SII-SWORD/CoKE huggingface dataset:
Golgi apparatus membrane protein TVP38/TMEM64 (Golgi_membrane_TVP38/TMEM64)
Type: Family

The TVP38/TMEM64 family comprises Golgi apparatus membrane proteins that are implicated in vesicular trafficking and spindle migration. The proteins within this family are characterized by the presence of a VTT domain, which was previously known as the SNARE-assoc domain but was renamed due to the lack of evidence for association with SNARE proteins. The VTT domain is indicative of the family's role in cellular processes related to the transport of vesicles and the proper organization of spindle apparatus during cell division, which are critical for maintaining cellular function and integrity.
Calcium-dependent Lectin (Ca-dependent_lectin)
Type: Family

This family of proteins includes calcium-dependent lectins that play a crucial role in the innate immune defense. They are responsible for binding specific carbohydrate moieties such as mannose, fucose, and N-acetylglucosamine present on the surfaces of various microorganisms, which leads to the activation of the lectin complement pathway. Additionally, these proteins bind to late apoptotic and necrotic cells, as well as apoptotic blebs, facilitating their recognition and uptake by macrophages. This function is essential for the clearance of dying cells and may help to prevent an inflammatory response. Some members of this family have been implicated in the inhibition of viral infections, including SARS-CoV-2, by activating the complement system and reducing the associated inflammatory response.
SAGA-associated factor 11 (SGF11)
Type: Family

The SGF11 family proteins are components of the SAGA complex, a transcription regulatory histone acetylation (HAT) complex that activates transcription by remodeling chromatin and mediating histone acetylation and deubiquitination. Members of the SGF11 family participate in a subcomplex of SAGA that specifically deubiquitinates histone H2B, and are recruited to gene promoters by activators for transcription initiation. They are involved in nuclear receptor-mediated transactivation, mRNA binding and export from the nucleus, counteracting heterochromatin silencing, and are essential for the development of neuronal connectivity and the expression of ecdysone-induced genes.
Sorting Nexin Autophagy-related (Sorting_Nexin_Autophagy)
Type: Family

The Sorting Nexin family is involved in various intracellular trafficking processes, including cytoplasm to vacuole transport (Cvt), pexophagy, and mitophagy. Members of this family are essential for the survival of cells under severe endoplasmic reticulum stress and play a role in the endocytic pathway, retrieving proteins and sorting the v-SNARE protein SNC1. The PX domain within these proteins binds phosphatidylinositol 3-phosphate, facilitating peripheral membrane localization to perivacuolar punctate structures. Some members also contribute to meiosis, vegetative growth, asexual/sexual reproduction, virulence, and biosynthesis of virulence determinants like deoxynivalenol (DON).
Nematode receptor-like serpentine class alpha (Nematode_rcpt-like_serp_alpha)
Type: Family

This family of proteins includes G protein-coupled receptors (GPCRs) that are involved in chemosensory processes. Members of this family are implicated in the negative regulation of RAS/MAPK signaling pathways during certain developmental processes, such as vulva induction. They also play a role in the olfactory system, being required for the olfactory imprinting necessary for the response to specific odorants. These proteins signal through specific G-alpha protein subunits and are essential for the suppression of certain signaling pathways in response to environmental cues like food starvation.
HTH-type Metal-responsive Transcriptional Regulators (HTH_MetalResp_TranReg)
Type: Family

The protein family is comprised of helix-turn-helix (HTH) type transcriptional regulators involved in various cellular responses to environmental and intracellular signals. Members of the family function primarily as repressors or activators of gene expression. Several proteins within the family are responsive to metal ions, such as arsenic, antimony, bismuth, and zinc, regulating operons associated with metal resistance or homeostasis. For instance, some family members repress the ars operon and are derepressed by metalloids in their +III oxidation state. Others are involved in zinc homeostasis, repressing gene expression in the absence of zinc. Additionally, some regulators control genes related to lipid metabolism, hypoxic response, sporulation, and virulence. The family includes proteins that can bind to specific DNA sequences, with some showing metal ion-dependent binding regulation.
Pentapeptide repeat and BTB/POZ domain-containing protein (Pentapeptide-BTB/POZ_domain)
Type: Family

This family of proteins includes members that are involved in various cellular processes, such as resistance to antibiotics, particularly fluoroquinolones, by inhibiting DNA gyrase activity. Some proteins in this family mimic B-form DNA, potentially protecting DNA gyrase from fluoroquinolone action. Others are implicated in the ubiquitination pathway, serving as substrate-specific adapters for E3 ubiquitin-protein ligase complexes, leading to the proteasomal degradation of target proteins. Additionally, certain members are involved in the reorganization of host cell endosomal and lysosomal compartments during bacterial infection, promoting bacterial survival and virulence by recruiting kinesin-1 to the membrane of the Salmonella-containing vacuole and facilitating the extension of membrane tubules.
Group II Intron Splicing and Mobility/Defense (GrpII_Intron_Splice-Mob/Def)
Type: Family

The protein family includes multifunctional proteins that promote group II intron splicing and mobility, acting on both RNA and DNA. They have reverse transcriptase (RT) activity for intron duplication, maturase activity to facilitate splicing, and DNA endonuclease activity for site-specific DNA cleavage. Some members are involved in antiviral defense, synthesizing msDNA to protect against bacteriophages. Others are nuclear-encoded maturases required for mitochondrial group-II intron splicing, essential for mitochondrial biogenesis and metabolic pathways regulation during plant growth.
Proton-coupled symporters (H+-coupled_symporters)
Type: Family

This family of proteins is involved in the transport of various substrates across cellular membranes through a symport mechanism, where the transport of the substrate is coupled with the movement of protons into the cell. Members of this family function as osmosensors and osmoregulators, responding to osmotic shifts by importing osmolytes such as proline, glycine betaine, and other compatible solutes. Some proteins in this family are specific for the uptake of citrate, while others are more versatile and can transport a range of osmoprotectants including ectoine, pipecolic acid, and alpha-ketoglutarate. The activity of these transporters can be regulated by environmental factors such as osmotic stress, and some are inhibited by uncouplers like CCCP. Collectively, these proteins play a critical role in maintaining cellular homeostasis under varying environmental conditions.
Membrane-bound O-acyltransferase (MB_O-acyltransferase)
Type: Family

This family of proteins includes membrane-bound O-acyltransferases that are involved in various lipid modification processes. Members of this family are responsible for the acylation of proteins and lipids, which is crucial for their function and localization. Some proteins in this family catalyze the remodeling of glycosylphosphatidylinositol (GPI) anchors on GPI-anchored proteins, influencing cell integrity and apoptosis. Others are involved in the acetylation of alginate, affecting biofilm architecture and resistance to environmental stressors. Additionally, certain family members are implicated in the D-alanylation of teichoic acids in bacterial cell walls, contributing to cell wall charge and resistance to lysozyme. The family also includes enzymes that catalyze the N-terminal palmitoylation of signaling molecules such as Hedgehog proteins, which is essential for proper signaling and development. Overall, these enzymes play significant roles in cell signaling, structural integrity, and host-pathogen interactions.
Ribonuclease D-like (RNase_D-like)
Type: Family

This family of proteins is involved in the post-transcriptional modification of precursor tRNA molecules. Members of this family function as exonucleases, initiating the hydrolysis of RNA at the 3'-terminus and subsequently releasing 5'-mononucleotides. This enzymatic activity is essential for the proper processing of tRNA precursors, which is a critical step in the maturation of tRNAs before they are functional in protein synthesis.
Mitochondrial Acyl-CoA Synthetase Medium-Chain (Mitochondrial_ACSM)
Type: Family

The ACSM family catalyzes the activation of fatty acids by CoA to form acyl-CoA, a crucial step in fatty acid metabolism. Members of this family are capable of activating medium-chain fatty acids, with some showing specificity for C6-12 fatty acids or a preference for isobutyrate among C2-6 fatty acids. Additionally, certain members can activate carboxylate-containing xenobiotics, such as benzoate, and lipoate to lipoyl-nucleoside monophosphate. Lipoate activation is more efficient with GTP, particularly for the (R)-enantiomer. The family is characterized by its membership in the ATP-dependent AMP-binding enzyme family and is regulated by monovalent cations like potassium and rubidium.
Bacterial PTS System Sugar-Specific EIIC/EIIB (PTS_Sugar-EIIC/EIIB)
Type: Family

The protein family is involved in the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which is a key carbohydrate transport and phosphorylation mechanism in bacteria. Members of the family function as integral membrane proteins that form the translocation channel for specific sugars, facilitating their uptake into the cell. The PTS system operates by phosphorylating the sugar substrates during their transport across the membrane. Different proteins within the family are specific for various sugars, including lactose, cellobiose, galactose, lichenan, N,N'-diacetylchitobiose, oligo-beta-mannosides, and potentially other related carbohydrates. The EIIC domain is common among these proteins, forming the translocation channel and binding site for the sugars. Some members also contain the EIIB domain, which is involved in the phosphorylation transfer to the sugar substrate. The family plays a crucial role in the cellular uptake and metabolism of carbohydrates, affecting bacterial growth and adaptation to available sugar sources.
Protease transcriptional activator prtT (prtT)
Type: Family

The prtT family comprises transcription factors that are primarily involved in the regulation of protease gene expression, which is essential for protein utilization and degradation. Members of this family activate the transcription of various proteases, including serine alkaline proteases, metalloproteases, aspergillopepsins, sedolisins, and dipeptidyl-peptidases. Additionally, some members are implicated in the regulation of secondary metabolite biosynthesis clusters, such as those for diterpenes, polyketides, and mycotoxins, and may play roles in sporulation, virulence, and resistance to environmental stresses.
Inositol Monophosphatase Superfamily (Inositol_monoP_superfamily)
Type: Family

The inositol monophosphatase superfamily is characterized by its ability to dephosphorylate various substrates, playing a crucial role in different metabolic pathways. Members of this family are involved in the sulfur-activation pathway, converting adenosine 3'-phosphate 5'-phosphosulfate (PAPS) to adenosine 5'-phosphosulfate (APS) and 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP, thus regulating the flux of sulfur. Some members also hydrolyze inositol phosphates, such as inositol 1,4-bisphosphate, and are implicated in histidine biosynthesis by dephosphorylating histidinol-phosphate to histidinol. The family includes proteins that contribute to salt tolerance and may act as negative regulators of stress-responsive genes by modulating inositol phosphate turnover. Activity of these enzymes is often regulated by ions like Li(+), Na(+), Ca(2+), and K(+).
Protein O-Glucosyltransferase/Glycosyltransferase 90 (O-Glucosyltr/Glycosyltrsf_90)
Type: Family

The protein family is involved in the post-translational modification of proteins through O-glycosylation, specifically targeting extracellular EGF repeats and other consensus sequence motifs. Members of the family function as glycosyltransferases, transferring glucose or xylose from UDP-sugars to serine residues within specific consensus sequences. This modification plays a crucial role in protein folding, stability, and signaling, with notable involvement in the Notch signaling pathway, which is essential for various developmental processes. Some family members also participate in lipopolysaccharide core biosynthesis and glycosphingolipid modification, indicating a diverse set of biological functions related to carbohydrate attachment.
FYVE, RhoGEF and PH domain-containing (FYVE_RhoGEF_PH)
Type: Family

The FYVE, RhoGEF and PH domain-containing protein family is involved in the regulation of the actin cytoskeleton and cell shape. Members of this family activate CDC42, a Ras-like Rho family GTPase, by facilitating the exchange of bound GDP for free GTP. This activation process is crucial for various cellular functions including the formation of filopodia and lamellipodia, cell polarity, cytokinesis, and potentially affects the lifespan of an organism. Some family members are also implicated in the activation of MAPK8 and may influence proangiogenic actions of VEGF in vascular endothelial cells. The family is characterized by the presence of multiple domains, including FYVE-type zinc fingers for endosomal localization, DH domains for interaction with GTPases, and PH domains for membrane association and lipid binding. These domains contribute to the diverse roles of the family in cellular signaling and morphology.
Neuroligin and Bile salt-activated lipase (Neuroligin/BSAL)
Type: Family

This family of proteins includes cell surface molecules involved in cell-cell interactions, particularly in the nervous system. Members of this family interact with neurexin family proteins to mediate synapse function and synaptic signal transmission. They play roles in the formation and maintenance of synaptic junctions, clustering of synaptic proteins, and modulation of signaling by inhibitory synapses. Some members are involved in the digestion of dietary lipids, hydrolyzing a range of substrates for nutrient absorption. They are also implicated in the protection of neurons against oxidative stress and in the development of the nervous system.
Diverse Catalytic Activities Enzymes (Diverse_Catalytic_Enzymes)
Type: Family

This family of proteins includes enzymes with diverse catalytic activities. Members are involved in the initiation of mRNA decay, hydrolysis of diadenosine polyphosphates, and reversible adenylation of nicotinate mononucleotide. The endoribonucleases in this family initiate mRNA decay by cleaving mRNA molecules. Other members hydrolyze diadenosine polyphosphates, such as Ap4A, to yield ADP, with a preference for Ap4A. Some proteins also catalyze the adenylation of nicotinate mononucleotide to form nicotinic acid adenine dinucleotide. The family encompasses proteins with a preference for specific substrates and those with broader substrate specificity.
Drosophila Developmental Transcription Regulators (Dros_DevTransReg)
Type: Family

The protein family includes transcriptional regulators involved in various developmental processes in Drosophila melanogaster. Members act as transcriptional activators or repressors, influencing gene expression for segment specification, antenna development, sex determination, and courtship behavior. Some proteins within the family are essential for axon growth and guidance, repelling axons from the midline by regulating expression of midline repellents and their receptors. Others are involved in chromatin structure regulation, facilitating transcriptional activity by promoting open chromatin conformations, and are essential for processes such as zygotic genome activation and dosage compensation. Additionally, members participate in the formation of chromatin insulator complexes, which define transcriptional domains and protect against position effect variegation. The family also includes proteins that play roles in morphogenesis of muscles, sensory cells, and appendages, as well as in the differentiation of neurons and maintenance of stem cell identities.
BhsA/McbA stress and biofilm-associated protein (BhsA/McbA_stress_biofilm_assoc)
Type: Family

This family of proteins is involved in the cellular response to stress conditions, particularly in the context of biofilm formation and resistance to copper. Members of this family are implicated in reducing the permeability of the outer membrane to copper ions, which may be a protective mechanism against copper toxicity. Additionally, some proteins within this family are associated with the regulation of biofilm formation, which is a collective behavior of bacteria that allows them to survive in harsh environments. Biofilm formation is a complex process that involves cell-cell and cell-surface interactions, and proteins in this family may influence this process by modulating these interactions. Furthermore, there are indications that certain members of this family may contribute to the protection of biofilms against oxidative stress, enhancing the survival of bacterial communities.
Synaptobrevin-like vesicular transport protein (Synaptobrevin-like_transport)
Type: Family

This family of proteins is involved in the intracellular transport processes, specifically in the targeting and fusion of transport vesicles with their respective target membranes. Members of this family play a crucial role in various vesicle-mediated transport pathways, including the transport of proteins from the early endosome to the lysosome, the export of chylomicrons from the endoplasmic reticulum to the Golgi apparatus, and the exocytosis of mediators during immune cell degranulation. They are also required for the fusion of late endosomes with lysosomes, lysosomal exocytosis regulated by calcium, and the formation of phagosomes. The presence of a longin domain in some members suggests a role in vacuolar localization and subcellular targeting.
Neuronal Differentiation E-box Binding Transcription Factors (NeuroDiff_E-box_TFs)
Type: Family

The protein family is comprised of transcription factors involved in the initiation of neuronal differentiation and various developmental processes. Members of the family are characterized by their ability to bind to E-box motifs (5'-CANNTG-3') in the promoter regions of target genes, thereby activating transcription. They play roles in the development of the GnRH axis, neuronal plasticity, and tissue-specific cell fate determination during embryogenesis, such as muscle or early B-cell differentiation. Some family members also participate in mesenchymal to epithelial transition and may interact with other proteins like ATOH7, MYOD1, and CDP2 to regulate gene expression. The presence of a 9aaTAD motif suggests a transactivation function. The family is also implicated in sex determination and may influence lifespan and metabolism.
Anterior Gradient and Thioredoxin Domain (AGR/TXD)
Type: Family

The AGR family proteins are involved in a variety of cellular processes, including the formation of cement glands, cell migration, differentiation, growth, and adhesion. Some members function as protein-disulfide reductases in the endoplasmic reticulum, promoting disulfide bond formation in client proteins through thiol-disulfide oxidase activity. Others are implicated in mucociliary clearance in the airway by regulating ciliary beat frequency in response to calcium signaling. Additionally, certain AGR proteins are associated with the post-transcriptional synthesis and secretion of mucins, such as MUC2, and may act as proto-oncogenes. The family includes proteins that may also play roles in antioxidant defense and response to viral infection.
DnaJ subfamily B/C chaperone co-factors (DnaJ_subfamily_B/C)
Type: Family

This family of proteins functions as co-chaperones that work in conjunction with HSPA8/Hsc70 to promote protein folding, trafficking, and prevent aggregation of client proteins. They are involved in the endoplasmic reticulum-associated degradation (ERAD) pathway, influencing HSPA8/Hsc70's ATPase and polypeptide-binding activities. Some members can also operate independently of HSPA8/Hsc70, particularly in the maturation of potassium channels by stabilizing nascent subunits and aiding in their assembly into tetramers. Overexpression of certain members leads to the formation of nuclear membranous structures, the function of which is not fully understood. Additionally, some members are implicated in the penetration of polyomavirus into the endoplasmic reticulum membrane during infection.
ZC3H12/N4BP1 Ribonuclease and Regulator (ZC3H12/N4BP1_RNase_Reg)
Type: Family

The ZC3H12/N4BP1 protein family includes endoribonucleases and regulatory proteins involved in various biological processes such as immune homeostasis, inflammation, glial differentiation, apoptosis, adipogenesis, and angiogenesis. Members of the family function as RNases, regulating mRNA and pre-miRNA levels, thereby influencing cytokine production, T-cell activation, and stress response. They also modulate ubiquitination processes, affecting signaling pathways like NF-kappa-B and JNK. Some members serve as tumor suppressors or restrict viral replication. The family is characterized by a C3H1-type zinc finger domain essential for RNA binding and a proline-rich domain necessary for oligomerization.
Immunoglobulin superfamily V-set and transmembrane domain-containing protein (IgSF_V-set/TM_domain)
Type: Family

This family of proteins includes members that are involved in various cellular processes, including immune response modulation, cell differentiation, and regulation of cell motility. Some proteins in this family function as inhibitors of T-cell proliferation and IL2 production, playing roles in immune regulation. Others are implicated in adipocyte differentiation by promoting the expression of specific transcription factors. Additionally, certain family members are involved in the negative regulation of cell motility, interacting with other proteins to influence cell migration, fusion, and morphology. Some proteins also participate in maintaining neural networks and enhancing calcium channel currents in photoreceptors, indicating a role in neural and visual functions.
Plant secondary metabolite cytochrome P450s (Plant_metabolite_P450s)
Type: Family

This family of proteins includes enzymes that are part of the cytochrome P450 superfamily, known for their involvement in the metabolism of a wide range of substrates through oxidation reactions. Members of this family play diverse roles in the biosynthesis of plant secondary metabolites, including the conversion of flavanones to flavones and isoflavones, the breakdown of chlorophyll, the biosynthesis of volatile compounds involved in plant defense, and the hydroxylation of fatty acids and triterpenes. These enzymes are pivotal in the formation of phytoalexins, pigments, and signaling molecules that contribute to plant development, defense mechanisms, and interactions with the environment.
FAD-dependent monooxygenase (FAD_monoxygenase)
Type: Family

This family of proteins includes FAD-dependent monooxygenases involved in various biosynthetic pathways, primarily in fungi. These enzymes catalyze key oxidative steps in the production of secondary metabolites with diverse biological activities, including antitumor agents, antifungal compounds, and pigments. They are responsible for hydroxylation reactions, oxidative rearrangements, and ring expansions that contribute to the structural complexity of the metabolites. The family members share a common feature of utilizing flavin adenine dinucleotide (FAD) as a cofactor for their enzymatic activity.