SII-SWORD/CoKE huggingface dataset:
ArsJ-associated glyceraldehyde-3-phosphate dehydrogenase (G3PDH_Arsen)
Type: Family

This entry represents ArsJ-associated glyceraldehyde-3-phosphate dehydrogenase (GAPDH 3), an enzyme that catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The reaction involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, which is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is exchanged with a second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG. This enzyme belongs to the glyceraldehyde-3-phosphate dehydrogenase family and is found in various organisms, including Nostoc sp. (strain PCC 7120) and Trichormus variabilis (strain ATCC 29413).
Transposase for transposon Tn5 (Tn5_transposase)
Type: Family

This entry represents the transposase for transposon Tn5, a protein that mediates the transposition of the Tn5 transposon in Escherichia coli. The transposase operates via a 'cut and paste' mechanism. Initially, the monomeric transposase binds to the 19 bp inverted DNA repeats flanking the transposon. Dimerization of the DNA-bound transposase then forms a synaptic DNA complex. The transposase nicks the first DNA strand, and excision of the transposon proceeds through a series of intermediates. Finally, the transposase mediates the insertion of the transposon at a new site by strand transfer. The activity of the wild-type transposase is very low and is further inhibited by dimerization with the transposase inhibitor (inh). This protein belongs to the transposase 11 family and is also associated with the IS4 family transposases.
Galactofuranose ABC transporter, galactofuranose-binding protein YtfQ (YtfQ_transport)
Type: Family

This entry represents the galactofuranose-binding protein YtfQ, which is part of the ABC transporter complex YtfQRT-YjfF involved in galactofuranose transport in Escherichia coli (strain K12). YtfQ binds to both alpha- and beta-galactofuranose. It belongs to the bacterial solute-binding protein 2 family.
Adenylyltransferase SelO (adnlytase_SelO)
Type: Family

Protein adenylyltransferase SelO is an enzyme that catalyzes the transfer of adenosine 5'-monophosphate (AMP) to serine, threonine, or tyrosine residues of target proteins, a process known as AMPylation. This enzyme belongs to the SELO family and is found in various bacterial species, including Escherichia coli and Salmonella. The AMPylation activity of SelO plays a role in regulating protein functions and may be involved in redox homeostasis. In Escherichia coli (strain K12), SelO is known to AMPylate specific proteins such as SucA at 'Thr-405' and GrxA on 'Tyr-13', influencing protein S-glutathionylation levels. The enzyme is activated under reducing conditions and cannot use GTP, CTP, or UTP as cosubstrates.
Photosynthetic complex putative assembly protein PuhB (puhB_PGC)
Type: Family

This entry represents the photosynthetic complex putative assembly protein PuhB. The protein is involved in the assembly of photosynthetic complexes, which are crucial for the photosynthetic process in organisms such as Rhodobacter capsulatus. The exact function of PuhB remains to be fully characterized, but it is believed to play a role in the organization and stabilization of photosynthetic components. Further studies are needed to elucidate the precise mechanisms by which PuhB contributes to photosynthesis.
1-hydroxy-gamma-carotene desaturase (hydcarot_desat_CrtD)
Type: Family

This entry represents 1-hydroxycarotenoid 3,4-desaturase, an enzyme that catalyzes the introduction of a C-3,4 double bond into 1'-hydroxy-gamma-carotene and rhodopin (1-hydroxylycopene) to yield 1'-hydroxytorulene and (3E)-3,4-didehydrorhodopin, respectively. It can also act on 1-hydroxy-all-trans-1,2-dihydro-neurosporene, 1,1'-dihydroxy-1,1',2,2'-tetrahydroneurosporene, and 1,1'-dihydroxy-1,1',2,2'-tetrahydrolycopene. This enzyme is probably involved in the synthesis of myxol, a gamma-carotene derivative, and may use FAD as a proton acceptor. The enzyme belongs to the carotenoid/retinoid oxidoreductase family and is found in various bacterial species, including Nonlabens dokdonensis and Flavobacterium sp.
1-hydroxycarotenoid 3,4-desaturase (carotdesatCrtD)
Type: Family

This entry represents the 1-hydroxycarotenoid 3,4-desaturase (CrtD), which belongs to the carotenoid/retinoid oxidoreductase family. The enzyme catalyzes the introduction of C-3,4 double bonds into 1-hydroxyneurosporene (1-HO-Neu) to yield demethylspheroidene (DMS). The preferred substrates for this enzyme include 1-hydroxy-neurosporene, 1-hydroxy-lycopene, and 1,1-dihydroxyneurosporene. Additionally, 3,4-didehydrolycopene derivatives such as 1,1-dihydroxy-3,4-didehydrolycopene, 1-methoxy-1-hydroxy-3,4-didehydrolycopene, and 1-hydroxy-3,4-didehydrolycopene are also efficiently converted. This enzyme is found in various bacterial species, including Cereibacter sphaeroides, Rubrivivax gelatinosus, and Rhodobacter capsulatus.
Probable dimethyl sulfoxide reductase chain YnfF (DMSO_reductase_YnfF)
Type: Family

The protein YnfF from Escherichia coli (strain K12) is a probable dimethyl sulfoxide (DMSO) reductase chain. It functions as a terminal reductase during anaerobic growth on various sulfoxide and N-oxide compounds. YnfF is also annotated as a selenate/tellurate reductase subunit. This protein belongs to the prokaryotic molybdopterin-containing oxidoreductase family, which is involved in various redox processes. The enzyme's activity is crucial for the anaerobic respiration of E. coli, allowing it to utilize alternative electron acceptors in the absence of oxygen.
Slam-dependent hemophilin, C-terminal domain (Slam_hemophilin_C)
Type: Domain

This entry represents the C-terminal domain of Slam-dependent hemophilins found in Acinetobacter baumannii, Haemophilus influenzae and related Gram-negative bacteria, which consists of a β-barrel. Hemophilins are part of a high affinity heme acquisition system . It functions as a hemophore that acquires heme from human hemoglobin and delivers the heme to its cognate receptor, HphR, facilitating transport of heme across the bacterial outer membrane . It can also acquire heme complexed to human serum albumin . It plays a supporting role for full virulence, acting as an accessory factor that enhances the process of heme uptake .
HTH-type transcriptional regulator BhcR (TransRegBhcR)
Type: Family

HTH-type transcriptional regulator BhcR is a protein found in Paracoccus denitrificans (strain Pd 1222). It functions as a transcriptional regulator of the bhc gene cluster, which is involved in glycolate and glyoxylate assimilation via the beta-hydroxyaspartate cycle (BHAC). The interaction of BhcR with the promoter region of the bhc gene cluster is negatively affected by glyoxylate.
CsxC family protein (Exosporium_prot_C)
Type: Family

Exosporium protein C (CsxC) is a protein found in Clostridium sporogenes (strain ATCC 15579). It is part of the CsxC family, which is characterized by its role in the exosporium, a protective layer surrounding the spore. The CsxC family proteins are involved in the formation and maintenance of this layer, which is crucial for the spore's resistance to environmental stresses. The exact function of CsxC in the exosporium is not fully understood, but it is believed to play a structural role. Further studies are needed to elucidate the specific mechanisms by which CsxC contributes to exosporium integrity and spore viability.
PPi-dependent phosphofructokinase (PFKA_PPi_Ttgales)
Type: Family

This entry represents pyrophosphate--fructose 6-phosphate 1-phosphotransferase (PPi-PFK), an enzyme that catalyzes the phosphorylation of D-fructose 6-phosphate, the first committing step of glycolysis. Unlike common ATP-dependent phosphofructokinases (ATP-PFKs), PPi-PFK uses inorganic phosphate (PPi) as a phosphoryl donor, making the reaction reversible. This allows PPi-PFK to function in both glycolysis and gluconeogenesis, effectively replacing the enzymes of both the forward (ATP-PFK) and reverse (fructose-bisphosphatase (FBPase)) reactions. The enzyme is found in various organisms, including Naegleria fowleri and Thermotoga maritima. In Naegleria fowleri, the enzyme is activated by AMP, which likely promotes its oligomerization. In Thermotoga maritima, the enzyme is non-allosteric. PPi-PFK belongs to the phosphofructokinase type A (PFKA) family, specifically the PPi-dependent PFK group II subfamily, clade 'Short' sub-subfamily.
Reactive chlorine resistance oxidoreductase RclA (chlor_oxi_RclA)
Type: Family

Reactive chlorine resistance oxidoreductase RclA is a probable pyridine nucleotide-disulfide oxidoreductase found in Escherichia coli (strain K12). It belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family and is likely involved in reactive chlorine species (RCS) stress resistance. This enzyme plays a role in protecting the cell from oxidative damage caused by reactive chlorine compounds.
Geranylgeranyl pyrophosphate synthase CRTE-like (GGPPSyn_CRT-like)
Type: Family

Geranylgeranyl diphosphate synthase CRTE (GGPPS) is an enzyme that catalyses the condensation of farnesyl diphosphate (FPP) and isopentenyl diphosphate (IPP) to yield geranylgeranyl diphosphate (GGPP) . This reaction is crucial for the biosynthesis of carotenoids and diterpenes. The enzyme belongs to the FPP/GGPP synthase family and is found in various organisms, including Cyanophora paradoxa and Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6). In Picosynechococcus sp., GGPPS catalyzes the sequential condensation of three molecules of IPP onto dimethylallyl diphosphate (DMAPP) to yield GGPP, playing a key role in the biosynthesis of terpenenoids .

This entry also includes Dimethylallyltranstransferase AmbP2 from Fischerella ambigua, a prenyltransferase involved in the biosynthesis of ambiguines, a family of hapalindole-type alkaloids . It catalyses the addition of isopentenyl diphosphate (IPP) onto dimethylallyl diphosphate (DMAPP) to form geranyl pyrophosphate (GPP) , however, it cannot use farnesyl diphosphate (FPP) or geranylgeranyl diphosphate (GGPP) .
UPF0336 family protein (UPF0336_fam)
Type: Family

This entry represents a family of proteins known as UPF0336. Members of this family are found in various Mycobacterium species, including Mycobacterium bovis, Mycobacterium leprae, Mycobacterium tuberculosis, and Mycolicibacterium paratuberculosis. The exact function of UPF0336 family proteins is currently unknown, but they are conserved across different bacterial species, suggesting a potentially important role. These proteins typically consist of around 158-159 amino acids. Further research is needed to elucidate their precise biological function.
Xylan 1,4-beta-xylosidase (Xylosidase_Xyl3A)
Type: Family

Xylan 1,4-beta-xylosidase (Xyl3A) from Xylanibacter ruminicola is a member of the glycosyl hydrolase 3 family. This enzyme is involved in the degradation of plant cell wall polysaccharides. It exhibits beta-xylosidase activity by hydrolyzing glycosidic linkages of beta-1,4-xylo-oligosaccharides of various lengths (X2 to X6), releasing xylose monomers. Additionally, it has a minor alpha-L-arabinofuranosidase activity but does not possess beta-D-glucosidase activity. Xyl3A acts synergistically with Xyn10D-Fae1A to increase the release of xylose from xylan.
Prenyl lipid carboxyl methyltransferase (Isoprenylcys_mtase)
Type: Family

This entry represents protein-S-isoprenylcysteine O-methyltransferase, an enzyme that catalyzes the methylation of isoprenylated cysteine residues in proteins. The enzyme exhibits activity towards prenyl lipids, including N-acetyl-S-farnesyl-L-cysteine (AFC) and S-farnesylthioacetic acid (FTA), an analog of AFC. It belongs to the class VI-like SAM-binding methyltransferase superfamily and is specifically categorized under the isoprenylcysteine carboxyl methyltransferase family. The enzyme is involved in the post-translational modification of proteins, which is crucial for their proper localization and function within the cell.
Arginine ABC transporter substrate-binding protein ArtI (ArtI_ABC_transporter)
Type: Family

This entry represents the putative ABC transporter arginine-binding protein ArtI from Escherichia coli (strain K12). ArtI is part of the ABC transporter complex ArtPIQMJ, which is involved in the transport of arginine. Proteins in this family belong to the bacterial solute-binding protein 3 family.
Lipid II isoglutaminyl synthase subunit MurT (isoglutsynth_MurT)
Type: Family

The lipid II isoglutaminyl synthase complex catalyzes the formation of alpha-D-isoglutamine in the cell wall lipid II stem peptide. The MurT subunit catalyzes the ATP-dependent amidation of the D-glutamate residue of lipid II, converting it to an isoglutamine residue. This function is essential for the proper formation and maintenance of the bacterial cell wall. The MurT subunit belongs to the MurCDEF family, specifically the MurT subfamily.
3-hydroxy-D-aspartate aldolase BhcC (HdxyAspAldBhcC)
Type: Family

3-hydroxy-D-aspartate aldolase (BhcC) is an enzyme that catalyzes the condensation of glyoxylate and glycine into (2R,3S)-beta-hydroxyaspartate ((3S)-3-hydroxy-D-aspartate). This enzyme plays a crucial role in the glyoxylate assimilation pathway known as the beta-hydroxyaspartate cycle (BHAC). In Paracoccus denitrificans, BhcC is essential for growth in the presence of glycolate and glyoxylate. The enzyme also catalyzes the cleavage of both D-erythro- and D-threo-3-hydroxyaspartate to glycine and glyoxylate, and can act on D-threonine, D-3-phenylserine, and D-3,4-methylenedioxyphenylserine. BhcC belongs to the DSD1 family of enzymes.
Cis-3-hydroxy-L-proline dehydratase, mandelate racemase/muconate lactonizing enzyme family (HProlDhtase)
Type: Family

Cis-3-hydroxy-L-proline dehydratase is an enzyme that catalyzes the dehydration of cis-3-hydroxy-L-proline (c3LHyp) to Delta(1)-pyrroline-2-carboxylate (Pyr2C). This enzyme is likely involved in a degradation pathway that converts c3LHyp to L-proline, allowing certain bacteria such as Roseibium aggregatum and Ancylobacter novellus to utilize c3LHyp as a sole carbon source. Additionally, the enzyme can catalyze the epimerization of c3LHyp to trans-3-hydroxy-D-proline (t3DHyp), although this is a competing reaction. The enzyme belongs to the mandelate racemase/muconate lactonizing enzyme family.
Beta-hydroxyaspartate dehydratase (BHydaspDhtse)
Type: Family

Beta-hydroxyaspartate dehydratase (BhcB) catalyzes the dehydration of (2R,3S)-beta-hydroxyaspartate ((3S)-3-hydroxy-D-aspartate) into iminosuccinate. This enzyme is essential for the growth of Paracoccus denitrificans in the presence of glycolate and glyoxylate, as it functions in glyoxylate assimilation via the beta-hydroxyaspartate cycle (BHAC).
Cyclic nucleotide-degrading phosphodiesterase (cyc_nuc_deg_phdiest)
Type: Family

This entry represents a family of cyclic nucleotide-degrading phosphodiesterases. These enzymes are involved in the hydrolysis of cyclic nucleotides, such as cAMP and cGMP, into their corresponding nucleoside monophosphates. Members of this family include uncharacterized proteins from various Mycobacterium species, such as Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97), Mycobacterium tuberculosis (strains CDC 1551 / Oshkosh and ATCC 25618 / H37Rv), and Mycobacterium leprae (strain TN). These proteins share sequence similarity and are classified under the AtsA family. The precise biological roles of these proteins in Mycobacterium species remain to be fully elucidated.
Peptidoglycan-N-acetylglucosamine deacetylase (PgAcgDac)
Type: Family

Peptidoglycan-N-acetylglucosamine deacetylase (BC_1974) from Bacillus cereus (strain ATCC 14579) catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan. This enzyme belongs to the polysaccharide deacetylase family and is involved in modifying the peptidoglycan structure, which is crucial for bacterial cell wall integrity and function. The activity of this enzyme is inhibited by the hydroxamate N-hydroxy-4-(naphthalene-1-yl)benzamide (NHNB).
Lipid II isoglutaminyl synthase subunit GatD (isoglutsynth_GatD)
Type: Family

The lipid II isoglutaminyl synthase complex catalyzes the formation of alpha-D-isoglutamine in the cell wall lipid II stem peptide. The GatD subunit catalyzes the hydrolysis of glutamine to glutamate and ammonia. The resulting ammonia molecule is channeled to the active site of MurT. This function is critical for the biosynthesis of bacterial cell walls, particularly in Streptococcus pneumoniae (strain ATCC BAA-255 / R6). GatD belongs to the CobB/CobQ family, specifically the GatD subfamily.
Iminosuccinate reductase BhcD (BhcD-like)
Type: Family

Iminosuccinate reductase BhcD is an enzyme that catalyzes the NADH-dependent reduction of iminosuccinate to L-aspartate . This enzyme is essential for the growth of Paracoccus denitrificans in the presence of glycolate and glyoxylate, as it functions in glyoxylate assimilation via the beta-hydroxyaspartate cycle (BHAC). BHAC consists of BhcA, BhcB, BhcC, and BhcD enzyme activities. It converts two molecules of glyoxylate into oxaloacetate without the loss of carbon as CO2, under consumption of one reducing equivalent and regeneration of the catalytic amino donor, which makes it one of the most efficient glyoxylate assimilation pathways . BhcD regenerates the amino group donor for the first step of the BHAC.
Endo-beta-N-acetylglucosaminidase H (Endoglyc_H)
Type: Family

This entry represents endo-beta-N-acetylglucosaminidase H, a member of the glycosyl hydrolase 18 family. These enzymes cleave asparagine-linked oligomannose and hybrid, but not complex, oligosaccharides from glycoproteins. The proteins matched by this entry include endo-beta-N-acetylglucosaminidase H from Streptomyces plicatus (UniProt: P04067) and endo-beta-N-acetylglucosaminidase from Flavobacterium sp. (strain SK1022) (UniProt: P80036).
DNA protection during starvation protein (DNA_prot_starvation)
Type: Family

The DNA protection during starvation protein (Dps) is a member of the Dps family, which plays a crucial role in protecting DNA from oxidative damage. This protection is achieved by sequestering intracellular Fe(2+) ions and storing them in the form of Fe(3+) oxyhydroxide mineral. The process involves the oxidation of two Fe(2+) ions by one hydrogen peroxide molecule, thereby preventing the production of hydroxyl radicals through the Fenton reaction. This protein is particularly important during periods of starvation or stationary phase, where it helps to maintain genomic integrity under stress conditions. The Dps protein from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) is a well-characterized example of this family.
L-aspartate--glyoxylate aminotransferase (AspGlyoxATase)
Type: Family

L-aspartate--glyoxylate aminotransferase (BhcA) from Paracoccus denitrificans (strain Pd 1222) is an enzyme that catalyzes the transamination of glyoxylate into glycine using L-aspartate as the preferred amino group donor. This enzyme is essential for the growth of P. denitrificans in the presence of glycolate and glyoxylate, functioning in glyoxylate assimilation via the beta-hydroxyaspartate cycle (BHAC). BhcA can also catalyze the reverse reaction in vitro and use L-serine and L-glutamate as amino group donors, albeit with much less efficiency than L-aspartate. BhcA belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family.
Oligopeptide ABC transporter permease OppC (OppC_permease)
Type: Family

This entry represents the oligopeptide ABC transporter permease OppC, also known as AmiD, found in Streptococcus pneumoniae. These proteins are part of the binding-protein-dependent transport system for oligopeptides and are likely responsible for the translocation of substrates across the membrane. They belong to the binding-protein-dependent transport system permease family, specifically the OppBC subfamily. The function of these proteins is crucial for the uptake of oligopeptides, which are essential for bacterial nutrition and metabolism.
Superoxide dismutase [Mn], archaeal (Superox_dis_Halo)
Type: Family

This entry represents superoxide dismutase [Mn] enzymes found in various archaeal species, including Halobacterium salinarum, Haloferax volcanii, and Haloarcula marismortui. These enzymes belong to the iron/manganese superoxide dismutase family and are responsible for the destruction of superoxide anion radicals, which are toxic to biological systems. The enzymes catalyze the dismutation of superoxide into oxygen and hydrogen peroxide, thus protecting cells from oxidative damage. The activity of these enzymes is crucial for the survival of organisms in environments with high oxidative stress. In some cases, the activity of these enzymes is regulated by inhibitors such as hydrogen peroxide, while they remain resistant to cyanide and azide inhibition.
15-cis-phytoene synthase (PhytoSynCyanob)
Type: Family

This entry represents 15-cis-phytoene synthase, also known as CrtB, which is involved in the biosynthesis of carotenoids. The enzyme catalyzes the condensation of two molecules of geranylgeranyl diphosphate (GGPP) to form prephytoene diphosphate (PPPP), followed by the rearrangement of the cyclopropylcarbinyl intermediate to yield 15-cis-phytoene. This enzyme is part of the phytoene/squalene synthase family and is found in various cyanobacteria, including Synechococcus elongatus and Synechocystis sp. The enzyme plays a crucial role in the carotenoid biosynthesis pathway, which is essential for the production of pigments that protect against photooxidative damage.
Glutamate dehydrogenase B (GluDhGdhB)
Type: Family

This entry represents glutamate dehydrogenases from Halobacterium salinarum, including Glutamate dehydrogenase B (GdhB) and NAD-specific glutamate dehydrogenase A (GdhX). These enzymes belong to the Glu/Leu/Phe/Val dehydrogenases family. Glutamate dehydrogenases are involved in the reversible oxidative deamination of glutamate to α-ketoglutarate and ammonia, playing a crucial role in nitrogen metabolism. The activity of NAD-specific glutamate dehydrogenase A is regulated by various solvents, including ethanol, acetone, acetonitrile, and 2-propanol, which inhibit its activity by 65 to 70%. Methanol and dimethyl formamide also inhibit the enzyme, albeit to a lesser extent. These enzymes are essential for the metabolic processes in Halobacterium salinarum, a halophilic archaeon.
Archaetidylinositol phosphate synthase, archaeal (archin_ph_syn)
Type: Family

Archaetidylinositol phosphate synthase (AIPS) is an enzyme that catalyzes the formation of archaetidylinositol phosphate (AIP) from CDP-archaeol (CDP-ArOH or CDP-2,3-bis-(O-phytanyl)-sn-glycerol) and 1L-myo-inositol 1-phosphate (IP or 1D-myo-inositol 3-phosphate). AIP is a precursor of archaetidyl-myo-inositol (AI), an ether-type inositol phospholipid ubiquitously distributed in archaeal membranes and essential for glycolipid biosynthesis in archaea. This enzyme belongs to the CDP-alcohol phosphatidyltransferase class-I family. The function of AIPS is conserved across various archaeal species, including Methanothermobacter thermautotrophicus, Pyrococcus horikoshii, Saccharolobus solfataricus, and Aeropyrum pernix.
Aldehyde dehydrogenase, thermostable (AlphKGSA_gudD)
Type: Family

This entry represents alpha-ketoglutaric semialdehyde dehydrogenase (GucD) and thermostable aldehyde dehydrogenase from Bacillus subtilis (strain 168) and Geobacillus stearothermophilus, respectively. These enzymes belong to the aldehyde dehydrogenase family and catalyze the NAD(P)(+)-dependent oxidation of alpha-ketoglutaric semialdehyde to alpha-ketoglutarate. The enzyme from Bacillus subtilis prefers NADP(+) over NAD(+) as a cosubstrate, while the enzyme from Geobacillus stearothermophilus oxidizes several aliphatic aldehydes, particularly c6-aliphatic aldehyde and hexanal, but does not oxidize benzaldehyde.