SII-SWORD/CoKE huggingface dataset:
Primate lentivirus group Gag polyprotein-like (Primate_lentivir_Gag_pol-like)
Type: Domain

The primate lentivirus group gag polyprotein family is involved in the assembly, budding, maturation, and infection stages of the viral replication cycle. These polyproteins form membrane associations and self-associations that result in the budding of an immature virion from the infected cell. They selectively bind and package genomic RNA, encapsulate and protect viral RNA, and act as nucleic acid chaperones during retrotranscription. They also mediate virion assembly by interacting with the plasma membrane and recruiting viral Env proteins. The conical core of the virus, which encapsulates the genomic RNA-nucleocapsid complex, is formed by these polyproteins and is disassembled upon virion entry into the host cell. They contain late-budding domains that recruit host ESCRT machinery for viral particle budding.
Cytochrome P450 Monooxygenases (Cytochrome_P450_Monoox)
Type: Family

The Cytochrome P450 family is a diverse group of enzymes that play a crucial role in the metabolism of a wide range of substrates, including fatty acids, steroids, xenobiotics, and insect hormones. These heme-thiolate monooxygenases are involved in various biological processes such as the biosynthesis of steroid hormones, detoxification of synthetic insecticides, and breakdown of fatty acids. They exhibit a remarkable ability to oxidize structurally unrelated compounds, often through hydroxylation reactions. Members of this family are also implicated in the synthesis of aromatic C18 estrogens from C19 androgens, known as aromatase activity. Additionally, some family members participate in the biosynthesis of secondary metabolites, such as antibiotics and mycotoxins, and in the metabolism of endocannabinoids. The Cytochrome P450 enzymes are characterized by their use of molecular oxygen, inserting one oxygen atom into substrates while reducing the second to water, with electrons supplied by NADPH via cytochrome P450 reductase.
Aldolase class II family, sugar metabolism enzymes (Aldolase_class_II_sugar_metab)
Type: Family

The aldolase class II family is involved in various metabolic pathways, including the degradation of sugars such as L-fucose, D-arabinose, and L-rhamnulose, as well as the anaerobic utilization of L-ascorbate. Members of this family catalyze key reactions such as the reversible cleavage of L-rhamnulose-1-phosphate to dihydroxyacetone phosphate and L-lactaldehyde, the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate, and the dehydration of methylthioribulose-1-phosphate. These enzymes play crucial roles in the metabolism of rare sugars, the salvage pathway of toxic by-products, and the biosynthesis of coenzymes. They operate through mechanisms involving retroaldol/aldol reactions or decarboxylation, often requiring metal ions for activity. The family includes several subfamilies such as MtnB, AraD/FucA, and RhaD, each with specific substrate preferences and functions.
Non-receptor tyrosine kinases involved in cell signaling (Non-receptor_tyrosine_kinases)
Type: Family

This family of proteins includes non-receptor tyrosine kinases that play crucial roles in various cellular processes. They are involved in signal transduction pathways that regulate immune responses, cell growth, survival, differentiation, cytoskeletal remodeling, cell adhesion, and migration. These proteins are activated by cell surface receptors and are essential for both innate and adaptive immunity. They also participate in the regulation of B-cell and T-cell receptor signaling, contributing to the development and function of lymphocytes. Additionally, they mediate responses to growth factors, cytokines, and environmental stresses, influencing processes like platelet activation, vascular development, and osteoclast maturation.
Immunoglobulin Heavy Variable (IgHV)
Type: Family

The Immunoglobulin Heavy Variable (IgHV) family includes proteins that are critical components of the adaptive immune system. Members of this family are involved in antigen recognition and are produced by B lymphocytes. The variable region of the immunoglobulin heavy chain, which is part of the B cell receptor, binds specific antigens, triggering immune responses. This region undergoes V-(D)-J rearrangement and somatic hypermutation, processes that contribute to the diversity of antibodies and their ability to mature in affinity for antigens. The family includes both functional immunoglobulin chains and probable non-functional open reading frames. Functional members mediate humoral immunity by forming antigen binding sites with light chains, leading to the elimination of antigens. Non-functional members may arise from gene rearrangement or mutation events that prevent the production of a viable immunoglobulin chain.
Nuclear hormone receptor family NR3 subfamily (Nuclear_hormone_rcpt_NR3)
Type: Family

The nuclear hormone receptor family NR3 subfamily proteins are ligand-activated transcription factors that regulate gene expression affecting cellular proliferation and differentiation in target tissues. They bind to specific DNA sequences and modulate the transcription of target genes involved in a wide range of physiological processes including metabolism, development, and homeostasis. Members of this family respond to steroid hormones such as estrogens, glucocorticoids, mineralocorticoids, androgens, and progesterone, and can function as transcriptional activators or repressors. They are composed of a modulating N-terminal domain, a DNA-binding domain, and a C-terminal ligand-binding domain. Some members are known to interact with coactivator and corepressor proteins, influencing their transcriptional activity. They are also involved in various signaling pathways and may play roles in apoptosis, chromatin remodeling, and maintaining insulin sensitivity.
Bacterial glucokinase (Bacterial_glucokinase)
Type: Family

The bacterial glucokinase family consists of ATP-dependent enzymes that catalyze the phosphorylation of glucose to produce glucose-6-phosphate. This reaction is a key step in the glycolytic pathway, allowing cells to utilize glucose for energy production. In some bacteria, such as E. coli, the role of glucokinase is not critical for glucose metabolism as glucose is often imported as glucose-6-phosphate via the phosphotransferase system (PTS). However, in conditions where PTS is not the primary glucose transport mechanism, glucokinase activity becomes more important. The family members are not active on other sugars like fructose, galactose, or mannose, indicating a specific role in glucose metabolism.
Cytidine and Deoxycytidylate Deaminase (Cyt/Deoxycyt_deaminase)
Type: Family

The cytidine and deoxycytidylate deaminase family encompasses enzymes that play a crucial role in pyrimidine metabolism. Members of this family are responsible for the hydrolytic deamination of cytidine and 2'-deoxycytidine, converting them into uridine and 2'-deoxyuridine, respectively. This reaction is essential for the recycling of cytidine and for the synthesis of uridine monophosphate (UMP). Some members of the family have also evolved to deaminate the cytosine moiety of certain antibiotics, such as blasticidin S, contributing to antibiotic resistance. The family is characterized by a conserved domain structure, with each monomer typically comprising a small N-terminal alpha-helical domain and two larger core domains that exhibit nearly identical tertiary structures.
Tryptophan--tRNA ligase (Trp-tRNA_synthetase)
Type: Family

The Tryptophan--tRNA ligase family comprises enzymes that catalyze the ligation of tryptophan to its corresponding tRNA, a critical step in the translation of the genetic code into proteins. These enzymes first activate tryptophan by ATP to form Trp-AMP and then transfer the activated amino acid to the acceptor end of tRNA(Trp). This reaction is essential for the incorporation of tryptophan into nascent polypeptide chains during mRNA translation. Members of this family are characterized by their membership in the class-I aminoacyl-tRNA synthetase family, which is known for its role in protein biosynthesis. The enzymes in this family are found across a wide range of organisms, indicating their fundamental role in cellular metabolism and genetic expression.
AraC/XylS family transcriptional regulators (AraC_XylS_family_regulators)
Type: Family

The AraC/XylS family proteins are transcriptional regulators that respond to specific environmental stimuli by activating or repressing the expression of various operons. Members of this family typically contain a helix-turn-helix (HTH) motif that facilitates DNA binding. They regulate diverse functions, including the metabolism of sugars such as L-rhamnose and L-arabinose, degradation of aromatic compounds like toluene and xylene, and control of virulence genes. The activators in this family, such as RhaS and RhaR, induce the expression of operons like rhaBAD and rhaT in response to L-rhamnose availability. Other members, like AraC, can function as both activators and repressors, regulating arabinose operons based on the presence or absence of arabinose. Some proteins within this family are involved in the response to environmental stresses or the regulation of genes important for pathogenicity.
Calcium-dependent Serine/Threonine Protein Kinases (CDPK_Ser/Thr_kinases)
Type: Family

Calcium-dependent protein kinases (CDPKs) are a family of serine/threonine protein kinases that play pivotal roles in calcium signaling pathways. They function as sensors and effectors of intracellular calcium levels, translating changes in calcium concentration into phosphorylation events that regulate various cellular processes. CDPKs are involved in a wide range of functions, including stress responses, cell cycle progression, cytokinesis, and motility. They are also implicated in the regulation of gene expression, development, and immune responses. CDPKs typically consist of a kinase domain, an autoinhibitory junction domain, and a calmodulin-like domain. The kinase activity of CDPKs is regulated by calcium binding, which induces conformational changes leading to autophosphorylation and activation of the kinase. This family is essential for the coordination of cellular responses to environmental cues and developmental signals across various organisms, particularly in plants and certain parasites.
FtsK/SpoIIIE/SftA cell division and DNA translocation (FtsK/SpoIIIE/SftA)
Type: Family

The FtsK/SpoIIIE/SftA family includes essential cell division proteins that coordinate cell division and chromosome segregation. Members of this family are involved in the assembly of the cell-division machinery and function as DNA motors that move double-stranded DNA in an ATP-dependent manner towards specific recombination sites within the replication terminus region. This movement is essential for the activation of the Xer recombinase, which facilitates chromosome unlinking by recombination. The proteins can also remove other proteins from DNA as they translocate, but this translocation stops at specific recombination sites to prevent the removal of essential recombinases. The family also includes proteins involved in specialized secretion systems, which export proteins from the cell, including virulence factors during infection. Additionally, some members are implicated in sporulation, aiding in the accurate completion of chromosome partitioning before the formation of the division septum.
Transcriptional regulatory Fis (Trans_regulatory_Fis)
Type: Family

The Fis family of DNA-binding proteins plays a crucial role in the regulation of ribosomal RNA transcription, directly activating rRNA promoters. Members of the Fis family are also involved in various other gene regulatory functions, such as preventing the initiation of DNA replication from oriC, binding to AT-rich sites in both coding and non-coding regions, and influencing DNA inversion processes. Their regulatory activities are essential for proper cellular function and gene expression modulation.
Antigen-presenting and immune regulatory MHC class I-related (MHC_class-I_related)
Type: Family

The protein family includes antigen-presenting molecules that display peptides or lipid antigens to T-cell receptors, contributing to immune surveillance and response. Members are involved in presenting foreign antigens, including microbial and tumor-derived peptides, to the immune system. Some act as ligands for receptors like KLRK1/NKG2D, mediating natural killer cell cytotoxicity. Others bind self and non-self glycolipids, presenting them to natural killer T-cells. The family also includes proteins that regulate humoral immunity by recycling IgG, extending its half-life, and transferring passive immunity. Additionally, some members bind to transferrin receptor, modulating iron uptake, while others are involved in stress-induced self-antigen recognition or immune regulation at the maternal-fetal interface. Overall, the family plays a crucial role in immune system regulation, pathogen defense, and maintaining homeostasis.
Rab GTPases family involved in membrane trafficking (Rab_GTPases_membrane_traffic)
Type: Family

The Rab family of small GTPases are key regulators of intracellular membrane trafficking, which encompasses the movement of vesicles between different cellular organelles and the plasma membrane. Members of this family cycle between an active GTP-bound state and an inactive GDP-bound state, enabling them to recruit various effectors responsible for vesicle formation, movement, tethering, and fusion. These proteins are involved in processes such as vesicular traffic, protein transport, endocytic recycling, cytokinesis, cell polarization, and ciliogenesis initiation. They also play roles in the regulation of cell survival, invasive migration, epithelial morphogenesis, and the maintenance of organelle identity and morphology. Additionally, they are implicated in the maturation and acidification of phagosomes, autophagy, and the oxidative stress response.
tRNA (adenine-N(6)-)-methyltransferase (tRNA_Adenine-N(6)_MTase)
Type: Family

The tRNA (adenine-N(6)-)-methyltransferase family is characterized by enzymes that specifically methylate the adenine at position 37 of tRNA(1)(Val) with the anticodon cmo5UAC. This methylation is a post-transcriptional modification that plays a crucial role in the stability and function of the tRNA molecule. The modification process is essential for the proper decoding of the genetic code and the fidelity of protein synthesis. Members of this family are part of the larger methyltransferase superfamily, sharing common structural features that facilitate the transfer of a methyl group from S-adenosylmethionine to the target adenine nucleotide. The activity of these enzymes is vital for cellular RNA metabolism and is conserved across various bacterial species.
Forkhead box domain-containing protein (FOX_domain-containing)
Type: Family

This family of proteins includes transcription factors that play key roles in various developmental processes, such as differentiation of hair follicles, pharyngeal arch development, and embryonic patterning. Members of this family are involved in the regulation of gene expression by binding to DNA consensus sequences and acting as either transcriptional activators or repressors. They are essential for the proper development and function of multiple tissues, including the liver, pancreas, lungs, and kidneys. Some proteins within this family are also implicated in the maintenance of cell viability and resistance to oxidative stress, as well as in the regulation of cell cycle and apoptosis. They are characterized by the presence of a forkhead box (FOX) domain, which is a conserved DNA-binding motif.
Nucleoside triphosphate/diphosphate phosphatase-like (Ntdp-like)
Type: Family

This entry represents the nucleoside triphosphate/diphosphate phosphatase (Ntdp) family and similar proteins mainly found in bacteria and archaea. Ntdp family proteins are characterised by their ability to hydrolyse nucleoside triphosphates and diphosphates. They exhibit nucleoside phosphatase activity towards a variety of nucleoside triphosphates (NTPs) and diphosphates (NDPs), including those of adenosine, guanosine, uridine, cytidine, and their deoxy counterparts. These enzymes play a role in nucleotide metabolism, contributing to the regulation of intracellular nucleotide pools and the maintenance of nucleotide balance within the cell. Some members of the Ntdp family are also implicated in bacterial virulence, influencing the production of hemolysins, nucleases, and other extracellular proteins, as well as affecting cell wall protein expression. The enzymatic activity of these proteins can be regulated by substrate concentration and the presence of non-hydrolyzable analogs .
Glutathione S-transferase superfamily (GST_superfamily)
Type: Family

The Glutathione S-transferase (GST) superfamily includes enzymes that play a crucial role in the detoxification of endogenous compounds and xenobiotics. Members of the family catalyze the conjugation of the tripeptide glutathione to a variety of hydrophobic and electrophilic substrates, facilitating their solubilization and excretion. Some family members also exhibit peroxidase activity, reducing lipid hydroperoxides, and are involved in isomerization reactions important for steroid hormone biosynthesis. Additionally, certain GSTs are structural components of the eye lens in squids and octopi, with limited enzymatic activity. The family contributes to various physiological processes, including cellular proliferation, protection against oxidative stress, and regulation of cell signaling pathways.
Cysteine synthase/Cystathionine beta-synthase (Cys_Synth/Cystath_Beta-Synth)
Type: Family

The cysteine synthase/cystathionine beta-synthase family is involved in the biosynthesis of cysteine, an essential amino acid. Members of this family catalyse the conversion of O-acetylserine (OAS) to cysteine through the elimination of acetate and addition of hydrogen sulfide . Some proteins within this family also have bifunctional activity, being able to catalyse the synthesis of L-3-cyanoalanine, which is involved in cyanide detoxification in plants . Cystathionine beta-synthases are implicated in the transsulfuration pathway, converting L-serine and L-homocysteine into L-cystathionine, a precursor to L-cysteine . This family also includes proteins that synthesise N-(2-amino-2-carboxyethyl)-L-glutamate, a precursor for antibiotics and siderophores like staphyloferrin B. Some proteins are regulated allosterically by S-adenosyl-methionine and may bind heme groups, affecting their redox sensitivity. The family plays a crucial role in maintaining sulfur amino acid levels, participating in redox regulation, and contributing to the synthesis of important biomolecules.
Thiolase-like superfamily, Thiolase (Thiolase-like_sf_Thiolase)
Type: Family

The Thiolase family proteins are involved in key metabolic processes, primarily catalyzing the thiolytic cleavage of 3-ketoacyl-CoA to form acetyl-CoA and a CoA ester that is two carbons shorter, a crucial step in the beta-oxidation pathway of fatty acid metabolism. This reaction is fundamental for the breakdown of fatty acids, enabling their conversion into acetyl-CoA, which enters the citric acid cycle for energy production. Some family members also catalyze the cleavage of beta-ketoadipyl-CoA to succinyl-CoA and acetyl-CoA, and are implicated in the metabolism of aromatic compounds. Additionally, certain thiolases are involved in the biosynthesis of jasmonic acid, a plant hormone associated with stress responses, and in the production of floral scent compounds. The family includes both peroxisomal and non-peroxisomal enzymes, with some members possessing a peroxisomal targeting signal for localization.
Leucine-rich repeat domain-containing protein (LRR_domain-containing)
Type: Family

This family of proteins includes a diverse range of functions, primarily associated with cellular signaling and regulation. Members are involved in innate immunity, acting as regulators of Toll-like receptor signaling pathways, and contributing to inflammatory responses. Some proteins within the family function as GTP-binding proteins, while others are involved in the MAPK pathway activation, acting as Ras effectors. The family also includes proteins that participate in the regulation of cell volume through the volume-regulated anion channel (VRAC), mediating ion transport in response to osmotic changes. Additionally, there are proteins that play roles in apoptosis, cell survival, and ubiquitination processes. The proteins are characterized by the presence of leucine-rich repeat (LRR) domains, which are typically involved in protein-protein interactions and may contribute to the diverse functional roles of the family.
Thiol-specific antioxidant peroxiredoxin (Peroxiredoxin)
Type: Family

The peroxiredoxin family proteins are thiol-specific peroxidases that catalyse the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols . They play a crucial role in cell protection against oxidative stress by detoxifying peroxides. Some family members act as sensors of hydrogen peroxide-mediated signalling events and may participate in signaling cascades of growth factors and tumor necrosis factor-alpha by regulating intracellular H2O2 concentrations. Additionally, certain peroxiredoxins are involved in the maintenance of physical strength, the regulation of NF-kappa-B activation in the cytosol, and may have a role in postmitotic motor neuron differentiation. They are also implicated in the antioxidant defense of photosynthesizing tissues and may contribute to longevity and the mitohormetic pathway. The family includes both cytosolic and mitochondrial members, with some localized to chloroplasts in plants.
Lipopolysaccharide Assembly Protein LptD (LptD)
Type: Family

The LptD family proteins are integral components of the bacterial outer membrane, primarily involved in the assembly of lipopolysaccharide (LPS). LPS is a key constituent of the outer leaflet of the outer membrane in Gram-negative bacteria, crucial for maintaining structural integrity and protecting against environmental stress. Members of the LptD family work in conjunction with LptE, another essential protein in the LPS transport machinery. The LptD proteins possess an N-terminal periplasmic domain that likely interacts with LptA and a C-terminal transmembrane domain that forms a beta-barrel structure and interacts with LptE. This interaction is vital for the proper insertion and assembly of LPS onto the cell surface. Some LptD proteins also contribute to resistance against solvents like n-hexane and are implicated in outer membrane permeability and envelope biogenesis.
DnaG Primase (DnaG_primase)
Type: Family

The DnaG primase family consists of RNA polymerases that synthesize short RNA molecules serving as primers for DNA polymerase during DNA replication. Members of this family are also involved in RNA degradation as part of the exosome complex and function as poly(A)-binding proteins, enhancing the interaction between heteromeric, adenine-rich transcripts and the exosome. The family includes proteins with an N-terminal zinc-binding domain, a central core domain with primase activity, and a C-terminal DnaB-binding domain. These enzymes are essential for DNA replication initiation and are found across various bacterial and archaeal species.
Type II DNA Topoisomerases (Type_II_DNA_Topoisomerases)
Type: Family

This family of proteins includes type II topoisomerases, which are enzymes that modulate the topological states of DNA. They are involved in processes requiring DNA strand separation such as replication, transcription, recombination, and repair. These proteins can introduce negative supercoils into DNA in an ATP-dependent manner, and are also capable of relaxing supercoils and decatenating interlinked DNA circles. They function by creating transient double-stranded breaks in the DNA and passing another segment of the DNA helix through this break before resealing it. Some family members are targets for antibiotics that inhibit their activity, which is crucial for bacterial viability and cell division.