SII-SWORD/CoKE huggingface dataset:
Visual system homeobox transcriptional regulators (VSX_homeobox_regulators)
Type: Family

The Visual system homeobox family comprises transcriptional regulators involved in the development and differentiation of various neuronal cell types and eye structures. Family members mediate the differentiation of V2a interneurons and play roles in eye development, including the specification and morphogenesis of the sensory retina, and the organization of the neuroretina. They regulate gene expression by binding to DNA consensus sequences, competitively inhibiting motor neuron gene transcription, and modulating the expression of genes involved in retinal development. These proteins are also implicated in the maintenance of neural retina identity and the regulation of canonical Wnt signaling. They participate in the development of retinal ganglion cells, promoting Hedgehog signaling and proliferation of retinal progenitor cells, and influence the differentiation of bipolar cells and rod cells within the inner nuclear layer.
Odorant-binding protein (Odorant-binding_protein)
Type: Family

This family of proteins is found in insects and it is involved in the olfactory system, specifically in the capture and transport of hydrophobic odorant molecules. Members of this family are thought to be present in the fluid surrounding olfactory sensory dendrites, where they play a role in transporting these odorants through the aqueous environment to the olfactory receptors . This process is essential for the perception of smells. Some members, like odorant-binding protein 59a from Drosophila, are also implicated in hygrotaxis behavior, which is the ability to detect and respond to humidity levels .
Transcriptional Repressor and Histone Methyltransferase (TR-Histone_Methyltrans)
Type: Family

This family of proteins includes transcriptional repressors and histone methyltransferases. Members are involved in various biological processes such as neural development, neuronal differentiation, and steroidogenesis. Some proteins in this family act on histone H3 lysine residues, modifying chromatin structure and influencing gene expression. Others play roles in oligodendrocyte differentiation and remyelination following nerve injury. Additionally, certain family members are implicated in spermatid development and fertility, with functions that include the regulation of spermatocyte-specific genes.
RING-CH-type E3 ubiquitin-protein ligase (RING-CH-type_E3_ubiq-ligase)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases with a RING-CH-type zinc finger domain essential for their ligase activity. These enzymes facilitate the transfer of ubiquitin from E2 ubiquitin-conjugating enzymes to specific substrate proteins, thereby tagging them for various cellular processes. The ubiquitination can lead to different outcomes, including protein degradation, cellular signaling, and trafficking. Members of this family are involved in several cellular processes such as T-cell proliferation, lysosome homeostasis, and autophagy regulation. They are known to promote mixed polyubiquitination on certain targets, which can inhibit autophagy or regulate inflammatory responses by targeting components of the inflammasome for degradation.
Zinc finger MYND domain-containing protein 10 (ZMYND10)
Type: Family

The ZMYND10 family is implicated in the organization and motility of axonemal structures, which are essential components of cilia. Family members play a crucial role in the pre-assembly of inner and outer dynein arms, which are necessary for the proper construction of the axoneme, the core structure of cilia responsible for their motility. Through these functions, the ZMYND10 family may indirectly influence the transcription of dynein proteins, thereby regulating ciliary movement.
Centrosomal protein of 76 kDa (CEP76)
Type: Family

The CEP76 family comprises centrosomal proteins that play a crucial role in ensuring proper centriole duplication. Members of the CEP76 family are essential for maintaining the fidelity of cell division by restricting centriole duplication to a single event per cell cycle, thereby preventing centriole reduplication. This regulatory function is vital for cell cycle progression and genomic stability.
Adhesion and Centrosome-associated Protein (Adhesion_Centrosome_assoc)
Type: Family

This family of proteins is involved in cellular adhesion systems, contributing to the organization of various types of cell-cell adherens junctions, including homotypic, interneuronal, and heterotypic connections. Members of this family may facilitate the linkage between the nectin-afadin and E-cadherin-catenin systems via alpha-actinin, potentially playing a role in the organization of the actin cytoskeleton at adherens junctions. They are also implicated in cell motility, localizing to the leading edge of moving cells and possibly influencing cell movement through Rac signaling activation. Additionally, these proteins act as centrosome maturation factors, maintaining pericentriolar material integrity and aiding proper microtubule nucleation at mitotic spindle poles. They are involved in ciliogenesis by recruiting specific components to the cilia, indicating a role in cellular signaling and structure.
SCF Complex F-box/Wd Repeat-Containing Protein (SCF_F-box/WD-repeat)
Type: Family

This family of proteins includes components of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which are involved in the recognition and binding of specific substrate proteins, often following phosphorylation. These proteins facilitate the ubiquitination and subsequent proteasomal degradation of their target proteins, thereby regulating protein turnover and contributing to the control of various cellular processes. Some family members are implicated in critical signaling pathways, such as those governing limb development and possibly Wnt signaling, highlighting their role in developmental and cell signaling pathways.
Neurotrophin receptor-related death domain-containing protein (Neurotrophin_rcpt-DD)
Type: Family

This family of proteins includes receptors that modulate signaling pathways for cell survival, differentiation, and apoptosis. They interact with neurotrophins such as NGF, BDNF, NTF3, and NTF4, with varying affinities for mature and precursor forms. Members of this family can form heterodimeric complexes, influencing neuronal development and synaptic plasticity. They are involved in the regulation of the actin cytoskeleton, RHOA inactivation, and insulin-dependent glucose uptake by modulating the translocation of GLUT4. Additionally, these proteins contribute to the circadian regulation of clock genes and metabolic genes in the brain and liver. Some members also have roles in immune response and can interact with viral proteins.
Cardiac-enriched FHL2-interacting (CEFIP)
Type: Family

This family of proteins is implicated in the regulation of cardiomyocyte hypertrophy. Members are known to interact with the FHL2 protein and play a significant role in the activation of the calcineurin/NFAT signaling pathway, which is crucial for cardiac muscle cell growth and function.
Pituitary tumor-transforming gene 1 protein-interacting (PTTG1IP)
Type: Family

The PTTG1IP protein family is involved in the regulation of nuclear translocation of the pituitary tumor-transforming gene 1 (PTTG1) protein. Members of this family are thought to play a role in facilitating the movement of PTTG1 into the nucleus, where it can perform its functions related to cell cycle regulation and tumor transformation. The precise mechanisms by which the PTTG1IP family members assist in the nuclear translocation of PTTG1 and their potential additional roles in cellular processes remain to be fully elucidated.
Transcriptional Regulators and Tumor Expansion (TransReg_TumorExp)
Type: Family

The protein family is involved in various cellular processes including transcriptional regulation and tumor cell expansion. Members act as transcriptional coactivators, enhancing the activity of MEF2C and MYOD1, which are crucial for skeletal muscle differentiation. Additionally, they play a role in down-regulating specific promoter activities and activating NF-kappa-B, a key transcription factor. The family is implicated in promoting anchorage-independent growth, metastasis to lung, bone, and brain, and inducing chemoresistance. These functions suggest a significant role in both normal cellular differentiation and pathological conditions such as cancer.
Cytochrome P450 71D (CYP450_71D)
Type: Family

The Cytochrome P450 71D family comprises enzymes with monooxygenase activity, involved in the biosynthesis of various phytoalexins, which are antimicrobial and often antioxidative substances produced by plants in response to pathogen attack. Members of the family catalyze hydroxylation reactions, adding hydroxyl groups to specific substrates such as 5-epiaristolochene and premnaspirodiene, leading to the production of compounds like capsidiol and solavetivone. These reactions are crucial for the plant's defense mechanism. The enzymes show variability in their substrate specificity and efficiency of hydroxylation steps. Some members are inhibited by compounds like ancymidol and ketoconazole, indicating a potential for regulation of their activity.
Epithelial Junction Adhesion Regulator (EJ_Adhesion_Regulator)
Type: Family

This family of proteins is involved in cellular adhesion and integrity, particularly in the formation and maintenance of tight junctions in epithelial cells. They play a crucial role in the epithelial apical junction complex and are implicated in the transepithelial migration of leukocytes. These proteins interact with JAML, a transmembrane protein on leukocytes, to mediate the activation of gamma-delta T-cells, which are important for tissue homeostasis and repair. The signaling cascade triggered by this interaction involves PI3-kinase and MAP kinases, leading to T-cell proliferation and the secretion of cytokines and growth factors that promote epithelial tissue repair. Additionally, in humans, these proteins serve as receptors for Coxsackievirus B and adenoviruses, facilitating microbial infection.
Pentatricopeptide repeat domain-containing protein (PPR_domain-containing)
Type: Family

This family of proteins features the pentatricopeptide repeat (PPR), which is a sequence motif known to mediate sequence-specific RNA binding. Members of this family are implicated in post-transcriptional processes within organelles, such as RNA editing, stability, and processing. The PPR motif typically consists of 35 amino acids and is often repeated in tandem. Proteins in this family are suggested to play roles in embryogenesis and may function as transcriptional regulators. The presence of a WQQ domain in one member indicates a specific structural feature that could be involved in protein-protein or protein-RNA interactions, potentially contributing to the regulatory functions of these proteins.
C-type Lectin Domain Family 1 (C-type_Lectin_Domain_Fam1)
Type: Family

The C-type lectin domain family 1 is characterized by its members containing C-type lectin-like domains. These proteins function as receptors with diverse roles, including cell-cell interaction and immune response. Members of the family, such as CLC1B in humans and mice, act as platelet receptors for PDPN and signal through a cascade involving SRC and SYK tyrosine kinases, leading to PLCG2 activation. They also play a role in microbial infections by acting as receptors for snake venom proteins like rhodocytin and facilitating the capture of pathogens such as HIV-1 by platelets. In invertebrates, such as in the case of LEC2_MEGRO, these lectins bind to specific carbohydrate structures, agglutinate cells, and may be involved in defense mechanisms.
Kelch/BTB domain-containing protein (Kelch/BTB_domain_protein)
Type: Family

This family of proteins includes members that contain Kelch motifs, which are typically involved in protein-protein interactions, and may also feature BTB/POZ domains that participate in protein oligomerization and interactions with other cellular components. These domains are often found in proteins that play roles in diverse cellular processes including cytoskeleton organization, cell morphology, signal transduction, and regulation of transcription. The presence of these domains suggests that the family members may be involved in similar functions, although the specific roles can vary widely among individual proteins and across different species.
MMS22L-TONSL complex component (MMS22L-TONSL_complex_comp)
Type: Family

This family of proteins is involved in the maintenance of genome integrity during DNA replication by promoting homologous recombination-mediated repair of double-strand breaks at stalled or collapsed replication forks. Members of this family are components of the MMS22L-TONSL complex, which is essential for the assembly of RAD51 filaments on single-stranded DNA, a critical step in the homologous recombination process. These proteins act as histone readers, recognizing and binding newly synthesized histones, particularly unmodified histone H4 at Lys-20 and histone H3.1. They are recruited to double-strand breaks after histone replacement by histone chaperones and the eviction of the replication protein A complex from these sites, facilitating the recruitment of RAD51 and subsequent DNA repair.
Platelet Glycoprotein Ib-IX-V Complex (GPIb-IX-V_Complex)
Type: Family

The Platelet Glycoprotein Ib-IX-V Complex family comprises proteins that play a crucial role in hemostasis. Members of this family, including GPIb alpha, GPIb beta, GPIX, and GPV, form a receptor complex on the surface of platelets. This complex binds to von Willebrand factor (vWF), facilitating platelet adhesion to damaged blood vessel walls. The interaction is essential for the formation of platelet plugs, which are critical in preventing blood loss following vascular injury. The GPIb-V-IX complex serves as the vWF receptor and is involved in the orientation and membrane insertion of its components, ensuring proper function and stability of the receptor on the platelet surface.
Immune receptor domain-containing protein (Immune_rcpt_domain)
Type: Family

This family of proteins is involved in immune system processes, including the innate and adaptive immune responses. Members act as cell surface receptors that can enhance T-cell activation, regulate Toll-like receptor signaling, and mediate cytokine production. Some proteins in the family are implicated in the regulation of macrophage and dendritic cell activation, as well as in the phagocytosis of apoptotic cells and cellular debris. They may also participate in antigen presentation and the anti-viral response. Additionally, certain family members are involved in the regulation of microglial functions, such as proliferation, migration, phagocytosis, and the response to oxidative stress, which are crucial for brain homeostasis and the immune response in the central nervous system.
MORN repeat-containing protein 4 (MORN4)
Type: Family

The MORN repeat-containing protein 4 family is characterized by its role in neuronal response to injury. Members of this family are implicated in the promotion of axonal degeneration following neuronal damage due to toxic insult or trauma. In addition to this conserved function, the Drosophila homolog has a specialized role in the visual system, where it organizes rhabdomeric components to enhance the fidelity of phototransduction in dark-adapted photoreceptors and contributes to the stability of specific phototransduction proteins, ensuring proper termination of the light response.
Speedy/Ringo cell cycle regulator (Speedy-Ringo_regulator)
Type: Family

This family of proteins is involved in the regulation of cell cycle progression, particularly the G1/S phase transition and meiotic G2/M progression. Members of this family bind and activate cyclin-dependent kinases (CDK1 and CDK2), facilitating cell cycle transitions without promoting CDK2 phosphorylation. They induce conformational changes in the T-loop of CDK2, which allows for kinase activation. Additionally, they can interfere with CDKN1B-mediated inhibition of CDK2 and are implicated in cell survival during DNA damage. In oocytes, they stimulate maturation by activating the MAPK cascade and cdc2-cyclin B complex, and are necessary for polyadenylation. They also play roles in the spindle-assembly checkpoint by recruiting components to kinetochores and are involved in the correct localization of Aurora B during prometaphase.
Viral replication and host interaction regulator (Viral_replicn-host_int_reg)
Type: Family

This family of proteins includes multifunctional components involved in various cellular and viral processes. Members of this family play essential roles in virus replication cycles, acting as viroporins to form ion conductive pores, altering cell permeability, and facilitating ion and small molecule transport. They are involved in viral RNA replication regulation, protease activity as cofactors, and innate immune response inhibition by targeting host proteins. Some members contain a protease-helicase domain essential for viral polyprotein processing and genome replication, enhancing RNA-dependent RNA polymerase activity. They also package viral RNA into nucleocapsids, regulate transcription, and modify membranes to scaffold virus replication complexes. Additionally, they possess ribonuclease activity, which can inhibit interferon production. In contrast, other members regulate the export of proteins from the endoplasmic reticulum to the cell surface, with implications in both cellular and viral contexts.
Cell Division and Developmental Signaling Domain-Containing Protein (CellDiv_DevSignal_Domain)
Type: Family

This family of proteins includes members involved in critical cellular and developmental processes. Some proteins in this family are essential for male reproductive functions, playing a key role in the formation of sperm cells during spermiogenesis and being necessary for successful fertilization. They may participate in the assembly of the manchette, a structure important in sperm development. Other members are implicated in the regulation of the mitotic spindle, a cellular apparatus crucial for cell division, and are thought to be particularly important in the context of neurogenesis. Additionally, certain proteins are components of complexes that modulate signaling pathways, such as the Hedgehog signaling pathway, which is vital for proper limb development. Collectively, the family encompasses proteins with functions in cell division, developmental signaling, and reproductive biology.
Centriolar and ciliogenesis-associated protein (Centriolar_ciliogenesis_assoc)
Type: Family

This family of proteins is involved in the process of ciliogenesis, which is the formation of cilia on the surface of cells. Cilia are small, hair-like structures that protrude from the cell body and are involved in movement and sensory functions. Members of this family are essential for the proper anchoring of centrioles, which are structures that serve as the main organizing centers for microtubules and are crucial for the formation of cilia. The proteins in this family play a significant role in ensuring that centrioles are correctly positioned at the cell's apical surface, thereby facilitating the formation of functional cilia.
Cytochrome b5 domain-containing (Cytochrome_b5_domain)
Type: Family

The cytochrome b5 family is characterized by a domain that binds heme under oxidizing conditions. Members of this family are involved in redox signaling pathways and are essential for the coordinated beating of multiple cilia. The cytochrome b5 domain-containing proteins function as radial spoke stalk proteins, which are likely to play a role in the regulation of ciliary motion, possibly through redox-mediated mechanisms.
Polyamine Binding and Protein Trafficking (PolyBind_ProtTraffic)
Type: Family

The protein family includes members that are involved in polyamine binding and protein trafficking. Some members, like the prostatic spermine-binding proteins from mouse and rat, are glycoproteins that bind various polyamines and are regulated by androgens in the prostate. These proteins are functionally equivalent across species and are implicated in the binding of polyamines. Other members, such as the pancreatic adenocarcinoma up-regulated factor in humans, play a crucial role in tumor progression and metastasis in pancreatic cancer, influencing cell migration and invasion via specific signaling pathways. Additionally, the zymogen granule membrane protein 16 from humans, rats, and mice, which belongs to the jacalin lectin family, is suggested to have a role in the formation of zymogen granules by acting as a linker molecule in the trans-Golgi network. This family's diverse functions reflect its involvement in both intracellular trafficking and extracellular interactions.
Mitochondrial rRNA Methyltransferase NSUN4 (Mito_rRNA_Mtase_NSUN4)
Type: Family

The NSUN4 family of proteins is involved in the biogenesis and assembly of mitochondrial ribosomes. Members of this family are 5-methylcytosine rRNA methyltransferases that play a crucial role in the maturation of the mitochondrial ribosome small subunit (SSU) by methylating 12S rRNA, as well as potentially methylating 16S rRNA of the large subunit (LSU). The methylation process is enhanced by the presence of MTERFD2/MTERF4, which also targets NSUN4 to the LSU. The family's function is critical for ensuring the proper assembly of SSU and LSU, which is a final step in ribosome biogenesis. Additionally, some members may methylate cytosine in rRNAs and tRNAs at multiple sites, which could influence the translation of specific codons. All family members belong to the class I-like SAM-binding methyltransferase superfamily within the RsmB/NOP family.
LRP2-binding protein (LRP2-binding)
Type: Family

This family of proteins may be involved in the regulation of LRP2, a multi-ligand receptor protein that plays a critical role in cellular uptake and signaling. The members of this family are thought to serve as adapter molecules that influence the function of LRP2, potentially affecting its interactions with various ligands or modulating its activity within different signaling pathways. The precise mechanisms by which these proteins regulate LRP2 function remain to be fully elucidated, but their conserved role across different species suggests a fundamental importance in cellular physiology related to LRP2-mediated processes.
NFATC2-Interacting & DNA Repair (NFATC2-Int_DNA_Repair)
Type: Family

The NFATC2-interacting protein family is involved in the regulation of NFAT-driven transcription of cytokine genes in T-helper 2 (Th2) cells. Members of the family enhance cytokine expression by recruiting PRMT1 to promoters, facilitating histone methylation and acetylation. They also play a role in DNA repair by stabilizing the association of double strand breaks with the nuclear periphery during homologous recombination. Additionally, they down-regulate the formation of poly-SUMO chains, indicating a multifaceted role in cellular regulation and response to damage.
Differentiation & Development-Associated Protein (Diff-Dev_Assoc_Protein)
Type: Family

This family of proteins is involved in cellular differentiation and development. Members of this family appear to play roles in the process of cell differentiation, which is crucial for the development of specialized cell types from more generic precursor cells. Additionally, some proteins within this family are implicated in cell-cell adhesion, a process that is essential for the formation of structured tissues and organs during development. The exact functions of several members remain uncharacterized, suggesting that the family may have diverse roles in various biological processes related to cellular development and differentiation.