SII-SWORD/CoKE huggingface dataset:
L-prolyl-[peptidyl-carrier protein] dehydrogenase (ProlPCPDhRedW)
Type: Family

L-prolyl-[peptidyl-carrier protein] dehydrogenase, also known as L-prolyl-[prolyl-carrier protein] dehydrogenase, is an enzyme involved in the biosynthesis of undecylprodigiosin in Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145). This enzyme catalyzes the desaturation of L-prolyl-[prolyl-carrier protein] to yield 1H-pyrrole-2-carbonyl-[prolyl-carrier protein]. It belongs to the acyl-CoA dehydrogenase family. The function of this enzyme has been supported by experimental evidence (PubMed:11514230, PubMed:11880032).
NADPH-dependent hydrogenase/sulfhydrogenase 1 subunit gamma (sulfhyd_HydG)
Type: Family

This entry represents the gamma subunit of NADPH-dependent hydrogenase/sulfhydrogenase 1, also known as sulfhydrogenase 1 subunit gamma. This enzyme complex is found in Pyrococcus furiosus and functions as an NADPH-dependent hydrogen-evolving hydrogenase with sulfur-reducing activity. The beta and gamma subunits form the sulfur-reducing component that catalyzes the cytoplasmic production of hydrogen sulfide in the presence of elemental sulfur. This activity is not exhibited with NAD and is not active in the presence of sodium sulfate, sodium sulfite, sodium thiosulfate, or cysteine. The enzyme's activity is stimulated by rubredoxin at pH 7.6 but not by ferredoxin. This enzyme may play a role in hydrogen cycling during fermentative growth.
Tungsten-containing formylmethanofuran dehydrogenase subunit FwdC (FMH_DH_FwdC)
Type: Family

This entry represents the tungsten-containing formylmethanofuran dehydrogenase subunit FwdC. Proteins in this family catalyze the reversible oxidation of CO2 and methanofuran (MFR) to N-formylmethanofuran (CHO-MFR). This enzyme is oxygen-labile and belongs to the FwdC/FmdC family. The activity of this enzyme is crucial for the metabolic processes in various methanogenic archaea, including Methanococcus maripaludis, Methanothermobacter thermautotrophicus, Methanocaldococcus jannaschii, Methanothermobacter marburgensis, and Methanothermobacter wolfeii. The enzyme can only oxidize formylmethanofuran and is not inactivated by cyanide.
Chemoreceptor glutamine deamidase/glutamate methylesterase CheD (CheD_Thtga)
Type: Family

Chemoreceptor glutamine deamidase/glutamate methylesterase CheD is an enzyme found in Thermotoga maritima, which plays a crucial role in the modification of chemoreceptors (MCPs). CheD deamidates glutamine residues on MCPs, a modification necessary for the proper transmission of conformational signals to the CheA kinase. Additionally, CheD demethylates methylated glutamate residues on chemoreceptors Mcp2 and Mcp4, and enhances the activity of CheC. This enzyme belongs to the CheD family and is essential for the chemotactic signaling pathways in bacteria.
Cell wall elongation/penicillin-binding protein regulator TseB (regulator_TseB)
Type: Family

This entry represents the cell wall elongation/penicillin-binding protein regulator TseB. The TseB protein is involved in the regulation of cell wall elongation and penicillin-binding proteins in Bacillus subtilis (strain 168). The exact function of TseB remains uncharacterized, but it is believed to play a role in maintaining cell wall integrity and proper cell division. Further studies are required to elucidate the precise mechanisms by which TseB regulates these processes.
NADPH-dependent hydrogenase/sulfhydrogenase 1 subunit alpha (sulfhyd_HydA)
Type: Family

This entry represents the alpha subunit of NADPH-dependent hydrogenase/sulfhydrogenase 1, also known as sulfhydrogenase 1 subunit alpha. This protein is part of a bifunctional enzyme complex that functions as an NADPH-dependent hydrogen-evolving hydrogenase with sulfur-reducing activity. It may play a role in hydrogen cycling during fermentative growth. The alpha and delta subunits form the hydrogenase component that catalyzes the reduction of protons to evolve hydrogen. This protein belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit family.
Pantoate kinase, GHMP family (Panto_kinase)
Type: Family

Pantoate kinase is an enzyme that belongs to the GHMP kinase family, specifically the PoK subfamily. It is responsible for phosphorylating (R)-pantoate to form (R)-4-phosphopantoate, a crucial step in the coenzyme A (CoA) biosynthesis pathway. ATP is the preferred phosphate donor for this reaction, although UTP can also serve as a donor with lower efficiency. This enzyme is found in Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1).
Glucose import system permease protein GlcT (GlcT_permease)
Type: Family

This entry represents the glucose import system permease protein GlcT, 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).
alpha-IPM synthase (IPMS)
Type: Family

2-isopropylmalate synthase (IPMS) is an enzyme that catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). This reaction represents the first step in the leucine biosynthesis pathway. Members of this family belong to the alpha-IPM synthase/homocitrate synthase family. The enzyme is not inhibited by leucine and, in some cases, also displays a low citramalate synthase activity, using pyruvate as a substrate. However, it is unable to use 2-oxoglutarate. This family includes proteins from various archaeal species such as Sulfolobus acidocaldarius, Saccharolobus solfataricus, Ignicoccus hospitalis, and Sulfurisphaera tokodaii.
HTH-type transcriptional regulator CatM (HTH_CatM)
Type: Family

The HTH-type transcriptional regulator CatM is a protein found in Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1). It positively regulates the expression of catA, catBCIJFD, and benPK in response to cis,cis-muconate. CatM binds to the catB-catM intercistronic region, a specific sequence upstream of catA, and the benPK promoter region. Additionally, it can repress pca genes. This protein belongs to the LysR transcriptional regulatory family.
Methane monooxygenase component C (MethMoxCompC)
Type: Family

Methane monooxygenase component C (mmoC) from Methylococcus capsulatus is responsible for the initial oxygenation of methane to methanol in methanotrophs. This enzyme also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic, and heterocyclic compounds. The component C is the iron-sulfur flavoprotein of soluble methane monooxygenase (sMMO).
Cell division protein CdvC (cell_div_CdvC)
Type: Family

Cell division protein CdvC is a member of the AAA ATPase family and is involved in the cell division machinery of Sulfolobus acidocaldarius. The CdvA, CdvB, and CdvC proteins polymerize between segregating nucleoids and persist throughout cell division, forming a successively smaller structure during constriction. The MIT domain of CdvC is involved in interaction with CdvB. This protein plays a crucial role in the division process, ensuring proper segregation and constriction of the cell.
Oxalate oxidoreductase subunit beta (OxalOxred_beta)
Type: Family

Oxalate oxidoreductase subunit beta 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).
Methane monooxygenase component A gamma chain (MethMoxGammaMmoZ)
Type: Family

Methane monooxygenase (MMO) is an enzyme complex found in methanotrophic bacteria that catalyzes the initial oxygenation of methane to methanol. The gamma chain of the methane monooxygenase component A, also known as mmoZ, plays a crucial role in this process. This subunit is responsible for the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic, and heterocyclic compounds. The enzyme is essential for the metabolism of methane in methanotrophs, such as Methylosinus trichosporium and Methylococcus capsulatus. The gamma chain is a part of the hydroxylase component of the enzyme complex, which is involved in the binding and activation of molecular oxygen for the oxidation of methane.
Carbonic anhydrase, gamma-class (carb_anhyd)
Type: Family

Carbonic anhydrases (CAs) are enzymes that catalyze the reversible hydration of carbon dioxide. This entry represents the gamma-class carbonic anhydrase family, which includes enzymes that are important for growth on acetate. In Methanosarcina thermophila, the carbonic anhydrase (MSTHT_0588) is likely an extracellular enzyme that may support a H(+)/CH(3)COO(-) symport mechanism and/or conversion of CO(2) to HCO(3)(-), thus removing excess CO(2) produced by growth on acetate. These enzymes play a crucial role in maintaining cellular pH and ion balance by facilitating the rapid interconversion of CO(2) and bicarbonate.
Methane monooxygenase regulatory protein B (MethMoxRegMmoB)
Type: Family

Methane monooxygenase regulatory protein B (MmoB) is a component of the soluble methane monooxygenase (sMMO) complex found in methanotrophic bacteria such as Methylosinus trichosporium and Methylococcus capsulatus. The MmoB protein acts as a regulator of electron flow through the sMMO complex, switching the enzyme from an oxidase to a hydroxylase in the presence of the substrate. This regulatory function is crucial for the proper catalytic activity of the sMMO complex, enabling the oxidation of methane to methanol. MmoB belongs to the TmoD/XamoD family, which includes proteins involved in similar regulatory roles in other monooxygenase systems.
Methane monooxygenase component A beta chain (MethMoxA_beta)
Type: Family

Methane monooxygenase component A beta chain is responsible for the initial oxygenation of methane to methanol in methanotrophs. This enzyme also catalyzes the monohydroxylation of a variety of unactivated alkenes, alicyclic, aromatic, and heterocyclic compounds. The enzyme is found in species such as Methylosinus trichosporium and Methylococcus capsulatus. The beta chain is a crucial component of the methane monooxygenase complex, playing a significant role in the oxidation process.
Phospho-furanose lactonase (PhFuoseLconase)
Type: Family

Phospho-furanose lactonase catalyzes the hydrolysis of D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate. It is also capable of hydrolyzing carboxy 1,4-lactones. This enzyme belongs to the metallo-dependent hydrolases superfamily, specifically the phosphotriesterase family. The enzyme is found in Mycoplasmopsis synoviae (strain 53) and Mycoplasmopsis agalactiae (strain NCTC 10123 / CIP 59.7 / PG2).
NurA family nuclease (NurA_nuclease)
Type: Family

The DNA double-strand break repair nuclease NurA is involved in the repair of DNA double-strand breaks (DSBs). It likely acts in conjunction with HerA to stimulate the resection of the 5' strand, producing the long 3' single-strand required for RadA loading. NurA exhibits 5' endonuclease activity as well as both 5' and 3' exonuclease activities. The exonuclease activity of NurA is stimulated in the presence of HerA. This protein belongs to the NurA family and is characterized by its role in DNA repair mechanisms.
Sarcosine reductase complex component B subunit beta (Sarcosine_GrdF)
Type: Family

Sarcosine reductase complex component B subunit beta is involved in the first step of sarcosine reductase. The substrate is bound to component PB via a Schiff base intermediate. The PB-activated substrate is then nucleophilically attacked by the selenol anion of component PA, transforming it into a carboxymethylated selenoether and the respective amine. Component PC acts to form acetyl phosphate, leaving component PA in its oxidized state. Finally, component PA is reduced by the thioredoxin system to start a new catalytic cycle of reductive deamination. This protein belongs to the GrdB/GrdF/GrdH family.
Homoisocitrate dehydrogenase (HICDH)
Type: Family

Homoisocitrate dehydrogenase (HICDH) is an enzyme that catalyzes the NAD-dependent oxidation and decarboxylation of (2R,3S)-homoisocitrate, (2R,3S)-homo(2)-isocitrate, and (2R,3S)-homo(3)-isocitrate into 2-oxoadipate, 2-oxopimelate (2-oxoheptanedioate), and 2-oxosuberate, respectively. These substrates are intermediates in the biosynthesis of biotin and 7-mercaptoheptanoate, a moiety of coenzyme B in methanoarchaea. The enzyme is also capable of producing 2-oxoazelate from (2R,3S)-homo(4)-isocitrate in vitro, although this substrate is likely not physiologically relevant. HICDH is unable to use any isomer of isocitrate or isopropylmalate as a substrate, and NADP as an oxidant. This enzyme belongs to the isocitrate and isopropylmalate dehydrogenases family.
MPN499 family protein (MPN499)
Type: Family

This entry represents the MPN499 family protein, which is currently uncharacterized. The protein is found in Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1) and is encoded by the MPN_499 gene. The specific function of this protein family remains unknown.
Trehalase 2 (Trehalase_2)
Type: Family

Trehalase 2 is an enzyme that catalyzes the hydrolysis of alpha,alpha-trehalose into two molecules of D-glucose. It belongs to the glycosyl hydrolase 15 family and is found in Sulfolobus acidocaldarius. This enzyme plays a crucial role in carbohydrate metabolism by breaking down trehalose, a disaccharide sugar. The activity of trehalase 2 is essential for organisms that utilize trehalose as a source of energy and carbon.
Preflagellin peptidase (Arch_preflagellin_pept)
Type: Family

Preflagellin peptidases, also known as FlaK, are enzymes that cleave the N-terminal leader peptide from preflagellins. This processing is necessary for the assembly of flagellins into a flagellum structure. These enzymes belong to the peptidase A24 family, specifically the archaeal preflagellin peptidase subfamily. They are found in various archaeal species, including Methanococcus maripaludis, Methanococcus voltae, and Methanocaldococcus jannaschii.
HTH-type sugar sensing transcriptional regulator TrmB (tran_reg_TrmB)
Type: Family

The HTH-type sugar sensing transcriptional regulator TrmB is a protein family involved in the regulation of sugar metabolism in archaea. Members of this family, such as those found in Pyrococcus furiosus (Q9HGZ9) and Thermococcus litoralis (Q7LYW4), contain an N-terminal DNA-binding domain and a C-terminal sugar-binding domain. TrmB proteins function by inhibiting the transcription of the trehalose/maltose transport gene cluster (malE operon) and, in some cases, the maltodextrin transport gene cluster (mdxE operon). This inhibition is achieved through binding to operator sequences in the promoters, preventing polymerase recruitment and transcription. The repressor activity of TrmB is regulated by the binding of various sugars, which can act as inducers or corepressors. For instance, maltose and trehalose binding results in the derepression of the malE operon, while glucose binding causes stronger repression of both the malE and mdxE operons.
4-epi-cubebol synthase (epi-cubol_syn)
Type: Family

4-epi-cubebol synthase is an enzyme that belongs to the terpene synthase family. It catalyzes the conversion of (2E,6E)-farnesyl diphosphate (FPP) to yield the bicyclic sesquiterpenol 4-epi-cubebol via a 1,10-cyclization. This process requires the abstraction of the pyrophosphate from FPP to yield a (E,E)-germacradienyl cation. The enzyme contains a conserved Asp-Asp-Xaa-Xaa-Xaa-Glu (DDXXXE) motif, which is important for its catalytic activity, presumably through binding to Mg(2+). The only accepted substrate for this enzyme is (2E,6E)-farnesyl diphosphate (FPP). This enzyme has been characterized in Streptosporangium roseum (strain ATCC 12428 / DSM 43021 / JCM 3005 / KCTC 9067 / NCIMB 10171 / NRRL 2505 / NI 9100).
Pentalenene oxygenase (PentlenOxigase)
Type: Family

Pentalenene oxygenase is an enzyme that catalyzes the conversion of pentalenene to pentalen-13-al through stepwise oxidation via pentalen-13-ol. This enzyme plays a crucial role in the biosynthesis of the neopentalenolactone antibiotic. It belongs to the cytochrome P450 family, which is known for its diverse catalytic activities involving the oxidation of organic substrates. The enzyme is encoded by the ptlI gene in Streptomyces avermitilis, a bacterium known for producing various secondary metabolites with pharmaceutical importance.
1-deoxy-11-beta-hydroxypentalenate dehydrogenase (HdxpentlteDhPtlF)
Type: Family

This entry represents 1-deoxy-11-beta-hydroxypentalenate dehydrogenase, an enzyme involved in the biosynthesis of pentalenolactone antibiotics. The enzyme catalyzes the oxidation of 1-deoxy-11-beta-hydroxypentalenic acid to 1-deoxy-11-oxopentalenic acid. Members of this family belong to the short-chain dehydrogenases/reductases (SDR) family. The proteins matched by this entry are found in various Streptomyces species, including Streptomyces exfoliatus, Streptomyces arenae, and Streptomyces avermitilis.
Pentalenene synthase (PentlnSyn)
Type: Family

Pentalenene synthase is an enzyme that catalyzes the cyclization of farnesyl diphosphate (FPP) to the tricyclic sesquiterpene pentalenene. This reaction is a key step in the biosynthesis of the pentalenolactone family of antibiotics, which are produced by various Streptomyces species. The enzyme belongs to the terpene synthase family and contains a conserved Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif that is important for its catalytic activity, presumably through binding to Mg(2+).
Alpha-L-rhamnosidase, ulvan degradation (Rhamnosidase_Flavobac)
Type: Family

Alpha-L-rhamnosidase is an enzyme that may be involved in the degradation of ulvan, the main polysaccharide component of the cell wall of Ulvales (green seaweed). Ulvan is composed of disaccharide building blocks comprising 3-sulfated rhamnose (Rha3S) linked to D-glucuronic acid (GlcA), L-iduronic acid (IduA), or D-xylose (Xyl). This enzyme belongs to the glycosyl hydrolase 78 family. The protein is found in Formosa agariphila (strain DSM 15362 / KCTC 12365 / LMG 23005 / KMM 3901 / M-2Alg 35-1).
1-deoxypentalenic acid 11-beta-hydroxylase (DxPntBtaHylase)
Type: Family

1-deoxypentalenic acid 11-beta-hydroxylase is an enzyme that catalyzes the conversion of 1-deoxypentalenic acid to 11-beta-hydroxy-1-deoxypentalenic acid. This reaction is a key step in the biosynthesis of the antibiotic pentalenolactone. The enzyme belongs to the PhyH family and is found in various Streptomyces species, including Streptomyces arenae, Streptomyces avermitilis, and Streptomyces exfoliatus. The enzyme plays a crucial role in the production of pentalenolactone and neopentalenolactone antibiotics, which have significant biological activities.
Neopentalenolactone/pentalenolactone D synthase (Neo-PentlctneDsynPtlE)
Type: Family

This entry represents neopentalenolactone/pentalenolactone D synthase enzymes, which belong to the FAD-binding monooxygenase family. These enzymes catalyze the flavin-dependent Baeyer-Villiger oxidation of 1-deoxy-11-oxopentalenic acid to either pentalenolactone D or neopentalenolactone D. This reaction is a crucial step in the biosynthesis of the respective antibiotics. The enzymes are found in various Streptomyces species, including Streptomyces arenae, Streptomyces avermitilis, and Streptomyces exfoliatus.
Pentalenolactone F synthase (PentlctneF_syn)
Type: Family

This entry represents pentalenolactone F synthase, an enzyme that catalyzes the Fe(2+) and alpha-ketoglutarate-dependent oxidation of pentalenolactone D to pentalenolactone F. This enzyme is involved in the biosynthesis of the pentalenolactone antibiotic. Additionally, it can catalyze the oxidation of pentalenolactone D to pentalenolactone E. In Streptomyces avermitilis, the enzyme also mediates the production of PL308 and possibly neopentalenolactone E in the presence of neopentalenolactone D. This enzyme belongs to the TfdA dioxygenase family and its activity is regulated by ascorbate.
Pectinesterase B (Pectinest_B)
Type: Family

Pectinesterase B (PemB) is an enzyme that belongs to the pectinesterase family. It is involved in the degradation of methylated oligogalacturonides present in the periplasm. This enzyme is more active on methylated oligogalacturides than on pectin. Pectinesterase B is found in bacteria such as Dickeya dadantii (strain 3937) and Pectobacterium parmentieri. The enzyme plays a crucial role in the breakdown of pectin, a major component of plant cell walls, facilitating bacterial invasion and infection.
Mannosylglucosylglycerate synthase (manno_glu_gly_synth)
Type: Family

Mannosylglucosylglycerate synthase (MGG synthase) is an enzyme that catalyzes the synthesis of mannosylglucosylglycerate (MGG) from glucosylglycerate (GG) and GDP-mannose. This enzyme belongs to the glycosyltransferase group 1 family and is found in Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8). The enzyme plays a crucial role in the biosynthesis of compatible solutes, which are important for the organism's adaptation to high-temperature environments. The enzyme's activity is essential for the production of MGG, a compound that helps in stabilizing proteins and cellular structures under stress conditions.
Pentalenolactone synthase (PentlenlactSyn)
Type: Family

Pentalenolactone synthase is an enzyme that catalyzes the final step in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone. This enzyme mediates the oxidative rearrangement of pentalenolactone F to pentalenolactone. It belongs to the cytochrome P450 family, which is known for its role in the oxidative metabolism of various substrates. The enzyme is found in Streptomyces exfoliatus and Streptomyces arenae, where it plays a crucial role in the production of pentalenolactone, a compound with antibiotic properties.
GrgA family transcription factor (GrgA_tf)
Type: Family

This entry represents the GrgA family transcription factors, which belong to the chlamydial CPn_0623/CT_504/TC_0791 family. Members of this family include uncharacterized proteins such as TC_0791 from Chlamydia muridarum, CPn_0623 from Chlamydia pneumoniae, and CT_504 from Chlamydia trachomatis. These proteins are thought to play roles in transcription regulation within chlamydial species, although their precise functions remain to be fully elucidated. The family is characterized by conserved sequence motifs and structural features typical of transcription factors.
Endo-beta-N-acetylglucosaminidase F3 (Endoglyc_F3)
Type: Family

Endo-beta-N-acetylglucosaminidase F3 (Endo F3) is an enzyme that catalyzes the endohydrolysis of the di-N-acetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins. It is capable of hydrolyzing bi- and triantennary glycans. The presence of a core-bound fucose significantly enhances Endo F3 activity on biantennary and, presumably, triantennary oligosaccharides. This enzyme belongs to the glycosyl hydrolase 18 family and is found in the bacterium Elizabethkingia meningoseptica.
MPN337 family protein (MPN337)
Type: Family

This entry represents the MPN337 family of proteins, which includes uncharacterized proteins such as MG241 from Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37) and MPN_337 from Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1). The exact function of these proteins is currently unknown. Further research is needed to elucidate their roles in the respective organisms.