SII-SWORD/CoKE huggingface dataset:
Putative phosphonoacetaldehyde dehydrogenase (Put_phosphonoacetaldehyde_DH)
Type: Family

This family of genes are members of the

NAD-dependent aldehyde dehydrogenase family. These genes are observed in Ralstonia eutropha (strain JMP134) (Alcaligenes eutrophus), Sinorhizobium meliloti 1021, Burkholderia mallei ATCC 23344, Burkholderia thailandensis (strain E264/ATCC 700388/DSM 13276/CIP 106301), Burkholderia cenocepacia (strain AU 1054), Burkholderia pseudomallei K96243 and Burkholderia pseudomallei (strain 1710b), Burkholderia xenovorans (strain LB400), Burkholderia sp. (strain 383) (Burkholderia cepacia (strain ATCC 17760/NCIB 9086/R18194)) and Polaromonas sp. (strain JS666/ATCC BAA-500) in close proximity to the PhnW gene (

) encoding 2-aminoethyl phosphonate aminotransferase (which generates phosphonoacetaldehyde) and PhnA (

) encoding phosphonoacetate hydrolase (not to be confused with the alkylphosphonate utilization operon protein PhnA modelled by

). Additionally, transporters believed to be specific for 2-aminoethyl phosphonate are often present. PhnW is, in other organisms, coupled with PhnX (

) for the degradation of phosphonoacetaldehyde (

), but PhnX is apparently absent in each of the organisms containing this aldehyde reductase. PhnA, characterised in a strain of Pseudomonas fluorescens that has not yet had its genome sequenced, is only rarely found outside of the PhnW and aldehyde dehydrogenase context. For instance in Rhodopseudomonas and Bordetella bronchiseptica, where it is adjacent to transporters presumably specific for the import of phosphonoacetate. It seems reasonably certain then, that this enzyme catalyses the NAD-dependent oxidation of phosphonoacetaldehyde to phosphonoacetate, bridging the metabolic gap between PhnW and PhnA. We propose the name phosphonoacetaldehyde dehydrogenase and the gene symbol PhnY for this enzyme. The structure of PhnY has been solved .

Putative phosphonoformaldehyde dehydrogenase (PhpJ), an aldehyde dehydrogenase homologue reportedly involved in the biosynthesis of phosphinothricin tripeptides in Streptomyces viridochromogenes DSM 40736, is also included in this entry .
L-lysine 6-transaminase (L-lysine_6-transaminase)
Type: Family

The immediate product of the reaction of L-lysine 6-transaminase, also called lysine epsilon-aminotransferase (LAT) on lysine, 2-aminoadipate 6-semialdehyde, becomes 1-piperideine 6-carboxylate, or P6C. This product may be converted subsequently to pipecolate or alpha-aminoadipate, lysine catabolites that may be precursors of certain secondary metabolites .
HhH-GPD-type base excision DNA repair protein (HhH-GPD_base_excis)
Type: Family

This entry describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes.
Formyl-CoA:oxalate CoA-transferase (Formyl_CoA_transfer)
Type: Family

CoA-transferases are found in organisms from all kingdoms of life. They catalyse reversible transfer reactions of coenzyme A groups from CoA-thioesters to free acids. There are at least three families of CoA-transferases, which differ in sequence and reaction mechanism:

Family I consists of CoA-transferases for 3-oxoacids (

,

), short-chain fatty acids (

,

) and glutaconate (

). Most use succinyl-CoA or acetyl-CoA as CoA donors.

Family II consists of the homodimeric alpha-subunits of citrate lyase and citramalate lyase (

,

). These enzymes catalyse the transfer of acyl carrier protein (ACP) with a covalently bound CoA derivative, but can accept free CoA thioesters as well.

Family III consists of formyl-CoA:oxalate CoA-transferase , succinyl-CoA:(R)-benzylsuccinate CoA-transferase , (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase , succinyl-CoA:mesaconate CoA-transferase and butyrobetainyl-CoA:(R)-carnitine CoA-transferase . These CoA-transferases occur in prokaryotes and eukaryotes, and catalyse CoA-transfer reactions in a highly substrate-and stereo-specific manner .

Family III CoA-transferase family member formyl-CoA transferase transfers coenzyme A from formyl-CoA to oxalate. It forms a pathway, together with oxalyl-CoA decarboxylase, for oxalate degradation; decarboxylation by the latter gene regenerates formyl-CoA. The two enzymes typically are encoded by a two-gene operon .
Oxalyl-CoA decarboxylase (Oxalyl-CoA_decarboxylase)
Type: Family

Oxalate accumulation from amino-acid catabolism is toxic and leads to acute disorders in mammals. Gut microflora are therefore pivotal in maintaining a safe intestinal oxalate balance through oxalate degradation. A number of bacteria, including Oxalobacter formigenes from the human gut, can carry out oxalate degradation via a two-step process :

Formyl-CoA transferase (frc;

) catalyses the transfer of the CoA moiety from formyl-CoA to oxalate.

Oxalate decarboxylase (oxc;

) catalyses the formation of formyl-CoA and carbon dioxide from oxalyl-CoA.

This entry represents the enzyme oxalyl-CoA decarboxylase (

), which binds one metal ion (usually magnesium) and one thiamine pyrophosphate (TPP) per subunit as cofactors .
Guanylate kinase (Guanylate_kinase)
Type: Family

Guanylate kinase, also called GMP kinase, is essential for recycling GMP and indirectly, cGMP. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP . Guanylate kinase is a highly conserved monomer and is important for the activation of various antiviral drugs.
YcaO-related McrA-glycine thioamidation protein (Methan_mark_1)
Type: Family

Members of this protein family were previously designated 'methanogenesis marker protein 1', now named as YcaO-related McrA-glycine thioamidation protein, which is universal in and restricted to methanogenic archaea. It shares homology with YcaO (ribosomal protein S12 methylthiotransferase) and its homologues involved in ATP-dependent formation of heterocycles in thiazole/oxazole-modified peptide antibiotics .
Methanogenesis marker protein 2 (Methan_mark_2)
Type: Family

Members of this protein family are only found archaeal methanogens. They show sequence similarity AIR synthase related protein N-and C-terminal domains (

and

). The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis .
Methyl coenzyme M reductase system, component A2 (Me_Coenz_M_Rdtase_A2)
Type: Family

The enzyme that catalyses the final step in methanogenesis, methyl coenzyme M reductase (MCR), contains alpha, beta, and gamma chains . In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed component A2 of the methyl coenzyme M reductase system . The MCR systems is formed of 3 components: A, B (HS-CoB) and C (MCR itself). Component A contains A1, an F420-reducing hydrogenase; A2, an ATP-binding protein; A3a, an uncharacterised iron-containing protein; and A3b, a methyl-viologen-reducing (F420-nonreducing) hydrogenase .
Phosphonate degradation operon associated (Phosphonate_degrad-assoc)
Type: Family

This entry represents a group of bacterial proteins found adjacent to other genes implicated in the catabolism of phosphonates and contain a series of five invariant histidines, the domain in general has only four. Most members contain

.
Methanogenesis marker domain 9 (Methan_mark_9)
Type: Domain

The exact function of this protein is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs may be metal-binding transcription factor. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins.
Radical SAM methyltransferase MA_4551-like (MA_4551-like)
Type: Family

Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens, including Methyl coenzyme M reductase-arginine methyltransferase Mmp10. Mmp10 is encoded near the gene for methyl coenzyme M reductase, whose product it modifies. The C-terminal region contains an unusual form of cobalamin-binding domain. Mmp10 is a cobalamin-requiring radical SAM methyltransferase that creates the methylarginine modification to methyl coenzyme M reductase .
Putative radical SAM enzyme, CHP03279 family (CHP03279_fam)
Type: Family

Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cut-off score for this model, 700 bits, excludes homologues from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialised, conserved function, perhaps related to photosynthesis. A distantly related protein family,

, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Methanogenesis marker 11 protein (Methan_mark_11)
Type: Family

Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it .
Ni-sirohydrochlorin a,c-diamide reductive cyclase complex, component CfbD (CfbD)
Type: Family

Ni-sirohydrochlorin a,c-diamide reductive cyclase complex, component CfbD is involved in the biosynthesis of coenzyme F430. Coenzyme F430 is an ancillary factor for methyl-coenzyme M reductase, an enzyme that mediates methane biogenesis in methanogens. CfbD catalyzes both the six-electron reduction of the tetrahydroporphyrin ring system and the gamma-lactamization of the c-acetamide side chain of Ni-sirohydrochlorin a,c-diamide, to produce the last intermediate in F430 biosynthesis .
Methanogenesis marker protein 15 (Methan_mark_15)
Type: Family

Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it . Related proteins include the BadF/BadG/BcrA/BcrD ATPase family (

), which includes an activator for (R)-2-hydroxyglutaryl-CoA dehydratase.
Methanogenesis marker 16 metalloprotein (Methan_mark_16)
Type: Family

Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of a 4Fe-4S domain (

).
CoB--CoM heterodisulphide reductase, subunit B (CoB/CoM_hetero-S_Rdtase_bsu)
Type: Family

This entry represents subunit B (HdrB) from CoB--CoM heterodisulphide reductase (or heterodisulphide reductase; Hdr;

), an iron-sulphur protein found in methanogenic archaea . Hdr catalyses the reversible reduction of the heterodisulphide (CoM-S-S-CoB) to the thiol-coenzymes: coenzyme M (H-S-CoM) and coenzyme B (H-S-CoB). Hdr is composed of three subunits: hdrA (subunit A), hdrB (subunit B) and hdrC (subunit C). Hdr forms a complex with the F420-non-reducing hydrogenase (Mvh), which provides the reducing equivalents to the heterodisulphide reductase.

All processes in methanogenesis lead to the formation of a mixed disulphide bond between coenzyme-M and coenzyme-B, by a reaction in which coenzyme B reduces methyl-CoM, leading to formation of methane and a CoB-CoM heterodisulphide . There are two different systems that are capable of reducing the CoB-CoM heterodisulphide, using either H2 or a reduced cofactor F420 as electron donors .

HdrB may have a function in energy transduction. Some archaea species have two copies, HdrB1 and HdrB2.
Coenzyme F420 hydrogenase subunit beta, archaea (FrhB_archaea)
Type: Family

This entry represents the beta subunit of coenzyme F420 hydrogenase (FRH) (

) found exclusively and universally in methanogenic archaea . Active coenzyme F420 hydrogenase forms a heterocomplex of three subunits: alpha (

), beta and gamma (

). This enzyme reduces the physiological low-potential two-electron acceptor coenzyme F420, and the artificial one-electron acceptor methylviologen. The enzyme complex is tightly associated with the redox cofactors: nickel, flavin adenine dinucleotide (FAD), and iron-sulphur cluster (2-13 Fe atoms per alpha/beta/gamma unit of the FRH) .
CoB--CoM heterodisulphide reductase, subunit C (CoB/CoM_hetero-S_Rdtase_csu)
Type: Family

This entry represents subunit C (HdrC) from CoB--CoM heterodisulphide reductase (or heterodisulphide reductase; Hdr;

), an iron-sulphur protein found in methanogenic archaea . Hdr catalyses the reversible reduction of the heterodisulphide (CoM-S-S-CoB) to the thiol-coenzymes: coenzyme M (H-S-CoM) and coenzyme B (H-S-CoB). Hdr is composed of three subunits: hdrA (subunit A), hdrB (subunit B) and hdrC (subunit C). Hdr forms a complex with the F420-non-reducing hydrogenase (Mvh), which provides the reducing equivalents to the heterodisulphide reductase.

All processes in methanogenesis lead to the formation of a mixed disulphide bond between coenzyme-M and coenzyme-B, by a reaction in which coenzyme B reduces methyl-CoM, leading to formation of methane and a CoB-CoM heterodisulphide . There are two different systems that are capable of reducing the CoB-CoM heterodisulphide, using either H2 or a reduced cofactor F420 as electron donors .

HdrC may carry electrons from hydrogenase to hdrA. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate.
Coenzyme F420 hydrogenase, subunit gamma (Coenz_F420_hydrogenase_gsu)
Type: Family

This entry represents the gamma subunit of coenzyme F420 hydrogenase (FRH) (

) found exclusively and universally in methanogenic archaea . Active coenzyme F420 hydrogenase forms a heterocomplex of three subunits: alpha (

), beta (

) and gamma. This enzyme reduces the physiological low-potential two-electron acceptor coenzyme F420, and the artificial one-electron acceptor methylviologen. The enzyme complex is tightly associated with the redox cofactors: nickel, flavin adenine dinucleotide (FAD), and iron-sulphur cluster (2-13 Fe atoms per alpha/beta/gamma unit of the FRH) .
Coenzyme F420 hydrogenase, subunit alpha (Coenz_F420_hydrogenase_asu)
Type: Family

This entry represents the beta subunit of coenzyme F420 hydrogenase (FRH) (

) found exclusively and universally in methanogenic archaea . Active coenzyme F420 hydrogenase forms a heterocomplex of three subunits: alpha, beta (

) and gamma (

). This enzyme reduces the physiological low-potential two-electron acceptor coenzyme F420, and the artificial one-electron acceptor methylviologen. The enzyme complex is tightly associated with the redox cofactors: nickel, flavin adenine dinucleotide (FAD), and iron-sulphur cluster (2-13 Fe atoms per alpha/beta/gamma unit of the FRH) .
Phosphonopyruvate decarboxylase (Phosphono-pyrv_decarboxylase)
Type: Family

This entry represents phosphonopyruvate, a decarboxylase enzyme that produces phosphonoacetaldehyde (Pald), which is the second step in the biosynthesis phosphonate-containing compounds. Since the preceding enzymatic step, PEP phosphomutase (AepX,

) favours the substrate PEP energetically, the decarboxylase is required to drive the reaction in the direction of phosphonate production.

Pald is a precursor of natural products including antibiotics like bialaphos and phosphonothricin in Streptomyces species, phosphonate-modified molecules such as the polysaccharide B of Bacteroides fragilis , the phosphonolipids of Tetrahymena pyriformis , the glycosylinositolphospholipids of Trypanosoma cruzi . This gene generally occurs in prokaryotic organisms adjacent to the gene for AepX. Most often an aminotransferase (aepZ) is also present which leads to the production of the most common phosphonate compound, 2-aminoethylphosphonate (AEP).
HTH-type transcriptional regulator ArgP (ArgP)
Type: Family

ArgP (formally known as IciA) is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon . ArgP mutants convey canavanine (an L-arginine structural homologue) sensitivity . ArgP also affects lysine biosynthesis in E. coli through regulating dapB Gene .
Phage/plasmid-like protein (Phg/plasmid-like_prot)
Type: Family

Members of this uncharacterised protein family are found in various Mycobacterium phage genomes, in Streptomyces coelicolor plasmid SCP1, and in bacterial genomes near various markers that suggest lateral gene transfer. Their function is unknown.
Outer membrane protein assembly factor BamB (BamB)
Type: Family

Outer membrane protein (OMP) assembly factor BamB, also known as YfgL in Escherichia coli, is part of the outer membrane protein assembly Bam complex (composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE), which is involved in assembly and insertion of β-barrel proteins into the outer membrane . Although BamB is not essential in E. coli, it serves an important function in the BAM complex, significantly increasing the folding efficiency of some OMPs in vivo and in vitro. It was suggested that BamB serves as a scaffolding protein in the Bam complex by optimally orienting the flexible periplasmic domain of BamA for interaction with other BAM components and chaperones .
Outer membrane protein assembly factor BamD (BamD)
Type: Family

Outer membrane protein assembly factor BamD, also known as YfiO in Escherichia coli, is part of the outer membrane protein assembly Bam complex (composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE), which is involved in assembly and insertion of β-barrel proteins into the outer membrane . In E. coli, the N-terminal of BamD may interact with various proteins as a chaperone to assist in the folding and insertion of proteins into the outer membrane. The C-terminal region of BamD may serve as the link between BamA, BamC and BamE .
ATP synthase subunit beta, bacterial and archaeal (Alt_ATPase_F1_bsu)
Type: Family

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 to drive the synthesis of ATP.

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea . These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This entry represents the F1 beta subunit of this apparent second ATP synthase.
Alternate ATP synthase, F0complex, subunit A (Alt_ATP_synth_F0_Asu)
Type: Family

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 to drive the synthesis of ATP.

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea . These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This entry represents the F0 subunit A of this apparent second ATP synthase.
Phosphonate metabolism protein PhnP (Phosphonate_metab_PhnP)
Type: Family

This family of proteins found in operons encoding phosphonate C-P lyase systems as is observed in Escherichia coli and is a member of the metallo-beta-lactamase superfamily (

). Instances of this protein are associated with the C-P lyase, but not all genomes containing the C-P lyase system contain phnP.
Phosphonate metabolism protein, transferase hexapeptide repeat family (Phosphonate_tfrase_rpt)
Type: Family

This family of proteins contains copies of the Bacterial transferase hexapeptide repeat family (

) and is only found in operons encoding the phosphonate C-P lyase system (

). Many C-P lyase operons, however, lack a homologue of this protein.
Selenium-dependent molybdenum hydroxylase system protein, YqeB family (Se-dep_Mo_hydrolase_YqeB)
Type: Domain

Members of this protein family are probable accessory proteins for the biosynthesis of enzymes with labile selenium-containing centres, different from selenocysteine-containing proteins .
Molybdenum cofactor cytidylyltransferase (Mo_hydrolase_YgfJ)
Type: Family

Members of this protein include MocA, which transfers cytosine from CTP to molybdopterin during molybdopterin cytosine dinucleotide (MCD) cofactor biosynthesis. It is distantly related to MobA (Molybdopterin-guanine dinucleotide biosynthesis protein A) .
Selenium-dependent xanthine dehydrogenase (Xdh)
Type: Family

Members of this protein resemble conventional xanthine dehydrogenase enzymes, which depend on molybdenum cofactor - molybdopterin bound to molybdate with two sulfur atoms as ligands. But all members of this family occur in species that contain markers for the biosynthesis of enzymes with a selenium-containing form of molybdenum cofactor. The member of this family from Enterococcus faecalis has been shown to act as a xanthine dehydrogenenase, and its activity if dependent on SelD (selenophosphate synthase), selenium, and molybdenum .
Probable molybdopterin-containing oxidoreductase, FAD-binding subunit (Molybdo-cont_Rdtase_FAD-bd_su)
Type: Family

This entry represents a group of proteins from gammaproteobacteria, including Uncharacterized protein YgfM from Escherichia coli, which has been suggested to be the FAD-binding subunit of a molydbopterin-containing selenate reductase . This family seems to be related to the FAD-binding subunit of a molybdopterin-containing selenate reductase from Rhodobacter sphaeroides , but this protein is not included in this group.
Molybdenum-binding protein YgfN/XdhD (Mo-bd_YgfN/XdhD)
Type: Family

This family consists of YgfN, whose function is not clear. YgfN was identified as a molybdenum-binding subunit of a putative molydbopterin-containing selenate reductase complex consisting of proteins YgfK, YgfM and YgfN . However, another study showed that a mutation in the gene (b2881) encoding this protein conferred sensitivity to adenine, which is associated with impaired synthesis of guanine nucleotides from adenine during purine salvage . YgfN is also known as XdhD, as it has been suggested to be a molybdenum-containing protein of the xanthine oxidase family .
Putative aminohydrolase SsnA (Aminohydrolase_SsnA)
Type: Family

Members of this protein family are found exclusively in genomes that contain putative set of labile selenium-dependent enzyme accessory proteins as well as homologues of a labile selenium-dependent purine hydroxylase. A mutant in this gene in Escherichia coli had improved stationary phase viability. The function of this protein is unknown.
Putative selenate reductase YgfK (Se_rdtase_YgfK)
Type: Family

Members of this protein family are found in genomic regions associated with selenium and/or purine metabolism .
Putative carbamoyltransferase YgeW (Carbamoyltransferase_YgeW)
Type: Family

Members of this protein family include the ygeW gene product of Escherichia coli. The function of this protein is unknown. Members show some homology to ornithine carbamoyltransferase and aspartate carbamoyltransferase (carbamoyltransferase), and may belong to the carbamoyltransferases in function. Members often are found in a large, conserved genomic region associated with purine catabolism .