SII-SWORD/CoKE huggingface dataset:
Phenolic Acid Decarboxylase UbiD-like (PAD_UbiD-like)
Type: Family

This family of proteins is involved in the non-oxidative decarboxylation and detoxification of phenolic derivatives. Members of this family function under both aerobic and anaerobic conditions, catalyzing the reversible decarboxylation of compounds such as 4-hydroxybenzoate and vanillate. Some members may also decarboxylate salicylate and 3,4-dihydroxybenzoate. The activity of these enzymes can be modulated by various ions and is sensitive to oxygen levels in some cases. They play a role in the microbial metabolism of phenolic compounds, which can be toxic to cells at high concentrations.
Archaeosine Synthase Type 1 (Archaeosine_synthase_1)
Type: Family

This family of proteins is involved in the biosynthesis of archaeosine, a unique modified nucleoside found in the dihydrouridine loop of archaeal tRNAs. Members of this family catalyze the transformation of 7-cyano-7-deazaguanine (preQ0)-modified tRNA into different intermediates leading to archaeosine-tRNA. This modification involves either the addition of L-lysine to form a q0N lysine adduct or the conversion of a nitrile group to a formamidine group. The enzymes can utilize various amino donors such as glutamine, asparagine, or ammonium for the conversion process, highlighting their functional versatility within the biosynthetic pathway of archaeosine.
Mycobacterial FAS-II 3-oxoacyl-ACP reductase (FAS-II_3-oxoacyl-ACP_reductase)
Type: Family

This family of proteins is involved in the fatty acid elongation system FAS-II, which is crucial for mycolic acid biosynthesis in mycobacteria. Members of this family function as enzymes catalyzing the NADPH-dependent reduction of beta-ketoacyl derivatives, a key step in the FAS-II cycle. These proteins show a preference for long-chain substrates and can also utilize CoA derivatives in vitro. The activity of these enzymes is regulated by phosphorylation, which impacts mycolic acid production. Additionally, some members are inhibited by isoniazid, a drug used to treat tuberculosis, through the formation of an isonicotinoyl-NADP adduct that binds to the active site. Structural dynamics play a role in their function, with conformational changes upon NADPH binding facilitating the transition between inactive and active states and product release.
2-Methylcitrate Dehydratase (2-Methylcitrate_Dehydratase)
Type: Family

This family of proteins is involved in the catabolism of short chain fatty acids through both the tricarboxylic acid cycle and the 2-methylcitrate cycle. Members of this family catalyze the dehydration of 2-methylcitrate to produce the cis isomer of 2-methyl-aconitate. Additionally, these enzymes may also facilitate the dehydration of citrate and the hydration of cis-aconitate.
Esterase and Immunogenic RsiV-related (Esterase_Immunogenic_RsiV)
Type: Family

This family of proteins includes esterases and immunogenic proteins. The esterases in this family are capable of hydrolyzing ester substrates with varying carbon chain lengths, showing high efficiency with short to medium-chain lengths. They exhibit enzymatic activity against acetate, butyrate, and caprylate, with decreasing activity towards longer fatty acids such as laurate, myristate, and caproate, and weak activity against palmitate. Additionally, members of this family are recognized for their immunogenic properties, although specific functions related to immune response are not detailed in the provided annotations.
RHS domain-containing protein (RHS_domain)
Type: Family

This family of proteins includes Rhs elements, which are characterized by a conserved amino-terminal fragment of approximately 141 kDa, followed by a variable C-terminal region. The conserved N-terminal region suggests a shared structural framework or function among family members, while the divergent C-terminus indicates potential specialization for different roles or interactions. Although the exact functions of these proteins are not fully understood, they are considered nonessential but may have significant roles in the cell's natural ecology, possibly contributing to intercellular interactions or environmental adaptability.
Type-4 uracil-DNA glycosylase (Type-4_UDG)
Type: Family

This family of proteins is involved in the repair of DNA by recognizing and excising uracil, which can appear in DNA due to cytosine deamination or misincorporation during DNA synthesis. Members of this family can process uracil in various DNA contexts, including double-stranded DNA with U/G or U/A pairings and single-stranded DNA. They are characterized by a pseudo-FCL region that binds to DNA and participates in catalysis, especially in duplex DNA. This region includes an alpha helix and loop structure, which is stabilized by a [4Fe-4S](2+) cluster. The activity of these enzymes is regulated by the presence of uracil and apurinic/apyrimidinic sites, which can act as inhibitors.
Alanyl-tRNA Editing Domain-Containing Protein (Alanyl-tRNA_Edit-Domain)
Type: Family

This family of proteins is involved in the quality control of protein synthesis. Members of this family function in trans to correct mischarged tRNA molecules, specifically by removing incorrect amino acids from tRNA(Ala). They ensure that tRNA(Ala) is not erroneously charged with serine or glycine, which is crucial for maintaining the fidelity of protein translation. These proteins belong to the class-II aminoacyl-tRNA synthetase family and possess an editing domain known as AlaX-M, which is responsible for their editing activity. The recognition of the mischarged tRNA(Ala) by these proteins may depend on the acceptor stem of the tRNA molecule.
Hydroxyproline Metabolism Enzyme (Hydroxyproline_Metab_Enz)
Type: Family

This family of proteins includes enzymes that are involved in the metabolism of hydroxyproline, a modified amino acid. Members of this family are primarily responsible for the dehydration of trans-3-hydroxy-L-proline (t3LHyp) to Delta(1)-pyrroline-2-carboxylate (Pyr2C), a reaction that is part of a degradation pathway leading to the production of L-proline. This allows organisms to utilize t3LHyp as a sole carbon source. Some members also exhibit epimerase activity, converting t3LHyp to its cis isomer, as well as trans-4-hydroxy-L-proline to its cis isomer, although with lower efficiency. The family is characterized by a lack of proline racemase activity, despite being related to the proline racemase family.
Divalent-cation tolerance CutA (CutA_tolerance)
Type: Family

This family of proteins is associated with the cellular response to divalent cations. Members of this family are implicated in the mechanism of resistance to heavy metals, suggesting a role in detoxification or maintaining metal ion homeostasis. The precise molecular function may involve interaction with metal ions, possibly sequestering them or participating in transport processes to mitigate the toxic effects of heavy metal accumulation.
Beta-galactosidase (Beta-galactosidase)
Type: Family

This family of proteins includes enzymes that catalyze the hydrolysis of beta-galactosides into monosaccharides. Members of this family are characterized by their ability to break down lactose and other beta-galactosides, which is a key step in the metabolism of carbohydrates. These enzymes are widely distributed in nature, being found in various organisms including bacteria, yeasts, plants, and animals. They play important roles in processes such as lactose digestion in mammals, plant cell wall degradation, and the catabolism of glycolipids and glycoproteins. The activity of these enzymes is essential for the utilization of galactose-containing sugars as an energy source and for the maintenance of cellular functions related to carbohydrate processing.
Molybdate/tungstate import ATP-binding (Molybdate/tungstate_ABC-ATPase)
Type: Family

This family of proteins is involved in the transport of molybdate and tungstate across the cell membrane. They are part of the ATP-binding cassette (ABC) transporter complex WtpABC, which is responsible for the uptake of these oxyanions. Members of this family are ATP-binding proteins that provide the necessary energy for the transport process by hydrolyzing ATP. They are essential for the proper function of the WtpABC complex, ensuring the availability of molybdate and tungstate for cellular processes.
Siroheme Decarboxylase (Siroheme_Decarboxylase)
Type: Family

This family of proteins is involved in the biosynthesis of heme b, an essential component of hemoproteins. Members of this family catalyze the decarboxylation of siroheme to produce didecarboxysiroheme, a precursor in the biosynthetic pathway. The enzymatic activity involves a two-step decarboxylation process where siroheme is first converted to monodecarboxysiroheme and subsequently to didecarboxysiroheme. Additionally, the activity of these enzymes is modulated by the redox state of bound heme b, with stimulation observed in the presence of reducing agents such as sodium dithionite.
Plant immune system effector (Plant_immune_effector)
Type: Family

This family of proteins includes effectors involved in the recognition of non-host organisms by the immune system. Members of this family are capable of eliciting a hypersensitive response, which is a rapid and localized cell death at the site of infection. This response is a defense mechanism used by plants to prevent the spread of infection by pathogens. The proteins within this family play a crucial role in the interaction between host plants and pathogenic bacteria, contributing to the plant's ability to recognize and respond to microbial invaders.
Siroheme decarboxylase beta subunit-like (AhbB-like)
Type: Family

This family of proteins is involved in the biosynthesis of haem b, a component of haemproteins. Members of this family function as sirohaem decarboxylases, catalysing the sequential decarboxylation of sirohaem to form didecarboxysirohaem. This reaction is a key step in the conversion of sirohaem to haem b . The activity of these enzymes is modulated by the redox state of bound haem b, with reduced haem b stimulating enzymatic activity. Additionally, sodium dithionite can enhance the activity of these proteins, indicating a regulatory mechanism sensitive to redox conditions.
Tetrahydromethanopterin:alpha-L-glutamate ligase (THMPT_Glu_ligase)
Type: Family

This family of proteins catalyzes the ATP or GTP-dependent ligation of L-glutamate to tetrahydromethanopterin, resulting in the formation of tetrahydrosarcinapterin. This enzymatic activity is crucial for the biosynthesis of coenzymes involved in methanogenesis, a form of anaerobic respiration used by certain microorganisms. Members of this family are characterized by their similarity to the RimK family, specifically within the MptN subfamily, indicating a shared evolutionary origin and functional characteristics.
Bifunctional IPC transferase/DIPP synthase (IPC_transferase/DIPP_synth)
Type: Family

This family of proteins is involved in the biosynthesis of di-myo-inositol phosphate (DIP), an organic solute found in microorganisms that inhabit hot environments. Members of this family exhibit bifunctional enzymatic activity, catalyzing two distinct steps in the DIP biosynthetic pathway. The first step involves the condensation of CTP and L-myo-inositol-1-phosphate to form CDP-L-myo-inositol. The second step is the synthesis of di-myo-inositol-1,3'-phosphate-1'-phosphate (DIPP) from CDP-L-myo-inositol and L-myo-inositol-1-phosphate. These enzymes are characterized by two domains: the N-terminal section, which is similar to the MobA family, and the C-terminal section, which belongs to the CDP-alcohol phosphatidyltransferase class-I family.
tRNA(Ile2) 2-agmatinylcytidine synthetase (TiaS)
Type: Family

This family of proteins includes ATP-dependent agmatine transferases that are responsible for the post-transcriptional modification of tRNA(Ile2). Specifically, these enzymes catalyze the formation of 2-agmatinylcytidine at the wobble position of the tRNA, which is crucial for accurate decoding during protein synthesis. The modification alters the codon specificity of tRNA(Ile2), enabling it to recognize the AUA codon in addition to the canonical AUG, thereby expanding the genetic code's capacity for protein translation.
Peptidase C56 Deglycase (Peptidase_C56_Deglycase)
Type: Family

This family of proteins functions as deglycases, catalyzing the deglycation of Maillard adducts formed between amino groups of proteins and reactive carbonyl groups of glyoxals. They repair proteins glycated by methylglyoxal and glyoxal, releasing lactate or glycolate and reactivating proteins by reversing glycation. These proteins deglycate cysteine, arginine, and lysine residues, acting on early glycation intermediates to prevent the formation of advanced glycation endproducts (AGE) that can cause irreversible damage. Additionally, these proteins exhibit proteolytic activity, cleaving at the carboxyl side of residues in the P1 position, showing both trypsin- and chymotrypsin-like specificities.
Magnetosome CDF Transporter (Magnetosome_CDF_Transporter)
Type: Family

This family of proteins is involved in the biogenesis of magnetosomes, which are intracellular organelles that allow magnetotactic bacteria to orient themselves along geomagnetic fields. Members of this family are essential for both the formation of magnetosome vesicles and the biomineralization process within these vesicles, likely by binding and transporting iron. They are characterized by a C-terminal domain that forms a V-shaped, dimeric metallo-chaperone-like fold, which is implicated in binding metal cations and is essential for the protein's dimerization. The proteins are part of the cation diffusion facilitator (CDF) transporter family and are believed to require heterodimerization with MamM for stability. Some members have been shown to be capable of inducing magnetosome membrane biogenesis when coexpressed with other magnetosome-related genes.
Long-chain-fatty-acid--AMP ligase FadD28 (LCFA-AMP_ligase_FadD28)
Type: Family

This family of proteins is involved in the biosynthesis of phthiocerol dimycocerosate (PDIM), a unique cell wall lipid characteristic of pathogenic mycobacteria. Members of this family function as enzymes that catalyze the activation of long-chain fatty acids into acyl-adenylates (acyl-AMP). These activated intermediates are subsequently transferred to a multifunctional polyketide synthase for further elongation. The activity of these proteins is essential for the production of PDIM, which plays a role in the pathogenicity of mycobacteria by contributing to the arrest of host phagosome maturation.
F420-non-reducing hydrogenase Vhu, subunit U (F420-Hydrogenase_large-U)
Type: Family

This family of proteins includes subunits of F420-non-reducing hydrogenase Vhu, subunit U and related archaeal proteins. These hydrogenases typically contain nickel and iron within their active sites and are involved in energy metabolism by coupling the oxidation of hydrogen with the reduction of various electron acceptors . Vhu consists of three subunits, vhuA, vhuG and vhuU . The vhuU subunit is very small (only 25 amino acids) and is post-translationally processed by cleavage of the C-terminal end. This very small hydrogenase subunit contains selenocysteine within a conserved amino-acid sequence which shown to be involved in Ni coordination.
Isobutyryl-CoA Mutase/GTPase Domain-Containing Protein (IcmF/GTPase_domain)
Type: Family

This family of proteins catalyzes the reversible interconversion of isobutyryl-CoA and n-butyryl-CoA, with some members also acting on pivalyl-CoA and isovaleryl-CoA, through radical chemistry. Members possess a GTPase domain, which functions as a chaperone aiding in cofactor delivery and holo-enzyme assembly. This domain also plays a role in cofactor repair by powering the ejection of inactive cofactor and facilitating its reactivation. The proteins are characterized by a 5'-deoxyadenosylcobalamin binding region, a P-loop GTPase domain, a structured linker region for dimerization, and a C-terminal substrate-binding domain. They do not exhibit methylmalonyl-CoA mutase activity or convert 3-hydroxybutyryl-CoA to 2-hydroxyisobutyryl-CoA. Some members have ATPase activity, while others do not.
Alginate biosynthesis AlgK (Alginate_biosynth_AlgK)
Type: Family

This family of proteins is implicated in the biosynthesis of alginate, a biopolymer that plays a crucial role in the formation of biofilms by certain bacteria. Members of this family are thought to contribute to the polymerization process of mannuronate, a key monomer in the production of alginate. Alginate is a significant component of the extracellular matrix in bacterial biofilms and is involved in various functions including protection against environmental stress and the immune system of hosts. The proteins in this family share a common evolutionary origin and are characterized by specific sequence features that define their role in alginate polymerization.
2Fe2S Plant-type Ferredoxin (2Fe2S_Ferredoxin)
Type: Family

This family of proteins includes iron-sulfur proteins known as ferredoxins. They play a crucial role in electron transfer across a variety of metabolic processes. These proteins contain a 2Fe2S cluster, which is essential for their function in redox reactions. The members of this family are involved in numerous biological functions, including but not limited to photosynthesis, nitrogen fixation, and the metabolism of sulfur and iron.
Beta-RFA-P synthase (Beta-RFA-P_synthase)
Type: Family

This family of proteins catalyzes the condensation of 4-hydroxybenzoate or 4-aminobenzoate with 5-phospho-alpha-D-ribose 1-diphosphate. The reaction produces beta-ribofuranosylphenol 5'-phosphate or beta-ribofuranosylaminobenzene 5'-phosphate, respectively. While 4-hydroxybenzoate is biosynthesized by methanogenic archaea, 4-aminobenzoate can also be utilized as a substrate when available in the growth medium. These enzymes play a role in the biosynthesis of cofactors and secondary metabolites that are essential for the survival and function of these archaeal organisms.
Conjugal Transfer TraC-like (Conjugal_Transfer_TraC)
Type: Family

This family of proteins is involved in bacterial conjugation, which is a process of horizontal gene transfer. The proteins facilitate the transfer of genetic material, such as plasmids, between bacterial cells. This is often mediated through the formation of a pilus that connects donor and recipient cells, allowing for the transfer of DNA. The TraC protein is typically associated with the transfer of Ti plasmids in Agrobacterium tumefaciens, which are responsible for the transfer of genes that can cause plant tumors. The presence of a TraC-like protein in other bacteria suggests a similar role in conjugative transfer.
Pyrroline-2-carboxylate reductase-like (Pyr2C_reductase-like)
Type: Family

This family of proteins includes enzymes that are primarily involved in the biosynthesis and degradation of L-proline. Members of this family are capable of catalyzing the reduction of Delta(1)-pyrroline-2-carboxylate (Pyr2C) to L-proline, which is an important process in proline metabolism. Some enzymes within this family can also reduce Delta(1)-piperideine-2-carboxylate (Pip2C) to L-pipecolate, and may participate in the metabolism of D-proline and D-lysine. The preferred electron donor for these reactions is NADPH, although NADH can also be used. Additionally, these enzymes may play a role in the degradation of trans-3-hydroxy-L-proline (t3LHyp), contributing to the ability of certain organisms to utilize t3LHyp as a sole carbon source. The family belongs to the broader ornithine cyclodeaminase/mu-crystallin superfamily but does not exhibit ornithine cyclodeaminase activity.
CBASS cyclic nucleotide synthase (CBASS_cN_synthase)
Type: Family

This family of proteins includes cyclic nucleotide synthases that are part of the CBASS (cyclic oligonucleotide-based antiphage signaling system), which provides immunity against bacteriophage infections in bacteria. These proteins synthesize cyclic nucleotides in response to phage infection, serving as second messenger signals that activate various effectors, leading to bacterial cell death and abortive phage infection. The family members are involved in the synthesis of specific cyclic oligonucleotides, such as 3',3',3'-cyclic AMP-AMP-AMP (cAAA) and 3',3'-c-di-AMP, although they cannot use GTP as a substrate. They are regulated by complex formation with other proteins and DNA, and mutations in these proteins can affect the immunity conferred against phage infection. The proteins also have a role in the disassembly complex, interacting with other proteins to regulate their activity.
3,5-Dihydroxyphenylacetyl-CoA Synthase (DPA-CoA_Synthase)
Type: Family

This family of proteins is involved in the biosynthesis of nonproteinogenic amino acids that are key components in the production of certain antibiotics. Specifically, these enzymes catalyze the Claisen condensation of malonyl-CoA molecules to form 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA), a precursor in the synthesis of (S)-3,5-dihydroxyphenylglycine (Dpg). Dpg is an important building block for antibiotics such as balhimycin, vancomycin, and teicoplanin. The enzymatic activity requires the cooperation with dehydratases for the aromatization process. Structurally, these proteins are part of the thiolase-like superfamily and are related to the chalcone and stilbene synthases.
Alpha-ketoglutarate-dependent hydroxylase (Alpha-KG_dependent_hydroxylase)
Type: Family

This family of proteins includes alpha-ketoglutarate-dependent hydroxylases involved in the biosynthesis of nonproteinogenic amino acids that are components of various antibiotics. Members of this family catalyze the hydroxylation of specific amino acids, such as L-enduracididine, L-arginine, and L-ornithine, introducing a hydroxyl group at the beta carbon position. These enzymatic reactions contribute to the production of modified amino acids like beta-hydroxyenduracididine, (3S)-hydroxy-L-arginine, and (3S)-hydroxy-L-ornithine, which are essential for the activity of peptide antibiotics including mannopeptimycin, viomycin, and capreomycin. The family is characterized by a broad substrate specificity and the ability to produce specific stereoisomers of hydroxylated amino acids.
Anthranilate Synthase Beta Subunit (AS_beta_subunit)
Type: Family

This family of proteins is involved in the biosynthesis of anthranilate, a precursor in the L-tryptophan biosynthetic pathway. They form a part of a heterotetrameric complex, functioning as the glutamine-binding beta subunit. This subunit exhibits glutamine amidotransferase activity, producing ammonia from glutamine. The ammonia then reacts with chorismate in a reaction catalyzed by the alpha subunit to generate anthranilate. In conditions where the beta subunit is absent, the alpha subunit can compensate by directly converting chorismate into anthranilate using an elevated concentration of ammonia.
Metallo-beta-lactamase-like hydrolase (MBL-like_hydrolase)
Type: Family

This family of proteins is potentially involved in bacterial cellular processes related to adherence or the development of biofilms. Members of this family are characterized by their similarity to the metallo-beta-lactamase superfamily, which suggests they may have a hydrolase activity that interacts with beta-lactam antibiotics. The exact biochemical function and mechanism of action within the cell adherence or biofilm formation context remain to be fully elucidated.