SII-SWORD/CoKE huggingface dataset:
Nucleolus and neural progenitor protein (Nepro)
Type: Family

This family includes Nucleolus and neural progenitor protein from mouse (Nepro) and similar animal sequences. Nepro may play a role in cortex development as part of the Notch signalling pathway. Downstream of Notch, it may repress the expression of proneural genes and inhibit neuronal differentiation thereby maintaining neural progenitors . It may also be involved in preimplentation embryo development . In humans, NEPRO (also known as Ribonuclease MRP subunit P64, Rmp64), which is required for the activity of human RNase MRP , interacts with multiple protein subunits of RMRP and is implicated in Anauxetic dysplasia 3 .
Proline-rich transmembrane domain-containing protein (PRRT_domain-containing)
Type: Family

This family of proteins is characterized by a proline-rich region and transmembrane domains, suggesting a role in cell adhesion, signaling, or as structural components of the cell membrane. The exact biological functions of these proteins may vary across different tissues and organisms. They could be involved in the formation of protein complexes, interacting with other membrane or cytosolic proteins, and may participate in signaling pathways that regulate cellular processes. The proline-rich motifs within these proteins might mediate interactions with SH3 domains or other proline-binding domains, which are common in signaling proteins. Additionally, the transmembrane domains indicate that these proteins are likely to be integral to the membrane, potentially acting as receptors or channels.
Mitochondrial ribosomal protein bS21 (Mitoribosomal_bS21)
Type: Family

This family of proteins includes components of the mitochondrial ribosome, also known as mitoribosomes. These proteins are integral to the mitoribosome's structure and function, which is specialized for the synthesis of proteins encoded by the mitochondrial genome. Some of these proteins are essential for the formation of the mitochondrial respiratory chain's transmembrane subunits. Mitoribosomes are closely associated with the mitochondrial inner membrane, allowing for the cotranslational integration of nascent polypeptides directly into the membrane.
Unconventional myosin-XVI (Myosin-XVI)
Type: Family

This family of proteins includes unconventional myosins with ATPase activity, which are involved in intracellular movements. Members of this family interact with actin filaments and are thought to transport membranous compartments within cells. They play a role in brain development by targeting the catalytic subunit of protein phosphatase 1. Additionally, these proteins are involved in the activation of PI3K and the recruitment of the WAVE1 complex, which is important for regulating neuronal morphogenesis.
Mitochondrial gene expression regulator (Mito_gene_expr_regulator)
Type: Family

This family of proteins is involved in mitochondrial biogenesis and the regulation of mitochondrial gene expression. Members of this family are thought to play a role in the assembly of the mitochondrial respiratory chain, particularly influencing the synthesis and stability of cytochrome c oxidase (COX). They may act as translational activators of mitochondrial mRNAs, contributing to the coordination of mitochondrial and nuclear gene expression during cellular energy metabolism. The proteins in this family are characterized by their mitochondrial localization and are conserved across various species, indicating a fundamental role in the mitochondrial function.
U7 snRNA-associated Sm-like (U7_snRNA_Sm-like)
Type: Family

This family of proteins appears to be involved in the U7 small nuclear ribonucleoprotein (snRNP) complex, which plays a crucial role in the 3'-end processing of histone pre-mRNAs. Members of this family are implicated in the stabilization of U7 snRNA levels and are essential for the transition from the G1 to S phases of the cell cycle. They exhibit specific binding to U7 snRNA and interact with the downstream cleavage product of histone pre-mRNA, suggesting a specialized function in histone gene expression regulation.
Pyridoxamine phosphate oxidase-like (PMP_oxidase-like)
Type: Family

This family of proteins includes enzymes that are involved in the biosynthesis of vitamin B6, which is an essential cofactor for a wide range of enzymatic reactions. Members of this family catalyze the oxidation of pyridoxamine 5'-phosphate (PMP) to pyridoxal 5'-phosphate (PLP), the active form of vitamin B6. The reaction is crucial for maintaining the levels of PLP within the cell, which in turn supports various metabolic processes including amino acid, glucose, and lipid metabolism. These enzymes are typically flavin-dependent and utilize molecular oxygen to oxidize PMP to PLP, releasing hydrogen peroxide as a byproduct.
Endoplasmic Reticulum Co-molecular Chaperone (ER_Co-chaperone)
Type: Family

This family of proteins is involved in the regulation of protein folding within the endoplasmic reticulum. Members of this family are thought to act as co-molecular chaperones, assisting in the proper folding of proteins under various conditions, including high-temperature stress. This function is critical for maintaining cellular homeostasis and ensuring the correct conformation of proteins that are essential for various cellular processes.
ER body metal ion sequestration protein (ER_body_metal_sequester)
Type: Family

This family of proteins may play a role in the sequestration of excess cytosolic iron and manganese into the endoplasmic reticulum, potentially reducing metal ion toxicity. These proteins are not essential for the accumulation of endoplasmic reticulum body components, including the protein PYK10.
Leaf Development Regulator (Leaf_Dev_Regulator)
Type: Family

This family of proteins functions as transcription factors involved in cell differentiation. They play a crucial role in leaf development and morphogenesis by regulating the expression of knox homeobox genes and other determinants of leaf polarity. Members of this family can form dimers through a conserved C-terminal domain and may interact with other proteins to exert their regulatory functions. Some proteins in this family are also implicated in the regulation of flowering by binding to specific promoters and forming functional complexes with other factors.
Axonemal dynein light chain domain-containing protein (Axonemal_dynein_LC_domain)
Type: Family

This family of proteins is implicated in the process of spermiogenesis and is considered crucial for male fertility. Members of this family are believed to play a role in the dynamics of the manchette, a structure involved in shaping the spermatid head, as well as in the assembly of the sperm flagellum, which is essential for sperm motility.
Extracellular matrix and enzyme regulator (ECM-enzyme_regulator)
Type: Family

This family of proteins includes components involved in the structural organization of cellular compartments and regulation of enzymatic activity. Members of this family are known to participate in the formation of extracellular matrix structures, as well as in the regulation of signal transduction pathways by modulating the activity of specific enzymes. One protein is involved in the construction of the stalk tube matrix that houses certain cell types, while another acts as an inhibitor of cyclic nucleotide phosphodiesterase, thereby affecting the enzyme's affinity for its substrate.
Extended Synaptotagmin & KAHRP-like protein (Ext_Synaptotagmin/KAHRP-like)
Type: Family

This family of proteins includes members that are involved in cellular interactions and signaling processes. Some proteins in this family are thought to mimic human histidine-rich glycoproteins to facilitate the anchoring of binding complexes with endothelial cell receptors. These interactions are critical in the establishment of connections between cells and the extracellular matrix, playing a role in processes such as cell adhesion and possibly in immune evasion or pathogenesis in the case of parasitic proteins. The family also encompasses proteins that belong to the extended synaptotagmin family, suggesting a potential role in membrane trafficking or signaling due to the presence of the C2 domain, which is known to bind to phospholipids and participate in calcium-dependent cellular processes.
Coiled-coil-helix-coiled-coil-helix domain-containing protein (CHCH_domain-containing_protein)
Type: Family

This family of proteins includes members that are characterized by the presence of a coiled-coil-helix-coiled-coil-helix (CHCH) domain. These proteins are typically involved in mitochondrial functions, particularly in the mitochondrial intermembrane space. They may play roles in mitochondrial dynamics, including the regulation of mitochondrial morphology and distribution. Some family members contain a cysteine motif that is important for their function in the intermembrane space, where they may be involved in redox processes or the import and folding of other mitochondrial proteins. The exact functions of these proteins can vary among different organisms and may be influenced by the presence of additional domains or motifs.
MORN repeat-containing protein (MORN_repeat_protein)
Type: Family

This family of proteins contains MORN repeat motifs and is suggested to play a role in the process of spermatogenesis. The MORN motif, which stands for Membrane Occupation and Recognition Nexus, is typically involved in membrane binding and recognition. Proteins with MORN repeats are implicated in various cellular processes, including signal transduction, cytoskeletal organization, and membrane trafficking. Given the annotations for the mouse and human proteins, it is likely that members of this family are involved in reproductive biology, particularly in the development and function of sperm cells.
NPAT LisH domain-containing protein (NPAT_LisH)
Type: Family

This family of proteins is involved in cell cycle regulation, specifically required for the progression through the G1 and S phases and for S phase entry. Members of this family are known to activate transcription of histone genes, including those for histone H2A, H2B, H3, and H4, which are essential for DNA packaging during cell division. Some members also interact with other proteins such as MIZF to regulate additional promoters like ATM and PRKDC. The activation of gene transcription is partly achieved through the recruitment of the NuA4 histone acetyltransferase complex to promoters. A characteristic feature of this family is the presence of a LisH domain, which is crucial for their role in activating histone gene transcription.
GAMETE CELL DEFECTIVE 1 mitochondrial (GCD1_mitochondrial)
Type: Family

The GAMETE CELL DEFECTIVE 1 family proteins are mitochondrial-associated factors essential for plant fertility, playing a critical role in both male and female gametophyte functions and development. They ensure the integrity of female gametic mitochondria and are involved in various developmental processes such as embryo apical-basal and dorsal-ventral patterning, endosperm development, and central vacuole dynamics. These proteins modulate the expression of genes related to these processes and are implicated in triggering programmed cell death for endosperm cellularization and maturation. Additionally, they are crucial for microspore development, pollen production, germination, and mitochondrial-driven cell-to-cell communication in embryo sacs, facilitating reciprocal signaling between central and egg cells.
SSU Processome Component (SSU_Processome_Comp)
Type: Family

This family of proteins is involved in the early stages of ribosome biogenesis, specifically in the assembly of the small subunit (SSU) processome. These proteins are found in the nucleolus and are associated with the nascent pre-ribosomal RNA. They collaborate with ribosome biogenesis factors, an RNA chaperone, and ribosomal proteins to facilitate RNA folding, chemical modifications, structural rearrangements, and cleavage. Additionally, they contribute to the targeted degradation of pre-ribosomal RNA by the RNA exosome. A key regulatory function of these proteins is to prevent the premature recruitment of the helicase DHX37 during the pre-ribosomal RNA processing stages.
Actin dynamics regulator (Actin_dynamics_regulator)
Type: Family

This family of proteins is essential for maintaining epithelial cell integrity by modulating the actin cytoskeleton. Members of this family are known to enhance actin polymerization. They achieve this by preventing actin-capping proteins from binding to actin filaments, thereby promoting the growth of the actin network which is crucial for various cellular processes.
Nematode Serpentine Receptor Class Epsilon (Serpentine_rcpt_epsilon)
Type: Family

This family of proteins includes members that are characterized as serpentine receptors, which are likely to function as G protein-coupled receptors (GPCRs). These receptors typically have a seven-transmembrane domain structure and are involved in signal transduction processes. They are known to play roles in various physiological processes by responding to a range of stimuli such as ligands, which can be small molecules, peptides, or proteins. The activation of these receptors often leads to a cascade of intracellular events resulting in cellular responses. Given their designation as class epsilon receptors, they may have specific functions or ligand preferences within the broader context of nematode sensory and signaling systems.
Cytoskeleton-associated protein 2-like (CKAP2-like)
Type: Family

This family of proteins is involved in the organization and stability of the cytoskeleton, specifically through association with microtubules. Members of this family play a crucial role in the formation of the mitotic spindle, which is essential for proper chromosome segregation during cell division. They are also important for the progression of the cell cycle, particularly in neural progenitor cells. A characteristic feature of these proteins is the presence of a KEN box domain, which is necessary for their interaction with the APC/C-Cdh1 complex, leading to their ubiquitination and subsequent degradation.
SOX30 Transcription Factor (SOX30_TF)
Type: Family

The SOX30 family of transcription factors is characterized by its dual role in gene regulation, functioning as both an activator and a repressor. Members of the SOX30 family recognize and bind to a specific DNA sequence motif, predominantly favoring guanine-rich regions adjacent to the core 5'-ACAAT-3' sequence. The family is involved in the regulation of its own transcription and is essential for the activation of genes required for spermiogenesis. Additionally, the SOX30 family plays a role in modulating Wnt signaling pathways by repressing the transcription of CTNNB1 and by directly binding to the CTNNB1 protein, which hinders its interaction with TCF7L2/TCF4, thereby inhibiting the signaling cascade.
Intermediate Filament Keratin-like (IF_Keratin-like)
Type: Family

This family of proteins includes members that are part of the intermediate filament network within the cytoskeleton. Intermediate filaments are fibrous proteins that provide mechanical support and maintain the structural integrity of cells. They play a crucial role in cell shape, stability, and the organization of the cytoplasm. These proteins are involved in cell-cell adhesion and are essential for the proper functioning of epithelial cells. They also contribute to the resilience and mechanical properties of hair, nails, and the outer layer of the skin. Due to their structural role, mutations in these proteins can lead to a variety of skin disorders and other diseases.
Putative E3 ubiquitin-protein ligase LIN (E3_ubiquitin-ligase_LIN)
Type: Family

This family of proteins includes putative E3 ubiquitin-protein ligases that are implicated in the rhizobial infection process. Members of this family are believed to play a crucial role in the formation of infection threads, as well as in the growth, differentiation, and maintenance of nodules during the symbiotic interaction between rhizobia and leguminous plants. The involvement of these proteins in the early steps of infection thread formation suggests a significant function in the establishment of symbiosis, which is essential for the biological nitrogen fixation process in legumes.
Leucine-rich repeat and IQ domain-containing protein (LRR-IQ_domain_protein)
Type: Family

This family of proteins contains leucine-rich repeat (LRR) and IQ motifs, which are typically involved in protein-protein interactions and mediating complex formation. The LRR domains are known for their role in the immune response, cell adhesion, and signal transduction, due to their structural versatility and ability to bind various ligands. The IQ motif is a calmodulin-binding sequence that is often associated with the regulation of calcium-mediated signaling pathways. Members of this family are likely to be involved in cellular processes that require specific and regulated interactions with other proteins, possibly acting as scaffolds or regulators in signal transduction pathways. The exact functions of these proteins may vary among different organisms and could be influenced by their tissue-specific expression and interaction with other cellular components.
Nematode Receptor-Like/GPCR1 (NRL-GPCR1)
Type: Family

This family of proteins includes receptors that are typically involved in signal transduction processes. They are characterized by their ability to bind ligands and initiate a cellular response, commonly through the activation of G-proteins. These receptors are integral membrane proteins that may play a role in various biological processes, including sensory perception, regulation of immune responses, and homeostasis maintenance. The diversity within this family reflects the range of ligands they can bind and the different signaling pathways they can engage.
BPTI/Kunitz domain-containing protein (BPTI/Kunitz_domain)
Type: Family

This family of proteins includes inhibitors that possess a BPTI/Kunitz domain, which is known for its role in protease inhibition. Members of this family are involved in various biological processes, including the regulation of proteolytic pathways, such as those involved in blood coagulation, fibrinolysis, and inflammation. The domain's inhibitory activity is typically directed against serine proteases, and it functions by binding to the active site of the target protease, thereby preventing substrate access and catalysis. The presence of this domain in allergens like Ani s 1 suggests a role in immune response, where it may protect the allergen from degradation or modulate host immune functions. The diversity of proteins containing the BPTI/Kunitz domain reflects the versatility and importance of this inhibitory mechanism in various physiological contexts.
Tumor necrosis factor receptor superfamily member 8 (TNFR_superfamily_member_8)
Type: Family

This family of proteins includes receptors that interact with TNFSF8/CD30L. Members are involved in the regulation of cellular growth and the transformation of activated lymphoblasts. They also play a role in gene expression regulation through the activation of the NF-kappa-B pathway.
Ribonuclease H2 subunit C (RNase_H2_subunit_C)
Type: Family

The RNase H2 subunit C family comprises non-catalytic subunits of the RNase H2 complex, an endonuclease that degrades RNA in RNA:DNA hybrids. The family plays a crucial role in DNA replication by potentially facilitating the removal of RNA primers from Okazaki fragments on the lagging strand. Additionally, it is involved in the repair process by excising single ribonucleotides embedded in DNA:RNA duplexes, maintaining genomic stability.
Chloroplast Fatty Acid Desaturase CarF (Chloroplast_FAD_CarF)
Type: Family

The CarF family of fatty acid desaturases is involved in the biosynthesis of chloroplast-specific phosphatidylglycerol molecular species. Members of the CarF family catalyze the introduction of a trans double bond close to the carboxyl group of palmitic acid. This specific enzymatic activity is crucial for the formation of phosphatidylglycerol with a distinct fatty acid composition, which is essential for proper chloroplast function and plant development. The histidine box domains within these proteins are key for binding the catalytic metal ions necessary for the desaturation process.
Zinc finger BED domain-containing protein (Zinc_finger_BED)
Type: Family

This family of proteins includes transcriptional repressors that interact with a specific DNA consensus sequence to regulate gene expression, potentially in a tissue-specific manner. Members of this family are involved in the negative regulation of postnatal growth, particularly affecting muscle and organ development in females. They play a critical role in myoblast differentiation and mitochondrial activity, primarily through the repression of IGF2 transcription. Additionally, these proteins are implicated in the cell cycle control of myoblasts and may influence the transcription of E2F family members. They also contribute positively to the cell cycle and survival of pancreatic beta cells, influencing cell adhesion and the formation of cell-to-cell junctions, which may affect beta cell differentiation and function. Furthermore, they are associated with insulin sensitivity and glucose metabolism.
F-box only protein 24 (F-box_protein_24)
Type: Family

The F-box only protein 24 family comprises proteins that serve as substrate-recognition components within the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex. Members of this family are involved in targeting specific protein substrates for ubiquitination, marking them for proteasomal degradation. This regulatory mechanism is crucial for various cellular processes, including cell cycle progression, signal transduction, and transcription. The precise substrates and biological roles may vary among different organisms and tissue types, reflecting the diverse functions of the SCF complex in maintaining cellular homeostasis.
Mitochondrial ATP Synthase Subunit 6 (ATP_Synthase_Subunit_6)
Type: Family

This family of proteins is involved in the synthesis of ATP via the mitochondrial membrane ATP synthase, also known as Complex V. These proteins are part of the F(0) domain of the enzyme, which is responsible for proton translocation across the membrane. The proton gradient required for this process is established by the respiratory chain's electron transport complexes. The ATP synthesis occurs in the F(1) catalytic domain and is mechanically coupled to proton translocation through a rotary mechanism of the central stalk subunits. Members of this family are also implicated in conferring tolerance to various abiotic stresses, likely by ensuring cellular energy homeostasis under such conditions.
Izumo sperm-egg fusion (Izumo_fusion)
Type: Family

This family of proteins is involved in the process of sperm-egg fusion, a critical event in fertilization. Members of this family are characterized by their role in mediating the recognition and binding between sperm and oocyte membranes, facilitating the fusion of these two distinct gametes. The proteins are typically expressed in the testis and are present on the surface of sperm cells. They are essential for the species-specific recognition that ensures fertilization occurs only between gametes of the same species, thus contributing to reproductive isolation and speciation.
C-type lectin domain-containing protein 5A (CLEC5A)
Type: Family

This family of proteins includes cell surface receptors that play a crucial role in osteoclastogenesis and inflammatory responses. They are known to signal through the phosphorylation of TYROBP. In humans, these proteins also serve as macrophage receptors for dengue virus serotypes 1-4, triggering pro-inflammatory cytokine release without facilitating viral entry.