SII-SWORD/CoKE huggingface dataset:
Microtubule-severing AAA ATPase (MT-severing_AAA_ATPase)
Type: Family

This family of proteins is involved in the dynamic regulation of microtubule networks within cells. Members of this family possess ATPase activity and are capable of severing microtubules in an ATP-dependent manner. They play crucial roles in cellular processes such as cytokinesis, membrane trafficking, and the maintenance of axonal integrity. Some family members are implicated in the biogenesis and remodeling of complex microtubule arrays found in axons, spindles, and cilia. They are also associated with the ESCRT-III complex, contributing to abscission during cytokinesis and nuclear envelope reassembly. Additionally, they participate in the regulation of lipid droplet distribution and size, and are involved in the DNA damage response.
Small GTPase superfamily, Rab (Small_GTPase_Rab)
Type: Family

The Rab family of small GTPases is a group of proteins that play a crucial role in regulating intracellular membrane trafficking. They are involved in various stages of vesicular transport, including vesicle formation, movement, tethering, and fusion with target membranes. Members of the Rab family cycle between an inactive GDP-bound form and an active GTP-bound form, recruiting different downstream effectors necessary for vesicular trafficking processes. They are key regulators in processes such as exocytosis, endocytic recycling, and ciliogenesis. Some Rabs are involved in specific pathways like insulin-induced glucose transporter trafficking to the plasma membrane, which is important for glucose homeostasis. Others participate in the establishment and maintenance of cell polarity, neurotransmitter release, and the assembly of tight junctions. The Rab family also has roles in autophagy, axonogenesis, and the regulation of endoplasmic reticulum dynamics.
PfkB Carbohydrate Kinase (PfkB_Carbo_kinase)
Type: Family

The PfkB carbohydrate kinase family encompasses enzymes that catalyze the phosphorylation of various sugars and sugar derivatives, playing key roles in metabolic pathways. Members of this family are involved in the phosphorylation of adenosine, fructose, inositol, tagatose, and deoxygluconate, among others, contributing to the synthesis of AMP, starch formation, phytic acid biosynthesis, and the Entner-Doudoroff pathway. The family includes enzymes such as adenosine kinase, fructokinase, inositol 3-kinase, tagatose kinase, and 2-dehydro-3-deoxygluconokinase. These enzymes are regulated by various factors including substrate inhibition, competitive inhibition by analogs, and the presence of potassium ions. Some members are also involved in the metabolism of antimycobacterial compounds, indicating a potential role in therapeutic pathways.
Sterol Desaturase and Related Enzymes (Sterol_Desaturase_Related)
Type: Family

The sterol desaturase family is involved in various crucial biological processes, including the biosynthesis of sterols such as cholesterol and ergosterol, which are essential components of cell membranes and precursors to steroid hormones and vitamins. Members of this family function as enzymes that introduce double bonds into sterol molecules, a key step in the formation of complex sterols. They are also involved in the desaturation and hydroxylation of fatty acids, contributing to the production of signaling molecules and the regulation of lipid metabolism. Additionally, some members participate in the synthesis of very-long-chain alkanes, which are important for the formation of protective waxy layers in plants, contributing to cuticular permeability and drought tolerance. The family includes enzymes such as lathosterol oxidase, Delta(7)-sterol 5(6)-desaturase, and methylsterol monooxygenase, which catalyze various desaturation, hydroxylation, and decarbonylation reactions in sterol and sphingolipid biosynthesis pathways.
Chromosome partition protein MukB/SMC (MukB/SMC)
Type: Family

The MukB/SMC protein family is essential for chromosome condensation, segregation, and cell cycle progression. Members function as homodimers and are involved in negative DNA supercoiling, which helps organize and compact chromosomes. The family proteins may facilitate chromosome segregation by condensing DNA from both sides of a centrally located replisome during cell division. They feature a hinge domain that allows homodimerization, forming a V-shaped structure, and are characterized by large intramolecular coiled coil regions.
Type-B Carboxylesterase/Lipase (Type-B_Carboxylest/Lipase)
Type: Family

The Type-B Carboxylesterase/Lipase family encompasses enzymes involved in diverse biological processes including the detoxification of xenobiotics, activation of ester and amide prodrugs, metabolism of lipids, and hydrolysis of various ester substrates. Members of this family exhibit hydrolytic activity towards compounds such as palmitoylcarnitine, retinyl esters, xenobiotics, and pyrethroid pesticides. Some are implicated in the biosynthesis of mycotoxins like patulin, while others participate in the degradation of fumonisin B1 or play roles in cell adhesion, virulence, and reproductive biology. The family's broad substrate specificity reflects its involvement in lipid metabolism, with some members preferentially acting on short-chain fatty acid esters, while others target long-chain fatty acid esters or triglycerides. The family's functional diversity is further exemplified by its role in the synthesis of fatty acid ethyl esters and involvement in reverse cholesterol transport. Collectively, the Type-B Carboxylesterase/Lipase family plays a crucial role in various physiological and biochemical pathways across different species.
VPS10-related sortilin family receptors (VPS10-sortilin)
Type: Family

The VPS10-related sortilin family proteins function as sorting receptors within the Golgi compartment, essential for the intracellular sorting and delivery of soluble vacuolar proteins. They are involved in multiple trafficking cycles between the late Golgi and prevacuolar endosome-like compartments. Family members like sortilin also act as clearance receptors on the cell surface, mediating transport from the Golgi to lysosomes, endosomes, and possibly from the endoplasmic reticulum to the Golgi. They play roles in neuronal apoptosis, osteogenic differentiation, adipocyte storage vesicle formation, and protection against oxidative stress. Some subfamily members are implicated in synaptic plasticity, regulation of dendritic spine density, and cell migration, proliferation, and adhesion, contributing to processes such as atherosclerosis and renal ion homeostasis.
Origin Recognition Complex 1/Cell Division Control Protein 6 (ORC1/CDC6)
Type: Family

The ORC1/CDC6 family includes proteins that are key regulators of DNA replication. Members of the family are involved in the initiation of DNA replication by binding to origins of replication, which is often ATP-dependent. They play a role in the assembly of the pre-replication complex necessary to commence DNA replication. Some family members also participate in checkpoint controls to ensure DNA replication is completed before mitosis begins. Additionally, certain proteins within the family have roles in transcriptional silencing, chromatin structure modulation, and cell cycle control of replication. They may bind to specific DNA sequences, such as the ARS consensus sequence in some species, and can interact with other proteins like the MCM helicase complex to regulate the replication process.
IolE/XylA/MocC-like (IolE/XylAMocC-like)
Type: Family

The IolE/XylA/MocC family proteins are primarily involved in the metabolism of inositol and its derivatives. They catalyse the dehydration of inosose to 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione, a key step in the catabolism of inositol. Inosose dehydratases from this family convert 2-keto-myo-inositol to D-2,3-diketo-4-deoxy-epi-inositol. Additionally, some members are implicated in the reversible interconversion of 2-keto-myo-inositol to 1-keto-D-chiro-inositol. The family also includes proteins involved in the catabolism of rhizopine, xylose, and other sugars, highlighting a broader role in carbohydrate metabolism. The enzymes exhibit a diverse range of substrate specificities and activities, including epimerisation of ketoses and dehydration reactions, contributing to various metabolic pathways across different organisms.
Carbohydrate Metabolism HTH-type Transcriptional Regulators (Carb_Metab_HTH_regulators)
Type: Family

The protein family is comprised of helix-turn-helix (HTH) type transcriptional regulators that are involved in the repression or activation of various operons related to carbohydrate transport and metabolism. Members of this family function as repressors for operons such as aga, ula, gat, and glycerol-3-phosphate regulon, or as activators like the fuc operon. They respond to specific inducers, which can lead to the de-repression of the target genes. The regulators bind to DNA and modulate the transcription of genes involved in the utilization of sugars like N-acetyl galactosamine, lactose, L-fucose, and galactitol. Some members are also involved in carbon catabolite repression and the regulation of genes encoding metabolic enzymes. The activity of these regulators is crucial for the efficient utilization of carbohydrates and for the adaptive response of bacteria to different environmental nutrient sources.
Glycosyl Hydrolase Family 18 (Glycosyl_Hydrlase_18)
Type: Family

The glycosyl hydrolase 18 family encompasses a diverse group of proteins with a range of functions, including chitin degradation, tissue remodeling, and modulation of cell proliferation and motility. Members of this family are involved in various biological processes such as immune responses, fertilization, and symbiotic signaling. Some proteins possess chitinase activity, playing roles in host defense against pathogens and in the molting process of arthropods. Others, lacking chitinase activity, such as Chitinase-3-like protein 1 from human act as carbohydrate-binding lectins or participate in signaling pathways. The family includes proteins that contribute to inflammatory responses, facilitate bacterial invasion, and regulate apoptosis in different tissues. Additionally, some members are involved in the regulation of insulin-like peptide signaling, affecting cell proliferation and differentiation.
FAD-dependent oxidoreductase 2 (FAD-oxidoreductase_2)
Type: Family

The FAD-dependent oxidoreductase 2 family is characterised by its members' ability to catalyse various redox reactions, often involving the reduction of electron acceptors using FAD as a cofactor. Members of this family are involved in diverse biological processes, including the anaerobic conversion of glycerol 3-phosphate to dihydroxyacetone, steroid degradation, and the reduction of unsaturated compounds such as urocanate, acrylate, and fumarate. These enzymes play crucial roles in metabolic pathways across different organisms, contributing to energy conservation, detoxification, and the biosynthesis of important compounds.

This family includes the anaerobic G-3-P dehydrogenase subunit B (GlpB), 3-oxosteroid dehydrogenase, urocanate reductase and FRD/SDH among others, each with specific substrates and functions, reflecting the versatility and adaptability of these enzymes to various environmental and physiological conditions. Urocanate reductase (UrdA) catalyses the two-electron reduction of urocanate to dihydrourocanate, which is present at higher concentrations in subjects with type 2 diabetes, and directly impairs glucose tolerance and insulin signaling at the level of insulin receptor substrate (IRS) through activation of p38 gamma (MAPK12)-p62-mTORC1. UrdA from the gut bacteria S.parasanguinis may contribute to the pathogenesis of type 2 diabetes by producing the microbial metabolite dihydrourocanate .
Tyrosinase and Hemocyanin (Tyrosinase/Hemocyanin)
Type: Family

The Tyrosinase family includes copper-containing oxidases involved in pigment formation, such as melanins and other polyphenolic compounds. Members catalyze the hydroxylation of tyrosine to DOPA and the oxidation of DOPA to DOPA-quinone, which are key steps in melanin biosynthesis. Some family members also function in the oxidation of mono- and o-diphenols to o-diquinones, contributing to defense mechanisms against various stress factors. Additionally, the family encompasses hemocyanins, which are oxygen carriers in mollusks and arthropods. The family's diverse roles reflect its involvement in pigmentation, defense, and oxygen transport.
Plant and Fungal Acyltransferase (Plant_Fungal_Acyltransferase)
Type: Family

The acyltransferase family is involved in a diverse range of biosynthetic processes in plants and fungi, including the production of secondary metabolites such as polyketides, terpenoids, and alkaloids. These enzymes catalyze the transfer of acyl groups from acyl-CoA donors to various acceptors, playing crucial roles in the synthesis of phytohormones, mycotoxins, volatile organic compounds, and other bioactive molecules. They contribute to plant defense mechanisms by producing phytoalexins and other antimicrobial compounds. Additionally, they are involved in the formation of flavor and aroma compounds in fruits. The family includes enzymes that modify the trichothecene skeleton in the biosynthesis of trichothecene mycotoxins and others that participate in the biosynthesis of mannosylerythritol lipids, which enhance the availability of water-insoluble substrates.
DENR/SUI1 Translation Initiation Factor (DENR/SUI1_TIF)
Type: Family

The DENR/SUI1 family includes proteins involved in the initiation phase of translation. Members of this family are implicated in various functions related to translation initiation, such as scanning and recognition of the initiation codon, and promoting the recruitment of aminoacylated initiator tRNA to the P site of 40S ribosomes. Some proteins in this family may also facilitate the release of deacylated tRNA and mRNA from recycled 40S subunits after post-termination ribosomal complexes are dissociated into subunits. Additionally, certain DENR family members play a role in modulating the translational profile of a subset of mRNAs, particularly in cancer-related processes when recruited by oncogenes. The SUI1 domain present in these proteins is suggested to be involved in RNA binding, which is crucial for their function in translation.
ABC Transporter ATP-Binding (ABC_transp_ATP-bind)
Type: Family

The protein family is involved in the transport of various substrates across cellular membranes using ATP-binding cassette (ABC) transporters. These proteins are responsible for energy coupling within their respective ABC transporter complexes, facilitating the import or export of substances such as nickel, peptides, dipeptides, glutathione, and potentially other divalent metal ions. Some family members are implicated in bacterial resistance to antimicrobial peptides, while others contribute to virulence and are necessary for processes like genetic competence or sporulation. The transport systems can be specific for certain substrates, such as nickel or glutathione, or may have broader specificity, as seen with oligopeptide transporters that can handle a range of peptide lengths.
Protein N5-glutamine methyltransferase (N5-glutamine_MTase)
Type: Family

The N5-glutamine methyltransferase family is responsible for the post-translational modification of class 1 translation termination release factors. Members of the family methylate the glutamine residue within the universally conserved GGQ motif of these release factors, which is essential for proper termination of protein synthesis. This methylation is crucial for the accuracy and efficiency of the translation termination process. The family includes both bacterial and eukaryotic proteins, with some members also involved in the methylation of mitochondrial translation release factors. The activity of these enzymes ensures the fidelity of protein synthesis by modifying the release factors that recognize stop codons and promote the disassembly of the ribosomal complex.
Glycosyltransferase 2/OpgH subfamily (Glycosyltr_2/OpgH_subfam)
Type: Family

The Glycosyltransferase 2 family, specifically the OpgH subfamily, is involved in the biosynthesis of osmoregulated periplasmic glucans (OPGs), which are important for bacterial response to osmotic stress. Members of this subfamily transfer glucose from UDP-glucose to various lipid carriers, forming glucans that play a role in the protection and structural integrity of bacterial cells. Some members are also implicated in the biosynthesis of non-bilayer-forming membrane lipids and cellulose, contributing to membrane stability and cell wall structure, respectively. The cellulose synthase members of the family are activated by c-di-GMP and are involved in the production of extracellular cellulose for mechanical and chemical protection, particularly in multicellular bacterial communities.
Iron-sulfur cluster assembly and transfer HesB/IscA (Fe-S_cluster_asmbl/transfer)
Type: Family

The HesB/IscA family is involved in the assembly and transfer of iron-sulfur (Fe-S) clusters, which are critical for various cellular processes. Members of this family can transfer Fe-S clusters to apo-ferredoxin and other recipient proteins, acting catalytically through multiple cycles of cluster formation and transfer. They play a role in recruiting intracellular free iron, facilitating the assembly of transient Fe-S clusters in IscU, a scaffold protein for cluster formation. This process occurs in the presence of IscS, L-cysteine, and the thioredoxin reductase system TrxA/TrxB. Some members are also implicated in the maturation of mitochondrial 4Fe-4S proteins and may bind intermediates of Fe/S cluster assembly. The family includes proteins that function under oxidative stress and iron limitation, such as SufA, which is part of the sufABCDSE gene cluster.
Universal ribosomal protein uL10 (Ribosomal_protein_uL10)
Type: Family

The universal ribosomal protein uL10 family is involved in the structural and functional composition of the ribosome, specifically forming part of the ribosomal stalk. The ribosomal stalk is crucial for the interaction of the ribosome with GTP-bound translation factors during protein synthesis. Members of the uL10 family play a central role in recruiting these factors, which are essential for the translation process. The interaction with translation factors enhances the GTPase activity, which is necessary for the translocation step of protein elongation. The uL10 family proteins are functionally equivalent to the E.coli protein L10 and are a key component in the large ribosomal subunit, contributing to the peptidyl transferase center and the exit tunnel for nascent polypeptide chains.
CDP-alcohol phosphatidyltransferase class-I (CDP-alcohol_PTase-I)
Type: Family

The CDP-alcohol phosphatidyltransferase class-I family is involved in the biosynthesis of acidic phospholipids, which are critical components of cell membranes. Members of this family function as enzymes that catalyze the transfer of a phosphatidyl group from CDP-diacylglycerol to various acceptor molecules. For instance, some family members transfer the phosphatidyl group to glycerol-3-phosphate to form phosphatidylglycerophosphate, the committed step in the synthesis of acidic phospholipids. Others catalyze the synthesis of cardiolipin by transferring a phosphatidyl group to phosphatidylglycerol. Cardiolipin is a key phospholipid in mitochondrial membranes, essential for maintaining mitochondrial integrity and function. Additionally, some enzymes within this family can catalyze the formation of archaetidylserine in lipid biosynthesis. The activity of these enzymes is crucial for cell membrane structure and function, impacting processes such as cell morphology, cytokinesis, and stress response.
Protein/nucleic acid deglycase (Prot/Nucl_acid_deglycase)
Type: Family

The protein family is involved in the cellular defense against glycation and oxidative stress. Members of the family function as protein and nucleotide deglycases, catalyzing the deglycation of Maillard adducts formed between amino groups of proteins or nucleotides and reactive carbonyl groups of glyoxals. They repair methylglyoxal- and glyoxal-glycated proteins, releasing repaired proteins and lactate or glycolate. They deglycate cysteine, arginine, and lysine residues in proteins, reactivating them by reversing glycation. They also repair glycated guanine in nucleotides and nucleic acids, thus participating in a nucleotide repair system named guanine glycation repair (GG repair). Additionally, some members have been reported to possess chaperone, protease, and metal-binding activities, contributing to cell protection against oxidative stress and cell death. They may also be involved in mitochondrial function, autophagy of dysfunctional mitochondria, and inflammatory responses.
NAD-dependent DNA ligase B (NAD_dep_DNA_ligaseB)
Type: Family

The NAD-dependent DNA ligase B family comprises enzymes that play a crucial role in DNA replication, recombination, and repair. Members of this family are responsible for catalyzing the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA. They utilize NAD as a coenzyme and as the energy source for the reaction. The enzymes are characterized by their ability to join broken DNA strands, thereby maintaining the integrity and continuity of the genetic information during cell division and in response to DNA damage.
Proton-linked Monocarboxylate Transporter (Proton-linked_MCT)
Type: Family

The Monocarboxylate Transporter (MCT) family comprises proteins that facilitate the proton-linked transport of monocarboxylates across the plasma membrane. Members of this family play diverse roles in the transport of metabolites such as lactate, pyruvate, ketone bodies, and thyroid hormones, contributing to various physiological processes including pH regulation, metabolic homeostasis, and hormone distribution. Some family members are also involved in the efflux of specific metabolites and secondary metabolites, including mycotoxins and antibiotics, in various organisms. The transport mechanism often involves symport or antiport with protons and is typically regulated by substrate concentration, pH, and other factors. The MCT family is part of the major facilitator superfamily (MFS) and is characterized by a common structural framework that facilitates the transport activity.
Multifunctional Developmental and Immune Receptor (Dev_Immune_Receptor)
Type: Family

The protein family is involved in a variety of developmental processes, immune responses, and cellular signaling pathways. Members of the family function as cell surface receptors, contributing to neurite outgrowth inhibition, brain development, and axon migration. They also play roles in synapse formation and maintenance in the nervous system, acting as ligands for presynaptic receptors and regulating excitatory synapse development. Some family members are involved in the innate immune response, mediating B-cell activation via lipopolysaccharide interaction. Others modulate chondrocyte differentiation, collagen fibrillogenesis, and bone morphogenetic protein signaling. Additionally, the family includes proteins that regulate TGF-beta activation, influencing microglia function and immune signaling. The family also encompasses proteins that contribute to wound healing, cholesterol homeostasis, and energy expenditure regulation.