SII-SWORD/CoKE huggingface dataset:
Formate-dependent cytochrome c nitrite reductase, c552 subunit (Cyt_c_NO2Rdtase_formate-dep)
Type: Family

Members of this protein family represent cytochrome c552, a component of cytochrome c nitrite reductase, which is known more formally as nitrite reductase (cytochrome; ammonia-forming,

). Nitrite can be reduced by several enzymes:

reduces nitrite all the way to ammonia, rather than to ammonium hydroxide (ammonia:ferricytochrome-c oxidoreductase),

(ammonium-hydroxide:NAD(P)+ oxidoreductase),

nitrite reductase (NO-forming) (nitric-oxide:ferricytochrome-c oxidoreductase).

Some examples of

occur in a seven gene system that enables formate-dependent nitrite reduction, but it can also be found in simpler contexts. All members of this protein family, however, do belong to the formate-dependent system of nitrite reduction.
Cytochrome c nitrite reductase, small subunit (NrfH)
Type: Family

This entry represents NrfH, a tetraheme cytochrome c. NrfH is the cytochrome c nitrite reductase small subunit, and forms a heterodimer with NrfA, the catalytic subunit. While NrfA can act as a monomer, NrfH can bind to and anchor NrfA in the membrane and enable electron transfer to NrfA from quinones .
Cytochrome b558/566, subunit A (Cyt_b558/566_suA)
Type: Family

This entry represents CbsA, a novel, highly glycosylated, mono-haem cytochrome b558/566 found in Sulfolobus acidocaldarius and several other members of the Sulfolobales, a branch of the Crenarchaeota . Encoded at the same locus as CbsA are: CbsB, a hydrophobic protein, SoxL, a Rieske iron-sulphur protein, SoxN, a predicted membrane-bound b-type cytochrome b, and OdsN, a protein of unknown function. Transcriptional studies suggest that these proteins may form a complex analogous to the cytochrome bc1 complex. The redox-active subunits of this complex would consist of CbsA, SoxL and SoxN, while CbsB and OdsN would be additional non-redox-active subunits.
Cytochrome b558/566, subunit B (Cyt_b558/566_suB)
Type: Family

This entry represents CbsB, a hydrophobic protein which is found in Sulfolobus acidocaldarius and several other members of the Sulfolobales, a branch of the Crenarchaeota . Encoded at the same locus as CbsB are: CbsA, a high potential cytochrome b558/566, SoxL, a Rieske iron-sulphur protein, SoxN, a predicted membrane-bound b-type cytochrome b, and OdsN, a protein of unknown function. Transcriptional studies suggest that these proteins may form a complex analogous to the cytochrome bc1 complex. The redox-active subunits of this complex would consist of CbsA, SoxL and SoxN, while CbsB and OdsN would be additional non-redox-active subunits. A possible function for CbsB, based on its hydrophobicity, would be to anchor CbsA to the membrane.
CRISPR-associated protein Cas7/Csc2 (CRISPR-assoc_prot_Cas7/Csc2)
Type: Family

This entry represents the type I-D Cas7/Csc2 family of Cas proteins that are strictly associated with the Cyano subtype of CRISPR/Cas locus and found in several species of Cyanobacteria and several archaeal species. This family is designated Csc2 for CRISPR/Cas Subtype Cyano protein 2, as it is often the second gene upstream of the core cas genes, cas3-cas4-cas1-cas2 . Structural analysis of T. pendens Csc2 revealed that it forms a core RRM-like domain, flanked by three peripheral insertion domains: a lid domain, a zinc-binding domain and a helical domain. Csc2 binds single-stranded RNA in vitro in a sequence-independent manner .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated helicase Cas3' (CRISPR-assoc_helicase_Cas3')
Type: Family

This entry represents a family of Cas proteins that are strictly associated with the Cyano subtype of CRISPR/Cas locus and found in several species of Cyanobacteria and several archaeal species. These proteins contain helicase motifs and appear to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
CRISPR-associated protein Csc1 (CRISPR-assoc_prot_Csc1)
Type: Family

This entry represents the type I-D Csc1 family of Cas proteins that are strictly associated with the Cyano subtype of CRISPR/Cas locus and found in several species of Cyanobacteria and several archaeal species. This family is designated Csc1 for CRISPR/Cas Subtype Cyano protein 1, as it is often the first gene upstream of the core cas genes, cas3-cas4-cas1-cas2 . Type I-D cascade is capable of specifically binding ssRNA.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Alpha-ribazole phosphatase, CobZ (Ribazole_CobZ)
Type: Family

This family includes the experimentally characterised CobZ of the methanogenic archaeon Methanosarcina mazei (Methanosarcina frisia), and other archaeal proteins found similarly next to or very near to other cobalamin biosynthesis genes. CobZ replaces the alpha-ribazole-phosphate phosphatase (

) called CobC in analogous bacterial pathways for cobalamin biosynthesis under anaerobic conditions . CobZ possesses phosphatase activity and is capable of converting alpha-ribazole-5'-phosphate to alpha-ribazole .
Alpha-ribazole phosphatase, CobC (Ribazole_CobC)
Type: Family

In Salmonella typhimurium LT2, under anaerobic conditions, CobU (

and

), CobT (

), CobC (

) and CobS (

) catalyse reactions in the nucleotide loop assembly pathway, which convert adenosylcobinamide (AdoCbi) into adenosylcobalamin (AdoCbl). CobT and CobC are involved in 5,6-dimethylbenzimidazole activation whereby 5,6-dimethylbenzimidazole is converted into its riboside, alpha-ribazole. The second branch of the nuclotide loop assembly pathway is the cobinamide (Cbi) activation branch where AdoCbi or adenosylcobinamide-phosphate is converted into the activated intermediate AdoCbi-GDP by the bifunctional enzyme CobU. CobS catalyses the final step in adenosylcobalamin biosynthesis, which is the condensation of AdoCbi-GDP with alpha-ribazole to yield adenosylcobalamin.

Members of this entry include the known CobC protein of Salmonella and Escherichia coli species, and homologous proteins found in cobalamin biosynthesis regions in other bacteria. CobC is alpha-ribazole phosphatase (

) and, like many phosphatases, can be closely related in sequence to other phosphatases with different functions. Close homologues excluded from this entry include proteins with duplications.
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 1 (OHCU_decarboxylase-1)
Type: Domain

Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalysed by this OHCU decarboxylase in Mus musculus (Mouse) . Homologues of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented in this entry.
N-ATPase, AtpR subunit-like (AtpR-like)
Type: Family

Membrane protein with three predicted transmembrane segments, two of which contain conserved Arg residues. AtpR genes are found in the N-ATPase (archaeal-type F1-Fo-ATPase) operons and are predicted to interact with the conserved Glu/Asp residues in the c subunits, regulating the assembly and/or function of the membrane-embedded ring of 'c' (proteolipid) subunits .

This entry also includes AtpR like proteins found in bacteria. Some of them have been annotated as ATP synthase protein I (atpI). However, their function still need to be verified.
tRNA 2-selenouridine synthase (SelU)
Type: Family

Modified nucleosides present at the wobble position increase the capabilities of tRNA to decode multiple synonymous mRNA codons which differ in the third nucleoside. tRNA 2-selenouridine synthase (SelU) is involved in the post-transcriptional modification of the uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln). It catalyzes the conversion of 2-thiouridine (S2U-RNA) to 2-selenouridine (Se2U-RNA) .
Tagatose/fructose phosphokinase (Tagatose/fructose_Pkinase)
Type: Family

This entry represents a family of hexose kinases that includes the tagatose-6-kinases from the carbohydrate kinase PfkB family (LacC subfamily), 1-phosphofructokinases and 6-phosphofructokinases isozyme 2 from the carbohydrate kinase PfkB family.

Tagatose-6-phosphate kinase (

) is part of the tagatose-6-phosphate pathway of lactose degradation.

Fructose 1-phosphate kinase (also known as 1-phosphofructokinase) acts in concert with the fructose-specific phosphotransferase system (PTS), which phosphorylates fructose during transport to fructose-1-phosphate. The action of 1-phosphofructokinase results in beta-D-fructose-1,6-bisphosphate and is an entry point into glycolysis (

).
Pyridine nucleotide-disulphide oxidoreductase family protein, N-terminal (Pyridine_nucleo_diS_OxRdtase_N)
Type: Domain

Members of this entry include the N-terminal sequence regions of (probable) bifunctional proteins whose C-terminal sequences are SelD (selenide, water dikinase) the selenium donor protein necessary for selenium incorporation into protein (as selenocysteine), tRNA (as 2-selenouridine), or both. However, some members of this family occur in species that do not show selenium incorporation, and the function of this protein in these species is unknown.
Flagella basal body P-ring formation protein FlgA, SAF domain (SAF_FlgA)
Type: Domain

This entry describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. FlgA, is required for P-ring assembly in bacterial flagella of taxa such as Salmonella enterica or Escherichia coli. It consists of two domains, a SAF domain and a β-barrel domain responsible for binding to FlgI, a P-ring component protein . SAF domain is structurally similar to antifreeze protein Type III and related proteins that share in common the so-called β-clip fold.
Rieske iron-sulphur protein SoxL2 (Rieske_Fe-S_SoxL2)
Type: Family

This iron-sulphur protein is found in a contiguous genomic region with subunits of cytochrome b558/566, and appears to be part of a cytochrome bc1-analogous system .
Selenium cofactor biosynthesis protein YqeC (YqeC)
Type: Family

This uncharacterised protein family includes YqeC from Escherichia coli. A phylogenetic profiling analysis shows correlation with SelD, the selenium donor protein, even in species where SelD contributes to neither selenocysteine nor selenouridine biosynthesis . Instead, this family appears to mark a selenium-dependent molybdenum hydroxylase maturation system.
Uric acid permease UacT-like (UacT-like)
Type: Family

This family includes uric acid transporters such as UacT (YgfU) from Escherichia coli , and PucK and PucJ from Bacillus subtilis .
CRISPR associated protein Cas10d/Csc3 (CRISPR-assoc_prot_Cas10d/Csc3)
Type: Family

This entry represents the type I-D Cas10d/Csc3 family of Cas proteins that are strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc3 for CRISPR/Cas Subtype Cyano protein 3, as it is often the third gene upstream of the core cas genes, cas3-cas4-cas1-cas2 . Type I-D CRISPR/Cas proteins contain characteristic features of both type I and type III systems, the most prevalent CRISPR-Cas systems. Type I-D system is capable of specifically binding ssRNA. Type I systems use a short protospacer adjacent motif (PAM) to discriminate between self and non-self DNA, a functionality retained in Cas10d/Csc3.

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Ureidoglycolate dehydrogenase (Ureidoglycolate_dehydrogenase)
Type: Family

This protein converts ureidoglycolate to oxalureate in the non-urea-forming catabolism of allantoin (

). The pathway has been characterised in Escherichia coli and is observed in the genomes of Enterococcus faecalis (Streptococcus faecalis) and Bacillus licheniformis.
Allantoate amidohydrolase (Allantoate_amidohydrolase)
Type: Family

This protein catalyses the breakdown of allantoate , first to ureidoglycine by hydrolysis and then decarboxylation of one of the two equivalent ureido groups. Ureidoglycine then spontaneously exchanges ammonia for water resulting in ureidoglycolate. This enzyme is an alternative to allantoicase (

) which releases urea.
Pilus assembly, Flp-type CpaB (Pilus_assmbl_Flp-typ_CpaB)
Type: Family

Members of this protein family are the CpaB protein of Flp-type pilus assembly. Similar proteins include the FlgA protein of bacterial flagellum biosynthesis.
Allantoinase (Allantoinase)
Type: Family

This entry includes allantoinases mainly from bacteria and eukaryotes but also from some archaeal species. Allantoinase catalyses the conversion of allantoin (5-ureidohydantoin) to allantoic acid by hydrolytic cleavage of the five-member hydantoin ring . The proteins in this family are all in the vicinity of other genes involved in the processes of xanthine/urate/allantoin catabolism.
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 2 (OHCU_decarboxylase-2)
Type: Domain

Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) has been recently been shown to be catalysed by this protein in Mus musculus (Mouse) . Homologues of this protein are found adjacent to and fused with uricase in a number of prokaryotes, represented by this entry. This entry is a separate (but related) from that represented by

.
Pyruvate dehydrogenase E1 component subunit alpha/BCKADH E1-alpha (PdhA/BkdA)
Type: Family

This entry includes pyruvate dehydrogenase E1 component subunit alpha (PdhA) from Bacillus subtilis and 3-methyl-2-oxobutanoate dehydrogenase subunit alpha (BkdA) from Mycobacterium tuberculosis.

The pyruvate dehydrogenase complex catalyses the overall conversion of pyruvate to acetyl-CoA and CO2. It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).
Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit, subgroup y (Pyrv_DH_E1_asu_subgrp-y)
Type: Family

Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH) . This entry represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc. The pyruvate dehydrogenase complex catalyses the overall conversion of pyruvate to acetyl-CoA and carbon dioxide. It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).
DNA phosphorothioation system sulfurtransferase DndC (SulphurTrfase_DndC)
Type: Family

This entry describes the DndC protein from the dnd (degradation during electrophoresis) operon. The dnd phenotype reflects a sulphur-containing modification to DNA . The operon is sparsely and sporadically distributed among bacteria. The examples known so far include Actinobacteria, Firmicutes, Gammaproteobacteria, Cyanobacteria. DndC is suggested to be a sulphur transferase.
DNA sulphur modification protein DndD (DNA_S_DndD)
Type: Family

This entry describes the DndD protein encoded by an operon associated with a sulphur-containing modification to DNA . The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Alpha-ketoglutarate dehydrogenase (Alpha-ketoglut_DH)
Type: Family

Several bacterial species have a paralog to homodimeric form of the pyruvate dehydrogenase E1 component (see model

), often encoded next to L-methionine gamma-lyase gene (mdeA). The member from a strain of Pseudomonas putida was shown to act on alpha-ketobutyrate, which is produced by MdeA. This model serves as an exception model to

, as other proteins hitting

should be identified as the pyruvate dehydrogenase E1 component.
DGQHR-containing domain (DGQHR-contain_dom)
Type: Domain

This highly divergent, uncharacterised domain has several absolutely conserved residues, including a QR pair and FxxxN motif. Its most striking feature, however, is a near invariant pentapeptide motif DGQHR. While the function is unknown, members occur in contexts that suggest extensive lateral gene transfer (LGT), and several have been annotated as putative bacteriophage proteins.
Cyclohexa-1,5-dienecarbonyl-CoA hydratase (Dienoyl_CoA_hydratase)
Type: Family

This entry describes cyclohexa-1,5-dienecarbonyl-CoA hydratase, also called dienoyl-CoA hydratase, which acts on the product of benzoyl-CoA reductase (

). Benzoyl-CoA is a common intermediate in the degradation of many aromatic compounds, and this enzyme is part of an anaerobic pathway for dearomatization and degradation .
Benzoyl-CoA reductase, bzd-type, N subunit (Benzoyl-CoA_Rdtase_bzd_nsu)
Type: Family

Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyses the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Benzoyl-CoA reductase, bzd-type, O subunit (Benzoyl-CoA_Rdtase_bzd_osu)
Type: Family

Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyses the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Benzoyl-CoA reductase, bzd-type, Q subunit (Benzoyl-CoA_Rdtase_bzd_qsu)
Type: Family

Members of this family are the Q subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyses the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
4-hydroxybenzoyl-CoA reductase, gamma subunit (4hydrxbenzoyl-CoA_Rdtase_gsu)
Type: Family

4-Hydroxybenzoyl-CoA reductase (4-HBCR) is a member of the xanthine oxidase (XO) family of molybdenum cofactor containing enzymes. It catalyses the irreversible removal of a phenolic hydroxy group by reduction, yielding water and benzoyl-CoA, which is a common intermediate in the anaerobic degradation of aromatic compounds.

4-HBCR has a heterodimer subunit compositon of alpha2-beta2-gamma2. 4-HBCR contains two molybdopterins, four [2Fe-2S], two [4Fe-4S] clusters and two FADs . A ferredoxin with two [4Fe-4S] clusters functions as the natural electron donor. The enzyme is reversibly inactivated by cyanide, titanium(III) citrate and dithionite. Dithionite and azide bind directly to equatorial ligation sites of the Mo atom .

This entry represents the gamma subunit (HcrC) of this three-subunit enzyme. It is 17 kDa in size and has two [2Fe-2S] clusters .
4-hydroxybenzoyl-CoA reductase, alpha subunit (4hydrxbenzoyl-CoA_Rdtase_asu)
Type: Family

4-Hydroxybenzoyl-CoA reductase (4-HBCR) is a member of the xanthine oxidase (XO) family of molybdenum cofactor containing enzymes. It catalyses the irreversible removal of a phenolic hydroxy group by reduction, yielding water and benzoyl-CoA, which is a common intermediate in the anaerobic degradation of aromatic compounds.

4-HBCR has a heterodimer subunit compositon of alpha2-beta2-gamma2. 4-HBCR contains two molybdopterins, four [2Fe-2S], two [4Fe-4S] clusters and two FADs . A ferredoxin with two [4Fe-4S] clusters functions as the natural electron donor. The enzyme is reversibly inactivated by cyanide, titanium(III) citrate and dithionite. Dithionite and azide bind directly to equatorial ligation sites of the Mo atom .

This entry represents the largest chain, alpha (HcrA) of 4-hydroxybenzoyl-CoA reductase. It is 82 kDa in size and contains a Mo-cofactor-binding site .
4-hydroxybenzoyl-CoA reductase, beta subunit (4hydrxbenzoyl-CoA_Rdtase_bsu)
Type: Family

4-Hydroxybenzoyl-CoA reductase (4-HBCR) is a member of the xanthine oxidase (XO) family of molybdenum cofactor containing enzymes. It catalyses the irreversible removal of a phenolic hydroxy group by reduction, yielding water and benzoyl-CoA, which is a common intermediate in the anaerobic degradation of aromatic compounds.

4-HBCR has a heterodimer subunit compositon of alpha2-beta2-gamma2. 4-HBCR contains two molybdopterins, four [2Fe-2S], two [4Fe-4S] clusters and two FADs . A ferredoxin with two [4Fe-4S] clusters functions as the natural electron donor. The enzyme is reversibly inactivated by cyanide, titanium(III) citrate and dithionite. Dithionite and azide bind directly to equatorial ligation sites of the Mo atom .

This entry represents the second largest chain, beta (HcrB, 35 kDa), of the enzyme 4-hydroxybenzoyl-CoA reductase. In Thauera aromatica, there is an additional domain in the beta-subunit, which probably has an extra iron-sulphur cluster .
Xanthine dehydrogenase D subunit (Xanthine_dehydrogenase_dsu)
Type: Family

This gene has been characterised in Bacillus subtilis as the molybdopterin binding-subunit of xanthine dehydrogenase (pucD), acting in conjunction with pucC, the FAD-binding subunit and pucE, the FeS-binding subunit. The more common XDH complex (

) includes the xdhB gene which is related to pucD. It appears that most of the relatives of pucD outside of this narrow clade are involved in other processes as they are found in unrelated genomic contexts, contain the more common XDH complex and/or do not appear to process purines to allantoin.
tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC, C-terminal (tRNA_S-uridine_synth_MnmC_C)
Type: Domain

In Escherichia coli, the protein previously designated YfcK is now identified as the bifunctional enzyme MnmC. It acts, following the action of the heterotetramer of GidA and MnmE, in the modification of U-34 of certain tRNA to 5-methylaminomethyl-2-thiouridine (mnm5s2U). In other bacteria, the corresponding proteins are usually but always found as a single polypeptide chain, but occasionally as the product of tandem genes. The N-terminal region, or subunit, contains methyltransferase activity and is known as MnmC2. This entry represents the C-terminal region of the multifunctional protein, referred to as MnmC1 .
Xanthine dehydrogenase E subunit (Xanthine_dehydrogenase_esu)
Type: Family

This protein has been characterised in Bacillus subtilis as the iron-sulphur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (

) includes the xdhA gene as the Fe-S cluster binding component.
Xanthine dehydrogenase C subunit (Xanthine_dehydrogenase_csu)
Type: Family

This protein has been characterised in Bacillus subtilis as the FAD binding-subunit of xanthine dehydrogenase (pucC), acting in conjunction with pucD, the molybdopterin-binding subunit and pucE, the FeS-binding subunit.
6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase (Dearomat_hydrolase)
Type: Family

6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase is a ring-hydrolysing enzyme invloved in the anaerobic metabolism of aromatic enzymes by way of benzoyl-CoA, as seen in Thauera aromatica , Geobacter metallireducens, and Azoarcus sp. (strain EbN1). Note that Rhodopseudomonas palustris uses a different pathway to perform a similar degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.