SII-SWORD/CoKE huggingface dataset:
RNA-binding protein 25 (RBM25)
Type: Family

This family of proteins is involved in the regulation of alternative pre-mRNA splicing and plays a role in apoptotic cell death. Members of this family includes RNA-binding protein 25 (RBM25) from human and its orthologue from S.pombe U1 snRNP-associated protein usp107. RBM25 modulates the expression of the apoptotic factor BCL2L1 by influencing the ratio of its isoforms. They are capable of binding to specific RNA sequences, which promotes the selection of certain splice sites, affecting the generation of different mRNA isoforms . It is also involved in the generation of an abnormal and truncated splice form of SCN5A in heart failure . S. pombe usp107 is a component of the U1 snRNP particle and may contribute to the recognition and binding of pre-mRNA 5'-splice sites .
Tetratricopeptide repeat domain-containing protein (TPR_domain_protein)
Type: Family

This family of proteins contains tetratricopeptide repeat (TPR) motifs, which are known to mediate protein-protein interactions. These interactions are crucial for the assembly of multiprotein complexes. The TPR motif consists of 34 amino acids and forms a helix-turn-helix structure. Proteins in this family are involved in a variety of cellular processes, including the regulation of transcription, cell cycle control, and mitochondrial and peroxisomal functions. Due to the versatility of the TPR motif, members of this family may act as scaffolding proteins, adaptors, or regulators in different signaling pathways and cellular compartments.
Cobalt transport CbiQ (Cobalt_transport_CbiQ)
Type: Family

This family of proteins is involved in the transport of metal ions across cellular membranes, specifically cobalt. Members of this family are components of the energy-coupling factor (ECF) transporter complex, which plays a crucial role in the uptake of cobalt ions. The complex has been shown to facilitate cobalt import when expressed in E. coli and may also have the capacity to transport nickel, albeit with much lower affinity. The function of these proteins is essential for organisms that require cobalt as a micronutrient for various biochemical processes.
Neurotrophin-activated signaling adaptor (Neurotrophin_sig_adaptor)
Type: Family

This family of proteins is involved in signal transduction pathways related to neuronal development, regeneration, and synaptic signaling. Members of this family promote sustained MAP-kinase signaling through a Rap1-dependent mechanism, which is activated by neurotrophins. They serve as docking sites for complexes like CRKL-C3G, facilitating sustained ERK activation. These proteins are implicated in the localization and activation of receptor tyrosine kinases, such as EPHA4, and enhance JAK/STAT signaling in cooperation with SNTA1. They are also involved in the recruitment of RAPGEF2 to late endosomes, contributing to neurite outgrowth. Additionally, they may modulate stress-induced apoptosis in melanoma cells via the MEK/ERK pathway.
Endonuclease/Polynucleotide Kinase Domain-Containing Protein (Endo/PolyKinase_Domain-Protein)
Type: Family

This family of proteins includes enzymes with endonuclease activity that are involved in mRNA surveillance and DNA repair or recombination processes. Members of this family are capable of recognizing and binding specific polyubiquitinated proteins, which facilitates their recruitment to sites of action such as stalled ribosomes or DNA damage. Within the context of mRNA surveillance, these proteins play a role in the No-Go Decay (NGD) pathway, where they mediate the cleavage of mRNAs in response to ribosome collisions, thereby contributing to the maintenance of cellular homeostasis. In addition to their role in mRNA cleavage, some family members also possess 5'-polynucleotide kinase activity, which may be important in DNA repair mechanisms. The domains present in these proteins, such as the Smr domain, are responsible for their enzymatic activities and specific interactions with other proteins or nucleic acids.
Anaerobic Bacterial Peroxidase-Related (Anaerobic_Peroxidase-Rel)
Type: Family

This family of proteins includes enzymes that play a crucial role in the oxidative stress defense system of certain obligate anaerobic bacteria. Members of this family function as terminal components of an NADH peroxidase system, utilizing NADH:rubredoxin oxidoreductase and rubredoxin as electron transport intermediaries to reduce hydrogen peroxide. They are involved in the detoxification of hydrogen peroxide, thereby protecting the cell from oxidative damage. Some family members also exhibit NADH oxidase activity, although this is significantly less pronounced compared to their peroxidase activity. The proteins are characterized by their ability to transfer electrons and reduce peroxide substrates, indicating a primary function in the cellular response to oxidative stress.
C. elegans Developmental and Neuronal Protein (Celegans_DevNeuronal_Protein)
Type: Family

This family of proteins is involved in various developmental and morphogenetic processes in Caenorhabditis elegans. Members of this family play crucial roles in epithelial tube development, including the morphogenesis and function of unicellular tubes within the excretory system such as the canal cell, duct cell, and pore cell. They are also implicated in cuticle development, alae formation, and vulval lumen shaping, which are essential for larval development. Additionally, these proteins are associated with neuronal functions, including neurite growth and maintenance, as well as sensory neuron permeability and behavior responses such as chemotaxis, osmotic avoidance, and mating. Some family members contain a ZP domain, which is important for protein localization and secretion.
Inosine-uridine nucleoside hydrolase (IUN_hydrolase)
Type: Family

This family of proteins is involved in the hydrolysis of the N-glycosidic bond of purine and pyrimidine nucleosides, resulting in the separation of ribose and the base. The enzymatic activity varies with different substrates, showing a preference for adenosine, followed by guanosine, inosine, xanthosine, cytidine, and uridine. The members of this family are characterized by their ability to act on commonly occurring nucleosides, playing a role in nucleotide metabolism.
Chloroplast-associated Reproductive Support & Metal Ion Transport (Chloro_ReproSupport/MetalTrans)
Type: Family

This family of proteins includes essential components involved in plant reproductive processes, specifically female gametogenesis and embryogenesis. Members of this family are believed to play a crucial role in ensuring an adequate energy supply within chloroplasts during these critical stages of plant development. Additionally, a member of this family from a bacterial source is implicated in metal ion transport, potentially facilitating nickel incorporation, which is a key step in the activation of certain enzymes such as urease. However, this bacterial protein is not essential for the enzyme's catalytic activity but may be part of a high-affinity nickel transport system.
Acetyltransferase Enzymes (Acetyltransferase_Enz)
Type: Family

This family of proteins includes enzymes that catalyze the transfer of acetyl groups from acetyl coenzyme A to various acceptor substrates, resulting in the release of CoA and the formation of an acetylated product. Members of this family exhibit substrate specificity, with preferences for amino acids such as L-threonine, L-serine, and L-methionine, among others. They are also capable of acetylating other compounds like thiamine pyrophosphate. The enzymatic activity of these proteins is crucial for various cellular processes, including the modification of proteins and metabolites, which can affect their function, stability, or localization.
Centrosome-associated WD domain-containing protein (Centrosome-WD_assoc)
Type: Family

This family of proteins is involved in various cellular processes related to centrosome function and ciliogenesis. Members of this family are essential for the proper formation and anchoring of the mitotic spindle to centrosomes during cell division. They are required for the localization of specific centriole satellite proteins to the centrosome, which is crucial for maintaining normal mitotic spindle morphology. Additionally, these proteins play a role in the biogenesis of cilia by participating in the removal of certain protein complexes from the mother centriole and facilitating the formation of ciliary vesicles. They are also implicated in the docking of vesicles to the basal body, a step necessary for ciliogenesis, potentially aiding the docking of vesicles containing specific small GTPases.
WD repeat-containing protein 62 (WDR62)
Type: Family

This family of proteins includes WD repeat-containing protein 62 (WDR62), a microcephaly-related, microtubule (MT)-associated protein (MAP) that localises to the spindle pole and regulates spindle organisation by recruiting katanin to the spindle pole by forming a complex with TPX2/Aurora A . It has been suggested to be an adaptor protein between its recruiting factor TPX2/Aurora A and the effector katanin to orchestrate the regulation of spindle dynamics. The microtubule-binding affinity of WDR62 is autoinhibited through JNK phosphorylation-induced intramolecular interaction . It is implicated in the development of the cerebral cortex, influencing both the proliferation and migration of neurons . Additionally, these proteins are involved in the duplication of centrioles, specifically the mother-centriole-dependent process. This function appears to be mediated through the formation of a complex at the centrosome, which sequentially incorporates CEP152, CDK5RAP2, and CEP63, and ultimately recruits CDK2, an enzyme essential for the duplication of centrioles .
Aromatic Amino Acid Catabolism Transcriptional Regulators (AAA_Catabolism_Regulators)
Type: Family

This family of proteins includes transcriptional activators involved in the regulation of various metabolic processes. Members of this family are responsible for the expression of genes related to the catabolism of aromatic amino acids, such as activating the transcription of aminotransferases and decarboxylases. They also play a role in the response to environmental stress by binding to specific response elements in the DNA to mediate the induction of genes encoding transporters, which may be involved in acid resistance and ammonia transport. Additionally, some family members are associated with the biosynthesis of pigments through the activation of gene clusters involved in the degradation of amino acids like L-tyrosine.
Cysteine protease inhibitor I42 (Cys_protease_inhibitor_I42)
Type: Family

This family of proteins includes inhibitors of cysteine proteases. Members of this family are characterized by their ability to block the substrate-binding site of target cysteine proteases through a tripartite wedge formed by the BC, DE, and FG loops. The BC loop, in particular, is noted for interacting with the catalytically active cysteine and histidine residues of the protease catalytic center. These proteins play a protective role by inhibiting the activity of cysteine proteases, which may be released by damaged intracellular vesicles or are otherwise active within the organism. The inhibition of these proteases is crucial for regulating proteolytic processes and maintaining cellular integrity.
Oocyte-to-zygote transition regulator (Oocyte-zygote_transition_reg)
Type: Family

This family of proteins includes inactive phosphatases and pseudophosphatases that are essential for the oocyte-to-zygote transition in Caenorhabditis elegans. Members of this family are involved in the regulation of the cortical actin cytoskeleton's polarization and rearrangement during oocyte maturation and post-fertilization. They function in a redundant manner to localize specific kinases and other proteins to the cortex and cytoplasmic foci, influencing kinase activity and ensuring proper cellular organization and eggshell formation. Additionally, some members contain N-terminal destruction box motifs that target them for proteasomal degradation.
Transcriptional Regulator for Metabolic and Drug Resistance Pathways (Metabolic/Drug-Res_Regulator)
Type: Family

This family of proteins includes transcription factors involved in the regulation of gene expression in response to environmental changes. Members of this family can act as activators or repressors. They are known to regulate genes involved in metabolic pathways, such as the catabolism of quinic acid, allowing organisms to utilize it as a carbon source. Additionally, they can confer resistance to antifungal agents by activating or repressing genes associated with drug resistance. These proteins typically bind to specific DNA sequences in the promoters of target genes to exert their regulatory functions.
Perforin-1 pore-forming (Perforin-1_pore-forming)
Type: Family

The Perforin-1 family includes pore-forming proteins that are essential for granzyme-mediated programmed cell death and immune defense against virus-infected or neoplastic cells. Members of the family can insert into target cell membranes when bound to calcium, oligomerize, and form large pores. This action facilitates the passage and uptake of cytotoxic granzymes into target cells, promoting cytolysis and apoptosis. The family is characterized by a MACPF domain responsible for pore formation, an EGF-like domain connecting MACPF and C2 domains, and a C2 domain for calcium-dependent lipid membrane binding. The C2 domain's calcium binding induces structural rearrangements, leading to oligomerization and the insertion of transmembrane beta-strands into the membrane as amphipathic beta-hairpins. These proteins are also involved in delivering cationic cargo proteins and releasing mature caspase-7 into the extracellular space.
Enterotoxin complex component (Enterotoxin_cmpnt)
Type: Family

This family of proteins includes components of an enterotoxin complex known for its role in causing gastroenteritis through food-borne pathogens. Members of this family are involved in binding to erythrocytes and are associated with cytotoxic activity, contributing to the diarrheal symptoms observed during infection.
Outer_spore_wall_assembly (Spore_wall_assembly)
Type: Family

This family of proteins is involved in the assembly of the spore wall, a critical process in the formation of spores in yeast. Members of this family may also play a role in modulating ribosomal DNA transcription, suggesting a potential regulatory function in addition to their structural role in spore wall formation.
Mitochondrial antiviral-signaling domain-containing protein (MAVS)
Type: Family

This family of proteins serves as an adapter in the innate immune defense against viruses. It operates downstream of sensors that detect viral replication by-products, coordinating the activation of key transcription factors and the induction of antiviral cytokines. The proteins in this family contain domains essential for interaction with viral RNA sensors and for recruiting and activating IRF3, a transcription factor involved in interferon signaling. They play a role in both peroxisomal and mitochondrial signaling pathways, which lead to an antiviral state within the cell. The peroxisomal proteins quickly induce defense factors independently of interferons, while the mitochondrial counterparts initiate a delayed, interferon-dependent response to reinforce and sustain antiviral defenses. Additionally, these proteins are implicated in preventing apoptosis and activating the NLRP3 inflammasome, further contributing to the immune response.
RING-type E3 ubiquitin ligase ATL (RING-type_E3_ligase_ATL)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases that exhibit in vitro E3 ligase activity, mediating protein monoubiquitination. Members are involved in plant defense signaling by monoubiquitinating phosphorylated BIK1 in response to pathogen detection. They contain a RING-type zinc finger domain that is responsible for binding to E2 ubiquitin-conjugating enzymes, a characteristic feature that suggests a role in the ubiquitination pathway.
Protein SSUH2 homolog (SSUH2_homolog)
Type: Family

SSUH2 protein is implicated in the biological process of odontogenesis, which is the complex development of teeth. Members of this family are homologous proteins that share a conserved function across different species, including zebrafish, mice, and humans. The role of the SSUH2 in odontogenesis suggests their involvement in the tooth development .
YEATS domain-containing (YEATS_domain)
Type: Family

The YEATS domain-containing protein family is characterized by its ability to recognize and bind acylated histones, particularly those that are crotonylated. Members of this family function as chromatin reader components of the super elongation complex (SEC), which is essential for enhancing the catalytic rate of RNA polymerase II transcription. This is achieved by alleviating transient pausing of the polymerase along the DNA. The YEATS domain facilitates the specific recognition of acetylated and crotonylated histones, with a higher binding affinity for crotonylated histones, especially at certain lysine residues. This interaction is crucial for the regulation of gene transcription, including oncogenic gene expression in the context of acute myeloid leukemia. Additionally, the family plays a significant role in hematopoietic stem cell maintenance by binding to active gene promoters and enhancers, thereby influencing histone methylation states and preserving stem cell identity.
SSM1 domain-containing protein (SSM1_domain)
Type: Family

This family of proteins may be involved in cellular processes such as transcription and phosphate metabolism. One member is suggested to have a role in the inactivation of 6-azauracil, which could indicate a function in nucleotide metabolism or detoxification. Another member is implicated in phosphate metabolic processes. The exact biochemical activities and mechanisms of action within this family remain to be fully characterized.
Thioredoxin domain-containing protein 11 (Thioredoxin_dom-contain_11)
Type: Family

The Thioredoxin domain-containing protein 11 family is part of the protein disulfide isomerase family, suggesting a role in the formation of proper protein disulfide bonds. Members of this family may function as redox regulators, particularly in the folding of Dual Oxidase (DUOX) proteins. They are implicated in the thyroid hydrogen peroxide generating system by interacting with DUOX1 and DUOX2, forming part of a larger multiprotein complex. Although they associate with DUOX proteins, they are not independently capable of assisting in hydrogen peroxide production.
Exon junction complex-associated protein (EJC-associated_protein)
Type: Family

This family of proteins includes components of the exon junction complex (EJC), which is involved in mRNA splicing and metabolism. Members of this family are implicated in the regulation of splicing, particularly in the modulation of apoptotic gene isoforms. They are known to bind RNA and are associated with the ASAP complex, which has roles in both splicing inhibition and the promotion of apoptosis. These proteins can induce chromatin condensation in response to apoptotic signals and have been shown to regulate the expression of specific cyclins in leukemia cells.
Mitochondrial Serine Protease LACTB (Mito_Ser_Protease_LACTB)
Type: Family

The LACTB family comprises mitochondrial serine proteases that regulate mitochondrial lipid metabolism. These enzymes are involved in modulating the levels of PISD, a key enzyme in the conversion of phosphatidylserine to phosphatidylethanolamine, impacting the lipid composition within mitochondria. The precise mechanism, whether through direct proteolysis of PISD or another lipid metabolism protein, remains unclear. Additionally, members of the LACTB family have been identified as tumor suppressors, capable of inhibiting the proliferation of cancer cells, likely through their role in mitochondrial lipid metabolism regulation.
Ras-responsive element-binding protein 1 (RREB1)
Type: Family

The RREB1 family comprises transcription factors that bind specifically to RAS-responsive elements in gene promoters. Members of the family are involved in various cellular processes, including the repression of the angiotensinogen gene, regulation of transcriptional activities of AR and NEUROD1, and promotion of brown adipocyte differentiation. They may also play a role in Ras/Raf-mediated cell differentiation, enhancing calcitonin expression. Additionally, they have been implicated in the negative regulation of CDKN2A expression, influencing susceptibility to certain tumors.
Nodulation factor sulfotransferase (Nod_factor_sulfotransferase)
Type: Family

This family of proteins is involved in the biosynthesis of nodulation factors, which are key signaling molecules in symbiotic relationships between certain plants and nitrogen-fixing bacteria. Members of this family are believed to participate in the sulfation process of the nod factor by transferring sulfate from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to specific positions on N-acetylglucosamine residues. This modification is crucial for the biological activity of nod factors, influencing the establishment of symbiosis and the subsequent development of root nodules where nitrogen fixation occurs.
Regulatory Factors in Gene Expression and Cell Death (RegFact_GeneExpr_CellDeath)
Type: Family

The protein family in question appears to be involved in regulatory functions within the cell, with one member identified as a probable transcription factor that may influence gene expression by binding to regulatory regions, specifically modulating the expression of homeobox protein lin-39 in the vulval lineage. Another member is implicated in promoting programmed cell death, potentially interacting with cell cycle regulatory factors and synthetic multivulva class B proteins, while functioning independently of certain known cell death pathways. The functions of the third member remain uncharacterized. Collectively, the family seems to play roles in gene regulation and cell fate determination.
Giardia Variant Surface Antigen (Giardia_VSA)
Type: Family

This family of proteins is characterized by the presence of a CXXC motif repeat, which suggests a potential role in binding to other proteins or possibly to DNA. Members of this family are known as variant surface proteins (VSPs) in Giardia, which indicates that they may be involved in antigenic variation, a mechanism that pathogens use to evade the host immune response. VSPs are typically found on the surface of the trophozoite stage of the parasite and are thought to play a role in host-parasite interactions, possibly by facilitating attachment to the host's intestinal epithelium or by protecting the parasite from the host's immune system.
Rho GTPase-activating Regulators (Rho_GAP_Regulators)
Type: Family

This family of proteins includes Rho GTPase-activating proteins (GAPs) that are involved in the regulation of the Rho family of small GTPases, particularly the Rac-type GTPase. Members of this family function by catalyzing the conversion of the active GTP-bound form of these GTPases to their inactive GDP-bound state, thereby controlling their activity and downstream signaling pathways. These proteins play a crucial role in various cellular processes, including the regulation of cytoskeletal dynamics and cell morphology. One member is specifically implicated in maintaining the inactivation of a particular Rho GTPase at the apex of pollen tubes, which is essential for the regulation of polar cell growth in plants.