SII-SWORD/CoKE huggingface dataset:
Glycosyl Hydrolase Family 16 (Glycosyl_Hydrlase_16)
Type: Family

The glycosyl hydrolase 16 family is involved in the hydrolysis of glycosidic bonds in complex carbohydrates. Members of this family play diverse roles, including the degradation of cellulosic substrates, the cleavage of beta-1,4-linkages in agarose, and the recognition of microbial cell wall components by the immune system. Some proteins within the family act as extracellular glycosidases important in fungal pathogenesis, cell wall assembly, and regeneration. Others are involved in innate immune responses, binding to specific polysaccharides like beta-1,3-glucan to activate defense cascades. Additionally, the family includes enzymes that degrade sulfated polysaccharides such as porphyran and kappa-carrageenan. The broad substrate specificity and functional diversity highlight the family's role in both microbial metabolism and host defense mechanisms.
DEAD box ATP-dependent RNA helicases (DEAD_box_RNA_helicases)
Type: Family

The DEAD box helicase family is characterized by its involvement in various RNA metabolic processes including ribosome biogenesis, mRNA degradation, and translation initiation. Members of this family are ATP-dependent RNA helicases that unwind double-stranded RNA in both 5'- and 3'-directions and exhibit RNA-dependent ATPase activity. They play roles in cellular responses to environmental stresses such as cold, oxidants, and pH changes. Some subfamilies are implicated in the assembly of ribosomal subunits and may work in conjunction with cold shock proteins. Others are involved in CRISPR immunity, acting as endonucleases and helicases. The family includes subfamilies such as CshA, CshB, DbpA, DeaD/CsdA, and DDX21/DDX50, each with specific functions and regulatory mechanisms.
Polycomb group and chromatin remodeling factors (PcG_chromatin_remod_factors)
Type: Family

This family of proteins includes Polycomb group (PcG) components and related factors that are involved in chromatin remodeling and transcriptional repression. They play a crucial role in maintaining the repressive state of genes, including homeotic genes, throughout development. Members of this family are characterized by their ability to recognize and bind specific methylated lysine residues on histone proteins, acting as 'readers' of post-translational modifications. This binding can lead to chromatin compaction and gene silencing. Some members also participate in DNA damage repair by promoting homologous recombination. Additionally, they may be involved in cell proliferation, differentiation, and the regulation of ubiquitin-dependent protein degradation. The family includes proteins with MBT repeats, SAM domains, and other domains that contribute to their function in gene regulation and chromatin structure.
Major Facilitator Superfamily Trehalose Transporter (MFS_Trehalose_Transporter)
Type: Family

The Major Facilitator Superfamily (MFS) Trehalose Transporter subfamily consists of proteins that function primarily as facilitative transporters for trehalose, a disaccharide sugar. Members of the family mediate the bidirectional transfer of trehalose across cell membranes, without transporting other sugars such as maltose, sucrose, or lactose. These transporters are responsible for the distribution of trehalose synthesized in the fat body to other tissues, which is crucial for regulating trehalose levels in the hemolymph and providing a carbon source for cellular metabolism. Some members within the family have been identified as high-capacity transporters, while others have low-capacity transport capabilities. Additionally, there are homologs that fail to transport trehalose, suggesting a potential divergence in function or regulation within the family.
SEC23/SEC24 family, SEC24 subfamily (SEC23_SEC24_subfamily)
Type: Family

The SEC23/SEC24 family, specifically the SEC24 subfamily, comprises proteins that are integral components of the coat protein complex II (COPII). These proteins are involved in the formation of transport vesicles from the endoplasmic reticulum (ER). The primary functions of the SEC24 subfamily include facilitating the physical deformation of the ER membrane to form vesicles and selecting cargo molecules for transport to the Golgi apparatus. The SEC24 proteins play a central role in cargo selection within the COPII complex, with some members showing specificity for certain cargo motifs or types, such as GPI-anchored proteins or those containing cytoplasmic DxE or LxxLE motifs. The SEC24 subfamily is essential for the maintenance of the early secretory pathway and has implications in various cellular processes, including viral infection, cell size patterning, and development of male gametophytes.
Plant Fructan Metabolism Enzymes (Fructan_Metab_Enzymes)
Type: Family

The glycosyl hydrolase 32 family is involved in the hydrolysis and synthesis of fructans, which are fructose-based polymers found in plants. Members of this family function as enzymes that break down various types of fructans, including inulin-type beta-(2,1)-fructans and levan-type beta-(2,6)-linked fructans, into fructose units. Some enzymes within this family also exhibit transferase activity, contributing to fructan biosynthesis by catalyzing the production of fructan oligosaccharides from sucrose. These activities are essential for plant processes such as sucrose partitioning during seed development, stress response, and the mobilization of sucrose to sink organs. The family includes fructan exohydrolases, beta-fructofuranosidases, and fructosyltransferases, which are regulated by various factors, including sucrose inhibition.
LacD aldolase (LacD_aldolase)
Type: Family

The LacD aldolase family consists of enzymes that catalyze the cleavage and formation of specific sugar phosphates. Members of this family are known to function as tagatose 1,6-diphosphate aldolases, which are involved in carbohydrate metabolism, particularly in the Leloir pathway for galactose catabolism. Some members, identified as sulfofructosephosphate aldolases, specifically cleave 6-deoxy-6-sulfo-D-fructose 1-phosphate (SFP) to produce dihydroxyacetone phosphate (DHAP) and 3-sulfolactaldehyde (SLA). These enzymes can also catalyze the reverse reaction, demonstrating their role in both the breakdown and synthesis of sugar phosphates. The LacD aldolase family is characterized by its ability to perform these reactions, which are essential for the utilization and conversion of various sugars within bacterial metabolic pathways.
Thioredoxin family ResA/DsbE subfamily (Thioredoxin_ResA/DsbE_sf)
Type: Family

The thioredoxin family ResA/DsbE subfamily consists of thiol-disulfide oxidoreductases that play a crucial role in the synthesis of c-type cytochromes. Members of this family are involved in reducing disulfide bonds in apocytochrome c, which is a necessary step before heme can be covalently attached. Some proteins within this family may also participate in the formation of disulfide bonds in periplasmic proteins or act as disulfide oxidoreductases in the biogenesis of cytochromes c. Additionally, certain members are implicated in sporulation and redox reactions through reversible oxidation of their active center dithiol to a disulfide, catalyzing dithiol-disulfide exchange reactions.
Methionine Synthase/Corrinoid (Met_Synthase/Corrinoid)
Type: Family

The Methionine Synthase and Corrinoid Protein family encompasses enzymes that are involved in the transfer of methyl groups in various biological processes. Methionine synthases catalyze the transfer of a methyl group from methyl-cobalamin or methyltetrahydrofolate to homocysteine, producing methionine, an essential amino acid. These enzymes are modular, containing distinct domains for substrate binding and activity, including the Hcy-binding, pterin-binding, B12-binding, and AdoMet activation domains. Other family members act as methyl group carriers in methanogenesis and the degradation of quaternary amines, transferring methyl groups between different proteins or to tetrahydrofolate, contributing to carbon dioxide fixation or anaerobic respiration. The family is characterized by the presence of corrinoid prosthetic groups and is involved in pathways such as the Wood-Ljungdahl pathway and the metabolism of various amine compounds.
Bacterial Solute-Binding Protein 2 (Bact_Solute-Bind_Prot2)
Type: Family

The bacterial solute-binding protein 2 family includes periplasmic proteins that function primarily in chemotaxis and transport systems. Members of the family are involved in high-affinity uptake systems, binding various sugars and autoinducer 2 (AI-2) molecules. They are part of ABC transporter complexes, delivering ligands to permeases for import into the cell. Some proteins within the family also play roles in transcriptional induction of genes in response to specific signals, such as plant-derived monosaccharides, and do not interact with transport systems. The family is characterized by a calcium-binding site similar to EF-hand proteins, which is essential for their sugar-binding function.
Type II toxin-antitoxin system RNase (Type_II_TA_system_RNase)
Type: Family

The PINc/VapC protein family consists of toxic components of type II toxin-antitoxin (TA) systems, functioning primarily as ribonucleases (RNases). Members of the family are involved in various cellular processes including plasmid stability, bacterial cell trafficking, and post-transcriptional regulation of metabolism. They exhibit sequence-specific endoribonuclease activity, targeting ssRNA and sometimes tRNA, leading to inhibition of translation and cell growth when overexpressed. The toxicity of these proteins is counteracted by their cognate antitoxins, which neutralize their RNase activity. Some family members are implicated in inducing host cell death upon bacterial cell lysis during infection. The TA systems may play roles in monitoring the nutritional supply and physiological state of the cell, linking catabolic and anabolic reactions, and contributing to bacterial dormancy under stress conditions.
RTX toxin and mannuronan C5-epimerase (RTX_toxin/Mannuronan_C5-epim)
Type: Family

This family of proteins includes a variety of bacterial exotoxins that share a common feature in their structure, a Gly-rich region implicated in calcium binding. These proteins are involved in targeting host cells and disrupting their normal function, often by forming pores in the cell membrane, leading to cell lysis. Some members of this family are bifunctional, possessing additional enzymatic activities such as adenylate cyclase activity, which can interfere with host cell signaling pathways. The toxins are typically associated with virulence and contribute to the pathogenicity of the bacteria by damaging host tissues and evading the immune response. Other members of the family are involved in the modification of specific biopolymers, contributing to the formation of structures necessary for bacterial survival.
Phosphotransferase System Sugar-Specific Components (PTS_Sugar-Specific_Components)
Type: Family

The Phosphoenolpyruvate-dependent Sugar Phosphotransferase System (PTS) is a major carbohydrate active transport system that catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The PTS is involved in the transport of various sugars including beta-glucosides, sucrose, trehalose, N-acetylmuramic acid, and MurNAc-GlcNAc. It consists of multiple domains: EIIC forms the translocation channel with a substrate-binding site; EIIB is phosphorylated by phospho-EIIA on a cysteinyl or histidyl residue, depending on the sugar, and transfers the phosphoryl group to the sugar substrate; EIIA is phosphorylated by phospho-HPr on a histidyl residue and transfers the phosphoryl group to EIIB. The system plays a key role in the uptake and phosphorylation of sugars, facilitating their utilization as carbon and energy sources, and is involved in the regulation of various cellular processes.
Phosphopantetheinyl Transferase Superfamily (P-Pant_transferase_sf)
Type: Family

The P-Pant transferase superfamily, specifically the AcpS and Gsp/Sfp/HetI/AcpT families, consists of enzymes that play a crucial role in the activation of carrier proteins involved in various biosynthetic pathways. These enzymes transfer the 4'-phosphopantetheine moiety from coenzyme A to a serine residue on acyl-carrier-proteins (ACPs) or peptidyl-carrier proteins (PCPs). This post-translational modification is essential for converting inactive apo-carrier proteins into their active holo-forms, enabling them to carry acyl groups for fatty acid synthesis, as well as for the production of polyketides, nonribosomal peptides, and other secondary metabolites. The modification is also necessary for the function of proteins involved in the synthesis of lysine and other metabolites, playing a significant role in growth, development, and the production of antibiotics and pigments. The family's enzymes are also implicated in virulence and are inhibited by various antifungal compounds.
Transcription factors Myb-like (MYB_TF)
Type: Family

The Myb family of transcription factors is characterised by their ability to bind specific DNA sequences and regulate gene expression across a variety of biological processes. Members of the Myb family are involved in the control of cell proliferation, differentiation, and development in both plants and animals . In plants, they play crucial roles in secondary cell wall biosynthesis, cell cycle regulation, auxin response, abiotic stress response, and reproductive development . In animals, they are key regulators of hematopoietic progenitor cell proliferation and differentiation, male meiosis, and germline integrity . Some members act as transcriptional activators, while others function as repressors. The family is also implicated in the regulation of metabolic pathways and response to environmental stimuli.
Protein Tyrosine Phosphatase (PTP)
Type: Family

The protein tyrosine phosphatase family is involved in various cellular processes including cell cycle regulation, cell proliferation, motility, and invasive activity. Members of this family have dual specificity, dephosphorylating proteins with phosphotyrosine or phosphoserine residues. They play roles in mitotic progression, particularly the G1 to S phase transition, and are implicated in cancer metastasis and cardiac hypertrophy. Some members are involved in cytokinesis, chromosome segregation, and spindle assembly. Others have functions in cilia formation and maintenance, and in the DNA damage response, acting as regulators of checkpoints and promoting exit from mitosis. The family includes non-receptor class CDC14 subfamily members, which are essential for coordinating nuclear division with cytokinesis and are involved in transcription regulation of ribosomal genes.
FAD-dependent monooxygenase, fungal (FAD_mOase_fung)
Type: Family

This FAD-dependent monooxygenase family consists of enzymes involved in the biosynthesis of various fungal secondary metabolites, including meroterpenoids, indole-diterpenes, and polyketides. These metabolites often exhibit bioactive properties such as mycotoxicity, immunosuppression, and inhibition of mammalian ion channels or enzymes. Family members catalyse critical oxidation steps, including epoxidation, hydroxylation, and oxidative rearrangements, which are essential for constructing complex molecular architectures and functional groups. The versatility of these enzymes allows for the generation of diverse metabolites through regio- and stereo-specific modifications, contributing to the metabolic richness of fungal species .
4-hydroxybenzoyl-CoA thioesterase (4-hydroxybenzoyl-CoA_TE)
Type: Family

The 4-hydroxybenzoyl-CoA thioesterase family is involved in diverse metabolic processes, including the biosynthesis of phylloquinone (vitamin K1) and fatty acids. Members of the family exhibit hydrolase activity, catalyzing the cleavage of thioester bonds in various substrates. Some enzymes specifically hydrolyze 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) in the vitamin K1 biosynthetic pathway, while others are involved in phospholipid metabolism or the production of medium to long-chain fatty acids and beta-keto fatty acids. These fatty acids may contribute to processes such as cuticular wax synthesis, suberin biosynthesis, and the development of floral organs. The family includes enzymes with specificity for acyl-ACP substrates and others that act on acyl-CoA thioesters with varying chain lengths and degrees of saturation.
F420-dependent glucose-6-phosphate dehydrogenase/mer (F420-G6PD/mer)
Type: Family

The F420-dependent glucose-6-phosphate dehydrogenase family encompasses enzymes that catalyze the oxidation of glucose 6-phosphate (G6P) to 6-phosphogluconolactone, utilizing the coenzyme F420. This reaction is a key step in the pentose phosphate pathway, which provides reducing power and precursors for nucleotide synthesis. Members of this family are also involved in the bioreductive activation of prodrugs, such as the anti-tuberculosis drug PA-824, by supplying reduced F420 to other enzymes. Additionally, these enzymes play a role in mycobacterial resistance to oxidative stress by consuming G6P. The family includes the mer subfamily, which comprises enzymes like phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase, involved in the biosynthesis of complex lipids in mycobacteria, contributing to their virulence and cell wall structure.
Acyl-protein thioesterase 1-2/Carboxylesterase-like (LYPA1-2/EST-like)
Type: Family

This family of proteins includes enzymes that exhibit a variety of hydrolytic activities, primarily acting on ester bonds. Acyl-protein thioesterase 1/2 are involved in the hydrolysis of fatty acids from S-acylated cysteine residues in proteins, a process known as depalmitoylation, which is important for the regulation of protein localization and function . Some proteins within this family show a preference for palmitoylated G-alpha proteins as substrates. Lysophospholipase-like protein 1 is a palmitoyl thioesterase that catalyses depalmitoylation of CGAS and KCNMA1, acting as a regulator of innate immunity . Other members display broader substrate specificity, including carboxylesterase activity, which may be involved in the degradation of various compounds, such as Carboxylesterase SOBER1 from Arabidopsis thaliana, which functions as a negative regulator of the hypersensitive response (HR) triggered by the bacterial type III effector protein AvrBsT . The activities of these proteins are essential for diverse biological processes, including signal transduction, lipid metabolism, and the regulation of protein modifications.
Deoxyribonucleoside Kinase (Deoxyribonucleoside_kinase)
Type: Family

This family of proteins includes enzymes that are involved in the salvage pathway of nucleotide synthesis. They are responsible for the phosphorylation of deoxyribonucleosides, which is a critical step in the generation of deoxyribonucleotide triphosphates (dNTPs) necessary for DNA replication and repair. Members of this family exhibit a range of substrate specificities, with some phosphorylating purine deoxyribonucleosides and others pyrimidine deoxyribonucleosides. Additionally, certain members are known to phosphorylate nucleoside analogs, which are compounds used as antiviral and chemotherapeutic agents.
Mitochondrial Carrier (Mitochondrial_Carrier)
Type: Family

This family of proteins is involved in the transport of various metabolites, nucleotides, and cofactors across the mitochondrial inner membrane. Members of this family function as carriers, facilitating the exchange of substances such as carnitine, acylcarnitines, amino acids, and NAD(+), among others. They play essential roles in metabolic processes including the urea cycle, fatty acid beta-oxidation, amino acid degradation, and mitochondrial energy metabolism. Some members are also implicated in maintaining tissue differentiation, magnesium homeostasis, and mitochondrial protein synthesis. The transport mechanisms include both counter-exchange and uniport, and are regulated by various inhibitors.
Transcription/DNA replication regulator (Transcr_DNA_Rep_Reg)
Type: Family

The protein family is involved in various aspects of transcriptional regulation and DNA replication. Members of the family function as components of larger complexes that interact with DNA and transcription factors to modulate gene expression . Some members, like Nuclear transcription factor Y subunit gamma, recognise specific DNA motifs, such as the CCAAT box, and are involved in the activation or repression of gene transcription. Others participate in chromosomal DNA replication, contributing to the synthesis of DNA strands and ensuring replication fidelity through proofreading exonuclease activity. The family also includes proteins that regulate the accessibility of chromatin by promoting nucleosome sliding, thus facilitating transcription and DNA repair. Overall, the family plays critical roles in maintaining cellular functions by regulating the expression of genes and ensuring the accurate replication of the genome.
Trace Amine-Associated Receptor (TAAR)
Type: Family

The Trace Amine-Associated Receptor (TAAR) family includes G-protein coupled receptors that are predominantly expressed in the olfactory epithelium. They are known to bind trace amines, which are biogenic amines found in very low concentrations in mammalian tissues. While some TAARs are orphan receptors with unknown ligands, others are activated by specific trace amines such as beta-phenylethylamine, p-tyramine, octopamine, tryptamine, and trimethylamine. These receptors are implicated in various physiological functions, including olfaction and the detection of social cues. The exact roles of TAARs in vertebrates remain speculative, but they are thought to be involved in neurotransmission and innate behavioral responses.
Bacterial cell wall metabolism enzyme (Cell_wall_metabolism_enzyme)
Type: Family

This family of proteins includes enzymes involved in bacterial cell wall metabolism. Members of this family function as murein hydrolase activators, endopeptidases, and transglycosylases. They play roles in cell division by activating cell wall hydrolases for septal murein cleavage and daughter cell separation. Some act on polyglycine interpeptide bridges in the peptidoglycan layer, facilitating cell wall expansion, remodeling, and autolysis. Others are involved in the maturation of the spore cortex peptidoglycan or in the degradation of host proteins like elastin, contributing to pathogenicity. The family includes proteins with peptidase M23B domain known for lysostaphin-like endopeptidase activity, and some members are implicated in virulence as they may degrade host tissues or participate in immune evasion.
Class-IV Pyridoxal-Phosphate-Dependent Aminotransferase (Class-IV_PLP-Dep_Aminotrnsfr)
Type: Family

The Class-IV Pyridoxal-Phosphate-Dependent Aminotransferase family comprises enzymes that catalyze the transfer of amino groups from amino acids to alpha-keto acids via a ping-pong mechanism. Members of this family are involved in the metabolism of branched-chain amino acids such as leucine, isoleucine, and valine, as well as D-amino acids including D-alanine, D-leucine, D-aspartate, D-glutamate, D-aminobutyrate, D-norvaline, and D-asparagine. These enzymes play crucial roles in processes such as the synthesis of bacterial cell wall components and the biosynthesis of p-aminobenzoate (PABA), a precursor of tetrahydrofolate. The family includes both specific branched-chain-amino-acid aminotransferases and D-alanine aminotransferases, as well as multifunctional enzymes with aminodeoxychorismate lyase activity, contributing to folate biosynthesis.