SII-SWORD/CoKE huggingface dataset:
N-acyl homoserine lactonase AiiA (AHLLactAiiA)
Type: Family

N-acyl homoserine lactonase AiiA is an enzyme that belongs to the metallo-beta-lactamase superfamily. It catalyzes the hydrolysis of N-acyl homoserine lactones (AHLs), which are signaling molecules used in quorum sensing by various bacteria. The enzyme shows activity towards both short- and long-chain AHLs, with or without 3-oxo substitution at the C3 position, and has maximum activity on C10-AHL. AiiA enzymes from different Bacillus species, including Bacillus thuringiensis and Bacillus cereus, have been characterized. The enzyme is completely inhibited by Cu(2+) and Ag(+), and partially inhibited by Cr(2+), Pb(2+), and Fe(2+). It is not affected by Mg(2+), Ca(2+), Mn(2+), Co(2+), Ni(2+), Zn(2+), Cd(2+), or chelating agents such as EDTA, 2,2'-bipyridine, and o-phenanthroline.
Bifunctional 2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase (KDG_KDGal_kin_Halo)
Type: Family

This entry represents bifunctional enzymes that exhibit both 2-dehydro-3-deoxygluconokinase and 2-dehydro-3-deoxygalactonokinase activities. These enzymes are involved in the degradation of glucose via the semi-phosphorylative Entner-Doudoroff pathway and galactose catabolism. They catalyze the phosphorylation of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG) and the phosphorylation of 2-keto-3-deoxygalactonate (KDGal) to produce 2-keto-3-deoxy-6-phosphogalactonate (KDPGal). The enzymes belong to the carbohydrate kinase PfkB family and are found in Haloferax volcanii.
Citrate synthase, Haloferax volcanii (Cit_synth_Halo_CitZ)
Type: Family

Citrate synthase (EC 2.3.3.1) is an enzyme that catalyses the first step of the citric acid cycle (Krebs cycle), which is the condensation of oxaloacetate and acetyl-CoA to form citrate. This enzyme is a key regulatory point in the cycle and is found in a wide range of organisms, including the archaeon Haloferax volcanii. The citrate synthase from Haloferax volcanii, encoded by the citZ gene, belongs to the citrate synthase family. It might regulate the synthesis and function of enzymes involved in later enzymatic steps of the Krebs cycle. This entry represents citrate synthase proteins from Haloferax volcanii and related archaeal species.
Peroxynitrite isomerase (PeroxynitIsom)
Type: Family

This entry represents peroxynitrite isomerases, which belong to the nitrobindin family. These proteins form a 10-stranded antiparallel beta-barrel structure capable of accommodating a hydrophobic ligand in its interior. The fold hosts a heme group located in a wide surface cleft. The primary function of these proteins is to scavenge peroxynitrite and protect free L-tyrosine against peroxynitrite-mediated nitration by acting as peroxynitrite isomerases that convert peroxynitrite to nitrate. This activity likely plays a role in peroxynitrite sensing and the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively). These proteins are also able to bind nitric oxide (NO) in vitro and may act as sensors of peroxynitrite levels in vivo.
Medium/long-chain-fatty-acid--CoA ligase FadD6 (FACL_FadD6)
Type: Family

Medium/long-chain-fatty-acid--CoA ligase FadD6, also known as long-chain-fatty-acid--CoA ligase FadD6, is an enzyme found in Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv). This enzyme catalyzes the activation of medium and long-chain fatty acids by converting them into acyl-coenzyme A (acyl-CoA) esters. This process is crucial for the uptake and metabolic trapping of fatty acids within the bacterial cell. FadD6 may also play a significant role in channeling fatty acids into triacylglycerol (TAG) for storage, which is particularly important during the dormancy phase of Mycobacterium tuberculosis. The enzyme belongs to the ATP-dependent AMP-binding enzyme family.
Indole-3-glycerol phosphate synthase, archaeal (Indglycph_syn_Halo_TrpC)
Type: Family

Indole-3-glycerol phosphate synthase (IGPS) is an enzyme that catalyses the conversion of 1-(2-carboxyphenylamino)-1-deoxyribulose-5-phosphate to indole-3-glycerol phosphate, a key step in the biosynthesis of tryptophan. This enzyme is part of the TrpC family and is found in various archaeal species, including Haloferax volcanii, Halobacterium salinarum, and Haloarcula marismortui. IGPS plays a crucial role in the tryptophan biosynthesis pathway, which is essential for the production of this important amino acid. The enzyme's structure and function are conserved across different species, highlighting its evolutionary significance.
RIO-type serine/threonine-protein kinase Rio1 (RIO1_kinase)
Type: Family

RIO-type serine/threonine-protein kinase Rio1 is a serine/threonine-protein kinase that is capable of autophosphorylation and can phosphorylate proteasome subunit alpha 1 (PsmA1) in vitro. Despite having a protein kinase domain, it is proposed to function predominantly as an ATPase. This protein belongs to the protein kinase superfamily, specifically the RIO-type Ser/Thr kinase family. The protein is found in Haloferax volcanii, a species of archaea.
Phthiotriol/phenolphthiotriol dimycocerosates methyltransferase (PthPhpthDimycoMt)
Type: Family

This entry represents phthiotriol/phenolphthiotriol dimycocerosates methyltransferases, which are enzymes that catalyze the methylation of the lipid moiety of intermediate compounds such as phthiotriol and glycosylated phenolphthiotriol dimycocerosates. This methylation process results in the formation of phthiocerol dimycocerosates (DIM A) and glycosylated phenolphthiocerol dimycocerosates (PGL). These enzymes belong to the methyltransferase superfamily and are found in various Mycobacterium species, including Mycobacterium bovis, Mycobacterium tuberculosis, Mycobacterium ulcerans, Mycobacterium leprae, and Mycolicibacterium smegmatis. The enzymes play a crucial role in the biosynthesis of complex lipids that are important for the pathogenicity and survival of these bacteria.
Endonuclease VIII Nei2 (Endonuc_Nei2)
Type: Family

This entry represents endonuclease VIII Nei2, a member of the FPG family. Endonuclease VIII Nei2 is involved in the base excision repair of DNA damaged by oxidation or mutagenic agents. It functions as a DNA glycosylase that recognizes and removes damaged bases, and has AP (apurinic/apyrimidinic) lyase activity. The enzyme introduces nicks in the DNA strand by cleaving the DNA backbone through beta-delta elimination, generating a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. This protein is found in Mycobacterium tuberculosis (strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh) and Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97).
Rad50/Mre11 complex component (Mre11_Halo)
Type: Family

The DNA double-strand break repair protein Mre11 is a crucial component of the Rad50/Mre11 complex, which plays a significant role in the early steps of DNA double-strand break (DSB) repair. Mre11 binds to DSB ends and exhibits both double-stranded 3'-5' exonuclease activity and single-stranded endonuclease activity. In polyploid organisms, the Rad50/Mre11 complex appears to restrain the repair of double-strand breaks by homologous recombination, allowing another pathway to act as the primary mode of repair. The nuclease activity of Mre11 is regulated by Rad50. This protein belongs to the MRE11/RAD32 family.
Menaquinone reductase (MkRedMenJ)
Type: Family

Menaquinone reductase, also known as MenJ, is an enzyme that catalyzes the reduction of a single double bond in the isoprenoid tail of menaquinone (MK-9) in mycobacteria, likely the beta-isoprene unit. This reaction forms the predominant form of menaquinone found in mycobacteria, MK-9(II-H2). The enzyme belongs to the geranylgeranyl reductase family and is essential for the survival of Mycobacterium tuberculosis in host macrophages. The enzyme is found in various strains of Mycobacterium, including Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155), Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv), and Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh).
3-phenylpropionate/cinnamic acid dioxygenase subunit beta (3PPDioc_HcaF)
Type: Family

This entry represents the beta subunit of the multicomponent 3-phenylpropionate/cinnamic acid dioxygenase enzyme complex. This enzyme complex is responsible for the conversion of 3-phenylpropionic acid (PP) and cinnamic acid (CI) into their respective dihydrodiol forms, 3-phenylpropionate-dihydrodiol (PP-dihydrodiol) and cinnamic acid-dihydrodiol (CI-dihydrodiol). The beta subunit, encoded by the hcaF gene, is a part of the bacterial ring-hydroxylating dioxygenase beta subunit family. This family is characterized by its role in the hydroxylation of aromatic compounds, facilitating their breakdown and utilization by bacteria. The function of this enzyme complex is crucial for the metabolism of aromatic compounds in various bacterial species, including Escherichia coli and Shigella species.
Outer membrane protein Omp38 (Omp38)
Type: Family

Outer membrane protein Omp38 is a member of the outer membrane OOP (TC 1.B.6) superfamily. This protein functions as a porin, facilitating the transport of molecules across the outer membrane. In Acinetobacter baumannii, Omp38 has been shown to induce apoptosis in human cell lines through caspase-dependent and AIF-dependent pathways. The protein can localize to the mitochondria, leading to the release of proapoptotic molecules such as cytochrome c and apoptosis-inducing factor (AIF). Additionally, Omp38 binds peptidoglycan, contributing to cell wall maintenance. The periplasmic domain of Omp38, particularly residues 221-339, is involved in binding peptidoglycan and diaminopimelate, a component of peptidoglycan.
3-phenylpropionate/cinnamic acid dioxygenase subunit alpha (3PPDioc_HcaE)
Type: Family

This entry represents the alpha subunit of the 3-phenylpropionate/cinnamic acid dioxygenase enzyme complex. This multicomponent dioxygenase converts 3-phenylpropionic acid (PP) and cinnamic acid (CI) into their respective dihydrodiol forms, 3-phenylpropionate-dihydrodiol (PP-dihydrodiol) and cinnamic acid-dihydrodiol (CI-dihydrodiol). The alpha subunit is a part of the bacterial ring-hydroxylating dioxygenase alpha subunit family, which is involved in the initial steps of the degradation of aromatic compounds. This enzyme complex is found in various bacterial species, including Escherichia coli and Shigella species. The function of this enzyme is crucial for the microbial metabolism of aromatic compounds, contributing to the breakdown and utilization of these compounds as carbon sources.
DGGGPL reductase (Dggglyphlred_Halo)
Type: Family

Digeranylgeranylglycerophospholipid reductase (DGGGPL reductase) is an enzyme involved in the biosynthesis of archaeal membrane lipids. It catalyzes the reduction of 2,3-digeranylgeranylglycerophospholipids (unsaturated archaeols) into 2,3-diphytanylglycerophospholipids (saturated archaeols). This enzyme can fully reduce the unsaturated isoprenoid side chains of membrane phospholipids and glycolipids and is also capable of reducing the omega-position isoprene of dolichol phosphate. It belongs to the geranylgeranyl reductase family, specifically the DGGGPL reductase subfamily. The enzyme is found in Haloferax volcanii, an archaeal species known for its extremophilic properties.
(2E,6E)-farnesyl diphosphate synthase (FPP_synthase)
Type: Family

This entry represents (2E,6E)-farnesyl diphosphate synthase, an enzyme that catalyzes the sequential condensations of isopentenyl pyrophosphate (IPP) with dimethylallyl diphosphate (DMAPP) to yield geranyl diphosphate (GPP) and with GPP to yield (2E,6E)-farnesyl diphosphate (E,E-FPP). The enzyme contains two aspartate-rich DDxxD motifs, designated as FARM (the first aspartate-rich motif) and SARM (the second aspartate-rich motif). It belongs to the FPP/GGPP synthase family. This enzyme plays a crucial role in the biosynthesis of isoprenoids, which are essential components of various biological processes.
UDP-glucose 6-dehydrogenase AglM (UDPGDh_AglM)
Type: Family

UDP-glucose 6-dehydrogenase AglM is an enzyme involved in the assembly of a N-linked pentasaccharide that decorates the S-layer glycoprotein and flagellins in Haloferax volcanii. It plays a crucial role in the biosynthesis of the hexuronic acids found at both positions 2 and 3 of the pentasaccharide. The activity of this enzyme improves as salinity decreases. AglM belongs to the UDP-glucose/GDP-mannose dehydrogenase family.
Dolichyl-phosphate hexose transferase (DPhHxTase)
Type: Family

Dolichyl-phosphate hexose transferase is a glycosyltransferase that belongs to the glycosyltransferase 2 family. This enzyme is responsible for adding a monosaccharide to dolichol phosphate, thereby generating one of the three monosaccharide-modified dolichol phosphates. The specific subunit onto which additional sugars are added is not known. This protein is found in Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2), where it is encoded by the gene HVO_1613.
Olefin beta-lactone synthetase (OlefBLtnSyn)
Type: Family

Olefin beta-lactone synthetase is an enzyme involved in the biosynthesis of olefins. It catalyzes the conversion of beta-hydroxy acid substrates to beta-lactones in the presence of ATP. This enzyme can use various stereoisomers of 2-hexyl-3-hydroxydecanoic acid and 2-alkyl-3-hydroxyalkanoic acids as substrates. The enzyme is part of the ATP-dependent AMP-binding enzyme family and has been studied in organisms such as Stenotrophomonas maltophilia (strain K279a) and Xanthomonas campestris pv. campestris (strain ATCC 33913).
N-acyl homoserine lactonase AttM (AHLLactAttM)
Type: Family

N-acyl homoserine lactonase AttM is an enzyme that belongs to the metallo-beta-lactamase superfamily. This enzyme is involved in the hydrolysis of N-acyl homoserine lactones (AHLs), which are signaling molecules used in quorum sensing by various bacteria. The enzyme is characterized by its ability to disrupt quorum sensing, thereby affecting bacterial communication and potentially influencing pathogenicity. The AttM enzyme has been identified in several bacterial species, including Agrobacterium fabrum, Rhizobium johnstonii, Azorhizobium caulinodans, and Rhizobium radiobacter. The enzyme's activity is dependent on the presence of metal ions, which are essential for its catalytic function.
ATP-dependent DNA ligase LigA (LigA_Halo)
Type: Family

This entry represents ATP-dependent DNA ligases, specifically the LigA type found in various halophilic archaea. DNA ligases are essential enzymes that seal nicks in double-stranded DNA during DNA replication, recombination, and repair. These enzymes utilize ATP to catalyze the formation of a phosphodiester bond between adjacent nucleotides, ensuring the integrity and continuity of the DNA molecule. Members of this family are crucial for maintaining genomic stability and are found across different species of halophilic archaea, including Haloquadratum walsbyi, Natronomonas pharaonis, Halorubrum lacusprofundi, Halobacterium salinarum, Haloferax volcanii, and Haloarcula marismortui. These proteins belong to the ATP-dependent DNA ligase family, characterized by their ability to use ATP as a cofactor in the ligation process.
D-2-hydroxyacid dehydrogenase (Dhydh_Halo)
Type: Family

This entry represents D-2-hydroxyacid dehydrogenase, an enzyme that catalyzes the stereospecific NAD(P)H-dependent reduction of 2-ketocarboxylic acids into the corresponding D-2-hydroxycarboxylic acids. The enzyme can utilize both NADPH and NADH as reductants, with a marked preference for NADPH. It exhibits broad substrate specificity, favoring 2-ketocarboxylic acids with unbranched chains of 4-5 carbon atoms. This enzyme belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family and is found in Haloferax mediterranei.
Lateral flagellin LafA (lat_flg_LafA)
Type: Family

Lateral flagellin LafA is a protein found in Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633). It is the subunit protein that polymerizes to form the filaments of bacterial flagella, which are essential for lateral flagellar synthesis and swarming motility. This protein belongs to the bacterial flagellin family.
Methenyltetrahydrofolate cyclohydrolase (MthfCyhylase)
Type: Family

Methenyltetrahydrofolate cyclohydrolase (MTHF cyclohydrolase) is an enzyme that plays a crucial role in the metabolism of one-carbon (C1) and two-carbon (C2) units. This enzyme is part of the cyclodeaminase/cyclohydrolase family and is required for the interconversion of 5,10-methenyltetrahydrofolate to 10-formyltetrahydrofolate. The enzyme is essential for the folate-mediated one-carbon metabolic pathway, which is vital for nucleotide biosynthesis and amino acid metabolism. The protein is found in various organisms, including Methylorubrum extorquens, where it is encoded by the fchA gene. The enzyme's activity is crucial for the proper functioning of cellular metabolism, particularly in processes involving the transfer of one-carbon units.
Assimilatory nitrate reductase NasA (Nitr_red_NasA)
Type: Family

Assimilatory nitrate reductase NasA is a key enzyme involved in the first step of nitrate assimilation. It catalyzes the reduction of nitrate to nitrite, using ferredoxin as the electron donor. This enzyme can also use reduced methyl viologen but neither NADPH nor NADH as electron donors. The activity of NasA is inhibited by cyanide and azide. This protein belongs to the prokaryotic molybdopterin-containing oxidoreductase family, specifically the NasA/NapA/NarB subfamily. The enzyme is found in Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4).
PGN N-acetylglucosamine deacetylase (PGN_GlcNAc_Dac)
Type: Family

Peptidoglycan-N-acetylglucosamine deacetylase (PGN GlcNAc deacetylase) is an enzyme that catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan. This activity is crucial for modifying the peptidoglycan layer of bacterial cell walls, which can affect bacterial resistance to lysozyme and other environmental stresses. The enzyme is known to act on cell wall peptidoglycan from both Gram-positive bacteria, such as Bacillus cereus and Bacillus subtilis, and Gram-negative bacteria, such as Helicobacter pylori. It also acts on soluble chitin substrates and N-acetylchitooligomers but is not active on acetylated xylan. The deacetylase activity is regulated by hydroxylation on Pro-179 and is inhibited by CuCl(2), ZnCl(2), and the hydroxamate N-hydroxy-4-(naphthalene-1-yl)benzamide (NHNB). This enzyme belongs to the polysaccharide deacetylase family.
Lycopene beta cyclase (LycopCyc)
Type: Family

Lycopene beta cyclase (LycopCyc) is an enzyme that catalyzes the double cyclization reaction converting lycopene to beta-carotene. This enzyme also converts neurosporene to the monocyclic beta-zeacarotene but does not cyclize zeta-carotene. It belongs to the lycopene cyclase family and is regulated by the bleaching herbicide 2-(4-methylphenoxy)triethylamine hydrochloride (MPTA). The enzyme is found in Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805).
N-acetylglucosamine deacetylase (GlcNAc_deacetylase)
Type: Family

Peptidoglycan-N-acetylglucosamine deacetylase (PgdA) is an enzyme found in Streptococcus pneumoniae (strain ATCC BAA-255 / R6) that catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan. This modification confers resistance to host lysozyme and contributes to pneumococcal virulence. The enzymatic activity of PgdA is inhibited by EDTA in vitro. This enzyme plays a crucial role in the bacterial cell wall integrity and pathogenicity.
Enoyl-CoA hydratase DpgD (EnCoAhydt_DpgD)
Type: Family

Enoyl-CoA hydratase DpgD is a member of the enoyl-CoA hydratase/isomerase family, found in Amycolatopsis orientalis. This enzyme is involved in the biosynthesis of the nonproteinogenic amino acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg), which is crucial for the production of the antibiotics vancomycin and teicoplanin. DpgD catalyzes the syn-addition of a water molecule across the double bond of a trans-2-enoyl-CoA thioester, resulting in the formation of a beta-hydroxyacyl-CoA thioester. It may also act as a dehydratase, facilitating the aromatization of the DPA-S-DgpA or DPA-S-CoA intermediate. Additionally, DpgD can utilize non-physiological substrates such as crotonyl-CoA and beta-methylcrotonyl-CoA.
Acidic tetraheme cytochrome c3 TmcA (c3_cytochr_TmcA)
Type: Family

Acidic tetraheme cytochrome c3 TmcA is a protein found in Desulfocurvibacter africanus. This protein is involved in electron transfer processes, specifically exchanging electrons with the basic cytochrome c3. The protein is characterized by the presence of four heme groups, which are essential for its function in electron transport.
Sulfate respiration complex protein HmcC (sulf_resp_HmcC)
Type: Family

This entry represents the sulfate respiration complex protein HmcC, also known as high-molecular-weight cytochrome c (HmcC). HmcC is part of a transmembrane protein complex that facilitates electron flow from the periplasmic hydrogenase to cytoplasmic enzymes involved in sulfate reduction. The protein is encoded by the DVU_0534 gene in Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough). HmcC belongs to the NrfD family and plays a crucial role in the electron transport chain associated with sulfate respiration.
2-isopropylmalate synthase LeuA2 (IPMS_Lepto)
Type: Family

This entry represents 2-isopropylmalate synthase 2 (LeuA2) from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601). The enzyme catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-ketoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate). It exhibits high alpha-isopropylmalate synthase activity and low citramalate synthase activity. This protein belongs to the alpha-IPM synthase/homocitrate synthase family, specifically the LeuA type 1 subfamily.
1-phosphofructokinase (pfkB_Halo)
Type: Family

1-phosphofructokinase (pfkB) from Haloferax volcanii catalyzes the ATP-dependent phosphorylation of fructose-1-phosphate to fructose-1,6-bisphosphate. This enzyme plays a crucial role in the utilization of fructose as a sole carbon and energy source. It belongs to the carbohydrate kinase PfkB family, which is characterized by its involvement in carbohydrate metabolism. The enzyme's function is essential for the metabolic pathways that convert fructose into usable energy forms within the cell.
Sulfate respiration complex protein HmcE (sulf_resp_HmcE)
Type: Family

The sulfate respiration complex protein HmcE is part of a high-molecular-weight cytochrome c (HMWC) complex. This complex, which includes ORF2, ORF3, ORF4, ORF5, and ORF6 in the HMC operon, forms a transmembrane protein assembly that facilitates electron flow from the periplasmic hydrogenase to the cytoplasmic enzymes responsible for sulfate reduction. This process is crucial for the energy metabolism of Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough). The HmcE protein plays a significant role in the electron transfer chain, contributing to the reduction of sulfates in the cytoplasm.
Non-specific acid phosphatase (Acid_Phosphatase_PhoC)
Type: Family

This entry represents non-specific acid phosphatases, including major phosphate-irrepressible acid phosphatases from various bacterial species such as Providencia stuartii and Morganella morganii. These enzymes belong to the class A bacterial acid phosphatase family. Acid phosphatases catalyse the hydrolysis of phosphate esters, releasing inorganic phosphate. They play a role in phosphate metabolism and are typically active at acidic pH. The proteins in this entry are characterized by their ability to function independently of phosphate repression, which is a regulatory mechanism in some bacteria.