SII-SWORD/CoKE huggingface dataset:
Glycosyltransferase family GT2 and GT47 (Glycosyltrans_GT2/GT47)
Type: Family

The GT2 glycosyltransferase family is involved in various biological processes across different organisms. In fungi, members of this family maintain the cell wall's outer surface by synthesizing an unknown extracellular or cell wall polysaccharide, essential for plant-fungal interactions and hyphal growth on solid matrices. They also play roles in infection-related morphogenesis, pathogenesis, stress tolerance, and hyphal hydrophobicity, potentially through the glycosylation of heat shock proteins and other substrates, affecting growth, pathogenicity, and cell wall integrity. Another subset of this family, the glycosyltransferase 47 family, is crucial for heparan-sulfate biosynthesis, adding glucuronic acid and N-acetylglucosamine units to heparan sulfate chains, which is vital for cellular functions in higher organisms.
Autophagy and Host Defense Regulator (Autophagy_HostDef_Reg)
Type: Family

The protein family is involved in the regulation of autophagy and host defense mechanisms. Members promote autophagosome maturation by facilitating the production of PtdIns(3)P and antagonizing negative regulators of the PI3K/PI3KC3 complex. They bind various phosphoinositides and recruit complexes to autophagosomes, influencing their fusion with lysosomes. Additionally, they regulate lipid and glycogen homeostasis and may act as tumor suppressors. Some members inhibit PIK3C3 activity, negatively regulate endosome maturation, and affect endocytic trafficking. They are also involved in the immune response, promoting NADH oxidase activity and affecting TLR signaling, as well as regulating pro-inflammatory cytokine production following pathogen infection.
BAH domain-containing protein (BAH_domain_protein)
Type: Family

This family of proteins includes members with a BAH domain, which is implicated in chromosomal localization and gene regulation. One characterized function within this family is the determination of tissue-specific identity, particularly in the context of developmental processes. For example, a member of this family in Drosophila is involved in the development of eye morphology and can induce ectopic wing formation when overexpressed. This suggests that the family may play a role in the regulation of morphogenetic pathways and the expression of genes responsible for tissue identity and development.
Intracellular Vesicle Transport-Associated (IVT-Associated)
Type: Family

This family of proteins appears to be involved in intracellular vesicle transport, a critical process for the trafficking of molecules within cells. The proteins may play a role in the movement of vesicles between different cellular compartments, ensuring the proper distribution of proteins, lipids, and other substances necessary for cell function and signaling.
SKI2 subfamily ATP-dependent RNA helicases (SKI2_subfamily_helicases)
Type: Family

The helicase family, specifically the SKI2 subfamily, is characterized by proteins that exhibit nucleic acid unwinding activity, which is essential for various aspects of RNA and DNA metabolism. Members of this family are involved in processes such as RNA surveillance, splicing, and ribosome biogenesis. One member, DDX60, is known to play a role in the innate immune response by regulating type I interferon and interferon-inducible gene expression upon viral infection. It can bind to single-stranded RNA, double-stranded RNA, and double-stranded DNA, and enhances the interaction of RIGI with double-stranded RNA, exhibiting antiviral activity against specific viruses.
Phosphatidylinositol transfer protein/CRAL-TRIO domain (PITP/CRAL-TRIO)
Type: Family

The protein family is characterized by its involvement in lipid transfer and membrane trafficking. Members of the family are non-classical phosphatidylinositol transfer proteins (PITPs) that exhibit phosphatidylinositol-binding/transfer activity. They play a role in activating phospholipase D1, modulating ArfGAP function, and inhibiting phosphatidylcholine degradation. Additionally, the family is implicated in the regulation of post-Golgi membrane-trafficking events, resistance to oxidative stress, and the inhibition of fatty acid synthase activity under specific metabolic conditions. The presence of CRAL-TRIO domains suggests a role in binding small lipophilic molecules, potentially contributing to diverse cellular processes including signal transduction and membrane trafficking.
Xaa-Pro dipeptidase-like (X-Pro_dipept-like)
Type: Family

Xaa-Pro dipeptidase specialises in the hydrolysis of dipeptides where the C-terminal residue is either proline (Xaa-Pro) or hydroxyproline . These enzyme preferentially cleave Gly-Pro dipeptides but are also capable of processing other dipeptides with a prolyl residue, such as Ala-Pro, Met-Pro, Phe-Pro, Val-Pro, and Leu-Pro . It plays a crucial role in collagen metabolism by breaking down the high concentration of imino acids present in collagen . Additionally, the human homologue is known to be regulated by specific inhibitors, which can indirectly influence inflammatory processes by affecting the CARD8 inflammasome .
Tectonic-like complex component protein (Tectonic-like_complex_comp)
Type: Family

This family of proteins includes components of the tectonic-like complex, which is localized at the transition zone of primary cilia. These proteins play a crucial role in maintaining the ciliary structure and are essential for ciliogenesis. They act as a barrier to prevent the diffusion of transmembrane proteins between the cilia and plasma membranes. Additionally, they are involved in the sonic hedgehog (SHH) signaling pathway, which is important for developmental processes.
YY1-Associated Transcriptional Regulator (YY1-Transcr_Regul)
Type: Family

The protein family in question is involved in various cellular processes including chromatin remodeling, transcriptional regulation, DNA repair, replication, and cell cycle regulation. Members of the family are known to associate with complexes that include proteins such as YY1, SIN3A, and HDAC1, indicating a role in transcriptional repression. Additionally, the family plays a crucial role in B cell lymphopoiesis, highlighting its importance in immune system development. The association with the INO80 complex and enhancement of transcription activation by YY1 suggests a multifaceted role in gene expression control.
LTO1 complex adapter protein (LTO1_adapter)
Type: Family

This family of proteins is involved in the biogenesis of the large ribosomal subunit and initiation of translation. Members of this family form a complex with YAE1 or its homologs, functioning as a target-specific adapter that recruits apo-ribosomal-like proteins to the cytosolic iron-sulfur protein assembly (CIA) machinery. This interaction is essential for the maturation of iron-sulfur clusters that are crucial for the functionality of ribosomal proteins and other iron-sulfur cluster-dependent enzymes. Additionally, these proteins may have a role in proline metabolism and the regulation of reactive oxygen species (ROS) production, highlighting their potential involvement in cellular metabolic regulation and response to oxidative stress.
Pectin Methylation Modulator (Pectin_Meth_Modulator)
Type: Family

This family of proteins is involved in the modulation of cell wall physiology, particularly through the regulation of pectin methylation status. Members of this family are implicated in various developmental processes, including seed germination, hypocotyl elongation, reproductive organ development, and embryo development. They act as regulators of pectin methylesterification, affecting cell separation and elongation. Some members are also involved in the plant's response to root-knot nematode infection and play a role in gravitropic responses by influencing auxin efflux. The family includes proteins that are essential for the proper development of roots, rosettes, and embryos, particularly in the context of cell wall modification and testa rupture during seed germination.
Chromatin-remodeling and transcription coactivator (Chromatin_remod/trans_coact)
Type: Family

This family of proteins includes components of the SWI/SNF chromatin remodeling subcomplex GBAF, which is involved in modifying chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. These proteins may also be associated with BRD4-mediated gene transcription regulation. Additionally, a related protein is a part of the Mediator complex, acting as a coactivator in the transcription of RNA polymerase II-dependent genes by serving as a bridge between gene-specific regulatory proteins and the basal transcription machinery.
F-box/kelch-repeat domain-containing protein (F-box/Kelch-repeat)
Type: Family

This family of proteins includes members that contain an F-box domain and often kelch repeats. The F-box domain is crucial for the interaction with SKP1-like (ASK) proteins, which are part of the SCF (SKP1-cullin-F-box) E3 ubiquitin ligase complex. These complexes play a significant role in the ubiquitination pathway, where they are responsible for the recognition and targeting of specific substrate proteins for ubiquitination, followed by proteasomal degradation. The ubiquitination process is a key regulatory mechanism for controlling protein levels and function in eukaryotic cells, affecting various cellular processes such as cell cycle progression, signal transduction, and transcriptional regulation.
Transcriptional Regulator and Chromatin Remodeler (Trans_Reg/Chrom_Remod)
Type: Family

The protein family is involved in transcriptional regulation and chromatin remodeling. Members of the family function as transcriptional activators, interacting with various transcriptional activators and cofactors to modulate gene expression. They play roles in the regulation of the circadian clock by controlling the transcriptional activity of core components such as CLOCK and BMAL1/2. They also influence the expression of genes like MMP3, impacting processes like stromelysin expression. The family includes proteins that may have significance in embryonic and postnatal development, as well as neuronal differentiation. Some members possess an atypical PHD domain that negatively modulates cofactor binding, suggesting a complex regulatory mechanism within chromatin structure and transcriptional machinery.
Armadillo Repeat & Ser/Thr Protein Kinase (Armadillo-Ser/Thr_Kinase)
Type: Family

This family of proteins includes armadillo repeat-containing proteins involved in male fertility and sperm motility, specifically by promoting autophagic degradation of ribosomes during spermatogenesis to supply energy for sperm flagellar motility. Additionally, the family encompasses serine/threonine-protein kinases that play a role in the spatial and temporal control of cortical activities in mitotic and postmitotic cells, plasma membrane function in developing pollen, cell expansion, cell elongation, and embryo development.
Environmental Response Regulator (Env_Response_Regulator)
Type: Family

This family of proteins includes transcription factors that are involved in the regulation of gene expression in response to environmental conditions. One member of this family acts as a negative regulator by controlling the expression of genes that are regulated by abscisic acid, which is a plant hormone that plays a key role in stress responses and developmental processes.
E3 ubiquitin-protein ligase RNF220-like (E3_ubiq-ligase_RNF220-like)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases that are involved in the ubiquitination and subsequent proteasomal degradation of specific substrates, such as SIN3B. These proteins also function independently of their ligase activity, stabilizing CTNNB1 through deubiquitination mediated by USP7, which in turn promotes Wnt signaling. Additionally, they play a role in the regulation of the nuclear lamina structure, which is crucial for maintaining the integrity of the nucleus. The family is characterized by its diverse functions in cellular signaling pathways and structural maintenance.
Spaetzle/Toll ligand-like (Spz/Toll_ligand-like)
Type: Family

This family of proteins includes neurotrophins that function as ligands for Toll and Toll-related receptors, playing a pivotal role in the development and function of the central nervous system. They are involved in the establishment of dorsal-ventral polarity during embryonic development, motor axon targeting, neuronal survival, and synaptic targeting at the neuromuscular junction. Some members are implicated in the immune response regulation in the tracheal system. They activate signaling pathways such as the Toll signaling pathway and a Tollo and JNK pathway, which are essential for various developmental and immune processes.
Zinc finger and G patch domain-containing protein (ZnF-G_patch_domain)
Type: Family

This family of proteins includes members with zinc finger domains, which are typically involved in DNA binding and transcriptional regulation. The presence of G patch domains suggests a role in RNA processing or repair mechanisms. These domains are known to mediate protein-RNA interactions, which are crucial in various cellular processes including splicing, transcription, and translation. The proteins in this family are likely to have diverse functions related to gene expression regulation and RNA metabolism, reflecting the multifunctional nature of zinc finger and G patch domain-containing proteins.
B-cell PI3K Activation and Signaling Adapters (B-cell_PI3K-Signaling_Adptrs)
Type: Family

The protein family is involved in B-cell development and signaling, acting as an adapter linking B-cell receptor (BCR) signaling to the phosphoinositide 3-kinase (PI3K)-Akt pathway. It supports BCR and PI3K activation by providing a docking site for PIK3R1 and complements the role of CD19. Additionally, it connects Toll-like receptor (TLR) signaling to PI3K activation, regulating inflammatory cytokine production and is implicated in natural killer cell PI3K activation. The family also plays a role in B-cell survival through REL activation. Another function includes promoting BCR-induced Ca(2+) mobilization from intracellular stores and facilitating Lyn-mediated phosphorylation of IP3 receptors.
Dermatan-Sulfate Isomerase (Dermatan-Sulfate_Isomerase)
Type: Family

The dermatan-sulfate isomerase family is involved in the biosynthesis of dermatan sulfate, a type of glycosaminoglycan/mucopolysaccharide. Members of this family are responsible for the conversion of D-glucuronic acid to L-iduronic acid (IdoUA) residues, a key step in the formation of dermatan sulfate. This process is crucial for the proper function of various biological systems, as dermatan sulfate plays a significant role in cell signaling, coagulation, and the modulation of enzyme activities. The family includes both active epimerases and epimerase-like proteins that may have a regulatory or yet undefined role in dermatan sulfate biosynthesis.
DnaJ Homolog Subfamily C Member 16 (DnaJ_C16_autophagy_reg)
Type: Family

The DnaJ homolog subfamily C member 16 family is involved in the cellular autophagy process, specifically in the regulation of autophagosome size. Autophagosomes are key structures in autophagy, a mechanism by which cells degrade and recycle cytoplasmic components. The members of the DnaJ homolog subfamily C member 16 family play a crucial role in ensuring that autophagosomes are formed with the appropriate dimensions, which is essential for the proper turnover of cellular materials and maintenance of cellular homeostasis.
Serine/Threonine/Tyrosine-Interacting Phosphatase (STYX-Interacting_Phosphatase)
Type: Family

This family of proteins includes catalytically inactive phosphatases that interact with serine, threonine, and tyrosine residues. Members of this family function as nuclear anchors for MAPK1/MAPK3, also known as ERK1/ERK2, thereby modulating cell-fate decisions and cell migration through the spatiotemporal regulation of these kinases. Additionally, they are involved in inhibiting the degradation of substrates by preventing the assembly of the SCF E3 ubiquitin-protein ligase complex through binding to the F-box of FBXW7. These proteins also play a role in spermatogenesis, highlighting their importance in developmental processes.
Telomeric Repeat-Binding Domain-Containing Protein (TRBD-Containing_Protein)
Type: Family

This family of proteins is involved in the regulation and protection of telomeres, the repetitive nucleotide sequences at the ends of chromosomes. Members of this family bind specifically to telomeric DNA sequences, playing a crucial role in maintaining telomere integrity and length. They are components of the shelterin complex, which is essential for protecting chromosome ends from being recognized as DNA damage and prevents inappropriate processing by DNA repair pathways. Additionally, these proteins are implicated in the regulation of the mitotic spindle, contributing to proper cell division. Some family members also interact with microtubules and are involved in transcriptional regulation, including the control of histone levels and centromere function.
Serine/threonine kinase-like (Ser/Thr_kinase-like)
Type: Family

This family of proteins includes serine/threonine kinases and putative kinases. Some members are predicted to be catalytically inactive due to the absence of conserved active site residues, yet they may retain other functional roles within the cell. One member is reported to phosphorylate specific substrates, suggesting a role in signaling or regulatory pathways. The family belongs to the larger protein kinase superfamily and shares homology with other serine/threonine kinases, indicating a potential involvement in phosphorylation-dependent processes.
Ankyrin repeat and MYND domain-containing protein 2 (Ankyrin-MYND_dom_contain_2)
Type: Family

The Ankyrin repeat and MYND domain-containing protein 2 family is implicated in the cellular process of trafficking signaling proteins to cilia. Members of this family play a crucial role in the proper localization of signaling molecules, which is essential for the function of cilia in sensory perception and signal transduction. In particular, the family is involved in the dendritic transport of receptor-type guanylate cyclases to cilia in sensory neurons, which is necessary for calcium signaling in response to stimuli such as nitric oxide. This function is critical for the behavioral avoidance response in organisms, highlighting the family's importance in sensory and physiological processes.
CONSTANS-like zinc finger regulators (CONSTANS-like_ZF)
Type: Family

This family of proteins includes members that are characterized by the presence of zinc finger domains, suggesting a role in DNA binding and regulation of gene expression. The CONSTANS-like proteins within this family are likely involved in the regulation of flowering time and other developmental processes in plants, as implied by their similarity to the CONSTANS protein, which is known to control the timing of flowering in response to photoperiod. Additionally, one member of this family is involved in the regulation of chloroplast protein import, indicating a broader role in chloroplast function and development.
Thioredoxin-related transmembrane domain-containing protein (TMX_domain-containing)
Type: Family

This family of proteins contains a thioredoxin domain and is involved in redox reactions, where it catalyzes the reversible oxidation of its active center dithiol to a disulfide and facilitates dithiol-disulfide exchange reactions. Members of this family inhibit an alternative triglyceride biosynthesis pathway, thus regulating triacylglycerol accumulation. They function as protein disulfide isomerases, aiding in the formation and reduction of disulfide bonds, particularly of transmembrane proteins at the endoplasmic reticulum membrane. They are also involved in the endoplasmic reticulum-associated degradation pathway, targeting folding-defective polypeptides. Additionally, these proteins play a role in the regulation of platelet aggregation, endoplasmic reticulum-mitochondria contact sites, and calcium flux between these organelles.
Tricalbin domain-containing protein (Tricalbin_domain)
Type: Family

This family of proteins may be involved in membrane trafficking processes. Members are characterized by the presence of C2 domains, which in some cases show Ca(2+)-dependent phospholipid binding, suggesting a role in membrane interactions and signaling. The C2 domains bind to various phospholipids, including phosphatidylserine and phosphoinositides. Additionally, some members contain an SMP-LTD domain, which is a barrel-like structure capable of binding and transferring glycerophospholipids between bilayers. The combination of these domains indicates a functional role in lipid transport and membrane organization.
CTLH complex component protein (CTLH_complex_component)
Type: Family

This family of proteins is involved in the ubiquitin-proteasome system, specifically as components of the CTLH E3 ubiquitin-protein ligase complex. They interact with UBE2H to facilitate ubiquitination and subsequent proteasomal degradation of specific target proteins, such as the transcription factor HBP1. Additionally, these proteins play a role in the endocytic pathway, being required for the internalization and degradation of the GABA receptor GABRA1. They are also implicated in cellular responses to the extracellular matrix, mediating cell spreading and cytoskeletal changes in response to THBS1. A characteristic feature of these proteins is the presence of a LisH domain, which is important for dimerization and may contain a nuclear targeting signal.
Ankyrin repeat and death domain-containing protein (Ankyrin-DD_containing_protein)
Type: Family

This family of proteins includes members with ankyrin repeats and a death domain, suggesting a role in protein-protein interactions and apoptotic signaling pathways. Some proteins in this family are involved in the regulation of immune responses, such as the inhibition of type I interferon-induced antiviral activity and the modulation of NF-kappa-B activation, which is a key factor in inflammatory and immune responses. The presence of ankyrin repeats indicates that these proteins may be involved in mediating interactions with other cellular proteins, potentially influencing various signaling cascades and cellular functions.
Polycomb group PRC1-like complex component (PcG_PRC1-like_component)
Type: Family

This family of proteins includes components of Polycomb group (PcG) multiprotein PRC1-like complexes, which are essential for maintaining the transcriptionally repressive state of various genes, such as Hox genes, during development. These proteins are involved in chromatin remodeling and histone modification, specifically contributing to the monoubiquitination of histone H2A at a conserved lysine residue, which results in a heritable change in chromatin expressibility. Some members may bind to specific chromatin regions, potentially influencing the target specificity of the PRC1 complex. Certain proteins within this family may also have functions independent of the PRC1 complex, such as roles in embryonic stem cells or binding to modified DNA to facilitate repression of specific genomic loci.
Tumor necrosis factor receptor superfamily decoy receptor (TNFRSF_decoy_receptor)
Type: Family

This family of proteins includes decoy receptors that interact with various tumor necrosis factor superfamily ligands. They play a crucial role in regulating osteoclastogenesis by acting as decoy receptors for TNFSF11/RANKL, neutralizing its function and inhibiting osteoclast activation. These proteins are also involved in promoting osteoclast apoptosis, thus contributing to bone homeostasis, which is influenced by the local balance between TNFSF11 and the decoy receptors. Additionally, they may have a role in preventing arterial calcification and can act as decoy receptors for TNFSF10/TRAIL, providing protection against apoptosis. The binding of TNFSF10/TRAIL to these receptors can block the inhibition of osteoclastogenesis.