPQRCSGVWPAEGVPFLCVIERRSSGRTMTAWSAGLATACQNGREPSSERGEGLVHLAKFSRDVKQSPGGGGLTDARHNIAVSGRLRELIAPSVASPLRQLGEALGSTLQETAGCNNGQDQPTSTSEGDEAGCCVTPGHPAPTAGLTSGGPESGEEYGGAAAEPVTIQPSGQTVPGTDDYVSTLAPRRSAMTRAGACAASGISGAVEELDGKNTKIFAEGMCYRDVPLVSELGSDGPLHIGAKAPLVDGSQPCSFPSDVPSLLSPMPERHTTEMNGSRTPSNGGVITIEDQKVRPLGVGPVGLTASSVQEQCLSDWSLKSPWGNNPSSSTRAEQCLVPDGGFAGPPGGCNGGGTEEPPIWAMLKSYDETTIPSFCIRVGPGEPFLFGRSSKCHATTTDTYVSSVQFSILYKSEAQEMNGAIKVSYLQDYRSEGRAEGVHSASPTSASHLCSEVLAGRKVRLRDNSVNGTYVNVKRVGRGRTCVLHDQDLITFRMGSSRFFLGFKFLLTDIRGVPLNATPATSISSRPTVAPGSSATSRRGTPHFYQCVSESVGTVSRGGSASEVSVPNRLSSDLGRRIAGGGHSGGGVESSRRGGTPITRRSRGRRCSTGAHSREVIEWKIGEEMLGKGGNAEVFLGMNLTNGKLIAVKRVPLPRVAMGDGGGRDVQQQYRCLQEEIKVLSKAVHPNIVQYYGSSQNDSYFNILLEFVPGGSLRHLLDNFGVLSPVVICSYLGQTLEGLFYLHKNNIVHSDLKAANILITDRGRVKLSDFGTARLLNRQRGHSQECQDVRMPPGNSADSGALLTLHVAGTLRWMAPELLRDSCGPTVASDIWSVGCVLIEMLSGEGPWYEYDFESEEELINLLMYTSEPPEVPECQTLPELTTIAKKCLTLVPEERPTCEQLLRYVRHAKEQLELVWEDLV", "metadata": {"id": "G0TYZ9", "cluster": 22761039, "interpro_all": ["IPR000253", "IPR011009", "IPR000719", "IPR017441", "IPR008271", "IPR008984"], "interpro_used": ["IPR008271", "IPR000253", "IPR017441"], "interpro_unused": ["IPR000719", "IPR011009", "IPR008984"]}, "task_type": "autoregressive"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein should contain a Domain of unknown function DUF6535 domain that constitutes an integral membrane region within a large family of fungal proteins. This domain likely contains three transmembrane helices and is sometimes found in two copies, although its specific biological function remains unknown. It is expressed in Laetiporus sulphureus 93-53 and has UniProt annotations Transmembrane helix.", "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, 3418, 1927, 5435, 2347, 4855, 17136, 3786, 1015, 3418, 1988, 14879, 1925, 12328, 3260, 3031, 2651, 43, 3103, 3416, 1927, 8697, 2697, 18, 2052, 3418, 3205, 5461, 2559, 9117, 12789, 1930, 1977, 8929, 2435, 1922, 2288, 9425, 16, 2876, 2496, 2487, 3933, 2347, 4497, 5435, 18, 2176, 1977, 3198, 1922, 21744, 14245, 1924, 1957, 13528, 2027, 1957, 6156, 17, 4522, 1930, 2258, 20709, 15010, 9117, 7864, 18, 3], "output": "PATAALSNSYFAAAERISALSLTLITAFISIIVRTWLHLWHFWRRGLANRKVPEIIGWLPFLLQIAYIISAMVVSLGFFIVATVAFTLMTPEWGAIVALIRAIRHIFSRGPFYKLSNDWTAFEEHCLNVNYQDDLLEDVIRPRLRAASAEEALSVIRDPTVSSLIAEERGLKTIAQLNESETSQSGETHLSGTSPVIVNGLWFNYSTRFSTFLTTHERIIALILFLCGLILFIDTLSPLCSYKSPQTWYFLVFATKLAWGPISYLLIPVSKRWNSALLIEVDAAAKDDTFLIDILKHRAIKIRDPTKIAQITMDAMFTTLGA", "metadata": {"id": "A0A165DN30", "cluster": 25909231, "interpro_all": ["IPR045338"], "interpro_used": ["IPR045338"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein belongs to the Elongator complex protein 5 family, which serves as a component of the accessory subcomplex within the eukaryotic Elongator complex. This complex is primarily required for the modification of uridine nucleosides at the wobble position of tRNAs to generate 5-methoxy-carbonylmethyl and 5-carbamoylmethyl groups, in addition to playing roles in transcriptional elongation and histone acetylation. It has been detected in Chlamydomonas schloesseri and exhibits UniProt keyword tags Cytoplasm, Nucleus, and tRNA processing. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 1920, 7846, 3061, 2796, 2213, 25, 3416, 16, 2154, 10634, 1966, 43, 4594, 1927, 1920, 15954, 5736, 19667, 2651, 1920, 10825, 7846, 3061, 2796, 18, 2052, 2796, 1977, 5985, 3414, 1958, 1920, 6295, 1927, 26104, 18015, 1036, 2019, 1920, 26334, 6936, 1952, 3507, 1927, 20770, 1942, 5655, 25, 17, 17954, 17, 14201, 21312, 1930, 25, 17, 17742, 10921, 21312, 2671, 16, 1922, 2459, 1942, 14797, 5456, 1922, 5224, 9971, 1930, 6632, 10339, 18, 2176, 2258, 2252, 3330, 1922, 14667, 10480, 2966, 6012, 1979, 18842, 1930, 9826, 20709, 11121, 2538, 14392, 5239, 16, 5607, 16, 1930, 10089, 4587, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MRQGRSQATVVRLVDLTGTLAPVAAEAAASAPRSASAGGPDVEYVDLHSDPWGWHRGAAATAQPGQGAADQEAAAGPGPGSAAAAAAAAAAGAAAGAATAAGRGAGPLVSLDDLLDQLVRPASQSAQTPDAGRGGVCVVLGCLSSLVERYGGVGNGGSGCGGGGADGGGGGEWAALALVEALQRAPAVSCVLASVHTDLHSEAAVEGLRRAASCVLQLGALTDLQQRLAAAALQGSGRAQQLHGGALAGRLDCRTRRRTGRVKVESELYSISLQPAAPGAGGGAAAAAATAAPAVHFFAMPPQVDAPDPKALLRLQPPASAASSAAAPAAAPAGGGGGGAAAPGVAAGAAGAGGAGQPLGLMGGVGTAEELARAVGSSMRLTLTEEERRAKQAVVLPYQHTGTGLRGPAAAAYAAGDHAGYLPPAAGGRGPGAAGGAGAAGGGGEAAGAVGGPGARGGGLGHILYVRDSASEQDSDQDLDEDLDI", "metadata": {"id": "A0A836BCP0", "cluster": 27477042, "interpro_all": ["IPR019519"], "interpro_used": ["IPR019519"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein incorporates a Mur ligase, C-terminal domain that facilitates the sequential addition of amino acids to UDP-N-acetylmuramic acid during bacterial peptidoglycan biosynthesis. Adopting a dihydrofolate reductase-like fold, this domain is responsible for binding the incoming amino acid substrate in enzymes such as MurC, MurD, MurE, and MurF, as well as in folylpolyglutamate synthase and cyanophycin synthetase. Additionally, the protein includes a Mur ligase, central domain that functions as the ATP-binding catalytic module in the MurC, MurD, MurE, and MurF enzymes responsible for the stepwise assembly of the bacterial peptidoglycan stem peptide. This domain shares structural similarity with ATPase domains and is also present in folylpolyglutamate synthetase and cyanophycin synthetase, where it drives ATP-dependent ligation reactions for folate metabolism and cyanophycin storage. In addition, the protein has a Folylpolyglutamate synthetase conserved site that belongs to the ATP-dependent enzyme responsible for adding polyglutamate tails to folate and its derivatives, thereby aiding in the retention of the intracellular folate pool. This site is situated within the active site in a large interdomain cleft adjacent to an ATP-binding P-loop motif. It is produced by uncultured Clostridium sp and is classified with UniProt keywords Cell cycle, Magnesium, and Cytoplasm.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 19683, 43, 6185, 11905, 16, 45, 17, 4262, 3418, 1988, 11374, 1920, 9454, 2459, 1927, 3835, 4576, 1942, 18500, 17, 56, 17, 6894, 23010, 29085, 1935, 2687, 2409, 4543, 24183, 8132, 18, 20478, 43, 11842, 27851, 11386, 17, 3189, 3728, 16, 2052, 3418, 1977, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 4510, 1922, 5038, 2427, 1966, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 16, 1966, 2486, 1966, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 8921, 1930, 26898, 25818, 3665, 18185, 18, 4950, 16, 1920, 2213, 5921, 43, 6185, 11905, 16, 4101, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 6804, 9059, 1922, 1920, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 5038, 5061, 1958, 1920, 13846, 5957, 1927, 1920, 4543, 24183, 4402, 4207, 18, 2052, 3418, 16495, 4346, 6796, 1956, 9444, 4682, 1930, 1977, 2222, 2481, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 1930, 26898, 25818, 3665, 18185, 16, 2597, 2176, 15435, 4498, 17, 3100, 11102, 5298, 1958, 13761, 4714, 1930, 26898, 25818, 3665, 7451, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 5305, 3200, 1988, 14440, 1942, 1920, 4498, 17, 3100, 4113, 5061, 1958, 8013, 16115, 26697, 21084, 18103, 1942, 13761, 1930, 2496, 8383, 16, 6113, 8379, 1941, 1922, 1920, 7521, 1927, 1920, 4776, 13761, 5562, 18, 2052, 3200, 1977, 18287, 2651, 1920, 3500, 3200, 1922, 43, 3103, 13633, 2954, 1921, 14649, 6811, 1942, 1925, 4498, 17, 2743, 58, 17, 5881, 5219, 18, 2176, 1977, 4152, 2007, 5269, 21058, 21156, 2056, 1930, 1977, 5947, 1956, 20709, 11569, 2024, 4048, 16, 13148, 16, 1930, 5239, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MELSELLTGLTYEVLKGTVERKIRKVTDGHDFVGKALERGATALVIQSEECYERWIRALYGYPARKMKVIGITGTKGKTTTACMVQQLLNYGGHKTESCQIQAYLHEMVVAGCDSVVMEVSSQGLKLKRTAGIRFEVGIFTEYLQCKHLLFLQSKVGIGNADDPWYEEIFEGTECEKITYCFGIRYRLGMADGKRQAEEIEIELPLPGHFNVYIREGLKKIRIPGRMELAAAWRDGMVFVDYAHNAMSLKSILQMLKERRYEMGEVAGRYADFTVITTDNPRYEEPGEIIKDILTGMKRSGDVIIIAGKGHETYQEIQGIRYEMDDRKLVKEITCTQILSNDTENIGERDVFVCIKGYCRCEDFLPDSRNVTIIRVSDTRYALALMSAGLIGTVRVDTGRRILSSYNTTPNLGRDHIGTSEHADFEGCGGGCVQMDYHALDIRKICRRDNSMAAAAAVRYLGVENETREYADGRIVVVFGCGGNRSTNGAYVVVEDRREAVRYAIENRK", "metadata": {"id": "A0A1C6FPS1", "cluster": 9844456, "interpro_all": ["IPR018109", "IPR036565", "IPR004101", "IPR036615", "IPR013221", "IPR000713", "IPR035911", "IPR005761"], "interpro_used": ["IPR004101", "IPR013221", "IPR018109"], "interpro_unused": ["IPR036615", "IPR035911", "IPR036565", "IPR000713", "IPR005761"]}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein features a Low-density lipoprotein (LDL) receptor class A conserved site that functions as a calcium-dependent ligand-binding module, primarily interacting with LDL and other positively charged substrates. This cysteine-rich domain utilizes a conserved cluster of acidic residues to mediate high-affinity interactions essential for cholesterol transport, endocytosis, and complement activation. Furthermore, the protein includes 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. In addition, the protein has a Frizzled domain that functions as an extracellular binding interface for Wnt glycoproteins. Also known as a cysteine-rich domain (CRD), it adopts a predominantly alpha-helical structure stabilized by ten conserved cysteines forming a network of disulfide bonds. This module is found in diverse signaling proteins, including Frizzled family receptors, receptor tyrosine kinases, and secreted Wnt antagonists. It is present in Strigamia maritima (European centipede) (Geophilus maritimus) and is classified with UniProt keywords Signal-anchor and Transmembrane.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 4075, 43, 2330, 17, 3824, 9694, 12, 8017, 13, 3148, 2921, 43, 5305, 3200, 1988, 4088, 1966, 43, 5016, 17, 3100, 5207, 17, 2743, 9059, 16, 5985, 8615, 1956, 8017, 1930, 2303, 6629, 9516, 6249, 18, 2052, 8666, 17, 5536, 3418, 18127, 43, 5305, 4377, 1927, 9931, 4248, 1942, 8265, 2149, 17, 5173, 3719, 4415, 1958, 5463, 4860, 16, 11914, 16, 1930, 5508, 2936, 18, 3677, 16, 1920, 2213, 5921, 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, 1922, 2459, 16, 1920, 2213, 2258, 43, 9081, 18559, 2824, 3418, 1988, 4088, 1966, 1925, 5329, 2743, 6854, 1958, 7028, 16268, 18, 2222, 3171, 1966, 43, 8666, 17, 5536, 3418, 12, 29509, 13, 16, 2176, 24032, 43, 7700, 4595, 17, 11514, 3170, 12017, 2007, 5656, 5305, 22446, 7402, 43, 3504, 1927, 11830, 9031, 18, 2052, 9059, 1977, 2435, 1922, 6445, 3197, 2697, 16, 2710, 9081, 18559, 2824, 3416, 4086, 16, 3148, 6941, 7784, 16, 1930, 8366, 7028, 10515, 18, 2176, 1977, 2481, 1922, 2114, 1950, 14981, 1019, 13081, 2265, 1019, 12, 6785, 20674, 7438, 1021, 13, 12, 14136, 24888, 5277, 1036, 13081, 2265, 1957, 13, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 17, 13333, 1930, 9117, 18, 3], "output": "MEEIDLPISIQQILENNSFNGGIVQIGNKNSVTICTAAEQLTLPKLSWLDEGLDLALDTFYMELQLDKDKRLIKLEELFHSSLLHDWANDAPYTEQFEMTFLIPLKNLPDDGIEDALAAIIPDRVLIVLDGFDEINKSQRQNVLRVMYRQRFYDATVIITSRCGEFYVRAEDLSECEVSRFVNNISPHCDVERLNSIANINPELFQCPLFIVLFCSLFNCIIKNSLTKDKKSFTKNFDIFDVSDKSSDCEKKILYEFGKMIKGWQKMSLFKTTSHFEAFHRSILDFIVAYAIWLDCSNLLDYLKKFISLYSNVEECIWDLISRNKLTKMGVVSGRIKKVCILDDDDDFGVLPDVLIPQLRLIVTNGNQIPHDELFSYLIDFHVFQIYLQSFKVINSKRNTIINLNSQTINKLPANFDSGGIDCLRRFTTALKVESLVKCELLENTFTSRHKLVDIFSLLPTSAEAVVVVKTSHSGYKKITYLNVNTPDRDILWSVLKVTTVSILRCLSNHFLNAFNTLPSCWPGFNKFRNLKCLELQMLGILKPSDHIDSLVKCILSLSVTNLSFHVEIKDDIEFPKCISVHNCEHTLVSDLLECVKLKLFLKVQFIINPDVWTDIVRKTNIDVRIVYHRSNTKDFKVGSVNTCIRRKEMDPKTIMEEIDLTASIQRNSPSGGILQIGNENMYSTFIIIKKLEFALKEIYKQLTLPKLSWLDEGLDLALDTFYMELQLDKLIESKPGYGKTTLCIKLLHDWANDAPYTEQFEMTFLIPLKNLPDDGIEDALARGKRVLIVLDGFDEINKSQRQNVLRVMYRQRFYDATVIITSRCGEFYVRAEDLENVKYTITGIIINLKIENRAIKKTGIMAINIKTEPNFLQDNSFNRGIIKIGYVDSITVMKEIYKQLSLPKLSWMDGGIDFTLDKFYMELELDDRVKQLIMLECIKLLYDWANDEPYTAQFKLAFLIPLKNLPKDGIEEGLAAILPDWRIDNLTVLIVLDGFDELSNGMKQNVLRVVYRQIYYEATVVLTCRSGEFIVQDLERASLYCDILRLEKVAQSNPELQLIICTEEHNEVPNQITMDVIIISMTTCISELEKEFSETNSSRYGYEETKHDSTEFSLFDDSSPEESNTVDNNLTSVEYPVSSNDTENDLNMWLNNDVTFNGSDNFSRSFELDSEQEKISFYYGPEITIDTSMFTHTMKETTTGKTSQMYTHPITQLSASWGFGNSDAIVTPTSVNPQSVVTKSASEGSQCRHRTLSFCDDVSSYNSWECNLWLKEYLCYILEPMCVDEVAVPPCNSLCKAAKKGCEAQILCAGLGNGEACKHNEYRCSDTTCIPGTWWCDGVMDCEQGDDEKDCHPRNRNPEAENCNDCLVKKLEFALKEIYKSNCNRLLIESKPGYGKTTLCIKCGIDKEDLMDIIMKRGKEKIFGTAAFKREFSNVKYTITGIAFLSSCSENIEELDTQTKLYAMMKLQFDICPLTEKVYKLGFLVKHAGLLRQFCNYMPFHSYASSFSFEELEKVKCINFILDFQFGTKIDHVECKLFGKNIKEFNGERDRKEWYENVSKGMIHFEELSLILCMGLSPNIWEIISLIQKLKEVCCAKTSYTLNTLSVYSIFNVNFDNIIDNKSYTSVTVCTAVEAVENCRDYLSDKRLIKLEELFDSSSNCNRLAIIPDCGIDKEDLMDIIMKKIFGTAAFKREFSPCAVGNDSNESEAKNLEFALDIFKYDCNRILIEGKPGFGKTTLRIIKEAGKNEIFSTPAFKREYPGVKYIITGIKENEIVKFMNDTALFRIPTKETRLSNVSSESGGAYYWDVNPSLSSDRAFNMELLTLKKIFMSSPLTYLPNLAGATTEFEKWQLVSYYNSIVDKFITGSPTLEAVFRCDVFPSAT", "metadata": {"id": "T1IS78", "cluster": 846052, "interpro_all": ["IPR020067", "IPR036790", "IPR036055", "IPR023415", "IPR002172", "IPR007111", "IPR027417"], "interpro_used": ["IPR023415", "IPR007111", "IPR020067"], "interpro_unused": ["IPR002172", "IPR027417", "IPR036790", "IPR036055"]}, "task_type": "infilling"} {"instruction": "I am designing a protein that has the following properties: The protein is assigned to 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 derived from Chloroflexota bacterium. 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, 6304, 1942, 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, 3595, 2037, 10107, 18222, 7336, 14061, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MPPQRASGTNTATTAAHATNNPNRNLRDTSPSQPDWASVNACPANRPAVRQPPPDSARSVSLGQEGYRISRTGDSCCIFAARRPCKDCPVEESAAIPRAHGHPMMTSAAIGACVGLLVAAALGVRYLSQVQEAAAAKAPVETYTVATGPIRSELAYSGLVSSVQQATVTPPSAGMLATVDVEVGRTVRAGDRIASLASESLPLQVQQAQADLQAAEARRAQLLTGPRATDVAGARAVLAAAEARLAQLSTPSLADVAAARATLATAQASVASSELAGDNSRAQLLGAIATACATNFSFGLPCGSADVPLSLDAQAAAESFLTSRAGDARSDLGARAVAVLTANAAYRTAIGNAAAARDNVAAARAKLEALGNPSAAEVSTQRAQIATARDTLEAKLTPYTEADMQAVNATISRAQAQTAIAEANLARTIVRAPFDGMVTQRMVEPGTNVTLQTPVLMLAAKGVEVRITLRDTDAPRISAGLAAEIAISGEERPLVGRVRQIAPSGDARAHTVDVIVAVDDPTGRLRPGTLAQVRLLTVQKANAIIVPASALITEGTAARVFTMVDGTVRIRTVTTGLADHLNVEVTDGLRAGDLVIVAGQNTLHEGQAVRPAR", "metadata": {"id": "A0A3L7X0L8", "cluster": 1245979, "interpro_all": ["IPR006143"], "interpro_used": ["IPR006143"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein features 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 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. Furthermore, the protein includes a MacB-like, ATP-binding domain that functions as the catalytic component of ABC transporter systems, including MacB macrolide exporters and the LolCDE lipoprotein release complex. It binds and hydrolyzes ATP via conserved Walker A and B motifs to energize the transmembrane transport of substrates such as antibiotics or lipoproteins. It is derived from candidate division BRC1 bacterium ADurb.BinA364 and has UniProt annotations Hydrolase.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 4075, 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, 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, 3677, 16, 1920, 2213, 5921, 43, 3433, 1014, 17, 3189, 16, 4498, 17, 2743, 3418, 1988, 4088, 1966, 1920, 6804, 4594, 1927, 7219, 9054, 3771, 16, 2710, 3433, 1014, 23929, 2261, 12660, 2045, 1930, 1920, 3004, 8293, 3695, 9694, 4012, 2796, 18, 2176, 6876, 1930, 7222, 20887, 4498, 3454, 5305, 20138, 43, 1930, 44, 8277, 1942, 2066, 2693, 2606, 1920, 9117, 4860, 1927, 6249, 2427, 1966, 7560, 2014, 18393, 18, 2176, 1977, 3595, 2037, 6610, 8451, 2387, 5800, 14061, 2041, 5223, 18, 8768, 12779, 8760, 1930, 2258, 20709, 15010, 20748, 18, 3], "output": "MLVLENATKTYIKDGKEVRALDGVSLAVPAGEALLRPDSGRVSVDGQDPYAMGPEARAMLRARVIGFVFQQFAETRADELIERFQLADRANHLPAELSTGQKQRAALARALLNRPVREGGAALMVTHDAQADHLATRIVAIDRGRLQEHAAAPSRQTEFVVARGPSGCGKSTLLLTAGHLAPYLTVRENVLAASLALRLPGKLLLADEPTGNLDPGNASVVLEHIADF", "metadata": {"id": "A0A1V5GM36", "cluster": 3476878, "interpro_all": ["IPR003593", "IPR003439", "IPR015854", "IPR017911", "IPR027417"], "interpro_used": ["IPR003593", "IPR003439", "IPR017911"], "interpro_unused": ["IPR015854", "IPR027417"]}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein contains a Rubrerythrin, diiron-binding domain that adopts a ferritin-like four-alpha-helix bundle fold to coordinate a diiron-oxo center. It typically functions as the N-terminal component of rubrerythrin proteins, playing a key role in the cellular response to oxidative stress. In addition, the protein is included in the Ferritin-like superfamily, which encompasses a diverse class of di-iron carboxylate proteins characterized by a four-helical bundle fold involved in iron storage, detoxification, and redox catalysis. Members range from iron-sequestering ferritins and bacterioferritins to DNA-protecting DPS proteins and enzymes like ribonucleotide reductases that perform oxidative reactions. These proteins typically assemble into multisubunit complexes with hollow interiors that solubilize mineral cores or house active sites across animals, plants, and microorganisms. It is present in 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, 5461, 43, 10010, 1936, 6907, 5856, 1921, 16, 26028, 2830, 17, 2743, 3418, 1988, 24032, 43, 15552, 17, 3189, 3006, 17, 4595, 17, 7864, 14142, 3728, 1942, 11865, 43, 26028, 2830, 17, 18588, 4102, 18, 2176, 5745, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 10010, 1936, 6907, 5856, 1921, 2697, 16, 14797, 43, 3834, 2770, 1922, 1920, 3689, 2644, 1942, 5163, 3071, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 15552, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2921, 1927, 2137, 17, 5680, 20877, 2697, 4378, 2007, 43, 3006, 17, 11514, 14142, 3728, 3286, 1922, 5680, 7451, 16, 18169, 16, 1930, 9366, 15408, 18, 4678, 3109, 2037, 5680, 17, 23504, 1941, 15552, 1036, 1930, 14027, 28079, 3027, 21881, 1942, 2678, 17, 15145, 25450, 2697, 1930, 5038, 3189, 18347, 4749, 11386, 1036, 1988, 2385, 5163, 5298, 18, 2144, 2697, 5745, 17421, 2460, 13564, 2255, 1983, 1932, 5048, 1956, 20010, 18110, 1036, 1988, 28911, 2606, 8463, 15715, 2014, 5953, 3500, 3402, 3436, 3555, 16, 4793, 16, 1930, 11679, 18, 2176, 1977, 2481, 1922, 14061, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MFNSIEDVLDFAREKEQDAYSELAKQEIRHRIVIIKNLELEKALLTTEKSKKLYSDLAQIVEDRELQNVYEKYLKGDFYLELAGRMLDAGMKKLFTEMRKGNVEIASHPKSLAIENAMLLALERERGSHIFKNLAADELEHQTSIQG", "metadata": {"id": "A0A7X8BM77", "cluster": 4281765, "interpro_all": ["IPR012347", "IPR009078", "IPR003251"], "interpro_used": ["IPR003251", "IPR009078"], "interpro_unused": ["IPR012347"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein should contain 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. Moreover, the protein is associated with 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. It occurs in Olpidium bornovanus and corresponds to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 3066, 5531, 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, 3950, 16, 1920, 2213, 1977, 2458, 1956, 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, 2176, 5110, 1922, 2865, 10984, 7408, 1989, 8813, 24883, 1957, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "RTISYAVTYLGGSVGFSDGDPHHIFDDAEVLRPTVYVGGPGDLKRFRQGVIDSVSVKGWFGKKAFWRAYRSKGEALRRGRLAKDGCWGRIAFSPTGVATLASYYDYGSYGGSHVGPPLPCNEIKLRDVAEMSHCARDEPNPRGEVCIRGHSVFGGYFGDTARTADVLSSDGWLATGDVGEWLPNGTLKFVGPEKVERSLTSSRLINQAFVYGEPDRPGLVAVIVPDEEGLAAVTAVSVFPAVIFAVLLLSLLRPLRDTRRKTHDVRSPRFFNGISKN", "metadata": {"id": "A0A8H7ZWR2", "cluster": 4887963, "interpro_all": ["IPR000873", "IPR042099"], "interpro_used": ["IPR000873", "IPR042099"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein features 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. Also, it is part of 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 has been detected in Sphingobacterium corticibacterium and is annotated with UniProt keywords Cell membrane, Protein transport, and Cell inner membrane.\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, 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, 2222, 16, 2176, 1977, 3131, 1927, 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, 2258, 2252, 3330, 1922, 13502, 12022, 8106, 26073, 2341, 18842, 1989, 1930, 1977, 10633, 1956, 20709, 11569, 2024, 3260, 16, 2213, 4860, 16, 1930, 2024, 6671, 3260, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MKYLSSIFFVLFCTTVFIQTKAQEKNIDQNIIYSKEAQASGTKGVLGVEFIVEKDGQLSSIHIADSIGSVRTKQKIHVPIDVKKTAEKRWMAGQLGPRAVEAQPNEPPGGMGAFRTWIGQNYNYPLEATRNKVNGTITAEEAIRVIKKSRPWKPAIVKGKPVRAKFTLPIILNTHDINDRPEISARPLGGYNDFLGADIADSLKSTIARLPAWKPGMVNGISIPINNNIVDTFDIEPTIRFVVNKDGRLSDYEIVKNLGYG", "metadata": {"id": "A0A4Q6XMU8", "cluster": 7097041, "interpro_all": ["IPR051045", "IPR006260", "IPR037682"], "interpro_used": ["IPR037682", "IPR051045"], "interpro_unused": ["IPR006260"]}, "task_type": "infilling"} {"instruction": "I am designing a protein that has the following properties: 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 features a Ribosomal RNA large subunit methyltransferase K/L-like methyltransferase domain that catalyzes the methylation of guanine residues in RNA, targeting substrates such as the 23S ribosomal RNA or tRNA. In *Escherichia coli*, it specifically modifies guanine at positions 2445 and 2069 of the 23S rRNA prior to its assembly into the 50S subunit, while in other contexts, it may associate with a THUMP domain to facilitate tRNA dimethylation. Also, the protein contains a THUMP domain that functions as an RNA-binding module to capture the 3'-end of substrates, particularly the CCA-terminus of tRNAs, thereby positioning them for modification by associated catalytic domains. Adopting an \u03b1/\u03b2 fold, it is found in enzymes responsible for diverse RNA processing events, including methylation, pseudouridylation, and thiouridylation, across all domains of life. It is found in Jiulongibacter sediminis. 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, 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, 4075, 43, 11196, 3146, 3103, 5903, 16478, 53, 19, 54, 17, 3189, 16478, 3418, 1988, 17097, 1920, 5547, 1927, 16904, 4248, 1922, 3146, 16, 5133, 6249, 2427, 1966, 1920, 3020, 1036, 11196, 3146, 2014, 10089, 18, 1922, 14, 10210, 5178, 14, 16, 2176, 4475, 25436, 16904, 2019, 6490, 20953, 1015, 1930, 16560, 1026, 1927, 1920, 3020, 1036, 9067, 3432, 1942, 2496, 5957, 2460, 1920, 2761, 1036, 5903, 16, 2679, 1922, 2303, 11144, 16, 2176, 2278, 11774, 1956, 43, 1913, 6807, 3418, 1942, 6628, 10089, 9780, 1943, 18, 2222, 16, 1920, 2213, 5461, 43, 1913, 6807, 3418, 1988, 4088, 1966, 1925, 3146, 17, 2743, 9059, 1942, 7573, 1920, 23, 11, 17, 2482, 1927, 6249, 16, 4443, 1920, 13980, 17, 7822, 1927, 20770, 16, 6113, 12158, 3581, 1958, 6295, 2007, 2458, 6804, 4682, 18, 20478, 1925, 160, 19, 161, 3728, 16, 2176, 1977, 2435, 1922, 5038, 5061, 1958, 6445, 3146, 4587, 3916, 16, 2710, 5547, 16, 11520, 18330, 14458, 6055, 16, 1930, 15331, 18330, 14458, 6055, 16, 3436, 2136, 4682, 1927, 3308, 18, 2176, 1977, 2435, 1922, 14280, 1944, 2188, 26073, 2341, 1915, 6276, 1980, 15472, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MEPYLMTAKTLSGLESILAKEIEELGGLKVEKGKRIVYFEGNDGLMMKANLGLRTALSILIPFAEFQAKNENELYQETLDIPWEDIFSLRNTFSIQSVVGGEYFNHSKYVALKVKDAIADRFRKVTGRRPNVDPKDADYQINVHINRDRCTLSFDSSGKTLDKRGYRLKSNEAPINECLAAGIILKSGWDKKRCIYDPMSGSGTFGIEAALIGRNMAPGMKRRFSFQNWADFNQELFYQIKDELKAQETELQTEIYCSDIEKQNLSIITENAVRAGVIDDLTIEHLDYFKSSKRCDSGVAFLNPPYGERMNLDHSKETYKAIGDQLKQHYTNCDAWVISSNMPAMKAFGLKAESKEMVFNGGLECRLQHYKLF", "metadata": {"id": "A0A0P7CAW3", "cluster": 8021846, "interpro_all": ["IPR000241", "IPR054170", "IPR029063", "IPR004114"], "interpro_used": ["IPR029063", "IPR000241", "IPR004114"], "interpro_unused": ["IPR054170"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: It is part 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. Furthermore, the protein falls within 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. It originates from Cladocopium goreaui. What would its protein sequence look like?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 2176, 1977, 3131, 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, 3677, 16, 1920, 2213, 12182, 2651, 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, 2176, 22970, 2037, 23415, 24724, 10984, 1989, 20380, 5376, 15444, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "AALLDTCDARARFAEAQVTQLMQLMEAQQQNQGLLPTGLPWPQGRSHLPTPEAHLPQRSLQQAFGGAKSEKSNPWEMEGSPASDEQDSNQSGRIERHMEQEQRRLAKKLRPKQTLRGYLEELRSEDPRCIFIVRRINKLGFRSKTALESHYSKFGKVLQVCVAHSKVKPLPNSGQTARTRPGNFGLVVMQSPAAVKKVLDKGSTHIIDGVEVSVHKYQPSGFDDEVNEEEDEKMETSMTGAEFRGQPRRVPKETEEIVTSGSTQTGGSSTKGSSHSGSGSSGGGINSGDTDDWNRQESGSSNSSLGSDVKGAQDQFLGPSLPLEVKAERGWRKATRRGNLKPGAPWLGIWMPSSSNGAGSVELECRATSLLQQVLGLDPPQPRSSSPPASELSFDLVSYQSQSAAVCPPARRVETRADIEATFNSCPTHFLDSAKKLSGSSVSGEERIKRAWKAGQWAKAVADGRCLSPNRTPQLDLRPRFYAVLRATGVSLPTICRSAGTYWGIIGDLTSSSSITHGFPSELEAKIYFAGAGIVDYDLVLAESAVEPYVLSWPLGEEEDGEAEATVLVAMRREGGILLVLPQTFLPRQLVSEGNQGNLEGIFGPSQVFTVPAIIIEDEIVSPTGTDVDVMVIDCSIDVVKHMRAFTYQEELVYNYDEDSPYALPSMDALLPKIRTWVSQAVDMRVGFYTPEEAEGAEETPATPRRRKPPAKATPLGGGAKPKRPTTATLATEMRGILDALPQITKQLTVMSERQTLLESRLAVVPTAKASAAALGSTLSTSLPGPPPPVSDLVKSLQPPPRTQERASLGLLASPGIAKQLEVEELAEERLEGLKGSSLSSDGALAQAVLAQSKALTSLVAQIASSQNDPLSELTGSSSTAGTRGAATRSRLQLELAQHKGLFFQSVLQSMSRRMAPTSNPSATAMELLERGVSGVRYLERFGGYGRVKELGQIQYQVMMIMDFLMAENYLAAMDGVALLAVTLEQAALDGGRMELATLLCLQEDPPASIFVNRQLSSTSRARSFAPLADQRWVTCALAFLKEMEVISNKRNEMNAAGRVGFEASSEGSGRLNERWTRLHEDGIQFEKEEPEPNPLSTMLDFSTWAICLPRWILRCRTAFSWHLWRSFTATWRDPCDASTTAFPLPVPHPGCFSEKGLKHKKISRLAWARKKLLHIVVFSLNYMYLGRFPTRSELERRPNAEQMKVFERLRSLIAVCGEGEQQFIAVPGRSGPELGAALLQMERFADLHPELSQSYVQRKPVKFKEDKHLLPFADHPELLPYRSLDASRLKIVGTGEWPMADFLSGPLWLPFQEPRFLLHGEPDDVSVWPVFRREERSENLKLAKLWDSKGILRLHRKPLMRDHFCKTFNAYKNRHLDRQIGDRRIPNSRERAIDGPSHHLPPGFLLTNLRVEPFVEQVVGSVTDRRDFYHQAKISEERAQSNMLAFAFSEEELDGTRALEEARSTQPTKKQRESVGDGFGLLAEGADDLAVEGKWFPCFGSLFQGDHLGVEFALKAHEEVLQRGGLLESTRRLFGHALFPLQRQIEGLIIDDYFAIGCEPITTSPLNTFASKALAKARCIYEAAGLEGSVEKDIDAQNVFKAAGAEIISSAAAVQRGLTLVGAPVEKRLALAALSLRAARLRFASSKLLARLAGSWTSVLLYRRCLTSSVDFFFKLGAEAEASGPNTAVPLTRKVAQELVLLSALSPVAVSNIAVKYNEKVCASDASLGLGAVVSAKVDPETVEVLWLGSDKKGCYSKLDAPAAALLAAAGEEVAEPCGPDHLKAPKRGPLLYFDFVEFFGGSGRVSSCVAALGHSVAPCLDLTASKHYDMTDERLLEWCLYMIEEGRFKAFLTEPPCTTFSPAAHPAVRSYVEPEGFDRRCPKTRLGNVLAFRSFVLLRHGRKFGRPCGKEQPRRSKMAWMRAWRALKRLGFCEAVIASCQFASPHKKEFIFLLHGLDPLRLEVKCPGGHSHVKIQGQLTKGSAVYTWPLAEHLAKEFSRVLRLGCAFEERGPDVFGLESVVSNDVLLTEKWRTRKCWHWKRKSHINVLEAHGGLGVLAAAASDQPDSRFVALMDSRVAKGALAKGRSSADGLQRTCKRSSAIQVAFGLYPGWNFAPTRLNIADDPTRRVPVRSPVPLSVRKGLSQQQIQSRAERRKGIELVATRVARQDTLNRRTKLLSDFRCWLFEVHKVSLSQLLSAKPPDPEEICKWLTAYGQDMFLSGKAYGKFAETINAVAQARPVIRKQLVGAWDLAFAWQSDEPGEHHPALPLSILLAIVALALLWGWPLEASVISLTWCGLLRIGEVLIAERGDLIPPEDSMPGVLFGLLRIRTPKTRGRAARHQAARIDPPDVLSLLSAVYGKCPSSTRLWPYSAATLRKRFCCLLAGVGLATEKIKGRYPFSLGSLRPGGATHMLLESEDSEKVRRRGRWVTNKVMEIYLQEILYTTFAETLDRQTKIRVNQLAGNFTKILGQSVAFLNSAIPPTTWWNLFQTKDDELLDQSGLAGDGSLNVAVENDRWPPTEPSLGEWHVPSAEASTDQTYVVSLSHRDLQELREMLRLKSARSEADLSEILSQLQHLLEELQAPHGCLNAEKIMQATSLIQLAKQQLSLMHADCRSRMAEISMSTAAHAPPFPQIPFDASLGAPPGFGRGFFPGHSAQDR", "metadata": {"id": "A0A9P1CUN7", "cluster": 9359660, "interpro_all": ["IPR013762", "IPR012677"], "interpro_used": ["IPR012677", "IPR013762"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein can be placed in the Regulatory protein YycH/YycI, domain 2 superfamily, which regulates the essential histidine kinase YycG within the bacterial periplasm. Members of this family are membrane-anchored proteins that form a ternary complex with YycG to modulate its kinase activity and control crucial cellular processes. It originates from Ligilactobacillus murinus DSM 20452 = NBRC 14221. 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, 2112, 1998, 5396, 1922, 1920, 4948, 2213, 67, 3204, 19, 67, 2773, 1033, 16, 3418, 22, 13975, 16, 2154, 7014, 1920, 4415, 13873, 4016, 67, 2773, 1029, 2651, 1920, 4543, 20171, 18, 4678, 1927, 2052, 3416, 2032, 3260, 17, 17199, 2697, 1988, 2386, 43, 18734, 2796, 1956, 67, 2773, 1029, 1942, 8480, 2496, 4016, 2455, 1930, 2285, 6608, 3689, 4028, 18, 2176, 22970, 2037, 3650, 19167, 2341, 14357, 8898, 6185, 22214, 10964, 16368, 8982, 33, 8789, 15618, 13680, 4716, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "MLFSVVFTALIWVTPVYFQRLAGMAAPDKTRVVNDDTNTTDKKKLTDVYRPVSITVTDKRSSSRLLSNRIDVVDLMMTSLEGSKITDISEPETVSKSEYLKLVQTPRSYQLNYGSELSFGVLKQYLAEQPAKSENYSFDRIVISYDGSKVYFLDDAGLKVYKAKLTKYDKAKLNNVHKNKGLKRYKLSYEYQNGRLIQYYEEQLTVPRHSYLYNKENVGMYVTRLLGTEKSSTSSLTTREQDGVTIYSDDSGQKLSIRDKTGLITYTDYLTDETGRQNWTLDDHLTNDFTDLEQLGVSLADVKYSEYDIQEKNVIYRSYIAGFPVISARDFGTYQIQNRVRSKKLVFSQCSLQVPVPAAGKAVTLKPTKEILPDLQSTDVDLGKISDIQIGYTVSQNSTASLVIDLTPTYFVKYNNVWINYQDLISGKKWGDNDNEF", "metadata": {"id": "A0A0R2BJH2", "cluster": 9627346, "interpro_all": ["IPR042274"], "interpro_used": ["IPR042274"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I'm looking for a protein that has the following function: 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. Additionally, the protein carries 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. It is present in Flammeovirga sp. SJP92. Give the sequence.", "tokenized_instruction": [2, 51, 11, 55, 12300, 1958, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 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, 4950, 16, 1920, 2213, 16252, 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, 2176, 1977, 2481, 1922, 2300, 2595, 1021, 14127, 4223, 2056, 18, 13550, 1034, 11884, 18, 7031, 1920, 3244, 18, 3], "output": "METFELRNYKGQVHRFQFENALIVFLPTVSSKLDKEHLHLLKKQMKVITKHVQNIFVIVHQNEEEISKVLKKKNFPFPILADSKARIAKQLQCYLLPIGIVQRSSFLYNINGALLFRKTFMSNIEEHFEFIYSPTE", "metadata": {"id": "A0A150AFY4", "cluster": 10822775, "interpro_all": ["IPR000866", "IPR036249"], "interpro_used": ["IPR036249", "IPR000866"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "To achieve this function:\nThe protein contains a N-acetylmuramidase domain that confers N-acetylmuramidase (lysozyme) activity to degrade bacterial peptidoglycan. Commonly found in bacteria and viruses, it often serves as the C-terminal catalytic unit of bacteriophage endolysins. It is expressed in Myoviridae sp. ct3pM2.\nWhat amino acids must be placed in the masked gaps?", "tokenized_instruction": [2, 1942, 6230, 2052, 2347, 30, 1920, 2213, 5461, 43, 56, 17, 6894, 23010, 29085, 9200, 3418, 1988, 16556, 56, 17, 6894, 23010, 29085, 9200, 12, 18581, 13, 2455, 1942, 17069, 4543, 24183, 18, 5384, 2435, 1922, 4802, 1930, 6241, 16, 2176, 3868, 10634, 1966, 1920, 45, 17, 4262, 6804, 5344, 1927, 24613, 16239, 19010, 2925, 18, 2176, 1977, 3198, 1922, 15924, 3026, 10828, 2056, 18, 3369, 23081, 8224, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MKNGLTNEMIKDLANRLFLSDGRPQILFEGHIMYKEFHKKFPDEYKRLELAKEIDEECALKATSWGMFQIMGFESHEKQLELMYYFMNNSGCLKELNAYDQKLRNAYENFKNKIGIEPALLKAVQIVEAAGRDGRDLAYLCKKFSTVFYPKWDKSKYFGGLGNHNLCGCKDVFEFVHKMSKEKDWAGFAKKYNGPGYAQ", "metadata": {"id": "A0A8S5TDP1", "cluster": 11260523, "interpro_all": ["IPR024408"], "interpro_used": ["IPR024408"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein has 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. It is found in Isorropodon fossajaponicum endosymbiont JTNG4.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2258, 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, 2176, 1977, 2435, 1922, 4911, 18858, 22178, 1916, 22220, 14174, 21851, 27999, 22868, 19077, 2001, 1031, 52, 1031, 2029, 1006, 18, 3], "output": "MKDFTPSELETHLKHNHPLMLDVREQWEWDKCHFDKARLLPMGEIMTSLDNPPLDKSEETVLICHHGIRSMQAVATESSKSIIVVTADSNTTSLMV", "metadata": {"id": "A0A7R6NZG1", "cluster": 11401642, "interpro_all": ["IPR001763", "IPR036873"], "interpro_used": ["IPR001763"], "interpro_unused": ["IPR036873"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is grouped in 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. Also, the protein includes a Replication factor A, C-terminal domain that binds and stabilizes single-stranded DNA intermediates to prevent reannealing during DNA metabolism. Found in eukaryotes and archaea, this domain plays an essential role in DNA replication, recombination, and repair, typically functioning as part of the 70kDa subunit. In addition, the protein is included in the DNA damage-induced apoptosis suppressor protein family, which functions as a stress-induced anti-apoptotic factor that facilitates DNA repair and cell survival. These proteins act to suppress cell death in response to DNA damage, thereby preventing genomic lesions, and are frequently overexpressed in cancer tissues where they promote malignant growth. It is identified in Elysia marginata.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 10809, 1922, 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, 2222, 16, 1920, 2213, 5921, 43, 5158, 2991, 43, 16, 45, 17, 4262, 3418, 1988, 6876, 1930, 19658, 2957, 17, 10338, 2678, 12386, 1942, 4625, 1964, 6288, 5243, 1941, 2409, 2678, 4714, 18, 2435, 1922, 15021, 1930, 21501, 16, 2052, 3418, 5705, 1925, 4415, 2770, 1922, 2678, 5158, 16, 7827, 16, 1930, 5059, 16, 5745, 7295, 1966, 3131, 1927, 1920, 3895, 30493, 5903, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 2678, 4293, 17, 2719, 4091, 9241, 2213, 3416, 16, 2154, 4088, 1966, 43, 3071, 17, 2719, 2246, 17, 6353, 2991, 1988, 11374, 2678, 5059, 1930, 2024, 3298, 18, 2144, 2697, 4033, 1942, 4400, 2024, 3539, 1922, 2644, 1942, 2678, 4293, 16, 6113, 8444, 4935, 4518, 16, 1930, 2032, 5467, 10593, 1922, 2539, 3878, 2597, 2611, 5527, 6558, 2905, 18, 2176, 1977, 2899, 1922, 2349, 2012, 2126, 9027, 5499, 18, 3], "output": "MTGRSSRVLLAATVTEIGCGPYVYPACPQCHLSRCPKCSSVYKPEDIYYRFRLCATITDFLSTANITAFGEKYYSLSEELVKLAIEQTFVGQSLLFGFKVNPLVLFQADNSSAQKIRSDLIAVQIALQGKPNQNFRTVSRNVVNFLYTKGTAALATSPAQSVSPLVCERSQTESVCSNSSLLSESELRSLLDITNLDVAVSTSPTKKSSKDLQSLMMSVENNQEANEHCVRRSKSTFSKANQNSENKGKKRKNRCATKLHDVSPKGNVTTQKGLSSGICSVRSELESYEIKTQNQTLGRELREPENQSLYLCEDKKGKNIDCDTLLRSLKNSVTKLNPVTLSQFKLVNNLSLSASPADSDSDMDVTKNLPSQIEPSRINQTTKPSDSHLKCVLEEFPESENLNDFLKAGPFHFKIKVKKNVGTWQSTQGKTETSQEYVNYISYEILAKEKKNSTNRRESKHKRNKPELRENNLELSPNLPILDRAQKLLEDIYDFFGGVGLTSQQAQSLRRKSNENVTLPSPEPGEESIHISKLENSFSISEESKKSLDILPAGIYMNKNDSLKWSGDKHQLAVQEVNSSTDYSISFNHELVAQNDSESLQNSKKDFTISNPLSVGMRTMNPLIGCAHGSPQLDASIGHLKKFFSESFFNSSVSTPTTGNRKVRFKKRRKEIFSCLKKQQSAQEIDVSNCHSQDLFESPIQAATSKSLQVSMVSKCDASIQSPLFFSHDGSGSQELFSSEDPDSSHPQSSKSELPEEQHTVEQTLSSNIWTLSQGYRETNRDSLDLFSPSTSQNFCYCKLTQLETSGMLDVFFGVTASKLNQKILGLDKKSVSQLPRQQVLLSDVVNDSLTTKDGLCELVRYIEERYKTLAEPLDKANLSSIRLSCDSSVQKIKRMYRKTKRILERKGNRKDVFSNLSCSSPYDISDQEMYSKTPVISLLDSINNLNDNAPLVLPQIHQETSSQGEKIFRKVLCNVSDAEKNSSILKKFGCASEKETNQINCFNHDKCDCSEEWPQLDHISFANVNEHFVCANVTTAPESTNRVYCTPTPCGASTNADFETASRNSKGYKPTGEQKDEQQVDECNLECMNPPLIYHLKNCTQLFDLFDNSCVTPSSMQEQCCRSQNSHESFHDFEIISHLPVPNPKRKNLKVNHQGNPSKMDPTCAFGMNFSHGLKASTGQSIPSI", "metadata": {"id": "A0AAV4HGH5", "cluster": 12702045, "interpro_all": ["IPR043522", "IPR012340", "IPR013955"], "interpro_used": ["IPR012340", "IPR013955", "IPR043522"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We aim to build a protein that does the following:\nThe protein has a DUF4283 domain that is found in plant proteins and is hypothesized to function as a binding or guiding region due to its association with a diverse range of other domains. It is characterized by the presence of two highly conserved tryptophan residues. In addition, the protein is grouped in the Endonuclease/exonuclease/phosphatase superfamily, which comprises magnesium-dependent enzymes involved in intracellular signaling, DNA repair, and lipid metabolism. Representative members include DNase I, AP endonucleases, and sphingomyelinases, which share a structural core consisting of a beta-sandwich fold and a duplicated alpha+beta motif. It is present in Thlaspi arvense (Field penny-cress).\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 2258, 43, 4855, 10432, 4839, 1010, 3418, 1988, 1977, 2435, 1922, 4496, 2697, 1930, 1977, 7149, 1942, 2347, 1966, 43, 2743, 2014, 19096, 3031, 2810, 1942, 2496, 3279, 1956, 43, 6445, 3109, 1927, 2303, 4682, 18, 2176, 1977, 4378, 2007, 1920, 2990, 1927, 2288, 3626, 5305, 13489, 4248, 18, 1922, 2459, 16, 1920, 2213, 1977, 10809, 1922, 1920, 18697, 19, 24966, 19, 8167, 13975, 16, 2154, 12936, 13148, 17, 3100, 5038, 3286, 1922, 4776, 3197, 16, 2678, 5059, 16, 1930, 4486, 4714, 18, 5051, 4678, 3951, 12861, 51, 16, 2100, 18697, 1036, 16, 1930, 28057, 2319, 16, 2154, 7948, 43, 4346, 4728, 7600, 1927, 43, 4666, 17, 18038, 3728, 1930, 43, 19479, 4595, 15, 4666, 5219, 18, 2176, 1977, 2481, 1922, 1913, 24605, 10984, 21502, 4480, 12, 3559, 4959, 16323, 17, 18401, 1036, 13, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MNRKKKSHRALVESSKLARVLSTPSAATISKIKNSSPSFAGTSNTGALATDSDAAETDDSAGVPFVFIPDENIEAAKEEFKEIIFARFHGNSPPMGRIIGVVNALWARTGPQIPVELRDVPYLLFNKESLSRIATALGKPVSLAPETEQKENFQVAKMESCQTPQCDVLGGRDQAADRCQSPKGKDRVFEENQAAPEGRDRNTCDPSPSEVERSCEAAKFRGYDLKASKHVGTAEAPRVVEPPFYLVNRMESSPRIVVVWDPFVSVFIYQASFVYGFNQGNEHQGLWEELSILNATTPAARFPLTVIGDFNQIIQLNQHSNHNALVIDDLFEAQEKWLPYTWWNNQAINPISKKIDHALINQVWASFLSLRRQVCKPFKFFHHVLKNFYKRHYSGISERVREQAAKVGVLQTAESKYYRRRSRVRWADVGDKNTVFYHRTVAQRVPRNHIHFLNCRNSSPLSVHAHQVLDIGQSMFVHSPWSSDFNPEEALLTSAVAKEERSSPSESICKRSKLLSGIFDTSGDIAVLSPTEEKNQTEDSSPSAQAVTCGIFILAENVSFTVMTFGMEEFNLAIQDAPDSYAEFLEPLQSDHAACLFRLPRALLTSPNPFVATAEHPERVKWQQLL", "metadata": {"id": "A0AAU9SK72", "cluster": 13121339, "interpro_all": ["IPR025558", "IPR036691"], "interpro_used": ["IPR025558", "IPR036691"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein according to this functional description: The protein includes a Small ribosomal subunit protein uS2 conserved site that defines a family of proteins integral to the small ribosomal subunit across all domains of life, including the eukaryotic P40 laminin receptor and mitochondrial homologs. Also, the protein falls within the Nucleotide-diphospho-sugar transferase superfamily, which catalyzes the transfer of sugar moieties from activated donor molecules, such as nucleotide diphospho-sugars, to specific acceptor molecules to form glycosidic bonds. These enzymes play a critical role in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides. Also, the protein is classified under the UTP--glucose-1-phosphate uridylyltransferase family, which catalyzes the reaction between UTP and alpha-D-glucose 1-phosphate to produce diphosphate and UDP-glucose. Also known as UDP-glucose pyrophosphorylase, this enzyme generates the universal activated glucose donor essential for glucosyl transfer reactions and carbohydrate synthesis, and functions as a homooctamer in *Saccharomyces cerevisiae*. It occurs in Rhododendron griersonianum and is described by UniProt keywords Nucleotidyltransferase, Ribonucleoprotein, and Ribosomal protein.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 5921, 43, 2858, 11196, 5903, 2213, 2022, 1028, 5305, 3200, 1988, 16737, 43, 3416, 1927, 2697, 12328, 1942, 1920, 2858, 11196, 5903, 3436, 2136, 4682, 1927, 3308, 16, 2710, 1920, 10825, 26007, 15261, 3148, 1930, 4596, 14279, 18, 2222, 16, 1920, 2213, 12182, 2651, 1920, 5489, 17, 11791, 2609, 1037, 17, 9523, 13763, 13975, 16, 2154, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 6282, 4206, 16, 2427, 1966, 5489, 11791, 2609, 1037, 17, 15592, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2144, 5038, 3918, 43, 4140, 2770, 1922, 1920, 8132, 1927, 2054, 11926, 16, 22012, 16, 1930, 18686, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 27412, 17, 17, 3817, 17, 21, 17, 5413, 3674, 19743, 2199, 9961, 3416, 16, 2154, 17097, 1920, 3227, 2192, 27412, 1930, 4595, 17, 46, 17, 3817, 21, 17, 5413, 1942, 5074, 23266, 1930, 18500, 17, 3817, 18, 2222, 3171, 1966, 18500, 17, 3817, 20661, 2609, 2247, 24605, 1021, 16, 2052, 4113, 12399, 1920, 10321, 4128, 3817, 6282, 4415, 1958, 3351, 11731, 3856, 5298, 1930, 10590, 4271, 16, 1930, 4088, 1966, 43, 16350, 24402, 8835, 1922, 14, 16285, 10628, 14, 18, 2176, 5110, 1922, 11490, 12308, 2830, 2398, 8885, 6114, 1022, 1989, 1930, 1977, 2910, 2007, 20709, 11569, 2797, 4090, 2199, 9961, 16, 18347, 6657, 16, 1930, 11196, 2213, 18, 3], "output": "MTIHSAVIQKLLSTNAHLGRRVAAHHFKIYTYGARNGVTIIDSDKTLICIRNACHFISNLVRQKGKFLFVNTNPLCDDIVDQMTKRIGCGADSSWRLGGFLTNSGSPKKFRSRNKKLHLGSTQPPDCVVIMDTERKSSVIFEADKLQIPIVGLVNSDMPWDVYKRITYPVPANDSVKFVYLFCNLITKTFLVEQKRFQEVDNKQLSLTKDENRYFDTVVLVAFIGEESENLKQTMTSSSKDETPVIPYESLDLTSDDPVETKQLLDKLVVIKLNSALGTKMGFSGPRSATEVCNGLSYLDLIINQIESLNSKHGCNVPLILMNTIRTHDGTLKVVEKYSQKNIDILPLCQNRSHPVSRGRDSEDESVLFDHHELFLSLKNTGTLEALLLQGKEYILVVKYDNLGTLIDSKILNHLIQNRIQYCTELSEMAQMPGKNSLEKSKLVDTGNLWMNLKVVKRLVETDGKNVENYPLSKSFDRAIDVNVPHSRFQPMMSTSDLFLFQSDLYSYGDSLIRNSARTNSLNPCIELGPEFEKLSDFQSRFKSIPSIIELDSLKVMGDVWFGTGITLKGKVTIIAKPGVKLEIPDGVVIENKEISDPSDI", "metadata": {"id": "A0AAV6JH23", "cluster": 14400999, "interpro_all": ["IPR029044", "IPR001865", "IPR005706", "IPR018130", "IPR023591", "IPR002618", "IPR016267"], "interpro_used": ["IPR018130", "IPR029044", "IPR016267"], "interpro_unused": ["IPR023591", "IPR001865", "IPR002618", "IPR005706"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that will have the following function: The protein can be placed in the 7TM chemosensory receptor family, which comprises insect gustatory and odorant receptors that function as seven-transmembrane ligand-gated ion channels. These proteins exhibit high sequence divergence consistent with an ancient origin and include homologs in nematodes, such as the *Caenorhabditis elegans* protein Egl-47. It is found in Culex quinquefasciatus (Southern house mosquito) (Culex pungens) and corresponds to UniProt keyword Cell membrane, Transducer, and Transmembrane helix.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 27, 15375, 24760, 12680, 3148, 3416, 16, 2154, 12936, 11422, 26416, 2548, 1930, 12685, 2031, 4086, 1988, 2347, 1966, 5260, 17, 9117, 5207, 17, 12336, 4755, 5628, 18, 2144, 2697, 5987, 2149, 3244, 11227, 3499, 1956, 1925, 17364, 4853, 1930, 3951, 14279, 1922, 19669, 16, 2427, 1966, 1920, 14, 22418, 10861, 14, 2213, 25943, 17, 4261, 18, 2176, 1977, 2435, 1922, 6710, 2783, 9012, 5089, 19427, 3349, 7482, 12, 9257, 5953, 9719, 13, 12, 6710, 2783, 15809, 7470, 13, 1930, 8852, 1942, 20709, 11121, 2538, 2024, 3260, 16, 14848, 16, 1930, 9117, 7864, 18, 3], "output": "MELVNLFNSLYVSSCRIVQRNGHYHVYHRNVVSTFIGPLVICGITGFCGGTITLERLHFFLQSTAELSSLARYVSLTAIVLILTVWCLVQRSKVFKLLESLISYDRHSCRLINGRQPAIKLRLAKTGITFICLTYAVLLGIRAFMCLTYYLEFGPHTTILLFGAGLLELYFYLHQLFMQHFAEQFSERYRLLRCQLRPSSVRTLVRSVKLYDRLVLMQEIFADTFGVQLLLSTLLTFLDCAIITYHSIHMLGMGVSAITVAIESVFLIPRVLLFFGLTYQFERLSFEEQEFKNAIKSLQYEATEEHSEDYLNFLDLINLKLMTESPKITACGLFTVNLQVFYNVFAAIVTYIMILFQFRDFEK", "metadata": {"id": "A0A1S4KKJ6", "cluster": 15434335, "interpro_all": ["IPR013604"], "interpro_used": ["IPR013604"], "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 includes a Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain that functions as a glycoside hydrolase to cleave N-acetylglucosamine-containing linkages. It is typically found in enzymes that release N-glycans from glycoproteins or in flagellar proteins that hydrolyse peptidoglycan. It is present in Parcubacteria group bacterium.", "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, 5921, 43, 7338, 11731, 17, 11424, 16239, 17, 4666, 17, 56, 17, 6894, 22988, 5360, 16408, 2051, 17, 3189, 3418, 1988, 4088, 1966, 43, 7533, 2261, 20748, 1942, 21252, 56, 17, 6894, 22988, 17454, 17, 3165, 19949, 18, 2176, 1977, 5745, 2435, 1922, 5038, 1988, 4012, 56, 17, 15509, 2037, 16268, 2014, 1922, 24154, 2697, 1988, 21686, 1021, 24183, 18, 2176, 1977, 2481, 1922, 2096, 18021, 7972, 2341, 18339, 2210, 14061, 18, 3], "output": "MFLLLTSKGWRIEAIRTEDEKIQFAQLELQLQIHQEKNNPLENYLQSKHHGDFVKVAELIQKSCEKYNIPFEITLAIAILESGYGTSRIAQEKQNFFAIGAYDWNPYNSASDFSDLSLEEAIDYQILILKNDYFVRYKNLEEIAKNYCRNWRSWLEEVKFIAREVTEIFPKNVKYEQIK", "metadata": {"id": "A0A847Y633", "cluster": 16224270, "interpro_all": ["IPR002901"], "interpro_used": ["IPR002901"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein is grouped in the GrpE nucleotide exchange factor family, which functions as an essential co-chaperone for the Hsp70/DnaK molecular chaperone system. As an asymmetric homodimer, it binds to the ATPase domain of DnaK to catalyze the rapid dissociation of ADP, thereby facilitating nucleotide exchange and ATP rebinding. This activity regulates the chaperone cycle necessary for protein folding and the heat shock response in prokaryotes and eukaryotic mitochondria. It occurs in Berkelbacteria bacterium and exhibits UniProt keyword tags Coiled coil, Cytoplasm, and Stress response. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 16945, 1021, 5489, 6818, 2991, 3416, 16, 2154, 4088, 1966, 1925, 4415, 2081, 17, 14044, 1958, 1920, 12886, 19, 2678, 1040, 3272, 14044, 2433, 18, 1966, 1925, 11474, 21189, 16, 2176, 6876, 1942, 1920, 9444, 3418, 1927, 2678, 1040, 1942, 18170, 1920, 4052, 9182, 1927, 9828, 16, 6113, 12440, 5489, 6818, 1930, 4498, 25884, 2378, 18, 2052, 2455, 7014, 1920, 14044, 4048, 4680, 1958, 2213, 10328, 1930, 1920, 5631, 7418, 2644, 1922, 28149, 1930, 10825, 6489, 18, 2176, 5110, 1922, 8310, 20133, 7972, 2341, 18339, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 17524, 9121, 16, 5239, 16, 1930, 3071, 2644, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MIYPYLELSLIILYNELRMLKKKIQELEQKIKELEDGWRRTQADFENYRKRTEAERGEILNLLKADFLTKITPVLDNFRRAFEHAPDDEFSKGIKQIEKQLENILLSEGLQKIPADTGDKFDPNLHEAITHEPNKKIPSDHIIAEVESGWMFANKVIKPAKVRVSKGKK", "metadata": {"id": "A0A7C3UE92", "cluster": 16719024, "interpro_all": ["IPR000740", "IPR013805", "IPR009012"], "interpro_used": ["IPR000740"], "interpro_unused": ["IPR009012", "IPR013805"]}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein is a member of the von Willebrand factor A-like domain superfamily, which functions as a versatile protein-interaction module involved in ligand binding and the assembly of multiprotein complexes. Spanning both extracellular proteins like integrins and collagens as well as intracellular machinery, these domains facilitate diverse biological events including cell adhesion, migration, signal transduction, and DNA repair. Furthermore, 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. Additionally, the protein possesses a TonB-dependent receptor, plug domain that acts as an independently folding channel gate within bacterial outer membrane receptors, blocking the pore until ligand binding induces conformational changes to open the pathway. It facilitates the high-affinity, energy-dependent uptake of specific substrates into the periplasmic space by coupling with the TonB-ExbBD complex. It is identified in Lutibacter sp. Hel_I_33_5.\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, 14147, 30067, 2991, 43, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 2213, 17, 2835, 9059, 3286, 1922, 5207, 2743, 1930, 1920, 5957, 1927, 20677, 5684, 5048, 18, 13346, 2321, 5329, 2697, 3189, 15563, 1930, 5621, 1036, 1966, 2486, 1966, 4776, 10853, 16, 2144, 4682, 6628, 6445, 3933, 3916, 2710, 2024, 6141, 16, 5049, 16, 2733, 8201, 16, 1930, 2678, 5059, 18, 3677, 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, 4950, 16, 1920, 2213, 14465, 43, 16501, 1014, 17, 3100, 3148, 16, 15998, 3418, 1988, 8016, 1966, 1925, 6407, 10328, 4999, 11898, 2651, 4543, 7642, 3260, 4086, 16, 7472, 1920, 8554, 4801, 5207, 2743, 6387, 8523, 2840, 1942, 4437, 1920, 3374, 18, 2176, 11374, 1920, 2149, 17, 5173, 16, 3844, 17, 3100, 5047, 1927, 2487, 6249, 2460, 1920, 24334, 5230, 2007, 7590, 1956, 1920, 16501, 1014, 17, 1975, 6936, 1007, 2796, 18, 2176, 1977, 2899, 1922, 10908, 4397, 2422, 2056, 18, 3091, 41, 51, 41, 3401, 41, 25, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MKKCMFVISFFVVSFSVTSQTKKKTTLIWDTSYSMIDQLIKFSNEVILNESFDIKEGKWERLKNLFFTDGNESIDDFPAFFSNPVQIISSTGKAENSKLIVEVSNRVSLKGVVEDISGPLSNVTVISKQERVNTVTNEKGENTLRVKALKSKTKNVLLTDGRGVLDEVTVVSERKEIGYSTQSIGEEDISHLDTDVKRAVKGKFSGLKIQNNLIVMDGIIISETDSGIGNSGNGSKGIISKTQFVDKTNKYGTLGVNGVLLITTKTGSPDNGVNSKKKIKLKAKNIDEAFNIYLDQRKLNKTNVDFFFNVATYFKNWGLLALVYKYEENHLYSEAIVLYKRLVEYNPKVTQLYRNLAIAYKRNGLYKKASDFSGLLKSINYEYKNLVALNKDSIQLAEFDLQIVNPQKRYFNWLHTEKDEKIRLENEKNHGYGLEEFFITSKDITVYHNFGKANQTKEEKIISLVDLNKKLNILTLDIKKNISKEIHFLNTYFSKNPNTSVELFNSIYDGVSSFNNLLNVKGDEIKKIAKLSNGQFIDLSNEQYEITITKGDIVEFRYIGKMVNTGNRLENKDKTATDDVDLSQFLGRGNNMSILGNQYGTHINPDNVKSITYLKGLAATGTTPTYNEDVVAISNNLPYMSKLINEYLLKRILSNVLELVSKNDFSTQFKEAQNVYNNIDRNNLVRPFFKDNITYKTRIVFEWNEFDIGKWIFNISYLGKLTGNNNVPTYFR", "metadata": {"id": "A0A559S0A4", "cluster": 20286749, "interpro_all": ["IPR008969", "IPR012910", "IPR037066", "IPR011990", "IPR036465"], "interpro_used": ["IPR036465", "IPR011990", "IPR012910"], "interpro_unused": ["IPR008969", "IPR037066"]}, "task_type": "infilling"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein belongs to 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. In addition, 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 has been characterized in Pirellulaceae bacterium.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 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, 1922, 2459, 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, 2258, 2252, 4378, 1922, 13774, 1992, 5617, 1972, 3336, 14061, 18, 3], "output": "MPRRSLTSLRVLVTGASSGIGRELVLELARQGSRVVAMARREERLVALEEDA", "metadata": {"id": "A0A925DB43", "cluster": 20610982, "interpro_all": ["IPR036291", "IPR002347"], "interpro_used": ["IPR002347", "IPR036291"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein features a SnoaL-like domain that functions as a polyketide cyclase, typically involved in catalyzing ring closure steps during polyketide biosynthesis. This domain is structurally characterized by a distorted \u03b1-\u03b2 barrel fold. Moreover, the protein is grouped in the NTF2-like domain superfamily, which constitutes a versatile structural fold characterized by a \u03b2-\u03b1(2)-\u03b2 insertion. This domain scaffolds diverse functional roles, ranging from facilitating nuclear protein transport in NTF2 to supporting enzymatic activity in dioxygenases and structural roles in type IV secretion systems. It is native to Bradyrhizobium sp. cir1.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 4075, 43, 3437, 20827, 17, 3189, 3418, 1988, 4088, 1966, 43, 4286, 18540, 2261, 16526, 16, 5745, 3286, 1922, 29601, 6335, 10408, 5983, 2409, 4286, 18540, 2261, 8132, 18, 2052, 3418, 1977, 12171, 4378, 2007, 43, 22797, 160, 17, 161, 19560, 3728, 18, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 5891, 6680, 17, 3189, 3418, 13975, 16, 2154, 14879, 43, 20425, 4346, 3728, 4378, 2007, 43, 161, 17, 160, 12, 22, 13, 17, 161, 7413, 18, 2052, 3418, 10603, 6445, 3183, 5456, 16, 6485, 2037, 12440, 4254, 2213, 4860, 1922, 5891, 6680, 1942, 6184, 8145, 2455, 1922, 23652, 10465, 2432, 2319, 1930, 4346, 5456, 1922, 2601, 4370, 5512, 3771, 18, 2176, 1977, 6196, 1942, 20152, 5004, 2061, 23156, 2056, 18, 3252, 1009, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MSLEARISRLEDIERLRERVVEFFEHCDTGGSTGEAMEDLFADLAQTFCLHYAGNYVFDVRPGSDTAYGHWSAWETPVLSKRDGQWYWLNWDQTIKFFVPVSDSWEQADRIVEQRLSHGAYNPKALASLFLPDGCFESGDLKCVGRPAGKAVWGCFVHRHSYR", "metadata": {"id": "A0A7W6SR30", "cluster": 21345371, "interpro_all": ["IPR032710", "IPR037401"], "interpro_used": ["IPR037401", "IPR032710"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein is grouped in 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, 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. It is produced by Pelagibacterium lacus.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 1977, 10809, 1922, 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, 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, 2176, 1977, 4152, 2007, 7874, 29284, 7972, 2341, 18842, 1989, 7511, 1957, 18, 3], "output": "MEHQVMRLKNKTAVVTGGASGIGRASAIRLSAEGAKILVADISERAGMSVAEEIRDAGHQATFLKVDMAKEDEISAMIDKAVSLYGSCDILFNNAGVAGESLENTTPESLRRVIDINLNGPFFACMYAIPVMKKQGGGVIINTGSIGGIKSSGRSPAYAASKGGLLLATRTFARIAGGDNIRVNAVCPGSVDTEQTIEHMGNPSSPEGFEAAQARRLSRIPLGRAATADDIAKAVVFLASDEAAYITGESLVVDGGVLA", "metadata": {"id": "A0A369W4A6", "cluster": 21411175, "interpro_all": ["IPR036291", "IPR002347"], "interpro_used": ["IPR002347", "IPR036291"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I'm looking for a protein that has the following function: The protein is categorized in the Glutaredoxin-like, plant II family, which functions as a glutathione-dependent thioltransferase involved in maintaining cellular redox homeostasis. Restricted to plants, these proteins utilize a redox-active CXXC motif within a thioredoxin fold to reduce protein disulfides or mixed glutathione-protein disulfides, thereby regulating DNA synthesis, signal transduction, and oxidative stress responses. In addition, the protein is classified under 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. Furthermore, the protein contains a Glutaredoxin domain that functions as a glutathione-dependent thioltransferase to reduce protein disulfide bonds using a redox-active CXXC motif within a thioredoxin fold. It facilitates electron transfer from NADPH and glutathione to target substrates, playing a critical role in DNA synthesis, signal transduction, and defense against oxidative stress. It is identified in Lactuca virosa and features UniProt keywords Redox-active center. 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, 19406, 1919, 9754, 17, 3189, 16, 4496, 2890, 3416, 16, 2154, 4088, 1966, 43, 9153, 17, 3100, 13914, 9961, 3286, 1922, 8231, 3689, 9366, 7622, 18, 6715, 1942, 4793, 16, 2144, 2697, 12561, 43, 9366, 17, 3500, 5639, 21487, 5219, 2651, 43, 23684, 3728, 1942, 4412, 2213, 11830, 1036, 2014, 4985, 9153, 17, 2213, 11830, 1036, 16, 6113, 6773, 2678, 4271, 16, 2733, 8201, 16, 1930, 5163, 3071, 3387, 18, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 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, 3677, 16, 1920, 2213, 5461, 43, 19406, 1919, 9754, 3418, 1988, 4088, 1966, 43, 9153, 17, 3100, 13914, 9961, 1942, 4412, 2213, 11830, 9031, 2193, 43, 9366, 17, 3500, 5639, 21487, 5219, 2651, 43, 23684, 3728, 18, 2176, 11374, 4995, 3856, 2037, 11908, 1930, 9153, 1942, 2758, 6249, 16, 14797, 43, 4140, 2770, 1922, 2678, 4271, 16, 2733, 8201, 16, 1930, 9720, 3316, 5163, 3071, 18, 2176, 1977, 2899, 1922, 5641, 29394, 2787, 5360, 1930, 4075, 20709, 11569, 9366, 17, 3500, 4102, 18, 7031, 1920, 3244, 18, 3], "output": "MAMVTMEVAKYLVVIFSKTSCCMCHTIKTLINNFGSNLVVYELDGHPNGQQLEDELKAVGCKLSVAVVFIGLQLLGGSNEIMSLHLKGELAQLLKW", "metadata": {"id": "A0AAU9P8Y9", "cluster": 21601803, "interpro_all": ["IPR011905", "IPR002109", "IPR036249"], "interpro_used": ["IPR011905", "IPR036249", "IPR002109"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would the protein sequence be if I wanted a protein that could perform the following function: It is part of the Ribonuclease P family, which functions as a site-specific endonuclease responsible for generating mature tRNAs by catalyzing the removal of the 5'-leader sequence from pre-tRNA. The protein component of this ribonucleoprotein complex plays an essential auxiliary role by binding to the 5'-leader sequence and broadening the substrate specificity of the catalytic RNA moiety. Additionally, the protein is associated with 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. In addition, the protein is classified under 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. It has been characterized in Geovibrio thiophilus and exhibits UniProt keyword tags Hydrolase and tRNA processing.", "tokenized_instruction": [2, 4663, 2962, 1920, 2213, 3244, 1998, 2647, 51, 14624, 43, 2213, 1988, 2578, 2385, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 18347, 2051, 58, 3416, 16, 2154, 4088, 1966, 43, 3200, 17, 2487, 18697, 5061, 1958, 9155, 6665, 20770, 2007, 29601, 1920, 6025, 1927, 1920, 25, 11, 17, 17442, 3244, 2037, 2097, 17, 10089, 18, 1920, 2213, 4594, 1927, 2052, 18347, 6657, 2796, 5705, 1925, 4415, 21549, 2770, 2007, 2743, 1942, 1920, 25, 11, 17, 17442, 3244, 1930, 23701, 1920, 4510, 4896, 1927, 1920, 6804, 3146, 11804, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 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, 1922, 2459, 16, 1920, 2213, 1977, 5947, 2441, 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, 2176, 2258, 2252, 4378, 1922, 14136, 2165, 2377, 3940, 15331, 24888, 5277, 1036, 1930, 9826, 20709, 11121, 2538, 14392, 20748, 1930, 10089, 4587, 18, 3], "output": "MNQRLKSSERLKKKSDYLKVLRGKKCAGRLITVYWNACDCEQSRFGFITGKKVSKKAVDRNRLRRYFKEFCRKNKSLFPAKRDFVFRALPGAGKASHDEIDNEALRLVEKIASEIPADRTY", "metadata": {"id": "A0A3R5XWB5", "cluster": 21997167, "interpro_all": ["IPR020568", "IPR014721", "IPR000100"], "interpro_used": ["IPR000100", "IPR014721", "IPR020568"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to make a protein that can have this function: The protein incorporates a 6-hydroxymethylpterin diphosphokinase MptE-like domain that catalyzes the conversion of 6-hydroxymethyl-7,8-dihydropterin to its diphosphate form using ATP. This reaction is critical for the biosynthesis of pterin-containing C1-carriers, such as tetrahydrofolate and tetrahydromethanopterin, in archaea and bacteria. It occurs in Planctomycetota bacterium. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 19683, 43, 26, 17, 29078, 2410, 16654, 11791, 2609, 18655, 15840, 1021, 17, 3189, 3418, 1988, 17097, 1920, 7309, 1927, 26, 17, 29078, 17, 27, 16, 28, 17, 11842, 2410, 16654, 1942, 2496, 23266, 2386, 2193, 4498, 18, 2052, 3227, 1977, 4140, 1958, 1920, 8132, 1927, 19147, 1921, 17, 3165, 8817, 17, 8974, 16, 2427, 1966, 21196, 27851, 1930, 21196, 23568, 9286, 2410, 16654, 16, 1922, 21501, 1930, 4802, 18, 2176, 5110, 1922, 4720, 2341, 13386, 19446, 3857, 14061, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MLISREDAPRVRAAAEDSMSGNPFDFSGDGGGFEGLEGLGLEGLVGPSGLPADPAVLERNLMALSGRNRALAERIAGAVSRAGVVLEIGADGVVTGTLEGRRLGSARRAGAEAEKLAESVDPAECAAACVLGFGLGHHVRALQERLGMKSLVVVFEPDVGLLRAVLERVDHSGWLALGRCVIVTDAEDAAGLTRSIRGMEGLIALGVRIIEHAPSRARLGDDAARFGRTMGEVVRSTRTHVVTTLVHAPVTLRNMVMNADRYASCAGITALKNSCVGVPAVTVAAGPSLQKNLALLGEPGVRERVVIIAAQTVLKPMLAAGIRPHFVTALDHHELSGRFYEGLTAEDVRGVRLVVEPKANPAILEKFPGEILVTQEKVLDDLIGTDLVRDLGELPAGATVAHLSYYLARYLGCDPVIMIGQDLGFTDGQYYAAGAAIHRVWQGELNHERSLEMLEWERVARMRANLRRVPSQDGRTIYTDEQMATYLAQFEAEFQKDTLAGLAVIDATEGGAAKKHTTAMPLREALERFARAERPALPETAGGAREAASVREALRAHFERLIADARAIRAASDETAERLTEIAESRVDTRGANAIVAEVQATGHRVRAMKPAFPLVEFINQTGVLNRFKADRLIELAGADPLERQRRQAERDIQNVRWIGQAADELARQLAQGIAVLDGARSKATRDEPEPECSVGREPVRAEVFVLCDPGYGGLGVARDLGEAVWRGRDALDLTLRRALLCGRGCSVRVLTPDPRKTGELLRRAGLEAEPRVVVEPVDPARWRERARAIGRARACASDGWRGGVAQTTVFDEMLDPKTVGEIMDRRGVDAAVLIGADWALVDPVLLDALIDRHAEAPDRHQIVFSQAVPGLGGCVLSRSAVRSLEQLQDIGSPLGTVGGLLGYVPVNTQTDPIGTTLCVRVEPAVRDAGVRLIADAAPGRRLIASALERLGERAGDSSALQSVRAVEMSRAFMVPRTLVLELCPGRLSSGVFGAWKRGGPRPTERGAVDFARAHALLRELTSAREDAVVVFDGPGDPLMHPGALDFVRLADELGAACVSLRTDLLREGVEPDEIFVSGLGVLSVDVLATEPATYAALTGVDRHRFVVERLGRIADARAMGETGLKSPWIQPRMTRCDAVIDQVEGFYDAWIMTVGSAVIDPQPVWVSDRVRPLPMPEGRALQIERETLRVRSDGVVCDASWRAVRRLNAFDEGLAGAVRAWRAVLEQGGRSRMAAGAAA", "metadata": {"id": "A0A3M2CFC8", "cluster": 24196301, "interpro_all": ["IPR002826"], "interpro_used": ["IPR002826"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein is classified under the Beta-lactam antibiotic response regulator family, which functions as an integral membrane sensor that detects beta-lactam antibiotics and transduces signals to the cytoplasm. Upon acylation of a conserved serine residue, these proteins activate a zinc protease domain to cleave a transcriptional repressor, resulting in the derepression of antibiotic resistance genes. Furthermore, the protein should have 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. It is present in Adhaeribacter swui and is linked to UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 4666, 17, 15294, 7267, 2644, 7888, 3416, 16, 2154, 4088, 1966, 1925, 12328, 3260, 6443, 1988, 19998, 4666, 17, 15294, 7560, 1930, 30334, 1036, 4771, 1942, 1920, 5239, 18, 4073, 11337, 1943, 1927, 43, 5305, 8468, 6181, 16, 2144, 2697, 6980, 43, 7997, 7154, 3418, 1942, 21252, 43, 5224, 14434, 16, 3864, 1922, 1920, 13343, 3124, 1927, 7267, 3554, 2628, 18, 3677, 16, 1920, 2213, 3066, 2162, 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, 2176, 1977, 2481, 1922, 21918, 29164, 26073, 2341, 1915, 3476, 15444, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 7864, 18, 3], "output": "MPLLFSYILKVSFCLGAIYLFYYSILRPLTFFNWNRWYFLVGTGLCFFIPLIAVSGIWESMPEPIVIKYIPSIAAVRNTTFVRLEPVSNSYSMWDWLLLLIIGGYVLLFIRTLVQVFSLVRLRRKANLISNVGAKIYHINGHIQPFSFWNSVFINRTLHPEEDLLKIIRHELVHVRQAHTLDIIWMELVCILNWFNPFVWLLRQQVRQNLEFISDHQVLQSGTDKKHYQYLLLQVTGQPNFRLANQFNFSPLKNRIVMMNKIPSAKRHLAKFLLVVPLSAGLLFACREVKAQVPSENKNLVTHRHEGQNIILAEFQDGTQEKFDISTEVGKKAFMQAQKFFGDSYNPADVSRGWSEGFKTLLKRNPDIAQIKWRYDIDQLNKNDFPFIADRLYITLKSGVEKVYPIESKTDLAKVENELGKLPLFPPPPPTVSIVKY", "metadata": {"id": "A0A7G7GEM0", "cluster": 26351671, "interpro_all": ["IPR052173", "IPR008756"], "interpro_used": ["IPR052173", "IPR008756"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The 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 is derived from Candidatus Sulfopaludibacter sp. SbA3. 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, 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, 3595, 2037, 14550, 1031, 1957, 5141, 8228, 5277, 7408, 7972, 2341, 1915, 2056, 18, 7760, 12779, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MPVQELANAAELLSAADKPLAEKLLLQGQARDPQSKWPRRLGRLYAEALAGADAAYAKLARQKLEESQDPELLATAGHFVFTSNLPDGQVLGKAYVERALQLDPQSVPAHAARARMHQPADGSAAALARQAESSFFKGDRDAARKDATSALQQAQKSTTDPDYGTAIYQANMVLGMIAMSDHDRKSAVKCMLAAADAPSTEELAYYVSSAPYQLPGMLLADGERESVLQFLARFAKTCVADRKELLASADLIRHGQKPVWYPAAD", "metadata": {"id": "A0A2N9MAU0", "cluster": 26923198, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein is assigned to the The FYVE, RhoGEF and PH domain-containing family, which regulates the actin cytoskeleton and cell morphology by functioning as guanine nucleotide exchange factors (GEFs) for the Rho GTPase CDC42. Utilizing DH domains for catalytic activity alongside PH and FYVE domains for membrane and endosomal targeting, these proteins facilitate GDP-GTP exchange to drive processes such as filopodia formation, cell polarity, and cytokinesis. Also, the protein should include a Dbl homology (DH) domain that functions as a guanine nucleotide exchange factor (GEF) for Rho family GTPases, such as Rho, Rac, and CDC42, by catalyzing the exchange of GDP for GTP. Structurally composed of an elongated $\\alpha$-helix bundle, it is typically located immediately N-terminal to a pleckstrin homology (PH) domain, forming a module where the DH domain mediates specific GTPase activation and oligomerization. Furthermore, 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. It originates from Amorphochlora amoebiformis and contains UniProt keyword associations 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, 1977, 6304, 1942, 1920, 1920, 27976, 1961, 16, 28589, 7726, 1930, 2087, 3418, 17, 3165, 3416, 16, 2154, 7014, 1920, 4718, 11612, 1930, 2024, 6076, 2007, 7295, 1966, 16904, 5489, 6818, 2790, 12, 15022, 1036, 13, 1958, 1920, 10585, 14809, 15790, 18, 10232, 6781, 4682, 1958, 6804, 2455, 17764, 2087, 1930, 27976, 1961, 4682, 1958, 3260, 1930, 16514, 5133, 16, 2144, 2697, 6628, 15217, 17, 9319, 6818, 1942, 9265, 4028, 2427, 1966, 24137, 3337, 16, 2024, 12432, 16, 1930, 20825, 18, 2222, 16, 1920, 2213, 3066, 3951, 43, 6594, 1024, 9039, 12, 6781, 13, 3418, 1988, 4088, 1966, 43, 16904, 5489, 6818, 2991, 12, 15022, 13, 1958, 10585, 3416, 18390, 16, 2427, 1966, 10585, 16, 7195, 16, 1930, 15790, 16, 2007, 29601, 1920, 6818, 1927, 15217, 1958, 9319, 18, 12171, 7179, 1927, 1925, 16158, 8, 38, 4595, 8, 17, 7864, 14142, 16, 2176, 1977, 5745, 4810, 6183, 56, 17, 4262, 1942, 43, 6483, 12940, 2156, 5572, 9039, 12, 2087, 13, 3418, 16, 7402, 43, 9059, 2597, 1920, 6781, 3418, 10412, 2487, 14809, 2936, 1930, 17371, 18, 3677, 16, 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, 2176, 22970, 2037, 16237, 20845, 1019, 27714, 27511, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MNAILDVFNKYTKFFALYITSDRYYGKTKGKKGLLELFSKLILISLDIQGRIDKALQDMKDIAGKVNKAMERFAKSLSKVYKGTFSPILESDFGKKMKKIRDCKAILFNDMLLLAVPMPTVVVPYTKVYLRQRNGFSERVGKTETKKRTLNPVVRAMAKAILAGESQSGKSVTRYSESCFVIWDEDYLSSDDYMGTASINLLSKLDPKKWLSLHGSSISDVTKTNKKEVGEKVTGQIRVRPQKDTTGRVLVPAIEGSNKDSYIPIMRVEICSEEKKVIGTFELTGKYVTCYQSATLFLTSEGKPIQRIPRYVLLLRELRKRSQTSEMIELEQKLWDTSIIAPHRSYHSESSDGKVVQGSLEYVSVAILEGKNLVAMDYGESSDWVEGRTAQKEAKGKQAEFNFVARSKLNQLGRIDIIAQPDSGIYTNTFAGEVAICATRAPTPDFRKSCEKDIPPHFLMGSVESNLSDPFINNSGKELSKA", "metadata": {"id": "A0A7S0GTI4", "cluster": 28933664, "interpro_all": ["IPR000008", "IPR035892", "IPR035899", "IPR000219", "IPR051092"], "interpro_used": ["IPR051092", "IPR000219", "IPR000008"], "interpro_unused": ["IPR035899", "IPR035892"]}, "task_type": "infilling"} {"instruction": "The protein has a MADS MEF2-like, N-terminal domain that acts as a eukaryotic transcriptional regulator by binding DNA and forming homo- or heterodimers. This Type II MADS domain features a distinct alpha-helix position at the dimerization interface compared to SRF-like counterparts and is essential for homeotic regulation in plants and immediate-early development in animals. In addition, the protein belongs to the MADS-box/MEF2 Transcription Factor family, which functions as transcription factors regulating diverse developmental processes through the formation of DNA-binding homo- and heterodimers. In plants, these proteins control floral organ identity and flowering time, whereas in animals, they are key regulators of muscle development, neuronal differentiation, and cell survival. Furthermore, the protein has a MADS-box domain that serves as a DNA-binding and dimerization module essential for transcriptional regulation in eukaryotes. It functions as a dimer, utilizing an anti-parallel coiled coil to recognize the DNA major groove and N-terminal extensions to contact the minor groove, while a beta-sheet stabilizes the protein interface. This domain is critical for diverse developmental events, including cell proliferation, differentiation, and tissue specification. It is present in Wallemia hederae and exhibits UniProt keyword tags Nucleus 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, 2258, 43, 9133, 1036, 22473, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 8016, 1966, 43, 10825, 5224, 7888, 2007, 2743, 2678, 1930, 7402, 16350, 17, 2014, 21523, 18, 2052, 2601, 2890, 9133, 1036, 3418, 4075, 43, 4493, 4595, 17, 7864, 3507, 2019, 1920, 13640, 6854, 2452, 1942, 23730, 17, 3189, 11482, 1930, 1977, 4415, 1958, 4502, 3153, 3640, 1922, 4793, 1930, 8426, 17, 3120, 2740, 1922, 3555, 18, 1922, 2459, 16, 1920, 2213, 14440, 1942, 1920, 9133, 1036, 17, 5758, 19, 22473, 3213, 2991, 3416, 16, 2154, 4088, 1966, 3213, 2790, 6773, 6445, 5878, 4028, 2596, 1920, 3337, 1927, 2678, 17, 2743, 16350, 17, 1930, 21523, 18, 1922, 4793, 16, 2144, 2697, 2285, 20741, 3090, 6833, 1930, 15346, 2367, 16, 3417, 1922, 3555, 16, 2611, 2032, 3834, 9098, 1927, 3760, 2740, 16, 5121, 4155, 16, 1930, 2024, 3298, 18, 3677, 16, 1920, 2213, 2258, 43, 9133, 1036, 17, 5758, 3418, 1988, 10634, 1966, 43, 2678, 17, 2743, 1930, 13640, 9059, 4415, 1958, 5224, 3640, 1922, 15021, 18, 2176, 4088, 1966, 43, 7632, 16, 10232, 1925, 2246, 17, 6110, 17524, 9121, 1942, 9967, 1920, 2678, 3044, 15920, 1930, 56, 17, 4262, 20917, 1942, 5217, 1920, 5857, 15920, 16, 2679, 43, 4666, 17, 11130, 19658, 1920, 2213, 6854, 18, 2052, 3418, 1977, 4140, 1958, 6445, 5878, 3916, 16, 2710, 2024, 4031, 16, 4155, 16, 1930, 2960, 14674, 18, 2176, 1977, 2481, 1922, 4821, 3847, 13794, 20938, 1930, 9826, 20709, 11121, 2538, 14392, 5607, 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": "MGRRKISIRPLKDDRNRKVTFSKRCNGMFKKAYELSVLCSVDIAIIAFDSDGKLHEFSSGNIEKILMKYTEHNGDSNVKGPRDYCDDHDSDDGEGGGGGGGGSAIHDSRDADTAEPETDHHQHHHTHAMTQSQSPRASSSVKQEGAIERDEREVKPRIEVDSAVDEGIATGYANASTPAHHPHSPAHAPPPRSPKHTLSPYNMATSFLSPNAGSGVAQSDQLLNWQYAQMHAAHMMQQQQQVASQVRSNQHSSNSSNNSNSNTQSSQFLSPTAPYTNTHTAQPPPPPPFFSPGIPNIPIGGLPWYASIPPLAWPPPNASANVNAQTQQQQQQQLPQALLMDPFQFPLDGLPTAEPFQWPVPKEDSGGMGVSTQAAQPQQQQQQQQTPLAANANANSNSTTNSNSDTNTPSHSHSVSAGSDHNAHTHAHSSPSHHPHQHHHHSPRQKRARKS", "metadata": {"id": "A0A4T0FW79", "cluster": 1216852, "interpro_all": ["IPR050142", "IPR033896", "IPR002100", "IPR036879"], "interpro_used": ["IPR033896", "IPR050142", "IPR002100"], "interpro_unused": ["IPR036879"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\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. Additionally, the protein falls within 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 has been characterized in Meloidogyne graminicola.\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, 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, 12182, 2651, 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, 2258, 2252, 4378, 1922, 4221, 2642, 2021, 17151, 8604, 26386, 10173, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MYRQYKIGESLPTRKKQQIENLFTVHRIFKKIRETNALANYVDSTVAGEELADFNITTNNNNNEFNSLNISTTTINNNNNKFENNISKTYKEVKLQLLKEKLKNKKESGFSQHQIAKLTGVSQSFQKEEEIITTTTTNTDNNDEFNNLSYLNRRPNTQTSSSNM", "metadata": {"id": "A0A8S9ZBK6", "cluster": 4530500, "interpro_all": ["IPR009057", "IPR036388"], "interpro_used": ["IPR036388", "IPR009057"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein carries a 5'-3' DNA helicase ZGRF1-like, N-terminal domain that forms the predicted all-beta N-terminus of eukaryotic proteins such as ZGRF1 and Mte1, which function in homologous recombination and telomere maintenance. These parent proteins facilitate the repair of replication-blocking DNA lesions and interact with helicases, although this specific domain has not been directly implicated in nuclear focus formation. Additionally, the protein is associated with the DNA Repair Helicase ZGRF1 family, which acts as a 5'-3' DNA helicase involved in repairing replication-blocking lesions and enhancing homologous recombination. These proteins stimulate RAD51 strand exchange, recruit RPA2, and upregulate EXO1-mediated end resection, while also facilitating the branch migration of Holliday junctions and the dissociation of D-loops. It has been detected in Morchella conica CCBAS932.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 16252, 43, 25, 11, 17, 23, 11, 2678, 15318, 68, 2299, 5739, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 4952, 1920, 4396, 2136, 17, 4666, 56, 17, 7822, 1927, 10825, 2697, 2427, 1966, 68, 2299, 5739, 1930, 4638, 12474, 16, 2154, 2347, 1922, 8725, 7827, 1930, 12025, 6291, 18, 2144, 6162, 2697, 6628, 1920, 5059, 1927, 5158, 17, 7472, 2678, 4518, 1930, 6310, 1956, 29919, 16, 2876, 2052, 2487, 3418, 2258, 2084, 2252, 4103, 6835, 1922, 4254, 3691, 3337, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 2678, 5059, 15318, 68, 2299, 5739, 3416, 16, 2154, 8016, 1966, 43, 25, 11, 17, 23, 11, 2678, 15318, 3286, 1922, 5059, 1941, 5158, 17, 7472, 4518, 1930, 9221, 8725, 7827, 18, 2144, 2697, 9084, 15897, 5984, 6818, 16, 5608, 16454, 1028, 16, 1930, 21617, 18930, 1009, 17, 3434, 2482, 6953, 16, 2679, 2222, 12440, 1920, 6089, 5049, 1927, 14451, 27539, 11245, 1930, 1920, 9182, 1927, 46, 17, 11109, 18, 2176, 2258, 2252, 3330, 1922, 2803, 15404, 11560, 1019, 1962, 6102, 4928, 7972, 1036, 11436, 1028, 18, 3], "output": "MSENSHSSQAAPIDEYRVLWTAQKKQKLKKWHDGFLRFHKFNKRLLVYDDARHTVEDFKGTVVQDLTPLFTSVVKRKQQIQAVNTLISSETPNQANRHGPWGPNSRFPPQTPMQQRPTNMGMSLQHSVRANNNTQHPHSYKGRSLGQAQSLPTRIEQSGPQVSDAATSSTSYRPPLNALGGPPSPNRRLNQPSKQQAPLEPPQNHLSSFSDAARPLEPPLKHSRTNNIFSNPAPVNKSTPNLVIDTDSDDELFGSPPDPASASKRSLNGSKNQYNDPRAFKPPSKGKTISSPEKTPSRGRVAMSNTDVDSNPITSSGDESEKEKEPFEPLVTTGKILLGNTAKRKRTKLLCQRPSPVAPKERPTDTKASKASSPPTVIGKVPDEDLAMVDFANDAPIPPPPAVKKNLSAFKFRPPTRIEEKEDTVEYQKEHDIGPWSSEALFLFDWRPPGMREKGNKILISLVADMYLRGRDTIEEGDDLEFENHLVRNATPTPHQRPMAAAAPAQRPNRISNPNPPIQQLRIRRKKAPSCPAPPHVNRGSLNLNGFDINSASPPPAQETDLRAGEGSNPRISQPLPNDRSSAAPLRNPQVAVERESVAKKPRKEPVHQNKSDDKGKGIANDAQYR", "metadata": {"id": "A0A3N4KT32", "cluster": 5528634, "interpro_all": ["IPR052800", "IPR018838"], "interpro_used": ["IPR018838", "IPR052800"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should contain a 2-oxo acid dehydrogenase lipoyl binding site that is located in the E2 dihydrolipamide acyltransferase component of multienzyme complexes, such as pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, and branched-chain 2-oxo acid dehydrogenase. It anchors the lipoyl cofactor essential for catalyzing the oxidative decarboxylation of 2-oxo acids to acyl-CoA. Also, it is part of the 2-oxoacid dehydrogenase family, which primarily functions as the dihydrolipoamide succinyltransferase (E2) component of the 2-oxoglutarate dehydrogenase (OGDH) complex to catalyze the conversion of 2-oxoglutarate to succinyl-CoA within the Krebs cycle. Some members also participate in the pyruvate dehydrogenase complex or translocate to the nucleus to succinylate histones, thereby linking cellular respiration and energy metabolism with epigenetic gene regulation. Additionally, the protein possesses a Biotin/lipoyl attachment domain that covalently binds biotin or lipoic acid cofactors to a conserved lysine residue positioned within a flattened 8-stranded beta-barrel. This domain facilitates catalytic carboxyl or acyl transfer reactions and serves as an essential component in metabolic multi-enzyme complexes, including pyruvate dehydrogenase and the glycine cleavage system. It has been detected in Trueperaceae bacterium. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 3066, 5531, 43, 22, 17, 18588, 2687, 9294, 3178, 10921, 2743, 3200, 1988, 1977, 4810, 1922, 1920, 6602, 11842, 8257, 5482, 11337, 9961, 4594, 1927, 2779, 14896, 5048, 16, 2427, 1966, 11867, 9294, 16, 22, 17, 18588, 16542, 17488, 9294, 16, 1930, 16484, 17, 4659, 22, 17, 18588, 2687, 9294, 18, 2176, 27127, 1920, 3178, 10921, 15155, 4415, 1958, 29601, 1920, 5163, 22429, 1943, 1927, 22, 17, 18588, 4576, 1942, 11337, 17, 10027, 18, 2222, 16, 2176, 1977, 3131, 1927, 1920, 22, 17, 18588, 29272, 9294, 3416, 16, 2154, 5985, 4088, 1966, 1920, 11842, 8257, 6952, 16408, 1021, 13791, 2199, 9961, 12, 6602, 13, 4594, 1927, 1920, 22, 17, 18588, 16542, 17488, 9294, 12, 24507, 1023, 13, 2796, 1942, 18170, 1920, 7309, 1927, 22, 17, 18588, 16542, 17488, 1942, 13791, 2199, 17, 10027, 2651, 1920, 25362, 4048, 18, 2673, 4678, 2222, 7352, 1922, 1920, 11867, 9294, 2796, 2014, 26377, 1942, 1920, 5607, 1942, 13791, 9075, 15808, 16, 6113, 9486, 3689, 11695, 1930, 3844, 4714, 1956, 8542, 2359, 3640, 18, 4950, 16, 1920, 2213, 14465, 43, 8622, 19, 3178, 10921, 8576, 3418, 1988, 16590, 6876, 8622, 2014, 3178, 8643, 2687, 21362, 1942, 43, 5305, 9082, 6181, 11814, 2651, 43, 26931, 28, 17, 10338, 4666, 17, 19560, 18, 2052, 3418, 11374, 6804, 9943, 2014, 11337, 3856, 5298, 1930, 10634, 1966, 1925, 4415, 4594, 1922, 4487, 2779, 17, 4113, 5048, 16, 2710, 11867, 9294, 1930, 1920, 10646, 6404, 2433, 18, 2176, 2258, 2252, 3330, 1922, 6228, 2116, 9914, 14061, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MATDVKVPSAGESISEVFIGAWLKQPGDRVEVDEPVVELETDKATLDVPAPTAGVLLEVLKKEGDSAAIGEVIARIDETAAAGQGAPVAAATGGAAATPAPAAPAPSA", "metadata": {"id": "A0A951YKF6", "cluster": 5622702, "interpro_all": ["IPR003016", "IPR050537", "IPR000089", "IPR011053"], "interpro_used": ["IPR003016", "IPR050537", "IPR000089"], "interpro_unused": ["IPR011053"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein incorporates a Alcohol dehydrogenase-like, N-terminal domain that functions as the catalytic core for a diverse family of oxidoreductases, including zinc-dependent alcohol dehydrogenases and quinone oxidoreductases. It typically adopts a GroES-like fold to catalyze the reversible oxidation of alcohols to aldehydes or ketones using NAD or NADP cofactors, often utilizing coordinated zinc ions for activity. In addition to enzymatic roles, it can perform structural functions, such as in the mammalian lens protein zeta-crystallin. Also, the protein should have a Enoylreductase domain that catalyzes the reduction of enzyme-bound 2-enoyl intermediates during polyketide and fatty acid biosynthesis. This domain serves as a key catalytic component in polyketide synthases, mammalian fatty acid synthases, and mitochondrial enoyl-[acyl-carrier-protein] reductases. It is also found in various dehydrogenases belonging to the medium-chain and short-chain dehydrogenase/reductase superfamilies. Additionally, the protein can be placed in the Trans-enoyl reductase-like family, which comprises fungal enzymes that function within gene clusters to mediate the biosynthesis of secondary metabolites, such as lovastatin, oxaleimide, and tenellin-type 2-pyridones. Structurally, these members possess an N-terminal GroES-like fold and a C-terminal NAD(P)-binding Rossmann fold, playing roles in processes ranging from iron stress tolerance to host infection. It is found in Cercospora zeae-maydis SCOH1-5.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 19683, 43, 4284, 9294, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 4728, 1958, 43, 6445, 3416, 1927, 27388, 1036, 16, 2710, 7997, 17, 3100, 4284, 9294, 1036, 1930, 25093, 27388, 1036, 18, 2176, 5745, 24032, 43, 8947, 1918, 17, 3189, 3728, 1942, 18170, 1920, 10743, 6638, 1927, 21773, 1942, 25075, 2014, 21876, 1036, 2193, 6577, 2014, 24221, 21362, 16, 3868, 10232, 11651, 7997, 6982, 1958, 2455, 18, 1922, 2459, 1942, 8145, 5456, 16, 2176, 2112, 2385, 4346, 4088, 16, 2427, 1966, 1922, 1920, 6492, 8540, 2213, 18943, 17, 24572, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 2066, 10921, 3510, 10410, 3418, 1988, 17097, 1920, 3378, 1927, 4113, 17, 4124, 22, 17, 2066, 10921, 12386, 2409, 4286, 18540, 2261, 1930, 5934, 2687, 8132, 18, 2052, 3418, 10634, 1966, 43, 3834, 6804, 4594, 1922, 4286, 18540, 2261, 8921, 1036, 16, 6492, 5934, 2687, 8921, 1036, 16, 1930, 4596, 2066, 10921, 17, 37, 11337, 17, 9685, 17, 2213, 39, 11386, 1036, 18, 2176, 1977, 2222, 2435, 1922, 3425, 9294, 1036, 10588, 1942, 1920, 3649, 17, 4659, 1930, 3662, 17, 4659, 9294, 19, 11386, 8587, 21341, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2127, 17, 2066, 10921, 11386, 17, 3189, 3416, 16, 2154, 12936, 8697, 5038, 1988, 2347, 2651, 2359, 5859, 1942, 8265, 1920, 8132, 1927, 4067, 6926, 16, 2427, 1966, 18412, 11680, 16, 18512, 14209, 16408, 1021, 16, 1930, 5656, 20912, 17, 2601, 22, 17, 24828, 3965, 18, 12171, 16, 2144, 4678, 7150, 1925, 56, 17, 4262, 8947, 1918, 17, 3189, 3728, 1930, 43, 45, 17, 4262, 6577, 12, 58, 13, 17, 2743, 18215, 8890, 3728, 16, 14797, 5456, 1922, 4028, 6485, 2037, 5680, 3071, 6555, 1942, 4423, 2909, 18, 2176, 1977, 2435, 1922, 28856, 9890, 1019, 6116, 3336, 17, 2278, 15783, 2160, 2977, 1009, 17, 25, 18, 3], "output": "MAADHSLPLPDRQRAIKVVEASTVRLENEVPLPKLEDEDVLVRVHCVALNPFDWKSLDLSPAPGSTFGCDVAGEVVAVGAKCRNNINVGDRVFGPVKGNASDAPENGGFAEYATIREVVAWKVPEGMQLEHAATLGMSLMTVGLALHYMLNIPLPLDSPEKNGPGRHVFIYGGGTATGTLAVQCAALSGMQPVVACSPRHFARMKSLGAVACFDYHIATVADDVREFTNNSLAEALDCITDSASMNICYNALGEQGGRYVGLDQFPIRSHTRRDVRPEWIVAWTVSGEAIRWKRPYARAPRPKHKVFGQSWNPVAQKLLDAGALQTHPVDVRSGGLAAIPDGVDALRKGLTDGRKLVYCIV", "metadata": {"id": "A0A6A6FQX9", "cluster": 10307770, "interpro_all": ["IPR013154", "IPR011032", "IPR036291", "IPR020843", "IPR047122"], "interpro_used": ["IPR013154", "IPR020843", "IPR047122"], "interpro_unused": ["IPR011032", "IPR036291"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein has a CheW-like domain that mediates protein-protein interactions in bacterial chemotaxis signaling pathways, functioning as a bridge to couple the CheA histidine kinase to transmembrane sensory receptors. It adopts a structure composed of two $\\beta$-sheet subdomains forming loose five-stranded $\\beta$-barrels stabilized by a hydrophobic core. This adaptor module is found in various signaling proteins, including CheW, CheA, and CheV, where it facilitates the assembly of the chemotactic signal transduction complex. In addition, the protein is included in the bacterial chemotaxis sensor histidine kinase CheA family, which functions as a central signal transducer in chemotaxis by autophosphorylating in response to chemoreceptor inputs. These proteins transfer the phosphate group to response regulators, such as CheB and CheY, to modulate flagellar motor activity and control swimming behavior. It occurs in uncultured bacterium and features UniProt keywords Transferase.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 19461, 17, 3189, 3418, 1988, 10412, 2213, 17, 2213, 3719, 1922, 4543, 16884, 3197, 3873, 16, 7295, 1966, 43, 11925, 1942, 15116, 1920, 10003, 1019, 13873, 4016, 1942, 9117, 6893, 4086, 18, 2176, 24032, 43, 3170, 7179, 1927, 2288, 8, 38, 4666, 8, 17, 11130, 30103, 7402, 21425, 3628, 17, 10338, 8, 38, 4666, 8, 17, 19560, 1036, 12017, 2007, 43, 7919, 4728, 18, 2052, 15077, 9059, 1977, 2435, 1922, 3425, 3197, 2697, 16, 2710, 19461, 16, 10003, 1019, 16, 1930, 10003, 1020, 16, 2597, 2176, 11374, 1920, 5957, 1927, 1920, 20513, 2733, 8201, 2796, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4543, 16884, 6443, 13873, 4016, 10003, 1019, 3416, 16, 2154, 4088, 1966, 43, 4101, 2733, 14848, 1922, 16884, 2007, 20369, 2199, 2287, 1922, 2644, 1942, 13534, 5943, 7344, 1924, 10230, 18, 2144, 2697, 3856, 1920, 5413, 2210, 1942, 2644, 9098, 16, 2427, 1966, 10003, 1014, 1930, 10003, 1012, 16, 1942, 8480, 24154, 4842, 2455, 1930, 2285, 15781, 3379, 18, 2176, 5110, 1922, 5269, 21058, 14061, 1930, 4075, 20709, 11569, 13763, 18, 3], "output": "KTVLERLKGSVSIETKVGEGTSFLLKVPLTLAIIKALMFRATEKLYAVPLSSVVEIVRAQAAEVHIVERREVIRLRDEVLPLVRLSSLIDGEKGSQKKLFIVVVQQGDRKYGLAVDRLVGEEELVLKALDDQLVATELVS", "metadata": {"id": "D7R138", "cluster": 10846618, "interpro_all": ["IPR051315", "IPR036061", "IPR002545"], "interpro_used": ["IPR002545", "IPR051315"], "interpro_unused": ["IPR036061"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: It is part of the Ribosome-inactivating protein, subdomain 2 superfamily, which encompasses bacterial and plant toxins, such as shiga and ricin, that inhibit eukaryotic protein synthesis. These proteins function by inactivating the 60S ribosomal subunit through the specific N-glycosidic cleavage of an adenine base from 28S rRNA. This structural subdomain features an irregular topology and supports the catalytic site defined by conserved glutamate and arginine residues. It has been detected in Diversispora epigaea.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 2176, 1977, 3131, 1927, 1920, 12794, 17, 20862, 2213, 16, 27517, 22, 13975, 16, 2154, 21569, 4543, 1930, 4496, 13599, 16, 2427, 1966, 18963, 1019, 1930, 27417, 16, 1988, 2875, 10825, 2213, 4271, 18, 2144, 2697, 2347, 2007, 20862, 1920, 3276, 1036, 11196, 5903, 2596, 1920, 2487, 56, 17, 7533, 12546, 6404, 1927, 1925, 15643, 5170, 2037, 3158, 1036, 9067, 18, 2052, 4346, 27517, 4075, 1925, 11499, 13678, 1930, 7825, 1920, 6804, 3200, 3608, 2007, 5305, 7627, 1930, 9732, 4248, 18, 2176, 2258, 2252, 3330, 1922, 5479, 1937, 21086, 7680, 24145, 18, 3], "output": "MTAIQDVIQEPSHTYYTKLRVINKTVMKSKMTGRFFSVPAQNLYNKYRETMIGNQRVSLKGYRLETRIRIANPNIVRCKKICTSPKKGARIIWLESGESTSNFGNEINTSTSAIDLTKNYGRQSNHIKKEPFGQNNNTRSAKEPENSDDEEVVILKDNSDSERQNWPNPFEIDFLDIKEPNDVTMILCRIGDLITDNIPEYLGIKIDKKNVYKLTGAVGDFQSVSENEQHHVRWDPIVKGKFTATHNGKTSKSHDSKNHLTACSTIKKNAVRPLDVATFNDTERANANTNIVTETEVYNWMQGEKRIRPYVLSIVDEEVLLYLYYHLPSNLFAPDNTINDFFTQLAYNDLSDPIAIHQFVENKYPSFVKKSKKVNNVYQSEEKEITSENESQSSQIIPHAILDTSANNSLYIGTSYNVPITIGTGEDSITIIILLSTRKESRNAFNTEKLQVSEVN", "metadata": {"id": "A0A397IBP0", "cluster": 11526427, "interpro_all": ["IPR016139"], "interpro_used": ["IPR016139"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the specific amino acid spans required to infill the masked sequence regions. Function: The protein has a Signal transduction histidine kinase, phosphotransfer (Hpt) domain that acts as a histidine-containing intermediate in bacterial phosphorelay signal transduction systems. This module facilitates the shuttling of phosphoryl groups from a sensor kinase receiver domain to a terminal response regulator, thereby regulating complex cellular processes such as chemotaxis and gliding motility. Moreover, the protein has 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 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. It is native to Magnetospirillum aberrantis SpK and is described by UniProt keywords Transmembrane helix, Cell membrane, and Coiled coil.", "tokenized_instruction": [2, 5655, 1920, 2487, 3835, 2687, 23658, 3414, 1942, 6510, 1024, 1920, 17476, 3244, 3451, 18, 2347, 30, 1920, 2213, 2258, 43, 2733, 8201, 13873, 4016, 16, 8078, 17204, 12, 26280, 13, 3418, 1988, 8016, 1966, 43, 13873, 17, 3165, 6129, 1922, 4543, 3421, 15208, 1012, 2733, 8201, 3771, 18, 2052, 9059, 11374, 1920, 26340, 3961, 1927, 12556, 2671, 2037, 43, 6443, 4016, 12608, 3418, 1942, 43, 4262, 2644, 7888, 16, 6113, 6773, 2796, 3689, 4028, 2427, 1966, 16884, 1930, 6534, 2117, 9254, 18, 3950, 16, 1920, 2213, 2258, 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, 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, 2176, 1977, 6196, 1942, 14634, 3106, 23576, 11560, 1989, 9801, 1937, 2056, 1040, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 7864, 16, 2024, 3260, 16, 1930, 17524, 9121, 18, 3], "output": "MALWHVEQITARFLIIAMSVSAVLAALVSGAVAWRQFEGERHMWSINDRATAAIVHSLAANPSLSCAEVTDSRGRLLAATAAAGCDAPVDSTLWVDRSALTAAARADAQLTALVFLLLSAAMVISSVFALRATVMAPLDRLNRDELGRVVTAYNGLLDRIDAHNAELEDARTQAVAAAQAKSRFLATMSHEIADVIWQSTESLLGIINDILDLSRIEAGKVRITPAPTNPAAIVREVAGALDATARALRQVVMNLVGNAVKFTETGTVSVSLGRHGERLEITVTSTTRRHGGTGLGLSISRQLVDLMGGRIDATSTLGTGSTFRVLLPLIETSTDNPVNQWLLRSQLERLGYEVEIHSNGALALDAFRKGTEFAAVVTDYHMPVMDGLDLARAIRATADTVEECLKAGMDTVVTKPVSLQDMASALSLRAGTTRTTSPCHPGPPPSPATRADMAALFSATADDLRRAITASLAAGDSRELSEAAGRALEQAAKAEDWLKIRPLAARLAALDIETRAALNAPLDETEVSDGLRSNARLSSAMQDVARLNAIALQEPTPFAADVDYEGHHLGRLAIATAAKVETNPRPRRTPMHGVLGTVELLRETPLTLEQRKYKGLRLDLVTAPDLPEWILADALRADTGIGIATSELARLFEPFRQADPTAATARPRHDPASATIDAGRVLAAEEAPNQRVPIIGMTADAFFTEAPLLDAEILAAVCGPDHSLASAALSLGATRLGLT", "metadata": {"id": "A0A7C9QV67", "cluster": 11574031, "interpro_all": ["IPR011006", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR036641", "IPR004358", "IPR008207", "IPR001789"], "interpro_used": ["IPR008207", "IPR005467", "IPR001789"], "interpro_unused": ["IPR004358", "IPR011006", "IPR036097", "IPR003661", "IPR036890", "IPR036641"]}, "task_type": "infilling"} {"instruction": "The protein is included in the Transposon, En/Spm-like family, which includes En/Spm-like transposable elements such as Tdc1 from carrot. The precise function of these proteins is currently unknown. It occurs in Sesamum angolense. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 1977, 3063, 1922, 1920, 18808, 16, 2066, 19, 19064, 17, 3189, 3416, 16, 2154, 5921, 2066, 19, 19064, 17, 3189, 12935, 2115, 5362, 2427, 1966, 6888, 5800, 2037, 3669, 1991, 18, 1920, 8162, 2347, 1927, 2144, 2697, 1977, 5077, 5435, 18, 2176, 5110, 1922, 9924, 1976, 1989, 3409, 2456, 3355, 1021, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MRRRIPVCTWVMRRRGWFSMPPGQLYDLLIKTKMVRLMMPLWNGCTQSQLVSVAELVNIKAESHISKQIYDRISQWTDHILSHDHTLPLDYYSTKKLMKDLDLLIRKIDAYKNGCMLYWNDDIIWTTASFVKNLDGFAPHSPSNPKHFIDIYLDSLIKELQDLWHVGVLTRDNAENETFTIHAAFMWTLDDLPTYKMAFGWSSIDATGCRVLERKVARPRLTGEQIRDWVENFSPAVEELRLHDMKSNDCHVFMQKLILIAFCKMLPELVEPRRNDDLCMNNTCIQWSIFNYSGRASGGSKKREDGFRWITSHNCLDIKARLRIGCLSLLVLLHPPDCKLGIMQLSTNPSQLHPSTEIFVGAFNLFDDTFRQDDPNIKELVATQFKKYKNRFKRCIEVAFQEEETIPTLQVVTDNHLYDLHDPNGIQLVVELFLANQQGTGTSRSANCESNDKSDEDRFDEDYETE", "metadata": {"id": "A0AAE2BTL7", "cluster": 12075210, "interpro_all": ["IPR004242"], "interpro_used": ["IPR004242"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein incorporates a PTS system mannose/sorbose-specific IIA subunit domain that functions as a cytoplasmic component of the bacterial phosphotransferase system (PTS) to facilitate carbohydrate uptake. It accepts a phosphoryl group from the phosphocarrier protein HPr and transfers it to a specific IIB subunit, thereby driving the transport and phosphorylation of sugars such as mannose or sorbose. In addition, the protein is included in the Bacterial PTS system sugar-specific components family, which mediates the simultaneous transport and phosphorylation of carbohydrates via the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). These proteins facilitate the transfer of a phosphoryl group to specific sugars, such as mannose, fructose, and N-acetylgalactosamine, during uptake and may also participate in bacterial chemotaxis or phage infection. It is identified in Candidatus Tectomicrobia bacterium RIFCSPLOWO2_02_FULL_70_19 and has UniProt annotations Kinase and Sugar transport. What would be a viable protein sequence for the function described above? Output the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 8618, 2433, 17936, 19, 20029, 2217, 17, 2487, 17433, 5903, 3418, 1988, 4088, 1966, 43, 6823, 4594, 1927, 1920, 4543, 8078, 9961, 2433, 12, 8618, 13, 1942, 6628, 10590, 5047, 18, 2176, 5861, 1036, 43, 12556, 2210, 2037, 1920, 8078, 15339, 29158, 2213, 18542, 1930, 19180, 2176, 1942, 43, 2487, 19795, 5903, 16, 6113, 9228, 1920, 4860, 1930, 4050, 1927, 15592, 2427, 1966, 17936, 2014, 20029, 2217, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4543, 8618, 2433, 9523, 17, 2487, 4178, 3416, 16, 2154, 10412, 1920, 5710, 4860, 1930, 4050, 1927, 16282, 3454, 1920, 8078, 9356, 18425, 12631, 2010, 17, 3100, 9523, 8078, 9961, 2433, 12, 8618, 13, 18, 2144, 2697, 6628, 1920, 3856, 1927, 43, 12556, 2210, 1942, 2487, 15592, 16, 2427, 1966, 17936, 16, 15102, 16, 1930, 56, 17, 6894, 5411, 2131, 17454, 16, 2409, 5047, 1930, 2278, 2222, 7352, 1922, 4543, 16884, 2014, 10503, 2909, 18, 2176, 1977, 2899, 1922, 14550, 1031, 1957, 18671, 4575, 4913, 15129, 2126, 14061, 12424, 2792, 2030, 1971, 5265, 41, 5725, 41, 4125, 41, 3895, 41, 2282, 1930, 2258, 20709, 15010, 4016, 1930, 9523, 4860, 18, 4663, 2962, 1998, 43, 8978, 2213, 3244, 1958, 1920, 2347, 2910, 3538, 35, 6647, 1920, 3835, 2687, 3244, 18, 3], "output": "MIGLVLVGHGDLPEALLQTASSVLSGAAQMRAVCLRTDEDQARFTEEIERAVREVDSGEGIIVMTDMMGGTPTNAALAMLNRQDVEVVTGVNLPMLLKVPFIKGKTVHEAARFLVEYGRRNLAQPSEMLRALKQESDRKPKES", "metadata": {"id": "A0A1F7TDN5", "cluster": 12448076, "interpro_all": ["IPR051471", "IPR004701", "IPR036662", "IPR033887"], "interpro_used": ["IPR033887", "IPR051471"], "interpro_unused": ["IPR036662", "IPR004701"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein is categorized in the Small subunit of serine palmitoyltransferase-like family, which substantially enhances the catalytic activity of serine palmitoyltransferase (SPT) during the first committed step of sphingolipid biosynthesis. Members of this family possess a conserved hydrophobic central domain predicted to reside in the membrane and are essential for conferring full enzymatic activity to the SPT complex. It is produced by Parascedosporium putredinis and is annotated with UniProt keywords Endoplasmic reticulum 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, 1977, 10234, 1922, 1920, 2858, 5903, 1927, 8468, 25997, 9961, 17, 3189, 3416, 16, 2154, 7878, 9515, 1920, 6804, 2455, 1927, 8468, 25997, 9961, 12, 19375, 13, 2409, 1920, 2561, 18925, 3537, 1927, 13502, 16113, 8132, 18, 4678, 1927, 2052, 3416, 7150, 43, 5305, 7919, 4101, 3418, 4396, 1942, 17305, 1922, 1920, 3260, 1930, 2032, 4415, 1958, 21510, 4125, 8145, 2455, 1942, 1920, 19375, 2796, 18, 2176, 1977, 4152, 2007, 5336, 3051, 9890, 2457, 5366, 3510, 15472, 1930, 1977, 10633, 1956, 20709, 11569, 13355, 12279, 1930, 9117, 7864, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "MAVVTSFVKWLELKKYQLEVTFSVYIYTPIEKFIFWSFVFLLAGLTVITMVLYLPHHIIFLINRACFYARGDSVDVLEMTKEALAQGALNPGVADTATTTIASAVEAATEMVRDL", "metadata": {"id": "A0A9P1GUR7", "cluster": 14110017, "interpro_all": ["IPR024512"], "interpro_used": ["IPR024512"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a protein with the following function: The protein is included in the Six-bladed beta-propeller, TolB-like superfamily, which forms a structural domain consisting of six 4-stranded beta-sheet motifs that serves as a scaffold for diverse biological activities ranging from enzymatic catalysis to transport. Members of this family include enzymes like quinoprotein glucose dehydrogenase, signaling components such as the LDL receptor, and the periplasmic TolB protein, where the domain mediates protein-protein interactions within the Tol-dependent translocation system. It has been detected in Mytilus galloprovincialis (Mediterranean mussel). Please generate the amino acid sequence for this protein.", "tokenized_instruction": [2, 51, 2150, 14246, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 3798, 17, 22707, 1007, 4666, 17, 5062, 13728, 16, 21930, 1014, 17, 3189, 13975, 16, 2154, 4952, 43, 4346, 3418, 7600, 1927, 3798, 24, 17, 10338, 4666, 17, 11130, 8277, 1988, 10634, 1966, 43, 7281, 1958, 6445, 3933, 4209, 6485, 2037, 8145, 15408, 1942, 4860, 18, 4678, 1927, 2052, 3416, 3951, 5038, 3189, 9012, 6657, 3817, 9294, 16, 3197, 4178, 2427, 1966, 1920, 8017, 3148, 16, 1930, 1920, 24334, 21930, 1014, 2213, 16, 2597, 1920, 3418, 10412, 2213, 17, 2213, 3719, 2651, 1920, 21930, 17, 3100, 7849, 2433, 18, 2176, 2258, 2252, 3330, 1922, 3057, 2583, 1957, 9354, 12964, 11800, 3349, 19337, 12, 16825, 26874, 1938, 13, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MGNCELGKHKFTKGKLLKASLKVLLNYNIRCIDFTVNNKNEILFAAPPGKELLAVSASGSVKSVIQASPMVILAIHLTKHGDLIIGMRDQGQKYPITERSSRQVAIFDEKYTRKSVFEFDSTGKKLFNYAGRIATDSNDYVYVVDWMDNDLRGQIVGINKSGHKIFSYTGHPFYNTDDVPLVPLDIAVTPSDVILISDRNNHTLHALNPKGELCGIQLTQNIGIILPYSLSVDSEGFLVIGCTSYNGEDDKAKIFVVKLLV", "metadata": {"id": "A0A8B6GJU5", "cluster": 14255636, "interpro_all": ["IPR011042"], "interpro_used": ["IPR011042"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe 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. Additionally, the protein should have a Signal transduction histidine kinase, phosphotransfer (Hpt) domain that acts as a histidine-containing intermediate in bacterial phosphorelay signal transduction systems. This module facilitates the shuttling of phosphoryl groups from a sensor kinase receiver domain to a terminal response regulator, thereby regulating complex cellular processes such as chemotaxis and gliding motility. Also, 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. It is produced by Stagnimonas aquatica and is connected to UniProt keyword Membrane, Transmembrane helix, and Two-component regulatory system.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 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, 4950, 16, 1920, 2213, 3066, 2162, 43, 2733, 8201, 13873, 4016, 16, 8078, 17204, 12, 26280, 13, 3418, 1988, 8016, 1966, 43, 13873, 17, 3165, 6129, 1922, 4543, 3421, 15208, 1012, 2733, 8201, 3771, 18, 2052, 9059, 11374, 1920, 26340, 3961, 1927, 12556, 2671, 2037, 43, 6443, 4016, 12608, 3418, 1942, 43, 4262, 2644, 7888, 16, 6113, 6773, 2796, 3689, 4028, 2427, 1966, 16884, 1930, 6534, 2117, 9254, 18, 2222, 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, 2176, 1977, 4152, 2007, 23891, 3223, 1980, 9259, 15849, 1019, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 3260, 16, 9117, 7864, 16, 1930, 2288, 17, 4594, 4948, 2433, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MHARTVAAPRLGRLSLRWKLLLVLGLLDFDSYQALLGALLEQSLREQERLAAQIGAAVNAADLRFFDRHGTPLAVWDWSESPVTGAALPSARQALYCQKQCVQQVFVPAFDRDGVEVIIRVGRSLASSLLAPTPPLWGRQLMAVTDAARLLPLLRAYGQAALSIKPLSVSVVGGQAEALFVKDDSAAAVVFLLLMPSLRRLRAVSLALPLLAEQRFAEARALMLALMGAEAASEAKSRFLAVMSHEIRTPMNGISATTLLAVLDDVLDFSKIEAGQIRIEWRPVALRELVMYVDPVLPTVVRADPVRLRQILFNLCSNAIKVTDDRARIRLRVADTGIGMGPEVRQRLFRPFQQGGRIEVDSSPGEGSEFRVELDLPLGETAAECEVLTSYLRSAGATLVAADSPEHRDYWLEEDRYRNLERPLRAALLLDALALLSGRRARVAERQGRLILVAEDHPTNRLVIGAQLQRLGYAAEEMDGFRLAREIRALEAVGQRPGRLPIIALTAKPATLEHLAARLRRWVPARAPHSTPPVDFEALRAIFAELAQAGEQGAQPRLLGLAHKLKGSVRFVGAPALASALAQLRAALAQVLSAYAELSDWLQQRRSQPRPLGAVHSFLGYLGYRNLVEHNERQARGTGRASESLAVDLVADLTAIEARQAALRAVAREHRPQHFFKQLAGADVALLVRLDAPPIEAAPLVGRLGQLPDPTRQLVAAARIRQDVLRFESVAVLGLLVSSQRHLGWRDEIDGLNRIALALSDKLERLGLLELLQLSPLSPEQQERVRVIRHVEGCLLTFASAAYEKRLRLFTARGRVLVRIEPLAGELSTTRRYGGTGLGLSICKALVEAMPPLWSAELLRGVAVAVSLRDESSREAIHLRRHGDPPDSAEVDADTPGALPAPVVSASELAEDGVQALARLAGRDYAALLTDLHMPDALSGEIEQCRAVGMDDFLLHGDDPELLELVLQDFQRINAPLLEEGLRGPLAPEQ", "metadata": {"id": "A0A3N0VLJ8", "cluster": 14340287, "interpro_all": ["IPR011006", "IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR036641", "IPR004358", "IPR008207", "IPR001789"], "interpro_used": ["IPR001789", "IPR008207", "IPR005467"], "interpro_unused": ["IPR004358", "IPR011006", "IPR036097", "IPR003661", "IPR036890", "IPR036641"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein contains a Manganese/iron superoxide dismutase N-terminal domain that forms the alpha-helical hairpin structure of the Fe/Mn-SOD enzyme, which catalyzes the disproportionation of toxic superoxide radicals into molecular oxygen. This domain supports the binding of manganese or iron cofactors and facilitates the assembly of the enzyme into homodimers or homotetramers, serving as a primary defense against oxidative stress in prokaryotes and mitochondria. It is expressed in Porphyromonadaceae bacterium and exhibits UniProt keyword tags Metal-binding and Oxidoreductase.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 5461, 43, 19516, 19, 5680, 10738, 16679, 56, 17, 4262, 3418, 1988, 4952, 1920, 4595, 17, 11514, 14565, 3170, 1927, 1920, 2650, 19, 5890, 17, 4546, 4113, 16, 2154, 17097, 1920, 17375, 1943, 1927, 6161, 10738, 12467, 2460, 3272, 4612, 18, 2052, 3418, 7825, 1920, 2743, 1927, 19516, 2014, 5680, 21362, 1930, 11374, 1920, 5957, 1927, 1920, 4113, 2460, 29227, 2014, 16350, 28959, 13190, 16, 13915, 1966, 43, 3065, 9720, 3316, 5163, 3071, 1922, 28149, 1930, 6489, 18, 2176, 1977, 3198, 1922, 17376, 5134, 3947, 7324, 1972, 3336, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 6048, 17, 2743, 1930, 27388, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MKFELIQLIAFHHGKHLAGYVNTPYAADALEPAISAET", "metadata": {"id": "A0A9D5WFX2", "cluster": 14891531, "interpro_all": ["IPR019831", "IPR036324"], "interpro_used": ["IPR019831"], "interpro_unused": ["IPR036324"]}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein carries 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. Also, the protein includes 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 is categorized in the Serine/threonine and dual-specificity kinase family, which phosphorylates diverse substrates, including transcription factors and histones, to regulate critical cellular processes such as the cell cycle, DNA damage repair, and apoptosis. These kinases also function in developmental contexts and stress responses, influencing signaling pathways related to pre-mRNA splicing, mTORC1 activity, and cytoskeletal organization. It is derived from Pristionchus mayeri and carries UniProt keyword assignments ATP-binding, Serine/threonine-protein kinase, and Transferase.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 16252, 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, 2222, 16, 1920, 2213, 5921, 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, 1977, 10234, 1922, 1920, 8468, 19, 13143, 1930, 7064, 17, 4896, 4016, 3416, 16, 2154, 18360, 6445, 6249, 16, 2710, 3213, 2790, 1930, 15808, 16, 1942, 5741, 4140, 3689, 4028, 2427, 1966, 1920, 2024, 4048, 16, 2678, 4293, 5059, 16, 1930, 4091, 18, 2144, 7784, 2222, 2347, 1922, 5878, 11144, 1930, 3071, 3387, 16, 11623, 3197, 3873, 2712, 1942, 2097, 17, 3616, 8490, 16, 13694, 2455, 16, 1930, 14787, 5901, 18, 2176, 1977, 3595, 2037, 17618, 2156, 2001, 2072, 1957, 2278, 18842, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 16, 8468, 19, 13143, 17, 2213, 4016, 16, 1930, 13763, 18, 3], "output": "PSRPSPLWPWCARGIVELSRHRPLSLRPLAAAAVDGRPSKLLHHAPPSSGILAASSSSNLASDVALVAPMTSAAEVSQEVKDAIAAVARSMVGVDEQVARKRKSSKASTNSLSKISSSKTRTKPSTEGEYQGSSKSDADSEVAKDSGEYRNHYEVLEFLGKGTFGQVVKAWKKGTNEIVAIKILKKFNFVRAFECFQHKSHTCLVFEMLEQNLYDFLKQNKFTKSLGLIHADLKPENIMLVDPQNQPFRVKVIDFGSASHRSKAFKESIDMWSLGCVIAELFLGWPLYPGSSKAARFFKETKPHESSPVGTPSSWRLKNVDELDIHRVSRYNQVTVPSFDEDPMNQVCERMDRTVTHLAIYNSTSYFNTALKRMKVCMRGRPPGTIPVTNPATATVAPVAAAAPTAVQNAADIMNYYAVAANPISLNSLVSYGQMQQMQQAAAVAALPQSLMPQFVPISVIDHQLLAAQANYQAVAQFPFGHQKFQLNLPALQLPAGAPQNANVTQQPQPLMNAPAPATLAAAPLQPEVPKPHAIGQQAGIANNNLATLNTNIQNLIAAAANGNIDDVDDGPGSSMRAAGVRQNAARNALNGQDLRPLIEVKPEPKMEPIDDGYPRAYLGQPGPSQPVAAAMANPYDQTLLHHLAGAVAAHNAAMFQQRRRPTDHQPPPCRRSRRGLIMDISRKRKAEPAAGHHYPLPPMRLESHQQEELLRAQPVAVSSYKLIKNEVLVSPHPSYARQGQIEVSILSRLSNENAEEPLPMNNIRPIVQQVLTALMKLVTNTYLQSRYYRAPEIILGLPEYDQIRYIVQTQGNPPMHMLEAATDSTMIHIKSKETRKYIFSSLDDEFVALLKRMLVLNQDQRITPFEALQHPFVSPSSVAAPQTPLRVSGIPGAAIHPQQVNMNAAYYQAAPANLLPTTSRPTFAVPTAAALFQPDLLNRTAAAQPSFEDWAQPALQEPSRPLQHVSVTQLQQLAMRHAARPLLHHQPLIQQQQPQVPKQEVITLGATNPLYHPNTSRVIQTNNSRAGKTAVVMSNQQLAAAAAAAANPMANQLTAALG", "metadata": {"id": "A0AAN5DEU0", "cluster": 15175804, "interpro_all": ["IPR011009", "IPR000719", "IPR017441", "IPR008271", "IPR050494"], "interpro_used": ["IPR017441", "IPR000719", "IPR050494"], "interpro_unused": ["IPR011009", "IPR008271"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein belongs to the ClpP/crotonase-like domain superfamily, which comprises a diverse group of enzymes sharing a repeated \u03b2/\u03b2/\u03b1 structural unit, including Clp and tail-specific proteases involved in protein degradation, as well as crotonases and biotin-dependent carboxyltransferases. Also, the protein should feature a Enoyl-CoA hydratase/isomerase conserved site that stabilizes an enolate anion intermediate derived from an acyl-CoA substrate via a characteristic oxyanion hole. Found in the crotonase superfamily, this domain supports diverse catalytic activities, including hydration, isomerization, and dehalogenation, typically within a conserved trimeric structural core. In addition, it is part of the Enoyl-CoA hydratase, C-terminal superfamily, which represents the alpha-helical C-terminal domain found in enoyl-CoA hydratases and related enzymes. This domain serves a structural role, likely facilitating the trimerisation of the protein complex. It occurs in Chloroflexota bacterium.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 14440, 1942, 1920, 18017, 1034, 19, 9442, 5405, 2051, 17, 3189, 3418, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 5038, 10763, 43, 5116, 161, 19, 161, 19, 160, 4346, 5344, 16, 2710, 18017, 1930, 5281, 17, 2487, 12447, 3286, 1922, 2213, 4877, 16, 1966, 2486, 1966, 9442, 5405, 2319, 1930, 8622, 17, 3100, 9943, 18580, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 2066, 10921, 17, 10027, 22420, 3857, 4127, 19, 25510, 5305, 3200, 1988, 19658, 1925, 2066, 8649, 10985, 6129, 3595, 2037, 1925, 11337, 17, 10027, 4510, 3454, 43, 6293, 20004, 8150, 1916, 13356, 18, 2435, 1922, 1920, 9442, 5405, 2051, 13975, 16, 2052, 3418, 7825, 6445, 6804, 4209, 16, 2710, 16561, 16, 27027, 16, 1930, 2028, 7289, 2404, 1943, 16, 5745, 2651, 43, 5305, 29177, 4346, 4728, 18, 1922, 2459, 16, 2176, 1977, 3131, 1927, 1920, 2066, 10921, 17, 10027, 22420, 3857, 4127, 16, 45, 17, 4262, 13975, 16, 2154, 4972, 1920, 4595, 17, 11514, 45, 17, 4262, 3418, 2435, 1922, 2066, 10921, 17, 10027, 22420, 3857, 4127, 1036, 1930, 2712, 5038, 18, 2052, 3418, 10634, 43, 4346, 2770, 16, 3205, 12440, 1920, 20085, 6284, 1927, 1920, 2213, 2796, 18, 2176, 5110, 1922, 10107, 18222, 7336, 14061, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MPAEPRGEWAPPSDVDAVHAATGTGTDLVLTRENALTAEMSWGMGRVLRVLSEDATGGDIGTLPMGDEGQPASYRPARAERYPAVAIRDALALACDLAVADPTARFGALQVRRAVGRSRALELLWGGDWVEAAEAASAGLVNRVTAEGPSSSMTLMKRAAHRAVEMSLEQAAAEGARAFREKRTPRFRGHGAVALLTLNRPERRVRACVITGAPPAFCACPFPVLAAVNGPAAGAGFRGLVADWALTWLLVAAGAVLEETMRWASELLETDSLMQARAFATAD", "metadata": {"id": "A0A535HXC4", "cluster": 17000541, "interpro_all": ["IPR029045", "IPR018376", "IPR001753", "IPR014748"], "interpro_used": ["IPR029045", "IPR018376", "IPR014748"], "interpro_unused": ["IPR001753"]}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein is classified under the Sphingomyelinase C/Sphingomyelin phosphodiesterase 2-like family, which functions as neutral sphingomyelinases or phospholipase C enzymes to hydrolyze sphingolipids like sphingomyelin and inositol phosphosphingolipids into ceramide and phosphocholine. These proteins regulate lipid metabolism and contribute to vesicle budding from the plasma membrane, with specific members localizing to mitochondria or the secretory pathway. In addition, 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 native to bacterium and is described by UniProt keywords Hydrolase, Sphingolipid metabolism, and Transmembrane helix.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 1977, 5947, 2441, 1920, 28057, 2051, 45, 19, 28057, 24821, 22, 17, 3189, 3416, 16, 2154, 4088, 1966, 5459, 28057, 2319, 2014, 17570, 45, 5038, 1942, 7222, 6931, 13502, 18954, 3189, 28057, 1930, 16246, 8078, 3508, 7969, 2029, 18954, 2460, 16926, 1930, 8078, 11603, 18, 2144, 2697, 5741, 4486, 4714, 1930, 4672, 1942, 11502, 15909, 2037, 1920, 3582, 3260, 16, 1956, 2487, 4678, 29507, 1942, 6489, 2014, 1920, 11518, 3374, 18, 1922, 2459, 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, 6196, 1942, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 20748, 16, 13502, 16113, 4714, 16, 1930, 9117, 7864, 18, 3], "output": "MKQTKNFPLRVLTFNVWGLKIGPLHISDVILLQEVWCPSIANFLIREMHTQTLRFHRFTSPDEWFVGKGAVAADIHVTMRLQQLRQLQSWVAGLEHHIPSVIAGQFRESLTDTFSARHGQADGHTYFVDRSYHVYVFLLTPKQSRLDLTMVDSERIKPTLQEIIVHNPIPINGNMISARDIQARMDRIASALHRSKSGYPYHVYQPGRGTWRGPLGNGLLMLSRFPIDTKQGIVRVINTHLGSGKKPLDFNFSPSSLEYCVFRHWAIHKPKMHDRNERIDMLNDAERPYSDHCAVLSTVGIR", "metadata": {"id": "A0A7Y5H1L1", "cluster": 17734621, "interpro_all": ["IPR036691", "IPR005135", "IPR038772"], "interpro_used": ["IPR038772", "IPR005135"], "interpro_unused": ["IPR036691"]}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein includes a Ion transport domain that mediates the selective passage of sodium, potassium, and calcium ions across membranes. It features a six-transmembrane helix topology with a pore-forming loop between the final two helices that determines ion selectivity. This domain functions in various assemblies, including tetrameric potassium channels and inositol 1,4,5-trisphosphate-gated receptors involved in endoplasmic reticulum calcium release. Additionally, the protein is a member of the Two pore calcium channel protein 1, plant family, which mediates calcium flux and functions as a major ROS-responsive Ca2+ channel. It regulates essential physiological processes such as germination and stomatal movement, in addition to playing a role in defense responses. It has been detected in Eutreptiella gymnastica and is connected to UniProt keyword Ion channel and Repeat. 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, 5921, 43, 4755, 4860, 3418, 1988, 10412, 1920, 5328, 11008, 1927, 5227, 16, 9057, 16, 1930, 5016, 6982, 3436, 5726, 18, 2176, 4075, 43, 3798, 17, 9117, 7864, 13678, 1956, 43, 8554, 17, 7402, 5881, 2192, 1920, 3948, 2288, 12789, 1988, 13554, 4755, 9008, 18, 2052, 3418, 4088, 1922, 3425, 16137, 16, 2710, 30442, 9057, 5628, 1930, 16246, 21, 16, 24, 16, 25, 17, 6349, 25324, 17, 12336, 4086, 3286, 1922, 13355, 12279, 5016, 4012, 18, 4950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 2288, 8554, 5016, 4999, 2213, 21, 16, 4496, 3416, 16, 2154, 10412, 5016, 8220, 1930, 4088, 1966, 43, 3044, 4742, 17, 8487, 5497, 15, 4999, 18, 2176, 7014, 4415, 5005, 4028, 2427, 1966, 14609, 1930, 23075, 5829, 16, 1922, 2459, 1942, 14797, 43, 2770, 1922, 9720, 3387, 18, 2176, 2258, 2252, 3330, 1922, 24048, 20483, 24866, 11560, 1019, 26024, 3676, 21788, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 4755, 4999, 1930, 6865, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "LQTVLVTLPELRTIVLLLGLYVFFFAWMGVVLYRDQGSAFFMSLPESMWSLICLLTTVNFPDVMIASVTHSRLNFLYFFLFTGFGIFYLMNRTISTTAQAYTETYNDYQADGRAQEEALLREAFDLLRQGRPALELQELVPVFGQLNRRPDLPPIDDDNCRLLLAAVDSNGTGSCELG", "metadata": {"id": "A0A7S1IFU2", "cluster": 22206351, "interpro_all": ["IPR005821", "IPR044581"], "interpro_used": ["IPR005821", "IPR044581"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the protein function: The protein should contain a BRO N-terminal domain that functions as a DNA-binding module within a widespread superfamily of viral and bacterial proteins. Originally characterized in baculovirus Bro proteins, it occurs either as a stand-alone unit or combined with other domains in temperate phages and bacteria. It is expressed in Lampropedia aestuarii. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 3066, 5531, 43, 4188, 56, 17, 4262, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 9059, 2651, 43, 9360, 13975, 1927, 4324, 1930, 4543, 2697, 18, 10398, 4378, 1922, 26647, 4188, 2697, 16, 2176, 5110, 3108, 1966, 43, 2924, 17, 4298, 5344, 2014, 4252, 1956, 2303, 4682, 1922, 21533, 18273, 1930, 4802, 18, 2176, 1977, 3198, 1922, 12503, 2928, 19258, 12893, 1031, 12169, 21094, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MSNSITSSNFHFDDHLVRLIQDGDSTWFHAGDVMNALDYAATSRSSKVCAHIPEIWKGVKPIHTLGGTQSALFLQEQGLYFFLGRSDKPKALPFQMWVYGEVLPSIRKTGSYKVGQQQELAIDETAESIRRDSIGSIIERLTSRVQQSNTYPVEVFMPLVNAVLRKAGLDFVHRSGHSALPISFAQELEDRLTSLGRVFHPMTSPNFHDVIAIRRILSGMDPKTGQKDSRCTAILPAKNPTLEPEVRRANKRSTSSPAALPSPCSAC", "metadata": {"id": "A0A4S5BN44", "cluster": 23361730, "interpro_all": ["IPR003497"], "interpro_used": ["IPR003497"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should contain a Reverse transcriptase, RNA-dependent DNA polymerase domain that catalyzes the synthesis of DNA from an RNA template. It is typically associated with mobile genetic elements, such as retrotransposons, retroviruses, and group II introns, where it facilitates replication and transposition. It originates from Mucuna pruriens (Velvet bean) (Dolichos pruriens) and is annotated with UniProt keywords Membrane, 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, 5531, 43, 5267, 13335, 16, 3146, 17, 3100, 2678, 6479, 3418, 1988, 17097, 1920, 4271, 1927, 2678, 2037, 1925, 3146, 7662, 18, 2176, 1977, 5745, 2458, 1956, 8785, 3299, 5362, 16, 2427, 1966, 27181, 2101, 16, 26371, 16, 1930, 2210, 2890, 15778, 16, 2597, 2176, 11374, 5158, 1930, 22596, 18, 2176, 22970, 2037, 3422, 17864, 23563, 15960, 12, 6217, 1961, 1031, 21266, 13, 12, 17837, 2108, 1951, 23563, 15960, 13, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 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": "NNHKASSLKTMKAKRSKSEAALYIKFQGQYDILIVSLYVDDLIFMRNNIKMMSDFKNDMMKTFEVIDLDLMNYFFGIEKDDGAPKIDASHYRNLVRSLLYLIVTQLNANLFIVELLNTLLRYLQSMKEFRQAELTRVNTRPDRLRLSQVRHVPTVYVLQPSGPIKSSPIELTESATQLRGHLSTSLASMSLLENLPRPSGRSS", "metadata": {"id": "A0A371F6X9", "cluster": 24577171, "interpro_all": ["IPR013103"], "interpro_used": ["IPR013103"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein has 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. Moreover, the protein contains a Glycosyltransferase subfamily 4-like, N-terminal domain that constitutes the N-terminal Rossmann-fold structure of GT-B family enzymes, including MshA and family 1 subfamily 4 members, and participates in glycosyltransferase activity. It has been detected in Candidatus Thermofonsia Clade 1 bacterium.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 2258, 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, 3950, 16, 1920, 2213, 5461, 43, 20067, 9961, 16227, 24, 17, 3189, 16, 56, 17, 4262, 3418, 1988, 14879, 1920, 56, 17, 4262, 18215, 8890, 17, 3728, 3170, 1927, 4637, 17, 44, 3416, 5038, 16, 2710, 19864, 1019, 1930, 3416, 21, 16227, 24, 4678, 16, 1930, 17241, 1922, 20067, 9961, 2455, 18, 2176, 2258, 2252, 3330, 1922, 14550, 1031, 1957, 21465, 2101, 2126, 11315, 21, 14061, 18, 3], "output": "MRIGINILYLRPSCVDGAYVYARRLLDSLALLDSENAYYVYLNWNFLARQRFLRYFHEQVLLPLHALRHRLDVVHSLHLTHPFFLPCRSVMTLHDTRGNGARRATRVITDSEFAKREMMAHFGLRADKIDVIHLSISPSALPASSYVHKNIPRLLEAFATIQAEFPHELVLIGKLPNNVTPEGADVFVVASLYEGFGLPALEAQAADVALVCSQAASLPEVAGDGAYYFDPYDVLRAKGHANLQRFSWQRTAYQTLEVYRKVAQRREAADFAMPSPNFQPVIFMVPGLGGDIYGFRKQVIRFFAQTDAAIRAHYGVRQPYIAAISGMLTQRVRTTGYVPDAHLPILMRQSLAQALRVCLRDSTLRQS", "metadata": {"id": "A0A2M8PEL4", "cluster": 24978484, "interpro_all": ["IPR001296", "IPR028098"], "interpro_used": ["IPR001296", "IPR028098"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: The protein can be placed in the Integral membrane protein EMC3/TMCO1-like family, which comprises eukaryotic and archaeal members of the Oxa1 superfamily that function as transmembrane domain insertases and intramembrane chaperones. These proteins, including EMC3 and TMCO1, facilitate the insertion and folding of multi-pass membrane proteins into lipid bilayers and play a role in ER calcium homeostasis. It is produced by Candidatus Iainarchaeum archaeon and corresponds to UniProt keyword Coiled coil and Transmembrane helix. 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, 12328, 3260, 2213, 2391, 12981, 19, 5072, 4879, 1009, 17, 3189, 3416, 16, 2154, 12936, 10825, 1930, 22367, 4678, 1927, 1920, 28905, 1009, 13975, 1988, 2347, 1966, 9117, 3418, 12844, 2319, 1930, 9857, 8591, 18098, 18, 2144, 2697, 16, 2710, 2391, 12981, 1930, 5072, 4879, 1009, 16, 6628, 1920, 7413, 1930, 10328, 1927, 2779, 17, 4675, 3260, 2697, 2460, 4486, 21992, 1930, 3918, 43, 2770, 1922, 2668, 5016, 7622, 18, 2176, 1977, 4152, 2007, 14550, 1031, 1957, 11640, 4058, 15618, 20051, 1989, 13470, 1916, 1930, 8852, 1942, 20709, 11121, 2538, 17524, 9121, 1930, 9117, 7864, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MVFISPEIDLLLIALMLVTIFNTVSTIVRNRIMGKGHMEEIKKKQKEFKELMEKTDKDSQKRLKELEQELLETNLKMMKASMPTMLLSLGIVTVLWPWLQAEYSQYTFPIVGSWLFYYIVISLIFSIIISKVQKIILKA", "metadata": {"id": "A0A497JGR4", "cluster": 26946007, "interpro_all": ["IPR002809"], "interpro_used": ["IPR002809"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is grouped in the Protein RETICULATA-related family, which comprises plant proteins involved in the differential development of bundle sheath and mesophyll cell chloroplasts. It is derived from Brassica carinata (Ethiopian mustard) (Abyssinian cabbage) and corresponds to UniProt keyword Plastid and Transit peptide.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2213, 18905, 5499, 17, 2712, 3416, 16, 2154, 12936, 4496, 2697, 3286, 1922, 1920, 5611, 2740, 1927, 14142, 14730, 1930, 23037, 30338, 11560, 2024, 24627, 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, 1930, 8852, 1942, 20709, 11121, 2538, 19754, 1930, 16361, 4207, 18, 3], "output": "MSRYFELQRSVVMRWLMQFAKLAMECGVGVFTKTAAEYERRRENFFNELEYYSIRSFEIVRGVPVTSRRLDSHGMVEEAECGGANSSEHRLSVKKTCIEAGFRESLADDLFLVVLADVVIILLCLCVHVRSQEWSETNRGEAALLSARPVLEMT", "metadata": {"id": "A0A8X7U7R9", "cluster": 28476625, "interpro_all": ["IPR021825"], "interpro_used": ["IPR021825"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that has this function description: 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 should contain 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. It is derived from bacterium TMED46. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 2052, 2347, 8418, 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, 1920, 2213, 3066, 5531, 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, 2176, 1977, 3595, 2037, 14061, 22377, 15005, 1016, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MNKVSNAGKIWGEFYKNKKIDWVRYDKKDSRYFEDLIKSDYGKILIQCINFLGKDEDIKILEAGCGVGEMAISLSMNYNVKAFDYNKEALKICNKLNNILCKKVVLYIDDLLDLKVEKEKYNFIYNQAVLEYFTHEEKIICIKNLKKILEEEGIIVFVCQNTNSTYNNNDFINQPNVYNCNIDYVKKLFIENNFEILFYDGLYTSKVFTNFLLPKYMNENIKYYVWKIMDFLYFPSFIRRKYNLQFVVCAKILK", "metadata": {"id": "A0A3R8ALE4", "cluster": 1169038, "interpro_all": ["IPR041698", "IPR029063"], "interpro_used": ["IPR029063", "IPR041698"], "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 Nitrite/Sulfite reductase ferredoxin-like domain that functions as a structural element within sulfite and nitrite reductases, facilitating the six-electron reduction of sulfite to sulfide or nitrite to ammonia. This domain adopts a ferredoxin-like alpha/beta sandwich fold, with two copies typically forming a single structural unit that contributes to the assembly and reactivity of the hemoprotein component. In addition, the protein is categorized in the Nitrite and sulfite reductase 4Fe-4S domain-containing protein family, which utilizes a 4Fe-4S domain to transfer electrons from ferredoxin for the reduction of nitrite to ammonium and sulfite to sulfide. These enzymes are essential for nitrogen and sulfur assimilation, including the biosynthesis of sulfur-containing amino acids and cofactors, often functioning within the chloroplast. It is derived from Actinophytocola xanthii and corresponds to UniProt keyword Iron-sulfur, Metal-binding, and Iron.", "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, 15988, 19, 5141, 2394, 11386, 25304, 22389, 10960, 17, 3189, 3418, 1988, 4088, 1966, 43, 4346, 6149, 2651, 5141, 2394, 1930, 15988, 11386, 1036, 16, 12440, 1920, 3798, 17, 4995, 3378, 1927, 5141, 2394, 1942, 21135, 2014, 15988, 1942, 14880, 18, 2052, 3418, 24032, 43, 25304, 22389, 10960, 17, 3189, 4595, 19, 4666, 18038, 3728, 16, 1956, 2288, 9425, 5745, 7402, 43, 2957, 4346, 5344, 1988, 7624, 1942, 1920, 5957, 1930, 8229, 1927, 1920, 3243, 6657, 4594, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 1920, 15988, 1930, 5141, 2394, 11386, 15338, 1021, 17, 26814, 3418, 17, 3165, 2213, 3416, 16, 2154, 18127, 43, 15338, 1021, 17, 26814, 3418, 1942, 3856, 14354, 2037, 25304, 22389, 10960, 1958, 1920, 3378, 1927, 15988, 1942, 11944, 1930, 5141, 2394, 1942, 21135, 18, 2144, 5038, 2032, 4415, 1958, 6634, 1930, 12585, 22317, 16, 2710, 1920, 8132, 1927, 12585, 17, 3165, 3835, 4576, 1930, 21362, 16, 3868, 7295, 2651, 1920, 17471, 18, 2176, 1977, 3595, 2037, 4718, 2688, 2355, 23338, 1019, 15213, 3907, 1930, 8852, 1942, 20709, 11121, 2538, 5680, 17, 12585, 16, 6048, 17, 2743, 16, 1930, 5680, 18, 3], "output": "MATRTYQDRCPGVFRPWAADDGAIVRLRVPGGRISPDALLNLQLRGIGTEGGAVAAGLVDAVAAAGLLPSRTHELVRNILVSPLTGLHGGALLADPALAGLGGRFLFVLDDGRGDVARRDLDLGLVALDAARAASELARLAGEFTRVRGTGPSASWHVDELPDPSVLGAGVPRHPGRRLEVLAVPDGLVRRPLAERLAGAAGLVVTPWRGIVVEESSRVVDAAERYGDGTVLLTRRARLDLRPVVRALDDVQLRIGATGWGPVVPADRATEVAADPPPPGRVLGAD", "metadata": {"id": "A0A1Q8CY65", "cluster": 1861923, "interpro_all": ["IPR051329", "IPR005117", "IPR036136"], "interpro_used": ["IPR005117", "IPR051329"], "interpro_unused": ["IPR036136"]}, "task_type": "infilling"} {"instruction": "The protein includes a Peptide chain release factor domain that mediates the termination of protein synthesis in bacteria, mitochondria, and chloroplasts. It functions as a core component of type I release factors, such as RF1 and RF2, to facilitate the release of the nascent polypeptide chain from the ribosome. It originates from Morella rubra.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 5921, 43, 4207, 4659, 4012, 2991, 3418, 1988, 10412, 1920, 12462, 1927, 2213, 4271, 1922, 4802, 16, 6489, 16, 1930, 24627, 18, 2176, 4088, 1966, 43, 4728, 4594, 1927, 2601, 51, 4012, 2790, 16, 2427, 1966, 7751, 1009, 1930, 7751, 1028, 16, 1942, 6628, 1920, 4012, 1927, 1920, 16861, 13022, 4659, 2037, 1920, 12794, 18, 2176, 22970, 2037, 2253, 11560, 1019, 10010, 5524, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "GFTVERIVASNWPILDESESDWKSHAAAIAQSIHLKPDIWDDPMHAGKISHEHGSLMGKMKEVGAFERELLEHIDLRMRRNSKEKELQALLSRELDSCSCYIEVYWNNIFRFSSRDVNTVCFADDTGHLRYSGSDDNFCKLFWLPDESHKAVVLSEPNHQIKRRMKKLVLRLDLLSRELNMVKLAREEDDAEMESESLKALNRAHWQMRYLSQVAES", "metadata": {"id": "A0A6A1VJQ8", "cluster": 7196362, "interpro_all": ["IPR005139", "IPR045853"], "interpro_used": ["IPR005139"], "interpro_unused": ["IPR045853"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: 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 occurs in Parcubacteria group bacterium and is described by UniProt keywords Membrane, Transmembrane, and Transmembrane helix. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 51, 12914, 1942, 3036, 30, 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, 5110, 1922, 2096, 18021, 7972, 2341, 18339, 2210, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MKSFSFLGLFFSFLIILFFSFYFFATGKFFIQGPKIILLNPKEDIRTESRLIKIEGKIKGQIKNLTINNEKLYIGEDGVFNQKINLASGLNKIVLKAEDQNNRSDIITRKIFVIQ", "metadata": {"id": "A0A931VHV9", "cluster": 7702294, "interpro_all": ["IPR013783"], "interpro_used": ["IPR013783"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein should have a Zinc finger, RING-type conserved site that binds two zinc atoms in a \"cross-brace\" motif and functions primarily as an E3 ubiquitin ligase. This cysteine-rich domain facilitates substrate recognition and mediates protein-protein interactions essential for the ubiquitination pathway. Additionally, 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. It is produced by viral metagenome and is annotated with UniProt keywords Metal-binding, Ubl conjugation pathway, and Zinc-finger.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 2162, 43, 7997, 8497, 16, 6335, 17, 2601, 5305, 3200, 1988, 6876, 2288, 7997, 9030, 1922, 43, 6, 3567, 17, 18303, 1972, 6, 5219, 1930, 4088, 5985, 1966, 1925, 10968, 6526, 11905, 18, 2052, 8666, 17, 5536, 3418, 11374, 4510, 5708, 1930, 10412, 2213, 17, 2213, 3719, 4415, 1958, 1920, 11758, 3374, 18, 4950, 16, 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, 2176, 1977, 4152, 2007, 4324, 16552, 2225, 1930, 1977, 10633, 1956, 20709, 11569, 6048, 17, 2743, 16, 4803, 1024, 14122, 3374, 16, 1930, 7997, 17, 8497, 18, 3], "output": "MEQCGVCGIDLPSDANNPTCPLCRRLLHEEDNDDNEIQMQTDRIFEGLEFNMEEEITHDHMMEVSGAIHLRIVPKEDYDRIEVTVFNDERFPNLKWYAFRERIQHVDWSTELQHIRNDNVRMIVRYQPDIWLNIRAITACKHAFCISCLLKWYRVAQTRAEEEHIRQLMIDINTQNHCRNNPDQTYGTAASYILELNDTARAFRYRFGRIEEDRAQIVTE", "metadata": {"id": "A0A6C0LZF3", "cluster": 7968681, "interpro_all": ["IPR001841", "IPR013083", "IPR017907"], "interpro_used": ["IPR017907", "IPR013083"], "interpro_unused": ["IPR001841"]}, "task_type": "infilling"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. 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. Additionally, the protein has a DEAD/DEAH-box helicase domain that functions as an ATP-dependent nucleic acid-binding module essential for unwinding RNA structures during metabolism. It facilitates diverse cellular processes, including pre-mRNA splicing, ribosome biogenesis, and translation, by coupling ATPase activity with helicase function via the conserved motif III. 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. It is present in Kamptonema sp. SIO1D9 and contains UniProt keyword associations Antiviral defense and Hydrolase.", "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, 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, 2258, 43, 9535, 19, 30097, 1023, 17, 5758, 15318, 3418, 1988, 4088, 1966, 1925, 4498, 17, 3100, 11079, 2687, 17, 2743, 9059, 4415, 1958, 26801, 3146, 4061, 2409, 4714, 18, 2176, 11374, 6445, 3689, 4028, 16, 2710, 2097, 17, 3616, 8490, 16, 12794, 13008, 16, 1930, 6410, 16, 2007, 7590, 9444, 2455, 1956, 15318, 2347, 3454, 1920, 5305, 5219, 4337, 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, 2176, 1977, 2481, 1922, 25271, 26834, 6666, 2056, 18, 5998, 8098, 1007, 1026, 1930, 5461, 20709, 11121, 2538, 5253, 10129, 9720, 1930, 20748, 18, 3], "output": "MRITLLPLFSRQNPDSQHCPLGCQGQCKIKQISQLGQDSPASTLEAKVIFNTAFTNDGKSLGAYLPAFLHKKYRILGLYPTIELVRDQKYQLENYHQLVRVEQNKATGRRGSRFSELRKAIGNRRIILTNPDIFHLITHLSYPNLHIFGEHQETALINSMLLLRHSREQSRPLRFLFTSATANANFVEQLKKSGFTVETVQGEYLSKDREDAPEQDSNSLDWLNLNLEKIAQILKDEKPRKGRGLVILSGIVGDQERSKTREELENTPKPILIVGTSAVDVGVDFEVHLLIFEFSQYQAFVLIPSWMKWIWQKIQAELQENNLVDRHQFNTEIAANVFNGETVKGKTRGKERKELKARTQKLRESVTNDLCHIYGERFQNKERQWFVWDENQSRFYTYDLLRLLPHTEVEVISKKDFFTALETANRSTFEFNERYLKIYLRLRELEICTLTELEGLFLSGHPQQTALNQALEDLEFLSFVHRLIDSQDKAYACAFNQDALLLESLKWKIDRCTHSDPYIFPCPLSLHQVETYRKVSDKLNPHKRVDSLYGAELGRTYSPDYLLYTLTQTPDLYFADEFLGYRQISERIELHFEEVNSMARVHRVVSQLKQKLEPEILVREVTTDLSTFLQRLGRLGRRSGSPPTFEQYRYYWGGLQAQGMLNALKAIFQSVRDELLHFRGSSTLQAATRWLEIGEPFSLKLETDCLTLVPVAKDPRSHWKIRNTLFLPPTFG", "metadata": {"id": "A0A6P1AIK1", "cluster": 8910940, "interpro_all": ["IPR054712", "IPR017575", "IPR011545", "IPR050079", "IPR014001", "IPR001650", "IPR027417"], "interpro_used": ["IPR014001", "IPR011545", "IPR001650"], "interpro_unused": ["IPR017575", "IPR054712", "IPR027417", "IPR050079"]}, "task_type": "infilling"} {"instruction": "The protein I want to design has this role: It is part of the Calcium-activated chloride channel regulator family, which mediates calcium-activated chloride conductance and regulates mucus production, secretion, and tissue inflammation in the innate immune response. These proteins contain a metalloprotease region responsible for autoproteolytic processing and can function as tumor suppressors or cell adhesion factors through interactions with integrins. Additionally, the protein contains 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 present in Rotaria sp. Silwood1. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 2176, 1977, 3131, 1927, 1920, 5016, 17, 4128, 9140, 4999, 7888, 3416, 16, 2154, 10412, 5016, 17, 4128, 9140, 11977, 1930, 7014, 16428, 3372, 16, 5512, 16, 1930, 2960, 4531, 1922, 1920, 8539, 3743, 2644, 18, 2144, 2697, 5531, 43, 28629, 2051, 3031, 5061, 1958, 5728, 9218, 1021, 6586, 4587, 1930, 2112, 2347, 1966, 2798, 21664, 2014, 2024, 6141, 2790, 2596, 3719, 1956, 15563, 18, 4950, 16, 1920, 2213, 5461, 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, 2481, 1922, 30029, 3027, 1019, 2056, 18, 4059, 15269, 1009, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MQSRAPIDLVCIVDQSGSMGGQKIALLKKTLIDIVDQLGELDRLAIISFNTGAIDRSHGLKRMTQQ", "metadata": {"id": "A0A822FU73", "cluster": 9469823, "interpro_all": ["IPR051266", "IPR002035", "IPR036465"], "interpro_used": ["IPR051266", "IPR002035"], "interpro_unused": ["IPR036465"]}, "task_type": "autoregressive"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein is associated with the Antitoxin MazE-like family, which functions as the antitoxin component of a type II toxin-antitoxin (TA) system, typically binding to and neutralizing its cognate toxin to prevent cell death or growth arrest. It occurs in Rhodospirillales bacterium.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 1977, 2458, 1956, 1920, 10310, 9754, 14476, 17, 3189, 3416, 16, 2154, 4088, 1966, 1920, 10310, 9754, 4594, 1927, 43, 2601, 2890, 9165, 17, 10310, 9754, 12, 4410, 13, 2433, 16, 5745, 2743, 1942, 1930, 12130, 2496, 15786, 9165, 1942, 4625, 2024, 3539, 2014, 2905, 8048, 18, 2176, 5110, 1922, 11490, 3106, 23576, 11560, 3955, 14061, 18, 3], "output": "MPVSAKRLSTWAPDVGSPAFKAEITNESERRRKAASRDKVRAQGLRPIQIARRQSRLIAASRYEAEDQAFIDA", "metadata": {"id": "A0A938KX94", "cluster": 9753763, "interpro_all": ["IPR021558"], "interpro_used": ["IPR021558"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein should include a NUDIX hydrolase domain that functions as a pyrophosphohydrolase, hydrolyzing a wide range of organic pyrophosphates including nucleoside diphosphates linked to other moieties (NDP-X), such as oxidized (d)NTPs, dinucleotide coenzymes, and capped RNAs. This activity allows the domain to sanitize the nucleotide pool by degrading potentially mutagenic oxidized nucleotides and to regulate the levels of various metabolic intermediates and signaling compounds. It has been detected in Rhodospirillales bacterium.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 3066, 3951, 43, 28416, 2416, 20748, 3418, 1988, 4088, 1966, 43, 20661, 2609, 8601, 21524, 16, 7222, 9046, 43, 4743, 3109, 1927, 6805, 24937, 1036, 2710, 18015, 23266, 1036, 4624, 1942, 2303, 16706, 12, 8026, 1034, 17, 66, 13, 16, 2427, 1966, 11339, 12, 46, 13, 29676, 1036, 16, 21302, 22051, 1036, 16, 1930, 22069, 8624, 18, 2052, 2455, 5731, 1920, 3418, 1942, 6867, 2078, 6931, 1920, 5489, 5562, 2007, 18192, 5063, 21977, 11339, 9519, 1930, 1942, 5741, 1920, 2428, 1927, 3425, 4487, 12386, 1930, 3197, 4300, 18, 2176, 2258, 2252, 3330, 1922, 11490, 3106, 23576, 11560, 3955, 14061, 18, 3], "output": "MTTDNLIEKIGLAVLRGSQLLVVRNRDTSEIREELSCDIDEASLDYIGEYRDDAANDKGSKVRECLWFDTEHGDVTQLSKIIRDQILPDLRVRGFLAPAVEGESWLFLVPGGRVEVGESPTETLKRIRLYRGELAGNGIKMANEID", "metadata": {"id": "A0A6N2DUA8", "cluster": 10089423, "interpro_all": ["IPR015797", "IPR000086"], "interpro_used": ["IPR000086"], "interpro_unused": ["IPR015797"]}, "task_type": "infilling"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: It is part of the Nucleotide-diphospho-sugar transferase superfamily, which catalyzes the transfer of sugar moieties from activated donor molecules, such as nucleotide diphospho-sugars, to specific acceptor molecules to form glycosidic bonds. These enzymes play a critical role in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides. Also, the protein is classified under the GNT1/Glycosyltransferase 8 family, which encompasses enzymes involved in the modification of glycans and the biosynthesis of oligosaccharides. Members include N-acetylglucosaminyltransferases that modify N-linked glycans, glycogenins that initiate glycogen synthesis via self-glucosylation, and galactinol synthases involved in producing osmoprotectants. Collectively, these proteins contribute to cellular metabolism, stress responses, and structural integrity across diverse organisms. It occurs in Emiliania huxleyi (strain CCMP1516).", "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, 5489, 17, 11791, 2609, 1037, 17, 9523, 13763, 13975, 16, 2154, 17097, 1920, 3856, 1927, 9523, 16706, 2037, 4128, 6282, 4206, 16, 2427, 1966, 5489, 11791, 2609, 1037, 17, 15592, 16, 1942, 2487, 12641, 4206, 1942, 2386, 7533, 12546, 9031, 18, 2144, 5038, 3918, 43, 4140, 2770, 1922, 1920, 8132, 1927, 2054, 11926, 16, 22012, 16, 1930, 18686, 18, 2222, 16, 1920, 2213, 1977, 5947, 2441, 1920, 9005, 6613, 19, 20067, 9961, 28, 3416, 16, 2154, 21569, 5038, 3286, 1922, 1920, 6295, 1927, 15509, 1930, 1920, 8132, 1927, 22012, 18, 4678, 3951, 56, 17, 6894, 22988, 5360, 8547, 2199, 18580, 1988, 11675, 56, 17, 4624, 15509, 16, 13302, 2925, 1988, 11051, 13302, 4271, 3454, 3543, 17, 3351, 21385, 16, 1930, 9479, 21092, 8921, 1036, 3286, 1922, 7144, 9405, 18018, 2341, 2356, 18, 10182, 16, 2144, 2697, 4672, 1942, 3689, 4714, 16, 3071, 3387, 16, 1930, 4346, 7996, 3436, 6445, 7373, 18, 2176, 5110, 1922, 2391, 25600, 10306, 5897, 19776, 10676, 1033, 12, 3943, 25993, 5113, 7912, 1016, 13, 18, 3], "output": "MFVISNFTTIAVVSLVWTKTRRSIVLLSDGGLDKAHKRHSPTLTCLAVQLDAWSLEYDKVVSLDTDIVRRNIDHRRTAATRGGRTADGMLVLTPSRDVYEAMRRAAAFTRSYDSGDQGFLADEVQEAYIWHPFPRRIHALEDEVEKRVKFPFGFEFYGNVNSFFLTEGGAMIPMIPTHTAFRLALPAQRLFSVSTPAAALDSKWGFNALAFFASRNVAWYELPRRYHLGWCVQP", "metadata": {"id": "A0A0D3JMT2", "cluster": 10270924, "interpro_all": ["IPR050587", "IPR029044"], "interpro_used": ["IPR029044", "IPR050587"], "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 assigned to the Bacterial anti-sigma-factor serine-protein kinase family, which negatively regulates sigma factor activity to modulate transcriptional responses to environmental stress or developmental changes. Members phosphorylate antagonist proteins, such as RsbV or SpoIIAA, preventing the sigma factor from forming a holoenzyme with RNA polymerase. Some members also bind and potentially hydrolyze ATP and GTP. Also, the protein is associated with 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. It occurs in Actinomycetales bacterium.", "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, 6304, 1942, 1920, 4543, 2246, 17, 5139, 17, 2991, 8468, 17, 2213, 4016, 3416, 16, 2154, 7191, 7014, 5139, 2991, 2455, 1942, 8480, 5224, 3387, 1942, 4813, 3071, 2014, 5878, 2840, 18, 4678, 18730, 8151, 2697, 16, 2427, 1966, 4366, 21441, 2014, 18055, 3907, 5025, 16, 8444, 1920, 5139, 2991, 2037, 7402, 43, 20403, 14896, 1956, 3146, 6479, 18, 2673, 4678, 2222, 4566, 1930, 5063, 7222, 6931, 4498, 1930, 9319, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 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, 2176, 5110, 1922, 4718, 13386, 3949, 1918, 14061, 18, 3], "output": "MRNSVNGWGSARRIDACEVDEGGWGAGRRAPTEGWSRSFTRDTVARWGVGRLADAAELLTSELVTNAVKAAARLVQGSLVIEAWDPESDLPVMEDPAPGAESGRGLRIVDAVSNGWDPELPVRQPHPLRLVRAYQGEQSIAENDPETLFRVRDGLRALVPGPVRAATFAAVPAAVGGAAFVDPQDPRLVRVWLHYEAGSGGKVVWCQLDVPAPDGAGR", "metadata": {"id": "A0A970Z5Y6", "cluster": 11811523, "interpro_all": ["IPR050267", "IPR036890"], "interpro_used": ["IPR050267", "IPR036890"], "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 Diphthamide synthesis DPH1/DPH2 family, which mediates the first step in the biosynthesis of diphthamide, a unique post-translational modification of a histidine residue on translation elongation factor 2 (EF2). Members of this family function as 2-(3-amino-3-carboxypropyl)histidine synthase subunits, generating the specific modified residue that serves as the target for ADP-ribosylation by diphtheria toxin. It is native to Ananas comosus var. bracteatus.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 11791, 1963, 5482, 4271, 5679, 8600, 19, 5679, 6951, 3416, 16, 2154, 10412, 1920, 2561, 3537, 1922, 1920, 8132, 1927, 11791, 1963, 5482, 16, 43, 5008, 2753, 17, 8414, 6295, 1927, 43, 13873, 6181, 1990, 6410, 9971, 2991, 22, 12, 8485, 1028, 13, 18, 4678, 1927, 2052, 3416, 2347, 1966, 22, 17, 12, 23, 17, 3835, 17, 23, 17, 15750, 20194, 2199, 13, 13873, 8921, 6991, 16, 9155, 1920, 2487, 4795, 6181, 1988, 10634, 1966, 1920, 2758, 1958, 9828, 17, 29117, 3017, 2007, 29479, 2126, 9165, 18, 2176, 1977, 6196, 1942, 7381, 3676, 2008, 13650, 4953, 18, 18303, 2341, 5376, 1031, 1957, 18, 3], "output": "MEADDAHRLLPPPLLTLNLTLDERYPNSRGRRRRRRRREEGPFAQRGDLPPPLELRLRGPQDRASPPLGRRAPRRAPAPEGLLMYLVLADPTYGACCVADRAAAALSADLLVHYGHSCLVPVPSSLLAAAVRSAFPDPPPPRASPSRAPSSSSPPSTRRGPSSSDAPRPPSPNRRVWTRSSSWPTAGFTSRRSGVGAEALRALPDPGLDPFSLLLADALRSDADDVPVLYVFVDIRVDPTRLSPMATRTSSSPRQNRSPPARS", "metadata": {"id": "A0A6V7PJP4", "cluster": 16210277, "interpro_all": ["IPR016435", "IPR042263"], "interpro_used": ["IPR016435"], "interpro_unused": ["IPR042263"]}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein belongs to the Glycoside hydrolase family 71 family, which comprises alpha-1,3-glucanases. In fission yeast, members such as Agn1 hydrolyse septum-edging material and act in concert with endo-1,3-beta-glucanases to achieve efficient cell separation. It occurs in Puccinia coronata f. sp. avenae and contains UniProt keyword associations Signal.\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, 14440, 1942, 1920, 7533, 2261, 20748, 3416, 5858, 3416, 16, 2154, 12936, 4595, 17, 21, 16, 23, 17, 18798, 2319, 18, 1922, 16150, 5688, 16, 4678, 2427, 1966, 21790, 1009, 21686, 1021, 17026, 17, 3347, 6066, 3485, 1930, 4033, 1922, 21799, 1956, 16239, 17, 21, 16, 23, 17, 4666, 17, 18798, 2319, 1942, 6230, 5807, 2024, 7106, 18, 2176, 5110, 1922, 24236, 3665, 2126, 5548, 5499, 48, 18, 2056, 18, 16959, 3336, 1930, 5461, 20709, 11121, 2538, 5253, 2733, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MRLLPTLRGVVKTLVFLDVVLWAQPAASSALNSSSSPRLVFAHFITGLTVNYSRDAFALNVGLPDEWQLQQVKSAYESADAVKTTYGTPFVTSFVPLSAQLLINGRPLVSTFSGEANKLGAEDLSSGWQEALKAPLARLDPSTAVSDNPVVDGIMTWNSWPTGTENISTLIDHQFQSNASPCFFTHYKDKNWIYKSDDNLYINRWMKLISMPDPPDFVQIIWLKMSDYFIKWYKTGARPTIEEDTVHFNYRPHSINAIASSDTLPATQLRIRIGDMQQSFGNITRSEVNTFTAPWNGHTGEVEVALLDSTGNESILSKSTSGAGPALLPRGIMFLSLFMYHASLYQLWSDWSSQLTLAASHGIKLFLSLDMSVIQTAEDVTTWGNPPLDALFIPAWSSRSSQKLYMAGVSWNDYGESHYVGPRLGTPPADTTWLDGFDHQSPINASVSADAVYVATYLSATSTALMKRHGEVPISNEIKTYNFNYAA", "metadata": {"id": "A0A2N5U924", "cluster": 16549636, "interpro_all": ["IPR005197"], "interpro_used": ["IPR005197"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Target Function: The protein incorporates a PAS fold-4 domain that functions as a structural sensory module found in archaea, bacteria, and eukaryotes. It recognizes a diverse range of ligands, including oxygen, substituted aromatic hydrocarbons, dodecanoic acids, and autoinducers, to mediate signal transduction in response to environmental stimuli. In addition, 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. Additionally, the protein incorporates 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. It is identified in Verrucomicrobiota bacterium and is linked to UniProt keywords Transmembrane, Transmembrane helix, and Coiled coil.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 19683, 43, 9233, 3728, 17, 24, 3418, 1988, 4088, 1966, 43, 4346, 6893, 9059, 2435, 1922, 21501, 16, 4802, 16, 1930, 15021, 18, 2176, 16197, 43, 6445, 3109, 1927, 6908, 16, 2710, 4612, 16, 11798, 10761, 22318, 16, 12621, 13126, 8643, 4576, 16, 1930, 27485, 4600, 5675, 16, 1942, 8265, 2733, 8201, 1922, 2644, 1942, 4813, 5458, 18, 1922, 2459, 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, 4950, 16, 1920, 2213, 19683, 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, 2176, 1977, 2899, 1922, 3566, 3176, 13055, 1935, 15129, 3940, 3857, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 16, 9117, 7864, 16, 1930, 17524, 9121, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "LAVAIWTFSVLMGLLSARPTAQQFWVNIGFLGVVWLALVPAITLALVFIPATHELILKRDWVNGVVRESYGLLLKLVHSPPLYRQQTMLVLLGGLTPWAANLLHLAGLVPRSWLHFRLLEITPVARDAVIEHMNDAMLVLDAQDRIVDAVTLRDCPDLVRRLRETGAVQTEIALGQANDGRAFDLRVSPLFRRQAEQERERLIQELQDALGNVNLLSGLLPICASCKRIRDDRCPDCVQKLYPEIAQPGTAESGARALSPAWLAFALAYTGRGAWLTRSVLTAWFWVFAGFAYVCNLASLVLDPTPFSFALSGLLLAWGLFCNPAAQRLFHTTARQAIGQTADRRNRFVGRLAMLRDMTEGYWNQLESFIQRRSSAKFTHGL", "metadata": {"id": "A0A9E2VNH7", "cluster": 17025738, "interpro_all": ["IPR031621", "IPR000014", "IPR000700", "IPR035965", "IPR013656"], "interpro_used": ["IPR013656", "IPR000014", "IPR000700"], "interpro_unused": ["IPR031621", "IPR035965"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein includes a Lamin tail domain that adopts a globular immunoglobulin-like fold and functions as a structural module at the C-terminus of nuclear lamins and invertebrate intermediate filaments. It facilitates interactions with DNA and chromatin-binding proteins within the nuclear lamina, while prokaryotic homologs likely assist in tethering proteins to membrane structures. Additionally, the protein has a Phytase-like domain that likely incorporates PLC-like phosphodiesterase enzymatic activity. This repeated domain features highly conserved glutamate and aspartate residues that are predicted to facilitate this catalytic function. It is derived from Actinomycetota bacterium.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 5921, 43, 7962, 5281, 3418, 1988, 24032, 43, 20975, 11837, 17, 3189, 3728, 1930, 4088, 1966, 43, 4346, 9059, 2019, 1920, 45, 17, 7822, 1927, 4254, 7962, 1036, 1930, 26381, 6129, 11855, 18, 2176, 11374, 3719, 1956, 2678, 1930, 6338, 17, 2743, 2697, 2651, 1920, 4254, 14310, 16, 2679, 21545, 14279, 3205, 6589, 1922, 23991, 2697, 1942, 3260, 4061, 18, 4950, 16, 1920, 2213, 2258, 43, 9321, 2051, 17, 3189, 3418, 1988, 3205, 19683, 12897, 17, 3189, 24821, 8145, 2455, 18, 2052, 5116, 3418, 4075, 3626, 5305, 7627, 1930, 12878, 4248, 1988, 2032, 4396, 1942, 6628, 2052, 6804, 2347, 18, 2176, 1977, 3595, 2037, 4718, 13386, 19446, 3857, 14061, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "TTYGRCPDGTGGFGTTLSSTRGAANDCPAEAKVTVTFNEVESNGDLVGDFAELVNTGTEGFDLSTIVAPGEYYVLAEADFGFGLGGADSVRLFGPAGGSAGDEAIDTYTWATHAATTYGRCPDGTGDFTTTTSESSGGEPGDWVELVNNGVDPVDVGGFFFKDDDDARTFQIPAATSIAPGAYLVLDEADFGFGLGGADSARLFAADGSDGTGDFATTRTATKGAANQCVGDLVTEPWPGSQDVATVDEAGVLGGDISGLTYESTGTTTPGTLTATNTLTYPDGTGLPDTEGVTLGAGGSADGVYAATERNNASSGVSRPAILRWDVPAGEATLTVAANSGLEGIAFVPDSYLLEAGLVDETTGAAYDPTTYADHRGGLFLVGLEGNGQVYAYALDHTAGTFTRVADDTCEGRIGLVDVTDGAFAPETYYDRPAGMPNINNEGFTLAGGSECVEGVKPALWSDDSNDPTITADVTSAEPPSATGWYAGPVTVTFTCTPMSAPIVGDCPAPAVLDESGADQVVTGSVTAEVTVGGVKDGRTYRGDEPAGRCVASDATSDVDTCTVESMRNGRSVLVTATATDLAGNTASASKRFRVVFGASSKPRLLKPVKQKKQLSGAGRTMRASETQDHVTTWVRKAKVGKRTTGKKWKVGVLVGGTTTVIKLKVRGGYRFKDNDDSKAFYTIPDDSTRGAANDCSAAVRINEVTLIDSYTWLTHAATTYGRCPLAVNNGTGELVRLAKSGDTWSPSATHEWNLVDDLPFASGFPAVMDLHFEASTQQLWVVCDTGGFALREGTVTCVEDVDPVVVDGGTATTSVTVDVDLDAPSPLVQVLGARFNGGRYIVRRGDAFQVQA", "metadata": {"id": "A0A948CFW2", "cluster": 18209103, "interpro_all": ["IPR001322", "IPR036415", "IPR027372"], "interpro_used": ["IPR001322", "IPR027372"], "interpro_unused": ["IPR036415"]}, "task_type": "infilling"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein is a member of the Basic leucine zipper (bZIP) transcription factors family, which utilizes a characteristic bZIP domain to facilitate DNA binding and dimerization for the transcriptional regulation of diverse biological processes ranging from cell growth and development to stress responses and immunity. These proteins bind specific DNA sequences, such as cAMP response element (CRE) or activator protein 1 (AP-1) sites, to activate or repress gene expression and can interact with histone-modifying enzymes to influence chromatin structure. In addition, the protein includes a Basic-leucine zipper (bZIP) domain that functions as a DNA-binding and dimerization motif in eukaryotic transcription factors. It features a contiguous $\\alpha$-helix containing a basic region for DNA interaction and a leucine zipper that mediates parallel dimerization, forming a flexible fork structure that grips specific DNA sequences. It is native to Setomelanomma holmii and has UniProt annotations Coiled coil and Transcription regulation.", "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, 43, 7210, 1927, 1920, 5937, 12624, 27910, 12, 30450, 13, 3213, 2790, 3416, 16, 2154, 18127, 43, 6293, 30450, 3418, 1942, 6628, 2678, 2743, 1930, 13640, 1958, 1920, 5224, 3640, 1927, 6445, 3933, 4028, 6485, 2037, 2024, 2905, 1930, 2740, 1942, 3071, 3387, 1930, 7611, 18, 2144, 2697, 4566, 2487, 2678, 3709, 16, 2427, 1966, 6225, 2644, 6149, 12, 3478, 13, 2014, 9518, 2213, 21, 12, 2100, 17, 21, 13, 3402, 16, 1942, 6980, 2014, 9055, 2359, 2294, 1930, 2112, 6310, 1956, 6632, 17, 12691, 5038, 1942, 4039, 6338, 3170, 18, 1922, 2459, 16, 1920, 2213, 5921, 43, 5937, 17, 12624, 27910, 12, 30450, 13, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 1930, 13640, 5219, 1922, 10825, 3213, 2790, 18, 2176, 4075, 43, 20030, 8, 38, 4595, 8, 17, 7864, 3165, 43, 5937, 3031, 1958, 2678, 2835, 1930, 43, 12624, 27910, 1988, 10412, 6110, 13640, 16, 7402, 43, 9964, 15630, 3170, 1988, 17480, 1036, 2487, 2678, 3709, 18, 2176, 1977, 6196, 1942, 2735, 2225, 17576, 1947, 3368, 27350, 3907, 1930, 2258, 20709, 15010, 17524, 9121, 1930, 3213, 3640, 18, 3], "output": "EVGSARAVYLEKNRKAAVERRNRALKAEVELLKGGMRELMDIVGQHTHCGCVRPPLHVQPSESSLSPSKCRSKQKRQQEDLVEEARDSDSRLKLYVQREADRLAT", "metadata": {"id": "A0A9P4H6A8", "cluster": 18730372, "interpro_all": ["IPR004827", "IPR046347", "IPR051027"], "interpro_used": ["IPR051027", "IPR004827"], "interpro_unused": ["IPR046347"]}, "task_type": "infilling"} {"instruction": "The target protein must perform this role:\nIt is part of the Sushi domain-containing protein family, which is characterized by the presence of complement control protein (CCP) modules that mediate protein-protein interactions. These extracellular or membrane-bound proteins play regulatory roles in diverse biological processes, including the complement system, blood coagulation, cellular adhesion, and immune response. Also, the protein carries a Link domain that functions as a hyaluronan-binding region involved in extracellular matrix assembly, cell adhesion, and migration in vertebrates. It adopts a C-type lectin-like fold stabilized by two disulfide bonds and is commonly found in proteoglycans like aggrecan and receptors such as CD44. Additionally, the protein possesses a Sushi/SCR/CCP domain that mediates extracellular protein-protein interactions and recognition processes, particularly the binding of complement factors to fragments C3b and C4b. This module, also known as the Short Consensus Repeat (SCR), contains approximately 60 residues stabilized by two disulfide bridges between four invariant cysteines. It is identified in Oryzias latipes (Japanese rice fish) (Japanese killifish) and is associated with UniProt keywords Proteomics identification, Signal, and Transmembrane helix.\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, 3447, 7969, 3418, 17, 3165, 2213, 3416, 16, 2154, 1977, 4378, 2007, 1920, 2990, 1927, 5508, 2285, 2213, 12, 26123, 13, 10803, 1988, 8265, 2213, 17, 2213, 3719, 18, 2144, 5329, 2014, 3260, 17, 4124, 2697, 3918, 4948, 5456, 1922, 6445, 3933, 4028, 16, 2710, 1920, 5508, 2433, 16, 2877, 12441, 16, 3689, 6141, 16, 1930, 3743, 2644, 18, 2222, 16, 1920, 2213, 16252, 43, 3300, 3418, 1988, 4088, 1966, 43, 29614, 17, 2743, 3031, 3286, 1922, 5329, 4526, 5957, 16, 2024, 6141, 16, 1930, 5049, 1922, 14976, 18, 2176, 24032, 43, 45, 17, 2601, 13468, 17, 3189, 3728, 12017, 2007, 2288, 11830, 9031, 1930, 1977, 5384, 2435, 1922, 25185, 3189, 29979, 1930, 4086, 2427, 1966, 11699, 18, 4950, 16, 1920, 2213, 14465, 43, 3447, 7969, 19, 7572, 19, 26123, 3418, 1988, 10412, 5329, 2213, 17, 2213, 3719, 1930, 5708, 4028, 16, 4443, 1920, 2743, 1927, 5508, 2790, 1942, 6535, 8351, 1014, 1930, 10872, 1014, 18, 2052, 9059, 16, 2222, 3171, 1966, 1920, 3662, 7076, 6865, 12, 7572, 13, 16, 5461, 3993, 3276, 4248, 12017, 2007, 2288, 11830, 18142, 2192, 3006, 17004, 22446, 18, 2176, 1977, 2899, 1922, 19745, 10657, 4144, 29972, 12, 10405, 8674, 5724, 13, 12, 10405, 11321, 1974, 2471, 13, 1930, 1977, 2458, 1956, 20709, 11569, 14297, 4824, 16, 2733, 16, 1930, 9117, 7864, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MKSVKNQKETSGVFVLDLRNSSGFKGFSVAEKACASKSARLAECTRGWLHGGTVGTTVCNVAGGSLRAVDVRTENATEDAAHLDPPSFPYARLQEHSGFETGDELLYTCAPGYAMPGGDTSFSLLCDSSHVDYEDKYSDSYGDADHSLESQEEVHGETHQHGGRILERRGKVTFHSRQPEGVVEEGAKQEASDHHLIGHPRQELSQKHMFWFPSEAFQEEGYPVSTDSSTQTTQRTSGALSEESKEHNRDKGDTDDHDHYDDPDSHQEEDQDDHTKHPALHEDMGEHEEEPDRVLYGSREYDDGDDTPDDHHSIEDHDVEHPDVSKDDEIHDDRDSHESDGGRPHDIISVAAEKHQNVTQRGTGGKKNGESKTGTNVVKMADRPNEVEVRKPVPSSQIEHDSAAFPDLLEPSDSPSYSDTLDYDTQQAAPTRSWLDDLTEQPFQMGGQTVHNLPGEAGERGELEGDMRGTMCTGAVCAVATAVMVGVWCYRRQQQKSSAYEMNGKGQSQITQSQQIEMQQKVSLDELLHAVVQCFFSAFCIQDKATPCGDCGEWYGTVQICVKDQTEQESTLPVKVQQKQHREPDIQEKSEVVRTETAAATEEPVSVSQEVPDHQQSINVDHHHDDGEDDNNLERPDHPTTSREDHDDHYDEHPDDRDDVDDHHDDHDATKADTWLDSYPVAREKTTGRGHELDQGGVGKVQLGAAGTPDHGPAPPVHNGEAFTGVENCPPPPPVPSGRGPKVAAIIV", "metadata": {"id": "A0A3B3I6S3", "cluster": 19101468, "interpro_all": ["IPR016186", "IPR016187", "IPR000538", "IPR035976", "IPR053298", "IPR000436"], "interpro_used": ["IPR053298", "IPR000538", "IPR000436"], "interpro_unused": ["IPR016186", "IPR016187", "IPR035976"]}, "task_type": "infilling"} {"instruction": "Give me a peptide sequence capable of: The protein includes a Pesticidal crystal protein, domain I domain that constitutes the N-terminal helical bundle of *Bacillus thuringiensis* endotoxins, primarily responsible for membrane insertion and pore formation. Upon proteolytic activation in the insect gut, this domain facilitates the creation of cation-selective channels, leading to epithelial cell lysis. Additionally, the protein is included in the Galactose-binding-like domain superfamily, which functions as a versatile ligand-binding module characterized by a $\\beta$-sandwich structure with a jelly roll fold. Found in both eukaryotes and prokaryotes, this domain interacts with diverse targets ranging from cell-surface carbohydrates and phospholipids to membrane-anchored proteins and DNA complexes. It is identified in Bacillus thuringiensis subsp. medellin and features UniProt keywords Sporulation and Virulence.", "tokenized_instruction": [2, 7031, 2142, 43, 4207, 3244, 7131, 1927, 30, 1920, 2213, 5921, 43, 13417, 7161, 6561, 2213, 16, 3418, 51, 3418, 1988, 14879, 1920, 56, 17, 4262, 11514, 14142, 1927, 14, 14587, 1913, 4729, 24222, 14, 16366, 1036, 16, 5985, 5061, 1958, 3260, 7413, 1930, 8554, 3337, 18, 4073, 12712, 2936, 1922, 1920, 11422, 7660, 16, 2052, 3418, 11374, 1920, 13874, 1927, 9976, 17, 5328, 5628, 16, 4523, 1942, 4944, 2024, 8502, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 15996, 17, 2743, 17, 3189, 3418, 13975, 16, 2154, 4088, 1966, 43, 20425, 5207, 17, 2743, 9059, 4378, 2007, 43, 8, 38, 4666, 8, 17, 18038, 3170, 1956, 43, 8988, 11560, 1012, 12970, 3728, 18, 2435, 1922, 2321, 15021, 1930, 28149, 16, 2052, 3418, 9034, 1956, 6445, 4845, 6485, 2037, 2024, 17, 3154, 16282, 1930, 15619, 1942, 3260, 17, 17199, 2697, 1930, 2678, 5048, 18, 2176, 1977, 2899, 1922, 14587, 1913, 4729, 24222, 19615, 18, 2242, 20912, 1930, 4075, 20709, 11569, 23647, 1930, 9304, 18, 3], "output": "MNSFQNKNEYEILNAPSSISNIPNNYSKYPIANTLNQTMQNTNYKDWTNMCAIDNNLKSINPFEANLQNSLVGLFAITAAIASLLSAPITGGTSIAAGTAIAAAIIPILWPSQENNLPDKLLAISEATLYSFQDQRVREDALTRLESLKDSVKYFENAFTFWINNPNSTNTTTVRERFQEVNGRFVGSMAFFRAKNYEPILLSTYAQAARLHLLHLRDGITYAEKWNLSRQGDDMPGDLLYKEFNKYCNEYIEHCIKWYNESLSLLKSVGANWLEYNQYRTFLTASVLDVISLFSSYDPRLYKERLSVEILTRKLYTDPINYHRGISLEADESKYTLEPTLFTQLYTLTFYSNIFYNYMGHTNTYRYLSPDKIFAERSFGKQSSYIDKVPVIPNDKSIIYKIRAYDNHNGLFNVMYFGFWDGEKDQIQKIIGGSSTEIYIKNCTHRLADVISHDLDEKNKCYSFAWTSTTISLENEIKNDIITQIPAVKAYQLGVQSQVIKGPGHTGGDLINLKSNDYLRISCQHLSNVTKKYFVRIRYATNGSLNTRPIINITIPGMTPQGMVLDNTFSGTGYSNLEYQNFGYKEFLKEVTLNPNQSISLTLNRSDQNSNSILLLDRIEFLPITPSIRKSKEQQNLEKNQKTVNKLFFN", "metadata": {"id": "Q8VNX2", "cluster": 21357925, "interpro_all": ["IPR008979", "IPR038979", "IPR005638", "IPR005639", "IPR036716", "IPR036399", "IPR001178"], "interpro_used": ["IPR005639", "IPR008979"], "interpro_unused": ["IPR005638", "IPR036399", "IPR038979", "IPR036716", "IPR001178"]}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein falls within 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 can be placed in 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. It is expressed in Eptatretus burgeri (Inshore hagfish). 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, 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, 2112, 1998, 5396, 1922, 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, 2176, 1977, 3198, 1922, 2630, 3857, 4265, 1031, 1957, 4598, 4938, 1033, 12, 2346, 10647, 1936, 27710, 14422, 13, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MMALLYLLVAFSAIILHSAQSQVTGSHIVASKLQDKIMLPCFSEPWKSDVNNKLLWEFFYFINEEEKNVTIIEVIQMNKFAIAKMDEDHYDITEEQLKKGNLSISLYNPTIKDSGTYICSVENDAEKKVIASIEVLVPEHVDDCGCLSVYESCEDFLFFVGAGATLPTLSLLFPLVGSIICPPRIPQMLSRNTMKAKLRRRRKIIRKMDKTSLKLHSLNEENTEGTEILIDPQTLAKTKPSCPRPRVDNIV", "metadata": {"id": "A0A8C4R6S7", "cluster": 23059428, "interpro_all": ["IPR036179", "IPR013783"], "interpro_used": ["IPR013783", "IPR036179"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein is categorized in the FlgN-like superfamily, which functions as an export chaperone essential for flagellar assembly. Members of this family adopt a four-helix bundle structure to facilitate the export of hook-filament junction proteins, such as FlgK and FlgL, thereby enabling bacterial swimming and swarming motility. It originates from Sediminispirochaeta sp.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2300, 3223, 17, 3189, 13975, 16, 2154, 4088, 1966, 1925, 12660, 14044, 4415, 1958, 24154, 5957, 18, 4678, 1927, 2052, 3416, 14103, 43, 3006, 17, 7864, 14142, 3170, 1942, 6628, 1920, 12660, 1927, 17185, 17, 10797, 6910, 2697, 16, 2427, 1966, 2300, 1029, 1040, 1930, 2300, 4365, 16, 6113, 12180, 4543, 15781, 1930, 26149, 1941, 9254, 18, 2176, 22970, 2037, 6276, 1980, 15472, 10984, 24182, 3336, 3857, 2056, 18, 3], "output": "MAETVVHMKSILSQEVEGFGGAVERAEAIRNDIFKHDWKKLSQNLEKMEKLSTYLAALEKERVHIFENLRRELGAKENDGFYTVVVRLPEEEQNELSDLFRRLKSLVLQLQGVLWSVDAYTRSLSGTIYDIL", "metadata": {"id": "A0A9C8KW43", "cluster": 24130910, "interpro_all": ["IPR036679"], "interpro_used": ["IPR036679"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nThe protein should include 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 Luminiphilus sp and exhibits UniProt keyword tags 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, 3951, 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, 16410, 6285, 1970, 1957, 2056, 1930, 9826, 20709, 11121, 2538, 14392, 2733, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MCKPIVTRFSIPITLFVAMLLVSVSTQADNLYRYKNDVGGTVVDWRVPPEFAGSSGELQNKDLVKRLQQEATVERARLAKWDKFLLLRYSTVEDIDAARDRALRDLKIRLSILAQDLDAIAALRADIANTGRAIKEREAQVLEVTDSFDEDRSRFIQLQDVVLLRRSLSRDQTSAGTENRGYEVLNAQGQVVEVVPRQLSNQRTARNRLESVLARVADMERRGDVPLE", "metadata": {"id": "A0A937LXS5", "cluster": 25431799, "interpro_all": ["IPR018247"], "interpro_used": ["IPR018247"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\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. It is produced by Streptococcus virus MS1 and is classified with UniProt keywords Nucleotidyltransferase 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, 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, 15746, 3413, 3012, 1009, 1930, 1977, 5947, 1956, 20709, 11569, 2797, 4090, 2199, 9961, 1930, 13763, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MVDFIGQRKAKEFVKQRKYLPTFARYVAAELGYDCIFIENKVDDIRSIGAKNSLLKVTEEPPKNVHICMLAYTEGDVLSTDEVSHYLERFVKSSKDILKEGLALYLEKVQFFYDNIFEASSSNALKMVDWFKLKDTDNYIGYENRKIQDTEVLLANYGLLQLVGKNKLFAMNKLVKEVQEIGNSMVIVGAKKSGKRDMIELASSLAQPTLFVVQVAGMDTLISRSWVVTLLPYMAPMFSSPGQVQYLVQNHGKTREDALIPELFLEIAMAKCLGTVSTK", "metadata": {"id": "A0A1U9WR92", "cluster": 25587282, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein carries a Spen paralogue and orthologue C-terminal (SPOC) domain that mediates protein-protein interactions essential for transcriptional repression, specifically by recruiting corepressors such as SMRT/NcoR. It folds into a compact seven-stranded beta-barrel framed by six alpha-helices, displaying surface grooves and clefts optimized for binding partners. This domain is conserved in metazoan signaling proteins, including SHARP and MINT, where it regulates developmental processes. Moreover, it is part of 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 has been characterized in Trichonephila clavata (Joro spider) (Nephila clavata) and exhibits UniProt keyword tags RNA-binding. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 16252, 43, 6077, 1022, 16188, 2182, 1930, 11382, 2182, 45, 17, 4262, 12, 18055, 1030, 13, 3418, 1988, 10412, 2213, 17, 2213, 3719, 4415, 1958, 5224, 10084, 16, 4475, 2007, 17040, 4728, 29079, 1036, 2427, 1966, 28018, 1031, 19, 25165, 1005, 18, 2176, 16231, 2460, 43, 13726, 5260, 17, 10338, 4666, 17, 19560, 7673, 1007, 2007, 3798, 4595, 17, 12789, 16, 13867, 3154, 15920, 1036, 1930, 14649, 1036, 8944, 1958, 2743, 7228, 18, 2052, 3418, 1977, 5305, 1922, 24207, 1928, 3197, 2697, 16, 2710, 11707, 1930, 2360, 1031, 16, 2597, 2176, 7014, 5878, 4028, 18, 3950, 16, 2176, 1977, 3131, 1927, 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, 2258, 2252, 4378, 1922, 10477, 18128, 19167, 19887, 5499, 12, 7420, 1931, 26376, 13, 12, 7737, 19167, 19887, 5499, 13, 1930, 9826, 20709, 11121, 2538, 14392, 3146, 17, 2743, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MKTYELKYPHIWSGQFIVKGQRNPVKLNYVGGNVNVAVSALLRRRPIPHIRINRQVTPGYFPTFEENNTCLLTAQPYGRTLREKMDQIKSVKRSFSNYIKGKDSIIGITFLHPTEPGKRPFKAYVITPSEETSRLLARYAPDWYHSICDQLHFLVMISY", "metadata": {"id": "A0A8X6F2K4", "cluster": 27703767, "interpro_all": ["IPR016194", "IPR010912"], "interpro_used": ["IPR010912", "IPR016194"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Function:\nThe protein should feature a 2EXR domain that contains two conserved ExR motifs of potential functional significance and is predominantly found in fungi. It is found in Mollisiaceae sp. DMI_Dod_QoI.\nGiven the preceding functional annotation, generate the amino acids corresponding to the masked regions.", "tokenized_instruction": [2, 2347, 30, 1920, 2213, 3066, 5961, 43, 11416, 10024, 3418, 1988, 5461, 2288, 5305, 1975, 1005, 8277, 1927, 2889, 3183, 4550, 1930, 1977, 7700, 2435, 1922, 10520, 18, 2176, 1977, 2435, 1922, 20888, 1937, 19476, 2056, 18, 3931, 1033, 41, 12621, 41, 59, 26822, 18, 3258, 1920, 12141, 3183, 10452, 16, 5655, 1920, 3835, 4576, 3980, 1942, 1920, 17476, 3451, 18, 3], "output": "MDKRDTKKKSVKSKNKKFLKGDASIPPPPQARSINVGPLEAFPQYYIWMKDIKEENGTKTLCYLQPTTRKALDVSRACAESRKQVLAKDDTICVLNGDLLMIAYDKMSENYDGFTIWPWARNVHYLMLPSGLIPWWMNHAGLQDLRPFKEHNMRQLAKTMTDDNRVFEIDHDAIKVVKQIEDGVAVIPVFTLYKALPLKIFALKGWTADLGLYNHYGGMGIFKQLPNELQTMVWTAFIGEPGIRLPNRLPGKEETEVWRFGEGDATEMQNSNLLAEFSNLKELHFAMSERCIAESGGKTTECQRLVM", "metadata": {"id": "A0A8S9BFE8", "cluster": 449350, "interpro_all": ["IPR045518"], "interpro_used": ["IPR045518"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that can perform the following function: The protein carries 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 Lentisphaera araneosa HTCC2155.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 16252, 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, 10226, 3508, 20051, 5524, 20289, 2912, 5360, 5334, 24106, 19126, 18, 3], "output": "MYKFLLLLYVTLSCGAESVKIITYNVLYGFNHGKNIQEGQAWLKAQQADFIALQEMKGFDANKFAQLAKTWGHEHSYFYKRPHGMPLAFSSRFPISEVEELHKGVKRGFLKLKCRGIDFIVLHMTSQRLSARRQELNYISPTISELLKKKGKVIVLGDFNSLSPRDMKHLSELDDLLEEMRNTPRKKPNLNDNNFDIGIMTAFEDLGLVELCHQQLQGQKDLQGSFPSTLLEKIPNKEIQEKYLRRIDFILSDAISAKNLSQAAIPKEGDLEKISDHYPIIIELNN", "metadata": {"id": "A6DFG7", "cluster": 3718036, "interpro_all": ["IPR036691", "IPR005135"], "interpro_used": ["IPR005135"], "interpro_unused": ["IPR036691"]}, "task_type": "autoregressive"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein is classified under the Diverse Ion Transporter family, which functions in ion transport and pH regulation to support diverse biological processes including biomineralization and melanogenesis. These proteins modulate pH within specialized organelles, such as bacterial magnetosomes and mammalian melanosomes, to optimize enzymatic activity and facilitate maturation events like pigmentation. Also, the protein belongs to the Arsenical pump membrane protein, ArsB family, which functions as the inner membrane component of the arsenite-translocating ATPase complex involved in arsenic resistance. This hydrophobic protein acts as an anion channel containing multiple transmembrane regions and associates with the catalytic subunit ArsA to export toxic arsenite from the cell. Also, the protein should have a Citrate transporter-like domain that functions as a transmembrane transport component in CitM citrate transporters, NhaD Na+/H+ antiporters, and Na+/sulfate symporters. It mediates the translocation of substrates such as citrate and sulfate, often coupling transport to sodium ion gradients or proton exchange. It is expressed in Anaerolineae bacterium and is classified with UniProt keywords Cell membrane and Transmembrane helix.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 1977, 5947, 2441, 1920, 6445, 4755, 9054, 3416, 16, 2154, 4088, 1922, 4755, 4860, 1930, 2087, 3640, 1942, 3373, 6445, 3933, 4028, 2710, 4071, 29384, 1930, 5313, 3761, 18, 2144, 2697, 8480, 2087, 2651, 11021, 14487, 16, 2427, 1966, 4543, 14634, 4686, 1930, 6492, 5313, 4686, 16, 1942, 12714, 8145, 2455, 1930, 6628, 7655, 3916, 3189, 20542, 18, 2222, 16, 1920, 2213, 14440, 1942, 1920, 14241, 1923, 8912, 3260, 2213, 16, 9896, 1014, 3416, 16, 2154, 4088, 1966, 1920, 6671, 3260, 4594, 1927, 1920, 29466, 17, 12930, 2287, 9444, 2796, 3286, 1922, 14241, 3554, 18, 2052, 7919, 2213, 8016, 1966, 1925, 10985, 4999, 3165, 3137, 9117, 3451, 1930, 14162, 1956, 1920, 6804, 5903, 9896, 1019, 1942, 12660, 6161, 29466, 2037, 1920, 2024, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 11599, 9054, 17, 3189, 3418, 1988, 4088, 1966, 43, 9117, 4860, 4594, 1922, 12366, 1035, 11599, 10538, 16, 5331, 2015, 4049, 15, 19, 50, 15, 2246, 24095, 1036, 16, 1930, 4049, 15, 19, 8767, 29148, 2718, 2045, 18, 2176, 10412, 1920, 7849, 1927, 6249, 2427, 1966, 11599, 1930, 8767, 16, 3868, 7590, 4860, 1942, 5227, 4755, 12741, 2014, 8433, 6818, 18, 2176, 1977, 3198, 1922, 11381, 8419, 3336, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MAWRKSALVFLRSSHLRMALGAFLLASEPETGAFTLLGRLLDTHGNPLSEAQVSLHFSGLTEEQALKLEVKRPNFRPLTKTVSIELSKGGGSAELIDLGELTLIALELLHKTTAAMLGAVLVLLGSQAASLFNPDWYFLMIFVAMVEETGFFQWLAFAAYRAAGGQPWRLMVVLTFLTGLVEIALKLGLNPLTLLFPEVLAANIGGTATLIGTPPNILIGSYALMLLMRWRYGTAYRLAEEIDSAALLEHLREDARLAGPRLHLTPALTALLGAVVLMVWVRPVSALQEVGVIHWIADVVKGLAGESPLLAMLLMPFTAAMLPVAAYLSKAVPGGESGLFFWALSLGASLGGNATLFPVSYMRFLIDGLPITIISVVIATIWLLVRFVALMASSLGVKAGEEARLGETESQPDGHFTLRFQWPQEAARLVHRRDWAFWFAAAVFGGTLLSFERAVQAIDFEVIFLLVGMFSALLDNVIAVLLMAPITAGFSFGDFLVNVAPVAFASLLLTQPALFQRTAVVGAGMLALFDVEHMVHEVDWTTLLFFMALFVQLWPSALLSGVIDNIIGSAPNLVAAGIAERAG", "metadata": {"id": "A0A7C7QNK0", "cluster": 5818871, "interpro_all": ["IPR000802", "IPR004680", "IPR051475"], "interpro_used": ["IPR051475", "IPR000802", "IPR004680"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein should have a Domain of unknown function DUF7027 domain that constitutes a likely \u03b1-helical transmembrane segment found primarily in uncharacterised proteins from nematodes and arthropods. In addition, the protein is included in the Lysosomal-associated transmembrane transporter family, which mediates the intracellular transport of nucleosides and amino acids across lysosomal and endosomal membranes. These proteins regulate lysosomal dynamics by facilitating EGFR degradation, activating mTORC1 signaling, and exporting ceramide from late endosomes. Some members also participate in embryogenesis or negatively regulate TGFB1 signaling in specific cell types. It is found in Plectus sambesii and exhibits UniProt keyword tags Transmembrane helix.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 2162, 43, 3418, 1927, 5435, 2347, 4855, 1038, 4618, 4282, 3418, 1988, 14879, 43, 3205, 160, 17, 11514, 9117, 5367, 2435, 5985, 1922, 23229, 3495, 2697, 2037, 19669, 1930, 21680, 13816, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 12097, 17, 2458, 9117, 9054, 3416, 16, 2154, 10412, 1920, 4776, 4860, 1927, 18015, 1036, 1930, 3835, 4576, 3436, 12097, 1930, 16514, 5726, 18, 2144, 2697, 5741, 12097, 5565, 2007, 12440, 5775, 4877, 16, 8019, 13694, 3197, 16, 1930, 12660, 1941, 16926, 2037, 5058, 14978, 18, 2673, 4678, 2222, 7352, 1922, 18453, 2014, 7191, 5741, 5525, 5090, 3197, 1922, 2487, 2024, 3584, 18, 2176, 1977, 2435, 1922, 6483, 2341, 1957, 2235, 5873, 12924, 1033, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 7864, 18, 3], "output": "MDFNPNHSGLKILGVVEVTIASAVMALLVTVFTGVALCLAVIVSSALLIICIVVAHCLVAFNVLRPYQTTRLVFAIFVVMFVSRASVVHASQIIFEPKWQCCCCHLALMLTSDSKLMHPWVGIQKKNGQLLYPTLVVKGEEARTTEQTPEDKPGIVGIIYTMYLVVHCMRYLHGARRLEER", "metadata": {"id": "A0A914WVR0", "cluster": 5867904, "interpro_all": ["IPR054291", "IPR051115"], "interpro_used": ["IPR054291", "IPR051115"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe protein is categorized in the Protein of unknown function DUF123 family, which comprises uncharacterized archaeal and bacterial proteins containing a putative GIY-YIG domain homologous to UvrC DNA repair proteins. These proteins typically possess a C-terminal extension with semi-conserved cysteine and histidine residues, suggesting a potential function as a zinc-binding nucleic acid interaction domain. It is derived from Bacillus sp. J14TS2.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 5739, 4553, 3416, 16, 2154, 12936, 24528, 22367, 1930, 4543, 2697, 3165, 43, 6770, 7217, 1012, 17, 19929, 1029, 3418, 8725, 1942, 5819, 15618, 2678, 5059, 2697, 18, 2144, 2697, 5745, 7150, 43, 45, 17, 4262, 7140, 1956, 8762, 17, 5305, 8666, 1930, 13873, 4248, 16, 3783, 43, 2889, 2347, 1966, 43, 7997, 17, 2743, 11079, 2687, 2835, 3418, 18, 2176, 1977, 3595, 2037, 14587, 2056, 18, 52, 3745, 1973, 1028, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MKAMDYSIGASDTKLGCFHFSKGYYVYVGSAKRNIYLQIVDIQTYPGDEGECKLDCRCFSHLFYLFPDALYAIKAFMPKDEEAITIGQARVNRHIQMDKKKRWHIDYLRPFQRLLQENAGSMPIKGFGSS", "metadata": {"id": "A0A919WX78", "cluster": 7517305, "interpro_all": ["IPR002837"], "interpro_used": ["IPR002837"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein is assigned to the Heat shock protein DnaJ, cysteine-rich domain superfamily, which constitutes the central zinc-dependent structural element of Hsp40/DnaJ molecular chaperones. This domain features a V-shaped $\\beta$-hairpin topology that coordinates two zinc atoms and contributes to the chaperone's ability to bind unfolded polypeptides and regulate Hsp70 (DnaK) ATPase activity. It occurs in Spinactinospora alkalitolerans.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 1977, 6304, 1942, 1920, 5631, 7418, 2213, 2678, 1013, 16, 8666, 17, 5536, 3418, 13975, 16, 2154, 14879, 1920, 4101, 7997, 17, 3100, 4346, 6149, 1927, 6418, 4241, 19, 2678, 1013, 3272, 18098, 18, 2052, 3418, 4075, 43, 64, 17, 9132, 8, 38, 4666, 8, 17, 14565, 13678, 1988, 10675, 2288, 7997, 9030, 1930, 7624, 1942, 1920, 14044, 11, 61, 3682, 1942, 4566, 17416, 18633, 1930, 5741, 12886, 12, 2678, 1040, 13, 9444, 2455, 18, 2176, 5110, 1922, 7707, 11686, 9890, 1019, 25178, 4575, 3823, 2075, 18, 3], "output": "MSTCRTCNGTGEGERHDWPPPGSRIDIITTDDDGERVTRHQPCHACAGS", "metadata": {"id": "A0A852TS90", "cluster": 9111085, "interpro_all": ["IPR036410"], "interpro_used": ["IPR036410"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein is associated with 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. Furthermore, the protein includes a FG-GAP repeat that adopts a beta-propeller structure and functions as a ligand-binding domain, notably within the N-terminus of integrin alpha chains. Containing conserved FG and GAP motifs and potential Ca2+ binding sites, it mediates diverse processes including cell-cell interactions and host-pathogen recognition across eukaryotes and bacteria. It is native to Deltaproteobacteria bacterium.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 1977, 2458, 1956, 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, 3677, 16, 1920, 2213, 5921, 43, 13320, 17, 5750, 6865, 1988, 24032, 43, 4666, 17, 5062, 13728, 3170, 1930, 4088, 1966, 43, 5207, 17, 2743, 3418, 16, 7388, 2651, 1920, 56, 17, 7822, 1927, 8920, 4595, 7835, 18, 3165, 5305, 13320, 1930, 5750, 8277, 1930, 2889, 5497, 15, 2743, 3402, 16, 2176, 10412, 6445, 4028, 2710, 2024, 17, 2024, 3719, 1930, 4423, 17, 7055, 5708, 3436, 15021, 1930, 4802, 18, 2176, 1977, 6196, 1942, 9649, 9218, 1021, 10296, 14061, 18, 3], "output": "MRKFDLFMTLPLLLTAACIDEVSEGEKCATVDDTAAPDDATTDLEGSVPDTAEDDIDEIDDDTAAGDTDDDTECADRDEDGLCDEDDGCPDEPTLTEPTACGCDPSLVPGTFVDSGQTIGSGVGNRGTFTDSGARLDSFVDTVGLLADFDQDGDLDVVTGAHNRSSADSRLYLNDGAAHFTDSGVRFATGNYVTNNGAGTGFGGVSFGGLAAWAITVGDVNGDSYDDILIGVHGASNQIHLNNGAGGFLGDVDADGDLDAVVGIGGGPGSEVWINDGTGAFTDSGQALVANNASHSTITDIDYDGDLDVIFSDMNDGEGRFTLGQHIGVGIASQGHGVGDVNGDGLVDMVLAAEFQSGALFLNSCAVAEADDDTLEDDTAGGDTAKMLIGDLDGDSDLDLFLVSAFHPDEVWLNDGTSMGLGDFNNDSWPDFAVGNHSDSRSTYAYTGSTFGDPTSNASTLSADGANGGARIYL", "metadata": {"id": "A0A2E7UNC3", "cluster": 9558453, "interpro_all": ["IPR013517", "IPR028994"], "interpro_used": ["IPR028994", "IPR013517"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein should feature a Tail specific protease domain that adopts a crotonase-like fold formed from repeated \u03b2/\u03b2/\u03b1 units comprising two perpendicular \u03b2-sheets surrounded by \u03b1-helices. It is conserved across diverse lineages, functioning in enzymes such as tricorn proteases and C-terminal processing peptidases, as well as in the animal retinol-binding protein 3. Moreover, the protein is a member of the ClpP/crotonase-like domain superfamily, which comprises a diverse group of enzymes sharing a repeated \u03b2/\u03b2/\u03b1 structural unit, including Clp and tail-specific proteases involved in protein degradation, as well as crotonases and biotin-dependent carboxyltransferases. Furthermore, the protein should have a DnaJ domain that functions as a molecular co-chaperone by binding to Hsp70 proteins and stimulating their ATPase activity. This action stabilizes the interaction between Hsp70 and unfolded polypeptide substrates to assist in protein folding, translocation, and degradation. The domain structurally consists of a four-helix bundle with a specific charged surface required for the Hsp70 interaction. It originates from Candidatus Daviesbacteria bacterium RIFCSPHIGHO2_01_FULL_41_23 and is annotated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 3066, 5961, 43, 5281, 2487, 7154, 3418, 1988, 24032, 43, 9442, 5405, 2051, 17, 3189, 3728, 5333, 2037, 5116, 161, 19, 161, 19, 160, 5701, 10351, 2288, 15201, 161, 17, 14685, 16006, 2007, 160, 17, 12789, 18, 2176, 1977, 5305, 3436, 6445, 10439, 16, 7295, 1922, 5038, 2427, 1966, 12258, 5578, 12447, 1930, 45, 17, 4262, 4587, 24050, 1036, 16, 1966, 2486, 1966, 1922, 1920, 4027, 23256, 17, 2743, 2213, 23, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 18017, 1034, 19, 9442, 5405, 2051, 17, 3189, 3418, 13975, 16, 2154, 12936, 43, 6445, 2210, 1927, 5038, 10763, 43, 5116, 161, 19, 161, 19, 160, 4346, 5344, 16, 2710, 18017, 1930, 5281, 17, 2487, 12447, 3286, 1922, 2213, 4877, 16, 1966, 2486, 1966, 9442, 5405, 2319, 1930, 8622, 17, 3100, 9943, 18580, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 2678, 1013, 3418, 1988, 4088, 1966, 43, 3272, 2081, 17, 14044, 2007, 2743, 1942, 12886, 2697, 1930, 9868, 2310, 9444, 2455, 18, 2052, 4615, 19658, 1920, 2835, 2192, 12886, 1930, 17416, 13022, 6249, 1942, 6589, 1922, 2213, 10328, 16, 7849, 16, 1930, 4877, 18, 1920, 3418, 12171, 7543, 1927, 43, 3006, 17, 7864, 14142, 1956, 43, 2487, 9516, 3154, 3414, 1958, 1920, 12886, 2835, 18, 2176, 22970, 2037, 14550, 1031, 1957, 10022, 2062, 7972, 2341, 18339, 14061, 12424, 2792, 24888, 2509, 5265, 41, 3287, 41, 4125, 41, 4353, 41, 3020, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MIDNISIFNYNTLVQIYLQNNMLKIPSQKLFGKLLILIIVFTISEIYDKIKENYWNNISDAELLDLFKLSLTQNGTSLSMSGEQKNNVLTTVVGSVLTSLAPAGRSGLYTEKQEQQLKNTVANINPEKDLYKDLGLSAKLAQDKSPEAQEKLKALTYAKDTLTQADTKKRYDANQVEPTFFSKIADPSLNALIFDLRGNIGGAIDATAYFLGYFLGKGQYAFDFYHKGEKYKQIVILVDQNTQSSAEIMAAALKKYHVGVVLGVPTKGLVHSLTLRDDNQPIEGRGVDPDISIKDPDWPQKLLLYFNNSSLVETVKSLLVGLGLGREYFTKNPVLQQKAFTEKQEALFTVAKFENKDKLLEAVSKTAEKGASETAVQQAYATQSSSGILYIQFKKFSPTSLDEFQKTFESYKGYLPFKTMTDKLPSVSWGTVERVFPLDNQISSKEKYSIF", "metadata": {"id": "A0A1F5IR33", "cluster": 10027476, "interpro_all": ["IPR029045", "IPR001623", "IPR036869", "IPR005151"], "interpro_used": ["IPR005151", "IPR029045", "IPR001623"], "interpro_unused": ["IPR036869"]}, "task_type": "infilling"} {"instruction": "I am interested in designing a protein that can perform the following function: The protein is categorized in the Stage III sporulation protein AH-like family, which mediates intercellular signaling and forespore engulfment. In sporulating bacteria, these proteins form a gated channel connecting the mother cell and forespore to coordinate sigma factor gene expression, while their broad distribution across bacteria, archaea, and eukaryotes implies a wider conserved function beyond sporulation. It is found in Syntrophomonadaceae 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, 1977, 10234, 1922, 1920, 3587, 4337, 23647, 2213, 9646, 17, 3189, 3416, 16, 2154, 10412, 15685, 3197, 1930, 25811, 2074, 1021, 25787, 2017, 18, 1922, 9130, 4765, 4802, 16, 2144, 2697, 2386, 43, 12336, 4999, 15031, 1920, 7999, 2024, 1930, 25811, 2074, 1021, 1942, 11865, 5139, 2991, 2359, 2294, 16, 2679, 2310, 4949, 3282, 3436, 4802, 16, 21501, 16, 1930, 15021, 10715, 43, 12172, 5305, 2347, 6844, 23647, 18, 2176, 1977, 2435, 1922, 14913, 2789, 20050, 7324, 1972, 3336, 14061, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 2213, 35, 3], "output": "MMMVFKRKQIVILALILLIVVAGYLQYSYKQEGTLADNEGKLGEAVYVDNEIYNEEFTETDLNLVGSIDDQTNITASKIANDYFVQAQMSKEQSRSEATESLRTITEDINASVDIKDEAHSKMMDIVENTDKEVRIETLINKMGFEESFILFADNGSIDIVVKTPSLSTSQTAQITDIVTRQADVEVADIHIRTMF", "metadata": {"id": "A0A7X6UL50", "cluster": 10227133, "interpro_all": ["IPR024232", "IPR038503"], "interpro_used": ["IPR024232"], "interpro_unused": ["IPR038503"]}, "task_type": "autoregressive"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein should include a Signal recognition particle SRP54 GTPase domain that functions as a P-loop NTPase to regulate the targeting of nascent secretory proteins to the endoplasmic reticulum or plasma membrane. Located within the SRP54 subunit or its prokaryotic homolog Ffh, this domain binds GTP to coordinate the docking of the ribosome-polypeptide complex to the SRP receptor. Moreover, the protein has a Flagellar biosynthesis protein FlhF, GTPase domain that functions as a signal-recognition particle (SRP)-type GTPase essential for the placement and assembly of polar flagella. This C-terminal domain shares homology with the SRP54 subunit and regulates the correct localization and number of flagella during biosynthesis. 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. It has been characterized in Geobacter sp. 60473 and is annotated with UniProt keywords Cell projection, Protein transport, and Bacterial flagellum protein export.", "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, 3951, 43, 2733, 5708, 7022, 19939, 5651, 14809, 3418, 1988, 4088, 1966, 43, 58, 17, 5881, 29676, 2051, 1942, 5741, 1920, 5133, 1927, 16861, 11518, 2697, 1942, 1920, 13355, 12279, 2014, 3582, 3260, 18, 4810, 2651, 1920, 19939, 5651, 5903, 2014, 2496, 21545, 5928, 10735, 1023, 16, 2052, 3418, 6876, 9319, 1942, 11865, 1920, 10909, 1927, 1920, 12794, 17, 13022, 2796, 1942, 1920, 19939, 3148, 18, 3950, 16, 1920, 2213, 2258, 43, 24154, 8132, 2213, 2300, 1023, 1038, 16, 14809, 3418, 1988, 4088, 1966, 43, 2733, 17, 5708, 7022, 12, 19939, 13, 17, 2601, 14809, 4415, 1958, 1920, 9555, 1930, 5957, 1927, 5676, 26538, 18, 2052, 45, 17, 4262, 3418, 16495, 9039, 1956, 1920, 19939, 5651, 5903, 1930, 7014, 1920, 5550, 5363, 1930, 2529, 1927, 26538, 2409, 8132, 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, 2176, 2258, 2252, 4378, 1922, 14136, 7972, 2341, 1915, 2056, 18, 3276, 20939, 1930, 1977, 10633, 1956, 20709, 11569, 2024, 11244, 16, 2213, 4860, 16, 1930, 4543, 7030, 10757, 2213, 12660, 18, 3], "output": "MLVKTFEAVDMSEALRMVKAELGPDAMIISSKKERKKGFFGFFSKPVIKVTAALEVKPRQPAMLENSMLAPLARELKDLRLKVEQMTRQEAEAKARAAEAQSREESAAAAEAQAPAARAKEAGAEQSAEKAEADPAPAKAPQAEIEKASGGIKAALRVVVTELHRKGLERGAIRAVMPQAFKSAIKCSGPLTVKKNGPRIIALVGPTGVGKTTTIAKLAAHYALREGHRAALITIGVPVEVAATAAELEAAIELHSDKELILIDTAGRSHKDSEKIEELKGFLESRFAIEIHLCLAATTRFTKLDESESYGSIVNAHLRTKFPLSYFTTGQRVPEDLEIATPGRLAGLVLGESKQPNPYREAQEQHLSAKEEFNPRSIPKQDLEEMKKILFKTLADHLKPEARKGGTVETIRSFLDNFRVGAVEQLKTYSRIMDREVVEIVERFGVLPVSRVI", "metadata": {"id": "A0AA86MI27", "cluster": 10775616, "interpro_all": ["IPR003593", "IPR020006", "IPR047040", "IPR027417", "IPR000897"], "interpro_used": ["IPR000897", "IPR047040", "IPR003593"], "interpro_unused": ["IPR020006", "IPR027417"]}, "task_type": "infilling"} {"instruction": "Here is the protein function: The protein belongs to the Cytochrome c-type biogenesis protein CcsA family, which serves as an essential component of the system II pathway for c-type cytochrome biogenesis. This protein is required for the maturation of c-type cytochromes in chloroplasts and bacteria, where it is sometimes designated as CcsB or ResC. Additionally, the protein possesses 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. It occurs in Corynebacterium imitans and exhibits UniProt keyword tags Membrane, Transmembrane, and Transmembrane helix. Generate the corresponding amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 2213, 2347, 30, 1920, 2213, 14440, 1942, 1920, 9387, 45, 17, 2601, 13008, 2213, 17267, 1019, 3416, 16, 2154, 10634, 1966, 1925, 4415, 4594, 1927, 1920, 2433, 2890, 3374, 1958, 45, 17, 2601, 9387, 13008, 18, 2052, 2213, 1977, 3414, 1958, 1920, 7655, 1927, 45, 17, 2601, 9387, 1036, 1922, 24627, 1930, 4802, 16, 2597, 2176, 1977, 8929, 10176, 1966, 17267, 1014, 2014, 7615, 18, 4950, 16, 1920, 2213, 14465, 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, 2176, 5110, 1922, 2233, 17151, 7972, 2341, 18842, 1989, 2042, 16503, 1036, 1930, 9826, 20709, 11121, 2538, 14392, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 5655, 1920, 3980, 3835, 2687, 3244, 18, 3], "output": "MLVNTTMAELSDLTFRTAFIIYIVALLMSCVYYGRVLAVVDARRERSEKRMQEHAEAKVAVGAGGPAVVEKQLPSEQDLDEAYEARVANARKWSGMTQALVWFGVALHLVAFVTRGIAAQRFPLGNLYEYILFMTAVIMVAAAIVIGRKGWHTIWPWLLFPMVVAMFLNSTVFHMKAAPVVPALQSYWLPVHVSTVSIGASVGIVSGVFALLYLLRMWQPKGEEHGFIGKIVHPLPSAKTLDQITYKTAIITLPLFGIGIVFGAIWAEVAWGRPWNWDAKETVSMITWILYAAYLHARATAGWKNSKAAWINVFALAMTIFNMTYVNTVIAGLHSYAGLN", "metadata": {"id": "A0A076NLM1", "cluster": 15123002, "interpro_all": ["IPR002541", "IPR017562", "IPR045062"], "interpro_used": ["IPR017562", "IPR002541"], "interpro_unused": ["IPR045062"]}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein should have a Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase anticodon-binding domain that specifically recognizes and binds to the anticodon region of cognate tRNAs. This domain is an essential component of class I aminoacyl-tRNA synthetases for methionine, valine, leucine, and isoleucine, ensuring translational fidelity by anchoring the tRNA to facilitate the attachment of the amino acid to the 2'-hydroxyl group. Additionally, the protein includes a Aminoacyl-tRNA synthetase, class Ia domain that catalyzes the specific attachment of isoleucine, methionine, valine, leucine, cysteine, or arginine to their cognate tRNAs. Utilizing a characteristic Rossmann fold, this domain couples the aminoacyl group to the 2'-hydroxyl of the tRNA acceptor stem. Furthermore, the protein is included in the Leucine-tRNA ligase family, which functions as a class Ia aminoacyl-tRNA synthetase to catalyze the specific attachment of leucine to its cognate tRNA. These alpha monomers utilize a Rossmann fold catalytic domain to couple the aminoacyl group to the 2'-hydroxyl of the tRNA and feature a unique editing domain insertion typical of prokaryote-like lineages. It is found in Candidatus Puniceispirillum sp and is associated with UniProt keywords ATP-binding, Nucleotide-binding, and Protein biosynthesis. 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, 2162, 43, 2295, 2001, 2199, 19, 2326, 2199, 19, 9906, 2199, 19, 24467, 1978, 2199, 17, 10089, 18185, 11693, 28615, 17, 2743, 3418, 1988, 4475, 16197, 1930, 6876, 1942, 1920, 11693, 28615, 3031, 1927, 15786, 20770, 18, 2052, 3418, 1977, 1925, 4415, 4594, 1927, 2921, 51, 3835, 14645, 17, 10089, 18185, 1036, 1958, 12417, 16, 21884, 16, 12624, 16, 1930, 25398, 16, 14435, 8414, 14013, 2007, 20816, 1920, 10089, 1942, 6628, 1920, 8576, 1927, 1920, 3835, 2687, 1942, 1920, 22, 11, 17, 9420, 2210, 18, 4950, 16, 1920, 2213, 5921, 43, 3835, 14645, 17, 10089, 18185, 16, 2921, 11640, 3418, 1988, 17097, 1920, 2487, 8576, 1927, 25398, 16, 12417, 16, 21884, 16, 12624, 16, 8666, 16, 2014, 9732, 1942, 2310, 15786, 20770, 18, 10232, 43, 6293, 18215, 8890, 3728, 16, 2052, 3418, 14002, 1920, 3835, 14645, 2210, 1942, 1920, 22, 11, 17, 9420, 1927, 1920, 10089, 12641, 4402, 18, 3677, 16, 1920, 2213, 1977, 3063, 1922, 1920, 12624, 17, 10089, 11905, 3416, 16, 2154, 4088, 1966, 43, 2921, 11640, 3835, 14645, 17, 10089, 18185, 1942, 18170, 1920, 2487, 8576, 1927, 12624, 1942, 2496, 15786, 10089, 18, 2144, 4595, 13256, 12561, 43, 18215, 8890, 3728, 6804, 3418, 1942, 15116, 1920, 3835, 14645, 2210, 1942, 1920, 22, 11, 17, 9420, 1927, 1920, 10089, 1930, 5961, 43, 5008, 10454, 3418, 7413, 5939, 1927, 16809, 7229, 17, 3189, 10439, 18, 2176, 1977, 2435, 1922, 14550, 1031, 1957, 15809, 2927, 1937, 10984, 3027, 11560, 1989, 2056, 1930, 1977, 2458, 1956, 20709, 11569, 4498, 17, 2743, 16, 5489, 17, 2743, 16, 1930, 2213, 8132, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "CGGAAEREQDTFDTFFESSWYFLRYADPTHKDGFSAAAAAYWMPVDQYIGGVEHAVLHLLYSRFFTRALSHVGYLDLDEPFAGLMTQGMVCHQTFKDKDGKWLFPTDVTKDGDHWVETATGAKVDAGRIEKMSKSKRNVVDPELIIETYGADTARLFMLSDSPPERDMEWTESGVEGASRFLKRVWRMAHDTNLPPAGTALPDQLGNSALAAVRMAHKSILALSADIENFRFNRAVAQLHMLTNAIADIKMDEAGAGAAKRFAVETLTRLLSPLAPHVAEDIWQKLGYDTLLAQSSWPKADAALAIDDEIEIGVQVNGKLRDTIKLERDCPNDIAETTALASASVQRYLDGKTPKKIIVVQNRIINVVA", "metadata": {"id": "A0A937GYW1", "cluster": 15991118, "interpro_all": ["IPR002300", "IPR002302", "IPR013155", "IPR014729", "IPR009080"], "interpro_used": ["IPR013155", "IPR002300", "IPR002302"], "interpro_unused": ["IPR009080", "IPR014729"]}, "task_type": "autoregressive"} {"instruction": "\"The protein carries 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 is expressed in Flavobacterium micromati and is annotated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 16252, 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, 1977, 3198, 1922, 7732, 12022, 7709, 1968, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MAIVYAVIFVFLILVLIINQKSYAYASGHFHKNKASNHINFEIGSLKKSAKDNGKIFNNIAIYLIPLSIFFFTGSVKRRLALFFVTKGLVNRYRPFAYITHNEIEKLSLRAKEKFSLTAFGFMFFAISYSSFYKDSKLKSLIWILAIIGTLLGVLIGGLVGTAIAFGIIRIHKNASKPIELWGDNKIITLNFKREITICLVCVGITEIEKINSIDKIIAGRWDIFSQGYWLTDSLTGLFEDIVDYDIQNSFFSGDACYFRALSGKHFPTD", "metadata": {"id": "A0A1M5R1P2", "cluster": 17875788, "interpro_all": ["IPR036938", "IPR000326"], "interpro_used": ["IPR000326"], "interpro_unused": ["IPR036938"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein falls within the Sporulation protein YtxC family, which consists of uncharacterised proteins strictly conserved across endospore-forming Firmicutes. These proteins are typically localized uniformly within the mother cell cytoplasm, as observed in *Bacillus subtilis*. It is found in Christensenellaceae bacterium. 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, 12182, 2651, 1920, 23647, 2213, 24412, 21487, 3416, 16, 2154, 7543, 1927, 23229, 3495, 2697, 14470, 5305, 3436, 22868, 2074, 1021, 17, 7402, 24474, 18, 2144, 2697, 2032, 5745, 6579, 14474, 2651, 1920, 7999, 2024, 5239, 16, 1966, 2528, 1922, 14, 14587, 14745, 14, 18, 2176, 1977, 2435, 1922, 20898, 19018, 5870, 1972, 3336, 14061, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MQTVSVNTLEYEIDVAALLTRRLQRVPCGTEIAVSSASGGREALVRLRSEAERDALCEALAALLLRDAANFELARIINDMPLTLEEKQRVLPEAIKTAHEAAEVRREGIGETGNASLTMDAERVKEMLRAHFDGNDHLNLEGFLRFRMQDVLRAFELYALCAAEELMLQTEYLELMRVLSVLVRLQQPRIREVSLILHADGSCTITDDTDARIECEGCGAAAGAASELVNLLVALAPARIIVYDLSCGCCAELSQVLLQVFEDRVSFFR", "metadata": {"id": "A0A942AXT3", "cluster": 20500538, "interpro_all": ["IPR014199"], "interpro_used": ["IPR014199"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein should contain a Cellulosome anchoring protein cohesin domain that mediates the assembly of the cellulosome complex by binding to complementary dockerin domains. It serves as a structural module within scaffoldin proteins to integrate and organize hydrolytic enzymes for efficient cellulose degradation. Also, the protein should contain a Cadherin-like beta-sandwich-like domain that adopts a seven-stranded structure congruent with cadherins and is predicted to function in carbohydrate binding based on its frequent fusion with cell-wall-binding and glycohydrolase domains. Widespread in bacteria, it is often associated with Fibronectin Type III (FNIII) and S-layer homology regions. Also, the protein is grouped 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 Eubacteriaceae bacterium CHKCI005 and is annotated with UniProt keywords Signal, Membrane, and Transmembrane helix.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 3066, 5531, 43, 18485, 4283, 20816, 2213, 22822, 3418, 1988, 10412, 1920, 5957, 1927, 1920, 18485, 4283, 2796, 2007, 2743, 1942, 8862, 9170, 16654, 4682, 18, 2176, 10634, 1966, 43, 4346, 9059, 2651, 7281, 1921, 2697, 1942, 13780, 1930, 25681, 26702, 5038, 1958, 5807, 12343, 4877, 18, 2222, 16, 1920, 2213, 3066, 5531, 43, 8875, 17, 3189, 4666, 17, 18038, 17, 3189, 3418, 1988, 24032, 43, 5260, 17, 10338, 3170, 17891, 1956, 8875, 1036, 1930, 1977, 4396, 1942, 2347, 1922, 10590, 2743, 2454, 1990, 2496, 6439, 5289, 1956, 2024, 17, 4821, 17, 2743, 1930, 4235, 8601, 21524, 4682, 18, 9360, 1922, 4802, 16, 2176, 1977, 3868, 2458, 1956, 12848, 2601, 4337, 12, 9945, 10831, 13, 1930, 61, 17, 4757, 9039, 3451, 18, 2222, 16, 1920, 2213, 1977, 10809, 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, 4791, 7972, 2341, 18339, 1972, 3336, 14061, 2016, 17564, 1033, 24316, 1930, 1977, 10633, 1956, 20709, 11569, 2733, 16, 3260, 16, 1930, 9117, 7864, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MKKFIRAMSLSIALCSTQLSPGDTVTVTVGYSSSEPLVGHSFADRNNMSGSSAPTSDCLQFLSWYDSPAASGEIVVTRAEGSSGTTGKLVFLGTPSEQPSEPEKESSNLLKSLTVSNYSCSVPYEVESLDIKAVPVDSTPAAGSGLEKRHYTIAATLSPDFSPDVMDYHCQVPYETTALDINAICSKDGYNPRVYTISVTRKDPHSSRLKSIFTCTVPYETESLHITAVPEDSAATIITVSCEDQEDSLYYIDATRLAQSAEEEQEIGIAVFVLYLKRNNRKSLLFALLPVLPVSAASSATLTVSRGADITVKYPSDIFDYTPGSSGQTSLTLGTITLEVKDTTSVTVSTQSPQEEDPPEEQPATLSPAFNPDQPADSDASISIQNNKLKASGVTNVTVTVRAAPPDAPALDSLEIPDVQSDPDAVVELSDLSLASEGVTDITVTVLSIVEAQLFPSFEEQSEPGAQIENNILIPGSTSRITEDSNSSPAGTTQLIVAIAVVVIGAG", "metadata": {"id": "A0A143ZS18", "cluster": 25057526, "interpro_all": ["IPR025883", "IPR008965", "IPR002102"], "interpro_used": ["IPR002102", "IPR025883", "IPR008965"], "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 possesses a F-box associated beta-propeller, type 1 domain that functions as a subunit of SCF E3 ubiquitin ligase complexes, primarily in plants. Typically located C-terminal to F-box domains, this $\\beta$-propeller structure helps facilitate the ubiquitination and subsequent degradation of target proteins. It has been detected in Protea cynaroides.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 48, 17, 5758, 2458, 4666, 17, 5062, 13728, 16, 2601, 21, 3418, 1988, 4088, 1966, 43, 5903, 1927, 12437, 10968, 6526, 11905, 5048, 16, 5985, 1922, 4793, 18, 5745, 4810, 45, 17, 4262, 1942, 48, 17, 5758, 4682, 16, 2052, 8, 38, 4666, 8, 17, 5062, 13728, 3170, 12612, 6628, 1920, 11758, 1930, 4521, 4877, 1927, 2758, 2697, 18, 2176, 2258, 2252, 3330, 1922, 2174, 1019, 23836, 15742, 3726, 18, 3], "output": "MVVEEEGCLCLLNPATKEYKRIPDPEILAKRPPYYVFKDYGFGYSPRTDEYKVVVIRGYKIEENIHNDSWVYTLGTNSSWRLIEGSTYWIHTGSHALVNGALHWMAISDMPGFSILLISFDLGDEKFRLLSLPKSLSQEDINHMGLLESDGFLSLCHWMADGKFDVWIMKDYGDEQS", "metadata": {"id": "A0A9Q0KJD9", "cluster": 25316482, "interpro_all": ["IPR006527", "IPR017451"], "interpro_used": ["IPR006527"], "interpro_unused": ["IPR017451"]}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has this function description: The protein is assigned to the MlaA lipoprotein family, which acts as a lipid-anchored outer membrane component of the Mla ABC transport system responsible for maintaining membrane asymmetry through phospholipid transport. Also known as VacJ, this protein is required for the intercellular spreading of *Shigella flexneri*. It is identified in Gammaproteobacteria bacterium and is classified with UniProt keywords Signal. 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, 2646, 5025, 9694, 3416, 16, 2154, 8016, 1966, 43, 4486, 17, 17199, 7642, 3260, 4594, 1927, 1920, 2646, 1019, 7219, 4860, 2433, 5061, 1958, 8231, 3260, 13337, 2596, 14608, 4860, 18, 2222, 3171, 1966, 7017, 1013, 16, 2052, 2213, 1977, 3414, 1958, 1920, 15685, 13405, 1927, 14, 25698, 5795, 3239, 1033, 14, 18, 2176, 1977, 2899, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 5947, 1956, 20709, 11569, 2733, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MAVQMINRVVIGFLLPLILLGLSACASVPEGTEYAVDPLEGMNRSINRFNTDFDNTIAKPVAKGYQAITPDPLDRGFTNFFHNLADINSAANNLFQLKPGRAITDVGRLCVNTTIGLLGFIDVASDIGIPEYKEDMGQTLGYWGYEESTYIMLPMLGPSTVRDFIGKTGDVFMNPIYYTSEGVYWTLLAFRYVDLRADLLRASKVVEEAVIDPYAFMRESYLQKRRFDIYDGDPPLEDDLFFDDI", "metadata": {"id": "A0A8T3KU93", "cluster": 25470403, "interpro_all": ["IPR007428"], "interpro_used": ["IPR007428"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein is categorized in the The Autophagy-related protein 5 family, which coordinates autophagosome formation during macroautophagy and the cytoplasm-to-vacuole targeting pathway. Members of this family are covalently conjugated to Atg12 and bind Atg16, forming a complex essential for enclosing cytoplasmic components and delivering them to the lysosome or vacuole for degradation. Furthermore, the protein should have a Autophagy protein ATG5, UblA domain that constitutes the N-terminal ubiquitin-like region involved in autophagic vesicle formation. It conjugates with ATG12 to facilitate an E3-like ligase activity required for the lipidation and membrane recruitment of ATG8 family proteins. It is identified in Myodes glareolus (Bank vole) (Clethrionomys glareolus).", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10234, 1922, 1920, 1920, 6661, 17, 2712, 2213, 25, 3416, 16, 2154, 10675, 21631, 3337, 2409, 10133, 19847, 17539, 1930, 1920, 5239, 17, 1942, 17, 20309, 5133, 3374, 18, 4678, 1927, 2052, 3416, 2032, 16590, 6765, 1942, 9353, 3112, 1930, 4566, 9353, 3672, 16, 7402, 43, 2796, 4415, 1958, 17439, 11934, 6823, 4178, 1930, 16310, 3581, 1942, 1920, 19171, 2014, 20309, 1958, 4877, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 6661, 2213, 23289, 16, 4803, 5148, 3418, 1988, 14879, 1920, 56, 17, 4262, 6526, 17, 3189, 3031, 3286, 1922, 15319, 11502, 3337, 18, 2176, 14749, 1956, 9353, 3112, 1942, 6628, 1925, 10968, 17, 3189, 11905, 2455, 3414, 1958, 1920, 4486, 1943, 1930, 3260, 6067, 1927, 9353, 1025, 3416, 2697, 18, 2176, 1977, 2899, 1922, 22893, 1918, 27494, 1936, 19574, 12, 10596, 2984, 1021, 13, 12, 2965, 5856, 2001, 3542, 1036, 27494, 1936, 19574, 13, 18, 3], "output": "MTDDKDVLRDVWFGYLLLPRVSYLTLVTDKVKKFEYEGTPLKWRIPTCFTLYQDEITEREAEPYHFQKAMRQEDVSEIW", "metadata": {"id": "A0AAW0HUA0", "cluster": 338115, "interpro_all": ["IPR007239", "IPR048939", "IPR042527"], "interpro_used": ["IPR007239", "IPR048939"], "interpro_unused": ["IPR042527"]}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is classified under the Calcium-dependent protein kinase (CDPK) family, which functions as a sensor and effector of intracellular calcium signaling by translating calcium concentration changes into serine/threonine phosphorylation events. These enzymes typically integrate a catalytic domain with a calmodulin-like regulatory domain to enable direct activation by calcium, playing critical roles in stress responses, cell cycle progression, and development, particularly in plants and specific parasites. Additionally, the protein should contain 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. Moreover, the protein should feature 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 has been characterized in Klebsormidium nitens (Green alga) (Ulothrix nitens) and features UniProt keywords ATP-binding, Serine/threonine-protein kinase, and Transferase.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 5016, 17, 3100, 2213, 4016, 12, 26707, 1040, 13, 3416, 16, 2154, 4088, 1966, 43, 6443, 1930, 7917, 1927, 4776, 5016, 3197, 2007, 24751, 5016, 3110, 2840, 2460, 8468, 19, 13143, 4050, 3916, 18, 2144, 5038, 5745, 13780, 43, 6804, 3418, 1956, 43, 17537, 17, 3189, 4948, 3418, 1942, 8675, 3083, 2936, 2007, 5016, 16, 14797, 4140, 5456, 1922, 3071, 3387, 16, 2024, 4048, 4380, 16, 1930, 2740, 16, 4443, 1922, 4793, 1930, 2487, 9687, 18, 4950, 16, 1920, 2213, 3066, 5531, 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, 3950, 16, 1920, 2213, 3066, 5961, 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, 2258, 2252, 4378, 1922, 22981, 2076, 9734, 7904, 2099, 12, 4524, 4326, 1019, 13, 12, 3570, 2195, 3027, 1039, 7904, 2099, 13, 1930, 4075, 20709, 11569, 4498, 17, 2743, 16, 8468, 19, 13143, 17, 2213, 4016, 16, 1930, 13763, 18, 3], "output": "MRNTARVPTPPGTIFYILRSDATGMFDSFYRLRYDQRILGRHKGTDYLLDNTWGSSSLIVPADNFRPCKLPSKGKNLSLIYPDTWRRVRARKESPDYSLRGGTPGYKTPVDDRVYVGFGHRTTAGPKGERAITDPTCVVQHDGRFYLQTVPRTTLANKDFGFNRHFKDMYTVKEEIGRGSFGRTHIIPKSSMISEAAIMDVHREVQILSLLSGHEGIVEFMAAYEDLMNVYIVMETAVAYMHEKNVIHRDIKPENFIFANEKDNIIKAIDFGLSYKCQENETVKEKADEWSVGVLTYILLIGTRPFFGRTDSEIFKAVLRDEPDIDNADLSLPAREALDHPWLRDRSAMPVQPGCGSSDTRSGLDSTRHICNDRTESLQACLIDPRGWTIVHDFGQTCPGEDPRCISSHGDELLCIEWLRPLTVLSTTESPEVKHNPFVWRLDVKSWQMSFAEVEAQLAEAKSQKGGTVAVKILCQGGELMDDILSNQGPYKEATAVELVWQILVVGSPFFVAPEVLKQAYNLAKDFLKRLLNRNVESRAT", "metadata": {"id": "A0A1Y1IL39", "cluster": 4004005, "interpro_all": ["IPR050205", "IPR011009", "IPR000719", "IPR017441", "IPR008271"], "interpro_used": ["IPR050205", "IPR017441", "IPR000719"], "interpro_unused": ["IPR008271", "IPR011009"]}, "task_type": "infilling"} {"instruction": "Provide the structural infilling for the masked sequence. Target activity: The protein is included in 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. Moreover, the protein is included in the OsmC/Ohr superfamily, which comprises peroxiredoxins such as the osmotically inducible protein C (OsmC) and the organic hydroperoxide resistance protein (Ohr) that function in the detoxification of organic hydroperoxides. These stress-response proteins typically adopt a swapped dimer fold characterized by a mixed beta-sheet and buried helix topology. It is expressed in Isoptericola sediminis.", "tokenized_instruction": [2, 3394, 1920, 4346, 6510, 3961, 1958, 1920, 17476, 3244, 18, 2758, 2455, 30, 1920, 2213, 1977, 3063, 1922, 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, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 9405, 1030, 19, 5622, 1005, 13975, 16, 2154, 12936, 11456, 3030, 21269, 2427, 1966, 1920, 13951, 2169, 9376, 2213, 45, 12, 9405, 1030, 13, 1930, 1920, 6805, 25461, 6211, 3554, 2213, 12, 5622, 1005, 13, 1988, 2347, 1922, 1920, 18169, 1927, 6805, 25461, 29508, 18, 2144, 3071, 17, 2644, 2697, 5745, 14103, 43, 3476, 6688, 7632, 3728, 4378, 2007, 43, 4985, 4666, 17, 11130, 1930, 20516, 7864, 13678, 18, 2176, 1977, 3198, 1922, 10301, 1967, 29902, 6276, 1980, 15472, 18, 3], "output": "MTDQTVEDAPAAVTPSPTDPLWVERTGTAVFTPGELLKIALAACAGMSSDTKFENGKDMEDDRYPVLSEIACTVGRTLKAGAEVPPAEFLPPQDRTYRGFSARGATVEIGPSSEGSRVLGDDYETTIRVFEIDLSGLDEKTRAKTLLLAQRSIDR", "metadata": {"id": "A0A849K756", "cluster": 5594845, "interpro_all": ["IPR015946", "IPR036102"], "interpro_used": ["IPR015946", "IPR036102"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Target Function: The protein should include a Replication termination factor 2 RING-finger domain that forms a single functional Zn2+ ion-binding site and plays a critical role in managing replication stress. This domain associates with mRNA processing factors to facilitate the correct splicing of the *rtf1* transcript, thereby indirectly regulating replication termination at specific barriers. It is present in Octactis speculum.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 3066, 3951, 43, 5158, 12462, 2991, 22, 6335, 17, 8497, 3418, 1988, 4952, 43, 2957, 3183, 21061, 15, 4755, 17, 2743, 3200, 1930, 5705, 43, 4140, 2770, 1922, 14432, 5158, 3071, 18, 2052, 3418, 14162, 1956, 3616, 4587, 2790, 1942, 6628, 1920, 5550, 8490, 1927, 1920, 14, 4341, 5739, 14, 5291, 16, 6113, 10818, 6773, 5158, 12462, 2019, 2487, 8304, 18, 2176, 1977, 2481, 1922, 5843, 2131, 1937, 2187, 7705, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "FLLRDTEDACNWHKDSKLCRRVEHIVSSGAIFSCPVSGAEACGRAGDRRRSAVTQSSSFGCFVCGAKVHTQNDVLKGSPDGTWKGQLTRGQSPMRDVTTLHLHRLGLPHHRFVAFWKCGHVVSEKSFKEMLRMILLNPGARNENLLSPRPDRVAGVGV", "metadata": {"id": "A0A7S2DXW5", "cluster": 7209086, "interpro_all": ["IPR006735", "IPR027799"], "interpro_used": ["IPR027799"], "interpro_unused": ["IPR006735"]}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe 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 found in 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, 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, 2435, 1922, 14061, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MSLGNHTLNQLEHTLKQGQDLRLLPTREKNHFTSKEAVERDLTIRAVRARVQNLQRLDEEKASIALTEATERLRTLGLSEEKALQVLSPVVRGEISRALEGLHNVHGASKIKPLLSQVMQPLQKVWQGVAGAGKTFSVRQIAEEARLAGIAVQGFAPSAAAAGQLSKEAGLDAQAGMVAAKDFLALLKKAKVHSARVLFVGDVRQLSPVEAGNPFLLRQKDPTLQAAVRIINQGDVVQGLAHLNERIAEHSTEKGRILIDAGVASQEPLAREELQSALRSVAQLSLHDLTTSFLAPTRGQMEAIERTLTSTDQFITLQSHLLKREPSNDQKKLWIVDEDIQRNTGTTRIVLDES", "metadata": {"id": "A0A965VBK1", "cluster": 9132073, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein is included 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. Furthermore, the 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. It is derived from Propioniciclava sinopodophylli.", "tokenized_instruction": [2, 6647, 1920, 3835, 2687, 3244, 1958, 43, 2213, 1988, 17436, 2052, 2347, 30, 1920, 2213, 1977, 3063, 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, 3677, 16, 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, 2176, 1977, 3595, 2037, 5062, 14207, 24410, 15777, 3132, 22178, 13384, 1033, 18, 3], "output": "MGRREELGDAAIAVVSAAGLKGLTHRAVDTMAEVPAGTTSNYFRTRQALVDAVADRIEQRDLEVWAALSAPPETFEAFTHWLGAFARAMVVDHGELSRVRFSLFMADPDRYAPGHDRFLGSVAGALQLLGVEGSDVVAPAFLDYLDGVILHGTTVRPNAVPTAEVIAANLARLAGY", "metadata": {"id": "A0A4V6MV26", "cluster": 10689160, "interpro_all": ["IPR009057", "IPR001647"], "interpro_used": ["IPR009057", "IPR001647"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "What would be the complete amino acid sequence of a protein with the following function: The protein has 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. Furthermore, the protein should feature 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. Furthermore, the protein is grouped 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 is present in Gammaproteobacteria bacterium and has UniProt annotations Transcription regulation.", "tokenized_instruction": [2, 4663, 2962, 1998, 1920, 4080, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 2258, 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, 3677, 16, 1920, 2213, 3066, 5961, 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, 3677, 16, 1920, 2213, 1977, 10809, 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, 1977, 2481, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 2258, 20709, 15010, 3213, 3640, 18, 3], "output": "MIKKPITKQNRVNLRYQKIIDTLILDISKGRYCVGEKLPTEAVLCSRFKVSRYTVREALRRLDELSLVTRRRGSGTIVKMREPXKQYIQTLSNVGELLKYPPDTSLKVIKVEEVTTDNKLARKIGCKPHIKWSRIQCVRTTKDETPICLVEIYVKPKFSDVVRYIGLDDTPVYSLIEKHFNQPVGKVDIELYADTITSNGANQLKVKPETPALVVTRRYSNPPSXYFEISIIEXPAGRFTYTMELEQKWGTGGRFT", "metadata": {"id": "A0A2E4GHN2", "cluster": 11653673, "interpro_all": ["IPR050679", "IPR028978", "IPR000524", "IPR011663", "IPR036388", "IPR036390"], "interpro_used": ["IPR000524", "IPR011663", "IPR050679"], "interpro_unused": ["IPR036390", "IPR036388", "IPR028978"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein is included in the Protein of unknown function DUF4386 family, which is currently functionally uncharacterised. It has been detected in Caldisericales bacterium and is described by UniProt keywords Membrane, Transmembrane, 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, 1977, 3063, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 4745, 1016, 3416, 16, 2154, 1977, 5077, 9346, 23229, 3495, 18, 2176, 2258, 2252, 3330, 1922, 2570, 15783, 21052, 2612, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "EWFTLFQTNRFEAFSRLGVINMLTLSLSIPIYLAFNQAFRKERPLLTAFASVLFFVGTAVYLSSNTVFALFSVSQQFSAASASQKLFLEAAGQSLLQQGADLTSGTILGLLMTQIAGLLTTSAMARGKVFGKWIGWAGLIGYGIMTVFFILTSFFPTLYDKAMLIAAPGALIMMAYQLMLARKFFQLGAVEKRKQ", "metadata": {"id": "A0A7X7X8Y4", "cluster": 15443124, "interpro_all": ["IPR025495"], "interpro_used": ["IPR025495"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am interested in designing a polypeptide chain that can perform the following function: It is part of the Protein Kre1 family, which comprises GPI-anchored plasma membrane proteins involved in the structural assembly of cell wall 1,6-beta-glucan without enzymatic activity. These proteins can function as receptors for the yeast K1 viral toxin to facilitate lethal channel formation, while members such as Pga1 are also required for oxidative stress responses, host cell adhesion, and biofilm formation. It originates from Wickerhamomyces pijperi (Yeast) (Pichia pijperi). 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, 2176, 1977, 3131, 1927, 1920, 2213, 17716, 1009, 3416, 16, 2154, 12936, 17497, 17, 17199, 3582, 3260, 2697, 3286, 1922, 1920, 4346, 5957, 1927, 2024, 4821, 21, 16, 26, 17, 4666, 17, 18798, 2979, 8145, 2455, 18, 2144, 2697, 2112, 2347, 1966, 4086, 1958, 1920, 5688, 16185, 4324, 9165, 1942, 6628, 10470, 4999, 3337, 16, 2679, 4678, 2427, 1966, 25546, 1009, 2032, 2222, 3414, 1958, 5163, 3071, 3387, 16, 4423, 2024, 6141, 16, 1930, 9638, 3337, 18, 2176, 22970, 2037, 11980, 12940, 1915, 8527, 29249, 4269, 1013, 2116, 1033, 12, 5688, 13, 12, 7271, 7969, 1019, 4269, 1013, 2116, 1033, 13, 18, 2112, 6253, 5655, 1920, 3835, 2687, 3244, 3980, 1942, 2052, 13022, 4659, 35, 3], "output": "MKFQQILTVASFGLHTITAIVIPTSIPLAITVSAEQQFTTKVTSSYSSTEPTNVLDTVTEEYKNYVEERTRYPAQEHFEKEDSLFNRWLEPRAKKYSYSELEKIRKDYYDNKLGSGATRASPFPLPLFLDLLAPPRRKSTPAVAEINNRTTTVLEKRHYSNRNSGYHFLSPSSSLVFPTITPVAHHVKAVHAIEAITTTTPTTTHIQEPTFYYDNQGIRHTYSQQFRTHKSLASPVPKGIIGLGSLGGRVGDVRSYEFGTLTF", "metadata": {"id": "A0A9P8QBH5", "cluster": 16464186, "interpro_all": ["IPR031452"], "interpro_used": ["IPR031452"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein features a Protein of unknown function DUF1573 domain that constitutes a conserved N-terminal region in hypothetical proteins from bacteria such as *Rhodopirellula baltica*, *Bacteroides thetaiotaomicron*, and *Porphyromonas gingivalis*. In addition, the protein falls within 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 Bacteroidetes bacterium ADurb.Bin028 and is described by UniProt keywords Signal.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 4075, 43, 2213, 1927, 5435, 2347, 4855, 5739, 5071, 1010, 3418, 1988, 14879, 43, 5305, 56, 17, 4262, 3031, 1922, 15148, 2697, 2037, 4802, 2427, 1966, 14, 11490, 2011, 2952, 11560, 5617, 4641, 21788, 14, 16, 14, 27978, 14646, 3940, 3857, 22980, 1022, 14, 16, 1930, 14, 17376, 5134, 3947, 1934, 22118, 14, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 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, 26808, 14061, 2041, 5223, 18, 8768, 11636, 1025, 1930, 1977, 2910, 2007, 20709, 11569, 2733, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MKTKLLLFALILCSSFVFGQNKDFESPAKTSKQSIILFKSKVSKKPVKITNVQTSCGCAAADWSREEITNKKKQKISIVYVEGQDEPIQLQIKGEVLPSDTQEQAIENKTNVSKKENKTKSMNQKKKKINNNLVYDFGKIKHESEAKAVFVFKDSRIIGKFTKYAYVY", "metadata": {"id": "A0A1V6I0M7", "cluster": 19586382, "interpro_all": ["IPR011467", "IPR013783"], "interpro_used": ["IPR011467", "IPR013783"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to design a protein that has the following function: The protein contains a PseI/NeuA/B-like domain that adopts an N-terminal TIM-barrel fold and functions as the substrate-binding catalytic core in enzymes such as NeuB and PseI. It facilitates the condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc) to synthesize N-acetylneuraminic acid (Neu5Ac). Moreover, it is part of the PseI/Nans/NeuA/B acid synthase family, which catalyzes the formation of sialic acids, such as N-acetylneuraminic acid (Neu5Ac), through the condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc) or its phosphorylated derivatives. These enzymes typically feature an N-terminal domain responsible for binding sugar substrates and a C-terminal antifreeze-like (AFL) domain structurally similar to type III antifreeze proteins. Furthermore, the protein is classified under 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 has been detected in Candidatus Nomurabacteria bacterium GW2011_GWA2_41_25. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 5461, 43, 5971, 1033, 19, 2866, 1019, 19, 44, 17, 3189, 3418, 1988, 24032, 1925, 56, 17, 4262, 2267, 17, 19560, 3728, 1930, 4088, 1966, 1920, 4510, 17, 2743, 6804, 4728, 1922, 5038, 2427, 1966, 2866, 1014, 1930, 5971, 1033, 18, 2176, 11374, 1920, 16112, 1927, 8078, 9356, 18425, 12631, 2010, 12, 9110, 13, 1930, 56, 17, 6894, 8890, 17454, 12, 7338, 1948, 13, 1942, 15541, 56, 17, 6894, 2912, 9280, 8547, 1935, 2687, 12, 2866, 27704, 13, 18, 3950, 16, 2176, 1977, 3131, 1927, 1920, 5971, 1033, 19, 3529, 1036, 19, 2866, 1019, 19, 44, 2687, 8921, 3416, 16, 2154, 17097, 1920, 3337, 1927, 20436, 4576, 16, 2427, 1966, 56, 17, 6894, 2912, 9280, 8547, 1935, 2687, 12, 2866, 27704, 13, 16, 2596, 1920, 16112, 1927, 8078, 9356, 18425, 12631, 2010, 12, 9110, 13, 1930, 56, 17, 6894, 8890, 17454, 12, 7338, 1948, 13, 2014, 2496, 7199, 8383, 18, 2144, 5038, 5745, 5961, 1925, 56, 17, 4262, 3418, 5061, 1958, 2743, 9523, 6249, 1930, 43, 45, 17, 4262, 12244, 2329, 6931, 17, 3189, 12, 18957, 13, 3418, 12171, 2551, 1942, 2601, 4337, 12244, 2329, 6931, 2697, 18, 3677, 16, 1920, 2213, 1977, 5947, 2441, 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, 2258, 2252, 3330, 1922, 14550, 1031, 1957, 9684, 9280, 7972, 2341, 18339, 14061, 8997, 23437, 1009, 41, 8997, 8398, 41, 4353, 41, 2637, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MIIAECGHNANGSMKHMKLQINEAKKCGADIAKFQVYDIDKIMTPDNPVYMELKMCQLDKEELKELADYCEKIDIEFCASAFDPERVGWLEEVGVKRHKLASRSIYDAETIKAMEATGKPIIASLGMINEKQGIPSITNSEFLYCVAEYPAIITEEMFPKDFKFYAGFSDHTIGIKWTKEAVRRGATIIEKHFTLDQRLPGCDQAGSSDPKEFKEFIDWVRLYEKNG", "metadata": {"id": "A0A0G0VTU8", "cluster": 20548603, "interpro_all": ["IPR013785", "IPR013132", "IPR051690"], "interpro_used": ["IPR013132", "IPR051690", "IPR013785"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has this function description: The protein is included in the Axonemal dynein light chain family, which plays a dynamic role in flagellar and cilial motility across eukaryotes. These proteins form part of the axoneme core structure and interact directly with the N-terminal half of dynein heavy chains to facilitate microtubule-based movement. It is present in Artemia franciscana (Brine shrimp) (Artemia sanfranciscana) and is connected to UniProt keyword Coiled coil and Motor protein. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 2052, 2347, 8418, 30, 1920, 2213, 1977, 3063, 1922, 1920, 9980, 30426, 18188, 3696, 4659, 3416, 16, 2154, 5705, 43, 5760, 2770, 1922, 24154, 1930, 15714, 1024, 9254, 3436, 15021, 18, 2144, 2697, 2386, 3131, 1927, 1920, 9980, 17800, 4728, 3170, 1930, 6310, 4103, 1956, 1920, 56, 17, 4262, 4768, 1927, 18188, 7881, 7835, 1942, 6628, 10544, 17, 2454, 5829, 18, 2176, 1977, 2481, 1922, 20897, 6026, 28740, 8337, 1019, 12, 29221, 25184, 13, 12, 20897, 6026, 6867, 7134, 2412, 10368, 7241, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 17524, 9121, 1930, 4842, 2213, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MSCKSLSFSLLSYKKPVLVTNNFCEGSTSTGKTDESGLICQETLNSILRPRTWIDDEGAAWMQEVSSTPGSRTDVIALRERLNYKLRQRQSRPVGFCPIRRELYSQCFDELIRQTSINCSESGLLLVEVRDEISTSMNALIQLYESAVAYTVSKDLKFQKDEEGVKNNIDDLKNKIQGLETELKSLHIQFEREKEEMEEKFKLKEGELLSQIESLENTNKTIKATLQSLLTPSSKQEEF", "metadata": {"id": "A0AA88HYL3", "cluster": 23057587, "interpro_all": ["IPR019347"], "interpro_used": ["IPR019347"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the intended role of my protein: The protein has a Mitochondrial carrier protein, transmembrane region repeat that forms the structural core of transporters found in the inner mitochondrial membrane or peroxisomes. Typically present in three tandem copies, these repeats assemble into a six-helix channel-like structure that mediates the translocation of substrates, such as ADP/ATP and phosphate, through a conformational shift. Furthermore, it is part of the Mitochondrial and Peroxisomal Carrier Protein family, which mediates the translocation of essential cofactors including coenzyme A (CoA), FAD, FMN, and AMP across organelle membranes. Belonging to the mitochondrial carrier superfamily, these transporters likely function via a counter-exchange mechanism to import substrates into the matrix from the cytosol, relying on internal regions for peroxisomal targeting. It is native to Denticeps clupeoides (denticle herring) and features UniProt keywords Transmembrane helix. Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 30, 1920, 2213, 2258, 43, 4596, 9685, 2213, 16, 9117, 3031, 6865, 1988, 4952, 1920, 4346, 4728, 1927, 10538, 2435, 1922, 1920, 6671, 4596, 3260, 2014, 28990, 18, 5745, 2481, 1922, 2559, 10361, 9425, 16, 2144, 9569, 17421, 2460, 43, 3798, 17, 7864, 4999, 17, 3189, 3170, 1988, 10412, 1920, 7849, 1927, 6249, 16, 2427, 1966, 9828, 19, 4498, 1930, 5413, 16, 2596, 43, 8523, 5950, 18, 3677, 16, 2176, 1977, 3131, 1927, 1920, 4596, 1930, 28765, 9685, 2213, 3416, 16, 2154, 10412, 1920, 7849, 1927, 4415, 21362, 2710, 22051, 43, 12, 10027, 13, 16, 14134, 16, 29599, 16, 1930, 3681, 3436, 19309, 5726, 18, 10588, 1942, 1920, 4596, 9685, 13975, 16, 2144, 10538, 3205, 2347, 3454, 43, 5836, 17, 6818, 2856, 1942, 2582, 6249, 2460, 1920, 4526, 2037, 1920, 11689, 16, 21119, 1990, 4495, 3451, 1958, 28765, 5133, 18, 2176, 1977, 6196, 1942, 17071, 3944, 1036, 2111, 3481, 1021, 12363, 12, 17071, 3283, 3656, 8641, 13, 1930, 4075, 20709, 11569, 9117, 7864, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "HTLAHTRSLTHTHTLAHTHTHTLAHTHTHTRSLTHTHTLAHTHTHARTHTHTRSHTHTHTRTHTHTPHTLPHTHTRTHTTQSHTTHTLTHTHSHTHARTHTHARHTHTHTRSLSHTHTHARTTHTLAHTHTHTLAHTHTHARTHTHARSHTHTHTHARSHTLAHTLAHTHTLAHTHTLAHTHARTHTHTRSHTHTHTTRTHTRSHTHTLSHTHTLAHTHTRSHTHTHTRSHTRSHTRSHTRSHTLAHTLAHTLAHTHARTHTRSHTHTLAHTHTHARTHTHTLALTHTHTLAHTHTRLLTHTHTHACSHTHTLIHTHTHSFTHSFTHTHTHSFTRTRTHSFTHSHAHTRTHTHTHAHTRTHSHSHTHIHTRTLAHTLAHTRTHTHTRAHTRTHSFARTRTHTRTRTHTRTRTHTHTHTHSHSHSFTHTLTLTHSLLLPPLAVGVVNVLVTTPLWVVNTRLKLQGAKFRNADIRPTDYEGIVDAFVRIVQDEGAGALWNGTFPSLLLVLNPAVQFMIYEGLKRQLRRGLLRELSSTEVFLIGAVAKAVATTATYPLQTAQSILRFGGHRAAAARGSRLLSGLRGVAYLLVSRVRTYGVLGLFKGLEAKLLQTVLTAALMFLIYENIASATFSIMGVKRPLARR", "metadata": {"id": "A0A8C4B4E0", "cluster": 23451314, "interpro_all": ["IPR052217", "IPR018108", "IPR023395"], "interpro_used": ["IPR018108", "IPR052217"], "interpro_unused": ["IPR023395"]}, "task_type": "autoregressive"} {"instruction": "Assume the biological function is as follows:\nThe protein includes a Cyclin-like domain that functions as a structural core composed of a duplicated five-helix fold, where one helix is typically surrounded by the others. This domain is a defining feature of diverse regulatory proteins, including cyclins, transcription factor IIB (TFIIB), and the retinoblastoma tumor suppressor. Additionally, the protein has a Cyclin, N-terminal domain that regulates cyclin-dependent kinases (CDKs) to control nuclear cell division cycles. This all-alpha fold domain binds catalytic partners, such as p34(cdc2) or cdk2, to form complexes like the Maturation Promoting Factor (MPF) essential for G1/S and G2/M transitions. It originates from Vitrella brassicaformis (strain CCMP3155).\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 5921, 43, 8180, 17, 3189, 3418, 1988, 4088, 1966, 43, 4346, 4728, 7179, 1927, 43, 19479, 3628, 17, 7864, 3728, 16, 2597, 2340, 7864, 1977, 5745, 16006, 2007, 1920, 4991, 18, 2052, 3418, 1977, 43, 11266, 5961, 1927, 6445, 4948, 2697, 16, 2710, 29201, 16, 3213, 2991, 19795, 12, 27935, 1014, 13, 16, 1930, 1920, 25526, 2798, 9241, 18, 4950, 16, 1920, 2213, 2258, 43, 8180, 16, 56, 17, 4262, 3418, 1988, 7014, 8180, 17, 3100, 7784, 12, 9727, 1036, 13, 1942, 2285, 4254, 2024, 8451, 6355, 18, 2052, 2136, 17, 4595, 3728, 3418, 6876, 6804, 7228, 16, 2427, 1966, 9234, 1006, 12, 28190, 13, 2014, 18664, 16, 1942, 2386, 5048, 3189, 1920, 7655, 7356, 2991, 12, 5438, 1038, 13, 4415, 1958, 8533, 19, 61, 1930, 9616, 19, 55, 10673, 18, 2176, 22970, 2037, 16986, 11560, 1019, 19503, 6102, 2231, 1937, 12, 3943, 25993, 7170, 19126, 13, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MPFRSTHYLPVPPAQSSVGTTQGKPGAPYSRPMQALSCAFRKGPAHDIRSVTAGYAKSCPYRSTGAVGVGGHGKEILPHKLTASTHGYGGHSHLLVGKHDQGSHSAYSTMGKSVSTKAIMTQTKCDAPRQSSDHPDMPIPTGQSAHSRRPNLTLQAVREPITVPITHHRGSSPMGMDLDTHDHKPHGSSGRFGESAALCAHLPPHKPGITRAISYGGSSVSSGQDTAMVEGESAGMLLSSPFPGIDLFGVPDQPAEVLREINAIAETLLMDPEQLQLIRDAPNAIKGCYRSEVDCTINPDMTTDQPAGQGSPAHTQPMRTAPITARDRRKVVQWMSEVCQSLRWQMKTFLTSVNALDRFLKYSTGAGLQEYFEDRSVPQLSAFVRAAPYLRSVHQVKTIQLDIMDTLSGRFLLKTPIDFAVLYLSSLKHHPDLTYFRMYGTHVSVPGSHLVAATLIQLIQYVEPSLIPVSIHRELCADVFKLEYSSTDSGQLGGAEGDMGIIAEGVNVMEIAHKLIHLVIHSQHLDDPDVRTKLLETTQQEGATYLLRHRHRRTPHPGEATTNKGVVTVLSGDKVLSLTRSISLTVDDHTAATAPPEWTASTSAPSSTSSEEDSEGGYPSTPTMSGTPSTPCDASMDQSPPTPSRSPGGGGGPTQPIQTAHLPVLSVACLFIDAIASRGYLPMIIEVIVCVLGAACMRLLNRMHYDESESTNGDSDASSM", "metadata": {"id": "A0A0G4GRL4", "cluster": 26968885, "interpro_all": ["IPR039361", "IPR013763", "IPR036915", "IPR006671"], "interpro_used": ["IPR013763", "IPR006671"], "interpro_unused": ["IPR036915", "IPR039361"]}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: The protein is assigned to 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 originates from Deinococcus sonorensis KR-87 and carries UniProt keyword assignments Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 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, 22970, 2037, 2028, 3522, 4879, 2437, 1957, 9337, 2073, 3355, 1937, 6203, 17, 5783, 1930, 16252, 20709, 11121, 2538, 18306, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MNYAASLAVVVILTFFFPLTVRIGVAYGLPRTLATVALAAVLTFVAATLLIRWQVARYRQAAESVEEARRQVNLDPQNPRAYFVGGEHLASLLLRLGRRREAAEMIDRYARLGGARESEIVALQTALSQAERRQRRGTHLGRGN", "metadata": {"id": "A0AAU7UBX5", "cluster": 28600587, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "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 Mur ligase, central domain that functions as the ATP-binding catalytic module in the MurC, MurD, MurE, and MurF enzymes responsible for the stepwise assembly of the bacterial peptidoglycan stem peptide. This domain shares structural similarity with ATPase domains and is also present in folylpolyglutamate synthetase and cyanophycin synthetase, where it drives ATP-dependent ligation reactions for folate metabolism and cyanophycin storage. Moreover, the protein is included in the UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase family, which catalyzes the ATP-dependent addition of meso-diaminopimelate (or L-lysine in some species) to the UDP-N-acetylmuramoyl-L-alanyl-D-glutamate precursor during the biosynthesis of bacterial peptidoglycan. Also known as MurE, these enzymes typically feature a three-domain structure comprising an N-terminal substrate-binding domain, a central ATP-binding domain, and a C-terminal domain responsible for binding the incoming amino acid. Moreover, the protein should contain a Mur ligase, C-terminal domain that facilitates the sequential addition of amino acids to UDP-N-acetylmuramic acid during bacterial peptidoglycan biosynthesis. Adopting a dihydrofolate reductase-like fold, this domain is responsible for binding the incoming amino acid substrate in enzymes such as MurC, MurD, MurE, and MurF, as well as in folylpolyglutamate synthase and cyanophycin synthetase. It has been detected in Lachnospiraceae bacterium and features UniProt keywords Cell division, Cell shape, and Cell wall biogenesis/degradation.", "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, 6185, 11905, 16, 4101, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 6804, 9059, 1922, 1920, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 5038, 5061, 1958, 1920, 13846, 5957, 1927, 1920, 4543, 24183, 4402, 4207, 18, 2052, 3418, 16495, 4346, 6796, 1956, 9444, 4682, 1930, 1977, 2222, 2481, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 1930, 26898, 25818, 3665, 18185, 16, 2597, 2176, 15435, 4498, 17, 3100, 11102, 5298, 1958, 13761, 4714, 1930, 26898, 25818, 3665, 7451, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 18500, 17, 56, 17, 6894, 23010, 29085, 10921, 8056, 16323, 1024, 17, 46, 17, 7627, 17, 22, 16, 26, 17, 21121, 2011, 11593, 5148, 2057, 11905, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 2459, 1927, 23577, 17, 21121, 2011, 11593, 5148, 2057, 12, 2014, 54, 17, 9082, 1922, 2673, 3038, 13, 1942, 1920, 18500, 17, 56, 17, 6894, 23010, 29085, 10921, 17, 54, 17, 10527, 16323, 1024, 17, 46, 17, 7627, 7897, 2409, 1920, 8132, 1927, 4543, 24183, 18, 2222, 3171, 1966, 6185, 1021, 16, 2144, 5038, 5745, 5961, 43, 2559, 17, 3418, 3170, 10351, 1925, 56, 17, 4262, 4510, 17, 2743, 3418, 16, 43, 4101, 4498, 17, 2743, 3418, 16, 1930, 43, 45, 17, 4262, 3418, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 6185, 11905, 16, 45, 17, 4262, 3418, 1988, 11374, 1920, 9454, 2459, 1927, 3835, 4576, 1942, 18500, 17, 56, 17, 6894, 23010, 29085, 1935, 2687, 2409, 4543, 24183, 8132, 18, 20478, 43, 11842, 27851, 11386, 17, 3189, 3728, 16, 2052, 3418, 1977, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 4510, 1922, 5038, 2427, 1966, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 16, 1966, 2486, 1966, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 8921, 1930, 26898, 25818, 3665, 18185, 18, 2176, 2258, 2252, 3330, 1922, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 1930, 4075, 20709, 11569, 2024, 8451, 16, 2024, 5989, 16, 1930, 2024, 4821, 13008, 19, 4877, 18, 3], "output": "MRQTKKLLQELNCRCIRGELPREVKQVAYDSRNVEPGGLFVCIRGSRQDGHAFIRGAWKEDNSSQEAAKQQKYCVLETPDTRAALASIARQWFDNPQEKLKIVGVTGTKDGKKCGLIGTIEVCYGTWQQTIRNTTPESYELYEILRKMVDQGCQYVVMEVSSQALAGEHADFAEYMACKHRLFCQCRIGIFNQDDPYWQEMWRGSSCEKVLRYRIGKNQGEMEAASENSWNVVVNAPGKFSIYNSLAAISVAEQYQIPEKAIEKAIVDYAHNAMALDALLRTLRDYHPGRIICIFGCGGNRAAERRFQMGEVAGRLADLVVVTTDNIPDRGQAIAYGISHAKPGDIVVIAGKGHETYQEINGEKYPMDDRKLAMKCKVWEAVERGAVVILTEKGKTSTVWMIWKMFTAKLHRVDGIMFEAAVFTNLREDHIGTYGFSRQADYCADRVQLLRGSDRLGVQYHLNLHTLQVPGRIEMLPVSPRFIVPREEDPEKIADEICLGLEAAKGKYGR", "metadata": {"id": "A0A943GXK6", "cluster": 14128257, "interpro_all": ["IPR036565", "IPR004101", "IPR036615", "IPR013221", "IPR000713", "IPR035911", "IPR005761"], "interpro_used": ["IPR013221", "IPR005761", "IPR004101"], "interpro_unused": ["IPR000713", "IPR036565", "IPR035911", "IPR036615"]}, "task_type": "infilling"} {"instruction": "The protein incorporates a CheB methylesterase domain that functions as a response regulator in bacterial chemotaxis by catalyzing the demethylation of methyl-accepting chemotaxis proteins (MCPs). This domain removes methyl groups from gamma-glutamyl methyl ester residues to modulate sensory adaptation and is regulated through phosphorylation by the histidine kinase CheA. It is derived from Gammaproteobacteria bacterium and contains UniProt keyword associations Hydrolase.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 19683, 43, 10003, 1014, 4963, 8342, 2051, 3418, 1988, 4088, 1966, 43, 2644, 7888, 1922, 4543, 16884, 2007, 29601, 1920, 20254, 1927, 4963, 17, 26170, 16884, 2697, 12, 11942, 1036, 13, 18, 2052, 3418, 21890, 4963, 2671, 2037, 7034, 17, 25345, 4963, 9603, 4248, 1942, 8480, 6893, 7810, 1930, 1977, 4335, 2596, 4050, 2007, 1920, 13873, 4016, 10003, 1019, 18, 2176, 1977, 3595, 2037, 7034, 9218, 1021, 10296, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 20748, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MKNLENASAEATGPSSKPDSHVPSPATLELRKVHIAIASDSLRKVVLSESLHPGLMDHLAASEAEVLILDLHDDIEHDEAVLDALLDDSLARWHTTLLRKIVELASRESGIDVSLTEGMDSGMYALDSGSVAMGEDRVFPGQTPLGALPADIPAAFVLAQHLGTRFVSLLAEQLDRETPLRVCRPQVGHVLRHTVELHPAPGKAPYAPSIDLVVEDVARRYPARSGVILFSGLGDMSSMPDAARDTGLVEVSASPEELAQRLVRHFNSLNQRSYLENALKDRGLPVPIVFNDISALTLKEPRSKGEVAMSVWVLGASLGGPEALKRFGQVLIAPVEERLVINSVGDGRKGLREMHRRGGLVWAQDSSSCV", "metadata": {"id": "A0A7C1TI87", "cluster": 334279, "interpro_all": ["IPR035909", "IPR000673"], "interpro_used": ["IPR000673"], "interpro_unused": ["IPR035909"]}, "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 YfhO family, which comprises largely uncharacterised proteins, including some annotated as putative ABC transporter permeases. Transcription of these genes is regulated by the YvrGHb two-component system and occurs in sporulation medium. It is expressed in Planctomycetota bacterium and is annotated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "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, 29962, 10647, 3416, 16, 2154, 12936, 6318, 23229, 3495, 2697, 16, 2710, 2673, 10633, 1966, 6770, 7219, 9054, 6191, 2319, 18, 3213, 1927, 2144, 2628, 1977, 4335, 2007, 1920, 67, 23663, 2509, 1014, 2288, 17, 4594, 2433, 1930, 5110, 1922, 23647, 3649, 18, 2176, 1977, 3198, 1922, 4720, 2341, 13386, 19446, 3857, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MRCAAWICLGLAGAAVQLIPTAELSLLSTRQGRTHPQAAEGNNKNNNNTNSPPLGGLGGGTNNHRAQKKQAGDNNNSNSNNTNSPPLNQANPQTPTIDPVVIWATPGGQIESARRANPIEWNLYVGPIILILLASIGFAQGWPGIRLLYHLPLFNAGAPARALSVAWVAWAIKGALALAVVLAVAGLTLGQHLAESPEKFFDGDWRAATALVHGAALIARLADSAQRLTLLSAGGALAIALGLFLSLRSRNHLLPFLPYSREHLDPRPLGGPLFPDSHTMSAIEQTARGGRLLRLDESASGIGDVLNRRLVEVMTTIDPGSAYRGGASRISRPEVIGHPALDLFAVTCILSTRELRHPRLDSAWLVPRAVGASRTVALGLVTSGQLNQLTDHCVVPAKAADAPDRMDLKLTAGDGGWLVISEAWYPGWKATVNGADVEVTPANHALMALPYEPSSVRLGTVLSALAALFALVHVLRRRRRAVATSRPRPADLLAESLPTATLAGLALPNLFGAGGLGGGANNPRAPKNALAGILASPTRAAPALLLLPWLAALGAQALAVTHLRAEVEAVTALPDSAPPILLLLGADGLLTRLARPNLATAWGIKELLPYVVFPLKQVLAQDEFFVYRRQPPAGLSSEAPVRSATWEAGSLESSRPVPAGEVVVRLF", "metadata": {"id": "A0A2D5W9Z7", "cluster": 2666204, "interpro_all": ["IPR018580"], "interpro_used": ["IPR018580"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe protein should have a Meta/HslJ (DUF306) domain that constitutes a putative secreted or outer-membrane component implicated in diverse phenotypes such as bacterial motility, novobiocin resistance, and protozoan virulence. It features a pair of conserved cysteine residues that are predicted to form a structural disulfide bond. It is native to Sphingomonas glacialis.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 3066, 2162, 43, 5880, 19, 28578, 1013, 12, 4855, 10892, 14265, 13, 3418, 1988, 14879, 43, 6770, 8366, 2014, 7642, 17, 3260, 4594, 6835, 1922, 6445, 6568, 2427, 1966, 4543, 9254, 16, 9441, 15193, 3665, 3554, 16, 1930, 23583, 13642, 1928, 9304, 18, 2176, 4075, 43, 3715, 1927, 5305, 8666, 4248, 1988, 2032, 4396, 1942, 2386, 43, 4346, 11830, 5403, 18, 2176, 1977, 6196, 1942, 13502, 10480, 27424, 1937, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MFAAFSPDAGVSHPAERGPSDHVWVLEKFQTGTWACNSIGPGKLKWENISGQMHGKLATDGASARIIKWSIDQKGLSVRFADGSSARFVSERVIERGMEVATLRFNSDHTVTVVGCDNARVVAIANRFWLRVETAR", "metadata": {"id": "A0A502FSU0", "cluster": 2834863, "interpro_all": ["IPR005184", "IPR038670"], "interpro_used": ["IPR005184"], "interpro_unused": ["IPR038670"]}, "task_type": "infilling"} {"instruction": "I want to make a protein that can have this function: The protein is grouped in the The TEC1/TEAD Transcription Factor family, which comprises transcription factors central to the Hippo signaling pathway that regulate cell proliferation, apoptosis, and organ size control. These proteins bind specific DNA sequences to mediate the expression of effectors like YAP1 and WWTR1/TAZ, and in fungi, they regulate gene expression involved in sporulation and conidium development. Furthermore, the protein should contain a TEA/ATTS domain that binds DNA within eukaryotic transcription factors, adopting a three-helix bundle structure with a homeodomain fold. It utilizes a specific recognition helix to interact with DNA, an activity that can be modulated by the phosphorylation of conserved serine residues on the binding surface. It is present in Henningerozyma blattae (strain ATCC 34711 / CBS 6284 / DSM 70876 / NBRC 10599 / NRRL Y-10934 / UCD 77-7) (Yeast) (Tetrapisispora blattae) and carries UniProt keyword assignments Coiled coil, Nucleus, and Transcription regulation. Can you generate its sequence?", "tokenized_instruction": [2, 51, 12914, 1942, 5144, 43, 2213, 1988, 2112, 2162, 2052, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 1920, 18671, 1009, 19, 12459, 1007, 3213, 2991, 3416, 16, 2154, 12936, 3213, 2790, 4101, 1942, 1920, 25771, 3197, 3374, 1988, 5741, 2024, 4031, 16, 4091, 16, 1930, 3090, 3081, 2285, 18, 2144, 2697, 4566, 2487, 2678, 3709, 1942, 8265, 1920, 2294, 1927, 13066, 3189, 28146, 1930, 6010, 29361, 19, 18579, 16, 1930, 1922, 10520, 16, 2611, 5741, 2359, 2294, 3286, 1922, 23647, 1930, 30084, 1989, 2740, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 12459, 19, 3099, 1036, 3418, 1988, 6876, 2678, 2651, 10825, 3213, 2790, 16, 20478, 43, 2559, 17, 7864, 14142, 3170, 1956, 43, 4502, 17166, 3728, 18, 2176, 18127, 43, 2487, 5708, 7864, 1942, 6310, 1956, 2678, 16, 1925, 2455, 1988, 2112, 1998, 9985, 2007, 1920, 4050, 1927, 5305, 8468, 4248, 1990, 1920, 2743, 3154, 18, 2176, 1977, 2481, 1922, 14618, 2989, 6506, 3105, 1019, 18208, 3519, 3336, 12, 3943, 11037, 26952, 3242, 19, 16341, 5374, 11068, 19, 10964, 3895, 8851, 1016, 19, 8789, 15618, 7991, 6576, 19, 5214, 1005, 1024, 67, 17, 9359, 4857, 19, 8577, 1007, 5517, 17, 27, 13, 12, 5688, 13, 12, 28000, 1937, 1937, 21086, 18208, 3519, 3336, 13, 1930, 16252, 20709, 11121, 2538, 18306, 17524, 9121, 16, 5607, 16, 1930, 3213, 3640, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MNEKPNHANLRQIPIKSIPDKEDKPFRNLAPDSDPINNPQGEDEAINSNLQKKINDDEINDISSSSLESTSSSLKNYTQLSKTRVFDVFTQDVKNIDSNSDDTNSLQKSNDSKFDEIQDLDIFQLDELINNKIKEDFLKKLRKNNNNNNYNNKSIEDAKNIENLRDTDNIKSNNQSDHTNINLINSGSGKLLNEDTLSKKYPINKLSNSILERGTKPIPLNQLSLTSKISQARTVLDKPIISNTPLTSTQSNIPTNSNTSSISNPEPIDTKNISNTQNKSSNTPSSLTPQTGKSHDNDKWTAEVENAFVESLHLIIKNGPNKIKVLNKGYGRNELISMYILDKSGELRTKKQISSHIQVWKKAILNKISCNEDLEVQEKEINKLIENGAEQNEENIKKFNTIFEEILRKHNYRENSIDSSNSLSNSLSSLHSDKSNFDNSDSLYQELPKRYESPQLEYAKTIYQQVDNLKCVPITYPSLESQDITEEEKLAINKILQDAETLKRQQRLLIDKNWNESKLLLNQNNANTIREFSGEQTIDTSSNSKNLRKQIDINLEENHSSTVNERNEQKFQNTESNESLLQNKHNTINISNQIPFNKGFAKPPMGITPTWGMFPPYGPGLGYSPTHFQSPTVMRYPINNQQNRSFVDFQTQYNRVNPNYYSPLNTNFQRYSNSPSSRTGRTSPFNVNLNMESNLRDASYHESSNLQDNSTTEHQTFRQGLTSRPDQNKNSISSSSYENIESSIEDNDK", "metadata": {"id": "I2H921", "cluster": 2955503, "interpro_all": ["IPR000818", "IPR038096", "IPR050937"], "interpro_used": ["IPR050937", "IPR000818"], "interpro_unused": ["IPR038096"]}, "task_type": "autoregressive"} {"instruction": "Design a protein's amino acid sequence that will have the following function: The protein belongs to 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 is categorized in the RING-H2 finger protein ATL1/ATL16-like family, which comprises plant ubiquitin ligases containing a RING-H2 domain. These proteins play central roles in regulating plant defense responses, programmed cell death, and carbon/nitrogen nutrient balance, with some members localizing to plasma membrane lipid rafts to trigger specific cell death pathways. In addition, 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 originates from Cannabis sativa (Hemp) (Marijuana) and is linked to UniProt keywords Ubl conjugation pathway.", "tokenized_instruction": [2, 3036, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 14440, 1942, 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, 1977, 10234, 1922, 1920, 6335, 17, 4881, 8497, 2213, 9118, 1009, 19, 9118, 3672, 17, 3189, 3416, 16, 2154, 12936, 4496, 6526, 22423, 3165, 43, 6335, 17, 4881, 3418, 18, 2144, 2697, 3918, 4101, 5456, 1922, 6773, 4496, 9720, 3387, 16, 13839, 2024, 3539, 16, 1930, 5056, 19, 6634, 8708, 6766, 16, 1956, 2673, 4678, 29507, 1942, 3582, 3260, 4486, 21001, 1942, 6086, 2487, 2024, 3539, 3873, 18, 1922, 2459, 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, 22970, 2037, 14664, 22939, 12, 3243, 1034, 13, 12, 15617, 13, 1930, 1977, 4624, 1942, 20709, 11569, 4803, 1024, 14122, 3374, 18, 3], "output": "MEFNERQMESLMVAGLWCCQSDPSFRPSIKQVVNILNFEAPLPNLRPKLPKPMYFAHSLNMDSTSYTTSTDTTTTRDQFQYTSSSSYTDSSTSAGLSRPTHKILVTVRRGLDTSVLQSIPVLVFQPEDFKDGLECAVCLSDLAQGEKARLLPKCNHGFLFIGDRSRLDPN", "metadata": {"id": "A0A7J6IAA7", "cluster": 3359536, "interpro_all": ["IPR044600", "IPR001841", "IPR013083"], "interpro_used": ["IPR013083", "IPR044600", "IPR001841"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein contains 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. Also, the protein belongs to the Cytochrome P450, E-class, group I family, which comprises heme-containing mono-oxygenases that typically function within a two-component system requiring an NADPH-dependent reductase. These enzymes catalyze the oxidation of diverse substrates, facilitating essential processes such as xenobiotic detoxification and steroid metabolism in vertebrates, as well as alkaloid biosynthesis in plants. It has been characterized in Acaulospora morrowiae and is annotated with UniProt keywords Metal-binding, Monooxygenase, and Oxidoreductase.\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, 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, 2222, 16, 1920, 2213, 14440, 1942, 1920, 9387, 12088, 16, 47, 17, 2921, 16, 2210, 51, 3416, 16, 2154, 12936, 10954, 17, 3165, 8914, 17, 25298, 1036, 1988, 5745, 2347, 2651, 43, 2288, 17, 4594, 2433, 8887, 1925, 11908, 17, 3100, 11386, 18, 2144, 5038, 18170, 1920, 6638, 1927, 6445, 6249, 16, 12440, 4415, 4028, 2427, 1966, 29821, 18169, 1930, 9507, 4714, 1922, 14976, 16, 1966, 2486, 1966, 29951, 8132, 1922, 4793, 18, 2176, 2258, 2252, 4378, 1922, 18699, 11677, 21086, 2803, 2438, 7955, 1930, 1977, 10633, 1956, 20709, 11569, 6048, 17, 2743, 16, 8914, 13966, 16, 1930, 27388, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MLKLNLFTSGFDWISITLIFLFLYVSKYPLPIIGNLHQAIFHKIGDIDFGTWSFHLREKYGETFEVYLGSLNRFFVRPKVNGLSELEMNDGLIFNNDKKSWSRNRKFVSQDLFDKVECNWTSGVVIDFATWIRCFMTDILSSTLTGSPAVCPLSESLKTWFNSLPFFVAIPRYLRYNLPILSSINRHYLNNAKRLEDEILGLLDMLLTMNIRDHNEPAEDDEPMKDEEIRDNVMDISLTSSDSTEEIDSIFANDMTRPVTSNDLEKLVYMEAAIKETLRMFPVTPLVPRSLTNPETLLGLMHNKNVWEEPHKFNPDRFLKDTEKIQKKFFVPFGGGCRICPGYYNYCKRENPLPGPLRTVVTGDPESLDKIYNPSLKTLQSPKFLREFAGITQCSISKSEYTPEMKKSYEFLEKVIKRREQLESLPGGQAVGDGNSFCYFIYHIFHNPLCKERLLYNWPAGQLFFISQYS", "metadata": {"id": "A0A9N9CZ75", "cluster": 5215756, "interpro_all": ["IPR001128", "IPR017972", "IPR002401", "IPR036396"], "interpro_used": ["IPR017972", "IPR002401"], "interpro_unused": ["IPR036396", "IPR001128"]}, "task_type": "infilling"} {"instruction": "The protein is grouped in the Peptidoglycan biosynthesis protein MurJ family, which functions as a lipid II flippase essential for bacterial cell wall synthesis. These proteins translocate the peptidoglycan precursor lipid II from the cytosolic face of the membrane to the extracellular side, enabling the incorporation of its glycopeptide moiety into the growing cell wall mesh. It is derived from Salvia splendens (Scarlet sage) and is described by UniProt keywords Peptidoglycan synthesis, Cell shape, and Cell membrane.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 1977, 10809, 1922, 1920, 24183, 8132, 2213, 6185, 1013, 3416, 16, 2154, 4088, 1966, 43, 4486, 2890, 16405, 5506, 4415, 1958, 4543, 2024, 4821, 4271, 18, 2144, 2697, 26377, 1920, 24183, 7897, 4486, 2890, 2037, 1920, 9410, 6171, 1927, 1920, 3260, 1942, 1920, 5329, 4159, 16, 12180, 1920, 8629, 1927, 2496, 8821, 8253, 11804, 2460, 1920, 6552, 2024, 4821, 10238, 18, 2176, 1977, 3595, 2037, 14623, 2126, 12002, 5233, 1036, 12, 10218, 6088, 26524, 13, 1930, 1977, 2910, 2007, 20709, 11569, 24183, 4271, 16, 2024, 5989, 16, 1930, 2024, 3260, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MNKRTGSGYSCQYERRQPGLIHFVSAHFGANQYKTRRHSLFPTDSPLQNPPSPIGRPSLRFSQAEASPRRFRGIQAQVVVPTGDKSVSAATLVGVATLVSKILGLLREVIMASVFGVGGFSSSLLGGVNGPIHIIMSTTLSKLPEERGKKLFQHLYAPGLWIMAEGQIIREIAIKQLKMMTPCIVLAGPVGLGIASVSDDIELFLFLAWACYPNYVYTGSSNTNKHLQCLVCNLAYDPQVYLPSWFLFLSLDAYLLVIAPLGALSSITVLPLVPKFSKLLLPIFSVMRSLVEPIIHILFERCEFDSSASALVSSLVAVFYALGDGKRPFLVSAGAVALNAVLDWLSVSRFNLLLKRKLSGLSSYAAMIYPTTLLLICCITSNITTSVAYNLMHVSVAFGLIGFFVPAVLLHLHSDSEEMQAYLGWDIQVSDLMEVTAEVALGFNPIVAVANSRALPGSALKLTQFQLKSEMIKARIAFDLSIAFRAEKSLSSSPHKDDFSHPVATAFKYCTFDKSKYAWVLPTTIMFLVGGVVGAFVYIFPDFVVQIFGYMSAQGNDVLPCISPALSSSLVALTSRLNGYFSGKFLLCFSPVKTSSWESLANDLERALLLCMVFLACDYLNTDSLGTPFFIAKDLLGAKGLALSTSFTAALSVLILFHASTLLSRYNLMMELFTLLMAGNLRGSELLSGPPTACAKLYVLKT", "metadata": {"id": "A0A8X8XH75", "cluster": 5607473, "interpro_all": ["IPR004268"], "interpro_used": ["IPR004268"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the intended role of my protein: The protein incorporates a Cyclic nucleotide-binding conserved site that mediates the interaction with cAMP or cGMP to regulate signal transduction. This domain typically folds into a structure composed of three alpha-helices and a distinctive eight-stranded antiparallel beta-barrel, maintained by invariant glycine residues. It is found in diverse proteins, including prokaryotic catabolite gene activators, cyclic nucleotide-dependent kinases, and vertebrate ion channels. Also, 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 incorporates 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 found in Amphiprora paludosa and is annotated with UniProt keywords Transmembrane helix, cGMP-binding, and Transmembrane. Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 30, 1920, 2213, 19683, 43, 9821, 5489, 17, 2743, 5305, 3200, 1988, 10412, 1920, 2835, 1956, 6225, 2014, 15958, 1942, 5741, 2733, 8201, 18, 2052, 3418, 5745, 16231, 2460, 43, 3170, 7179, 1927, 2559, 4595, 17, 12789, 1930, 43, 15308, 5066, 17, 10338, 28892, 4666, 17, 19560, 16, 5514, 2007, 17004, 10646, 4248, 18, 2176, 1977, 2435, 1922, 6445, 2697, 16, 2710, 21545, 3115, 3016, 2394, 2359, 15497, 16, 9821, 5489, 17, 3100, 7784, 16, 1930, 13416, 4755, 5628, 18, 2222, 16, 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, 19683, 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, 2435, 1922, 26747, 8478, 1019, 5755, 2009, 5360, 1930, 1977, 10633, 1956, 20709, 11569, 9117, 7864, 16, 15958, 17, 2743, 16, 1930, 9117, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "MNPTTRRTQQTAANSGASTTWWQSVHRTEQELSRVLFRRQQQYQQQGPRYGVLAASALSVAVLGYVGTTAYWQTKEQEEQEENARINTAQPHQFWPDATLLIAPPQVARMQSAMWAPTPNSTTTTADEAALARGRSTLWNMTSPDFAELETKYRVNWRRPLGEGAFGAVYLATNRSTGERVAVKKISQRFTNQAAFQNEMGALLEIQKAGGHPHINGMQDHFVQPPSQQQQQQNNHKSDYGYFYLVLDLISGGEMFDHLCHAGPYSEADAARLIREVASAMNFLHGIGIVHGDLKPENLMLSSKEAAKAVIKVVDFGCARSHVMEQAQAQAAQTAKQAQQSSTRSTLASWGFGGSWSRTPSDDKAIEDADDDVDDEEEEPFDYQTQGTANTPAYSPPEVLLLKRSDDIKKRNTPIEPSFDMWAVGVILYIMLTGVHPFDLYGNATDQEIEDAVLSGKKPPLGKSALTAHLSPDATNLIELLLEWNPQRRLTAHQLLDHPWVKGETARTQVIADSDKRLRAYRAYKTKLEAKAFADMISASADNAADAYYAAKQQATNTTGGGGGNGDVDVNKKMSLIEISFSRFDPDNKGFITAKELRKLVGNDDPNAASEIPNDERLSMSCFSDILAGNMKNKHFPKGHMIYKEGEIGNAMYFINSGSVEVFTKDGYRSTRHAGEFFGEGALLNPKKTRSASIRALTPIHVMEISRDYFEKYMSSDSDVKVKLREKDKARKRQRAKTLLQLHQNTKEKLYKKGDKLFQKGERTTDLFILSEGDVWLQAKGQDVISVDMGEICGEHSAVFGRPRNVDAVCKSDECKALVLHARDFQKLLSTQPHFKESIREICLRREFQKALCVDTGKPFPKDEKDLKAAFDFVASHSGNTEFIEFDGLKSLLHNFDPTYTEEDMLDILESLDLDETGRISWSEFKRIFGMDGGAAATKEKPRTSRDWRRKKWKR", "metadata": {"id": "A0A7S2YCT2", "cluster": 5687292, "interpro_all": ["IPR050205", "IPR018488", "IPR000595", "IPR018490", "IPR011992", "IPR018247", "IPR002048", "IPR011009", "IPR000719", "IPR017441", "IPR014710", "IPR008271"], "interpro_used": ["IPR018488", "IPR000719", "IPR017441"], "interpro_unused": ["IPR008271", "IPR002048", "IPR018490", "IPR050205", "IPR011009", "IPR018247", "IPR011992", "IPR000595", "IPR014710"]}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe 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. Furthermore, the protein is assigned to 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 belongs to the Beta-phosphoglucomutase-like family, which comprises enzymes belonging to the HAD-like hydrolase superfamily that metabolize phosphorylated carbohydrates. These proteins typically catalyze the interconversion of glucose phosphates or the dephosphorylation of various sugar phosphates, playing key roles in glycolysis and the pentose phosphate pathway. It is present in Alphaproteobacteria bacterium.\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, 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, 3677, 16, 1920, 2213, 1977, 6304, 1942, 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, 14440, 1942, 1920, 4666, 17, 8078, 22988, 1947, 26455, 4127, 17, 3189, 3416, 16, 2154, 12936, 5038, 10588, 1942, 1920, 2430, 17, 3189, 20748, 13975, 1988, 3074, 2606, 7199, 16282, 18, 2144, 2697, 5745, 18170, 1920, 8590, 12766, 2045, 2001, 1927, 3817, 26473, 2014, 1920, 16881, 1927, 3425, 9523, 26473, 16, 14797, 3834, 5456, 1922, 13393, 1930, 1920, 9412, 2217, 5413, 3374, 18, 2176, 1977, 2481, 1922, 4595, 9218, 1021, 10296, 14061, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MPRMTADLHPKAVIFDCDGVLLDSEYQVYDATAPPLIESVCNLIGVPVTPTMMQAYRERRRWQASGSPMERLQLTLKPTGFWNHFTPHIYSGFDQPNTLPEHCLVIEDSANGVKAGVAAGMTVWAVFETMPDIHAAIRTRLPHLLKEGALMHVLTPMGVHVEAEIANQFHGLENHLETIPHAQTLVESLAVPKAVGKPAPDVYLHAARQIGGFVGGKHCDDTHGDMLRDAGAV", "metadata": {"id": "A0A949XJ03", "cluster": 7626466, "interpro_all": ["IPR051600", "IPR036412", "IPR006439", "IPR041492", "IPR023214", "IPR023198"], "interpro_used": ["IPR023214", "IPR006439", "IPR051600"], "interpro_unused": ["IPR036412", "IPR041492", "IPR023198"]}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: The protein possesses a Cyanophage baseplate Pam3 plug gp18 domain that functions as a structural plug within the baseplate of cyanophages, where it assembles into a hexamer to fix the core helical bundle of the wedge onto the hub. Adopting an immunoglobulin-like fold, it embeds between the tube initiator helices to stabilize the assembly required for DNA injection. It has been detected in Caudoviricetes sp.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 14465, 43, 26898, 4151, 2106, 5170, 6722, 11888, 1010, 15998, 4882, 3928, 3418, 1988, 4088, 1966, 43, 4346, 15998, 2651, 1920, 5170, 6722, 1927, 26898, 4151, 2286, 16, 2597, 2176, 17421, 1036, 2460, 43, 25602, 1942, 4011, 1920, 4728, 11514, 14142, 1927, 1920, 22034, 6131, 1920, 13988, 18, 20478, 1925, 11837, 17, 3189, 3728, 16, 2176, 17746, 1036, 2192, 1920, 6723, 23467, 12789, 1942, 13448, 1920, 5957, 3414, 1958, 2678, 4107, 18, 2176, 2258, 2252, 3330, 1922, 10268, 14127, 2927, 14652, 2056, 18, 3], "output": "MQVIPISQIGAQTLNITLNNQVFQLRIMDKGSAGIFMPYRGFPGDLMFADQKGFTNPSFKGFNDRYVLYWLEPGEESIGLDVKNGTRNIALSVLCLDRRRLVNF", "metadata": {"id": "A0A6G5XWX4", "cluster": 8356577, "interpro_all": ["IPR054252"], "interpro_used": ["IPR054252"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein possesses 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 found in Clostridiaceae bacterium and is described by UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14465, 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, 2435, 1922, 17938, 14773, 1972, 3336, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 9117, 7864, 18, 3], "output": "MASKEYKFVKSLLFGDDSLSPEQAKTRMLVMYLFTGVITTIVNFIFFTAFNELVPFHYDVTLFKWEFDLFLLVNQTIAWLASVIVAYITNRAFVFVSNGNYIKEFFIFATARIVSFFLVELGTFSLFLLLLENVMKIPQETHLFYVFQIDITALYVIKLMNSVILVILNFVMSKIFVFKKNDNKAESIANSKMQEEYEEGSANE", "metadata": {"id": "A0A972A515", "cluster": 8939242, "interpro_all": ["IPR007267"], "interpro_used": ["IPR007267"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "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. In addition, the protein is a member of the CbbQ/NirQ/NorQ/GpvN family, which comprises ATPases that facilitate the assembly and activation of diverse macromolecular complexes, including gas vesicles for buoyancy and the carbon-fixing enzyme RuBisCO. These proteins also act as regulatory activators for nitrite and nitric oxide reductases involved in denitrification and assist in the formation of active methanol dehydrogenase. Furthermore, the protein has a ChlI/MoxR, AAA lid domain that forms an $\\alpha$-helical structure at the C-terminus of AAA domains to support ATP-dependent activities. It is present in magnesium-chelatase subunits, such as ChlI and ChlD, where it facilitates ATP-dependent activation and chelation steps. Additionally, this domain functions in MoxR proteins to assist in the chaperone-mediated assembly of enzymatic complexes. It is found in Salinirubellus salinus and contains UniProt keyword associations Plasmid.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 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, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 5529, 1014, 1055, 19, 12951, 1055, 19, 3990, 1055, 19, 4882, 1020, 1022, 3416, 16, 2154, 12936, 28132, 1988, 6628, 1920, 5957, 1930, 2936, 1927, 6445, 21815, 5048, 16, 2710, 4422, 8319, 1958, 3168, 3759, 3970, 1930, 1920, 5056, 17, 23871, 4113, 10010, 16409, 18, 2144, 2697, 2222, 4033, 1966, 4948, 15497, 1958, 15988, 1930, 10233, 7491, 11386, 1036, 3286, 1922, 26319, 3123, 1930, 6589, 1922, 1920, 3337, 1927, 3500, 8570, 9294, 18, 3677, 16, 1920, 2213, 2258, 43, 17906, 1033, 19, 2661, 10024, 16, 13835, 13096, 3418, 1988, 4952, 1925, 8, 38, 4595, 8, 17, 11514, 3170, 2019, 1920, 45, 17, 7822, 1927, 13835, 4682, 1942, 3373, 4498, 17, 3100, 4209, 18, 2176, 1977, 2481, 1922, 13148, 17, 11749, 7234, 6991, 16, 2427, 1966, 17906, 1033, 1930, 17906, 1007, 16, 2597, 2176, 11374, 4498, 17, 3100, 2936, 1930, 28526, 5983, 18, 4950, 16, 2052, 3418, 4088, 1922, 2661, 10024, 2697, 1942, 6589, 1922, 1920, 14044, 17, 3434, 5957, 1927, 8145, 5048, 18, 2176, 1977, 2435, 1922, 30128, 1996, 26166, 11560, 1957, 30128, 1957, 1930, 5461, 20709, 11121, 2538, 5253, 5609, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MSNDTSTSTTSSVLAPATLHERLQRAVGEAVVGQEAAKTTIATRVAAAAGLPAKRIQLTPDVLPADITGTQLYNEQEGAFEFRRGPVRAMPKAQAALLEAMEEGRVSVDGETHSLPSPFFVVATQNPLDVSAPSSDDALVDILTTADERERDDKRRRQASPYTLTPEAIHSARGLVNAPSPRALIGVQRAAKARAAIERRAYVIPEDIKRVAIDALCHRLTIELLGETLDATAVPTMVSAPASDTPLATDGGEVVTQLTTALLAGGHVLLEGAPGVFSNAVIADEINMAGTYPLPESQLDRFMFHLTAIHVSAPIKQYLVALMRSLETDSRAAAEQAPRGDTEAAR", "metadata": {"id": "A0A9E7UD33", "cluster": 9363876, "interpro_all": ["IPR003593", "IPR011703", "IPR050764", "IPR041628", "IPR027417"], "interpro_used": ["IPR003593", "IPR050764", "IPR041628"], "interpro_unused": ["IPR011703", "IPR027417"]}, "task_type": "infilling"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein possesses a AWS domain that is a cysteine-rich motif typically found associated with the SET domain in eukaryotic histone-lysine N-methyltransferases. It serves as a conserved component of transcriptional regulators involved in chromatin modification, such as Nsd1, although its specific molecular function remains uncharacterized. Also, the protein features a SETD2/Set2, SET domain that functions as a histone-lysine N-methyltransferase specifically targeting histone H3 at Lys-36 to regulate transcription elongation, DNA repair, and p53-mediated checkpoints. Beyond chromatin regulation, this domain mediates genomic stability during mitosis by methylating alpha-tubulin and contributes to antiviral defense through STAT1 methylation. In addition, the protein has a SET domain that functions as a protein methyltransferase, typically methylating lysine residues on histones to modulate chromatin structure and gene activity. This beta-rich domain forms a knot-like structure that binds S-adenosylmethionine (SAM) and contains a conserved tyrosine residue essential for catalysis. It originates from Kalanchoe fedtschenkoi (Lavender scallops) (South American air plant) and exhibits UniProt keyword tags Chromosome, Nucleus, and S-adenosyl-L-methionine.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 6727, 1036, 3418, 1988, 1977, 43, 8666, 17, 5536, 5219, 5745, 2435, 2458, 1956, 1920, 2735, 3418, 1922, 10825, 6632, 17, 9082, 56, 17, 28253, 18, 2176, 10634, 1966, 43, 5305, 4594, 1927, 5224, 9098, 3286, 1922, 6338, 6295, 16, 2427, 1966, 4246, 7240, 16, 2876, 2496, 2487, 3272, 2347, 4497, 24528, 18, 2222, 16, 1920, 2213, 4075, 43, 2735, 9091, 19, 2735, 1028, 16, 2735, 3418, 1988, 4088, 1966, 43, 6632, 17, 9082, 56, 17, 16478, 4475, 5133, 6632, 8170, 2019, 3629, 17, 3480, 1942, 5741, 3213, 9971, 16, 2678, 5059, 16, 1930, 5105, 17, 3434, 28799, 18, 6844, 6338, 3640, 16, 2052, 3418, 10412, 4935, 5057, 2409, 12611, 2007, 4963, 2287, 4595, 17, 9332, 1930, 7624, 1942, 10129, 9720, 2596, 15664, 5547, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 2735, 3418, 1988, 4088, 1966, 43, 2213, 16478, 16, 5745, 4963, 2287, 9082, 4248, 1990, 15808, 1942, 8480, 6338, 3170, 1930, 2359, 2455, 18, 2052, 4666, 17, 5536, 3418, 4952, 43, 26646, 17, 3189, 3170, 1988, 6876, 61, 17, 29283, 23568, 11215, 12, 2235, 13, 1930, 5461, 43, 5305, 6941, 6181, 4415, 1958, 15408, 18, 2176, 22970, 2037, 17338, 5584, 6802, 5788, 1973, 22132, 8323, 1033, 12, 21875, 18168, 7350, 6012, 2523, 13, 12, 6061, 5339, 4433, 4496, 13, 1930, 9826, 20709, 11121, 2538, 14392, 5597, 16, 5607, 16, 1930, 61, 17, 29283, 17, 54, 17, 12417, 18, 3], "output": "MVCHCKPPCDGGLGCGEECLNRMLNIECVRGTCPCGDHCSNQQFQERKYAKLKSFKSGKKGYGLCSEEDIGRGQFLIEYVGEVLDMPAYEARQKDYASKGHKHFYFMTLNGSEVIDACSKGNLGRFINHSCEPNCRTEKWMVNGEICIGLFAVRSIKKGEEVTFDYNYVRVFGAAAKKCDCGSSQCRGFIGGDPLNCEVVAHDSEEDDAEDLETVMIDTQSDTIDRTEIISTTKSANVDEIQDAAESSVRESVHIDAHGEIESSMDLSTSSVSLSRQIENANETMHLTRAPFTQHVEDMLSKYSSSSGIDTCMEEKVTNKASKSYKSESSSLTEGPGNSIYECIDANLKTYPDNVEVDQEPPRSSSTKKSAISSSSRKSTNSRFPKVMSKKSALIANKSKKFSDVSCRHEVVVEKLNELLDSGGGISKRKVQNFGIYNCFFYLASKKTKFFLTTVLNGYACLLCNSCT", "metadata": {"id": "A0A7N0TNE1", "cluster": 9693925, "interpro_all": ["IPR006560", "IPR003616", "IPR050777", "IPR001214", "IPR046341", "IPR044437"], "interpro_used": ["IPR006560", "IPR044437", "IPR001214"], "interpro_unused": ["IPR046341", "IPR050777", "IPR003616"]}, "task_type": "autoregressive"} {"instruction": "The protein possesses 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. Additionally, the protein should contain 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. Also, the protein falls within the Heme chaperone HemW-like family, which functions as a heme chaperone catalyzing the insertion of heme into hemoproteins. Members of this family, such as HemW, are closely related to the oxygen-independent coproporphyrinogen III oxidase HemN but lack specific N-terminal motifs and are often present in species that do not synthesize heme *de novo*. It is identified in Erysipelotrichia bacterium and contains UniProt keyword associations Cytoplasm, Metal-binding, and S-adenosyl-L-methionine. Design a protein sequence that will have the functional description above.", "tokenized_instruction": [2, 1920, 2213, 14465, 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, 4950, 16, 1920, 2213, 3066, 5531, 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, 2222, 16, 1920, 2213, 12182, 2651, 1920, 10954, 14044, 3243, 1018, 17, 3189, 3416, 16, 2154, 4088, 1966, 43, 10954, 14044, 29601, 1920, 7413, 1927, 10954, 2460, 3243, 14070, 18, 4678, 1927, 2052, 3416, 16, 2427, 1966, 3243, 1018, 16, 2032, 6538, 2712, 1942, 1920, 4612, 17, 3484, 3725, 17351, 11119, 30338, 5572, 2404, 4337, 10488, 3243, 1022, 2308, 3630, 2487, 56, 17, 4262, 8277, 1930, 2032, 3868, 2481, 1922, 3038, 1988, 2608, 2084, 15541, 10954, 14, 2028, 9441, 14, 18, 2176, 1977, 2899, 1922, 2668, 2012, 25535, 29168, 4698, 2126, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 5239, 16, 6048, 17, 2743, 16, 1930, 61, 17, 29283, 17, 54, 17, 12417, 18, 3036, 43, 2213, 3244, 1988, 2832, 2162, 1920, 3183, 8418, 3538, 18, 3], "output": "MKKLKPRCLKAKTKSQKTTNKINSLYIHIPFCEHLCHYCDFAKLFYDENLANKYLDVLFSEIDSYQIKKVKTIYIGGGTPSSLNISQLEKLLKKVTPFLSAGGEFSFELNVENITLEKLKLLKFYGVNRLSIGVQSTNLEILKSLNRQHSFVEVEKNYYLARELGFNNISLDLIYGTPKQNIEILEKDLENLLKLNPEHLSIYELSIHPNTVFYLNNIKPLDEDESRKQYNLILKILRNRGYKRYEIANFAKPNYQSKHNLTYWQNKNYYGVGLGAHGYIKNLRYQNTKSLTKYLKGEIIYEKEILSLEDEEKYFWITNLRLEEGFKIDEYISRYGKKRFQRRIDQLKQTGLFKYMIKSNNQVRLNDDGLMLLDYLLIEII", "metadata": {"id": "A0A970N2U8", "cluster": 9728311, "interpro_all": ["IPR013785", "IPR034505", "IPR006638", "IPR004559", "IPR007197"], "interpro_used": ["IPR006638", "IPR007197", "IPR004559"], "interpro_unused": ["IPR034505", "IPR013785"]}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein is classified under 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. In addition, the protein possesses 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. It is present in Deltaproteobacteria bacterium RIFCSPLOWO2_12_FULL_60_19 and exhibits UniProt keyword tags Cell inner membrane, Cell membrane, and Transmembrane helix.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 1977, 5947, 2441, 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, 1922, 2459, 16, 1920, 2213, 14465, 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, 2176, 1977, 2481, 1922, 9649, 9218, 1021, 10296, 14061, 12424, 2792, 2030, 1971, 5265, 41, 2369, 41, 4125, 41, 3276, 41, 2282, 1930, 9826, 20709, 11121, 2538, 14392, 2024, 6671, 3260, 16, 2024, 3260, 16, 1930, 9117, 7864, 18, 3], "output": "MTRFLNSQTLILIGCSLFVVYLAGITIQNYVKAYFDREFYLLFWNSLKFALGTPFKKLFMVMSLIPFIIPGILSTIAWILLLSFSIYSMGGMVWAEAIHLYPLVFLLMAGSSTFTTFRRVTLPLMRPAMFSVLLVGVPARISVFTTKIFLAIHQFPSDFGLAGAGVLFYQKITRREERYATVTGKGYRPRVIDLGPWKYVTCASASFIPYYGVPSMELLERVTLANYHYILLTSVIAWITVKSKVPGRAFLDNMTFIPIAMPGIVLGVAYLTKFMPYGIRAASASMIQINRELEEASFASGFVAGWIYISIIALRELSTSILLYSYSMVLLLVAMAFVARKFGAKIGIAEPLVMLLYGSIRSAPIGEPGAAYSCAISFLIGTYLAWINERTNPKIGLINLVVMGVFGLESAPAAFRNMDTSLEEAALTALIMFIRSIESFEVPAYAVTLLAISTAFFIFLLAVIFPVFILIWSNYPLAITAFKNSFILSVGSATLVMLSLIWVYLTLPIPIYGTMWVLLLGGTWLQTFTKVILPLLMPSTVLSIMAFDLWEGGQYTYVCALGVL", "metadata": {"id": "A0A1F9KBN0", "cluster": 10008032, "interpro_all": ["IPR000515", "IPR035906"], "interpro_used": ["IPR035906", "IPR000515"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\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. It is found in Massilimicrobiota timonensis.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 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, 1977, 2435, 1922, 3411, 5912, 4913, 15129, 3940, 3857, 2267, 2290, 3355, 1937, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MDYHKHNSAHLGARKLEIENVKLMLPYHQHLKELYYEKYDNFISILGDRGLGKTSIMLTIIDEIKLLVPDDMSDNSDILGWIIVTLENMFYRIENIRDYIDSFRNSAKNSYMNSRHYFCDKGEAQDQVIDLIAP", "metadata": {"id": "A0A1Y4SVU9", "cluster": 10753778, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate a protein sequence that will be able to perform the following function: The protein possesses a YDG domain that is found in a wide variety of bacterial cell surface proteins. This presumed domain contains a highly conserved YDG motif near the N-terminus and is likely related to the MBG domain. It is found in Clostridia bacterium and is described by UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 67, 18641, 3418, 1988, 1977, 2435, 1922, 43, 4743, 5386, 1927, 4543, 2024, 3154, 2697, 18, 2052, 15326, 3418, 5461, 43, 3626, 5305, 67, 18641, 5219, 4931, 1920, 56, 17, 7822, 1930, 1977, 3205, 2712, 1942, 1920, 5667, 1029, 3418, 18, 2176, 1977, 2435, 1922, 17938, 14773, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MDISKAVLSIHSAVVGNKVYDGTTAAVISDVVLNGLIPGESLEAGVDYTVSGLFGNANAGNDIPVTVSVTPTTTEKAANYAVSGTGSFMANITKKALVISGVSATNRAYDGTSAVVLAGGALGGVAATDTGSVSFSLGVGAMADAKAGSGKPVSTNIVLTGAKAANYSLTQPAGITVDISKAALSIHGADIANKVYNGTTAATVSNLTFSGLASGESLEAGVDYTVSSLFDSANAGNNIPVTVSVTLATTEKATNYAVSGTGSFMADITPRGLTGGVVVDVDNTTGQAALVDEGDMLRANTSGVSVPGTLTVSYQWYRNGATIAGATLASYTVGNLSADPAGTSFTVKVTGTGNYMGTLESAAKVVSQLPLAGSISITGSTAVGNTLSLDASLLTPAAATYDIIWMRGDVPIGGATGVDYTIVREDVGKTLSVVITATGNYTGTKRASLRISAGGISGSSPYVPAYAILNQTGRATVDLTAGSTLVSAEQFSQLMALNADKPVVMRGRGYNITFPQGSMRSIGGYSGDLNFGISFNMGAHYAAIKSAAGDDFILMLQFIHSGPLPGTAQVSIYVGTQYAGQSLQYLYYNPQAGKLEPMQTATVDTNGYITVTQDHCSSYAVTFYGPIDIPKTGDSEPGIWGWLIAGISAWGMIAILTSWGPKRKHPGRTF", "metadata": {"id": "A0A965UB23", "cluster": 11238141, "interpro_all": ["IPR041248"], "interpro_used": ["IPR041248"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein should feature 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. Furthermore, the protein belongs to the Histone lysine demethylase/ribosomal histidine hydroxylase NO66-like family, which comprises bifunctional JmjC domain-containing metalloenzymes that regulate chromatin remodeling and ribosome biogenesis. These proteins utilize Fe(II) and alpha-ketoglutarate cofactors to catalyze the oxidative demethylation of specific histone H3 lysine residues and the hydroxylation of ribosomal proteins, such as L27a and L16. It is derived from Acropora cervicornis (Staghorn coral) and contains UniProt keyword associations Nucleus, Metal-binding, and Iron.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 3066, 5961, 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, 3677, 16, 1920, 2213, 14440, 1942, 1920, 6632, 9082, 21732, 2051, 19, 11196, 13873, 16324, 2239, 7283, 17, 3189, 3416, 16, 2154, 12936, 29491, 16097, 30271, 3418, 17, 3165, 8969, 6802, 1022, 16367, 1988, 5741, 6338, 8378, 1930, 12794, 13008, 18, 2144, 2697, 12561, 2650, 12, 2890, 13, 1930, 4595, 17, 21471, 16542, 17488, 21362, 1942, 18170, 1920, 5163, 20254, 1927, 2487, 6632, 8170, 9082, 4248, 1930, 1920, 21319, 1927, 11196, 2697, 16, 2427, 1966, 12051, 13827, 1930, 7554, 1016, 18, 2176, 1977, 3595, 2037, 10428, 7540, 5524, 6545, 5670, 1005, 11110, 12, 23891, 2509, 5578, 17358, 13, 1930, 5461, 20709, 11121, 2538, 5253, 5607, 16, 6048, 17, 2743, 16, 1930, 5680, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MKRKNRAPSTSATSPDGKKKKMGHENAGESSSLEAFFNEHWEKKPLFVKRGNADFYGSLFSKKDLESVLKKEEAEGKTELLNESGRVNLKHIKAAGVSVQFHTCLVGADAFVFEPGSQGLAPQFDELETFILQEASPDLELSDIGEASHEFDMEPGDLLQENSWGNMMTSALSRAIEKAMESDVEYRKGLPVNISSFMGTKVKPSNNPRTAFTDGLDKLLKGLVHHLNPDKAVDEPRKGKKKAVAPFDDNKIRLSHPDHVRVLIGDLSDGVPAEEETEESEESEKNDNKKDKKNDKKKTEGEDEDGGSDKESDAFDNGEAGDEYMLVLHSVKNKRASHMMRDKFVMVSSLKLPEKERLSLVKSLWDHGLLEIMDTTKSIDFSSPQRVLESLLSLDSILFIEDMSLLRYQPDRFKDEVWKLLESLETYFLEGKTKWKLFKPLQELPQYYPRGIVFFPTPIDEKEHTLYLAITTFGIKETEETEGQHMNEEEAESIMRDFFAGRLPPFKKYYESDEDMSEAEEEDDDEKGSGKDKAKTKEKPAKETKGKNKKDQDCEEEMGDPSPCSTLQFPFRYKDALQQITAD", "metadata": {"id": "A0AAD9VED6", "cluster": 13476004, "interpro_all": ["IPR003347", "IPR039994"], "interpro_used": ["IPR003347", "IPR039994"], "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 has a Two component regulator propeller repeat that typically comprises 14 tandem repeats located at the N-terminus of two-component regulator proteins. These repeats are predicted to fold into two $\\beta$-propeller structures that may function in recruiting other proteins or interacting with DNA. Also, 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 should contain a PorZ, N-terminal beta-propeller domain that functions as an essential component of the type-IX secretion system (T9SS) machinery. Predominantly found in Bacteroidetes such as *Porphyromonas gingivalis*, this N-terminal region adopts a seven-stranded \u03b2-propeller fold. It is present in Bacteroidales bacterium.", "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, 2258, 43, 2288, 4594, 7888, 5062, 13728, 6865, 1988, 5745, 12936, 2607, 10361, 9569, 4810, 2019, 1920, 56, 17, 7822, 1927, 2288, 17, 4594, 7888, 2697, 18, 2144, 9569, 2032, 4396, 1942, 3728, 2460, 2288, 8, 38, 4666, 8, 17, 5062, 13728, 4061, 1988, 2278, 2347, 1922, 17040, 2303, 2697, 2014, 8615, 1956, 2678, 18, 2222, 16, 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, 3066, 5531, 43, 4572, 1011, 16, 56, 17, 4262, 4666, 17, 5062, 13728, 3418, 1988, 4088, 1966, 1925, 4415, 4594, 1927, 1920, 2601, 17, 13848, 5512, 2433, 12, 62, 1026, 5590, 13, 10853, 18, 7700, 2435, 1922, 26808, 2427, 1966, 14, 17376, 5134, 3947, 1934, 22118, 14, 16, 2052, 56, 17, 4262, 3031, 24032, 43, 5260, 17, 10338, 161, 17, 5062, 13728, 3728, 18, 2176, 1977, 2481, 1922, 24323, 3955, 14061, 18, 3], "output": "MVKRIYILLSFIFVGICKVHTQPAIGQWRDYYAFNDATVSGLSEVDITALSAIPQKQITLVGYKSGNIDLVYENTKRVVSLPFIKDKSLVYVSTDFGLVVIDPDRLEVKDTYFIVENAGTLKVNRLVAWISYERWSREQFFTDPAAECRGVTADETHLLALEKVGGNDILWMNSGSGFSSNAIQKYSLQGEKLELVSSYLFGGTPKVADCIPLENNALAVADNKFFHIDASANMVVAASGAYDAAFGNFWNPFIAHTFSDGRWSYYADWFFVASWGGGLYKLNSGTLAEHYNPDNSTLQSVFPGQPYCRIAGMDIDPKFPYYSAIGTSRIISLTVSPSGIIWLALARDNGLFAFRPRDANGNLFSNEVTALAFDRDGYLWLGTNQGVLVSYNPHRVLQGVYLLETEEVTCIDVDGGNRKWFGTAKSGVYLFSADGTKQIHHFNTKNSPLYRSNASEPANTFDKVYAFPNPVRPNYSGVITIAGLMDNSVVKDGKNRNGQRVATGVYLIFCSDSKGEQAAVTKLLFVKRELSISGSKLYCAVANGYFTYDTENGELNKYTPMLGSKCINHFYYFSNGKFWAATSQGVYSASTNDPLLWVEVDRPFDETLGVSIGFQKIAAEFNGLVIISPTDHSVHTPTGPFSFNHDAVRVKADPRNPNVGNLWVANSEVPNPISVLTAHGVWKSLSPGNDVEASSDDIYLKETSFQKIKIPDVVEGLAPSNTILSIKAHPVTGEVFIATDKGLIAITDIAGNIVYETRSNGGLATW", "metadata": {"id": "A0A9E0A4J7", "cluster": 13756324, "interpro_all": ["IPR048954", "IPR011110", "IPR015943"], "interpro_used": ["IPR011110", "IPR015943", "IPR048954"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "To achieve this function:\nThe protein is categorized in the Protein of unknown function DUF4330 family, which comprises functionally uncharacterised proteins containing a single completely conserved glycine residue. Some members are annotated as the dihydrolipoamide dehydrogenase (E3) component of the Pyruvate/2-oxoglutarate dehydrogenase complex. It is found in Salinirubellus salinus and is annotated with UniProt keywords 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, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 10432, 6498, 1008, 3416, 16, 2154, 12936, 9346, 23229, 3495, 2697, 3165, 43, 2957, 5796, 5305, 10646, 6181, 18, 2673, 4678, 2032, 10633, 1966, 1920, 11842, 8257, 6952, 16408, 1021, 9294, 12, 10968, 13, 4594, 1927, 1920, 11867, 19, 22, 17, 18588, 16542, 17488, 9294, 2796, 18, 2176, 1977, 2435, 1922, 30128, 1996, 26166, 11560, 1957, 30128, 1957, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4663, 3835, 4576, 4902, 1998, 5396, 1922, 1920, 17476, 11349, 35, 3], "output": "MQLLDDDGRLFGIVNVVDALAVLLFVSLLVAGVAVVGGFGSESAQQLSVGDRSSAGPQAGNVTVTDLSVSGASEPGTATVYARVEIEGALETNGTVVSLDAGGETLNTSTTPVRVETTVPADVAMAVKEVAPTADPSRYRLSLALDIETARVEGSDQFAGRTVSIGETTAVRIETTVQNSVAASVSVGDTYRVNGGSVGRVVDVRAYPTPDRRFGGQTLSLGQSIPFRTTSYDVTGTVVGLGSSVPPGEAAELDAGTAERLGNRTLATVTEVERANATVVLESESGEIFARNHTDNGLRFHARPLTVGRTVTFDLGTVRVTGNVTSIEREPATRYATVELGEQPVYVAEREDGPGQRFTYADRPLPVGSTLAITGAEYGDAYRIDGQALATITDVRTTVPFRTASYNLTGSIVAVGDTGLTTDSRRFLSLGLELETVVRNGETTTTVTVDLESVDPAVAPVLEDVTLTLDLTTRR", "metadata": {"id": "A0A9E7QZ70", "cluster": 14157605, "interpro_all": ["IPR025480"], "interpro_used": ["IPR025480"], "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 categorized in the SIS family GmhA and DiaA subfamilies, which comprise proteins with distinct roles in bacterial envelope biogenesis and replication initiation. GmhA catalyzes the isomerization of sedoheptulose 7-phosphate to produce precursors for lipopolysaccharides essential to Gram-negative outer membranes, while DiaA regulates chromosomal replication by interacting with the DnaA initiator protein. Furthermore, the protein can be placed in the SIS domain superfamily, which functions as a phosphosugar-binding module involved in phosphosugar isomerization or transcriptional regulation. Structurally defined by a three-layer $\\alpha$-$\\beta$-$\\alpha$ sandwich fold, it serves either a catalytic role in enzymes or binds phosphorylated sugar substrates to modulate gene expression in transcriptional regulators. It is found in Desulfuromonadales bacterium C00003093.", "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, 10234, 1922, 1920, 19149, 3416, 5711, 2722, 1930, 25141, 1019, 24167, 16, 2154, 13817, 2697, 1956, 4493, 5456, 1922, 4543, 11262, 13008, 1930, 5158, 6035, 18, 5711, 2722, 17097, 1920, 27027, 1927, 6276, 28600, 1031, 8658, 27, 17, 5413, 1942, 5074, 10416, 1958, 15614, 1036, 4415, 1942, 8604, 17, 3136, 7642, 5726, 16, 2679, 25141, 1019, 7014, 9220, 5158, 2007, 8615, 1956, 1920, 2678, 1019, 23467, 2213, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 19149, 3418, 13975, 16, 2154, 4088, 1966, 43, 8078, 20490, 13279, 17, 2743, 9059, 3286, 1922, 8078, 20490, 13279, 27027, 2014, 5224, 3640, 18, 12171, 3608, 2007, 43, 2559, 17, 4757, 8, 38, 4595, 8, 17, 8, 38, 4666, 8, 17, 8, 38, 4595, 8, 18038, 3728, 16, 2176, 10634, 3108, 43, 6804, 2770, 1922, 5038, 2014, 6876, 7199, 9523, 6249, 1942, 8480, 2359, 2294, 1922, 5224, 9098, 18, 2176, 1977, 2435, 1922, 30311, 18916, 3947, 7324, 2612, 14061, 24948, 6787, 26494, 1010, 18, 3], "output": "MNQRITATCSQIQDLLAMFAGGGQLLIAAGAAFQPPAVTLGSDQMLLTAMMNAGPSNALQLLRDEVMENEQPVALLTVAREQEGQLLCELVESELFGVGEFCRQQNAELTRLATQMGVAQLLSGHFTYRLGFDRPVLQFDQRLVRHYRSLGSARHLLLILNDGSPLCRDGIDICLELGTDSVPRQLELALIA", "metadata": {"id": "A0A1E7ID43", "cluster": 14313456, "interpro_all": ["IPR046348", "IPR050099"], "interpro_used": ["IPR050099", "IPR046348"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is assigned to the Conserved hypothetical protein CHP02574, addiction module family, which likely functions as a component of a bacterial toxin-antitoxin system involved in programmed cell death. These short proteins are typically encoded on the main chromosome in pairs with plasmid stabilisation proteins, forming a functional module composed of a stable toxin and an unstable antitoxin. It is produced by Terriglobia bacterium. The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 6304, 1942, 1920, 5305, 15148, 2213, 2016, 1034, 11636, 5071, 1006, 16, 12067, 9059, 3416, 16, 2154, 3205, 4088, 1966, 43, 4594, 1927, 43, 4543, 9165, 17, 10310, 9754, 2433, 3286, 1922, 13839, 2024, 3539, 18, 2144, 3662, 2697, 2032, 5745, 7905, 1990, 1920, 2730, 5597, 1922, 5803, 1956, 5609, 5722, 6284, 2697, 16, 7402, 43, 3183, 9059, 7179, 1927, 43, 4700, 9165, 1930, 1925, 11976, 10310, 9754, 18, 2176, 1977, 4152, 2007, 11420, 17780, 18311, 14061, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MRYLRLRTESSSTIYERSVIRLTIAGPPRGSPLTNAQRDELDRRLDELDREGPTGIPWEEVFRNIRSRR", "metadata": {"id": "A0A953S1E9", "cluster": 15103177, "interpro_all": ["IPR013406"], "interpro_used": ["IPR013406"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein has a Peptidase S8/S53 domain that functions as a serine endopeptidase utilizing a characteristic Asp-His-Ser catalytic triad found in subtilisin and sedolisin families. This domain is widely distributed across all domains of life and includes the kexin subfamily, which specializes in processing proproteins by cleaving C-terminally to paired basic amino acids. Furthermore, the protein should feature a Peptidase S8 subtilisin serine active site that functions as the catalytic center for subtilase-type serine proteases, mediating peptide bond hydrolysis via a conserved Asp-His-Ser triad. This active site utilizes a charge relay system similar to, but evolved independently from, the trypsin family. In addition, the protein is associated with the The subtilisin-like serine protease family, which comprises peptidase S8 enzymes that catalyze the proteolytic cleavage of various substrates, typically preferring hydrophobic or small residues with a P4 arginine or lysine. These proteases regulate diverse biological processes ranging from cholesterol homeostasis and lysosome biogenesis to pathogenicity and transcription factor activation via regulated intramembrane proteolysis. It is identified in Theionarchaea archaeon (strain DG-70-1) and is connected to UniProt keyword Hydrolase.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 2258, 43, 24050, 13808, 19, 8357, 1010, 3418, 1988, 4088, 1966, 43, 8468, 16239, 9626, 2410, 9200, 10232, 43, 6293, 4138, 17, 4167, 17, 2375, 6804, 21845, 2435, 1922, 14745, 1921, 1930, 6276, 23747, 1921, 5767, 18, 2052, 3418, 1977, 5673, 6533, 3436, 2136, 4682, 1927, 3308, 1930, 5921, 1920, 3364, 10960, 16227, 16, 2154, 5180, 4517, 1922, 4587, 12031, 7229, 2925, 2007, 28634, 45, 17, 18328, 1942, 7304, 5937, 3835, 4576, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 24050, 13808, 14745, 1921, 8468, 3500, 3200, 1988, 4088, 1966, 1920, 6804, 4102, 1958, 14444, 2051, 17, 2601, 8468, 12447, 16, 10239, 4207, 5403, 9128, 3454, 43, 5305, 4138, 17, 4167, 17, 2375, 21845, 18, 2052, 3500, 3200, 18127, 43, 7051, 22092, 2433, 2551, 1942, 16, 2308, 10764, 6407, 2037, 16, 1920, 9527, 3416, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 1920, 14745, 1921, 17, 3189, 8468, 7154, 3416, 16, 2154, 12936, 24050, 13808, 5038, 1988, 18170, 1920, 12712, 6404, 1927, 3425, 6249, 16, 5745, 4458, 8641, 7919, 2014, 2858, 4248, 1956, 43, 9068, 9732, 2014, 9082, 18, 2144, 12447, 5741, 6445, 3933, 4028, 6485, 2037, 5463, 7622, 1930, 19171, 13008, 1942, 15903, 1930, 3213, 2991, 2936, 3454, 4335, 9857, 8591, 15439, 18, 2176, 1977, 2899, 1922, 1920, 2001, 3983, 24145, 13470, 1916, 12, 3943, 9665, 17, 3895, 17, 21, 13, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 20748, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MKKGFSLVLIGVLVLSFYVPVAAPEGEMVSLIFEGESVNMLAAQVPLATLGIVLASPHITEVFKDAREVMDISGSVMDAYTLEELGDLPDNYYNYMVLVAIIDTGVYPLHPCLYPRVIGGISFAPGEPIVASNCAVLLPETDLWAIAIMNYAPPESWFTDPIKVFPKDGSGVPSSVVMEGLDHAIQQRKLGGTGFDGWDPEDRLVDKATLTGIVVSAAAGNPVHTRVGMDIVYGIPGIGGDMFPYDDQQIIYFSSRGPTTSAYPPNSIAIMSGTSSACPAVSGAALLLAAWQKTNLPNYDKYAQGEGYLNVPNALQKLKDGVCWWGGSKTWSTGPLGPGETYDIVIKVDKDTARIEFYVQSSVRTAYSYYYDSVNIYEDDCFSITDPDPGRQLCPIEASGCINNGEWKEHYIWSKYPTHDLDMYVFDPNGYAYLDGAQYYSPEREMYLIPNPYWLRVCEIVNDKVAMRNVIEGAGGIVTIEYEMRYLPYPPRADGEDSDIFETGAQEVWGETGAGSGQEDSWGDADNHYHGTVCAGAYPGYIIVPLLGMAPLAEIYAYNCTGGAEGLPIDVISMSLGDGPALNTVSTPGCAKTSIGVGAAADDCRRKPDVLACGVYAMQGFAKPSEIRNAIIQGAVPPDMGYGRCLRGTNLRIDICLSNVTYLNPGNQNPWLGDSGKIRIVVEGDWTNWDEMLCDVTVTETEDVSPGTAVVIFELWWFNDQIIENPVPGTYTILIFGY", "metadata": {"id": "A0A151F0B9", "cluster": 16310180, "interpro_all": ["IPR000209", "IPR036852", "IPR023827", "IPR023828", "IPR050131", "IPR015500"], "interpro_used": ["IPR000209", "IPR023828", "IPR050131"], "interpro_unused": ["IPR015500", "IPR023827", "IPR036852"]}, "task_type": "infilling"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein should contain a Peptidase M14, carboxypeptidase A domain that functions as a zinc-dependent metallopeptidase to hydrolyze C-terminal amino acids from diverse substrates, including digestive proteins and cytosolic tubulin. These enzymes are typically expressed as inactive zymogens with a globular propeptide that shields the catalytic site, which coordinates the metal ion using conserved histidine and glutamate residues. Also, the protein is categorized in the Cytosolic carboxypeptidase family, which includes metallocarboxypeptidases that catalyze the deglutamylation of tubulin and other target proteins by removing polyglutamate side chains from their C-terminal tails. This modification regulates microtubule integrity and kinesin motor transport, while also influencing antiviral defense responses and cell pluripotency. It is derived from Symbiodinium necroappetens.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 3066, 5531, 43, 24050, 8510, 1006, 16, 15750, 9626, 2410, 9200, 43, 3418, 1988, 4088, 1966, 43, 7997, 17, 3100, 8969, 24897, 1942, 7222, 6931, 45, 17, 4262, 3835, 4576, 2037, 6445, 6249, 16, 2710, 15486, 2697, 1930, 9410, 9332, 18, 2144, 5038, 2032, 5745, 3198, 1966, 9078, 15856, 6847, 1956, 43, 20975, 5062, 8253, 1988, 19397, 1036, 1920, 6804, 3200, 16, 2154, 10675, 1920, 6048, 4755, 2193, 5305, 13873, 1930, 7627, 4248, 18, 2222, 16, 1920, 2213, 1977, 10234, 1922, 1920, 9410, 15750, 9626, 2410, 9200, 3416, 16, 2154, 5921, 8969, 22780, 7221, 9626, 2410, 30413, 1988, 18170, 1920, 3744, 26697, 27302, 1943, 1927, 9332, 1930, 2303, 2758, 2697, 2007, 11340, 16115, 26697, 21084, 4159, 7835, 2037, 2310, 45, 17, 4262, 18103, 18, 2052, 6295, 7014, 10544, 7996, 1930, 19378, 4842, 4860, 16, 2679, 2222, 11623, 10129, 9720, 3387, 1930, 2024, 18962, 18, 2176, 1977, 3595, 2037, 17246, 25435, 2457, 10341, 3444, 11555, 3355, 18, 3], "output": "MQMLSDLARWPVEPEACIVARAHPGETHASWVMRGVMEFLMGDPMAGRTRTNLDAVDLNRHHHDDSAPETKGLKSALQSRRRGIFAIANASDGDRLVSLMASRTHLLDAAGTSRSEIRAQDAVEVGGEHLLLQAGQEKLCTPFSRLALTAAGKEVLALRLGNQSAQHRVEAQSCLAQLAWLLVPMLNPDGVAEAQEGELLAFIDIHSHGVGRVAAASQGYKYSLTIESSLCARH", "metadata": {"id": "A0A812IYI6", "cluster": 17036769, "interpro_all": ["IPR050821", "IPR000834"], "interpro_used": ["IPR000834", "IPR050821"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein is associated with the Putative surface bspA-like protein family, which is implicated in interactions with host tissues and likely plays a role in adherence or invasion processes during the infection cycle. These proteins potentially function by binding to host cell surfaces or extracellular matrix components. Also, the protein is grouped 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. Furthermore, the protein should have a BspA-type LRR region repeat that forms an \u03b1/\u03b2 horseshoe fold to facilitate protein-protein interactions. This motif is notably present in BspA-like surface antigens of *Trichomonas vaginalis*. It is derived from Candidatus Methanomethylophilaceae archaeon.\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, 6770, 3154, 28915, 1019, 17, 3189, 2213, 3416, 16, 2154, 1977, 6835, 1922, 3719, 1956, 4423, 3878, 1930, 3205, 5705, 43, 2770, 1922, 7015, 2014, 6254, 4028, 2409, 1920, 2909, 4048, 18, 2144, 2697, 5063, 2347, 2007, 2743, 1942, 4423, 2024, 7553, 2014, 5329, 4526, 4178, 18, 2222, 16, 1920, 2213, 1977, 10809, 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, 3677, 16, 1920, 2213, 3066, 2162, 43, 28915, 1019, 17, 2601, 13947, 3031, 6865, 1988, 4952, 1925, 160, 19, 161, 15638, 10647, 1021, 3728, 1942, 6628, 2213, 17, 2213, 3719, 18, 2052, 5219, 1977, 7388, 2481, 1922, 28915, 1019, 17, 3189, 3154, 7769, 1927, 14, 10477, 10480, 10120, 1937, 14, 18, 2176, 1977, 3595, 2037, 14550, 1031, 1957, 17348, 18403, 7766, 1972, 3336, 13470, 1916, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "YDNGEAVLSSAAGAVAFVIMLVIPTVYWKATSTNLYLSSSPSYAATGADGVESVYPYIAIGVYEASVSDGRMLSYADALTPAPGSDYQQWNFYQWTLYKMMANSSASETGLADSAGPYADSTSSYSKLFIECFCNRVLYAGNALGGQTISDHHHPKSAFWDLPKSDGGIVFGFSEPGDQVWSNIGWMLHTNIGSRLAYVMAADAVAVTFEESGLRYRTMSGCGGHEFGVVSVGYKAFYGCSAIESVDLGSVKVVSVSKVGPYAFYGCEALKSLEMPGEGVLVCSGAFGMCFYGCRSLASLDLSGVSKIGAKAFPYCDGLTEIASVVIEDGVSSLGRSAFSECKAITSLEVGSAGGEAIEPTADSLRGHVFTGSSMVLDMVSLDPYDLSKTLNGTTFEGTYNGSSTVSGMKAYAHTAVSGATPKADATNNQFKSYTVMGTKNSQSMLGLGPVYNSWGSMGEFVGDAVARAILPSSGWTGAAYSNCSLRVGGFWAIGPSAGVSCLDGCDSLIDAVSLVGYTGSPVNLSVPSTVTGTKAFANCASLASLTIPGTGLESASFTGSGAAIGTKAISGTVSSVGEYAFYGCASLAGLTDVGPNAFYRLAFRD", "metadata": {"id": "A0A8T4FNS5", "cluster": 21088627, "interpro_all": ["IPR026906", "IPR032675", "IPR053139"], "interpro_used": ["IPR053139", "IPR032675", "IPR026906"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein is classified under the L-Aspartase-like superfamily, which comprises enzymes such as L-aspartate ammonia-lyase, class II fumarases, and argininosuccinate lyases that catalyze the reversible deamination of L-aspartic acid or related substrates to produce fumaric acid. These proteins typically assemble into functionally active tetramers with active sites located in clefts between subunits, utilizing a carbanion mechanism. Additionally, they often feature a separate regulatory site where the substrate acts as an activator in the presence of a divalent metal ion. Moreover, the protein is a member of the Phenylalanine ammonia-lyase family, which catalyses the non-oxidative deamination of L-phenylalanine to trans-cinnamic acid, a crucial step in phenylpropanoid biosynthesis. These enzymes utilize a 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) cofactor formed from a post-translationally cyclised Ala-Ser-Gly triad and share a common structural fold with histidine ammonia lyases. In plants and fungi, members often contain a C-terminal multi-helix domain that may regulate enzymatic stability and metabolic response. Additionally, the protein should feature a Phenylalanine/histidine ammonia-lyase active site that catalyzes the elimination of ammonia from L-phenylalanine or L-histidine to produce trans-cinnamate or urocanic acid. This catalytic center relies on a conserved Ala-Ser-Gly triad that undergoes post-translational cyclization to form an essential electrophilic dehydro-alanine (DHA) residue. It is derived from Apiospora kogelbergensis.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 5947, 2441, 1920, 54, 17, 12053, 2051, 17, 3189, 13975, 16, 2154, 12936, 5038, 2427, 1966, 54, 17, 12878, 14880, 17, 23928, 16, 2921, 2890, 13203, 9041, 4127, 1036, 16, 1930, 8918, 11096, 27186, 2010, 23928, 1036, 1988, 18170, 1920, 10743, 30097, 8547, 1943, 1927, 54, 17, 23047, 2687, 2014, 2712, 6249, 1942, 5074, 13203, 28867, 2687, 18, 2144, 2697, 5745, 17421, 2460, 9346, 3500, 26568, 1956, 3500, 3402, 4810, 1922, 14649, 1036, 2192, 6991, 16, 10232, 43, 3697, 8150, 1916, 2856, 18, 4950, 16, 2611, 3868, 5961, 43, 5850, 4948, 3200, 2597, 1920, 4510, 8016, 1966, 1925, 9518, 1922, 1920, 2990, 1927, 43, 21610, 6048, 4755, 18, 3950, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 17388, 14880, 17, 23928, 3416, 16, 2154, 13928, 1918, 1920, 2447, 17, 5163, 30097, 8547, 1943, 1927, 54, 17, 17388, 1942, 2127, 17, 23765, 1935, 2687, 16, 43, 6608, 3537, 1922, 7971, 20194, 9286, 1960, 8132, 18, 2144, 5038, 12561, 43, 23, 16, 25, 17, 11842, 17, 25, 17, 4963, 18574, 17, 13380, 17, 20697, 10457, 17, 24, 17, 2340, 12, 6519, 1037, 13, 15155, 5333, 2037, 43, 2753, 17, 8414, 1954, 3637, 3495, 10527, 17, 2375, 17, 3376, 21845, 1930, 7948, 43, 3059, 4346, 3728, 1956, 13873, 14880, 23928, 1036, 18, 1922, 4793, 1930, 10520, 16, 4678, 3868, 5531, 43, 45, 17, 4262, 2779, 17, 7864, 3418, 1988, 2278, 5741, 8145, 5057, 1930, 4487, 2644, 18, 4950, 16, 1920, 2213, 3066, 5961, 43, 17388, 19, 13873, 14880, 17, 23928, 3500, 3200, 1988, 17097, 1920, 9570, 1927, 14880, 2037, 54, 17, 17388, 2014, 54, 17, 13873, 1942, 5074, 2127, 17, 23765, 2010, 2014, 14984, 8337, 1935, 2687, 18, 2052, 6804, 4102, 12850, 1990, 43, 5305, 10527, 17, 2375, 17, 3376, 21845, 1988, 14928, 2753, 17, 8414, 25267, 1942, 2386, 1925, 4415, 6105, 10029, 28936, 17, 10504, 12, 13440, 13, 6181, 18, 2176, 1977, 3595, 2037, 20655, 9890, 1019, 6235, 20178, 7519, 8134, 18, 3], "output": "MSQLFPVVSFSELLVAQQERIASSINNVFVDSQTLTVADVVAVSRYLSQVTVTDEAAQAIQECSNIVQEKLAQGEVIYGVNTGFGGSADQRTDAVDRLQQRLFTLLMAGITSDSETDPMVCSSISPTTCMPEAWVRASMLVRLNSLAAGASGVRIQITDRLAAMLNHDIVPLVPLRGSISASGDLGPLSYVGGVLQGKKYVSAYFGPREGGVDGQKPRKLMRADKALEQAQLPPLGVQAKEGLAIVNGTAFSAGVAALAAYECSCLAALSQVLTAMTVEALCGTDESFDPFVAGVRPHPGQVDSAHNMFRFLRGSRLVNSADFLASGTLRQDRYAVRTASQWIGPVIEDFQLAYAQISTELNSVTDNPLIDRHGHGGKGRIVHGGNFQAKAITSAVEKLRQGLQSLGRMLFSQCTELINPSTNRGLPPNLVADDPATSFLFKGTDIMAAALTSELGFLANPVGSHVQTAEMGNQGINSLALISARYTLKAVDVFSQLAAAHLVAVCQAVDLRVRSHALAAPGTTLAEAGSTTPNASPFLGMAGKRVYDFVRGELKVPPHHRGSRVRR", "metadata": {"id": "A0AAW0QEE8", "cluster": 21228790, "interpro_all": ["IPR001106", "IPR024083", "IPR008948", "IPR022313", "IPR005922"], "interpro_used": ["IPR008948", "IPR005922", "IPR022313"], "interpro_unused": ["IPR001106", "IPR024083"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein features a Tc1-like transposase, DDE domain that serves as the catalytic core responsible for transposon mobilization. Adopting an RNase H-like fold with a characteristic DDE motif of acidic residues, it acts as an endonuclease to nick the 5'-end of the transposon DNA. Furthermore, the protein is a member of the Oligosaccharyl transferase complex subunit OST3/OST6 family, which comprises alternative integral membrane subunits of the oligosaccharyl transferase (OST) complex in the endoplasmic reticulum. These proteins are essential for recruiting the fully active complex responsible for transferring oligosaccharides from dolichyl pyrophosphate to asparagine residues on nascent polypeptides. Consequently, they play a critical role in ensuring efficient N-linked glycosylation of soluble and membrane-bound proteins. In addition, the protein is associated with the Ribonuclease H superfamily, which comprises the catalytic domains of diverse polynucleotidyl transferases characterized by a conserved 3-layer $\\alpha/\\beta/\\alpha$ fold. This superfamily includes enzymes such as RNase H, retroviral integrases, transposases, and exonucleases that utilize this domain to catalyze nucleic acid backbone cleavage or transfer during DNA replication, repair, and recombination. It originates from Hemibagrus guttatus and is associated with UniProt keywords Disulfide bond, Magnesium, and Transposable element.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 4075, 43, 5283, 1009, 17, 3189, 12935, 2051, 16, 6758, 1021, 3418, 1988, 10634, 1966, 1920, 6804, 4728, 5061, 1958, 18808, 14586, 18, 20478, 1925, 9843, 50, 17, 3189, 3728, 1956, 43, 6293, 6758, 1021, 5219, 1927, 9931, 4248, 16, 2176, 8016, 1966, 1925, 18697, 1942, 12657, 1920, 25, 11, 17, 2482, 1927, 1920, 18808, 2678, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 14691, 7364, 2199, 13763, 2796, 5903, 17677, 1010, 19, 17677, 1016, 3416, 16, 2154, 12936, 5012, 12328, 3260, 6991, 1927, 1920, 14691, 7364, 2199, 13763, 12, 17677, 13, 2796, 1922, 1920, 13355, 12279, 18, 2144, 2697, 2032, 4415, 1958, 17040, 1920, 5437, 3500, 2796, 5061, 1958, 21902, 22012, 2037, 17837, 2108, 2199, 24937, 1942, 23677, 4248, 1990, 16861, 18633, 18, 7099, 16, 2611, 3918, 43, 4140, 2770, 1922, 14435, 5807, 56, 17, 4624, 12082, 1927, 6622, 1930, 3260, 17, 4124, 2697, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 1920, 18347, 2051, 50, 13975, 16, 2154, 12936, 1920, 6804, 4682, 1927, 6445, 15176, 2626, 4090, 2199, 13763, 1036, 4378, 2007, 43, 5305, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 18, 2052, 13975, 5921, 5038, 2427, 1966, 9843, 50, 16, 16599, 27252, 1036, 16, 12935, 2319, 16, 1930, 24966, 1036, 1988, 12561, 2052, 3418, 1942, 18170, 11079, 2687, 10787, 6404, 2014, 3856, 2409, 2678, 5158, 16, 5059, 16, 1930, 7827, 18, 2176, 22970, 2037, 28881, 7972, 2299, 1957, 7660, 3857, 1031, 1957, 1930, 1977, 2458, 1956, 20709, 11569, 11830, 5403, 16, 13148, 16, 1930, 12935, 2115, 6149, 18, 3], "output": "MNGAMYREILSKNLLPSARALKMKHFKVLEWPSQSPDLNPIENLWRELICMEEWAKLPATNMLVEKVEQMMEWALQPQRQCSVCSVFVYISVLCVSVGVFGVLFVGFKMLFCVFGCIFFLVCCGLVYISVVGVYLVVFSFFCFGFWGFVYFSDLKCVLVFCVLVFFFFLMYISVCWCILCNYVITESKLTYSSTFSTRLFFTVVDYDEGADVFQDTFDLQRIGFASEQLAKWIHDRTDVQIRVFRPPNYSNNLEFIYNKTGWAMAALCVVFAMTSGQMWNHIDEQDVQGQQDVQDEQDVQGQQDEQDVQDEQDVKRGWVFQHDNDPKHTARATKEWLRKKIRVAQRQPQNITALEESSRRSVIRMNGEKFRRFVKSPPRNYSVIVMFTLVWLVYISVCVLVKSGLCALVYIIWGFVYISCLVIFSDFKCILVEILSLCAQANEEYQVLANSWRQLNMNSAPTFMHFPAKGKPKRAGTIALALLVSLVGGLLYLRRRGPPYAHKNPQNGQVDVRDEQDGR", "metadata": {"id": "A0AAE0PSY9", "cluster": 21847716, "interpro_all": ["IPR021149", "IPR036397", "IPR038717"], "interpro_used": ["IPR038717", "IPR021149", "IPR036397"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is categorized in the Protein of unknown function DUF2232 family, which consists of uncharacterized proteins found in bacteria and eukaryotes. It is produced by Pyramimonas obovata and corresponds to UniProt keyword Membrane, Transmembrane, and Transmembrane helix.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 6680, 4553, 1028, 3416, 16, 2154, 7543, 1927, 24528, 2697, 2435, 1922, 4802, 1930, 15021, 18, 2176, 1977, 4152, 2007, 12113, 1980, 9259, 2384, 5122, 3857, 1930, 8852, 1942, 20709, 11121, 2538, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MMAAQIALLSGAAARNLHPLHTLLTRRVDLPTRELSTTSTRRVGFLGSQNIGAARGQQRQIKPCADAGAAAFAGLAYYLGTALRLEAHLGSFLPLPIVIAGLQRAISYVLIHGLMALSLSVLWSMRLPWSVTIPIRENLLAMVAAQMSTLAEQMGALMGISGTPALHWIYTILLSKIAPPGFCRAPKVIQRMLFGPTAETTRKRIQKHGLRGAWVGARLGCGGMSEENYASLQQKTQAMVETAMLAGAARWNPRVAAKVLAVTALLLAILASVVRSGGMLVSLAISSYLLILIFVVVIVNSLTYLLLLHVLY", "metadata": {"id": "A0A7S0WLD0", "cluster": 22301570, "interpro_all": ["IPR018710"], "interpro_used": ["IPR018710"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein has a Flagellar protein FlgJ, N-terminal domain that is directly involved in the assembly of the flagellar rod structure. It originates from Teichococcus coralli and is connected to UniProt keyword Cell projection, Cilium, and Flagellum. 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, 24154, 2213, 2300, 1029, 1013, 16, 56, 17, 4262, 3418, 1988, 1977, 4103, 3286, 1922, 1920, 5957, 1927, 1920, 24154, 6275, 3170, 18, 2176, 22970, 2037, 3602, 2108, 8256, 17358, 12191, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2024, 11244, 16, 28997, 16, 1930, 7030, 10757, 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": "MEPVTLSPPPQARKLARQLETSFAAELLRAARPQQKAGGLAGRGAGGDAFDSFMDEALGAAMVARGGLGLAPMLEKAIAGRAAGAPR", "metadata": {"id": "A0A845BQ84", "cluster": 22474073, "interpro_all": ["IPR019301"], "interpro_used": ["IPR019301"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is included in the Protein of unknown function DUF6627, PA2779-like family, which comprises uncharacterized proteins of approximately 130 amino acids found primarily in Proteobacteria. Members of this family are distinguished by an extremely hydrophobic region at or near the C-terminus, consisting almost entirely of bulky hydrophobic residues such as valine, isoleucine, leucine, and phenylalanine. It is found in Gammaproteobacteria bacterium and is annotated with UniProt keywords Signal, Transmembrane, and Membrane.\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, 2213, 1927, 5435, 2347, 4855, 17136, 8166, 1027, 16, 3838, 28362, 1026, 17, 3189, 3416, 16, 2154, 12936, 24528, 2697, 1927, 3993, 8761, 3835, 4576, 2435, 5985, 1922, 22266, 18, 4678, 1927, 2052, 3416, 2032, 12080, 2007, 1925, 8113, 7919, 3031, 2019, 2014, 4931, 1920, 45, 17, 7822, 16, 7600, 5365, 11668, 1927, 22605, 7919, 4248, 2427, 1966, 21884, 16, 25398, 16, 12624, 16, 1930, 17388, 18, 2176, 1977, 2435, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 2733, 16, 9117, 16, 1930, 3260, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MRNIRDLTAGFISMLFLTVCLISPKAKVADFLQRKDVQQAVKNSGMELQQVISGVESMTPFITFIVLLITDIAGYTDIFPFVVKKAQAAMVSPIKATPNTILNMDAEIDLIAKNIDSIPAGGDALAII", "metadata": {"id": "A0A525CAV3", "cluster": 22576598, "interpro_all": ["IPR046735"], "interpro_used": ["IPR046735"], "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 possesses a Outer membrane protein beta-barrel domain 3 domain that functions as a structural transmembrane anchor by forming a $\\beta$-barrel in the outer membrane. It is characteristically associated with TonB-dependent receptors involved in nutrient transport, though it is also found in other proteins within the outer membrane $\\beta$-barrel superfamily. Additionally, the protein is associated with 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 is derived from Niabella ginsenosidivorans and is connected to UniProt keyword Signal.", "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, 14465, 43, 7642, 3260, 2213, 4666, 17, 19560, 3418, 23, 3418, 1988, 4088, 1966, 43, 4346, 9117, 13333, 2007, 7402, 43, 8, 38, 4666, 8, 17, 19560, 1922, 1920, 7642, 3260, 18, 2176, 1977, 6293, 2169, 2458, 1956, 16501, 1014, 17, 3100, 4086, 3286, 1922, 8708, 4860, 16, 4170, 2176, 1977, 2222, 2435, 1922, 2303, 2697, 2651, 1920, 7642, 3260, 8, 38, 4666, 8, 17, 19560, 13975, 18, 4950, 16, 1920, 2213, 1977, 2458, 1956, 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, 1977, 3595, 2037, 21946, 21512, 1019, 27601, 27545, 7408, 15525, 17182, 1036, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 18, 3], "output": "MRLKRSAIILLLAVFHLTVHSQNAIVKGQLVDSAEHRNLQHAVISLLNAKDSVLVRYGRADEKGNFTISNADTGHYVIMITHPYFADIFDSITLAPSQTLDLGILNMLSKLKMLEEVVVKSGAPIRVKGDTTIYTADSFKVRDGANVEELLKKLPGIQVDKDGKITAMGETVKNVLVDGEEFFGSDPGIATKNLDAKNIQEVQVYDKKSDQATFTGIDDGSKEKTINLKLKDNAKKGYFGKAEAGGGTDGRFNNSLMANSFKNKRKLSAYGIMSNTGNLNLNWDDETKYGGGSNVELMDGGGIAIFSGGDNYNYSGGIPTNWNWGLNYSNKFNQDKNSLNTSYKGVKINAPDSYESNSRTYLADSVWSTNNRSNSYGTTVKNNINGTFESKIDSANTIKITAKAYSNSSKNYTNFYSESLTPENGFINKNYRASQNESDKYTLNTTALWMHKFKKANRTFSFNIDVNLVDGNSKGQLNSNLVFYNNGDSTGNSRIDQRNSSRNNSQNYTAKATYTEPLFKDSYLELSYSALVYKSAVVRDVFDKGADDQYNTLIDSLSNHYNFDYLGHSPGANFKITKKKYNFTVGGAVGFYNYRQNNTTLGVVRKYNFTNYFPRANFQYKFKPSESLSIYYNGRTSAPNIDDLQPILVNTDPLNIKTGNPLLKPSFTHNLSLNFNSYNMLKDRYIGGYISWNLTQNAFSTLSSYRDSIRVYQTVNTNGVTSVYGGMWGGIGFKKAHMRLNFNPQLNYNKGVDLIERNGIVNQNTSEYTNISFNTYLSKNKDSVYDLGIGPKIVYTNSHASINTASNVSYFNYGITGYVWFQLPLRFEIRSDVDVNLQKKDARFKGSYNYTVWNATLSKKIAKNKFEVKASVNDILNQNQRYTRNISGSMLYEQSSLLLRRYALLSFLWNFTNNNTKAPSSN", "metadata": {"id": "A0A1A9HY52", "cluster": 25709257, "interpro_all": ["IPR013784", "IPR041700"], "interpro_used": ["IPR041700", "IPR013784"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to make a polypeptide chain that will have the following function description: The protein is assigned to the Retrovirus-related Pol polyprotein family, which mediates the replication and integration of retroviral and retrotransposon genetic material into host genomes. This polyprotein encodes multiple enzymatic activities, including a reverse transcriptase for DNA synthesis, an RNase H for RNA degradation, and an integrase for genomic insertion. It also functions as an aspartyl protease that processes Gag and Pol precursors into mature, functional units. Also, the protein should feature a Integrase zinc-binding domain that coordinates zinc ions and is found in a wide variety of integrase proteins responsible for viral genome integration. Furthermore, the protein has 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 is derived from Iris pallida (Sweet iris). 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, 6304, 1942, 1920, 23987, 17, 2712, 2492, 6240, 5684, 3416, 16, 2154, 10412, 1920, 5158, 1930, 7122, 1927, 16599, 1930, 27181, 1916, 3299, 3485, 2460, 4423, 7313, 18, 2052, 6240, 5684, 9937, 3137, 8145, 4209, 16, 2710, 43, 5267, 13335, 1958, 2678, 4271, 16, 1925, 9843, 50, 1958, 3146, 4877, 16, 1930, 1925, 27252, 1958, 4935, 7413, 18, 2176, 2222, 4088, 1966, 1925, 12053, 2199, 7154, 1988, 4028, 9819, 1930, 2492, 10416, 2460, 6665, 16, 3183, 5701, 18, 2222, 16, 1920, 2213, 3066, 5961, 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, 3677, 16, 1920, 2213, 2258, 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, 1977, 3595, 2037, 17187, 12574, 3825, 12, 15190, 17187, 13, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MLHNQVPNRGIGEVHLLIMRFMGFYLKIQKKLHQSRDDHFDFIMIRLHMLYRRSYDGLLLRCLSENKAKQILREAHDGVCGAHQPGPKLQDRIRRMGYYWPSMIADAVDYARRCKACQIHADFIHQPSEFLHSTVASWPFEAWDMDIIGPINPPSVKGHRFILALTDYFSKWAEEAVPLVEVKTSNVISFIKHHVIYRFGIHRRIIHDNGPQFASQAFY", "metadata": {"id": "A0AAX6IBA8", "cluster": 62, "interpro_all": ["IPR001584", "IPR041588", "IPR050951", "IPR012337", "IPR036397"], "interpro_used": ["IPR050951", "IPR041588", "IPR001584"], "interpro_unused": ["IPR012337", "IPR036397"]}, "task_type": "autoregressive"} {"instruction": "I need a protein that performs the following role: The protein should feature a WD40-like beta-propeller repeat that typically folds into a multi-bladed beta-propeller structure to serve as a stable scaffold for protein-protein or protein-DNA interactions. Acting as a platform for the assembly of molecular complexes, this domain mediates diverse cellular functions including signal transduction, transcriptional regulation, and ubiquitin ligase activity. In addition, the protein falls within the Six-bladed beta-propeller, TolB-like superfamily, which forms a structural domain consisting of six 4-stranded beta-sheet motifs that serves as a scaffold for diverse biological activities ranging from enzymatic catalysis to transport. Members of this family include enzymes like quinoprotein glucose dehydrogenase, signaling components such as the LDL receptor, and the periplasmic TolB protein, where the domain mediates protein-protein interactions within the Tol-dependent translocation system. It is derived from Myxococcales bacterium. 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, 17907, 4241, 17, 3189, 4666, 17, 5062, 13728, 6865, 1988, 5745, 16231, 2460, 43, 2779, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 1942, 7120, 1966, 43, 4700, 7281, 1958, 2213, 17, 2213, 2014, 2213, 17, 2678, 3719, 18, 8290, 1966, 43, 6631, 1958, 1920, 5957, 1927, 3272, 5048, 16, 2052, 3418, 10412, 6445, 3689, 4088, 2710, 2733, 8201, 16, 5224, 3640, 16, 1930, 6526, 11905, 2455, 18, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 3798, 17, 22707, 1007, 4666, 17, 5062, 13728, 16, 21930, 1014, 17, 3189, 13975, 16, 2154, 4952, 43, 4346, 3418, 7600, 1927, 3798, 24, 17, 10338, 4666, 17, 11130, 8277, 1988, 10634, 1966, 43, 7281, 1958, 6445, 3933, 4209, 6485, 2037, 8145, 15408, 1942, 4860, 18, 4678, 1927, 2052, 3416, 3951, 5038, 3189, 9012, 6657, 3817, 9294, 16, 3197, 4178, 2427, 1966, 1920, 8017, 3148, 16, 1930, 1920, 24334, 21930, 1014, 2213, 16, 2597, 1920, 3418, 10412, 2213, 17, 2213, 3719, 2651, 1920, 21930, 17, 3100, 7849, 2433, 18, 2176, 1977, 3595, 2037, 21464, 11748, 1918, 14061, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MDVRSIALLVGLALGLGCQINSGGVGTGGGSAGVGTETGEGGTTLPPVLTDDGGTTTPGGTTEPPPGTGSDGTTGLDGSSSGSGDTGDPMLPRPDPYGVAVPLTELNDALGAADDDPTLRQDQREIYFASTRLGDEDIFVATRASVDVPFDTPMIVGGNISTFSQETTPELSRDGTLLLFASDRRGNGLEIYYTTRASMASLSWALPQPLPALSSMAHESAATPQHDQATLLFCSDRMPTDGGADIWRAAFDPGTVMVSDLQRVAELASPALDCPGNSNADMTWLSFESGRTGTQGGQDLWVAQRTAEGDGYWPPYNLSELNTAAEDGDPWVSADMQTIYFSSNRTGNYDLYMARQVP", "metadata": {"id": "A0A956FGJ9", "cluster": 48622, "interpro_all": ["IPR011042", "IPR011659"], "interpro_used": ["IPR011659", "IPR011042"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein features a Type II secretion system protein GspF domain that functions as an integral inner membrane platform for the type II secretion machinery, type IV pili, and archaeal flagella. It is present in Chloroflexota bacterium and is described by UniProt keywords Cell membrane 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, 4075, 43, 2601, 2890, 5512, 2433, 2213, 5022, 1034, 1038, 3418, 1988, 4088, 1966, 1925, 12328, 6671, 3260, 6631, 1958, 1920, 2601, 2890, 5512, 10853, 16, 2601, 4370, 7547, 1033, 16, 1930, 22367, 26538, 18, 2176, 1977, 2481, 1922, 10107, 18222, 7336, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MPTNTLLFLSAAAAVLSAIAWVRASYQARQQTRHMKRRLGIKSRWDDAFEIDDEQLLDPTTEVPERRSADLKFKPSEALGLVVVIGLVSYILVELLLTQGPFISTCLAILCALTVPWLLLRSRRDRRLLALELVAREIGDPASEEFSLVVREVRLGGSIDDSLEALEKRMPSADLEVMVTALKVQRQEEIKTMMAEPKFTSYLMPILSIGALALLNRTIPHFLDVLFWTIPGLIVLTVFILMQIGGFLLIQRFARVKIMVLFIGDIFDASQRGKDLAAKLKANFTRQLPMVAELMANALRAGMSLQGIAGGNLIKSMGALSQTLIERQRT", "metadata": {"id": "A0A951KGW3", "cluster": 356510, "interpro_all": ["IPR018076", "IPR042094"], "interpro_used": ["IPR018076"], "interpro_unused": ["IPR042094"]}, "task_type": "infilling"} {"instruction": "Please generate an amino acid sequence that is capable of: The protein is a member of the Bacterial cell division SPOR domain-containing protein family, which facilitates bacterial cell division by associating with the septal ring to promote cell constriction and septal peptidoglycan synthesis. Members typically utilize a SPOR domain to bind peptidoglycan, targeting the protein to the division septum where it interacts with other divisome components. Furthermore, the protein includes 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 Chromatiaceae bacterium and is described by UniProt keywords Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 4543, 2024, 8451, 9130, 3418, 17, 3165, 2213, 3416, 16, 2154, 11374, 4543, 2024, 8451, 2007, 26284, 1956, 1920, 16458, 6335, 1942, 5527, 2024, 19837, 1930, 16458, 24183, 4271, 18, 4678, 5745, 12561, 43, 9130, 3418, 1942, 4566, 24183, 16, 5133, 1920, 2213, 1942, 1920, 8451, 17026, 2597, 2176, 9034, 1956, 2303, 6421, 23854, 3870, 4178, 18, 3677, 16, 1920, 2213, 5921, 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, 6068, 19476, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MGGENGMDEAGKKRLVGAAVVIALAVIFVPMLLEEGTDDGLGDPIHIPARPALDSDAQAALEDALEAAEEDLVLPLPAPEPPGIEPEIDVAASSATGPISDDPAAATGTGPNQTARPAAVPSAAAASGTGDRPATAGNAAPAAASGNQTAAGPRPVPPGAQSWVVQVASVRQPEAARRLQDELRGKGYPAFVEQAEVNGLTWYRVRVGPEVDRARANDVSARITRETAHKPLVQRYQ", "metadata": {"id": "A0A6I7Q163", "cluster": 5442438, "interpro_all": ["IPR052521", "IPR007730", "IPR036680"], "interpro_used": ["IPR052521", "IPR007730"], "interpro_unused": ["IPR036680"]}, "task_type": "autoregressive"} {"instruction": "I have a partial protein sequence with masked gaps. Based on this function, predict the missing amino acids: The protein possesses a MucB/RseB, N-terminal domain that negatively modulates the activity of sigma factors RpoE and AlgU by stabilizing their inhibitory partners under non-stress conditions. This domain plays a key role in regulating stress responses and the differentiation of *Pseudomonas aeruginosa* into alginate-producing forms. Additionally, the protein carries a MucB/RseB, C-terminal domain that mediates interaction with the anti-sigma factor RseA. This binding stabilizes RseA to negatively modulate sigma-E activity under non-stress conditions, or contributes to the differentiation of *Pseudomonas aeruginosa* into an alginate-producing form in the context of MucB. It is produced by Abyssibacter profundi and has UniProt annotations Periplasm and 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, 14465, 43, 3422, 1014, 19, 4366, 13495, 16, 56, 17, 4262, 3418, 1988, 7191, 13112, 1920, 2455, 1927, 5139, 2790, 4822, 6802, 1930, 4326, 1032, 2007, 14384, 2310, 5431, 7228, 2441, 2447, 17, 3071, 2961, 18, 2052, 3418, 5705, 43, 3834, 2770, 1922, 6773, 3071, 3387, 1930, 1920, 4155, 1927, 14, 13461, 10830, 14, 2460, 17987, 17, 7144, 4952, 18, 4950, 16, 1920, 2213, 16252, 43, 3422, 1014, 19, 4366, 13495, 16, 45, 17, 4262, 3418, 1988, 10412, 2835, 1956, 1920, 2246, 17, 5139, 2991, 4366, 5376, 18, 2052, 2743, 19658, 4366, 5376, 1942, 7191, 8480, 5139, 17, 47, 2455, 2441, 2447, 17, 3071, 2961, 16, 2014, 7624, 1942, 1920, 4155, 1927, 14, 13461, 10830, 14, 2460, 1925, 17987, 17, 7144, 2386, 1922, 1920, 4491, 1927, 3422, 1014, 18, 2176, 1977, 4152, 2007, 2186, 2012, 12924, 7972, 2341, 1915, 3150, 2652, 1033, 1930, 2258, 20709, 15010, 20171, 1930, 2733, 18, 3], "output": "MASRARKAPFPKTDCHMLQRLTIAVAVAASSVVGSSQAADRSAQDWLAKMSVYRTGEQLETMRVIHRFSNGQEDERLISLTGDAREIVRSDGEVLLPKVSTVDLETLRLHYEFSRGVVDRVADRACQGVALSPRDEFRFGYGDALEQFLFTSVGYPETILDQALEPAIDTEGFREIRHGGPEPTLRLEDDLRVVGQSTRVFPGAQTPVTHILLTDGLATVSVFAAESKLPARMVDEFHVAVVGEVPARTVEQIGNSLSRTTPTPEAVRTQNYEGVVRCLLPRERVVMVDERGQSAQLCIDVLTGVPLRIALLDGQSHWMVESLPPGFKVFRGVSSIGAVHAYG", "metadata": {"id": "A0A363UKD1", "cluster": 7504520, "interpro_all": ["IPR033436", "IPR038484", "IPR033434", "IPR005588"], "interpro_used": ["IPR033434", "IPR033436"], "interpro_unused": ["IPR038484", "IPR005588"]}, "task_type": "infilling"} {"instruction": "Assume the biological function is as follows:\nThe protein incorporates a Thiol:disulfide interchange protein DsbD, N-terminal domain domain that facilitates the correct folding of secreted proteins within the bacterial periplasm by mediating electron transfer in the disulfide bond formation pathway. It functions by interacting with the C-terminal domain of DsbD to accept electrons and subsequently reducing oxidized disulfide bond isomerases such as DsbC, DsbE, and DsbG. It occurs in Hyphomicrobiales bacterium.\nGenerate the missing fragments of this polypeptide chain.", "tokenized_instruction": [2, 10336, 1920, 3933, 2347, 1977, 1966, 6052, 30, 1920, 2213, 19683, 43, 13914, 30, 11830, 26139, 2213, 15136, 1007, 16, 56, 17, 4262, 3418, 3418, 1988, 11374, 1920, 5550, 10328, 1927, 8366, 2697, 2651, 1920, 4543, 20171, 2007, 10239, 4995, 3856, 1922, 1920, 11830, 5403, 3337, 3374, 18, 2176, 4088, 2007, 8615, 1956, 1920, 45, 17, 4262, 3418, 1927, 15136, 1007, 1942, 5861, 14354, 1930, 5326, 5526, 11339, 11830, 5403, 25510, 1036, 2427, 1966, 15136, 1030, 16, 15136, 1021, 16, 1930, 15136, 1029, 18, 2176, 5110, 1922, 2483, 25808, 1935, 7839, 1918, 14061, 18, 5655, 1920, 6814, 6535, 1927, 2052, 13022, 4659, 18, 3], "output": "MRYLFSRLAAAVLXILXWQGMAQAMSGPWIELPNARARLIMTGEPMSGTLLAIPPILDWSRSENVASAEVQFPAPKRFGDEYGQSIGYKHRVVFPINIKLINPEKLALTIPPMFSTSADVSNIMAKAVKSLPLNVPEQLKASFSVMETSGKVPVLEIKIPASLPEKISETETHQLWHLPLYGIPRKQSPWGADMRLTIIGKNISFEQYFALDAPNGLEIELDDEWKTYWRSPGDSGGRPSKLVLDTFLGICREVCIPVTRFSAGPADIPVEDIFVEGPSNWFL", "metadata": {"id": "A0A2A5G7E5", "cluster": 10093298, "interpro_all": ["IPR028250"], "interpro_used": ["IPR028250"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein possesses 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. Furthermore, 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 has been detected in Pithovirus LCPAC302 and carries UniProt keyword assignments ATP-binding.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 1920, 2213, 14465, 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, 3677, 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, 2258, 2252, 3330, 1922, 10795, 10647, 11074, 5236, 4302, 12981, 11636, 1930, 16252, 20709, 11121, 2538, 18306, 4498, 17, 2743, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MKITCPVQLKDHQKPVVKQIWNRLTHDKEFSYGLKVGIIAPSYQSLHSEDGWLSWVDKYGIDIEFTLSFFDKVASEGLFLIFDEFHKATRKSSTHFACAALVHTPGDKEEHYPQILRMLGIVTEYRMFYLKPFTSQYEWEDYEKLSGVKVNNICKELYHEYLKQYVTFSMKQPKTSIKTTMLNCFLEDVDGGQWNMGSITIGLKYIERGKLNSMINYVKKSLKENTRKKVQKQLKRKYMTDEMYITLRLMRKHNRYWKGLCKDMFNYILNFVYERSGIIANFQKSSNDSWCLIISPGVGAESISLHDKVQSAGRVNRVGVKSDSKIMIIYSKQGDVETKEVMFPADYPAYIEGEKDKDLVKKLASLNIKYIDTSDTGLGKTHVTLCLAWYLQKRRYSSIISHKGNISHPWLIRKLESKKKYNYISTKACKKYSDRCRVGLISSLGQLIRFCSKKNPFVAFDEYTTKPQDLEMINRGIGYLQRGVGWNGYFVLCIGARDLQHQYYDLDPIKPDVMNGKTKNIDHGDYPREILITPDHFHTRVSVLNCMVKKSTIAKNLLGN", "metadata": {"id": "A0A481Z7J7", "cluster": 10507499, "interpro_all": ["IPR006935", "IPR027417"], "interpro_used": ["IPR006935", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein is associated with 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 native to Nocardioides aromaticivorans and is linked to UniProt keywords 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, 1977, 2458, 1956, 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, 6196, 1942, 9812, 3082, 12363, 10761, 2068, 8846, 3355, 1930, 1977, 4624, 1942, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MSTLHDQLADLADAAPTGGPVPGLWQQGVRRQRRRRNARLGAVAAAVVVVAALAGLLRTTAPEEPEPVQVPFGELHLPRMVYPPDPWAESTTTPGPLAAIGTASKFEPTGIRGHVESFAAFGVSAVDGSAVFLDLPWTGEDGFGPGGPVLSPDGTKVAWVRYTGGTEPVVNGFAVLDTMTGRARRLSDPDNPVIKGMDVSGLTFSGDSRYLEVSYSLTGSDADRAHSLVLWDVATGARRVAEPAGRYWLPNMGSAPAGTVWSRGDRTFTFDPVTGRTTSERSGFKVVQASYGPERSFAAIAFGETDQADWRLFVGASPRDVRQVRLDMVPEQLLGWRDATHVVIRDLPTGRAVEVDLATLVSTDLRLDVSEDLFDLPSYAADLWANPLVDGVRPPDASDPRTPWWFAGPGIALLAAAAFVTWWRRRV", "metadata": {"id": "A0A7Z0CQ90", "cluster": 10575284, "interpro_all": ["IPR015943"], "interpro_used": ["IPR015943"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein is included 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. It originates from Legionella birminghamensis and carries UniProt keyword assignments Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 4080, 1920, 13022, 4659, 3244, 2007, 15325, 1920, 17476, 3451, 1956, 1920, 5550, 3835, 4576, 18, 2347, 30, 1920, 2213, 1977, 3063, 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, 2176, 22970, 2037, 27836, 5870, 29477, 8134, 1930, 16252, 20709, 11121, 2538, 18306, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MLNFNPIAHLFIMKIFLKFSVNILAKLFYKQQAIKAIEEENVEGLKELLKQSYGGLLPNIKRKCKDKKFLRDLAIEKDSLAIVDFLFNDGMGVSYKDRFLAIAVQHNSRKVINYLVRKGYTLTLDKLPLLSQKVKDLADRGYIRESQLVAGLEGYLFLEKNLKPICIASTSFVQGKLKNHRGCKELLAFFFEFNTDSVNKINEVETGLIHCSLVICEKMPSEYNKTLYSSLASYISVHSPQQGRVPYLNNETDLRTAHARSLDTLEKPEQLRDYAKNNKAEKPLKAITPVKTELKTYIDACIAEPEKSGQGNVLITLASLTIANFCNLIATRGR", "metadata": {"id": "A0A378I7X7", "cluster": 12801637, "interpro_all": ["IPR036770"], "interpro_used": ["IPR036770"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein is assigned to 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 is found in Saprolegnia parasitica (strain CBS 223.65). The above is the intended function of my protein. Generate the amino acid sequence.", "tokenized_instruction": [2, 1920, 2213, 1977, 6304, 1942, 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, 1977, 2435, 1922, 9235, 15828, 3223, 2126, 16445, 1019, 12, 3943, 16341, 16975, 18, 4459, 13, 18, 1920, 3538, 1977, 1920, 11214, 2347, 1927, 3057, 2213, 18, 5655, 1920, 3835, 2687, 3244, 18, 3], "output": "MLHVVTPRYTHALHEACQCSALGNSSVGLMLDPDAGSEATFIADMAARRASGKIVALSLGGQHGAAMRPRWPTFFVSSLLTKYGLDDIDLDLEDGVPQGLPIITNLINGVKQLKQKIGERL", "metadata": {"id": "A0A067BG91", "cluster": 16822627, "interpro_all": ["IPR017853"], "interpro_used": ["IPR017853"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is associated with 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 present in Amycolatopsis sp. M39.\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, 2458, 1956, 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, 2481, 1922, 20306, 4879, 5148, 27747, 8362, 2056, 18, 12123, 1026, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MPQMPKTAQADRSAVVRQLVSVTSDTQDGDQSLNHGEPIADHHDRSMTAVATRTGQSASRPGSASRPHESPSAAPRLPRSTIPRDSRRAARRLREAVLAGVLRRLARPARASRTDLQEAIKEVGEQCPFSTSTRRRDAPDRLPVRDATRTVRDQRTEYMTPPAERPGTVQTGAVEIPGGARREGESHAWVDVWTGGWWAHDPTNARRLRVPGPSSGTHALVHNLWISARSVQNALFGHRYRLSIEFAPADTRPPRTARWQNSTMACRNTDYWGTDVTSFDLHAPGTDSWRVREDFAHVSLVMLGVPAHQTGGQ", "metadata": {"id": "A0A178XC07", "cluster": 18778155, "interpro_all": ["IPR038765"], "interpro_used": ["IPR038765"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I'm looking for a protein that has the following function: The protein is classified under the TMEM14 family, which comprises transmembrane proteins that adopt a three-helical bundle structure and function in fatty acid export or heme biosynthesis. In plants, members like FAX1 mediate plastid fatty acid release essential for pollen wall biogenesis, while animal homologs are required for normal heme production. It originates from Oryza meridionalis and contains UniProt keyword associations Transmembrane helix. 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, 22414, 3745, 3416, 16, 2154, 12936, 9117, 2697, 1988, 14103, 43, 2559, 17, 11514, 14142, 3170, 1930, 2347, 1922, 5934, 2687, 12660, 2014, 10954, 8132, 18, 1922, 4793, 16, 4678, 3189, 5685, 7653, 8265, 19754, 5934, 2687, 4012, 4415, 1958, 12206, 4821, 13008, 16, 2679, 4027, 14279, 2032, 3414, 1958, 2791, 10954, 3372, 18, 2176, 22970, 2037, 19745, 1019, 6902, 13756, 2996, 1937, 1930, 5461, 20709, 11121, 2538, 5253, 9117, 7864, 18, 7031, 1920, 3244, 18, 3], "output": "MRSSESDRITPRTPHIPPISPESKCPTIATAQSRGGEVARENEGAGDHHHHLLLPPPPPPCRGHPFPSLATSSQCCARPGRSRRRALLRCSAVSELAPAASAAYGALLLGGGAFAYVRSGSKGSIFGGLSGSALMGIAYYLMQSPETKAIGDAVGFGSAFLFASVFGIRLYNTRKLVPSGLLLVLSLGVLGVFYSAYLQDKV", "metadata": {"id": "A0A0E0DHI8", "cluster": 19596314, "interpro_all": ["IPR005349", "IPR044890"], "interpro_used": ["IPR005349"], "interpro_unused": ["IPR044890"]}, "task_type": "autoregressive"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein falls within the Unconventional Myosin ATPase family, which comprises actin-dependent motor proteins with ATPase activity that facilitate intracellular transport and cellular organization. By binding membranous compartments via divergent tails, these myosins are essential for processes such as stereocilia arrangement in hair cells, opsin transport in photoreceptors, and the formation of epithelial brush borders. In addition, the protein should include a Myosin head, motor domain-like domain that functions as an ATP-dependent molecular motor, typically forming the globular N-terminal head of myosin heavy chains to interact with actin and generate mechanical force. This conserved fold is also present in fungal chitinases, where it plays a critical role in hyphal tip growth and chitin synthesis. 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 present in Myotis brandtii (Brandt's bat) and exhibits UniProt keyword tags Actin-binding and ATP-binding.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 12182, 2651, 1920, 25623, 20126, 1923, 10863, 9444, 3416, 16, 2154, 12936, 4718, 17, 3100, 4842, 2697, 1956, 9444, 2455, 1988, 6628, 4776, 4860, 1930, 3689, 5901, 18, 2007, 2743, 22890, 10436, 3454, 13609, 18103, 16, 2144, 10863, 1036, 2032, 4415, 1958, 4028, 2427, 1966, 26692, 10401, 2126, 13002, 1922, 7018, 2094, 16, 26430, 4860, 1922, 19102, 16, 1930, 1920, 3337, 1927, 4944, 19668, 19607, 18, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 10863, 4469, 16, 4842, 3418, 17, 3189, 3418, 1988, 4088, 1966, 1925, 4498, 17, 3100, 3272, 4842, 16, 5745, 7402, 1920, 20975, 56, 17, 4262, 4469, 1927, 10863, 7881, 7835, 1942, 6310, 1956, 4718, 1930, 5655, 5821, 5495, 18, 2052, 5305, 3728, 1977, 2222, 2481, 1922, 8697, 16588, 2319, 16, 2597, 2176, 5705, 43, 4140, 2770, 1922, 27125, 7933, 2905, 1930, 16588, 4271, 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, 2481, 1922, 15924, 3600, 17154, 16373, 12, 17154, 1031, 11, 61, 11579, 13, 1930, 9826, 20709, 11121, 2538, 14392, 4718, 17, 2743, 1930, 4498, 17, 2743, 18, 3], "output": "MDGWMDGWMDGYSPPTRGTSAKPGLYCGSAVLQEVPATLAGQFKQSLDQLMKILTNCQPSFIRCIKPNEHRAARVLSFPPPGPGQCSSCHPPHRQDTGLPDPTRTLCFCPQSADSSRQKKPLVMREAGHREGQLLAGL", "metadata": {"id": "S7NEX9", "cluster": 21079277, "interpro_all": ["IPR036961", "IPR001609", "IPR027417", "IPR051567"], "interpro_used": ["IPR051567", "IPR001609", "IPR027417"], "interpro_unused": ["IPR036961"]}, "task_type": "infilling"} {"instruction": "I need a protein that performs the following role: The protein is assigned to the Sialidase family, which catalyzes the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, and alpha-(2->8)-glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, and glycolipids. As members of glycoside hydrolase family 33, these enzymes modify cell surface glycans and can act as pathogenic factors in bacterial infections. It is expressed in Bacteroidales bacterium and is connected to UniProt keyword Signal. Please generate this protein's amino acid sequence.", "tokenized_instruction": [2, 51, 2942, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 6304, 1942, 1920, 12952, 9200, 3416, 16, 2154, 17097, 1920, 9128, 1927, 4595, 17, 12, 22, 17, 34, 23, 13, 17, 16, 4595, 17, 12, 22, 17, 34, 26, 13, 17, 16, 1930, 4595, 17, 12, 22, 17, 34, 28, 13, 17, 7533, 12546, 19949, 1927, 4262, 20436, 2687, 4248, 1922, 22012, 16, 16268, 16, 1930, 14193, 2049, 3753, 18, 1966, 4678, 1927, 7533, 2261, 20748, 3416, 3401, 16, 2144, 5038, 11675, 2024, 3154, 15509, 1930, 2112, 4033, 1966, 8070, 2790, 1922, 4543, 5024, 18, 2176, 1977, 3198, 1922, 24323, 3955, 14061, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 2733, 18, 11586, 5655, 2052, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MKRNILLYALLFFAGISTAIAQENIFSESFKKGIPVQITNNRDKGYAIRLADDGTTVTSGNASYNEEEIWYFVGNAEQFRLYSLKGGKKLALKLDGTAAEAAATMRPAKEATTLTLTKQEKGGYAISPAGNPELSFNMFGGAGRDIKLYSSQDEGSHWTIREVDTKRPLVIKYNALTEGGFDTNTRIGNIAITIDGNTSNIMLSKENLPEASTCYLPHGATFSIAPGLVCHGWKMDINGGEGIAGQQLPQKGMEVTVNIDVDKENKYQYLFYSPDEEGIPYRIPAIVTTANGYVFAINDYRPCGNDIGFGEVDLVMRHSTKGGSEWDGHSWSEPVKIADGVGKEAKETWLTGFGDPAVVADRERNEILVMSVCGNRVCWHGNYGAGTPENPENPNRMARLRIKYNEETGEWEASQPKEVTYEIYPLFKDKDGKAHVGSMFIGAGRMAQSRMIKVGDYYRIYCAVWAVETASYRHHNYALYSDDFGETWHLLGELGNDFNDSPAPYGNEPKCEELPDGSVLLSSRKGHGRYFNVFHYTNFEKAEGYWDGAVATDEVGDLKFGSNDTNGEPLLVGNILFQSVPTGDSRSNVAIFYKPLSDDPATYTPTELSKGWKKIPVSDRGSAYSSMCILPDGNIGIYYEEEPGGYSMVYVPVNIEKAVGKFTYTERLSDKCGTCGEGKYEGIVTVE", "metadata": {"id": "A0A928GJT8", "cluster": 22246259, "interpro_all": ["IPR026856", "IPR036278"], "interpro_used": ["IPR026856"], "interpro_unused": ["IPR036278"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence for a protein that will have the following function: The protein is assigned to the Macrolide Exporter MacB family, which consists of non-canonical ABC transporters that typically function as the inner membrane component of tripartite efflux systems like MacAB-TolC. Utilizing ATP hydrolysis, these proteins actively export substrates to confer macrolide resistance, while variants such as PvdT secrete siderophores for iron acquisition. In addition, the protein should have 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. Furthermore, the protein incorporates a ABC3 transporter permease, C-terminal domain that functions as the transmembrane component of various ATP-binding cassette (ABC) type 3 systems, mediating substrate translocation across the inner membrane. It participates in diverse biological processes, ranging from lipoprotein release via the LolCDE complex and antimicrobial efflux to bacterial cell division as part of the FtsX septal ring component. It is present in Cytophagales bacterium CG18_big_fil_WC_8_21_14_2_50_42_9 and is associated with UniProt keywords Cell membrane and Transmembrane helix.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 1920, 23929, 2261, 12660, 1915, 3433, 1014, 3416, 16, 2154, 7543, 1927, 2447, 17, 9452, 7219, 10538, 1988, 5745, 2347, 1966, 1920, 6671, 3260, 4594, 1927, 8027, 24707, 11247, 3771, 3189, 13421, 1014, 17, 21930, 1030, 18, 10232, 4498, 9128, 16, 2144, 2697, 11182, 12660, 6249, 1942, 7909, 23929, 2261, 3554, 16, 2679, 4936, 2427, 1966, 5774, 18314, 15989, 22940, 14820, 1958, 5680, 6165, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 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, 3677, 16, 1920, 2213, 19683, 43, 7219, 1010, 9054, 6191, 2051, 16, 45, 17, 4262, 3418, 1988, 4088, 1966, 1920, 9117, 4594, 1927, 3425, 4498, 17, 2743, 12992, 12, 7219, 13, 2601, 23, 3771, 16, 10239, 4510, 7849, 3436, 1920, 6671, 3260, 18, 2176, 17241, 1922, 6445, 3933, 4028, 16, 6485, 2037, 9694, 4012, 3454, 1920, 3004, 8293, 3695, 2796, 1930, 8003, 11247, 1942, 4543, 2024, 8451, 1966, 3131, 1927, 1920, 17022, 1039, 16458, 6335, 4594, 18, 2176, 1977, 2481, 1922, 22953, 4151, 5411, 1918, 14061, 7294, 3928, 41, 9769, 41, 3313, 41, 14888, 41, 28, 41, 2900, 41, 2607, 41, 22, 41, 2761, 41, 3858, 41, 29, 1930, 1977, 2458, 1956, 20709, 11569, 2024, 3260, 1930, 9117, 7864, 18, 3], "output": "MLYSYLKIAFRNLIRHKAFSILNIAGLAVGIAAALVIFLVVNFELSFDTFHAKKDRIYRVVNEFMHAAGKDYQTGVPFPFGEALKTDYPQLGKVAMTFGAYNTQISVIDEEGNIGKKFKEEAGAFFAGPEFFEVFDYHWLAGNPKKALAEPNMAVLTQSEAEKYFGDWHQALGKQLKLDNQTLVQVTGILEDVPYNSDFQQEVIVSYATLRSLFSENDFTNWGSVSSGVQCYILLPEGTTEASFNRLLVSFLKKHYPKNKNTYKLQPLSDLHFNPNYPPPSFRSITKQTITSLELIGLFILVIACINFVNLATAQALGRAKEAGVRKVLGSNRGQLIWQFLGETFVIVLIAVLSAILLVQLVLPWVQPISNLPESFNLYAAPHLLLFLFGIIVSVTFLSGFYPALVLSGFQPIQALKSKMTIQTLGGISLRKSLVVLQFSVAQVLIIATLIAICQMNFIRQKDLGFNQRAVLLVEIPDDSLAQAKMHHLKNQFAALPGVERVSFNFSAPLSGSSSSSNFGFTSTTKDEDFPLNIKAADADYFSTFQLRFAAGR", "metadata": {"id": "A0A2M6GIA4", "cluster": 22976895, "interpro_all": ["IPR003838", "IPR025857", "IPR050250"], "interpro_used": ["IPR050250", "IPR025857", "IPR003838"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Output the amino acid sequence for a protein that performs this function: The protein should include 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 Erysipelotrichaceae bacterium and is linked to 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, 3066, 3951, 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, 2668, 2012, 25535, 29168, 4698, 9914, 14061, 1930, 1977, 4624, 1942, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MLMKKDRLIKLGILAGLTIIVSLLVCFVDKAPIGPKATVVGMSHINGFFRDIFKFSKFWYVITNLLGYLAILLCLCFAGIGALQLWAGKGLKKVDRNIVALGCLYVVVILLYVIFEKAEINCRPVIMPGETDPEASFPSSHTMLALTVFCSAPWVGNRYLKDANIRKIFTIVMYVLAAVMVVGRLLSGVHWFTDIIASILISATLLYAFRIVLDFIKPKKKTVRK", "metadata": {"id": "A0A928A0C4", "cluster": 24921601, "interpro_all": ["IPR036938", "IPR000326"], "interpro_used": ["IPR000326"], "interpro_unused": ["IPR036938"]}, "task_type": "autoregressive"} {"instruction": "A protein is required to perform the following role:\nThe protein possesses 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. Moreover, the protein should contain 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 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 Vreelandella salicampi and has UniProt annotations Transferase.\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, 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, 3950, 16, 1920, 2213, 3066, 5531, 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, 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, 12110, 5182, 4702, 5870, 20734, 3456, 1033, 1930, 2258, 20709, 15010, 13763, 18, 2176, 5077, 2258, 17476, 3451, 1988, 2942, 1942, 1998, 8924, 18, 3394, 1920, 6368, 3835, 4576, 18, 3], "output": "MSDSPEHADYATLVEHHPFMLNRFLPDTTLVYVNDMVGEEERRQWHEHYAQFTPEAPRHQLINCVGGAVGIDVTARMEARTALEINEERYALAQQAAGFGVDKPLTFTEWLSRLHPDDVERCSKAVNEQLLVQGRGQVFERDTSGAPLRLIGTHLDIQQFAYAVSHDLRQPLRMVNSYLQLLTRELGMILGILDYSRVGRKTSPMEWVDSRAVLDDVMVHIKGDWPEVYASRDELTRLLQNLLDNALKYQVDVQDNGIGIAPEQQDRLFGVFTRLQPRSRFKISVTSPGEGDGSCFTFTLPITRHYQDSAMATFFEANPDALIGKRWLPKGDSHWIEWTNTAFFGDDGSLMFIQWEWHPERDEIVWDAQCYRMLGLSPSEGNEFIIEFRYQTASGYLWSLKSVQQELSRSNQELENDLSDDAQEMIHFAREGAERMDKGFLKPMLTESGGHVEKGTTPDVTITGHQQACEWEGTGIGLAICKRIVEHHEG", "metadata": {"id": "A0A7Z0LJG1", "cluster": 28956235, "interpro_all": ["IPR036890", "IPR005467", "IPR003661", "IPR036097", "IPR001610", "IPR000014", "IPR000700", "IPR035965", "IPR013656", "IPR013655", "IPR052162", "IPR004358"], "interpro_used": ["IPR013655", "IPR000700", "IPR005467"], "interpro_unused": ["IPR013656", "IPR000014", "IPR004358", "IPR001610", "IPR052162", "IPR036097", "IPR035965", "IPR003661", "IPR036890"]}, "task_type": "infilling"} {"instruction": "What is a possible amino acid sequence that could have the following functional description: The protein is classified under the The Hemocyanin/hexamerin family, which comprises homologous proteins including oxygen-transporting hemocyanins found in arthropod and mollusc haemolymph and non-oxygen-binding hexamerins used for storage in insects. These proteins typically assemble into hexamers or larger cylindrical oligomers and possess copper-binding domains that share structural similarity with tyrosinases. Additionally, the protein carries a Hemocyanin, N-terminal domain that comprises the structural N-terminal region of invertebrate hemolymph proteins, functioning in oxygen transport within crustacean and cheliceratan hemocyanins or nutrient storage within insect hexamerins. These homologous proteins typically assemble into hexamers, though the hexamerin variants lack the oxygen-binding capacity of their counterparts. Additionally, the protein possesses a Hemocyanin/hexamerin middle domain that functions as a core structural component in arthropod oxygen-transporting hemocyanins and insect storage hexamerins. It contributes to the copper-binding center essential for oxygen transport in hemocyanins, sharing homology with the active site of tyrosinases, while providing a stable scaffold in non-oxygen-binding hexamerins. It is expressed in Camponotus floridanus (Florida carpenter ant) and contains UniProt keyword associations Signal and Storage protein.", "tokenized_instruction": [2, 4663, 1977, 43, 3216, 3835, 2687, 3244, 1988, 2578, 2162, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 5947, 2441, 1920, 1920, 3243, 26924, 19, 25602, 1921, 3416, 16, 2154, 12936, 8725, 2697, 2710, 4612, 17, 27038, 3243, 26924, 1036, 2435, 1922, 21680, 1986, 1930, 20888, 7801, 7105, 23059, 1930, 2447, 17, 4612, 17, 2743, 25602, 2925, 2251, 1958, 7451, 1922, 13340, 18, 2144, 2697, 5745, 17421, 2460, 25602, 1036, 2014, 4327, 18677, 14160, 1930, 7150, 9541, 17, 2743, 4682, 1988, 7948, 4346, 6796, 1956, 27083, 1036, 18, 4950, 16, 1920, 2213, 16252, 43, 3243, 26924, 16, 56, 17, 4262, 3418, 1988, 12936, 1920, 4346, 56, 17, 4262, 3031, 1927, 26381, 3243, 23059, 2697, 16, 7295, 1922, 4612, 4860, 2651, 24191, 22076, 1022, 1930, 11749, 2927, 5524, 3285, 3243, 26924, 1036, 2014, 8708, 7451, 2651, 11422, 25602, 2925, 18, 2144, 8725, 2697, 5745, 17421, 2460, 25602, 1036, 16, 4170, 1920, 25602, 1921, 4936, 3630, 1920, 4612, 17, 2743, 4796, 1927, 2310, 11482, 18, 4950, 16, 1920, 2213, 14465, 43, 3243, 26924, 19, 25602, 1921, 5576, 3418, 1988, 4088, 1966, 43, 4728, 4346, 4594, 1922, 21680, 1986, 4612, 17, 27038, 3243, 26924, 1036, 1930, 11422, 7451, 25602, 2925, 18, 2176, 7624, 1942, 1920, 9541, 17, 2743, 4102, 4415, 1958, 4612, 4860, 1922, 3243, 26924, 1036, 16, 10763, 9039, 1956, 1920, 3500, 3200, 1927, 27083, 1036, 16, 2679, 5453, 43, 4700, 7281, 1922, 2447, 17, 4612, 17, 2743, 25602, 2925, 18, 2176, 1977, 3198, 1922, 6225, 23557, 1031, 1957, 19386, 1022, 1957, 12, 19386, 16549, 9583, 4942, 13, 1930, 5461, 20709, 11121, 2538, 5253, 2733, 1930, 7451, 2213, 18, 3], "output": "MKAIALFLAAVCLAQATQVPVHTADKTYLVKQKNIYELFWHVDQPTVYHPELYQKARYFNFEDNVASFNDQVAVTEFLQRLKHGIIPRGVVFSGPQHFHEAVNLFHVFHSAKDFDTFYNAAVWARFNVNEYVYIYALSVAVLHRPDTKHIRVPPAYEVLPYYFFNEEVIHQAHHIALGNTQNAVKKTVGSVDYYYIPANYSDWYIVHDHGVSDYHKLSFFTEGVGLPSFYIASIHAFPHWLNSVKHNLPQFVRGELYLYLHQQILARYNLERLSHNVGEVDYVDVNRPVVPYYPTLQHPNGASFPQRPVGFKIPVHMHEDIQALQDAHVRISDAIASGHIVDANGNPIDIYKTVDGLNQLGNIIQGNADSVNPGYYGHLDVLYRKVFGVTPVHHTTSNHVVPSALDLLSTRLRDPLFYGIYKNIVSYWTKYKQHLPKYTHEELVFPGVHVESVTVDKLVTFFDHFDSLINNAVSVSSHKEAQSTVIKARQNRLNHKPFSFHITVHSDKNVKAIVRVFIGPKYNVHGHEVDISETHHHFLELDQWVVDLVSGTNKIERSSHESVYVTPDEVPSDVLYKKVVKALEGGEAFTYPEQLYGFPDRLIIPRGKKEGLQFKLFVAVSHFDETAAVHVDSPVWGSNVVDARSLGYPLDRPIPFNFTEVPNFHIRDVVITHKQVDDLNQINV", "metadata": {"id": "E1ZXZ4", "cluster": 1813884, "interpro_all": ["IPR008922", "IPR013788", "IPR000896", "IPR005203", "IPR037020", "IPR005204", "IPR036697", "IPR014756"], "interpro_used": ["IPR013788", "IPR005204", "IPR000896"], "interpro_unused": ["IPR005203", "IPR008922", "IPR037020", "IPR014756", "IPR036697"]}, "task_type": "autoregressive"} {"instruction": "A protein has the following role:\nThe protein can be placed in the Protein of unknown function DUF6082 family, which comprises components of biosynthetic gene clusters, including the kanamycin pathway in *Streptomyces kanamyceticus*. Predominantly found in Actinobacteria, these proteins are associated with saccharide biosynthesis. It is identified in Amycolatopsis australiensis and contains UniProt keyword associations Membrane, Transmembrane, and Transmembrane helix.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 17136, 13895, 1028, 3416, 16, 2154, 12936, 4178, 1927, 14041, 2359, 5859, 16, 2710, 1920, 19404, 3374, 1922, 14, 22874, 12916, 26984, 1972, 2002, 1957, 14, 18, 7700, 2435, 1922, 29130, 16, 2144, 2697, 2032, 2458, 1956, 14175, 2205, 3695, 8132, 18, 2176, 1977, 2899, 1922, 20306, 4879, 5148, 27747, 8362, 9417, 24222, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MRTSLRIRTRRLALVAAVSAAGAACVLLVDWAHLSDIGQAYGGVSALIATIGVFGVAASLHSAILLFAVEHPEYLQCWGGYSVENNGLSGQYDLDGVRRNIAHFFEGELGREYWKVVEQQFRRAEAGGPPTPWDVGFGLALGGVAVGAAGGWLVRRLASRFLSPLSFPLLDRIDGALGQVRESRRAGIRDERQLKATSYRAFCNLVFLNYYSMYHSHESWMSGKDKGRRRRAFLNRSGVEVGGPPPAGPDDAVATSR", "metadata": {"id": "A0A1K1S4H4", "cluster": 1936355, "interpro_all": ["IPR045728"], "interpro_used": ["IPR045728"], "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 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 originates from Vitis vinifera (Grape) and carries UniProt keyword assignments Transmembrane helix, Transferase, and Receptor.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 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, 22970, 2037, 29677, 1036, 11132, 19582, 12, 18673, 13, 1930, 16252, 20709, 11121, 2538, 18306, 9117, 7864, 16, 13763, 16, 1930, 3148, 18, 3], "output": "MIIRFNRGVRLDWKGISYLHENSRLRIIHRDLKPSNVLLDGDMQGSLHEVRMELTLLKYGYMAPEYAMEGLYSSKSDVFSFGVLLLEMLTGRKNSGFHLSGMGLSLLSYVSLFRVVAL", "metadata": {"id": "A0A438H1K1", "cluster": 2697159, "interpro_all": ["IPR011009", "IPR000719", "IPR008271"], "interpro_used": ["IPR011009", "IPR008271"], "interpro_unused": ["IPR000719"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein is classified under 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. Additionally, the protein is assigned 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. In addition, 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. It has been characterized in Spirochaetaceae bacterium 4572_59. 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, 5947, 2441, 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, 4950, 16, 1920, 2213, 1977, 6304, 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, 1922, 2459, 16, 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, 2176, 2258, 2252, 4378, 1922, 22075, 25588, 9215, 1972, 3336, 14061, 30321, 1028, 41, 4777, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MAAMEITVLVIEDQLALREYLRKILEKEAYRVLTASSGKEALALLKKQDPDIILLDLLLPERRHWLFSKNRIRILSCWI", "metadata": {"id": "A0A1W9V4V8", "cluster": 9949726, "interpro_all": ["IPR050595", "IPR011006", "IPR001789"], "interpro_used": ["IPR011006", "IPR050595", "IPR001789"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: The protein should feature a Tyrosine-protein kinase ephrin type A/B receptor-like domain that functions as the intracellular catalytic unit of ephrin type A and B receptors, mediating signal transduction by transferring a phosphate group from ATP to specific tyrosine residues on substrate proteins. This kinase activity regulates essential cellular processes, including differentiation, adhesion, motility, and growth. Also, the protein falls within 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 is native to Tupaia chinensis (Chinese tree shrew) and is described by UniProt keywords Glycoprotein. 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, 5961, 43, 6941, 17, 2213, 4016, 21717, 2601, 43, 19, 44, 3148, 17, 3189, 3418, 1988, 4088, 1966, 1920, 4776, 6804, 5344, 1927, 21717, 2601, 43, 1930, 44, 4086, 16, 10239, 2733, 8201, 2007, 21902, 43, 5413, 2210, 2037, 4498, 1942, 2487, 6941, 4248, 1990, 4510, 2697, 18, 2052, 4016, 2455, 7014, 4415, 3689, 4028, 16, 2710, 4155, 16, 6141, 16, 9254, 16, 1930, 2905, 18, 2222, 16, 1920, 2213, 12182, 2651, 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, 1977, 6196, 1942, 9037, 4302, 2126, 6790, 8134, 12, 7185, 6694, 6606, 2370, 13, 1930, 1977, 2910, 2007, 20709, 11569, 11424, 18, 4663, 2962, 2496, 2213, 3244, 8120, 3189, 35, 3], "output": "MARAGEVQVDQTSFPQETVLQDTGAREELPERTPPMERGASSAHLGTTALKERQFQPDAHLAPGLRKGLEPLEDAELAPQDSSALGASRPSGQHPAVQGFYCPEGTGLDWQPCPPGTYSPEPGLGSWSECRACDGGRFCPEANATEAGGQCREGFFCSRGSTRPNPEAGTEAAAGPCPRGHYCPKGSAVPQPCPPGTFGPRIKLSSEAACSPCLPSHHCGSAGLAHPSGPCSDGFFCLRGALVPNGSLGDGTSGPCPAGHFCPPGTVTPRPCPAGTYNALPAQGRCEPCPQGFFCLANTSLVVGKECPAGHYCPASTAFPSQFPCPRGTYKPQKGGVRKSDCTPCEPGSFQPIPGATSVEDCQPCPAGWFCSLAGLSSPEALCEGGWYCPGASVSGHSPDAICPTGHSCPPGSPEPRLCPPGQYQDEPGRSICKMCPAGKFCPLGIQGPGSRPIWPVDCPAGYYCPLGTQTPTQHPCPGGTFRERPGARSAKDCRPCRAGQFCSDSGAGKRLPDGPCSAGYYCPPGQTSATPTSFRCPPGFSCPEGSPQPRACANGTFQPQEAQGSCEPCPAGFYCEASGTGPAARGPSLCLQGYFCPLGSHSATAHPCPRGTFGPRRGAAAELDCELCPAGMFCSSEGLPQPSGLCQSAYYCTGGAVSPTPIKHRVEAPGLSGNDVCPSGFFCPQGTGFPVPCPSGFYSSVPGLDSKEQCQPCPPGHYCSRPGLPSALEAGLCDAGYICLGGSTVPSPSDRIHGYRCPPGFHCPPGAHSELPCKPGTFSPLPGADACLPCPEGTYCHQAATVEPSTCPKGYYCEGGAASPTPQRNLAFPLNGPCPQGHYCPEGTLYPVPCPEGTMRNSPGGTSEGSCGLCLAGSFCPSVGLRSPTGSCVASSDCLSDPSASSPIALPCPQRLVVRRDWAQMNRRSTAPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPSGRKVSSLRISQGVLTNGRAQRQDPVNFA", "metadata": {"id": "L9L2D9", "cluster": 10219266, "interpro_all": ["IPR009030", "IPR011641"], "interpro_used": ["IPR011641", "IPR009030"], "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 is included in the Ureohydrolase domain superfamily, which encompasses enzymes sharing a 3-layer $\\alpha-\\beta-\\alpha$ architecture that hydrolyze non-peptide carbon-nitrogen bonds, including arginase, agmatinase, and histone deacetylases. These enzymes are critical for arginine metabolism and the urea cycle, catalyzing reactions such as the conversion of arginine to urea and ornithine or agmatine to putrescine. They function across diverse pathways ranging from nitrogen excretion and polyamine biosynthesis to histidine degradation. It occurs in Okeania sp. SIO2D1.", "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, 3063, 1922, 1920, 6794, 8601, 21524, 3418, 13975, 16, 2154, 21569, 5038, 10763, 43, 23, 17, 4757, 8, 38, 4595, 17, 38, 4666, 17, 38, 4595, 8, 9335, 1988, 7222, 6931, 2447, 17, 4207, 5056, 17, 6634, 9031, 16, 2710, 26132, 16, 2260, 3368, 28010, 4127, 16, 1930, 6632, 19489, 1036, 18, 2144, 5038, 2032, 4140, 1958, 9732, 4714, 1930, 1920, 10505, 4048, 16, 29601, 5298, 2427, 1966, 1920, 7309, 1927, 9732, 1942, 10505, 1930, 26918, 2014, 2260, 3368, 4425, 1942, 5366, 2808, 11388, 18, 2611, 2347, 3436, 6445, 3873, 6485, 2037, 6634, 11093, 1930, 27883, 8132, 1942, 13873, 4877, 18, 2176, 5110, 1922, 12167, 5376, 10306, 2056, 18, 17139, 7240, 18, 3], "output": "MGPDAYRTAGLEAALGALGHTVTERGNVAATPAKTADSPAPHLHQPHETIGWTAALADATELAAKDGMPILLGGALTSTTTTWTIARESEA", "metadata": {"id": "A0A6P0XAP4", "cluster": 11430361, "interpro_all": ["IPR023696"], "interpro_used": ["IPR023696"], "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 features a Aldehyde dehydrogenase domain that oxidizes a wide variety of aliphatic and aromatic aldehydes using NADP as a cofactor. This catalytic region relies on conserved cysteine and glutamic acid residues and is found in dimeric or tetrameric enzymes across bacteria, fungi, and mammals. Additionally, the protein is classified under the The Aldehyde/histidinol dehydrogenase superfamily, which encompasses NAD(P)-dependent oxidoreductases that catalyze the conversion of various aldehydes and alcohols, such as L-histidinol, into their corresponding carboxylic acids. These enzymes, characterized by a conserved 3-layer $\\alpha/\\beta/\\alpha$ structural domain and a catalytic cysteine, include aldehyde dehydrogenases that oxidize diverse aliphatic and aromatic substrates as well as histidinol dehydrogenases essential for the final step of histidine biosynthesis. It has been detected in Caenorhabditis japonica.", "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, 18727, 9294, 3418, 1988, 3618, 4517, 43, 4743, 5386, 1927, 22234, 1930, 10761, 25075, 2193, 24221, 1966, 43, 15155, 18, 2052, 6804, 3031, 12850, 1990, 5305, 8666, 1930, 18626, 2687, 4248, 1930, 1977, 2435, 1922, 18150, 2014, 30442, 5038, 3436, 4802, 16, 10520, 16, 1930, 9902, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 1920, 18727, 19, 27507, 22816, 1945, 9294, 13975, 16, 2154, 21569, 6577, 12, 58, 13, 17, 3100, 27388, 1036, 1988, 18170, 1920, 7309, 1927, 3425, 25075, 1930, 21773, 16, 2427, 1966, 54, 17, 27507, 22816, 1945, 16, 2460, 2310, 3980, 18708, 4576, 18, 2144, 5038, 16, 4378, 2007, 43, 5305, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 4346, 3418, 1930, 43, 6804, 8666, 16, 3951, 18727, 9294, 1036, 1988, 3618, 2606, 6445, 22234, 1930, 10761, 6249, 1966, 2486, 1966, 27507, 22816, 1945, 9294, 1036, 4415, 1958, 1920, 3948, 3537, 1927, 13873, 8132, 18, 2176, 2258, 2252, 3330, 1922, 22418, 27096, 18, 3], "output": "XKLYQIGDPLDRSTAHGPQNHLAARLDGHGLFFPPTILSNVDDDVLRRANDTEFGLAAGVFTLRFCDVSKPGRFETGTIHLNKLIEYVQKSVKDGAKVEVGGENFAASEESFGPIMCISSFDDDDIEKDASKSLRVAEVTFFNRF", "metadata": {"id": "A0A8R1HRL8", "cluster": 12607050, "interpro_all": ["IPR016161", "IPR016163", "IPR015590"], "interpro_used": ["IPR015590", "IPR016161"], "interpro_unused": ["IPR016163"]}, "task_type": "infilling"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: It is part of 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. Additionally, the protein includes 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 derived from Haloprofundus marisrubri and is associated with UniProt keywords 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, 2176, 1977, 3131, 1927, 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, 4950, 16, 1920, 2213, 5921, 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, 3595, 2037, 23226, 2216, 19073, 10249, 1957, 13081, 19025, 2255, 3027, 1930, 1977, 2458, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MDGSYIEDDYSGTGAVLGGEAYALGVVFDEDEDQLAIRRDGTVLYAVGLDDEPLEVQRGEDYASADGENPERRIDFQASFDALETDDSFAVESRVVGSVVEEVQNYADIVVVVDDGSSRNRGYGAALQTLFVEGKQRNAGGDVQRLLRRQQECSADIVIGSRFTGINTLTNLGLGTFRKSERIGDTQSGFRAYGPHARKRGYAIDEIGIKIRYDLEDTYDRPLTTLGVPGFISAFAGLSVGYWGFFASVFAIVHQSLRSVRSPHLLRLLSRAGQYGCPLTIRETLVDIAQSHGFRGLVVHEPRLIEEKPVEAPIVVGLPAYNEEKSDRTAERAAAAGAVVVRHSSLVVIDADGQHDDVASEIPLYRRFGLWVRAIESLAEDDTLGSSMEASTDILFTHNPLLHGYSVVKGVLRLIERSMFEYGQSGEFPLALVGLSGLLLLV", "metadata": {"id": "A0A0W1RC76", "cluster": 12727804, "interpro_all": ["IPR001173", "IPR050256", "IPR029044"], "interpro_used": ["IPR050256", "IPR001173"], "interpro_unused": ["IPR029044"]}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein should include a Macro domain that recognizes and binds mono- or poly-ADP-ribose and related NAD metabolites, serving as a regulatory module in ADP-ribosylation signaling. Structurally characterized by a mixed \u03b1/\u03b2 fold with a central hydrophobic cleft, this domain is found across eukaryotes, bacteria, and viruses, where it participates in chromatin biology, DNA repair, and transcriptional regulation. Also, the protein is categorized 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 has been detected in candidate division WOR-3 bacterium JGI_Cruoil_03_51_56.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 3066, 3951, 43, 10133, 3418, 1988, 16197, 1930, 6876, 8914, 17, 2014, 4286, 17, 9828, 17, 17870, 1930, 2712, 6577, 6926, 16, 13915, 1966, 43, 4948, 9059, 1922, 9828, 17, 29117, 3017, 3197, 18, 12171, 4378, 2007, 43, 4985, 160, 19, 161, 3728, 1956, 43, 4101, 7919, 14649, 16, 2052, 3418, 1977, 2435, 3436, 15021, 16, 4802, 16, 1930, 6241, 16, 2597, 2176, 17241, 1922, 6338, 7256, 16, 2678, 5059, 16, 1930, 5224, 3640, 18, 2222, 16, 1920, 2213, 1977, 10234, 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, 2258, 2252, 3330, 1922, 6610, 8451, 4315, 17, 23, 14061, 52, 6121, 41, 2345, 22914, 1970, 41, 5167, 41, 4892, 41, 4489, 18, 3], "output": "MNNRNQLTKSFRNLTITVLSGDVAGAIKRRGGKEIEDEAMKKGPVHAAVMGQDLATNSALITKPALGTGVGGFPLDKAGRLMIDAVIAHKAFGKALESTPQENGIAITEQPVDAIVNAANNRFWMGGGEPGLAITTSAGKLPARYCIATLSSLAEASRLNLETIAFSHKNNLPKEVRFVLFTADAQ", "metadata": {"id": "A0A235BXI2", "cluster": 12837081, "interpro_all": ["IPR002589", "IPR043472"], "interpro_used": ["IPR002589", "IPR043472"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: It is part 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. In addition, the protein features a RDD domain that functions as a Na+(Li+, K+)/H+ antiporter. This region contains two predicted transmembrane helices and is named for a conserved motif comprising one arginine and two aspartates. Additionally, the protein includes 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 present in Microcystis aeruginosa Ma_MB_F_20061100_S20D and exhibits UniProt keyword tags Transferase and Transmembrane helix.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 2176, 1977, 3131, 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, 1922, 2459, 16, 1920, 2213, 4075, 43, 8695, 1007, 3418, 1988, 4088, 1966, 43, 4049, 15, 12, 2336, 15, 16, 53, 15, 13, 19, 50, 15, 2246, 24095, 18, 2052, 3031, 5461, 2288, 4396, 9117, 12789, 1930, 1977, 10314, 1958, 43, 5305, 5219, 10351, 2340, 9732, 1930, 2288, 12878, 1036, 18, 4950, 16, 1920, 2213, 5921, 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, 2481, 1922, 10572, 2298, 1937, 10830, 2488, 41, 5667, 41, 48, 41, 3956, 24307, 1008, 41, 5159, 1008, 1007, 1930, 9826, 20709, 11121, 2538, 14392, 13763, 1930, 9117, 7864, 18, 3], "output": "MSFCINPHCPKPKSITESRYCQSCGSDLLLNGKYRVTNLLSAKGGFGNTYEVIDERKIPKVLKVLTYDSSKAIDLFQQEANLLKQLNHPGIPKGENYFIYHPRESQTALHCLVMEKIAGIDLEEHQKQRGFKPIDYNLALDWLSQLANILHEVHKHKFYHRDIKPSNIILKPDGQLVLIDFGAARQVTKTVLAGGKNTGIYTPGYAPPEQSLGHSVPQSDFYALGKTFVFLLTGKEPSDPKIYNINTNEFNWRKYAPNIPSRLADFIDNLMAEKPINRPKDTKTLLKIITDIKANPHQTKKTKNSAPEKPKIIPIPNPALISVFAAISPSYAGFWLRFKASVIDSFIVLIVAALLGGYICFRLQQWSTFQDLNLNFNIPKEIWVYYAAGLSAAGTTIIGFALFIAAIIYNIQAKVNFTHEHIAILTALGLGIVIKWLYYVFLEYLFKATIGKMFFDLSVTDSQGRRISFARANRRYLLKYLSTAPLYLGFLLAAWTKKKRALHDMISGTQIRKKK", "metadata": {"id": "A0A552EBF5", "cluster": 15241345, "interpro_all": ["IPR011009", "IPR000719", "IPR010432", "IPR008271"], "interpro_used": ["IPR011009", "IPR010432", "IPR008271"], "interpro_unused": ["IPR000719"]}, "task_type": "autoregressive"} {"instruction": "Provide the amino acid sequence of a protein with the following function: The protein features a SRR1-like domain that functions as a signaling module involved in regulating the circadian clock input pathway and maintaining normal oscillator function. It modulates the expression of clock-regulated genes in plants through phytochrome signaling, influences heme-regulated rhythms and cell proliferation in mammals, and contributes to microtubule stability in yeast. It is found in Strongyloides papillosus (Intestinal threadworm).", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 4581, 7011, 17, 3189, 3418, 1988, 4088, 1966, 43, 3197, 9059, 3286, 1922, 6773, 1920, 10507, 10357, 5877, 3374, 1930, 8231, 2791, 25539, 2347, 18, 2176, 13112, 1920, 2294, 1927, 10357, 17, 4335, 2628, 1922, 4793, 2596, 25512, 2072, 4191, 3197, 16, 8061, 10954, 17, 4335, 16622, 1930, 2024, 4031, 1922, 9902, 16, 1930, 7624, 1942, 10544, 5057, 1922, 5688, 18, 2176, 1977, 2435, 1922, 3206, 2199, 12363, 14668, 13650, 12, 6139, 18205, 16620, 13, 18, 3], "output": "MDSDGFVIVAKRRSCKPKLKIDEMNFIYPCTIEISFKRTNENVCRAINQLTKDKYINMFLTLLEKILNGDRISKIKCYGIGHFGELDGSGTYQLALLILIQKHYNISVTIQEPILNDVEINYINNYPFFEYISGDDLTSIEISESQNDYVLFFIPHGEDEMYEGILKTHNNEKQRQKMIILGNVLDDISITYKNISNFKYWKEYYDVCKKHILPTYSKCMGAFNNTCLMYN", "metadata": {"id": "A0A0N5BDD7", "cluster": 16271296, "interpro_all": ["IPR012942", "IPR040044"], "interpro_used": ["IPR012942"], "interpro_unused": ["IPR040044"]}, "task_type": "autoregressive"} {"instruction": "An incomplete protein sequence has the following functional profile:\nThe protein can be placed 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. Moreover, the protein carries a TonB-dependent receptor, plug domain that acts as an independently folding channel gate within bacterial outer membrane receptors, blocking the pore until ligand binding induces conformational changes to open the pathway. It facilitates the high-affinity, energy-dependent uptake of specific substrates into the periplasmic space by coupling with the TonB-ExbBD complex. In addition, the protein contains a TonB-dependent receptor-like, beta-barrel domain that forms a bacterial outer membrane channel enclosing a gating plug domain. It facilitates the high-affinity active transport of scarce substrates, such as iron-siderophores and vitamin B12, by interacting with the TonB complex to transduce energy for pore opening. It has been characterized in Fidelibacterota bacterium and is described by UniProt keywords Cell outer membrane, TonB box, and Transmembrane beta strand.\nPlease supply the amino acids for the masked tokens.", "tokenized_instruction": [2, 1925, 9876, 2213, 3244, 2258, 1920, 2894, 3183, 5174, 30, 1920, 2213, 2112, 1998, 5396, 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, 3950, 16, 1920, 2213, 16252, 43, 16501, 1014, 17, 3100, 3148, 16, 15998, 3418, 1988, 8016, 1966, 1925, 6407, 10328, 4999, 11898, 2651, 4543, 7642, 3260, 4086, 16, 7472, 1920, 8554, 4801, 5207, 2743, 6387, 8523, 2840, 1942, 4437, 1920, 3374, 18, 2176, 11374, 1920, 2149, 17, 5173, 16, 3844, 17, 3100, 5047, 1927, 2487, 6249, 2460, 1920, 24334, 5230, 2007, 7590, 1956, 1920, 16501, 1014, 17, 1975, 6936, 1007, 2796, 18, 1922, 2459, 16, 1920, 2213, 5461, 43, 16501, 1014, 17, 3100, 3148, 17, 3189, 16, 4666, 17, 19560, 3418, 1988, 4952, 43, 4543, 7642, 3260, 4999, 17439, 11934, 43, 12568, 15998, 3418, 18, 2176, 11374, 1920, 2149, 17, 5173, 3500, 4860, 1927, 16937, 6249, 16, 2427, 1966, 5680, 17, 22940, 14820, 1930, 6111, 17492, 16, 2007, 8615, 1956, 1920, 16501, 1014, 2796, 1942, 30334, 3844, 1958, 8554, 9497, 18, 2176, 2258, 2252, 4378, 1922, 26209, 30466, 2422, 7336, 14061, 1930, 1977, 2910, 2007, 20709, 11569, 2024, 7642, 3260, 16, 16501, 1014, 5758, 16, 1930, 9117, 4666, 5984, 18, 11586, 9042, 1920, 3835, 4576, 1958, 1920, 17476, 26923, 2099, 18, 3], "output": "MIFKFKFYFFFIFIIITVLDAQSDRVSGKIRGRAVDAMTKDPLXGANVLLLPVESGRGTMVSYMGYASTXIQSIEVSPGATTEILCSMGVEAIEGQEVNVVAESMENTVDVKSVVTVIANAGGVVKTEAGRSRGIHMRGGRSGEVAFYVDGILTNDPVDRSQGVQIDAMSGIVTVVTKSGSKQNYSGNLIFETDQISNNNSVYNNGYGKYNLAGSNIVSPRSIKLPHSXYTHPMGTFKMTFSPPSSGFNAIISASFEDKATNTLGKNTAWRLMISTFEHYNNYGSGENXSYKDFHYLSTRLDWVYYAENNGWYDPKTRIWKEDDLSGGTNNNPVQLSXXPYEEQAFYYYYYTQGNQFDLSTGMWSSESEKVVYYNSLDSVAHFKEFDEKEYASYLFGDDDFQRSNDLWAYRGNMHNGYYYDRKSVSTHSSIEFQLNTQWSIRNAAKFGFKTTASTMDYRDIQFENKYENNDFILMSGLRWDYFDPNVESLKTSLLVDDGXVERXPAKVKIKLSYGYFVQFPQYAEMYQNVYADISSGLPLVGNPNITPEETIQYQFGLAHKLRTYPVLIEGQVASVTVMEMEDYAKIKGIEFKLKLNNFSNLNREYXYLYIFDSDRPXPVKEYPMEFDITHSVKFNLNYYLPARNSNSFIGRLTSDWNFNFQYKSLDMRVEKYXNNFSMYLDIRNVFNWVNTTYVYSYSGEPDTNGIISSAEEAYDTHLQLWRSLLXNPYNYSSARYFXFGINLWFTNENGEFVIPNLITGVYSVKQVKYSGDQLYKMPVSNFTDKESIDVLTISKGGFSAEFGEQFGGPFPGLKKYLSFYXSGSYESYSHSISKGDWLXDYYKTLEGSRRLSLQIQLTDANGLPLISDNYFVIAYNQRWHEAGTWYIPAFLDDESNDIFNVYTFGPGRPRSHANQNPYFDSYNYEPLSGSAYVPRLGINFNASDKTAIYTNSPTLGLEIISFFKDQMNLATNTGDIDYTWMSAKGTGSSGNLATGAPYTPTDIYGKAQEIGSKRMPGRPPVFERSRYLQYIGDTXPISGN", "metadata": {"id": "A0A2E0CZY7", "cluster": 17801395, "interpro_all": ["IPR013784", "IPR012910", "IPR037066", "IPR039426", "IPR000531", "IPR036942"], "interpro_used": ["IPR013784", "IPR012910", "IPR000531"], "interpro_unused": ["IPR036942", "IPR039426", "IPR037066"]}, "task_type": "infilling"} {"instruction": "The protein is classified under 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. Also, the protein should have 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. Moreover, the protein has 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. It is found in Alkalicaulis satelles and is associated with UniProt keywords Hydrolase and Protease.\nEvaluate this biological role and generate the missing polypeptide segments.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 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, 2222, 16, 1920, 2213, 3066, 2162, 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, 3950, 16, 1920, 2213, 2258, 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, 2176, 1977, 2435, 1922, 25178, 3375, 13004, 1036, 5784, 10371, 1930, 1977, 2458, 1956, 20709, 11569, 20748, 1930, 7154, 18, 4323, 2052, 3933, 2770, 1930, 5655, 1920, 6814, 13022, 7492, 18, 3], "output": "MRANSSLLWTLVLAGVIALTVRTLVFQPFTIPSDSMRPALEPGDRGRVFERLPERGDIVVFTPPHAPRTAYIKRVIGLPGDMVTVSGARYQVWQEILEGGRGYLVHDAGPGPLTEFGPVLVPDGHVFVLGDNRSIIGRADRVLLSVRPDFSLWKPWTWTRIRTGRTFLSLDPEPRYVAVAKWPYGWSRLSLPLAPPLPVVHINGAPVPRGLVGEETRLSSDGEMTESRDSRAAAPEGPGMAPVDH", "metadata": {"id": "A0A5M6ZL03", "cluster": 19286217, "interpro_all": ["IPR036286", "IPR000223", "IPR019758", "IPR019757", "IPR019533"], "interpro_used": ["IPR036286", "IPR019533", "IPR019758"], "interpro_unused": ["IPR000223", "IPR019757"]}, "task_type": "infilling"} {"instruction": "Design the missing regions for a protein's amino acid sequence that will have the following function: The protein can be placed 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. In addition, the protein includes a Pyrrolo-quinoline quinone repeat domain that forms a \u03b2-propeller structure found in diverse bacterial quinoproteins, particularly dehydrogenases. It functions by binding the redox coenzyme pyrrolo-quinoline quinone (PQQ) to facilitate enzymatic redox reactions. In addition, the protein is categorized in 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 identified in Kangiellaceae bacterium and features 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, 2112, 1998, 5396, 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, 1922, 2459, 16, 1920, 2213, 5921, 43, 23878, 1037, 17, 9012, 8419, 25093, 6865, 3418, 1988, 4952, 43, 161, 17, 5062, 13728, 3170, 2435, 1922, 6445, 4543, 9012, 14070, 16, 4443, 9294, 1036, 18, 2176, 4088, 2007, 2743, 1920, 9366, 22051, 23878, 1037, 17, 9012, 8419, 25093, 12, 15564, 1055, 13, 1942, 6628, 8145, 9366, 5298, 18, 1922, 2459, 16, 1920, 2213, 1977, 10234, 1922, 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, 2899, 1922, 23940, 19918, 1972, 3336, 14061, 1930, 4075, 20709, 11569, 2733, 18, 3], "output": "MTWFATNATWLSTRVFNRVLLFISVLCGFHPLAQAAPGDLLWTHTTSDQIRSSAALAQDQALTPGAFGATIIDSPVLAPDGTIYVSTSAGLHAVSPLGEQQWIYSSNFSGTRSAAVGPNGVSNISTSPVVAPDGTIYVGSFDDHLYAINPNGTLKWRFETGGDIAPPAIFATGGKIDASPVISSTNTIYIPSWDKNFYALTPFGLEMWHFTTDDVLAATPTLGNDDSPLIDSTGTLYLGSTSKHFYAIETTATGLQSGYWPTLGHNAQRQFHAIDTDGDGTIDAKDSDDDNDNFPDESNSATISWGTIYFGDHDGFLNAMSSSGELLWQYGEIYVPRNSLHALDADGNLVWVFDASQGDIVFGSSDGIVYMVDSDGTELWRLIYLPARDGNLYALDRSGNLVWSYDTGEWLLT", "metadata": {"id": "A0A2E2VSN1", "cluster": 21891779, "interpro_all": ["IPR018391", "IPR002372", "IPR011047", "IPR015943"], "interpro_used": ["IPR015943", "IPR002372", "IPR011047"], "interpro_unused": ["IPR018391"]}, "task_type": "infilling"} {"instruction": "The protein features 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 is found in Seminavis robusta. Here is the functional description of a protein. Can you give me the amino acid sequence?", "tokenized_instruction": [2, 1920, 2213, 4075, 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, 1977, 2435, 1922, 19381, 9188, 1036, 5786, 1019, 18, 3410, 1977, 1920, 3183, 8418, 1927, 43, 2213, 18, 2112, 6253, 7031, 2142, 1920, 3835, 2687, 3244, 35, 3], "output": "MSSSSVWVQLYYNKGKDEPEGRPTSVKKPNDPLIVVAPAQKQQQRLEFCRTWSSEGNHLPYNLLAKSYDDLQRQIQGDSDLEEFIQISNTPAVLAWERGSDGSPTGFPGEIAAPFSGSNVSSISTSTLGHIQKVFQAALLVRDKRKCVVSGTQYREGSGNVQAAHIIPVAAKKRVLEQAKICSIYDTCNGMLLESTLHKAFDSYLWCLNENGVFCVSDAERHQKKIKEYGIAKYRSNVLDLSGDNFPTKATLRARHALFQSKVDKAKNQGNKKS", "metadata": {"id": "A0A9N8DSF0", "cluster": 22910968, "interpro_all": ["IPR003615"], "interpro_used": ["IPR003615"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Provide the amino acid sequence of a protein with the following function: It 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. Also, the protein is classified under 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. Additionally, the protein belongs to the Tryptophan synthase, alpha chain family, which catalyzes the aldol cleavage of indole-3-glycerol phosphate to indole and glyceraldehyde 3-phosphate during the final step of tryptophan biosynthesis. This component functions in concert with the beta subunit, existing as a separate polypeptide in bacteria and plants or as a fused domain in fungi, to facilitate the production of L-tryptophan. It is found in Leptospiraceae bacterium and corresponds to UniProt keyword Amino-acid biosynthesis, Aromatic amino acid biosynthesis, and Lyase.", "tokenized_instruction": [2, 3394, 1920, 3835, 2687, 3244, 1927, 43, 2213, 1956, 1920, 2894, 2347, 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, 2222, 16, 1920, 2213, 1977, 5947, 2441, 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, 4950, 16, 1920, 2213, 14440, 1942, 1920, 13489, 8921, 16, 4595, 4659, 3416, 16, 2154, 17097, 1920, 11174, 1945, 6404, 1927, 18050, 17, 23, 17, 9244, 5413, 1942, 18050, 1930, 22447, 23, 17, 5413, 2409, 1920, 3948, 3537, 1927, 13489, 8132, 18, 2052, 4594, 4088, 1922, 21799, 1956, 1920, 4666, 5903, 16, 6124, 1966, 43, 5850, 13022, 1922, 4802, 1930, 4793, 2014, 1966, 43, 10305, 3418, 1922, 10520, 16, 1942, 6628, 1920, 3372, 1927, 54, 17, 13489, 18, 2176, 1977, 2435, 1922, 24060, 11979, 1972, 3336, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 3835, 17, 2687, 8132, 16, 10761, 3835, 2687, 8132, 16, 1930, 23928, 18, 3], "output": "MTVNNESNLAQYIGQRQSARGGGPVYMPYLTVGDPDFDSTVQFAVQMIDAGADILELGIPFSDPTADGPVIQAAIVRALGHPDFSMRRVFSVAKAIHTQRPEVPLVFLSYMNPVLNGLNPAPRINFQARPEDADRLMYDTAAALDSFLQQCVESGVQALVIPDLPFDQPEAILIRERLERYGVHQILMVAPNTSDERLNRICEAASGFIYYVTSLGVTGIRKDLQLPADLKSRIARIRERSGVPVMAGFGINTPGQIEPLRGVVDGIIVGSLHHRIIGELGASAAGQLVDATAGFVAACNQS", "metadata": {"id": "A0A961IIS9", "cluster": 23837643, "interpro_all": ["IPR013785", "IPR011060", "IPR002028"], "interpro_used": ["IPR013785", "IPR011060", "IPR002028"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein contains a DUF4912 domain that adopts an immunoglobulin-like (Ig-like) fold and is found in uncharacterized bacterial proteins, such as TP_0359 from *Treponema pallidum*. It is produced by Deltaproteobacteria bacterium CG07_land_8_20_14_0_80_38_7. Can you generate its sequence?", "tokenized_instruction": [2, 3410, 1977, 1920, 3183, 8418, 1927, 43, 13022, 4659, 51, 12914, 1942, 3036, 30, 1920, 2213, 5461, 43, 4855, 10432, 12118, 1028, 3418, 1988, 24032, 1925, 11837, 17, 3189, 12, 7021, 17, 3189, 13, 3728, 1930, 1977, 2435, 1922, 24528, 4543, 2697, 16, 2427, 1966, 6213, 41, 21770, 1026, 2037, 14, 2171, 21851, 6666, 12574, 10015, 1035, 14, 18, 2176, 1977, 4152, 2007, 9649, 9218, 1021, 10296, 14061, 7294, 14099, 41, 7559, 41, 28, 41, 2036, 41, 2607, 41, 20, 41, 3729, 41, 3738, 41, 27, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MRKKKTVKKSFSSKKQLSKKTGLIKKAEALRKKTTKKVKTSKIAAKTLIRKNKNGDLKPKKTVKTKKQFALSKSTKEKKHSKLIKPKSFSKKKTNKVTLFEELIIEAKTDSTVHEQSRIEESKFDLGIPENAKAMPEHELPSSYNKDQAVILTVSPHFVFAYWEVTNNSMHEAVSKIGYNTKLTLRFYDITLSSNPDHSPHWDIEVFDRLGNWYLKLDYPEQKLTLDIGLKNEFGNFYPLTRSNTIKLPRTTLADPGPLKWMIVTDLGDKITTDIEDYTDADLELLRKILGPHFFDLLIKGKFSTIEGSNLEAVFQEISSFRLRQDSSSSPTMWSNH", "metadata": {"id": "A0A2M7A0A3", "cluster": 24815130, "interpro_all": ["IPR032585"], "interpro_used": ["IPR032585"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein I want to design has this role: The protein belongs to the 5-oxoprolinase subunit C family, which catalyzes the ATP-dependent cleavage of 5-oxoproline to L-glutamate as part of the glutathione degradation pathway. In *Bacillus subtilis*, this protein also regulates sporulation by binding the inhibitor PxpB (KipI) to prevent its suppression of kinase A. In addition, the protein has a Carboxyltransferase domain, subdomain A and B domain that constitutes the N-terminal portion of the carboxyltransferase component in biotin-dependent enzymes like urea carboxylase and urea amidolyase. It interacts with subdomains C and D to facilitate the ATP-dependent carboxylation of urea, although variants such as *Bacillus subtilis* KipA lack catalytic residues and function primarily as structural binding partners. It occurs in Halalkalibacter hemicellulosilyticusJCM 9152 and is linked to UniProt keywords ATP-binding and Hydrolase. What would the amino acid sequence be?", "tokenized_instruction": [2, 1920, 2213, 51, 12914, 1942, 3036, 2258, 2052, 2770, 30, 1920, 2213, 14440, 1942, 1920, 25, 17, 18588, 15743, 11413, 5903, 45, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 6404, 1927, 25, 17, 18588, 15743, 2053, 1942, 54, 17, 7627, 1966, 3131, 1927, 1920, 9153, 4877, 3374, 18, 1922, 14, 14587, 14745, 14, 16, 2052, 2213, 2222, 7014, 23647, 2007, 2743, 1920, 4106, 15194, 16752, 12, 8191, 10984, 13, 1942, 4625, 2496, 6412, 1927, 4016, 43, 18, 1922, 2459, 16, 1920, 2213, 2258, 43, 9943, 9961, 3418, 16, 27517, 43, 1930, 44, 3418, 1988, 14879, 1920, 56, 17, 4262, 7717, 1927, 1920, 9943, 9961, 4594, 1922, 8622, 17, 3100, 5038, 3189, 10505, 29073, 1930, 10505, 28813, 26558, 2051, 18, 2176, 9034, 1956, 30103, 45, 1930, 46, 1942, 6628, 1920, 4498, 17, 3100, 9943, 1943, 1927, 10505, 16, 2876, 4936, 2427, 1966, 14, 14587, 14745, 14, 8191, 4302, 3630, 6804, 4248, 1930, 2347, 5985, 1966, 4346, 2743, 7228, 18, 2176, 5110, 1922, 4217, 5135, 12498, 7972, 2341, 1915, 25482, 1992, 11677, 2869, 2002, 1957, 30271, 1035, 6550, 8982, 1930, 1977, 4624, 1942, 20709, 11569, 4498, 17, 2743, 1930, 20748, 18, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 35, 3], "output": "MTIEIVKAGLLTTVQDTGRIGFQKAGVSIGGAMDIDAIQIANVLVGNDENEAALEVTMTGPTMQFNESVMFAITGGDLSPKLNGAQIPLNRPIIAKREMNFPFIKSKMDVVLILPLREACK", "metadata": {"id": "W4QA09", "cluster": 26811553, "interpro_all": ["IPR003778", "IPR052708"], "interpro_used": ["IPR052708", "IPR003778"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that can perform the following function: The protein is categorized in the VapC family, which functions as the toxic component of a toxin-antitoxin (TA) module. Members are ribonucleases that often act as endonucleases specifically targeting initiator tRNA (fMet) to inhibit translation, while lacking activity against DNA. Moreover, the protein has 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 native to Nitrospiraceae bacterium and is annotated with UniProt keywords Hydrolase, Magnesium, and Metal-binding.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10234, 1922, 1920, 16697, 1030, 3416, 16, 2154, 4088, 1966, 1920, 6161, 4594, 1927, 43, 9165, 17, 10310, 9754, 12, 4410, 13, 9059, 18, 4678, 2032, 18347, 2319, 1988, 3868, 4033, 1966, 18697, 1036, 4475, 5133, 23467, 10089, 12, 5620, 1946, 13, 1942, 2875, 6410, 16, 2679, 7046, 2455, 3316, 2678, 18, 3950, 16, 1920, 2213, 2258, 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, 6196, 1942, 16665, 10984, 5524, 1972, 3336, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 20748, 16, 13148, 16, 1930, 6048, 17, 2743, 18, 3], "output": "MRSGRRQRNIGVKRRPAVEDRKRVVIDTNLLVRYLTDDDPVKAKAVDALLNKAGSGEIKILVPSSVIAELVWVLESSYNMESAGLAELVDAVLNTPGVEVTDKSIIKSALKLYRAKKIDMIDAWIIEFAKDAGVGAIYTFDKKHFKDAEGIEARSP", "metadata": {"id": "A0A349ELY9", "cluster": 28691104, "interpro_all": ["IPR029060", "IPR002716", "IPR022907"], "interpro_used": ["IPR022907", "IPR002716"], "interpro_unused": ["IPR029060"]}, "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 includes a tRNA synthetases class I, catalytic domain that serves as the Rossmann-fold core of cysteinyl-tRNA synthetases, driving the ATP-dependent formation of cysteinyl-adenylate. This domain utilizes characteristic HIGH and KMSKS motifs for ATP binding to specifically aminoacylate the 2'-OH of the tRNA acceptor end, maintaining high fidelity despite lacking an editing mechanism. In addition, the protein should have a Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase anticodon-binding domain that specifically recognizes and binds to the anticodon region of cognate tRNAs. This domain is an essential component of class I aminoacyl-tRNA synthetases for methionine, valine, leucine, and isoleucine, ensuring translational fidelity by anchoring the tRNA to facilitate the attachment of the amino acid to the 2'-hydroxyl group. Also, the protein contains a Methioninyl-tRNA synthetase core domain that functions as the catalytic center of class I methionine-tRNA ligases, adopting a Rossmann fold to mediate the ATP-dependent formation of methionyl-adenylate. It contains conserved ATP-binding motifs and facilitates the specific attachment of methionine to the 2'-hydroxyl of the cognate tRNA, distinguishing it from related enzymes by the absence of an editing insertion. It has been detected in Candidatus Parcubacteria bacterium and is annotated with UniProt keywords Metal-binding, Protein biosynthesis, and Zinc.", "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, 5921, 43, 10089, 18185, 1036, 2921, 51, 16, 6804, 3418, 1988, 10634, 1966, 1920, 18215, 8890, 17, 3728, 4728, 1927, 20368, 1921, 2199, 17, 10089, 18185, 1036, 16, 9228, 1920, 4498, 17, 3100, 3337, 1927, 20368, 1921, 2199, 17, 23052, 18, 2052, 3418, 18127, 6293, 2149, 1930, 7477, 13254, 1036, 8277, 1958, 4498, 2743, 1942, 4475, 3835, 14645, 2010, 1920, 22, 11, 17, 5622, 1927, 1920, 10089, 12641, 2482, 16, 8231, 2149, 14013, 4281, 7046, 1925, 10454, 2856, 18, 1922, 2459, 16, 1920, 2213, 3066, 2162, 43, 2295, 2001, 2199, 19, 2326, 2199, 19, 9906, 2199, 19, 24467, 1978, 2199, 17, 10089, 18185, 11693, 28615, 17, 2743, 3418, 1988, 4475, 16197, 1930, 6876, 1942, 1920, 11693, 28615, 3031, 1927, 15786, 20770, 18, 2052, 3418, 1977, 1925, 4415, 4594, 1927, 2921, 51, 3835, 14645, 17, 10089, 18185, 1036, 1958, 12417, 16, 21884, 16, 12624, 16, 1930, 25398, 16, 14435, 8414, 14013, 2007, 20816, 1920, 10089, 1942, 6628, 1920, 8576, 1927, 1920, 3835, 2687, 1942, 1920, 22, 11, 17, 9420, 2210, 18, 2222, 16, 1920, 2213, 5461, 43, 2295, 2001, 1921, 2199, 17, 10089, 18185, 4728, 3418, 1988, 4088, 1966, 1920, 6804, 4102, 1927, 2921, 51, 12417, 17, 10089, 22423, 16, 20478, 43, 18215, 8890, 3728, 1942, 8265, 1920, 4498, 17, 3100, 3337, 1927, 2295, 2001, 2199, 17, 23052, 18, 2176, 5461, 5305, 4498, 17, 2743, 8277, 1930, 11374, 1920, 2487, 8576, 1927, 12417, 1942, 1920, 22, 11, 17, 9420, 1927, 1920, 15786, 10089, 16, 15589, 2176, 2037, 2712, 5038, 2007, 1920, 3905, 1927, 1925, 10454, 7413, 18, 2176, 2258, 2252, 3330, 1922, 14550, 1031, 1957, 2096, 18021, 7972, 2341, 18339, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 6048, 17, 2743, 16, 2213, 8132, 16, 1930, 7997, 18, 3], "output": "MAKSFLITTPIYYVNDEPHLGHAFTTLAADVYTRFLKNQGKKVFFLTGTDEHGLKIAEIAEEKGKNPKEFCDEISEKFKKTWKELLIEYDFFVRTTDEYHELAVKKFIEILKKKNQIYQKEYKGLYCVGCEKFLTEKELENGLCPAHRKAPQKVKEKNYFLKVKDKLSKIKSLIEKDKLKIFPEFAKKEALGLLKQSLDDLSISREKERVKWGIEFPGDKTQLVYVWFDALINYISAVGFATNKKKFERWWKKSFVIHFIGKDILKFHAIFWPAMLISAKIKIPNQLAVHGFFTVEGQKMSKSLGNVIRPKELIEKFGSDGTRYLILSQFPFGEDGDIRISKLIEKYNADLAFGLGNLVLRVLNLAKKQNISLRKIVAQKSIENEVKKRKNNYQKLLINFGFFESLKEIWDLIHFCDKYIDKEKPWEKKENSKKVILNLVFCLKEISRMLLPFCPQKSKEIQEQIEGKRKLEPLFKKI", "metadata": {"id": "A0A7C4JHL4", "cluster": 698240, "interpro_all": ["IPR013155", "IPR023457", "IPR015413", "IPR033911", "IPR014729", "IPR032678", "IPR009080"], "interpro_used": ["IPR032678", "IPR013155", "IPR033911"], "interpro_unused": ["IPR023457", "IPR015413", "IPR009080", "IPR014729"]}, "task_type": "autoregressive"} {"instruction": "Complete the polypeptide chain sequence by replacing the masked regions with the correct amino acids. Function: The protein contains a Peptidase S8/S53 domain that functions as a serine endopeptidase utilizing a characteristic Asp-His-Ser catalytic triad found in subtilisin and sedolisin families. This domain is widely distributed across all domains of life and includes the kexin subfamily, which specializes in processing proproteins by cleaving C-terminally to paired basic amino acids. Additionally, the protein possesses a Y4bN peptidase domain that functions as a serine endo- or exo-peptidase within the subtilase superfamily, utilizing a conserved Asp/His/Ser catalytic triad structurally distinct from trypsin. Found primarily in bacterial subtilisin homologues, this domain is often stabilized by calcium ions and can operate in diverse intra- or extracellular environments, including extreme temperatures and pH levels. Also, the protein can be placed in the Peptidase S8, subtilisin-related family, which comprises serine endopeptidases that function as pro-protein convertases within the secretory pathway. These enzymes cleave polypeptide precursors at specific basic sites to generate biologically active forms of diverse targets, including peptide hormones, receptors, and viral glycoproteins. It is found in Nitrospira sp and contains UniProt keyword associations Hydrolase, Protease, and Serine protease.", "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, 24050, 13808, 19, 8357, 1010, 3418, 1988, 4088, 1966, 43, 8468, 16239, 9626, 2410, 9200, 10232, 43, 6293, 4138, 17, 4167, 17, 2375, 6804, 21845, 2435, 1922, 14745, 1921, 1930, 6276, 23747, 1921, 5767, 18, 2052, 3418, 1977, 5673, 6533, 3436, 2136, 4682, 1927, 3308, 1930, 5921, 1920, 3364, 10960, 16227, 16, 2154, 5180, 4517, 1922, 4587, 12031, 7229, 2925, 2007, 28634, 45, 17, 18328, 1942, 7304, 5937, 3835, 4576, 18, 4950, 16, 1920, 2213, 14465, 43, 67, 14919, 1022, 24050, 3418, 1988, 4088, 1966, 43, 8468, 16239, 17, 2014, 18930, 17, 24050, 2651, 1920, 14444, 2051, 13975, 16, 10232, 43, 5305, 4138, 19, 4167, 19, 2375, 6804, 21845, 12171, 4493, 2037, 9527, 18, 2435, 5985, 1922, 4543, 14745, 1921, 18541, 16, 2052, 3418, 1977, 3868, 12017, 2007, 5016, 6982, 1930, 2112, 15336, 1922, 6445, 5153, 17, 2014, 5329, 8114, 16, 2710, 9848, 7750, 1930, 2087, 2428, 18, 2222, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 24050, 13808, 16, 14745, 1921, 17, 2712, 3416, 16, 2154, 12936, 8468, 16239, 9626, 2410, 30413, 1988, 2347, 1966, 1965, 17, 2213, 14450, 2319, 2651, 1920, 11518, 3374, 18, 2144, 5038, 21252, 13022, 10416, 2019, 2487, 5937, 3402, 1942, 5655, 12186, 3500, 4952, 1927, 6445, 4845, 16, 2710, 4207, 10224, 16, 4086, 16, 1930, 4324, 16268, 18, 2176, 1977, 2435, 1922, 16665, 10984, 5524, 2056, 1930, 5461, 20709, 11121, 2538, 5253, 20748, 16, 7154, 16, 1930, 8468, 7154, 18, 3], "output": "MPPRDDLKHILLSASEGIAFTPVTGFPAGERPALTARQNRFLHANRLVGEVDTAIQQHMQMVQTGLDATSLENRQGTPIEVLNVRVEENGKTSATVFVPESRIEFFKRKFQTYRDNAQTDPTGTDSFWMDDAERPQDTARVQTWEVWLRKGFHQKLLDNATRFNIRISQHRMAFQECEICLITSSQDSLAKEDAAGFFVDLPPREQADWANDLARRIQHSTENAPAVCIANDMDSYDPSWGAVDHNGHGTQVAGVALFEDIAKHLGHANPIQLTHRLESVKILPPAVNAPQRRRVFCLAVTASGRNINGRPTAWSASLDKISVGLNDDLSIDDAQKQLFIVSAGNAQSWNALSVGGITHKAVSNDPTTHGWNLLAPPGDLSPRSRTSVVWTEKDWPIKPDIVFEAGPFKCSRDTSAATAAVARMAAILHGEYPNLWPETIRGLLVHSADWTPEMLLNGQALANINSSSRTCLISQQTIQPFIRGEDDDGRLAQSANFKEMNLHRLPWPQDYLREYGITQIKLRVTLYSYASHQLRFDLQRPLEMSDTFRQRVNRQDRTEGEAREVQDTSANWYLGPRVRNRGIAVMPEGGWWKVRKHLNRSNQTARYALIITLESENQELDIYSQIQTEIANMTAVAVATRTEAFRVADPDAEITAGVSFDIEGRIPTEGLPGNAALKIDAVDAVRIADLLIQAVLSPLVGFSFLDTGIHRQHALISPSLAQGQNQEELYGYITQESASRAIRDTLQPTDYPARNLLESIENPNYIHDGTIVSDDPDLSVLTTGHDVKNTLLRTFGYGIPNLEIARFSASYYVEPSPSRRIPIQQSISSDIWKGTAGQLADQGL", "metadata": {"id": "A0A955UBR3", "cluster": 1345472, "interpro_all": ["IPR000209", "IPR036852", "IPR015500", "IPR034074"], "interpro_used": ["IPR000209", "IPR034074", "IPR015500"], "interpro_unused": ["IPR036852"]}, "task_type": "infilling"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs 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. It is expressed in Bradyrhizobium diazoefficiens SEMIA 5080.", "tokenized_instruction": [2, 6647, 1920, 2340, 17, 12317, 3835, 2687, 3244, 1958, 43, 13022, 4659, 1988, 17436, 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, 2176, 1977, 3198, 1922, 20152, 5004, 2061, 23156, 19106, 6802, 6167, 2099, 8762, 1019, 2761, 4476, 18, 3], "output": "MGWEKNDFHHEERLSEDGQESYLDYLITTAQTSLLIEAKRAQVNFGGVPALRRAPMRGSWAKSGDLRKAILQARDYGRTKGVGFCAVTNGDAWVIFPVNRRDLVSFDDTHAVVFRTAESALHDDREEFLALLSRESVIDGSLEQQLLGGDSNQIENRRLNRIYDKSFSKITRQTMFSSIEDEIVTAFSEELISANPELLEKAYVETADRMRFDDRIKMSVVRRDQVLRSRPLRPVGRDGAKGVGAKFTSVKVKAQPLALLTLGLVGAGKTTFLRYVETISGKAFFDQTKKPPAAHWLYVDFRNFSKTLSPRTHIFEAILNYIKAHPALGDYETTIAPAYEEEVANLTRGPLGGLKANKAALDEQIGKILLKEYEEGAPYCRRILSYASKSQACFLVIDNVDQVEETTIQDAIFLDAVAIAREANLSLVIAMRDATYVKNRSSAVFDAFTFDAIYIDPPDVQSVLSKRFTIANHLLKDKTFEVVSDGGAKVTVSDASRVVDMLSASVLGTDVGQLIEVSATGDVRLALRMTKQFLQFGYSTSYRAYQAFLKTGHYDFPIHEAIRAIMFGNQSIYRDEFSPILNPFDAKTGRSESQFLRVYVMSALIAAATTKEFQGIEASEIISSLERMGFSSRITNKIITDLIKARVCFSRSHQEYSSESVLVPTRLCGYIVRELLGRLVFLETVIFDTFIYGDQVWEEIKGGMKSVYAEQNTVRRFKIRKSIAKQFFDWIEQEVQKLCVEASRRNLGPFWTSNPITRMRPAFEGELERAFRSAVRNYGSAKEQDEIKLPLFQQQIDN", "metadata": {"id": "A0A837C3I9", "cluster": 1389012, "interpro_all": ["IPR027417"], "interpro_used": ["IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein falls within 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 identified in Victivallales bacterium.\nThis is the biological role of the target protein. Complete its masked polypeptide sequence.", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 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, 2899, 1922, 8159, 2113, 2214, 3955, 14061, 18, 2052, 1977, 1920, 3933, 2770, 1927, 1920, 2758, 2213, 18, 4080, 2496, 17476, 13022, 3244, 18, 3], "output": "IEGANSSIHADGSQNWVFDLRNDCMGEASMALAANVNDFIYSCPAFSGGPRAAPTSASYGLVAWTMLGTIACATALGEPRWNERVFRCLLANLRTTGPSGFRYWETDRLNLAPHYESWLWACFLWAYRQTGYEPFRERASRAIGLTMAGLLPLAWLVRVEDTAEHRAWLRQVAADLLAFQDATNEAYGTSEAPLIQANGDPLCDLLYTTNFAFVGLHEAVAVTGDAPEHPQLDGGWFRAFDFGRWDYWASNADLGWGAWQMGCSYWDFTADCCIPAECVTRLIDEMFGNGSLALGGRLQNQPRWREGNDASNGVYYGDDNARAGNRLEDATLQGKGWRYYPDEWRWTNGLQQERARMGCGAIREEVGGAGKGAYGPPADLREAADRLAAFLCRIQVHSIESGWTQGWIAAILALR", "metadata": {"id": "A0A9E1XNY7", "cluster": 3382049, "interpro_all": ["IPR008928"], "interpro_used": ["IPR008928"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "It is part of the U1 snRNP 70 kDa and U11/U12 snRNP 35 kDa family, which comprises components of the spliceosomal U1 small nuclear ribonucleoprotein (snRNP) complex essential for pre-mRNA splicing and 5' splice-site recognition. These proteins utilize an RNA recognition motif (RRM) to bind the U1-snRNA loop I and facilitate spliceosome assembly, while some members also participate in the minor spliceosome for U12-type introns. Additionally, the family plays roles in broader cellular contexts, including oogenesis, meiotic segregation, and nutritional signaling pathways. Additionally, 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. Furthermore, the protein is included in 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 is native to Planoprotostelium fungivorum.\nGenerate the missing structural regions for this protein.", "tokenized_instruction": [2, 2176, 1977, 3131, 1927, 1920, 22978, 11970, 6708, 3895, 6713, 1930, 22978, 1009, 19, 22978, 1028, 11970, 6708, 3259, 6713, 3416, 16, 2154, 12936, 4178, 1927, 1920, 10708, 4969, 22978, 2858, 4254, 18347, 6657, 12, 11970, 6708, 13, 2796, 4415, 1958, 2097, 17, 3616, 8490, 1930, 25, 11, 10708, 17, 3200, 5708, 18, 2144, 2697, 12561, 1925, 3146, 5708, 5219, 12, 5162, 1035, 13, 1942, 4566, 1920, 22978, 17, 11970, 2175, 5881, 51, 1930, 6628, 10708, 4283, 5957, 16, 2679, 2673, 4678, 2222, 7352, 1922, 1920, 5857, 10708, 4283, 1958, 22978, 1028, 17, 2601, 15778, 18, 4950, 16, 1920, 3416, 5705, 5456, 1922, 11462, 3689, 11144, 16, 2710, 57, 3761, 16, 16205, 12707, 16, 1930, 9369, 3197, 3873, 18, 4950, 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, 3677, 16, 1920, 2213, 1977, 3063, 1922, 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, 1977, 6196, 1942, 4720, 11552, 18092, 12191, 1989, 10520, 15525, 24277, 18, 5655, 1920, 6814, 4346, 3451, 1958, 2052, 2213, 18, 3], "output": "MITTYLDTRDTAFDPYDIYKGVEDIDNDLFVSLIAPETTEDSLRKFFRLYNLEPLRIVVLRDKSERALPYAYVQFMMLDGARIHIQKAKVNRTLFIAKMEKSITSAELRDLMESYGRVDHDDAIKAHSSMKANKQRWVVEWATSNNDPDALGIDRNNIFIGGLGKIDSISLVNKESDPTEEETESGVRSAFAFVRFNDSKSSGMAIEQKTKRRVNKFYSNYYNPPYFAPMGMPMNYGYAPQMAYTVPPPIYNQPPPPPSMDSSLAPTPAEAHHNMMMNGGPPVTQHIQQQQQQQNPAYLPQYHNKHPGTKTFSAQKNELDEESKALVSSLTALSLDRAPPATRWASGMTQEPRGPADGCEVDQASIARLATHNRVTIIKNHQTNKSKGCGFVKFLTRNPVTTTKESLMERFSAYQNGALWNDKRIRVQYCESQEMPNMMYPPPWSGFPQQPPREGYARALLGKEDEKGNT", "metadata": {"id": "A0A2P6NF73", "cluster": 3629735, "interpro_all": ["IPR012677", "IPR035979", "IPR000504", "IPR051183"], "interpro_used": ["IPR051183", "IPR000504", "IPR012677"], "interpro_unused": ["IPR035979"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein incorporates a RNA polymerase sigma-70 ECF-like, HTH domain that functions as a C-terminal DNA-binding module in sigma factors to regulate extracytoplasmic functions (ECF). It enables bacteria to respond to external environmental stimuli and is typically controlled by interactions with anti-sigma and anti-anti-sigma factors. 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. Furthermore, 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. It is native to Pyrinomonadaceae bacterium and carries UniProt keyword assignments Transcription regulation. 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, 19683, 43, 3146, 6479, 5139, 17, 3895, 3270, 1038, 17, 3189, 16, 5334, 1023, 3418, 1988, 4088, 1966, 43, 45, 17, 4262, 2678, 17, 2743, 9059, 1922, 5139, 2790, 1942, 5741, 3439, 2355, 11302, 4088, 12, 3270, 1038, 13, 18, 2176, 10217, 4802, 1942, 4409, 1942, 5771, 4813, 5458, 1930, 1977, 5745, 4642, 2007, 3719, 1956, 2246, 17, 5139, 1930, 2246, 17, 2246, 17, 5139, 2790, 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, 3677, 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, 2176, 1977, 6196, 1942, 6487, 3522, 3947, 7324, 1972, 3336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 3213, 3640, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MSETAYQPREITLLLQAWSNGNRKGLDELLPLVYDELHRQAHRFLRRERQNHTLQTTALIHEAYLNLIEQNRVEWQNREHFFAISANMMRRILVNYANARQRKKRGGSAENLELDESFLIPALKTGIDLLALDEALTRLAKMDKRQEQIVELRYFSGLTIDETADVLGVSPATIKRDWKMTKAWLHRELSGKDGTRELA", "metadata": {"id": "A0A925FL76", "cluster": 4846519, "interpro_all": ["IPR053812", "IPR039425", "IPR014284", "IPR011517", "IPR013324", "IPR036388"], "interpro_used": ["IPR053812", "IPR036388", "IPR014284"], "interpro_unused": ["IPR013324", "IPR039425", "IPR011517"]}, "task_type": "autoregressive"} {"instruction": "Target Function: The protein carries a eukaryotic Dullard phosphatase domain that functions as a putative phosphatase found in a family of proteins including Dullard and NLI interacting factor (NIF)-like phosphatases. Furthermore, the protein is categorized in the Mitochondrial import inner membrane translocase subunit TIM50 family, which acts as an essential, dynamic component of the TIM23 complex to mediate the translocation of transit peptide-containing proteins across the mitochondrial inner membrane. These proteins facilitate the transfer of preproteins from the TOM complex and direct them to the TIM23 channel for import. Furthermore, the protein features a FCP1 homology domain that functions as the catalytic unit of protein serine phosphatases, specifically dephosphorylating the C-terminal domain (CTD) of RNA polymerase II. This metal-dependent phosphohydrolase module utilizes a conserved DxDx(T/V) motif to facilitate catalysis and substrate recognition. It is derived from Leishmania martiniquensis and contains UniProt keyword associations Protein phosphatase.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 16252, 43, 10825, 13247, 5148, 8544, 8167, 3418, 1988, 4088, 1966, 43, 6770, 8167, 2435, 1922, 43, 3416, 1927, 2697, 2710, 13247, 5148, 8544, 1930, 9092, 1033, 8615, 2991, 12, 17719, 13, 17, 3189, 19131, 18, 3677, 16, 1920, 2213, 1977, 10234, 1922, 1920, 4596, 2582, 6671, 3260, 12930, 2051, 5903, 2267, 3382, 3416, 16, 2154, 8016, 1966, 1925, 4415, 16, 5760, 4594, 1927, 1920, 2267, 4553, 2796, 1942, 8265, 1920, 7849, 1927, 16361, 4207, 17, 3165, 2697, 3436, 1920, 4596, 6671, 3260, 18, 2144, 2697, 6628, 1920, 3856, 1927, 10719, 10355, 2037, 1920, 5970, 2796, 1930, 3083, 3581, 1942, 1920, 2267, 4553, 4999, 1958, 2582, 18, 3677, 16, 1920, 2213, 4075, 43, 6437, 5113, 9039, 3418, 1988, 4088, 1966, 1920, 6804, 5344, 1927, 2213, 8468, 19131, 16, 4475, 13517, 2199, 2287, 1920, 45, 17, 4262, 3418, 12, 15898, 13, 1927, 3146, 6479, 2890, 18, 2052, 6048, 17, 3100, 8078, 8535, 24605, 1021, 9059, 18127, 43, 5305, 14852, 30170, 12, 62, 19, 64, 13, 5219, 1942, 6628, 15408, 1930, 4510, 5708, 18, 2176, 1977, 3595, 2037, 18344, 14196, 3573, 3355, 1937, 1930, 5461, 20709, 11121, 2538, 5253, 2213, 8167, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MDGERETSAAPTPFFRGLSGRLEPPQENHYRGGGGGSSAGGATPPSSATTTPTAPPGSQQQRSGGGRAGGSSDVSGTDSSGSAHNGPARYIRNQPKNTSPIDASAHPSLLPEPLPTSYQNTGRYDVHLPITLDRDTHVNVYVAFLGTYCDPLMDSIDKQRILGGLRLFRAIIDNSPIAYLFQQRNAIPITSWFDVYDVLDNYNALLQLQQLHEGNGEKQRQPSSSGRFTAAAENGIKAMPSTLAPVSTLITQVSQNRAASGGSGGSTGSRQRVHATELVERVRHKKCLILDVDETLVHSRPHLHRFLEAVAPLFEVVVFTASEHCSVVGTTYVKDLSLLGRNLEQVDPCDEELLRLIPVLEALAEADT", "metadata": {"id": "A0A836H8U4", "cluster": 5404755, "interpro_all": ["IPR011948", "IPR004274", "IPR036412", "IPR023214", "IPR050365"], "interpro_used": ["IPR011948", "IPR050365", "IPR004274"], "interpro_unused": ["IPR023214", "IPR036412"]}, "task_type": "infilling"} {"instruction": "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. In addition, the protein includes 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 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. It is native to marine bacterium AO1-C and exhibits UniProt keyword tags Transmembrane, Membrane, and TPR repeat.\nBased on this target activity, infill the masked gaps in the sequence.", "tokenized_instruction": [2, 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, 1922, 2459, 16, 1920, 2213, 5921, 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, 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, 2176, 1977, 6196, 1942, 10789, 14061, 16707, 1009, 17, 45, 1930, 9826, 20709, 11121, 2538, 14392, 9117, 16, 3260, 16, 1930, 22288, 6865, 18, 2454, 1990, 2052, 2758, 2455, 16, 6510, 1024, 1920, 17476, 11349, 1922, 1920, 3244, 18, 3], "output": "MKPWQFIFKAQFLFYGCWILVLGSLTLQVKAQELVDSLEVALKDNQANAATKAKILSELVVQKILRLAETHTDSTNRIIAYHSSGFIEYRKGRYSKALMWYKKALRLIDRDNHAGKDVATYYQQALGGYEAVGDQRNRAVIYNAIGNVYNKRTEYQSAMKYYQKSLTLHQKLDSLTSYPDPGTQTSLLGICLKITHKTKDKTARATSLFYIGDVYALLKDYKKALTYYEKSLQLRLEQKDKSEAAASYNNIGKIYNQLGEGANLLGTAATFYHAGYPNEALEYYQEALALSEKLGEKLLKAQIKIGIGQALLTNKKYQAAITQTSEGYALARKHQLKFQIIFKNISDSLINAENIKTAASLEQKRKYEVAQQRQLLQQQKKEALLAAELKQQKRQRVLSIFGMSVTKWDSELKKQNNLKRDAVFKAQETMQKKIAQDLHDGVGQLLVALRLNLEATATPMEKNRKVWKLTIALEHLLDNTFSGSQINHYFECYNLQKRYRESIEINTYRIVQELTSNVMKHAKATEVELQLTGIGLLNIRSRVDFLAGNVSFESGENGGTCVKITLPMKSNVNHSSDKMLKGDILVAEIYAYRDIKTAEEYHTYRKLGMVYARKGDYAKALAGIGRICRIKGEYYKALEYFYDKALEFYQKARWLINEVRNKSHLVVAKDAAQMLSNAFAQIKNYEQAYRFVLILVLLLFAYYRYRIRQQHNAFQLLDKITQDVRSISHLAMPNLIKSDGYEVDDYLYIHFEDNGQGFDSTKIKN", "metadata": {"id": "A0A1Q3GJ97", "cluster": 5479489, "interpro_all": ["IPR036890", "IPR005467", "IPR011712", "IPR011990", "IPR019734"], "interpro_used": ["IPR011990", "IPR019734", "IPR005467"], "interpro_unused": ["IPR011712", "IPR036890"]}, "task_type": "infilling"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein has a Dockerin type I repeat repeat that forms a calcium-binding loop-helix motif within the dockerin domain to mediate binding with cohesin. This interaction is essential for assembling the cellulosome complex in Gram-positive anaerobes, facilitating the degradation of crystalline cellulose by enzymes such as endoglucanases. Furthermore, the protein features 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 should include 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 native to Phycisphaeraceae 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, 2258, 43, 9170, 16654, 2601, 51, 6865, 6865, 1988, 4952, 43, 5016, 17, 2743, 5881, 17, 7864, 5219, 2651, 1920, 9170, 16654, 3418, 1942, 8265, 2743, 1956, 22822, 18, 2052, 2835, 1977, 4415, 1958, 26358, 1920, 18485, 4283, 2796, 1922, 8604, 17, 2843, 29163, 1918, 16, 12440, 1920, 4877, 1927, 14631, 12343, 2007, 5038, 2427, 1966, 16239, 22988, 7241, 4127, 1036, 18, 3677, 16, 1920, 2213, 4075, 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, 3066, 3951, 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, 6196, 1942, 25511, 9119, 29164, 9914, 14061, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MRLRLWGRILELAASGEMGRRASVAATGMLGVAVAGGVSRADEPCPSSCDLGVYAANIGDMDGDGVSDVAVCDPMAGVVEIFGGDGSLLCRLTAPMEEGLFGFAVFPVCDVDGDGFPEIAVASLTDYDQEFPGGIIHLYSVVKCKEVAYLKNVDGVAAPAVSLVGDLDGDGTVGYADLLMLLAGLGGEDLEADPYALDVNADGVVDFADAVELLGLEGTQAVSACEASVAALVSGSESLLNDPMYTGVLGACGEVLSQGPIGCLICAIRCGSHMKKAAECVFSQRRRIAELCDPLADQGRIFEYTECFREQRLATTRCLQDVAGAAGSCGSCIYKCFRAL", "metadata": {"id": "A0A7L9BMX1", "cluster": 11141094, "interpro_all": ["IPR002105", "IPR036439", "IPR018247", "IPR002048", "IPR028994"], "interpro_used": ["IPR002105", "IPR018247", "IPR002048"], "interpro_unused": ["IPR028994", "IPR036439"]}, "task_type": "autoregressive"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein possesses a SH2 domain that functions as a regulatory module in intracellular signaling cascades by recognizing and binding specific phosphotyrosine-containing peptide motifs in a strictly phosphorylation-dependent manner. It mediates protein-protein interactions by docking onto phosphorylated targets, typically recognizing residues C-terminal to the tyrosine, and is commonly found within kinases, adaptor molecules, and structural proteins. Furthermore, the protein falls within the Immunoreceptor signaling adapters family, which functions as essential linkers in signaling pathways downstream of T-cell, B-cell, and mast cell receptors. These proteins mediate interactions via SH2 domains and proline-rich regions to facilitate kinase activation, calcium mobilization, and the induction of transcription factors like NF-kappa-B and NFAT, thereby regulating cell development, activation, and apoptosis. It is produced by Paramuricea clavata (Red gorgonian) (Violescent sea-whip).", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 14465, 43, 19124, 3418, 1988, 4088, 1966, 43, 4948, 9059, 1922, 4776, 3197, 15967, 2007, 15667, 1930, 2743, 2487, 29552, 17, 3165, 4207, 8277, 1922, 43, 14470, 4050, 17, 3100, 5222, 18, 2176, 10412, 2213, 17, 2213, 3719, 2007, 10909, 6131, 7199, 4845, 16, 5745, 15667, 4248, 45, 17, 4262, 1942, 1920, 6941, 16, 1930, 1977, 5384, 2435, 2651, 7784, 16, 15077, 4206, 16, 1930, 4346, 2697, 18, 3677, 16, 1920, 2213, 12182, 2651, 1920, 8613, 3342, 1924, 3197, 21054, 1036, 3416, 16, 2154, 4088, 1966, 4415, 25247, 1922, 3197, 3873, 5863, 1927, 62, 17, 2024, 16, 44, 17, 2024, 16, 1930, 9731, 2024, 4086, 18, 2144, 2697, 8265, 3719, 3454, 19124, 4682, 1930, 12958, 17, 5536, 3451, 1942, 6628, 4016, 2936, 16, 5016, 14586, 16, 1930, 1920, 4408, 1927, 3213, 2790, 3189, 4651, 17, 12093, 17, 44, 1930, 16537, 16, 6113, 6773, 2024, 2740, 16, 2936, 16, 1930, 4091, 18, 2176, 1977, 4152, 2007, 3167, 15861, 5376, 19887, 5499, 12, 2312, 20380, 3827, 10306, 1022, 13, 12, 7088, 1918, 3025, 9309, 17, 2003, 2049, 13, 18, 3], "output": "MAGRLEENYEDPNQISGDQADSDEFEQEDYEIPDTSELPKKAPQETPKKSHFNPKNIFNRSPSKKGLPSVPSKGDKKKTTKKEVPPAPLATPAPPVPENKLSPSRQLPNPGGKGIIGKLRGEKADKRHSMGSLPSLPTDKVDSKTKNQGSESPKLPPKPLPVKPLPEKPAPKERPVANQQQKPEPPSKQPQKSKTQLLQHQPWFHGSTSKTVVADILKSTKKDGAYLVRNSSRDPGQSTMSILYKGEIRHLNMPCDTNGHYRLGDSGVERFKNIEELVTYFTKHDVEFSAGGKTHLTHACRKSS", "metadata": {"id": "A0A6S7I009", "cluster": 11774821, "interpro_all": ["IPR051751", "IPR000980", "IPR036860"], "interpro_used": ["IPR000980", "IPR051751"], "interpro_unused": ["IPR036860"]}, "task_type": "autoregressive"} {"instruction": "Predict the masked amino acids. The target function is: The protein is included in the CRISPR-associated protein Cas1, NMENI subtype family, which functions as a variant of the Cas1 component within the CRISPR-Cas prokaryotic defense system. This system provides immunity against foreign genetic elements through the coordinated action of Cas proteins and CRISPR RNA. In addition, the protein can be placed in the CRISPR-associated endonuclease Cas1 family, which functions as a key component of the bacterial and archaeal CRISPR adaptive immune system to provide protection against mobile genetic elements. These proteins act as dsDNA endonucleases that facilitate the integration of spacer DNA into the CRISPR cassette and are essential for the transcription and processing of CRISPR clusters into crRNA. Additionally, some members exhibit ssDNA exonuclease activity and are capable of binding both single- and double-stranded DNA. It is found in Hydrogenedentota bacterium and carries UniProt keyword assignments Magnesium, Metal-binding, and Antiviral defense.", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 1977, 3063, 1922, 1920, 12509, 17, 2458, 2213, 4373, 1009, 16, 2943, 28131, 8856, 3416, 16, 2154, 4088, 1966, 43, 6031, 1927, 1920, 4373, 1009, 4594, 2651, 1920, 12509, 17, 4373, 21545, 9720, 2433, 18, 2052, 2433, 4558, 7611, 3316, 12400, 3299, 5362, 2596, 1920, 11651, 4615, 1927, 4373, 2697, 1930, 12509, 3146, 18, 1922, 2459, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 12509, 17, 2458, 18697, 4373, 1009, 3416, 16, 2154, 4088, 1966, 43, 3834, 4594, 1927, 1920, 4543, 1930, 22367, 12509, 7617, 3743, 2433, 1942, 3394, 6202, 3316, 8785, 3299, 5362, 18, 2144, 2697, 4033, 1966, 16397, 18697, 1036, 1988, 6628, 1920, 7122, 1927, 17060, 2678, 2460, 1920, 12509, 12992, 1930, 2032, 4415, 1958, 1920, 3213, 1930, 4587, 1927, 12509, 5859, 2460, 2345, 10378, 18, 4950, 16, 2673, 4678, 5987, 15063, 24966, 2455, 1930, 2032, 7131, 1927, 2743, 2321, 2957, 17, 1930, 4825, 17, 10338, 2678, 18, 2176, 1977, 2435, 1922, 6201, 1919, 1939, 7336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 13148, 16, 6048, 17, 2743, 16, 1930, 10129, 9720, 18, 3], "output": "MSYHIVHILSHGSYISVDRSEILCVVVCARGVSERYKPIGKTVGLPRIVHEKIIYGKVENQAYVLDIIGVGKYWRLYFSSFDKAGPNAREKRLAEHPINAMHGLCPLLGIHHKFKFKSDPLVYLSFTEDENFSMDTFIKGFAKRYRGNTKPLKIPLIRDLDLGFLVMKTKEYERRAPIFSSNSLSELIQNGAVILHCDSQIFQRQIERQGEFADELWNPLWKYLEENKVEEGACAKVLNYAYAVMGAIVHRSIIAYDLMEPMRPFCDLMLLVEMRIKMPKKTKVLDAIDRYINMVAECF", "metadata": {"id": "A0A7C4YZU7", "cluster": 13005132, "interpro_all": ["IPR050646", "IPR002729", "IPR042206", "IPR042211", "IPR019855"], "interpro_used": ["IPR019855", "IPR050646"], "interpro_unused": ["IPR042211", "IPR042206", "IPR002729"]}, "task_type": "infilling"} {"instruction": "\"The protein contains 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. Additionally, it is part of 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. It is present in Leptolyngbya sp. IPPAS B-1204.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 5461, 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, 4950, 16, 2176, 1977, 3131, 1927, 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, 2176, 1977, 2481, 1922, 16976, 26558, 2029, 4864, 1019, 2056, 18, 5416, 4302, 1036, 44, 17, 6103, 1006, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MNYAEIAAWSKPAAQLSAHVTTALAVPLASEAQLNACTNAVIFRAADGTGRVNWSTTNGGSGVCWVHAGITQTPRPITRPVMTSVTAGTPLQVAVADGSTVVLTGKSAATPSNSEAAAPTVSPGTAARSPDGEIIASIPQGTVDGGWVAQEYLQYRALAVTLTTTLILAPKVLNGVPRSAIITTAGSLDSANQVLEVEVAVTNGGNLNVRSGPGGEIVGSTSDEWVEIEGGGWVSQHHLASGNAKAEVMASGGVNIRNTVVLTGQVERGWVEL", "metadata": {"id": "A0A3M9ZAY4", "cluster": 13332971, "interpro_all": ["IPR052354", "IPR003646"], "interpro_used": ["IPR003646", "IPR052354"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein carries a Domain of unknown function DUF5600 domain that forms a helical structure within EH-domain-containing ATPase 2 (EHD2) proteins. It establishes extensive contacts with the G-domain. Furthermore, the protein has a ShKT domain that functions as a potent potassium channel inhibitor in sea anemone toxins and serves as a regulatory module in diverse enzymes and extracellular matrix proteins. Stabilized by three disulfide bridges and six conserved cysteines, this compact fold is found in association with metallopeptidases and oxidoreductases, potentially conferring ion channel-modulatory activity in non-venomous contexts. Furthermore, the protein features a Dynamin, N-terminal domain that functions as the catalytic GTPase component of the dynamin superfamily, driving membrane remodeling events such as vesicle scission and organelle division. It hydrolyzes GTP to power mechanical constriction during processes including endocytosis, cytokinesis, and pathogen resistance in eukaryotic cells. It is derived from Bursaphelenchus xylophilus (Pinewood nematode worm) (Aphelenchoides xylophilus) and contains UniProt keyword associations Disulfide bond.\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, 16252, 43, 3418, 1927, 5435, 2347, 4855, 17968, 9889, 3418, 1988, 4952, 43, 11514, 3170, 2651, 12429, 17, 3418, 17, 3165, 9444, 22, 12, 12429, 9091, 13, 2697, 18, 2176, 22799, 6475, 9070, 1956, 1920, 49, 17, 3418, 18, 3677, 16, 1920, 2213, 2258, 43, 2044, 19385, 3418, 1988, 4088, 1966, 43, 6828, 9057, 4999, 4106, 1922, 9309, 9860, 3947, 1021, 13599, 1930, 10634, 1966, 43, 4948, 9059, 1922, 6445, 5038, 1930, 5329, 4526, 2697, 18, 12017, 2007, 2559, 11830, 18142, 1930, 3798, 5305, 22446, 16, 2052, 13726, 3728, 1977, 2435, 1922, 3279, 1956, 8969, 24897, 1036, 1930, 27388, 1036, 16, 5063, 21510, 4755, 4999, 17, 22470, 2455, 1922, 2447, 17, 15540, 2080, 11144, 18, 3677, 16, 1920, 2213, 4075, 43, 22653, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 6804, 14809, 4594, 1927, 1920, 22653, 13975, 16, 9228, 3260, 8378, 3916, 2427, 1966, 11502, 30198, 2001, 1930, 19309, 8451, 18, 2176, 7222, 20887, 9319, 1942, 4215, 5821, 19837, 2409, 4028, 2710, 11914, 16, 20825, 16, 1930, 7055, 3554, 1922, 10825, 2094, 18, 2176, 1977, 3595, 2037, 13579, 2575, 29476, 2072, 1957, 9639, 18239, 12, 17541, 15269, 18827, 11055, 13, 12, 12274, 29476, 28226, 3726, 9639, 18239, 13, 1930, 5461, 20709, 11121, 2538, 5253, 11830, 5403, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MCKGKVENNKEDLNSENVIKWLMERFAASPVIMFLGQYSVGKTSMIKYLCNKDYPGASVHYGKEPHIVQGLTLTEDNRFPFQSLKIFGSAFSSRLQGEEQTTKRQYGFNQVVRFLCDKVDMVILMFDTTKCLRGNEEKLRIVLNKADMVDEASMIRVRGALMWGLSKVIQTPIMNTFKEDYLELFHEIQLTVSRCTSRKVNDLIKRIELVKTHAGLMTMFAADRVKQKFAEFRIKQRKAPADLPDVEDYRKAALETTKKHWVKEDPKMKYDELPSDSLKSCFQDLVKAVNEAPVHIPSQLSTESSEEKIKDKKKDKKKNKEKKRMKANGFNLFAMKPVVTLVLGYQYRSRGNNGAHVDRNGDYYNYNDNYRSINNNFNNVIDGCRDGGTDCAKSKHLCEDNTYRSFMAVECPLTCGKCYNAKVVPVEKRHSFERFHSPPLAEAEIGPEPTTDSFVAAALNAPILKHMSFLDTPGILSGLDISDELKQVINEVPKVYIGSFTRELKDKSIMMGGRFSFSDNEKGMQKLMKNLNDFIENDIPKALAASKPKSNKSSKVQSDGDHKLSALTQCVLSQGRFYNFPGSNNYGVVNDFYWDSSQLDQNRNRMN", "metadata": {"id": "A0A1I7RMW7", "cluster": 13496601, "interpro_all": ["IPR040990", "IPR045063", "IPR031692", "IPR027417", "IPR003582", "IPR051943"], "interpro_used": ["IPR040990", "IPR003582", "IPR045063"], "interpro_unused": ["IPR031692", "IPR027417", "IPR051943"]}, "task_type": "infilling"} {"instruction": "Return only the raw amino acid sequence for a protein with function: The protein is assigned to 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. In addition, 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. It is found in Ignavibacteriales bacterium.", "tokenized_instruction": [2, 7215, 2444, 1920, 7429, 3835, 2687, 3244, 1958, 43, 2213, 1956, 2347, 30, 1920, 2213, 1977, 6304, 1942, 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, 1922, 2459, 16, 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, 2176, 1977, 2435, 1922, 12046, 9188, 7972, 2341, 18339, 2612, 14061, 18, 3], "output": "MLSWSELPQHPIIIAHRGASATAPENTLTAFSQAIECGVNAIELDVRLTNDNRVVVIHDSHLRRTTNGKGNVHESSLSELKMYSAGSWFHKKYTDERIPTLTEVIELVHGRVGINIELKHEGSRREGNILVEQTVKIVEQYRAEQLVMFSSFNHALVQYAKILNKNIIRGILFHTYCVPFYSPPKKLKEISASFLICNKHLLRKRLIDVAHQHNIQTGIYTINTEESLTKALRYGVDCIFTDDPKTILTCLKHSFR", "metadata": {"id": "A0A932IJJ5", "cluster": 13567724, "interpro_all": ["IPR030395", "IPR017946"], "interpro_used": ["IPR017946", "IPR030395"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I am designing a protein that has the following properties: The protein is assigned 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. Moreover, the protein is categorized in the HAD-like hydrolase domain-containing protein family, which is characterized by a haloacid dehalogenase-like hydrolase domain that catalyzes the hydrolysis of various substrates. These proteins typically participate in dehalogenation reactions or other hydrolytic processes fundamental to cellular metabolism and pathway regulation. It is identified in Candidatus Uhrbacteria bacterium GW2011_GWF2_39_13. 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, 6304, 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, 3950, 16, 1920, 2213, 1977, 10234, 1922, 1920, 2430, 17, 3189, 20748, 3418, 17, 3165, 2213, 3416, 16, 2154, 1977, 4378, 2007, 43, 23226, 29272, 2028, 7289, 2404, 2051, 17, 3189, 20748, 3418, 1988, 17097, 1920, 9128, 1927, 3425, 6249, 18, 2144, 2697, 5745, 7352, 1922, 2028, 7289, 2404, 1943, 5298, 2014, 2303, 26702, 4028, 8829, 1942, 3689, 4714, 1930, 3374, 3640, 18, 2176, 1977, 2899, 1922, 14550, 1031, 1957, 23476, 16007, 2422, 2126, 14061, 8997, 23437, 1009, 41, 8997, 6680, 41, 3886, 41, 2590, 18, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MEKNSLTYIRSCLDSLKPIYPLVAGDAESQYGFCPGIKAVIFDIYGTLLVSDSGDFRQEKLSETRLSALLGKSVLHIKDENKNRAVHEIIGKYNDYIKKHHGESKSSGIEYPEINIVDLWDSVISGLAADNLLETPLPDIDLKLIAIVFELSLNPIYPMPFMTELIRLIESKPLISGVVSNAQFYTPLIMNYFLDNEISFSEHIKAFKDDLNIFSYKFGMSKPGVELFETAVSRLSNNYNIRPEETIFIGNDMLNDIYPAKSAGFKTVLFTGDARSLRRRKEHPLVNSLKADYVIRDLKELPHIIGI", "metadata": {"id": "A0A0G0MKF2", "cluster": 14268944, "interpro_all": ["IPR051828", "IPR036412", "IPR023214"], "interpro_used": ["IPR023214", "IPR051828"], "interpro_unused": ["IPR036412"]}, "task_type": "autoregressive"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein has a FG-GAP repeat that adopts a beta-propeller structure and functions as a ligand-binding domain, notably within the N-terminus of integrin alpha chains. Containing conserved FG and GAP motifs and potential Ca2+ binding sites, it mediates diverse processes including cell-cell interactions and host-pathogen recognition across eukaryotes and bacteria. Moreover, the protein belongs to the Integrin alpha chain family, which functions as the regulatory alpha subunit of integrin heterodimers to mediate cell adhesion to the extracellular matrix and intracellular signaling. These transmembrane proteins feature a large extracellular N-terminal beta-propeller domain that determines ligand specificity, often recognizing acidic peptide motifs, and a short cytoplasmic tail. By associating with a specific beta subunit, the alpha chain modulates receptor binding properties and facilitates connections between the extracellular environment and the cytoskeleton. Moreover, the protein is grouped 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 has been characterized in Planctomycetota bacterium and corresponds to UniProt keyword Glycoprotein.", "tokenized_instruction": [2, 3258, 1920, 2758, 2347, 16, 4663, 2032, 1920, 5550, 3835, 4576, 1958, 1920, 17476, 3244, 11349, 35, 2347, 30, 1920, 2213, 2258, 43, 13320, 17, 5750, 6865, 1988, 24032, 43, 4666, 17, 5062, 13728, 3170, 1930, 4088, 1966, 43, 5207, 17, 2743, 3418, 16, 7388, 2651, 1920, 56, 17, 7822, 1927, 8920, 4595, 7835, 18, 3165, 5305, 13320, 1930, 5750, 8277, 1930, 2889, 5497, 15, 2743, 3402, 16, 2176, 10412, 6445, 4028, 2710, 2024, 17, 2024, 3719, 1930, 4423, 17, 7055, 5708, 3436, 15021, 1930, 4802, 18, 3950, 16, 1920, 2213, 14440, 1942, 1920, 8920, 4595, 4659, 3416, 16, 2154, 4088, 1966, 1920, 4948, 4595, 5903, 1927, 8920, 21523, 1942, 8265, 2024, 6141, 1942, 1920, 5329, 4526, 1930, 4776, 3197, 18, 2144, 9117, 2697, 5961, 43, 3103, 5329, 56, 17, 4262, 4666, 17, 5062, 13728, 3418, 1988, 13554, 5207, 4896, 16, 3868, 15667, 9931, 4207, 8277, 16, 1930, 43, 3662, 6823, 5281, 18, 2007, 26284, 1956, 43, 2487, 4666, 5903, 16, 1920, 4595, 4659, 13112, 3148, 2743, 3879, 1930, 11374, 10005, 2192, 1920, 5329, 3515, 1930, 1920, 11612, 18, 3950, 16, 1920, 2213, 1977, 10809, 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, 2258, 2252, 4378, 1922, 4720, 2341, 13386, 19446, 3857, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 11424, 18, 3], "output": "MRCLHKSSNALLLLAIFALPATSQIAFGPVQSSPMGAPHPLEAFADLDQDGDIDGVGLDPAGFVPVVPQPLGVAMGDLDEDGDVDLVTTSATPKVVTLLFVAGSSFTRVDFAVQTVGPPTVLDGNGGFAPPQPFVSPDPIPSDALPADVNGDGHVDFVYHVLSPAPLLRMAVNDGPKVGVGDFDGDGDDDIVLVDETSNLAQPESYTLKVFRQDVSGFAAPTTVTTSLQPFGNFGLGAVFPMIGFAFPSQENHLVVFRGDVALSLPQALDAQAPFGTSSMKIADMTNDGFPDLVRVGPDPTDPLTHITSLSPMGHAGYVQQGFIHPILWKLEDAGGQGVPGIDVTFTTPNGPVVVTTDANGIARQFEAPSDVFLRETNAQITNLASVQRTLEVTYLHERPAIPLWVAVDLPRTPNVLGGTQPFMGGFLTTVQAMYDAFVFGGLSVVVQVYGYDAALGFPQNLIVSDPVFLTLVALYRNVFPSDLQVAGFDGHLDIILGRESLLAGDGQGSCSFTYSDVPSGAGPNFSVHTVDVDSDGFDDLVLRGIHEIAVNLTNPNPSFLYTSSGMVVAQAGATNAAPGMLVTYAGTLHTSLLMPEPELGLLP", "metadata": {"id": "A0A7C5AC50", "cluster": 15613896, "interpro_all": ["IPR013517", "IPR013783", "IPR000413", "IPR028994", "IPR008964"], "interpro_used": ["IPR013517", "IPR000413", "IPR013783"], "interpro_unused": ["IPR008964", "IPR028994"]}, "task_type": "infilling"} {"instruction": "Output the one-letter amino acid sequence for a polypeptide chain that performs this function: The protein is classified under the Protein-tyrosine phosphatase-like superfamily, which encompasses a diverse group of enzymes including receptor and non-receptor tyrosine phosphatases, dual specificity phosphatases, and lipid phosphatases like PTEN. Members of this family share a core structure of a central parallel beta-sheet flanked by alpha-helices and utilize a conserved C(X)5R active site motif to catalyze dephosphorylation via a cysteinyl-phosphate intermediate. These enzymes play critical regulatory roles in signal transduction pathways, such as the MAP kinase pathway, as well as cell cycle control, growth, and differentiation. Furthermore, the protein can be placed in the Tyrosine/serine-protein phosphatase IphP-type family, which comprises dual-specificity enzymes that dephosphorylate both tyrosine and serine/threonine residues. Notable members include the cyanobacterial IphP, which displays MAP kinase phosphatase activity, and the mycobacterial PtpB, which demonstrates triple specificity toward phosphotyrosine, phosphoserine/threonine, and phosphoinositides. Also, the protein should feature a Protein-tyrosine phosphatase active site that catalyzes the removal of phosphate groups from tyrosine residues or exhibits dual specificity for serine/threonine and tyrosine substrates. This enzymatic activity is crucial for regulating mitogenic signal transduction, cell cycle control, and cellular differentiation. It is expressed in Acidimicrobiales bacterium.", "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, 2213, 17, 6941, 8167, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 5038, 2710, 3148, 1930, 2447, 17, 3148, 6941, 19131, 16, 7064, 4896, 19131, 16, 1930, 4486, 19131, 3189, 9496, 18, 4678, 1927, 2052, 3416, 7948, 43, 4728, 3170, 1927, 43, 4101, 6110, 4666, 17, 11130, 20185, 2007, 4595, 17, 12789, 1930, 12561, 43, 5305, 45, 12, 66, 13, 25, 1005, 3500, 3200, 5219, 1942, 18170, 16881, 3454, 43, 20368, 1921, 2199, 17, 5413, 6129, 18, 2144, 5038, 3918, 4140, 4948, 5456, 1922, 2733, 8201, 3873, 16, 2427, 1966, 1920, 4446, 4016, 3374, 16, 1966, 2486, 1966, 2024, 4048, 2285, 16, 2905, 16, 1930, 4155, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 6941, 19, 8468, 17, 2213, 8167, 5416, 15870, 17, 2601, 3416, 16, 2154, 12936, 7064, 17, 4896, 5038, 1988, 13517, 9075, 2321, 6941, 1930, 8468, 19, 13143, 4248, 18, 11892, 4678, 3951, 1920, 21897, 1024, 5416, 15870, 16, 2154, 10750, 4446, 4016, 8167, 2455, 16, 1930, 1920, 21424, 14990, 1014, 16, 2154, 7706, 10073, 4896, 4205, 29552, 16, 8078, 26337, 19, 13143, 16, 1930, 23546, 1036, 18, 2222, 16, 1920, 2213, 3066, 5961, 43, 2213, 17, 6941, 8167, 3500, 3200, 1988, 17097, 1920, 6025, 1927, 5413, 2671, 2037, 6941, 4248, 2014, 9826, 7064, 4896, 1958, 8468, 19, 13143, 1930, 6941, 6249, 18, 2052, 8145, 2455, 1977, 6608, 1958, 6773, 23644, 2733, 8201, 16, 2024, 4048, 2285, 16, 1930, 3689, 4155, 18, 2176, 1977, 3198, 1922, 2687, 1980, 1935, 7839, 1918, 14061, 18, 3], "output": "MDIRYDVVHTDGVARRLVLERAANVRDLGGFATPDGLTAFGRVLRADQLGMLTDGDVAMLREGAAVVRTVDLRGLDEVGALGRGRLADAGVDHLHLPIRDRANDPEVLAARRGRTPAQVYLDQLEQAPVRYLAAVEALTADGTSVIHCTAGKDRTGLSAMLVLGALGVADDAIVDDYAATARVPSDVKQASRDPNADAFWADYTRHADTADVQTDASMSVIMRELLELVDGRWGGIPEYFAAYDATPLIDGLRRRLLA", "metadata": {"id": "A0A960I6H0", "cluster": 16939973, "interpro_all": ["IPR029021", "IPR026893", "IPR016130"], "interpro_used": ["IPR029021", "IPR026893", "IPR016130"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein includes a LysM domain that serves as a widespread peptidoglycan-binding module in bacteria and a chitin-binding motif in eukaryotes. Adopting a \u03b2-\u03b1-\u03b1-\u03b2 fold, this small globular domain is often found attached to catalytic units in cell wall-degrading enzymes and plays a role in specific plant-bacteria recognition signaling. It is produced by Verrucomicrobiota 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, 5921, 43, 3629, 1035, 3418, 1988, 10634, 1966, 43, 9360, 24183, 17, 2743, 9059, 1922, 4802, 1930, 43, 16588, 17, 2743, 5219, 1922, 15021, 18, 20478, 43, 161, 17, 160, 17, 160, 17, 161, 3728, 16, 2052, 2858, 20975, 3418, 1977, 3868, 2435, 8765, 1942, 6804, 5701, 1922, 2024, 4821, 17, 18192, 5038, 1930, 5705, 43, 2770, 1922, 2487, 4496, 17, 4802, 5708, 3197, 18, 2176, 1977, 4152, 2007, 3566, 3176, 13055, 1935, 15129, 3940, 3857, 14061, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MPSDKPIVDYKIQEGDEIKAANQLTSDFIVAGKTIRVPSGSPQGLPQPAVVESAAGLVQSLWTIARAHKTSVKLAEGAAPAVPEKSSAAAE", "metadata": {"id": "A0A3E1EEU2", "cluster": 18408672, "interpro_all": ["IPR018392", "IPR036779"], "interpro_used": ["IPR018392"], "interpro_unused": ["IPR036779"]}, "task_type": "infilling"} {"instruction": "The protein belongs to 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. In addition, the protein is a member 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 found in Fonsecaea nubica.\nInfill the missing gaps for a protein with this description.", "tokenized_instruction": [2, 1920, 2213, 14440, 1942, 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, 1922, 2459, 16, 1920, 2213, 1977, 43, 7210, 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, 2435, 1922, 23160, 4127, 3375, 5376, 13232, 3821, 3375, 18, 6510, 1024, 1920, 6814, 11349, 1958, 43, 2213, 1956, 2052, 8418, 18, 3], "output": "MSDTSNVPGGHFFVTPRHDDTFAKSGAAAIALLARSDLDAAAKEVVEAAKQAGRKDTPKVLKTVEQEFGTLDVVINNASRMEVWKPIHETDVEDWWSTWEKTIITISSAGALTTSSGGSAYQGTKTAQIRLNDFLHPGGVKTEVGTTMPDYMHHLLVAEPELPADTLVWLTRERLAKKDEIVEKDLLKLKLREYEFINPLKGDPTNLKVLVTGASKGIGRATVIALRVDTSDVAAVDKAIKVNLKGTYLVTRATLPLLLKGNGMKEYGDQSLLAYAIREWLAGRYVSVPWDMEGL", "metadata": {"id": "A0A178BW82", "cluster": 18783756, "interpro_all": ["IPR036291", "IPR002347"], "interpro_used": ["IPR002347", "IPR036291"], "interpro_unused": []}, "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 included in the Six-bladed beta-propeller, TolB-like superfamily, which forms a structural domain consisting of six 4-stranded beta-sheet motifs that serves as a scaffold for diverse biological activities ranging from enzymatic catalysis to transport. Members of this family include enzymes like quinoprotein glucose dehydrogenase, signaling components such as the LDL receptor, and the periplasmic TolB protein, where the domain mediates protein-protein interactions within the Tol-dependent translocation system. It is native to Quillaja saponaria (Soap bark tree).", "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, 3063, 1922, 1920, 3798, 17, 22707, 1007, 4666, 17, 5062, 13728, 16, 21930, 1014, 17, 3189, 13975, 16, 2154, 4952, 43, 4346, 3418, 7600, 1927, 3798, 24, 17, 10338, 4666, 17, 11130, 8277, 1988, 10634, 1966, 43, 7281, 1958, 6445, 3933, 4209, 6485, 2037, 8145, 15408, 1942, 4860, 18, 4678, 1927, 2052, 3416, 3951, 5038, 3189, 9012, 6657, 3817, 9294, 16, 3197, 4178, 2427, 1966, 1920, 8017, 3148, 16, 1930, 1920, 24334, 21930, 1014, 2213, 16, 2597, 1920, 3418, 10412, 2213, 17, 2213, 3719, 2651, 1920, 21930, 17, 3100, 7849, 2433, 18, 2176, 1977, 6196, 1942, 2571, 10888, 14174, 9235, 12502, 3027, 1019, 12, 2577, 2026, 18399, 6694, 13, 18, 3], "output": "MGKLRIPASPMVGFTNGMETVRGGTEFVIITFHRKDCICPFAPELEYVCERPLEPRFDKKSGDLYNADAYLGLQVVGPPGG", "metadata": {"id": "A0AAD7Q8B7", "cluster": 19452920, "interpro_all": ["IPR011042"], "interpro_used": ["IPR011042"], "interpro_unused": []}, "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 Pentapeptide repeat that adopts a right-handed beta-helical structure to function as a DNA mimic, exhibiting size, shape, and electrostatic similarity to B-form DNA. This structural mimicry facilitates interactions with DNA-binding proteins, such as DNA gyrase, often conferring resistance to fluoroquinolones or protecting against microcin B17 toxicity. Also, the protein is a member of the Pentapeptide repeat and BTB/POZ domain-containing protein family, which encompasses proteins with diverse roles ranging from fluoroquinolone resistance via DNA gyrase inhibition to substrate recognition in E3 ubiquitin-protein ligase complexes. Some members also contribute to bacterial virulence by reorganizing host endosomal compartments and recruiting kinesin-1 to facilitate intracellular survival. It has been detected in Chloroflexota bacterium and is associated with UniProt keywords 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, 3066, 5961, 43, 9412, 24010, 6865, 1988, 24032, 43, 3659, 17, 17105, 4666, 17, 11514, 3170, 1942, 2347, 1966, 43, 2678, 10223, 16, 12196, 3081, 16, 5989, 16, 1930, 12452, 6796, 1942, 44, 17, 2386, 2678, 18, 2052, 4346, 10223, 6907, 11374, 3719, 1956, 2678, 17, 2743, 2697, 16, 2427, 1966, 2678, 9430, 2051, 16, 3868, 21510, 3554, 1942, 23619, 24909, 2014, 15145, 3316, 10572, 1921, 10360, 1027, 5532, 18, 2222, 16, 1920, 2213, 1977, 43, 7210, 1927, 1920, 9412, 24010, 6865, 1930, 29034, 19, 2510, 1011, 3418, 17, 3165, 2213, 3416, 16, 2154, 21569, 2697, 1956, 6445, 5456, 6485, 2037, 23619, 13048, 3554, 3454, 2678, 9430, 2051, 3523, 1942, 4510, 5708, 1922, 10968, 6526, 17, 2213, 11905, 5048, 18, 2673, 4678, 2222, 4672, 1942, 4543, 9304, 2007, 1964, 7023, 3903, 4423, 16514, 10436, 1930, 17040, 19378, 17, 21, 1942, 6628, 4776, 3298, 18, 2176, 2258, 2252, 3330, 1922, 10107, 18222, 7336, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MTLSNWAPIAYRLVVGIPASLRWWKGATPDWPDTLWDRLRMGESGDVPVRESVSALAAQQQADTAERSLIDERLQNGAAMLGSNLLSVERPAEYHQQVMRSLCAFVRHPATDGSVTTAGGRREDVEVAVADLRWAMLQSVNLSSARVPSHLLDMNLAGASLANARLRRALFIGADLTGANLEGAAQLDSARADAGDPPVLDGVLDADTGKALVWRVGPLHLDLLALVVALTVVSVVTTIRNLGLVVGGVIALIIAGWRGWVADQQRLAGIYALRRVAERTISSCHENQMETDAACGLDLHGDLHLVPPLDMAEKARFANLSGADVSGAQFAGGSESPARGLTQ", "metadata": {"id": "A0A6B1GHB7", "cluster": 21598777, "interpro_all": ["IPR001646", "IPR051082"], "interpro_used": ["IPR001646", "IPR051082"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate the missing amino acid spans for a protein that performs the following role: The protein should have 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 SpaA-like, prealbumin fold domain subgroup 3 domain that serves as a stalk component in bacterial cell surface proteins. It typically adopts a prealbumin-like fold and contains an intramolecular isopeptide bond for structural stability. It is derived from Frigoribacterium sp. SL97 and features UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 2162, 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, 19361, 1019, 17, 3189, 16, 2097, 15721, 3728, 3418, 6200, 23, 3418, 1988, 10634, 1966, 43, 19447, 4594, 1922, 4543, 2024, 3154, 2697, 18, 2176, 5745, 24032, 43, 2097, 15721, 17, 3189, 3728, 1930, 5461, 1925, 18083, 10301, 8253, 5403, 1958, 4346, 5057, 18, 2176, 1977, 3595, 2037, 9081, 3827, 3027, 7972, 2341, 18842, 1989, 2056, 18, 2788, 8528, 1930, 4075, 20709, 11569, 9117, 7864, 18, 3], "output": "MSLLRASVRPRRRALSFAAFATASLLAAVAVTQAVSPAPAQAAAALSCDQNTIYATAGQGQFVAINVAANGLDAYAFTNGAANNSNGNTLARYDSAAGAVTTVANANPSGAPASTLRGAVNPVTGIYYYATGGDPSTISAYDPKTAFSTQGLLFVVASNAVYRLNDETIPTTAGTTSLAATKLTDLPTGTNSPGIAFSSDGYLYVSSGMQIIKLDSSSGNYANTLTGKADVTGRWKSGDQFALKVDGGNLSSPSTATTSGTANGVQAQKAGAALAIPARTYTVSQTAGNVTDDATVASGSGNTAQFTFPAATSADGTDVVCTFANTVAAISAAASDDTGTTASGTSLRVGAPGVLADDAGTDLTVTSNTQPAHGQATVAADGSYDGGGGTSTSTVTITVTPVSSDDVATARAGQALVVDAASGVLANDSGTGLTAAVATGPSHGSLVLGRDGSYRYVPADGFSVTVLPSAVDDTATAASGTPTTIAGSDLTSNDDGLDTTVTAVSTPGHGTASVTPSGDVVYTPADDFSGTDAFDYTVTDGQGGTDTDDSVDAVAGAPLDVPAGRGLLANDGGTGPLTAAVATAPSHGTVVVSPDGSFVYTPEKGFSGTDSFTYTLTDGNGVTSTATAAHLDGPGVLGNDFGTGLTAAVETGPQHGTATVATNGEFDYTPAPGFSGTDTVTYQVTDAAGRTSTATVTITVKPVAVDLANDLGTGLRVTDHGTPAHGAVTVDADGSWSYTPDAGTSGTDSFEYQVTDASGQTATARAWVIVGDLALSNDSGTGLSGALDGAPRHGDVTVAKDGSYVYTPATGFSGTDTFTYTATDAEGQKSTGIVTVVVVPDAVDDVLGTDLRAEIVDAPTHGTATIAAGGTITYTPADGFSGTDQLTYRAADASGGSDVATVTIHVGPIAAHGVLSNDKGTDLTAKVTDQPKAGTVTTGPDGSYTYTPKPGTSGKDTFGYEVTDGNGQKGTGTVTIVVAPKAVDDVATTAVTPAPHGTVTVAPDGTFDYTPAPGFSGDDIVVYTVTDRDGGTDAATVTVTVTPRAIDDRYTTPAATTLVTSVGTPAHGTIVTQPDGSAAYTPEAGFSGTDHVEYTATDASGRGTKAVATIVVGALAVDDAGATRAGTPLTVDATHGVLANDSGSKPGFSGVDAFTYTATDAEGQIRTGTVTITVLPTAVDDGASTPADTTLTVAAPGVLGNDLGTGLCVTGTGTATHGTVTIDAGGRDGGTATATVRITVGVKAIDDEGTTIAGQRLVSGKVGGVLGNDDGSALWVALASKPSHGTVTMTRDGSYEYVPDAGFVGADSFITVLGAAVAVDDEQRGTTDHPVAVDVTANDAPTEGATFDRGTVVIVDPATGDGVSTLTVPEQGTWTTDTAGETVQAVVTVSFPMILSATQLAFTGSASVLGIAAMALLGVALGLALSRRGRRVVGPIRGRRRAENTVSDVIAGTANPFSPANNGLGVGRGDKIGVVGRIPGLQAGNGDFTEVSRMTTPAISNITSYSDLASCNSSTRLADYSTTYRCAVYTPATGFSGTDTFQYTTTGTDTFTYTATDSEGASTTSTVTATVTVTVAPRASSVAVAPEAVDDAVQVTAGGNDAATTPNGTTVTTPASAGLAADQGTATAGRPLSVDAAKGLTSTKAGTAVTVAEPGVLGNDVVDDSPVGGTVADQPLVVDVVADGHVTVAAPGVLGNDVGSGLTVSVPAPGLLVNDLGTGLTSLTATIDGRPAHGTVDLAKDGSYVYAPLVYAPTTGYSGPDAVTYAVADRDYTATDASGQTSRATVTVVDGTVVFTPAKGFDSKASVQYRV", "metadata": {"id": "A0A9E8QGI4", "cluster": 22565967, "interpro_all": ["IPR048834", "IPR006311"], "interpro_used": ["IPR006311", "IPR048834"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein possesses a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. Moreover, the protein should feature a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. It is present in Nitrospiraceae bacterium.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 14465, 43, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 2176, 1977, 2481, 1922, 16665, 10984, 5524, 1972, 3336, 14061, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MLKLGVLASGRGSNFQSIIESTENGCLKGKAEIAVLIVDKEEAFARKRARNHGIAEVWGFMRIVRKPLIDAFPNRIMNIHPALLPAFPGLHAQQQAVDYGVRVSGCTVHARILTEEHRIYPEAIRLYAEGRLSVENRKVNIAAARTPQSGFTNPLPGNLNPKDSPTKDAYFERIRDELNARAVDLVVLAFVDEGMDTGPVIIQSAVPVAPDDTEETLS", "metadata": {"id": "A0A7X7WTB9", "cluster": 8212935, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR001555", "IPR002376"], "interpro_unused": ["IPR036477", "IPR004607"]}, "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 categorized in the The NmrA-like oxidoreductase family, which functions as a redox sensor responding to intracellular NADPH/NADP(+) levels to regulate nitrogen metabolite repression and secondary metabolite biosynthesis. These proteins undergo NADPH-dependent conformational changes, switching between a stabilized dimer and a monomer that binds argininosuccinate synthase to inhibit nitric oxide synthesis and prevent apoptosis. Furthermore, family members contribute to the enzymatic production of bioactive compounds, including mycotoxins and indole alkaloids, through complex redox and cyclization reactions. Additionally, the protein contains a NmrA-like domain that functions as a negative transcriptional regulator or redox sensor using an atypical short-chain dehydrogenase/reductase (SDR) fold. It retains an NAD(P)-binding motif but often lacks catalytic dehydrogenase activity due to altered active site residues, serving instead to modulate targets such as the fungal transcription factor AreA. Moreover, 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. It occurs in Aspergillus versicolor CBS 583.65.", "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, 10234, 1922, 1920, 1920, 5923, 1019, 17, 3189, 27388, 3416, 16, 2154, 4088, 1966, 43, 9366, 6443, 10884, 1942, 4776, 11908, 19, 24221, 12, 15, 13, 2428, 1942, 5741, 6634, 9483, 10084, 1930, 4067, 9483, 8132, 18, 2144, 2697, 4978, 11908, 17, 3100, 8523, 2840, 16, 10880, 2192, 43, 12017, 7632, 1930, 43, 11287, 1988, 6876, 8918, 11096, 27186, 2010, 8921, 1942, 2875, 10233, 7491, 4271, 1930, 4625, 4091, 18, 3677, 16, 3416, 4678, 4672, 1942, 1920, 8145, 3372, 1927, 13570, 4300, 16, 2710, 5078, 20223, 1930, 18050, 22390, 16, 2596, 2796, 9366, 1930, 25267, 5298, 18, 4950, 16, 1920, 2213, 5461, 43, 5923, 1019, 17, 3189, 3418, 1988, 4088, 1966, 43, 3136, 5224, 7888, 2014, 9366, 6443, 2193, 1925, 10834, 3662, 17, 4659, 9294, 19, 11386, 12, 4035, 1005, 13, 3728, 18, 2176, 21645, 1925, 6577, 12, 58, 13, 17, 2743, 5219, 2308, 3868, 13012, 6804, 9294, 2455, 2810, 1942, 5520, 3500, 3200, 4248, 16, 13915, 5974, 1942, 8480, 4845, 2427, 1966, 1920, 8697, 3213, 2991, 3403, 18, 3950, 16, 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, 2176, 5110, 1922, 17604, 3162, 5670, 4051, 16341, 4804, 1010, 18, 4459, 18, 3], "output": "MSLVVITGATGTQGGSVARQLAKNPAWKVRGLTRNAQSTKARELKTLGVEMVTADLNDARTLPEAFEGATAIFCVTFFWDIATTEGIDAATKGELQQFINVVQVAAKLPTLRHLVLSVMPNCETLSGGILPCPHWDAKARGGEYVKRELPQLAAKTTYVWMGWYVDNLAGQPLMKPQPYLGKYIIAQPSKPDAIVPVAGVVEVNTGITVQSILAQPEKTHGKYVPKLTDLISWTAIAEGWSKYTGETAVYAEISDSEFEKLVGPSFGPEIARQFRFSEEYPDWYTYHPEDTLSLKDLGVGEEVLGFYKGLEYFKSQIQP", "metadata": {"id": "A0A1L9PPH4", "cluster": 681857, "interpro_all": ["IPR036291", "IPR008030", "IPR051164"], "interpro_used": ["IPR051164", "IPR008030", "IPR036291"], "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 Extensin-like, C-terminal domain that constitutes the C-terminus of bacterial proteins resembling plant extensins. These proteins are putative cell wall glycoproteins that likely function to strengthen the cell wall structure in response to mechanical stress. It has been characterized in Myxococcota bacterium and has UniProt annotations Signal.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 19683, 43, 11899, 6777, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 14879, 1920, 45, 17, 7822, 1927, 4543, 2697, 18994, 4496, 11899, 6777, 1036, 18, 2144, 2697, 2032, 6770, 2024, 4821, 16268, 1988, 3205, 2347, 1942, 17976, 1920, 2024, 4821, 3170, 1922, 2644, 1942, 5821, 3071, 18, 2176, 2258, 2252, 4378, 1922, 21464, 26941, 7336, 14061, 1930, 2258, 20709, 15010, 2733, 18, 3], "output": "MIKTFVLVFTLIFGLVPTASAAKKKARKRNLDRKCGMRTPVTIPGGKIGKIQYMNGRKKAKPVMDCRTALGRFYSYRYIKNSSDLSRHAVGLGIDIYGITTADGKTYTVARLLRQLACDLDRSHYFRAILTPDADRDHRDHFHLSVYAHREKRTRPSSKRVWQVVRQRRASNRRVIRKKHHRKKLSELRRSGTVFRLGPYLKALYRLYPIFSANGGISSILVSSDYQKGLGLGKTCEGHPRARGKYRTTLIEYQVFSYPWVKRLPKLGN", "metadata": {"id": "A0A948E7Z3", "cluster": 1359965, "interpro_all": ["IPR009683"], "interpro_used": ["IPR009683"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The protein is classified under the Protein of unknown function DUF389 family, which consists of conserved hypothetical proteins with no characterized function. Members of this family are predicted to be integral membrane proteins. It has been characterized in Microgenomates bacterium 39_6 and features UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2213, 1927, 5435, 2347, 4855, 10892, 9485, 3416, 16, 2154, 7543, 1927, 5305, 15148, 2697, 1956, 2239, 4378, 2347, 18, 4678, 1927, 2052, 3416, 2032, 4396, 1942, 1998, 12328, 3260, 2697, 18, 2176, 2258, 2252, 4378, 1922, 12517, 19824, 29187, 14061, 3886, 41, 26, 1930, 4075, 20709, 11569, 9117, 7864, 18, 3], "output": "MKHLNLKSLEKRAIEEIRPDGVKANNIYLIIGSMLVAPFIDPIVSLVVLVFVTSFIFWLLNLAHLDLNQINPPLLWFWPKSSDTSAGIAVAISLVPPISLGIILGAELAMFFYAKSGRKNSLQDLILLSIFSALIASFARSGNFKKVFKAVGSLFLVIGAPEALLIDNFFVALIIGIISAYATFYLIAQDMVNFTGQINNFVINF", "metadata": {"id": "A0A101HWV8", "cluster": 1503850, "interpro_all": ["IPR005240"], "interpro_used": ["IPR005240"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Functionally defined as:\nIt is part of the Six-bladed beta-propeller, TolB-like superfamily, which forms a structural domain consisting of six 4-stranded beta-sheet motifs that serves as a scaffold for diverse biological activities ranging from enzymatic catalysis to transport. Members of this family include enzymes like quinoprotein glucose dehydrogenase, signaling components such as the LDL receptor, and the periplasmic TolB protein, where the domain mediates protein-protein interactions within the Tol-dependent translocation system. Also, the protein should have a WD40-like beta-propeller repeat that typically folds into a multi-bladed beta-propeller structure to serve as a stable scaffold for protein-protein or protein-DNA interactions. Acting as a platform for the assembly of molecular complexes, this domain mediates diverse cellular functions including signal transduction, transcriptional regulation, and ubiquitin ligase activity. It is found in Theionarchaea archaeon and is annotated with UniProt keywords Membrane, Transmembrane, and Transmembrane helix.\nDetermine the correct amino acid sequences for the masked regions.", "tokenized_instruction": [2, 9346, 3608, 1966, 30, 2176, 1977, 3131, 1927, 1920, 3798, 17, 22707, 1007, 4666, 17, 5062, 13728, 16, 21930, 1014, 17, 3189, 13975, 16, 2154, 4952, 43, 4346, 3418, 7600, 1927, 3798, 24, 17, 10338, 4666, 17, 11130, 8277, 1988, 10634, 1966, 43, 7281, 1958, 6445, 3933, 4209, 6485, 2037, 8145, 15408, 1942, 4860, 18, 4678, 1927, 2052, 3416, 3951, 5038, 3189, 9012, 6657, 3817, 9294, 16, 3197, 4178, 2427, 1966, 1920, 8017, 3148, 16, 1930, 1920, 24334, 21930, 1014, 2213, 16, 2597, 1920, 3418, 10412, 2213, 17, 2213, 3719, 2651, 1920, 21930, 17, 3100, 7849, 2433, 18, 2222, 16, 1920, 2213, 3066, 2162, 43, 17907, 4241, 17, 3189, 4666, 17, 5062, 13728, 6865, 1988, 5745, 16231, 2460, 43, 2779, 17, 22707, 1007, 4666, 17, 5062, 13728, 3170, 1942, 7120, 1966, 43, 4700, 7281, 1958, 2213, 17, 2213, 2014, 2213, 17, 2678, 3719, 18, 8290, 1966, 43, 6631, 1958, 1920, 5957, 1927, 3272, 5048, 16, 2052, 3418, 10412, 6445, 3689, 4088, 2710, 2733, 8201, 16, 5224, 3640, 16, 1930, 6526, 11905, 2455, 18, 2176, 1977, 2435, 1922, 1920, 2001, 3983, 24145, 13470, 1916, 1930, 1977, 10633, 1956, 20709, 11569, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3415, 1920, 5550, 3835, 2687, 3709, 1958, 1920, 17476, 3451, 18, 3], "output": "MLSAMSDRLWKTNNLLWLLLLAGLAGGLIFVGLGSGNPGMSARGTNVKRLFCSPSIDGFPSFSADGERIAFVSNRDDWRYFTFTFWPRWSPDGTKIVFISDRNGNSEICVMDADGSNEINVSKIVFTSDRDGNHEIYVMNPDGSNQKRLTNTTSWEGSPAWSPDGQRRLTRDSAADGGPIWSPDGTKIVFTSDRDCNDEIYIMDSDGSNLRRLSPPAPGRLFVVLTGVFLAGIPSILWLHQNTAGKDQNPVYGLSTNFLFSFTVGFVLIYLGARVTKVEEVTVQKAFGAALIGALCSKIIYKTTWKKASAVFVIYSAVFLTLILISMGVLTPFLQESIEFSATIEGFLASITIRNMSEPPVVVTGIYADGRMMDYGIDIVLSKVVLHMEDGTKLTFVVEYQAGTRGWNSRTWILFGKIAFTAESLEEKNFDLDIWVAIYVMDSDGNNMERLTAYPCRKNNPWEDSQSSWSPDGTTQIAFTSNREGSSDIYVMNTDGSNTRNFAEEFACSWCCSVSNEVILMTVLIASFLVMSYLDRITAFLAVYPWGDLVGYVLVLPSLPMMDCEREDSDVLVLKSQRPGLSSKELDLSSYGIPPG", "metadata": {"id": "A0A8J7XHH1", "cluster": 1989140, "interpro_all": ["IPR011042", "IPR011659"], "interpro_used": ["IPR011042", "IPR011659"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein should include a Aspartate kinase conserved site that catalyzes the phosphorylation of aspartate, initiating the biosynthesis of lysine, threonine, isoleucine, and methionine. This region provides catalytic activity in both monofunctional enzymes and bifunctional isozymes, such as those fused with a homoserine dehydrogenase domain. In addition, the protein should contain a ACT domain that functions as a conserved regulatory binding fold involved in the allosteric control of enzymes within amino acid and purine metabolism. It typically adopts a ferredoxin-like topology, where pairs of domains form an eight-stranded antiparallel sheet to bind ligands, such as serine, at the interface. This module is found in a variety of proteins, including 3-phosphoglycerate dehydrogenase and chorismate mutases, across archaea, bacteria, and plants. Furthermore, the protein should feature a Aspartate/glutamate/uridylate kinase domain that catalyzes the phosphorylation of aspartate, glutamate, or uridylate to drive amino acid or nucleotide biosynthesis. This domain often functions as a key regulatory checkpoint in prokaryotes and plants, controlling the production of lysine, threonine, and methionine via feedback inhibition by these end-products. It is present in Armatimonadota bacterium and is annotated with UniProt keywords Diaminopimelate biosynthesis, Amino-acid biosynthesis, and Transferase.\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, 12878, 4016, 5305, 3200, 1988, 17097, 1920, 4050, 1927, 12878, 16, 12410, 1920, 8132, 1927, 9082, 16, 13143, 16, 25398, 16, 1930, 12417, 18, 2052, 3031, 4558, 6804, 2455, 1922, 2321, 8914, 15802, 5038, 1930, 29491, 4911, 16367, 16, 2427, 1966, 2690, 10305, 1956, 43, 16350, 26337, 9294, 3418, 18, 1922, 2459, 16, 1920, 2213, 3066, 5531, 43, 4033, 3418, 1988, 4088, 1966, 43, 5305, 4948, 2743, 3728, 3286, 1922, 1920, 14772, 2285, 1927, 5038, 2651, 3835, 2687, 1930, 19700, 4714, 18, 2176, 5745, 24032, 43, 25304, 22389, 10960, 17, 3189, 13678, 16, 2597, 5803, 1927, 4682, 2386, 1925, 5066, 17, 10338, 28892, 11130, 1942, 4566, 6908, 16, 2427, 1966, 8468, 16, 2019, 1920, 6854, 18, 2052, 9059, 1977, 2435, 1922, 43, 5386, 1927, 2697, 16, 2710, 23, 17, 8078, 14966, 2010, 9294, 1930, 25952, 18538, 2010, 2446, 2319, 16, 3436, 21501, 16, 4802, 16, 1930, 4793, 18, 3677, 16, 1920, 2213, 3066, 5961, 43, 12878, 19, 7627, 19, 3674, 19743, 2010, 4016, 3418, 1988, 17097, 1920, 4050, 1927, 12878, 16, 7627, 16, 2014, 3674, 19743, 2010, 1942, 9265, 3835, 2687, 2014, 5489, 8132, 18, 2052, 3418, 3868, 4088, 1966, 43, 3834, 4948, 11714, 1922, 28149, 1930, 4793, 16, 7138, 1920, 3372, 1927, 9082, 16, 13143, 16, 1930, 12417, 3454, 6491, 3523, 2007, 2144, 2482, 17, 4461, 18, 2176, 1977, 2481, 1922, 6011, 1968, 3947, 12595, 3857, 14061, 1930, 1977, 10633, 1956, 20709, 11569, 21121, 2011, 11593, 5148, 2057, 8132, 16, 3835, 17, 2687, 8132, 16, 1930, 13763, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MIVMKFGGTSVGSGQRIRAVHDICAAGIEERPVVVVSAVKGVTDLLLRAAEEAALCGKSSEIKNLLDECQSLLQGLHLLRELTLRTRDAVASYGERLSARITASYFRLRGVEAEARMKQAFSMLPESEIPVVTGFIGKDQHGQVTTLGRGGSDYSAALIRILPAVSFDEAAELAYFGAKVLHPRTIEPAITTGIPVLVKNSFFPEDPGTTILPGTEVLNLRSTRMLEAPGFLHSVFSVFHSHGLSIDVISTSEVSVSLTLDNAENLEEAMKELGLGVAGRIFTVLGKEEINVEMISQGASRINITFVVSDHDADRAVRCLHDEFFSDPRAHFQQIAQIHAGICDDLQVPLSAKAYDAWDVGMLTSSEFTQAKPLGAALRVKEIQIWTDVSGIMTGDPRVVPHAKEGAVKAITSKKGITCDIAQVSVEQGRSIICLVGEGIKTT", "metadata": {"id": "A0A9D6DV48", "cluster": 5365055, "interpro_all": ["IPR036393", "IPR045865", "IPR054352", "IPR002912", "IPR001048", "IPR005260", "IPR001341", "IPR042199", "IPR018042"], "interpro_used": ["IPR018042", "IPR002912", "IPR001048"], "interpro_unused": ["IPR005260", "IPR045865", "IPR054352", "IPR042199", "IPR001341", "IPR036393"]}, "task_type": "infilling"} {"instruction": "Come up with a polypeptide chain sequence that has the following functional description: The protein is grouped in the Protein of unknown function DUF1269 family, which consists of uncharacterized proteins predicted to be membrane-associated. Members of this family typically contain two or more transmembrane segments, though their specific biological function remains experimentally undetermined. It originates from hydrothermal vent metagenome. Give me the sequence.", "tokenized_instruction": [2, 10449, 2353, 1956, 43, 13022, 4659, 3244, 1988, 2258, 1920, 2894, 3183, 8418, 30, 1920, 2213, 1977, 10809, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 5739, 4684, 1026, 3416, 16, 2154, 7543, 1927, 24528, 2697, 4396, 1942, 1998, 3260, 17, 2458, 18, 4678, 1927, 2052, 3416, 5745, 5531, 2288, 2014, 2253, 9117, 7492, 16, 4170, 2310, 2487, 3933, 2347, 4497, 9568, 27115, 18, 2176, 22970, 2037, 26959, 14654, 16552, 2225, 18, 7031, 2142, 1920, 3244, 18, 3], "output": "MEQIGPLQLLVIGFADPQLDGSILSELVSASDSGTIRIVDVLGVYKDEAGNVAAAQMSDLTQDEAMTYGAWIGALIGLGAGGVDGAEIGALAGAMSALDEYEYGLDAEAVATIAQDIPAGGAAMLAIIEHTWAIGFRNAMRDSGGVLIAQDFLSPEALIALGAGA", "metadata": {"id": "A0A3B0REK6", "cluster": 6900014, "interpro_all": ["IPR009200"], "interpro_used": ["IPR009200"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "The protein exhibits the following characteristics:\nThe protein is a member of the Conserved oligomeric Golgi complex subunit 8 family, which acts as a component of the peripheral membrane COG complex involved in intra-Golgi protein trafficking. Furthermore, the protein is a member of 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. It has been detected in Bifiguratus adelaidae and is connected to UniProt keyword Golgi apparatus, Protein transport, and Transport.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 1977, 43, 7210, 1927, 1920, 5305, 19206, 10277, 2796, 5903, 28, 3416, 16, 2154, 8016, 1966, 43, 4594, 1927, 1920, 5009, 3260, 17082, 2796, 3286, 1922, 5153, 17, 10277, 2213, 9604, 18, 3677, 16, 1920, 2213, 1977, 43, 7210, 1927, 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, 2176, 2258, 2252, 3330, 1922, 10740, 7694, 5524, 1031, 1957, 23846, 5148, 10828, 1930, 1977, 7951, 1942, 20709, 11121, 2538, 10277, 11161, 16, 2213, 4860, 16, 1930, 4860, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MTEAALDTSRHDLVLSLLHSKGQGLLSLPLASLQQEPQRLIKATSNVDQRLDDLRAHLDGFESMVTDVMNSCKDFDQLLDLLEIPQLMETCVRNGYYQEAMDLSAHVTRLANRHSQLQLIRLLQKPIRLPVAMNIVGNLRRMRTFMLELEREVEKSSEFVSKNQREFKQRFVYDATQYTSIFQSSTPRSRSISESHSAPPPASTIVTTSLLPTYLSSILTQLMYCGMSLGRVGLDFRHLVCDEFEANFASKIEFATKSRIPPSQWMVSRTFNSTNIMDDLERSKSLSCPALAHFTNGVLSAFNALRPLAPISLFPKLRDKVPSHDHNDISIPDANAIEAFVTTYVRCVVSYLHRCLCRGVYGSKNLEEVFKIWLPQTAEIGTKEDKEPSTEKEADVTTRAGTEATSNSERDSDIAPAKDTNGIKDTNDSIDGVNERHHEESTPTWLANYVDHDLQSLVLDEYQSIVKARDVQIDTEVEVSAFLDVRSELESILDNHDSEVKLLQSIQHQTQQTLAFMGRGEMELRVAFLKCRRLYFQALFIKKAIDLLREHLFEVTTDLTKTLLDILRKYLPQVNDTASMMWSIVDGMLTTTGAPPKASQSSFSSPPQIILDTLLRQVSAQLQAYLDAYATMYIADSDLEQVKVFEGAASSADADGDADTISAPVDHQEE", "metadata": {"id": "A0A261Y356", "cluster": 8712135, "interpro_all": ["IPR007255", "IPR016159"], "interpro_used": ["IPR007255", "IPR016159"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Infill the masked sequence for this function: The protein includes 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. Also, the protein is included in 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. Moreover, the protein should contain 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 originates from Rhodnius neglectus and carries UniProt keyword assignments Nucleotidyltransferase, Hydrolase, and Transferase.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 5921, 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, 2222, 16, 1920, 2213, 1977, 3063, 1922, 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, 3950, 16, 1920, 2213, 3066, 5531, 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, 22970, 2037, 11490, 8635, 1957, 18256, 1957, 1930, 16252, 20709, 11121, 2538, 18306, 2797, 4090, 2199, 9961, 16, 20748, 16, 1930, 13763, 18, 3], "output": "NNNPREYKFKEKSCNDITIYTYNCRTLMGLSEVRRDGEQCVNINNNITFYHNGKGVRISKIIWKLEPKVGKRSRLKIIQVYAPTTASTEEELEEDMNAKIGKNEGEKATGMFSYGERNERGKRLVEFADGQTKNEIDFFIIDKKDIVQDVDVDNGINTGSDHQILNSKNYESILKKNLKIYRKREDQDVEEQLKEIEEIPNEIKKLLERRRRLKRTGKAKVEFAEICKLIRIKWREVKQCIRQQQIGTSKMISIKDANGRVRREINEIADVICESLQECYTENKWEEEKGFHDSWSVLEEEIHYVIVLVGLLCKLFNTCLATKTIPEIWKKGKLINRIGDTLESAITPNQTGFKKNHSTNDNILDFEKAFDRVKIDVILKTLKNRGIEKIYMNIFECIYGRQGDVPSAKVFNVILDEAFSNMEWQGRGVRINGEWLNVIKAMLEDLIREVTKVGLAINGKKTKIMYLNCDENTQILKIITKEGEWEEVVRRCSLGWSAFNKYKHLLRSKVEIEHKALSAKIIKKLRVTVRSMARIMLGITRKDKKKKQWITWAGHIVRTKDERWSKKIIEWYPREMKRKVCGGVTWMRVARDRREWERLKTVYSTVWLYQDLKENIKLEQLLAEMQNVEWDVGGTGFLINKNQEKNIISYKSYSEYYEHLKMALDEDICKYTIIMGESNKLFIMNTFFKKKESRKWTWISPRAIKMILKPGIEKKKWEYKPRYLRQSTVIKKTTCEVTEAREICNRRKWSNEKKLNELKETIDSGKSYYKNLYSRDVGDKIEETRNLKEGKAGGIDGITNEEIKAGGNLLFKKGDRQEIKNYRPINLLSVVYKIFMAVITVIQQLIRKSKDYNFPLILLFIKAKLFFKIENTGREIEIKRGLLKFADDIVLIGKSILEGEEEIESTDSFIYLGQKKLFRTCVLPTIIYGCETWTEQSLLVDVGKIVTERKWNRGRPSRTWEEEFRK", "metadata": {"id": "A0A0P4VWD0", "cluster": 14040685, "interpro_all": ["IPR043502", "IPR036691", "IPR005135", "IPR043128", "IPR000477"], "interpro_used": ["IPR000477", "IPR043128", "IPR005135"], "interpro_unused": ["IPR036691", "IPR043502"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein has a Rho GTPase-activating protein domain that stimulates the intrinsic GTPase activity of Rho family small G proteins, such as Rho, Rac, and Cdc42, to promote their transition from an active GTP-bound form to an inactive GDP-bound state. This regulation of molecular switches controls critical cellular processes, including cell adhesion, motility, and actin cytoskeleton organization. Structurally, this domain, also known as the breakpoint cluster region-homology (BH) domain, is composed of seven $\\alpha$-helices. Additionally, the protein possesses 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. Moreover, the protein is associated with the Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein family, which functions as GTPase-activating proteins (GAPs) that regulate ARF and RHO small GTPases to modulate the actin cytoskeleton, membrane trafficking, and cell signaling. These proteins are activated by binding to specific phosphoinositides, particularly phosphatidylinositol 3,4,5-trisphosphate, and facilitate cytoskeletal reorganization events such as those required for anthrax toxin internalization. It is found in Timema monikensis.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 2258, 43, 10585, 14809, 17, 8019, 2213, 3418, 1988, 11803, 1920, 7598, 14809, 2455, 1927, 10585, 3416, 2858, 49, 2697, 16, 2427, 1966, 10585, 16, 7195, 16, 1930, 15790, 16, 1942, 5527, 2310, 4832, 2037, 1925, 3500, 9319, 17, 4124, 2386, 1942, 1925, 9078, 15217, 17, 4124, 3360, 18, 2052, 3640, 1927, 3272, 21529, 3562, 4140, 3689, 4028, 16, 2710, 2024, 6141, 16, 9254, 16, 1930, 4718, 11612, 5901, 18, 12171, 16, 2052, 3418, 16, 2222, 3171, 1966, 1920, 24698, 4377, 3031, 17, 9039, 12, 9710, 13, 3418, 16, 1977, 7179, 1927, 5260, 8, 38, 4595, 8, 17, 12789, 18, 4950, 16, 1920, 2213, 14465, 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, 3950, 16, 1920, 2213, 1977, 2458, 1956, 1920, 13720, 17, 5750, 1956, 10585, 17, 5750, 3418, 16, 9808, 6865, 1930, 2087, 3418, 17, 3165, 2213, 3416, 16, 2154, 4088, 1966, 14809, 17, 8019, 2697, 12, 11349, 13, 1988, 5741, 13720, 1930, 10585, 2858, 18390, 1942, 8480, 1920, 4718, 11612, 16, 3260, 9604, 16, 1930, 2024, 3197, 18, 2144, 2697, 2032, 4128, 2007, 2743, 1942, 2487, 23546, 1036, 16, 4443, 16927, 23, 16, 24, 16, 25, 17, 6349, 25324, 16, 1930, 6628, 14787, 18062, 3916, 2427, 1966, 2690, 3414, 1958, 14228, 3013, 9165, 12071, 18, 2176, 1977, 2435, 1922, 2367, 3368, 2399, 5909, 3355, 1937, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MLANMLVLGELVRANKLCWVVLDHLLEIINDQPNMLAESGEPPDSANMLGWSFIISNKCSNNTNMLANIPNKLGSISFHSPFTTEEEECEKAEDDYGVPPPIYPPPPLPDESVYDELQSVISGHSSSCNDPYEDISLVKSLGSSSKSPSQTSNSFPMPSSISPTQKKQIIDITNKNIKPGARSDSWSFFNTVSNDDLYSNVSITGCPTSSESVSPSLLSDLEGLQYNSSDDDSYSTVNSQSHLSVQNELYENWNLSSVDPLFENSPLNCDTSSKNVKLLSTSNTPPISNKILTSSYGKINKVSAQQQHPTTSSLTEEGISLIPPVPPRRFDSMTITGSVKSVDQLSLPEARTSVDKSCQADSTLEREETDSNITSTPTSQPEIPTTTPVDSVPPKQRLARWYSMKRAIQLVTDNPDKDKSTNITRPNLLLHKVSPYSGSLFRLTGTSDRNKELAQRWCVLAEGKLSCFQDKTASEIKEVVPLESIMSVNVSWKGRHSVFGSASTTDRRVWMQKILESLTKVFPMRISSDFTRAGWCFLKEGVSGLWNLAWILLHKRTLMQDNSNDSPPTKEKGPMLLVDFPGQALYFQMDTARETTMWRVAVRVAAVDNGPNLAQQQLTSGTNSAVTRLLTLFRQDAWAVQLSKSEYSEYDVGSVLKRFFRDLPEPLFTTELHAQLCEIADGKFGNRKLIGHLYFIHEQHEKNLMPVDNLAAIWGPTLMHLECDEYQSWSSLESGVVTHLISMYPSLFDVDTKPSGDLKVWIYIDSKDSGNCVNVTIHPQRQAGEVCVELASKTGALVRPMHHTERVLDTVLRWGYWSDADCKDNCLVLTRNTTFKEADILTKQPMTMCGELRFADQKSKKLNEWKIEDIVWYFGHEPKRNPHMRSRDAPYFGCTIAGTSKEEQLRWVGAMLGGEFPQGLLPSPILLVTTQHNFLALTSSPSSPSDSCIDTDSIYIANGSDIDDRSSIYSNVPNTEYGSTSSILSVPLRSAHEKRTLPSQSVIFEFKDEIVSQDILKLDPLAQLNQSLEHVAWSSPMIARRNRSSGADNAVFYNVAADYKPSATGDEIHCFELSFYCLTNGTLQEADLRKAICTVKDDVPTIVDKCVNFIYAHGSMSEGIYRRSHQDLLAQYRRALEQLPPINFVTAEELIREKKMLEVLERYHASNTSVPHNEFPSHQLTLEEVVLGSFKNYLFEFSQAKLSYYKDKSGSN", "metadata": {"id": "A0A7R9E336", "cluster": 16479815, "interpro_all": ["IPR052227", "IPR011993", "IPR001849", "IPR008936", "IPR000198"], "interpro_used": ["IPR000198", "IPR001849", "IPR052227"], "interpro_unused": ["IPR011993", "IPR008936"]}, "task_type": "infilling"} {"instruction": "Resolve the missing spans in this masked protein sequence to achieve the following biological role: The protein is a member of the Two-component system sensor histidine kinase family, which functions as a bacterial membrane-associated sensor that undergoes autophosphorylation on a histidine residue upon detecting environmental signals. These kinases subsequently transfer the phosphoryl group to a cognate response regulator, modulating gene expression related to virulence, stress resistance, and homeostasis. Some members also exhibit phosphatase activity to further regulate the signaling pathway. Furthermore, the protein is grouped 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. In addition, the protein should include a Bacterial nitrate/nitrite sensing (NIT) domain that serves as a sensor module in signal transduction pathways to detect nitrate or nitrite concentrations. It regulates gene expression, cell motility, and enzyme activity by coupling ligand binding to downstream effector domains such as histidine kinases, transcription regulators, or diguanylate cyclases. It is produced by Lipingzhangella halophila and contains UniProt keyword associations Transferase, Transmembrane helix, and Two-component regulatory system.", "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, 2288, 17, 4594, 2433, 6443, 13873, 4016, 3416, 16, 2154, 4088, 1966, 43, 4543, 3260, 17, 2458, 6443, 1988, 14928, 22009, 1990, 43, 13873, 6181, 4073, 9227, 4813, 4771, 18, 2144, 7784, 5326, 3856, 1920, 12556, 2210, 1942, 43, 15786, 2644, 7888, 16, 10871, 2359, 2294, 2712, 1942, 9304, 16, 3071, 3554, 16, 1930, 7622, 18, 2673, 4678, 2222, 5987, 8167, 2455, 1942, 2520, 5741, 1920, 3197, 3374, 18, 3677, 16, 1920, 2213, 1977, 10809, 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, 1922, 2459, 16, 1920, 2213, 3066, 3951, 43, 4543, 12628, 19, 15988, 9306, 12, 7904, 13, 3418, 1988, 10634, 1966, 43, 6443, 9059, 1922, 2733, 8201, 3873, 1942, 4277, 12628, 2014, 15988, 3295, 18, 2176, 7014, 2359, 2294, 16, 2024, 9254, 16, 1930, 4113, 2455, 2007, 7590, 5207, 2743, 1942, 5863, 7917, 4682, 2427, 1966, 13873, 7784, 16, 3213, 9098, 16, 2014, 4325, 13785, 9075, 16526, 1036, 18, 2176, 1977, 4152, 2007, 3178, 1941, 1011, 15409, 20178, 5148, 23226, 24888, 5148, 1930, 5461, 20709, 11121, 2538, 5253, 13763, 16, 9117, 7864, 16, 1930, 2288, 17, 4594, 4948, 2433, 18, 3], "output": "MRSPRTRSVRFRILTVVLIYLTVPQGLALIDQQRLHPEVGAPTDALGNPDDLEAARSETDDAVQEFEGIQESDILEVVEPATSAVDDGSLGSREAFDYYTGMSDGYLAILTTAAREELLQEDALLAAGIAAGGLAAHSATESAVIDLPPHLRERHEEGPIPDEVAAGDTWQQAVGGVAESNREVEYATAEHLRAGVAVVAGLVGVALSILVSVRMARRLIKETTDRSGQGVDAADVGPSRLAFQIHTGEAKLRQNVNDVIVNLARRNQSLLHRQLKLFDNLERHAEGLLILSGSLPGRGWSRPMPVVDVIRAASTEVEEYTRVLLAELIENATLSSPQTSEVLVRGRDVANGFAVLLADPPELDLAKRTELGHFVVATLARRHGPRSILSVDEQPGVEENQAKAAVAAEGRHHAEPAAGTAAAQGLPPSGEEEPAHPSPAARTRGLPRRVRQANLVPQLRDDEADPPPGTADGWTRGRNDDPPTGSDPAHSAPPSADDLEGNHQPLLTLVPLAGFAVAVAAERRATLIHIADPEAARERVRNMQDQVDQLDSTRQSITTLNDPEMTARGIALARGPQQHHRFVQQVGQVQQSEEMARLRELENAVVEAGPTASAEPMATGIIVLKEQIEDVAHNQLPNLVRRLTRELDDLNWAFDEARMVAIQSARQVDDPDQLRELFLLDHLATRMRSVFPMSSVGLTGGAVTDVIHEVEDGGLGMSEQSLQQANEIKVHLRDSPYGGVTAIVLLEGPQPTHTPTGETSHPPKHRPSPPPRQDNGGDRPPEQVHSMMSAMQA", "metadata": {"id": "A0A7W7RL96", "cluster": 17433699, "interpro_all": ["IPR036890", "IPR013587", "IPR010910", "IPR050428"], "interpro_used": ["IPR050428", "IPR036890", "IPR010910"], "interpro_unused": ["IPR013587"]}, "task_type": "infilling"} {"instruction": "A protein is required to perform the following role:\nThe protein includes 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 is categorized in the Bacterial Sigma Factor Regulator family, which regulates gene transcription during stress response and sporulation by controlling sigma factor activity. Members typically employ phosphatase and kinase activities to modulate signal transduction pathways, often utilizing PAS domains to sense cellular energy levels or environmental stimuli. In addition, the protein incorporates a PPM-type phosphatase-like domain that catalyzes the Mg2+- or Mn2+-dependent dephosphorylation of phosphoserine and phosphothreonine residues. It functions as a versatile regulatory module in signaling pathways across prokaryotes and eukaryotes, controlling processes such as stress responses, metabolism, and sporulation by reversing the action of protein kinases. It is present in Spirochaetaceae bacterium and contains UniProt keyword associations 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, 5921, 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, 1977, 10234, 1922, 1920, 4543, 5139, 2991, 7888, 3416, 16, 2154, 7014, 2359, 3213, 2409, 3071, 2644, 1930, 23647, 2007, 7138, 5139, 2991, 2455, 18, 4678, 5745, 4417, 8167, 1930, 4016, 4209, 1942, 8480, 2733, 8201, 3873, 16, 3868, 10232, 9233, 4682, 1942, 7534, 3689, 3844, 2428, 2014, 4813, 5458, 18, 1922, 2459, 16, 1920, 2213, 19683, 43, 8748, 17, 2601, 8167, 17, 3189, 3418, 1988, 17097, 1920, 14756, 15, 17, 2014, 26737, 15, 17, 3100, 16881, 1927, 8078, 26337, 1930, 8078, 5856, 1021, 12530, 4248, 18, 2176, 4088, 1966, 43, 20425, 4948, 9059, 1922, 3197, 3873, 3436, 28149, 1930, 15021, 16, 7138, 4028, 2427, 1966, 3071, 3387, 16, 4714, 16, 1930, 23647, 2007, 26526, 1920, 4615, 1927, 2213, 7784, 18, 2176, 1977, 2481, 1922, 22075, 25588, 9215, 1972, 3336, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 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": "MAFTAAHSLRRSFVLTLAVLYSVAARHLTRNYVERYATARNILEQNRIRSLLGRETALAAAEATALSQLGSYQRLFRDQTIFIAAAGSRRPANPGDRWFFETTALRDEAGTMVGVAGTTSVIVNGEGQILAYRDRAIIEHNARVALFDQPADRAVLGETLAALASTRISAGGLIPELGWYNLVMVEDSLVIGPGDFVPFLRPLGALTAAANQVAKGDYRLNLALENRNETGVAERTSELAESRDRLLGSIRSGRLIQTSILPSEDFAFFRPLPDGFCAAVVDCTGPADDSGRLLQRLHLALLDNLRAAKDTAHLENLPLFLTDRDGPRQIDGARLHLGFERSGQADLPVHRLPGLSAAGFLNHLAASWRQPLTRQAAAIESFELPMPDAGGGAAPTPEEKRTLVNLTVFLTSCLKLADDQAIVGWLRNEADYFVSTRNQSITAAVVLDLTGSADFWINVNYDAFLDEIRVWINGMDLSTFLASLVEHDERQLVDADRIDIYQDMPPVLLRLRYGGAPVTAALAALLATVLSLSLILGIVLVQLDQLVLLAGAFRFMTGRINDYTAHLEQMRDMAEHLGAHHLWLRPLDTVGGHGVPGAFMTMMAASLLNRIAATGGLDIALCRYRRPQAVLEFSGAGCGGGQRFHLVSDGILDLPGGEHGFSACAAWQGLHGQRDDLCLF", "metadata": {"id": "A0A356EGY2", "cluster": 19054720, "interpro_all": ["IPR052016", "IPR003660", "IPR036457", "IPR001932"], "interpro_used": ["IPR003660", "IPR052016", "IPR001932"], "interpro_unused": ["IPR036457"]}, "task_type": "infilling"} {"instruction": "Identify and generate the missing sequence components for a protein functioning as described: The 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 is expressed in Ligilactobacillus araffinosus DSM 20653 and is associated with UniProt keywords Coiled coil.", "tokenized_instruction": [2, 3512, 1930, 5655, 1920, 6814, 3244, 4178, 1958, 43, 2213, 7295, 1966, 2910, 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, 1977, 3198, 1922, 3650, 19167, 2341, 14357, 8898, 20289, 2040, 11096, 1957, 10964, 16560, 3786, 1930, 1977, 2458, 1956, 20709, 11569, 17524, 9121, 18, 3], "output": "MRRKVLIGLGVILLAVVFIGFGFTKNVEVQKEYEQAMERSFQNAAKRKQDDPQAERNIKQLDLYMKAKTALGLNVLVRRSSAYATEIEEAQNQLASFERLYDESIYAKAKHLKHENDQFLAPACPLKSEHKGMTQTKKYEYQAAKINQRNYDQAKKIFDQAADADHAIECNEEGNYAKSNTLLTSILKYRGIKERYYD", "metadata": {"id": "A0A0R1ZGZ9", "cluster": 19373384, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Function:\nThe protein is classified under 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 Sediminibacterium sp 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, 1977, 5947, 2441, 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, 6276, 1980, 11566, 7972, 2341, 18842, 1989, 2056, 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": "MKKWIGAMFLVTLMQTAFAQDFKKVETAVAKKASLETTAEGYYWKSKIYAGLAKDPAAKYPKADPEFALAVKSGQEPFFEVYLKSFKDGVAAFGEKDIIFTKGWSSNKQPFDTTTLMYAGNLKSPEVVDVYKYVLIQSIEKKDKAQFEKYYAVAEKDEKVASFEAQTAANSLSEIECQMYGDMFMSARNEENLNQNFAAAFNVGISYYNQYTALDDQFGNNIRALQQLAKFKAQQDSIKKLNLALDAPMKAKVDQRSVDFLATLYSSKRDKNRANQKLYDELDAKFNKYDQLHDKYQSLLLNNYEAAKTEYDKDAVDQLYKSLEDYIKWKDAAANFDRGVVLSYANQNAGNVENTMKHYTRMIDANYPEEKWFEFRADFIDKNMTAPEAKANFYLDKAADAYKKAYNMNNTNKPVAPKDPKKKLAFDAIEWIENAFNIIKDKPTLTRSEKNVAA", "metadata": {"id": "A0A9D9RGW7", "cluster": 20750030, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Please generate an amino acid sequence that is capable of: 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. Moreover, the protein is categorized 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. It is produced by Phototrophicales bacterium.", "tokenized_instruction": [2, 11586, 5655, 1925, 3835, 2687, 3244, 1988, 1977, 7131, 1927, 30, 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, 3950, 16, 1920, 2213, 1977, 10234, 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, 2176, 1977, 4152, 2007, 10066, 1997, 2688, 2046, 1918, 14061, 18, 3], "output": "MPGEHILLIDSDRTAADAMVKAILQPKMYHTHCATTADEAFATMQRIKPDLILVSLDSTPEASLDLLRKLSSQ", "metadata": {"id": "A0A2M8PLB4", "cluster": 22004484, "interpro_all": ["IPR011006", "IPR001789"], "interpro_used": ["IPR001789", "IPR011006"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein has a PocR domain that functions as a ligand-binding module with a novel variant of the PAS-like fold, capable of binding small hydrocarbon derivatives such as 1,3-propanediol. It has been detected in bacterium and contains UniProt keyword associations Membrane, Transmembrane, and Transmembrane helix.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 2258, 43, 18660, 1005, 3418, 1988, 4088, 1966, 43, 5207, 17, 2743, 9059, 1956, 43, 4008, 6031, 1927, 1920, 9233, 17, 3189, 3728, 16, 7131, 1927, 2743, 2858, 21638, 8383, 2427, 1966, 21, 16, 23, 17, 5062, 23223, 11149, 18, 2176, 2258, 2252, 3330, 1922, 14061, 1930, 5461, 20709, 11121, 2538, 5253, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 3], "output": "MAKSALSSISFENPPEMERLLNKYKSGNMPSIFCDEEDESLLGNNGKDIINIYLAGFSKTYNIPLYLFPIPNNSNISQKSQEDISRNFHDFMMSCEMLQSLGDDIPRPNKECHKDCIEKILHLKKNKKVLAYMCCVGMISFAVPVYVSDRIIGVLLTKCYKPKEANNWKSGLIQMYNCQSNYWDDQINDMEWQSIYQHIPTENSDIWAESKRRILLCEEMLNIKPNELLDIIEKKLKDDKISEITLEYAESFLMKHLNQASEYLTEILSQKYRLEKDSIIGWIRAEMGSSLSLEDGFWHKIQWCRIHPKMGVRKTR", "metadata": {"id": "A0A7C4FNW7", "cluster": 22509390, "interpro_all": ["IPR018771"], "interpro_used": ["IPR018771"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has the following function: The protein should include a Basic-leucine zipper (bZIP) domain that functions as a DNA-binding and dimerization motif in eukaryotic transcription factors. It features a contiguous $\\alpha$-helix containing a basic region for DNA interaction and a leucine zipper that mediates parallel dimerization, forming a flexible fork structure that grips specific DNA sequences. It is expressed in Didymella exigua CBS 183.55. Please generate its protein sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 1920, 2894, 2347, 30, 1920, 2213, 3066, 3951, 43, 5937, 17, 12624, 27910, 12, 30450, 13, 3418, 1988, 4088, 1966, 43, 2678, 17, 2743, 1930, 13640, 5219, 1922, 10825, 3213, 2790, 18, 2176, 4075, 43, 20030, 8, 38, 4595, 8, 17, 7864, 3165, 43, 5937, 3031, 1958, 2678, 2835, 1930, 43, 12624, 27910, 1988, 10412, 6110, 13640, 16, 7402, 43, 9964, 15630, 3170, 1988, 17480, 1036, 2487, 2678, 3709, 18, 2176, 1977, 3198, 1922, 2811, 2229, 5870, 1975, 7694, 1019, 16341, 16228, 18, 4288, 18, 11586, 5655, 2496, 2213, 3244, 18, 3], "output": "MNVSSRLHPGTPIVPRAQSTGAEPTLMQPRKVNSEVRKQQNRIASRNYREKRKRKLQQLQQLLEDDDPSELQTRTRSKSPYEDRSCSESVGYERSIASSSPHIATVLGNLESPHLDHTATANQTWSETPFIPSIEQPLRPVTCLQSLSYNMGTPTATSYPVWSTIPSVASTGYVTTDPAHQSMYSSRASIWPSFECFYSGSVHQQTNIPSTVSYATLWQHNTSEDVPAGIAIDPHGWRYYTYGPS", "metadata": {"id": "A0A6A5R6Z6", "cluster": 788164, "interpro_all": ["IPR004827"], "interpro_used": ["IPR004827"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein falls within the Trp repressor/replication initiator superfamily, which comprises DNA-binding proteins that function as transcriptional regulators or replication initiation factors. Members such as the Trp repressor form intertwined helical dimers that repress tryptophan biosynthesis genes specifically in the presence of L-tryptophan, while structurally related proteins like DnaA assemble at the origin of replication to trigger bacterial chromosomal DNA synthesis. Additionally, the protein is assigned to the Transposase IS3/IS911 family, which mediates efficient DNA transposition in *Escherichia coli* insertion elements and other bacterial systems. It typically features an N-terminal helix-turn-helix (HTH) motif followed by a leucine zipper motif that facilitates oligomerization. It has been characterized in Poribacteria bacterium.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 12182, 2651, 1920, 7259, 14434, 19, 5158, 23467, 13975, 16, 2154, 12936, 2678, 17, 2743, 2697, 1988, 2347, 1966, 5224, 9098, 2014, 5158, 6035, 2790, 18, 4678, 2427, 1966, 1920, 7259, 14434, 2386, 27332, 17860, 1919, 11514, 13351, 1988, 9055, 13489, 8132, 2628, 4475, 1922, 1920, 2990, 1927, 54, 17, 13489, 16, 2679, 12171, 2712, 2697, 3189, 2678, 1019, 17421, 2019, 1920, 4853, 1927, 5158, 1942, 6086, 4543, 9220, 2678, 4271, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 12935, 2051, 1977, 1010, 19, 1977, 12118, 1009, 3416, 16, 2154, 10412, 5807, 2678, 22596, 1922, 14, 10210, 5178, 14, 7413, 5362, 1930, 2303, 4543, 3771, 18, 2176, 5745, 4075, 1925, 56, 17, 4262, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 3489, 2007, 43, 12624, 27910, 5219, 1988, 11374, 17371, 18, 2176, 2258, 2252, 4378, 1922, 4572, 26073, 2341, 18339, 14061, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MEMMTDFLRSLGGATVKSVAGKFGINANRLSEWVLCDGGEVVSVQPQVPPPSPPAERAVGVVEVEYQADGRRRWSHDAKAYIVGETLKPRGLAKDGKLVLPAPDPDEHVEFAPVKVEIVFRGVSIKLSGDTAAPRIAEIA", "metadata": {"id": "A0A7X3RCT9", "cluster": 2304956, "interpro_all": ["IPR002514", "IPR010921"], "interpro_used": ["IPR010921", "IPR002514"], "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 EF-hand domain pair superfamily, which functions as a calcium-binding module composed of two adjacent EF-hand units forming a four-helix bundle. This domain coordinates calcium ions in a pentagonal bipyramidal configuration within a twelve-residue loop, serving as a critical regulatory or structural element in diverse proteins such as calmodulin, troponin C, and S100 family members. Additionally, the protein has 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 Oryzias latipes (Japanese rice fish) (Japanese killifish) and features UniProt keywords Coiled coil, Cytoplasm, and Cytoskeleton.", "tokenized_instruction": [2, 5655, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 1977, 10234, 1922, 1920, 8485, 17, 3897, 3418, 3715, 13975, 16, 2154, 4088, 1966, 43, 5016, 17, 2743, 9059, 7179, 1927, 2288, 6811, 8485, 17, 3897, 5701, 7402, 43, 3006, 17, 7864, 14142, 18, 2052, 3418, 10675, 5016, 6982, 1922, 43, 9412, 13481, 8446, 3553, 25238, 1923, 9674, 2651, 43, 12367, 17, 6181, 5881, 16, 13915, 1966, 43, 4140, 4948, 2014, 4346, 6149, 1922, 6445, 2697, 2427, 1966, 17537, 16, 18714, 45, 16, 1930, 12678, 3416, 4678, 18, 4950, 16, 1920, 2213, 2258, 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, 19745, 10657, 4144, 29972, 12, 10405, 8674, 5724, 13, 12, 10405, 11321, 1974, 2471, 13, 1930, 4075, 20709, 11569, 17524, 9121, 16, 5239, 16, 1930, 11612, 18, 3], "output": "MEPSLWRRGPQGGGLSCGMGDGQEQDHYEERLKEVFDSFDASGCGSLTPEELADLARVDFQQFKTALIQVLYSTFPGAQEEQEAPPPTASPEIQPKFVKDVNPADGSLEDNDDSAVPRKRERWNSQESSSDEFEAEGQMHLWNPDGPSTPRGWDGHAARSELLVLCESLGLEPGADALLDPDEQMDVQEFVSRLMTQPKPPTPSASTPYRQLKRHHSTQSFDELDDGAGHAAAERVLDVWMDEGVENGVEILQSLSVEPDGRLNLCDLAAALESELLVTKNGEIREKEKIRSDLEKAEKQKSQLASEVDERHAAIERANSLNLRRLEQEHKERLGAVRAKIKEEESLLRDHLSISLKENRRLETELLDGAEELEEAQGQILKLQRSLESLMKRSSYEAQCRELQDRIDELQAELQDLHPLSKGHAPTHKALSEELESQEVQPFSLSLEAEMMLERLKEQHLQQMEELQEQLEIKVNEFNRRLEKQQEIHEVRSHAQELQNQLEGAELKPAAGGEELQSRGAEVGPFRQQLQEALRVSADLEEQLKALEVQQEISKLKEEQEELLEARKEEKSELERRLSAEWEQEKDALEVSHENQLRVRLEEKAQLDLQRNETLQVLLEEEMLRLVVDQEEKENSLREQWERERAKLEEHHEEVLHLKEEWEKEKLQLEEDYEGMIQERLGKEKEKLEEKEKMEREAAEERELLEERHREAALERSEAGRLAQENLALRKKISALEEGDLNQEELLETLERLKKEKSAAEDQNGVLAERNAQSAAHLERLQLKEREGPPAEGHARVAACVSALEAELTNALEDTCELREKAARSQLSQILAERQNADREVGVLQTQLAKAQEKVKTEEENLQAAARQNDSLKREVAVLHKKLLHTQEKNRTLEAELHSSGKKMFREEAKAREKVHQLDATILSLSKHKQAGQASALKALEQENAALKRELQAQREQGSQLLESFQAQLVGLLPPSPHRVQRGHRAEEPENLQEPMAEQRAAHADSCRRIGGLCRSLQLEDATPALLHALLQNQDRLSGSKRYGRRSTPEFLETTSGVPSVAPLSVRLEAELRRACEELEMAVGRRIPAFSSTTATPLFSWVLRAALASFKAEIRHLLENVEQSELMKEVEQIQQQAGLQREKAEAEIEKFGDVDPSSADLLLQEERIKQLSPGMESDPGIGSEEQKASLSLRHQEELGALREEMLSTEEKEQLLRKMEELKEQHAVEEVKVKFEEEKGELVRRLTEQWEGRILEERLQLQEQSEQRERRMKELSSKHGEERSALRGELQKLRDDVQKAAETFKRQSRRLAQLENRNSQLSQQLARLKADLKAAQQEKEQHLLRLENERLQADARGLRNDLVQCEAARSGAEWENLQLENEALKAQMSRLS", "metadata": {"id": "A0A3B3HMZ3", "cluster": 2813292, "interpro_all": ["IPR011992", "IPR002048"], "interpro_used": ["IPR011992", "IPR002048"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "I want to build a protein that can perform the following function: It is part of the Bacterial polysaccharide biosynthesis and export family, which mediates the production, regulation, and transport of capsular and extracellular polysaccharides essential for bacterial virulence. Members function as autophosphorylating tyrosine-protein kinases, lipopolysaccharide chain-length determinants, or components of ATP-driven export complexes. These proteins coordinate the polymerization and translocation of polysaccharides across the inner membrane to the cell surface. 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 has been detected in Desulfatirhabdium butyrativorans.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2112, 2385, 1920, 2894, 2347, 30, 2176, 1977, 3131, 1927, 1920, 4543, 17167, 8132, 1930, 12660, 3416, 16, 2154, 10412, 1920, 3372, 16, 3640, 16, 1930, 4860, 1927, 22590, 1930, 5329, 18686, 4415, 1958, 4543, 9304, 18, 4678, 2347, 1966, 20369, 2199, 2287, 6941, 17, 2213, 7784, 16, 15614, 4659, 17, 3471, 9873, 16, 2014, 4178, 1927, 4498, 17, 6446, 12660, 5048, 18, 2144, 2697, 11865, 1920, 11486, 1930, 7849, 1927, 18686, 3436, 1920, 6671, 3260, 1942, 1920, 2024, 3154, 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, 2258, 2252, 3330, 1922, 30311, 1968, 5004, 13385, 2457, 2308, 3553, 1968, 15525, 17182, 1036, 18, 3], "output": "MSATQPKSRDDEITERDLFGSIPKALDINPFEGINLDEIAVKPPRKEALDEEDLIEINPIQGVDLEEISAVPVAATDTEEHLEIVEINPIEEEHVEGLNDIHPSPAALAAGLAVSTDGMPSSPKAAFFQKLKGLFSRKTSVSSEPSPPPPIQDKPTQPQQKSETKLPKPSAAPPVSEKVKPKGFMKPLRKPFGNGGGPALTPQLVKQAFNYAEIYRIREKILSSLDGKVHKVVMAASPYDGTGNTFMISVLGLNAASYTQLNLLLVDLNMRRPQLHLAFGLPLDQGFGDIAQGLVHWSDVVKDTELPNLKLISAGAPVKDLARYLNKDFLESFLSDLKSEYDMVLLDTSPVMVRNRNNVDPILLGRMSDVVIVISRNKYTSRNALVSTVQAIAQDGGNIIGIVYNH", "metadata": {"id": "A0A7C4VZL2", "cluster": 3871358, "interpro_all": ["IPR050445", "IPR027417"], "interpro_used": ["IPR050445", "IPR027417"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given this biological function:\nThe protein should contain a Tetratricopeptide repeat protein 21A/21B C-terminal ARM domain that functions as a structural component of intraflagellar transport (IFT) proteins TTC21A and TTC21B. It participates in retrograde ciliary transport as part of IFT complex A and is essential for cilium assembly and sperm flagellar formation. Furthermore, the protein belongs to 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 derived from Xenopus laevis (African clawed frog).\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 3066, 5531, 43, 12470, 3319, 21305, 6865, 2213, 2900, 1019, 19, 2900, 1014, 45, 17, 4262, 6011, 3418, 1988, 4088, 1966, 43, 4346, 4594, 1927, 5153, 20631, 7852, 4860, 12, 22416, 13, 2697, 19914, 4716, 1019, 1930, 19914, 4716, 1014, 18, 2176, 17241, 1922, 14492, 17542, 4860, 1966, 3131, 1927, 22416, 2796, 43, 1930, 1977, 4415, 1958, 28997, 5957, 1930, 6283, 24154, 3337, 18, 3677, 16, 1920, 2213, 14440, 1942, 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, 3595, 2037, 14545, 25042, 12, 7050, 6958, 2172, 1007, 23707, 13, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MSKMAWSIADAEDLEKSWLLLADIYIKSGKYDIATELLKRCSLAINKAYEFLGFIMEKEQWYKDAAANYGGAALALSRGGLQVLKDRPTYPKIKKEILAKHRLLLLYNKVGGEEQLVQFYTSALISLCNHFRLAWDYSNQSNPAVDFNFGCLGLRK", "metadata": {"id": "A0A974CI99", "cluster": 4368386, "interpro_all": ["IPR056834", "IPR011990", "IPR040364"], "interpro_used": ["IPR056834", "IPR011990"], "interpro_unused": ["IPR040364"]}, "task_type": "infilling"} {"instruction": "I am designing a polypeptide chain with the following function: The protein is assigned to the Protein of unknown function DUF6789 family, which comprises functionally uncharacterised proteins found in bacteria and archaea. These proteins are likely membrane proteins. It is derived from Phreatobacter aquaticus and is associated with UniProt keywords 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, 1977, 6304, 1942, 1920, 2213, 1927, 5435, 2347, 4855, 17136, 7950, 1026, 3416, 16, 2154, 12936, 9346, 23229, 3495, 2697, 2435, 1922, 4802, 1930, 21501, 18, 2144, 2697, 2032, 3205, 3260, 2697, 18, 2176, 1977, 3595, 2037, 17252, 5376, 4575, 7972, 2341, 1915, 15849, 1957, 1930, 1977, 2458, 1956, 20709, 11569, 9117, 7864, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MFLKARLGILPAFQPYDSVQTTLVAAFGTGLPPSVLWILSFLNGAVVLGFLFGQAYRWLPGTCGATKGLVFGLTGWIAMGLLFFPMIGMGFFAAQSPAGAAASLLSLAMIVTYSVTMGMVYAALERAGKP", "metadata": {"id": "A0A4D7QU88", "cluster": 6344612, "interpro_all": ["IPR046739"], "interpro_used": ["IPR046739"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein is a member of the HipA Serine/Threonine-Protein Kinase family, which constitutes the toxin component of bacterial type II toxin-antitoxin systems involved in multidrug tolerance and persistence. These kinases phosphorylate glutamate-tRNA ligase to trigger the stringent response and inhibit essential cellular processes like translation, an activity that is typically neutralized by a cognate antitoxin. Furthermore, the protein should contain a HipA-like, C-terminal domain that mediates bacterial persistence and cell division control, functioning as the toxic component of a toxin-antitoxin system. It typically associates with the antitoxin HipB to neutralize toxicity and autoregulate the *hip* operon. This domain is also found in serine/threonine kinases such as CtkA, where it aids in inducing host inflammation via NF-kappa-B phosphorylation. Furthermore, the protein should include a HipA N-terminal subdomain 1 domain that functions as a structural component of the bacterial serine/threonine kinase HipA, an enzyme involved in multidrug tolerance. This region represents the first of two subdomains formed in the N-terminus by the disruption of the beta-sheet architecture by a P loop motif. It is derived from Ignavibacteria bacterium and corresponds to UniProt keyword Transferase.\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, 7679, 1019, 8468, 19, 13143, 17, 2213, 4016, 3416, 16, 2154, 14879, 1920, 9165, 4594, 1927, 4543, 2601, 2890, 9165, 17, 10310, 9754, 3771, 3286, 1922, 16398, 6555, 1930, 10804, 18, 2144, 7784, 18730, 7627, 17, 10089, 11905, 1942, 6086, 1920, 16801, 2644, 1930, 2875, 4415, 3689, 4028, 3189, 6410, 16, 1925, 2455, 1988, 1977, 5745, 22982, 2007, 43, 15786, 10310, 9754, 18, 3677, 16, 1920, 2213, 3066, 5531, 43, 7679, 1019, 17, 3189, 16, 45, 17, 4262, 3418, 1988, 10412, 4543, 10804, 1930, 2024, 8451, 2285, 16, 7295, 1966, 1920, 6161, 4594, 1927, 43, 9165, 17, 10310, 9754, 2433, 18, 2176, 5745, 14162, 1956, 1920, 10310, 9754, 7679, 1014, 1942, 25885, 5532, 1930, 24643, 4056, 1920, 14, 7679, 14, 15675, 18, 2052, 3418, 1977, 2222, 2435, 1922, 8468, 19, 13143, 7784, 2427, 1966, 3369, 7640, 16, 2597, 2176, 8494, 1922, 7834, 4423, 4531, 3454, 4651, 17, 12093, 17, 44, 4050, 18, 3677, 16, 1920, 2213, 3066, 3951, 43, 7679, 1019, 56, 17, 4262, 27517, 21, 3418, 1988, 4088, 1966, 43, 4346, 4594, 1927, 1920, 4543, 8468, 19, 13143, 4016, 7679, 1019, 16, 1925, 4113, 3286, 1922, 16398, 6555, 18, 2052, 3031, 4972, 1920, 2561, 1927, 2288, 30103, 5333, 1922, 1920, 56, 17, 7822, 2007, 1920, 7561, 1927, 1920, 4666, 17, 11130, 9335, 2007, 43, 58, 5881, 5219, 18, 2176, 1977, 3595, 2037, 12046, 9188, 7972, 2341, 18339, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 13763, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MIVEVMLHGQLLGTAEWNADKKSSTFQYNNEMVKVIEPSPIIMPTEERIFETPDEFGNVMMKEWLKQRELSIDDINPVDRLTYVGKRGMGALEYIPANHREDDNRLIDISELDKDSLTEILRIGTSVGGARAKALIAIKRDKYKKIKEIRPGDIIQPKGYSYWILKIDGANSESTLHEENGRFHFLTKRFDRTDNGEKIHMQTFSALAGIDYKIQKASNYETFNVVARNQDDHVKNFSFLMNKDGNWQISPAYDICFSYSQGGTWTNVHQSSINNAILEEVVSAVNQWSKIATEIDIPQEKIQYINKYLRIKDFYNRDHINFHNLPYLLSDSMIYNVAKSVLESKKEASFSNKQNLGESEGMGKIEFAYYKLAKEAGIEILFRVMKRLQLSYKQYEQQYRRMLGKYDNFTKDDLLDFAKKFGIKKA", "metadata": {"id": "A0A7V1LFZ3", "cluster": 8082088, "interpro_all": ["IPR012893", "IPR017508", "IPR052028"], "interpro_used": ["IPR052028", "IPR012893", "IPR017508"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "\"The protein can be placed in the Protein-tyrosine phosphatase-like superfamily, which encompasses a diverse group of enzymes including receptor and non-receptor tyrosine phosphatases, dual specificity phosphatases, and lipid phosphatases like PTEN. Members of this family share a core structure of a central parallel beta-sheet flanked by alpha-helices and utilize a conserved C(X)5R active site motif to catalyze dephosphorylation via a cysteinyl-phosphate intermediate. These enzymes play critical regulatory roles in signal transduction pathways, such as the MAP kinase pathway, as well as cell cycle control, growth, and differentiation. Moreover, the protein should include a Dual specificity phosphatase, catalytic domain that catalyzes the dephosphorylation of phosphoserine, phosphothreonine, and phosphotyrosine residues using a conserved cysteinyl-phosphate intermediate. Structurally distinguished by a shallow active site pocket that accommodates diverse substrates, this domain functions as a key regulator in mitogenic signal transduction pathways, such as the MAP kinase cascade, and cell cycle control. Moreover, the protein has a Tyrosine-specific protein phosphatase domain that catalyzes the dephosphorylation of tyrosine residues using a conserved active site cysteine and a cysteinyl-phosphate intermediate. Crucial for regulating signal transduction pathways and cell cycle control, this domain influences cell growth and differentiation through the precise modification of signaling proteins. It structurally consists of a central parallel beta-sheet flanked by alpha-helices that support the conserved PTP signature motif. It originates from Steinernema glaseri and is classified with UniProt keywords Hydrolase.\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 2213, 17, 6941, 8167, 17, 3189, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 5038, 2710, 3148, 1930, 2447, 17, 3148, 6941, 19131, 16, 7064, 4896, 19131, 16, 1930, 4486, 19131, 3189, 9496, 18, 4678, 1927, 2052, 3416, 7948, 43, 4728, 3170, 1927, 43, 4101, 6110, 4666, 17, 11130, 20185, 2007, 4595, 17, 12789, 1930, 12561, 43, 5305, 45, 12, 66, 13, 25, 1005, 3500, 3200, 5219, 1942, 18170, 16881, 3454, 43, 20368, 1921, 2199, 17, 5413, 6129, 18, 2144, 5038, 3918, 4140, 4948, 5456, 1922, 2733, 8201, 3873, 16, 2427, 1966, 1920, 4446, 4016, 3374, 16, 1966, 2486, 1966, 2024, 4048, 2285, 16, 2905, 16, 1930, 4155, 18, 3950, 16, 1920, 2213, 3066, 3951, 43, 7064, 4896, 8167, 16, 6804, 3418, 1988, 17097, 1920, 16881, 1927, 8078, 26337, 16, 8078, 5856, 1021, 12530, 16, 1930, 29552, 4248, 2193, 43, 5305, 20368, 1921, 2199, 17, 5413, 6129, 18, 12171, 12080, 2007, 43, 17272, 3500, 3200, 10154, 1988, 16848, 1036, 6445, 6249, 16, 2052, 3418, 4088, 1966, 43, 3834, 7888, 1922, 23644, 2733, 8201, 3873, 16, 2427, 1966, 1920, 4446, 4016, 9861, 16, 1930, 2024, 4048, 2285, 18, 3950, 16, 1920, 2213, 2258, 43, 6941, 17, 2487, 2213, 8167, 3418, 1988, 17097, 1920, 16881, 1927, 6941, 4248, 2193, 43, 5305, 3500, 3200, 8666, 1930, 43, 20368, 1921, 2199, 17, 5413, 6129, 18, 6608, 1958, 6773, 2733, 8201, 3873, 1930, 2024, 4048, 2285, 16, 2052, 3418, 8061, 2024, 2905, 1930, 4155, 2596, 1920, 8162, 6295, 1927, 3197, 2697, 18, 2176, 12171, 7543, 1927, 43, 4101, 6110, 4666, 17, 11130, 20185, 2007, 4595, 17, 12789, 1988, 3373, 1920, 5305, 14990, 9983, 5219, 18, 2176, 22970, 2037, 21557, 1915, 19319, 1019, 23545, 18842, 1930, 1977, 5947, 1956, 20709, 11569, 20748, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MIDKVIDHLYLSDAGSVIGLRAKKNLSEHLITHVLTISAAPPSIWRQLHVRLRXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXVDDAIEGGGNVLVHCEAGVSRSVTVVAAYLMRKFEWTAEKAILAMGYRADAETLALAQEYRNWCADSGIIPQTGTLDGVRRLDDKQINDEKKVEGVSYMFVFAXXXXIFXXXXDLLGNNLLESTLNFFIQHARPIAGPNSGFVRQLNVFR", "metadata": {"id": "A0A1I7Y975", "cluster": 9815610, "interpro_all": ["IPR000340", "IPR029021", "IPR000387", "IPR020422"], "interpro_used": ["IPR029021", "IPR000340", "IPR000387"], "interpro_unused": ["IPR020422"]}, "task_type": "infilling"} {"instruction": "The protein falls within the Ribonuclease H superfamily, which comprises the catalytic domains of diverse polynucleotidyl transferases characterized by a conserved 3-layer $\\alpha/\\beta/\\alpha$ fold. This superfamily includes enzymes such as RNase H, retroviral integrases, transposases, and exonucleases that utilize this domain to catalyze nucleic acid backbone cleavage or transfer during DNA replication, repair, and recombination. It has been characterized in Acrobeloides nanus. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 12182, 2651, 1920, 18347, 2051, 50, 13975, 16, 2154, 12936, 1920, 6804, 4682, 1927, 6445, 15176, 2626, 4090, 2199, 13763, 1036, 4378, 2007, 43, 5305, 23, 17, 4757, 8, 38, 4595, 19, 38, 4666, 19, 38, 4595, 8, 3728, 18, 2052, 13975, 5921, 5038, 2427, 1966, 9843, 50, 16, 16599, 27252, 1036, 16, 12935, 2319, 16, 1930, 24966, 1036, 1988, 12561, 2052, 3418, 1942, 18170, 11079, 2687, 10787, 6404, 2014, 3856, 2409, 2678, 5158, 16, 5059, 16, 1930, 7827, 18, 2176, 2258, 2252, 4378, 1922, 10428, 16248, 6012, 3726, 3529, 1957, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MEASKASNVDRKLKRAKVMKRHFTANRHRSIVFTNEKLFTIEERLQKPKSWFGPLSLSTTKLIWFSLSKVSKSIKSIEKCFENICCHGRGSLWRSFMDSSTRLYIKTSSTGHIEIFPRRRRLWKWILRDGFHPSKECTAHIPELNAMDYSVWSILETSACSKPHKTVESLKRSLTKIWDEEIRWSG", "metadata": {"id": "A0A914E2L1", "cluster": 10756546, "interpro_all": ["IPR036397"], "interpro_used": ["IPR036397"], "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 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. Moreover, the protein is grouped in the CTF18-RFC complex component family, which functions as part of the CTF18-RFC complex to ensure sister chromatid cohesion and genome stability. These proteins facilitate the ATP-dependent loading of the sliding clamp PCNA onto primed and gapped DNA and exhibit weak ATPase activity stimulated by primed DNA, RPA, and PCNA. Furthermore, 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 has been detected in Chaetoceros tenuissimus and is linked to UniProt keywords Nucleus.", "tokenized_instruction": [2, 13818, 1920, 6814, 23658, 1922, 2052, 17476, 2213, 3244, 1942, 6230, 1920, 2894, 3933, 2770, 30, 1920, 2213, 19683, 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, 3950, 16, 1920, 2213, 1977, 10809, 1922, 1920, 29124, 3928, 17, 7751, 1030, 2796, 4594, 3416, 16, 2154, 4088, 1966, 3131, 1927, 1920, 29124, 3928, 17, 7751, 1030, 2796, 1942, 6486, 14611, 28829, 21275, 1930, 3843, 5057, 18, 2144, 2697, 6628, 1920, 4498, 17, 3100, 6693, 1927, 1920, 17324, 10209, 14381, 6131, 14979, 1930, 5750, 7438, 2678, 1930, 5987, 5015, 9444, 2455, 5449, 2007, 14979, 2678, 16, 16454, 16, 1930, 14381, 18, 3677, 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, 2258, 2252, 3330, 1922, 13297, 19446, 2337, 1951, 5656, 8694, 12924, 23084, 1930, 1977, 4624, 1942, 20709, 11569, 5607, 18, 3], "output": "MSNEPPFNDDDLINDFYEEPDEYPDEFDIPEEYMEELQKDDNNVDLPLNQDNDVMMEESEKPEVPSHVSFDTNEVQFKSHKSDLYSFEMKQEGDVMEAVNWKTQNSKNSIVQKTKVNTAPEAQLIQFSNKNEFYNVSRDVQYLRQQEKPVADASLLGITMKELIKRADALERKKDVEHGVQQHRNEEKDRLWVDKHSPQNFSDLLSDERINREVLRSLRAWDPYVFGKTPEQTNDKRPDLKNRVILLSGPAGVGKTTLAHIIAKHAGYRPIEVNASSIGKKDVMAGRPNCLILDEVDGADAKSSINALVNIIKADKPDPNAKKHKHAPALRPLLPYAKCFDVSPPSANRFVSRLKAVLSAEGGDIRSCLFTLQFAAARAREMALNKQKKNQDMIGANDVLVDITAALSKIFKKFKGKSKSSRDVERILQAADVFGDNSKILDSCWTAHEWLSCVDVFRSFKTSVASNNVSEHRTMQKWHIPSAIAACHLLARYQSEANVGLVDKFLEGLPPSVKSGINKHQLVSDILPYCLWLLRAVSSLDVLKKEEKNAFFAHVQTLRSLGLTYVHVRGKIPPLMKELLAHETTVAGLRAKEEGREANVVAEEKDDVHMVNQSSTSTIPSKKLTTKDPKSIPKKKAASNFLGIGAASNTGSGIIIDKVIRFKYQKGFTQAVRLPCTKRDLFCHKVMNEKNQPPSGERYSGKQKWRTSERFQINKKMATNESTFMTIDNDTIPVNRQKRQKLDAVDHDNETMENEHEPPKRPVYFQQQQADQADATTTSDERSASVLTERVTRAMESSTLNIKATYLRRPIIFICNRMTLVGGGSMLHRLVEGSNALGGNGLGLKDQRSDMGGTLMFFMNIANISYVDPTLDRCRVETRPDIQLSMREITDSSGQGIGSLNKDEDDSRDYGTRVMNMRLEPEIDRVSRYKGVSEQEKNKKEDQESNKKQVTSPNTRAKAARTARKAAQVGFDRSKGRVKY", "metadata": {"id": "A0AAD3DCC8", "cluster": 11845978, "interpro_all": ["IPR003593", "IPR003959", "IPR053016", "IPR027417"], "interpro_used": ["IPR003959", "IPR053016", "IPR003593"], "interpro_unused": ["IPR027417"]}, "task_type": "infilling"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is included in the GAF-like domain superfamily, which comprises regulatory modules structurally similar to the PAS domain found in signaling proteins such as phosphodiesterases, cyclases, and phytochromes. These domains typically function as sensor modules that bind small molecules like cAMP and cGMP to allosterically regulate enzymatic activity or serve as chromophore attachment sites for light detection in plants and bacteria. Furthermore, 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. Moreover, 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. It is expressed in Branchiostoma floridae (Florida lancelet) (Amphioxus) and is linked to UniProt keywords Coiled coil.\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, 4357, 1038, 17, 3189, 3418, 13975, 16, 2154, 12936, 4948, 10803, 12171, 2551, 1942, 1920, 9233, 3418, 2435, 1922, 3197, 2697, 2427, 1966, 24821, 1036, 16, 16526, 1036, 16, 1930, 25512, 2072, 4191, 1036, 18, 2144, 4682, 5745, 2347, 1966, 6443, 10803, 1988, 4566, 2858, 4206, 3189, 6225, 1930, 15958, 1942, 14772, 2169, 5741, 8145, 2455, 2014, 7120, 1966, 25801, 8576, 3402, 1958, 3696, 3805, 1922, 4793, 1930, 4802, 18, 3677, 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, 3950, 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, 2176, 1977, 3198, 1922, 6089, 14356, 4575, 3368, 19386, 1021, 12, 19386, 26448, 5484, 13, 12, 9141, 3940, 1039, 1957, 13, 1930, 1977, 4624, 1942, 20709, 11569, 17524, 9121, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MSQVQFAMVPSPPKGPSPSGSKAPTPLGEEHASPTLHALTQVMGRIQGMREEKKRRLEESREEAQRLASKVPIDIIDVRCYMVDKLLPTLILGVEKLLREVERRGLEHTEGVTRDEASPYFRGMQEVSEQLKREVMSYQDTRLARVKAEARQKREEREMSERLFHHWIRDEDGNVQLSLVQSALRSFKEIVAHLPEDIQAVSAFSINVSHWPIIELDEMDDALSLSEDELDLQVSEMTEATSVSQGTSVAPQVSDEGAEKEGKVPEAAVEKGEKEGEKEGGEKEGEKETEEKAAEEEPKEVQEEKAEEEKTEGDAKEEGKIEESKTEESKTEEEKAAAPMEEVKEEPAEEATTATDEKKKEEAAEEKNAEKKEEGMSEEQQKEASEEAETSQPEKEVTAAAEARTEATETKREGEEETTVTVTTESEKPEVKEPETAVRDEATESDLLPPMTPDLNRSSSQMTQMTGTSVFDENSLNLNQFVQLVETFLGDHYVETEEEKMSRLAKARRDAISARHKYLLDQLFEKWDNDGSGFLDLEEVQTILLKYKKKYRLHDNRMNRREFRTFIEDVVHQLPGDDNECFEAVMEYLRAGGASMDPVYRAVFNALYKDQEAHGGNKKISAYIAMLERTPDDAPLMLGKAMYKDMKGISFASVESGKPIHVPRVMMHGNIHLWNPDRKDLGIDTMADPHDRSIFVTHEISFFQGIAKAFSVAFHYIDIRRKILRIAESAVHWIHRRVLRKMMTTDKSGNSKLYEDPQRLERKDNLFRDYLFKSVTNSETVTADAYGERHELRELPHAEQREVTRMLKILQSAHKEVEKESAGAEKKRVLGSDPETILTHLSDIVVISLVEHTSKSQDAGRPQAFSPPPGSSASTDTNATIDAALKAEMAKSFVRRWRRNHEQLTKDWLNDDKVTFNPINYLAQYLMRNNPRYSNFARQLESTRRVESLKAQKELEPTDETGKGLGQEAFEKKDPEKETPAIAEVAEGEETGEETAEKKEKDGQKEGGQEDAADKPEEKPEEQQEQVSQDIPETEGPKEPAEVPTKTRTGRVSVTFSSEPPQMLGNPYHEAVDRLVGYIQSGKEGMEAAIIKKARASLSVERSYTERIRGDARKKWLQLIKIAAETNDLQPSRGETLLRYVAVQEVDGSFMVVPLKDHRKRVFGMSVNVKQIDVYMVEPGAKEHDFTAFPLRDNDGRAVAVVDISIGPHGAVSKHGSVPAQYLYNWAF", "metadata": {"id": "A0A9J7KKJ8", "cluster": 13112529, "interpro_all": ["IPR011992", "IPR018247", "IPR002048", "IPR029016"], "interpro_used": ["IPR029016", "IPR018247", "IPR002048"], "interpro_unused": ["IPR011992"]}, "task_type": "infilling"} {"instruction": "Given this biological function:\nThe protein should include a Cthe_2314-like HEPN domain that functions as a nucleotide-binding module with putative metal-independent endoribonuclease activity, typically serving as the toxin component in prokaryotic toxin-antitoxin systems to cleave cellular RNA. It has been characterized in Staphylococcus equorum.\nReplace the masked placeholders with the appropriate amino acid spans.", "tokenized_instruction": [2, 3258, 2052, 3933, 2347, 30, 1920, 2213, 3066, 3951, 43, 3369, 4116, 41, 10577, 1006, 17, 3189, 3357, 1022, 3418, 1988, 4088, 1966, 43, 5489, 17, 2743, 9059, 1956, 6770, 6048, 17, 3484, 16239, 3027, 20226, 2626, 2051, 2455, 16, 5745, 13915, 1966, 1920, 9165, 4594, 1922, 21545, 9165, 17, 10310, 9754, 3771, 1942, 21252, 3689, 3146, 18, 2176, 2258, 2252, 4378, 1922, 13452, 3009, 17279, 18, 14732, 1920, 17476, 4368, 14658, 1956, 1920, 4703, 3835, 2687, 23658, 18, 3], "output": "MLFNRMNLLIRNYTYTMFYYLFPDFKEEDYTKQFNFNYFSEYFFIQLKKNEISFHKAINKLKEKDLNITHNQHPQFISSGITKCENGIVTAGVGMCLEKTIEIINKNKDNQGIHDEVWYKSPGSKGQSVELQGFSIFELLGHIIVNIYDVKFYALDKIRNSNEFDDAAKHRHNYTTSQKVKEIMDGML", "metadata": {"id": "A0AAW7AM57", "cluster": 14011553, "interpro_all": ["IPR041394"], "interpro_used": ["IPR041394"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the intended role of my protein: The protein incorporates 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. Moreover, 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. Moreover, the protein should contain a AAA+ lid domain that forms the \u03b1-helical C-terminal bundle of the AAA+ module, typically facilitating oligomerization and the conformational mechanics driven by ATP hydrolysis. It is present in Ceratobasidium sp. AG-Ba and is annotated with UniProt keywords Mitochondrion and Mitochondrion outer membrane. Please provide the amino acid sequence.", "tokenized_instruction": [2, 3410, 1977, 1920, 11214, 2770, 1927, 3057, 2213, 30, 1920, 2213, 19683, 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, 3950, 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, 3950, 16, 1920, 2213, 3066, 5531, 43, 13835, 15, 13096, 3418, 1988, 4952, 1920, 160, 17, 11514, 45, 17, 4262, 14142, 1927, 1920, 13835, 15, 9059, 16, 5745, 12440, 17371, 1930, 1920, 8523, 18041, 6446, 2007, 4498, 9128, 18, 2176, 1977, 2481, 1922, 6580, 8286, 7972, 12924, 7408, 1989, 2056, 18, 2260, 17, 6813, 1930, 1977, 10633, 1956, 20709, 11569, 30017, 1930, 30017, 7642, 3260, 18, 11586, 3394, 1920, 3835, 2687, 3244, 18, 3], "output": "MDGQPSYVPTLGLSGIAAGDAIQLPPCALDAMWKSQAMNKVDPRALPPSCYLEDALSQLRTTLLPKVQHNAAHVVLGSQIVEPTLALFCPIEGGEYVIDATVKELAEKTNSEVQVIDMAQVAADRWGVFGESALGLKLTGYLLNEATIPDNPYTRYYEPLGANTANASLFEVFWNKVIKCDPPADRANLAAPLSTAPSDAPSDGSTPRPRIVYIRDFGLLSSQAQKWFPALYSAIRARRTGGLGPESPVTHPTTIVFGFCPYPPTTSSPSSGYVACTCSLCVPGGKGPGNLSDTDFAREKRLKERFEKWDKGTLLKDLPVFNPQVKIAKDMTRPGIKLESGPGFVEQTGITSTEKTSTHDLGASQAELGQIKDTGLEPRNTEEWVDVKIKPEDAKQSDDLAKPADDTAPKYPSLSATNPYSLASSYTFPYTPPGLGLQSVYEQKLDGYFRSCIIAPAKRNVDLERTSRESRLQELNELRLRVVVGAMSGVIEGEAGLSILKGKREVDGTGPDDHEMSIGWEKRLLDATELNAIVDRALETSMRSDQDAKSEGAIRLTWAELQQAWLAHQTAEEKRKAWKASNGFSKEQDDNTEESSTDEVIAKIKSEGLDEYERQWIDYIVSPAKLAATFEDVHLPSEIIDTIRSTVSLPLLYPEAFQSGILKDQTNTGALLFGPTGTGKALVVKALAKESGARMLTVNPSIIVNQYYMNSGQILYSVFKLAQRLKPCLVFIEGIETLASSETSNSTLLNHLVQAFDRLSDPSVIVIGATDRPFDINHAVLRHLTCRLLIDLPELDARERILKNMLRDEKLAADVSNSELAKKTDGFSGSDLKHLCVTAAREALKDMVNFSGPSREDEITKASKPNIKETQAGHVNNTKNGSELQARILTTTHFMRALTRVSPLKSHSQDALSEIRKWNSKFGTGARETPDNGLLS", "metadata": {"id": "A0A8H8NA10", "cluster": 14293359, "interpro_all": ["IPR003593", "IPR041569", "IPR003959", "IPR051701", "IPR027417"], "interpro_used": ["IPR003959", "IPR003593", "IPR041569"], "interpro_unused": ["IPR051701", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "The protein is classified under the Phage tail tube protein-like family, which comprises structural proteins that polymerize to form the tail tube of bacteriophages. These components create a conduit for viral genome delivery and are identified in both active phage particles and integrated prophage sequences. It occurs in Gemmatimonadaceae bacterium. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 1977, 5947, 2441, 1920, 10503, 5281, 6723, 2213, 17, 3189, 3416, 16, 2154, 12936, 4346, 2697, 1988, 4593, 2606, 1942, 2386, 1920, 5281, 6723, 1927, 24613, 1036, 18, 2144, 4178, 7762, 43, 26622, 1958, 4324, 3843, 4868, 1930, 2032, 2899, 1922, 2321, 3500, 10503, 5569, 1930, 6714, 8839, 2170, 3709, 18, 2176, 5110, 1922, 10607, 3368, 2265, 12502, 3825, 1972, 3336, 14061, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MATQIGTNIIVGYKVEGTINTPPGATGAKQLRFTPGAGLALSKADIRSNEVRNDGLSSMGRHGSRMVQGSYGGELAVGAFDELLEAVMRSTWVAAVAITNATMTSITTTTSTIVAAAGSWLTQGVRVGDIVRLTGHSTTANNSKNLRVLAVTATTITVPTGDLTADAVADASFTLTILRKVKNGATPVRRSFYFDEYNQDIDQSEVFGGNRIVSMKITGQPDGMALIEFGVMGLSSDTLATAASPYFTTPTLNTATALVFADAKIRFNGVDIGIGTGFELTYQIGAGVQPVIGSTAGRDVSDAAARLAGSLSLIREDLS", "metadata": {"id": "A0A7W1PGR5", "cluster": 15074646, "interpro_all": ["IPR044000"], "interpro_used": ["IPR044000"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to this functional description: The protein is classified under the Small subunit processome component 20 family, which functions as a core component of the small subunit (SSU) processome essential for the biogenesis of the eukaryotic small ribosomal subunit. Members of this family associate with U3 small nucleolar RNA (snoRNA) within the nucleolus to facilitate the folding, modification, and cleavage of pre-18S rRNA. Additionally, they are implicated in the targeted degradation of pre-ribosomal RNA by the RNA exosome during quality control. Additionally, the protein includes a HEAT, type 2 repeat that forms a rod-like helical structure composed of pairs of antiparallel alpha-helices to function as a protein-protein interaction surface. These repeats are frequently found in cytoplasmic proteins involved in intracellular transport processes. Additionally, the protein is grouped in 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. It is expressed in Proboscia inermis.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2052, 3183, 8418, 30, 1920, 2213, 1977, 5947, 2441, 1920, 2858, 5903, 2585, 2225, 4594, 2036, 3416, 16, 2154, 4088, 1966, 43, 4728, 4594, 1927, 1920, 2858, 5903, 12, 4577, 1032, 13, 2585, 2225, 4415, 1958, 1920, 13008, 1927, 1920, 10825, 2858, 11196, 5903, 18, 4678, 1927, 2052, 3416, 11774, 1956, 63, 1010, 2858, 23770, 3146, 12, 3437, 27532, 13, 2651, 1920, 27542, 1942, 6628, 1920, 10328, 16, 6295, 16, 1930, 6404, 1927, 2097, 17, 17659, 9067, 18, 4950, 16, 2611, 2032, 6835, 1922, 1920, 5154, 4877, 1927, 2097, 17, 11196, 3146, 2007, 1920, 3146, 20235, 2409, 3455, 2285, 18, 4950, 16, 1920, 2213, 5921, 43, 5631, 16, 2601, 22, 6865, 1988, 4952, 43, 6275, 17, 3189, 11514, 3170, 7179, 1927, 5803, 1927, 28892, 4595, 17, 12789, 1942, 2347, 1966, 43, 2213, 17, 2213, 2835, 3154, 18, 2144, 9569, 2032, 5467, 2435, 1922, 6823, 2697, 3286, 1922, 4776, 4860, 4028, 18, 4950, 16, 1920, 2213, 1977, 10809, 1922, 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, 2176, 1977, 3198, 1922, 2680, 17413, 1019, 21317, 7395, 1036, 18, 3], "output": "TIQSMADPFVPMLTLCIQHGDKASVQQNNEILFTSLQCLGILLKWNLPQSKICSQTLGPPVLKLLQGCCGVGNGGAAGGKQDLRMGCFKALILLISLDNRDRHLSAQTTEQQSSKLPKDASMDETEELLNTPMPLSPKQMKVLISLLHSAILENTEQLSSATFGLIKSIVSRRYISAEFYDLMVVVLKLSVQSQKESIRQQCCQIFLQFLMDYPLESKRIEQHLRQIVLNIQYEYQDGRLSALNLLTSVTTKFPTALLEEHCQLLFLPMVLQLVNDSSSECRQAVADCLMALFRNVGVEKIHLLYDYMVRWIGGGDGDECAQSLQLKRTSAQLFG", "metadata": {"id": "A0A7S0CDN2", "cluster": 15339429, "interpro_all": ["IPR011989", "IPR016024", "IPR000357", "IPR021133", "IPR052575"], "interpro_used": ["IPR052575", "IPR021133", "IPR011989"], "interpro_unused": ["IPR000357", "IPR016024"]}, "task_type": "autoregressive"} {"instruction": "What would the amino acid sequence be if I wanted a polypeptide chain capable of the following function: The protein can be placed 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. In addition, the protein is included in the RmlC-like jelly roll fold superfamily, which adopts a mainly beta jelly roll topology and functions as a dTDP-sugar isomerase, specifically dTDP-4-dehydrorhamnose 3,5-epimerase. This domain catalyzes a key step in the biosynthesis of L-rhamnose, a saccharide essential for the virulence of certain pathogenic bacteria. Moreover, the protein has 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. It is derived from Tunturiibacter lichenicola and is associated with UniProt keywords Oxidoreductase.", "tokenized_instruction": [2, 4663, 2962, 1920, 3835, 2687, 3244, 1998, 2647, 51, 14624, 43, 13022, 4659, 7131, 1927, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 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, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 10625, 8293, 17, 3189, 8988, 11560, 1012, 12970, 3728, 13975, 16, 2154, 24032, 43, 4994, 4666, 8988, 11560, 1012, 12970, 13678, 1930, 4088, 1966, 43, 7711, 10274, 17, 9523, 25510, 16, 4475, 7711, 10274, 17, 24, 17, 28936, 5004, 17652, 2217, 23, 16, 25, 17, 13872, 9213, 2051, 18, 2052, 3418, 17097, 43, 3834, 3537, 1922, 1920, 8132, 1927, 54, 17, 23120, 2217, 16, 43, 14175, 2205, 3695, 4415, 1958, 1920, 9304, 1927, 4908, 8070, 4802, 18, 3950, 16, 1920, 2213, 2258, 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, 2176, 1977, 3595, 2037, 6367, 1031, 18330, 26073, 2341, 1915, 28088, 29902, 1930, 1977, 2458, 1956, 20709, 11569, 27388, 18, 3], "output": "MTTSLKDGTMIDKMAQFDLPQEIADSEQKKPWQSGQYAKTLFKKHDLRVVLILMENAAKMKEHHADGTLSVQVLKGQIRFTVHGKPHDLKTGELITLGASIRHEVEALQDSAFLLTISWPSNQDLLAMKHRGYGT", "metadata": {"id": "A0A7W8IFL5", "cluster": 16501088, "interpro_all": ["IPR013096", "IPR014710", "IPR011051"], "interpro_used": ["IPR011051", "IPR014710", "IPR013096"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Given the target function, what are the correct amino acids for the masked sequence gaps? Function: The protein is a member of the RNA binding protein HABP4/SERBP1-like family, which comprises proteins that bind RNA, G4 quadruplexes, and purine motif triplexes to regulate transcription, pre-mRNA splicing, and mRNA stability. Members such as SERBP1 function as ribosome preservation factors, associating with EEF2 to stabilize inactive ribosomes and protect them from degradation during nutrient starvation. It is native to Polytomella parva.", "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, 43, 7210, 1927, 1920, 3146, 2743, 2213, 6192, 12425, 19, 2375, 10013, 17, 3189, 3416, 16, 2154, 12936, 2697, 1988, 4566, 3146, 16, 14036, 22566, 1918, 16, 1930, 19700, 5219, 10073, 1039, 1918, 1942, 5741, 3213, 16, 2097, 17, 3616, 8490, 16, 1930, 3616, 5057, 18, 4678, 2427, 1966, 2375, 10013, 2347, 1966, 12794, 12698, 2790, 16, 26284, 1956, 11150, 6680, 1942, 13448, 9078, 18654, 1930, 9145, 3581, 2037, 4877, 2409, 8708, 12767, 18, 2176, 1977, 6196, 1942, 25276, 2225, 11560, 1019, 19995, 1019, 18, 3], "output": "WPPPGGPPPAVAPPADAAPAEEAAAVTPEPEVNQLTLQEYELKPLAKVSADDQVPFAVRSKTSKVEKADAKKTNAKGNDRRTRNGGKNTNASAAPKINMGDFPSLGATLEEKRRNLNKVVETRSIDASDNVVYIEYQYNNEPVKTEKPERR", "metadata": {"id": "A0A7S0YTW5", "cluster": 20474051, "interpro_all": ["IPR039764"], "interpro_used": ["IPR039764"], "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 include a DnaJ domain that functions as a molecular co-chaperone by binding to Hsp70 proteins and stimulating their ATPase activity. This action stabilizes the interaction between Hsp70 and unfolded polypeptide substrates to assist in protein folding, translocation, and degradation. The domain structurally consists of a four-helix bundle with a specific charged surface required for the Hsp70 interaction. Also, the protein has a Ubiquitin interacting motif conserved site that recognizes and binds ubiquitin, serving as a specific targeting signal for monoubiquitination. Often occurring in tandem arrays, this motif is found in proteins involved in ubiquitin metabolism, including proteasome subunits and ligases, where it frequently cooperates with other ubiquitin-associated domains. It is produced by Dunaliella tertiolecta (Green alga) and exhibits UniProt keyword tags Coiled coil, Repeat, and TPR repeat.", "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, 3951, 43, 2678, 1013, 3418, 1988, 4088, 1966, 43, 3272, 2081, 17, 14044, 2007, 2743, 1942, 12886, 2697, 1930, 9868, 2310, 9444, 2455, 18, 2052, 4615, 19658, 1920, 2835, 2192, 12886, 1930, 17416, 13022, 6249, 1942, 6589, 1922, 2213, 10328, 16, 7849, 16, 1930, 4877, 18, 1920, 3418, 12171, 7543, 1927, 43, 3006, 17, 7864, 14142, 1956, 43, 2487, 9516, 3154, 3414, 1958, 1920, 12886, 2835, 18, 2222, 16, 1920, 2213, 2258, 43, 6526, 8615, 5219, 5305, 3200, 1988, 16197, 1930, 6876, 6526, 16, 13915, 1966, 43, 2487, 5133, 2733, 1958, 8914, 15571, 1943, 18, 3868, 6966, 1922, 10361, 10517, 16, 2052, 5219, 1977, 2435, 1922, 2697, 3286, 1922, 6526, 4714, 16, 2710, 9993, 6991, 1930, 22423, 16, 2597, 2176, 5467, 23230, 1036, 1956, 2303, 6526, 17, 2458, 4682, 18, 2176, 1977, 4152, 2007, 23513, 12498, 5870, 10766, 7794, 3857, 12, 4524, 4326, 1019, 13, 1930, 9826, 20709, 11121, 2538, 14392, 17524, 9121, 16, 6865, 16, 1930, 22288, 6865, 18, 3], "output": "MKLTREESRSLLELPLDGELEDSQIKSAFKRLALIWHPDKNRDRTEEASEKFKQINAAYARLTGSDESDDEIDEEDFADLSELFPMFLFSLFGGMPMGGGGRARGRGGGMGGMPFGDVPSFVFSSGGPRGSRGGFSYGPPPGFFGGMPFDMYDDEEDDDFSDDYTESDEWTTDDDDDDEYEDPLPRSNGAGMKGRAGFARAPAREARPAPPPGPPSDNPLLLRFIKQHQLPRPVMLSRTDTSITLTVDRKGEAEAEGVMLLGKVLFELHFKKAEGNHPWSILSSSSAQSKPTTFAVQNLDPGSKYTFRGRAGMESIEQGKGLIWGGFSVDSSYVTAAANQPSTSARAAAASGTSPEANGAQAGPGAAGAPMSKAASKRNKKKAKRQNAQGAKAEEEEEEEESAGADGTPVAARAGTAATAGARAVPTASTQAPPKQQQQQQQQQPEPRQQAKKGGGKGGKKQGQAKQQQQQQEPEEDKQAKAEEAKRQAQKDAAIAAALARAAADYEEGAAKIKRQQDLHKQRQAEREAAQAAAQAARLQAEQEAARQREQAEAQRAAQAAHLNRQRESAAAAASPSSASAGSSSSRPGAAVAGGGRGRGRRQGGQAAGLSPADQQAEDARLAAALDAQQQRLQQQLLEEEEQLALAIKASLESAALEGIPPPAPEPL", "metadata": {"id": "A0A7S3QU48", "cluster": 20838887, "interpro_all": ["IPR001623", "IPR036869", "IPR003903"], "interpro_used": ["IPR001623", "IPR003903"], "interpro_unused": ["IPR036869"]}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: The protein can be placed in the Septum formation initiator FtsL/DivIC family, which acts as an essential component of the cell division machinery required for vegetative and sporulation septum formation. These proteins typically feature an N-terminal coiled-coil domain and form a heterodimer that is critical for the stabilization and localization of the division apparatus. Additionally, the protein is classified under the Cell division protein DivIC family, which is essential for vegetative and sporulation septum formation. It localizes to the septum to form a trimeric complex with DivIB and FtsL, functioning to stabilize FtsL against RasP cleavage. It occurs in Facklamia hominis and is annotated with UniProt keywords Coiled coil.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 17026, 3337, 23467, 17022, 1024, 19, 6421, 1935, 3416, 16, 2154, 8016, 1966, 1925, 4415, 4594, 1927, 1920, 2024, 8451, 10853, 3414, 1958, 18823, 1930, 23647, 17026, 3337, 18, 2144, 2697, 5745, 5961, 1925, 56, 17, 4262, 17524, 17, 9121, 3418, 1930, 2386, 43, 15672, 1988, 1977, 4140, 1958, 1920, 10281, 1930, 5363, 1927, 1920, 8451, 11161, 18, 4950, 16, 1920, 2213, 1977, 5947, 2441, 1920, 2024, 8451, 2213, 6421, 1935, 3416, 16, 2154, 1977, 4415, 1958, 18823, 1930, 23647, 17026, 3337, 18, 2176, 18440, 1942, 1920, 17026, 1942, 2386, 43, 29177, 2796, 1956, 6421, 2023, 1930, 17022, 1024, 16, 7295, 1942, 13448, 17022, 1024, 3316, 6520, 1034, 6404, 18, 2176, 5110, 1922, 3186, 16244, 14981, 1019, 3344, 15472, 1930, 1977, 10633, 1956, 20709, 11569, 17524, 9121, 18, 3], "output": "MSEIVKNQKILNFKRSYMSFFIHFAAIICLAFALISCVTAFKQTQNKYQAVQLEYQRSQDPEYLAKLARRDDDYQIFSNTKEKPKESKDSNKMQMKKARAHKALSQSQAQLTEAQYFYSKEGEIIFDIESDKM", "metadata": {"id": "A0AAJ1V3W4", "cluster": 21226452, "interpro_all": ["IPR039076", "IPR007060"], "interpro_used": ["IPR007060", "IPR039076"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: 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 include a DEAD/DEAH-box helicase domain that functions as an ATP-dependent nucleic acid-binding module essential for unwinding RNA structures during metabolism. It facilitates diverse cellular processes, including pre-mRNA splicing, ribosome biogenesis, and translation, by coupling ATPase activity with helicase function via the conserved motif III. In addition, the protein should feature a Primosomal protein N' 3' DNA-binding domain that specifically recognizes and binds the 3' end of the leading-strand arm within replication fork structures. Found at the N-terminus of the bacterial ATP-dependent helicase PriA, this domain acts as a sensor to stabilize arrested forks and facilitate the assembly of the primosome for DNA replication restart. It is present in Candidatus Kinetoplastibacterium oncopeltii TCC290E and contains UniProt keyword associations Isomerase, Hydrolase, and Zinc.", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 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, 3951, 43, 9535, 19, 30097, 1023, 17, 5758, 15318, 3418, 1988, 4088, 1966, 1925, 4498, 17, 3100, 11079, 2687, 17, 2743, 9059, 4415, 1958, 26801, 3146, 4061, 2409, 4714, 18, 2176, 11374, 6445, 3689, 4028, 16, 2710, 2097, 17, 3616, 8490, 16, 12794, 13008, 16, 1930, 6410, 16, 2007, 7590, 9444, 2455, 1956, 15318, 2347, 3454, 1920, 5305, 5219, 4337, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 2610, 4969, 2213, 56, 11, 23, 11, 2678, 17, 2743, 3418, 1988, 4475, 16197, 1930, 6876, 1920, 23, 11, 2482, 1927, 1920, 4523, 17, 5984, 6011, 2651, 5158, 15630, 4061, 18, 2435, 2019, 1920, 56, 17, 7822, 1927, 1920, 4543, 4498, 17, 3100, 15318, 17618, 1019, 16, 2052, 3418, 8016, 1966, 43, 6443, 1942, 13448, 17398, 24487, 1930, 6628, 1920, 5957, 1927, 1920, 2610, 4283, 1958, 2678, 5158, 27016, 7446, 18, 2176, 1977, 2481, 1922, 14550, 1031, 1957, 15838, 9574, 26073, 2341, 18842, 1989, 25601, 9551, 3907, 18920, 24069, 1021, 1930, 5461, 20709, 11121, 2538, 5253, 25510, 16, 20748, 16, 1930, 7997, 18, 3], "output": "MPIQNKLSISYNWLCVALNLPLFSIFDYKSINIINVGSRVVVPFGKRTLIGIVIKILEKPSIDASYVKEVLEILDDLPPFPQDWLKLLEFTADYYQRPLGNVMFSVIPLPLRSLSSYRGKRTLGGPIVKLGKSDDKMSPLIILPSIKKYDAILNDEQKKAVSIINSLKEFKAILLYGITGSGKTEVYLRAARNILQNSNKQILFLIPEINLTPQLEKSVRDSLAGIVNYEDILVMHSKLTMKSKLDVWYRVQCSKARVLLGTRMSIFAPFNNIGLIVIDEEHDTSYKQQNGLRYSARDLGVWRARHLNIPIILGSATPSLETWNNAIIGHYLRIYLKKKARDFSQNDIKLVNTKKFRPNNGLTAPLIEAIKDRLKKKEQSLIFINRRGYSPVFCCFSCDWISKCPRCTAFTVLHNTSNNESRLQCHHCGYCMISPLSCPECGDQDLRPIGSGTQRVEEALIGLFPNANIVRIDADSTKCKGSLSSLLNDVNNGNVDILIGTQMLAKGHDFLRVSLVGVINSDAMIFCQNFRAPEHLFSQLMQVSGRAGRHLNGGEVLIQTSFPEHMIYKFVINQDYDGFAKYSLNLRSIANLPPYSYQALLSVESKNLRIAMDFLHKSKNIIKEKVSFEFNYLSDITCYDPIPSRIVRIADIERAQMLVEGKHRSLLITFLKVWLRHISRLPNNKNKIKWYIEVDPLEI", "metadata": {"id": "M1LVG7", "cluster": 21533708, "interpro_all": ["IPR011545", "IPR014001", "IPR001650", "IPR027417", "IPR005259", "IPR041222", "IPR042115", "IPR041236", "IPR050880"], "interpro_used": ["IPR014001", "IPR011545", "IPR041222"], "interpro_unused": ["IPR001650", "IPR042115", "IPR050880", "IPR005259", "IPR041236", "IPR027417"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein according to the following functional description: The protein belongs to 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 have a Dihydroorotate dehydrogenase, catalytic domain that catalyzes the FAD-dependent conversion of dihydroorotate to orotate in *de novo* pyrimidine biosynthesis or 5,6-dihydrouracil to uracil in degradation. It utilizes electron acceptors such as quinone, fumarate, or NAD+ and is localized to bacterial membranes, yeast cytosol, or eukaryotic mitochondria. In addition, the protein is included in the Dihydroorotate dehydrogenase, class 2 family, which catalyzes the stereospecific oxidation of (S)-dihydroorotate to orotate as the fourth step in de novo pyrimidine biosynthesis. These membrane-associated monomers utilize a bound FMN cofactor and respiratory quinones as electron acceptors, and are structurally characterized by a catalytic TIM barrel fused to an N-terminal alpha-helical domain. It originates from Candidatus Levybacteria bacterium RIFCSPHIGHO2_01_FULL_40_15b and is annotated with UniProt keywords Flavoprotein and Oxidoreductase.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 1920, 2894, 3183, 8418, 30, 1920, 2213, 14440, 1942, 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, 2162, 43, 11842, 30232, 3857, 2057, 9294, 16, 6804, 3418, 1988, 17097, 1920, 14134, 17, 3100, 7309, 1927, 11842, 30232, 3857, 2057, 1942, 25027, 3857, 2057, 1922, 14, 2028, 9441, 14, 21611, 8132, 2014, 25, 16, 26, 17, 11842, 9280, 10401, 1942, 22761, 1922, 4877, 18, 2176, 18127, 4995, 27916, 2427, 1966, 25093, 16, 28343, 16, 2014, 6577, 15, 1930, 1977, 6579, 1942, 4543, 5726, 16, 5688, 11689, 16, 2014, 10825, 6489, 18, 1922, 2459, 16, 1920, 2213, 1977, 3063, 1922, 1920, 11842, 30232, 3857, 2057, 9294, 16, 2921, 22, 3416, 16, 2154, 17097, 1920, 26692, 19302, 6638, 1927, 12, 61, 13, 17, 11842, 30232, 3857, 2057, 1942, 25027, 3857, 2057, 1966, 1920, 8776, 3537, 1922, 2028, 9441, 21611, 8132, 18, 2144, 3260, 17, 2458, 13256, 12561, 43, 4124, 29599, 15155, 1930, 5481, 25093, 1036, 1966, 4995, 27916, 16, 1930, 2032, 12171, 4378, 2007, 43, 6804, 2267, 19560, 10305, 1942, 1925, 56, 17, 4262, 4595, 17, 11514, 3418, 18, 2176, 22970, 2037, 14550, 1031, 1957, 10157, 16924, 2422, 2126, 14061, 12424, 2792, 24888, 2509, 5265, 41, 3287, 41, 4125, 41, 3040, 41, 2461, 1014, 1930, 1977, 10633, 1956, 20709, 11569, 7732, 6657, 1930, 27388, 18, 3], "output": "MSVEIRSAIDAAHRNIVHPYLTRGEAQNDREIAHERALKLMEMAQRIPLAVEITDRMFSYDDPILRTSFAGLEAPNPLGIAAGFDKNARVHRFLGQGLGFGTVTVGSIAKVEYGGNARPRIFDLPNSRGLINRMSFPGEGSRSAVETLRADRRSRPYLLIVNFAASRPSFDAGRQIEDYGIVSDELADFGDEGEANVSSPNTPGVRGLQETDAFSDLADVVIPVYLHRGKPVRFKFGPDLETEKLHKNAQTIIDKKGSGITITNTSTGAEIRKGLSGRDVHREEQGGISGLPITQKALEASHRLYDYIGDEIPIHRIGGIMNVRDVWDALTYGGATTVDVYTAFVRQETSTPNFAYYILRDLVKAMRAYGMTSMADFKGIRGKRVPFPKT", "metadata": {"id": "A0A1F6I753", "cluster": 21661421, "interpro_all": ["IPR013785", "IPR050074", "IPR005719", "IPR005720"], "interpro_used": ["IPR013785", "IPR005720", "IPR005719"], "interpro_unused": ["IPR050074"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a protein I want to design: It is part of the Dodecin family, which comprises small dodecameric flavoproteins that bind riboflavin and other flavins within a protective aromatic tetrade structure. These proteins safeguard flavins against light damage by quenching their excited states and facilitating the degradation of riboflavin to lumichrome. Moreover, the protein can be placed in the Dodecin-like superfamily, which forms small dodecameric assemblies that bind flavins such as riboflavin and lumichrome with broad specificity. These proteins contain a unique aromatic tetrade binding pocket where ligands are stacked between tryptophan residues, potentially serving as waste-trapping devices for flavin metabolites. It has been detected in Hyphomonas beringensis. 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, 2176, 1977, 3131, 1927, 1920, 12621, 1940, 1921, 3416, 16, 2154, 12936, 2858, 12621, 19384, 9213, 1935, 7732, 14070, 1988, 4566, 28849, 1930, 2303, 26758, 1036, 2651, 43, 6337, 10761, 12470, 3695, 3170, 18, 2144, 2697, 7672, 11056, 2211, 26758, 1036, 3316, 3696, 4293, 2007, 16721, 2310, 14043, 4376, 1930, 12440, 1920, 4877, 1927, 28849, 1942, 5491, 2108, 4191, 18, 3950, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 12621, 1940, 1921, 17, 3189, 13975, 16, 2154, 4952, 2858, 12621, 19384, 9213, 1935, 16137, 1988, 4566, 26758, 1036, 2427, 1966, 28849, 1930, 5491, 2108, 4191, 1956, 4949, 4896, 18, 2144, 2697, 5531, 43, 5008, 10761, 12470, 3695, 2743, 10154, 2597, 6908, 2032, 24669, 2192, 13489, 4248, 16, 5063, 13915, 1966, 10437, 17, 16815, 6985, 1958, 26758, 6926, 18, 2176, 2258, 2252, 3330, 1922, 2483, 25808, 9259, 8310, 19017, 8362, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MGSAAGIERQIIGTSNVSVDDAIERGLTAAHIKYGAPTWFNVGNVRGIIDNGRVSHYEVTLELGFDTAEKAPEAGDYFRSACRGKPLHRMRPSLDVRY", "metadata": {"id": "A0A062UM50", "cluster": 21830099, "interpro_all": ["IPR009923", "IPR025543", "IPR036694"], "interpro_used": ["IPR009923", "IPR036694"], "interpro_unused": ["IPR025543"]}, "task_type": "autoregressive"} {"instruction": "What amino acids belong in the masked regions of a protein with this function: The protein is included in the Lactose permease-like family, which comprises integral membrane proteins functioning as cation-dependent symporters for substrates ranging from carbohydrates to amino acids. Bacterial members facilitate the uptake of beta-galactosides and other sugars, while eukaryotic homologues such as MFSD12 import cysteine into organelles like melanosomes to regulate pigmentation. In addition, the protein is assigned 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 is identified in Macrostomum lignano.", "tokenized_instruction": [2, 4663, 3835, 4576, 6784, 1922, 1920, 17476, 3451, 1927, 43, 2213, 1956, 2052, 2347, 30, 1920, 2213, 1977, 3063, 1922, 1920, 21021, 6191, 2051, 17, 3189, 3416, 16, 2154, 12936, 12328, 3260, 2697, 7295, 1966, 9976, 17, 3100, 29148, 2718, 2045, 1958, 6249, 6485, 2037, 16282, 1942, 3835, 4576, 18, 4543, 4678, 6628, 1920, 5047, 1927, 4666, 17, 9479, 17079, 1930, 2303, 15592, 16, 2679, 10825, 18541, 2427, 1966, 23778, 7240, 1028, 2582, 8666, 2460, 14487, 3189, 5313, 4686, 1942, 5741, 20542, 18, 1922, 2459, 16, 1920, 2213, 1977, 6304, 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, 1977, 2899, 1922, 26967, 4575, 23010, 1035, 12975, 9286, 18, 3], "output": "QIFQAISILYVTALTATPGWHLFACCLLAGLMPGGIVPLLPWASLPDVIQVVLVIHVMQLGSHVRFCTLTYLLVSCRFGKKLSLQIGSVGTAFYFMVTAAGVLGANALL", "metadata": {"id": "A0A1I8G3F2", "cluster": 22078740, "interpro_all": ["IPR039672", "IPR036259"], "interpro_used": ["IPR039672", "IPR036259"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein possesses 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. Additionally, the protein falls within 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 has been characterized in Corynespora cassiicola Philippines and is linked to UniProt keywords Transmembrane helix. I want a protein with the function described above.", "tokenized_instruction": [2, 1920, 2213, 14465, 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, 4950, 16, 1920, 2213, 12182, 2651, 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, 2258, 2252, 4378, 1922, 2233, 17151, 3508, 8846, 10499, 3907, 4879, 5148, 24919, 2613, 1930, 1977, 4624, 1942, 20709, 11569, 9117, 7864, 18, 51, 12914, 43, 2213, 1956, 1920, 2347, 2910, 3538, 18, 3], "output": "MDQIPPQELARLAGEDRGPLVKILVISFTSFAFTAVALRCYSRINYYPRVTWDDWFILLAMVFSSITTTMQIFGKSSWLTDAGTGRHLIFLDLAAVTRVLKFLYFSITCYGIGLTFSKMAILLQYRCLFASKKSRVVLYLVMGFVVAYGIASTCTAVFSCVPIDAFWYIQKKATARCLDQNAVFIAISSLNVFSNIVILCLPVGKVLSLDIPSTHRVALVYTLFIGVVICVIAAFRINALIEVSGHPEDSTWFSVPAAYLSSIEANLAIVCACVPVLGPLVARPASSYPFSEGGVASSKELKGSISWSTSRNGDPELEWA", "metadata": {"id": "A0A2T2N667", "cluster": 22784023, "interpro_all": ["IPR049326", "IPR052337"], "interpro_used": ["IPR049326", "IPR052337"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that has this function description: The protein is classified under the Peptide antibiotic immunity-related family, which confers immunity to specific peptide antibiotics such as the DNA replication inhibitor microcin B17. These proteins can function independently or in concert with other factors to induce the SOS repair system as a protective mechanism. Furthermore, the protein should have a Pentapeptide repeat that adopts a right-handed beta-helical structure to function as a DNA mimic, exhibiting size, shape, and electrostatic similarity to B-form DNA. This structural mimicry facilitates interactions with DNA-binding proteins, such as DNA gyrase, often conferring resistance to fluoroquinolones or protecting against microcin B17 toxicity. It is present in Lachnospiraceae bacterium. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2258, 2052, 2347, 8418, 30, 1920, 2213, 1977, 5947, 2441, 1920, 4207, 7267, 7611, 17, 2712, 3416, 16, 2154, 16556, 7611, 1942, 2487, 4207, 7560, 2427, 1966, 1920, 2678, 5158, 4106, 10572, 1921, 10360, 1027, 18, 2144, 2697, 2112, 2347, 6407, 2014, 1922, 21799, 1956, 2303, 2790, 1942, 4769, 1920, 17668, 5059, 2433, 1966, 43, 6337, 2856, 18, 3677, 16, 1920, 2213, 3066, 2162, 43, 9412, 24010, 6865, 1988, 24032, 43, 3659, 17, 17105, 4666, 17, 11514, 3170, 1942, 2347, 1966, 43, 2678, 10223, 16, 12196, 3081, 16, 5989, 16, 1930, 12452, 6796, 1942, 44, 17, 2386, 2678, 18, 2052, 4346, 10223, 6907, 11374, 3719, 1956, 2678, 17, 2743, 2697, 16, 2427, 1966, 2678, 9430, 2051, 16, 3868, 21510, 3554, 1942, 23619, 24909, 2014, 15145, 3316, 10572, 1921, 10360, 1027, 5532, 18, 2176, 1977, 2481, 1922, 7511, 11619, 3106, 11979, 1972, 3336, 14061, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MQVARKGLIMVEDFSEWKLQGEEIEQCLIQGQTIGQIEDSLVVRDCIFDNVTFVDCDFTKSDFTNVLFRKCDFSNCVVADSSFYKVRFERCKLVGTNMSEGFFKETEFYQVLGSYSNFSESKWNKSQLEGSIFKNAYFNHNEFKNMEFKSCELRSASFLQNKLEGMDFTTCHIEGLEVGIAEIKGMKVTTAQAIGFLNLLQLNIL", "metadata": {"id": "A0A3D3RKT5", "cluster": 24440255, "interpro_all": ["IPR001646", "IPR052949"], "interpro_used": ["IPR052949", "IPR001646"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to design a protein that has the following 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 is native to Porphyromonadaceae bacterium and exhibits UniProt keyword tags Membrane, Transmembrane, and Transmembrane helix. Please generate its amino acid sequence.", "tokenized_instruction": [2, 51, 12914, 1942, 3036, 43, 2213, 1988, 2258, 1920, 2894, 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, 1977, 6196, 1942, 17376, 5134, 3947, 7324, 1972, 3336, 14061, 1930, 9826, 20709, 11121, 2538, 14392, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 11586, 5655, 2496, 3835, 2687, 3244, 18, 3], "output": "MKLKPSLFPAILLLAVLAIQLLPGCTPSPERSRLEHIEAIIDEHPDSAMILIDSVDTAALRSDRDRALYGMLLTEALDKNHQNPSNDPLITSAINYFADKGERRREMIATYYGARVQYLNNDFSHAIVRFFRAKEIAEELSEHFWHGMAARGISDIYYKSFNRAEQLKFAKEEFDNLSKAQRQPYLNYALLDYATAIYNYGDYKSAIAFSRQILDSADTYNDIYLKVDALKLLGLANMSTREFSSAILIFENLLNSTFANSSDSLYLCLAYIGDNKPILAKRLFSKVSNGEPSLRLAVSHRINEASGNYRAALSDLNALYDSRDSVLRDYIKMPASTSTLDYLHMEKEKNKATLETSRKSLFLIILGLGFLVLLLSYFFHLYILKQKREIEDSVLLAEALKEQLSLEVSKHEMTVVSSNRKIEEYDKKISDAKTTIKELLSSKYEVLEDVCQILRECDNSAAAKRKIANVMTSFINEISLDGKKLDMLEERVNEIYGNVMKEIRKDLPDMKEIDYNLYLFMILGISNPSISILLKEKKINAVYDRKRRLKDKIKALSPVLQSKYMAPFS", "metadata": {"id": "A0A3B8R0B3", "cluster": 24640691, "interpro_all": ["IPR011990"], "interpro_used": ["IPR011990"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "We aim to build a protein that does the following:\nThe protein can be placed in the Mediator of RNA polymerase II transcription subunit 26 family, which functions as a component of the Mediator complex to regulate the transcription of nearly all RNA polymerase II-dependent genes. This subunit specifically facilitates the transition between the transcriptional initiation and elongation phases. Moreover, the protein should contain a Transcription factor IIS, N-terminal domain that functions as a protein interaction module characterized by a conserved LW motif and a compact four-helix bundle structure. This domain is found in various nuclear proteins, including transcription elongation factors like TFIIS and Elongin A, as well as the Mediator complex subunit MED26. Also, the protein features a Transcription elongation factor TFIIS/CRSP70 N-terminal domain that forms a four-helix bundle structure within transcription elongation factor S-II (TFIIS). While the full-length protein enables RNA Polymerase II to bypass transcriptional pause sites by stimulating mRNA cleavage, this specific N-terminal region is not essential for the elongation activity. It is produced by Folsomia candida (Springtail) and corresponds to UniProt keyword Activator, Nucleus, and Transcription regulation.\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 11370, 1927, 3146, 6479, 2890, 3213, 5903, 3179, 3416, 16, 2154, 4088, 1966, 43, 4594, 1927, 1920, 11370, 2796, 1942, 5741, 1920, 3213, 1927, 6737, 2136, 3146, 6479, 2890, 17, 3100, 2628, 18, 2052, 5903, 4475, 11374, 1920, 4832, 2192, 1920, 5224, 6035, 1930, 9971, 7643, 18, 3950, 16, 1920, 2213, 3066, 5531, 43, 3213, 2991, 2890, 1036, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 43, 2213, 2835, 9059, 4378, 2007, 43, 5305, 21251, 5219, 1930, 43, 13726, 3006, 17, 7864, 14142, 3170, 18, 2052, 3418, 1977, 2435, 1922, 3425, 4254, 2697, 16, 2710, 3213, 9971, 2790, 3189, 27935, 1036, 1930, 7846, 1921, 43, 16, 1966, 2486, 1966, 1920, 11370, 2796, 5903, 2242, 4684, 18, 2222, 16, 1920, 2213, 4075, 43, 3213, 9971, 2991, 27935, 1036, 19, 17982, 1034, 4618, 56, 17, 4262, 3418, 1988, 4952, 43, 3006, 17, 7864, 14142, 3170, 2651, 3213, 9971, 2991, 61, 17, 2890, 12, 27935, 1036, 13, 18, 2679, 1920, 4125, 17, 3471, 2213, 10217, 3146, 6479, 2890, 1942, 10344, 5224, 25863, 3402, 2007, 9868, 3616, 6404, 16, 2052, 2487, 56, 17, 4262, 3031, 1977, 2084, 4415, 1958, 1920, 9971, 2455, 18, 2176, 1977, 4152, 2007, 17802, 2204, 6026, 14550, 12, 11858, 11578, 13, 1930, 8852, 1942, 20709, 11121, 2538, 9518, 16, 5607, 16, 1930, 3213, 3640, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "MLARGAKSYGFDGEGTARLWLIGRPTNMLKTFVSFVMLSLPLEFNAAPVPLEDGWMRIHVCFYFTMKATANTGLSLVHVHLGVCTENTHPRSDDTSTLTIIKTATTTTTNLGRRRDNNNNNKLLREIGATAAKGKTTPGLMQQSPVILTQRLIDAVDDSYHVKDMGAIIEVLETKRINDEKLAKRAKNLVKKWRDAVLVNEQQQSGGGGGGRPVNGNSDSSPQLMTASRISPNALHNSNSLSPRILNNLTSNNNNRNGQQQQQVGRHSSSPSLRVSSPSQFGNKAKSPSCGPIISSSPLNNNNNTNKMMTSTIEDGAERMNAGPPSKKARHGIANGGIFEGTLDDPSLALLDDLSKDSMTSAVLSGAPSPASIILGDSALTSPAMSGGEGESASETLLCGQDDNQVNVVAEVVAPVQKRGRKKKQKTNEMDGFGFPGGVTPQKDENLRGTVHRLSMEIFDDDHRFPPTPDISPVPPPPPLERKPIPKPHITAALSRQRNEISLLPHEPTPPPPPVIPPTADEPLDSKKKRKRDKLSRLPPIDPQTLEELKNFKFDVPSEDEEAKSKPEIETENATSLTSTNESNAENIKNNIAEADFVDVSPKIEDTSGPDDPSTIPQIVVSSTTLPQTIDEMDTSEQAEEKIGNLNGNLDKDGLFKEWQEVVAVESFKGDLLHILPYTIIDFRVFGRVCCSGFLAYCVLREKIRRRGKNVAKLAPKEKKNRQNCTIFPPPPSSPSSSSSSAGLLLQVLEQLPVTKELLETTRLGKTINVFRGLHVPGGHLRSIGGYNSNSSSIPSAVVAAVSSPRLNSYAPNVEVVARTNAANKRLRRASDNSDGSSSKAVSNMSSSKPSLFSSIPENEGSAVDHGANNVNDQPEGNTQTLRIHKQIAQAKQESMVRRDDPVMKSDFVKEYLHSQNKQIEKKNRGENNATTTISFPTESEIAPPLIASKIDWGDSEDEDDQEQPEADAPAPREIDDSEVERLHL", "metadata": {"id": "A0A226DWV9", "cluster": 26889600, "interpro_all": ["IPR042376", "IPR003617", "IPR035441", "IPR017923"], "interpro_used": ["IPR042376", "IPR017923", "IPR003617"], "interpro_unused": ["IPR035441"]}, "task_type": "infilling"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein features a Domain of unknown function DUF7344 domain that is a presumed helix-turn-helix (HTH) motif found in uncharacterised archaeal sequences. It has been characterized in Halorubrum kocurii JCM 14978.\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, 3418, 1927, 5435, 2347, 4855, 1038, 8966, 6609, 3418, 1988, 1977, 43, 15326, 7864, 17, 5165, 17, 7864, 12, 5334, 1023, 13, 5219, 2435, 1922, 23229, 3495, 22367, 3709, 18, 2176, 2258, 2252, 4378, 1922, 23226, 3176, 2377, 1989, 6235, 18021, 21094, 14904, 1035, 14094, 7950, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MTDALYDDGEQVSDNWDAVFKSSVPLPESAAPSARPSDPEALRLQLYHTHLPVSAVFDALHSAADDLPDSLVTGCQRLEAEQQDGATFLSAEPRRQLLASLSDAPPDRMLAEMGFVTWDADPLVASRGPRFDE", "metadata": {"id": "M0NIW3", "cluster": 1677283, "interpro_all": ["IPR055768"], "interpro_used": ["IPR055768"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Predict the masked amino acids. The target function is: The protein belongs to the Phosphatase and SH3 domain-containing protein family, which exhibits phosphatase activity towards protein tyrosine residues, such as EGFR and ZAP70, and phosphorylated steroid compounds essential for development. These enzymes regulate the accumulation of receptor-type tyrosine kinases, while their constituent SH3 domains interact with dynamin to potentially inhibit endocytic pathways. In addition, the protein is associated with 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 present in Parastrongyloides trichosuri (Possum-specific nematode worm).", "tokenized_instruction": [2, 5660, 1920, 17476, 3835, 4576, 18, 1920, 2758, 2347, 1977, 30, 1920, 2213, 14440, 1942, 1920, 8167, 1930, 18824, 3418, 17, 3165, 2213, 3416, 16, 2154, 9826, 8167, 2455, 5681, 2213, 6941, 4248, 16, 2427, 1966, 5775, 1930, 24427, 4618, 16, 1930, 7199, 9507, 4300, 4415, 1958, 2740, 18, 2144, 5038, 5741, 1920, 4858, 1927, 3148, 17, 2601, 6941, 7784, 16, 2679, 2310, 18690, 18824, 4682, 6310, 1956, 22653, 1942, 5063, 2875, 17674, 3873, 18, 1922, 2459, 16, 1920, 2213, 1977, 2458, 1956, 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, 2481, 1922, 5336, 14342, 26983, 6012, 3726, 10477, 1951, 18330, 12, 2776, 1989, 17, 2487, 18827, 11055, 13, 18, 3], "output": "MPRRIYAVRHCQREDNINSPLSDKGRNIQGPALTRRFKNIPLDETTTILLGDKNNKIFIEPGLIECLTMCTYDPILKKWPTIEVGWNDENCKPKDNDQILLVSHASPMAAINGSGLFVCSSFNDTTHLSAKSVNWQKSFPQFESDNYVFSSPMDRTCIDPPGCWNVRKLKEKFPKIDLRLRDTIEGILKKCSHDILVGHWTYPSQGSISIYDETS", "metadata": {"id": "A0A0N5A5E3", "cluster": 1999322, "interpro_all": ["IPR013078", "IPR029033", "IPR051710"], "interpro_used": ["IPR051710", "IPR013078"], "interpro_unused": ["IPR029033"]}, "task_type": "infilling"} {"instruction": "Design an amino acid sequence that will be able to perform the following function: The protein is associated with 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. In addition, the protein falls within the P-type ATPase, transmembrane domain superfamily, which constitutes the ten-helix membrane-spanning region of P-type (E1-E2) ATPases that utilize ATP hydrolysis to drive the active transport of ions and phospholipids. These transporters alternate between E1 and E2 conformations to pump substrates, including protons, alkali metals, and heavy metals, across bacterial and eukaryotic membranes. Furthermore, the protein features 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. It occurs in Eutreptiella gymnastica and is described by UniProt keywords Metal-binding and Transmembrane helix.", "tokenized_instruction": [2, 3036, 1925, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 1977, 2458, 1956, 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, 1922, 2459, 16, 1920, 2213, 12182, 2651, 1920, 58, 17, 2601, 9444, 16, 9117, 3418, 13975, 16, 2154, 14879, 1920, 5656, 17, 7864, 3260, 17, 13346, 3031, 1927, 58, 17, 2601, 12, 11123, 17, 6602, 13, 28132, 1988, 12561, 4498, 9128, 1942, 9265, 1920, 3500, 4860, 1927, 6982, 1930, 15619, 18, 2144, 10538, 14263, 2192, 11123, 1930, 6602, 12526, 1942, 8912, 6249, 16, 2710, 15948, 16, 25178, 11570, 16, 1930, 7881, 11570, 16, 3436, 4543, 1930, 10825, 5726, 18, 3677, 16, 1920, 2213, 4075, 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, 2176, 5110, 1922, 24048, 20483, 24866, 11560, 1019, 26024, 3676, 21788, 1930, 1977, 2910, 2007, 20709, 11569, 6048, 17, 2743, 1930, 9117, 7864, 18, 3], "output": "IGGTINQEGLLHIQATKLGDETMLSQILKAVQEAQTNKAPIQAVADTVAGLFVPAVILIAVCSLLVWLGCGYLNLYPSEWRGSESVVVFTLRFFIASLVVACPCAMGLATPTAVMVGSGVGALHGLLIKGGGPLEAASRIDAILFDKTGTLTQGNIQVVEAKLLTTGTDAMEAWRLIGGAEASSGHP", "metadata": {"id": "A0A7S1IWR4", "cluster": 7011175, "interpro_all": ["IPR023299", "IPR018303", "IPR023298", "IPR023214", "IPR001757"], "interpro_used": ["IPR023214", "IPR023298", "IPR018303"], "interpro_unused": ["IPR023299", "IPR001757"]}, "task_type": "autoregressive"} {"instruction": "Can you generate a protein's amino acid sequence given the following functional description? The protein belongs to 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. Moreover, the 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. Also, the protein has a Cdc23 domain that functions as the APC8 subunit of the anaphase-promoting complex (APC), playing a structural role in this E3 ubiquitin ligase machinery. It works in concert with other subunits, such as CDC27 and CDC16, to regulate cell cycle progression and the onset of anaphase. It has been detected in Ectocarpus siliculosus (Brown alga) (Conferva siliculosa) and is annotated with UniProt keywords Mitosis, Cell division, and TPR repeat.", "tokenized_instruction": [2, 2112, 6253, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 3258, 1920, 2894, 3183, 8418, 35, 1920, 2213, 14440, 1942, 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, 3950, 16, 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, 2222, 16, 1920, 2213, 2258, 43, 28190, 1010, 3418, 1988, 4088, 1966, 1920, 9187, 1025, 5903, 1927, 1920, 20826, 17, 7356, 2796, 12, 9187, 13, 16, 14797, 43, 4346, 2770, 1922, 2052, 10968, 6526, 11905, 10853, 18, 2176, 10997, 1922, 21799, 1956, 2303, 6991, 16, 2427, 1966, 28190, 1027, 1930, 7137, 3672, 16, 1942, 5741, 2024, 4048, 4380, 1930, 1920, 4727, 1927, 20826, 18, 2176, 2258, 2252, 3330, 1922, 7495, 7095, 1034, 1957, 16105, 11677, 1957, 12, 8084, 4326, 1019, 13, 12, 7909, 7302, 16105, 11677, 1019, 13, 1930, 1977, 10633, 1956, 20709, 11569, 12611, 16, 2024, 8451, 16, 1930, 22288, 6865, 18, 3], "output": "MDVGEFERASQAFGNKSWPAAAAAGSVPGGLYSRARFLGWYSLFLAGERRREEESQLTDALQRRRLVNPHLKTLHAELSQCDQAGTLDAFGLYIYAAVLKALREEGRGGAGGTGGNTPTPTTPHSSGGGGGANSLGGSGGGAFVTPRARAPSGGRGDATGGGGGTTSTEKTAVTTATAQEVLARSLRLFPYNWSAWLDLASLCLETDTFFLQHLLVEQHLSKDALAILDDLEPSFPCSSYVLSQTAVAHYHLRNFDQGHDDFKELRRRDPLRMEGLDVFSNILYVKECKAELSFLAHTTNKSAPLRPETNCIIGNYYSLKGQHEKAVTYFLKALRLDRRCLSAWTLMGHEFIELKNSGAAVESYRQAVDINPKDYRAWYGLGQAYEILHMHLYAIYYYKRATALRPYDARMWIAMGQCLEKLGKSAEAISTYERAMANDDREGIALAQLAKLYDGAGRKDSAAKCYETMLANRSADGDNSSAEEGMHFLCLYYKNKGDYTRASKMANGLLDYTGTSREAALAVLREIRSIMETRQHQAAESSALPQPHNANNSHDDVSLDGGSGRPLFTPRAATGSSHHDGSGAGGSQLFNANNSGLGGSVRGATRAAAGTFPTPTPRRPGRVRNGVSPGTGGGGGGAAGGGAGSGTPGYRLMGNSGGGTSLAPRSPEDMSVAMSLGSSDEDDDGGALARYSPGIATPVATGHGGAGAGHDGSPEAGGDGQGEESLSDILSP", "metadata": {"id": "D7FLS8", "cluster": 7708649, "interpro_all": ["IPR007192", "IPR011990", "IPR019734"], "interpro_used": ["IPR011990", "IPR019734", "IPR007192"], "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 should include 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. Also, the protein falls within the His-Me finger superfamily, which comprises diverse endonuclease proteins found in all forms of life that are involved in efficient, nonspecific DNA cleavage. Also known as HNH nucleases, these proteins feature a structural core consisting of a $\\beta$-hairpin and an $\\alpha$-helix that coordinates a single catalytic metal ion essential for enzymatic activity. Also, the protein features a NUMOD4 domain that functions as a putative DNA-binding motif commonly found in homing endonucleases and related proteins. It is produced by Salmonella phage GEC_vB_N5 and is classified with UniProt keywords Hydrolase.", "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, 3066, 3951, 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, 2222, 16, 1920, 2213, 12182, 2651, 1920, 4167, 17, 2142, 8497, 13975, 16, 2154, 12936, 6445, 18697, 2697, 2435, 1922, 2136, 4952, 1927, 3308, 1988, 2032, 3286, 1922, 5807, 16, 12720, 2678, 6404, 18, 2222, 3171, 1966, 9888, 1023, 29305, 16, 2144, 2697, 5961, 43, 4346, 4728, 7600, 1927, 43, 8, 38, 4666, 8, 17, 14565, 1930, 1925, 8, 38, 4595, 8, 17, 7864, 1988, 10675, 43, 2957, 6804, 6048, 4755, 4415, 1958, 8145, 2455, 18, 2222, 16, 1920, 2213, 4075, 43, 2403, 1986, 1006, 3418, 1988, 4088, 1966, 43, 6770, 2678, 17, 2743, 5219, 5384, 2435, 1922, 20621, 18697, 1036, 1930, 2712, 2697, 18, 2176, 1977, 4152, 2007, 11681, 10503, 3929, 1030, 41, 16535, 41, 56, 1015, 1930, 1977, 5947, 1956, 20709, 11569, 20748, 18, 3], "output": "MEGFKPIPEYPEYLVSEKGEIYSTISNKYLKPTINGKGYYHFAVREDTNKYKWLQLHRVICRVYGNLPSLDSEMEVDHNDRNKLNILPSNLVAREKKDHYDKTTLERGKTIGGTRCIVCNKRIHSGREYCINCSPVKQTKSPEITAEQIEYWVSKYSWTRAAKELNLSDNGLRKRYTKLTGKSPKEIKKSG", "metadata": {"id": "A0A7S9SRF0", "cluster": 12151000, "interpro_all": ["IPR044925", "IPR003615", "IPR010902"], "interpro_used": ["IPR003615", "IPR044925", "IPR010902"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Infill the masked sequence for this function: 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. Furthermore, the protein should feature 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 has been detected in Bacteroidetes bacterium HLUCCA01 and is annotated with UniProt keywords TPR repeat.", "tokenized_instruction": [2, 6510, 1024, 1920, 17476, 3244, 1958, 2052, 2347, 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, 3677, 16, 1920, 2213, 3066, 5961, 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, 2258, 2252, 3330, 1922, 26808, 14061, 8429, 1978, 3375, 6924, 1930, 1977, 10633, 1956, 20709, 11569, 22288, 6865, 18, 3], "output": "MPELKETLLELSEKIVDLNKAGTGLRHIGDDLLRYEKETTGAVEMYRKALKVWPEHVGLRIVVERSIRIGGETPDVLQNKFPDDIESQRFLRELDQMKLEIMESADPQTEPHKIKEDQAYVRFMLGSVCQLLDYHEKLNELFISLDALGLHEDAFAATLVKLDRIAEAKTVLFNCIS", "metadata": {"id": "A0A0P7WH71", "cluster": 14000005, "interpro_all": ["IPR011990", "IPR019734"], "interpro_used": ["IPR011990", "IPR019734"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Here is the functional description of a protein I want to design: 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. Additionally, the protein should feature 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. It is found in Desulfobacteraceae bacterium. 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, 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, 4950, 16, 1920, 2213, 3066, 5961, 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, 2176, 1977, 2435, 1922, 30311, 5883, 9914, 14061, 18, 11586, 5655, 1920, 3835, 2687, 3244, 1958, 2052, 2213, 18, 3], "output": "MIGPALVNQLLKDTWEVRVLSRRPFNPNLFVDHVDCMFGDIRDINFLQTAMKGVDVAFHLAAKLHINNPSPKQSEEYHHINVDGALKVAQAAIKAKVKRLVHFSTIGVYGPSVAIEPYQETSSLNPQSLYALSKIRSEEGILKLFHGQKQSSAVILRLSAVYGPRLQGNYRTLVKALQRGLFWPVGNGENRRTMIYIDDMVRAAILAAEHPKAAGNIFNVTDGKIHTLNDVLNAIAFALGKTPPGFHLPGRPVQVFSSLTDHLSNALRLPVPGLRNLVDKMMEDVAVSGEKICNDLSFIPRYDLEHGWQAALCRQSKNAS", "metadata": {"id": "A0A7X1L7K7", "cluster": 20057503, "interpro_all": ["IPR001509", "IPR036291"], "interpro_used": ["IPR036291", "IPR001509"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: The protein should contain a KAP family P-loop domain that functions as a predicted NTPase, often characterized by the insertion of transmembrane helices that anchor the catalytic core to the intracellular side of the membrane. This domain is found in diverse proteins including Kidins220/ARMS and PifA across bacteria and animals. 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 derived from Cardiobacterium valvarum F0432 and is classified with UniProt keywords Transmembrane helix.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 1920, 2213, 3066, 5531, 43, 17367, 3416, 58, 17, 5881, 3418, 1988, 4088, 1966, 43, 4396, 29676, 2051, 16, 3868, 4378, 2007, 1920, 7413, 1927, 9117, 12789, 1988, 13333, 1920, 6804, 4728, 1942, 1920, 4776, 4159, 1927, 1920, 3260, 18, 2052, 3418, 1977, 2435, 1922, 6445, 2697, 2710, 4816, 2925, 4460, 1008, 19, 9715, 1930, 22452, 1019, 3436, 4802, 1930, 3555, 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, 3595, 2037, 21129, 7972, 2341, 18842, 1989, 2326, 19313, 1989, 17930, 7514, 1028, 1930, 1977, 5947, 1956, 20709, 11569, 9117, 7864, 18, 3], "output": "MTNQDTSSPNDPNQKAFIPEDLFERTKIAEMLVDGNWGTGKTVFCHRLENYINNDNPLFVLLSKIIQYLKDKDDRNQADKISIAKAGGLAIIEALVTSLVAELPNEDELGNSIAALKQALSDYAAENPLVIFIDELDRCKPLFTFERQLEESIKHRYGQHIDSQRYLTQISLPGIPASGIISNTHQYIKNLINSTLFNNFMISLHNISLRNAETIIRYFNFYVKNLCIRVYNKKATVQEVSSFLGIEEQRVLTLITMYPNYNQMQEFIDFLTKRSLLDWVSMDKTADDIVTRFSVNKIEELISDIAFYKIFRILQNEIEENNNQEYNSNLDSFFPHCPSENYKHIQTIYIDAFEYDHTNIITNSARKVLWPVAKTLTKESIKNIGNTVQQRIEKLFQKEESESQAFALDMLEVIKHIFDIPNVKFIDKFIKFRIQLPIPKNGNAEFNNFLRTKRINSLTIDLAILLFYCIILYVIDPSNNNRLLHSELESIPIRSLLDQGYVLLHFKEK", "metadata": {"id": "G9ZG52", "cluster": 22542870, "interpro_all": ["IPR011646", "IPR027417"], "interpro_used": ["IPR011646", "IPR027417"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We are engineering a protein with the following requirements:\nThe protein contains a BD-FAE-like domain that adopts an \u03b1/\u03b2-hydrolase fold with a Ser-Asp-His catalytic triad to primarily function as a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans. This versatile scaffold also supports diverse hydrolytic activities across organisms, including kynurenine formamidase activity in tryptophan degradation, isoprenylcysteine demethylation in plants, and immunogenic lipase activity in bacterial pathogenesis. Furthermore, the protein should feature 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. Also, the protein is included in the GDXG lipolytic enzyme family, which comprises proteins with a conserved GDXG motif that primarily function as esterases and lipases to hydrolyze short-chain fatty esters. These enzymes display broad functional diversity, with roles ranging from the regulation of MalT and MelA activity to plant cell wall degradation and tryptophan metabolism. Additionally, some members are involved in maintaining mycobacterial cell envelope permeability and detoxifying organophosphorus compounds. It is native to Verrucomicrobiota bacterium.\nReplace the masked tokens with the appropriate sequence.", "tokenized_instruction": [2, 2038, 2032, 9325, 43, 2213, 1956, 1920, 2894, 8456, 30, 1920, 2213, 5461, 43, 5238, 17, 5685, 1021, 17, 3189, 3418, 1988, 24032, 1925, 160, 19, 161, 17, 20748, 3728, 1956, 43, 2375, 17, 4138, 17, 4167, 6804, 21845, 1942, 5985, 2347, 1966, 43, 29491, 4635, 1944, 10921, 1930, 6894, 23665, 26389, 3500, 1990, 2796, 4613, 23665, 1036, 18, 2052, 20425, 7281, 2222, 7825, 6445, 26702, 4209, 3436, 7373, 16, 2710, 23523, 24684, 2053, 2386, 25238, 2051, 2455, 1922, 13489, 4877, 16, 26690, 2199, 23159, 7595, 20254, 1922, 4793, 16, 1930, 18835, 16653, 2455, 1922, 4543, 6559, 18, 3677, 16, 1920, 2213, 3066, 5961, 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, 2222, 16, 1920, 2213, 1977, 3063, 1922, 1920, 7113, 1039, 1029, 3178, 6586, 4113, 3416, 16, 2154, 12936, 2697, 1956, 43, 5305, 7113, 1039, 1029, 5219, 1988, 5985, 2347, 1966, 26389, 1036, 1930, 16653, 1036, 1942, 7222, 6931, 3662, 17, 4659, 5934, 16785, 18, 2144, 5038, 4434, 4949, 3183, 5935, 16, 1956, 5456, 6485, 2037, 1920, 3640, 1927, 15505, 1930, 4221, 1019, 2455, 1942, 4496, 2024, 4821, 4877, 1930, 13489, 4714, 18, 4950, 16, 2673, 4678, 2032, 3286, 1922, 8231, 21424, 2024, 11262, 8828, 1930, 15289, 7649, 3090, 16847, 1957, 4300, 18, 2176, 1977, 6196, 1942, 3566, 3176, 13055, 1935, 15129, 3940, 3857, 14061, 18, 14732, 1920, 17476, 26923, 2099, 1956, 1920, 4703, 3244, 18, 3], "output": "MKLIVDVPYREGSPVWRVDIALPEASAGDKNGGRSSICYWAQRGYVGVSRWLRAHASDYNIDPNRVGAFGHSAGAHLVAFDAGPWPEPSSLVNAACAVATPTDLAGSREVNRFPGATAEAPPFLLIHGVTDGTVPVEAKNVNLFLLDAMGHDPLPTHEAILRFQSDLARRWQLERASEQGFGFERVSAFDLNHDGKLSRDEWIEPAEMDAWRGRSPRPGRKNLPVSPPGTTPRPDRPQPRAVILNVHGGGWSAGVRYRLLGEAPFPACIEDVKCAVMLGVCPKGAGEDERRTLARRCSPLTYVNHGRDFAAALRAAGPLIDAFFYTTIGARAGVLAPGTDEMFARIDRGQNNV", "metadata": {"id": "A0A938GUJ6", "cluster": 22689426, "interpro_all": ["IPR029058", "IPR049492", "IPR018247", "IPR050300"], "interpro_used": ["IPR049492", "IPR018247", "IPR050300"], "interpro_unused": ["IPR029058"]}, "task_type": "infilling"} {"instruction": "A synthetic protein is tasked with the following:\nThe protein should have a Malate synthase, TIM barrel domain that forms the central catalytic core of the enzyme, creating the active site cleft alongside a C-terminal helical domain. It catalyzes the aldol condensation of glyoxylate with acetyl-CoA to produce malate as part of the glyoxylate bypass in bacteria, fungi, and plants. Also, the protein is associated with the Malate synthase A family, which functions as a key enzyme in the glyoxylate cycle by catalyzing the condensation of acetyl-CoA with glyoxylate to form malate. This activity enables organisms such as bacteria, fungi, and plants to assimilate two-carbon compounds as carbon sources, effectively bypassing specific steps of the tricarboxylic acid cycle. It occurs in Solirubrobacterales bacterium.\nIt has masked regions. Complete the sequence.", "tokenized_instruction": [2, 43, 6830, 2213, 1977, 3909, 1919, 1956, 1920, 2894, 30, 1920, 2213, 3066, 2162, 43, 24260, 8921, 16, 2267, 19560, 3418, 1988, 4952, 1920, 4101, 6804, 4728, 1927, 1920, 4113, 16, 11124, 1920, 3500, 3200, 14649, 17764, 43, 45, 17, 4262, 11514, 3418, 18, 2176, 17097, 1920, 11174, 1945, 16112, 1927, 3376, 6644, 2010, 1956, 6894, 17, 10027, 1942, 5074, 24260, 1966, 3131, 1927, 1920, 3376, 6644, 2010, 10344, 1922, 4802, 16, 10520, 16, 1930, 4793, 18, 2222, 16, 1920, 2213, 1977, 2458, 1956, 1920, 24260, 8921, 43, 3416, 16, 2154, 4088, 1966, 43, 3834, 4113, 1922, 1920, 3376, 6644, 2010, 4048, 2007, 29601, 1920, 16112, 1927, 6894, 17, 10027, 1956, 3376, 6644, 2010, 1942, 2386, 24260, 18, 2052, 2455, 10217, 7373, 2427, 1966, 4802, 16, 10520, 16, 1930, 4793, 1942, 18226, 2010, 2288, 17, 5056, 4300, 1966, 5056, 5777, 16, 7098, 10344, 1941, 2487, 5983, 1927, 1920, 12258, 26431, 2687, 4048, 18, 2176, 5110, 1922, 2638, 1996, 2255, 15129, 2422, 3955, 14061, 18, 2176, 2258, 17476, 3451, 18, 4080, 1920, 3244, 18, 3], "output": "MRRVQVTGGVGDQARVLSDDSLNVCKGRQRHLDAGAMLAFLAEIREILESHRPGRAQDDDQPLTLTPAPKAFLCDFQANLFDAVQGTTELTRPDGRVYRPGEEVATHGDLPRLAADGRGQFLLLPKLEGHLEARLGLELVAALHDAFEGRRRETGLSARPLRRSETARGDEDALTPPRANVIAGPTRVASTLVNGEAVSASFVDFGRFMTHNG", "metadata": {"id": "A0A7J9YV61", "cluster": 24508648, "interpro_all": ["IPR011076", "IPR006252", "IPR001465", "IPR048356", "IPR046363"], "interpro_used": ["IPR001465", "IPR006252"], "interpro_unused": ["IPR046363", "IPR011076", "IPR048356"]}, "task_type": "infilling"} {"instruction": "The protein can be placed in the SGNH hydrolase superfamily, which encompasses a diverse group of esterases and lipases characterized by a three-layer \u03b1/\u03b2/\u03b1 fold and a conserved Ser/Acid/His catalytic triad. These enzymes utilize a unique hydrogen bond network to stabilize the active site and are found in proteins ranging from viral haemagglutinin-esterase surface glycoproteins to bacterial thioesterases. It is native to Helicosporidium sp. ATCC 50920.\nBased on this functional description, predict the missing amino acid spans.", "tokenized_instruction": [2, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 10075, 21677, 20748, 13975, 16, 2154, 21569, 43, 6445, 2210, 1927, 26389, 1036, 1930, 16653, 1036, 4378, 2007, 43, 2559, 17, 4757, 160, 19, 161, 19, 160, 3728, 1930, 43, 5305, 2375, 19, 2687, 19, 4167, 6804, 21845, 18, 2144, 5038, 12561, 43, 5008, 6201, 5403, 3504, 1942, 13448, 1920, 3500, 3200, 1930, 2032, 2435, 1922, 2697, 6485, 2037, 4324, 7105, 17003, 1921, 17, 26389, 3154, 16268, 1942, 4543, 30215, 2319, 18, 2176, 1977, 6196, 1942, 11279, 9890, 9734, 2056, 18, 11037, 30468, 3520, 18, 2454, 1990, 2052, 3183, 8418, 16, 5660, 1920, 6814, 3835, 2687, 23658, 18, 3], "output": "MRRRASVSLGDRVRLRNFVRKLASGEPVSGDYVSDLSSYFRRVTSNVTIHQGGIPGILNLKADIIFIELAINDVMHQYKEGHGLRRLRYLQTNADICGSVAEYYAQPMLAYRALLFDEVARHAYMVDAVVEMVRAEARALGSDEPWGPSDEAALERELAPPMFKNNSTAGFDLRTVSPAFPHPATALHGQGQGSRLAFGYLRDQSGQSRANVSCTNCYCPLYNLYPTRVNLTLEDPTPEINDRLDILGICIAGSPIWPEIGFLGGSISDSGGPNKGVHFASCLELHIGPYHERLIRKALGYARRPATVELAFHTFQPEHGEMDPAAFMSRDLMHPDPVGNDKISTGVVLLGEDMRRLVVELDMRLDEVAAAAPIPFKAGWAFQPGRFRQLFTSICMRSDPAGPL", "metadata": {"id": "A0A059LNX1", "cluster": 26150834, "interpro_all": ["IPR036514"], "interpro_used": ["IPR036514"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Target Function: The protein belongs to the SOB-five-like family, which comprises plant-specific proteins that function as positive modulators of endogenous cytokinin levels during development. These proteins contain the conserved SOFL-A and SOFL-B domains necessary for regulating specific cytokinin N-glucosides derived from biosynthetic intermediates. It is derived from Ziziphus jujuba (Chinese jujube) (Ziziphus sativa) and is annotated with UniProt keywords Cytokinin biosynthesis and Cytokinin signaling pathway.\nPredict the masked residues for this protein.", "tokenized_instruction": [2, 2758, 2347, 30, 1920, 2213, 14440, 1942, 1920, 24998, 17, 3628, 17, 3189, 3416, 16, 2154, 12936, 4496, 17, 2487, 2697, 1988, 2347, 1966, 2843, 17455, 1927, 5355, 4192, 15020, 2428, 2409, 2740, 18, 2144, 2697, 5531, 1920, 5305, 18026, 1024, 17, 43, 1930, 18026, 1024, 17, 44, 4682, 4680, 1958, 6773, 2487, 4192, 15020, 56, 17, 28507, 1036, 3595, 2037, 14041, 12386, 18, 2176, 1977, 3595, 2037, 28666, 22030, 2102, 1957, 8212, 13267, 7972, 12, 7185, 8212, 13267, 5873, 13, 12, 28666, 22030, 2102, 1957, 22939, 13, 1930, 1977, 10633, 1956, 20709, 11569, 4192, 15020, 8132, 1930, 4192, 15020, 3197, 3374, 18, 5660, 1920, 17476, 4248, 1958, 2052, 2213, 18, 3], "output": "MGTEECSSSESGWTMYIASYAANEEDFGSDDSMASDASSGPSYQQYYHGRTNKKEKKSSGEKNTKRKPVEEDDAECSSCGDDNDAKSKKRVTYQTSHCKESHGKKDKKQSTNKNN", "metadata": {"id": "A0A6P3Z591", "cluster": 26792318, "interpro_all": ["IPR044670"], "interpro_used": ["IPR044670"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Generate an amino acid sequence for a protein that will have the following function: The protein is assigned to 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 originates from Geodia barretti (Barrett's horny sponge).", "tokenized_instruction": [2, 5655, 1925, 3835, 2687, 3244, 1958, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 6304, 1942, 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, 22970, 2037, 14136, 7408, 1019, 24101, 1033, 12, 24101, 11, 61, 15579, 1012, 19757, 13, 18, 3], "output": "MGPTEVQYQHWISEVLISSGSTWTTVTSVGDGGSLMLLLHSFPEFWFSWRHQLKAFCKDYHVAVDMRGYGDMDQPVGSSEYSLNHLT", "metadata": {"id": "A0AA35QWG2", "cluster": 28973604, "interpro_all": ["IPR029058"], "interpro_used": ["IPR029058"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to build a protein that will have the following function: The protein is grouped in the Bacterial/plant glycogen synthase family, which comprises enzymes responsible for the elongation of linear glycogen and starch chains in bacteria and plants. These proteins catalyze the transfer of a glucosyl moiety from an activated donor, such as UDP-glucose or ADP-glucose, to the nonreducing end of a preexisting alpha(1->4) glucan primer. Moreover, the protein should feature a Starch synthase, catalytic domain domain that catalyzes the synthesis of glycogen or starch in bacteria and plants using ADP-glucose as the glucose donor. This enzymatic region is distinct from animal glycogen synthases, which utilize UDP-glucose, and is responsible for polysaccharide chain elongation. Furthermore, 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 produced by Paenibacillus terrae and is associated with UniProt keywords Glycogen biosynthesis and Glycosyltransferase.", "tokenized_instruction": [2, 51, 12914, 1942, 10071, 43, 2213, 1988, 2832, 2162, 1920, 2894, 2347, 30, 1920, 2213, 1977, 10809, 1922, 1920, 4543, 19, 4496, 13302, 8921, 3416, 16, 2154, 12936, 5038, 5061, 1958, 1920, 9971, 1927, 4258, 13302, 1930, 12912, 7835, 1922, 4802, 1930, 4793, 18, 2144, 2697, 18170, 1920, 3856, 1927, 43, 3351, 11731, 11804, 2037, 1925, 4128, 6282, 16, 2427, 1966, 18500, 17, 3817, 2014, 9828, 17, 3817, 16, 1942, 1920, 28309, 2219, 1941, 2482, 1927, 43, 21604, 4595, 12, 21, 17, 34, 24, 13, 18798, 6194, 18, 3950, 16, 1920, 2213, 3066, 5961, 43, 12912, 8921, 16, 6804, 3418, 3418, 1988, 17097, 1920, 4271, 1927, 13302, 2014, 12912, 1922, 4802, 1930, 4793, 2193, 9828, 17, 3817, 1966, 1920, 3817, 6282, 18, 2052, 8145, 3031, 1977, 4493, 2037, 4027, 13302, 8921, 1036, 16, 2154, 12561, 18500, 17, 3817, 16, 1930, 1977, 5061, 1958, 17167, 4659, 9971, 18, 3677, 16, 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, 4152, 2007, 25726, 8635, 7972, 10401, 5277, 1036, 11420, 3336, 1930, 1977, 2458, 1956, 20709, 11569, 13302, 8132, 1930, 20067, 9961, 18, 3], "output": "MNILFAAAEAHPFIKTGGLADVIGALPKALRQAACDVRIILPKYTGIPDTYKKSLRPVTVKHVSVGWRDQYCGVEELTLDGIKVYFIDNEYYFGRDGIYGYMDDGERFSFFNRAILEVLPDLNFQPDILHCHDWHTAMVPLLLNANYRHLPFYVDIRTVFTIHNLLYQGDFPYEVLTELLNLDSSYFTPEGVEYHGRLNFMKGGLTYSDHVTTVSPTYAEEIQTEFYGYGLEGLLRKLGAQGRLSGIVNGIDIKSYNPATDHRIYTKYRTSLAKKKENKIGLQKELGLPVRPDVPLIAMVTRLVDMKGLNLVTRVLDEIMYDDDIQFVVLGTGDPAFEHWFREAAGRYPLKMSAQLGFNEPLSRKIYAASDMYLMPSRFEPCGISQLLALRYGSIPIVRETGGLNDTVHAYNESTGEGNGFSFKNYNAHDMLHTIRRAVDFYRQPEHWSKLTSTAFAGEYSWDVSAGAYLDIYRSLTGNE", "metadata": {"id": "A0A4U2PQT8", "cluster": 27957297, "interpro_all": ["IPR001296", "IPR011835", "IPR013534"], "interpro_used": ["IPR011835", "IPR013534", "IPR001296"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "For a newly designed protein, its function is dictated by the following:\nThe protein should feature a Mur ligase, C-terminal domain that facilitates the sequential addition of amino acids to UDP-N-acetylmuramic acid during bacterial peptidoglycan biosynthesis. Adopting a dihydrofolate reductase-like fold, this domain is responsible for binding the incoming amino acid substrate in enzymes such as MurC, MurD, MurE, and MurF, as well as in folylpolyglutamate synthase and cyanophycin synthetase. Also, the protein includes a Mur ligase, central domain that functions as the ATP-binding catalytic module in the MurC, MurD, MurE, and MurF enzymes responsible for the stepwise assembly of the bacterial peptidoglycan stem peptide. This domain shares structural similarity with ATPase domains and is also present in folylpolyglutamate synthetase and cyanophycin synthetase, where it drives ATP-dependent ligation reactions for folate metabolism and cyanophycin storage. Furthermore, the protein can be placed in the UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase family, which catalyzes the ATP-dependent addition of meso-diaminopimelate (or L-lysine in some species) to the UDP-N-acetylmuramoyl-L-alanyl-D-glutamate precursor during the biosynthesis of bacterial peptidoglycan. Also known as MurE, these enzymes typically feature a three-domain structure comprising an N-terminal substrate-binding domain, a central ATP-binding domain, and a C-terminal domain responsible for binding the incoming amino acid. It is native to Oscillospiraceae bacterium and carries UniProt keyword assignments Peptidoglycan synthesis, Cell division, and Cell cycle.\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, 5961, 43, 6185, 11905, 16, 45, 17, 4262, 3418, 1988, 11374, 1920, 9454, 2459, 1927, 3835, 4576, 1942, 18500, 17, 56, 17, 6894, 23010, 29085, 1935, 2687, 2409, 4543, 24183, 8132, 18, 20478, 43, 11842, 27851, 11386, 17, 3189, 3728, 16, 2052, 3418, 1977, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 4510, 1922, 5038, 2427, 1966, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 16, 1966, 2486, 1966, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 8921, 1930, 26898, 25818, 3665, 18185, 18, 2222, 16, 1920, 2213, 5921, 43, 6185, 11905, 16, 4101, 3418, 1988, 4088, 1966, 1920, 4498, 17, 2743, 6804, 9059, 1922, 1920, 6185, 1030, 16, 6185, 1007, 16, 6185, 1021, 16, 1930, 6185, 1038, 5038, 5061, 1958, 1920, 13846, 5957, 1927, 1920, 4543, 24183, 4402, 4207, 18, 2052, 3418, 16495, 4346, 6796, 1956, 9444, 4682, 1930, 1977, 2222, 2481, 1922, 17802, 2199, 13811, 4121, 26697, 21084, 18185, 1930, 26898, 25818, 3665, 18185, 16, 2597, 2176, 15435, 4498, 17, 3100, 11102, 5298, 1958, 13761, 4714, 1930, 26898, 25818, 3665, 7451, 18, 3677, 16, 1920, 2213, 2112, 1998, 5396, 1922, 1920, 18500, 17, 56, 17, 6894, 23010, 29085, 10921, 8056, 16323, 1024, 17, 46, 17, 7627, 17, 22, 16, 26, 17, 21121, 2011, 11593, 5148, 2057, 11905, 3416, 16, 2154, 17097, 1920, 4498, 17, 3100, 2459, 1927, 23577, 17, 21121, 2011, 11593, 5148, 2057, 12, 2014, 54, 17, 9082, 1922, 2673, 3038, 13, 1942, 1920, 18500, 17, 56, 17, 6894, 23010, 29085, 10921, 17, 54, 17, 10527, 16323, 1024, 17, 46, 17, 7627, 7897, 2409, 1920, 8132, 1927, 4543, 24183, 18, 2222, 3171, 1966, 6185, 1021, 16, 2144, 5038, 5745, 5961, 43, 2559, 17, 3418, 3170, 10351, 1925, 56, 17, 4262, 4510, 17, 2743, 3418, 16, 43, 4101, 4498, 17, 2743, 3418, 16, 1930, 43, 45, 17, 4262, 3418, 5061, 1958, 2743, 1920, 22201, 3835, 2687, 18, 2176, 1977, 6196, 1942, 7799, 3106, 11979, 1972, 3336, 14061, 1930, 16252, 20709, 11121, 2538, 18306, 24183, 4271, 16, 2024, 8451, 16, 1930, 2024, 4048, 18, 5660, 1920, 17476, 3835, 4576, 1942, 20809, 2052, 18, 3], "output": "MKLIDILNNIEYKCNNFQPNFEISDDSHDFAGELYNKGVRVFAVQQDISLPDDAVEKLNTIAITGTKGKTSVSFMLKSVYEAAGHKVGVIGSTGTYIGDKEYETADTAIIEATSQGFKMDRTYGIEFNTGIFTNLSPDHIGDQCKKVIINADSDNYDEIINGIDYSFGNGEFHVGDNKLTTQFTFAEDNIAACARRDGLSYNEIKQGLSKAFVKGRMKTLFDTIKLYNPKRIISVFGCGGNRSKRFEKIEDIISDILIGMHKTDGKYEIIPNRRDAIKYEEIEGVQYPFDEREVVFTSLRELEQQGDLIIFDSRKAITPSDMFVCLKGFTFKIVVDDTRKFLALSSANFFGRPANSTPESYLLHKYYKEMLDAGCGNEHKDFEEYLNCKKMIFTCPLITVSEDSLKNPSAEIDLKTPGRFSLCNAALAEIVPIEKDYTVIIDFAHNEFSVLRRYGMGEVIGANSDLSIITSDNSEALRIASKGDIVLLIGKGHEM", "metadata": {"id": "A0A928IWY3", "cluster": 2213526, "interpro_all": ["IPR036565", "IPR004101", "IPR036615", "IPR013221", "IPR035911", "IPR005761"], "interpro_used": ["IPR004101", "IPR013221", "IPR005761"], "interpro_unused": ["IPR036615", "IPR035911", "IPR036565"]}, "task_type": "infilling"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: 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. Additionally, the protein includes a HYDIN/VesB/CFA65-like immunoglobulin-like domain that stabilizes associated protease domains, co-defines substrate specificity, and may facilitate bacterial surface binding or secretion. This structural module is found C-terminal to the catalytic domain in the *Vibrio cholerae* serine protease VesB, as well as in eukaryotic proteins such as HYDIN. It is found in Pontibacter qinzhouensis and is described by UniProt keywords Cell projection, Cilium, and Cytoplasm.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 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, 4950, 16, 1920, 2213, 5921, 43, 2993, 1921, 19, 5634, 1014, 19, 18456, 5964, 17, 3189, 11837, 17, 3189, 3418, 1988, 19658, 2458, 7154, 4682, 16, 2081, 17, 16737, 4510, 4896, 16, 1930, 2278, 6628, 4543, 3154, 2743, 2014, 5512, 18, 2052, 4346, 9059, 1977, 2435, 45, 17, 4262, 1942, 1920, 6804, 3418, 1922, 1920, 14, 23280, 22105, 14, 8468, 7154, 5634, 1014, 16, 1966, 2486, 1966, 1922, 10825, 2697, 2427, 1966, 2993, 1921, 18, 2176, 1977, 2435, 1922, 15065, 4397, 2422, 8165, 1022, 19902, 8134, 1930, 1977, 2910, 2007, 20709, 11569, 2024, 11244, 16, 28997, 16, 1930, 5239, 18, 3], "output": "MYLSEERTYSFGAVRVLEQGTPVPFTLTNVLGTMPAKLAPGAQVTFTITFKPAAGGPRFAELLLETTITNLEDIVLKASAAPFQLNAKTNSTASHVKIIKGGYVTIKANVEENDLYKAAFRLIVLTMGLQDLHLTGTPAATITGRDPGDFSLDPTSDEESPLVIKLGGQGTRLPVTYSVVAGNGQVELSGENN", "metadata": {"id": "A0A5C8KDP8", "cluster": 820603, "interpro_all": ["IPR053879", "IPR013783"], "interpro_used": ["IPR013783", "IPR053879"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "The protein exhibits the following characteristics:\nThe protein possesses a BED-type zinc finger domain that serves as a DNA-binding module in cellular regulatory factors and transposases found in animals, plants, and fungi. Characterized by conserved aromatic positions and a zinc-coordinating cysteine/histidine motif, it plays key roles in processes such as chromatin insulation and transcriptional regulation. Also, the protein carries a Hermes transposase DNA-binding domain that confers specific DNA-binding capabilities to the Hermes transposase. This domain enables the recognition of specific DNA sequences, facilitating the recruitment of the transposase to transposon ends during DNA transposition. Moreover, the protein carries a HAT C-terminal dimerisation domain that mediates the formation of extremely stable dimers at the C-terminus of transposases belonging to the Activator (hAT) superfamily. It is native to Musca domestica (House fly) and carries UniProt keyword assignments Metal-binding, Zinc-finger, and Nucleus.\nDeduce the missing amino acid spans from the masked sequence.", "tokenized_instruction": [2, 1920, 2213, 9826, 1920, 2894, 3779, 30, 1920, 2213, 14465, 43, 7497, 17, 2601, 7997, 8497, 3418, 1988, 10634, 1966, 43, 2678, 17, 2743, 9059, 1922, 3689, 4948, 2790, 1930, 12935, 2319, 2435, 1922, 3555, 16, 4793, 16, 1930, 10520, 18, 4378, 2007, 5305, 10761, 6490, 1930, 43, 7997, 17, 19355, 8666, 19, 13873, 5219, 16, 2176, 5705, 3834, 5456, 1922, 4028, 2427, 1966, 6338, 19151, 1929, 1930, 5224, 3640, 18, 2222, 16, 1920, 2213, 16252, 43, 19432, 1918, 12935, 2051, 2678, 17, 2743, 3418, 1988, 16556, 2487, 2678, 17, 2743, 13693, 1942, 1920, 19432, 1918, 12935, 2051, 18, 2052, 3418, 10217, 1920, 5708, 1927, 2487, 2678, 3709, 16, 12440, 1920, 6067, 1927, 1920, 12935, 2051, 1942, 18808, 9618, 2409, 2678, 22596, 18, 3950, 16, 1920, 2213, 16252, 43, 16133, 45, 17, 4262, 7632, 6284, 3418, 1988, 10412, 1920, 3337, 1927, 8113, 4700, 13351, 2019, 1920, 45, 17, 7822, 1927, 12935, 2319, 10588, 1942, 1920, 9518, 12, 16133, 13, 13975, 18, 2176, 1977, 6196, 1942, 7841, 1019, 11070, 1019, 12, 5953, 11716, 13, 1930, 16252, 20709, 11121, 2538, 18306, 6048, 17, 2743, 16, 7997, 17, 8497, 16, 1930, 5607, 18, 11481, 3005, 1920, 6814, 3835, 2687, 23658, 2037, 1920, 17476, 3244, 18, 3], "output": "MSKNEAIENSCNVDISMDEDRLFLIKAKLDHLGDEISPNLVACRFCHSVLKYTTRTTSNLVRHKCYIAKMKNPTNDDFLKEKASFTSIFTKIRKGEFKIGNITGRNLVACRICNHIYKFNGRSTSNLVKHKCYIRKLKENAFASAEEEESEFNVDASLTEDTCFSEEKSQFNADASLTEDTCFSEDDPLNNNNNEYVADPFNYSAIKCKLLNGELKINNREGLVACRICYKIYKSNKRSTSNLVKHKCYMEIEENSAKDNNENDRVDSPTDFPEIDSLLGIKSKILSGEYKISCKQGRSNVSKLVVCRICYNIYKYNLSSTSNLVKHKCYLKQAEENNASIETEWSIENCRSFKMVEDAGFKKLVEFLISLGATYGKCLDVIKSEISSIKDIGFGLTADIWSDTYLNQSFRRLLGINVINGKACTKQNIIVKAKRLLNYFNTYNHITCMTRLIQDAIQNVCGNVPAVNTLYKNCVNIVKHLSGDTVYAMFSFVGKNWQEISQHNHKDNEIVEISQININEESNATLHLVIVYIHRLRKLCAVEPKDLEIIKELKAKLLKYFDSSIMPNDTVERERIKSECKKIMETYLEEDLATNEEIDGDNNASTSAEIEMYEGIQIKFSDNFNVLQWWHQNKNTFPLLYKTSCKVLNVSINNIMFLHCNLENFDLETFFINENNVESSGEYNLSPKRKNAYVWCIFGKVENEGALTKEAVGKKCAKPDGNEPKTGSNVWHIFGTIENRYNEQLHPGSGEEEKSEGYIKKLRENAFAEELNTEIKTEKEELLTTFTEENMEERSNVWTIFGNVEDPRGQELYTDSYRCELSIENARSLAGSWNIFGKIQNELGQELYVSADFKQEAVRIFQLDINSVLPNITTISGKIDDIYTTFLIFTMHYVRYGSLCDLEKYAVIVTDKEINMTTAFAGKFQQSTPIKSFMENFYTTINDILNIFEPFQDALKVLQDVTTIHKIALFLFPPANKLIQYKDDIFSDFIAQPDKTQNISAVDHAAPASMAYSKDIISLARNFIADKKYIIHHK", "metadata": {"id": "A0A1I8NKX5", "cluster": 5400721, "interpro_all": ["IPR008906", "IPR018473", "IPR012337", "IPR003656", "IPR052035", "IPR036236"], "interpro_used": ["IPR003656", "IPR018473", "IPR008906"], "interpro_unused": ["IPR012337", "IPR036236", "IPR052035"]}, "task_type": "infilling"} {"instruction": "Generate a protein according to these design specifications: The protein belongs to 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 has 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 produced by Luteibaculum oceani and has UniProt annotations TPR repeat.", "tokenized_instruction": [2, 5655, 43, 2213, 3147, 1942, 2144, 3036, 22437, 30, 1920, 2213, 14440, 1942, 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, 2258, 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, 4152, 2007, 12867, 26073, 18021, 5277, 1035, 13563, 1033, 1930, 2258, 20709, 15010, 22288, 6865, 18, 3], "output": "MRILSFLSTSLLVITLNAQKLPQYVNGKEAYKQILNEEIQFPQVNLKTLECGYISTIFHVDVNGEIDSVFYRNTGLNNAFDEKVQAFASKIEKFNSFKGKNGKASSYFVFQPVGFLFSDKVCPSWNKLSSDSNWVHKDSVFYYPEHNIYRDSRNISNIIFRDKGLELVNDGKYKEAISYFEEGMAFEPENDFYPYNLGICYYHIRKIDKACEYLKTAKKMGNKYAKSVYKEKCNF", "metadata": {"id": "A0A5C6UUE4", "cluster": 5556839, "interpro_all": ["IPR011990", "IPR019734"], "interpro_used": ["IPR011990", "IPR019734"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nIt is part of the Small GTPase family, which constitutes a superfamily of regulatory GTP hydrolases that function as molecular switches by cycling between active GTP-bound and inactive GDP-bound states. These proteins share a conserved 20kDa catalytic domain featuring distinct loop regions, including Switch I and II, which mediate conformational changes essential for interaction with downstream effectors. They play critical roles in diverse cellular activities such as signal transduction, cytoskeletal reorganization, nucleocytoplasmic transport, and vesicular trafficking. Additionally, 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 produced by Hydra vulgaris (Hydra) (Hydra attenuata).\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, 2858, 14809, 3416, 16, 2154, 14879, 43, 13975, 1927, 4948, 9319, 30337, 1988, 2347, 1966, 3272, 21529, 2007, 11061, 2192, 3500, 9319, 17, 4124, 1930, 9078, 15217, 17, 4124, 4376, 18, 2144, 2697, 7948, 43, 5305, 2036, 30493, 6804, 3418, 29931, 4493, 5881, 3451, 16, 2710, 6195, 51, 1930, 2890, 16, 2154, 8265, 8523, 2840, 4415, 1958, 2835, 1956, 5863, 13066, 18, 2611, 3918, 4140, 5456, 1922, 6445, 3689, 4209, 2427, 1966, 2733, 8201, 16, 14787, 18062, 16, 2797, 3107, 11302, 4860, 16, 1930, 16168, 9604, 18, 4950, 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, 4152, 2007, 22420, 22621, 12, 22420, 13, 12, 22420, 5693, 5499, 13, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MSKEDIVSKTVSEPVVRFAIVGAPKVGKSAISVRFREIFFGDDHITYELKDTANEVDVLSFMLAEDILKLIDSHLSKDSNEGKNMLCYALGKSLAKLYHAGFWEMSAADNYESTYGPIRPQNINKTRNVDDFRNNTKSVLNQQNSKTDGFKKNSLGYLLLENFAMNDLAFAMANVPDSSSIKRERLAKPIRKLGVNQIAFENRDNEKDQPTKDAKANQENIPDLVQKTNSQTISSSISTVILKTTNSAPVSQINLPFVTQTNMKNLYNKRYSFGPEYDLCRIFKGRSEKKSTRMKISAIFKQANLLTRRYISEYQPGVENNYVSHISWATCIAVVYSIDDRLISNKNDLDHLRVVTSDEAMIVEAFFSTTNKPINPVKKISLDNSNTYLKKSRKSQDAHKTDDHKETEKSRKEKFRISDTDSLDSNSSKLNLNNKITETNLNSIAIPQTKSTSAQQANSIPLSQTMSMNNDNSPLANWNALM", "metadata": {"id": "A0A8B6XNL2", "cluster": 10565063, "interpro_all": ["IPR027417", "IPR051065", "IPR001806"], "interpro_used": ["IPR001806", "IPR027417"], "interpro_unused": ["IPR051065"]}, "task_type": "infilling"} {"instruction": "A protein has the following role:\nThe 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. Additionally, it is part of 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 uncultured Caudovirales phage.\nComplete the masked structural regions.", "tokenized_instruction": [2, 43, 2213, 2258, 1920, 2894, 2770, 30, 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, 4950, 16, 2176, 1977, 3131, 1927, 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, 5269, 21058, 10268, 20165, 1918, 10503, 18, 4080, 1920, 17476, 4346, 3451, 18, 3], "output": "MRASEFIVEYKLSVSKDTDGVAVKATAGGKNLRLDPQTVWVDERYHGQGIARDMYDHLKELGYTITVWETEQTPAEKFIADIYDEYPQTFQNNHMFELKPSTSRRGAVEVYWFQAYPLRSGVGSRAMQVLQDSQAALTKFYRRQGFKPIMKGGRSLSWEPLEEISRDRLERYARARQRLNTSYEIYHADEPTKIVDRERYESDVDYDLRLRRGTGIMEFAEGIRAYHGNQFTDSREGAEYYAGDDGYVVVVDLDVKNPYIIKAQGYDGIYDRRLGDWIPFSRKQIRVISKDDTFMGENFADGKVKGKSVTDLRRKAKAASGEKAKMYHWCANMKSGRKKNKGHAEFFFDEQGVRSWDQTDAGRGFWNKHRGEDAVMPFGSEEFARAREHGVALTLVPWDKGQVLSRAGRQVDTRQERMFEADTPADAQRYYQDYIGGIDTEQLHAPMWGQEEANSVLRRWQELQASRPGRVKRAGASCNG", "metadata": {"id": "A0A6J5LVI6", "cluster": 15208106, "interpro_all": ["IPR016181", "IPR000182"], "interpro_used": ["IPR000182", "IPR016181"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "We aim to build a protein that does the following:\nThe protein carries a Short-chain dehydrogenase/reductase conserved site that characterizes the catalytic core of NAD- or NADP-dependent oxidoreductases. This region features two perfectly conserved residues, a lysine and a tyrosine, with the tyrosine directly participating in the catalytic mechanism. Additionally, the protein can be placed 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 is present in Branchiostoma floridae (Florida lancelet) (Amphioxus).\nWhat sequences should replace the masked placeholders?", "tokenized_instruction": [2, 2038, 3774, 1942, 10071, 43, 2213, 1988, 3731, 1920, 2894, 30, 1920, 2213, 16252, 43, 3662, 17, 4659, 9294, 19, 11386, 5305, 3200, 1988, 26735, 1920, 6804, 4728, 1927, 6577, 17, 2014, 24221, 17, 3100, 27388, 1036, 18, 2052, 3031, 4075, 2288, 19981, 5305, 4248, 16, 43, 9082, 1930, 43, 6941, 16, 1956, 1920, 6941, 4103, 9505, 1922, 1920, 6804, 2856, 18, 4950, 16, 1920, 2213, 2112, 1998, 5396, 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, 1977, 2481, 1922, 6089, 14356, 4575, 3368, 19386, 1021, 12, 19386, 26448, 5484, 13, 12, 9141, 3940, 1039, 1957, 13, 18, 4663, 3709, 3066, 14732, 1920, 17476, 4368, 14658, 35, 3], "output": "TGCDSGFGFGLAKRLDSLGFTVFAGCLLADSGGVQAAVRQVKDRLPTGSKGLYALVNNAMAAYRRVMEVNTFGTVRVTKAFLPLVRRAKGRVVNISTKAAMEFFSDALRHEMHKWGVKVVIVENNVEDVVKEDYGMEYFDFKMEQLRLYEGSKKLRAECSSRLSTVQIDVTDDGQGVWQPGEIEWVSSVGGLCAGPLAAGYSMPSSFARATDIVLPAVYKKFAEDLR", "metadata": {"id": "C3ZEQ2", "cluster": 16757419, "interpro_all": ["IPR036291", "IPR020904", "IPR002347"], "interpro_used": ["IPR020904", "IPR036291"], "interpro_unused": ["IPR002347"]}, "task_type": "infilling"} {"instruction": "The desired role of my protein is: The protein is grouped in the Large ribosomal subunit protein uL4-like family, which encompasses bacterial uL4 and eukaryotic uL4c/m proteins integral to the large ribosomal subunit. These proteins typically feature a globular surface domain with finger-like projections that extend into the rRNA core to organize and stabilize its tertiary structure during mRNA-directed protein synthesis. It originates from candidate division WWE3 bacterium GW2011_GWF1_42_14 and is described by UniProt keywords Ribonucleoprotein, Ribosomal protein, and rRNA-binding. Please design the protein's amino acid sequence.", "tokenized_instruction": [2, 1920, 9465, 2770, 1927, 3057, 2213, 1977, 30, 1920, 2213, 1977, 10809, 1922, 1920, 3103, 11196, 5903, 2213, 3570, 1006, 17, 3189, 3416, 16, 2154, 21569, 4543, 3570, 1006, 1930, 10825, 3570, 25077, 19, 55, 2697, 12328, 1942, 1920, 3103, 11196, 5903, 18, 2144, 2697, 5745, 5961, 43, 20975, 3154, 3418, 1956, 8497, 17, 3189, 11512, 1988, 9676, 2460, 1920, 9067, 4728, 1942, 25681, 1930, 13448, 2496, 10832, 3170, 2409, 3616, 17, 6554, 2213, 4271, 18, 2176, 22970, 2037, 6610, 8451, 6010, 24336, 14061, 8997, 23437, 1009, 41, 8997, 5739, 41, 3858, 41, 2607, 1930, 1977, 2910, 2007, 20709, 11569, 18347, 6657, 16, 11196, 2213, 16, 1930, 9067, 17, 2743, 18, 11586, 3036, 1920, 2213, 11, 61, 3835, 2687, 3244, 18, 3], "output": "MKKQVLDKKGNKVEEITLHDEVFKAEPNNNVLVQYIRVYTTNQRTGTSKVKNKAEVAGGGAKPWRQKGTGRARAGSSRSPIWVHGGVTHGPLPKDWTLKLPKKMKKLAMRSALSLKEAADSLFVVNDFGVDKISTSAMSTAVKTLGLKGSVLYVWNKKDEKVMKSISNLTNIRAAYAGSLNPYDLISAKTVLFEKDAILDINERFKK", "metadata": {"id": "A0A0G1BPT4", "cluster": 16820637, "interpro_all": ["IPR002136", "IPR013005", "IPR023574"], "interpro_used": ["IPR013005"], "interpro_unused": ["IPR023574", "IPR002136"]}, "task_type": "autoregressive"} {"instruction": "Generate a protein's amino acid sequence that will be able to perform the following function: The protein can be placed in 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. Also, the protein belongs to the Polysaccharide Degradation Enzymes family, which comprises enzymes that hydrolyze specific glycosidic bonds to degrade complex polysaccharides, including unsaturated rhamnogalacturonan disaccharides and ulvan from green seaweed cell walls. These proteins preferentially cleave unsaturated 4-deoxy-L-threo-hex-4-enopyranosiduronic acid residues to facilitate complete polymer breakdown. Additionally, some members are implicated in regulating bacterial surface properties in response to the presence of plant cells. Moreover, the protein is included in the Glycosyl hydrolase, family 88 family, which functions as an unsaturated glucuronyl hydrolase responsible for the hydrolytic release of unsaturated glucuronic acids from oligosaccharides generated by polysaccharide lyases. It is expressed in Pelagibacterium sp. H642.", "tokenized_instruction": [2, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1988, 2832, 1998, 4236, 1942, 2385, 1920, 2894, 2347, 30, 1920, 2213, 2112, 1998, 5396, 1922, 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, 2222, 16, 1920, 2213, 14440, 1942, 1920, 17167, 4877, 5038, 3416, 16, 2154, 12936, 5038, 1988, 7222, 6931, 2487, 7533, 12546, 9031, 1942, 17069, 2796, 18686, 16, 2710, 19172, 23120, 27395, 10366, 1928, 2054, 11926, 1930, 3570, 25777, 2037, 4524, 19636, 3831, 2024, 12430, 18, 2144, 2697, 10662, 21252, 19172, 24, 17, 16333, 17, 54, 17, 6841, 1037, 17, 7142, 17, 24, 17, 2066, 18499, 27545, 10015, 26242, 2687, 4248, 1942, 6628, 4080, 4593, 13630, 18, 4950, 16, 2673, 4678, 2032, 6835, 1922, 6773, 4543, 3154, 3879, 1922, 2644, 1942, 1920, 2990, 1927, 4496, 2094, 18, 3950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 20067, 20748, 16, 3416, 5744, 3416, 16, 2154, 4088, 1966, 1925, 19172, 17102, 2199, 20748, 5061, 1958, 1920, 26702, 4012, 1927, 19172, 17102, 1935, 4576, 2037, 22012, 3999, 2007, 17167, 23928, 1036, 18, 2176, 1977, 3198, 1922, 7874, 29284, 7972, 2341, 18842, 1989, 2056, 18, 26841, 6852, 18, 3], "output": "MKLDTFFDTFAEQYQHYKRGDWCYEDGCIYRGLLLLDGVDPRGPWFGHLKRLVDSQVGNDGSLAGYDIEEFNIDNILSGRALIALHVRTGEKKYRLAAERLAEQLERHPRIGRGNYWHKLRYPYQVWLDGLYMGLPFQIEYGKAFGKPELVDDAIVQLKSALELLADPATGLYSHGYDEAREQRWADKRTGRSQALWSRALGWLAMALVDVREAIGPELAAQAGLDEAIAVFAKRVARHQREDGRWNQVTDQPELEGNYPESSATAMFAYFFLVGERLGISGVDGEIGLKALAGLREHALAAGPDGEPVLGAICHVAGLGGFDGRYRDGTAAYYVSERLQPNDAKGVGPFMMAVAEARRRDRLGEAAVTENAGFPASARAGAPRG", "metadata": {"id": "A0AA51U0N4", "cluster": 18235785, "interpro_all": ["IPR008928", "IPR012341", "IPR010905", "IPR052043"], "interpro_used": ["IPR008928", "IPR052043", "IPR010905"], "interpro_unused": ["IPR012341"]}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to create: The protein is classified under the Bacterial polysaccharide biosynthesis and export family, which mediates the production, regulation, and transport of capsular and extracellular polysaccharides essential for bacterial virulence. Members function as autophosphorylating tyrosine-protein kinases, lipopolysaccharide chain-length determinants, or components of ATP-driven export complexes. These proteins coordinate the polymerization and translocation of polysaccharides across the inner membrane to the cell surface. It occurs in Gammaproteobacteria bacterium and corresponds to UniProt keyword Coiled coil 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, 5947, 2441, 1920, 4543, 17167, 8132, 1930, 12660, 3416, 16, 2154, 10412, 1920, 3372, 16, 3640, 16, 1930, 4860, 1927, 22590, 1930, 5329, 18686, 4415, 1958, 4543, 9304, 18, 4678, 2347, 1966, 20369, 2199, 2287, 6941, 17, 2213, 7784, 16, 15614, 4659, 17, 3471, 9873, 16, 2014, 4178, 1927, 4498, 17, 6446, 12660, 5048, 18, 2144, 2697, 11865, 1920, 11486, 1930, 7849, 1927, 18686, 3436, 1920, 6671, 3260, 1942, 1920, 2024, 3154, 18, 2176, 5110, 1922, 7034, 9218, 1021, 10296, 14061, 1930, 8852, 1942, 20709, 11121, 2538, 17524, 9121, 1930, 9117, 7864, 18, 11586, 3394, 1920, 3835, 2687, 3244, 1958, 2052, 13022, 4659, 18, 3], "output": "MSNITLDEMVPLVTREASARRKTLLTIFAVVALLFLLLAAFWQKQYESYAHIYVDDKSVVAPILDQAPTQERNQANIAKQELFSAEILDKIMLEVPFIDENTGDVERERIRNEIIESTNVQNMNNQLIRIEFQDPDPSVAYRTVELYSNLFLAKTMKTSSDETNEAFDFIIDQVETYRNKLEDADRRLESFRAQYPGLSETGTGRLNDRVLELERELEQTQLLYAQADQRRRSLQRELSSESTNLARQAQADQLRSRISALQGEIDSLRLSYTDDYPDIIRLKQQIGDLENQAANPTQSSGGFGATLNSPVYQQLRSDLAAASAEADSLRSKINQLSILKEKEVERSTDSGRVEREYAELTRDYTI", "metadata": {"id": "A0A952LM56", "cluster": 19013366, "interpro_all": ["IPR050445"], "interpro_used": ["IPR050445"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "I want to make a polypeptide chain that will have the following function description: It is part of the The Biotin--acetyl-CoA-carboxylase ligase family, which functions as a bifunctional enzyme and transcriptional repressor involved in the regulation of biotin synthesis. Members such as BirA contain an N-terminal helix-turn-helix DNA-binding domain and a central catalytic domain, utilizing the reaction intermediate biotinyl-5'-AMP as a co-repressor to trigger dimerization and specific DNA binding. Additionally, the protein features a Biotin protein ligase, C-terminal domain that adopts an SH3-like barrel fold and is typically associated with prokaryotic bifunctional transcriptional repressors and eukaryotic enzymes involved in biotin utilization. In addition, the protein should feature a Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain that catalyzes the post-translational covalent attachment of biotin or lipoic acid cofactors to specific lysine residues on dependent metabolic enzyme complexes. This module mediates cofactor transfer from an adenylate intermediate to target proteins such as alpha-ketoacid dehydrogenases, utilizing a structure composed of a mixed beta-sheet and alpha-helices with a strictly conserved catalytic lysine. It has been characterized in Thioploca ingrica. 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, 1920, 8622, 17, 17, 6894, 17, 10027, 17, 29073, 11905, 3416, 16, 2154, 4088, 1966, 43, 29491, 4113, 1930, 5224, 14434, 3286, 1922, 1920, 3640, 1927, 8622, 4271, 18, 4678, 2427, 1966, 4349, 1019, 5531, 1925, 56, 17, 4262, 7864, 17, 5165, 17, 7864, 2678, 17, 2743, 3418, 1930, 43, 4101, 6804, 3418, 16, 10232, 1920, 3227, 6129, 8622, 2199, 17, 25, 11, 17, 3681, 1966, 43, 2081, 17, 14434, 1942, 6086, 13640, 1930, 2487, 2678, 2743, 18, 4950, 16, 1920, 2213, 4075, 43, 8622, 2213, 11905, 16, 45, 17, 4262, 3418, 1988, 24032, 1925, 18824, 17, 3189, 19560, 3728, 1930, 1977, 5745, 2458, 1956, 21545, 29491, 5224, 26446, 1930, 10825, 5038, 3286, 1922, 8622, 8422, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 8622, 2199, 2213, 11905, 12, 4149, 1024, 13, 1930, 3178, 10921, 2213, 11905, 12, 20880, 13, 6804, 3418, 1988, 17097, 1920, 2753, 17, 8414, 13577, 8576, 1927, 8622, 2014, 3178, 8643, 2687, 21362, 1942, 2487, 9082, 4248, 1990, 3100, 4487, 4113, 5048, 18, 2052, 9059, 10412, 15155, 3856, 2037, 1925, 23052, 6129, 1942, 2758, 2697, 2427, 1966, 4595, 17, 21471, 29272, 9294, 1036, 16, 10232, 43, 3170, 7179, 1927, 43, 4985, 4666, 17, 11130, 1930, 4595, 17, 12789, 1956, 43, 14470, 5305, 6804, 9082, 18, 2176, 2258, 2252, 4378, 1922, 15331, 2030, 21259, 13568, 6102, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MFHRILQVLADGQPHTVQELTSKLAISPTKLDDFIKTLITYGIKFSSLGASTYQLSENLELLEYSCLWVQLPEYTRQQIAHLEILDVVDSTNHYVLTPEKQRVPLICLAEYQTAGRGRQGRQWISPYASGLCLSIKQGYTRFNHSLGGLGIALAITVVRLLQAMGAQEIGLKWPNDILWRNRKLAGLLLETRIRNHRYEIVVGIGINVKMPVVELKTIEQPWVDLQTVLGQPISRNTLAAMLIEHCLQTLASYSQDGLTTFISDWYHFDLLYGQLVILENSTFDGHSVTEKTKRKSVIVTGKACGIDEQGALLLQIGDCKQRYFYGEARIQV", "metadata": {"id": "A0A090APJ0", "cluster": 19969296, "interpro_all": ["IPR045864", "IPR004408", "IPR003142", "IPR004143", "IPR008988", "IPR036388"], "interpro_used": ["IPR004408", "IPR003142", "IPR004143"], "interpro_unused": ["IPR036388", "IPR008988", "IPR045864"]}, "task_type": "autoregressive"} {"instruction": "The target protein must perform this role:\nIt 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. Also, the protein includes 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 has been characterized in Ignavibacteria bacterium GWC2_36_12 and carries UniProt keyword assignments TPR repeat.\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, 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, 5921, 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, 2258, 2252, 4378, 1922, 12046, 9188, 7972, 2341, 18339, 14061, 8997, 8054, 41, 3480, 41, 2369, 1930, 16252, 20709, 11121, 2538, 18306, 22288, 6865, 18, 5660, 1920, 3835, 4576, 1988, 6784, 1922, 1920, 17476, 4368, 14658, 18, 3], "output": "MQLLKTKSYLILFLSLFFQSCGLWDSFTTYFNLYYNASDFLIVPNSANQQFGKVIEKCSQILQFHPDGSYVDDALLMLGKSFYYQKNYQKGFWIGKTEMRLRNYESALQTLGTVRGQALADGREDILKDSFVEEIVYRISLITSSDDETIKAEVLYEMGKLYIKVNESQNAISAYNEVFEYSPSYEIEVGTKLELIFEIMRSENKFSDVYDQVDLETGITLIELNRLDEALDKLEYVDTAYVATKTSGVSYYQKASISQAPQEYILESGEKARIFKKYQNLTLQVNNYMDELFYVENPEEFTKDSIKYLAELNLYTEHLESLASFDTLSNRTDTTATDTTTTDSTMNDSTAVKDSTDDKLRVDQINIDSLFAERWEKDRVFPKKPVKSELSTDSLKSLLVKNKLELGNLFLTELELPDSAYYDYLNILSYYLTVNQETKADSLFNVIYERYKDQRIANAAANKLNKPLIDFDYDPAKDLYVEAESELLAPKALYASGWILENELSLYDSAAIVYDTMSVRYPQSEYSLKVRPKLTSYKLYKKAVEDSLQKEQVSPGTDKPLLPTEEDKVRKTNVDNTETVQSDTLHRGILNDPRRNPRRRFEQGEQAIREQKRDLFATGERKFQELIATQPESDLILETRLREDYQVAIGLSKQGKVLRTTGENEKALEAKYKLGELYQYNFQNFDSAAVQDSVTYVQDSLKVESLVLRNRNSRESSNVSEDYPNTSLHATVLYALGSNKDYESSIYKFYMLYKDFPQSLLLKRIDQEKFLADSLAVVSDS", "metadata": {"id": "A0A1G0QVR3", "cluster": 20904022, "interpro_all": ["IPR011990", "IPR019734"], "interpro_used": ["IPR011990", "IPR019734"], "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 Protein of unknown function DUF5960 family, which is found within biosynthetic gene clusters involved in the production of ribosomally synthesised and post-translationally modified peptides (RiPPs). It is native to Enterococcus aquimarinus.", "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, 2213, 1927, 5435, 2347, 4855, 17968, 10352, 1008, 3416, 16, 2154, 1977, 2435, 2651, 14041, 2359, 5859, 3286, 1922, 1920, 3372, 1927, 11196, 1954, 4271, 1919, 1930, 2753, 17, 8414, 1954, 4795, 5320, 12, 8936, 2523, 13, 18, 2176, 1977, 6196, 1942, 25390, 10059, 12874, 5572, 1957, 18, 3], "output": "MSDDLFGVVVDGRKLLFKYGESYNRFTDEYYHYVKSNTPVCFIENDLLKLMYKNGIDYFRVPKNKTLVGHDIAFVFKRSEENKITMFEFIEVQKY", "metadata": {"id": "A0A1L8QSX4", "cluster": 21944189, "interpro_all": ["IPR046004"], "interpro_used": ["IPR046004"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Generate a protein sequence that folds into a functional protein with the following function: The protein features a PPM-type phosphatase-like domain that catalyzes the Mg2+- or Mn2+-dependent dephosphorylation of phosphoserine and phosphothreonine residues. It functions as a versatile regulatory module in signaling pathways across prokaryotes and eukaryotes, controlling processes such as stress responses, metabolism, and sporulation by reversing the action of protein kinases. Additionally, the protein is assigned to the Protein phosphatase 2C family, which comprises monomeric serine/threonine specific protein phosphatases that require divalent cations, primarily magnesium or manganese, for catalytic activity. These enzymes exhibit broad substrate specificity and play roles in diverse signaling pathways, including the regulation of pyruvate dehydrogenase and receptor-like kinases. It is produced by Lactuca sativa (Garden lettuce).", "tokenized_instruction": [2, 5655, 43, 2213, 3244, 1988, 16231, 2460, 43, 3183, 2213, 1956, 1920, 2894, 2347, 30, 1920, 2213, 4075, 43, 8748, 17, 2601, 8167, 17, 3189, 3418, 1988, 17097, 1920, 14756, 15, 17, 2014, 26737, 15, 17, 3100, 16881, 1927, 8078, 26337, 1930, 8078, 5856, 1021, 12530, 4248, 18, 2176, 4088, 1966, 43, 20425, 4948, 9059, 1922, 3197, 3873, 3436, 28149, 1930, 15021, 16, 7138, 4028, 2427, 1966, 3071, 3387, 16, 4714, 16, 1930, 23647, 2007, 26526, 1920, 4615, 1927, 2213, 7784, 18, 4950, 16, 1920, 2213, 1977, 6304, 1942, 1920, 2213, 8167, 6921, 3416, 16, 2154, 12936, 14457, 8468, 19, 13143, 2487, 2213, 19131, 1988, 4350, 21610, 16525, 16, 5985, 13148, 2014, 19516, 16, 1958, 6804, 2455, 18, 2144, 5038, 5987, 4949, 4510, 4896, 1930, 3918, 5456, 1922, 6445, 3197, 3873, 16, 2710, 1920, 3640, 1927, 11867, 9294, 1930, 3148, 17, 3189, 7784, 18, 2176, 1977, 4152, 2007, 5641, 29394, 22939, 12, 26981, 23121, 3005, 13, 18, 3], "output": "MKIYGDSRVVLSRGGPTMHLSVDHKNELARIKISGGRVNDYNGLHVVGVLATSKSISDRQLKPYIIAKPKVIVNKRDDVAEFMILATNGLWDVISNDLECQVVRKCIDG", "metadata": {"id": "A0A9R1XKH7", "cluster": 22555052, "interpro_all": ["IPR015655", "IPR036457", "IPR001932"], "interpro_used": ["IPR001932", "IPR015655"], "interpro_unused": ["IPR036457"]}, "task_type": "autoregressive"} {"instruction": "Can you predict the missing sequence spans for a protein that performs the following role: 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 is a member of 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. In addition, 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. It is native to Planctomycetota bacterium.", "tokenized_instruction": [2, 2112, 6253, 5660, 1920, 6814, 3244, 23658, 1958, 43, 2213, 1988, 17436, 1920, 2894, 2770, 30, 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, 1977, 43, 7210, 1927, 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, 1922, 2459, 16, 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, 2176, 1977, 6196, 1942, 4720, 2341, 13386, 19446, 3857, 14061, 18, 3], "output": "MARILVVDDSATQRDMVQILLEEAGHTDLQMKEVDGLEVVRTVRENWPQIPVVLMTQYGSQEQLGRIVSELLEVVESRTKRDEMTAALRSVQRAEMEDQLHQLDCFDQASVFRIVLALKEALVNAIDHGNLELDSKLRELETVVYRLEPDAVSYTISDEGPGFDPSQIPDPRYFSERGNTITMVKQREHKPTAQLAPCVLQADDGKPALEIIHQQQPHLVITETIAAEALRLGASNFIPKKVLEFVIGNDPRQASRLVAFLNNEYHRLAEQRRIQPPYCDRKVDPENLVKASGRGLMLIQTFMDDV", "metadata": {"id": "A0A3M1VFM0", "cluster": 23089796, "interpro_all": ["IPR050595", "IPR011006", "IPR036890", "IPR001789"], "interpro_used": ["IPR011006", "IPR050595", "IPR001789"], "interpro_unused": ["IPR036890"]}, "task_type": "infilling"} {"instruction": "\"The protein should include a Myc-type, basic helix-loop-helix (bHLH) domain that functions as a sequence-specific transcription factor involved in cellular differentiation and proliferation. It utilizes two amphipathic helices separated by a loop to mediate homo- or heterodimerization, enabling the adjacent basic region to bind the E-box DNA motif (CANNTG). This domain is found in eukaryotic regulators like Myc and Max, where it modulates gene expression as an activator or repressor depending on the dimer composition. Moreover, the protein contains a Nuclear receptor coactivator 1-3 bHLH domain that acts as a transcriptional coactivator for steroid and nuclear receptors to mediate ligand-dependent gene activation. It facilitates responses to hormones and metabolites and is required to control energy balance between white and brown adipose tissues. Additionally, this domain participates in glucose metabolism regulation by modulating specific target gene expression. Additionally, the protein is included in the Nuclear receptor coactivator family, which functions as a ligand-dependent molecular switch to stimulate transcriptional activity through interaction with nuclear receptors, including those for steroids, retinoids, thyroid hormones, and prostanoids. These proteins play a central role in assembling multisubunit coactivator complexes that facilitate chromatin remodeling and the recruitment of general transcription factors. It is native to Austrofundulus limnaeus (Annual killifish).\"\nFill in the missing sequence spans for a protein designed to meet this specification.", "tokenized_instruction": [2, 6, 1920, 2213, 3066, 3951, 43, 5078, 17, 2601, 16, 5937, 7864, 17, 5881, 17, 7864, 12, 24735, 13, 3418, 1988, 4088, 1966, 43, 3244, 17, 2487, 3213, 2991, 3286, 1922, 3689, 4155, 1930, 4031, 18, 2176, 18127, 2288, 26747, 21494, 12789, 6239, 2007, 43, 5881, 1942, 8265, 16350, 17, 2014, 15672, 2466, 16, 12180, 1920, 6811, 5937, 3031, 1942, 4566, 1920, 47, 17, 5758, 2678, 5219, 12, 8734, 16960, 13, 18, 2052, 3418, 1977, 2435, 1922, 10825, 9098, 3189, 5078, 1930, 7531, 16, 2597, 2176, 13112, 2359, 2294, 1966, 1925, 9518, 2014, 14434, 6362, 1990, 1920, 7632, 5128, 18, 3950, 16, 1920, 2213, 5461, 43, 4254, 3148, 22706, 21, 17, 23, 24735, 3418, 1988, 8016, 1966, 43, 5224, 22706, 1958, 9507, 1930, 4254, 4086, 1942, 8265, 5207, 17, 3100, 2359, 2936, 18, 2176, 11374, 3387, 1942, 10224, 1930, 6926, 1930, 1977, 3414, 1942, 2285, 3844, 6766, 2192, 4511, 1930, 8084, 8564, 3878, 18, 4950, 16, 2052, 3418, 17241, 1922, 3817, 4714, 3640, 2007, 10871, 2487, 2758, 2359, 2294, 18, 4950, 16, 1920, 2213, 1977, 3063, 1922, 1920, 4254, 3148, 22706, 3416, 16, 2154, 4088, 1966, 43, 5207, 17, 3100, 3272, 6195, 1942, 9084, 5224, 2455, 2596, 2835, 1956, 4254, 4086, 16, 2710, 2690, 1958, 13039, 16, 26885, 1036, 16, 6918, 10224, 16, 1930, 4876, 9286, 3753, 18, 2144, 2697, 3918, 43, 4101, 2770, 1922, 26358, 13564, 2255, 1983, 1932, 22706, 5048, 1988, 6628, 6338, 8378, 1930, 1920, 6067, 1927, 3335, 3213, 2790, 18, 2176, 1977, 6196, 1942, 7162, 4199, 2652, 9605, 2784, 26243, 1957, 12, 7780, 11321, 1974, 2471, 13, 18, 6, 11928, 1922, 1920, 6814, 3244, 23658, 1958, 43, 2213, 4609, 1942, 9572, 2052, 14674, 18, 3], "output": "MSGLGENSMEPLSSENRKRKLSTCESKYIEELAELISANLSDIDSFNVKPDTPSSRITARATDGRGAGRYECARTDCLQVFTCSSTLLKLPHYDTPGLGCERKRREQKCAILKETVRQIRQIKEQGEWRSLSFGWGMAGRAGPASFCLIG", "metadata": {"id": "A0A2I4BE18", "cluster": 23245083, "interpro_all": ["IPR011598", "IPR056193", "IPR036638", "IPR017426"], "interpro_used": ["IPR011598", "IPR056193", "IPR017426"], "interpro_unused": ["IPR036638"]}, "task_type": "infilling"} {"instruction": "The protein is categorized in 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. Also, the protein carries a Outer membrane protein, beta-barrel domain that adopts a membrane-bound beta-barrel fold structure found in a diverse range of outer membrane proteins. It has been detected in Rhodobiaceae bacterium and is associated with UniProt keywords Signal. Generate a protein's amino acid sequence with this function.", "tokenized_instruction": [2, 1920, 2213, 1977, 10234, 1922, 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, 2222, 16, 1920, 2213, 16252, 43, 7642, 3260, 2213, 16, 4666, 17, 19560, 3418, 1988, 24032, 43, 3260, 17, 4124, 4666, 17, 19560, 3728, 3170, 2435, 1922, 43, 6445, 3109, 1927, 7642, 3260, 2697, 18, 2176, 2258, 2252, 3330, 1922, 11490, 18311, 1972, 3336, 14061, 1930, 1977, 2458, 1956, 20709, 11569, 2733, 18, 5655, 43, 2213, 11, 61, 3835, 2687, 3244, 1956, 2052, 2347, 18, 3], "output": "MKKFAILSIASLMTLSVAHAEQPTQYFAVGYKMMTLDSGVVELDMTGTQLTYGKRINEKFVIEGNMVTYLDADVLEVTSLDLSALYYPLNNQFHVRLGVSDGEVELEGLSADESSELLGVGYSWLVGSSSGVRLEYTTASYGDLDADGFTLSVAARF", "metadata": {"id": "A0A349J4W2", "cluster": 24136690, "interpro_all": ["IPR011250", "IPR027385"], "interpro_used": ["IPR011250", "IPR027385"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "Here is the functional description of a polypeptide chain I want to design: The protein is grouped in the Protein of unknown function DUF998 family, which comprises uncharacterized proteins with no currently defined biological function. It is derived from Serinibacter arcticus and has UniProt annotations Membrane, Transmembrane, 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, 1977, 10809, 1922, 1920, 2213, 1927, 5435, 2347, 4855, 1038, 26234, 3416, 16, 2154, 12936, 24528, 2697, 1956, 2239, 5077, 3608, 3933, 2347, 18, 2176, 1977, 3595, 2037, 2375, 11566, 7972, 2341, 1915, 23937, 1957, 1930, 2258, 20709, 15010, 3260, 16, 9117, 16, 1930, 9117, 7864, 18, 2112, 6253, 5655, 2496, 3244, 35, 3], "output": "MTSKRVGALLWILTLAYWPLQVLVAGRWPEPYSWSANYISDLGATLCGTVTDDGPARAVCSPEHEWWNIGLAFVGVLTALGAVLLSRGRRTAERVGLLLVMAGGLAVVVTAVVPFDVDTDVHDLAALAQFVLQILGMVVLAFTLRTRGRVAFAVVTLVMVLVAGAGFAAFLSEGHLGFGVGIVERVAFDTLTLWTVVAGLFLVGGRESGVRVRGSRR", "metadata": {"id": "A0A2U1ZXS5", "cluster": 26860147, "interpro_all": ["IPR009339"], "interpro_used": ["IPR009339"], "interpro_unused": []}, "task_type": "autoregressive"} {"instruction": "A polypeptide chain has masked sequences and the function is characterized by this:\nThe protein is classified under the NinB superfamily, which functions as a bacteriophage recombinase that participates in the early stages of genetic recombination by acting as a functional equivalent to the host RecFOR complex. It assists in loading the RecA strand exchange protein onto single-stranded DNA coated with ssDNA-binding proteins and typically exists as an intertwined dimer with unusual structural folds. It originates from Methylophilaceae phage P19250A.\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, 12117, 1014, 13975, 16, 2154, 4088, 1966, 43, 24613, 21366, 1988, 17241, 1922, 1920, 3120, 5143, 1927, 3299, 7827, 2007, 8290, 1966, 43, 3183, 6582, 1942, 1920, 4423, 2090, 8467, 2796, 18, 2176, 6589, 1036, 1922, 6693, 1920, 21534, 5984, 6818, 2213, 6131, 2957, 17, 10338, 2678, 7242, 1956, 15063, 17, 2743, 2697, 1930, 5745, 8655, 1966, 1925, 27332, 17860, 1919, 7632, 1956, 12236, 4346, 16231, 18, 2176, 22970, 2037, 4963, 7766, 1972, 3336, 10503, 23969, 28498, 1019, 18, 6510, 1024, 1920, 5550, 3835, 4576, 18, 3], "output": "MEANKFLWGRLYKVHLLCGHLFLTEQKTINGQQIESYFSQLGWSIESISQFTGYLPMEIQVPYVRSTTDLTVEQFSLYI", "metadata": {"id": "A0A2H4FX38", "cluster": 28971993, "interpro_all": ["IPR036619"], "interpro_used": ["IPR036619"], "interpro_unused": []}, "task_type": "infilling"} {"instruction": "Restore the missing amino acid spans for a protein sequence with this functional profile: The protein should contain a Formyl transferase, N-terminal domain that functions as the N-terminal component of enzymes catalyzing formyl group transfers, including methionyl-tRNA formyltransferase and glycinamide ribonucleotide transformylase. This domain facilitates diverse metabolic roles, ranging from the modification of initiator tRNA for IF2 recognition during translation initiation to specific steps in de novo purine biosynthesis and formate production. In addition, the protein should feature a Phosphoribosylglycinamide formyltransferase active site that catalyses the transfer of a formyl group to 5'-phosphoribosylglycinamide in the third step of de novo purine biosynthesis. This conserved region utilizes an essential aspartic acid residue to facilitate the catalytic mechanism. It has been detected in Synechococcus sp. ARS1019.", "tokenized_instruction": [2, 12900, 1920, 6814, 3835, 2687, 23658, 1958, 43, 2213, 3244, 1956, 2052, 3183, 5174, 30, 1920, 2213, 3066, 5531, 43, 29285, 13763, 16, 56, 17, 4262, 3418, 1988, 4088, 1966, 1920, 56, 17, 4262, 4594, 1927, 5038, 29601, 29285, 2210, 19180, 16, 2710, 2295, 2001, 2199, 17, 10089, 29285, 9961, 1930, 4235, 4058, 16408, 1021, 18347, 4749, 4331, 15499, 18, 2052, 3418, 11374, 6445, 4487, 5456, 16, 6485, 2037, 1920, 6295, 1927, 23467, 10089, 1958, 2647, 1028, 5708, 2409, 6410, 6035, 1942, 2487, 5983, 1922, 2028, 9441, 19700, 8132, 1930, 25741, 3372, 18, 1922, 2459, 16, 1920, 2213, 3066, 5961, 43, 3421, 2023, 11731, 17038, 3665, 5482, 29285, 9961, 3500, 3200, 1988, 13928, 1918, 1920, 3856, 1927, 43, 29285, 2210, 1942, 25, 11, 17, 3421, 2023, 11731, 17038, 3665, 5482, 1922, 1920, 4563, 3537, 1927, 2028, 9441, 19700, 8132, 18, 2052, 5305, 3031, 18127, 1925, 4415, 23047, 2687, 6181, 1942, 6628, 1920, 6804, 2856, 18, 2176, 2258, 2252, 3330, 1922, 26734, 8256, 2056, 18, 9896, 13100, 1026, 18, 3], "output": "MPAFSDPSDHQAGEQALLQPPMQNTPTTLSGGSNFEALATAVKAGRLNAEIVLLVVNNPGCGAVKNRERLDQELVRSFNAVQVDAVLLNIHPSLLPSFRGLDAVGQALEAGVCISGCTVHKSDNHESLAARIHRQEHRLLPHAVQLAASRWSQGPPIRLGVMASGNTRAERLQIPHTVIDHRVWVMAGWMRIVTPVLIGAFAGRLVSEELDAGPIIAQAAVPVL", "metadata": {"id": "A0A2D6Y4E7", "cluster": 20300585, "interpro_all": ["IPR002376", "IPR036477", "IPR004607", "IPR001555"], "interpro_used": ["IPR002376", "IPR001555"], "interpro_unused": ["IPR004607", "IPR036477"]}, "task_type": "infilling"}