SII-SWORD/CoKE huggingface dataset:
Transcription activator-like effector protein (TALE)
Type: Family

This family of proteins functions as transcription factors in plant cells, where they bind to specific DNA sequences and activate gene expression. They contain a central DNA-binding region with tandem core repeats, each recognizing a single DNA base through a base-specifying residue. These proteins play a role in plant-pathogen interactions by inducing a hypersensitive response in resistant plants, leading to cell death and limiting pathogen spread. In susceptible plants, they can manipulate host gene expression to facilitate infection. The activation domain is crucial for their function in planta, and they possess nuclear localization signals for transport into the nucleus. They are characterized by their ability to act as avirulence factors, triggering plant defense mechanisms when recognized by specific plant resistance genes.
Phenazine biosynthesis oxidase (Phenazine_biosynth_oxidase)
Type: Family

This family of proteins is involved in the biosynthesis of phenazine, an antibiotic and nitrogen-containing heterocyclic compound that plays a significant role in virulence, competition, and biological control. Members of this family catalyze multiple oxidation reactions in the final stages of core phenazine biosynthesis. They are responsible for the oxidation of hexahydrophenazine-1,6-dicarboxylic acid and tetrahydrophenazine-1-carboxylic acid, leading to the production of phenazine-1,6-dicarboxylic acid and phenazine-1-carboxylic acid. These enzymes are also involved in synthesizing reduced forms of phenazines, which are likely the active end products in a biological context.
Phytoene synthase-related (Phytoene_synthase-rel)
Type: Family

This family of proteins is involved in the biosynthesis of carotenoids, a class of pigments that play various roles in photosynthesis and photoprotection in plants and microorganisms. Members of this family catalyze the first committed step in carotenoid biosynthesis, which is the head-to-head condensation of two molecules of geranylgeranyl diphosphate (GGPP) to form prephytoene diphosphate (PPPP). This is followed by a rearrangement to produce phytoene, the colorless precursor of various carotenoids. Some members are known to specifically synthesize the 15-cis-phytoene isomer. The activity of these enzymes can be regulated by factors such as phosphate ions, squalestatin, and substrate concentration.
LDH2/MDH2 Oxidoreductase (LDH2/MDH2_Oxidoreductase)
Type: Family

This family of proteins includes enzymes that function as oxidoreductases, primarily acting on the CH-OH group of donors with NAD+ or NADP+ as acceptors. Members of this family are involved in various metabolic processes, including the biosynthesis of coenzyme M and methanopterin. They exhibit catalytic activity towards substrates such as oxaloacetate, sulfopyruvate, and alpha-ketoglutarate, but not pyruvate. The enzymes show a preference for NADH over NADPH as a coenzyme in their reactions. The family plays a role in the reduction of sulfopyruvate to (R)-sulfolactate, which is a key step in the biosynthetic pathways of coenzyme M and methanopterin, compounds essential for certain methanogenic archaea.
tRNA-splicing ligase RtcB (RtcB_ligase)
Type: Family

This family of proteins is involved in the critical cellular process of tRNA splicing and maturation. Members of this family function by catalyzing the ligation of tRNA halves following intron removal, a key step in tRNA processing that ensures the proper functioning of tRNAs during protein synthesis. They are characterized by their ability to join RNA molecules with 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA molecules with 5'-hydroxy ends, thereby generating mature tRNAs that are essential for the translation of genetic information into proteins.
F(420)H(2) dehydrogenase complex subunit H (F420H2_dehydrogenase_H)
Type: Family

This family of proteins is involved in the energy-conserving electron transfer system in methylotrophic methanogens. Members function as a component of the F(420)H(2) dehydrogenase complex, which is crucial for the metabolism of these organisms when they grow on substrates such as methanol or methylamines. These proteins catalyze the oxidation of methanophenazine to dihydromethanophenazine and shuttle electrons from reduced coenzyme F(420) to methanophenazine via FAD and iron-sulfur centers. This process is coupled with proton translocation across the cytoplasmic membrane, conserving energy in the form of a proton gradient. Additionally, some members can oxidize F(420)H(2) with various quinones, indicating a broader role in the redox reactions within the cell membrane.
HTH-type transcriptional regulator LrpA (HTH-LrpA_regulator)
Type: Family

This family of proteins includes helix-turn-helix (HTH) type transcriptional regulators known as LrpA. Members of this family are involved in the negative regulation of their own transcription. They function by binding DNA and interfering with the recruitment of RNA polymerase (RNAP) to the promoter complex, thus inhibiting the association of RNAP with the TBP-TFB complex. The DNA-binding activity is attributed to the presence of an N-terminal domain with an HTH motif, while the C-terminal domain exhibits mixed alpha/beta characteristics, which is common among various RNA- and DNA-binding domains. These proteins are capable of binding to specific DNA sequences that overlap the transcriptional start site of their own promoters.
Sulredoxin-like (SDX-like)
Type: Family

This family of proteins is characterized by a similarity to sulredoxins, which suggests a potential involvement in cellular redox processes. However, the exact biochemical function of these proteins has not been established, and further research is necessary to elucidate their role in the cell.
Class-III Pyridoxal-Phosphate-Dependent Aminotransferase LysJ (Class-III_PLP-Dep_Atrans_LysJ)
Type: Family

This family of proteins is involved in the biosynthesis of the amino acids arginine and lysine. Members of this family function as transaminases, enzymes that catalyze the transfer of an amino group from a donor to an acceptor molecule, typically utilizing pyridoxal phosphate as a cofactor. These proteins specifically participate in the conversion of semialdehyde intermediates, which are part of the metabolic pathways leading to the production of arginine and lysine. As members of the class-III pyridoxal-phosphate-dependent aminotransferase family, they share a common evolutionary origin and mechanistic features with other enzymes in this class.
DNA Double-Strand Break Repair Mre11/Rad50 Complex (DSB_Repair_Mre11/Rad50)
Type: Family

This family of proteins is involved in the cellular response to DNA double-strand breaks (DSBs), a critical form of DNA damage. Members of this family function as part of a protein complex that includes Rad50 and is essential for the early steps of DSB repair. They exhibit a dual enzymatic activity, possessing both double-stranded 3'-5' exonuclease and single-stranded endonuclease capabilities. These proteins are responsible for binding to the broken DNA ends, processing them, and coordinating the recruitment of additional factors necessary for DNA repair. The nuclease activity of these proteins is modulated by their interaction with Rad50, ensuring a regulated response to DNA damage. Their immediate recruitment to sites of chromosomal DNA damage, such as that caused by gamma irradiation, underscores their role in maintaining genomic stability.
DNA Double-strand Break Repair Helicase (DSB_Repair_Helicase)
Type: Family

This family of proteins is involved in the cellular response to DNA double-strand breaks (DSBs), a critical type of DNA damage. Members of this family function in DSB repair by collaborating with the NurA nuclease to initiate resection of the 5' DNA strand, thereby generating a 3' single-stranded DNA overhang. This overhang is essential for the recruitment and loading of the RadA recombinase, which facilitates homologous recombination repair. These proteins possess DNA-dependent ATPase and DNA helicase activities, enabling them to unwind DNA structures such as Holliday junctions, splayed-arm DNA, and blunt-ended double-stranded DNA. Their ATPase activity is modulated by the presence of DNA, with a preference for linear double-stranded DNA, and can be stimulated by specific protein interactions. The structural domains of these proteins include an N-terminal HAS-barrel domain for interaction with NurA, a central RecA-like catalytic core, and a C-terminal four-helix bundle.
DNA double-strand break repair nuclease NurA (DSB_repair_nuclease_NurA)
Type: Family

This family of proteins is involved in the cellular response to DNA double-strand breaks (DSBs), a critical type of DNA damage. Members of this family function in DSB repair by processing DNA ends to facilitate the subsequent steps of repair. They exhibit nuclease activities that are essential for the resection of DNA strands, creating the necessary single-stranded DNA overhangs for the loading of repair proteins. These nucleases typically act in conjunction with other proteins, such as HerA, to stimulate the resection process. Some family members have been shown to possess both single-stranded endonuclease activity and 5'-3' exonuclease activity on DNA substrates. The regulation of their nuclease activities can be influenced by interactions with other proteins, such as SSB, which can inhibit their function.
Trehalose Synthase Glycosyltransferase (Trehalose_synthase_GT)
Type: Family

This family of proteins is involved in the synthesis of trehalose, a type of sugar, from ADP-glucose and glucose. The enzymes in this family are capable of catalyzing a reversible reaction, although the equilibrium is significantly biased towards the production of trehalose. While they predominantly use ADP-glucose as a glucose donor, they exhibit lower activity with UDP-glucose and GDP-glucose as alternative substrates. The family falls under the glycosyltransferase group 1, specifically within the glycosyltransferase 4 subfamily, indicating a shared structural motif and evolutionary origin.
Brz Transcriptional Regulator (Brz_Regulator)
Type: Family

This entry represents a group of small proteins mainly from Halobacteria including Transcriptional regulator Brz. Brz is known to activate transcription of bacteriorhodopsin and phytoene synthase. It may interact with DNA or RNA via the zinc finger domain . These proteins are predicted to adopt a zinc β-ribbon fold in which the last zinc coordinating residue is histidine instead of the commonly found cysteine. This kind of substitution has been already observed in other zinc β-ribbon domains from transcription factors, methytransferases and ribosomal proteins. Mutation of the cysteine and histidine residues has a pronounced effect on the Brz function .
Mevalonate 3,5-bisphosphate decarboxylase (MVD_Decarboxylase)
Type: Family

This family of proteins catalyzes the ATP-independent decarboxylation of (R)-mevalonate 3,5-bisphosphate to isopentenyl phosphate. They are involved in an alternative mevalonate pathway, distinct from the classical route, which is utilized by extreme acidophiles of the Thermoplasmatales order. This alternative pathway progresses through mevalonate 3-phosphate instead of mevalonate 5-phosphate. Members of this family do not show decarboxylase activity on mevalonate, mevalonate 3-phosphate, mevalonate 5-phosphate, or mevalonate 5-pyrophosphate.
Bacterial Sortase Class E (Sortase_Class_E)
Type: Family

This family of proteins functions as transpeptidases that anchor surface proteins to the bacterial cell wall. They recognize specific peptide motifs, with a preference for sequences containing Leu-Ala-x-Thr-Gly over Leu-Pro-x-Thr-Gly. These enzymes exhibit substrate specificity that includes cleaving not only the Thr-Gly motif but also the Ala-X bond, with certain amino acid combinations being preferred substrates. They are involved in the attachment of chaplin proteins such as ChpA, ChpB, and ChpC to the cell wall, with differential importance for the attachment of ChpC. The absence of these enzymes results in developmental defects in aerial hyphae formation, indicating a role in bacterial morphogenesis.
L-arabinose transport ATP-binding (L-arabinose_ABC_transporter)
Type: Family

This family of proteins is involved in the transport of L-arabinose across cellular membranes. Members of this family are part of a binding-protein-dependent transport system, which is an ATP-binding cassette (ABC) transporter system. These proteins are likely responsible for the hydrolysis of ATP, which provides the necessary energy for the active transport of L-arabinose into the cell. The ABC transporter superfamily to which these proteins belong is characterized by its ability to transport various molecules across membranes in a process that is coupled with ATP hydrolysis.
Bacterial Transpeptidase (Bacterial_Transpeptidase)
Type: Family

This family of proteins includes transpeptidases that are key components in bacterial cell wall synthesis. They are responsible for forming peptide cross-links between glycan strands in the peptidoglycan layer, which is crucial for maintaining cell wall integrity and shape. These enzymes are part of the divisome complex that orchestrates the synthesis of the septal cross wall during cell division. Members of this family are also the targets of beta-lactam antibiotics, which inhibit their activity by acylating an essential serine residue at the active site, leading to the weakening of the cell wall and ultimately bacterial cell death.
Type IV-like pilus-associated transformation protein (T4P_transformation_protein)
Type: Family

This family of proteins is involved in the process of bacterial transformation, specifically through the formation and function of type IV-like pili. These pili are essential for DNA uptake during transformation, as they are believed to extend and retract dynamically, facilitating the binding and internalization of external DNA into the bacterial cell. Members of this family are crucial for the DNA binding step that precedes the integration of new genetic material into the bacterial genome, playing a key role in horizontal gene transfer and genetic diversity.
Cell envelope sensor kinase (Cell_env_sensor_kinase)
Type: Family

This family of proteins includes sensor components of two-component regulatory systems, which are typically involved in responses to environmental stimuli. Members of this family function as membrane-associated protein kinases that phosphorylate their cognate response regulators. The phosphorylation event typically occurs in response to changes in the cell envelope and is part of a signaling process that can lead to the activation of transcription, such as that of RNA polymerase sigma-E factor. This regulatory mechanism plays a crucial role in maintaining cell envelope stability under varying conditions.
RNA-guided DNA endonuclease domain-containing protein (RNA-guided_DNA_endonuclease)
Type: Family

This family of proteins includes RNA-guided DNA endonucleases that are associated with insertion sequence elements. They are characterized by their ability to cleave double-stranded DNA when guided by a specific RNA molecule. The cleavage occurs downstream of a transposon-associated motif, resulting in staggered cuts 15-21 bases from the motif and producing 5'-overhangs. These proteins are also capable of binding to a specific RNA derived from the 3' end of their own gene and the right end of the insertion sequence, as well as adjacent downstream sequences. The family is distinguished by having domains in the N-terminal and C-terminal regions that are similar to those found in transposase 2 and transposase 35, respectively, suggesting a role in transposition-related activities.
2-amino-4-ketopentanoate thiolase beta subunit (AKP_thiolase_beta)
Type: Family

This family of proteins is involved in the ornithine fermentation pathway . Members of this family catalyse the thiolytic cleavage of 2-amino-4-ketopentanoate (AKP) with coenzyme A (CoA) to produce acetyl-CoA and alanine. The reaction is a key step in the conversion of ornithine to various end products. These enzymes exhibit strict specificity for their substrate AKP. Regulatory features include inhibition by compounds such as p-chloromercuribenzoate and acetyl-CoA, with some members also being sensitive to N-ethylmaleimide.
Diadenylate Cyclase CdaS-like (DAC_CdaS-like)
Type: Family

This family of proteins includes diadenylate cyclases, enzymes that catalyze the formation of cyclic di-AMP (c-di-AMP) from two ATP molecules. Cyclic di-AMP is a second messenger involved in various cellular processes such as growth, DNA repair, and cell wall homeostasis. Members of this family are characterized by an N-terminal region that may influence enzymatic activity and oligomerization. While some members can also utilize ADP as a substrate, they generally exhibit slower activity with ADP and may possess weak ADPase activity. The proteins are implicated in critical bacterial lifecycle stages, including sporulation and spore germination, and are differentially regulated by various sigma factors.
Bacterial Cell Wall Biosynthesis Protein (Cell_Wall_Biosynth_Protein)
Type: Family

This family of proteins is involved in bacterial cell wall biosynthesis. They possess a bifunctional mechanism with distinct domains responsible for different stages of peptidoglycan formation. The N-terminal domain functions as a transglycosylase/glycosyltransferase, which is not inhibited by penicillin and is responsible for the polymerization of glycan chains, forming linear strands of peptidoglycan. The C-terminal domain exhibits transpeptidase activity, which is sensitive to penicillin and is crucial for cross-linking peptide subunits in the cell wall. The proteins are known to bind lipid II intermediates and are capable of hydrolyzing thiolester analogs of cell wall precursors. Their activity is influenced by various factors, including the presence of detergents and antibiotics, with specific detergents enhancing or inhibiting their glycosyltransferase activity, and antibiotics like moenomycin and vancomycin affecting them differently.
Metal-staphylopine ABC transporter permease (Staphylopine_ABC_permease)
Type: Family

This family of proteins is involved in the transport of divalent metal ions across bacterial membranes. They are components of the ABC transporter complex CntABCDF, also known as Opp1, which is responsible for the uptake of metals in complex with the metallophore staphylopine. These proteins play a crucial role in the translocation of substrates such as nickel, cobalt, zinc, copper, and iron. Their activity is essential for various cellular processes, including virulence and enzyme activity regulation, such as urease. The presence of certain metals can influence the import efficiency of others, indicating a regulatory mechanism for metal ion uptake based on availability and possibly competition among ions.
DNA Protection During Starvation (DPS)
Type: Family

This family of proteins is involved in the protection of DNA during conditions of stress such as starvation. They function by binding and sequestering intracellular Fe(2+) ions, converting them to Fe(3+) oxyhydroxide mineral. This process is coupled with the detoxification of hydrogen peroxide, as the proteins catalyze the oxidation of Fe(2+) ions in the presence of hydrogen peroxide, thereby preventing the formation of hydroxyl radicals through the Fenton reaction. The sequestration and oxidation activities help in storing iron in a safe form and protect DNA from oxidative damage.
SecD/SecF protein-export membrane protein (SecD/SecF_export)
Type: Family

This family of proteins is involved in the process of protein export across the cell membrane. Members of this family are integral to the translocation machinery that guides newly synthesized proteins from the cytoplasm to their final destinations outside the cell or within the cell membrane. They play a crucial role in maintaining cellular function by ensuring that proteins reach their correct location, which is essential for a variety of cellular processes and overall cellular homeostasis.
tRNA Cytidine Acetyltransferase (tRNA_Cytidine_AcTrnsfr)
Type: Family

This family of proteins includes enzymes that are responsible for the acetylation of cytidine in tRNA molecules. Specifically, they catalyze the formation of N(4)-acetylcytidine at the wobble position of tRNA(Met), which is a modification that can affect the stability and function of the tRNA. These enzymes utilize acetyl-CoA as the acetyl group donor and require ATP (or GTP) to carry out the reaction. The acetylation process is important for the proper decoding of the genetic code during protein synthesis and may also play a role in the regulation of tRNA function and expression.
2-alkyl-3-oxoalkanoate reductase (2-alkyl-3-oxoalkanoate_rdct)
Type: Family

This family of proteins is involved in the biosynthesis of olefins, a class of hydrocarbons. Members of this family function as enzymes that catalyze a reversible reaction where 2-alkyl-3-oxoalkanoic acids are reduced to 2-alkyl-3-hydroxyalkanoic acids, utilizing NADPH as a cofactor. This reaction is stereospecific, indicating that these enzymes have a precise control over the stereochemistry of the product formed. The oxidative reaction prefers syn-2-decyl-3-hydroxytetradecanoic acid as a substrate, while the reductive reaction can process (2R/S)-2-hexyl-3-ketodecanoic acid. The activity of these enzymes is crucial for the production of olefins, which are important components in various biological processes and industrial applications.
Exopolysaccharide Production Regulator (EPS_Regulator)
Type: Family

This family of proteins is involved in the regulation of exopolysaccharide biosynthesis. Members of this family function as negative regulators, acting to decrease the production of exopolysaccharides, which are high-molecular-weight polysaccharides that are secreted by microorganisms into their environment. These molecules play key roles in biofilm formation, cellular adhesion, and protection against environmental stresses. By modulating the synthesis of exopolysaccharides, proteins in this family are likely to be critical for the control of bacterial biofilm development and the maintenance of cell surface properties.
DNA double-strand break repair ATPase (DSB_repair_ATPase)
Type: Family

This family of proteins is involved in the cellular response to DNA double-strand breaks (DSBs), a critical form of genetic damage. Members of this family function as part of a larger complex, which includes Mre11, and play a key role in the initial steps of DSB repair. They are responsible for controlling the dynamic balance between two essential processes: DNA end bridging and DNA resection. This regulation is achieved through ATP-dependent structural changes in the complex. Additionally, these proteins feature a unique zinc-hook domain that facilitates the formation of a V-shaped homodimer through the coordination of zinc ions, which is essential for their function in DNA repair.
MIP/Aquaporin Lactic Acid Transporter (MIP/AQP_LacticAcid_Trans)
Type: Family

This family of proteins includes transporters that facilitate the transmembrane diffusion of various small molecules. Members of this family are involved in the cellular metabolism of lactic acid, as they transport lactic acid across the cell membrane. Additionally, these proteins can transport other uncharged solutes such as urea and hydrogen peroxide (H2O2). While some family members are also capable of transporting water, glycerol, and dihydroxyacetone, others are selective and do not transport these compounds. The physiological role of these proteins is likely broader than just lactate metabolism, as they can handle a range of solutes, reflecting the diverse functions of the MIP/aquaporin superfamily to which they belong.