SII-SWORD/CoKE huggingface dataset:
BTB/POZ domain-containing protein and Galectin-3-binding (BTB-POZ/Galectin-3-binding)
Type: Family

This family of proteins includes members with a BTB/POZ domain and galectin-3-binding capabilities. The BTB/POZ domain is known for its role in protein-protein interactions, which can be crucial for various cellular processes. Some members of this family are involved in promoting integrin-mediated cell adhesion, which is essential for cell-cell interactions and cellular signaling. Additionally, certain proteins within this family may play a role in stimulating host defense mechanisms against viruses and tumor cells, potentially contributing to immune surveillance and cancer prevention.
Cholesterol transport domain-containing protein (Cholesterol_transport)
Type: Family

This family of proteins is involved in the non-vesicular transport of cholesterol between cellular membranes, particularly from the plasma membrane to the endoplasmic reticulum. Members contain unique domains that bind cholesterol and phosphatidylserine, enabling them to serve as molecular bridges facilitating cholesterol transfer. These proteins play a significant role in maintaining cholesterol homeostasis within cells. Some family members are also implicated in autophagy regulation, tumor progression, and the formation of endoplasmic reticulum-plasma membrane contact sites in response to cholesterol levels.
Microtubule-associated protein 7 domain-containing protein (MAP7_domain-containing)
Type: Family

This family of proteins is involved in the stabilization and assembly of microtubules. Members are known to associate dynamically with microtubules and may play significant roles during the polarization and differentiation of epithelial cells. They are also implicated in the formation of intercellular contacts and may interact with other proteins, such as TRPV4, to mediate their redistribution towards the cell membrane, potentially linking cytoskeletal microfilaments and influencing cell shape and signaling.
Tensin Phosphatase (Tensin_PTEN_phosphatase)
Type: Family

The Tensin phosphatase family is involved in various cellular processes including cell migration, proliferation, and cytoskeletal organization. Members of the family promote cell migration by interacting with integrins and the cytoplasmic tail of ITGB1, leading to the disassembly of actin stress fibers. They regulate the stability and degradation of receptors like EGFR and MET, influencing cell survival and proliferation. The family includes protein and lipid phosphatases that are essential for myofibroblast differentiation, extracellular matrix deposition, and podocyte maintenance. They play roles in signal transduction, linking pathways to the cytoskeleton, and in the regulation of the PI3K-AKT pathway. Additionally, they are involved in the regulation of mTORC1 activity in response to glucose conditions and are essential for maintaining the integrity of the glomerular filtration barrier. The family also contributes to the remodeling of the extracellular matrix and is implicated in cartilage development.
SR-related and CTD-associated factor (SR-CTD_assoc_factor)
Type: Family

The SR-related and CTD-associated factor family includes proteins involved in the regulation of mRNA processing and stability. Members of the family function as anti-terminator proteins, preventing early mRNA termination during transcription. They achieve this by suppressing the use of early, alternative poly(A) sites, which prevents the generation of non-functional truncated proteins. These proteins associate with the phosphorylated C-terminal heptapeptide repeat domain (CTD) of RNA polymerase II's largest subunit, POLR2A, and bind nascent RNA to inhibit premature transcript cleavage and polyadenylation. Some family members also act as positive regulators of transcript elongation or are involved in alternative splicing regulation, contributing to the complexity of gene expression.
Homocysteine S-methyltransferase (Hcy_S-methyltransferase)
Type: Family

The Homocysteine S-methyltransferase family comprises enzymes that catalyze the transfer of a methyl group from S-methylmethionine (SMM) to various substrates, including homocysteine, adenosyl-L-homocysteine (AdoMet), and selenocysteine. These enzymes play a role in the SMM cycle in plants, which is involved in the regulation of AdoMet levels, a key methyl donor for numerous methylation reactions. Some family members show specificity for DL-homocysteine over DL-cysteine and do not possess selenocysteine methyltransferase activity, while others can methylate selenocysteine and are involved in selenium detoxification. Activity of these enzymes can be inhibited by L-methionine, indicating a regulatory mechanism for controlling enzyme function. The family is involved in essential metabolic pathways that contribute to amino acid processing and potentially to the detoxification of harmful compounds.
Serine/Threonine Proteases with Immune and Developmental Roles (Ser/Thr_Proteases_Immune/Dev)
Type: Family

This family of proteins includes serine proteases with diverse biological functions, primarily involved in immune responses. Members are characterized by their proteolytic activity, with some having a specific role in the melanization-mediated immune response, where they cleave substrates to activate cascades such as the prophenoloxidase system. This process is crucial for pathogen recognition and defense in invertebrates. Other members are implicated in morphogenesis and development, contributing to processes like germ-band retraction and dorsal closure. Some proteins within the family are inactive but still play essential roles in immune responses or development by interacting with other proteins or pathways. The family also includes threonine proteases, which may be involved in proteolysis. The presence of a clip domain in some members suggests a structural feature that is important for their function.
WD repeat-containing striatin (WD_repeat_striatin)
Type: Family

This family of proteins is characterized by the ability to bind calmodulin in a calcium-dependent manner, suggesting a role in calcium signaling pathways. Members are implicated in various cellular processes, including scaffolding or signaling, and may influence dendritic Ca(2+) signaling. Some proteins within this family are involved in the regulation of the cell cycle in response to external signals, such as pheromones in yeast. Additionally, certain members are required for developmental processes, such as the formation of mature fruiting bodies during early sexual development in fungi.
Disintegrin and Metalloproteinase Domain-Containing (ADAM_Metalloproteinase)
Type: Family

The Disintegrin and metalloproteinase domain-containing (ADAM) protein family includes transmembrane metalloproteases involved in the ectodomain shedding of various transmembrane proteins, including cytokines, adhesion proteins, and growth factor precursors. These proteases are essential for development, tissue homeostasis, and cell signaling. They play roles in the proteolytic release of cell-surface proteins such as TNF-alpha, interleukin receptors, and Notch, influencing pathways like inflammation, hemostasis, and neurogenesis. Some family members are involved in the regulation of cell fate decisions during development by modulating signaling pathways such as Notch. They are regulated by propeptide domains via a cysteine switch mechanism and interact with tetraspanins for substrate selectivity and cellular trafficking.
THEM6/lcsJ thioesterase (THEM6_lcsJ_thioesterase)
Type: Family

The THEM6/lcsJ thioesterase family is involved in the biosynthesis of various bioactive compounds, including oxaleimides, lipopeptide antibiotics, and linear lipopeptides. Members of this family function as thioesterases, playing a crucial role in the processing and maturation of secondary metabolites. They participate in complex biosynthetic pathways, often involving polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS), to produce molecules with diverse biological activities such as cytotoxic, antimalarial, antiviral, antibacterial, antifungal, antitumor, and phytotoxic properties. The family's thioesterases are responsible for hydrolyzing thioester bonds, facilitating the release of synthesized compounds from the synthetase enzymes, and potentially aiding in the modification and maturation of the bioactive products.
Site-specific recombinase/transposase-related (Recombinase/Transposase-rel)
Type: Family

This family of proteins includes enzymes involved in site-specific recombination and transposition processes. Members of this family function as resolvases, catalyzing the resolution of cointegrated replicons to produce the final transposition products. These proteins are also related to transposases, which are enzymes that facilitate the movement of DNA segments within the genome. The family encompasses proteins with similarity to both site-specific recombinase resolvases and transposases from different subfamilies, indicating a potential role in DNA recombination and repair mechanisms.
Dynamin-binding and Rho GEF (Dynamin-Rho_GEF)
Type: Family

The Dynamin-binding protein family is characterized by its role as guanine nucleotide exchange factors (GEFs), primarily for CDC42, influencing various intracellular processes. Family members are involved in the organization of the actin and microtubule cytoskeleton, regulation of apical junctions, and spindle orientation in epithelial cells, contributing to lumenogenesis and ciliogenesis. Some members are implicated in membrane trafficking between the cell surface and the Golgi. Additionally, certain proteins within the family are associated with cell polarity, cytokinesis, and septum formation in yeast, as well as renal ciliogenesis and kidney development in zebrafish. The family's functions are critical for maintaining cellular structure and facilitating cell fusion during zygote formation.
Chromodomain-helicase-DNA-binding (CHD)
Type: Family

The CHD family proteins are ATP-dependent chromatin remodelers that regulate transcription by altering chromatin structure. They are involved in various cellular processes including transcriptional repression and activation, chromatin boundary establishment, and co-transcriptional RNA processing. Members of the family act as transcriptional repressors by recruiting histone H1 to target genes and suppressing apoptosis mediated by p53. They also serve as negative regulators of the Wnt signaling pathway by modulating beta-catenin activity. Some members function as transcriptional coactivators for nuclear receptors and are implicated in osteogenesis. The family plays a role in the cellular response to oxidative stress and may regulate rRNA production. Additionally, they are involved in neuronal differentiation, cell cycle regulation, DNA repair, and viral infection response.
BSD domain-containing protein (BSD_domain-containing)
Type: Family

This family of proteins includes members that are involved in various cellular processes. Some proteins within this family play a role in adipocyte differentiation, where they are implicated in the signaling pathways that lead to the phosphorylation of key proteins involved in cell growth and metabolism. Specifically, they promote the phosphorylation of AKT1, which is a crucial step in the activation of mTORC2 signaling after growth factor stimulation. Other members of this family are associated with ubiquitin metabolism and are necessary for the control of DNA replication. The functions of some proteins in this family have not been characterized, suggesting a potential diversity of roles across different species.
Epithelial Barrier and Cell Signaling Protein (Epithelial_Barrier/Signaling)
Type: Family

This family of proteins includes members that are involved in various cellular processes, including cell adhesion, cell cycle regulation, and cell-extracellular matrix interactions. Some proteins in this family are essential for the organization of cellular junctions and the maintenance of barrier functions in epithelial tissues. Others have roles in the protection and renewal of epithelial surfaces, as well as in differentiation. Certain family members are implicated in tumor suppression and may influence cancer cell proliferation through interactions with growth factor receptors, leading to cell cycle arrest and modulation of apoptosis. The family also contains proteins that are important for the structural integrity of basement membranes and may participate in cell-matrix signaling pathways.
H-rev107 Phospholipase/Acyltransferase (H-rev107_PLA/AT)
Type: Family

The H-rev107 family proteins are multifunctional enzymes with both phospholipase A1/2 and acyltransferase activities. They catalyze the calcium-independent release of fatty acids from glycerophospholipids at the sn-1 or sn-2 position, with a higher activity for PLA1 over PLA2 for most substrates. Additionally, they exhibit O-acyltransferase activity, transferring fatty acyl groups from glycerophospholipids to lysophospholipids. They also show N-acyltransferase activity, transferring fatty acyl groups from phosphatidylcholine and other glycerophospholipids to the primary amine of phosphatidylethanolamine, forming N-acylphosphatidylethanolamine, a precursor for N-acylethanolamines. Some family members are involved in organelle degradation during eye lens terminal differentiation, contributing to lens transparency. Others may act as host factors for picornaviruses, facilitating viral genome release into the cytoplasm. The C-terminal transmembrane domain is essential for targeting to damaged organelles.
Developmental and Hematopoietic Transcription Factors (Dev/Hematopoietic_TF)
Type: Family

The protein family is comprised of transcription factors that play crucial roles in developmental processes, hematopoiesis, and immune system function. Members of the family are involved in the regulation of gene expression by binding to specific DNA motifs, such as the 5'-TGACCA-3' sequence, and may act as transcriptional repressors or corepressors. They are associated with chromatin remodeling complexes and are essential for processes like B-cell formation, T-lymphocyte differentiation, and survival during thymocyte development. Some members negatively regulate the JAK/STAT pathway, affecting developmental pathways in insects. The family also includes proteins that may interact with the P53-signaling pathway, contributing to tumor suppression. The diverse functions of the family reflect its involvement in controlling cell fate decisions and responses to developmental signals across different organisms.
Phosducin-like chaperone and apoptosis regulator (Phosducin-like_chap/apop_reg)
Type: Family

This family of proteins is involved in various cellular processes, including acting as chaperones for specific receptors, such as the angiogenic VEGF receptor KDR/VEGFR2, by increasing their stability through the inhibition of ubiquitination and degradation. Members of this family are known to interact with the chaperonin-containing T-complex (CCT), modulating its activity and consequently affecting the folding of cytoskeletal actin. Additionally, these proteins play a role in the cellular response to heat shock by working alongside other chaperone complexes. They are also implicated in the regulation of apoptosis through the modulation of caspase activation.
Phosducin-like regulator (Phosducin-like_reg)
Type: Family

This family of proteins is involved in various cellular processes, including the regulation of visual phototransduction and the integration of photoreceptor metabolism. Members of this family function as co-chaperones for CCT in the assembly of heterotrimeric G protein complexes and facilitate the assembly of Gbeta-Ggamma and RGS-Gbeta5 heterodimers. They also play roles in hedgehog signaling and ciliary function. Some members inhibit the transcriptional activation activity of the cone-rod homeobox CRX, which is important in visual function. Additionally, they are implicated in the regulation of G protein signaling by modulating the assembly of G protein subunits.
cTAGE and MIA/OTOR (cTAGE_MIA/OTOR)
Type: Family

The cTAGE and MIA/OTOR family proteins are involved in the transport of large cargos from the endoplasmic reticulum (ER) to the Golgi apparatus. They facilitate the incorporation of these cargos into membrane-bound carriers, particularly those too bulky for standard COPII-coated vesicles. Key functions include the specific loading of collagen VII (COL7A1) into transport carriers and the secretion of lipoproteins, which is crucial for cholesterol and triglyceride homeostasis. The family members interact with COPII coat subunits SEC23A and SEC23B via proline-rich domains containing PPP motifs. Additionally, they are involved in the assembly of COPII components at ER exit sites and may interact with other ER-resident proteins to facilitate cargo transport. While some members are associated with tumor antigens, the primary role of the family appears to be in the specialized secretion process, particularly in cells with specific secretory pathways.
Eukaryotic initiation factor 2B subunits alpha/beta/delta (eIF2B_alpha/beta/delta)
Type: Family

This family of proteins includes eukaryotic initiation factor 2B (eIF2B) subunits alpha, beta, and delta. These proteins form part of the eIF2B complex, which is essential for protein synthesis initiation. The complex catalyzes the exchange of GDP for GTP on the eIF2 gamma subunit, a critical step in the formation of the pre-initiation complex. The activity of these proteins is regulated by the phosphorylation state of the eIF2 alpha subunit; phosphorylation represses their guanine nucleotide exchange factor activity, thereby reducing the availability of initiator methionyl-tRNA to the ribosome and controlling global protein synthesis. Certain conditions, such as the integrated stress response, can modulate the activity of these proteins through specific inhibitors like ISRIB, which can stimulate their activity irrespective of the phosphorylation state of eIF2.
Receptor-like Defense Trigger (RLP_Defense_Trigger)
Type: Family

This family of proteins is involved in plant defense mechanisms. Members of this family act as receptors that recognize specific pathogen-associated molecular patterns (PAMPs) or microbe-associated molecular patterns (MAMPs), triggering immune responses. These responses can include the release of reactive oxygen species (ROS), emission of stress-related phytohormones like ethylene, and hypersensitive cell death. Some family members are known to confer resistance to bacterial pathogens and parasitic plants by recognizing specific molecular patterns presented by the invading organism.
Complement System Regulators and Virion Entry Mediators (ComplSys_Reg/VirEntry_Med)
Type: Family

The protein family is involved in the regulation of the complement system, a critical component of the innate immune response. Members of the family include glycoproteins that inhibit complement activation on self cells by binding to specific markers, accelerating the decay of C3 convertase, and acting as cofactors for factor I to degrade C3b. Some family members also mediate cellular responses by interacting with receptors, aiding in pathogen phagocytosis and destruction. Additionally, certain proteins within the family are associated with lipid metabolism and may influence tissue-bound complement fragments, competing with physiological inhibitors. The family also includes a protein that aids in viral entry into host cells by participating in the dissolution of virion membranes.
Plant secondary metabolite acyltransferase (Plant_metabolite_acyltrans)
Type: Family

This family of proteins is involved in the modification of plant secondary metabolites through the transfer of acyl groups from donor molecules such as malonyl-CoA, coumaroyl-CoA, and other acyl-CoAs to acceptor molecules, which are often phenolic glucosides or anthocyanins. These modifications typically involve the addition of malonyl, coumaroyl, or other acyl groups to specific hydroxyl groups of the acceptor compounds. The enzymatic activity of these proteins plays a crucial role in the biosynthesis and diversification of plant secondary metabolites, which can serve various functions including pigmentation, defense against herbivores and pathogens, and plant-environment interactions. The proteins in this family are characterized by a conserved HXXXXD motif essential for their acyltransferase activity and are inhibited or regulated by various compounds and metal ions.
C-type lectin domain-containing protein (C-type_lectin_domain)
Type: Family

This family of proteins includes receptors and elements of receptor complexes involved in various biological processes. Members of this family have roles in the immune system, such as mediating phagocytosis enhancement and functioning as receptors for defense collagens and pulmonary surfactant proteins. Some are implicated in vascular development, including angiogenesis and hematopoietic precursor cell interactions. Additionally, certain family members are involved in the development of the nervous system, contributing to neurite outgrowth, elongation, and motor axon guidance. The family also contains receptors for hyaluronate, which may be involved in cell adhesion and signaling pathways. The diverse functions of these proteins reflect their involvement in intercellular communication and cellular response to environmental cues.
Atos Homolog Transcription Regulators (ATOS_Transcription_Regulators)
Type: Family

The ATOS family comprises transcription regulators that synchronize transcriptional and translational programs to promote macrophage invasion of tissues. Members of the family contain transactivation domains (TADs), which are essential for the transcriptional activation of a subset of target genes. The family plays a crucial role in adjusting transcription and translation of genes involved in metabolic processes and mitochondrial bioenergetics, facilitating macrophage tissue invasion. Some members are implicated in inducing the transcriptional expression of metabolic enzymes and translational regulators, thereby modulating mitochondrial function and energy production to support macrophage function.
Polycomb group RING finger (PcG_RING_finger)
Type: Family

This family of proteins includes transcriptional repressors that are components of Polycomb group (PcG) multiprotein PRC1-like complexes. These complexes are essential for maintaining the transcriptionally repressive state of numerous genes, such as Hox genes, during development. The proteins act through chromatin remodeling and histone modification, specifically by mediating the monoubiquitination of histone H2A at lysine 119, which leads to heritable changes in chromatin expressibility. Additionally, some family members have roles in regulating the activity of RNF2 ubiquitin ligase within the PRC1-like complex. Certain proteins in this family are also involved in the silencing of one copy of the X chromosome in female mammals and may influence histone demethylation levels.
Mitochondrial Carrier Antiporter (Mito_Carrier_Antiporter)
Type: Family

This family of proteins includes mitochondrial carriers that function as antiporters, exchanging dicarboxylates and sulfur oxoanions across the inner mitochondrial membrane. Some members are implicated in the transport of specific metabolites such as oxaloacetate and sulfate, and may play roles in metabolic pathways like leucine biosynthesis. The exact function of some carriers remains to be determined, although they do not mediate citrate export from mitochondria to cytoplasm.