SII-SWORD/CoKE huggingface dataset:
DNA Repair Helicase ZGRF1 (DNA_Repair_Helicase_ZGRF1)
Type: Family

This family of proteins includes 5'-3' DNA helicases that are involved in DNA repair processes, particularly in the repair of replication-blocking DNA lesions. They are known to be recruited to sites of DNA damage and enhance homologous recombination (HR) by directly stimulating the strand exchange activity of RAD51. These proteins facilitate recombinational repair post RAD51 recruitment and are not essential for RAD51 loading at damage sites. They also enhance HR by upregulating EXO1-mediated DNA end resection at double-strand breaks. Additionally, they are necessary for the recruitment of RPA2, a replication protein, to DNA damage sites. These helicases contribute to the initiation of the G2/M checkpoint in the cell cycle but are not involved in maintaining it. They possess enzymatic activities that promote the branch migration of Holliday junctions and the dissociation of D-loops and DNA flaps, which are critical steps in DNA repair and recombination.
Ankyrin Repeat and EF-hand Domain-containing (Ankyrin-EF-hand)
Type: Family

The Ankyrin repeat and EF-hand domain-containing protein family is characterized by the presence of ankyrin repeats and EF-hand domains, suggesting a role in calcium signaling and protein-protein interactions. Members of this family, such as Ankyrin repeat domain-containing protein 23, are implicated in energy metabolism and may act as molecular links between stretch-induced signaling pathways and muscle gene expression. The precise functions of other members remain to be fully elucidated, but the structural motifs suggest a potential involvement in cellular signaling and regulatory processes.
Kinetochore-associated protein 1 (KNTC1)
Type: Family

This entry includes KNTC1 (also known as ROD) proteins, a crucial component of the mitotic checkpoint, ensuring cells do not exit mitosis prematurely . KNTC1 is required for the assembly of essential complexes onto kinetochores, including dynein-dynactin and MAD1-MAD2 in mammals, and dynein-dynactin and mdf-1-mdf-2 in C. elegans. KNTC1 is the major subunit of the RZZ (ROD-Zwilch-ZW10) complex, which plays a significant role in spindle assembly, kinetochore-microtubule attachment, and spindle pole separation . The RZZ complex also recruits proteins like spdl-1 to kinetochores, regulates the attachment of the NDC80 complex to microtubules, and is implicated in nuclear envelope breakdown. These proteins are vital for chromosome segregation, embryonic development, and maintaining genomic stability during cell division.
Primary Cilium-Associated Jouberin (Cilium-Associated_Jouberin)
Type: Family

This family of proteins is involved in various cellular processes related to ciliogenesis and vesicle trafficking. They are essential for the formation of primary non-motile cilia and play a role in the recruitment of specific proteins to the basal body of the cilium. These proteins are also components of a complex that acts as a barrier at the transition zone of primary cilia, preventing the diffusion of transmembrane proteins between the cilia and plasma membranes. Additionally, they are implicated in neuronal differentiation and act as positive modulators of classical Wnt signaling, which is crucial for ciliary signaling during the embryonic development of the cerebellum.
Ubiquitin-editing complex component (UEC_component)
Type: Family

This family of proteins is involved in the regulation of inflammatory signaling pathways. Members of this family act as essential components of a ubiquitin-editing protein complex, which includes TNFAIP3, ITCH, and TAX1BP1. They play a role in ensuring the transient nature of the signaling pathways by promoting the association of TNFAIP3 with RIPK1 following TNF stimulation. They facilitate the deubiquitination of 'Lys-63' polyubiquitin chains on RIPK1 and the subsequent formation of 'Lys-48'-linked polyubiquitin chains, leading to the proteasomal degradation of RIPK1. This activity effectively terminates the activation of NF-kappa-B mediated by TNF or LPS. Additionally, these proteins are involved in recruiting STAMBP to the E3 ubiquitin-ligase SMURF2, targeting it for ubiquitination and subsequent degradation by the 26S proteasome. They also contain a PPxY motif, which is known to mediate interactions with the NEDD4 E3 ubiquitin ligase.
GEF and Ubiquitin-Proteasome Regulators (GEF_Ubiquitin-Prot_Reg)
Type: Family

The protein family in question appears to encompass proteins with roles in cellular signaling and regulation. One member, ECT2L_HUMAN, is suggested to function as a guanine nucleotide exchange factor (GEF), which implies a role in activating GTPases, critical for various cellular processes including cell division and differentiation. The other two members, FBX16_HUMAN and FBX16_MOUSE, are likely involved in the ubiquitin-proteasome pathway, recognizing phosphorylated proteins to facilitate their ubiquitination and subsequent degradation. This indicates a role in protein turnover and regulation of signaling pathways through targeted protein degradation. The family, therefore, seems to be involved in the regulation of cellular processes through modulation of protein activity and turnover.
Fasciclin-like AGP (Fasciclin-like_AGP)
Type: Family

This family of proteins may function as cell surface adhesion molecules. Members of this family are characterized by their similarity to fasciclin-like arabinogalactan proteins, which are known to play a role in cell-cell interactions and communication. These proteins may be involved in various biological processes where cell adhesion is required, although their specific functions in these processes remain to be fully elucidated.
Mitochondrial translation and respiration regulator (Mito_transl_resp_regulator)
Type: Family

This family of proteins is involved in the regulation of mitochondrial protein translation and respiration. Members of this family play a role in mitochondria-mediated cell death and may function as scaffolding proteins or stabilizers of respiratory chain supercomplexes. They have the ability to bind GTP, which suggests a regulatory role in mitochondrial function. These proteins are part of the TRAFAC class YlqF/YawG GTPase family, specifically the NOA1 subfamily, indicating a conserved mechanism of action across different species.
G-protein coupled receptor Mth-like (GPCR_Mth-like)
Type: Family

This family of proteins includes G-protein coupled receptors (GPCRs) that are likely involved in signal transduction processes. GPCRs are a large family of cell surface receptors that respond to a variety of external signals and activate intracellular signaling pathways through the binding and activation of G-proteins. The specific subfamily mentioned, Mth, suggests that these proteins may share structural and functional characteristics with the Methuselah (Mth) receptors, which have been implicated in the regulation of lifespan and stress responses in Drosophila. While the exact functions of the Mth-like receptors in this family are not detailed, they are presumed to play roles in physiological processes through the reception of extracellular signals and subsequent activation of downstream signaling cascades.
Actin-polarity regulatory (Actin_polarity_regulatory)
Type: Family

This family of proteins is involved in the regulation of cellular polarity and actin cytoskeleton organization. Members of this family play a crucial role in the spatial orientation of cell growth and division. They are essential for the proper localization of specific proteins to the plasma membrane, which is a key factor in maintaining polarized cell growth. Additionally, these proteins are involved in the formation and stabilization of actin structures, such as actin cables and patches, which are important for cell shape and motility. The family's functions are critical in various organisms for processes like budding in yeast and hyphal tip growth in filamentous fungi.
Plant N-acetyltransferase (Plant_NAT)
Type: Family

This family of proteins includes N-acetyltransferases that play a role in plant development and growth. Members are involved in processes such as cell elongation, apical hook formation in seedlings, and auxin homeostasis, which may influence organogenesis and plant biomass. Some family members exhibit histone acetyltransferase activity, impacting gene expression by modifying histones and thereby regulating traits like grain weight and yield. The family is characterized by a conserved acetyltransferase domain, suggesting a shared enzymatic function across different plant species.
Glucose-responsive signaling protein (Glucose_resp_signaling)
Type: Family

This family of proteins includes members involved in signal transduction pathways, particularly in the response to glucose availability. One characterized member functions in the glucose/cAMP-signaling pathway, which is essential for maintaining basal levels of cAMP and generating a glucose-induced cAMP response. The family likely plays a role in cellular processes that respond to environmental changes, although the specific functions of some members remain uncharacterized.
Plant DnaJ domain-containing protein (Plant_DnaJ_domain)
Type: Family

This family of proteins is involved in plant development, particularly in the structural organization of cellular compartments. Members of this family play a role in gravitropic signal transduction, influencing pH changes and auxin distribution, which are critical for plant orientation and growth responses to gravity. Some members are associated with the localization and activity of auxin efflux carrier components, affecting lateral auxin transport.
C-Maf-inducing protein (CMIP)
Type: Family

This family of proteins is involved in the signaling pathways of T-cells. Members of this family are implicated in the transmission of signals that lead to the activation of specific transcription factors, such as c-Maf, which is associated with the differentiation of T-helper 2 (Th2) cells. The proteins may have distinct roles depending on the isoform, with some isoforms linking T-cell receptor-mediated signals to the activation of specific pathways critical for T-cell function and immune response.
Peroxisomal Protein Import DnaJ (Peroxisomal_DnaJ)
Type: Family

The DnaJ protein family is involved in the molecular chaperone system, which is essential for protein folding and quality control within the cell. Members of this family, such as DnaJ-like protein 1, are known to play a crucial role in peroxisomal protein import, ensuring the proper function of peroxisomes. Peroxisomes are cellular organelles that carry out various metabolic tasks, including the breakdown of fatty acids and the detoxification of hydrogen peroxide. By assisting in the import of proteins into peroxisomes, the DnaJ protein family contributes to maintaining the organelle's functionality and, consequently, the cell's metabolic balance.
Programmed cell death 2-like regulator (PDCD2-like_regulator)
Type: Family

This family of proteins is implicated in the regulation of transcriptional activation and cell cycle progression. Members of this family are known to suppress the activity of several transcription factors, including AP1, CREB, NFAT, and NF-kB, which are critical for various cellular processes. Additionally, these proteins have a role in modulating the cell cycle, specifically by delaying progression through the S phase. The regulatory functions suggest a potential involvement in controlling cell proliferation and response to cellular stress signals, which may be related to programmed cell death pathways.
Peroxisomal Membrane Protein PEX28-32 (Peroxisomal_Membrane_PEX28-32)
Type: Family

The PEX28-32 family is involved in the regulation of peroxisome number, size, and distribution within the cell. Members of this family are peroxisomal membrane proteins that play a role in peroxisome maintenance and dynamics. The family includes subfamilies such as PEX28 and PEX29, which share similar functions in peroxisome regulation but may have distinct roles or regulatory mechanisms within the broader context of peroxisome biogenesis and homeostasis.
MIT domain-containing protein 1 (MIT_domain_contain_protein1)
Type: Family

The MIT domain-containing protein 1 family is involved in the final stages of cell division, specifically in the abscission process that completes cytokinesis. Members of this family possess a MIT domain that interacts with the MIT-interacting motifs of ESCRT-III complex components, playing a crucial role in the separation of daughter cells. Additionally, the C-terminal domain of these proteins is known to bind lipid membranes enriched with acidic phosphoinositides, which is essential for their localization to the midbody during cell division. While all family members are implicated in cytokinesis, some appear not to be involved in endosomal transport, indicating a specialized function in cell division.
NEDD1 Spindle Assembly Protein (NEDD1_Spindle_Assembly)
Type: Family

This family of proteins is essential for the progression of mitosis, a critical phase of the cell cycle. Members of this family facilitate the nucleation of microtubules from the spindle, which is a key step in the formation of the mitotic spindle required for chromosome segregation. Additionally, these proteins may have a significant role in the embryonic development and differentiation of the central nervous system, suggesting a broader functional spectrum beyond mitotic spindle formation.
Chromatin-associated regulatory protein (Chromatin_regulatory_protein)
Type: Family

This family of proteins includes components involved in the regulation of gene expression through the modification of chromatin structure. Specifically, one member is known to function as a catalytic component of a histone deacetylase complex, which is responsible for the removal of acetyl groups from lysine residues on the N-terminal part of core histones. This deacetylation process is crucial for epigenetic repression and has significant roles in various cellular processes including transcriptional regulation, cell cycle progression, response to DNA damage, adaptation to osmotic stress, and developmental events. While some members of this family are uncharacterized, the characterized components suggest a broader involvement in chromatin remodeling and regulation of gene expression.
PhiA domain-containing protein (PhiA_domain)
Type: Family

This family of proteins is involved in the development of asexual reproductive structures in fungi, specifically in the formation of phialides and conidia, which are essential for spore production. Members of this family also serve as a general stress protectant for the fungus, particularly in competitive interactions with antagonistic bacteria.
F-box only substrate-recognition component (F-box_only_SRC)
Type: Family

This family of proteins serves as substrate-recognition components within SCF-type E3 ubiquitin ligase complexes. They are involved in the targeted ubiquitination and subsequent proteasomal degradation of specific proteins, notably the tumor suppressor p53. By recognizing and binding to p53, they facilitate its ubiquitination, which is a post-translational modification leading to the protein's degradation. This regulatory mechanism is crucial for controlling the cell cycle and preventing the accumulation of damaged DNA, thereby playing a significant role in maintaining cellular homeostasis and preventing tumorigenesis.
SXP/RAL-2-related (SXP/RAL-2_related)
Type: Family

This family of proteins is characterized by similarity to the SXP/RAL-2 family, which suggests a potential role in a variety of biological processes. Members of the SXP/RAL-2 family are often involved in host-parasite interactions, with some functioning as antigens in parasitic organisms. These proteins may be implicated in immune evasion or modulation, and could play a role in the life cycle of the parasites. The exact functions of individual family members can vary, and further research is necessary to fully elucidate the specific roles and mechanisms of action for these proteins.
N6-methyladenosine RNA Methylation Regulator (m6A_RNA_Methylation_Regulator)
Type: Family

This family of proteins includes components involved in the post-transcriptional modification of RNA, specifically through N6-methyladenosine (m6A) methylation. Members of this family play a crucial role in the efficiency of mRNA splicing and RNA processing. They are key regulators of m6A methylation, particularly influencing the modification of mRNAs at the 3'-UTR. These proteins are also implicated in maintaining the pluripotency of embryonic stem cells by modulating m6A methylation levels. Additionally, they are essential for the assembly and nuclear localization of certain RNA-modifying complexes, serving as a scaffold for other components and facilitating interactions with RNA-binding proteins.
Coiled-coil domain-containing protein Prefoldin subunit beta-like (CCD-Prefoldin_beta-like)
Type: Family

This family of proteins is characterized by the presence of a coiled-coil domain, which suggests a role in providing structural support and facilitating protein-protein interactions. Members of this family are similar to the prefoldin subunit beta, indicating a potential involvement in the stabilization of nascent polypeptide chains and the promotion of correct folding. Prefoldin is a molecular chaperone complex that captures and delivers unfolded proteins to the cytosolic chaperonin for facilitated folding.
Chitin Synthase Export/Cell Fusion Regulator (CHS_Export/Cell_Fusion_Reg)
Type: Family

This family of proteins is involved in various cellular processes related to the synthesis of chitin and cell fusion. Members of this family are known to form complexes that facilitate the export of specific cargo proteins, such as chitin synthase, to their proper cellular locations. Additionally, they play a role in the targeting of proteins to sites of polarized growth. Some family members act as scaffolds within the Golgi apparatus, retaining proteins required for cell fusion. The degradation of these proteins can trigger the release of cell fusion proteins, indicating a regulatory function in mating processes. Overall, the family is characterized by its involvement in the transport and regulation of proteins essential for chitin biosynthesis and cell fusion events.
Negative elongation factor A domain-containing protein (NELF-A_domain)
Type: Family

This family of proteins is involved in the regulation of transcription elongation by RNA polymerase II. Members of this family are essential components of the NELF complex, which interacts with the DSIF complex to induce transcriptional pausing. This action is antagonized by the P-TEFb kinase complex. The presence of an HDAg-like domain within these proteins is crucial for their role in transcriptional repression and their interaction with the RNA polymerase II complex. Additionally, these proteins have been implicated in playing a role in HIV-1 latency, potentially through the recruitment of PCF11 to paused RNA polymerase II. In Drosophila, the family member is also critical for postembryonic development.
N-acetyltransferase domain-containing protein (N-acetyltransferase_domain)
Type: Family

This family of proteins includes enzymes that are involved in the transfer of acetyl groups from acetyl-CoA to various substrates. Members of this family are typically referred to as N-acetyltransferases and are known to play a role in the modification of small molecules, proteins, and other macromolecules. This modification can alter the function, localization, or stability of the target molecules and is important in a wide range of biological processes including metabolism, signal transduction, and gene expression. The specific substrates and biological functions of the uncharacterized N-acetyltransferases in this family remain to be elucidated through experimental studies.
RCC1 domain-containing protein (RCC1_domain-containing)
Type: Family

This family of proteins is involved in various cellular processes, including transcriptional repression of satellite repeats and the regulation of histone methylation, specifically H3K36 methylation in centromeric regions. Members of this family work in conjunction with KDM8 to maintain genomic stability by ensuring proper mitotic spindle organization and chromosome segregation. Additionally, these proteins play a crucial role in cytoskeletal dynamics by regulating alpha-tubulin deacetylation and microtubule stability. This regulation is essential for cell migration and the induction of epithelial to mesenchymal transition (EMT) in response to TGF-beta signaling, potentially through the modulation of KDM8 activity.
Apoptosis-promoting protein (Apoptosis_promoter)
Type: Family

This family of proteins is involved in the regulation of programmed cell death or apoptosis. Members of this family have been shown to promote apoptosis when they are overexpressed. Apoptosis is a critical process in development and homeostasis in multicellular organisms, allowing the body to remove unwanted or damaged cells. Proteins that can induce apoptosis play important roles in immune responses, tissue remodeling, and the suppression of tumorigenesis.
Starch-Associated Glucan Phosphatase (Starch-Glucan_Phosphatase)
Type: Family

This family of proteins includes phosphoglucan phosphatases that are associated with starch granules and are involved in starch metabolism. Members of this family function to dephosphorylate phospho-oligosaccharides that accumulate during the night, playing a role in the regulation of starch degradation. These enzymes exhibit specificity for the glucan C3 and C6 positions, with some members showing a preference for the C6 position. The activity of these phosphatases is essential for the proper control of starch accumulation and is required for the initial steps of starch degradation at the granule surface. Additionally, these proteins possess a C-terminal polysaccharide-binding domain, which is necessary for their glucan phosphatase activity through interaction with the phosphatase domain.
Telomeric DNA-binding and transcriptional regulator (Telomeric_DNA-bd_trans-reg)
Type: Family

This family of proteins is involved in telomere maintenance and gene expression regulation. Members bind to specific telomeric DNA sequences and can act as transcriptional regulators. They play a role in regulating telomere length, either by promoting or inhibiting telomere elongation. Additionally, these proteins are capable of binding to promoter regions of genes, including ribosomal protein genes and rDNA loci, to activate transcription. Some family members also function as genome partitioners, contributing to chromatin organization and preventing the spread of transcriptional silencing or activation from affecting adjacent regions.
3-Keto-Steroid Reductase/17-beta-Hydroxysteroid Dehydrogenase (3KSR/17beta-HSD)
Type: Family

This family of proteins is involved in steroid-hormone metabolism and cholesterol biosynthesis. Members of this family function as bifunctional enzymes that catalyze the NADP(H)-dependent reduction of estrogens and androgens, thereby regulating the biological potency of these steroids. They are responsible for converting estrone to a more potent estrogen, 17beta-estradiol, and for converting dihydrotestosterone to less active forms. Some family members also convert progesterone to its inactive form. Additionally, these enzymes participate in the post-squalene phase of cholesterol biosynthesis as 3-ketosteroid reductases. The activities of these enzymes can be selectively inhibited by certain 4-methyl-4-aza-5alpha-androstane derivatives.