SII-SWORD/CoKE huggingface dataset:
Bacterial Cell Division Inhibitor SulA (SulA_CellDiv_inhibitor)
Type: Family

The SulA family includes cell division inhibitors that are part of the SOS system, which responds to DNA damage. Members of the SulA family accumulate in response to DNA damage, leading to the cessation of cell division and the formation of long, non-septate filaments. They function by binding to a polymerization-competent form of FtsZ, a key protein in the assembly of the bacterial Z ring, essential for cell division. The binding occurs in a 1:1 ratio in the presence of GTP, inhibiting FtsZ polymerization and thus preventing the formation of the Z ring. This action helps to prevent the segregation of damaged DNA into daughter cells, allowing time for DNA repair mechanisms to correct any damage before cell division resumes.
Arrestin domain-containing protein (Arrestin_domain-protein)
Type: Family

This family of proteins is involved in various cellular processes including endocytosis, ubiquitination, and signal transduction. Members act as adapter proteins, mediating the interaction between ubiquitin ligases and their substrates, which can lead to the ubiquitination and subsequent degradation of target proteins. Some proteins in this family are implicated in the regulation of G protein-coupled receptors (GPCRs) by affecting their cell surface expression and turnover. Others are involved in cellular responses to environmental stimuli, such as pH changes, by participating in the proteolytic cleavage of transcription factors. Additionally, certain members have roles in oxidative stress response, transcriptional repression, cell cycle arrest, and tumor suppression. The family also includes proteins that contribute to the maturation of immune cells and the resistance to toxins and stress.
RSE1/DDB1/CFT1/CPSF1 (RSE1/DDB1/CFT1/CPSF1)
Type: Family

The RSE1/DDB1/CFT1/CPSF1 protein family is involved in various essential cellular processes, including pre-mRNA splicing, DNA repair, cell cycle control, and pre-mRNA 3'-end formation. Members of the family play roles in the spliceosome, a complex that removes introns from pre-mRNAs, and in the recognition and repair of UV-induced DNA damage. They are also part of complexes that mediate ubiquitination and proteasomal degradation of proteins, contributing to genomic stability, transcription-coupled repair, and circadian rhythm regulation. Additionally, they are involved in the cleavage and polyadenylation specificity factor (CPSF) complex, crucial for polyadenylation-dependent pre-mRNA 3'-end formation.
Basic helix-loop-helix transcription factors (bHLH_transcription_factors)
Type: Family

The basic helix-loop-helix (bHLH) protein family includes transcription factors that play crucial roles in various developmental processes, including neurogenesis, myogenesis, and the differentiation of specific cell types. Members of this family are characterized by their ability to bind E-box DNA sequences (CANNTG) and modulate gene expression. They are involved in the activation or repression of target genes, often through dimerization with other bHLH proteins or transcription factors such as TCF3/E47. These proteins contribute to the formation and maturation of neurons, oligodendrocytes, and other cell lineages by regulating the expression of genes critical for cell fate determination and differentiation. Some family members also participate in the maintenance of circadian rhythms, auditory signaling, and the development of sensory organs. The bHLH domain is essential for DNA binding and transcriptional regulation, with some members also possessing domains for repressor or activator functions.
Major Facilitator Superfamily Sugar Transporters (MFS_Sugar_Transporters)
Type: Family

The Major Facilitator Superfamily (MFS) Sugar Transporter family encompasses a diverse group of integral membrane transport proteins involved in the facilitated transport of a wide variety of substrates across cellular membranes. Members of this family are primarily involved in the uptake of sugars such as glucose, fructose, galactose, and quinic acid, which can be catabolized as carbon sources. These transporters operate with varying affinities, enabling organisms to adapt to different concentrations of extracellular sugars. Some members also participate in symport mechanisms, coupling sugar transport with proton movement. Additionally, certain proteins within this family function as sensors in glucose-signaling pathways, although they do not transport glucose themselves. The family includes proteins that contribute to metabolic processes, adaptation to environmental changes, and the biosynthesis of natural products.
Mitochondrial Processing Peptidase/Ubiquinol-cytochrome c Reductase Complex (MPP/UQCRC_Complex)
Type: Family

The Peptidase M16 family includes catalytic and regulatory subunits of the mitochondrial processing protease (MPP), which is essential for cleaving mitochondrial targeting sequences from newly imported proteins, typically after an arginine at position P2. Members of this family are also found as components of the ubiquinol-cytochrome c oxidoreductase complex, part of the mitochondrial electron transport chain, which is crucial for oxidative phosphorylation and ATP synthesis. The family includes proteins involved in electron transfer, proton translocation, and the Q cycle. Some members are implicated in the processing of the Rieske protein and its mitochondrial targeting sequence when incorporated into complex III. The family also contains zinc proteases with diverse functions, including virulence factors that compromise host cell functions and enzymes required for bacteriocin production.
Cation-dependent O-methyltransferase (Cation-dep_OMT)
Type: Family

The Cation-dependent O-methyltransferase family is involved in the methylation of various substrates using S-adenosyl-L-methionine (SAM) as the methyl donor. Members of this family play crucial roles in the biosynthesis of phenylpropanoids, alkaloids, and flavonoids, contributing to plant cell wall reinforcement, pigmentation, and defense responses. They catalyze the O-methylation of compounds such as caffeoyl-CoA, norbelladine, and anthocyanins. Some members are implicated in the production of volatile phenylpropanoids in flowers, while others participate in the biosynthesis of bioactive compounds with potential anticancer properties. The family also includes enzymes involved in the modification of tRNA and the biosynthesis of macrolide antibiotics and polymethoxylated flavonoids.
Major Intrinsic Protein/Aquaporin (MIP/Aquaporin)
Type: Family

The MIP/aquaporin family is a group of membrane proteins that facilitate the transport of water and small solutes across cell membranes. Members of this family are characterized by their ability to form channels that selectively allow the passage of water, glycerol, urea, and other small, non-charged molecules. These proteins are involved in various physiological processes, including osmoregulation, skin hydration, wound healing, and energy homeostasis. Aquaporins play a crucial role in maintaining water balance in cells and are found in a wide range of organisms, from bacteria to humans. Some family members also participate in the transport of gases like carbon dioxide and ammonia, contributing to processes such as nitrogen support in symbiotic relationships and gas exchange.
Cytochrome P450 monooxygenase, fungi (Cytochrome_P450_fung)
Type: Family

The cytochrome P450 family is involved in the biosynthesis of a wide range of secondary metabolites in fungi, including mycotoxins, antibiotics, and other bioactive compounds. Members of this family are typically monooxygenases that catalyse the oxidation of organic substrates using a heme iron to insert one oxygen atom into the substrate while reducing the other oxygen atom to water. These enzymes play key roles in various biosynthetic pathways, often acting on specific intermediates to introduce hydroxyl groups, epoxidize double bonds, or catalyse other oxidative transformations. Their activities contribute to the structural diversification of natural products, which can result in compounds with antimicrobial, antitumor, anti-inflammatory, and psychotropic properties, as well as compounds involved in fungal development and pigmentation .
Mitochondrial import inner membrane translocase subunit TIM50 (TIM50)
Type: Family

The TIM50 family proteins are essential components of the TIM23 complex, which mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane. These proteins are required to direct preproteins in transit to the channel protein TIM23 and may facilitate the transfer of translocating proteins from the TOM complex to the TIM23 complex. Although some members have phosphatase activity in vitro, this activity may not be relevant in vivo. The TIM50 family plays a dynamic role in protein import and does not act as a structural subunit of the TIM23 complex.
Binding-protein-dependent transport system permease (BP-dependent_transpt_permease)
Type: Family

The binding-protein-dependent transport system permease family is involved in the translocation of various substrates across the bacterial inner membrane. Members of this family are typically part of ABC transporter complexes and are responsible for the import or export of substances such as oligopeptides, dipeptides, glutathione, nickel, and other divalent metal ions. These permease proteins play crucial roles in nutrient uptake, resistance to antimicrobial peptides, metal ion homeostasis, and virulence. They are essential for various cellular processes including sporulation, genetic competence, and maintaining urease activity. The family includes subfamilies like OppBC, which are specifically associated with oligopeptide transport, and others that may be involved in the transport of dipeptides or metal ions complexed with metallophores.
Amino acid-polyamine-organocation superfamily (APC_superfamily)
Type: Family

The amino acid-polyamine-organocation (APC) superfamily is a diverse group of membrane transport proteins that facilitate the exchange or uptake of amino acids, polyamines, and organocations across the cell membrane. Members of this superfamily are involved in various biological processes, including acid resistance, substrate exchange for energy conversion, and virulence against host immune responses. They operate through mechanisms such as antiport and symport, often with specificity for substrates like arginine, ornithine, agmatine, putrescine, and GABA. The transport activity of these proteins is frequently regulated by environmental factors such as pH, and they possess structural features like transmembrane helices and central cavities for substrate binding.
Voltage-gated ClC-type chloride channel (ClC-type_chloride_channel)
Type: Family

The ClC-type chloride channel family is involved in the transport of chloride ions across cell membranes. Members of this family are voltage-gated channels that play a role in maintaining cellular ion homeostasis. A subfamily within this group, ClcB, is implicated in acting as an electrical shunt for an outwardly-directed proton pump linked to amino acid decarboxylation, which is a part of the extreme acid resistance response in some bacteria. Additionally, certain plant members of this family are involved in chloride homeostasis, influencing chloroplast ultrastructure and photosynthetic electron transport. Other functions include assisting in nitrogen-fixing root nodule symbiosis and transporting chloride and fluoride with similar efficiency.
Respiratory burst oxidase/Ferric reductase (RBOH/FRE)
Type: Family

The RBOH/FRE family proteins are involved in various redox processes across different species. Members of the RBOH subfamily are calcium-dependent NADPH oxidases that generate superoxide, playing roles in pathogen response, reactive oxygen species (ROS) signaling, and regulation of cellular processes such as stomatal closing. The FRE subfamily members are metalloreductases, likely involved in iron and copper homeostasis, and include ferric chelate reductases that participate in iron mobilization and uptake. Some members also function in copper reduction and are implicated in responses to environmental stressors like copper deficiency. Dual oxidases, another subfamily, generate hydrogen peroxide for thyroid hormone synthesis and antimicrobial defense, with some having peroxidase activity. Collectively, these proteins are integral to cellular redox homeostasis, signaling, and defense mechanisms.
Hairy and Enhancer of Split/HEY-related (HES_HEY)
Type: Family

The HES/HEY protein family includes transcriptional repressors that play crucial roles in various developmental processes, including neurogenesis, myogenesis, and the regulation of circadian rhythms. Members of this family are characterized by their ability to bind DNA on N-box motifs and sometimes E-box motifs, typically acting as negative regulators of gene expression. They are involved in the Notch signaling pathway, contributing to cell fate determination and maintenance of precursor cells. The family is also implicated in cardiovascular development and somite segmentation. Key features include a basic helix-loop-helix domain, an Orange domain, and a C-terminal WRPW motif that mediates interaction with Groucho/TLE corepressors.
Fungal extracellular virulence-associated metalloproteinases (Fungal_virulence_M36)
Type: Family

The peptidase M36 family comprises secreted metalloproteinases that play a role in the assimilation of proteinaceous substrates. Many members are implicated as virulence factors, contributing to the pathogenicity of various organisms by degrading host proteins and facilitating invasion or evasion of the host immune response. These enzymes are characterized by their dependence on metal ions for activity and are inhibited by metalloprotease inhibitors. They are capable of hydrolyzing a variety of peptide bonds and may have substrate specificity, as some are known to cleave specific proteins like elastin or azocasein. The activity of these metalloproteinases is often regulated by metal ions and inhibitors, indicating a tight control of their proteolytic functions, which is crucial for the survival and virulence of the organisms that secrete them.
Neurexin-related cell adhesion and synaptic protein (Neurexin-related_CASP)
Type: Family

This family of proteins is involved in various aspects of neural development and function, including cell recognition, cell adhesion, synaptic junction formation, and signal transmission. Members of this family are typically found on the neuronal cell surface and play roles in the formation and maintenance of synaptic connections by interacting with other proteins such as neuroligins. They are also implicated in the organization of myelinated axons and may influence neurotransmitter release and postsynaptic receptor regulation. Some members are involved in the structural maturation of synapses and may participate in the modulation of growth factor signaling, as well as the regulation of calcium ion homeostasis in neurons.
Fibrinogen C-terminal domain-containing protein (Fibrinogen_C-term_domain)
Type: Family

This family of proteins includes members with diverse roles in innate immunity, angiogenesis, metabolism, and cell adhesion. They are characterized by the presence of a fibrinogen C-terminal domain, which is implicated in various interactions such as binding to carbohydrates, cell surface receptors, or acetylated structures. Some family members function as lectins that recognize specific carbohydrate moieties, initiating complement activation or modulating cell adhesion. Others are involved in vascular development and stability, competing for receptor binding sites and influencing signaling pathways that regulate endothelial cell survival, proliferation, and migration. Additionally, certain proteins within this family can impact lipid metabolism by modulating the activity of enzymes like lipoprotein lipase, influencing triglyceride and cholesterol levels.
RRT5/SRSF/Splicing Factor SR (RRT5_SRSF_SR)
Type: Family

The RRT5/SRSF/Splicing Factor SR family is involved in various aspects of RNA processing, including pre-mRNA splicing, rDNA transcription modulation, and mRNA export. Members of this family play roles in constitutive and alternative splicing, ensuring the accuracy of splicing and regulating splice site selection. Some proteins within this family are implicated in cell cycle progression, spermatogenesis, and response to oxidative stress. Others are involved in ribosome assembly and pre-rRNA processing, contributing to the maintenance of ribosomal subunit levels. The family includes proteins with RNA recognition motifs (RRMs) and serine/arginine-rich (SR) domains, which are characteristic of splicing factors and are essential for spliceosome assembly and function. The family's diverse functions reflect its members' involvement in critical cellular processes, including gene expression regulation, development, and response to cellular stress.
Major Facilitator Superfamily TsgA-like (MFS_TsgA-like)
Type: Family

This family of proteins is part of the major facilitator superfamily (MFS), which is one of the largest groups of secondary transporters. Members of this family are involved in facilitating the transport of various substrates across cellular membranes. The transport mechanism typically involves the use of a proton or sodium gradient to drive the transport process, functioning as symporters, antiporters, or uniporters. While the specific substrates for the TsgA homologs are not detailed in the provided annotations, the MFS transporters generally play a critical role in the uptake of nutrients, efflux of toxins, and maintenance of ion gradients, which are essential processes for cellular function and homeostasis.
Pterin-4-alpha-carbinolamine dehydratase (Pterin-4-alpha-carb_dehyd)
Type: Family

The pterin-4-alpha-carbinolamine dehydratase family includes enzymes involved in tetrahydrobiopterin biosynthesis. These enzymes play a role in preventing the formation of 7-pterins and in accelerating the conversion of dihydrobiopterin to quinonoid dihydrobiopterin. Additionally, they may have a regulatory function in the expression of related genes such as phhA. Tetrahydrobiopterin is an essential cofactor in the hydroxylation of aromatic amino acids and the production of neurotransmitters.
Radical SAM PqqA peptide cyclase/Mycofactocin maturase MftC-like (Radical_SAM_PqqE_MftC-like)
Type: Family

The Radical SAM superfamily is a diverse group of enzymes that perform a wide range of functions, all of which involve radical-based mechanisms. Members of this superfamily are characterised by their use of a [4Fe-4S] cluster to reductively cleave S-adenosylmethionine (SAM) to initiate radical formation. Functions within this family include the biosynthesis of various cofactors, modification of tRNA and rRNA, biotin synthesis, lipid metabolism, and the generation of radical species for use in various enzymatic transformations. Notable reactions catalysed by these enzymes include the formation of thioether bonds, oxidative decarboxylations, and the generation of complex organic molecules. Included in this family are PqqA peptide cyclase (PqqE) which is involved in the biosynthesis of pyrroloquinoline quinone (PQQ), Mycofactocin maturase MftC, an enzyme that catalyses the first step of the biosynthesis of the enzyme cofactor mycofactocin (MFT), Pre-heme d1 synthase which catalyses the removal of two propionate side chains from the intermediate 12,18-didecarboxysiroheme (DDSH) and may introduce the keto functions on rings A and B, yielding the heme d1 precursor dihydro-heme d1 , and other enzymes involved in the biosynthesis of other modified biomolecules, highlighting its critical role in microbial metabolism and physiology.
Metallo-dependent Hydrolases Superfamily (Metallo-dep_Hydrolases_sf)
Type: Family

The Metallo-dependent Hydrolases family encompasses enzymes that catalyze a variety of hydrolytic reactions, often involving cyclic amide bonds. Members of this family are involved in diverse biological processes, including the degradation of dihydropyrimidines, the hydrolysis of D-hydantoin derivatives, and the regulation of cytoskeletal dynamics. Some proteins within this family are necessary for axon guidance and neuronal growth cone collapse, playing a crucial role in neuronal development and cell migration. Others are implicated in the reductive pyrimidine degradation pathway, converting dihydropyrimidines to N-carbamyl-amino acids. Additionally, certain family members participate in the negative regulation of dendrite outgrowth. The family also includes uncharacterized proteins that may have roles in cellular metabolism and signaling.
Type I Cytokine Receptor (Type-I_Cytokine_Rcpt)
Type: Family

The Type I Cytokine Receptor family is characterized by its role in immune system regulation and hematopoiesis. Members of this family are involved in various signaling pathways, such as JAK/STAT, MAPK, and NOTCH, which lead to diverse biological effects including cell proliferation, differentiation, survival, and inflammation control. They are receptors for a range of cytokines, including interleukins, growth hormone, prolactin, and leptin, mediating responses like growth regulation, appetite control, and immune cell development. The receptors typically feature a WSXWS motif essential for proper folding and transport, and a box 1 motif necessary for interaction with JAK kinases. Some receptors also exist in soluble forms, acting as agonists or modulators of signaling. This family plays a critical role in both central and peripheral functions, affecting processes from bone metabolism to neural development and regeneration.
Immune Recognition and Response Modulators (Immune_Resp_Modulators)
Type: Family

This family of proteins includes components involved in the immune system's recognition and response to antigens. Members function as receptors on B and T lymphocytes, recognizing specific antigens to initiate adaptive immune responses. They also serve as effector molecules, mediating various immune functions such as antigen presentation, hypersensitivity reactions, and antibody-dependent cellular cytotoxicity. Some members are involved in the assembly and stabilization of major histocompatibility complex (MHC) class I molecules, facilitating antigen processing and presentation. Others are implicated in mucosal immunity, complement activation, and the clearance of pathogens and apoptotic cells. The family encompasses a range of immunoglobulins with distinct roles in humoral immunity, as well as proteins that interact with natural killer cells to trigger immune activation.
SLX1 structure-specific endonuclease (SLX1_endonuclease)
Type: Family

The SLX1 family consists of catalytic subunits of structure-specific endonucleases that play a crucial role in the resolution of DNA secondary structures, which arise during DNA repair and recombination processes. Members of this family exhibit endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA near junctions with single-stranded DNA. They are involved in maintaining the integrity of ribosomal DNA loci by re-starting stalled replication forks and have been shown to have Holliday junction resolvase activity in vitro. Some family members display a preference for specific DNA structures such as 5'-flap structures, simple Y, and replication fork-like structures, and are capable of generating ligatable, nicked products from these substrates.