SII-SWORD/CoKE huggingface dataset:
Serine/threonine-protein kinase (Ser_Thr_protein_kinase)
Type: Family

The protein family is involved in a wide range of cellular processes, including signal transduction, cell cycle regulation, apoptosis, and immune responses. Members of this family are serine/threonine-protein kinases that act as regulatory links between membrane-associated GTPases and downstream MAPK cascades, determining cell fate decisions such as proliferation, differentiation, and survival. Some family members also have roles in stress responses, apoptosis, and necroptosis, acting as sensors or effectors in these pathways. They are involved in the phosphorylation of various substrates, including MAP kinase kinases, integrins, and histones, influencing pathways like JNK signaling, integrin-mediated signal transduction, and inflammatory responses. The family includes both catalytically active kinases and predicted pseudokinases with regulatory functions.
AAA ATPase domain-containing protein (AAA_ATPase_domain)
Type: Family

This family of proteins is characterized by the presence of AAA ATPase domains, suggesting a role in various cellular processes that require ATP hydrolysis. Members are involved in critical functions such as cell division, growth, protein degradation, vesicle fusion, and organelle biogenesis. They participate in the unfolding of substrate proteins, disassembly of protein complexes, and the regulation of proteasomal degradation pathways. Some proteins in this family are implicated in the endoplasmic reticulum-associated degradation (ERAD) process, ribosome biogenesis, and the response to endoplasmic reticulum stress. They also contribute to the maintenance of protein quality control by mediating the extraction and degradation of misfolded or damaged proteins. Additionally, these proteins play roles in the formation and reassembly of the Golgi apparatus during mitosis, DNA damage response, and autophagy.
Krueppel C2H2-type zinc-finger (Krueppel_C2H2_ZnF)
Type: Family

The Krueppel C2H2-type zinc-finger protein family is characterized by a conserved zinc-finger domain that mediates DNA binding and is involved in transcriptional regulation. Members of this family function predominantly as transcriptional repressors or activators, influencing various biological processes including development, differentiation, apoptosis, and metabolism. Some proteins within this family are known to interact with chromatin-modifying proteins, such as SETDB1 and TRIM28/KAP1, to establish repressive chromatin states. Others are involved in maintaining genomic imprints through DNA methylation. The family also includes proteins that regulate lipid metabolism, neuron death, and retrotransposon repression in embryonic stem cells. The diversity of functions reflects the broad role of Krueppel C2H2-type zinc-finger proteins in gene expression and cellular homeostasis.
tRNA pseudouridine synthase D (TruD_pseudoU_synthase)
Type: Family

The TruD family of pseudouridine synthases is responsible for the post-transcriptional modification of uracil-13 in transfer RNAs (tRNAs) to pseudouridine, a process that contributes to the stability and function of tRNA molecules. Pseudouridine synthases catalyze the isomerization of specific uridine residues in RNA, forming the C-glycoside isomer pseudouridine. This modification is ubiquitous and vital for the proper folding and codon recognition properties of tRNA. Members of the TruD family are characterized by their specific activity towards uracil-13 in tRNAs, playing a crucial role in the maintenance of the translational apparatus and protein synthesis.
Major Facilitator Superfamily (MFS) Transporters (MFS_Transporters)
Type: Family

The protein family is part of the major facilitator superfamily (MFS), which is one of the largest groups of secondary transporters. Members of this family are involved in a variety of functions, including the transport of a wide range of substrates across cell membranes. Specific subfamilies within this group confer resistance to multiple drugs by transporting harmful compounds out of the cell, while others are involved in the uptake of nutrients such as di- and tripeptides through a proton-dependent mechanism. Some members are implicated in the biomineralization process, likely transporting forms of iron, and others may function as antiporters exchanging different cations for protons. The diversity of functions reflects the versatility of the MFS in adapting to various substrates and transport needs within the cell.
SsuD/RutA monooxygenase (SsuD_RutA_monooxygenase)
Type: Family

The SsuD/RutA protein family includes monooxygenases that catalyze diverse desulfonation reactions, crucial for sulfur metabolism and pyrimidine degradation. Members of the SsuD subfamily are involved in the desulfonation of aliphatic sulfonates, converting them into aldehydes and sulfite, thus participating in sulfur compound utilization. The RutA subfamily members are pyrimidine monooxygenases that catalyze the ring opening of pyrimidine between N-3 and C-4 through a unique flavin hydroperoxide-catalyzed mechanism, yielding ureidoacrylate peracid and FMN-N(5)-oxide. This reaction is part of the uracil catabolic pathway and is essential for the regeneration of FMN, which is critical for various cellular processes. The family also includes enzymes like sulfoquinovose monooxygenase, which is involved in the degradation of sulfoquinovose, and dimethylsulfone monooxygenase, which participates in the dimethyl sulfide degradation pathway. These enzymes are characterized by their requirement for FMNH2 or FMN and their specificity for various sulfonated substrates.
ATP-binding cassette transporter C-like (ABC_transporter_C-like)
Type: Family

The ABC transporter C family is involved in various transport activities across cell membranes. Members of this family actively extrude physiological compounds and xenobiotics, contributing to cellular detoxification and multidrug resistance. They transport a wide range of substrates, including glutathione conjugates, cyclic nucleotides, bile acids, steroid conjugates, and drugs. Some members mediate the release of nucleoside triphosphates, playing a role in homeostasis. Others are involved in the regulation of epithelial ion and water transport, fluid homeostasis, and the regulation of pH and ion content in epithelial fluid layers. The family also includes proteins that may function in the secretion of metabolites and in the protection of the producing organism from self-toxicity.
Protocadherin/Cadherin-related Cell Adhesion (Protocadherin/Cadherin-CA)
Type: Family

The Protocadherin/Cadherin-related family is a group of calcium-dependent cell-adhesion proteins that play a crucial role in the establishment and maintenance of specific neuronal connections in the brain. Members of this family are involved in cells self-recognition and non-self discrimination, contributing to the sorting of heterogeneous cell types. They mediate homophilic trans-interactions through their cadherin domains, which bind calcium ions and facilitate adhesion. Some family members also participate in intermicrovillar adhesion, controlling the packing of microvilli at the apical membrane of epithelial cells and contributing to epithelial brush border differentiation. Additionally, certain protocadherins are implicated in synaptic reorganization underlying long-term memory and may be involved in regulating cell migration during developmental processes.
Complex I Subunit 2 (Complex_I_Subunit_2)
Type: Family

The Complex I Subunit 2 family comprises core subunits of the mitochondrial membrane respiratory chain NADH dehydrogenase, also known as Complex I. These proteins are essential for the catalytic activity and assembly of Complex I, which is responsible for the initial step in the mitochondrial electron transport chain. Complex I catalyzes the transfer of electrons from NADH to ubiquinone, a process fundamental to cellular respiration and energy production. Members of this family are believed to be part of the minimal assembly required for catalysis, indicating a conserved role across various species in facilitating efficient electron transfer and contributing to the proton gradient generation across the mitochondrial inner membrane.
LysR-type transcriptional regulator (LTTR)
Type: Family

The LysR-type transcriptional regulator (LTTR) family is a diverse group of proteins that function as transcriptional regulators in bacteria. Members of this family are involved in various cellular processes, including metabolism, virulence, and response to environmental changes. They typically act as activators or repressors by binding to specific DNA sequences near the promoters of target genes, often requiring small molecule coeffectors for activity. The LTTRs control genes related to amino acid metabolism, such as those involved in arginine and lysine pathways, flagellar assembly, and pectinase gene expression. They also regulate their own expression and can influence the expression of virulence factors. The activity of these regulators is modulated by ligand binding, which affects their DNA-binding ability and, consequently, the transcription of associated genes.
Bifunctional lipid A modification and metabolic enzymes (Lipid_A_modif_metabolic_enz)
Type: Family

This family of proteins includes enzymes with bifunctional activities, primarily involved in the modification of lipid A, which is a component of the bacterial outer membrane. The enzymes catalyze the oxidative decarboxylation of UDP-glucuronic acid to UDP-4-keto-arabinose and the addition of a formyl group to UDP-4-amino-4-deoxy-L-arabinose, resulting in UDP-L-4-formamido-arabinose. These modifications are crucial for bacterial resistance to polymyxin and other cationic antimicrobial peptides. Additionally, the family encompasses various dehydrogenases involved in steroid biosynthesis, as well as epimerases/dehydratases that participate in carbohydrate and nucleotide sugar metabolism, contributing to diverse biological processes such as cell wall biosynthesis and steroid hormone production.
AspA/AstE family (AspA/AstE_fam)
Type: Family

The AspA/AstE family is characterized by enzymes that play roles in amino acid metabolism and detoxification. Members of the Succinylglutamate desuccinylase subfamily catalyze the conversion of N(2)-succinylglutamate into succinate and glutamate, a reaction important in the arginine and proline metabolism pathway. The Aspartoacylase subfamily members are involved in the deacetylation of N-acetylaspartic acid (NAA) to produce acetate and L-aspartate, which is significant for maintaining white matter in the brain and acts as a scavenger of NAA in other tissues. Another subfamily includes enzymes that deacetylate mercapturic acids in kidney proximal tubules, playing a role in detoxification.
Transferase hexapeptide repeat (Trans_hexapeptide_repeat)
Type: Family

The transferase hexapeptide repeat family is characterized by its members' ability to catalyze the transfer of acetyl groups from acetyl-CoA to various substrates. Key functions include the biosynthesis of diaminopimelate, an intermediate in lysine biosynthesis, through the acetylation of tetrahydrodipicolinate, and the modification of antibiotics such as chloramphenicol and streptogramin, conferring bacterial resistance. Members of the DapH subfamily are involved in lysine biosynthesis, while others modify UDP-4-amino sugars in glycosylation pathways or inactivate antibiotics. The hexapeptide repeats are a distinctive feature that suggests a common structural fold facilitating the acetyltransferase activity.
RNR Ribonuclease (RNR_Ribonuclease)
Type: Family

The RNR ribonuclease family is characterized by its involvement in RNA processing and degradation. Members of this family exhibit 3'-5' exoribonuclease activity, releasing 5'-nucleoside monophosphates and participating in the maturation of structured RNAs such as rRNA, snRNA, snoRNA, and mRNAs. Some family members are implicated in mRNA degradation by hydrolyzing single-stranded polyribonucleotides processively from the 3' to 5' direction. Others are part of the RNA exosome complex, contributing to cellular RNA processing and degradation events, including the turnover of unstable mRNAs and surveillance pathways to prevent translation of aberrant mRNAs. Certain subfamilies, such as DIS3L2, specialize in recognizing and degrading polyuridylated RNAs, playing roles in cell proliferation and mitosis. The family's function is essential for maintaining RNA stability and integrity, ensuring proper gene expression and cellular homeostasis.
Cold shock domain-containing protein (Cold_shock_domain)
Type: Family

This family of proteins is associated with cellular responses to cold shock and includes factors that bind to DNA and RNA. Members are involved in various processes such as transcriptional activation, mRNA stabilization, translational repression, and DNA repair. They often recognize and bind specific nucleotide motifs and play roles in the regulation of gene expression under cold stress conditions. Some proteins within this family can also affect cell viability at low temperatures, inhibit DNA replication, and contribute to persister cell formation. Additionally, certain members are implicated in the sorting of RNAs within exosomes, potentially influencing RNA stability and intercellular communication.
Cytochrome P450 family 2 (Cytochrome_P450_fam2)
Type: Family

The Cytochrome P450 2 family comprises enzymes involved in the metabolism of fatty acids, steroids, retinoids, and xenobiotics. They function as monooxygenases, catalyzing the insertion of one oxygen atom from molecular oxygen into substrates, while reducing the second oxygen atom to water, using electrons from NADPH via cytochrome P450 reductase. Members of this family exhibit diverse substrate specificities, including hydroxylation of carbon-hydrogen bonds, epoxidation of double bonds, and metabolism of arachidonic acid and its conjugates. They are implicated in the synthesis of bile acids and steroid hormones, activation of vitamin D precursors, and the oxidative metabolism of various endogenous compounds and drugs. Some members also possess peroxidase and isomerase activities, modulating eicosanoid signaling and contributing to the breakdown of prostaglandins. The family plays a role in the regulation of physiological processes and the detoxification of potentially harmful substances.
Disulfide bond formation protein B (DsbB)
Type: Family

The DsbB family is involved in the formation of disulfide bonds in periplasmic proteins, which is a crucial post-translational modification for protein folding and stability. Members of this family function by oxidizing the DsbA protein, which in turn forms disulfide bonds in substrate proteins. Some members, classified under the DsbI subfamily, are part of a redox system with DsbL, mediating the formation of essential disulfide bonds in specific target proteins such as AssT. The activity of DsbB is essential for the proper functioning of various proteins, including enzymes like PhoA and structural proteins like OmpA. The redox state of the periplasm, influenced by DsbB, can also affect regulatory pathways, such as the PhoP-regulated transcription pathway.
Ubiquitin carboxyl-terminal hydrolase (Ub_carboxyl-term_hydrolase)
Type: Family

The ubiquitin carboxyl-terminal hydrolase family, also known as deubiquitinating enzymes (DUBs), plays a crucial role in various cellular processes by cleaving ubiquitin from ubiquitinated proteins, thus regulating protein turnover and preventing degradation. Members of this family are involved in cell cycle regulation, DNA repair, transcriptional regulation, autophagy, and signal transduction. They exhibit specificity for different ubiquitin linkages and substrates, including histones, signaling receptors, and structural proteins, thereby influencing pathways such as NF-kappa-B activation, TGF-beta receptor signaling, and the spindle assembly checkpoint. Their activities contribute to the maintenance of protein homeostasis, genomic stability, and cellular response to stress and damage.
Triose Phosphate/Phosphate Translocator (TPT_transporter)
Type: Family

The TPT transporter family is involved in the transport of various substances across cellular membranes. Members of this family function as nucleotide-sugar transporters, facilitating the import of nucleotide-sugars such as GDP-mannose, UDP-glucose, and UDP-galactose into the Golgi lumen or endoplasmic reticulum. These transport processes are essential for the synthesis of glycoproteins, glycolipids, and oligosaccharides, impacting cell wall composition, glycosylation, and other cellular functions. Some family members also transport sugar phosphates like triose phosphates, phosphoenolpyruvate, and glucose-6-phosphate, playing roles in photosynthesis, carbon fixation, and metabolic pathways. The family includes antiporters specific for GDP-fucose, which are involved in fucosylation processes essential for cell signaling and development. Overall, the TPT transporter family is crucial for various biosynthetic pathways and cellular homeostasis.
Lipid Phosphate Formation and Regulation (Lipid_Phosphate_FormReg)
Type: Family

The protein family is involved in the phosphorylation of various lipids, acting as lipid kinases with a range of specificities and functions. Members of the family catalyze the formation of lipid phosphates such as sphingosine-1-phosphate, dihydrosphingosine 1-phosphate, phosphatidic acid, and ceramide 1-phosphate, which play roles in cell signaling, proliferation, apoptosis, stress response, and membrane trafficking. Some family members also possess acetyltransferase activity and are involved in epigenetic regulation and inflammatory responses. The family includes sphingosine kinases, diacylglycerol kinases, ceramide kinases, and other lipid kinases with unidentified substrates. These enzymes are key in lipid metabolism and are implicated in various cellular processes, including the production of lipoteichoic acid, mitochondrial protein import, and the regulation of programmed cell death in plants.
RluA Pseudouridine Synthase (RluA_PseudoU_synthase)
Type: Family

The RluA family of pseudouridine synthases is responsible for the isomerization of specific uridine residues to pseudouridine in various RNA molecules, a modification that can influence RNA stability, folding, and function. Members of the family exhibit substrate specificity for different types of RNA, including ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA). They play crucial roles in the assembly and function of ribosomes, the translation of mitochondrial mRNAs, and the regulation of mRNA splicing. The family includes enzymes with dual-specificity that modify both rRNA and tRNA, as well as those that target mitochondrial RNAs or function in the nucleus to modify pre-mRNAs. This post-transcriptional modification is essential for maintaining the proper structure and function of the RNA molecules and, consequently, for the accurate translation of the genetic code.
Major Facilitator Superfamily Efflux Transporters (MFS_Efflux_Transporters)
Type: Family

The Major Facilitator Superfamily (MFS) Efflux Transporters family is involved in the active transport of a variety of substrates across cellular membranes. Members of this family play crucial roles in the efflux of diverse compounds, including purine ribonucleosides (such as inosine and guanosine), sugars, and antibiotics like chloramphenicol. The transporters contribute to various physiological functions, such as maintaining intracellular concentration of sugars, conferring resistance to toxic compounds, and protecting cells against toxic purine base analogs. Some family members are implicated in quinolone resistance, functioning as efflux pumps for hydrophilic quinolones. The family belongs to the major facilitator superfamily and includes several subfamilies, such as NepI, MdtL, SotB, and PbuE, each with specific substrate preferences and roles in bacterial metabolism and defense mechanisms.
UPF0213 domain-containing protein (UPF0213_domain)
Type: Family

This family of proteins is characterized by the UPF0213 domain. The specific functions of these proteins are not well-defined, but they are widespread in bacteria and archaea, suggesting a conserved role in cellular processes. Proteins in this family may be involved in various cellular functions, but without additional experimental data, their precise biological roles remain speculative. The UPF0213 domain itself does not provide sufficient information to predict specific functions, and further research is needed to elucidate the activities and mechanisms of these proteins in the cell.
ATP-dependent DNA ligase (ATP-dep_DNA_ligase)
Type: Family

The ATP-dependent DNA ligase family is characterized by its members' ability to catalyze the joining of DNA strands to facilitate the repair of single and double-stranded breaks. This enzymatic activity is crucial during DNA replication, recombination, and repair processes. Members of this family are known to interact with other DNA repair proteins, such as XRCC1, and may have additional domains like the PARP-type zinc finger required for ligase activity. Some variants can use alternative nucleotides like ADP or NAD(+) and may be regulated by factors such as PCNA or inhibited by certain ions or conditions. This family plays an essential role in maintaining genomic integrity across various organisms, including bacteria, archaea, and eukaryotes.
Nickel-responsive transcriptional regulator (CopG/NikR_regulator)
Type: Family

The CopG/NikR family of transcriptional regulators is involved in the response to intracellular nickel concentrations. Members of this family function as transcriptional repressors or regulators, with some specifically repressing the nikABCDE operon when intracellular nickel levels are excessive. This operon is typically associated with nickel uptake and transport, suggesting a role for these regulators in metal ion homeostasis. The activity of these proteins is indicative of a metal-dependent regulatory mechanism, where binding of nickel ions likely induces conformational changes that affect DNA binding and transcriptional repression.
Plant Cytochrome P450 71 (Cytochrome_P450_71)
Type: Family

The Cytochrome P450 71 family is involved in a diverse array of biosynthetic processes for plant secondary metabolites, including the production of phytoalexins, alkaloids, and other compounds with roles in plant defense, flavor formation, and potential pharmaceutical applications. Members of this family are heme-thiolate monooxygenases that catalyze various oxidation reactions, such as hydroxylations, epoxidations, and aromatizations. These enzymes contribute to the synthesis of compounds like thymol, carvacrol, parthenolide, menthol, and coumarins, which have antimicrobial, anticancer, and other bioactive properties. The family's broad substrate specificity reflects its adaptation to different ecological niches and plant species.
Glycosyltransferase group 1 (Glycosyltransferase_grp1)
Type: Family

The glycosyltransferase group 1 family is involved in various biosynthetic pathways across different organisms, catalyzing the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Members of this family play crucial roles in the synthesis of important biological molecules such as mycothiol, a major redox buffer protecting bacteria against oxidative stress and antibiotics, and capsular polysaccharides, which are essential for bacterial virulence and biofilm formation. They are also involved in the production of lipopolysaccharides and exopolysaccharides, contributing to bacterial pathogenicity and environmental adaptability. Additionally, they participate in the biosynthesis of glycolipids and glycoproteins, impacting cell membrane structure and protein function.