SII-SWORD/CoKE huggingface dataset:
6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase (Dearomat_deydrogenase)
Type: Family

6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase is an enzyme found in the anaerobic metabolism of aromatic enzymes by way of benzoyl-CoA, as seen in Thauera aromatica , Geobacter metallireducens, and Azoarcus sp. (strain EbN1). The experimentally characterised form from T. aromatica uses only NAD+, not NADP+. Note that Rhodopseudomonas palustris uses a different pathway to perform a similar degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Xanthine dehydrogenase, accessory protein PucB (Xanthine_dehydrogenase_PucB)
Type: Family

Members of this protein family are PucB proteins found in Bacillus subtilis . The expression of this protein is located in an operon with the structural subunits of xanthine dehydrogenase, and has been found to be essential for XDH activity. Some members of this family appear to have a distant relationship to the MobA protein involved in molybdopterin biosynthesis, although this may be coincidental.
Pimeloyl-CoA dehydrogenase, small subunit (Pimeloyl_CoA_dehydrogenase_ssu)
Type: Family

Members of this protein family are PimD proteins, and can be found in Rhodopseudomonas palustris and Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Pimeloyl-CoA is a catabolite of benzoyl-CoA degradation, which occurs in R. palustris. This entry represents the small subunit
Pimeloyl-CoA dehydrogenase, large subunit (Pimeloyl_CoA_dehydrogenase_lsu)
Type: Family

Members of this protein family are PimC proteins that can be found in Rhodopseudomonas palustris and Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Pimeloyl-CoA, is a catabolite of benzoyl-CoA degradation, which occurs in R. palustris. This entry represents the large subunit.
Dicarboxylate-CoA ligase PimA (Dicarboxylate-CoA_ligase_PimA)
Type: Family

PimA, a member of a large family of acyl-CoA ligases, is found in a characteristic operon pimFABCDE for the metabolism of pimelate and related compounds. It is found, so far, in Bradyrhizobium japonicum and several strains of Rhodopseudomonas palustris. PimA from R. palustris was shown to be active as a CoA ligase for C(7) to C(14) dicarboxylates and fatty acids .
2-hydroxycyclohexanecarboxyl-CoA dehydrogenase (OH-benzo_CoA_DH_BadH)
Type: Family

This entry represents the enzyme 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase. The enzymatic properties the enzyme is homotetrameric, and not sensitive to oxygen. 2-hydroxycyclohexanecarboxyl-CoA dehydrogenaseis part of proposed pathway for degradation of benzoyl-CoA to 3-hydroxypimeloyl-CoA that differs from the analogous in Thauera aromatica. It also may occur in degradation of the non-aromatic compound cyclohexane-1-carboxylate .
Cyclohexanecarboxyl-CoA dehydrogenase (Cyc-hxne_CoA_dehydrogenase)
Type: Family

Cyclohex-1-ene-1carboxyl-CoA is an intermediate in the anaerobic degradation of benzoyl-CoA derived from various aromatic compounds, in Rhodopseudomonas palustris but not Thauera aromatica. The aliphatic compound cyclohexanecarboxylate, can be converted to the same intermediate in two steps. The first step is its ligation to coenzyme A. The second is the action of this enzyme, cyclohexanecarboxyl-CoA dehydrogenase.
Cyclohexanecarboxylate-CoA ligase (Cyclohxane-COOH-CoA_Ligase)
Type: Family

Cyclohexanecarboxylate-CoA ligase prepares the aliphatic ring compound, cyclohexanecarboxylate, for dehydrogenation and then degradation by a pathway also used in benzoyl-CoA degradation in Rhodopseudomonas palustris.
Botulinum neurotoxin transcription-activating sigma factor BotR (Tscrpt_reg_BotR)
Type: Family

Regulatory sigma-70 protein, BotR transcription regulator regulates neurotoxin production in Clostridium botulinum. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo .
2-ketocyclohexanecarboxyl-CoA hydrolase (Keto-benzo_CoA_Hydrolase)
Type: Family

2-ketocyclohexanecarboxyl-CoA hydrolase is a ring-opening enzyme that acts in catabolism of molecules such as benzoyl-CoA and cyclohexane carboxylate. It converts -ketocyclohexanecarboxyl-CoA to pimelyl-CoA. It is not sensitive to oxygen .
Catechol 2,3 dioxygenase (Catechol_2-3_dOase)
Type: Family

This entry represents catechol 2,3 dioxygenase (

), although some members have highly significant activity on catechol derivatives such as 3-methylcatechol, 3-chlorocatechol, and 4-chlorocatechol . Catechol 2,3 dioxygenase is also called metapyrocatechase, as it performs a meta-cleavage (an extradiol ring cleavage) in contrast to the ortho-cleavage (intradiol ring cleavage)performed by catechol 1,2-dioxygenase(

) also called pyrocatechase.
Allantoinase PuuE (PuuE)
Type: Domain

Allantoinase ([ec:]3.5.2.5) can hydrolyze allantoin((2,5-dioxoimidazolidin-4-yl)urea), one of the most important nitrogen carrier for some plants, soil animals, and microorganisms, to allantoate. DAL1 gene from Saccharomyces cerevisiae encodes an allantoinase. However, some organisms possess allantoinase activity but lack DAL1 allantoinase. In those organisms, a defective allantoinase gene, named puuE (purine utilization E), encodes an allantoinase that specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. PuuE allantoinase is related to polysaccharide deacetylase (DCA), one member of the carbohydrate esterase 4 (CE4) superfamily, that removes N-linked or O-linked acetyl groups of cell wall polysaccharides, and lacks sequence similarity with the known DAL1 allantoinase that belongs to the amidohydrolase superfamily. PuuE allantoinase functions as a homotetramer . Its monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCAs. It appears to be metal-independent and acts on a small substrate molecule, which is distinct from the common features of DCAs that are normally metal ion dependent and recognize multimeric substrates.
Biphenyl-2,3-diol 1,2-dioxygenase (DiOHbiphenyl_dOase)
Type: Family

Biphenyl-2,3-diol 1,2-dioxygenase (also called 2,3-dihydroxybiphenyl 1,2-dioxygenase) is the third enzyme of a pathway for biphenyl degradation. Many of the extradiol ring-cleaving dioxygenases, to which these proteins belong, act on a range of related substrates. Some members of this family may be found operons for toluene or naphthalene degradation, where other activities of the same enzyme may be more significant
(S)-ureidoglycine aminohydrolase (UGHY)
Type: Family

This entry represents the (S)-ureidoglycine aminohydrolase UGlyAH from bacteria and fungi, including UGlyAH from Escherichia coli and some plant homologues.

(S)-ureidoglycine aminohydrolase (UGHY or UGlyAH) is involved in the ureide pathway, a metabolic route of purine catabolism in plants, some bacteria and probably in some fungi where, uric acid is degraded into glyoxylate and ammonia . This enzyme is involved in the anaerobic nitrogen utilization via the assimilation of allantoin. It catalyses the second step in the allantoin degradation pathway, the deamination of the allantoin producing S-ureidoglycolate and ammonia from S-ureidoglycine .

The structure of UGlyAH from Arabidopsis thaliana (AtUGlyAH) has been studied. It contains two structurally similar β-barrel domains, called N and C (cupin) domains. AtUGlyAH binds a Mn ion through its C-terminal domain which acts as a molecular anchor to bind (S)-ureidoglycine. Its structure showed a bi-cupin fold with a conserved jelly roll-like β-barrel fold and an octameric functional unit. Several structural homologues of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features .
2-hydroxymuconic semialdehyde dehydrogenase (OHmuconic_semiald_DH)
Type: Family

Many aromatic compounds are catabolized by way of the catechol, via the meta-cleavage pathway, to pyruvate and acetyl-CoA. 2-hydroxymuconic semialdehyde dehydrogenase performs the second of seven steps in that pathway for catechol degradation.
4-hydroxy-2-oxovalerate aldolase (4OH_2_O-val_aldolase)
Type: Family

4-hydroxy 2-ketovalerate aldolase (also known as 4-hydroxy-2-ketovalerate aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA)) converts 4-hydroxy-2-oxopentanoate to acetaldehyde and pyruvate, the penultimate step in the meta-cleavage pathway for the degradation of phenols, cresols and catechol. Acetaldehyde is then converted by acetaldehyde dehydrogenase (acylating) (DmpF;

) to acetyl-CoA. The two enzymes are tightly associated. This family includes the Escherichia coli MhpE aldolase , the Pseudomonas DmpG aldolase, and the Burkholderia xenovorans BphI pyruvate aldolase . In Pseudomonas, the DmpG aldolase tightly associates with a dehydrogenase (DmpF) and is inactive without it . HOA has a canonical TIM-barrel fold with a C-terminal extension that forms a funnel leading to the active site . This family belongs to the DRE-TIM metallolyase superfamily.

DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core β(8)-α(8) motif with the eight parallel β strands forming an enclosed barrel surrounded by eight α helices. The domain has a catalytic centre containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name 'DRE-TIM' .
4-oxalocrotonate decarboxylase (4-oxalocrotonate_decarboxylase)
Type: Family

This entry represents 4-oxalocrotonate decarboxylase. This protein is characterised (indirectly) in Pseudomonas sp. (strain CF600) and was inactive except when co-expressed with DmpE, 2-oxopent-4-enoate hydratase, a homologous protein from the same operon . Both of these enzymes are active in the degradation of catechol, a common intermediate in the degradation of aromatic compounds such as benzoate, toluene, phenol, dimethylphenol (dmp), salicylate, etc.

This enzyme folds into unusual fold, the core of which contains 3 layers of β-sheet structure and looks like β-barrel and β-sandwich fused together with features brought from both . The 4-oxalocrotonate decarboxylases are structurally similar to fumarylacetoacetate hydrolases (FAH) and to members of FAH superfamily of enzymes . The latter are known to catalyse a remarkable variety of reactions and are essential in metabolic pathways that degrade aromatic compounds in prokaryotes and eukaryotes.
Salicylate 1-monooxygenase (Salicylate_mOase)
Type: Family

Members of this protein family are salicylate 1-monooxygenase, also called salicylate hydroxylase. This enzyme converts salicylate to catechol, which is a common intermediate in the degradation of a number of aromatic compounds (phenol, toluene, benzoate, etc.). The gene for this protein may occur in catechol degradation genes, such as those of the meta-cleavage pathway.
2-oxopent-4-enoate hydratase (2-oxopent-4-enoate_hydratase)
Type: Family

2-oxopent-4-enoate hydratase, which is also called 2-hydroxypent-2,4-dienoate hydratase is closely related to another gene found in the same operon, 4-oxalocrotonate decarboxylase, with which it interacts closely .
Benzoyl-CoA-dihydrodiol lyase (Benz-CoA_dihydrodiol_lyase)
Type: Family

In the presence of O2, the benzoyl-CoA oxygenase/reductase BoxBA BoxAB converts benzoyl-CoA to 2,3-dihydro-2,3-dihydroxybenzoyl-CoA . Members of this family, BoxC, homologous to enoyl-CoA hydratases/isomerases, hydrolyse this compound to 3,4-dehydroadipyl-CoA semialdehyde + HCOOH.
Benzoyl-CoA oxygenase/reductase BoxA (Benzoyl_CoA_Oase_BoxA)
Type: Family

Members of this protein family are BoxA, the A component of the BoxAB benzoyl-CoA oxygenase/reductase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. BoxA is a homodimeric iron-sulphur-flavoprotein and acts as an NADPH-dependent reductase for BoxB .
Benzoyl-CoA oxygenase BoxB (Benzoyl_CoA_Oase_BoxB)
Type: Family

Members of this protein family are BoxB, the B subunit of benzoyl-CoA oxygenase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation .
2-aminoethylphosphonate ABC transporter system, permease protein PhnU (AminoethylPonate_ABC_perm-PhnU)
Type: Family

The enzyme phosphonatase catalyses the degradation of 2-aminoethylphosphonate (AEP) in bacteria. This allows them to metabolise a range of organophosphonate compounds, including 2-aminoethylphosphonate, as a sole source of carbon, energy and phosphorus for growth . The C-P bond in phosphonoacetaldehyde (Pald) is hydrolysed and a bi-covalent Lys53ethylenamine/Asp12 aspartylphosphate intermediate is formed . This step can also be catalysed by C-P lyase , with some bacteria having the genes for both pathways and some only for one of them. The 2-aminoethylphosphonate ABC transport system functions in the transport of 2-aminoethylphosphonate across the membrane for utilisation in the bacterial cell .

PhnU is probably part of the phnSTUV complex involved in 2-aminoethylphosphonate import. It is found in a region of the salmonella typhimurium LT2 genome responsible for the catabolism of 2-aminoethylphosphonate via the phnWX pathway (

).
Putative 2-aminoethylphosphonate binding protein, ABC transporter (AminoethylPonate_ABC-bd)
Type: Family

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins .

This ABC transporter periplasmic substrate binding protein component is found in a region of the salmonella typhimurium LT2 genome responsible for the catabolism of 2-aminoethylphosphonate via the phnWX pathway (

).
Anthranilate 1,2-dioxygenase, large subunit (Anthranilate_1-2-diOase_lsu)
Type: Family

This entry represents a group of anthranilate 1,2-dioxygenase large subunit proteins from proteobacteria, including AndAc from Burkholderia cepacia and AntA from Acinetobacter baylyi. They are part of the multicomponent anthranilate dioxygenase, that converts anthranilate to catechol. Anthranilate (2-aminobenzoate) is an intermediate of tryptophan (Trp) biosynthesis and degradation . AndAc an also act on benzoate and salicylate but not on 2-chlorobenzoate or o-toluate .
Benzoate 1,2-dioxygenase, large subunit (Benzo_1-2-diOase_lsu)
Type: Family

Benzoate 1,2-dioxygenase (

) belongs to the larger family of aromatic ring-hydroxylating dioxygenases. Members of this family all act on benzoate, but may have additional activities on various benozate analogs. This entry describes the large subunit.
Anthranilate 1,2-dioxygenase, small subunit (Anthranilate_1-2-diOase_ssu)
Type: Family

This entry represents a group of anthranilate 1,2-dioxygenase small subunit proteins from proteobacteria, including AndAd from Burkholderia cepacia and AntB from Acinetobacter baylyi. They are part of the multicomponent anthranilate dioxygenase, that converts anthranilate to catechol. Anthranilate (2-aminobenzoate) is an intermediate of tryptophan (Trp) biosynthesis and degradation. Closely related paralogs typically are the benzoate 1,2-dioxygenase small subunit, among the larger set of ring-hydroxylating dioxygenases .
Benzoate 1,2-dioxygenase, small subunit (Benzo_1-2-diOase_ssu)
Type: Family

Benzoate 1,2-dioxygenase (

) belongs to the larger family of aromatic ring-hydroxylating dioxygenases. Members of this family should all act on benzoate, but several have additional known activities on various benozate analogs. Some members actually may be named more suitably according to such alternate an activity, such as 2-chlorobenzoate 1,2-dioxygenase (

).
DNA sulphur modification protein DndB (DNA_S_mod_DndB)
Type: Family

This is family of bacterial proteins likely to be necessary for binding to DNA and recognising the modification sites. Members are found in bacteria, archaea and on viral plasmids, and are typically between 354 and 474 amino acids in length. There is a conserved DGQHR sequence motif.

Included in this family is the DndB protein encoded by an operon associated with a sulphur-containing modification to DNA . DndB is described as a putative ATPase.
Hydroxypyruvate isomerase (Hydroxypyruvate_isomerase)
Type: Family

This enzyme interconverts tartronate semi-aldehyde (TSA, aka 2-hydroxy 3-oxopropionate) and hydroxypyruvate. The enzyme has been characterised and found to be specific for TSA, contain no cofactors, and have a rather high Km for hydroxypyruvate of 12.5 mM. The gene is often found in association with glyoxalate carboligase (which produces TSA), but has been shown to have no effect on growth on glyoxalate when knocked out . This is consistent with the fact that the gene for tartronate semialdehyde reductase (glxR) is also associated and may have primary responsibility for the catabolism of TSA.
Cysteine desulfurase DndA (Cysteine_desulfurase_DndA)
Type: Family

This entry describes DndA, a protein related to IscS and part of a larger family of cysteine desulfurases. It is encoded, typically, divergently from a conserved, sparsely distributed operon for sulphur modification of DNA. This modification system is designated dnd, after the phenotype of DNA degradation during electrophoresis. The system is sporadically distributed in bacteria, much like some restriction enzyme operons. DndB is described as a putative ATPase.
DNA phosphorothioation-dependent restriction protein DptG (Dnd_assoc_1)
Type: Family

A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation .
DNA phosphorothioation-dependent restriction protein DptH (Dnd_assoc_2)
Type: Family

A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation .
DNA phosphorothioation-dependent restriction protein DptF (Dnd_assoc_3)
Type: Family

A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation .
5-keto-4-deoxy-D-glucarate aldolase (GarL)
Type: Family

5-keto-4-deoxy-D-glucarate aldolase GarL is involved in step 2 of the subpathway that synthesizes D-glycerate from galactarate. It catalyses the reversible retro-aldol cleavage of both 5-keto-4-deoxy-D-glucarate and 2-keto-3-deoxy-D-glucarate to pyruvate and tartronic semialdehyde .
Succinylglutamate-semialdehyde dehydrogenase (SuccinylGlu_semiald_DH_AstD)
Type: Family

Succinylglutamic-semialdehyde dehydrogenase (or succinylglutamic semialdehyde dehydrogenase (SGSD, E. coli AstD, EC=1.2.1.71)) is the fourth enzyme in the arginine succinyltransferase (AST) pathway for arginine catabolism , and catalyzes the NAD+-dependent reduction of succinylglutamate semialdehyde into succinylglutamate . This pathway converts the carbon skeleton of arginine into glutamate, with the concomitant production of ammonia and conversion of succinyl-CoA into succinate and CoA.
Arginine N-succinyltransferase (Arginine_N-succinylTrfase)
Type: Family

Arginine N-succinyltransferase catalyses the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism via the arginine succinyltransferase pathway. Six major L-arginine-degrading pathways have been described for prokaryotes . Arginine succinyltransferase AstA (

) is the first enzyme of the succinyltransferase (AST) pathway operon consists of five genes . In a few species, such as Pseudomonas aeruginosa, arginine succinyltransferase consist of a heterodimer of subunits alpha (AstA) and beta (AruG) .

This family consists of the monomeric arginine N-succinyltransferase.
Arginine/ornithine succinyltransferase, alpha subunit (Arg/Orn_succinylTfrase_asu)
Type: Family

Arginine N-succinyltransferase catalyses the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism via the arginine succinyltransferase pathway. Six major L-arginine-degrading pathways have been described for prokaryotes . Arginine succinyltransferase AstA (

) is the first enzyme of the succinyltransferase (AST) pathway operon consists of five genes . In a few species, such as Pseudomonas aeruginosa, arginine succinyltransferase consist of a heterodimer of subunits alpha (AstA) and beta (AruG) .

Members of this protein family represent the alpha subunit of the arginine succinyltransferase heterodimer.
Acetyl/Succinylornithine transaminase family, bacteria (Ac/SucOrn_transaminase_bac)
Type: Family

This family consists of bacteria acetyl/succinylornithine transaminases.
Succinylornithine transaminase (

), catalyses the third of five steps in arginine succinyltransferase (AST) pathway, an ammonia-releasing pathway of arginine degradation. A number of sequences extremely closely related in sequence, found in different genomic contexts, are likely to act in different biological processes and may act on different substrates for example acetylornithine transaminase.
Glucarate dehydratase (Glucarate_dehydratase)
Type: Family

This entry represents glucarate dehydratase (

), which is involved in the first step of the degradation of D-glucaric acid. This enzyme converts D-glucarate (and L-idarate, a stereoisomer) to 5-dehydro-4-deoxyglucarate, which is subsequently acted on by GarL, tartronate semialdehyde reductase and glycerate kinase (,

).
Galactarate dehydratase GarD-like (GarD-like)
Type: Family

This entry includes GarD from Enterobacteriaceae and its homologues from other bacterial species.
5-dehydro-4-deoxyglucarate dehydratase (Dehydro-deoxyglucarate_dehyd)
Type: Family

5-dehydro-4-deoxyglucarate dehydratase (also called 5-keto-4-deoxy-glucarate dehydratase or KDGDH), is a member of the same family as dihydrodipicolinate synthase (DHDPS) . 5-dehydro-4-deoxyglucarate dehydratase is involved in glucarate metabolism, where it catalyses the dehydration and decarboxylation of 5-dehydro-4-deoxy-D-glucarate to 2,5-dioxopentanoate . In certain species of Enterobacteriaceae 5-dehydro-4-deoxy-D-glucarate is degraded to pyruvate and glycerate, instead of to 2,5-dioxopentanoate .