SII-SWORD/CoKE huggingface dataset:
SRY-related HMG-box transcription factor-like (SRY-related_HMG-box_TF-like)
Type: Family

The SRY-related protein family includes transcriptional regulators that play a crucial role in sex determination and differentiation . Members of this family, such as the Sex-determining region Y protein, are essential for male development, initiating the male sex determination process by influencing the development of supporting cell precursors as Sertoli cells. They are involved in various gene regulation aspects, including promoter activation or repression, and recognise specific DNA sequences to facilitate DNA bending . Additionally, they participate in pre-mRNA splicing and contribute to the maintenance of motor functions in dopaminergic neurons of the adult male brain . Some family members also have roles in embryonic development, organogenesis, and the differentiation of various cell types, including neuronal and endothelial cells .
Glutamate--cysteine ligase type 2, YbdK subfamily (GCL_type2/YbdK_subfam)
Type: Family

The glutamate--cysteine ligase type 2 family, specifically the YbdK subfamily, consists of ATP-dependent carboxylate-amine ligases. These enzymes exhibit weak glutamate--cysteine ligase activity, suggesting a potential role in the synthesis of gamma-glutamylcysteine (gamma-GC). Gamma-GC is a precursor to glutathione, a significant low-molecular-weight thiol compound. In certain halophilic archaea, these ligases catalyze the formation of gamma-GC as the main thiol compound instead of glutathione. The precise biological substrate and the full scope of functions for these enzymes remain to be elucidated, as the catalytic rates observed are low, raising questions about their role in vivo.
MADS-box/MEF2 Transcription Factor (MADS-box/MEF2_TF)
Type: Family

The MADS-box/MEF2 family proteins are transcription factors that play crucial roles in various developmental processes across a wide range of organisms. In plants, they are predominantly involved in the regulation of flower development, controlling floral organ identity, meristem determinacy, and flowering time. They function through the formation of homo- and heterodimers, which bind to specific DNA sequences to regulate gene expression. Some family members are also implicated in root development, seed development, and response to environmental cues like vernalization. In animals, MEF2 family members are key regulators of muscle development, neuronal differentiation, and survival, with additional roles in cell growth, survival, and apoptosis. They bind to MEF2 elements in gene promoters and are involved in muscle-specific, growth factor-induced, and stress-induced gene expression.
Tripartite motif-containing (TRIM/RBCC)
Type: Family

The TRIM/RBCC protein family is involved in various biological processes, including innate and adaptive immunity, cell cycle regulation, apoptosis, autophagy, and cellular differentiation. Members of this family function as E3 ubiquitin ligases, mediating the ubiquitination of target proteins for proteasomal degradation or other fates. They play key roles in antiviral defense by targeting viral proteins and regulating immune signaling pathways. Some TRIM proteins are involved in the regulation of cell proliferation, tumor suppression, and DNA damage response. Others participate in muscle cell differentiation and repair, as well as the regulation of calcium transport in epithelial cells. The family is characterized by a conserved tripartite motif comprising a RING-type zinc finger, one or two B-box-type zinc fingers, and a coiled-coil region, often followed by a variable C-terminal domain.
AAE Transporter (AAE_transporter)
Type: Family

The AAE transporter family is involved in the transport of various substrates across cellular membranes. Members of this family function as antiporters, exchanging one substance for another across the membrane, utilizing the gradient of one to move the other against its gradient. This mechanism is vital for maintaining cellular homeostasis and can be involved in the uptake of nutrients as well as the expulsion of toxins or by-products of metabolism. Specific members within this family have been identified to catalyze the electrogenic exchange of aspartate with alanine, and some are involved in the protection of cells from toxic by-products like methylglyoxal. The family includes several subfamilies, such as the YbjL and YidE subfamilies, indicating a diversity of functions and substrates among its members.
Centrin/CML-like (Centrin_CML-like)
Type: Family

The centrin family consists of calcium-binding proteins that play crucial roles in various cellular processes. Centrin is a protein involved in microtubule-organizing center structure and function, including centriole duplication and cell division . This entry also includes caltractin, obelin and some Calcium-binding proteins from Arabidopsis such as CML37 and 38 . Members of this entry are characterised by the presence of EF-hand domains, which are helix-loop-helix structural domains capable of binding calcium ions, and are involved in calcium signalling and regulation of various cellular activities.
Type-I 3-dehydroquinase (Type-I_3-dehydroquinase)
Type: Family

The type-I 3-dehydroquinase family is involved in the biosynthesis of aromatic amino acids through the chorismate pathway. Members of this family catalyze the cis-dehydration of 3-dehydroquinate (DHQ) to produce 3-dehydroshikimate, which introduces the first double bond of the aromatic ring. This reaction is the third step in the pathway and is crucial for the formation of aromatic compounds in various organisms. Some proteins within this family may also be inhibited by specific compounds and may have additional regulatory mechanisms affecting their activity.
Serine/Threonine Dehydratase (Ser/Thr_Dehydratase)
Type: Family

The serine/threonine dehydratase family is characterized by enzymes that catalyze the dehydration of serine and threonine to their respective alpha-keto acids, often as part of amino acid catabolism or biosynthesis. Members of this family are involved in the anaerobic formation of alpha-ketobutyrate and ammonia from threonine through a two-step reaction involving dehydration and nonenzymatic hydrolysis of enamine/imine intermediates. Some members are regulated allosterically by compounds such as isoleucine, valine, and AMP, and may have additional regulatory domains influencing their activity. The family includes D-serine dehydratases, which specifically act on D-serine, and L-threonine dehydratases, which are involved in isoleucine biosynthesis. These enzymes play crucial roles in nitrogen metabolism and are found across various organisms, including bacteria, plants, and animals.
Terpene synthase-like (Terpene_synthase-like)
Type: Family

This entry represents a group of terpene synthases from plants, fungi and bacteria . The terpene synthase family is involved in the biosynthesis of a wide variety of terpenoid compounds, which play diverse roles in physiology and ecology, such as plant defence against herbivores and pathogens, and have applications in medicine due to their antitumour, anti-inflammatory, and antibacterial properties . Members of this family are responsible for the conversion of prenyl diphosphate substrates into various terpenes, including monoterpenes, sesquiterpenes, and diterpenes. These enzymes are characterised by conserved motifs that are important for their catalytic activity, typically binding to Mg(2+) ions . The family includes enzymes involved in the production of phytohormones like gibberellins, as well as phytoalexins, volatile emissions, and oleoresin secretions. Some terpenes also serve as precursors for fragrances and flavourings, and have potential therapeutic applications.
Collagen superfamily (Collagen_superfamily)
Type: Family

The collagen family is characterized by its role in providing structural integrity to various tissues. Collagens are major components of the extracellular matrix and are involved in the formation of fibrils and networks that support the architecture of tissues such as skin, bone, cartilage, and basement membranes. They contribute to the physical properties of tissues, including elasticity and strength. Collagens also play roles in tissue development, growth, and repair. Some family members have specialized functions, such as mediating cell attachment, influencing cell morphology, and participating in angiogenesis. Certain collagens interact with other matrix proteins, like laminins and proteoglycans, to form complex meshworks. Some collagen types are involved in defense mechanisms, as seen in viral surface structures or in lung defense against inhaled pathogens. The diversity of domains within collagen chains, including triple-helical and non-collagenous domains, allows for the formation of various supramolecular assemblies and the execution of distinct biological functions.
Immunoglobulin Variable Light Chain (IgV_Light_Chain)
Type: Family

The Immunoglobulin Variable (IgV) protein family consists of variable domains of immunoglobulin light chains involved in antigen recognition. Members of this family are produced by B lymphocytes and exist as either membrane-bound or secreted glycoproteins. They play a crucial role in the humoral immune response by serving as receptors on B cells for specific antigen binding, which initiates clonal expansion and differentiation into plasma cells. Secreted forms act as antibodies to mediate the elimination of antigens. Each immunoglobulin possesses two antigen binding sites, formed by the variable domains of a heavy chain and an associated light chain. These domains undergo V-(D)-J rearrangement and somatic hypermutations, allowing for affinity maturation and adaptation to a diverse range of antigens. Some members are non-functional due to genetic alterations affecting the immunoglobulin chain synthesis.
Class-I pyridine nucleotide-disulfide oxidoreductase (Class-I_Pyr_Nuc-Dis_Oxidored)
Type: Family

This family of proteins is involved in redox reactions, where they play a crucial role in the transfer of electrons within cells. They are key components of various enzyme complexes, including the glycine cleavage system and alpha-ketoacid dehydrogenase complexes, which are essential for metabolic processes such as the conversion of pyruvate to acetyl-CoA and the degradation of glycine. Some members also participate in the reduction of mycothione, a unique antioxidant found in certain bacteria. Additionally, these proteins can have moonlighting functions, such as involvement in spermatazoa capacitation and acrosome reaction, or acting as serine proteases. Their activity is regulated by various factors, including the presence of metal ions and the formation of heterodimers.
ChlB/BchB/BchZ (ChlB/BchB/BchZ)
Type: Family

The ChlB/BchB/BchZ family includes proteins involved in the biosynthesis of chlorophylls and bacteriochlorophylls. Members of this family function as components of the dark-operative protochlorophyllide reductase (DPOR) complex, which catalyzes the light-independent reduction of ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is crucial for chlorophyll biosynthesis in photosynthetic organisms. The complex uses Mg-ATP and reduced ferredoxin as substrates. Some members are also involved in converting chlorophylls into bacteriochlorophylls by reducing ring B of the tetrapyrrole. Additionally, the family includes proteins that may play a role in the biosynthesis of the prosthetic group of nitrogenase (FeMo cofactor), which is essential for nitrogen fixation in certain bacteria.
Metal Ion Import ATP-binding (Metal_Ion_Import_ABC)
Type: Family

The protein family is involved in the import and transport of various metal ions across cellular membranes, utilizing ATP-driven transport systems. Members of the family are part of ABC transporter complexes, which are binding protein-dependent and responsible for energy coupling to the transport system. The family includes proteins that import essential nutrients such as vitamin B12, zinc, manganese, and possibly other metals, indicating a role in metal homeostasis and cellular nutrition. The transporters function by hydrolyzing ATP to provide the necessary energy for the translocation of their respective substrates through the membrane, contributing to the survival and virulence of the organisms.
UbiB protein kinase (UbiB_kinase)
Type: Family

The UbiB protein kinase family is involved in the regulation of aerobic coenzyme Q (ubiquinone) biosynthesis, specifically as regulators of UbiI activity. Ubiquinone is a vital lipid-soluble electron transporter within the electron transfer system in mitochondria and is essential for cellular respiration. Members of the UbiB family are likely to play a role in maintaining cellular energy processes and responding to oxidative stress. Some members are also implicated in the regulation of chloroplast lipid synthesis and modulation of chloroplast membrane composition in response to stress, as well as in the maintenance of photosynthetic electron transport by regulating the homeostasis of various prenyl-lipids.
HAD-like hydrolase superfamily (HAD-like_hydrolase_sf)
Type: Family

The HAD-like hydrolase superfamily protein family is involved in a variety of biochemical processes, including the degradation of phosphonates, the dephosphorylation of 2-phosphoglycolate as part of the DNA repair system, and the hydrolysis of pyrophosphate. Members of this family play crucial roles in cellular metabolism, such as the dissimilation of 2-phosphoglycolate formed during oxidative stress-induced DNA repair, controlling intracellular pyrophosphate pools, and recycling cell wall components. Some family members are also implicated in pathogenicity by modulating phosphatase activity through phosphorylation. The family includes phosphonoacetaldehyde hydrolases, phosphoglycolate phosphatases, pyrophosphatases, and tyrosine-protein kinases, highlighting its diverse functional repertoire in bacterial physiology and stress response mechanisms.
Threonylcarbamoyl-AMP synthase, SUA5 (TC-AMP_synthase_SUA5)
Type: Family

The SUA5 family, specifically the TsaC subfamily, consists of enzymes known as Threonylcarbamoyl-AMP synthases. These enzymes are universally required for the biosynthesis of a unique threonylcarbamoyl modification at position 37 (t(6)A37) on tRNAs that read codons starting with adenine. This modification is crucial for maintaining the accuracy of protein synthesis by ensuring proper codon recognition and the maintenance of the reading frame during translation. The enzymes catalyze the formation of threonylcarbamoyl-AMP (TC-AMP) from L-threonine, bicarbonate/CO2, and ATP, releasing diphosphate as a byproduct. Some members of the family may also participate in other cellular processes, such as telomere replication in eukaryotes. The family is characterized by a conserved domain and has members in a wide range of organisms, including bacteria, archaea, and eukaryotes.
Photosystem I iron-sulfur center (PSI_iron-sulfur_center)
Type: Family

The Photosystem I iron-sulfur center family comprises apoproteins that are crucial for the photochemical activity of Photosystem I (PSI), a plastocyanin-ferredoxin oxidoreductase. These proteins harbor two 4Fe-4S centers, named FA and FB, with FB serving as the terminal electron acceptor of PSI. Electrons are donated to ferredoxin by FB. The C-terminus of these proteins is involved in interactions with other PSI components, such as PsaA/B/D, and is necessary for the assembly of the PSI complex and the binding of PsaD and PsaE to PSI. The primary function of the family is to facilitate the conversion of photonic excitation into a charge separation, which sequentially transfers an electron from the donor P700 chlorophyll pair to a series of spectroscopically characterized acceptors, including A0, A1, FX, FA, and FB.
Ubiquitin and ubiquitin-like (Ubiquitin_ubiquitin-like)
Type: Family

The ubiquitin family is characterised by its role in post-translational modification, where ubiquitin or ubiquitin-like proteins are covalently attached to target proteins, influencing their stability, localization, or activity. Ubiquitination involves the conjugation of ubiquitin to lysine residues on substrates through an isopeptide bond, often leading to proteasomal degradation. However, ubiquitin also participates in non-proteolytic functions such as DNA repair, cell cycle regulation, endocytosis, and signal transduction . Polyubiquitin chains linked through different lysine residues or linearly through the N-terminal methionine can have distinct cellular roles. Some family members are involved in ribosome biogenesis as fusion proteins with ribosomal proteins, contributing to the structure and function of ribosomes. The family includes ubiquitin-like modifiers such as NEDD8, which regulate cell cycle and embryogenesis by modifying cullins and other proteins to alter E3 ligase activity .
Kazal-type Serine Protease Inhibitor (Kazal-type_SerProtInhib)
Type: Family

The Kazal-type serine protease inhibitor family is characterized by its ability to inhibit serine proteases. Members of this family play roles in various biological processes including anti-inflammatory and antimicrobial protection of mucous epithelia, skin integrity, and desquamation. They regulate the activity of defense-activating and desquamation-involved proteases such as kallikreins, trypsin, and elastase. The inhibitors are selective, with some members not inhibiting certain kallikreins. The family includes avian ovomucoids, which consist of three homologous, tandem Kazal family inhibitory domains and are known to inhibit trypsin. Human representatives of this family have been implicated in skin desquamation by inhibiting specific kallikreins.
Major Histocompatibility Complex/Immunoglobulin (MHC/Immunoglobulin)
Type: Family

The MHC class I and II protein families are integral to the adaptive immune system. MHC class I molecules, including beta-2-microglobulin, are expressed on nearly all nucleated cells and present endogenous peptide antigens to CD8+ T cells, playing a critical role in the immune response to intracellular pathogens and abnormal cells. MHC class II molecules are primarily expressed on professional antigen-presenting cells and present exogenous peptide antigens to CD4+ T cells, facilitating immune responses to extracellular pathogens. Both classes are involved in antigen processing and presentation, crucial for initiating specific immune responses. Immunoglobulin light chains, part of the immunoglobulin family, are essential for antibody diversity and specificity, contributing to the humoral immune response by recognizing and binding antigens.
Siroheme/cobalamin biosynthesis enzyme (Siro_Cobalamin_biosynth)
Type: Family

This family of proteins includes multifunctional enzymes involved in the biosynthesis of siroheme, a prosthetic group essential for various redox reactions and nitrogen and sulfur metabolism, including Siroheme synthase 1 (CysG1). These enzymes catalyse the sequential methylation of uroporphyrinogen III to form precorrin-2, followed by the NAD-dependent dehydrogenation to yield sirohydrochlorin, and finally, the ferrochelation to produce siroheme. Additionally, some members are involved in the methylation of precorrin-4 in cobalamin (vitamin B12) biosynthesis. The family also encompasses proteins that catalyze the initial methylation steps converting uroporphyrinogen III to precorrin-1 and precorrin-2, which are intermediates in both cobalamin and siroheme biosynthesis pathways.
Methionine Sulfoxide Reductase A (MsrA_MetSO_reductase)
Type: Family

The MsrA Met sulfoxide reductase family consists of enzymes that play a crucial role in cellular defense against oxidative stress. Members of this family are responsible for the repair of oxidized proteins by catalyzing the reduction of methionine sulfoxide to methionine, thereby restoring the function of these proteins. This reversible oxidation-reduction process is essential for maintaining protein function and preventing cellular damage caused by reactive oxygen species. The family is characterized by its ability to specifically reduce the S-enantiomer of methionine sulfoxide, highlighting its specialized role in protein repair mechanisms.
Apolipoprotein A1/A4/E (Apolipoprotein_A1/A4/E)
Type: Family

The apolipoprotein A1/A4/E family consists of proteins that are primarily involved in lipid transport and metabolism. Members of this family are key components of plasma lipoproteins, which are complexes that transport lipids through the bloodstream to various tissues. These apolipoproteins are amphipathic, meaning they can interact with both lipids and the aqueous environment, facilitating the formation, conversion, and clearance of lipoprotein particles such as high-density lipoproteins (HDL), very low-density lipoproteins (VLDL), chylomicrons, and their remnants. They play critical roles in reverse cholesterol transport, a process that moves cholesterol from peripheral tissues back to the liver for excretion. Additionally, some family members are involved in activating enzymes like lecithin cholesterol acyltransferase (LCAT) and lipoprotein lipase (LPL), which are essential for lipid metabolism. The family also includes proteins that influence plasma triglyceride levels and participate in spermatozoa motility.
Ubiquitin carboxyl-terminal hydrolases (Peptidase_C19)
Type: Family

The peptidase C19 family, also known as ubiquitin carboxyl-terminal hydrolases, encompasses deubiquitinating enzymes that play crucial roles in various cellular processes by removing ubiquitin from specific proteins and polyubiquitin chains. These enzymes are involved in the regulation of protein turnover, DNA damage repair, cell cycle progression, apoptosis, immune response, and signal transduction pathways such as Wnt and TGF-beta/BMP. They function by processing ubiquitin precursors, recycling ubiquitin molecules, editing polyubiquitin chains, and preventing proteasomal degradation of substrates. Some family members are also implicated in the regulation of mitophagy, endosomal protein recycling, and maintenance of circadian rhythm. The family includes enzymes that act as tumor suppressors, regulators of cell growth and differentiation, and modulators of inflammatory and antiviral responses.
Dihydroxy-acid dehydratase IlvD/Edd (DHAD_IlvD/Edd)
Type: Family

The IlvD/Edd family proteins are involved in the biosynthesis of branched-chain amino acids, specifically catalyzing the dehydration of dihydroxy-acid precursors into their corresponding 2-oxo-acids, which are the penultimate precursors to L-isoleucine and L-valine. These enzymes function by converting (2R,3R)-2,3-dihydroxy-3-methylpentanoate into 2-oxo-3-methylpentanoate and (2R)-2,3-dihydroxy-3-methylbutanoate into 2-oxo-3-methylbutanoate. The specificity of these enzymes for the (R) isomer of the substrate is noted, with no activity against the (S) isomer. The family's role is essential in the common pathway leading to the synthesis of branched-chain amino acids, which are vital for protein structure and metabolism. Due to the importance of this pathway, the IlvD/Edd family proteins are potential targets for the development of antifungal agents and herbicides.
ABC transporter ATP-binding protein (ABC_transporter_ATP-bind)
Type: Family

This family of proteins is involved in the transport of specific substrates across cellular membranes using ATP hydrolysis for energy. Members of this family are typically part of larger ABC transporter complexes, which are responsible for the import of substances such as aliphatic sulfonates and taurine. These proteins are characterized by their ability to bind and hydrolyze ATP, which provides the necessary energy for the transport process. They play a crucial role in the uptake of nutrients and other compounds that are essential for cellular function and metabolism.