SII-SWORD/CoKE huggingface dataset:
Circadian Clock Transcription Factors (Circadian_TF)
Type: Family

The protein family is involved in transcriptional regulation and forms a core component of the circadian clock, which is an internal time-keeping system that regulates physiological processes through circadian rhythms in gene expression. The family includes transcription factors that play roles in various biological processes such as angiogenesis, hematopoiesis, metabolism, cell motility, immune modulation, and response to hypoxia. Members of the family recognize specific DNA elements such as xenobiotic response elements (XRE), hypoxia response elements (HRE), and E-box elements, and they form heterodimers to activate or repress transcription. The family is also implicated in the development of the hypothalamo-pituitary axis, brain growth, visual and renal function, and cellular responses to environmental cues.
Inter-alpha-trypsin inhibitor heavy chain (ITIH)
Type: Family

The ITIH family proteins are involved in various biological processes, primarily acting as carriers or binding proteins for hyaluronan in serum. They play a crucial role in regulating the localization, synthesis, and degradation of hyaluronan, which is essential for cells during biological processes. Some members of the family are known to function as type II acute-phase proteins (APPs) that respond to inflammatory trauma and may contribute to liver development or regeneration. Additionally, certain ITIH family members have been implicated in tumor suppression, suggesting a potential role in cancer biology.
Bromodomain-containing chromatin reader (Bromo_chromatin_reader)
Type: Family

The bromodomain-containing protein family is characterized by the presence of bromodomains that specifically bind acetylated lysine residues on histones, facilitating the reading of epigenetic marks and the regulation of gene expression. Members of this family play key roles in chromatin remodeling, transcription regulation, and the maintenance of epigenetic memory across cell divisions. They are involved in various cellular processes including spermatogenesis, folliculogenesis, DNA-damage repair, and transcriptional activation of signal-inducible genes. Some family members also participate in the assembly of nucleosomes and the organization of higher-order chromatin structure. The family includes proteins that act as chromatin readers, recognizing acetylated histones throughout the cell cycle, and contributing to the transmission of epigenetic information and the regulation of transcription in response to external signals.
AP-1-like transcription factor yap1-like (AP-1-like)
Type: Family

This entry represents a family of fungal bZIP transcription factors, including AP-1-like transcription factor yap1 from Aspergillus flavus . Members are involved in the regulation of oxidative stress response, redox homeostasis, and various stress responses, including resistance to toxic compounds like arsenic and antifungal drugs. These proteins activate the transcription of genes encoding antioxidant enzymes, components of the cellular thiol-reducing pathways, and multidrug transporters. They are characterised by their ability to bind to specific DNA core binding sites, and their activity is modulated by the oxidation state of cysteine-rich domains, which affects their subcellular localization. Some members also play roles in iron regulation, metabolism control, and cell cycle regulation.
TEC1/TEAD Transcription Factor (TEC1_TEAD_TF)
Type: Family

The TEC1/TEAD family comprises transcription factors that play crucial roles in various biological processes, including organ size control, tumor suppression, cell proliferation, apoptosis, and developmental regulation. Members of the family are central to the Hippo signaling pathway, which restricts cell proliferation and promotes cell death to regulate organ growth and prevent tumorigenesis. They bind to specific DNA sequences, mediating gene expression of key pathway components like YAP1 and WWTR1/TAZ. Additionally, some family members are involved in the regulation of sporulation-specific genes, conidiophore development, and conidium maturation in fungi, where they bind to specific DNA sequences to regulate gene expression for morphological and chemical development during the life-cycle.
Collagen and Collagen-like Structural Proteins (Collagen_Structural_Proteins)
Type: Family

This family of proteins includes various types of collagen chains and collagen-like proteins that play crucial roles in the structural integrity and function of different tissues. Members of this family are involved in forming the extracellular matrix, providing tensile strength, and facilitating cell adhesion. They contribute to the formation of fibrillar and network-forming collagen, which are essential for the architecture of connective tissues, such as bone, cartilage, skin, and tendons. Some family members are involved in specialized functions, such as the formation of the egg case wall in certain species, participating in the protective cuticle layer in nematodes, or playing roles in the immune system by acting as pattern recognition receptors. Additionally, certain collagens may interact with components of the neuromuscular junction and influence the assembly of amyloid fibrils, indicating a diverse range of biological activities beyond structural support.
Olfactory G-protein coupled receptor 1 (Olfactory_GPCR1)
Type: Family

The olfactory receptor family is comprised of G-protein coupled receptors that are primarily involved in the detection of odorants. These receptors are integral membrane proteins that initiate a signal transduction cascade upon binding to specific molecules, leading to a sensory perception of smell. Each receptor is tuned to recognize a diverse array of chemical compounds, allowing for a broad range of olfactory sensations. Some members of the family have been shown to play roles beyond olfaction, such as in wound-healing processes and hair growth, indicating a multifunctional nature. The activation of these receptors typically involves G proteins, which can trigger various intracellular pathways, including the elevation of intracellular Ca(2+), activation of cAMP-dependent pathways, and phosphorylation of MAPKs.
Actin-regulating Serine/Threonine Kinase (Actin_reg-Ser/Thr_kinase)
Type: Family

This family of proteins includes serine/threonine kinases that play a crucial role in regulating actin filament dynamics and cytoskeletal organization. They act downstream of Rho family GTPase pathways and are involved in processes such as cell motility, cell cycle progression, and differentiation. Members of this family phosphorylate and inactivate actin-depolymerizing factors, leading to stabilization of the actin cytoskeleton. Some also participate in microtubule organization during mitosis and have roles in suppressing ciliogenesis. Additionally, certain members have dual specificity kinase activity, phosphorylating substrates on serine/threonine and tyrosine residues, and are implicated in spermatogenesis.
Cellular Communication Network Factor (CCN)
Type: Family

The CCN family is involved in a wide range of cellular processes including proliferation, adhesion, migration, differentiation, survival, and wound healing. Members of the family act as mitoattractants, mediate cell adhesion through heparin and divalent cations, and enhance growth factor-induced DNA synthesis. They play roles in angiogenesis, matrix remodeling, and bone turnover modulation. CCN proteins interact with integrins and other membrane receptors like NOTCH1, influencing stem cell function, myogenic differentiation, and inflammatory responses. They are implicated in tissue regeneration, endothelial cell function, and metabolic regulation in pancreatic beta-cells.
Arabidopsis F-box involved in BR signaling (F-box_BR-signaling)
Type: Family

This family of proteins includes components of SCF (SKP1-cullin-F-box) E3 ubiquitin ligase complexes, which are involved in the ubiquitination and subsequent proteasomal degradation of various target proteins. They play a crucial role in brassinosteroid signal transduction by mediating the inactivation of specific kinase inhibitors through competitive substrate binding and promotion of ubiquitination and degradation. These proteins are essential for regulating plant growth and development by modulating the stability of key signaling components.
Glycosyltransferase 29 (Sialyltransferase) (Glycosyltr_29_Sialyltrsf)
Type: Family

The glycosyltransferase 29 family is involved in the biosynthesis and modification of sialic acid-containing structures on glycoproteins and glycolipids. Members of this family catalyze the transfer of sialic acid through alpha-2,8-linkages, playing a crucial role in the formation of polysialic acid (PSA) chains and the synthesis of complex gangliosides. These enzymes are essential for neural cell plasticity, as they modify the embryonic neural cell adhesion molecule (N-CAM). They also contribute to the diversity of glycan structures by adding sialic acid to various acceptor substrates, including N-linked oligosaccharides and O-glycans. Their activity is implicated in the expression of PSA on glycoproteins and the synthesis of gangliosides such as GD1c, GT1a, GQ1b, GP1c, GT3, GD3, and potentially unusual sialylated lactosylceramide derivatives. The family's enzymes display substrate specificity, with some preferring substrates with alpha-2,3-linked terminal sialic acid and others showing a preference for O-glycans.
Family with sequence similarity 83 (FAM83) (FAM83)
Type: Family

The FAM83 family proteins are implicated in various signaling pathways, including the epidermal growth factor receptor (EGFR) signaling pathway. They are involved in activating downstream signaling cascades such as RAS/MAPK and PI3K/AKT/TOR, independent of EGFR activation. Some family members function as probable proto-oncogenes and are involved in cell proliferation, growth, migration, and epithelial to mesenchymal transition. They may also play roles in chromosome congression and alignment during mitosis, keratin cytoskeleton disassembly, and the structural organization and calcification of developing enamel. Additionally, they interact with other proteins like FBXW7 and KIF22, influencing the expression and signaling of MTOR, JUN, and MYC, and may regulate non-BMP target genes, suggesting roles in multiple signaling pathways.
LMO/RBTN Transcription Factors (LMO_RBTN_TF)
Type: Family

The LMO/RBTN protein family includes transcription factors and cofactors that play critical roles in hematopoietic development, neural lineage gene regulation, and motor neuron identity establishment. Members of the family, such as Rhombotin-1 and Rhombotin-2, are involved in specifying embryonic mesoderm to hematopoietic fate, often acting synergistically with other factors like TAL1/SCL and GATA1. They may also interact with DNA or other transcription factors to regulate gene expression within neural lineage cells. LIM domain only proteins (LMOs) like LMO3 and LMO4 function as transcription cofactors, influencing motor neuron identity and modulating gene expression in various developmental processes, including gastrulation and neurula stages. They can disrupt complexes like LDB1-LHX3, affecting interneuron gene expression, and act as positive cofactors for GATA transcription factors. The family is characterized by the presence of LIM zinc-binding domains, which are crucial for their interactions and functions.
AP-1 Transcription Factor bZIP (AP-1_TF_bZIP)
Type: Family

This family of proteins includes transcription factors that recognize and bind to specific DNA motifs, such as the AP-1 consensus sequence, to regulate gene expression. Members of this family are involved in various cellular processes, including the response to growth factors, amino acid starvation, and cellular stress. They function by forming dimers, often with proteins from the FOS family, to create an AP-1 transcription complex, enhancing DNA binding and transcriptional activity. Some are implicated in cell death pathways, steroidogenic gene expression, and the response to oncogenic signals. They share a characteristic bZIP domain that mediates DNA binding and dimerization.
Archaeal histone HMF (Archaeal_histone_HMF)
Type: Family

The archaeal histone HMF family is characterized by its ability to bind and compact DNA into nucleosome-like structures, typically involving 95 to 150 base pairs. These structures contain positive DNA supercoils, which are thought to increase the resistance of DNA to thermal denaturation. The formation of these nucleosome-like structures by the archaeal histone HMF family is analogous to the role of eukaryotic histones in chromatin organization, although the specific details of the structure and function may differ. The compacting of DNA by the family members is a critical aspect of DNA packaging within the cell, which is essential for maintaining DNA integrity and regulating gene expression.
Antp homeobox transcription factor (Antp_homeobox_TF)
Type: Family

The Antp homeobox family consists of sequence-specific transcription factors that play a crucial role in the developmental regulatory system. Members of this family are responsible for providing cells with specific positional identities along the anterior-posterior axis during embryonic development. They are characterized by the presence of a homeobox domain, which enables them to bind DNA and regulate the expression of target genes that are essential for the proper patterning and morphogenesis of tissues and organs.
GPCR Frizzled/Smoothened-like (GPCR_Fz/Smo-like)
Type: Family

This family of proteins includes members that are part of the G-protein coupled receptor Fz/Smo superfamily. They are characterized by a seven-transmembrane domain architecture typical of GPCRs and are implicated in signal transduction processes. Specifically, they play a role in the Wnt/beta-catenin signaling pathway, which is crucial for various developmental processes, cell proliferation, and differentiation. Some family members contain a Lys-Thr-X-X-X-Trp motif that is known to interact with the PDZ domain of Disheveled (Dvl) family members, a key interaction in the activation of the Wnt signaling pathway.
HTH-type LysR transcriptional regulators (HTH-type_LysR_regulators)
Type: Family

This family of proteins includes transcriptional regulators that typically contain a helix-turn-helix (HTH) motif, which is indicative of their role in DNA binding and regulation of gene expression. Members of this family are involved in various cellular processes, including the catabolism of specific compounds such as protocatechuate and sodium dodecyl sulfate (SDS), the regulation of operons related to nitrogen metabolism, malolactic fermentation, and the response to sulfur sources. They can act as activators or repressors of transcription, often responding to environmental cues or the presence of specific inducers. Some members are also known to regulate their own expression. The proteins are part of the LysR transcriptional regulatory family, which is one of the largest families of bacterial transcriptional regulators.
Retrovirus-related Pol polyprotein (Retrovirus_Pol_polyprotein)
Type: Family

The Retrovirus-related Pol polyprotein family is involved in the replication and integration of retroviral and retrotransposon genetic material into host genomes. Members of the family contain multiple enzymatic activities, including reverse transcriptase (RT), which converts RNA into dsDNA, and integrase (IN), which facilitates the integration of this DNA into the host genome. The RT activity includes DNA polymerase that can use DNA or RNA templates and ribonuclease H (RNase H) that degrades RNA in RNA-DNA hybrids. The integrase activity involves DNA cutting and joining reactions, crucial for the integration process. The family also includes aspartyl protease (PR) activity, which processes the Gag and Pol polyproteins into functional units. These proteins are essential for the life cycle of retroviruses and retrotransposons, enabling them to persist and propagate within host organisms.
Tripartite Motif and NHL Repeat Containing E3 Ligases (TRIM-NHL_E3_ligases)
Type: Family

The TRIM/NHL protein family includes E3 ubiquitin-protein ligases that play crucial roles in various cellular processes, including embryonic stem cell proliferation, neuronal functions, and innate immunity. Members of the family mediate ubiquitination of specific substrates, contributing to protein degradation pathways and post-transcriptional gene regulation. They are involved in neuroprotection, rapid ischemic tolerance, antiviral responses, and regulation of cell cycle transitions. Some family members interact with microRNAs and RNA-binding proteins to modulate gene expression, affecting processes like neural development and cell differentiation. The NHL domain, often forming a six-bladed beta-propeller, is a key feature for RNA targeting and protein-protein interactions, while the RING domain is essential for ligase activity.
N(4)/N(6)-adenine-specific DNA methyltransferase (N4_N6_ade-DNA_methylase)
Type: Family

The N(4)/N(6)-methyltransferase family is characterized by enzymes that predominantly act as type II methyltransferases, recognizing specific double-stranded DNA sequences and methylating adenine residues within these sequences. These modifications typically protect the DNA from cleavage by corresponding restriction endonucleases, thereby playing a crucial role in bacterial restriction-modification systems. Some family members are involved in bacteriophage exclusion (BREX) systems, providing immunity against bacteriophage infections by methylating bacterial DNA to facilitate self/non-self discrimination. The family includes enzymes with gamma and beta subtypes, with varying sequence specificities and methylation patterns. They are essential for gene expression regulation, transcriptional modification, and defense against foreign genetic elements.
Electron Transfer Iron-Sulfur Cluster-Binding Protein (ET_IronSulfur_Cluster-Binding)
Type: Family

This family of proteins is involved in various electron transfer processes within cellular respiration and metabolism. Members function as electron transfer units, often containing iron-sulfur clusters that facilitate the transfer of electrons between different components of the respiratory chain. These proteins are typically associated with the reduction or oxidation of compounds such as quinones, polysulfides, sulfites, and arsenates, playing a crucial role in anaerobic respiration. Some members are involved in the reduction of dimethyl sulfoxide and tetrathionate, or the oxidation of sulfite to sulfate. Others participate in the reduction of thiosulfate to sulfite and hydrogen sulfide, or the reduction of arsenate to arsenite. The family includes subunits of various reductase complexes, which are essential for the utilization of specific electron acceptors and may confer a growth advantage under certain environmental conditions.
Plant Biomass Hydrolyzing Esterase (Plant_Biomass_Hydrol_Est)
Type: Family

The protein family is involved in the hydrolysis of various plant biomass components, including xylan, polyvinyl alcohol, and plant cell wall esters. Members of the family possess esterase activity, with some showing specificity for acetylated xylans, cleaving acetyl side groups from the hetero-xylan backbone. Others are involved in the degradation of poly(3-hydroxybutyrate) and oxidized polyvinyl alcohol. Feruloyl esterases within the family hydrolyze ester bonds in arabinoxylans and pectin, aiding in plant cell wall degradation. The family includes proteins with modular structures, often comprising a catalytic module and a carbohydrate-binding module, indicating a gene fusion evolution. The family's broad substrate specificity and involvement in plant biomass degradation suggest a role in carbon cycling and biotechnological applications in biofuel production.
Two-component system histidine kinase (2C_system_His_kinase)
Type: Family

The protein family is involved in two-component signal transduction systems, which are prevalent in bacteria and plants. Members function as histidine kinases that autophosphorylate and transfer phosphate to response regulators, mediating cellular responses to environmental stimuli. They regulate processes such as cytokinin signaling, stress responses, cell cycle control, biofilm formation, and virulence. Some members act as cytokinin receptors, influencing plant development and stress signaling through MAPK cascades. Others participate in bacterial systems like the Rcs phosphorelay, affecting capsule synthesis and cell division. Additionally, certain kinases are involved in peroxide stress response and cell wall biosynthesis regulation.
BMP Lipoprotein (BMP_lipoprotein)
Type: Family

The BMP lipoprotein family comprises a group of membrane-associated proteins with diverse functions. Some members are involved in the uptake of nucleosides as part of ABC transporter complexes, with specificities ranging from purine nucleosides to all common nucleosides. These proteins may act as substrate-binding components of the transport system, displaying varying affinities for different substrates, including guanosine, inosine, adenosine, and riboflavin. Other members are described as immunogenic proteins, suggesting a role in immune response, although their specific functions remain unknown. Additionally, one member functions as a transcriptional activator, indicating a regulatory role in gene expression. The family is characterized by its similarity to the BMP lipoprotein family, suggesting a shared structural framework or evolutionary origin.
Cell Adhesion and Cytoskeletal Organization (Cell_Adh-Cytoskel_Orgn)
Type: Family

The protein family is involved in various cellular processes including cell adhesion, migration, cytoskeletal organization, and neural development. Members function in actin dynamics, serving as scaffolding molecules that influence actin polymerization and the assembly of actin filaments. They play roles in establishing cell morphology, motility, and interactions with the extracellular matrix. Some members are integral components of basement membranes, contributing to barrier selectivity and vascularization. Others mediate cellular responses to guidance cues in neuronal development and are involved in the Wnt signaling pathway. The family includes proteins that regulate synapse formation and maintenance, as well as those that participate in the architecture of epithelial cell junctions and myocardial remodeling.
Multiple antibiotic resistance protein MarA-like (MarA-like)
Type: Family

This protein family represents Multiple antibiotic resistance protein MarA from Salmonella typhimurium , Transcriptional regulator RamA from Klebsiella pneumoniae and similar bacterial transcriptional activators and regulatory proteins that are involved in various cellular responses such as antibiotic resistance, superoxide response, and DNA replication initiation. Some proteins within the family are known to bind specific DNA sequences, facilitating the binding of RNA polymerase to promoters, while others may influence the formation of nucleoprotein structures required for the function of replication origins. The family also encompasses proteins with probable regulatory functions that have not been fully characterised.