SII-SWORD/CoKE huggingface dataset:
KEOPS complex subunit CTAG/PCC1 (KEOPS_CTAG/PCC1)
Type: Family

This family of proteins is involved in the post-transcriptional modification of transfer RNAs (tRNAs). Specifically, they play a crucial role in the biosynthesis of the threonylcarbamoyladenosine (t(6)A) modification at position 37 adjacent to the anticodon in tRNAs that read codons starting with adenine. This modification is essential for the proper decoding of mRNA and the fidelity of protein synthesis. Members of this family are part of the KEOPS complex and contribute to the enzymatic activity that transfers the threonylcarbamoyl group from threonylcarbamoyl-AMP to the N6 group of adenosine at position 37 in tRNA. Additionally, these proteins can function as a dimerization module within the complex, facilitating the assembly and stability of the KEOPS complex.
Staphylopine dehydrogenase (Staphylopine_dehydrogenase)
Type: Family

This family of proteins includes enzymes that catalyze the NADPH-dependent reductive condensation of pyruvate with an intermediate to produce a compound known as staphylopine. Staphylopine is a metallophore involved in the transport and acquisition of essential metals such as nickel, cobalt, zinc, copper, and iron, which are critical for bacterial growth, especially within a host organism where metal availability is restricted. The synthesis of staphylopine by these enzymes is a key step in metal homeostasis and is likely to play a role in the virulence of bacteria that produce it. These enzymes are highly specific, as they do not utilize NADH or alpha-ketoglutarate as substitutes for NADPH and pyruvate, respectively.
Alpha-glucan branching enzyme (Alpha-glucan_branching_enzyme)
Type: Family

This family of proteins is involved in the modification of alpha-glucans, specifically in the creation of branch points within these molecules. The enzyme action involves cleaving alpha-1,4 glycosidic bonds and transferring the resulting oligosaccharides to an alpha-1,6 position, thus generating branched polysaccharides. The branching enzyme produces a variety of branch chain lengths, predominantly with degree of polymerization ranging from 5 to 30, with notable frequencies at lengths of 6 and 11. The catalytic mechanism of these proteins is of the alpha-retaining type. The family is characterized by a lack of activity towards alpha-galactosidase or pullulanase substrates, such as melibiose and pullulan, and does not process maltoheptaose, indicating an absence of alpha-amylase and 4-alpha-glucanotransferase activities. Members of this family typically contain a glycosyl hydrolase 57 domain and may have additional structural motifs, such as helix-hairpin-helix motifs, which are not essential for enzymatic function or thermal stability.
NiFe/NiFeSe hydrogenase small subunit (NiFe/NiFeSe_hyd_small_subunit)
Type: Family

This family of proteins includes small subunits of [NiFe] and [NiFeSe] hydrogenases, which are enzymes that catalyze the reversible oxidation of hydrogen gas. These hydrogenases play a crucial role in microbial energy metabolism by participating in the oxidative part of the fermentation process or in anaerobic respiration. The small subunit of these enzymes is typically involved in the maturation and stabilization of the active site, which contains nickel and iron or selenium atoms. The presence of selenium in some hydrogenases is thought to confer certain catalytic advantages, such as an increased tolerance to oxygen. Members of this family are found in a variety of microorganisms, including bacteria and archaea, and are integral to hydrogen cycling in a range of ecological niches.
tRNA (adenine(9)-N1)-methyltransferase (TRM10_methyltransferase)
Type: Family

This family of proteins includes enzymes that perform methylation, a type of chemical modification, on transfer RNA (tRNA) molecules. Specifically, they catalyze the addition of a methyl group to the nitrogen atom at position 1 of adenine at the ninth position (m1A9) in tRNA. This reaction is dependent on S-adenosyl-L-methionine (SAM) as the methyl donor. The methylation of tRNA is a critical process for the proper functioning of tRNA molecules during protein synthesis. Members of this family share a common structure characteristic of class IV-like SAM-binding methyltransferases.
Cytochrome c oxidase subunit 2-like (Cytochrome_c_oxidase_su2-like)
Type: Family

This family of proteins includes components of the respiratory chain that are involved in the terminal stage of aerobic respiration. They play a crucial role in energy production by catalyzing the reduction of oxygen to water. The proteins within this family are responsible for transferring electrons from a specific quinol to the catalytic core of the enzyme complex, which is composed of several subunits. The core subunits are essential for the enzyme's function, with one of them containing a bimetallic center crucial for the catalytic process. This center is formed by a heme group and a copper ion, which together facilitate the final electron transfer and subsequent reduction of oxygen.
NADPH-dependent hydrogen-evolving hydrogenase (NADPH-dep_hydrogenase)
Type: Family

This family of proteins includes subunits that are part of a bifunctional enzyme complex with NADPH-dependent hydrogen-evolving hydrogenase activity, coupled with sulfur reduction. These proteins are involved in hydrogen cycling during fermentative growth, catalyzing the reduction of protons to produce hydrogen gas. The complex typically does not exhibit activity with NAD, indicating specificity for NADPH as a cofactor. The family members are characterized by their role in energy metabolism, particularly under anaerobic conditions where alternative electron acceptors are utilized.
Hydrogenase large subunit (Hydrogenase_lg_subunit)
Type: Family

This family of proteins includes components of a bifunctional enzyme complex that is involved in hydrogen and sulfur metabolism. Members of this family are capable of catalyzing the reduction of protons to produce hydrogen gas, a process that is coupled with the reduction of sulfur compounds. These proteins are known to function during fermentative growth and can utilize both NAD and NADPH as electron donors for their enzymatic activity. The complex typically consists of multiple subunits, with the alpha and delta subunits forming the core hydrogenase component responsible for the hydrogen evolution reaction.
UDP-sugar dehydrogenase (UDP-sugar_DH)
Type: Family

This family of proteins includes enzymes that are responsible for the oxidation of specific nucleotide sugars, converting them into their respective uronic acid derivatives. The reaction involves the reduction of NAD(+) and is a key step in the biosynthesis of polysaccharides. Members of this family are characterized by a three-domain architecture, which includes a nucleotide binding domain, a helical domain that mediates dimerization, and a substrate binding domain that accommodates the sugar nucleotide substrate.
Heme-copper respiratory oxidase subunit 1 (Heme-copper_oxidase_sub1)
Type: Family

This family of proteins includes members that are integral components of the enzyme complex responsible for the terminal step of aerobic respiration. They are involved in the transfer of electrons from quinol to a binuclear center consisting of heme A3 and Cu(B), which is crucial for the catalytic reduction of oxygen to water. These proteins bind heme groups and play a pivotal role in the energy conversion process by maintaining the proton gradient across the biological membrane, thus contributing to ATP synthesis. Members of this family are characterized by their similarity to the heme-copper respiratory oxidase family.
NADPH-dependent Sulfhydrogenase Complex Subunit (NADPH_Sulfhydrogenase_Subunit)
Type: Family

This family of proteins includes components of a bifunctional enzyme complex that is involved in hydrogen and sulfur metabolism. Members of this family are involved in the cytoplasmic production of hydrogen sulfide in the presence of elemental sulfur and function as NADPH-dependent hydrogen-evolving hydrogenases. They are also known to have sulfur reducing activity. These proteins are not active with NAD or various sulfur oxyanions like sulfate, sulfite, thiosulfate, or with cysteine. The activity of these proteins is regulated by rubredoxin under certain pH conditions and is not stimulated by ferredoxin. They may have a role in hydrogen cycling during fermentative growth.
tRNA Cytosine-C(5)-Methyltransferase (tRNA_Cytosine-C(5)-MTase)
Type: Family

This family of proteins includes enzymes that catalyze the AdoMet-dependent methylation of cytosine in RNA molecules. They are responsible for the specific modification of cytosine at position 49 in tRNA, resulting in the formation of 5-methylcytosine (m5C49). The activity of these enzymes is modulated by the presence of the protein archease, which enhances substrate specificity and reduces aggregation. In the absence of archease, these enzymes exhibit broader substrate specificity, leading to methylation at various positions within tRNA and rRNA. Members of this family belong to the class I-like SAM-binding methyltransferase superfamily and are related to the RsmB/NOP family.
IucA/IucC-like synthase (IucA/IucC-like_synthase)
Type: Family

This family of proteins is involved in the biosynthesis of siderophores, specifically staphyloferrin B, which is a compound that bacteria use to sequester iron from the environment. Members of this family catalyze a key step in the biosynthetic pathway, which is the condensation of L-2,3-diaminopropionic acid with citryl-diaminoethane. This enzymatic activity is crucial for the survival of bacteria in iron-depleted environments, as it contributes to their ability to acquire essential nutrients and proliferate.
Glycosyl Hydrolase 121 (GH121)
Type: Family

This family of proteins includes enzymes with beta-L-arabinobiosidase activity, which are involved in the hydrolysis of L-arabinofuranose-beta-1,2-L-arabinofuranose disaccharides from various substrates. These enzymes exhibit specificity for certain arabinofuranose-containing disaccharides, particularly those unmodified and linked to hydroxyproline, but do not act on other arabinofuranose configurations. Additionally, they can demonstrate transglycosylation activity in the presence of 1-alkanols, transferring arabinofuranose residues while retaining their anomeric configuration.
Serine/threonine-protein acetyltransferase (Ser/Thr_acetyltransferase)
Type: Family

This family of proteins includes serine/threonine-protein acetyltransferases that are known to be translocated into host cells during infection. They are responsible for the acetylation of serine and threonine residues on host proteins. This modification can alter the function of the host proteins and is associated with the induction of a hypersensitive response in certain plant hosts that carry specific resistance genes. Members of this family are characterized by their enzymatic activity and their role in plant-pathogen interactions.
Actinobacterial Glucosamine Kinase (Actino_Glucosamine_Kinase)
Type: Family

This family of proteins includes enzymes that are responsible for the ATP-dependent phosphorylation of D-glucosamine (GlcN) to D-glucosamine 6-phosphate. These enzymes play a role in the metabolism of GlcNAc by incorporating exogenous GlcN into the bacterial GlcNAc metabolic pathways. They are characterized by their inability to phosphorylate maltose, indicating a specific substrate preference. Members of this family are typically found in actinobacteria and are involved in the utilization of GlcN derived from the degradation of chitosan, which is an important process for recycling and utilizing this amino sugar as a nutrient source.
Metallo-dependent Hydrolases FwdA/FmdA (Metallo-hydrolase_FwdA/FmdA)
Type: Family

This family of proteins includes metallo-dependent hydrolases that are characterized by their requirement for metal ions to catalyze the hydrolysis of various substrates. Members of this family, such as FwdA, are involved in fundamental biochemical processes and can have diverse substrate specificities, which may include nucleic acids, proteins, or small molecules. The metal ion acts as a cofactor, stabilizing the structure of the enzyme or participating directly in the catalytic mechanism. The precise functions of these enzymes can vary widely among different organisms and specific family members, but they generally play crucial roles in metabolism, regulation, and cellular signaling.
Damage-control nucleotide phosphatase I (DCN_phosphatase_I)
Type: Family

This family of proteins includes metal-dependent phosphatases that are thought to play a role in damage control by hydrolyzing phosphates from various substrates. Although their natural substrates remain unidentified, they exhibit activity against artificial substrates such as p-nitrophenyl phosphate. These enzymes are characterized by their ability to bind metal ions, which significantly enhances their phosphatase activity. They contain conserved motifs that are critical for their structure and function, including motifs that interact with a Fe-containing chromophore. The family is defined by specific conserved motifs, including a CxxC motif near the N-terminus, a GNFE motif close to the C-terminus, and a KC motif, which together form the substrate-binding cleft and are essential for activity.
Archaeal lipid biosynthesis protein FwdD (Archaeal_lipid_biosynth_FwdD)
Type: Family

This family of proteins includes FwdD, which is involved in the biosynthesis of archaeal membrane lipids. Members of this family are likely to participate in the formation of cyclic 2,3-diphosphoglycerate (cDPG) from 3-phosphoglycerate, a key intermediate in the biosynthetic pathway. The activity of these proteins is essential for the unique ether-linked membrane lipids characteristic of archaea, which contribute to their stability and functionality under extreme conditions. The proteins may possess enzymatic functions that are critical for the survival and adaptation of archaeal species in diverse and often harsh environments.
Hydrogenase Small Subunit-like (Hydrogenase_Small_Subunit-like)
Type: Family

This family of proteins includes subunits of a bifunctional enzyme complex that is involved in hydrogen and sulfur metabolism. Members of this family are involved in the catalytic process that reduces protons to produce hydrogen gas, a reaction that is part of fermentative growth in certain microorganisms. These proteins also exhibit sulfur-reducing activity, which may contribute to the sulfur cycle in their respective ecosystems. The enzyme complex typically requires cofactors such as NAD or NADPH for its activity. The family is characterized by the presence of a small subunit that is homologous to those found in [NiFe] and [NiFeSe] hydrogenases, indicating a conserved mechanism of action within this group.
Sulfhydrogenase gamma subunit-like (Sulfhydrogenase_gamma-like)
Type: Family

This family of proteins includes components of a bifunctional enzyme complex known for its role in hydrogen and sulfur metabolism. Members of this family are involved in the catalysis of hydrogen sulfide production in the cytoplasm, utilizing elemental sulfur as a substrate. They are also associated with hydrogen-evolving hydrogenase activity, contributing to hydrogen cycling under fermentative conditions. These proteins are capable of interacting with both NAD and NADPH during their enzymatic processes.
YsgD-like (YsgD-like)
Type: Family

This family of proteins is involved in various cellular processes. The specific functions of the family members may include enzymatic activity, structural roles, regulatory functions, or involvement in signaling pathways. Each protein within the family may have a distinct function or set of functions, which can be influenced by its structure, post-translational modifications, and interactions with other proteins or cellular components. The precise role of the family in cellular physiology can be diverse, ranging from metabolism to cell communication, and may be essential for maintaining cellular homeostasis and responding to environmental changes.
HdrA heterodisulfide reductase subunit (HdrA_heterodisulfide_rdct)
Type: Family

This family of proteins is involved in the energy metabolism process specific to certain archaea, particularly in the context of methanogenesis. Members of this family are components of a larger enzymatic complex that facilitates the reversible reduction of a heterodisulfide formed between coenzyme M (CoM-SH) and coenzyme B (CoB-SH) into their respective thiol forms. This reaction is a key step in the pathway that leads to methane production in methanogenic archaea. The proteins in this family are implicated in the methylotrophic pathway of methanogenesis, where methane is produced from methylated compounds, rather than the aceticlastic pathway, where methane is produced from acetate. The enzymatic activity of these proteins is crucial for the energy conservation and metabolic processes of methanogenic organisms.
Zinc metalloprotease TldD-like (Zinc_metalloprotease_TldD)
Type: Family

This family of proteins includes zinc metalloproteases that are capable of degrading various protein substrates such as azocasein in vitro. Members of this family are characterized by a conserved motif that is likely to constitute the active site necessary for their metalloprotease activity. These enzymes play a role in the proteolytic processing of other proteins, which is essential for various biological processes. The conserved motif typically includes a sequence of amino acids that coordinates the zinc ion required for the protease's catalytic function.
23S rRNA methylase regulatory peptide (23S_rRNA_methylase_reg)
Type: Family

This family of proteins includes peptides that regulate the synthesis of resistance proteins against erythromycin by a control mechanism. These peptides are typically found upstream of the erythromycin resistance protein gene and are involved in the response to the presence of the antibiotic, thereby contributing to the resistance phenotype in certain bacteria.
Sulfhydrogenase Complex Subunit Beta (Sulfhydrogenase_beta)
Type: Family

This family of proteins includes components of a bifunctional enzyme complex known for its role in hydrogen and sulfur metabolism. Members of this family are involved in the evolution of hydrogen gas and the reduction of sulfur. They exhibit activity with both NAD and NADPH and are implicated in the production of hydrogen sulfide in the cytoplasm when elemental sulfur is present. These proteins may be important for energy conservation in certain microbial fermentation processes.
CheY-P phosphatase CheC (CheY-P_phosphatase_CheC)
Type: Family

This family of proteins is involved in the regulation of chemotaxis by modulating the levels of phosphorylated CheY (CheY-P), which is a response regulator involved in flagellar motor control. Members of this family act as phosphatases, catalyzing the dephosphorylation of CheY-P to CheY, thereby reversing the signal transduction process and restoring normal CheY-P levels. Additionally, these proteins can interact with and inhibit CheD, a chemotaxis protein that modifies the chemoreceptor. They achieve this by mimicking a substrate recognition site of CheD, effectively acting as competitive inhibitors.
HdrC heterodisulfide reductase subunit C (HdrC_heterodisulfide_reductase)
Type: Family

This family of proteins is involved in the energy metabolism process specific to methanogenic archaea. They play a crucial role in the final step of methane biosynthesis, where they participate in the reduction of heterodisulfide bonds between coenzyme M (CoM-SH) and coenzyme B (CoB-SH). This reaction is essential for regenerating the reduced forms of these coenzymes, which are necessary for the methanogenic pathway. Members of this family are typically associated with the enzyme complex responsible for this reversible reaction, contributing to the energy conservation system in methanogens by coupling the reduction with the generation of a proton gradient used for ATP synthesis.
Riboflavin Transporter RibV (Riboflavin_Transporter_RibV)
Type: Family

This family of proteins is involved in the cellular uptake of riboflavin, which is a vital nutrient also known as vitamin B2. Riboflavin is essential for numerous cellular processes as it is a precursor for the synthesis of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), both of which are key cofactors in redox reactions. Members of this protein family are likely to function as transporters that facilitate the movement of riboflavin across cell membranes, ensuring its availability for metabolic processes within the cell.
tRNA Cytidine-2'-O-Methyltransferase (tRNA_Cytidine-2'-O-MTase)
Type: Family

This family of proteins includes enzymes that are responsible for the methylation of cytidine residues in tRNA molecules. Specifically, they catalyze the 2'O-methylation of cytidine at the 32nd position, resulting in the formation of 2'O-methylcytidine. This modification is crucial for the proper functioning of tRNA. The enzymes exhibit specificity for cytidine and are part of a larger superfamily of SAM-binding methyltransferases. They are related to the RNA methyltransferase TrmH family, which shares similar structural motifs and catalytic functions.
Polysaccharide Lyase 2 (PL_2)
Type: Family

This family of proteins includes enzymes that act on pectic substances by cleaving the glycosidic linkages between galacturonate residues. Members of this family are involved in the degradation of pectate, a component of the plant cell wall, by catalyzing the cleavage of polygalacturonate and oligogalacturonates to produce unsaturated digalacturonates. These enzymes play a role in various biological processes, including the breakdown of plant materials by microorganisms and possibly in plant metabolism and defense mechanisms.
Bifunctional sugar-1-phosphate nucleotidylyltransferase/acetyltransferase (Sugar-1P_NT/AT)
Type: Family

This family of proteins includes bifunctional enzymes that are involved in the synthesis of nucleotide sugars, which are essential for glycosylation processes. Members of this family exhibit multiple enzymatic activities, including acetyltransferase and nucleotidylyltransferase functions. They are capable of transferring an acetyl group to amino sugars such as glucosamine-1-phosphate and galactosamine-1-phosphate, as well as catalyzing the transfer of nucleotidyl groups to form nucleotide sugars like UDP-N-acetylglucosamine and UDP-N-acetylgalactosamine. Additionally, these enzymes can interconvert nucleotide sugars and their corresponding diphosphates, playing a crucial role in carbohydrate metabolism and the biosynthesis of glycoconjugates.
Structure-specific DNA repair endonuclease (DNA_repair_endonuclease)
Type: Family

This family of proteins includes structure-specific endonucleases that recognize and cleave various DNA structures during DNA repair processes. They exhibit a preference for cleaving at the 5' end of ds/ssDNA interfaces within 3' flap structures but also target bubble and Y-DNA structures, as well as both mobile and immobile Holliday junctions. Their activity is characterized by a preference for cutting after pyrimidine bases and the potential for progressive cleavage upstream of the initial site. These proteins play a role in nucleotide excision repair and their nuclease function is dependent on interaction with the PCNA heterotrimer. However, their activity can be inhibited by single-stranded DNA-binding proteins, even in the presence of PCNA.
Phr signaling regulator (Phr_regulator)
Type: Family

This family of proteins includes signaling molecules that play a crucial role in the regulation of genetic competence development in bacteria. They are secreted and subsequently need to be imported back into the cell to exert their function. Once inside, they act by inhibiting specific regulatory proteins, which in turn modulate the activity of transcription factors involved in genetic competence. Through this inhibition, they stimulate the expression of genes that are under the control of these transcription factors.