SII-SWORD/CoKE huggingface dataset:
Bacterial Transport-Associated Protein (Bact_Transport_Assoc)
Type: Family

This family of proteins is involved in transport processes within the cell. Members of this family share similarity with proteins from different bacterial species, suggesting a conserved role in cellular transport mechanisms. The exact substrates and transport pathways, however, are not specified in the provided annotations.
NAD(P)H nitroreductase (NAD(P)H_nitroreductase)
Type: Family

This family of proteins is involved in the reduction of nitroaromatic compounds. Members of this family are typically characterized by their ability to utilize NAD(P)H as an electron donor to convert nitro groups to amino groups through a reductive process. This biochemical activity is important for the detoxification of nitroaromatic compounds, which can be toxic and mutagenic to cells. The reduction process can also contribute to the activation of certain prodrugs that contain nitro groups. These enzymes are found across various bacterial species and may play a role in cellular responses to nitrosative stress.
CarD-like transcription regulator (CarD-like_regulator)
Type: Family

This family of proteins includes transcription factors that interact with RNA polymerase to control ribosomal RNA transcription. Members are involved in the regulation of replication and persistence during infection in some species. They also play a role in the response to various stresses, including starvation, oxidative, and genotoxic stress, and are important for maintaining rRNA levels under normal growth conditions.
SUA5 domain-containing protein (SUA5_domain)
Type: Family

This family of proteins is characterized by similarity to the SUA5 family, which is known to be involved in various cellular processes. Members of the SUA5 family typically share common structural features and are thought to play roles in the synthesis or modification of cellular components, although the specific functions of individual proteins within the family may vary. The exact biochemical activities and mechanisms of action of these proteins may include binding to other macromolecules, catalyzing chemical reactions, or regulating gene expression, but these functions are often determined by further experimental validation.
Exodeoxyribonuclease WalJ/YycJ-like (WalJ/YycJ-like)
Type: Family

This entry represents Exodeoxyribonuclease WalJ/YycJ from Streptococcus pneumoniae and similar prokaryotic 5'->3' double-stranded DNA exonucleases. Members of this family are involved in the WalK/WalR signal transduction pathway and may contribute to mutation mismatch repair (MMR) . They play a crucial role in ensuring the coordination of cell division with DNA replication and are potentially involved in cell wall metabolism . Most members of this family contain the metallo-beta-lactamase domain (

), indicating a shared structural framework and potential catalytic mechanism involving metal ions.
Extracellular DNA Utilization and Secretion System Component (Extracell_DNA_Util/SecSys_Comp)
Type: Family

This family of proteins includes components involved in the utilization of extracellular DNA as a nutrient and the assembly and function of secretion systems. Members are implicated in various cellular processes such as adhesion, colonization, biofilm maturation, and virulence. They play roles in the inner membrane, forming complexes essential for the assembly of functional pili or secretion machinery, and in some cases, mediate the energy-dependent secretion of extracellular factors like proteases and toxins.
Bacilysin biosynthesis H2HPP isomerase (Bacilysin_H2HPP_isomerase)
Type: Family

This family of proteins is involved in the biosynthesis of bacilysin, a nonribosomally synthesized dipeptide antibiotic composed of L-alanine and L-anticapsin. Members of this family function as isomerases, specifically catalyzing the allylic isomerization of endocyclic-delta(4),delta(8)-7R-dihydro-hydroxyphenylpyruvate to exocyclic-delta(3),delta(5)-dihydro-hydroxyphenylpyruvate. This reaction results in a mixture of olefin isomers. Bacilysin acts as an irreversible inactivator of the glutaminase domain of glucosamine synthetase, an enzyme involved in the biosynthesis of glucosamine-6-phosphate.
ABC-4 Integral Membrane (ABC-4_Integral_Memb_Prot)
Type: Family

The ABC-4 integral membrane protein family is involved in the transport of specific substrates across the cell membrane, functioning as part of ABC transporter complexes. Members of the family such as BceAB and YxdLM are implicated in the export of bacitracin and possibly in peptide resistance, respectively. These transporters utilize ATP hydrolysis to translocate their substrates and play a crucial role in the cellular response to antimicrobial peptides, contributing to the survival of the organism in hostile environments. The family's function in substrate specificity and energy coupling highlights its importance in cellular defense mechanisms.
Extradiol ring-cleavage dioxygenase (Extradiol_RC_dioxygenase)
Type: Family

This family of proteins includes extradiol ring-cleavage dioxygenases that are involved in the degradation of aromatic compounds with two hydroxyl groups at para positions. These enzymes catalyze the oxidative cleavage of aromatic rings, a critical step in the breakdown of various pollutants and toxins, such as gamma-hexachlorocyclohexane (gamma-HCH or lindane). The cleavage process consumes molecular oxygen and results in the formation of intermediate products that can be further metabolized for energy and carbon. Members of this family are characterized by their inability to process catechol, distinguishing them from meta-cleavage dioxygenases.
Flavonoid dioxygenase-like (Flavonoid_dioxygenase-like)
Type: Family

This family of proteins includes enzymes that are involved in the degradation of flavonoids, specifically catalyzing the dioxygenolytic cleavage of the O-heteroaromatic ring of flavonols. The enzymatic reaction results in the breakdown of compounds such as quercetin into smaller molecules, which is a key step in the catabolism of these plant-derived substances. The activity of these enzymes can be modulated by certain inhibitors, suggesting a level of regulatory control over their function.
Molybdopterin-guanine dinucleotide biosynthesis adapter (MGD_biosynthesis_adapter)
Type: Family

This family of proteins includes GTP-binding proteins that are involved in the biosynthesis and utilization of the molybdenum cofactor, specifically the Mo-molybdopterin guanine dinucleotide (Mo-MGD) form. Although they are not essential for the formation of Mo-MGD or for the activation of molybdoenzymes that utilize this cofactor, they may serve as adapter proteins that enhance the efficiency of these processes. Members of this family exhibit a weak intrinsic GTPase activity and can also bind other nucleotides such as ATP, TTP, and GDP, albeit with lower affinity compared to GTP.
Sulfide-quinone oxidoreductase (SQRD)
Type: Family

This family of proteins includes enzymes that are involved in the oxidation of sulfides, such as hydrogen sulfide, using quinones as electron acceptors. The reaction catalyzed by these enzymes leads to the formation of polysulfide products at the active site cysteine residues. These products are released when they reach a certain size, often as cyclooctasulfur. Members of this family are known to be inhibited by various compounds, including quinone analogs and cyanide, and can be inactivated by alkylation of the active site cysteine.
Cholesterol Oxidase Enzyme (Cholesterol_Oxidase)
Type: Family

The Cholesterol Oxidase family comprises enzymes that play a crucial role in the cholesterol degradation pathway. Members of this family are responsible for the oxidation and isomerization of cholesterol to cholestenone, which is a key initial step in breaking down cholesterol. These enzymes are characterized by their ability to catalyze the transformation of the 3-beta-hydroxy group of cholesterol and the subsequent isomerization of the double bond in the product, leading to the formation of cholest-4-en-3-one. This biochemical activity allows bacteria to utilize cholesterol as a sole carbon and energy source, and is also implicated in bacterial virulence. The family belongs to the broader GMC oxidoreductase family, although some members are noted to be highly divergent within this group.
HTH-type Metal-responsive Transcriptional Regulator (HTH_Metal-responsive_Reg)
Type: Family

This family of proteins includes helix-turn-helix (HTH) type transcriptional regulators that are responsive to metal ions. Members of this family are known to repress transcription of specific operons by binding to DNA. The presence of certain metal ions, such as cadmium or lead, can induce these proteins to release from the DNA, thereby lifting the repression and allowing gene expression. This regulatory mechanism is important for the cellular response to metal stress and may play a role in metal homeostasis and detoxification.
Bacteriocin Processing Enzyme (Bacteriocin_Proc_Enz)
Type: Family

The protein family includes enzymes involved in the processing of precursor peptides into their active forms. Members of the family are necessary for the maturation of bacteriocins, which are ribosomally synthesized antibacterial peptides. Specifically, the family is responsible for the conversion of inactive precursors such as microcin B17 (McbA) and trifolitoxin (TfxA) into their active bactericidal forms. These proteins play a crucial role in bacterial competition and survival by producing compounds that inhibit the growth of competing strains. The family exhibits similarity to nitroreductases, suggesting a potential shared mechanism or evolutionary relationship.
Light-responsive regulatory protein (Light-responsive_reg)
Type: Family

This family of proteins includes photoreceptors known as bacteriophytochromes and components of two-component regulatory systems. Bacteriophytochromes are light-sensitive and exist in two forms that are interconvertible by light, with absorption maxima in the red and far-red regions of the spectrum. They may also absorb green light and are implicated in regulating pigment synthesis for protection against intense light. The two-component system proteins function as final receptors in regulatory pathways responding to environmental stimuli, such as osmolarity changes or oxidative stress. They control downstream signaling cascades, which can lead to various cellular responses including adaptation to osmotic stress, cell wall biosynthesis, and virulence in pathogenic species. These proteins can be phosphorylated or unphosphorylated, with their activity and stability regulated accordingly to modulate the signaling pathways.
Transposase_8_domain-containing_protein (Transposase_8_domain)
Type: Family

This family of proteins includes members that are typically associated with mobile genetic elements, specifically insertion sequences. These proteins are related to transposases, which are enzymes that catalyze the movement of DNA segments within the genome. Members of this family are likely to play a role in the recombination events that lead to the insertion or excision of DNA elements, contributing to genomic diversity and evolution. The activity of these proteins is often regulated by various factors, including the availability of divalent cations such as calcium, which can influence their binding to DNA and catalytic activity.
Mitochondrial Isobutyryl-CoA Dehydrogenase (Mito_Isobutyryl-CoADH)
Type: Family

This family of proteins includes mitochondrial isobutyryl-CoA dehydrogenases that play a crucial role in the catabolism of valine, an essential branched-chain amino acid. Members of this family are primarily responsible for the oxidation of isobutyryl-CoA to methacrylyl-CoA, a critical step in the valine degradation pathway. Additionally, these enzymes have the ability to oxidize 2-methylbutanoyl-CoA, although with lower efficiency. Their activity is essential for the proper breakdown of valine, preventing the accumulation of toxic intermediates and maintaining metabolic balance.
Type VII toxin-antitoxin system antitoxin (Type_VII_TA_antitoxin)
Type: Family

This family of proteins includes probable antitoxin components of type VII toxin-antitoxin (TA) systems. Members of this family are thought to neutralize their cognate toxins through a mechanism that likely involves di-AMPylation or AMPylation. These antitoxins may bind nucleotides with varying affinities, with some showing a preference for TTP and ATP over ADP and AMP. The interaction between these antitoxins and their respective toxins is crucial for the regulation of the TA system, which plays a role in a variety of cellular processes including the response to stress.
Spore maturation protein B (SpmB)
Type: Family

The SpmB family includes proteins involved in spore core dehydration, suggesting a role in the transport of molecules into or out of the forespore, or in modifications of the cortex peptidoglycan structure during spore maturation. The family is named after Spore maturation protein B, which is a representative member. The functions of Inner membrane protein YjiG, also part of the SpmB family, are not well-characterized but are presumed to be related to spore maturation processes due to their family association.
Pyrimidine 5'-nucleotidase YjjG (Pyrimidine_5'-ntase_YjjG)
Type: Family

The YjjG family proteins are nucleotidases with high phosphatase activity towards non-canonical pyrimidine nucleotides and canonical nucleoside 5'-monophosphates such as UMP, dUMP, and dTMP. They exhibit house-cleaning functions in vivo, protecting cells from incorporation of potentially mutagenic nucleotides like 5-fluoro-2'-deoxyuridine monophosphate and 5-bromo-2'-deoxyuridine into DNA. These enzymes are strictly specific to pyrimidine substrates with 5'-monophosphates and do not act on nucleoside di- or triphosphates. The YjjG family's activity is crucial for thymine utilization through the thymine salvage pathway, as it catalyzes the hydrolysis of dUMP to deoxyuridine.
UV-induced DNA damage repair photolyase (UV-DNA_repair_photolyase)
Type: Family

This family of proteins includes members involved in the repair of UV-induced DNA damage, specifically (6-4) lesions. One characterized member functions as a photolyase, utilizing blue-light energy to catalyze the photoreactivation of (6-4) pyrimidine-pyrimidone photoproducts in both single-stranded and double-stranded DNA. The family is related to the iron-sulfur bacterial cryptochrome/photolyase (FeS-BCP) group, suggesting a conserved mechanism involving electron transfer facilitated by iron-sulfur clusters. The presence of uncharacterized members indicates potential functional diversity within the family.
YeaO-like (YeaO-like)
Type: Family

This entry represents a subclade of DUF488 domains lacking the catalytic residues common to the rhodanese-phosphatase superfamily. The C-terminal core strand is degenerate in this subclade .

Members of this family are uncharacterised proteins such as the E. coli YeaO protein and the Mycobacterium tuberculosis Rv3073c protein. They are conserved across different bacterial species, suggesting a potentially important biological role.
Cobalt-precorrin-5A hydrolase (CbiG_hydrolase)
Type: Family

This family of proteins is involved in the biosynthesis of cobalamin (vitamin B12), where they play a crucial role by catalyzing a specific hydrolysis step. Members of this family are responsible for the hydrolysis of the ring A acetate delta-lactone of cobalt-precorrin-5A. This reaction results in the removal of the C-20 carbon along with its attached methyl group, which is released as acetaldehyde. This step is essential in the transformation of cobalt-precorrin-5A into cobalt-precorrin-6A, a precursor in the biosynthetic pathway leading to the formation of cobalamin. The enzymatic activity of these proteins is critical for the proper progression of the cobalamin biosynthetic pathway.
2-oxoglutarate synthase subunit KorC (2-oxoglutarate_synth_KorC)
Type: Family

The 2-oxoglutarate synthase subunit KorC family includes proteins that are likely involved in the enzymatic conversion of 2-oxoglutarate to succinyl-CoA and CO2 in an ATP-dependent manner. This reaction is a key step in the Krebs cycle, an essential metabolic pathway for energy production in aerobic organisms. Members of the KorC family are typically found as part of a larger enzyme complex that catalyzes this transformation, playing a crucial role in cellular respiration and the regulation of energy metabolism.
dCTP Pyrophosphatase (dCTP_Pyrophosphatase)
Type: Family

This family of proteins is involved in the hydrolysis of deoxynucleoside triphosphates (dNTPs) into their corresponding nucleoside monophosphates, with a particular specificity for dCTP and its analogs, including modified forms such as 5-iodo-dCTP and 5-methyl-dCTP. The enzymatic activity serves a protective role, preventing the incorporation of these potentially harmful nucleotide analogs into DNA or RNA, thereby safeguarding the integrity of genetic material. The activity of these proteins is subject to inhibition by various agents, including divalent metal ions, the reaction end product pyrophosphate (PPi), dCDP, and certain pharmacological compounds like triptolide.
Polysaccharide Synthase/Transporter (PolySynth_Transporter)
Type: Family

This family of proteins includes members that are potentially involved in the biosynthesis and transport of polysaccharides. Some proteins in this family may play a role in the translocation of nascent O-polysaccharide molecules and/or their ligation to lipid A core units, which is a critical step in the assembly of bacterial cell wall components. The proteins are characterized by similarities to known polysaccharide synthases, suggesting a function in the synthesis of complex sugar chains that are essential for bacterial cell wall integrity and virulence.
Cytoskeleton-associated protease/Cytokinesis protein (CAP/Cytokinesis_protein)
Type: Family

This family of proteins includes enzymes with protease activity that are associated with the cytoskeleton and are implicated in muscle growth and neuromuscular junction maturation and stabilization. Members of this family may participate in cleaving specific muscle proteins, contributing to muscle function. Additionally, some members are involved in cytokinesis, the process of cell division, by recruiting other proteins to facilitate the synthesis of cellular structures necessary for cell separation.
Siderophore Hydrolyzing Esterase D (Siderophore_Hydrolase_D)
Type: Family

The Esterase D family is involved in the hydrolysis of siderophores, which are iron-chelating compounds crucial for microbial iron uptake and virulence. Members of this family display specificity towards various siderophores, including triacetylfusarinine C, bacillibactin, and enterobactin, facilitating the release of iron for metabolic use or storage. The family includes enzymes that can hydrolyze both iron-bound and apo forms of these siderophores, with some members showing equal efficiency in hydrolyzing different siderophore derivatives. This suggests a role not only in iron release but also in the degradation of iron-free chelators for cellular protection. The family is characterized by an alpha/beta-hydrolase fold and, in some cases, an atypical catalytic dyad.
Vanadium-dependent haloperoxidase (V-haloperoxidase)
Type: Family

This family of proteins includes enzymes that catalyze the halogenation of organic substrates using hydrogen peroxide. Members of this family are characterized by their ability to utilize vanadium as a cofactor in the oxidation of halides, such as chloride or bromide, to generate hypohalous acids. These acids can then react with various organic substrates to form halogenated products, which are significant in various biological and chemical processes. The enzymes are known for their role in the biosynthesis of halogenated metabolites, which can have diverse functions including antimicrobial activity.
RNA-directed DNA polymerase, mobile element (RdDP_mobile_element)
Type: Family

This family of proteins includes RNA-directed DNA polymerases from mobile genetic elements such as transposons. These enzymes are responsible for transcribing RNA into DNA, a process central to the mechanism of retrotransposition. Retrotransposons, which are a type of mobile element, use these polymerases to replicate themselves within the host genome. The activity of these enzymes can be modulated by various reagents, indicating a level of regulatory control over their function. Their activity is crucial for the mobility of genetic elements and can have significant impacts on genome stability and evolution.
Complex I Subunit 1 (ComplexI_Subunit1)
Type: Family

The Complex I Subunit 1 family is involved in the electron transport chain, a crucial step in cellular respiration. Members of this family are typically part of larger enzyme complexes such as NADH-ubiquinone oxidoreductase (Complex I) and formate hydrogenlyase, which are responsible for the transfer of electrons from donors like NADH to acceptors like ubiquinone. This process is fundamental for the generation of a proton gradient across the membrane, ultimately leading to ATP synthesis. Some members may also play a role in hydrogenase complexes, contributing to energy conservation in microorganisms through the oxidation of hydrogen gas.
Ketohexokinase-related (Ketohexokinase-related)
Type: Family

This family of proteins is involved in the metabolism of carbohydrates, specifically in the phosphorylation of fructose to produce fructose-1-phosphate. The enzymatic activity is essential for the utilisation of fructose as a source of energy and carbon skeletons. Members of this family require potassium for their activity and are inhibited by ADP, indicating a regulatory mechanism that integrates energy status with carbohydrate metabolism. The proteins in this family are structurally related, sharing a common fold typical of the PfkB (phosphofructokinase B) subfamily of carbohydrate kinases, which is characterised by a particular arrangement of β sheets and α helices.
Flagellar hook-length control (FliK)
Type: Family

This family of proteins is involved in the regulation of bacterial flagellar assembly, specifically by determining the length of the flagellar hook. The hook is a critical component of the flagellar structure, serving as a flexible joint that connects the basal body to the filament. Members of this family are characterized by a two-domain architecture, with a central region that functions as a hinge or connector. This structural feature is essential for their role in hook-length control, ensuring proper flagellar function and motility in bacteria.
Putative N-acetyltransferase and recombination-associated protein (N-acetyltrans/Recomb-assoc)
Type: Family

This family of proteins includes members that are putatively involved in diverse cellular processes. One member is suggested to have a role in increasing recombination centers, which could be important for DNA repair or recombination during meiosis. Another member is identified as a putative N-acetyltransferase, indicating a potential function in the modification of proteins or other molecules by acetyl groups. This enzymatic activity is often involved in the regulation of protein function and interactions, as well as in the metabolism of drugs and toxins. The functions of the other members remain uncharacterized, but they may share structural or functional similarities that are yet to be elucidated through experimental studies.