SII-SWORD/CoKE huggingface dataset:
Secondary Metabolite Biosynthesis Regulator (Sec_Metab_Biosynth_Reg)
Type: Family

This family of proteins includes transcription factors that regulate the expression of gene clusters involved in the biosynthesis of various secondary metabolites with biological activities. Members of this family are characterized by their ability to up-regulate genes responsible for the production of compounds such as isocyanide xanthocillin, lipopeptide antibiotics leucinostatins, and zearalenone, as well as down-regulate certain genes within these clusters. They are also involved in the regulation of genes for the biosynthesis of pestheic acid, a precursor of chloropupukeananes. These transcription factors are noted for containing a basic leucine zipper (bZIP) domain, which is a common motif in DNA-binding and dimerization for transcriptional regulation.
UDP-D-xylose:L-fucose alpha-1,3-D-xylosyltransferase (UDP-D-xylose:L-fucose_XylT)
Type: Family

This family of proteins includes enzymes that catalyze the transfer of D-xylose from UDP-alpha-D-xylose to L-fucose, a reaction likely involved in the biosynthesis of rhamnogalacturonan II (RG-II). RG-II is a complex pectic polysaccharide found in the primary cell wall and is crucial for cell wall integrity, particularly in rapidly growing plant tissues. These proteins share a conserved DXD motif, which is important for their enzymatic activity.
Kelch domain-containing protein 3-like (KLHDC3-like)
Type: Family

This entry represents human Kelch domain-containing protein 3 (KLHDC3) and similar proteins mainly found in animals. KLHDC3, also known as Testis intracellular mediator protein or PEAS, is the substrate-recognition component of a Cul2-RING (CRL2) E3 ubiquitin-protein ligase complex of the DesCEND (destruction via C-end degrons) pathway, which recognises a C-degron located at the extreme C terminus of target proteins, leading to their ubiquitination and degradation. This C-degron ris usually a motif of less than ten residues and can be present in full-length proteins, truncated proteins or proteolytically cleaved forms . The degradation process is particularly relevant for truncated selenoproteins that result from unsuccessful decoding events . Additionally, these proteins may play a role in the meiotic recombination process . Members of this family contain a Kelch-type β-propeller domain.
PiggyBac transposable element-derived (PiggyBac_TE-derived)
Type: Family

The PiggyBac transposable element-derived protein family is involved in DNA damage repair and gene expression regulation. Members of the family can bind to PGBD3-related transposable elements known as MER85s, which are non-autonomous 140 bp elements with PGBD3 terminal inverted repeats and no internal transposase ORF. One family member, the chimeric ERCC6-PGBD3 protein, is implicated in DNA repair post-UV irradiation and can function independently or synergistically with ERCC6. It also regulates gene expression, inducing interferon-like antiviral responses in the absence of ERCC6, and controls metabolism-related genes in its presence. The family plays a role in the cellular response to DNA damage and the fine-tuning of gene expression under different conditions.
TRAIP E3 ubiquitin-protein ligase (TRAIP_ubiq-protein_ligase)
Type: Family

The TRAIP family proteins are E3 ubiquitin ligases that play a crucial role in maintaining genome stability under replication stress. They regulate interstrand cross-link repair by ubiquitinating the MCM7 subunit of the CMG helicase complex, which influences the choice between repair pathways. The ubiquitination of MCM7 facilitates the recruitment of DNA glycosylase NEIL3 or, if cleavage fails, promotes CMG helicase unloading by the VCP/p97 ATPase for Fanconi anemia pathway engagement. TRAIP family members also participate in the repair of DNA-protein cross-links during DNA synthesis by targeting them for proteasomal degradation. Additionally, they have roles in mitotic spindle assembly checkpoint regulation and innate immune signaling, where they can negatively regulate NF-kappa-B activation and antiviral responses by ubiquitinating and degrading TNK1.
Gem-associated protein 5 (Gemin-5)
Type: Family

This entry represents Gemin-5, a protein involved in the assembly and function of small nuclear ribonucleoproteins (snRNPs), which are essential components of the spliceosome, the complex responsible for the splicing of pre-mRNA in eukaryotic cells . They recognise and bind to snRNAs and the 7-methylguanosine cap found on mRNA and snRNA molecules . They are part of the SMN complex, facilitating the formation of the core snRNP by delivering snRNAs to the complex. Additionally, they may interact with ribosomes and play a role in the regulation of protein synthesis. In Drosophila, is also described as a nuclear receptor cofactor in ecdysone-regulated gene expression during molting and puparium formation and it is essential in muscle and neuronal tissues for motor function, including climbing ability and flight .
A-kinase anchor protein 7 isoform gamma (AKAP7_isoform_gamma)
Type: Family

This family of proteins is involved in targeting cAMP-dependent protein kinase (PKA) to specific cellular locations, such as the membrane or cytoskeletal structures. In one context, the membrane-associated form of these proteins can reduce the activity of the epithelial sodium channel (ENaC), playing a role in sodium ion transport regulation. In its cytoplasmic form, the protein may regulate ENaC channel feedback inhibition by intracellular sodium. Additionally, some isoforms within this family may participate in the trafficking of other membrane proteins, such as aquaporin-2, to the plasma membrane, implicating a role in water transport and cellular homeostasis.
Coiled-coil and Forkhead-associated domain-containing protein (CC-FHA_domain)
Type: Family

This family of proteins includes members with coiled-coil domains and forkhead-associated domains, suggesting a role in mediating protein-protein interactions and potentially in DNA binding or the sensing of phosphorylation status. Coiled-coil domains are known to facilitate the oligomerization of proteins and are involved in a variety of biological processes including regulation of gene expression, cell division, and vesicle transport. Forkhead-associated domains are recognized for their ability to bind phosphopeptides and are often found in proteins involved in signal transduction, cell cycle control, and DNA repair. The presence of these domains indicates that the family may be involved in complex regulatory mechanisms within the cell, possibly acting as scaffolds or mediators in various signaling pathways or cellular structures.
Endoplasmic reticulum resident protein 44 (ERP44)
Type: Family

This family of proteins is involved in the regulation of the early secretory pathway by mediating thiol-dependent retention. They interact with substrate proteins through a conserved CRFS motif to form mixed disulfides. Additionally, these proteins can inhibit the calcium channel activity of ITPR1 and are implicated in the control of oxidative protein folding within the endoplasmic reticulum. They are essential for retaining certain oxidoreductases like ERO1A and ERO1B in the endoplasmic reticulum, suggesting a role in the maintenance of the redox environment.
Zinc finger matrin-type protein 3 (ZMAT3)
Type: Family

This family of proteins includes members that are recognized as direct targets of the p53/TP53 tumor suppressor gene. They are implicated in the TP53-dependent regulatory pathway that influences cell growth. These proteins may also have a role in the induction of apoptosis, potentially through mechanisms involving the modulation of TP53 expression and its localization to the nucleus and nucleolus.
Pumilio domain-containing protein (Pumilio_domain_protein)
Type: Family

This family of proteins includes RNA-binding proteins that are involved in the post-transcriptional regulation of gene expression. They are known to interact with the 3'-UTR regions of specific mRNAs, influencing their stability and turnover. Members of this family predominantly target mRNAs encoding membrane-associated proteins, playing roles in processes such as transmembrane transport and vesicular trafficking. They are implicated in the negative regulation of gene expression by promoting the deadenylation and decay of target mRNAs.
Peroxisomal membrane PEX28-32 (Peroxisomal_PEX28-32)
Type: Family

This family of proteins is involved in the biogenesis and maintenance of peroxisomes, which are key organelles in eukaryotic cells responsible for various metabolic processes including the beta-oxidation of fatty acids and the detoxification of hydrogen peroxide. Members of this family play a role in the regulation of peroxisome size, number, and distribution within the cell. They are integral to the peroxisomal membrane and may be involved in the formation of peroxisomal membrane contact sites, influencing the assembly of peroxisomal matrix proteins and the import of peroxisomal membrane proteins.
Zinc finger CCCH-type domain-containing protein (Zinc_finger_CCCH-type)
Type: Family

This family of proteins contains a zinc finger CCCH-type motif, which is typically involved in RNA binding and can play a role in post-transcriptional regulation of gene expression. Members of this family may be involved in processes such as mRNA splicing, translation, and degradation, as well as in the regulation of mRNA stability and transport. The CCCH-type zinc finger is characterized by the presence of three cysteine residues followed by one histidine residue within the motif. Proteins with this domain may interact with other proteins or nucleic acids, influencing various cellular pathways, including those related to development, immune response, and cell differentiation.
L-seryl-tRNA(Sec) kinase (Ser-tRNA(Sec)_kinase)
Type: Family

This family of proteins is involved in the biosynthesis of selenocysteine, an essential amino acid in some organisms. Members of this family catalyze the phosphorylation of seryl-tRNA(Sec), converting it to O-phosphoseryl-tRNA(Sec). This reaction is a crucial step in the formation of selenocysteine, which is then incorporated into selenoproteins. These proteins exhibit specificity for seryl-tRNA(Sec) and do not act on other tRNA species. The activity of these kinases is a key regulatory point in the selenocysteine biosynthetic pathway, which is vital for the production of proteins that contain this rare amino acid with important cellular functions, including antioxidant defense and redox regulation.
Non-classical Export Protein 102-like (NCE102-like)
Type: Family

This family of proteins is involved in non-classical protein export pathways, which facilitate the transport of proteins that lack a cleavable signal sequence. Members of this family play a role in membrane organization and may function as sensors of sphingolipids, influencing plasma membrane function. They are implicated in the formation of membrane compartments, such as MCCs, and the invagination of the plasma membrane at these sites. Additionally, they participate in eisosome organization and may serve as accessory subunits to core components of the export machinery. This pathway also serves as an alternative mechanism for the clearance or detoxification of damaged cellular material when traditional repair pathways are insufficient.
Zinc finger CCCH domain-containing protein (Zinc_finger_CCCH)
Type: Family

This family of proteins includes zinc finger CCCH domain-containing proteins which are characterized by their zinc finger motifs. These motifs are typically involved in binding to RNA or DNA and are essential for various biological processes including transcriptional regulation. Members of this family, such as the FRIGIDA-ESSENTIAL 1 protein in Arabidopsis, are known to function as transcriptional activators and play a role in plant developmental processes, such as the vernalization pathway which regulates flowering time. The zinc finger motif is crucial for their function in transcription activation.
WD repeat-containing protein 81 (WDR81)
Type: Family

The WD repeat WDR81 family proteins function as negative regulators of PI3 kinase/PI3K activity on endosomal membranes, influencing the phosphatidylinositol 3-phosphate content and thus affecting endosome dynamics including fusion, recycling, sorting, and transport. They are implicated in the lysosomal degradation pathway by facilitating the delivery of specific cargos for degradation. Additionally, they play roles in aggrephagy, the autophagic degradation of ubiquitinated protein aggregates, by modulating protein interactions and recruitment of autophagy-related proteins. These proteins are also involved in maintaining mitochondrial structure and organization.
Telomerase Complex Component (Telomerase_Complex_Comp)
Type: Family

This family of proteins includes components of the telomerase ribonucleoprotein complex, which plays a crucial role in the replication of chromosome termini. Members are involved in the stabilization and localization of vault RNA within the ribonucleoprotein vault particle, a structure implicated in nucleo-cytoplasmic transport. Some family members have a specific binding affinity for telomerase RNA, which may be indicative of an interaction with a region of RNA secondary structure.
ADP-ribosylation factor-binding (ARF-binding)
Type: Family

This family of proteins is involved in the regulation of membrane traffic, particularly through the trans-Golgi network. Members of this family are likely to interact with ADP-ribosylation factors, which are small GTP-binding proteins critical for vesicle formation and trafficking. The association with these factors suggests a role in the sorting of cargo proteins for transport to different destinations within the cell.
Chondroitin Sulfate Sulfotransferase (CS_Sulfotransferase)
Type: Family

This family of proteins functions as sulfotransferases, catalyzing the transfer of sulfate groups from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to specific hydroxyl groups of chondroitin sulfate A. The main activity involves the formation of chondroitin sulfate E by sulfating the C-6 hydroxyl group of the GalNAc 4-sulfate residue. Members of this family also contribute to the generation of highly sulfated structures by transferring sulfate to unique non-reducing terminal sequences of chondroitin sulfate. These modifications are similar to those found in thrombomodulin chondroitin sulfate. Additionally, there is evidence suggesting a potential role in B-cell receptor-mediated activation, which is important for B-cell development and regulation, although this function is not conclusively demonstrated in vivo. The activity of these enzymes is known to be inhibited by specific sulfated carbohydrate compounds.
AKNA Centrosomal and Transcription Regulator (AKNA_Centrosome-Trans_reg)
Type: Family

This family of proteins is involved in the organization of microtubules within centrosomes, playing a crucial role in cell delamination processes. They are essential for the delamination and retention of neural stem cells during neurogenesis and are implicated in the epithelial-to-mesenchymal transition in epithelial cells. These proteins function by enhancing centrosomal microtubule nucleation, recruiting nucleation factors, and stabilizing microtubule minus-ends, leading to the destabilization of microtubules at adherens junctions and facilitating the constriction of apical endfeet. Members of this family may also have a role as transcription factors, potentially regulating the expression of critical cell surface molecules involved in antigen-dependent B-cell development. However, the dual role as both microtubule organizers and transcription factors is not fully understood, and further evidence is needed to clarify these functions.
Chromatin target of PRMT1 (CTOP_PRMT1)
Type: Family

The Chromatin Target of PRMT1 (CTOP) protein family is involved in various cellular processes, including mRNA nuclear export, estrogen receptor target gene activation, and gene transcription regulation . Members of this family are components of the TREX complex, which is crucial for mRNA transcription, processing, and nuclear export, particularly associating with spliced mRNA. They also play a role in the export of intronless mRNAs and virus production . CTOP proteins interact with the methylosome complex, which includes PRMT1, PRMT5, MEP50, and ERH, to methylate H4R3 and activate transcription of genes, especially those implicated in glioblastomagenesis . Additionally, they are involved in the desumoylation and transactivation of ZNF148 target genes and are associated with 5-hydroxymethylcytosine on the chromosome.
Arabidopsis PWWP domain-containing (PDP_family_Arabidopsis)
Type: Family

The PDP family is involved in the regulation of gene expression through interaction with the PRC2 complex and modulation of the H3K27me3 level. Members of the PDP family, such as PDP1, PDP2, PDP3, and PDP6, are known to interact with MSI4/FVE and MSI5, which leads to the suppression of FLC, MAF4, and MAF5 expression. This suppression is crucial for promoting flowering in Arabidopsis thaliana. The PWWP domain present in these proteins suggests a role in chromatin-mediated regulation of gene expression, which is consistent with their involvement in histone methylation dynamics.
Tetratricopeptide repeat-containing protein (TPR-containing)
Type: Family

This family of proteins contains tetratricopeptide repeat (TPR) motifs, which are known to mediate protein-protein interactions. These motifs typically consist of 34 amino acids and form a helical structure that facilitates the assembly of multiprotein complexes. The proteins in this family are likely involved in various cellular processes through their role in the formation of these complexes. The specific functions of these proteins can vary widely, ranging from cell cycle regulation to protein transport, but they generally act as scaffolding proteins that bring other proteins together to form functional units.
Nectin and Poliovirus Receptor (Nectin/PVR)
Type: Family

The Nectin family proteins are involved in modulating T-cell signaling and can act as either costimulators or coinhibitors of T-cell function, depending on their receptor interactions. They play a crucial role in immune response by stimulating T-cell proliferation and cytokine production when binding to CD226, or inhibiting T-cell proliferation upon interaction with PVRIG. These proteins are also implicated in cell adhesion, formation of immunological synapses, and activation of NK cell cytotoxicity. Additionally, they serve as receptors for various viruses, facilitating microbial infection and influencing viral transport and immune evasion mechanisms. The family members contain an ITIM motif in their cytoplasmic region, which can bind SH2-containing phosphatases when phosphorylated.
Erythrocyte Invasion and Immune Modulation Protein (Erythrocyte_Invasion_ImmMod)
Type: Family

This family of proteins is implicated in the process of erythrocyte invasion by merozoites, which includes binding to erythrocyte surface proteins and possibly interacting with the host cytoskeleton to facilitate cell membrane rupture. Members of this family may also be involved in the formation and function of the food vacuole during the intraerythrocytic lifecycle of the parasite. Additionally, some proteins in this family have been suggested to bind to host proinflammatory cytokines, potentially modulating host immune responses during infection.
Ras-like GTPase Regulators (Ras-like_GTPase_Reg)
Type: Family

This family of proteins includes members that are involved in the regulation of cellular processes such as proliferation and arterial pressure. Some members may play a role in facilitating the release of atrial natriuretic peptide from cardiomyocytes, which is important for blood pressure regulation. Others are described as potent inhibitors of cellular proliferation, indicating a role in cell growth control. All members belong to the small GTPase superfamily and share similarity with the Ras protein family, suggesting a function related to molecular signaling and cellular dynamics.
Release factor glutamine methyltransferase, cyanobacteria-type (RF_glutamine_MTase_cyano)
Type: Family

This family of proteins includes Release factor glutamine methyltransferases (PRMC) mainly from cyanobacteria and uncharacterised plant sequences. PRMC is involved in the post-translational modification of class 1 translation termination release factors. Specifically, these enzymes catalyse the methylation of the glutamine residue within the universally conserved GGQ motif found in release factors RF1/PrfA and RF2/PrfB. This modification is crucial for the proper functioning of the release factors, which play a key role in terminating protein synthesis by prompting the disassembly of the ribosome from the mRNA and the newly synthesised polypeptide chain.
BTB and MATH domain-containing protein (BTB-MATH_domain_protein)
Type: Family

This family of proteins includes members that contain both BTB (Broad-Complex, Tramtrack and Bric a brac) and MATH (Meprin and TRAF Homology) domains. These domains suggest a role in protein-protein interactions, where the BTB domain is involved in the assembly of multimeric protein complexes, and the MATH domain is implicated in substrate recognition. One characterized member of this family is suggested to function as a substrate-specific adapter for an E3 ubiquitin-protein ligase complex, which is responsible for the ubiquitination and subsequent proteasomal degradation of target proteins. This indicates that the family may be involved in the ubiquitin-proteasome system, a critical pathway for protein degradation and regulation in eukaryotic cells.
Neuropeptide-activated GPCR (Neuropeptide-GPCR)
Type: Family

This family of proteins includes G-protein coupled receptors (GPCRs) that are involved in various signaling pathways. Members of this family are characterized by their ability to interact with G proteins and initiate intracellular second messenger cascades, typically involving phosphatidylinositol-calcium or cAMP. Specific functions identified within this family include the reception of neuropeptides such as nematocin and cardioactive peptide (CCAP), which influence behaviors like gustatory associative learning and male mating in nematodes, as well as cardiovascular regulation in insects. Some members may also modulate the activity of other receptors within the family, affecting intracellular signaling dynamics.
Cytochrome P450 20A1-like (CYP450_20A1-like)
Type: Family

This family of proteins includes members that are part of the cytochrome P450 superfamily, which are heme-thiolate proteins. These enzymes are involved in the metabolism of a wide variety of substrates, including xenobiotics, steroids, fatty acids, and drugs. They function primarily in the liver and are responsible for the oxidative metabolism of both endogenous and exogenous compounds. Their activity can result in the detoxification of substances or, conversely, the activation of compounds to more toxic forms. Cytochrome P450 enzymes are also important in the biosynthesis of steroid hormones and the metabolism of vitamins. They exhibit a characteristic spectral absorbance at 450 nm when bound to carbon monoxide, which is the basis for their naming. The diversity of reactions catalyzed by cytochrome P450 enzymes is large and includes hydroxylation, epoxidation, dealkylation, and reduction reactions.