SII-SWORD/CoKE huggingface dataset:
Bacterial Sigma Factor Regulator (Bact_Sigma-Reg)
Type: Family

The protein family described is involved in regulatory processes related to stress response and sporulation in bacteria. Members of the family function as regulators of sigma factors, which are proteins that control the transcription of specific sets of genes. They exhibit phosphatase activity, often dephosphorylating specific proteins to activate sigma factors in response to environmental or energy stress. Some members also have kinase activity and can phosphorylate other proteins, playing a role in signal transduction pathways. The family includes proteins that participate in the cross-regulation of carbon and glucose metabolisms, as well as proteins that act as independent regulators sensitive to osmosensory signals. They are characterized by the presence of domains such as PAS, which may sense cellular energy levels, and anti-sigma factor domains, which are involved in the regulation of sigma factor activity.
4-Toluene Sulfonate Uptake Permease (TSUP)
Type: Family

The 4-toluene sulfonate uptake permease (TSUP) family includes proteins involved in the transport of sulfonates and related compounds across cellular membranes. Members of the TSUP family are predominantly membrane transporters, which facilitate the uptake of substances like p-toluenesulphonate (TSA) and potentially export sulfite and various organosulfonates. These transporters are integral to the cellular processes that manage the import and export of sulfonate compounds, contributing to the metabolic versatility of the organisms in utilizing different sulfonated substrates as sources of sulfur or carbon, or in detoxification processes.
PHP domain-containing protein (PHP_domain)
Type: Family

This family of proteins includes enzymes that are involved in nucleotide metabolism and RNA processing. Members of this family are capable of hydrolyzing phosphate esters, such as the hydrolysis of the phosphate ester at carbon-1 of 5-phospho-D-ribose 1,2-cyclic phosphate to form ribose 2,5-bisphosphate. Additionally, they can catalyze the removal of 3'-phosphates from 3',5'-bis-phosphonucleotides and the successive hydrolysis of 5'-phosphomononucleotides from the ends of RNA and DNA oligonucleotides. Some family members are involved in the maturation of rRNA by trimming the 5'-end of rRNA precursors. The family includes enzymes that can hydrolyze both RNA and DNA substrates, with a preference for RNA, and can act on both single-stranded and annealed double-stranded nucleic acids, although with different efficiencies.
F420H(2)-dependent biliverdin reductase/Heme oxygenase (F420H2_bilvrd_red/Heme_oxyg)
Type: Family

The F420H(2)-dependent biliverdin reductase family is involved in the reduction of biliverdin to bilirubin, a potent antioxidant, which may play a role in protecting mycobacteria against oxidative stress, aiding the persistence of infections such as M.tuberculosis. Some members are less efficient at this reaction, suggesting alternative native substrates in vivo. The family also includes proteins from the heme oxygenase HugZ/HutZ family, which are involved in heme degradation to biliverdin, releasing iron and sometimes carbon monoxide. This process is crucial for heme iron utilization and may contribute to the pathogenicity of certain bacteria. Another member is involved in the biosynthesis of antibiotics tetracycline and oxytetracycline, catalyzing the reduction of their precursors. These proteins share common biochemical pathways but have diverse roles in microbial metabolism and pathogenicity.
Cyclic di-GMP and 3'3'-cGAMP-specific phosphodiesterases (Cyclic_di-GMP/3'3'-cGAMP_PDE)
Type: Family

This family of proteins includes cyclic di-GMP and 3'3'-cGAMP-specific phosphodiesterases. They are involved in the hydrolysis of cyclic dinucleotides, such as cyclic diguanylate (c-di-GMP) and 3'3'-cyclic GMP-AMP (3'3'-cGAMP), to linear nucleotides. These enzymes play key roles in bacterial signaling pathways, regulating processes such as motility, biofilm formation, and virulence. They act by modulating the levels of cyclic dinucleotides within the cell, which serve as secondary messengers. Some family members are regulated by metal ion binding or phosphorylation, which affects their catalytic activity. The proteins may contain specific domains, such as HD-GYP, that are crucial for their function and interaction with other proteins.
Type I restriction system S subunit (Type-I_RS_S_subunit)
Type: Family

This family of proteins includes specificity subunits of type I restriction-modification systems. They are responsible for recognizing specific DNA sequences and directing the restriction-modification complex to these sites. The proteins contain DNA recognition domains that determine the sequence specificity for methylation or cleavage. In conjunction with the modification (M) and restriction (R) subunits, they form complexes that can act as methyltransferases, modifying specific adenine residues within their recognition sequences to protect the host genome from cleavage. These complexes can also function as endonucleases, cleaving DNA at sites distant from the recognition sequence in an ATP-dependent manner, particularly when the recognition site is unmodified. The methylation state of the target sequence dictates whether the DNA is cut or modified, with hemimethylated sites being a signal for maintenance methylation.
26 kDa periplasmic antigen-related (26kDa_periplasmic_antigen)
Type: Family

This family of proteins includes both characterized and uncharacterized members. The characterized proteins are known as 26 kDa periplasmic immunogenic proteins, which are likely involved in the immune response, possibly as antigens recognized by the host's immune system during infection. The uncharacterized proteins, denoted as YggE in various bacterial species, have not been functionally described, and thus their role within the family remains speculative. Given the presence of both characterized and uncharacterized members, the overall function of this protein family cannot be conclusively determined without further experimental evidence or detailed bioinformatics analysis.
Sensor histidine kinase KdpD (Histidine_kinase_KdpD)
Type: Family

This family of proteins includes sensor histidine kinases known as KdpD, which are part of two-component regulatory systems, typically KdpD/KdpE. These proteins are involved in sensing environmental signals such as low potassium ion levels, osmotic imbalance, and other stresses. Upon sensing these signals, KdpD autophosphorylates and then transfers the phosphate group to KdpE, which acts as a transcriptional regulator. KdpE binds to promoter regions of target genes to modulate their expression. Some members of this family are also regulated by cyclic di-AMP, which acts as a negative regulator. The proteins are generally membrane-associated and play a role in various cellular responses, including the regulation of virulence factors and capsular polysaccharide production in certain species.
Methanogenesis-specific methyltransferase (Methanogen_methyltrans)
Type: Family

This family of proteins includes methyltransferases that play a crucial role in methanogenesis, a process of methane production in archaea. Members of this family are involved in transferring methyl groups from methylated corrinoid proteins or free cob(I)alamin to coenzyme M, which is a key step in the formation of the substrate for coenzyme-B sulfoethylthiotransferase. The methyltransferases are involved in different pathways, including the methanol pathway and the methylamines methanol pathway, as well as methanogenesis from methylated-thiols. They catalyze the transfer of a methyl group to the cobalt cofactor of a corrinoid protein and then to coenzyme M, facilitating the production of methane. The activity of these enzymes can be inhibited by chelating agents such as EDTA and EGTA.
Xyloglucan-specific glycosyl hydrolase (Xyloglucanase_GH74)
Type: Family

This family of proteins includes enzymes that primarily act on xyloglucan, a plant cell wall polysaccharide. Members of this family exhibit xyloglucanase activity, hydrolyzing the glucosidic bonds of unbranched glucose residues within xyloglucan to produce specific oligosaccharides. Some members are described as having oligoxyloglucan-reducing end-specific activity, cleaving the first two glycosyl segments from oligoxyloglucans. The enzymes show activity against substrates such as tamarind seed xyloglucan and cotton xyloglucan. They may have dual endo- and exo- modes of action or an endo-processive mode of action. The activity profile includes the production of oligosaccharides like XXXG, XLXG, XXLG, and XLLG, with varying activities on other polysaccharides. The family belongs to the glycosyl hydrolase 74 group, which is characterized by its specificity and mode of action towards xyloglucan-related substrates.
ExeA/AAA ATPase DNA-binding & secretion (ExeA_AAA_ATPase_DNA-bind)
Type: Family

The ExeA/AAA ATPase family includes proteins involved in various cellular processes such as general secretion pathways and DNA transposition. Members of the family may play regulatory roles in secretion systems, facilitating the export of proteins across membranes. Some proteins within the family function as ATP-dependent DNA activators, selecting target DNA sites for transposition, recruiting recombinases, and catalytically activating them. They exhibit non-specific DNA-binding properties and can polymerize into helical filaments around DNA. This activity is crucial for processes like target-primed replication and preventing self-integration into viral genomes, a mechanism known as target immunity. The family typically possesses an N-terminal DNA-binding region, a central ATPase module, and a C-terminal domain that can bind to double-stranded DNA.
Phage shock protein C (PspC)
Type: Family

This family of proteins is involved in cellular stress response, particularly under conditions where nutrient or energy availability is limited. Members of this family are implicated in transcription regulation, possibly through the modulation of gene expression related to the phage shock protein (psp) operon. They may play a crucial role in enhancing the survival of cells during environmental stresses that impact cellular energetics or membrane integrity.
HipA Serine/Threonine-Protein Kinase (HipA_Ser/Thr_kinase)
Type: Family

The HipA Ser/Thr kinase family includes proteins that function as toxins within type II toxin-antitoxin (TA) systems. Members of the family phosphorylate Glu-tRNA-ligase, leading to an increase in uncharged tRNA(Glu), which triggers the stringent response and results in amino acid starvation. This process inhibits cellular functions such as replication, transcription, translation, and cell wall synthesis, thereby reducing growth and contributing to multidrug resistance and persistence. Some family members induce dormancy and can be lethal in high concentrations. The toxic effects of these kinases are typically neutralized by their cognate antitoxins. The family plays a role in the regulation of bacterial persistence, a state associated with tolerance to antibiotics and possibly biofilm formation.
Periplasmic chaperone PpiD (PpiD_chaperone)
Type: Family

The PpiD chaperone family comprises periplasmic chaperones that serve as gatekeepers at the SecYEG translocon, a protein-conducting channel in the bacterial inner membrane. Members of the family facilitate the translocation of precursor proteins across the SecYEG complex by interacting with substrates during translocation. They are also involved in the release and possibly the early folding of newly synthesized secreted proteins at the periplasmic exit site of the Sec translocon. While one member has been implicated in bacteriophage T4 infection, suggesting a role in the penetration of the inner membrane by the bacteriophage injection machinery, the family generally does not exhibit peptidyl-prolyl isomerase activity. The family's structure typically includes an N-terminal helix for membrane anchoring and multiple periplasm-facing domains, with at least one or possibly two acting as chaperone domains and a parvulin-like domain that lacks catalytic activity.
Peptidase M20/M20A family hydrolases (Peptidase_M20/M20A_hydrolases)
Type: Family

The peptidase M20 family is composed of enzymes that catalyze the hydrolysis of various substrates, including dipeptides and specific amino acid derivatives. Members of the peptidase M20A subfamily, such as Xaa-Arg dipeptidases, are involved in metabolite repair mechanisms, specifically by hydrolyzing dipeptides with basic amino acids at the C-terminus, which may be by-products of carnosine synthesis. Other members of the peptidase M20 family, like p-aminobenzoyl-glutamate hydrolases, participate in the cleavage of p-aminobenzoyl-glutamate to p-aminobenzoate and glutamate, a process important in folate metabolism. Additionally, some enzymes, such as indole-3-acetyl-aspartic acid hydrolase, exhibit high substrate specificity, hydrolyzing compounds like indole-3-acetyl-aspartate to indole-3-acetic acid. The diverse functions of the peptidase M20 family reflect its role in various biological processes, including amino acid metabolism, peptide degradation, and plant hormone metabolism.
Membrane Transporter and Flippase (Membrane_Transporter-Flippase)
Type: Family

This family of proteins includes transporters that are involved in various cellular transport processes. Some members are responsible for the extrusion of multiple antimicrobial compounds, contributing to multidrug resistance. These proteins typically function as antiporters, exchanging ions like H+ or Na+ for organic cations across the cell membrane. Other members are involved in the biosynthesis of peptidoglycan, an essential component of bacterial cell walls, by transporting lipid-linked peptidoglycan precursors across the cytoplasmic membrane. Additionally, the family may include transporters for specific molecules such as flavin adenine dinucleotide (FAD) and possibly indole-3-acetic acid (IAA) or its derivatives, indicating a diverse range of substrate specificities and biological roles.
ATP-dependent Amino Acid Ligase (ATP-dep_AA_Ligase)
Type: Family

The protein family is involved in the biosynthesis of various peptide antibiotics and related compounds through ATP-dependent ligation of amino acids. Members of the family catalyze the formation of dipeptides by joining specific amino acids, which are then incorporated into larger bioactive molecules. These enzymes are typically part of operons or gene clusters that mediate the production of compounds such as bacilysin, dapdiamides, and isoquinoline alkaloids. The enzymes exhibit substrate specificity, with some recognizing small amino acids like alanine for the N-terminal end of dipeptides, while others have strict specificity towards arginine or can incorporate hydrophobic amino acids at the C-terminal end. The resulting compounds have roles in microbial defense and competition, and their biosynthetic pathways involve additional modifications like oxidation and cyclization.
Mitochondrial Glutaryl-CoA Dehydrogenase (Glutaryl-CoA_DH_mitochondrial)
Type: Family

The Glutaryl-CoA dehydrogenase family is involved in the mitochondrial oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and CO2, a crucial step in the catabolism of L-lysine, L-hydroxylysine, and L-tryptophan. Members of this family use electron transfer flavoprotein as an electron acceptor. The activity of these enzymes can be regulated by specific metabolites, such as MCPA-CoA, which is known to strongly inhibit the enzyme. Variants within this family may exist, including isoforms that are inactive, highlighting the potential for functional diversity within the family.
Nitrite reductase [NAD(P)H]-like (NasD-like)
Type: Family

This entry represents Nitrite reductase [NAD(P)H] from Bacillus subtilis and similar enzymes involved in nitrogen and sulfur metabolism from bacteria and fungi. Members of this family are responsible for the reduction of nitrite to ammonia, a step in nitrite assimilation, and the reduction of sulfite to sulfide, crucial for the biosynthesis of L-cysteine from sulfate. These processes are vital for the nitrogen and sulfur cycles in the environment and for the synthesis of essential amino acids in organisms. The family includes proteins with a 4Fe-4S domain, which is indicative of their involvement in electron transfer reactions during the catalysis of these reductions.
Zinc finger BED domain-containing (ZnF_BED_domain_contain)
Type: Family

The Zinc finger BED domain-containing protein family includes transcriptional regulators that interact with DNA and RNA, often binding to poly-guanine tracts to activate transcription. Members are involved in various developmental processes, such as vulval organogenesis, cell cycle regulation, and gonadal development. Some proteins within the family may also play roles in the biosynthesis of complex polyesters and in the regulation of distal tip cell migration. The BED domain is a characteristic feature that facilitates DNA-binding, suggesting a shared mechanism of action across the family in gene expression modulation and developmental regulation.
Hydrolase/Phosphoribosyltransferase-associated (Hydrolase/PRTase-associated)
Type: Family

This family of proteins includes enzymes with diverse hydrolytic activities. Some members are involved in the hydrolysis of the lactone ring of erythromycin, conferring resistance to this antibiotic. Other members are predicted to have phosphoribosyltransferase activity, which is typically associated with the synthesis of nucleotide precursors by transferring a phosphoribosyl group to purine or pyrimidine bases. The family appears to be functionally diverse, with some proteins containing domains indicative of a role in dienelactone hydrolase activity, which is involved in the breakdown of dienelactone, a compound related to environmental aromatic pollutants.
Lipopolysaccharide export system LptA (LPS_export_LptA)
Type: Family

This family of proteins is involved in the assembly and transport of lipopolysaccharide (LPS) across the bacterial cell envelope. Members of this family are essential for the translocation of LPS from the inner membrane to the outer membrane. They are believed to form a structural bridge between the inner and outer membranes, interacting with other Lpt proteins such as LptC and LptD to facilitate the movement of LPS through the periplasmic space. This process is critical for maintaining cell envelope integrity, viability, and pathogenicity in various bacterial species. Some family members are known to bind LPS directly and adopt a beta-jellyroll structure, which is characteristic of Lpt proteins in E. coli.
Type VII TA system antitoxin (Type-VII_TA_antitoxin)
Type: Family

This family of proteins functions as antitoxins within type VII toxin-antitoxin (TA) systems. They act by neutralizing their cognate toxins through a modification process known as di-AMPylation. This post-translational modification involves the transfer of adenylyl groups to specific targets, which in the context of TA systems, serves to inhibit the activity of the toxins and prevent cell damage or death. The antitoxins in this family are characterized by their ability to perform this enzymatic activity, which is crucial for the regulation of the TA system and the maintenance of cellular stability under stress conditions.
Caspase-related proteases and regulators (Caspase-related_regulators)
Type: Family

This family of proteins includes both catalytic and non-catalytic members with diverse roles in cellular processes. Catalytic members are involved in apoptosis, immune response, and inflammatory signaling pathways, often through the activation of NF-kappa-B and MAP kinase p38 pathways, and may also have ubiquitin ligase activity. Non-catalytic members act as inhibitors of apoptosis, protecting cells during development or affecting fertility. Some members are involved in epidermal differentiation and cornification, processing key proteins for skin maturation and barrier function. The family displays proteolytic activity with preferences for specific substrates and may also participate in DNA degradation in certain cell types.
GTPase and isobutyryl-CoA mutase domain-containing protein (GTPase/Isobutyryl-CoA_mutase)
Type: Family

This family of proteins includes GTPases with potential chaperone activity, involved in the assembly and repair of enzyme complexes. They may catalyze the reversible interconversion of isobutyryl-CoA and n-butyryl-CoA using radical chemistry. Some members also exhibit ATPase activity and are involved in cofactor delivery and holo-enzyme assembly. The family contains proteins with a P-loop GTPase domain that may act as a chaperone, and a 5'-deoxyadenosylcobalamin binding region homologous to ICM subunits. They may also participate in the repair of their cofactors, which can become inactivated during catalytic turnover.
Nucleic acid metabolism PIN/TRAM-domain-containing protein (Nucleic_acid_metab_PIN/TRAM)
Type: Family

This family of proteins is involved in nucleic acid metabolism, with some members functioning as ATP-dependent DNA helicases that promote Holliday junction branch migration and DNA unwinding. These proteins are implicated in DNA repair processes, particularly at low temperatures, and coordinate with other enzymes to facilitate the resolution of replication forks. Other members of this family possess RNase activity, suggesting a role in RNA metabolism. The presence of PIN and TRAM domains indicates a shared structural framework that may underlie their biochemical functions. The PIN domain is often associated with nuclease activity, while the function of the TRAM domain is less clear but may be involved in RNA binding or processing.
Tail sheath structural protein (Tail_sheath_structural)
Type: Family

This family of proteins includes Tail sheath protein from Bacteriophage T4 , the putative prophage major tail sheath protein from Pseudomonas aeruginosa and similar sequences from tailed bacteriophages and prokaryotic prophages that are involved in the assembly and structural integrity of bacteriophage tails. Members polymerise to form an extended helical structure around the baseplate-tail tube complex of the virus. These proteins are essential for the contraction mechanism during the infection process, where they shift from an extended to a contracted form. This conformational change is critical for driving the inner tail tube through the host cell envelope, creating a channel that allows for the ejection of viral DNA into the host cell, thus facilitating the infection cycle of the bacteriophage.
Polysaccharide Degradation Enzymes (PolySaccharide_Degr_Enz)
Type: Family

This family of proteins includes enzymes involved in the degradation of complex polysaccharides. Members of this family are characterized by their ability to hydrolyze specific glycosidic bonds within their respective substrates. Some act on unsaturated rhamnogalacturonan disaccharides, releasing unsaturated D-galacturonic acid and L-rhamnose, while others are involved in the breakdown of ulvan, a major component of green seaweed cell walls. These enzymes preferentially cleave unsaturated 4-deoxy-L-threo-hex-4-enopyranosiduronic acid in various oligosaccharide configurations, aiding in the complete degradation of the ulvan polymer. The family also includes proteins that may regulate bacterial surface properties in response to plant cell presence.