SII-SWORD/CoKE huggingface dataset:
Band 7/mec-2 domain-containing protein (Band7/mec-2_domain)
Type: Family

This family of proteins includes members that are involved in various cellular processes, such as the regulation of protease activity, hypersensitive response (HR)-like cell death, and mitochondrial function. Some proteins in this family are thought to regulate or encode a specific protease, influencing the stability of certain proteins. Others act as positive regulators of HR-like cell death and may be involved in potassium ion channel regulation. Additionally, certain members are associated with mitochondrial biogenesis and activity, including cardiolipin biosynthesis, mitochondrial membrane organization, and stress responses such as mitochondrial hyperfusion. These proteins may also play roles in cell migration, proliferation, T-cell activation, and calcium homeostasis.
Electron transfer and nitrogen metabolism enzyme (ET-N_metabolism_enzyme)
Type: Family

This family of proteins includes enzymes that are involved in electron transfer processes and nitrogen metabolism. Members of this family function as electron carriers, transferring electrons from NADPH or NADH to various acceptor molecules, often as part of P450 systems. These proteins are essential for the biosynthesis of steroid hormones and other metabolic processes in mitochondria. Additionally, some family members catalyze the synthesis of glutamate from glutamine and 2-oxoglutarate, playing a critical role in amino acid metabolism and the assimilation of nitrogen. The activity of these enzymes is regulated by various factors, including phosphorylation and the presence of specific substrates or inhibitors.
NAD(P)H-dependent reductase (NAD(P)H-dep_reductase)
Type: Family

The protein family is involved in various reductive processes, primarily acting as reductases that utilize NAD(P)H as an electron donor. Members of the family catalyze the reduction of azo bonds in aromatic azo compounds, quinones, and potentially other substrates, producing less reactive or toxic species. These activities are crucial for cellular detoxification pathways, including the metabolism of aromatic compounds and protection against oxidative stress. Some family members also participate in biosynthetic pathways, such as the production of meroterpenoids and arthripenoids, and may be involved in iron assimilation. The family includes enzymes that can reduce chromate, contributing to cellular defense mechanisms against chromate toxicity.
Receptor-type Tyrosine-protein Phosphatases/Ushers (RTP_Phos/Ushers)
Type: Family

The protein family includes receptor-type tyrosine-protein phosphatases and ushers, which are involved in a variety of biological processes including cell adhesion, migration, proliferation, differentiation, and angiogenesis. Members of the family play crucial roles in the maintenance and remodeling of blood vessels, as well as in the regulation of cell signaling pathways through their enzymatic activity of dephosphorylation. They are essential for normal brain development, auditory function, and vision, acting in complexes such as the USH2 complex for the maintenance of periciliary membrane complexes and hair bundle ankle formation. Additionally, they contribute to contact inhibition of cell growth, apoptotic cell death, and the suppression of immune responses. The family's phosphatases are involved in the regulation of energy metabolism and may also influence the differentiation of cells in bone and testis.
Cobalamin biosynthesis methyltransferase (Cobalamin_biosynth_MTase)
Type: Family

This family of proteins is involved in the biosynthesis of cobalamin (vitamin B12) and other related tetrapyrroles. Members of this family function as methyltransferases, catalyzing the transfer of methyl groups to specific carbon atoms within the tetrapyrrole ring. The enzymes typically methylate cobalt-precorrin-6B at C-15 followed by decarboxylation at C-12 to produce cobalt-precorrin-7, or they methylate precorrin-6Y at both C-5 and C-15 to form precorrin-8X. Some members are bifunctional and can perform both methylation steps in the pathway. The activity of these proteins is crucial for the proper formation of the corrin ring, which is a central component of cobalamin and related compounds. These compounds play essential roles in various biological processes, including DNA synthesis, fatty acid metabolism, and amino acid metabolism.
Leucine-rich repeat and signaling effector domain-containing protein (LRR-SigEffector_domain)
Type: Family

This family of proteins includes various members with roles in cellular signaling pathways, immune responses, and structural components of cells. Some act as effectors in the Ras-MAPK signaling cascade, regulating the activity of kinases such as Raf to modulate cell proliferation and differentiation. Others are involved in disease resistance in plants, recognizing specific pathogens and triggering immune responses. Certain family members are structural, contributing to the integrity of the sarcomeric M-band in muscle cells and influencing myocyte response to stress. Additionally, some proteins in this family are implicated in the regulation of nuclear import of growth factors, while others may participate in protein-protein interactions within signal transduction pathways. The family also includes proteins with enzymatic functions, such as adenylate cyclases that synthesize cAMP, a key second messenger in metabolic regulation, and protein phosphatases involved in dephosphorylation processes.
Membrane-associated guanylate kinase (MAGUK)
Type: Family

The MAGUK family proteins are multifunctional scaffolding proteins that play pivotal roles in cell polarity, tight junction biogenesis, and synaptic transmembrane protein anchoring. They are involved in various cellular processes including the regulation of neutrophil polarity, epithelial cell polarity, vascular lumen formation, and neuronal progenitor cell survival. These proteins are essential for the correct localization and trafficking of various cellular components, such as adherens junction proteins, myelin proteins, and vesicular markers. They also participate in signal transduction pathways, potentially influencing mTOR signaling and NF-kappa-B activation. Additionally, they have a role in the maintenance and organization of cerebellar progenitor cells and retinal development. The MAGUK family members contain characteristic domains such as PDZ, L27, and PRBH, which mediate their interactions with other proteins and membranes.
C2H2-type Zinc-Finger Transcription Regulators (C2H2-ZF_Transcription_Reg)
Type: Family

The protein family is characterized by members that function predominantly as transcription factors or transcriptional repressors involved in various developmental processes. These proteins play key roles in embryonic development, including heart and urogenital system formation, leg joint formation, hindgut patterning, and morphogenesis. They are also implicated in the regulation of gene expression related to H2O2 metabolism, the mitochondrial apoptotic cascade, and cellular differentiation pathways such as adipocyte differentiation and osteoblast suppression. Some family members are involved in tooth formation and kidney development. The proteins typically contain C2H2-type zinc-finger domains, which are essential for DNA-binding and transcriptional regulation, and some possess additional domains like KRAB for transcriptional repression. The family includes proteins with diverse functions across different species, unified by their structural features and roles in transcriptional regulation.
ApaG-like (ApaG-like)
Type: Family

This family of proteins is involved in various cellular processes. The specific functions of these proteins may include enzymatic activity, structural roles, signaling, or regulation of other proteins. Members of this family may be associated with metabolic pathways, cellular transport, or may act as receptors or channels. The exact function of this family of proteins can vary widely depending on the organism and the cellular context in which they are expressed.
Cortactin-binding and Actin Dynamics Regulator (Cortactin-Actin_Reg)
Type: Family

The protein family is involved in the regulation of actin dynamics and dendritic spine maintenance in neurons. Members of the family control the distribution of cortactin in hippocampal neurons, influencing dendritic spinogenesis. Some proteins within the family interact with filamin-A and F-actin, affecting cell migration from the ventricular zone and potentially inducing filamin-A degradation. Others regulate lamellipodial actin dynamics in a cortactin-dependent manner, impacting actin branch density and lamellipodial protrusion. Additionally, certain members exhibit antiangiogenic activity in endothelial cells, inhibiting cell proliferation, migration, and inducing apoptosis, and can inhibit tumor growth when expressed in tumor-associated vasculature.
Engrailed Homeobox Transcription Factors (Engrailed_Homeobox_TFs)
Type: Family

The engrailed homeobox family is a group of transcription factors characterized by the presence of a homeobox domain. These proteins play crucial roles in developmental processes, including the specification of body segmentation patterns, the development of the central nervous system, and limb patterning. They function as transcriptional regulators, with some members repressing activated promoters, while others act as activators. The family is also involved in maintaining the boundaries between different cell types during embryogenesis, promoting seam cell development and differentiation, and regulating gene expression to prevent cell fusion. Additionally, some members are implicated in shell and shell gland formation, as well as in the compartmentalization of the silk gland.
Trk/Ktr/HKT Potassium Transport (Trk_Ktr_HKT_K-transport)
Type: Family

The Trk/Ktr/HKT potassium transport family encompasses a variety of proteins involved in potassium uptake and regulation across different organisms. Members of the family participate in essential cellular processes such as maintaining osmotic balance, regulating cell volume, and contributing to the electrical excitability of cells. The family includes proteins that form part of constitutive potassium transport systems like TrkG and TrkH, which are regulated by binding to NAD(+) and NADH. Some members are involved in resistance to osmotic stress and antimicrobial peptides. Others are voltage-gated or calcium-gated potassium channels, which open in response to changes in membrane potential or the presence of calcium ions, respectively. The RCK N-terminal domain is a common feature within the family, binding NAD and other effectors to induce conformational changes that regulate potassium transport. While most family members are directly involved in potassium transport, some modulate the activity of other transporters or channels, highlighting the diversity of functions within this protein family.
Pyruvate:ferredoxin/flavodoxin oxidoreductase (Pyruvate:ferred/Flavod_OxRd)
Type: Family

The pyruvate:ferredoxin/flavodoxin oxidoreductase family comprises enzymes that catalyze the oxidative decarboxylation of various 2-oxoacids, such as pyruvate, 2-oxobutyrate, and 2-oxoglutarate, to form their CoA derivatives. These reactions are crucial for connecting glycolysis to other metabolic pathways like the Wood-Ljungdahl pathway and the tricarboxylic acid cycle. Members of this family are also involved in the reduction of ferredoxin or flavodoxin, which can subsequently provide reducing equivalents for processes such as nitrogen fixation. The family includes pyruvate synthase subunits, ketoisovalerate oxidoreductases, and oxalate oxidoreductases, highlighting its role in a diverse range of metabolic processes. Some members are sensitive to oxygen, and others are regulated by cofactors like magnesium ions and thiamine diphosphate.
Cyclopropane Fatty Acid Synthase/Methyltransferase (CFA/CMAS)
Type: Family

The CFA/CMAS family comprises enzymes that modify fatty acids and related molecules, primarily through the transfer of methyl groups from S-adenosyl-L-methionine (SAM). Members of this family are involved in the biosynthesis of mycolic acids, which are critical components of the mycobacterial cell wall, affecting cell envelope permeability, host immunomodulation, and persistence. The family includes mycolic acid methyltransferases that convert cis-olefins to trans-olefins and introduce methyl branches, cyclopropane mycolic acid synthases that form cyclopropane rings in mycolic acids, and enzymes involved in the biosynthesis of oxygenated mycolic acids such as methoxymycolate and ketomycolate. Some members also modify short-chain fatty acids and participate in the biosynthesis of antibiotics like novobiocin.
Glutamate/Leucine/Phenylalanine/Valine dehydrogenases (Glu_Leu_Phe_Val_DH)
Type: Family

The Glu/Leu/Phe/Val dehydrogenases family includes enzymes that catalyze the reversible oxidative deamination of glutamate to alpha-ketoglutarate and ammonia, a reaction that plays a central role in nitrogen metabolism. Members of this family are primarily NADP-specific, although some can utilize both NAD and NADP as cofactors, indicating potential roles in both anabolic and catabolic pathways. The enzymes are competitively inhibited by various compounds, suggesting a regulatory role in amino acid metabolism. The family is characterized by a broad taxonomic distribution, with members found in various organisms including yeasts, bacteria, and fungi.
CysQ/Inositol Monophosphatase (CysQ/Inositol_MonoPase)
Type: Family

The CysQ/Inositol Monophosphatase family comprises enzymes that primarily function as phosphatases with a broad specificity. They are involved in various metabolic processes, including the hydrolysis of adenosine 3',5'-bisphosphate (PAP) to adenosine 5'-monophosphate (AMP), a reaction that is central to the regulation of intracellular levels of PAP. Some family members also convert adenosine 3'-phosphate 5'-phosphosulfate (PAPS) to adenosine 5'-phosphosulfate (APS). Additionally, these enzymes participate in inositol phosphate metabolism, although with lower activity towards inositol phosphates compared to PAP. The family plays a role in sulfur metabolism by regulating the pools of PAP and PAPS in cells. Members of the CysQ/Inositol Monophosphatase family are characterized by their sensitivity to inhibition by lithium, which is of particular interest in the study of mood disorders where lithium salts are used therapeutically.
Metabotropic Glutamate Receptor (mGluR)
Type: Family

The G-protein coupled receptor 3 family is characterized by its members' ability to act as receptors for glutamate, which upon ligand binding, undergo conformational changes that trigger signaling via guanine nucleotide-binding proteins (G proteins). The signaling pathways modulate the activity of downstream effectors, such as adenylate cyclase, which is commonly inhibited by these receptors. The family plays a crucial role in various neural processes, including synaptic plasticity, neural network activity modulation, and visual signal transduction. Some members are involved in developmental processes like axon outgrowth regulation and eye development. The receptors may also participate in the CNS's central action of glutamate, influencing long-term potentiation and depression.
Glycosyl hydrolase 43 family arabinanases (GH43_arabinanases)
Type: Family

The glycosyl hydrolase 43 family is characterized by proteins that function primarily in the degradation of pectin, a major component of the plant cell wall. Members of this family are endo-1,5-alpha-L-arabinanases, which catalyze the hydrolysis of internal alpha-1,5-linked arabinofuranosyl residues in arabinan-containing polysaccharides. These enzymes are involved in the breakdown of linear 1,5-alpha-L-arabinan, a key process in the utilization of plant-derived carbohydrates. The activity of these enzymes is essential for the complete degradation of the plant cell wall, facilitating access to other cell wall components and contributing to the carbon cycle. The enzymes preferentially act on linear arabinan but can also process branched arabinan substrates, albeit at different efficiencies. The family includes both extracellular and intracellular enzymes, with some members displaying specificity towards short arabino-oligosaccharides.
Extracellular Zinc Metalloprotease M4 (Zinc_Metalloprotease_M4)
Type: Family

The Peptidase M4 family comprises extracellular zinc metalloproteases involved in a variety of biological processes, including pathogenesis, immune evasion, and protein activation. Members of this family have been implicated in the degradation of various substrates such as gastric mucus, elastin, collagen, and casein, which may contribute to ulcer formation, bacterial virulence, and tissue colonization. Some family members are known to cleave and activate other proteins, such as transglutaminase and cholera enterotoxin, playing roles in bacterial development and infection. The proteolytic activity of these enzymes is typically regulated by metal chelators, indicating their dependence on metal ions for function.
Rho GTPase-activating protein (Rho-GAP)
Type: Family

This family of proteins includes Rho GTPase-activating proteins (GAPs) that are primarily involved in the regulation of Rho-type GTPases. These proteins typically inactivate GTPases by accelerating the hydrolysis of GTP to GDP, thereby switching the GTPase from an active to an inactive state. Members of this family are implicated in various cellular processes, including signal transduction pathways, cell integrity, stress responses, polarized cell growth, bud site selection, and clathrin-mediated endocytosis. Some proteins within this family are also involved in the regulation of the actin cytoskeleton, contributing to cell contraction and the formation of stress fibers. Additionally, certain members interact with phosphoinositides, which may influence their localization and activity within the cell.
UBX domain-containing protein (UBX_domain-protein)
Type: Family

This family of proteins is involved in various cellular processes including ciliogenesis, endoplasmic reticulum-associated degradation (ERAD), and ubiquitin-dependent protein degradation. Members of this family function as ubiquitin-binding adapters or tethering factors, facilitating the recruitment of segregase VCP/p97 to specific protein complexes. They play roles in the regulation of protein turnover by mediating the degradation of misfolded proteins in the ER and the progression of DNA replication forks. Some members are also implicated in the disassembly of stress granules and may influence signaling pathways by controlling receptor expression levels. The family includes proteins with UBX domains that mediate interactions with VCP/p97 and may contain additional domains such as UBA and UIM, which are involved in binding ubiquitinated substrates and engaging NEDD8 modifications on cullins, respectively.
HRD1 family E3 ubiquitin-protein ligases (HRD1_E3_ubiq-ligases)
Type: Family

The HRD1 family of E3 ubiquitin-protein ligases is involved in the endoplasmic reticulum-associated degradation (ERAD) system, which mediates the ubiquitination and subsequent proteasomal degradation of misfolded or short-lived proteins in the endoplasmic reticulum (ER). Members of the HRD1 family accept ubiquitin from specific E2 ligases and transfer it to substrates, facilitating their removal from the ER and degradation. This process is crucial for maintaining protein homeostasis and ER quality control, and it protects cells from ER stress-induced apoptosis. Some family members also regulate various cellular processes, including cell cycle regulation, apoptosis, and cholesterol homeostasis, by targeting specific proteins such as p53, HMGCR, and components of the NADPH oxidase complex.
Beta-glucan modifying enzymes (Beta-glucan_modifiers)
Type: Family

This family of proteins includes enzymes predominantly involved in the hydrolysis and modification of beta-glucans. Members of this family are implicated in various biological processes, such as cell wall remodeling during growth, mating, and sporulation. They are active on substrates like laminarin and lichenan, and some are involved in the degradation of cellulosic biomass, catalyzing the release of glucose from cellobiose. Certain proteins within this family also contribute to pathogenicity, biofilm matrix formation, and immune response modulation in host organisms. Their activities are essential for maintaining cell wall integrity and facilitating cellular morphogenesis and adhesion.
Vitellogenin/Apolipophorin (Vitellogenin/Apolipophorin)
Type: Family

The Vitellogenin/Apolipophorin family includes proteins that serve as precursors for egg-yolk proteins, providing essential nutrients during the embryonic development of oviparous organisms. Vitellogenins are involved in sequestering calcium, iron, and other cations, and may influence life-span through autophagy and lysosomal lipolysis. Apolipophorins are major components of lipophorin, mediating lipid transport in hemolymph and forming lipoprotein particles. They may facilitate the movement of morphogens and be involved in yolk granule formation. Some members are implicated in the differentiation of honeybee larvae into queens and may bind toxins like tetrodotoxin.
PIH1 family, Kintoun subfamily (PIH1/Kintoun_subfamily)
Type: Family

The PIH1 family, specifically the Kintoun subfamily, is involved in the cytoplasmic pre-assembly of axonemal dyneins, which are essential for the motility of cilia and flagella across a range of species. Members of this family play a crucial role in organizing dynein arm complexes in the cytoplasm prior to their transport into the ciliary compartment via intraflagellar transport. Additionally, some members are implicated in pre-rRNA processing, snoRNP particle assembly, and regulation of gene transcription and mTORC1 complex activity.
Kininogen/Fetuin/Histidine-rich Glycoprotein (Kininogen_Fetuin_HRG)
Type: Family

The protein family includes kininogens, which serve as precursors to the vasodilator peptide bradykinin, affecting smooth muscle contraction, hypotension, and vascular permeability. They are involved in blood coagulation, positioning prekallikrein and factor XI for optimal interaction with factor XII. Kininogens also inhibit thiol proteases and thrombocyte aggregation. The family encompasses fetuins, which are involved in various biological processes including endocytosis, bone mineralization, and inhibition of proteases. Histidine-rich glycoproteins within the family bind ligands like heme and heparin, playing roles in immune clearance, cell adhesion, angiogenesis, and coagulation. They possess antiangiogenic and antimicrobial properties and can bind divalent metal ions. Members of the family are involved in reproductive processes, such as preventing premature zona pellucida hardening during fertilization. Overall, the family plays multifaceted roles in physiological regulation, including coagulation, inflammation, cell signaling, and tissue remodeling.
Sensor Histidine Kinase Regulatory (Sensor_HK_Regulatory)
Type: Family

The protein family is involved in various regulatory systems, primarily functioning as sensor histidine kinases in two-component signal transduction pathways. These proteins play key roles in adapting to environmental changes, controlling cell division and differentiation, and regulating circadian rhythms in cyanobacteria. They autophosphorylate in response to specific stimuli and transfer the phosphate to response regulators, modulating gene expression and cellular processes. Some members are involved in osmosensing, virulence, and photosystem regulation. The family includes proteins that localize to specific cell poles to guide cell division and proteins that form complexes with other circadian rhythm regulators, contributing to the robustness of circadian gene expression and adaptation to light/dark cycles.