SII-SWORD/CoKE huggingface dataset:
HAD-like Sugar Phosphate Phosphatase (HAD-like_SPP)
Type: Family

This family of proteins includes phosphatases that are part of the HAD-like hydrolase superfamily. Members of this family are involved in various metabolic processes, including glycerol biosynthesis, osmoadaptation, and the dephosphorylation of a range of sugar phosphates. Some proteins in this family contribute to cell wall integrity, virulence, and tolerance to certain stress conditions such as anaerobic environments or specific chemicals. The substrates for these enzymes include glycerol-1-phosphate, fructose-1-phosphate, mannitol 1-phosphate, sorbitol 6-phosphate, and other sugar phosphates, indicating a broad specificity within the family. The enzymes are characterized by their ability to catalyze the hydrolysis of phosphate ester bonds, which is a critical reaction in various biochemical pathways.
Secondary metabolite biosynthesis-associated protein (Sec-metab_biosynth-assoc)
Type: Family

This family of proteins is involved in the biosynthesis of various secondary metabolites, including mycotoxins, linear lipopeptides, antibiotics, and meroterpenoids. They are implicated in the activation and processing of amino acid precursors, the formation of polyketides, and the assembly of nonribosomal peptide synthetase (NRPS) products. These proteins may participate in the formation of enzyme complexes, catalyze the epimerization of amino acids, and contribute to the generation of structural diversity in natural compounds through the incorporation of unusual amino acids and fatty acids. The family includes proteins that may function in the oxidative processing of intermediates, the reduction of thioester-linked products, and the cyclization and rearrangement of molecular scaffolds to yield bioactive molecules with potential pharmacological properties.
Type IV pilus biogenesis and competence protein (Type_IV_pilus_biogenesis)
Type: Family

This family of proteins includes components involved in the biogenesis and function of type IV pili, which are filamentous structures on bacterial cell surfaces. These proteins are essential for pilus assembly, serving as a gateway for the pilus to traverse the outer membrane. Additionally, they are implicated in bacterial competence, facilitating the uptake of extracellular DNA, which can be a source of nutrients or genetic information for horizontal gene transfer. Some members may also act as channels for the entry of various substances, including heme and antimicrobial agents, into the bacterial cell.
Plant receptor-like serine/threonine-protein kinase (Plant_receptor-like_S/T_kinase)
Type: Family

This family of proteins includes receptor-like serine/threonine-protein kinases that play crucial roles in plant immunity and development. They are involved in the perception of pathogen-associated molecular patterns (PAMPs) and endogenous elicitors, triggering immune responses. Some members are responsible for the detection of specific bacterial proteins, leading to a series of intracellular events, such as protein cleavage, kinase chain release, and translocation to the nucleus to regulate transcription factors. Other members act as receptors for defense peptides or brassinosteroids, contributing to the regulation of plant growth, defense hormone expression, and feedback regulation of hormone biosynthesis. They may also possess dual specificity kinase activity, phosphorylating serine/threonine and tyrosine residues, and some have additional functions such as modulating seed size.
Precorrin Methyltransferase (Precorrin_MeTrfase)
Type: Family

The precorrin methyltransferase family is involved in the biosynthesis of cobalamin (vitamin B12). Members of this family are responsible for various methylation steps in the transformation of precorrin-2 into different intermediates leading towards the final cobalamin structure. These enzymes catalyze the methylation of specific carbon positions on the corrin ring, which is essential for the ring contraction and the formation of cobalt-factor intermediates. Some family members exhibit bifunctional activity, possessing both methyltransferase and isomerase domains, contributing to the conversion of higher precorrin forms into cobyrinate. The precise function of each enzyme varies, but all share the common goal of progressing the complex pathway of cobalamin biosynthesis through methyl group transfer and ring modification reactions.
Cytochrome c550/c551-like (Cytochrome_c550/c551-like)
Type: Family

The cytochrome c family is involved in various electron transfer processes within cells. Members of this family serve as electron carriers or as components of larger enzyme complexes that participate in respiratory and metabolic pathways. For instance, some cytochromes c are essential for organisms to utilize specific carbon sources for energy, such as cytochrome c550 in Pseudomonas aeruginosa which is essential for ethanol oxidation . Others are involved in the menaquinol:cytochrome c reductase complex, contributing to the electron transport chain . Certain family members act as natural electron acceptors for enzymes like formate dehydrogenase in the case of Cytochrome c-553, while others facilitate electron flow between respiratory complexes. The diversity of functions highlights the family's role in adapting to different environmental and metabolic conditions.
Sugar Phosphate Isomerase LacAB/RpiB (SPI_LacAB/RpiB)
Type: Family

This family of proteins includes enzymes that are involved in the isomerization of sugar phosphates, which is a critical step in various metabolic pathways. Members of this family catalyze the conversion of D-erythrulose 4-phosphate to D-erythrose 4-phosphate, a reaction that is part of the catabolism of D-apiose and other sugar alcohols like erythritol, L-threitol, and D-threitol. This allows certain bacteria to utilize these compounds as their sole carbon source. Some family members also catalyze the interconversion of ribulose-5-phosphate and ribose-5-phosphate, which is an important reaction in the pentose phosphate pathway. The activity of these enzymes can be regulated by various metabolites, indicating their role in the fine-tuning of cellular metabolic fluxes.
HepT RNase Toxin (HepT_RNase_toxin)
Type: Family

The HepT RNase toxin family comprises proteins that are likely toxic components of type VII toxin-antitoxin (TA) systems. Members of this family are predicted to function as RNases, which can inhibit cell growth when overexpressed. These toxins are typically neutralized by their cognate antitoxins, which are thought to act through AMPylation, a post-translational modification that can inactivate the RNase activity. The interaction between these toxins and antitoxins is crucial for the regulation of cellular processes and the maintenance of genomic stability. The HepT RNase toxin family is characterized by a conserved domain that is responsible for its ribonuclease activity, and members are found in various bacterial species.
NAD(P)H-dependent FMN reductase (NAD(P)H-dep_FMN_reductase)
Type: Family

This family of proteins includes NAD(P)H-dependent flavin mononucleotide (FMN) reductases that are involved in various biological processes, including the degradation of dimethyl sulfide and tryptophan. Members of this family catalyze the reduction of FMN to FMNH2, using NADH or NADPH as electron donors. Some proteins within this family are also capable of reducing FAD to FADH2. These reductases are implicated in the formation of two-component reduced FMN-dependent monooxygenase systems, which are essential for the metabolism of specific sulfonates and amino acids such as methionine. The activity of these enzymes is crucial for certain bacterial growth pathways and degradation processes.
Molybdate-responsive transcriptional regulator (Molybdate_resp_trans_reg)
Type: Family

This family of proteins includes transcriptional regulators that interact with molybdate. They function as sensors and regulators of molybdate transport and metabolism within the cell. Upon molybdate binding, these proteins undergo conformational changes that facilitate dimerization. The resulting dimer is capable of binding DNA, particularly upstream of operons like modABC, which are involved in molybdate transport. These proteins can act as repressors or enhancers of gene expression, affecting not only molybdate transport systems but also genes encoding molybdoenzymes. Some family members have been shown to bind tungstate as well. Structurally, these proteins are characterized by a winged helix-turn-helix motif for DNA interaction and a molybdate-binding domain that stabilizes the dimer upon ligand binding.
Glycosyl Hydrolase Family 31 (Glycosyl_Hydrolase_31)
Type: Family

The glycosyl hydrolase 31 family is involved in the degradation of various oligosaccharides. Members of this family catalyze the hydrolysis of glycosidic bonds, specifically liberating alpha-xylose from the non-reducing terminal glucose of xyloglucan oligosaccharides, which is crucial in xyloglucan degradation. Some enzymes within this family exhibit a preference for certain substrates, such as the alpha-(1-3)-isomaltosyl moiety, and are involved in the intracellular degradation of specific cyclic tetrasaccharides. The family's enzymes are characterized by their ability to recognize and cleave distinct linkages in oligosaccharides, contributing to diverse metabolic processes including the breakdown and utilization of complex carbohydrates.
Formate dehydrogenase cytochrome b556 subunit (FDH_cytochrome_b556_subunit)
Type: Family

This family of proteins includes subunits of formate dehydrogenases, which are enzymes that allow bacteria to use formate as a major electron donor in various types of respiration. Some members are involved in aerobic respiration, while others participate in anaerobic respiration, using nitrate as an electron acceptor. These proteins typically contain a cytochrome b556 component and may also have a menaquinone reduction site. They play a role in the generation of proton motive force and are associated with other systems such as dissimilatory nitrate reductase.
Thiamine pyrophosphate-dependent decarboxylase (TPP_dependent_decarboxylase)
Type: Family

The TPP enzyme family is involved in the biosynthesis of small molecule compounds through the decarboxylation of specific substrates. Members of this family catalyze the decarboxylation of sulfopyruvate to sulfoacetaldehyde, which is a step in the biosynthesis of coenzyme M (2-mercaptoethanesulfonic acid). Additionally, some members are responsible for the decarboxylation of phosphonopyruvate (PnPy) to phosphonoacetaldehyde (PnAA), a precursor in the biosynthesis of phosphinothricin tripeptide (PTT), a natural-product antibiotic and herbicide known as bialaphos (BA). The activity of some enzymes in the family is regulated by oxygen and can be inhibited at high temperatures, although reactivation is possible with reducing agents such as dithionite.
PTS system sugar-specific EIIB domain-containing protein (PTS_sugar-specific_EIIB)
Type: Family

This family of proteins is involved in the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which is a major carbohydrate active transport system. These proteins function by catalyzing the phosphorylation of incoming sugar substrates simultaneously with their translocation across the cell membrane. Members of this family are responsible for the transport of various sugars including N,N'-diacetylchitobiose, galactose, lichenan, cellobiose, and oligo-beta-mannosides. They contain a PTS EIIB type-3 domain that is phosphorylated by phospho-EIIA on a cysteinyl residue, which then transfers the phosphoryl group to the sugar substrate in coordination with the sugar uptake processed by the PTS EIIC type-3 domain.
FAD-binding Monooxygenase (FAD-binding_MO)
Type: Family

This family of proteins includes FAD-binding monooxygenases that are involved in various oxidative reactions. Members of this family catalyze Baeyer-Villiger oxidation reactions, converting ketones into esters or lactones, and are capable of acting on a range of substrates from long-chain aliphatic ketones to aromatic ketones. Some members are also involved in the enantioselective sulfoxidation of sulfides. Additionally, certain proteins within this family play a role in the activation of thiocarbamide-containing pro-drugs, transforming them into cytotoxic species that are effective against bacterial pathogens. These enzymes are also implicated in maintaining cell envelope integrity by regulating mycolic acid composition in response to environmental changes.
Aspartyl/Asparaginyl beta-hydroxylase domain-containing protein (Asp/Asn_beta-hydroxylase)
Type: Family

This family of proteins includes enzymes that may function as 2-oxoglutarate-dependent dioxygenases. These enzymes are involved in various biological processes, including the hydroxylation of specific residues in proteins, which can affect protein stability, localization, and interaction with other molecules. Some family members are implicated in the biosynthesis of ornithine lipids, which are important for membrane structure in certain organisms and contribute to symbiotic performance and acid tolerance.
Glycosyl Hydrolase Family 84 (Glycosyl_Hydrolase_84)
Type: Family

The glycosyl hydrolase 84 family is characterized by its ability to cleave N-acetylglucosamine (GlcNAc) from O-glycosylated proteins. Members of this family can utilize substrates such as p-nitrophenyl-beta-GlcNAc and 4-methylumbelliferone-GlcNAc in vitro, but do not act on p-nitrophenyl-beta-GalNAc or p-nitrophenyl-alpha-GlcNAc. The family includes enzymes that are inhibited by various compounds, including PUGNAc and metal ions, depending on the specific protein. Some members are also reported to bind acetyl-CoA and may have acetyltransferase activity, while others do not bind acetyl-CoA and lack histone acetyltransferase activity. The family's function is essential for the regulation of protein post-translational modifications through the removal of O-GlcNAc, impacting numerous cellular processes.
Aspartate-semialdehyde dehydrogenase-related (ASADH-related)
Type: Family

This family of proteins includes enzymes that are primarily involved in the biosynthesis of amino acids through catalytic activities. Members of this family are known to catalyze the NADPH-dependent formation of L-aspartate-semialdehyde from L-aspartyl-4-phosphate, a critical step in the biosynthetic pathway leading to various amino acids such as lysine, methionine, and threonine. Some members also have the ability to reduce malonyl-CoA to malonate semialdehyde, which is a key reaction in certain metabolic cycles. These proteins typically have a nucleotide-binding domain and a dimerization domain, indicating a common structural framework that supports their enzymatic functions. The activities of these enzymes are essential for the proper functioning of cellular metabolism and the synthesis of important biomolecules.
LRR Receptor-Like Ser/Thr Protein Kinase (LRR_Rcpt-Like_S/T_Kinase)
Type: Family

This family of proteins includes receptor-like serine/threonine-protein kinases with leucine-rich repeat (LRR) domains. These kinases are part of the protein kinase superfamily and play a crucial role in signal transduction pathways. They are involved in various cellular processes, including growth, differentiation, and immune response. The LRR domains typically facilitate protein-protein interactions, which are essential for the recognition of specific ligands or substrates, leading to the activation of the kinase domain and subsequent phosphorylation of target proteins.
SRC Kinase Signaling Inhibitor (SRCIN1)
Type: Family

The SRCIN1 family is involved in the regulation of the actin cytoskeleton and cell signaling pathways. Members of the family act as negative regulators of SRC kinase, activating CSK which in turn inhibits SRC activity. This inhibition impacts cell spreading and migration. In the nervous system, the family plays a role in dendritic spine morphology, calcium-dependent exocytosis, and possibly in neurotransmitter release or synapse maintenance. Additionally, some members are required for the normal development of intervertebral disks. The family also includes proteins that are involved in morphogenesis and may share similarity with yeast BUD6 in their role in actin cytoskeleton organization.
E3 ubiquitin-protein ligase domain-containing protein (E3_ubiquitin-ligase_domain)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases that are involved in various cellular processes, including the regulation of cell proliferation and apoptosis. They play a role in mediating ubiquitination and subsequent proteasomal degradation of specific target proteins. Some members are involved in the negative regulation of NOD2 signaling pathways by targeting RIPK2 for degradation. Others are implicated in the endoplasmic reticulum-associated degradation (ERAD) pathway, such as the ubiquitination of CANX. Additionally, certain family members are associated with the regulation of ER stress responses, including the activation of JNK signaling and the splicing of XBP1 mRNA. The family also includes proteins that may function in protein trafficking and localization, as well as in the sorting of vacuolar proteins.
CRISPR-associated exonuclease Cas4 (Cas4_exonuclease)
Type: Family

The CRISPR-associated exonuclease Cas4 family proteins are involved in the CRISPR adaptive immune system, which defends against mobile genetic elements such as viruses, transposable elements, and conjugative plasmids. Members of the Cas4 family are implicated in the processing of CRISPR clusters into CRISPR RNA (crRNA), which are transcribed and then target invading nucleic acids. Cas4 proteins typically exhibit 5' to 3' ssDNA exonuclease activity, and some have been shown to possess Mn(2+)-dependent endonuclease activity on circular ssDNA. They can also bind and potentially unwind dsDNA without the requirement for ATP. The endonuclease activity of Cas4 proteins contributes to the generation of crRNA by cleaving sequences complementary to foreign genetic elements.
HAD-like hydrolase domain-containing protein (HAD-like_hydrolase_domain)
Type: Family

This family of proteins includes members that are part of the HAD-like hydrolase superfamily. These proteins are characterized by a haloacid dehalogenase-like hydrolase domain, which suggests a role in catalyzing the hydrolysis of various substrates. The specific biochemical functions within this family may vary, but typically involve the cleavage of a covalent bond through the addition of water, a reaction fundamental to diverse metabolic processes. The presence of this domain indicates that the proteins may function in dehalogenation reactions or other hydrolytic processes, contributing to cellular metabolism and the regulation of various biological pathways.
Multiheme Cytochrome Electron Transporters (Multiheme_Cytochr_ET)
Type: Family

The protein family encompasses a group of multiheme cytochromes involved in various anaerobic respiratory processes. Members of the family are known to mediate electron transport in the reduction of Fe(3+) and sulfite to sulfide, acting as crucial components in the electron transfer chain under anaerobic conditions. While some members, such as OmcB, are specifically involved in Fe(3+) reduction, others like MccA and SirA catalyze the reduction of sulfite to sulfide. Notably, OmcC is not involved in Fe(3+) reduction, indicating a diversity of functions within the family. The family's role in these processes is essential for the survival of microorganisms in environments where oxygen is scarce or absent.
Neurogenic locus notch homolog (NOTCH_homolog)
Type: Family

The NOTCH family proteins are involved in cell-fate decisions and developmental processes. They function as receptors for membrane-bound ligands, such as Jagged and Delta proteins, to regulate differentiation, proliferation, and apoptosis. NOTCH proteins are essential in various biological contexts including hematopoiesis, cardiovascular development, thymic maturation, angiogenesis, and neurogenesis. They also play roles in left/right symmetry determination and tissue remodeling. Upon ligand binding, the NOTCH intracellular domain (NICD) translocates to the nucleus to form a transcriptional activator complex, influencing gene expression. The family's activity is crucial for various stages of development and can be involved in tumorigenesis when dysregulated.
Bromodomain-containing (Bromodomain_contain_prot)
Type: Family

The Bromodomain-containing protein family is involved in chromatin remodeling and regulation of transcription. Members act as coactivators and corepressors, influencing the expression of target genes. They bind to promoters, modulating histone acetylation, particularly at 'Lys-9' (H3K9ac), and recruit various proteins like BRCA1 and POU2F1. Some family members activate the Wnt signaling pathway by interacting with DVL1 and negatively regulating GSK3B, leading to dephosphorylation at 'Tyr-216'. They also play roles in cell cycle control, particularly in TP53-mediated cell-cycle arrest and transcriptional activation of TP53 target genes, promoting TP53 acetylation for efficient DNA binding. Additionally, certain members are involved in homologous recombination by orchestrating RAD51-RAD54 complex formation.
Regulators of mTOR signaling and Rac activation (mTOR-Rac_regulators)
Type: Family

This family of proteins includes guanine nucleotide exchange factors (GEFs) that activate Rac proteins by exchanging GDP for GTP, and are synergistically activated by phosphatidylinositol 3,4,5-trisphosphate and beta gamma subunits of heterotrimeric G proteins. Some members function as negative regulators of the mTORC1 and mTORC2 complexes, inhibiting their protein kinase activity and inducing autophagy. Others act as cholesterol-binding proteins that regulate mTORC1 signaling by sensing cholesterol sufficiency, disrupting interactions between GATOR1 and KICSTOR complexes to promote signaling, or inhibiting it during cholesterol starvation.
Transcription-coupled DNA damage response regulator-like (TC-DDR_regulator)
Type: Family

This family of proteins is involved in the regulation of transcription-coupled DNA damage response. Members of this family function by recruiting the ubiquitination machinery to RNA polymerase II, facilitating its polyubiquitination, removal, and subsequent degradation in cases where transcription-coupled nucleotide excision repair mechanisms fail to resolve DNA damage. Additionally, some members are implicated in the maintenance and activity of long-term repopulating hematopoietic stem cells and the formation of stress granules. Others are known to play a role in the nervous system, particularly in controlling copulatory organs during courtship. There is also involvement in telomere length regulation and DNA binding.

This family also includes pqn-59 which Modulates gene expression and cell fate specification during development and antagonises the activities of multiple heterochronic microRNAs such as lin-4 and let-7 miRNAs .
RING finger E3 ubiquitin-protein ligase (RING_finger_E3_ligase)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases that are involved in the ubiquitination and subsequent proteasomal degradation of various target proteins. They play roles in regulating transcription factors, particularly those with LIM domains, by mediating the degradation of their cofactors. This action allows the transcription factors to interact with other proteins and modulate gene expression. Some family members are involved in the regulation of telomere length and the random inactivation of the X chromosome during embryonic development. They also contribute to the establishment of proper protein complexes by regulating the stoichiometry of specific protein interactions. Additionally, they have roles in cellular processes such as axonal outgrowth and transcriptional regulation of hormone receptors.