SII-SWORD/CoKE huggingface dataset:
Succinyl-CoA:mesaconate CoA-transferase (Scnl_mescCoAtase)
Type: Family

Succinyl-CoA:mesaconate CoA-transferase is an enzyme involved in the methylaspartate cycle. It catalyzes the transfer of the CoA moiety from succinyl-CoA to mesaconate, generating mesaconyl-CoA (2-methylfumaryl-CoA) and succinate. This enzyme belongs to the CoA-transferase III family. In Haloarcula hispanica, the enzyme shows highest activity at 4 M KCl and does not require divalent ions for activity. It also exhibits high activity with methylsuccinate as a CoA-acceptor and low activity with glutarate, acrylate, and itaconate. However, it cannot use other CoA donors like acetyl-CoA, propionyl-CoA, butyryl-CoA, or acetoacetyl-CoA.
2,3-Digeranylgeranylglycerophospholipid reductase (DGGGPL_red)
Type: Family

This entry represents digeranylgeranylglycerophospholipid reductase, an enzyme involved in the biosynthesis of archaeal membrane lipids. The enzyme catalyzes the reduction of 2,3-digeranylgeranylglycerophospholipids (unsaturated archaeols) into 2,3-diphytanylglycerophospholipids (saturated archaeols). This process involves the hydrogenation of each double bond of the isoprenoid chains, leading to the formation of archaetidic acid from 2,3-di-O-geranylgeranylglyceryl phosphate (DGGGP). The enzyme is also active on upstream precursors of membrane lipid biosynthesis, such as 3-O-geranylgeranylglyceryl phosphate (GGGP) and geranylgeranyl diphosphate (GGPP). The physiological reducing agent for this enzyme is currently unknown. This enzyme belongs to the geranylgeranyl reductase family.
(R)-citramalate synthase (CitmalSynth_CimA)
Type: Family

This entry represents (R)-citramalate synthase (CimA), an enzyme found in Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601). CimA catalyzes the condensation of pyruvate and acetyl-coenzyme A to form (R)-citramalate. The enzyme shows strict substrate specificity for pyruvate and cannot use other alpha-keto acids such as alpha-ketoisovalerate, alpha-ketobutyrate, alpha-ketoisocaproate, alpha-ketoglutarate, or glyoxylate. The activity of CimA is regulated by the end-product isoleucine via feedback inhibition, which affects the binding of both pyruvate and acetyl-CoA. Structurally, CimA belongs to the alpha-IPM synthase/homocitrate synthase family and contains a catalytic N-terminal domain and a C-terminal regulatory domain, linked by a flexible region. The catalytic domain consists of a TIM barrel with the active site located at the center, composed of conserved residues from both subunits.
PTS phosphocarrier protein HPr (PTS-HPr)
Type: Family

Phosphocarrier protein HPr is a general (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The phosphoryl group from phosphoenolpyruvate (PEP) is transferred to the phosphoryl carrier protein HPr by enzyme I. Phospho-HPr then transfers it to the PTS EIIA domain. This protein is involved in fructose transport. Phosphorylation on Ser-47 inhibits the phosphoryl transfer from enzyme I to HPr. HPr belongs to the HPr family.
Fructose-bisphosphate aldolase class II (Fbpase2)
Type: Family

Fructose-bisphosphate aldolase class II (Fbpase class II) enzymes catalyse the aldol condensation of dihydroxyacetone phosphate (DHAP) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis. These enzymes are required for the utilization of fructose as a sole carbon and energy source and play a role in gluconeogenesis during growth on acetate, D-xylose, and casamino acids. The activity of these enzymes can be inhibited by EDTA. This entry represents the class II fructose-bisphosphate aldolase family, which includes proteins from various organisms such as Haloferax volcanii.
Olefin beta-lactone synthetase, Shewanella oneidensis (OlefBLtnSynShew)
Type: Family

Olefin beta-lactone synthetase is an enzyme involved in the biosynthesis of olefins. It catalyzes the conversion of 2-alkyl-3-hydroxyalkanoic acids to beta-lactones in the presence of ATP. This enzyme belongs to the ATP-dependent AMP-binding enzyme family. In Shewanella oneidensis, the oleABCD gene cluster is responsible for the production of 3,6,9,12,15,19,22,25,28-hentriacontanonaene, which may help the cells adapt to sudden drops in temperature. The function of this enzyme has been supported by experimental evidence (PubMed:20418444).
Sulfate respiration complex protein HmcD (sulf_resp_HmcD)
Type: Family

The sulfate respiration complex protein HmcD is part of a high-molecular-weight cytochrome c (HMWC) complex involved in electron transfer. This protein is encoded by the DVU_0533 gene in Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough). HmcD, along with other proteins in the HMC operon, forms a transmembrane protein complex that facilitates electron flow from the periplasmic hydrogenase to cytoplasmic enzymes responsible for sulfate reduction. This process is crucial for the organism's energy metabolism under anaerobic conditions.
Multifunctional alkaline phosphatase PehA (HdlasePehA)
Type: Family

This entry represents the multifunctional alkaline phosphatase PehA, a member of the alkaline phosphatase superfamily. PehA exhibits a broad substrate specificity, hydrolyzing phosphate diesters and phosphonate monoesters. It also acts on phosphate mono- and triesters, sulfate monoesters, and sulfonate monoesters. PehA can hydrolyze glyphosate monoesters and glyceryl glyphosate, although the latter has a much lower affinity. The enzyme's activity is stimulated by anions such as Cl(-), CH3COO(-), and SO4(2-) salts. PehA does not hydrolyze DNA or cGMP. This protein is found in Trinickia caryophylli and Rhizobium johnstonii.
MurNAc-alpha-1P uridylyltransferase (MurNAcPUrMurU)
Type: Family

N-acetylmuramate alpha-1-phosphate uridylyltransferase (MurU) is an enzyme that catalyzes the formation of UDP-N-acetylmuramate (UDP-MurNAc) from UTP and MurNAc-alpha-1P. This reaction is a crucial step in the recycling of peptidoglycan, an essential component of the bacterial cell wall. The enzyme is likely involved in a cell wall recycling pathway that bypasses the de novo biosynthesis of the peptidoglycan precursor UDP-MurNAc. The MurU enzyme from Caulobacter vibrioides has been shown to complement the fosfomycin sensitivity phenotype of a Pseudomonas putida mutant lacking murU, indicating its functional role in peptidoglycan recycling. This enzyme belongs to the nucleotidyltransferase MurU family.
F(420)H(2) dehydrogenase subunit D (F420_dehyd_FpoD)
Type: Family

The F(420)H(2) dehydrogenase subunit D is a component of the F(420)H(2) dehydrogenase (FPO complex), which is part of the energy-conserving F(420)H(2):heterodisulfide oxidoreductase system. This system plays a crucial role in the metabolism of methylotrophic methanogens, particularly when these organisms grow on methanol or methylamines. The FPO complex catalyzes the oxidation of methanophenazine to dihydromethanophenazine, shuttling electrons from F(420)H(2) via FAD and iron-sulfur (Fe-S) centers to methanophenazine, an electron carrier in the membrane. This redox reaction is coupled to proton translocation, conserving redox energy in a proton gradient. Additionally, the complex catalyzes the oxidation of F(420)H(2) with quinones such as 2,3-dimethyl-1,4-naphthoquinone, 2-methyl-1,4-naphthoquinone, and tetramethyl-p-benzoquinone. The subunit D belongs to the complex I 49 kDa subunit family.
Outer membrane protein OmpV (OmpV)
Type: Family

The outer membrane protein OmpV is a member of the MipA/OmpV family, which is found in various Vibrio species, including Vibrio anguillarum and Vibrio cholerae. These proteins are integral components of the bacterial outer membrane and are involved in maintaining membrane integrity and function. The OmpV protein from Vibrio cholerae is encoded by the ompV gene, while the corresponding protein in Vibrio anguillarum is referred to as Omp26La. Members of the MipA/OmpV family share significant sequence similarity and are characterized by their role in the bacterial outer membrane.
Fatty-acid O-methyltransferase (FAmtase_mtf2)
Type: Family

Fatty-acid O-methyltransferase (Mtf2) is an enzyme that modifies the hydroxy group of fatty acids through methylation. Oleate is identified as the most effective fatty acid acceptor for this enzyme. This protein belongs to the methyltransferase superfamily and is found in Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155). The enzyme plays a crucial role in the modification of fatty acids, which can impact various biological processes.
Oxalate oxidoreductase subunit alpha (OxalOxredalpha)
Type: Family

Oxalate oxidoreductase subunit alpha is an enzyme that catalyzes the anaerobic oxidation of oxalate using a broad range of electron acceptors, including ferredoxin and the nickel-dependent carbon monoxide dehydrogenase. This enzyme does not require coenzyme A as a cosubstrate and enables anaerobic growth on oxalate, which is used as an energy source by the bacteria Moorella thermoacetica (strain ATCC 39073 / JCM 9320).
UPF0167 protein CbrC (UPF0167_CbrC)
Type: Family

This entry represents the UPF0167 protein CbrC, which is involved in colicin E2 tolerance. The CbrC protein belongs to the UPF0167 family and is found in Escherichia coli (strain K12). The exact function of CbrC is not fully characterized, but it is known to play a role in the bacterial response to colicin E2. Colicins are a type of bacteriocin produced by some strains of Escherichia coli that can kill or inhibit the growth of other strains. The CbrC protein helps the bacteria to tolerate the presence of colicin E2, although the precise mechanisms are still under investigation.
Mycoplasma-type histidine triad protein HinT (M_plasma_HinT)
Type: Family

This entry represents a Mycoplasma-type histidine triad (HIT) protein, HinT. HIT proteins are characterized by a conserved histidine triad motif (HφHφHφ, where φ is a hydrophobic residue) and are involved in various biochemical processes, including nucleotide binding and hydrolysis. The specific function of this protein in Mesomycoplasma hyorhinis is not yet characterized, but it is presumed to play a role similar to other HIT proteins in nucleotide metabolism. Further studies are needed to elucidate its precise biological role.
NAD(P)-dependent benzaldehyde dehydrogenase (BenzalDHMdlD)
Type: Family

NAD(P)-dependent benzaldehyde dehydrogenase is an enzyme that catalyzes the conversion of benzaldehyde into benzoate in the (R)-mandelate degradation pathway. This enzyme can utilize either NAD or NADP as a cofactor. It belongs to the aldehyde dehydrogenase family and is encoded by the mdlD gene in Pseudomonas putida. The enzyme plays a crucial role in the metabolism of aromatic compounds, facilitating their breakdown and utilization as carbon sources.
Tyrosine isonitrile synthase (TyIsonSynPvcA)
Type: Family

L-tyrosine isonitrile synthase is an enzyme involved in the biosynthesis of rhabduscin, a tyrosine derivative that acts as a potent inhibitor of phenoloxidase, a key component of the insect's innate immune system. This enzyme is responsible for the synthesis of the isonitrile group on tyrosine, using the C2 of ribulose 5-phosphate as the source of the carbon atom. It belongs to the isocyanide synthase family and is found in Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / CCUG 14189 / LMG 1036 / NCIMB 9965 / AN6).
FPO subunit F (FPO_su_F)
Type: Family

The F420H2 dehydrogenase subunit F (FpoF) is a component of the F420H2 dehydrogenase (FPO complex), which is part of the energy-conserving F420H2:heterodisulfide oxidoreductase system. This membrane-bound electron transfer system plays a crucial role in the metabolism of methylotrophic methanogens, particularly when these organisms grow on methanol or methylamines. FpoF catalyzes the oxidation of methanophenazine to dihydromethanophenazine, shuttling electrons from F420H2, via FAD and iron-sulfur (Fe-S) centers, to methanophenazine, an electron carrier in the membrane. This process couples the redox reaction to proton translocation, conserving redox energy in a proton gradient. Additionally, FpoF catalyzes the oxidation of F420H2 with quinones such as 2,3-dimethyl-1,4-naphthoquinone, 2-methyl-1,4-naphthoquinone, and tetramethyl-p-benzoquinone. It may function both as an electron input module when connected to the membrane integral Fpo complex and as a soluble single subunit involved in the reoxidation of reduced ferredoxin in the cytoplasm.
Decorin-binding protein A (Decorin_bind_prot_A)
Type: Family

Decorin-binding protein A (DbpA) is a member of the decorin-binding protein family found in Borreliella burgdorferi, the causative agent of Lyme disease. This protein binds to decorin, a component of the extracellular matrix, which may facilitate the adherence of B. burgdorferi to collagen fibers in skin and other tissues. The interaction with decorin is crucial for the pathogen's ability to colonize and persist in the host. DbpA plays a significant role in the pathogenesis of Lyme disease by mediating bacterial attachment to host tissues.
N(G),N(G)-dimethylarginine dimethylaminohydrolase (DDAH)
Type: Family

This entry represents N(G),N(G)-dimethylarginine dimethylaminohydrolase from Pseudomonas aeruginosa (DDAH) and similar sequences specific to proteobacteria. DDAH is an enzyme that hydrolyses N(G),N(G)-dimethyl-L-arginine (ADMA) and N(G)-monomethyl-L-arginine (MMA) . These substrates are methylated derivatives of arginine, and their hydrolysis by DDAH plays a crucial role in regulating nitric oxide (NO) production by modulating the availability of arginine for nitric oxide synthase (NOS). DDAH activity is inhibited by zinc ions and competitively inhibited by lysine.
Glucose-binding protein GlcS (GlcS_GBP)
Type: Family

The Glucose-binding protein GlcS is a component of the ABC transporter complex GlcSTUV, which is involved in glucose uptake in Saccharolobus solfataricus. This protein binds glucose and can also bind galactose and mannose. The binding of glucose by GlcS is strongly inhibited by the presence of galactose and mannose. GlcS belongs to the bacterial solute-binding protein 1 family. The protein plays a crucial role in the transport and regulation of glucose and other sugars within the cell, facilitating their uptake and utilization.
Citrate synthase family (Cit_synThplmales)
Type: Family

Citrate synthase is an enzyme that catalyzes the first step of the citric acid cycle (Krebs cycle), which is the synthesis of citrate from oxaloacetate and acetyl-CoA. This enzyme is allosterically inhibited by NADH, indicating a regulatory role in cellular metabolism. Members of the citrate synthase family are found across various species, including Thermoplasma acidophilum and Saccharolobus solfataricus. These enzymes play a crucial role in energy production and metabolic regulation.
Glucose ABC transporter permease GlcU (GlcU_transporter)
Type: Family

This entry represents the glucose import system permease protein GlcU, which is part of the ABC transporter complex GlcSTUV involved in glucose uptake. The protein is responsible for the translocation of glucose across the membrane. It belongs to the binding-protein-dependent transport system permease family. The protein is found in Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2).
Fatty-acid--CoA ligase FadD21 (FAAL_FadD21)
Type: Family

This entry represents the fatty-acid--CoA ligase FadD21, also known as fatty-acid--AMP ligase FAAL21/FadD21. These enzymes belong to the ATP-dependent AMP-binding enzyme family and are involved in the activation of fatty acids by forming a fatty acyl-CoA thioester. The proteins matched by this entry are found in various Mycobacterium species, including Mycobacterium tuberculosis (strains CDC 1551 and H37Rv), Mycobacterium leprae (strain TN), and Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97). These enzymes play a crucial role in lipid metabolism, which is essential for the survival and pathogenicity of these bacteria.
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (dPGM_arch)
Type: Family

This entry represents 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase, an enzyme that catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. This enzyme belongs to the phosphoglycerate mutase family and is found in Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165). The enzyme plays a crucial role in the glycolytic pathway, facilitating the conversion of 3-phosphoglycerate to 2-phosphoglycerate, which is a key step in the metabolic process. The enzyme is characterized by its dependence on 2,3-bisphosphoglycerate for activity.
GTP-dependent dephospho-CoA kinase family (deph_CoA_kin_Thcocales)
Type: Family

GTP-dependent dephospho-CoA kinase (DPCK) catalyzes the GTP-dependent phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A (CoA). This enzyme is a member of the GTP-dependent DPCK family and is found in various archaeal species, including Pyrococcus horikoshii, Pyrococcus abyssi, Thermococcus onnurineus, Thermococcus kodakarensis, and Pyrococcus furiosus. The enzyme shows a strong preference for GTP as the phosphate donor, although it can also use UTP with lower efficiency and has weak activity with ATP. The proteins in this family are typically around 177-179 amino acids in length.
Lysyl aminopeptidase (lys_aminopep_Arch)
Type: Family

Lysyl aminopeptidase is an enzyme that hydrolyzes di-, tri- and tetrapeptides with a lysine as the N-terminal amino acid and with Gly, Lys, Ala, Phe or Glu in the second position. This enzyme belongs to the peptidase M42 family and is found in Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1). The enzyme plays a role in protein degradation and processing, contributing to the organism's ability to thrive in extreme environments. The lysyl aminopeptidase from Pyrococcus furiosus is encoded by the gene PF1861.
Rhamnosyl O-methyltransferase family (RhmsylMtase)
Type: Family

Rhamnosyl O-methyltransferase enzymes catalyze the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD). These enzymes are found in various strains of Mycobacterium, including Mycobacterium bovis, Mycobacterium leprae, and Mycobacterium tuberculosis. The proteins belong to the rhamnosyl O-methyltransferase family and share significant sequence similarity. The function of these enzymes is crucial for the modification of specific glycosylated compounds, which may play a role in the pathogenicity and survival of these bacteria.
Oxalate oxidoreductase subunit delta (OxalOxred_delta)
Type: Family

Oxalate oxidoreductase subunit delta is an enzyme that catalyzes the anaerobic oxidation of oxalate using a broad range of electron acceptors, including ferredoxin and the nickel-dependent carbon monoxide dehydrogenase. This enzyme does not require coenzyme A as a cosubstrate and enables anaerobic growth on oxalate, which is used as an energy source by the bacteria Moorella thermoacetica (strain ATCC 39073 / JCM 9320).
Leucine/methionine racemase (LeuMetRace)
Type: Family

Leucine/methionine racemase is an amino acid racemase with moderate substrate specificity. It is primarily active toward leucine, which is the preferred substrate, and methionine. The enzyme also exhibits lower levels of activity toward phenylalanine, alanine, and serine. It belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family. The activity of leucine/methionine racemase is strongly inhibited by several metal ions, including Co(2+), Zn(2+), Ni(2+), Cu(2+), and Fe(3+), as well as nonsubstrate amino acids such as L-arginine and L-lysine. The activity is completely abolished in the presence of hydroxylamine, an inhibitor of pyridoxal phosphate-dependent enzymes. This enzyme has been characterized in Thermococcus litoralis and Thermococcus kodakarensis.
Polysaccharide lyase 17 family (Alg_lyase)
Type: Family

Alginate lyase is an enzyme that catalyzes the depolymerization of alginate via a beta-elimination mechanism, cleaving the beta-1,4 glycosidic bond between two adjacent sugar residues. This enzyme acts specifically on alginate and each of its block structures, with the highest activity toward poly-beta-D-mannuronate (poly-ManA). It exhibits an exolytic mode of action, producing unsaturated monomers. Alginate lyase displays very low activity against poly-beta-D-glucuronate (poly-GlcA) and is not active on poly-alpha-D-galacturonate, hyaluronan, heparin, heparan sulfate, and chondroitin sulfate. This enzyme belongs to the polysaccharide lyase 17 family.
O6-methylguanine-DNA methyltransferase (DNA_protcyst_Mta_Thcoc)
Type: Family

Methylated-DNA--protein-cysteine methyltransferase (MGMT) is involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. This enzyme repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme, resulting in a suicide reaction where the enzyme is irreversibly inactivated. MGMT plays a crucial role in maintaining genomic stability by preventing mutations caused by alkylating agents. This family of enzymes is highly conserved across various species, including Pyrococcus horikoshii, Thermococcus barophilus, Pyrococcus sp. NA2, Thermococcus sibiricus, Thermococcus kodakarensis, Pyrococcus abyssi, and Thermococcus gammatolerans.
CoaD family phosphopantetheine adenylyltransferase (CoaD_Thcocales)
Type: Family

Phosphopantetheine adenylyltransferase (CoaD) is an enzyme that reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate. This enzyme belongs to the eukaryotic CoaD family and is found in various thermophilic archaea, including Thermococcus kodakarensis, Pyrococcus furiosus, Pyrococcus horikoshii, Thermococcus gammatolerans, and Pyrococcus abyssi. The CoaD family is characterized by its role in CoA biosynthesis, specifically in the conversion of 4'-phosphopantetheine to dephospho-CoA. The enzymes in this family share significant sequence similarity and functional properties.
Hexose phosphate transporter (Hexose_phos_transporter)
Type: Family

This entry represents hexose phosphate transporters, which are involved in the transport of hexose phosphates across cellular membranes. These transporters play a crucial role in carbohydrate metabolism by facilitating the movement of phosphorylated sugars, which are key intermediates in various metabolic pathways. The proteins matched by this entry are uncharacterized but are predicted to function as hexose phosphate transporters based on sequence similarity.
2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase (KDG_KDGal_kin)
Type: Family

This entry represents 2-dehydro-3-deoxygluconokinase (KDGK) and 2-dehydro-3-deoxygalactonokinase (KDGalK) enzymes. These enzymes are involved in the degradation of glucose and galactose via the semi-phosphorylative Entner-Doudoroff pathway. They catalyze the phosphorylation of 2-keto-3-deoxygluconate (KDG) and 2-keto-3-deoxygalactonate (KDGal) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal), respectively. Members of this family belong to the carbohydrate kinase PfkB family. The enzymes can utilize GTP as a phosphoryl donor and are found in various archaeal species such as Sulfurisphaera tokodaii, Thermoproteus tenax, and Saccharolobus solfataricus.