SII-SWORD/CoKE huggingface dataset:
YgfZ/GCV conserved site (YgfZ/GCV_T_CS)
Type: Conserved_site

This entry represents a conserved site, which includes includes the motif KGCYxGQE, that is found in glycine cleavage T-proteins, which are part of the glycine cleavage multienzyme complex (GCV) and in the bacterial tRNA-modifying protein YgfZ.

The glycine cleavage multienzyme complex (GCV) catalyses the catabolism of glycine in eukaryotes. GcvT (aminomethyltransferase,

) is a folate-dependent enzyme that catalyses the release of ammonia and the transfer of the methylene carbon unit (C1 unit) to tetrahydrofolate (H4folate) from the aminomethyl intermediate attached to the lipoate cofactor of H-protein . GCV is found in bacteria and the mitochondria of eukaryotes. Mutations in the human GcvT gene are known to cause nonketotic hyperglycinemia .
Putative selenium-binding protein YdfZ (Se-bd_putative_YdfZ)
Type: Family

This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system . Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Ribonuclease Y (Ribonuclease_Y)
Type: Family

Ribonuclease Y is an endoribonuclease that initiates mRNA decay . The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch . It also has been shown in Staphylococcus aureus that it catalyses the hydrolysis of both 2',3'-cyclic AMP and 2',3'-cyclic GMP into 3'-AMP and 3'-GMP, respectively, at the 3'-terminal of RNA .
Peptidase M20/DapE, YgeY (Peptidase_M20/DapE_YgeY)
Type: Family

Members of this protein family, including the YgeY protein of Escherichia coli, typically are found in extended genomic regions associated with purine catabolism. Homologues include peptidases and deacylases of the M20/M25 /M40 and DapE/ArgE families. The function is unknown.
Alternate ATP synthase, F0 complex, subunit b (Alt_ATP_synth_F0_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, including Methanosarcina barkeri, 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, CC and in principle may run in either direction. This entry represents the F0 subunit b of this apparent second ATP synthase.
Alternate ATP synthase, F0 complex, subunit C, bacterial/archaeal (Alt_ATP_synth_F0_Csu)
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, including Methanosarcina barkeri, 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 C of this apparent second ATP synthase.
Alternate ATP synthase, F1 complex, subunit gamma (Alt_ATP_synth_F1_gsu)
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, including Methanosarcina barkeri, 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 gamma subunit of this apparent second ATP synthase.
Alternate ATP synthase, F1 complex, subunit alpha (Alt_ATP_synth_F1_asu)
Type: Family

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, 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 alpha subunit of this apparent second ATP synthase.

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.
Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (BphB_TodD)
Type: Family

Members of this family occur as the BphD protein of biphenyl catabolism and as the TodD protein of toluene catabolism. Members catalyse the second step in each pathway and proved interchangeable when tested; the first and fourth enzymes in each pathway confer metabolic specificity. In the context of biphenyl degradation, the enzyme acts as cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (

), while in toluene degradation it acts as cis-toluene dihydrodiol dehydrogenase.
Ribulose bisphosphate carboxylase, type III (RuBisCO_III)
Type: Family

Type III ribulose bisphosphate carboxylase (RuBisCO) is composed of a large chain homodimer in a "head-to-tail" conformation. In contrast to type I RuBisCO, type III RuBisCO is composed solely of large subunits , or RuBisCO. These proteins act in a three-step pathway for conversion of the sugar moiety of AMP to two molecules of 3-phosphoglycerate . Many of these species in this entry use ADP-dependent sugar kinases, which form AMP, for glycolysis.
AMP phosphorylase (AMP_phosphorylase)
Type: Family

AMP phosphorylase is found in the Archaea, and only in those with a type III Rubisco enzyme. Most of the members previously were annotated as thymidine phosphorylase, or DeoA. The AMP metabolised by this enzyme may be produced by ADP-dependent sugar kinases .
Methylthioribulose-1-phosphate dehydratase (MethylthioRu-1-P_deHdtase_MtnB)
Type: Family

Members of this family are the methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway. This pathway allows methylthioadenosine, left over from polyamine biosynthesis, to be recycled to methionine.

Proteins in this entry also include the bifunctional enzyme MtnB/MtnX from bacteria and the probable bifunctional methylthioribulose-1-phosphate dehydratase/enolase-phosphatase E1 from plants.
Putative aminophosphonate oxidoreductase (NH2-phosphonate_OxRdtase)
Type: Family

This entry represents FAD-dependent oxidoreductases. Characterised proteins within this family include glycerol-3-phosphate dehydrogenase (

), sarcosine oxidase beta subunit (

) and a number of deaminating amino acid oxidases (

). These genes have been consistently observed in a genomic context including genes for the import and catabolism of 2-aminoethylphosphonate (AEP). If the substrate of this oxidoreductase is AEP itself, then it is probably acting in the manner of a deaminating oxidase, resulting in the same product (phosphonoacetaldehyde) as the transaminase PhnW, but releasing ammonia instead of coupling to pyruvate:alanine. Alternatively, it is reasonable to suppose that the various ABC cassette transporters which are also associated with these loci allow the import of phosphonates closely related to AEP which may not be substrates for PhnW.
S-adenosylmethionine decarboxylase proenzyme (S-AdoMet_deCOase_pro-enz)
Type: Family

Members of this protein family are the single chain precursor of the two chains of the mature S-adenosylmethionine decarboxylase as found in Methanocaldococcus jannaschii (Methanococcus jannaschii), Bacillus subtilis and a wide range of other species . S-adenosylmethionine decarboxylase catalyses the decarboxylation of S-adenosylmethionine to provide the aminopropyl moiety required for spermidine biosynthesis from putrescine.
2,3-diketo-5-methylthiopentyl-1-phosphate enolase (Diketo-Methiopentyl-P_enolase)
Type: Family

Members of this family are the methionine salvage pathway enzyme 2,3-diketo-5-methylthiopentyl-1-phosphate enolase, a homologue of RuBisCO . They catalyze the tautomerization of 2,3-diketo-5-methylthiopentane 1-phosphate (DK-MTP 1-P). This is an important step in the methionine salvage pathway in which 5-methylthio-D-ribose (MTR) derived from 5'-methylthioadenosine is converted to methionine. This protein family seems restricted to Bacillus subtilis and close relatives, where two separate proteins carry the enolase and phosphatase activities that in other species occur in a single protein, MtnC (

).
2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase (HAD-SF_hydro_IB_MtnX)
Type: Family

This entry represents 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase, MtnX, which is involved in methionine salvage and belongs to the HAD-superfamily hydrolases, subfamily IB . This enzyme is found in Bacillus subtilis and related species, paired with MtnW (

). In most species that recycle methionine from methylthioadenosine, the single protein MtnC replaces the MtnW/MtnX pair. In B. subtilis, mtnX was first known as ykrX.
Indolepyruvate ferredoxin oxidoreductase, beta subunit (Indolepyruvate_Fd_OxRdtase_bsu)
Type: Family

This entry represents the beta subunit of indolepyruvate ferredoxin oxidoreductase (IOR;

), an α(2)/β(2) tetramer whose cofactors include TPP, 4Fe4S, and 3Fe-4S. This enzyme is related to several other ketoacid oxidoreductases, including: the ketoacid oxidoreductases for pyruvate (

, POR), 2-ketoglutarate (

, KOR), and 2-oxoisovalerate (

, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactivated by oxygen, such as Pyrococcus furiosus and Methanobacterium thermoautotrophicum, and are inactivated by oxygen. IOR in Pyrococcus acts in the fermentation of all three aromatic amino acids, following removal of the amino group by transamination . In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate . In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase.
Coenzyme F390 synthetase (Coenzyme_F390_Synthase)
Type: Family

This enzyme, characterised in Methanobacterium thermoautotrophicum and found in several other methanogens, modifies coenzyme F420 by ligation of AMP (or GMP) from ATP (or GTP). On F420, it activates an aromatic hydroxyl group, which is unusual chemistry for an adenylyltransferase. This enzyme name has also been attached to numbers of uncharacterised genes which are instead likely to act as phenylacetate CoA ligase, based on their proximity to predicted indolepyruvate ferredoxin oxidoreductase (

) genes. The enzyme itself acts during transient exposure of the organism to oxygen .
Indolepyruvate oxidoreductase subunit IorA (IorA)
Type: Family

This entry represents the alpha subunit of indolepyruvate ferredoxin oxidoreductase (IOR;

), an α(2)/β(2) tetramer whose cofactors include TPP, 4Fe4S, and 3Fe-4S. This enzyme is related to several other ketoacid oxidoreductases, including the ketoacid oxidoreductases for pyruvate (

, POR), 2-ketoglutarate (

, KOR), and 2-oxoisovalerate (

, VOR). These multi-subunit enzymes typically are found in anaerobes, such as Pyrococcus furiosus and Methanobacterium thermoautotrophicum, and are inactivated by oxygen.
Phosphonate utilization transcriptional regulator PhnR (Tscrpt_reg_PhnR)
Type: Family

This entry represents proteins which are members of the wider GntR family (

), containing an N-terminal helix-turn-helix (HTH) motif. These proteins are found adjacent to, or inside of, operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio, Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii .
Transcription regulator, 2-aminoethylphosphonate utilisation-associated (Tscrpt_reg_AEP_util-assoc)
Type: Family

Proteins in this entry are members of the wider GntR family (

), containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to, or inside of, operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Aminoethylphosphonate utilisation-associated transcription regulator, LysR-type (Tscrpt_reg_LysR)
Type: Family

This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (

) and a periplasmic substrate-binding protein-like domain (

).
Phosphonate utilization associated transmembrane protein, putative (Phosphonate_util-assoc_TM_put)
Type: Family

Proteins in this entry appear to have transmembrane domains and may function as permeases. They are encoded in the vicinity of various types of operons for the catabolism of phosphonates in Vibrio, Pseudomonas, Polaromonas and Thiomicrospira.
Fe/S biogenesis protein NfuA (Fe/S_biogenesis_protein_NfuA)
Type: Family

This entry represents Fe/S biogenesis protein NfuA from gammaproteobacteria. This protein is involved in iron-sulphur cluster biogenesis under severe conditions such as iron starvation or oxidative stress. It binds a 4Fe-4S cluster and can transfer this cluster to apoproteins, thereby intervening in the maturation of Fe/S proteins. NfuA could also act as a scaffold/chaperone for damaged Fe/S proteins . An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization .
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, BphD (HOPD_hydrolase_BphD)
Type: Family

Members of this family are 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, or HOPD hydrolase, the BphD protein of biphenyl degradation. BphD acts on the product of ring meta-cleavage by BphC. Many species carrying bphC and bphD are capable of degrading polychlorinated biphenyls as well as biphenyl itself .
AAA+ ATPase ClpV1 (ATPase_T6SS_ClpV1)
Type: Family

ClpV is an AAA(+) ATPase that disassembles the type VI secretion system contracted sheath which resets the systems for reassembly of an extended sheath that is ready to fire again . The ClpV proteins are most similar to ClpB proteins within the Hsp100/Clp family, but cluster in a separate phylogenetic tree with a remarkable distance to ClpB . However, this entry also includes ClpB from Yersinia enterocolitica .

The type VI secretion system (T6SS), also known as CIS contractile injection system , is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath . Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA .
Chaperonin ClpB (Chaperonin_ClpB)
Type: Family

Members of this protein family include bacterial and plant ATP-dependent chaperone ClpB. This protein belongs to the AAA family of ATPases associated with various cellular activities. This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins .
Type VI secretion system protein TssM1-like (TssM1-like)
Type: Family

This entry includes TssM1, which is a component of the bacterial type VI secretion system (T6SS) .

The type VI secretion system (T6SS), also known as CIS contractile injection system , is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath . Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA .
Type IV / VI secretion system, DotU (T4/T6SS_DotU)
Type: Domain

At least two distinct groups of proteins, often encoded by adjacent genes, show sequence similarity due to homology between type IV secretion systems and type VI secretion systems. One is the IcmF family (

). The other group is the DotU family, which includes DotU from the Legionella pneumophila type IV secretion system. Many members of this protein family from type VI secretion systems have an additional C-terminal domain with OmpA/MotB homology

.
Type VI secretion system, OmpA-like domain, proteobacteria (OmpA-like_dom_proteobacteria)
Type: Domain

This entry represents a domain found at the C-terminal end of long forms of TssL, a component of type VI secretion systems (T6SS) , although other forms of TssL lack this domain. The domain shares homology with peptidoglycan-associating C-terminal regions of the Gram-negative bacterial outer membrane protein OmpA, the flagellar motor protein MotB, Pal, and other proteins. TssL is related to IcmH/DotU.
Type VI secretion system, lipoprotein SciN (T6SS_SciN)
Type: Family

One of the virulence mechanisms of Escherichia coli is the production of toxins from dedicated machineries called secretion systems. Seven secretion systems have been described, which assemble from 3 to up-to more than 20 subunits. These secretion systems derive from or have co-evolved with bacterial organelles such as ABC transporters (type I), type IV pili (type 2), flagella (type 3), or conjugative machines (type IV).

The type VI secretion system (T6SS) is present in most pathogens that have contact with animals, plants, or humans. T6SS exports Hcp (Haemolysin-Coregulated Protein) and a class of proteins named Vgr (Val-Gly Repeats), whose exact function is still speculative. In addition to Vgr and Hcp proteins, T6SS is characterised by the presence of an AAA+ Clp-like ATPase and of two additional genes icmF and dotU, encoding homologues of T4SS stabilising proteins .

SciN is a lipoprotein tethered to the outer membrane and expressed in the periplasm of E. coli, and is essential for T6SS-dependent secretion of the Hcp-like SciD protein and for biofilm formation .
Type VI secretion system, FHA domain-containing protein (T6SS_FHA)
Type: Family

Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis and Burkholderia mallei .
Glycoside hydrolase, family 1, beta-glucosidase (Glyco_hydro_1_beta-glucosidase)
Type: Family

Glycoside hydrolase family 1

comprises enzymes with a number of known activities; beta-glucosidase (

); beta-galactosidase (

); 6-phospho-beta-galactosidase (

); 6-phospho-beta-glucosidase (

); lactase-phlorizin hydrolase (

), (

); beta-mannosidase (

); myrosinase (

).

This enzyme represents beta-glucosidase, which catalyses the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose . It has a wide substrate specificity for beta-D-glucosides.

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Type VI secretion system protein TssE1-like (TssE1-like)
Type: Family

This entry includes TssE1, which is a baseplate component of the bacterial type VI secretion system (T6SS). It shares structural homology with T4 inner baseplate protein gp25 .

The type VI secretion system (T6SS), also known as CIS contractile injection system , is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath . Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA .
Type VI secretion system-associated, VCA0118 (T6SS-assoc_VCA0118)
Type: Family

Proteins in this entry, including VC_A0118 from Vibrio cholerae O1 biovar eltor str. N16961, are restricted to a subset of bacteria with the type VI secretion system, and are encoded among the type VI-associated pathogenicity islands. However, many species with type VI secretion lack a member of this family, suggesting that members of this family may be targets rather than components of the type VI secretion system.
Type VI secretion system-associated, VCA0119 (T6SS-assoc_VCA0119)
Type: Family

This entry represents one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (

). This group includes VCA0119 from Vibrio alginolyticus .
Type VI secretion system protein TssA-like (TssA-like)
Type: Family

This entry represents one of two related families in type VI secretion systems (T6SS) that contain an ImpA-related N-terminal domain (

). This group includes Rhizobium leguminosarum ImpA , thought to be an T6SS homologue .

This entry also includes TssA, which is a T6SS component forming dodecameric ring structures positioned at one end of the TssB/TssC sheath. .

The type VI secretion system (T6SS), also known as CIS contractile injection system , is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath . Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA .