SII-SWORD/CoKE huggingface dataset:
Wolbachia palindromic element (WPE) (WPE_wolbac)
Type: Domain

This domain conceptually resembles

, the Rickettsial palindromic element (RPE) domain. In both cases, a protein-coding palindromic element spreads through a genome, inserting usually in protein-coding regions. The additional protein coding sequence is thought to allow function of the host protein because of location in surface-exposed regions of the protein structure.
Copper transport repressor CopY/TcrY (Cu_transp_CopY/TcrY)
Type: Family

This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferable copper resistance) of an Enterococcus faecium (Streptococcus faecium) plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this entry are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Archaeoflavoprotein AfpA (Archaeoflavo_AfpA)
Type: Family

The prototypical member of this archaeal protein family is AF1518 from Archaeoglobus fulgidus. This homodimer with two non-covalently bound FMN cofactors can receive electrons from ferredoxin, but not from a number of other electron donors such as NADH or rubredoxin. It can then donate electrons to various reductases .
Archaeal dihydromethanopterin reductase (DmrX)
Type: Family

This entry describes one of two paralogous families of archaeal flavoproteins, the other being described by

. Proteins in this family have been recently characterised as dihydromethanopterin reductases .
Carboxysome shell carbonic anhydrase (Carboxysome_shell_carb_anhy)
Type: Family

This entry describes a carboxysome shell protein that proves to be a novel class, designated epsilon, of carbonic anhydrase. It tends to be encoded near genes for RuBisCo and other carboxysome shell proteins .
Carboxysome shell vertex protein CsoS4A (CsoS4A)
Type: Family

This entry describes the Carboxysome shell vertex protein CsoS4A (also known as carboxysome operon protein orfA). It distinguishes one of the two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins are components of other shells, for example, the ethanolamine utilization protein EutN/carboxysome structural protein Ccml of the ethanolamine degradation organelle of Nitrobacter hamburgensis. This protein, together with CsoS4B, forms vertices in the carboxysome .
Carboxysome shell vertex protein CsoS4B (CsoS4B)
Type: Family

This entry describes the Carboxysome shell vertex protein CsoS4B (also known as carboxysome operon protein orfB). It distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins are components of other types of shell such as the shell of the ethanolamine degradation organelle. This protein, together with CsoS4A, forms vertices in the carboxysome .
Nucleoside triphosphatase YtkD (Nudix_YtkD)
Type: Family

The proteins in this entry belong to the nudix family and includes the putative 8-oxo-dGTP diphosphatase YtkD from E. coli. These sequences share some sequence identity with Escherichia coli MutT but appear not to be functionally interchangeable with it. It functions, in conjunction with MutT, to protect vegetatively growing cells from DNA-damaging agents such as H2O2 or t-BHP (t-butylhydroperoxide) .
Phosphate butyryltransferase (Phosphate_butyryltransferase)
Type: Family

Members of this family are phosphate butyryltransferase enzymes, also called phosphotransbutyrylase. In general, this enzyme is found in butyrate-producing anaerobic bacteria, encoded next to the gene for butyrate kinase. Together, these two enzymes represent what may be the less common of two pathways for butyrate production from butyryl-CoA. The alternative is transfer of the CoA group to acetate by butyryl-CoA:acetate CoA transferase. This entry does not include the homologue from Thermotoga maritima, whose activity on butyryl-CoA is only 30 % of its activity with acetyl-CoA.
L-lactate oxidase (L_lactate_ox)
Type: Family

Members of this entry oxidize L-lactate to pyruvate, reducing molecular oxygen to hydrogen peroxide. The enzyme is known in Aerococcus viridans, Streptococcus iniae, and some strains of Streptococcus pyogenes where it appears to contribute to virulence.
Branched-chain phosphotransacylase (Brnchd-chn_Ptransacetylase)
Type: Family

This entry distinguishes branched-chain phosphotransacylases like that of Enterococcus faecalis from closely related subfamilies of phosphate butyryltransferase

, (

) and phosphate acetyltransferase

, (

). Members of this family and of

show considerable cross reactivity, and the occurrence of a member of either family proximate to an apparent leucine dehydrogenase will suggest activity on branched chain-acyl-CoA compounds.
CRISPR-associated protein, Cas02710 (CRISPR-assoc_prot_Cas02710)
Type: Family

This entry represents a family of Cas proteins encoded exclusively in the vicinity of CRISPR repeats and other Cas proteins in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia) .

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.
Cation/acetate symporter ActP (Cation/Ac_symporter_ActP)
Type: Family

This entry represents the cation/acetate symporter ActP from Gammaproteobacteria. ActP transports acetate and is also able to transport glycolate .
Urea carboxylase (Urea_COase)
Type: Family

Members of this family are ATP-dependent urea carboxylases, including characterised members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae (Baker's yeast). The allophanate hydrolase domain of the yeast enzyme is not included in this entry and is represented by an adjacent gene in O. sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from O. sagaranensis was shown to be highly active on acetamide and formamide as well as urea.
Allophanate hydrolase (Allophanate_hydrolase)
Type: Domain

Amidase signature (AS) enzymes are a large group of hydrolytic enzymes that contain a conserved stretch of approximately 130 amino acids known as the AS sequence. They are widespread, being found in both prokaryotes and eukaryotes. AS enzymes catalyse the hydrolysis of amide bonds (CO-NH2), although the family has diverged widely with regard to substrate specificity and function. Nonetheless, these enzymes maintain a core α/β/α structure, where the topologies of the N-and C-terminal halves are similar. AS enzymes characteristically have a highly conserved C-terminal region rich in serine and glycine residues, but devoid of aspartic acid and histidine residues, therefore they differ from classical serine hydrolases. These enzymes posses a unique, highly conserved Ser-Ser-Lys catalytic triad used for amide hydrolysis, although the catalytic mechanism for acyl-enzyme intermediate formation can differ between enzymes .

Examples of AS enzymes include:

Peptide amidase (Pam) , which catalyses the hydrolysis of the C-terminal amide bond of peptides.

Fatty acid amide hydrolases , which hydrolyse fatty acid amid substrates (e.g. cannabinoid anandamide and sleep-inducing oleamide), thereby controlling the level and duration of signalling induced by this diverse class of lipid transmitters.

Malonamidase E2 , which catalyses the hydrolysis of malonamate into malonate and ammonia, and which is involved in the transport of fixed nitrogen from bacteroids to plant cells in symbiotic nitrogen metabolism.

Subunit A of Glu-tRNA(Gln) amidotransferase ,a heterotrimeric enzyme that catalyses the formation of Gln-tRNA(Gln) by the transamidation of misacylated Glu-tRNA(Gln) via amidolysis of glutamine.

Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway . In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase.

In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene . Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it .

Allophanate hydrolase belongs to the Amidase signature enzyme family.
Cyanuric acid hydrolase/Barbiturase (AtzD/Barbiturase)
Type: Family

Cyanuric acid hydrolases (AtzD) and barbiturases are homologous and found almost exclusively in bacteria . AtzD hydrolyses cyanuric acid to release carboxybiuret, which spontaneously decarboxylates to biuret . Barbiturase catalyses the ring-opening of barbituric acid to ureidomalonic acid . Although the AtzD/barbiturase family have previously been suggested to belong to the amidohydrolase superfamily, bioinformatics analysis and the lack of bound metals imply that this might not be the case .
1-carboxybiuret hydrolase, AtzE subunit (Carboxybiuret_hydro_AtzE)
Type: Family

Amidase signature (AS) enzymes are a large group of hydrolytic enzymes that contain a conserved stretch of approximately 130 amino acids known as the AS sequence. They are widespread, being found in both prokaryotes and eukaryotes. AS enzymes catalyse the hydrolysis of amide bonds (CO-NH2), although the family has diverged widely with regard to substrate specificity and function. Nonetheless, these enzymes maintain a core α/β/α structure, where the topologies of the N-and C-terminal halves are similar. AS enzymes characteristically have a highly conserved C-terminal region rich in serine and glycine residues, but devoid of aspartic acid and histidine residues, therefore they differ from classical serine hydrolases. These enzymes posses a unique, highly conserved Ser-Ser-Lys catalytic triad used for amide hydrolysis, although the catalytic mechanism for acyl-enzyme intermediate formation can differ between enzymes .

Examples of AS enzymes include:

Peptide amidase (Pam) , which catalyses the hydrolysis of the C-terminal amide bond of peptides.

Fatty acid amide hydrolases , which hydrolyse fatty acid amid substrates (e.g. cannabinoid anandamide and sleep-inducing oleamide), thereby controlling the level and duration of signalling induced by this diverse class of lipid transmitters.

Malonamidase E2 , which catalyses the hydrolysis of malonamate into malonate and ammonia, and which is involved in the transport of fixed nitrogen from bacteroids to plant cells in symbiotic nitrogen metabolism.

Subunit A of Glu-tRNA(Gln) amidotransferase ,a heterotrimeric enzyme that catalyses the formation of Gln-tRNA(Gln) by the transamidation of misacylated Glu-tRNA(Gln) via amidolysis of glutamine.

This family refers to 1-carboxybiuret hydrolase subunit AtzE, which hydrolyzes 1-carboxybiuret to urea-1,3-dicarboxylate and NH3. As 1-carboxybiuret hydrolyzes spontaneously to biuret, AtzE was previously thought to use biuret as substrate, but this has since been corrected .
Bacteriochlorophyllide d C-20 methyltransferase (BchU)
Type: Family

Members of this protein family include bacteriochlorophyllide d C-20 (also known as methyltransferaseS-adenosylmethionine-dependent C-20 methyltransferase or BchU), part of the pathway of bacteriochlorophyll c production in photosynthetic green sulphur bacteria . The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produce bacteriochlorophyll d.

Methyltransferases (EC [ec:2.1.1.-]) constitute an important class of enzymes present in every life form. They transfer a methyl group most frequently from S-adenosyl L-methionine (SAM or AdoMet) to a nucleophilic acceptor such as oxygen leading to S-adenosyl-L-homocysteine (AdoHcy) and a methylated molecule . All these enzymes have in common a conserved region of about 130 amino acid residues that allow them to bind SAM . The substrates that are methylated by these enzymes cover virtually every kind of biomolecules ranging from small molecules, to lipids, proteins and nucleic acids . Methyltransferase are therefore involved in many essential cellular processes including biosynthesis, signal transduction, protein repair, chromatin regulation and gene silencing . More than 230 families of methyltransferases have been described so far, of which more than 220 use SAM as the methyl donor.
Acetate-CoA ligase [ADP-forming], alpha domain (AcCoA-synth-alpha)
Type: Domain

This group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which they have been characterised . In most species this protein is bifunctional, existing as fused α-β domains. In Pyrococcus and related species, however, the domains exist as separate polypeptides. This entry represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. One of these (along with its beta-domain partner) was characterised as ACS-II showing specificity for phenylacetyl-CoA . This entry excludes non-ACS-I paralogs.
Siderophore transporter, RhtX/FptX family (Siderophore_transpt_RhtX/FptX)
Type: Family

RhtX from Sinorhizobium meliloti 1021 and FptX from Pseudomonas aeruginosa appear to be single polypeptide transporters, from the major facilitator family for import of siderophores as a means to import iron. This function was suggested by proximity to siderophore biosynthesis genes and then confirmed by study of knockout and heterologous expression phenotypes.
Transcriptional repressor poly-beta-hydroxybutyrate-responsive (Tscrpt_rep_PHB_PhaQ)
Type: Family

Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family.
Pyruvate oxidase (Pyruvate_oxidase)
Type: Family

Members of this family are examples of pyruvate oxidase (

), such as POXB from Lactiplantibacillus plantarum , an enzyme with FAD and TPP as cofactors that catalyses the reaction pyruvate + phosphate + O2 + H2O = acetyl phosphate + CO2 + H2O2. It should not be confused with pyruvate dehydrogenase (

) as in Escherichia coli PoxB, although the E. coli enzyme is closely homologous and has pyruvate oxidase as an alternate name.
Thiamine kinase (Thiamine_kinase)
Type: Family

Members of this family are the ycfN gene product of Escherichia coli, now identified as the salvage enzyme thiamine kinase (ThiK), and additional proteobacterial homologues taken to be orthologs with equivalent function.
Penicillin-binding protein activator LpoB (LpoB)
Type: Family

This entry represents penicillin-binding protein activator LpoB. It has been suggested that penicillin-binding protein activator LpoB acts as a regulator of peptidoglycan synthesis that is essential for the function of penicillin-binding protein 1B (PBP1b) .
Phenylphosphate carboxylase, alpha subunit (Phenyl_P_COase_a)
Type: Family

Members of this protein family are the alpha subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This alpha subunit is homologous to the beta subunit and, more broadly, to UbiD family decarboxylases .
Phenylphosphate carboxylase, beta subunit (Phenyl_P_COase_b)
Type: Family

Members of this protein family are the beta subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This beta subunit is homologous to the alpha subunit and, more broadly, to UbiD family decarboxylases .
Phenylphosphate carboxylase, gamma subunit (Phenyl_P_COase_g)
Type: Family

Members of this protein family are the gamma subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. The gamma subunit has no known homologues.
Phenylphosphate carboxylase, delta subunit (Phenyl_P_COase_d)
Type: Family

Members of this protein family are the delta subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This delta subunit belongs to HAD family hydrolases.
Spore coat protein GerQ (Spore_coat_GerQ)
Type: Family

Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria) . This protein is cross-linked by a spore coat-associated transglutaminase.
GTP-binding protein Obg/CgtA (GTP-bd_Obg/CgtA)
Type: Family

This entry describes a universal, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure.

This is an essential GTPase which binds GTP, GDP and ppGpp with moderate affinity (with a twofold preference for GDP over GTP); shows high guanine nucleotide exchange rate constants for both nucleotides, and has a relatively low GTP hydrolysis rate. Deletion of the N terminus makes a protein that is non-functional in vivo but which retains nucleotide binding and GTPase activity. Required for cell cycle progression from G1 to S phase and for DNA replication .
Prolycopene isomerase (CrtISO)
Type: Family

This entry represents the Prolycopene isomerase (CrtISO) from Arabidopsis thaliana. Members of this family are predominantly found in plants and cyanobacteria.

CrtISO is a carotene cis-trans-isomerase (

) that converts 7,9,9'-tri-cis-neurosporene to 9'-cis-neurosporene and 7,9,9',7'-tetra-cis-lycopene (also known as prolycopene) into all-trans-lycopene .
Phytoene desaturase (Phytoene_desaturase)
Type: Family

This entry represents phytoene desaturase (PDS) from plants and cyanobacteria (blue-green algae). It is an essential carotenoid biosynthetic enzyme. It converts phytoene into zeta-carotene via the intermediary of phytofluene by the symmetrical introduction of two double bonds at the C-11 and C-11' positions of phytoene with a concomitant isomerization of two neighbouring double bonds at the C9 and C9' positions from trans to cis .

This entry does not include plant chloroplast transit peptides and the entry does not contain zeta-carotene desaturase, which is a closely related family in the same pathway.
Zeta-carotene desaturase (Zeta_caro_desat)
Type: Family

Zeta-carotene desaturase (also known as carotene 7,8-desaturase) catalyses two consecutive desaturations at positions C-7 and C-7' in the pathway from zeta-carotene to lycopene in plants and cyanobacteria .
Myxoxanthophyll biosynthesis, C-3',4' desaturase CrtD (Myxoxanthophyll_desat_CrtD)
Type: Family

This entry represents a family of proteins from cyanobacteria.

Members of this family include the Slr1293 protein, a carotenoid biosynthesis protein which was shown to be the C-3',4' desaturase (CrtD) of myxoxanthophyll biosynthesis in Synechocystis sp. (strain PCC 6803), and close homologues (presumed to be functionally equivalent) from other cyanobacteria, where myxoxanthophyll biosynthesis is either known or expected. This enzyme can act on neurosporene and so presumably catalyses the first step that is committed to myxoxanthophyll
.
Carotenoid/retinoid oxidoreductase (Carotenoid/retinoid_OxRdtase)
Type: Family

Phytoene is converted to lycopene by desaturation at four (two symmetrical pairs of) sites. This is achieved by two enzymes (4,4'-diaponeurosporene oxygenase or CrtP, and 4,4'-diaponeurosporenoate glycosyltransferase or CrtQ) in cyanobacteria (Gloeobacter being an exception) and plants, but by a single enzyme in most other bacteria and in fungi . This single enzyme is called the bacterial-type phytoene desaturase, or CrtI. Most members of this family are part of flavin containing amine oxidoreductase family. It is likely that all members act on either phytoene or on related compounds such as dehydrosqualene, for carotenoid biosynthesis.

This family also includes 4,4'-diapophytoene desaturase or CrtN which is required for the biosynthesis of the yellow-orange carotenoid staphyloxanthin in
Staphylococcus aureus
; 4,4'-diapolycopene oxygenase or CrtNb from
Methylomonas
which although involved in carotenoid biosynthesis is not a desaturase ; and 4,4'-diapolycopen-4-al dehydrogenase or CrtNc from
Bacillus indicus
.

Carotenoids are coloured compounds produced by plants, fungi, and microorganisms. Most animals lack the genes encoding carotenoid biosynthetic machinery and thus must obtain carotenoids from food. The pea aphid is an exception; its genome has been found to harbour genes for carotenoid biosynthesis, reflecting an ancestral transfer from a fungus .
Phosphoribosylaminoimidazole-succinocarboxamide synthase, Vibrio-type (SAICAR_synthase_Vibrio-typ)
Type: Family

This entry represents a protein family of phosphoribosylaminoimidazole-succinocarboxamide synthases (SAICAR synthetase or PUR7), significantly different in sequence from (

), which is predominantly found in the gammaproteobacteria Vibrio, Pseudoalteromonas, Pseudoalteromonas, Shewanella, Colwellia, and also in the primitive eukaryote Guillardia theta (Cryptomonas phi). This enzyme catalyses the seventh step in the de novo purine biosynthetic pathway; the ATP-dependent conversion of 5'-phosphoribosyl-5-aminoimidazole-4-carboxylic acid and aspartic acid to SAICAR .
Cytochrome c oxidase cbb3-type, CcoQ (Cyt_c_oxidase_cbb3_CcoQ)
Type: Family

Members of this protein family are restricted to the epsilon branch of the Proteobacteria. All members are found in operons containing the other three structural subunits of the cbb3 type of cytochrome c oxidase. These small proteins show remote sequence similarity to the CcoQ subunit in other cytochrome c oxidase systems, so this family is assumed to represent the epsilonproteobacterial variant of CcoQ.
Cytochrome c oxidase caa3 type assembly factor CtaG (Caa3-assmbl_CtaG)
Type: Family

CtaG is required for assembly of active cytochrome c oxidase of the caa3 type, as found in Bacillus subtilis . This entry represents CtaG from B.subtilis and other Bacilli.
Type-F conjugative transfer system pilin assembly thiol-disulphide isomerase TrbB (Thiol-disulphide_isomerase_rbB)
Type: Family

This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect . The protein is believed to be involved in pilin assembly . The protein is closely related to TraF (

) which is somewhat longer, lacks the cysteine motif and is apparently not functional as a disulfide bond isomerase.