SII-SWORD/CoKE huggingface dataset:
T cell receptor alpha variable region (TCR_alpha_variable)
Type: Family

This family of proteins includes variable regions of the alpha chain of T cell receptors (TRs), which are crucial for antigen recognition. These proteins are part of the alpha-beta TRs, which are antigen-specific and essential for the immune response. They are present on T lymphocytes and recognize peptide-major histocompatibility complex (pMH) complexes displayed by antigen-presenting cells (APCs). The interaction between TRs and pMH complexes triggers a cascade of intracellular events, starting with the activation of LCK kinase and subsequent phosphorylation of ITAM motifs on CD3 and CD247. This leads to the recruitment and activation of ZAP70, which then phosphorylates LAT to form the LAT signalosome. The signalosome coordinates downstream signaling pathways, including calcium, MAPK kinase, and NF-kB pathways, culminating in the activation of transcription factors vital for T cell proliferation, gene expression, and differentiation. The T cell repertoire is generated through V-(D)-J rearrangement in the thymus and is further refined to ensure self-tolerance and proper immune function.
Polygalacturonase-associated BURP domain-containing protein (PG-associated_BURP)
Type: Family

This family of proteins includes non-catalytic subunits of polygalacturonase as well as proteins containing a BURP domain at the C-terminus. Members of this family are involved in the regulation of plant cell size and growth, with some acting as chaperones for other proteins through the secretory pathway. The BURP domain is unique to plant proteins and plays a critical role in the function of these proteins, although the exact mechanisms are not fully understood.
Ribosome Assembly Protein 3 (Ribosome_Assembly_3)
Type: Family

This family of proteins is involved in the assembly of the 60S ribosomal subunit, a critical component of the eukaryotic ribosome. Members of this family play a key role in the biogenesis of this subunit, ensuring that protein synthesis within the cell is carried out efficiently. The proper formation of the 60S ribosomal subunit is essential for the translation of mRNA into polypeptides, which is a fundamental process in all living cells. Proteins in this family share a commonality in structure and function, indicative of their specialized role in ribosome assembly.
Fertilization and immune response mediator protein (Fert-Immune_med_protein)
Type: Family

This family of proteins includes members that are involved in various biological processes, including fertilization, signal transduction, and immune response. Some proteins in this family are known to play a role in the fertilization process by mediating the binding of sperm to the zona pellucida and facilitating the migration of spermatozoa into the oviduct. They may also be involved in promoting protein tyrosine phosphorylation as part of signal transduction pathways. Other members are implicated in the activation of neutrophils, including degranulation and superoxide production, and may influence neutrophil adhesion and migration by interacting with integrins and chemokine signaling. Additionally, these proteins can participate in neutrophil transendothelial migration and may enhance vascular integrity during this process.
Serine palmitoyltransferase small subunit (SPT_small_subunit)
Type: Family

This family of proteins is involved in the biosynthesis of sphingolipids, which are essential components of cell membranes and play a role in signal transduction and cell recognition. Members of this family function as part of a multisubunit enzyme complex known as serine palmitoyltransferase (SPT). This complex catalyzes the condensation of L-serine with activated acyl-CoA, typically palmitoyl-CoA, to form long-chain base precursors of sphingolipids. The catalytic core of the complex consists of a heterodimer formed by SPTLC1 and either SPTLC2 or SPTLC3. Proteins in this family enhance the catalytic activity of the complex and contribute to substrate specificity. The composition of the complex influences its preference for specific acyl-CoA substrates. Additionally, members of this family may have a role in localizing certain enzymes to the mitochondria-associated membranes, impacting the incorporation of fatty acids into specific phospholipids.
Protease Inhibitor I33 (Protease_Inhibitor_I33)
Type: Family

The protease inhibitor I33 family comprises proteins that function as aspartyl protease inhibitors. Members of this family are known to inhibit the activity of aspartic proteases such as pepsin. Aspartic proteases are a class of enzymes that play a crucial role in the digestive system by breaking down proteins into peptides. The inhibitors in the protease inhibitor I33 family bind to these enzymes and prevent them from degrading proteins, thereby regulating protease activity. This inhibition mechanism is important for controlling proteolytic processes and maintaining protein integrity in various organisms. Some family members are also recognized as immunodominant antigens, suggesting a role in immune response.
BPI fold-containing superfamily member (BPI_fold-superfamily_member)
Type: Family

This family of proteins includes lipid-binding components with a high affinity for certain phospholipids, such as dipalmitoylphosphatidylcholine. They are involved in the innate immune response, particularly in the upper airways, by reducing the surface tension of airway secretions and inhibiting biofilm formation by Gram-negative bacteria. Additionally, they regulate the proteolytic cleavage of specific sodium channels, contributing to the maintenance of airway surface liquid and mucus clearance. Some family members are also found in sweat, where they exhibit surfactant properties and may assist in temperature regulation through sweat spreading and evaporation. Others may play a role in oral cavity innate immunity.
Zein-alpha (Zein-alpha)
Type: Family

This family of proteins consists of seed storage proteins known as zeins, which are predominantly found in maize. Zeins accumulate in protein bodies within the endosperm of the maize seed and serve as a nutrient source during seed germination. They are characterized by their solubility in alcohol but insolubility in water, which distinguishes them from other seed storage proteins. Zeins are rich in proline and glutamine and have a role in determining the quality of the maize kernel, influencing its nutritional and industrial properties.
UPF0746 family, actin cytoskeleton organization (UPF0746_actin_org)
Type: Family

The UPF0746 family includes proteins that are implicated in the organization of the actin cytoskeleton and cytokinesis. One characterized member, Defective in tip formation protein A, is essential for the proper sorting of prestalk cells, tip formation during the mound stage, and fruiting body development in Dictyostelium discoideum. It may also play a role in cell adhesion. Other members of the family are uncharacterized, but based on similarity, they may share related functions in cellular structure and dynamics.
Schizosaccharomyces pombe Mam3/Map4 (S_pombe_Mam3/Map4)
Type: Family

The Mam3/Map4 family proteins are primarily involved in cell agglutination during the process of conjugation in Schizosaccharomyces pombe. These proteins are implicated in colony formation and may play a role in flocculation, a process where cells adhere together to form clumps or flocs. The family includes specific proteins such as Mam3 and Map4, which are specific to M and P cell types, respectively, and are essential for mating interactions. Other putative members of the family are believed to share similar functions in agglutination and flocculation, suggesting a conserved role within the family for these processes.
Bacterial Outer Membrane Factor (OMF) (Bacterial_OMF)
Type: Family

The Outer Membrane Factor (OMF) family proteins are involved in various transport and efflux processes across the bacterial outer membrane. Members of the family function as channels or conduits facilitating the export of diverse compounds, including antibiotics, toxins, and enzymes. The family includes proteins necessary for the secretion of calmodulin-sensitive adenylate cyclase-hemolysin, alkaline protease, and various other proteases. Some members, like TolC, are essential components of efflux systems that confer resistance to toxic substances by expelling them from the cell. These efflux systems are also implicated in bacterial virulence, contributing to the survival of pathogenic bacteria within the host. Additionally, the family encompasses proteins that participate in the import of molecules such as colicin E1. Structurally, the family is characterized by forming a 'channel-tunnel' that spans the outer membrane and periplasmic space, with a proximal end sealed by coiled helices.
DoxX-like inner membrane-associated oxidoreductase (DoxX-like_oxidoreductase)
Type: Family

This family of proteins includes members that are putatively involved in the degradation of aromatic compounds and may function as oxidoreductases. Some proteins within this family are suggested to play a role in the detoxification of catechol, which is essential for growth and viability in certain environmental conditions. The proteins are typically associated with the inner membrane and are characterized by their similarity to the DoxX family, indicating a potential shared functional framework or evolutionary origin.
Ribosomal-protein N-acetyltransferase (Ribosomal_N-acetyltransferase)
Type: Family

This family of proteins includes enzymes that catalyze the transfer of acetyl groups from acetyl coenzyme A to various substrates, including ribosomal proteins and nucleoid-associated DNA-binding proteins. Some members are known to modify specific ribosomal proteins, converting them into acetylated forms, which may affect their function or stability. Other members have broader substrate specificity, with activities extending to the acetylation and succinylation of proteins involved in nucleoid structure and function. The family also contains uncharacterized proteins that are predicted to have acetyltransferase activity based on sequence similarity.
Membrane Fusion Protein Cation Efflux System (MFP_Cation_Efflux)
Type: Family

This family of proteins is involved in the transport of metal cations across cellular membranes, conferring resistance to various heavy metals such as copper, silver, zinc, nickel, cobalt, and cadmium. Members of this family are typically part of larger efflux systems that actively expel toxic metal ions from the cell, thereby mitigating metal toxicity. These proteins are thought to function as part of a proton/cation antiporter mechanism, where the efflux of metal ions is coupled with the influx of protons, maintaining electrochemical gradients across the membrane. The family includes proteins that may act in concert with other components to form membrane-bound complexes essential for the energy-dependent efflux process.
ComF/GntX DNA utilization and transformation protein (ComF/GntX_DNA_util-trans)
Type: Family

This family of proteins is associated with bacterial competence for DNA uptake, suggesting a role in transformation processes. Members of this family are also implicated in gluconate metabolism, which indicates a potential involvement in the utilization of extracellular DNA as a nutrient. The proteins within this family share a similarity that categorizes them under the ComF/GntX group, reflecting a conserved function or structural characteristic across different bacterial species.
Short-chain Dehydrogenases/Reductases (SDR) (SDR_oxidoreductase)
Type: Family

The Short-chain Dehydrogenases/Reductases (SDR) family comprises enzymes with oxidoreductase activity, involved in various biosynthetic pathways. Members of the family participate in the synthesis of secondary metabolites such as botcinic acid, calbistrin A, and cladofulvin, which have roles in plant virulence, potential anti-leukemia properties, and fungal fitness, respectively. The family includes enzymes like polyketide synthases, trans-enoyl reductases, and cytochrome P450 monooxygenases. These enzymes catalyze key steps such as reduction of ketones to alcohols, methylation, hydroxylation, and dimerization reactions in the biosynthesis of complex polyketides and other metabolites.
Alkylbase DNA Glycosylase/Transcriptional Activator (Alkylbase_DNA_Glycosylase/TA)
Type: Family

This family of proteins is involved in the cellular response to DNA damage, specifically alkylation lesions. Members of this family function as DNA glycosylases that recognize and excise various alkylated bases from DNA, thereby initiating the base excision repair (BER) pathway. These enzymes hydrolyze the N-glycosidic bond between the damaged base and the sugar-phosphate DNA backbone, creating an abasic site that is further processed by other repair proteins. Some members also exhibit a bifunctional role, acting as transcriptional activators to regulate the expression of genes involved in alkylation damage resistance. Additionally, certain proteins within this family may participate in damage signaling by recognizing and binding to abasic sites without displaying glycosylase activity, potentially facilitating the recruitment of other repair factors.
Glycosyl Hydrolase 2 Domain-Containing Protein (GH2_Domain-Containing)
Type: Family

This family of proteins exhibits hydrolytic activity on glycosidic bonds. Members are involved in the degradation of various glycosides, including those with beta-galactosidic and beta-glucuronidic linkages. They catalyze the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides, as well as the removal of D-glucuronic acid side chains from polysaccharides. These enzymes play roles in the utilization of diverse carbon sources, the degradation of cell wall components in green seaweed, and potentially in the reactivation of glucuronide drug conjugates within the gastrointestinal tract. The family is characterized by a conserved domain indicative of the glycosyl hydrolase 2 superfamily.
FAD-linked Oxidoreductase/Transferase Type 4 (FAD-linked_OxidoTrans_Type4)
Type: Family

This family of proteins includes enzymes that are involved in oxidative reactions of various substrates such as glycolate and D-lactate. Members of this family function as oxidoreductases, often utilizing FAD as a cofactor. They are involved in metabolic pathways where they catalyze the oxidation of specific substrates to their corresponding products, such as the conversion of glycolate to glyoxylate or D-lactate to pyruvate. These enzymes are important for the metabolism of carbon sources and may interact with different electron acceptors, although the physiological acceptors are often unknown. Some family members are known to be stimulated by divalent cations, and their activity can be regulated by various inhibitors.
Cellulose Degradation Glycosyl Hydrolase 3 (Cellulose_Degrad_GH3)
Type: Family

The Glycosyl Hydrolase 3 family encompasses enzymes that play a crucial role in the degradation of cellulosic biomass. Members of this family, including beta-glucosidases, catalyze the hydrolysis of terminal, non-reducing beta-D-glucosyl residues, which results in the release of beta-D-glucose. This reaction is significant as it facilitates the last step in the breakdown of the inhibitory cellobiose, thereby contributing to cellulose degradation. Some family members also exhibit beta-xylosidase activity, which is involved in xyloglucan degradation, removing backbone 'G' units. These enzymes are found in various cellular locations, including the periplasmic space and lysosomes, indicating their diverse functional roles in different organisms.
GPI-anchor maturation lipid remodeler (GPI-anchor_lipid_remodeler)
Type: Family

This family of proteins is involved in the process of lipid remodeling, which is a crucial step during the maturation of glycosylphosphatidylinositol (GPI) anchors. Members of this family are required for the replacement of the diacylglycerol moiety with ceramides in GPI-anchor maturation, a modification that is essential for the maintenance of cell wall integrity in fungi and potentially in other organisms. The proteins are characterized by having distinct domains that interact with each other, suggesting a complex mechanism of action in the lipid remodeling process.
Transposase/Integrase Enzymes (Transposase-Integrase)
Type: Family

This family of proteins includes transposases and integrases, which are enzymes that catalyze the movement of DNA segments within genomes. Transposases are responsible for the cut-and-paste mechanism of transposable elements, allowing for the insertion of DNA at new genomic locations. Integrases typically facilitate the integration of viral DNA into the host genome, which is a critical step in the viral replication cycle. Members of this family share structural similarities and are involved in processes that contribute to genetic diversity and evolution.
Serine/threonine-protein phosphatase CPPED1 (STPP_CPPED1)
Type: Family

The CPPED1 family is part of the metallophosphoesterase superfamily and includes serine/threonine-protein phosphatases. Members of the CPPED1 family are involved in the dephosphorylation of AKT kinase family members, particularly at 'Ser-473'. This regulatory activity is crucial for controlling cell cycle progression and can promote cell apoptosis. Additionally, the CPPED1 family may have an inhibitory role in glucose uptake by adipocytes, suggesting a broader regulatory function in cellular metabolism and signaling pathways.
Tungsten-dependent aldehyde:ferredoxin oxidoreductase (W-dependent_AOR)
Type: Family

This family of proteins includes enzymes that are involved in the oxidative decarboxylation of aldehydes into their corresponding carboxylic acids, utilizing ferredoxin as an electron acceptor. Members of this family are characterized by the presence of tungsten in their active sites and are known to participate in various metabolic pathways, including glycolysis and gluconeogenesis. Some act in lieu of more common enzymes such as glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase, while others are involved in the fermentation of peptides. The activity of these enzymes is modulated by various compounds, with some enhancing and others inhibiting their function. They are sensitive to oxygen and can be inhibited by substances like arsenite, iodoacetate, and cyanide.
Molybdopterin Adenylyltransferase/MoaC-Related (MPT_Adenylyltrnsfr/MoaC-Rel)
Type: Family

This family of proteins includes enzymes involved in the biosynthesis of the molybdenum cofactor, which is essential for the activity of various molybdoenzymes. Members of this family are responsible for the adenylation of molybdopterin, a key step in the formation of the molybdenum cofactor. Additionally, some bifunctional proteins in this family also catalyze the conversion of (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate to cyclic pyranopterin monophosphate, another crucial reaction in the biosynthetic pathway. These activities are vital for the proper functioning of molybdoenzymes, which play roles in diverse biological processes including the metabolism of purines, pyrimidines, and pterins, and in the detoxification of sulfite and xanthine.
ABC transporter osmolyte uptake ATP-binding protein (ABC_osmolyte_uptake_ATP-bind)
Type: Family

This family of proteins is involved in the transport of various osmolytes across cellular membranes. Members of this family are part of ATP-binding cassette (ABC) transporter complexes, which are responsible for the energy-dependent uptake of specific substrates. These substrates include trimethylamine N-oxide (TMAO), glycine betaine, proline betaine, choline, and occasionally carnitine. The proteins are believed to couple the hydrolysis of ATP to the translocation of these osmolytes, facilitating the cell's response to osmotic stress and contributing to cryoprotection. The activity of these transport systems can be modulated by environmental conditions such as osmotic gradients and low temperatures.
Bacterial Sporulation-Associated (Bact_Sporulation_Assoc)
Type: Family

The protein family in question appears to be involved in bacterial sporulation processes. Members of this family may influence the activity or stability of sigma-G, a transcription factor critical for sporulation, and are likely required for the engulfment stage of spore formation. Some proteins within the family are suggested to play a role in cell wall metabolism during sporulation, enhancing amidase activity which is crucial for cell wall remodeling. Additionally, family members may function as autolysins, participating in cell wall hydrolases activities that are essential for various biological processes including cell separation, cell-wall turnover, and flagellar function, which is important for bacterial motility.
Glycosyl Hydrolase Family 39 (Glycosyl_Hydrolase_39)
Type: Family

The glycosyl hydrolase 39 family encompasses enzymes with diverse functions including the degradation of glycosaminoglycans and the hydrolysis of xylo-oligosaccharides. Members of the family such as beta-xylosidases are involved in the breakdown of xylan into xylose units, playing a role in the utilization of plant biomass. Other members, like alpha-L-iduronidases, are lysosomal hydrolases essential for the degradation of heparan sulfate and dermatan sulfate, crucial for lysosome function, autophagy, and the maintenance of various cellular and organ functions. Mutations in alpha-L-iduronidase can lead to lysosomal storage disorders, highlighting the importance of this family in human health.
Glutathione S-transferase Kappa/NadH (GST_Kappa/NadH)
Type: Family

The GST superfamily Kappa and NadH families are involved in various metabolic pathways. The Kappa family members, such as Glutathione S-transferase kappa 1 and kappa 2, primarily catalyze the conjugation of glutathione to a range of exogenous and endogenous compounds, facilitating their detoxification. This activity includes significant conjugating activity with substrates like 1-chloro-2,4-dinitrobenzene. Additionally, kappa 2 members are implicated in respiratory and lipid metabolism. The NadH family members, identified as 2-hydroxychromene-2-carboxylate isomerases, participate in the naphthalene catabolic pathway by catalyzing the reversible glutathione-dependent isomerization of specific substrates. They are also regulated by compounds such as salicylate, indicating a responsive adaptation to environmental or cellular conditions.
RNA-binding domain-containing protein (RNA-binding_domain)
Type: Family

This family of proteins is involved in RNA binding, which suggests a role in various RNA-related processes such as RNA metabolism, regulation of gene expression, or RNA splicing. Members of this family may interact with RNA molecules to influence their stability, structure, or function, and could be implicated in cellular responses to environmental changes or stress. The exact functions may vary among different organisms and could be essential for maintaining proper cellular function and homeostasis.
Alanine Aminotransferase (Ala_Aminotransferase)
Type: Family

This family of proteins is involved in amino acid metabolism, specifically in the biosynthesis and degradation of alanine. Members of this family function as aminotransferases, enzymes that catalyze the transfer of an amino group from an amino acid to a keto acid. The primary reaction mediated by these enzymes is the transamination of pyruvate and glutamate, resulting in the production of L-alanine and 2-oxoglutarate. This reversible reaction is a key step in the metabolic pathway, linking nitrogen and carbon metabolism. The enzymes typically require pyridoxal phosphate as a cofactor for their activity.