SII-SWORD/CoKE huggingface dataset:
Glycosyltransferase 28 family, UgtP subfamily (Glycosyltransf_28_UgtP)
Type: Family

The glycosyltransferase 28 family, specifically the UgtP subfamily, consists of processive diacylglycerol beta-glucosyltransferases involved in the biosynthesis of membrane glucolipids. These enzymes catalyze the transfer of glucose residues from UDP-glucose to diacylglycerol (DAG), forming various glycolipids such as beta-monoglucosyl-DAG, beta-diglucosyl-DAG, and beta-triglucosyl-DAG. Beta-diglucosyl-DAG is a predominant glycolipid in Bacillales and serves as a membrane anchor for lipoteichoic acid (LTA), which is crucial for cell envelope maintenance. Some members of the family can transfer up to three glucose residues, while others are limited to two. The family also includes monogalactosyldiacylglycerol synthases from plants, which are involved in the synthesis of the major structural component of photosynthetic membranes. These enzymes exhibit substrate preference and are essential for thylakoid membrane biogenesis and photosynthetic electron transport.
INO80/SWR1 chromatin remodeling helicase (INO80/SWR1_helicase)
Type: Family

The INO80/SWR1 helicase family is involved in chromatin remodeling and DNA repair. Members of this family function as ATPase components of various complexes, such as the INO80 and SWR1 complexes, which are responsible for shifting nucleosomes and exchanging histone variants. These activities lead to transcriptional regulation of selected genes and are essential for processes including DNA replication, DNA damage response, and mitotic chromosome segregation. Some family members are also implicated in developmental processes and the regulation of gene expression through histone modification exchange, contributing to cellular differentiation and response to environmental signals.
3-ketoacyl-CoA Thiolase (3-ketoacyl-CoA_Thiolase)
Type: Family

The Thiolase family proteins are enzymes that catalyze the final step of fatty acid oxidation. In this crucial metabolic process, they facilitate the cleavage of 3-ketoacyl-CoA to form acetyl-CoA and a CoA ester that is two carbons shorter than the original fatty acid. This reaction is a key part of the beta-oxidation pathway, which is essential for the breakdown of fatty acids to produce energy. Members of the Thiolase family are characterized by their membership in the thiolase-like superfamily, indicating a shared structural framework and evolutionary origin.
Eukaryotic ribosomal protein eL43 (Ribosomal_protein_eL43)
Type: Family

The eukaryotic ribosomal protein eL43 family is comprised of proteins that are components of the large ribosomal subunit (LSU) and are involved in protein synthesis within the cell. Members of the family bind to the 23S rRNA, which is a critical component of the peptidyl transferase center (PTC) in the LSU. This center catalyzes the formation of peptide bonds, polymerizing amino acids into polypeptide chains. The nascent polypeptides exit the ribosome through a tunnel in the LSU, where they interact with various protein factors for processing, targeting, and membrane insertion. Some members of the family are also suggested to have a putative zinc-binding function, although this is not universally noted across all family members.
Aldo/Keto Reductase Detoxification and Biosynthesis (AKR_Detox_Biosynth)
Type: Family

The Aldo/Keto Reductase (AKR) family is involved in detoxification and biosynthesis processes. Members of the family catalyze the reduction of aldehydes and ketones to their corresponding alcohols using NADPH as a cofactor. This family includes enzymes that protect against toxic compounds like aflatoxin B1, contribute to the biosynthesis of mycotoxins such as sterigmatocystin and aflatoxins, and participate in the production of secondary metabolites with roles in plant-pathogen interactions and potential pharmaceutical applications. Some members are implicated in cellular protection and stress responses by reducing reactive aldehydes. The broad substrate specificity of these enzymes reflects their diverse functions in various biological pathways.
Amino Acid-Polyamine-Organocation Superfamily YAT (APC_YAT)
Type: Family

The amino acid-polyamine-organocation (APC) superfamily, specifically the YAT family, consists of membrane-bound permeases with broad substrate specificity. These permeases are involved in the transport of a wide range of amino acids, including but not limited to asparagine, glutamine, alanine, cysteine, glycine, isoleucine, leucine, methionine, phenylalanine, serine, threonine, tyrosine, valine, arginine, lysine, and histidine. Some members also transport related compounds such as S-adenosylmethionine, proline, and polyamines. The family plays a crucial role in the utilization of amino acids as nitrogen sources, sensing extracellular amino acid levels, and regulating the expression of amino acid-metabolizing enzymes and permeases. The permeases can function as high-affinity transporters for specific amino acids or as general permeases with broader specificity, contributing to cellular nutrition and signaling.
Extracellular Matrix Assembly and Organization (ECM_Assembly_Org)
Type: Family

The protein family is involved in the structural integrity and organization of extracellular matrices in various tissues. Members of this family are major components of cartilage extracellular matrix and are involved in matrix assembly, promoting cell adhesion and playing roles in the formation of filamentous networks. Some proteins within the family interact with collagen, integrating collagen bundles and contributing to cell-binding. Others are involved in the organization of skeletal muscles and the formation of neuromuscular junctions. Additionally, certain members have roles in hemostasis, acting as molecular bridges in platelet adhesion or as chaperones for coagulation factors. The family also includes proteins that regulate cell shape and motility, as well as the proliferation and differentiation of neural stem cells, indicating a broader significance in tissue development and maintenance.
Rubredoxin electron transfer (Rubredoxin_ET)
Type: Family

The rubredoxin family comprises small nonheme iron proteins characterized by a single iron atom chelated to four cysteine residues. These proteins function predominantly as electron acceptors in various redox processes. They are involved in electron transfer chains, serving as intermediates or donors to various enzymes, including hydrogenase, pyruvate ferredoxin oxidoreductase, and superoxide reductase. Some family members participate in hydrocarbon hydroxylating systems, transferring electrons from NADH to rubredoxin reductase and alkane 1 monooxygenase. Others may play roles in oxidative stress defense systems or in hydrogen oxidation. The rubredoxin family is essential for diverse metabolic pathways, particularly in anaerobic and microaerophilic organisms, where they contribute to energy conservation and cellular protection against reactive oxygen species.
Snail/Krueppel C2H2-type Zinc-finger (Snail/Krueppel_Znf)
Type: Family

The Snail/Krueppel C2H2-type zinc-finger protein family is characterized by its role in transcriptional regulation, often acting as repressors that bind to E-box motifs. Members of this family are involved in various developmental processes, including neuronal differentiation, embryonic mesoderm formation, neural crest specification and migration, and tracheal morphogenesis. They modulate the action of bHLH transcription factors and are implicated in maintaining cell fate and polarity. Some family members also participate in stress responses, DNA repair, and chromatin insulation. They are essential in establishing transcriptional domains and may influence gene imprinting, cell adhesion, and proliferation. The family includes proteins with functions in the immune response, osteoblast maturation, and epithelial-mesenchymal transition, highlighting their diverse roles in cellular and developmental biology.
L-type Lectin-Domain Containing Receptor Kinases (L-type_Lectin-RKs)
Type: Family

The L-type lectin-domain containing receptor kinase family is involved in a variety of plant defense responses and developmental processes. Members of this family play key roles in resistance to pathogenic bacteria, fungi, and oomycetes, such as Pseudomonas syringae, Alternaria brassicicola, Phytophthora infestans, and Phytophthora capsici. Some proteins within the family are also implicated in the regulation of abscisic acid response during seed germination and in the negative regulation of salt tolerance. Additionally, certain members are essential for pollen development and male fertility, mediating processes like pollen exine assembly and aperture development. The family is characterized by an N-terminal leguminous lectin domain, which may be involved in ligand recognition and protein-protein interactions, and a C-terminal serine/threonine protein kinase domain, suggesting a role in signal transduction through phosphorylation. Some proteins are activated by autophosphorylation in response to stress conditions, while others may have catalytically inactive kinase domains.
Cytochrome P450, sterol 14-alpha demethylase (CYP450_sterol_14alpha_dmase)
Type: Family

The Cytochrome P450 family is involved in diverse oxidative reactions in the biosynthesis of sterols, including cholesterol in mammals and ergosterol in fungi. Members of this family function as monooxygenases that catalyze the removal of methyl groups from sterol substrates, such as lanosterol and eburicol, playing a critical role in membrane composition and synthesis of steroid hormones and bile acids. Some members are involved in the metabolism of oxysterols and neurosteroids, while others participate in the biosynthesis of secondary metabolites with various biological activities. The family is also a target for azole drugs, which inhibit the sterol 14-alpha demethylase activity, crucial for ergosterol biosynthesis and fungal growth.
Gas Vesicle Protein A (GvpA)
Type: Family

The Gas Vesicle Protein A (GvpA) family comprises proteins that form hollow, gas-filled proteinaceous nanostructures known as gas vesicles. These structures enable buoyancy control in various microorganisms, allowing them to position themselves at optimal depths for light or nutrient acquisition during planktonic growth. Gas vesicles are highly permeable to gas and are composed primarily of GvpA, which forms the protein shell. The family also includes minor components like GvpJ and GvpM, which may play roles in nucleating gas vesicle formation. The GvpA family proteins are involved in the formation of gas vesicles that are critical for the survival and adaptability of microorganisms in their respective aquatic or soil habitats.
SdhE FAD assembly factor (SdhE_FAD_assembly_factor)
Type: Family

The SdhE FAD assembly factor family consists of proteins that play a crucial role in the assembly of succinate dehydrogenase (SDH), a key enzyme complex in both the tricarboxylic acid cycle and the electron transport chain. These proteins are responsible for the flavinylation of the SdhA subunit of SDH, a process that involves the covalent attachment of the flavin adenine dinucleotide (FAD) cofactor. This post-translational modification is essential for the proper functioning of SDH, which catalyzes the oxidation of succinate to fumarate and the reduction of ubiquinone to ubiquinol. Members of the SdhE family may also be involved in the flavinylation of other flavoproteins, contributing to a range of metabolic and respiratory processes.
Globin-like Oxygen Transporters (Globin-like_OT)
Type: Family

This family of proteins includes members that are primarily involved in the transport and storage of oxygen. Some proteins in this family are known to bind heme groups, which facilitate the reversible binding of oxygen molecules. Certain members are also involved in redox signaling, electron transport, and may act as physiological sensors for oxygen. A subset of these proteins, known as neuroglobins, are involved in oxygen transport within the brain and exhibit hexacoordinate binding to an iron atom. These neuroglobins may also play a role in neuroprotection during oxidative stress by participating in anti-apoptotic activities. Other functions noted include nitrite reductase activity and the ability to bind and transport hydrosulfide, indicating a multifaceted role in cellular respiration and response to varying oxygen levels.
HssA/B-like serine-rich chaperone (HssA/B-like_chaperone)
Type: Family

The hssA/B family proteins are involved in the suppression of protein aggregation, particularly for proteins with long polyglutamine tracts. They function as chaperones that facilitate the degradation of polyQ aggregates by the proteasome, thus preventing the detrimental effects of protein misfolding and aggregation that can lead to cellular toxicity and disease. The family's role in proteostasis highlights its importance in maintaining cellular homeostasis and preventing proteopathies.
Coronaviruses polyprotein 1ab (Coronavir_polyprotein_1ab)
Type: Family

The coronaviruses polyprotein 1ab family is involved in the replication and transcription of viral RNA. It includes a multifunctional replicase polyprotein that contains enzymatic activities necessary for viral life cycle processes, such as RNA-directed RNA polymerase, helicase, and various proteinases. These enzymes participate in the formation of viral RNA cap structures, cleavage of the polyprotein into functional units, unwinding of RNA and DNA duplexes, and evasion of host immune responses. The family plays a critical role in the assembly of viral replication complexes, modulation of host cell survival pathways, inhibition of host translation, and manipulation of host membrane structures to facilitate viral replication.
DNA Repair and Maintenance Complex Component (DNA_Repair-Maintenance_Comp)
Type: Family

This family of proteins is involved in the maintenance and repair of DNA. Members of this family function as part of a protein complex that is crucial for the early steps of DNA double-strand break repair. They are known to bind to the ends of broken DNA strands and exhibit exonuclease and endonuclease activities, which are essential for processing DNA ends during repair. These proteins can have both double-stranded 3'-5' exonuclease activity and single-stranded endonuclease activity. Additionally, some family members are capable of cleaving DNA hairpin structures that can interfere with DNA replication and recombination. The nuclease activities of these proteins are typically regulated by interactions with other proteins, such as Rad50, which highlights their role in a larger DNA repair machinery.
DtxR/MntR Metal-Dependent Regulators (DtxR_MntR_Metal-Reg)
Type: Family

The DtxR/MntR family includes metal-dependent DNA-binding transcriptional regulators that control the expression of genes involved in metal homeostasis. Members of this family typically function as repressors or activators in response to specific metal ions. IdeR proteins are iron-dependent repressors that regulate iron metabolism, including siderophore biosynthesis and iron storage. MntR proteins are central regulators of manganese homeostasis, activating DNA binding in the presence of Mn(2+) to regulate manganese uptake and efflux systems. Some members also respond to other divalent metal ions, such as Cd(2+), but with lower affinity. The family plays a crucial role in maintaining metal ion balance within cells, which is essential for various physiological processes.
2-oxoacid dehydrogenase (2-oxoacid_dehydrogenase)
Type: Family

The 2-oxoacid dehydrogenase family is involved in crucial metabolic processes, catalyzing the conversion of 2-oxoglutarate to succinyl-CoA and CO2 as part of the 2-oxoglutarate dehydrogenase (OGDH) complex. This complex is a key component in the Krebs cycle, playing a pivotal role in energy production. The family includes dihydrolipoamide succinyltransferase (E2) components that form a core part of the OGDH complex, working in conjunction with other enzymatic components such as 2-oxoglutarate dehydrogenase (E1) and lipoamide dehydrogenase (E3). Some family members also participate in the pyruvate dehydrogenase (PDH) complex, contributing to the conversion of pyruvate to acetyl-CoA. Additionally, a subset of these proteins is involved in the succinylation of histones, indicating a nuclear role that intersects with gene regulation. The family's function is essential for cellular respiration and energy metabolism, as well as for the regulation of gene expression through epigenetic modifications.
Mitogen-activated protein kinase kinase kinase (MAP_kinase_kinase_kinase)
Type: Family

The MAP kinase kinase kinase (MAP3K) family is involved in a variety of cellular processes including signal transduction cascades, cell cycle regulation, stress responses, and immune system function. Members of this family activate downstream MAP kinase pathways by phosphorylating MAP2Ks, which in turn phosphorylate MAPKs, leading to the activation of transcription factors such as NF-kappa-B, AP1, and DDIT3. They play roles in plant defense, cytokinesis, cell differentiation, and responses to environmental stimuli like osmotic changes, heat shock, and oxidative stress. Some are involved in specific pathways like the innate immune MAP kinase signaling cascade, cell wall integrity signaling in fungi, and plant organ morphology regulation. Activation mechanisms include autophosphorylation and phosphorylation by other kinases, and some members possess regulatory domains like SAM and RA domains.
ThrE Dicarboxylate/Amino Acid Exporter (ThrE_Dicarb/AminoAcid_Exp)
Type: Family

The ThrE exporter family is involved in the transport of various substrates across the cell membrane. Members of this family function as transporters for dicarboxylates such as succinate, fumarate, and malate, as well as for amino acids like threonine and serine. These transporters are essential for the export of these metabolites, which plays a significant role in metabolic processes under both aerobic and anaerobic conditions. The activity of some family members is known to be dependent on the proton motive force and can be inhibited by specific ionophores. The coordinated action of certain subunits, such as YjjP and YjjB, is required for the efficient export of succinate, suggesting a complex interaction within the family to fulfill their function.
F-actin Monooxygenase Mical (F-actin_Monoox_Mical)
Type: Family

The Mical family proteins are multifunctional monooxygenases that mediate the depolymerization of F-actin by oxidizing specific methionine residues on actin, leading to actin filament disassembly and preventing repolymerization. They play a crucial role in various cellular processes, including cytoskeletal regulation, cell adhesion, migration, cytokinesis, and vesicle trafficking. Mical proteins are also involved in the regulation of the SRF signaling pathway, affecting gene transcription. Additionally, they function as Rab effector proteins, influencing vesicle transport and endocytic recycling. The family includes proteins that interact with components of the actin cytoskeleton and cell junctions, contributing to cell morphology, neurite outgrowth, and the assembly of junctional complexes.
Leucine-rich repeat and transmembrane domain-containing protein (LRR_TM_domain-containing)
Type: Family

This family of proteins includes a variety of members with diverse functions, primarily involved in cellular signaling, synaptic adhesion, and regulation of neuronal activity. Some act as inhibitors, such as those that inhibit TGF-beta signaling or phospholipase A2 activity. Others are involved in the immune response, bone homeostasis, and regulation of the JAK/STAT pathway. Notably, several members function as receptors that mediate axonal growth inhibition and neuronal plasticity, interacting with ligands like RTN4, OMG, and MAG, and are implicated in brain development and synaptic organization. Additionally, some proteins in this family are involved in the negative regulation of viral infection and in the formation of platelet plugs.
Glycosyl Hydrolase 18 Family Chitinases (Glycosyl_Hydrlase18_Chitinase)
Type: Family

The glycosyl hydrolase 18 family of chitinases encompasses enzymes with a variety of functions, primarily involved in the degradation of chitin, a key component of fungal cell walls and exoskeletal elements of some animals. These chitinases play crucial roles in defense mechanisms against chitin-containing fungal pathogens, contributing to plant and animal immunity. Some family members are involved in morphogenetic processes such as apical growth, cell division, and differentiation, as well as cell wall remodeling and maturation. Certain chitinases also exhibit bifunctional lysozyme activity or act as xylanase inhibitors, suggesting a broader role in plant defense against fungal pathogens. Additionally, some chitinases are implicated in physiological processes like seed germination and latex flow cessation. The family includes enzymes with varying substrate specificities and regulatory mechanisms, highlighting their adaptability and functional diversity.
Eukaryotic Initiation Factor 2 Gamma Subunit (eIF2G)
Type: Family

The eIF2G family plays a crucial role in the initiation phase of eukaryotic protein synthesis. Members of the eIF2G family are involved in the early steps of translation by forming a ternary complex with GTP and initiator tRNA. This complex is essential for the recruitment of the 40S ribosomal subunit and other initiation factors to form the 43S pre-initiation complex (43S PIC). The 43S PIC then binds to mRNA and scans for the start codon to form a 48S initiation complex. Following codon recognition, GTP hydrolysis leads to the release of the eIF2-GDP binary complex, allowing the 60S ribosomal subunit to join and form an 80S initiation complex capable of elongation. For eIF2G to participate in another round of initiation, GDP must be exchanged for GTP, a reaction facilitated by eIF-2B. The eIF2G family is part of the TRAFAC class translation factor GTPase superfamily and the classic translation factor GTPase family.
Beta-defensin antimicrobial peptides (Beta-defensin)
Type: Family

The beta-defensin family comprises peptides with a primary role in host defense, exhibiting broad-spectrum antimicrobial activity against Gram-negative and Gram-positive bacteria. Members of this family are characterized by their ability to permeabilize bacterial membranes, leading to bacterial cell death. Some beta-defensins also bind to bacterial lipopolysaccharides, potentially neutralizing their effects and contributing to immunoregulation. Additionally, certain atypical beta-defensins are involved in reproductive processes, such as facilitating sperm transport within the female reproductive tract, forming a sperm reservoir, and aiding in sperm protection against immunodetection. These functions are attributed to their glycosylation patterns, which impart a negative surface charge to the sperm glycocalyx. The family's role extends to the inhibition of lipopolysaccharide-mediated inflammation, further underscoring their importance in innate immunity and host defense.
Mycobacterial membrane protein Large (MmpL) (Mycobact_MmpL)
Type: Family

The MmpL family proteins are involved in the transport of diverse molecules across the inner membrane of bacteria, particularly in mycobacteria. They play crucial roles in the biosynthesis and secretion of cell wall components such as mycolic acids, sulfolipids, and trehalose monomycolate, which are critical for cell envelope integrity and virulence. Some members are also implicated in the export of siderophores, which are molecules that bind and transport iron, essential for bacterial growth. Additionally, certain MmpL proteins contribute to antibiotic resistance and fitness by exporting toxic compounds and drugs out of the cell. The family includes proteins that transport hopanoids, strengthening the cell envelope, and are involved in heme-iron acquisition systems.