SII-SWORD/CoKE huggingface dataset:
Non-receptor type tyrosine-specific phosphatase (NR_tyrosine_phosphatase)
Type: Family

This family of proteins includes non-receptor type tyrosine-specific phosphatases involved in a variety of cellular processes. They dephosphorylate receptor and non-receptor protein tyrosine kinases, regulating signaling pathways related to hematopoiesis, inflammation, cell proliferation and differentiation, glucose homeostasis, and immune system development. They play roles in T-cell receptor signaling, cytokine-mediated signaling, and growth factor receptor signaling, including negative regulation of insulin, EGF, and PDGF receptors. Some members are involved in the endoplasmic reticulum unfolded protein response and cell reorganization.
Innate Immunity and Apoptosis Regulator (Innate_Immune_Apopt_Reg)
Type: Family

The protein family is involved in the regulation of innate immune responses and apoptosis. Members act as negative feedback regulators, controlling excessive immune reactions by modulating pathways such as Toll-like receptor 4 (TLR4) and DDX58/RIG1-like helicases (RLH). They interact with key signaling molecules like TRAF6 to attenuate NF-kappa-B activation, and operate downstream from MAVS and upstream of NF-kappa-B and IRF3 in the RLH pathway. Additionally, family members function as negative regulators of the IAP family, inhibiting anti-caspase activity and promoting apoptosis. They induce the cleavage and inactivation of BIRC4, mediate TNF-alpha-induced apoptosis, and are involved in the mitochondrial apoptosis pathway. This includes promoting BAX translocation to mitochondria and cytochrome c release. They may also influence the cellular sensitivity to TRAIL and act as tumor suppressors by mediating resistance to apoptosis in cancer cells.
Sigma-2 receptor-like (Sigma-2_receptor-like)
Type: Family

This family of proteins includes intracellular receptors that are known to bind various drugs and are highly expressed in proliferating cells. They are thought to play a significant role in regulating cell survival, morphology, and differentiation. Members of this family may also act as regulators of cellular cholesterol homeostasis and potentially function as sterol isomerases. Additionally, they may influence the activity of certain cytochrome P450 enzymes, which are involved in drug metabolism and synthesis of cholesterol, steroids, and other lipids.
Homologous Recombination Repair RAD51 Paralog (HRR_RAD51_Paralog)
Type: Family

This family of proteins is involved in the homologous recombination repair (HRR) pathway, which is crucial for the repair of double-stranded DNA breaks that can occur during DNA replication or result from DNA-damaging agents. Members of this family are known to bind to single-stranded DNA (ssDNA) and exhibit DNA-dependent ATPase activity. They are part of the RAD51 paralog protein complex BCDX2, which functions in the BRCA1-BRCA2-dependent HR pathway. This complex operates downstream of BRCA2 recruitment and upstream of RAD51 recruitment, with a specific role in binding to the intersection of Holliday junctions and replication fork junctions. Additionally, these proteins are implicated in telomere maintenance and can stimulate Holliday junction resolution, contributing to genomic stability.
FK506-binding protein-like isomerase (FKBP-like_isomerase)
Type: Family

This family of proteins includes peptidyl-prolyl cis-trans isomerases (PPIases) that are known to accelerate the folding of proteins during protein synthesis. These enzymes facilitate the cis-trans isomerization of proline imidic peptide bonds in oligopeptides, which is a rate-limiting step during folding. Members of this family are involved in various cellular processes, including signal transduction, protein trafficking, and immune response. They are characterized by their ability to bind immunosuppressive drugs such as FK506 and rapamycin, which inhibit their isomerase activity. However, they are not inhibited by cyclosporin A, distinguishing them from some other PPIases.
Cell Cycle Progression and Pre-B-cell Leukemia Transcription Factor-Interacting (CCPG1/PBIP1)
Type: Family

The CCPG1 family proteins serve as assembly platforms for Rho protein signaling complexes, selectively modulating the guanine nucleotide exchange activity of specific Rho GTPases. They play a role in inhibiting the transcriptional activation and transforming activity of RHOA by limiting the exchange activity of MCF2L, without affecting CDC42 or MCF2's activity towards RHOA or CDC42. Additionally, the family includes proteins that regulate pre-B-cell leukemia transcription factors, inhibit DNA binding of PBX1-HOX complexes, and block E2A-PBX1 transcriptional activity. They also facilitate the tethering of estrogen receptor-alpha to microtubules, influencing its signaling pathway. Members of the CCPG1 family are implicated in cell cycle regulation and may have a role in Rho-mediated signaling pathways.
Mitochondrial ribosomal protein bL32 (Mitoribosomal_protein_bL32)
Type: Family

This family of proteins includes components of the mitochondrial ribosome, also known as mitoribosomes. These proteins are involved in the synthesis of mitochondrial genome-encoded proteins, which are essential for various cellular processes, including the mitochondrial respiratory chain. The mitoribosomes are closely associated with the mitochondrial inner membrane, allowing for the cotranslational integration of translation products into the membrane. This suggests a role in the production of transmembrane subunits that are critical for mitochondrial function and energy production within the cell.
Oxidative Stress Response Regulator (OxStress_Response_Reg)
Type: Family

This family of proteins is involved in promoting tolerance to various metals and oxidizing chemicals. Members of this family may function as transcription activators and are potentially involved in chromatin remodeling during stress responses. Some proteins in this family are known to interact with histone deacetylase HDA19, which may regulate gene expression. Additionally, certain members act as negative regulators of flowering, particularly under drought stress conditions, to possibly prevent premature flower development and ensure seed viability. The family includes proteins with kinase-inducible domains necessary for specific protein interactions.
Glycosyltransferase 8 (Glycosyltransferase_8)
Type: Family

The glycosyltransferase 8 family is characterized by its enzymatic function in post-translational modification of proteins. Members of this family are involved in the elongation of O-linked glucose residues that are attached to EGF-like repeats in the extracellular domain of Notch proteins. They achieve this by catalyzing the addition of xylose, thereby playing a crucial role in the modification of Notch signaling molecules, which are essential for various developmental processes. The precise action of these enzymes ensures the proper functioning of Notch protein interactions and signaling pathways.
WW domain-binding (WW_domain-binding)
Type: Family

The WW domain-binding protein family is characterized by its interaction with other proteins through PPxY motifs, which are known to mediate interactions with proteins such as WWOX and NEDD4. Members of this family are involved in various cellular processes, including acting as synapse-to-nucleus messengers that promote NMDA receptor-mediated excitotoxicity in neurons in a JUN-dependent manner. They are also implicated in inhibiting ubiquitination-mediated degradation, promoting phosphorylation and transcriptional activity of transcription factor JUN, and may play roles in T cell receptor signaling and apoptosis in T cells.
Ciliary function-associated GTPase (Ciliary_GTPase)
Type: Family

This family of proteins includes small GTPases involved in ciliary function and development. Members are cilium-specific and play a crucial role in controlling the microtubule-based axoneme structure of cilia. They are implicated in maintaining the association between intraflagellar transport (IFT) subcomplexes A and B, which is essential for ciliary signaling and function. These proteins are also involved in the development of the cerebral cortex by regulating the formation of a polarized radial glial scaffold and the migration and placement of interneurons. Although they bind GTP, their ability to hydrolyze it is unclear, with some members having an incomplete active site that likely contributes to the lack of GTPase activity.
Plant Cytochrome P450 78A (Cytochrome_P450_78A)
Type: Family

The Cytochrome P450 78A family is involved in various developmental processes in plants. Members of this family play crucial roles in regulating the growth of leaves, flowers, seeds, and fruits, often acting in a non-cell-autonomous manner. They are implicated in the timing of lateral organ formation and the duration of vegetative phases, such as the plastochron. Some family members function in association with others to regulate the relative growth of the shoot apical meristem and plant organs, as well as to stimulate cell proliferation in developing ovules, thereby promoting seed growth. The family operates through mechanisms that are distinct from classical phytohormones, suggesting the generation of unique mobile growth signals.
Serine/threonine-protein kinase NEK (STK_NEK)
Type: Family

This family of proteins includes serine/threonine kinases that play a crucial role in cell cycle regulation, particularly in mitotic progression and spindle dynamics. They are involved in the phosphorylation of various substrates, including histones and other kinases, which is essential for chromosome separation and cell division. Some members are also implicated in the regulation of ciliary biogenesis and organogenesis, as well as in maintaining renal tubular integrity. Additionally, one member is predicted to be catalytically inactive but is important for asymmetric cell division and embryogenesis, suggesting a regulatory function within the family.
Meteorin-like (Meteorin-like)
Type: Family

This family of proteins is involved in neurogenesis, specifically in glial cell differentiation and axonal network formation. Members of this family promote the differentiation of astrocytes and their transformation into radial glia, as well as the extension of axons in sensory ganglia neurons by activating satellite glia. Additionally, some family members function as hormones that are induced by exercise or cold exposure, leading to increased energy expenditure and improved glucose tolerance. These proteins contribute to the browning of white fat depots and stimulate immune cells to activate thermogenic and anti-inflammatory responses in adipose tissue. They are implicated in metabolic adaptations to cold temperatures.
Mediator complex subunit 1 (Mediator_complex_subunit_1)
Type: Family

This family of proteins functions as components of the Mediator complex, which is a coactivator essential for the regulated transcription of RNA polymerase II-dependent genes. These proteins act as a bridge, conveying information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. They are recruited to promoters through direct interactions with regulatory proteins and serve as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Some members of this family have specific roles in processes such as erythroid differentiation, embryogenesis, and development of various organs and systems.
Electron transfer flavoprotein regulatory factor 1 (ETFRF1)
Type: Family

The Electron transfer flavoprotein regulatory factor 1 family comprises proteins that function as regulators of the electron transfer flavoprotein (ETF) system. Members of this family are involved in promoting the removal of flavin from the ETF holoenzyme, which consists of the ETFA and ETFB subunits . This regulatory activity is crucial for the proper function of ETF, which plays a significant role in the mitochondrial electron transport chain and is essential for cellular respiration and energy production. The family belongs to the complex I LYR family, indicating that its members contain the LYR motif, which is associated with complex I assembly and function within the mitochondria.
MHC Class II Gamma Chain/Thyroglobulin (MHC-II_Gamma/Thyroglobulin)
Type: Family

The protein family includes two distinct groups with different functions. One group, the HLA/H-2 class II histocompatibility antigen gamma chains, plays a pivotal role in the immune system by stabilizing MHC class II alpha/beta heterodimers, facilitating antigen presentation, and interacting with CD44 to enhance T-cell responses. They also act as chaperones for CTSL and have antiviral properties against pathogens like Ebola virus and SARS-CoV-2. The other group, thyroglobulin, is essential for thyroid hormone synthesis, acting as a precursor for iodinated hormones T3 and T4. Thyroglobulin undergoes iodination and coupling of tyrosine residues, followed by proteolysis to release the hormones into the bloodstream. Both groups are critical for their respective physiological processes, with the former involved in immune defense and the latter in metabolic regulation.
Even-skipped homeobox domain-containing protein (Even-skipped_HD)
Type: Family

This family of proteins includes transcription factors that are characterized by the presence of an even-skipped homeobox domain. They are involved in various developmental processes, including the specification of neuronal cell types and pattern formation during embryogenesis. Members of this family can act as transcriptional repressors or activators, binding to specific promoter elements to regulate gene expression. They play crucial roles in motor neuron fate determination, posterior-specific pattern formation, and may influence the dorsoventral specification of mesodermal cell fate. The functions of these proteins are critical for proper segmentation and axial patterning in developing embryos across different species.
Homologous Recombination DNA-Binding Protein (HR_DNA-Binding_Protein)
Type: Family

This family of proteins is involved in DNA repair mechanisms, specifically through the promotion of homologous recombination. Members of this family exhibit structure-specific DNA-binding properties and are known to enhance the formation of DNA joint molecules, such as D-loops, which are critical intermediates in DNA repair and recombination processes. They interact with RAD51 and DMC1 recombinases to facilitate the search for homology and strand pairing during repair. Some members also have roles in the alternative lengthening of telomeres (ALT) pathway, which is significant in certain cancers. Additionally, they may cooperate with other proteins like WDR48/UAF1 to modulate the activity of enzymes involved in DNA repair, such as USP1-mediated deubiquitination of FANCD2. While some members show a strong preference for branched DNA structures, others bind with less affinity, indicating a range of DNA-binding properties within the family.
Axonemal Dynein Assembly Factor 4 (Dynein_assembly_factor_4)
Type: Family

This family of proteins is involved in the development of the cerebral neocortex, specifically in neuronal migration. Members of this family are also implicated in the regulation of estrogen receptor stability and proteasomal degradation, which is crucial for neuronal differentiation, survival, and plasticity. Additionally, these proteins function as axonemal dynein assembly factors, playing a vital role in ciliary motility, which is essential for the proper functioning of cilia.
Cation Diffusion Facilitator SLC30A (CDF_SLC30A)
Type: Family

This family of proteins is involved in zinc ion homeostasis within the early secretory pathway of cells. They are likely to form functional zinc ion:proton antiporter heterodimers with SLC30A5, although they probably have no intrinsic transporter activity on their own. These heterodimers facilitate the entry of zinc into the lumen of organelles along the secretory pathway. The proper regulation of zinc ion concentrations is crucial for the activation and folding of various enzymes, including alkaline phosphatases and those involved in the biosynthesis of phosphatidylinositol glycan anchors.
Major Latex-like (MLP-like)
Type: Family

This family of proteins includes members with a yet undefined role, which are known to be abundant in latex, constituting a significant portion of its soluble protein content. Some members of this family have been characterized to catalyze the formation of thebaine from its precursors, indicating a role in alkaloid biosynthesis. These enzymes function by facilitating the conversion of (7S)-salutaridinol 7-O-acetate into thebaine while minimizing the production of hydroxylated by-products through spontaneous allylic elimination. The activity of these enzymes can be slightly inhibited by certain substrates, suggesting a regulatory mechanism in the biosynthetic pathway. The diverse functions within this family reflect a range of biological roles, from enzymatic activity in secondary metabolism to yet-to-be-determined functions in plant physiology.
Bud site selection protein 4 (Bud4)
Type: Family

This family of proteins is involved in the regulation of cell polarity and morphogenesis, particularly in the process of bud site selection and septin organization at the bud neck during mitosis. Members of this family cooperate with other proteins to recognize spatial landmarks, which then serve as references for the establishment of polarity factors that coordinate budding, cytokinesis, and septation. In some species, these proteins also contribute to morphogenesis, adherence, colonization, and infection processes. They play a crucial role in the formation of septin ring structures and may influence the localization of hydrolytic enzymes necessary for cell separation.
Mitochondrial ribosomal protein bL33 (Mitoribosomal_protein_bL33)
Type: Family

This family of proteins includes components of the mitochondrial ribosome, also known as mitoribosomes. These proteins are involved in the synthesis of mitochondrial genome-encoded proteins. They play a crucial role in the mitochondrial respiratory chain by contributing to the production of essential transmembrane subunits. Mitoribosomes are attached to the mitochondrial inner membrane, allowing for the cotranslational integration of translation products into the membrane.
Archaemetzincin (Archaemetzincin)
Type: Family

This family of proteins includes enzymes with a probable role as zinc metalloproteases. Members of this family are characterized by their ability to bind zinc, which is essential for their catalytic activity. These enzymes are likely involved in the breakdown of various peptide substrates, utilizing the metal ion to hydrolyze peptide bonds. The family is part of the peptidase M54 group, suggesting a shared evolutionary origin and similar structural features among its members. The specific biological processes and substrates for these proteases may vary, but they are generally implicated in protein turnover and regulation.
Ribosomal Large Subunit bL36 (Ribosomal_LSU_bL36)
Type: Family

This family of proteins includes components of the large ribosomal subunit, specifically identified as bL36. Members of this family are involved in the assembly and function of ribosomes, which are essential for protein synthesis. In bacteria, these proteins are part of the 50S ribosomal subunit and play a role in the translation of mRNA into polypeptides. One member of this family is also noted to be a component of the mitochondrial ribosome in eukaryotes, indicating a conserved function in the translation machinery within mitochondria, which is responsible for synthesizing proteins encoded by the mitochondrial genome. These proteins are typically small and basic, and they contribute to the structure and stability of the ribosome.
Centromere-associated NAC/CAD complex protein (CENP-NAC/CAD_complex)
Type: Family

This family of proteins is involved in the structural and functional organization of centromeres. Members of this family are key components of the CENPA-NAC complex, which is crucial for kinetochore protein assembly, mitotic progression, and chromosome segregation. They are responsible for the recruitment of the CENPA-CAD complex and play a role in the incorporation of newly synthesized CENPA into centromeres. These proteins are necessary for the initial specific binding to CENPA nucleosomes, a critical step for centromere assembly. They are also required for proper chromosome alignment on the metaphase plate during cell division.
Glycosyltransferase_92 (GTase_92)
Type: Family

This family of proteins includes enzymes that are classified as glycosyltransferases, specifically within the glycosyltransferase 92 group. These enzymes are responsible for the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. This process is crucial for the synthesis of glycoconjugates, such as glycoproteins, glycolipids, and polysaccharides, which are essential components of cell membranes and extracellular matrices. The glycosyltransferase 92 family members are involved in various biological processes, including cell signaling, cell adhesion, and immune response, by modulating the structure and function of glycoconjugates. Their activity is vital for the proper functioning of cells and the organism as a whole.
Mouse Killer cell lectin-like receptors (Mouse_KLRs)
Type: Family

The Killer cell lectin-like receptor family in mice includes receptors expressed on natural killer (NK) cells. These receptors recognize class I MHC molecules, playing a crucial role in the regulation of NK cell activity and the immune response. They are involved in the surveillance against infected or transformed cells by inhibiting or activating NK cells upon interaction with their ligands. One member, T-cell surface glycoprotein YE1/48, specifically inhibits NK cells from lysing cells presenting H-2d alleles. The family's function is essential for maintaining the balance between immunity and self-tolerance, preventing autoimmunity while allowing effective responses against pathogens.
Dictyostelium Tiger (Dictyostelium_Tiger)
Type: Family

The Tiger protein family in Dictyostelium discoideum is involved in cell-cell recognition and signaling, essential for social amoebae aggregation and multicellular development. Members of the family, such as Contact site A protein, mediate cell binding through homophilic interactions, possibly elevating active sites into the extracellular space. Tiger proteins B1 and C1 are specifically implicated in kin discrimination, a critical process for the formation of multicellular structures. These proteins function in a non-diffusible manner, signaling between cells to regulate aggregation. Tiger protein D1 is suggested to regulate aggregation by activating tgrC1, while tgrC1 itself is a terminal node in the signaling pathway, activating tgrD1 and having both autonomous and non-autonomous functions. Collectively, the Tiger protein family represents a group of cell surface glycoproteins that coordinate the early stages of Dictyostelium development through intricate cell signaling mechanisms.
Growth-differentiation transition regulator (GDT_regulator)
Type: Family

This family of proteins includes members that are involved in the regulation of the transition between growth and differentiation. Some proteins in this family are predicted to be serine/threonine-protein kinases, which suggests a role in phosphorylation-dependent signaling pathways. However, certain members are predicted to be catalytically inactive, indicating potential regulatory or scaffolding roles rather than direct enzymatic activity. The presence of a protein kinase domain in the C-terminal section of some family members aligns them with the TKL Ser/Thr protein kinase family, while the N-terminal section is characteristic of the GDT family, suggesting a dual functionality or domain architecture.