SII-SWORD/CoKE huggingface dataset:
Secondary Metabolite Biosynthesis Oxidoreductase (Sec_Metab_Biosynth_Oxidored)
Type: Family

This family of proteins includes oxidoreductases involved in the biosynthesis of various secondary metabolites, such as diterpenes, mycotoxins, indole alkaloids, and meroterpenoids. Members of this family participate in gene clusters that mediate complex biosynthetic pathways, often acting as 'decorative enzymes' that modify precursor molecules through oxidation-reduction reactions. These modifications can include hydroxylation, prenylation, ring expansion, and structural rearrangements, contributing to the diversity of natural products with potential bioactive properties. The specific roles of these enzymes within their respective pathways can vary, with some members' functions remaining to be fully elucidated.
Collagen VI and Biomineralization Protein PIF (Collagen-VI/PIF)
Type: Family

This family of proteins includes collagen VI chains that serve as cell-binding proteins. They are involved in the formation of a network that supports cells in connective tissues. Collagen VI is important for maintaining the integrity of various organs and tissues throughout the body. Additionally, a member of this family, Protein PIF, plays a crucial role in the biomineralization process in marine organisms, specifically in the formation and growth of the nacreous layer of shells by promoting aragonite crystallization and binding to the organic matrix.
DNA polymerase eta (DNA_polymerase_eta)
Type: Family

The DNA polymerase eta family consists of specialized DNA polymerases involved in translesion synthesis (TLS), a DNA repair mechanism that allows DNA replication to proceed past lesions or distortions within the DNA helix. Members of the family are characterized by their ability to insert nucleotides opposite lesions, such as UV-induced pyrimidine dimers, with relaxed geometric constraints, leading to higher rates of misincorporation and low processivity. They often cooperate with other polymerase complexes, like POLZ, for complete bypass of DNA lesions. The family plays a crucial role in maintaining genomic stability by facilitating error-free or error-prone bypass of DNA damage, which is essential for cell survival following genotoxic stress. They also contribute to hypermutation at immunoglobulin genes and are involved in homologous recombination repair. The catalytic core of these enzymes features smaller fingers and thumb subdomains compared to high-fidelity polymerases, and their activity is regulated by the binding of a third divalent metal cation.
Rho GEF and signaling-related domain-containing protein (Rho_GEF_signaling-related)
Type: Family

This family of proteins includes members that are implicated in intracellular signaling and cytoskeleton dynamics. Some proteins within this family are suggested to function as guanine nucleotide exchange factors (GEFs), which are known to activate small GTPases by facilitating the exchange of GDP for GTP, thereby triggering various signaling pathways. Other members are uncharacterized but may share structural domains or sequence homology, suggesting potential roles in cellular processes related to signaling or cytoskeletal organization, particularly at the Golgi apparatus.
Receptor-like Ser/Thr Protein Kinase (RLK_Ser/Thr-Kinase)
Type: Family

This family of proteins includes receptor-like kinases that are predicted to function in signal transduction pathways. They are characterized by their kinase activity, specifically phosphorylating serine and threonine residues. These proteins are part of the larger protein kinase superfamily and are likely involved in various cellular processes, including growth, development, and response to environmental stimuli.
Rho-type GTPase guanine nucleotide-exchange factors (Rho-type_GEFs)
Type: Family

This family of proteins includes guanine nucleotide-exchange factors (GEFs) that specifically activate Rho-type GTPases, primarily Rho1, by catalyzing the exchange of GDP for GTP. These proteins play a crucial role in the regulation of cell wall biosynthesis, cell wall integrity, septum formation, and the organization of the actin cytoskeleton. They are involved in signaling pathways that control cell wall defects and coordinate actin deposition with cell wall biosynthesis during growth. Some family members also interact with additional Rho-type GTPases, such as Rho5, influencing their activation state and downstream signaling events.
U5 snRNP Complex Component (U5_snRNP_Component)
Type: Family

This family of proteins is essential for the process of pre-mRNA splicing, a critical step in gene expression where introns are removed and exons are joined to form a mature mRNA transcript. Members of this family are integral components of the spliceosome, a complex molecular machine that orchestrates the splicing process. Specifically, these proteins are part of the U5 small nuclear ribonucleoprotein (snRNP) complex and the U4/U6-U5 tri-snRNP complex, which are key building blocks of the spliceosome. Some members are also involved in the minor spliceosome pathway, which is responsible for the splicing of U12-type introns. The function of these proteins is conserved across a range of eukaryotic organisms, highlighting their importance in the cellular machinery.
Nephronectin domain-containing protein (Nephronectin_domain)
Type: Family

This family of proteins is involved in the regulation of kidney development and organ morphogenesis. Members of this family are known to interact with integrin alpha-8/beta-1, serving as functional ligands that regulate the expression of growth factors essential for these developmental processes. They also play roles in cell adhesion, spreading, and survival by binding to various integrins. Additionally, these proteins contribute to matrix assembly and may influence hair follicle morphogenesis. The presence of a MAM domain in some family members is critical for their localization at the cell surface, indicating a role in cell-matrix interactions.
Small GTPase RasD (Small_GTPase_RasD)
Type: Family

The RasD family proteins are small GTPases involved in various signaling pathways. Members of this family, such as the dexamethasone-induced Ras-related protein 1 and GTP-binding protein Rhes, play roles in the regulation of transcription and signal transduction. They are known to interact with components like the APBB1/FE65-APP complex, negatively regulating its transcriptional activity. Additionally, they are involved in G-protein-coupled receptor signaling and interact with heterotrimeric proteins, influencing functions such as locomotor activity and motor coordination, particularly within the striatum.
Ataxin-7-like transcription regulator (Ataxin-7-like_regulator)
Type: Family

This family of proteins is involved in neurodegeneration and transcription regulation. Members act as components of the STAGA transcription coactivator-HAT complex, mediating interactions with CRX, a photoreceptor cell-specific transcription factor, and contributing to CRX-dependent gene activation. They are also necessary for the stabilization of the microtubule cytoskeleton, which is crucial for maintaining cell structure and facilitating intracellular transport.
Serine/threonine-specific protein kinases (Ser/Thr-specific_kinases)
Type: Family

This family of proteins includes serine/threonine kinases that are involved in a variety of cellular processes. Members are known to phosphorylate substrates on serine and threonine residues, which is a key mechanism in regulating intracellular signaling pathways. Some proteins in this family have been shown to autophosphorylate and may also have the capacity to phosphorylate on tyrosine residues, although this activity towards other proteins is not clearly established. Functions attributed to these kinases include roles in secretory vesicle trafficking, ductal morphogenesis in the mammary gland, TGF-beta signaling, and vacuolar processing and morphology. The diverse functions suggest that these kinases are involved in both intracellular signaling and the regulation of cellular structures.
SAP domain-containing ribonucleoprotein (SAP_domain_ribonucleoprotein)
Type: Family

The SAP domain-containing ribonucleoprotein family includes SARNP from animals and its orthologues from yeast THO1 and mlo1. This family is involved in various cellular processes including DNA and RNA binding, transcriptional and translational control, and mRNA export. Members of the family have a higher affinity for single-stranded DNA and are known to bind scaffold/matrix attachment region DNA, as well as single-stranded RNA. They enhance the RNA unwinding activity of DDX39A and may play a role in cell growth, metabolism, and carcinogenesis. These proteins are components of the TREX complex, which is associated with spliced mRNA and is involved in coupling mRNA transcription, processing, and nuclear export . The complex is recruited to mRNA near the 5' end and functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. Additionally, the TREX complex is essential for the export of certain viral mRNAs and virus production. It also associates with DDX39B, which facilitates RNA binding of DDX39B and likely plays a role in mRNA export

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Solute Carrier Family 66 (SLC66) and Scramblase ANY1 (SLC66/Scramblase_ANY1)
Type: Family

The Solute Carrier Family 66 (SLC66) is involved in the bidirectional transport of phospholipids across the phospholipid bilayer, affecting membrane asymmetry. Members of the SLC66 family, such as scramblase ANY1 in yeast, facilitate the movement of phosphatidylserine (PS) and phosphatidylethanolamine (PE) between membrane leaflets. This activity is essential for proper lipid distribution in cellular membranes and may play a role in the endosome to trans-Golgi network trafficking pathway. The exact mechanism and the extent of PS scramblase activity within the family remain topics of scientific investigation.
Mitochondrial 3-hydroxyacyl-CoA dehydrogenase (Mito_3-hydroxyacyl-CoA_DH)
Type: Family

This family of proteins includes mitochondrial enzymes involved in the fatty acid beta-oxidation pathway. They catalyze the third step in the beta-oxidation cycle, specifically for medium and short-chain 3-hydroxy fatty acyl-CoAs ranging from C4 to C10 in length. Additionally, these proteins have a regulatory role in insulin secretion by inhibiting the activation of glutamate dehydrogenase 1, which is crucial for amino acid-induced insulin secretion regulation.
Mitochondrial inner membrane organizing protein (Mito_inner_membrane_organizer)
Type: Family

This family of proteins is involved in the structural organization of the mitochondrial inner membrane. Members of this family are known to interact with the mitochondrial contact site and cristae organizing system (MICOS) complex, as well as the sorting and assembly machinery (SAM) complex located in the mitochondrial outer membrane. These interactions are essential for maintaining the proper structure and function of the mitochondria, which is crucial for cellular energy production and metabolic processes.
High-affinity choline transporter (Choline_transporter)
Type: Family

This family of proteins includes high-affinity sodium-coupled choline transmembrane symporters. They function as electrogenic, voltage-dependent transporters with variable charge/choline stoichiometry. These proteins are crucial for acetylcholine synthesis, as they transport choline from the synaptic cleft into presynaptic nerve terminals following neurotransmitter release. The transport process is also influenced by chloride ions, which are likely regulatory rather than cotransported. The activity of these transporters is modulated by internalization and recycling between the cell surface and intracellular organelles. A specific motif in the C-terminal region is important for this regulation. The proteins are inhibited by hemicholinium 3 and are essential for cholinergic neuronal communication.
Plant Stress & Developmental Transcription Factors (Plant_Stress_Dev_TF)
Type: Family

The protein family described is involved in transcriptional regulation, with members acting as transcription factors that bind to specific DNA elements in gene promoters. These transcription factors play roles in plant stress responses, including cold, drought, and salt stress, as well as in sugar-repressed transcription. They contribute to various physiological processes such as stomatal closure, cold tolerance, and developmental adaptations like hypocotyl elongation, lateral root formation, leaf senescence, and somatic embryogenesis. The family includes both activators and repressors that recognize motifs like 5'-TATCCA-3' and 5'-ATCACA-3', and are involved in the regulation of genes associated with reactive oxygen species, auxin response, and embryonic development.
Cell Polarization and PKA Anchoring (Cell_Polariz_PKAAnc)
Type: Family

The protein family is involved in various cellular processes including cell polarization, division, and bud site selection. Members anchor regulatory subunits of protein kinase A (PKA) to mitochondria or the plasma membrane, potentially influencing apoptosis through BAD phosphorylation and inactivation. They may also facilitate PKA and G protein signal transduction by assembling multiprotein complexes and interacting with G-alpha proteins, linking signaling machinery to kinases. Additionally, they play a role in establishing bipolar budding patterns and localizing budding landmarks in yeast.
Meiotic Crossover Helicase (Meiotic_Crossover_Helicase)
Type: Family

This family of proteins includes ATP-dependent DNA helicases that play a crucial role in meiotic recombination. They are involved in the formation of crossovers and the complete synapsis of homologous chromosomes, which are essential for accurate chromosome segregation during meiosis. These helicases preferentially unwind DNA in the 3' to 5' direction and are specific to recombination events that result in interference-sensitive crossovers, also known as class I meiotic crossovers. Their activity is necessary for the proper formation of bivalents, structures formed by a pair of synapsed homologous chromosomes, ensuring genetic diversity and stability in the resulting gametes.
Arf-GAP domain and FG repeat-containing protein (Arf-GAP_FG-repeat_protein)
Type: Family

This family of proteins is involved in vesicular transport processes, particularly in vesicle docking and fusion events during acrosome biogenesis. Members of this family may also play a role in RNA trafficking or localization within cells. Additionally, certain proteins within this family can interact with viral components; for instance, they can act as cofactors for HIV-1 Rev, facilitating the export of Rev-responsive element-containing RNAs from the nucleus to the cytoplasm, which is a critical step in HIV-1 replication. The presence of FG repeats and occasionally N-P-F repeats within these proteins suggests a role in nucleocytoplasmic transport or cellular scaffolding.
Roquin domain-containing protein (Roquin_domain)
Type: Family

This family of proteins functions as post-transcriptional repressors, regulating mRNA stability by recognizing and binding to conserved stem loop motifs in the 3'-UTR of target mRNAs, leading to mRNA deadenylation and degradation. Members of this family are involved in controlling inflammatory responses and the differentiation of T cells by modulating the expression of specific genes. They also interact with miRNAs, influencing microRNA homeostasis and processing. Additionally, these proteins possess ubiquitin E3 ligase activity, pairing with various E2 enzymes to produce polyubiquitin chains, which can target proteins for degradation. They can bind to double-stranded RNA, which may regulate their E3 ligase activity.
Protein disulfide-isomerase TMX3 (PDI_TMX3)
Type: Family

The TMX3 family proteins are probable disulfide isomerases involved in the folding of proteins with disulfide bonds. They may function as dithiol oxidases and play a role in regulating redox signals. Members of the TMX3 family are also implicated in maintaining endoplasmic reticulum-mitochondria contact sites, which are crucial for cellular homeostasis and signaling. The presence of a di-lysine motif in these proteins suggests their localization to the endoplasmic reticulum, which is typical for type I membrane proteins. The TMX3 family is part of the larger protein disulfide isomerase family, which is essential for the proper formation of disulfide bonds in nascent proteins, thereby ensuring correct folding and functionality.
Glycosyl Hydrolase and Zinc Finger Regulators (GH-ZnFinger_Regulators)
Type: Family

This family of proteins includes enzymes and transcriptional regulators. The enzymatic members are involved in the breakdown of complex carbohydrates, such as dextran, which may influence bacterial adherence to surfaces like teeth. Other members of the family, characterized by zinc finger domains, are implicated in the regulation of gene expression, likely through binding to DNA and influencing transcriptional processes. These regulatory proteins are essential for various cellular functions and may have roles in development, differentiation, and maintenance of cellular states.
Cell surface hyaluronidase CEMIP/CEMIP2 (CEMIP/CEMIP2)
Type: Family

This family of proteins is involved in the metabolism of hyaluronic acid (HA), a major component of the extracellular matrix. It includes Cell migration-inducing and hyaluronan-binding protein (CEMIP) and Cell surface hyaluronidase (CEMIP2) which mediate the depolymerization of high-molecular-weight HA into intermediate-sized fragments . This process is crucial for various physiological functions, including the regulation of angiogenesis, heart development, and cell migration . CEMIP is known to bind HA and is implicated in the catabolism of HA in tissues such as the dermis and synovium. It may also play roles in pathological conditions by promoting epithelial-mesenchymal transition (EMT) and cancer progression . Additionally, these proteins can regulate cell adhesion and migration by modulating HA degradation at focal adhesion sites .
CR1/CR2 motif-containing transcription regulator (CR1/CR2-DNA-binding_regulator)
Type: Family

This family of proteins includes transcription factors that are characterized by their ability to bind DNA through specific motifs, such as CR1 and CR2, which mediate sequence-specific DNA binding. Members of this family are involved in the regulation of gene expression by binding to enhancer or promoter elements of target genes. For instance, some proteins within this family bind to the MYOD1 enhancer, playing a crucial role in muscle differentiation. Others are implicated in the transcriptional regulation of genes such as SLC2A4 and HD, or in the transcription of papillomavirus genes. The DNA-binding activity is essential for the transcriptional regulatory function of these proteins, which is a common feature shared by members of this family.
CUL4-DDB1 E3 ligase complex substrate receptor (CUL4-DDB1_E3_ligase_receptor)
Type: Family

This family of proteins appears to be involved in the ubiquitin-proteasome system, specifically as substrate receptors for the CUL4-DDB1 E3 ubiquitin-protein ligase complex. Members of this family may play a role in targeting proteins for ubiquitination and subsequent degradation, which is a critical process for maintaining cellular homeostasis. The presence of a DDB-box in at least one member suggests an interaction domain for binding to the DDB1 protein, which is a part of the E3 ligase complex. The ubiquitin-proteasome pathway is essential for various cellular processes, including cell cycle regulation, DNA repair, and signal transduction.
RNA polymerase II subunit 5-mediating protein (RNA_pol_II_subunit5-mediator)
Type: Family

This family of proteins is involved in the regulation of gene transcription and cellular growth signaling pathways. Members act as transcriptional repressors, working with corepressors to regulate transcription factors such as androgen receptors. Some family members are implicated in tumor suppression by inhibiting gene transcription that promotes anchorage-independent growth in cancer cells. They are also essential for cell survival in certain cancer types. These proteins play a role in maintaining signaling pathways that are critical for cell survival under normal conditions, by mediating negative feedback mechanisms that prevent excessive signaling. They can inhibit the activity of specific phosphatases in mitochondria, and are involved in the coordination of nutrient-sensitive gene expression in a manner dependent on the mTOR pathway. Additionally, they have a scaffolding function, capable of assembling a complex with prefoldin and other proteins involved in transcription and ubiquitination processes.
E3 ubiquitin-protein ligase CHFR (E3_ubiquitin-ligase_CHFR)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases involved in the antephase checkpoint of the cell cycle. They function by delaying the onset of mitosis in response to microtubule poisons, acting in early prophase before chromosome condensation. These proteins are implicated in signaling mitotic stress through the ubiquitination of target proteins, leading to their proteasomal degradation. They are known to mediate 'Lys-48'-linked ubiquitination, which targets proteins for degradation, and may also facilitate 'Lys-63'-linked ubiquitination, which is typically involved in signaling rather than degradation. Members of this family are believed to act as tumor suppressors and are involved in cell cycle arrest at G2/M. They contain FHA domains, which are important for their anti-proliferative properties and may interact with phosphorylated proteins, and PBZ-type zinc fingers, which bind poly(ADP-ribose) in a zinc-dependent manner, essential for their checkpoint function.
Diverse Functionality Domain-containing Protein (Diverse_Func_Domain-Protein)
Type: Family

This family of proteins includes a variety of functions, such as structural components in fibrous materials, antibacterial activity, and potential roles in cellular structure and regulation. One member is a core component of silk, contributing to the formation of a strong, insoluble, and chemically inert filament. Another exhibits antibacterial properties, suggesting a role in defense mechanisms. Other members are suggested to have roles in cellular structure or regulation, although their specific functions may not be fully characterized.
Nucleoredoxin-like (Nucleoredoxin-like)
Type: Family

This family of proteins includes probable thiol-disulfide oxidoreductases that are likely involved in various redox reactions. Members of this family may function in processes such as pollen tube growth and pollen function in plants, although some members do not require this activity for in vitro pollen tube growth. They may also be involved in the generation of lipid signaling molecules.
Autophagy Receptor and Signaling Regulator (Autophagy_Rcpt_SigReg)
Type: Family

The protein family functions as an autophagy receptor, playing a crucial role in selective macroautophagy, also known as aggrephagy. Members of the family serve as a bridge between polyubiquitinated cargo and autophagosomes, interacting with both the cargo destined for degradation and autophagy modifiers from the MAP1 LC3 family. They are involved in the formation and degradation of cytoplasmic ubiquitin-containing inclusions and the recruitment of ubiquitinated proteins to PML bodies in the nucleus. Additionally, they participate in the autophagy of peroxisomes in response to ROS. The family members may influence various cellular processes, including the activation of NFKB1, muscle cell signaling, cell differentiation, apoptosis, immune response, and K(+) channel regulation. They are implicated in endosome organization, vesicle transport, and activation of the NFE2L2/NRF2 pathway through interaction with KEAP1, promoting the expression of cytoprotective genes.