LiteFold/InterPro · Datasets at Hugging Face

IPR023961

23,961

Nitric oxide reductase FlRd-NAD(+) reductase

NO_rdtase_NorW

Family

1,149

false

This entry represents an accessory proteins for anaerobicnitric oxide (NO) reductase. It is thought to reduce the rubredoxin moiety of NOreductase.

[ "GO:0016731" ]

[ "oxidoreductase activity, acting on iron-sulfur proteins as donors, NAD or NADP as acceptor" ]

[ "molecular_function" ]

1

[ "HAMAP" ]

[ "MF_01313" ]

[ "NorW" ]

[ 1149 ]

1

[ "EC" ]

[ "1.18.1.-" ]

[ "EC:1.18.1.-" ]

1

[]

0

[]

0

[ "IPR050260" ]

[]

1

0

1

[ "Bacteria" ]

[ 1149 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Nitric oxide reductase FlRd-NAD(+) reductase

NO_rdtase_NorW

1

IPR023963

23,963

Methanobactin precursor, Mb-OB3b

Methanobactin_OB3b

Family

37

false

Methanobactins are siderophore-like copper-chelating natural products with considerable variety from species to species [ , , ]. The 11-residue methanobactin of Methylosinus trichosporium OB3b is derived from a 30-residue precursor. A very similar 31-residue precursor is found in the rice endophyte Azospirillum sp. B51...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF25751", "TIGR04071" ]

[ "Methanobactin", "methanobac_OB3b" ]

[ 25, 37 ]

2

[ "GP" ]

[ "GenProp0962" ]

[ "GP:GenProp0962" ]

1

[ "7fc0" ]

1

[ "PUB00060471", "PUB00106811", "PUB00106856", "PUB00160639", "PUB00160640" ]

[ "20961038", "26984926", "21900235", "15361623", "21254756" ]

[ "A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.", "Methanobactin and the Link between Copper and Bacterial Methane Oxidat...

[ 2010, 2016, 2011, 2004, 2011 ]

5

[]

0

null

[ "Pseudomonadota" ]

[ 37 ]

1

[]

0

true

Family

Methanobactin precursor, Mb-OB3b

Methanobactin_OB3b

9

IPR023965

23,965

Capreomycidine synthase

Capreomycidine_synthase

Family

144

false

Members of this family are capreomycidine synthases, which perform the second of two steps in the biosynthesis of 2S,3R-capreomycidine from arginine. The best characterised member is VioD from the biosynthetic pathway for viomycin [ ]. Capreomycidine is an unusual amino acid used by non-ribosomal peptide synthases (NRP...

[]

0

[ "NCBIFAM" ]

[ "TIGR03947" ]

[ "viomycin_VioD" ]

[ 144 ]

1

[ "GP" ]

[ "GenProp0909" ]

[ "GP:GenProp0909" ]

1

[ "4m2j", "4m2k", "4m2m" ]

3

[ "PUB00055106" ]

[ "15368581" ]

[ "Formation of the nonproteinogenic amino acid 2S,3R-capreomycidine by VioD from the viomycin biosynthesis pathway." ]

[ 2004 ]

1

[]

0

null

[ "Bacteria" ]

[ 144 ]

1

[]

0

true

Family

Capreomycidine synthase

Capreomycidine_synthase

7

IPR023966

23,966

Arginine beta-hydroxylase, Fe2/alpha-ketoglutarate-dependent

Arginine_beta-hydroxylase

Family

74

false

Members of this protein family are L-arginine beta-hydroxylase, members of a broader family of enzymes dependent on Fe(II), alpha-ketoglutarate, and molecular oxygen. Enzymes in the broader family but excluded by this model include clavaminate synthase, taurine dioxygenase, and prolyl-4-hydroxylase [ , ].

[]

0

[ "NCBIFAM" ]

[ "TIGR03946" ]

[ "viomycin_VioC" ]

[ 74 ]

1

[ "GP" ]

[ "GenProp0909" ]

[ "GP:GenProp0909" ]

1

[ "2wbo", "2wbp", "2wbq", "4m23", "4m25", "4m26", "4m27", "4m2c", "4m2e", "4m2f", "4m2g", "4m2i", "4ne0", "6alm", "6aln", "6alo", "6alp", "6alq", "6alr", "6dax", "6daz", "6db2", "6mp8", "6mp9", "6y0n", "6y12", "7vgl", "7vgn", "7y5f", "7y5i", "7y5p", "7yhe"...

34

[ "PUB00050101", "PUB00077127" ]

[ "19490124", "17967013" ]

[ "Structural basis for the erythro-stereospecificity of the l-arginine oxygenase VioC in viomycin biosynthesis.", "CD and MCD of CytC3 and taurine dioxygenase: role of the facial triad in alpha-KG-dependent oxygenases." ]

[ 2009, 2007 ]

2

[ "IPR014503" ]

[]

1

0

1

[ "Actinomycetes" ]

[ 74 ]

1

[]

0

true

Family

Arginine beta-hydroxylase, Fe2/alpha-ketoglutarate-dependent

Arginine_beta-hydroxylase

8

IPR023967

23,967

Conserved hypothetical protein CHP03996, oxidoreductase

CHP03996_oxidoreductase

Family

207

false

This protein family occurs in the vicinity of the putative mycofactocin biosynthesis operon in a number of Actinobacteria such as Frankia sp. and Rhodococcus sp. Family members contain a TIM-barrel fold commonly found in NADH:flavin oxidoreductase/NADH oxidase enzymes that use FMN/FAD as cofactor.

[]

0

[ "NCBIFAM" ]

[ "TIGR03996" ]

[ "mycofact_OYE_1" ]

[ 207 ]

1

[ "GP" ]

[ "GenProp0917" ]

[ "GP:GenProp0917" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "freshwater metagenome" ]

[ 191, 16 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP03996, oxidoreductase

CHP03996_oxidoreductase

4

IPR023968

23,968

Bacteriocin precursor, CLI3235 family, putative

Bacteriocin_CLI3235

Family

126

false

Members of this protein family are Cys-rich putative bacteriocin precursor peptides restricted to Clostridia but found in multiple species, with up to three per genome. They are found next to a CLI_3234 family radical SAM protein that may perform post-translational modification. This model describes approximately 35 re...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF27803", "TIGR04065" ]

[ "Bacteriocin_CLI3235", "ocin_CLI_3235" ]

[ 126, 111 ]

2

[ "GP" ]

[ "GenProp0945" ]

[ "GP:GenProp0945" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria" ]

[ 126 ]

1

[]

0

true

Family

Bacteriocin precursor, CLI3235 family, putative

Bacteriocin_CLI3235

8

IPR023969

23,969

Conserved hypothetical protein CHP04072, B12-binding/radical SAM-type

CHP04072_B12-bd/rSAM

Family

106

false

Members of this protein family occur in conserved genomic contexts highly suggestive of lipid biosynthesis, including an island shared between Kuenenia stuttgartiensis, which produces ladderanes [ ], and Desulfotalea psychrophila, which produces a different kind of unusual polyunsaturated hydrocarbon.

[]

0

[ "NCBIFAM" ]

[ "TIGR04072" ]

[ "rSAM_ladder_B12" ]

[ 106 ]

1

[]

0

[]

0

[ "PUB00055107" ]

[ "19220888" ]

[ "A comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis." ]

[ 2009 ]

1

[ "IPR034466" ]

[]

1

0

1

[ "Bacteria", "ecological metagenomes" ]

[ 102, 4 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP04072, B12-binding/radical SAM-type

CHP04072_B12-bd/rSAM

2

IPR023971

23,971

Selenoprotein GSU1558/SbtA-like

GSU1558/StbA-like

Family

26

false

Members of this protein family are small peptides found in the vicinity of a peptide modification-type radical SAM protein family, nearly always selenopeptides. Multiple members of this protein family occur in species with a selenocysteine incorporation systems and have a TGA stop codon at position that aligns with cys...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF27804", "TIGR04081" ]

[ "GSU1558_StbA-like", "" ]

[ 25, 26 ]

2

[ "GP" ]

[ "GenProp0956" ]

[ "GP:GenProp0956" ]

1

[]

0

[ "PUB00055953", "PUB00106225" ]

[ "21478363", "34730336" ]

[ "Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.", "New Role for Radical SAM Enzymes in the Biosynthesis of Thio(seleno)oxazole RiPP Natural Products." ]

[ 2011, 2021 ]

2

[]

0

null

[ "Pseudomonadati" ]

[ 26 ]

1

[]

0

true

Family

Selenoprotein GSU1558/SbtA-like

GSU1558/StbA-like

6

IPR023972

23,972

Conserved hypothetical protein CHP04069, acyl carrier-related

CHP04069_acyl_carrier-rel

Family

65

false

Members of this family are often related to an acyl carrier-like domain and are found in genomic contexts associated with a small Cys-rich peptide and a radical SAM protein which probably modifies the peptide.

[]

0

[ "NCBIFAM" ]

[ "TIGR04069" ]

[ "ocin_ACP_rel" ]

[ 65 ]

1

[ "GP" ]

[ "GenProp0945" ]

[ "GP:GenProp0945" ]

1

[]

0

[]

0

[]

0

null

[ "Bacillota" ]

[ 65 ]

1

[]

0

true

Family

Conserved hypothetical protein CHP04069, acyl carrier-related

CHP04069_acyl_carrier-rel

5

IPR023973

23,973

Methanobactin biosynthesis cassette protein MbnC-like

MbnC-like

Family

273

false

This entry represents a family of proteins from proteobacteria, including Methanobactin biosynthesis cassette protein MbnC from Methylosinus trichosporium, part of the he iron-containing heterodimeric MbnBC enzyme complex, which is central to the biosynthesis of methanobactins (Mbns), copper-binding metallophores isola...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF27805", "TIGR04061" ]

[ "MbnC-like", "AZL_007950_fam" ]

[ 273, 235 ]

2

[]

0

[ "7dz9", "7fc0", "7tcr", "7tcu", "7tcw", "7tcx" ]

6

[ "PUB00106909", "PUB00106910" ]

[ "35320042", "29348173" ]

[ "A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis.", "Methanobactins: Maintaining copper homeostasis in methanotrophs and beyond." ]

[ 2022, 2018 ]

2

[]

0

null

[ "Bacteria" ]

[ 273 ]

1

[]

0

true

Family

Methanobactin biosynthesis cassette protein MbnC-like

MbnC-like

3

IPR023974

23,974

His-Xaa-Ser system protein HxsD

HxsD

Family

547

false

This rare conserved hypothetical protein of small size occurs exclusively, and perhaps universally, in the context of a pair of (uncharacterised) radical SAM proteins, HxsC ( ) and HxsB ( ). Many members of this family have invariant motifs LYW and LLNDYxLRE, but PSI-BLAST starting from family members well below 20% pa...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF27806", "TIGR03976" ]

[ "HxsD", "chp_LLNDYxLRE" ]

[ 547, 451 ]

2

[ "GP" ]

[ "GenProp0921" ]

[ "GP:GenProp0921" ]

1

[]

0

[ "PUB00055953" ]

[ "21478363" ]

[ "Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification." ]

[ 2011 ]

1

[]

0

null

[ "Bacteria", "Nanobdellati", "metagenomes" ]

[ 538, 4, 5 ]

3

[]

0

true

Family

His-Xaa-Ser system protein HxsD

HxsD

4

IPR023975

23,975

Six-cysteine peptide SCIFF

Six-Cys_pep_SCIFF

Family

1,363

false

Members of this protein family are essentially universal in the class Clostridia and therefore highly abundant in the human gut microbiome. This short peptide is designated SCIFF, for Six Cysteines in Forty-Five residues. It is a presumed ribosomal natural product precursor, always found associated with a yet-uncharact...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF13165", "TIGR03973" ]

[ "SCIFF", "six_Cys_in_45" ]

[ 1363, 1360 ]

2

[ "GP" ]

[ "GenProp0919" ]

[ "GP:GenProp0919" ]

1

[]

0

[ "PUB00055953", "PUB00106801", "PUB00106802" ]

[ "21478363", "27410522", "32713052" ]

[ "Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.", "SkfB Abstracts a Hydrogen Atom from Cα on SkfA To Initiate Thioether Cross-Link Formation.", "The SCIFF-Derived Ranthipeptides Participate in Quorum Sensing in ...

[ 2011, 2016, 2020 ]

3

[]

0

null

[ "Bacteria", "unclassified sequences" ]

[ 1351, 12 ]

2

[]

0

true

Family

Six-cysteine peptide SCIFF

Six-Cys_pep_SCIFF

7

IPR023976

23,976

Conserved hypothetical protein CHP04031, Htur1727

CHP04031_Htur1727

Family

216

false

Members of this protein family show homology to the putative PaaH (or PaaB) subunit of the phenylacetate-CoA oxygenase complex. However, all members are found in the Halobacteriales in the vicinity of a radical SAM protein homologous to the PqqE protein of pyroquinoline quinone (PQQ) biosynthesis. Members are well-cons...

[]

0

[ "NCBIFAM" ]

[ "TIGR04031" ]

[ "Htur_1727_fam" ]

[ 216 ]

1

[ "GP" ]

[ "GenProp1065" ]

[ "GP:GenProp1065" ]

1

[]

0

[]

0

[ "IPR009359" ]

[]

1

0

1

[ "Halobacteriales" ]

[ 216 ]

1

[]

0

true

Family

Conserved hypothetical protein CHP04031, Htur1727

CHP04031_Htur1727

9

IPR023977

23,977

Copper-binding protein MbnP-like

MbnP-like

Family

579

false

Members of this rare protein family regularly occur next to a member of the MXAN_0977 subfamily ( ) of the di-heme cytochrome c peroxidase/MauG family ( ). MauG itself ( ) is a protein modification enzyme responsible for the tryptophan tryptophylquinone (TTQ) modification involved in methylamine dehydrogenase activatio...

[]

0

[ "NCBIFAM" ]

[ "TIGR04052" ]

[ "MbnP_like_WxW" ]

[ 579 ]

1

[ "GP" ]

[ "GenProp0940" ]

[ "GP:GenProp0940" ]

1

[ "7l6g" ]

1

[ "PUB00060471", "PUB00153588" ]

[ "20961038", "34074779" ]

[ "A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.", "Copper binding by a unique family of metalloproteins is dependent on k...

[ 2010, 2021 ]

2

[]

0

null

[ "Bacteria", "Durusdinium trenchii", "bioreactor metagenome" ]

[ 577, 1, 1 ]

3

[]

0

true

Family

Copper-binding protein MbnP-like

MbnP-like

4

IPR023978

23,978

Glucose-methanol-choline oxidoreductase, bacteria

GMC_oxidoreductase_bact

Family

784

false

This entry describes a set of dehydrogenases belonging to the glucose-methanol-choline oxidoreductase (GMC oxidoreductase) family. Members of the family are found in bacterial genome contexts containing also members of families and , and are proposed to be uniform in function.

[]

0

[ "NCBIFAM" ]

[ "TIGR03970" ]

[ "Rv0697" ]

[ 784 ]

1

[ "GP" ]

[ "GenProp0917" ]

[ "GP:GenProp0917" ]

1

[]

0

[]

0

[ "IPR012132" ]

[]

1

0

1

[ "Bacteria", "Geodia barretti", "ecological metagenomes", "uncultured marine group II/III euryarchaeote KM3_170_G02" ]

[ 718, 17, 48, 1 ]

4

[]

0

true

Family

Glucose-methanol-choline oxidoreductase, bacteria

GMC_oxidoreductase_bact

6

IPR023979

23,979

Conserved hypothetical protein CHP04014, B12-binding/radical SAM-type

CHP04014_B12-bd/rSAM

Family

113

false

Members of this family, which are found in methanogenic archaea, have both a B12 binding homology domain ( ) and a radical SAM domain ( ). They occur only once per genome. Some species that express proteins of this family also express a related protein with a similar domain architecture (see ).

[]

0

[ "SFLD", "NCBIFAM" ]

[ "SFLDG01217", "TIGR04014" ]

[ "B12-binding_methylthiotransfer", "B12_SAM_MJ_0865" ]

[ 111, 113 ]

2

[]

0

[ "9ccb" ]

1

[]

0

[ "IPR034466" ]

[]

1

0

1

[ "Archaea", "hydrocarbon metagenome" ]

[ 111, 2 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP04014, B12-binding/radical SAM-type

CHP04014_B12-bd/rSAM

6

IPR023981

23,981

Pre-mycofactocin glycosyltransferase

MftF

Family

1,295

false

Pre-mycofactocin glycosyltransferase MftF is a glycosyltransferase that catalyses the oligoglycosylation of pre-mycofactocin (PMFT), adding up to nine beta-1,4-linked glucose residues [ ]. It is involved in the biosynthesis of the enzyme cofactor mycofactocin (MFT), a redox cofactor which belongs to the family of ribos...

[ "GO:0016740" ]

[ "transferase activity" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR03965" ]

[ "mycofact_glyco" ]

[ 1295 ]

1

[ "EC", "GP", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "...

[ "2.4.1.-", "GenProp0917", "PWY-1901", "PWY-1961", "PWY-1981", "PWY-2021", "PWY-2881", "PWY-2901", "PWY-2902", "PWY-4421", "PWY-4801", "PWY-5094", "PWY-5105", "PWY-5129", "PWY-5139", "PWY-5160", "PWY-5161", "PWY-5268", "PWY-5284", "PWY-5286", "PWY-5310", "PWY-5312", "PWY-5...

[ "EC:2.4.1.-", "GP:GenProp0917", "METACYC:PWY-1901", "METACYC:PWY-1961", "METACYC:PWY-1981", "METACYC:PWY-2021", "METACYC:PWY-2881", "METACYC:PWY-2901", "METACYC:PWY-2902", "METACYC:PWY-4421", "METACYC:PWY-4801", "METACYC:PWY-5094", "METACYC:PWY-5105", "METACYC:PWY-5129", "METACYC:PWY-513...

201

[]

0

[ "PUB00096692", "PUB00096693" ]

[ "31113891", "33014324" ]

[ "Mycofactocin Is Associated with Ethanol Metabolism in Mycobacteria.", "Structure elucidation of the redox cofactor mycofactocin reveals oligo-glycosylation by MftF." ]

[ 2019, 2020 ]

2

[]

0

null

[ "Bacteria", "Halobacteriales", "ecological metagenomes" ]

[ 1241, 3, 51 ]

3

[]

0

true

Family

Pre-mycofactocin glycosyltransferase

MftF

6

IPR023982

23,982

Conserved hypothetical protein CHP04029, CMD-like

CHP04029_CMD-like

Family

764

false

Sequences in this family occur as the N-terminal domain of a fusion protein with a C-terminal peroxidase-like protein, or as discrete proteins encoded next to a peroxidase-like protein. The two partners regularly are encoded near to, and in the same genomes as, a putative FMN-dependent luciferase-like monooxygenase (LL...

[]

0

[ "NCBIFAM" ]

[ "TIGR04029" ]

[ "CMD_Avi_7170" ]

[ 764 ]

1

[ "GP" ]

[ "GenProp0935" ]

[ "GP:GenProp0935" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria" ]

[ 764 ]

1

[]

0

true

Family

Conserved hypothetical protein CHP04029, CMD-like

CHP04029_CMD-like

6

IPR023983

23,983

DNA sulphur modification system-associated protein 4

DNA_S_mod_dnd_assoc_4

Family

385

false

A DNA sulphur modification system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. Members of this protein family are strictly limited to species with the dnd operon, and are found close to the dnd operon on the chromosomes of species such as Nostoc sp. PCC 7120, G...

[]

0

[ "NCBIFAM" ]

[ "TIGR04062" ]

[ "dnd_assoc_4" ]

[ 385 ]

1

[ "GP" ]

[ "GenProp0701" ]

[ "GP:GenProp0701" ]

1

[]

0

[]

0

[ "IPR060766" ]

[]

1

0

1

[ "Bacteria", "ecological metagenomes" ]

[ 383, 2 ]

2

[]

0

true

Family

DNA sulphur modification system-associated protein 4

DNA_S_mod_dnd_assoc_4

2

IPR023984

23,984

Ribosomal peptide maturation radical SAM protein 1

rSAM_ocin_1

Family

944

false

Members of this family of peptide-modifying radical SAM proteins include BstC, BstF, and BstJ, three enzymes involved in the biosynthesis of the antibiotic bottromycin D from a ribosomally translated peptide precursor that lacks a leader peptide. They appear to perform methylations of carbon atoms [ , ]. Other members ...

[]

0

[ "SFLD", "NCBIFAM" ]

[ "SFLDF00324", "TIGR03975" ]

[ "bacteriocin_maturation", "rSAM_ocin_1" ]

[ 938, 931 ]

2

[ "GP" ]

[ "GenProp0861" ]

[ "GP:GenProp0861" ]

1

[]

0

[ "PUB00055015", "PUB00074064", "PUB00105079" ]

[ "20500830", "22983711", "22984777" ]

[ "Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family.", "Metagenome mining reveals polytheonamides as posttranslationally modified ribosomal peptides.", "Structure and biosynthesis of the antibiotic bottromycin D." ]

[ 2010, 2012, 2012 ]

3

[]

0

null

[ "Archaea", "Bacteria", "ecological metagenomes" ]

[ 2, 928, 14 ]

3

[]

0

true

Family

Ribosomal peptide maturation radical SAM protein 1

rSAM_ocin_1

8

IPR023985

23,985

Mycofactocin-dependent oxidoreductase

SDR_subfam_1

Family

6,952

false

Members of this protein subfamily are putative oxidoreductases belonging to the larger SDR family. All members occur in genomes that encode a cassette for the biosynthesis of mycofactocin, a proposed electron carrier of a novel redox pool. Characterised members of this family are described as NDMA-dependent, meaning th...

[]

0

[ "NCBIFAM" ]

[ "TIGR03971" ]

[ "SDR_subfam_1" ]

[ 6952 ]

1

[ "GP" ]

[ "GenProp0917" ]

[ "GP:GenProp0917" ]

1

[ "3oec", "3pgx", "3pxx", "3s55", "3sx2", "3t7c", "3tsc", "3uve", "4rgb", "5ej2" ]

10

[ "PUB00055045" ]

[ "21223593" ]

[ "Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners." ]

[ 2011 ]

1

[ "IPR002347" ]

[]

1

0

1

[ "Bacteria", "Didymella rabiei", "Halobacteriales", "metagenomes" ]

[ 6853, 1, 47, 51 ]

4

[]

0

true

Family

Mycofactocin-dependent oxidoreductase

SDR_subfam_1

8

IPR023986

23,986

Glycosyltransferase, putative, MSMEG0565 family

GlycosylTfrase_MSMEG0565

Family

1,016

false

A conserved gene cluster found sporadically from Actinobacteria to Proteobacteria to Cyanobacteria features a radical SAM protein, an N-acetyltransferase, an oxidoreductase, and two additional proteins whose functional classes are unclear. The metabolic role of the cluster is probably biosynthetic. This glycosyltransfe...

[]

0

[ "NCBIFAM" ]

[ "TIGR04047" ]

[ "MSMEG_0565_glyc" ]

[ 1016 ]

1

[ "GP" ]

[ "GenProp0939" ]

[ "GP:GenProp0939" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 1006, 10 ]

2

[]

0

true

Family

Glycosyltransferase, putative, MSMEG0565 family

GlycosylTfrase_MSMEG0565

8

IPR023987

23,987

Conserved hypothetical protein CHP03977, oxidoreductase

CHP03977_oxidoreductase

Family

229

false

This protein family occurs in the vicinity of the the putative mycofactocin biosynthesis operon in a number of Actinobacteria such as Frankia sp. and Rhodococcus sp., in Pelotomaculum thermopropionicum SI (Firmicutes), and in Geobacter uraniireducens Rf4 (Deltaproteobacteria). Family members contain a TIM-barrel fold c...

[]

0

[ "NCBIFAM" ]

[ "TIGR03997" ]

[ "mycofact_OYE_2" ]

[ 229 ]

1

[ "GP" ]

[ "GenProp0917" ]

[ "GP:GenProp0917" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "freshwater metagenome" ]

[ 212, 17 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP03977, oxidoreductase

CHP03977_oxidoreductase

7

IPR023988

23,988

Mycofactocin precursor peptide

MftA

Family

1,075

false

Mycofactocin precursor peptide MftA is the precursor peptide that leads to mycofactocin (MFT), a redox cofactor which belongs to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs) and is involved in alcohol metabolism of mycobacteria including Mycobacterium tuberculosis [ , ]. MftA...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF23709", "TIGR03969" ]

[ "MftA", "mycofactocin" ]

[ 1054, 1075 ]

2

[ "GP" ]

[ "GenProp0917" ]

[ "GP:GenProp0917" ]

1

[]

0

[ "PUB00096692", "PUB00096693", "PUB00096696", "PUB00155614" ]

[ "31113891", "33014324", "27158836", "36243697" ]

[ "Mycofactocin Is Associated with Ethanol Metabolism in Mycobacteria.", "Structure elucidation of the redox cofactor mycofactocin reveals oligo-glycosylation by MftF.", "The Radical S-Adenosyl-l-methionine Enzyme MftC Catalyzes an Oxidative Decarboxylation of the C-Terminus of the MftA Peptide.", "Comparative ...

[ 2019, 2020, 2016, 2022 ]

4

[]

0

null

[ "Bacteria", "Halobacteriales", "ecological metagenomes" ]

[ 1033, 6, 36 ]

3

[]

0

true

Family

Mycofactocin precursor peptide

MftA

9

IPR023989

23,989

Pre-mycofactocin synthase

MftD

Family

1,232

false

Pre-mycofactocin synthase MftD is involved in the biosynthesis of the enzyme cofactor mycofactocin (MFT), a ribosomally synthesized and post-translationally modified (RiPP) redox cofactor, and catalyses the oxidative deamination of AHDP (3-amino-5-[(4-hydroxyphenyl)methyl]-4,4-dimethyl-2-pyrrolidin-2-one), forming an a...

[]

0

[ "NCBIFAM" ]

[ "TIGR03966" ]

[ "actino_HemFlav" ]

[ 1232 ]

1

[ "EC", "GP" ]

[ "1.4.3.26", "GenProp0917" ]

[ "EC:1.4.3.26", "GP:GenProp0917" ]

2

[]

0

[ "PUB00096693", "PUB00096697" ]

[ "33014324", "31381312" ]

[ "Structure elucidation of the redox cofactor mycofactocin reveals oligo-glycosylation by MftF.", "MftD Catalyzes the Formation of a Biologically Active Redox Center in the Biosynthesis of the Ribosomally Synthesized and Post-translationally Modified Redox Cofactor Mycofactocin." ]

[ 2020, 2019 ]

2

[ "IPR012133" ]

[]

1

0

1

[ "Bacteria", "metagenomes" ]

[ 1208, 24 ]

2

[]

0

true

Family

Pre-mycofactocin synthase

MftD

6

IPR023990

23,990

Butyryl-CoA:acetate CoA-transferase

Butryl-CoA_acetate_CoA_Tfrase

Family

627

false

This enzyme represents one of at least two mechanisms for reclaiming CoA from butyryl-CoA at the end of butyrate biosynthesis (an important process performed by some colonic bacteria), namely transfer of CoA to acetate [ ]. An alternate mechanism transfers the butyrate onto inorganic phosphate, after which butyrate kin...

[ "GO:0019605" ]

[ "butyrate metabolic process" ]

[ "biological_process" ]

1

[ "HAMAP", "HAMAP", "NCBIFAM" ]

[ "MF_03227", "MF_03228", "TIGR03948" ]

[ "But_acet_CoA_trans", "But_CoA_trans", "butyr_acet_CoA" ]

[ 285, 623, 290 ]

3

[ "EC", "GP", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC" ]

[ "2.8.3.-", "GenProp0911", "PWY-5022", "PWY-5677", "PWY-7382", "PWY-7401", "PWY-8326" ]

[ "EC:2.8.3.-", "GP:GenProp0911", "METACYC:PWY-5022", "METACYC:PWY-5677", "METACYC:PWY-7382", "METACYC:PWY-7401", "METACYC:PWY-8326" ]

7

[]

0

[ "PUB00055058", "PUB00094482" ]

[ "19807780", "23468890" ]

[ "Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene.", "A proteomic view at the biochemistry of syntrophic butyrate oxidation in Syntrophomonas wolfei." ]

[ 2010, 2013 ]

2

[ "IPR046433" ]

[]

1

0

1

[ "Bacteria", "ecological metagenomes" ]

[ 617, 10 ]

2

[]

0

true

Family

Butyryl-CoA:acetate CoA-transferase

Butryl-CoA_acetate_CoA_Tfrase

5

IPR023991

23,991

Bacteriocin, class IIb, lactobin A/cerein 7B family

Bacteriocin_IIb_lactobn/cerein

Family

906

false

Members of this protein family are described variably as bacteriocins per se, one chain of a two-chain bacteriocin, or bacteriocin enhancer proteins. All members of the seed alignment occur in paired gene contexts with another member of the same protein family. This family includes bacteriocins that appear not to under...

[]

0

[ "NCBIFAM" ]

[ "TIGR03949" ]

[ "bact_IIb_cerein" ]

[ 906 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Candidatus Nitrososphaera evergladensis SR1", "ecological metagenomes" ]

[ 899, 1, 6 ]

3

[]

0

true

Family

Bacteriocin, class IIb, lactobin A/cerein 7B family

Bacteriocin_IIb_lactobn/cerein

3

IPR023992

23,992

Pre-heme d1 synthase NirJ

HemeD1_Synth_NirJ

Family

816

false

Heme D1 occurs in the cytochrome Cd1 subunit of nitrite reductase in species such as Pseudomonas stutzeri. NirJ is a radical SAM protein that contains two iron-sulfur clusters. It catalyzes the removal of two propionate side chains during heme D1 biosynthesis [ ]. In a number of species, distinct genes NirJ1 and NirJ2 ...

[ "GO:0003824", "GO:0051539" ]

[ "catalytic activity", "4 iron, 4 sulfur cluster binding" ]

[ "molecular_function", "molecular_function" ]

2

[ "SFLD", "NCBIFAM" ]

[ "SFLDF00393", "TIGR04051" ]

[ "heme_D1_biosynthesis_(NirJ-lik", "rSAM_NirJ" ]

[ 812, 816 ]

2

[]

0

[]

0

[ "PUB00097908" ]

[ "29076625" ]

[ "The Radical SAM enzyme NirJ catalyzes the removal of two propionate side chains during heme d1 biosynthesis." ]

[ 2017 ]

1

[ "IPR017200" ]

[]

1

0

1

[ "Bacteria", "unclassified sequences" ]

[ 801, 15 ]

2

[]

0

true

Family

Pre-heme d1 synthase NirJ

HemeD1_Synth_NirJ

3

IPR023993

23,993

S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, archaea

TYW1_archaea

Family

780

false

Members of this protein family are the archaeal protein TYW1 [ ], a radical SAM protein that catalyses the second step in creating the wye-bases, wyosine and derivatives such as wybutosine, for tRNA base modification [ ].

[ "GO:0016829", "GO:0051539", "GO:0008033" ]

[ "lyase activity", "4 iron, 4 sulfur cluster binding", "tRNA processing" ]

[ "molecular_function", "molecular_function", "biological_process" ]

3

[ "HAMAP", "NCBIFAM" ]

[ "MF_01921", "TIGR03972" ]

[ "TYW1_archaea", "rSAM_TYW1" ]

[ 713, 780 ]

2

[ "EC", "METACYC", "METACYC" ]

[ "4.1.3.44", "PWY-7285", "PWY-7286" ]

[ "EC:4.1.3.44", "METACYC:PWY-7285", "METACYC:PWY-7286" ]

3

[ "2yx0", "2z2u", "6djt" ]

3

[ "PUB00050155", "PUB00050182" ]

[ "17881823", "17727881" ]

[ "Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis.", "Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA." ]

[ 2007, 2007 ]

2

[ "IPR034556" ]

[]

1

0

1

[ "Archaea", "Eukaryota", "ecological metagenomes" ]

[ 748, 22, 10 ]

3

[]

0

true

Family

S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, archaea

TYW1_archaea

5

IPR023994

23,994

[NiFe]-hydrogenase assembly, chaperone, HybE

NiFe-hyd_HybE

Family

1,720

false

Members of this family are chaperones for the assembly of [NiFe] hydrogenases, in the family of HybE, which is specific for hydrogenase-2 of Escherichia coli. Members often have an additional N-terminal rubredoxin domain [ ].

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF11939", "TIGR03993" ]

[ "NiFe-hyd_HybE", "hydrog_HybE" ]

[ 1720, 1540 ]

2

[]

0

[ "2kc5" ]

1

[ "PUB00078075" ]

[ "19636963" ]

[ "1H, 13C and 15N resonance assignments of the chaperone HybE of hydrogenase-2 from Escherichia coli." ]

[ 2009 ]

1

[]

0

null

[ "Bacteria", "Durusdinium trenchii", "metagenomes" ]

[ 1698, 1, 21 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

[NiFe]-hydrogenase assembly, chaperone, HybE

NiFe-hyd_HybE

1

IPR023995

23,995

Oxygen-independent coproporphyrinogen-III oxidase-like protein HemZ

HemZ

Family

2,456

false

Members of this radical SAM protein family are HemZ, a protein involved in coproporphyrinogen III decarboxylation. Alternative names for this enzyme (EC ) include coproporphyrinogen dehydrogenase and oxygen-independent coproporphyrinogen III oxidase. The family is related to, but distinct from HemN, and in Bacillus sub...

[]

0

[ "SFLD", "NCBIFAM" ]

[ "SFLDF00310", "TIGR03994" ]

[ "oxygen-independent_coproporphy", "rSAM_HemZ" ]

[ 2431, 2447 ]

2

[]

0

[]

0

[ "PUB00055059" ]

[ "10498703" ]

[ "Transcriptional control of Bacillus subtilis hemN and hemZ." ]

[ 1999 ]

1

[ "IPR034505" ]

[]

1

0

1

[ "Bacteria", "Inoviridae sp. ctDEu7", "ecological metagenomes" ]

[ 2447, 1, 8 ]

3

[]

0

true

Family

Oxygen-independent coproporphyrinogen-III oxidase-like protein HemZ

HemZ

7

IPR023996

23,996

TonB-dependent outer membrane protein, SusC/RagA

TonB-dep_OMP_SusC/RagA

Family

91,056

false

This entry describes a clade of TonB-linked outer membrane proteins (OMP). Members of the family are restricted to the Bacteriodetes lineage (except for Gemmatimonas aurantiaca T-27 from the novel phylum Gemmatimonadetes) and occur in high copy numbers, with over 100 members from Bacteroides thetaiotaomicron VPI-5482 a...

[]

0

[ "NCBIFAM" ]

[ "TIGR04056" ]

[ "OMP_RagA_SusC" ]

[ 91056 ]

1

[ "GP" ]

[ "GenProp0941" ]

[ "GP:GenProp0941" ]

1

[ "5fq6", "5fq7", "5fq8", "5t3r", "5t4y", "6sli", "6slj", "6sln", "6sm3", "6sml", "6smq", "6z8i", "6z9a", "6zaz", "6zlt", "6zlu", "6zm1", "8a9y", "8aa0", "8aa1", "8aa2", "8aa3", "8aa4", "8ypt", "8ypu" ]

25

[ "PUB00016547", "PUB00055060", "PUB00055061" ]

[ "11717282", "15972517", "11553542" ]

[ "Biochemical analysis of interactions between outer membrane proteins that contribute to starch utilization by Bacteroides thetaiotaomicron.", "Sequence diversity and antigenic variation at the rag locus of Porphyromonas gingivalis.", "Molecular cloning of a Bacteroides caccae TonB-linked outer membrane protein...

[ 2001, 2005, 2001 ]

3

[]

0

null

[ "Bacteria", "Eukaryota", "unclassified Caudoviricetes", "unclassified sequences" ]

[ 90336, 44, 9, 667 ]

4

[]

0

true

Family

TonB-dependent outer membrane protein, SusC/RagA

TonB-dep_OMP_SusC/RagA

5

IPR023997

23,997

TonB-dependent outer membrane protein SusC/RagA, conserved site

TonB-dep_OMP_SusC/RagA_CS

Conserved_site

87,685

false

This entry describes a short conserved site found in the SusC/RagA family of outer membrane proteins from the Bacteriodetes. While many TonB-dependent outer membrane receptors are associated with siderophore import, this family seems to include generalized nutrient receptors that may convey fairly large oligomers of pr...

[]

0

[ "NCBIFAM" ]

[ "TIGR04057" ]

[ "SusC_RagA_signa" ]

[ 87685 ]

1

[]

0

[ "5fq6", "5fq7", "5fq8", "5t3r", "5t4y", "6sli", "6slj", "6sln", "6sm3", "6sml", "6smq", "6z8i", "6z9a", "6zaz", "6zlt", "6zlu", "6zm1", "8a9y", "8aa0", "8aa1", "8aa2", "8aa3", "8aa4", "8ypt", "8ypu" ]

25

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "unclassified Caudoviricetes", "unclassified sequences" ]

[ 86876, 59, 8, 742 ]

4

[]

0

true

Conserved_site

TonB-dependent outer membrane protein SusC/RagA, conserved site

TonB-dep_OMP_SusC/RagA_CS

9

IPR023998

23,998

Ferric aerobactin reductase IutB-like

FCR-like

Family

500

false

Members of this protein family are 2Fe-2S cluster binding proteins, found regularly in the context of siderophore transporters, including Ferric aerobactin reductase IutB from Vibrio vulnificus (FCR) [ , ]. Members are distantly related to FhuF from E. coli, a ferric iron reductase linked to removal of iron from hydrox...

[]

0

[ "NCBIFAM" ]

[ "TIGR03950" ]

[ "sidero_Fe_reduc" ]

[ 500 ]

1

[]

0

[]

0

[ "PUB00055062", "PUB00151532", "PUB00151533" ]

[ "14756576", "28150143", "32681432" ]

[ "FhuF, part of a siderophore-reductase system.", "IutB participates in the ferric-vulnibactin utilization system in Vibrio vulnificus M2799.", "VuuB and IutB reduce ferric-vulnibactin in Vibrio vulnificus M2799." ]

[ 2004, 2017, 2020 ]

3

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 493, 7 ]

2

[]

0

true

Family

Ferric aerobactin reductase IutB-like

FCR-like

3

IPR023999

23,999

Formate transporter FocA

Formate_transptr_FocA

Family

2,233

false

FocA (formate channel A) forms a pentameric formate-selective channel through the plasma membrane, involved in the bidirectional transport of formate during mixed-acid fermentation [ , , , , ]. It functions to maintain relatively constant intracellular formate levels during growth, using different mechanisms for efflux...

[ "GO:0015499", "GO:0015724", "GO:0016020" ]

[ "formate transmembrane transporter activity", "formate transport", "membrane" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "NCBIFAM" ]

[ "TIGR04060" ]

[ "formate_focA" ]

[ 2233 ]

1

[]

0

[ "3kcu", "3kcv", "3kly", "3klz", "3q7k", "9g49", "9g4d", "9i3k" ]

8

[ "PUB00055063", "PUB00060282", "PUB00060283", "PUB00060284", "PUB00101342", "PUB00101343" ]

[ "19940917", "21493860", "20041954", "20010838", "35390794", "35377837" ]

[ "Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel.", "pH-dependent gating in a FocA formate channel.", "Unexpected oligomeric structure of the FocA formate channel of Escherichia coli : a paradigm for the formate-nitrite transporter family of integral membrane proteins.", ...

[ 2009, 2011, 2010, 2010, 2022, 2022 ]

6

[ "IPR000292" ]

[]

1

0

1

[ "Bacteria", "Beauveria bassiana D1-5", "metagenomes" ]

[ 2229, 1, 3 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Formate transporter FocA

Formate_transptr_FocA

6

IPR024000

24,000

Conserved hypothetical protein CHP04046, FMN-dependent

CHP04046_FMN-dependent

Family

1,322

false

Members of this protein family belong to a conserved seven-gene biosynthetic cluster found sparsely in Cyanobacteria, Proteobacteria, and Actinobacteria. Distant homologies to characterised proteins suggest that members are enzymes dependent on a flavinoid cofactor.

[]

0

[ "NCBIFAM" ]

[ "TIGR04046" ]

[ "MSMEG_0569_nitr" ]

[ 1322 ]

1

[ "GP" ]

[ "GenProp0939" ]

[ "GP:GenProp0939" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "freshwater metagenome" ]

[ 1318, 4 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP04046, FMN-dependent

CHP04046_FMN-dependent

6

IPR024001

24,001

Cysteine-rich peptide, radical SAM maturase, CcpM

Cys-rich_pep_rSAM_mat_CcpM

Family

177

false

Members of this family are radical SAM enzymes that occur next to clostridial Cys-rich predicted bacteriocin (or other class of ribosomal natural product) precursors (see families and ). They include a TIGR04085 C-terminal additional 4Fe4S cluster-binding domain that is associated with peptide modification by radical S...

[]

0

[ "NCBIFAM" ]

[ "TIGR04068" ]

[ "rSAM_ocin_clost" ]

[ 177 ]

1

[ "GP" ]

[ "GenProp0945" ]

[ "GP:GenProp0945" ]

1

[]

0

[ "PUB00055953" ]

[ "21478363" ]

[ "Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification." ]

[ 2011 ]

1

[ "IPR023867" ]

[]

1

0

1

[ "Bacteria" ]

[ 177 ]

1

[]

0

true

Family

Cysteine-rich peptide, radical SAM maturase, CcpM

Cys-rich_pep_rSAM_mat_CcpM

9

IPR024003

24,003

Putative luciferase-like monooxygenase, KPN01858

Luciferase-like_KPN01858

Family

777

false

This protein family consists of luciferase-like monooxygenases (LLM), and include KPN_01858 from Klebsiella pneumoniae as a representative member. Most are from species that lack F420 biosynthesis, so the family is likely to bind FMN as its cofactor. This family is closely associated with a binding protein-dependent AB...

[]

0

[ "NCBIFAM" ]

[ "TIGR04027" ]

[ "LLM_KPN_01858" ]

[ 777 ]

1

[ "GP" ]

[ "GenProp0935" ]

[ "GP:GenProp0935" ]

1

[ "8k74" ]

1

[]

0

[]

0

null

[ "Bacteria", "Beauveria bassiana D1-5" ]

[ 776, 1 ]

2

[]

0

true

Family

Putative luciferase-like monooxygenase, KPN01858

Luciferase-like_KPN01858

5

IPR024005

24,005

Colanic acid biosynthesis, acetyltransferase, WcaF

Colanic_acid_synth_WcaF

Family

775

false

This acetyltransferase is believed to catalyze the addition of the acetyl group that is attached through an O linkage to the first fucosyl residue of the colanic acid repetitive unit (E unit) [ ].

[]

0

[ "NCBIFAM" ]

[ "TIGR04008" ]

[ "WcaF" ]

[ 775 ]

1

[]

0

[]

0

[ "PUB00008202" ]

[ "8759852" ]

[ "Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid." ]

[ 1996 ]

1

[]

0

null

[ "Gammaproteobacteria" ]

[ 775 ]

1

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Colanic acid biosynthesis, acetyltransferase, WcaF

Colanic_acid_synth_WcaF

5

IPR024006

24,006

Alternate signal-mediated exported protein, actinobacteria

Alt_signal_exp_actinobact

Family

688

false

Members of this Actinobacterial protein family contain the signal peptide domain , for the variant SipW form of the signal peptidase I family. The remainder of this protein, however, differs from families such as Peptidase_M73 ( ) and YqxM ( ) that share the same signal peptide domain. The two known targets for export ...

[]

0

[ "NCBIFAM" ]

[ "TIGR04089" ]

[ "exp_by_SipW_III" ]

[ 688 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "Opisthokonta", "metagenomes" ]

[ 682, 3, 3 ]

3

[]

0

true

Family

Alternate signal-mediated exported protein, actinobacteria

Alt_signal_exp_actinobact

8

IPR024007

24,007

[FeFe]-hydrogenase maturation HydG, radical SAM

FeFe-hyd_mat_HydG

Family

2,100

false

This entry describes the radical SAM protein HydG. It is part of an enzyme metallocentre maturation system, working together with GTP-binding protein HydF and another radical SAM enzyme, HydE, in H-cluster maturation in [FeFe] hydrogenases.

[]

0

[ "SFLD", "NCBIFAM" ]

[ "SFLDF00319", "TIGR03955" ]

[ "Fe_hydrogenase_maturase_(HydG-", "rSAM_HydG" ]

[ 1954, 2100 ]

2

[ "GP" ]

[ "GenProp0914" ]

[ "GP:GenProp0914" ]

1

[ "4rtb", "4wcx" ]

2

[]

0

[ "IPR034428" ]

[]

1

0

1

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 2004, 75, 21 ]

3

[]

0

true

Family

[FeFe]-hydrogenase maturation HydG, radical SAM

FeFe-hyd_mat_HydG

8

IPR024008

24,008

BsaA-like SipW-dependent biofilm matrix protein

BsaA

Family

331

false

Members of this largely Clostridial protein family contain the signal peptide, for the variant SipW form of the signal peptidase I family. The remainder of this protein, however, differs from families such as Peptidase_M73 ( ) and YqxM that share the same signal peptide domain. The two known targets for export by the S...

[]

0

[ "NCBIFAM" ]

[ "TIGR04090" ]

[ "exp_by_SipW_IV" ]

[ 331 ]

1

[]

0

[]

0

[ "PUB00106814" ]

[ "32737303" ]

[ "Temperature-regulated heterogeneous extracellular matrix gene expression defines biofilm morphology in Clostridium perfringens." ]

[ 2020 ]

1

[]

0

null

[ "Bacillota" ]

[ 331 ]

1

[]

0

true

Family

BsaA-like SipW-dependent biofilm matrix protein

BsaA

4

IPR024010

24,010

Colanic acid biosynthesis, glycosyl transferase, WcaE

Colanic_acid_synth_WcaE

Family

866

false

This entry represents the putative glycosyl transferase gene product of wcaE, which is thought to be involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species [ ].

[]

0

[ "NCBIFAM" ]

[ "TIGR04009" ]

[ "wcaE" ]

[ 866 ]

1

[]

0

[]

0

[ "PUB00008202" ]

[ "8759852" ]

[ "Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid." ]

[ 1996 ]

1

[]

0

null

[ "Beauveria bassiana D1-5", "Gammaproteobacteria" ]

[ 1, 865 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Colanic acid biosynthesis, glycosyl transferase, WcaE

Colanic_acid_synth_WcaE

9

IPR024011

24,011

Natural product biosynthesis luciferase-like monooxygenase domain

Biosynth_lucif-like_mOase_dom

Domain

2,022

false

This entry describes a type of bacterial luciferase-like monooxygenase (LLM) domain that regularly occurs within large non-ribosomal protein synthases/polyketide synthases, as well as smaller proteins. Luciferase-like monooxygenases include members that bind either FMN or F420. FMN is the more likely binding partner in...

[]

0

[ "NCBIFAM" ]

[ "TIGR04020" ]

[ "seco_metab_LLM" ]

[ 2022 ]

1

[]

0

[ "6ket" ]

1

[]

0

[ "IPR011251" ]

[]

1

0

1

[ "Bacteria", "Eukaryota", "ecological metagenomes" ]

[ 2014, 2, 6 ]

3

[]

0

true

Domain

Natural product biosynthesis luciferase-like monooxygenase domain

Biosynth_lucif-like_mOase_dom

2

IPR024013

24,013

Putative colanic acid polymerase WcaD

WcaD

Family

999

false

This entry represents WcaD proteins involved in colanic acid biosynthesis in bacteria. WcaD is a putative colanic acid polymerase that functions in slime polysaccharide biosynthesis [ ]. These proteins are multi-pass membrane proteins localised to the inner membrane with multiple transmembrane helices. Members are foun...

[]

0

[ "PFAM", "NCBIFAM" ]

[ "PF27321", "TIGR04010" ]

[ "WcaD", "WcaD" ]

[ 999, 872 ]

2

[]

0

[]

0

[ "PUB00008202", "PUB00106806" ]

[ "8759852", "34159784" ]

[ "Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid.", "Tracking Colanic Acid Repeat Unit Formation from Stepwise Biosynthesis Inactivation in Escherichia coli." ]

[ 1996, 2021 ]

2

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 996, 3 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Putative colanic acid polymerase WcaD

WcaD

4

IPR024014

24,014

FMNH(2)-dependent dimethylsulfone monooxygenase SfnG

DMSO2_SphG

Family

2,743

false

This family of FMNH2-dependent members of the luciferase-like monooxygenase (LLM) family includes SfnG, a monooxygenase that converts dimethylsulphone (DMSO2) to methanesulphonate [ ]. This step can be followed immediately by methanesulphonate sulphonatase (an alkanesulphonate monooxygenase - see ) for the FMNH2-depend...

[]

0

[ "NCBIFAM" ]

[ "TIGR04021" ]

[ "LLM_DMSO2_sfnG" ]

[ 2743 ]

1

[ "GP" ]

[ "GenProp0934" ]

[ "GP:GenProp0934" ]

1

[ "8t0u", "8t0w" ]

2

[ "PUB00055065" ]

[ "17768252" ]

[ "Transcriptional regulation of the sulfate-starvation-induced gene sfnA by a sigma54-dependent activator of Pseudomonas putida." ]

[ 2007 ]

1

[ "IPR050172" ]

[]

1

0

1

[ "Bacteria", "Eukaryota", "Halobacteriales", "metagenomes" ]

[ 2426, 296, 12, 9 ]

4

[ "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)" ]

[ 2 ]

1

true

Family

FMNH(2)-dependent dimethylsulfone monooxygenase SfnG

DMSO2_SphG

8

IPR024015

24,015

Pyridoxamine 5'-phosphate oxidase, probable FMN-dependent, Alr4036-like

Pyridox_Oxase_FMN-dep_Alr4036

Family

235

false

Pyridoxamine 5'-phosphate oxidase ( ) is an enzyme that is involved in the de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate. It oxidizes pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P. The enzyme requires the presence of flavin mononucleotide (FMN) as a cofactor, although there is ...

[]

0

[ "NCBIFAM" ]

[ "TIGR04026" ]

[ "PPOX_FMN_cyano" ]

[ 235 ]

1

[]

0

[ "2i51" ]

1

[ "PUB00001735", "PUB00002199", "PUB00002264", "PUB00055044", "PUB00155385" ]

[ "8586283", "1356963", "7896706", "20675471", "23897464" ]

[ "Molecular analysis of genes encoding phenazine biosynthesis in the biological control bacterium. Pseudomonas aureofaciens 30-84.", "Characterization of the complex pdxH-tyrS operon of Escherichia coli K-12 and pleiotropic phenotypes caused by pdxH insertion mutations.", "Sterol uptake induced by an impairment ...

[ 1995, 1992, 1995, 2010, 2013 ]

5

[ "IPR000659" ]

[]

1

0

1

[ "Bacteria", "Chlorophyta" ]

[ 226, 9 ]

2

[]

0

true

Family

Pyridoxamine 5'-phosphate oxidase, probable FMN-dependent, Alr4036-like

Pyridox_Oxase_FMN-dep_Alr4036

8

IPR024016

24,016

Conserved hypothetical protein CHP04064, radical SAM

CHP04064_rSAM

Family

17

false

Members of this family are radical SAM enzymes that occur co-clustered with Nif11-related bacteriocin precursors, as described by TIGRFAMs model . They could be involved a Nif11-class bacteriocin maturation.

[]

0

[ "NCBIFAM" ]

[ "TIGR04064" ]

[ "rSAM_nif11" ]

[ 17 ]

1

[ "GP" ]

[ "GenProp0861" ]

[ "GP:GenProp0861" ]

1

[]

0

[]

0

[ "IPR023867" ]

[]

1

0

1

[ "Bacteria", "bioreactor metagenome" ]

[ 16, 1 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP04064, radical SAM

CHP04064_rSAM

8

IPR024017

24,017

Petide cyclisation enzyme, radical SAM

Pep_cycl_rSAM

Family

31

false

Members of this family are radical SAM enzymes that appear to perform a cyclisation on an adjacent peptide from family [ ]. Genomes with the complete system include Streptococcus thermophilus LMD-9 and Lactococcus lactis subsp. cremoris MG1363, among others.

[]

0

[ "SFLD", "NCBIFAM" ]

[ "SFLDF00347", "TIGR04080" ]

[ "KxxxW_cyclic_peptide_maturase_", "rSAM_pep_cyc" ]

[ 12, 30 ]

2

[ "GP" ]

[ "GenProp0954" ]

[ "GP:GenProp0954" ]

1

[ "5v1q", "5v1s", "5v1t" ]

3

[ "PUB00055042" ]

[ "17921293" ]

[ "Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?" ]

[ 2007 ]

1

[]

0

null

[ "Bacteria" ]

[ 31 ]

1

[]

0

true

Family

Petide cyclisation enzyme, radical SAM

Pep_cycl_rSAM

6

IPR024018

24,018

Conserved hypothetical protein CHP04083, radical SAM

CHP04083_rSAM

Family

157

false

Members of this family are radical SAM enzymes, homologous to a variety of other peptide-modifying radical SAM, and found primarily in methanogenic archaea.

[]

0

[ "NCBIFAM" ]

[ "TIGR04083" ]

[ "rSAM_pep_methan" ]

[ 157 ]

1

[ "GP" ]

[ "GenProp0992" ]

[ "GP:GenProp0992" ]

1

[]

0

[]

0

[ "IPR023867" ]

[]

1

0

1

[ "Bacteria", "Methanobacteriota", "ecological metagenomes" ]

[ 4, 148, 5 ]

3

[]

0

true

Family

Conserved hypothetical protein CHP04083, radical SAM

CHP04083_rSAM

8

IPR024019

24,019

Conserved hypothetical protein CHP04096

CHP04096

Family

750

false

Members of this protein family show distant local sequence similarity to a number of S-adenosyl-methionine-dependent methyltransferases. The family is identified by Partial Phylogenetic Profiling as closely tied to the DNA phosphorothioation system (dnd), and members are found adjacent to dnd genes in at least 13 speci...

[]

0

[ "NCBIFAM" ]

[ "TIGR04096" ]

[ "dnd_rel_methyl" ]

[ 750 ]

1

[]

0

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 735, 15 ]

2

[]

0

true

Family

Conserved hypothetical protein CHP04096

CHP04096

5

IPR024020

24,020

Anti sigma-R factor, mycothiol system,RsrA

Anit_sigma_mycothiol_RsrA

Family

3,529

false

Members of this family are the anti-sigma-R factor RsrA, which contains a CXXC motif as a thiol-disulphide redox switch. It interacts with sigma-R. It regulates and is regulated by the mycothiol system, which occurs in many actinomycetes [ ].

[]

0

[ "NCBIFAM" ]

[ "TIGR03988" ]

[ "antisig_RsrA" ]

[ 3529 ]

1

[ "GP" ]

[ "GenProp0923" ]

[ "GP:GenProp0923" ]

1

[ "5frf", "5frh" ]

2

[ "PUB00055066" ]

[ "18430082" ]

[ "Mycothiol regulates and is regulated by a thiol-specific antisigma factor RsrA and sigma(R) in Streptomyces coelicolor." ]

[ 2008 ]

1

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 3497, 32 ]

2

[]

0

true

Family

Anti sigma-R factor, mycothiol system,RsrA

Anit_sigma_mycothiol_RsrA

4

IPR024021

24,021

[FeFe]-hydrogenase maturation HydE, radical SAM

FeFe-hyd_HydE_rSAM

Family

2,253

false

This entry describes the radical SAM protein HydE, one of a pair of radical SAM proteins, along with GTP-binding protein HydF, for maturation of [FeFe]-hydrogenase in Chlamydomonas reinhardtii and numerous bacteria [ , ].

[]

0

[ "SFLD", "NCBIFAM" ]

[ "SFLDF00348", "TIGR03956" ]

[ "FeFe_hydrogenase_maturase_(Hyd", "rSAM_HydE" ]

[ 1764, 2249 ]

2

[ "GP" ]

[ "GenProp0914" ]

[ "GP:GenProp0914" ]

1

[ "3ciw", "3cix", "3iix", "3iiz", "4jxc", "4jy8", "4jy9", "4jyd", "4jye", "4jyf", "5fep", "5fes", "5few", "5fex", "5fez", "5ff0", "5ff2", "5ff3", "5ff4", "7o1o", "7o1p", "7o1s", "7o1t", "7o25", "7o26", "8qmk", "8qml", "8qmm", "8qmn" ]

29

[ "PUB00055029", "PUB00055110" ]

[ "15082711", "16513746" ]

[ "Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase.", "Functional studies of [FeFe] hydrogenase maturation in an Escherichia coli biosynthetic system." ]

[ 2004, 2006 ]

2

[ "IPR034422" ]

[]

1

0

1

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 2203, 28, 22 ]

3

[]

0

true

Family

[FeFe]-hydrogenase maturation HydE, radical SAM

FeFe-hyd_HydE_rSAM

5

IPR024022

24,022

Transcription regulator HTH, surface antigen

Tscrpt_reg_HTH_surface_antigen

Family

162

false

This protein is found adjacent to various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK ...

[]

0

[ "NCBIFAM" ]

[ "TIGR04094" ]

[ "adjacent_YSIRK" ]

[ 162 ]

1

[]

0

[]

0

[ "PUB00055067" ]

[ "19865839" ]

[ "Streptococcal protective antigens (Spa): a new family of type-specific proteins of group A streptococci." ]

[ 2010 ]

1

[]

0

null

[ "Bacillati" ]

[ 162 ]

1

[]

0

true

Family

Transcription regulator HTH, surface antigen

Tscrpt_reg_HTH_surface_antigen

7

IPR024023

24,023

His-Xaa-Ser system radical SAM maturase HxsB

rSAM_paired_HxsB

Family

689

false

This entry describes HxsB, one of a pair of uncharacterised radical SAM proteins, regularly found in the context of a small protein with four or more repeats of the tripeptide His-Xaa-Ser (HXS). This enzyme may be be part of a peptide modification system.

[]

0

[ "NCBIFAM" ]

[ "TIGR03978" ]

[ "rSAM_paired_1" ]

[ 689 ]

1

[ "GP" ]

[ "GenProp0921" ]

[ "GP:GenProp0921" ]

1

[]

0

[]

0

[ "IPR023867" ]

[]

1

0

1

[ "Bacteria", "Nanobdellati", "metagenomes" ]

[ 683, 2, 4 ]

3

[]

0

true

Family

His-Xaa-Ser system radical SAM maturase HxsB

rSAM_paired_HxsB

5

IPR024024

24,024

D-alanyl transfer protein DltB

DltB

Family

2,201

false

Members of this protein family are DltB, part of a four-gene operon for D-alanyl-lipoteichoic acid biosynthesis that is present in the vast majority of low-GC Gram-positive organisms [ ]. It is an O-acyltransferase that catalyzes D-alanylation of both teichoic acid and lipoteichoic acid (LTA) [ ]. D-alanylation of LTA ...

[ "GO:0016746", "GO:0070395" ]

[ "acyltransferase activity", "lipoteichoic acid biosynthetic process" ]

[ "molecular_function", "biological_process" ]

2

[ "PIRSF", "NCBIFAM" ]

[ "PIRSF500216", "TIGR04091" ]

[ "DltB", "LTA_dltB" ]

[ 2068, 2185 ]

2

[ "EC", "GP", "GP", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METAC...

[ "2.3.1.-", "GenProp0958", "GenProp1398", "PWY-3602", "PWY-361", "PWY-4801", "PWY-4922", "PWY-5048", "PWY-5139", "PWY-5268", "PWY-5284", "PWY-5292", "PWY-5307", "PWY-5313", "PWY-5317", "PWY-5318", "PWY-5353", "PWY-5400", "PWY-5473", "PWY-5475", "PWY-5477", "PWY-5660", "PWY...

[ "EC:2.3.1.-", "GP:GenProp0958", "GP:GenProp1398", "METACYC:PWY-3602", "METACYC:PWY-361", "METACYC:PWY-4801", "METACYC:PWY-4922", "METACYC:PWY-5048", "METACYC:PWY-5139", "METACYC:PWY-5268", "METACYC:PWY-5284", "METACYC:PWY-5292", "METACYC:PWY-5307", "METACYC:PWY-5313", "METACYC:PWY-5317",...

221

[ "6bug", "6buh", "6bui", "8jem", "8jes", "8jf2" ]

6

[ "PUB00013853", "PUB00068169", "PUB00095085" ]

[ "7797557", "9158726", "30283133" ]

[ "Incorporation of D-alanine into lipoteichoic acid and wall teichoic acid in Bacillus subtilis. Identification of genes and regulation.", "The dlt operon in the biosynthesis of D-alanyl-lipoteichoic acid in Lactobacillus casei.", "Crystal structure of a membrane-bound O-acyltransferase." ]

[ 1995, 1996, 2018 ]

3

[ "IPR024194" ]

[]

1

0

1

[ "Bacteria", "metagenomes" ]

[ 2198, 3 ]

2

[]

0

true

Family

D-alanyl transfer protein DltB

DltB

9

IPR024025

24,025

SCIFF radical SAM maturase

SCIFF_rSAM_maturase

Family

1,701

false

Members of this protein family are predicted SPASM domain-containing radical SAM enzymes universally associated with Six Cysteines in Forty-Five protein, or SCIFF ( ), a predicted ribosomal natural product precursor that is nearly universal in the class Clostridia. Similarity of this family to radical SAM maturases (e....

[]

0

[ "NCBIFAM" ]

[ "TIGR03974" ]

[ "rSAM_six_Cys" ]

[ 1701 ]

1

[ "GP" ]

[ "GenProp0919" ]

[ "GP:GenProp0919" ]

1

[ "5wgg", "5why" ]

2

[ "PUB00055953", "PUB00106906" ]

[ "21478363", "28704043" ]

[ "Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.", "Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides." ]

[ 2011, 2017 ]

2

[ "IPR023867" ]

[]

1

0

1

[ "Bacteria", "unclassified sequences" ]

[ 1685, 16 ]

2

[]

0

true

Family

SCIFF radical SAM maturase

SCIFF_rSAM_maturase

5

IPR024026

24,026

3'-RNA ribose 2'-O-methyltransferase, Hen1, bacterial

3'-RNA_MeTfrase_Hen1_bac

Family

2,300

false

This entry represents bacterial Hen1, which is a 3' terminal RNA ribose 2'-O-methyltransferase that is involved in bacterial RNA repair [ ]. Hen1 forms a heterotetramer with Pnkp. The heterotetramer has been shown to repair transfer RNAs cleaved by ribotoxins in vitro [ ].

[]

0

[ "NCBIFAM" ]

[ "TIGR04074" ]

[ "bacter_Hen1" ]

[ 2300 ]

1

[ "GP" ]

[ "GenProp0948" ]

[ "GP:GenProp0948" ]

1

[ "4dqz", "4drf", "4e6n" ]

3

[ "PUB00055068", "PUB00056235" ]

[ "20007328", "19815768" ]

[ "Bacterial Hen1 is a 3' terminal RNA ribose 2'-O-methyltransferase component of a bacterial RNA repair cassette.", "Reconstituting bacterial RNA repair and modification in vitro." ]

[ 2010, 2009 ]

2

[ "IPR026610" ]

[]

1

0

1

[ "Bacteria", "Geodia barretti", "freshwater metagenome" ]

[ 2296, 3, 1 ]

3

[]

0

true

Family

3'-RNA ribose 2'-O-methyltransferase, Hen1, bacterial

3'-RNA_MeTfrase_Hen1_bac

4

IPR024027

24,027

Colanic acid biosynthesis, acetyltransferase, WcaB

Colanic_acid_synth_WcaB

Family

687

false

This protein family is one of the acetyl transferases involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species [ ].

[ "GO:0016747" ]

[ "acyltransferase activity, transferring groups other than amino-acyl groups" ]

[ "molecular_function" ]

1

[ "NCBIFAM" ]

[ "TIGR04016" ]

[ "WcaB" ]

[ 687 ]

1

[ "EC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC"...

[ "2.3.1.-", "PWY-3602", "PWY-361", "PWY-4801", "PWY-4922", "PWY-5048", "PWY-5139", "PWY-5268", "PWY-5284", "PWY-5292", "PWY-5307", "PWY-5313", "PWY-5317", "PWY-5318", "PWY-5353", "PWY-5400", "PWY-5473", "PWY-5475", "PWY-5477", "PWY-5660", "PWY-5679", "PWY-5710", "PWY-5794"...

[ "EC:2.3.1.-", "METACYC:PWY-3602", "METACYC:PWY-361", "METACYC:PWY-4801", "METACYC:PWY-4922", "METACYC:PWY-5048", "METACYC:PWY-5139", "METACYC:PWY-5268", "METACYC:PWY-5284", "METACYC:PWY-5292", "METACYC:PWY-5307", "METACYC:PWY-5313", "METACYC:PWY-5317", "METACYC:PWY-5318", "METACYC:PWY-53...

219

[]

0

[ "PUB00008202" ]

[ "8759852" ]

[ "Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid." ]

[ 1996 ]

1

[ "IPR005881" ]

[]

1

0

1

[ "Gammaproteobacteria", "Oryza sativa subsp. indica" ]

[ 686, 1 ]

2

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Family

Colanic acid biosynthesis, acetyltransferase, WcaB

Colanic_acid_synth_WcaB

7

IPR024028

24,028

Polynucleotide kinase-phosphatase, bacterial

PNKP_bac

Family

2,358

false

Members of this family are the bacterial polynucleotide kinase-phosphatase (Pnkp) enzymes that prepare broken RNA termini for sealing by RNA ligase [ ]. Their genes co-occur with genes for the 3' terminal RNA ribose 2'-O-methyltransferase Hen1, and the pair are thought to form a bacterial RNA repair cassette, where a c...

[]

0

[ "NCBIFAM" ]

[ "TIGR04075" ]

[ "bacter_Pnkp" ]

[ 2358 ]

1

[ "GP" ]

[ "GenProp0948" ]

[ "GP:GenProp0948" ]

1

[]

0

[ "PUB00055068", "PUB00055069" ]

[ "20007328", "17986465" ]

[ "Bacterial Hen1 is a 3' terminal RNA ribose 2'-O-methyltransferase component of a bacterial RNA repair cassette.", "Characterization of the 2',3' cyclic phosphodiesterase activities of Clostridium thermocellum polynucleotide kinase-phosphatase and bacteriophage lambda phosphatase." ]

[ 2010, 2007 ]

2

[]

0

null

[ "Bacteria", "Geodia barretti", "freshwater metagenome" ]

[ 2352, 5, 1 ]

3

[]

0

true

Family

Polynucleotide kinase-phosphatase, bacterial

PNKP_bac

6

IPR024029

24,029

Pyridoxamine 5-phosphate oxidase, FMN-dependent

Pyridox_Oxase_FMN-dep

Family

6,283

false

Pyridoxamine 5'-phosphate oxidase ( ) is an enzyme that is involved in the de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate. It oxidizes pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P. The enzyme requires the presence of flavin mononucleotide (FMN) as a cofactor, although there is ...

[]

0

[ "NCBIFAM" ]

[ "TIGR04025" ]

[ "PPOX_FMN_DR2398" ]

[ 6283 ]

1

[]

0

[]

0

[ "PUB00055044" ]

[ "20675471" ]

[ "Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria." ]

[ 2010 ]

1

[]

0

null

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 6237, 6, 40 ]

3

[]

0

true

Family

Pyridoxamine 5-phosphate oxidase, FMN-dependent

Pyridox_Oxase_FMN-dep

6

IPR024030

24,030

AIR synthase-related protein, sll0787 family

AIR_synthase-rel_sll0787

Family

884

false

This entry represents a family of uncharacterised proteins, including sll0787 from Synechocystis sp. PCC 6803. They resemble the C-terminal region of MSMEG_0567 from Mycobacterium smegmatis, where the N-terminal is a GNAT family N-acetyltransferase.

[]

0

[ "NCBIFAM" ]

[ "TIGR04049" ]

[ "AIR_rel_sll0787" ]

[ 884 ]

1

[ "GP" ]

[ "GenProp0939" ]

[ "GP:GenProp0939" ]

1

[]

0

[]

0

[ "IPR011413" ]

[]

1

0

1

[ "Bacteria", "Ricinus communis", "ecological metagenomes" ]

[ 880, 1, 3 ]

3

[]

0

true

Family

AIR synthase-related protein, sll0787 family

AIR_synthase-rel_sll0787

5

IPR024031

24,031

PPOX class F420-dependent enzyme, MSMEG_5819/OxyR family

MSMEG_5819/OxyR

Family

1,555

false

F420 (or 8-hydroxy-5-deazaflavin) is a coenzyme involved in redox reactions in methanogens. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. This subfamily...

[]

0

[ "NCBIFAM" ]

[ "TIGR04023" ]

[ "PPOX_MSMEG_5819" ]

[ 1555 ]

1

[ "GP" ]

[ "GenProp0002" ]

[ "GP:GenProp0002" ]

1

[]

0

[ "PUB00055044", "PUB00067298" ]

[ "20675471", "23621493" ]

[ "Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.", "Uncovering the Enzymes that Catalyze the Final Steps in Oxytetracycline Biosynthesis." ]

[ 2010, 2013 ]

2

[]

0

null

[ "Archaea", "Bacillati", "freshwater metagenome" ]

[ 6, 1524, 25 ]

3

[]

0

true

Family

PPOX class F420-dependent enzyme, MSMEG_5819/OxyR family

MSMEG_5819/OxyR

6

IPR024032

24,032

His-Xaa-Ser system radical SAM maturase HxsC

rSAM_paired_HxsC

Family

671

false

This entry describes HxsC, one of a pair of uncharacterised radical SAM proteins, regularly found in the context of a small protein with four or more repeats of the tripeptide His-Xaa-Ser (HXS). This enzyme may be be part of a peptide modification system.

[]

0

[ "SFLD", "NCBIFAM" ]

[ "SFLDG01103", "TIGR03977" ]

[ "Uncharacterised_Radical_SAM_Su", "rSAM_pair_HxsC" ]

[ 660, 663 ]

2

[ "GP" ]

[ "GenProp0921" ]

[ "GP:GenProp0921" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "Fermentimicrarchaeum limneticum", "metagenomes" ]

[ 666, 1, 4 ]

3

[]

0

true

Family

His-Xaa-Ser system radical SAM maturase HxsC

rSAM_paired_HxsC

4

IPR024033

24,033

Oxamate carbamoyltransferase subunit AllG, helical domain

OXTCase_su_AllG_h-dom

Homologous_superfamily

3,062

false

This superfamily represents a domain found in the N-terminal region of a conserved protein (YlbE) of unknown function from Escherichia coli K12. It consists of a mainly α orthogonal bundle . This domain is associated with and immediately N-terminal to another domain of unknown function defined by (DUF1116). Tis domain ...

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:1.10.10.660" ]

[ "" ]

[ 3062 ]

1

[]

0

[ "3clq" ]

1

[ "PUB00155434" ]

[ "38888336" ]

[ "Oxamic transcarbamylase of Escherichia coli is encoded by the three genes allFGH (formerly fdrA, ylbE, and ylbF)." ]

[ 2024 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "metagenomes" ]

[ 21, 2965, 5, 71 ]

4

[ "Escherichia coli (strain K12)" ]

[ 2 ]

1

true

Homologous_superfamily

Oxamate carbamoyltransferase subunit AllG, helical domain

OXTCase_su_AllG_h-dom

6

IPR024034

24,034

ATPase, F1/V1 complex, beta/alpha subunit, C-terminal

ATPase_F1/V1_b/a_C

Homologous_superfamily

66,049

false

This entry represents a domain that is found at the C terminus of the F1 ATP synthase beta subunit and in the C terminus of the V-ATPase alpha and beta subunits. Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some t...

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:1.10.1140.10" ]

[ "" ]

[ 66049 ]

1

[ "EC", "METACYC", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "...

[ "7.1.2.2", "PWY-7980", "R-BTA-1222556", "R-BTA-77387", "R-BTA-917977", "R-BTA-9639288", "R-BTA-983712", "R-CEL-1222556", "R-CEL-1268020", "R-CEL-163210", "R-CEL-77387", "R-CEL-8949613", "R-CEL-917977", "R-CEL-9639288", "R-CEL-983712", "R-CEL-9837999", "R-CFA-1268020", "R-CFA-163210...

[ "EC:7.1.2.2", "METACYC:PWY-7980", "REACTOME:R-BTA-1222556", "REACTOME:R-BTA-77387", "REACTOME:R-BTA-917977", "REACTOME:R-BTA-9639288", "REACTOME:R-BTA-983712", "REACTOME:R-CEL-1222556", "REACTOME:R-CEL-1268020", "REACTOME:R-CEL-163210", "REACTOME:R-CEL-77387", "REACTOME:R-CEL-8949613", "REAC...

72

[ "1bmf", "1cow", "1e1q", "1e1r", "1e79", "1efr", "1fx0", "1h8e", "1h8h", "1kmh", "1mab", "1nbm", "1ohh", "1qo1", "1sky", "1vdz", "1w0j", "1w0k", "2ck3", "2f43", "2hld", "2jdi", "2jiz", "2jj1", "2jj2", "2qe7", "2v7q", "2w6e", "2w6f", "2w6g", "2w6h", "2w6i"...

488

[ "PUB00020603", "PUB00020604", "PUB00068786", "PUB00068787", "PUB00068788", "PUB00068789" ]

[ "15473999", "15078220", "20450191", "18937357", "1385979", "9741106" ]

[ "The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio.", "Mechanisms of ATPases--a multi-disciplinary approach.", "Regulation and isoform function of the V-ATPases.", "New insights into structure-function relationships between archeal AT...

[ 2004, 2004, 2010, 2008, 1992, 1998 ]

6

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 977, 28860, 35506, 706 ]

4

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus",...

[ 23, 2, 3, 14, 1, 7, 2, 2, 24, 9, 2, 2, 39 ]

13

true

Homologous_superfamily

ATPase, F1/V1 complex, beta/alpha subunit, C-terminal

ATPase_F1/V1_b/a_C

3

IPR024035

24,035

MSMEG_0567 GNAT N-acetyltransferase

MSMEG_0567_GNAT

Domain

1,389

false

This entry includes proteins that belong to the GNAT family ( ), in which numerous characterised examples, though not all, are shown to be N-acetyltransferases or to interact with acetyl-CoA. In some instances, this is the N-terminal GNAT domain while in other members represents the full length, such as in sll0787 from...

[]

0

[ "NCBIFAM" ]

[ "TIGR04045" ]

[ "MSMEG_0567_GNAT" ]

[ 1389 ]

1

[ "GP" ]

[ "GenProp0939" ]

[ "GP:GenProp0939" ]

1

[]

0

[]

0

[]

0

null

[ "Bacteria", "ecological metagenomes" ]

[ 1378, 11 ]

2

[]

0

true

Domain

MSMEG_0567 GNAT N-acetyltransferase

MSMEG_0567_GNAT

5

IPR024036

24,036

tRNA-dihydrouridine synthase, putative, C-terminal

tRNA-dHydroUridine_Synthase_C

Homologous_superfamily

25,403

false

This entry represents a C-terminal four-helix bundle domain found in tRNA-dihydrouridine synthases [ ].

[ "GO:0016491" ]

[ "oxidoreductase activity" ]

[ "molecular_function" ]

1

[ "CATHGENE3D" ]

[ "G3DSA:1.10.1200.80" ]

[ "" ]

[ 25403 ]

1

[ "EC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC"...

[ "1.3.1.-", "PWY-2541", "PWY-5292", "PWY-5301", "PWY-5367", "PWY-5393", "PWY-5729", "PWY-5818", "PWY-5956", "PWY-5972", "PWY-5984", "PWY-6088", "PWY-6302", "PWY-6309", "PWY-6332", "PWY-6786", "PWY-6824", "PWY-6944", "PWY-6996", "PWY-7096", "PWY-7154", "PWY-7155", "PWY-7300...

[ "EC:1.3.1.-", "METACYC:PWY-2541", "METACYC:PWY-5292", "METACYC:PWY-5301", "METACYC:PWY-5367", "METACYC:PWY-5393", "METACYC:PWY-5729", "METACYC:PWY-5818", "METACYC:PWY-5956", "METACYC:PWY-5972", "METACYC:PWY-5984", "METACYC:PWY-6088", "METACYC:PWY-6302", "METACYC:PWY-6309", "METACYC:PWY-6...

35

[ "1vhn", "6ei9" ]

2

[ "PUB00032087" ]

[ "15103641" ]

[ "The 1.59 A resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima." ]

[ 2004 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 51, 24776, 110, 466 ]

4

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Homologous_superfamily

tRNA-dihydrouridine synthase, putative, C-terminal

tRNA-dHydroUridine_Synthase_C

9

IPR024037

24,037

Alternate ATP synthase, F1 complex, subunit epsilon

Alt_ATP_synth_F1_esu

Family

845

false

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel ...

[]

0

[ "NCBIFAM" ]

[ "TIGR03166" ]

[ "alt_F1F0_F1_eps" ]

[ 845 ]

1

[]

0

[]

0

[ "PUB00015307", "PUB00020603", "PUB00020604", "PUB00068786", "PUB00068787", "PUB00068788", "PUB00068789" ]

[ "9425287", "15473999", "15078220", "20450191", "18937357", "1385979", "9741106" ]

[ "F0F1-ATPase genes from an archaebacterium, Methanosarcina barkeri.", "The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio.", "Mechanisms of ATPases--a multi-disciplinary approach.", "Regulation and isoform function of the V-ATPases.", ...

[ 1997, 2004, 2004, 2010, 2008, 1992, 1998 ]

7

[ "IPR001469" ]

[]

1

0

1

[ "Bacteria", "Methanomicrobia", "ecological metagenomes" ]

[ 795, 26, 24 ]

3

[]

0

true

Family

Alternate ATP synthase, F1 complex, subunit epsilon

Alt_ATP_synth_F1_esu

1

IPR024038

24,038

MYXO-CTERM protein-sorting domain

MYXO-CTERM

Domain

1,469

false

This entry describes MYXO-CTERM, a C-terminal putative protein sorting domain, analogous to LPXTG ( ) and PEP-CTERM ( ). It is largely restricted to the Myxococcota, a division of the Deltaproteobacteria [ ].

[]

0

[ "NCBIFAM" ]

[ "TIGR03901" ]

[ "MYXO-CTERM" ]

[ 1469 ]

1

[]

0

[]

0

[ "PUB00103726" ]

[ "31975447" ]

[ "MYXO-CTERM sorting tag directs proteins to the cell surface via the type II secretion system." ]

[ 2020 ]

1

[]

0

null

[ "Bacteria", "Eukaryota", "Halobacteriales", "ecological metagenomes" ]

[ 1455, 6, 2, 6 ]

4

[]

0

true

Domain

MYXO-CTERM protein-sorting domain

MYXO-CTERM

9

IPR024041

24,041

Ammonium transporter AmtB-like domain

NH4_transpt_AmtB-like_dom

Domain

57,338

false

This ammonium transporter domain consists of a duplication of 2 structural repeats of five helices each plus one extra C-terminal helix. It has been described as a channel that spans the membrane 11 times [ ].

[ "GO:0008519", "GO:0072488", "GO:0016020" ]

[ "ammonium channel activity", "ammonium transmembrane transport", "membrane" ]

[ "molecular_function", "biological_process", "cellular_component" ]

3

[ "PFAM" ]

[ "PF00909" ]

[ "Ammonium_transp" ]

[ 57338 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "R-BTA-444411", "R-CFA-444411", "R-DDI-1237044", "R-DDI-1247673", "R-DDI-444411", "R-DRE-444411", "R-HSA-1237044", "R-HSA-1247673", "R-HSA-444411", "R-HSA-5619042", "R-HSA-9037628", "R-MMU-1237044", "R-MMU-1247673", "R-MMU-444411", "R-RNO-1237044", "R-RNO-1247673", "R-RNO-444411", ...

[ "REACTOME:R-BTA-444411", "REACTOME:R-CFA-444411", "REACTOME:R-DDI-1237044", "REACTOME:R-DDI-1247673", "REACTOME:R-DDI-444411", "REACTOME:R-DRE-444411", "REACTOME:R-HSA-1237044", "REACTOME:R-HSA-1247673", "REACTOME:R-HSA-444411", "REACTOME:R-HSA-5619042", "REACTOME:R-HSA-9037628", "REACTOME:R-M...

19

[ "1u77", "1u7c", "1u7g", "1xqe", "1xqf", "2b2f", "2b2h", "2b2i", "2b2j", "2nmr", "2nop", "2now", "2npc", "2npd", "2npe", "2npg", "2npj", "2npk", "2ns1", "2nuu", "3b9w", "3b9y", "3b9z", "3bhs", "3c1g", "3c1h", "3c1i", "3c1j", "3hd6", "4nh2", "5aex", "5aez"...

52

[ "PUB00031687" ]

[ "15361618" ]

[ "Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A." ]

[ 2004 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Megaviridae environmental sample", "unclassified sequences" ]

[ 1026, 31093, 24361, 1, 857 ]

5

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus",...

[ 22, 8, 25, 4, 1, 568, 13, 4, 23, 12, 3, 3, 22 ]

13

true

Domain

Ammonium transporter AmtB-like domain

NH4_transpt_AmtB-like_dom

3

IPR024042

24,042

TM1646-like domain superfamily

TM1646-like_dom_sf

Homologous_superfamily

2,424

false

This superfamily represents a domain consisting of a four helix bundle found in uncharacterised proteins.

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:1.20.120.490", "SSF158397" ]

[ "", "" ]

[ 2406, 2421 ]

2

[]

0

[ "2p61", "2qup", "5un5", "5un6", "6y06" ]

5

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "Ignicoccus islandicus DSM 13165", "ecological metagenomes" ]

[ 2397, 11, 1, 15 ]

4

[]

0

true

Homologous_superfamily

TM1646-like domain superfamily

TM1646-like_dom_sf

2

IPR024044

24,044

NifT/FixU barrel-like domain superfamily

NifT/FixU_barrel-like_dom_sf

Homologous_superfamily

1,181

false

This superfamily represents a barrel-like domain found in bacterial proteins NifT/FixU/MosB. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase, although perturbation of nifT expression in Klebsiella pneumoniae has only a limited e...

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:2.40.50.240", "SSF159203" ]

[ "", "" ]

[ 1181, 1181 ]

2

[]

0

[ "2jn4" ]

1

[ "PUB00006373" ]

[ "9139910" ]

[ "Identification and characterization of the nifV-nifZ-nifT gene region from the filamentous cyanobacterium Anabaena sp. strain PCC 7120." ]

[ 1997 ]

1

[]

0

null

[ "Bacteria", "metagenomes" ]

[ 1166, 15 ]

2

[]

0

true

Homologous_superfamily

NifT/FixU barrel-like domain superfamily

NifT/FixU_barrel-like_dom_sf

4

IPR024046

24,046

Flagellar assembly factor FliW domain superfamily

Flagellar_assmbl_FliW_dom_sf

Homologous_superfamily

4,295

false

This superfamily represents the structural domain of flagellar assembly factor FliW. It consists mainly of a β roll.

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:2.30.290.10", "SSF141457" ]

[ "", "" ]

[ 4293, 4295 ]

2

[]

0

[ "2aj7", "5dmb", "5dmd", "5jak" ]

4

[]

0

[]

0

null

[ "Bacteria", "Symbiodiniaceae", "metagenomes" ]

[ 4213, 2, 80 ]

3

[]

0

true

Homologous_superfamily

Flagellar assembly factor FliW domain superfamily

Flagellar_assmbl_FliW_dom_sf

6

IPR024047

24,047

MM3350-like superfamily

MM3350-like_sf

Homologous_superfamily

9,129

false

This domain superfamily is found in several uncharacterised proteins of unknown function. It consists of five α helices and a β roll.

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.10.290.30", "SSF159941" ]

[ "", "" ]

[ 8840, 9101 ]

2

[]

0

[ "2i1s" ]

1

[]

0

[]

0

null

[ "Archaea", "Bacteria", "Cyanophage S-TIM5", "Eukaryota", "metagenomes" ]

[ 251, 7862, 1, 870, 145 ]

5

[]

0

true

Homologous_superfamily

MM3350-like superfamily

MM3350-like_sf

9

IPR024049

24,049

eRF1, domain 1

eRF1_1_sf

Homologous_superfamily

7,136

false

The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [ ]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with doma...

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.30.960.10", "SSF55481" ]

[ "", "" ]

[ 7078, 7132 ]

2

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-72764", "R-BTA-9629569", "R-BTA-975956", "R-BTA-975957", "R-CEL-72764", "R-CEL-9629569", "R-CEL-975956", "R-CEL-975957", "R-DDI-72764", "R-DDI-975956", "R-DDI-975957", "R-DME-72764", "R-DME-9629569", "R-DME-975956", "R-DME-975957", "R-HSA-72764", "R-HSA-9010553", "R-HSA-9629...

[ "REACTOME:R-BTA-72764", "REACTOME:R-BTA-9629569", "REACTOME:R-BTA-975956", "REACTOME:R-BTA-975957", "REACTOME:R-CEL-72764", "REACTOME:R-CEL-9629569", "REACTOME:R-CEL-975956", "REACTOME:R-CEL-975957", "REACTOME:R-DDI-72764", "REACTOME:R-DDI-975956", "REACTOME:R-DDI-975957", "REACTOME:R-DME-7276...

36

[ "1dt9", "2lgt", "2llx", "2mq6", "2mq9", "3agk", "3e1y", "3e20", "3j5y", "3jag", "3jah", "3jai", "3vmf", "4af1", "4crn", "4d5n", "4d61", "5a8l", "5dmq", "5lzt", "5lzu", "5lzv", "6d90", "6hcf", "6hcm", "6ip8", "6p5n", "6xa1", "6zme", "7nwh", "7o80", "8ip8"...

35

[ "PUB00007747" ]

[ "10676813" ]

[ "The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis." ]

[ 2000 ]

1

[]

0

null

[ "Archaea", "Bacteria candidate phyla", "Eukaryota", "Megaviricetes", "metagenomes" ]

[ 1037, 2, 6025, 21, 51 ]

5

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 8, 1, 4, 4, 5, 6, 1, 9, 2, 1, 1, 6 ]

12

true

Homologous_superfamily

eRF1, domain 1

eRF1_1_sf

2

IPR024050

24,050

AICAR transformylase, insert domain superfamily

AICAR_Tfase_insert_dom_sf

Homologous_superfamily

5,235

false

This domain is found in the enzyme 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase (AICARFT). AICARFT can be part of a bifunctional enzyme catalysing the last two steps in de novo purine biosynthesis and having also an IMP (Inosine monophosphate) cyclohydrolase (IMPCHase) functional domain. The bifuncti...

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:1.10.287.440" ]

[ "" ]

[ 5235 ]

1

[ "EC", "EC", "METACYC", "METACYC", "METACYC", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "2.1.2.3", "3.5.4.10", "PWY-6123", "PWY-6124", "PWY-7234", "R-BTA-73817", "R-GGA-419140", "R-HSA-73817", "R-HSA-9725370", "R-MMU-73817", "R-RNO-73817", "R-SCE-73817", "R-SPO-73817" ]

[ "EC:2.1.2.3", "EC:3.5.4.10", "METACYC:PWY-6123", "METACYC:PWY-6124", "METACYC:PWY-7234", "REACTOME:R-BTA-73817", "REACTOME:R-GGA-419140", "REACTOME:R-HSA-73817", "REACTOME:R-HSA-9725370", "REACTOME:R-MMU-73817", "REACTOME:R-RNO-73817", "REACTOME:R-SCE-73817", "REACTOME:R-SPO-73817" ]

13

[ "1g8m", "1m9n", "1oz0", "1p4r", "1pkx", "1pl0", "1thz", "2b1g", "2b1i", "2iu0", "2iu3", "5uy8", "5uz0", "7mgq" ]

14

[ "PUB00025174" ]

[ "11323713" ]

[ "Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis." ]

[ 2001 ]

1

[]

0

null

[ "Bacteria", "Eukaryota", "Viruses", "metagenomes" ]

[ 1472, 3743, 2, 18 ]

4

[ "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Rattus norvegicus", "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)", "Schizosaccharomyces pombe (strai...

[ 3, 2, 2, 5, 1, 1, 3, 2, 1 ]

9

true

Homologous_superfamily

AICAR transformylase, insert domain superfamily

AICAR_Tfase_insert_dom_sf

8

IPR024051

24,051

AICAR transformylase, duplicated domain superfamily

AICAR_Tfase_dup_dom_sf

Homologous_superfamily

32,048

false

This domain is found in the enzyme 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase (AICARFT). AICARFT can be part of a bifunctional enzyme catalysing the last two steps in de novo purine biosynthesis and having also an IMP (Inosine monophosphate) cyclohydrolase (IMPCHase) functional domain. The bifuncti...

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:3.40.140.20" ]

[ "" ]

[ 32048 ]

1

[ "EC", "EC", "METACYC", "METACYC", "METACYC", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "2.1.2.3", "3.5.4.10", "PWY-6123", "PWY-6124", "PWY-7234", "R-BTA-73817", "R-DDI-73817", "R-GGA-419140", "R-HSA-73817", "R-HSA-9725370", "R-MMU-73817", "R-RNO-73817", "R-SCE-73817", "R-SPO-73817" ]

[ "EC:2.1.2.3", "EC:3.5.4.10", "METACYC:PWY-6123", "METACYC:PWY-6124", "METACYC:PWY-7234", "REACTOME:R-BTA-73817", "REACTOME:R-DDI-73817", "REACTOME:R-GGA-419140", "REACTOME:R-HSA-73817", "REACTOME:R-HSA-9725370", "REACTOME:R-MMU-73817", "REACTOME:R-RNO-73817", "REACTOME:R-SCE-73817", "REACT...

14

[ "1g8m", "1m9n", "1oz0", "1p4r", "1pkx", "1pl0", "1thz", "1zcz", "2b1g", "2b1i", "2iu0", "2iu3", "3zzm", "4a1o", "4ehi", "5uy8", "5uz0", "7mgq", "9ou7" ]

19

[ "PUB00025174" ]

[ "11323713" ]

[ "Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis." ]

[ 2001 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Viruses", "unclassified sequences" ]

[ 525, 25485, 5305, 16, 717 ]

5

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus",...

[ 6, 3, 2, 2, 1, 5, 1, 1, 4, 3, 2, 1, 12 ]

13

true

Homologous_superfamily

AICAR transformylase, duplicated domain superfamily

AICAR_Tfase_dup_dom_sf

2

IPR024052

24,052

Phosphopentomutase DeoB cap domain superfamily

Phosphopentomutase_DeoB_cap_sf

Homologous_superfamily

10,251

false

Phosphopentomutase is involved in the purine and pyrimidine salvage pathway of nucleotide synthesis. It catalyses a phosphotransfer on ribose and deoxyribose, converting D-ribose 1-phosphate to D-ribose 5-phosphate, and 2-deoxy-D-ribose 1-phosphate to 2-deoxy-D-ribose 5-phosphate [ ]. Phosphopentomutase is composed of ...

[ "GO:0008973" ]

[ "phosphopentomutase activity" ]

[ "molecular_function" ]

1

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.30.70.1250", "SSF143856" ]

[ "", "" ]

[ 10213, 9605 ]

2

[ "EC", "METACYC" ]

[ "5.4.2.7", "PWY-7180" ]

[ "EC:5.4.2.7", "METACYC:PWY-7180" ]

2

[ "3m7v", "3m8w", "3m8y", "3m8z", "3ot9", "3twz", "3tx0", "3un2", "3un3", "3un5", "3uny", "3uo0", "4lr7", "4lr8", "4lr9", "4lra", "4lrb", "4lrc", "4lrd", "4lre", "4lrf", "4n7t" ]

22

[ "PUB00014944", "PUB00055258" ]

[ "9692190", "21193409" ]

[ "Phosphopentomutase of Bacillus stearothermophilus TH6-2: the enzyme and its gene ppm.", "Bacillus cereus Phosphopentomutase Is an Alkaline Phosphatase Family Member That Exhibits an Altered Entry Point into the Catalytic Cycle." ]

[ 1998, 2011 ]

2

[]

0

null

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 10162, 12, 77 ]

3

[ "Arabidopsis thaliana", "Escherichia coli (strain K12)" ]

[ 1, 2 ]

2

true

Homologous_superfamily

Phosphopentomutase DeoB cap domain superfamily

Phosphopentomutase_DeoB_cap_sf

4

IPR024053

24,053

von Hippel-Lindau disease tumour suppressor, beta domain

VHL_beta_dom

Domain

2,314

false

von Hippel-Landau (pVHL) protein, the gene product of VHL, is a critical regulator of the ubiquitous oxygen-sensing pathway. It is conserved throughout evolution, as its homologues are found in organisms ranging from mammals to Drosophila and Caenorhabditis. pVHL acts as the substrate recognition component of an E3 ubi...

[]

0

[ "PFAM" ]

[ "PF01847" ]

[ "VHL" ]

[ 2314 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-CEL-1234176", "R-CEL-3232142", "R-CEL-8951664", "R-CEL-9706019", "R-CEL-983168", "R-DME-1234176", "R-DME-8951664", "R-DME-9706019", "R-DME-983168", "R-HSA-1234176", "R-HSA-3232142", "R-HSA-8951664", "R-HSA-9682706", "R-HSA-9694686", "R-HSA-9706019", "R-HSA-983168", "R-MMU-1234176"...

[ "REACTOME:R-CEL-1234176", "REACTOME:R-CEL-3232142", "REACTOME:R-CEL-8951664", "REACTOME:R-CEL-9706019", "REACTOME:R-CEL-983168", "REACTOME:R-DME-1234176", "REACTOME:R-DME-8951664", "REACTOME:R-DME-9706019", "REACTOME:R-DME-983168", "REACTOME:R-HSA-1234176", "REACTOME:R-HSA-3232142", "REACTOME:...

26

[ "1lm8", "1lqb", "1vcb", "3zrc", "3zrf", "3ztc", "3ztd", "3zun", "4ajy", "4awj", "4b95", "4b9k", "4bks", "4bkt", "4w9c", "4w9d", "4w9e", "4w9f", "4w9g", "4w9h", "4w9i", "4w9j", "4w9k", "4w9l", "4wqo", "5lli", "5n4w", "5nvv", "5nvw", "5nvx", "5nvy", "5nvz"...

138

[ "PUB00005233", "PUB00022097", "PUB00027102", "PUB00079586", "PUB00079587", "PUB00079588", "PUB00079589", "PUB00079591", "PUB00079592", "PUB00079593", "PUB00079594", "PUB00079595", "PUB00079596", "PUB00079597", "PUB00079598", "PUB00079599", "PUB00079600", "PUB00079601", "PUB000796...

[ "10205047", "12004076", "12050673", "17998064", "19671042", "19657325", "19414081", "19402056", "19261475", "19243301", "19216840", "15611513", "18095884", "17932373", "17255293", "17245122", "18323857", "16728571", "16531988", "16869749" ]

[ "Structure of the VHL-ElonginC-ElonginB complex: implications for VHL tumor suppressor function.", "Structure of an HIF-1alpha -pVHL complex: hydroxyproline recognition in signaling.", "Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL.", "The von hippel-lindau tumor suppressor pro...

[ 1999, 2002, 2002, 2007, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2004, 2008, 2008, 2007, 2007, 2008, 2006, 2006, 2005 ]

20

[]

0

null

[ "Bacteria", "Eukaryota", "ecological metagenomes" ]

[ 313, 1988, 13 ]

3

[ "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 1, 2, 3, 12, 2, 4 ]

6

true

Domain

von Hippel-Lindau disease tumour suppressor, beta domain

VHL_beta_dom

3

IPR024055

24,055

Translation initiation factor 2, alpha subunit, C-terminal

TIF2_asu_C

Homologous_superfamily

5,898

false

This superfamily represents the C-terminal domain of the translation initiation factor 2 alpha subunit. It adopts an α-β fold, containing five β strands, two α helices, and one loosely associated C-terminal α helix [ ].

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.30.70.1130", "SSF110993" ]

[ "", "" ]

[ 5868, 5889 ]

2

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-156827", "R-BTA-381042", "R-BTA-382556", "R-BTA-72649", "R-BTA-72695", "R-BTA-72702", "R-BTA-72731", "R-BTA-9840373", "R-DDI-156827", "R-DDI-382556", "R-DDI-72695", "R-DDI-72702", "R-DDI-72731", "R-DDI-9840373", "R-DME-156827", "R-DME-381042", "R-DME-382556", "R-DME-72649", ...

[ "REACTOME:R-BTA-156827", "REACTOME:R-BTA-381042", "REACTOME:R-BTA-382556", "REACTOME:R-BTA-72649", "REACTOME:R-BTA-72695", "REACTOME:R-BTA-72702", "REACTOME:R-BTA-72731", "REACTOME:R-BTA-9840373", "REACTOME:R-DDI-156827", "REACTOME:R-DDI-382556", "REACTOME:R-DDI-72695", "REACTOME:R-DDI-72702",...

83

[ "1q8k", "1yz6", "1yz7", "2aho", "2qmu", "2qn6", "3aev", "3cw2", "3j81", "3jap", "3qsy", "3v11", "5jb3", "5jbh", "5k0y", "6fec", "6fyx", "6fyy", "6gsm", "6gsn", "6i3m", "6i7t", "6jly", "6jlz", "6k71", "6k72", "6o81", "6o85", "6o9z", "6qg0", "6qg1", "6qg2"...

75

[ "PUB00030166" ]

[ "15341733" ]

[ "Solution structure of human initiation factor eIF2alpha reveals homology to the elongation factor eEF1B." ]

[ 2004 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Megaviricetes", "metagenomes" ]

[ 928, 3, 4901, 19, 47 ]

5

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae (strai...

[ 7, 1, 2, 2, 4, 2, 1, 4, 2, 1, 1, 13 ]

12

true

Homologous_superfamily

Translation initiation factor 2, alpha subunit, C-terminal

TIF2_asu_C

9

IPR024056

24,056

Apical membrane antigen 1 domain superfamily

Apmem_Ag1_dom_sf

Homologous_superfamily

2,077

false

A novel antigen of Plasmodium falciparum has been cloned that contains a hydrophobic domain typical of an integral membrane protein. The antigen is designated apical membrane antigen 1 (AMA-1) by virtue of appearing to be located in the apical complex [ ]. AMA-1 appears to be transported to the merozoite surface close ...

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:4.10.1010.10", "SSF82910" ]

[ "", "" ]

[ 2077, 2077 ]

2

[]

0

[ "1hn6", "1w81", "1w8k", "2j4w", "2j5l", "5nqg", "8qus", "8rek", "9dx6" ]

9

[ "PUB00008080", "PUB00008081" ]

[ "2701947", "2211675" ]

[ "Integral membrane protein located in the apical complex of Plasmodium falciparum.", "A merozoite receptor protein from Plasmodium knowlesi is highly conserved and distributed throughout Plasmodium." ]

[ 1989, 1990 ]

2

[]

0

null

[ "Plasmodium" ]

[ 2077 ]

1

[]

0

true

Homologous_superfamily

Apical membrane antigen 1 domain superfamily

Apmem_Ag1_dom_sf

2

IPR024057

24,057

Nucleoplasmin core domain

Nucleoplasmin_core_dom

Domain

4,236

false

This entry represents the core structural domain for the nucleoplasmin (Np) family of histone chaperone proteins. This core domain is formed by an 8-stranded β barrel [ ]. The three branches of the Np family, including nucleophosmin (NO38/B23), nucleoplasmin (Np), and nucleoplasmin-like proteins (NLP), bind core histon...

[]

0

[ "PFAM" ]

[ "PF03066" ]

[ "Nucleoplasmin" ]

[ 4236 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-DME-3899300", "R-DME-8869496", "R-DME-9833482", "R-HSA-180746", "R-HSA-3899300", "R-HSA-606279", "R-HSA-6804115", "R-HSA-8869496", "R-HSA-9692914", "R-HSA-9700645", "R-HSA-9725370", "R-HSA-9725371", "R-HSA-9821993", "R-HSA-9833482", "R-MMU-3899300", "R-MMU-606279", "R-MMU-6804115"...

[ "REACTOME:R-DME-3899300", "REACTOME:R-DME-8869496", "REACTOME:R-DME-9833482", "REACTOME:R-HSA-180746", "REACTOME:R-HSA-3899300", "REACTOME:R-HSA-606279", "REACTOME:R-HSA-6804115", "REACTOME:R-HSA-8869496", "REACTOME:R-HSA-9692914", "REACTOME:R-HSA-9700645", "REACTOME:R-HSA-9725370", "REACTOME:...

24

[ "1k5j", "1nlq", "1xb9", "1xe0", "2p1b", "2vtx", "3t30", "4n8m", "5ehd", "8as5", "8vhi", "8vhj", "8vhk" ]

13

[ "PUB00032376" ]

[ "15576029" ]

[ "The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus." ]

[ 2004 ]

1

[]

0

null

[ "Opisthokonta", "bird metagenome" ]

[ 4235, 1 ]

2

[ "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 8, 3, 23, 16, 14 ]

5

true

Domain

Nucleoplasmin core domain

Nucleoplasmin_core_dom

1

IPR024058

24,058

Cytochrome f transmembrane anchor

Cyt-f_TM

Homologous_superfamily

14,655

false

The cytochrome b6f integral membrane protein complex transfers electrons between the two reaction centre complexes of oxygenic photosynthetic membranes, and participates in formation of the transmembrane electrochemical proton gradient by also transferring protons from the stromal to the internal lumen compartment. The...

[]

0

[ "SSF" ]

[ "SSF103431" ]

[ "" ]

[ 14655 ]

1

[]

0

[ "1q90", "1vf5", "2d2c", "2e74", "2e75", "2e76", "2zt9", "4h0l", "4h13", "4h44", "4i7z", "4ogq", "4pv1", "6rqf", "7qrm", "7r0w", "7zxy", "7zyv", "9es7", "9es8", "9es9" ]

21

[ "PUB00002369", "PUB00005037", "PUB00005442" ]

[ "8027021", "8762139", "7631417" ]

[ "Structural aspects of the cytochrome b6f complex; structure of the lumen-side domain of cytochrome f.", "The heme redox center of chloroplast cytochrome f is linked to a buried five-water chain.", "Cytochrome f revealed." ]

[ 1994, 1996, 1995 ]

3

[]

0

null

[ "Bacteria", "Eukaryota" ]

[ 379, 14276 ]

2

[ "Arabidopsis thaliana", "Oryza sativa subsp. japonica", "Zea mays" ]

[ 7, 9, 8 ]

3

true

Homologous_superfamily

Cytochrome f transmembrane anchor

Cyt-f_TM

8

IPR024059

24,059

YopX-like, N-terminal

YopX-like_N

Homologous_superfamily

14

false

This superfamily represents a domain found in ORF041 from Bacteriophage 37, which forms a β sandwich structure similar to the N-terminal domain of YopX ( ).

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:2.60.430.10" ]

[ "" ]

[ 14 ]

1

[]

0

[ "2p84" ]

1

[]

0

[]

0

null

[ "Bacilli", "Staphylococcus phage 37" ]

[ 13, 1 ]

2

[]

0

true

Homologous_superfamily

YopX-like, N-terminal

YopX-like_N

5

IPR024060

24,060

Ureidoglycolate lyase domain superfamily

Ureidoglycolate_lyase_dom_sf

Homologous_superfamily

8,531

false

This superfamily represents the structural domain of ureidoglycolate lyase, and consists of a β structure known as a jelly roll.

[ "GO:0004848" ]

[ "ureidoglycolate hydrolase activity" ]

[ "molecular_function" ]

1

[ "CATHGENE3D" ]

[ "G3DSA:2.60.120.480" ]

[ "" ]

[ 8531 ]

1

[ "EC", "METACYC", "METACYC" ]

[ "4.3.2.3", "PWY-5694", "PWY-5705" ]

[ "EC:4.3.2.3", "METACYC:PWY-5694", "METACYC:PWY-5705" ]

3

[ "1xsq", "1xsr", "1yqc", "2bdr" ]

4

[]

0

[]

0

null

[ "Bacteria", "Eukaryota", "unclassified sequences" ]

[ 5873, 2568, 90 ]

3

[ "Arabidopsis thaliana", "Escherichia coli (strain K12)", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)", "Schizosaccharomyces pombe (strain 972 / ATCC 24843)", "Zea mays" ]

[ 16, 1, 1, 2, 1, 1, 4 ]

7

true

Homologous_superfamily

Ureidoglycolate lyase domain superfamily

Ureidoglycolate_lyase_dom_sf

8

IPR024061

24,061

NDT80, DNA-binding domain

NDT80_DNA-bd_dom

Domain

6,280

false

The NDT80 DNA-binding domain is found in the following proteins, which might all be involved in sensing nutritional status [ ]: Yeast meiosis-specific transcription factor NDT80, the key transcription factor that ultimately allows the continuation of meiosis after the successful completion of recombination. Emericella ...

[ "GO:0003677" ]

[ "DNA binding" ]

[ "molecular_function" ]

1

[ "PFAM", "PROFILE" ]

[ "PF05224", "PS51517" ]

[ "NDT80_PhoG", "NDT80" ]

[ 6233, 6241 ]

2

[]

0

[ "1m6u", "1m7u", "1mn4", "1mnn", "2etw", "2euv", "2euw", "2eux", "2euz", "2evf", "2evg", "2evh", "2evi", "2evj", "5h5p", "5yhu", "5zhu" ]

17

[ "PUB00022187", "PUB00055515", "PUB00163233" ]

[ "12411490", "16464624", "28623291" ]

[ "Structure of the sporulation-specific transcription factor Ndt80 bound to DNA.", "The Aspergillus nidulans xprG (phoG) gene encodes a putative transcriptional activator involved in the response to nutrient limitation.", "Crystal structure of the DNA-binding domain of Myelin-gene Regulatory Factor." ]

[ 2002, 2006, 2017 ]

3

[]

0

null

[ "Eukaryota", "Gimesia panareensis" ]

[ 6279, 1 ]

2

[ "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Rattus norvegicus", "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)" ]

[ 2, 15, 3, 5, 2, 7, 8, 1 ]

8

true

Domain

NDT80, DNA-binding domain

NDT80_DNA-bd_dom

1

IPR024062

24,062

Bacteriophage PBS2, uracil-glycosylase inhibitor

Phage_PBS2_Ugi

Homologous_superfamily

5

false

DNA glycosylases excise damaged or unconventional bases in DNA and initiate the base excision repair (BER) pathway to maintain genomic integrity. Of these, uracil-DNA glycosylase (UDG) excises uracil from DNA by cleavage of the N-glycosidic bond between uracil and deoxyribose sugar. Uracil residues in DNA arise as a re...

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.10.450.20", "SSF54441" ]

[ "", "" ]

[ 4, 5 ]

2

[]

0

[ "1eui", "1lqg", "1lqm", "1udi", "1ugh", "1ugi", "1uug", "2j8x", "2ugi", "2uug", "2zhx", "4lyl", "6lyd", "6lye", "8aim" ]

15

[ "PUB00022775", "PUB00024677", "PUB00027104", "PUB00055072" ]

[ "7552746", "9776748", "12136137", "7479702" ]

[ "Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex.", "X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG.", "Domain closure and action ...

[ 1995, 1998, 2002, 1995 ]

4

[]

0

null

[ "Ajellomyces dermatitidis (strain ER-3 / ATCC MYA-2586)", "Caudoviricetes" ]

[ 1, 4 ]

2

[]

0

true

Homologous_superfamily

Bacteriophage PBS2, uracil-glycosylase inhibitor

Phage_PBS2_Ugi

5

IPR024064

24,064

FdhE-like superfamily

FdhE-like_sf

Homologous_superfamily

5,451

false

This superfamily represents a domain found in formate dehydrogenase accessory protein FdhE and homologues. It consists of an N-terminal five-helical bundle, a tandem repeat of two rubredoxin-like domains and a C-terminal helix packed together.

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.90.1670.10", "SSF144020" ]

[ "", "" ]

[ 4315, 5423 ]

2

[]

0

[ "2fiy" ]

1

[]

0

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Viruses", "unclassified sequences" ]

[ 145, 5095, 108, 21, 82 ]

5

[ "Escherichia coli (strain K12)", "Zea mays" ]

[ 1, 1 ]

2

true

Homologous_superfamily

FdhE-like superfamily

FdhE-like_sf

4

IPR024065

24,065

DNA topoisomerase V, catalytic domain superfamily

TopoV_catalytic_dom_sf

Homologous_superfamily

7

false

DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single-or double-strand breaks, crossing the strands through one another, then resealing the breaks [ ]. These enzymes have several functions: to remove DNA supercoi...

[]

0

[ "SSF" ]

[ "SSF140979" ]

[ "" ]

[ 7 ]

1

[]

0

[ "2csb", "2csd", "3m6k", "3m6z", "3m7d", "3m7g", "4gfj", "5hm5", "8df7", "8df8", "8df9", "8dfb" ]

12

[ "PUB00005437", "PUB00016842", "PUB00020793", "PUB00020794", "PUB00040090", "PUB00055625", "PUB00055626" ]

[ "7770916", "11395412", "12596227", "12042765", "16395333", "20637419", "11353838" ]

[ "The mechanisms of DNA topoisomerases.", "DNA topoisomerases: structure, function, and mechanism.", "Phylogenomics of type II DNA topoisomerases.", "Cellular roles of DNA topoisomerases: a molecular perspective.", "Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerase...

[ 1995, 2001, 2003, 2002, 2006, 2010, 2001 ]

7

[]

0

null

[ "Bacteria", "Methanopyrus kandleri" ]

[ 5, 2 ]

2

[]

0

true

Homologous_superfamily

DNA topoisomerase V, catalytic domain superfamily

TopoV_catalytic_dom_sf

1

IPR024066

24,066

RGS, subdomain 1/3

RGS_subdom1/3

Homologous_superfamily

18,439

false

RGS (Regulator of G Protein Signalling) proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins [ ]. Upon activation by GPCRs, heterotrimeric G proteins exchange GDP for GTP, are released from the receptor, and dissociate into free, activ...

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:1.10.196.10" ]

[ "" ]

[ 18439 ]

1

[ "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOM...

[ "R-BTA-416476", "R-BTA-418594", "R-BTA-418597", "R-CEL-416476", "R-CEL-418594", "R-CEL-418597", "R-DME-195253", "R-DME-196299", "R-DME-209155", "R-DME-209190", "R-DME-209214", "R-DME-209360", "R-DME-209396", "R-DME-209413", "R-DME-209440", "R-DME-209461", "R-DME-418594", "R-DME-432...

[ "REACTOME:R-BTA-416476", "REACTOME:R-BTA-418594", "REACTOME:R-BTA-418597", "REACTOME:R-CEL-416476", "REACTOME:R-CEL-418594", "REACTOME:R-CEL-418597", "REACTOME:R-DME-195253", "REACTOME:R-DME-196299", "REACTOME:R-DME-209155", "REACTOME:R-DME-209190", "REACTOME:R-DME-209214", "REACTOME:R-DME-209...

66

[ "1agr", "1cmz", "1dk8", "1emu", "1ezt", "1ezy", "1zv4", "2af0", "2bt2", "2bv1", "2crp", "2dlr", "2dlv", "2ebz", "2gtp", "2i59", "2ihb", "2ihd", "2ik8", "2jm5", "2jnu", "2ode", "2oj4", "2owi", "2v4z", "3c7k", "3c7l", "4ekc", "4ekd", "5do9", "7y1p" ]

31

[ "PUB00000946", "PUB00006536", "PUB00015162", "PUB00015163", "PUB00046994", "PUB00071325" ]

[ "9108480", "10836135", "15090201", "10987813", "18434541", "23900842" ]

[ "Structure of RGS4 bound to AlF4--activated G(i alpha1): stabilization of the transition state for GTP hydrolysis.", "The regulator of G protein signaling family.", "RGS proteins: G protein-coupled receptors meet their match.", "Regulators of G protein signaling: a bestiary of modular protein binding domains....

[ 1997, 2000, 2003, 2000, 2008, 2013 ]

6

[]

0

null

[ "Eukaryota", "marine metagenome" ]

[ 18438, 1 ]

2

[ "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Homo sapiens", "Mus musculus", "Rattus norvegicus" ]

[ 8, 92, 12, 56, 64, 73 ]

6

true

Homologous_superfamily

RGS, subdomain 1/3

RGS_subdom1/3

9

IPR024067

24,067

Methylmalonyl-CoA mutase small subunit, N-terminal

Me-malonyl-CoA_mutase_sm_su_N

Homologous_superfamily

957

false

Methylmalonyl-CoA mutase ( ) catalyses the isomerization of succinyl-CoA to methylmalonyl-CoA during the synthesis of propionate from tricarboxylic acid-cycle intermediates in propionic acid fermentation. This entry represents the N-terminal portion of the catalytic domain found in methylmalonyl-CoA mutase small subuni...

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:1.10.196.20" ]

[ "" ]

[ 957 ]

1

[]

0

[ "1e1c", "1req", "2req", "3req", "4req", "5req", "6req", "7req" ]

8

[]

0

[]

0

null

[ "Bacteria", "freshwater metagenome" ]

[ 952, 5 ]

2

[]

0

true

Homologous_superfamily

Methylmalonyl-CoA mutase small subunit, N-terminal

Me-malonyl-CoA_mutase_sm_su_N

8

IPR024068

24,068

Rotavirus NSP2, N-terminal

Rotavirus_NSP2_N

Homologous_superfamily

2,791

false

Rotavirus non-structural protein 2 (NSP2) is a basic protein which possesses RNA-binding activity and is essential for genome replication [ ]. It may also be important for viral RNA packaging. This superfamily represents the N-terminal domain of Rotavirus NSP2.

[ "GO:0016817" ]

[ "hydrolase activity, acting on acid anhydrides" ]

[ "molecular_function" ]

1

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.90.1400.10", "SSF75574" ]

[ "", "" ]

[ 2791, 2791 ]

2

[ "EC", "METACYC" ]

[ "3.6.4.-", "PWY-7250" ]

[ "EC:3.6.4.-", "METACYC:PWY-7250" ]

2

[ "1l9v", "2gu0", "2r7c", "2r7j", "2r7p", "2r8f", "4g0a", "4g0j", "6auk", "6cy9", "6cya", "7pko", "7pkp", "9oft", "9ogq" ]

15

[ "PUB00008136" ]

[ "8380660" ]

[ "Nucleotide and amino acid sequence analysis of the rotavirus nonstructural RNA-binding protein NS35." ]

[ 1993 ]

1

[]

0

null

[ "Rotavirus" ]

[ 2791 ]

1

[]

0

true

Homologous_superfamily

Rotavirus NSP2, N-terminal

Rotavirus_NSP2_N

6

IPR024069

24,069

AF2212-like domain superfamily

AF2212-like_dom_sf

Homologous_superfamily

698

false

This domain superfamily is found in protein AF2212 (also known as putative antitoxin VapB21) from the archaean Archaeoglobus fulgidus, and other uncharacterised proteins belonging to the UPF0165 family. The structure of AF2212 has been solved ( ) but not published. The AF2212-like domain is irregular with few secondary...

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:4.10.1150.10" ]

[ "" ]

[ 698 ]

1

[]

0

[ "2nwt" ]

1

[]

0

[]

0

null

[ "Archaea", "Bacteria", "Geodia barretti", "ecological metagenomes" ]

[ 360, 327, 1, 10 ]

4

[]

0

true

Homologous_superfamily

AF2212-like domain superfamily

AF2212-like_dom_sf

4

IPR024071

24,071

S-Me-THD, C-terminal domain superfamily

S-Me-THD_C_sf

Homologous_superfamily

5,939

false

This β-barrel domain is found at the C-terminal of S-methyl thiohydantoin desulfurase from Variovorax sp. (S-Me-THD) and similar sequences mainly found in bacteria and fungi. S-Me-THD catalyses the hydrolysis of S-methyl-thiohydantoin-5-propanoate into hydantoin-5-propanoate and methanethiol, the third step in S-methyl...

[]

0

[ "CATHGENE3D" ]

[ "G3DSA:2.40.390.10" ]

[ "" ]

[ 5939 ]

1

[]

0

[ "2o3i" ]

1

[ "PUB00155448" ]

[ "38389448" ]

[ "Structure and Substrate Specificity of S-Methyl Thiourocanate Hydratase." ]

[ 2024 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "ecological metagenomes" ]

[ 194, 3505, 2168, 72 ]

4

[ "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)" ]

[ 1 ]

1

true

Homologous_superfamily

S-Me-THD, C-terminal domain superfamily

S-Me-THD_C_sf

2

IPR024072

24,072

Dihydrofolate reductase-like domain superfamily

DHFR-like_dom_sf

Homologous_superfamily

109,795

false

Dihydrofolate reductase (DHFR) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [ ], and important also in the conversion of deoxyuridine monophosphate to deo...

[]

0

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.40.430.10", "SSF53597" ]

[ "", "" ]

[ 109652, 109521 ]

2

[ "EC", "METACYC", "METACYC", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME", "REACTOME" ]

[ "1.5.1.3", "PWY-3841", "PWY-6614", "R-CEL-196757", "R-DME-196757", "R-HSA-1474151", "R-HSA-196757", "R-HSA-69205", "R-MMU-196757", "R-RNO-196757", "R-SCE-196757", "R-SPO-196757" ]

[ "EC:1.5.1.3", "METACYC:PWY-3841", "METACYC:PWY-6614", "REACTOME:R-CEL-196757", "REACTOME:R-DME-196757", "REACTOME:R-HSA-1474151", "REACTOME:R-HSA-196757", "REACTOME:R-HSA-69205", "REACTOME:R-MMU-196757", "REACTOME:R-RNO-196757", "REACTOME:R-SCE-196757", "REACTOME:R-SPO-196757" ]

12

[ "1ai9", "1ao8", "1aoe", "1boz", "1bzf", "1cd2", "1cz3", "1d1g", "1daj", "1ddr", "1dds", "1df7", "1dg5", "1dg7", "1dg8", "1dhf", "1dhi", "1dhj", "1dis", "1diu", "1dlr", "1dls", "1dr1", "1dr2", "1dr3", "1dr4", "1dr5", "1dr6", "1dr7", "1dra", "1drb", "1dre"...

715

[ "PUB00005107" ]

[ "2830673" ]

[ "A gene for dihydrofolate reductase in a herpesvirus." ]

[ 1988 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Plasmid R483", "Viruses", "unclassified sequences" ]

[ 1647, 94953, 10755, 1, 1107, 1332 ]

6

[ "Arabidopsis thaliana", "Caenorhabditis elegans", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus",...

[ 28, 1, 3, 2, 2, 6, 2, 2, 18, 4, 2, 3, 35 ]

13

true

Homologous_superfamily

Dihydrofolate reductase-like domain superfamily

DHFR-like_dom_sf

7

IPR024073

24,073

Argininosuccinate synthetase mutimerisation domain, C-terminal tail

AS_multimer_C_tail

Homologous_superfamily

4,864

false

The argininosuccinate synthetase (AS) monomer is composed of a nucleotide binding domain and a catalytic/multimerisation domain. The catalytic/multimerisation domain possesses a C-terminal tail, which is involved in protein dimerisation and tetramerisation [ ]. The tail contains two α helices. In a subset of bacterial ...

[ "GO:0042803" ]

[ "protein homodimerization activity" ]

[ "molecular_function" ]

1

[ "CATHGENE3D" ]

[ "G3DSA:1.10.287.400" ]

[ "" ]

[ 4864 ]

1

[ "EC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC" ]

[ "6.3.4.5", "PWY-4983", "PWY-4984", "PWY-5", "PWY-5154", "PWY-7400" ]

[ "EC:6.3.4.5", "METACYC:PWY-4983", "METACYC:PWY-4984", "METACYC:PWY-5", "METACYC:PWY-5154", "METACYC:PWY-7400" ]

6

[ "1k92", "1k97", "1kp2", "1kp3", "5us8", "6e5y" ]

6

[ "PUB00028813" ]

[ "11738042" ]

[ "The 1.6 A crystal structure of E. coli argininosuccinate synthetase suggests a conformational change during catalysis." ]

[ 2001 ]

1

[]

0

null

[ "Bacteria", "Eukaryota", "metagenomes" ]

[ 4690, 5, 169 ]

3

[ "Escherichia coli (strain K12)" ]

[ 1 ]

1

true

Homologous_superfamily

Argininosuccinate synthetase mutimerisation domain, C-terminal tail

AS_multimer_C_tail

4

IPR024074

24,074

Argininosuccinate synthetase, catalytic/multimerisation domain body

AS_cat/multimer_dom_body

Homologous_superfamily

29,737

false

The argininosuccinate synthetase (AS) monomer is composed of a nucleotide binding domain and a catalytic/multimerisation domain. The catalytic/multimerisation domain can be subdivided in the body of the domain and a C-terminal tail involved in multimerisation, though this tail is not present in all sequences. This entr...

[ "GO:0004055" ]

[ "argininosuccinate synthase activity" ]

[ "molecular_function" ]

1

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.90.1260.10", "SSF69864" ]

[ "", "" ]

[ 29626, 29552 ]

2

[ "EC", "METACYC", "METACYC", "METACYC", "METACYC", "METACYC", "REACTOME", "REACTOME", "REACTOME" ]

[ "6.3.4.5", "PWY-4983", "PWY-4984", "PWY-5", "PWY-5154", "PWY-7400", "R-BTA-70635", "R-HSA-70635", "R-MMU-70635" ]

[ "EC:6.3.4.5", "METACYC:PWY-4983", "METACYC:PWY-4984", "METACYC:PWY-5", "METACYC:PWY-5154", "METACYC:PWY-7400", "REACTOME:R-BTA-70635", "REACTOME:R-HSA-70635", "REACTOME:R-MMU-70635" ]

9

[ "1j1z", "1j20", "1j21", "1k92", "1k97", "1kh1", "1kh2", "1kh3", "1kor", "1kp2", "1kp3", "1vl2", "2nz2", "4nzp", "4u7j", "4xfj", "5us8", "6e5y", "6xnq", "7k5z" ]

20

[ "PUB00028813" ]

[ "11738042" ]

[ "The 1.6 A crystal structure of E. coli argininosuccinate synthetase suggests a conformational change during catalysis." ]

[ 2001 ]

1

[]

0

null

[ "Archaea", "Bacteria", "Eukaryota", "Siphoviridae sp. ctBLh2", "unclassified sequences" ]

[ 833, 23293, 4988, 1, 622 ]

5

[ "Arabidopsis thaliana", "Danio rerio", "Drosophila melanogaster", "Escherichia coli (strain K12)", "Homo sapiens", "Mus musculus", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Rattus norvegicus", "Saccharomyces cerevisiae...

[ 4, 1, 1, 1, 10, 3, 2, 7, 3, 1, 1, 11 ]

12

true

Homologous_superfamily

Argininosuccinate synthetase, catalytic/multimerisation domain body

AS_cat/multimer_dom_body

6

IPR024075

24,075

DNA-directed RNA polymerase, helix hairpin domain superfamily

DNA-dir_RNA_pol_helix_hairp_sf

Homologous_superfamily

4,070

false

The single subunit DNA-directed RNA polymerase (RNAP) that is encoded by bacteriophage T7 is the prototype of a class of relatively simple RNAPs that includes the RNAPs of the related phages T3 and SP6, as well as the mitochondrial and chloroplastic RNAPs [ ]. This superfamily represents a helix hairpin structural doma...

[ "GO:0003899" ]

[ "DNA-directed RNA polymerase activity" ]

[ "molecular_function" ]

1

[ "CATHGENE3D" ]

[ "G3DSA:1.10.287.260" ]

[ "" ]

[ 4070 ]

1

[ "EC", "REACTOME" ]

[ "2.7.7.6", "R-SCE-163282" ]

[ "EC:2.7.7.6", "REACTOME:R-SCE-163282" ]

2

[ "1aro", "1cez", "1h38", "1msw", "1qln", "1s0v", "1s76", "1s77", "2pi4", "2pi5", "3e2e", "3e3j", "4rnp", "6ymv", "6ymw", "8ap1", "8att", "8atv", "8atw", "8c5s", "8c5u", "8dh0", "8dh1", "8dh2", "8dh3", "8dh4", "8dh5", "8q63" ]

28

[ "PUB00003849" ]

[ "7526118" ]

[ "The phage RNA polymerases are related to DNA polymerases and reverse transcriptases." ]

[ 1993 ]

1

[]

0

null

[ "Bacteria", "Eukaryota", "Viruses", "feces metagenome" ]

[ 100, 3181, 788, 1 ]

4

[ "Arabidopsis thaliana", "Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)", "Oryza sativa subsp. japonica", "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)", "Zea mays" ]

[ 17, 1, 10, 1, 28 ]

5

true

Homologous_superfamily

DNA-directed RNA polymerase, helix hairpin domain superfamily

DNA-dir_RNA_pol_helix_hairp_sf

2

IPR024076

24,076

Rotavirus NSP2, C-terminal

Rotavirus_NSP2_C

Homologous_superfamily

2,797

false

Rotavirus non-structural protein 2 (NSP2) is a basic protein which possesses RNA-binding activity and is essential for genome replication [ ]. It may also be important for viral RNA packaging. This superfamily represents the C-terminal domain of the Rotavirus NSP2.

[ "GO:0016817" ]

[ "hydrolase activity, acting on acid anhydrides" ]

[ "molecular_function" ]

1

[ "CATHGENE3D", "SSF" ]

[ "G3DSA:3.30.428.20", "SSF75347" ]

[ "", "" ]

[ 2795, 2797 ]

2

[ "EC", "METACYC" ]

[ "3.6.4.-", "PWY-7250" ]

[ "EC:3.6.4.-", "METACYC:PWY-7250" ]

2

[ "1l9v", "2gu0", "2r7c", "2r7j", "2r7p", "2r8f", "4g0a", "4g0j", "6auk", "6cy9", "6cya", "7pko", "7pkp", "9oft", "9ogq" ]

15

[ "PUB00008136" ]

[ "8380660" ]

[ "Nucleotide and amino acid sequence analysis of the rotavirus nonstructural RNA-binding protein NS35." ]

[ 1993 ]

1

[]

0

null

[ "Bacillota", "Rotavirus" ]

[ 2, 2795 ]

2

[]

0

true

Homologous_superfamily

Rotavirus NSP2, C-terminal

Rotavirus_NSP2_C

2