SII-SWORD/CoKE huggingface dataset:
UPF0194 membrane-associated transport protein (UPF0194_transport)
Type: Family

This family of proteins includes members that are putatively involved in transport processes, possibly as components of efflux systems. Some proteins within this family may play a role in providing resistance or protection against certain environmental stressors or toxic compounds. For example, one member is implicated in a multi-component transporter system that confers protection against a specific killing factor. Another member is suggested to influence sensitivity to an antibiotic. However, the precise functions of most proteins in this family remain uncharacterized, and further research is needed to elucidate their biological roles.
Diverse Carboxylesterases and Gibberellin Receptors (Carboxylest/Gibb_receptor)
Type: Family

The protein family is characterized by enzymes that predominantly exhibit carboxylesterase activity, acting on various esters with differing acyl chain lengths. Members of the family are involved in diverse biological processes, including the biosynthesis of mycotoxins such as sterigmatocystin and aflatoxins, the formation of plant defense chemicals like tulipalins, and the metabolism of xenobiotic compounds. They play roles in the biosynthesis of phytohormones and monoterpenoid indole alkaloids, and in lipid metabolism by hydrolyzing triglycerides. Some family members also function as receptors for the plant hormone gibberellin, mediating growth and development responses. The family includes lactone-forming carboxylesterases that catalyze intramolecular transesterifications, and enzymes involved in the detoxification and degradation of plant-produced benzoxazolinones.
Leucine-rich repeat and fibronectin type-III domain-containing (LRFN)
Type: Family

The LRFN family proteins are involved in various cellular processes, primarily related to neural development and function. They act as cell adhesion molecules, mediating homophilic cell-cell adhesion in a calcium-independent manner, and are crucial for neurite outgrowth in hippocampal neurons. Members of this family are also implicated in the regulation and maintenance of excitatory synapses, often inducing the clustering of postsynaptic proteins. Some LRFN proteins enhance the cell surface expression of NMDA receptor subunits and may influence the redistribution of synaptic proteins to the cell periphery. The presence of a PDZ-binding motif in some family members suggests a role in protein-protein interactions at synapses. Additionally, certain LRFN proteins may have roles in axon guidance, phototransduction, and craniofacial and inner ear morphogenesis. The family includes proteins with leucine-rich repeat and fibronectin type III domains, which are characteristic structural features contributing to their functions.
Larval/pupal cuticle protein (Cuticle_Struct_Prot)
Type: Family

The cuticle protein family is comprised of structural proteins that are integral components of the exoskeleton in various arthropods, including insects, spiders, and ticks . These proteins are involved in the formation and stabilization of the cuticle, which serves as a protective layer and plays a crucial role in arthropod development and morphology. Members of the family are found in different stages of the life cycle, such as larval, pupal, and adult stages, and are associated with specific parts of the cuticle, including the endocuticle and the rigid cuticle. Some proteins within the family have been identified to bind chitin, suggesting a direct role in cuticle rigidity and structure. The family's proteins are essential for the proper differentiation of cuticular structures and may interact with epidermal cells to form stable cuticular layers that are critical for the arthropod's survival and adaptability.
Bacterial Diguanylate Cyclase (Diguanylate_Cyclase)
Type: Family

The Diguanylate Cyclase (DGC) family is responsible for the synthesis of cyclic-di-GMP (c-di-GMP), a bacterial second messenger that regulates cell surface-associated traits such as biofilm formation, cellulose production, and motility. Members of the family typically contain a GGDEF domain that catalyzes the condensation of two GTP molecules to form c-di-GMP. Some members are also involved in signal transduction pathways and may possess additional domains for sensory functions, such as oxygen sensing through a globin-fold domain. The activity of these enzymes can be regulated by various mechanisms, including allosteric inhibition by c-di-GMP itself, phosphorylation, or interaction with other proteins. The DGC family plays a crucial role in the transition between different bacterial lifestyles, impacting both environmental persistence and host-pathogen interactions.
Type IV Pilus and Type II Secretion System Core (T4P/T2SS_Core)
Type: Family

This family of proteins includes major and minor components of type IV pili (T4P) and type II secretion system (T2SS) core proteins. The T4P components are involved in functions such as twitching motility, cellular adherence, microcolony formation, resistance to neutrophil-mediated killing, and DNA uptake during transformation. They are essential for the assembly of pili, which are filamentous structures that extend and retract from the bacterial surface, facilitating movement and host interactions. The T2SS core proteins are pseudopilins that polymerize to form the pseudopilus, a structure required for the secretion of extracellular factors like proteases and toxins from the periplasm. These proteins are crucial for bacterial virulence and adaptation to various environments.
AB hydrolase (AB_hydrolase)
Type: Family

This family of proteins includes enzymes that are part of the AB hydrolase superfamily. Members of this family are involved in various biological processes, including pyrimidine catabolism, where they may facilitate the hydrolysis of carbamate, a reaction that can occur spontaneously. Some proteins within this family have been implicated in the biosynthesis of antibiotics, such as chlorotetracycline and anthracyclines, which exhibit high cytotoxicity and are used in cancer chemotherapy. They may also have roles in oxidative stress defense by detoxifying peroxoacids. Additionally, certain members exhibit esterase, lipase, and perhydrolase activities, and are capable of halogenating organic compounds in the presence of halides and hydrogen peroxide.
Anthranilate Synthase/Amidotransferase (Anth_synth/Amidotransfase)
Type: Family

The Anthranilate Synthase/Amidotransferase family is involved in the biosynthesis of anthranilate and 4-amino-4-deoxychorismate (ADC), which are intermediates in the production of L-tryptophan, p-aminobenzoate (PABA), and tetrahydrofolate. The family includes heterotetrameric and heterodimeric complexes that catalyze a two-step reaction. The first step involves a glutamine amidotransferase activity provided by the beta subunit, generating ammonia from glutamine. This ammonia, along with chorismate, is used in the second step, catalyzed by the alpha subunit, to produce anthranilate or ADC. Some members also possess additional enzymatic activities, such as indole-glycerolphosphate synthase and phosphoribosylanthranilate isomerase, contributing to multifunctional proteins in tryptophan biosynthesis. The family is subject to feedback inhibition by tryptophan and can be involved in auxin production and virulence factor synthesis in certain species.
Alpha-2-macroglobulin/Complement system (A2M/Complement_sys)
Type: Family

The alpha-2-macroglobulin family includes protease inhibitors that use a unique 'trapping' mechanism to inhibit all four classes of proteinases. Members contain a bait region with specific cleavage sites for different proteinases. Upon cleavage, a conformational change traps the proteinase, reducing its activity against high molecular weight substrates while remaining active against smaller substrates. A thioester bond is hydrolyzed post-cleavage, allowing covalent binding to the proteinase. Some family members play roles in the immune response by binding pathogens and mediating clearance through lysis or melanization. Others are involved in the complement system, acting as non-enzymatic components of C3 and C5 convertases, or as mediators of local inflammatory processes. The family also includes complement components that are central to the complement system activation and function in chronic inflammation as chemoattractants for neutrophils.
Helicase Hel308/SKI2-like (Hel308_SKI2-like)
Type: Family

The Helicase Hel308/SKI2 family includes ATP-dependent DNA and RNA helicases involved in various cellular processes such as DNA repair, ribosome quality control (RQC), and pre-mRNA splicing . Members of the Hel308 subfamily primarily function in the 3'-5' unwinding of DNA at stalled replication forks, contributing to the repair mechanism. They exhibit DNA-dependent ATPase activity and may also process branched DNA structures like Holliday junctions. The SKI2 subfamily members are implicated in the RQC pathway, resolving stalled ribosomes during problematic translation, and play a role in pre-mRNA splicing as part of the spliceosomal complex. This family also includes helicases involved in homology-driven double-strand break (DSB) repair, such as unwinding DNA for microhomology-mediated end-joining (MMEJ) and other related DSB repair pathways.
Prenyltransferase/isoprenoid biosynthesis (Prenyltransferase_related)
Type: Family

This family of proteins is found in bacteria, archaea, fungi and plants and includes enzymes involved in various prenyltransferase reactions, which are critical steps in the biosynthesis of diverse isoprenoid compounds. These enzymes transfer prenyl groups to acceptor molecules, playing roles in the synthesis of archaeal membrane lipids, chlorophylls, carotenoids, and other terpenoids. Some members catalyze the esterification of chlorophyllide and bacteriochlorophyllide with prenyl diphosphates, while others are involved in the elongation of carotenoids. Additionally, certain enzymes within this family participate in the biosynthesis of complex natural products with biological activities, such as fumagillin and erinacines, by catalyzing the transfer of prenyl groups or cyclization of diterpenes.
Insect Cytochrome P450 Detoxification (Insect_CytP450_Detox)
Type: Family

The cytochrome P450 family is involved in the metabolism of insect hormones and the breakdown of synthetic insecticides. Members of this family are necessary for resistance to certain insecticides like DDT and imidacloprid. Some proteins within the family enable insects to feed on furanocoumarin-producing plants by detoxifying xanthotoxin and other furanocoumarins. They also metabolize a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. The family includes enzymes that have adapted to metabolize various xenobiotic substances, contributing to the survival of insects in environments with toxic compounds.
Group II Amino Acid Decarboxylases (GrpII_AminoAcid_Decarb)
Type: Family

The Group II Decarboxylase family comprises enzymes that catalyze the decarboxylation of various amino acids, playing key roles in metabolic pathways. Members of the MfnA subfamily primarily decarboxylate L-tyrosine and L-aspartate, contributing to methanofuran biosynthesis and coenzyme A production, respectively. The Sphingosine-1-phosphate lyase subfamily members cleave phosphorylated sphingoid bases into fatty aldehydes and phosphoethanolamine, impacting lipid homeostasis, apoptosis, and stress responses. The Tyrosine decarboxylase subfamily is involved in tyramine production, which aids in acid resistance and gastrointestinal colonization, and can metabolize levodopa, affecting Parkinson's disease treatment. Other family members, such as Tryptophan decarboxylase, are involved in neurotransmitter synthesis. The family's diverse functions reflect its importance in various biological processes, including neurotransmission, stress response, lipid metabolism, and drug metabolism.
Ethylene and sulfur compound biosynthesis-related protein (Ethylene_sulfur-biosynth)
Type: Family

This family of proteins includes enzymes that are primarily involved in the biosynthesis of ethylene, a plant hormone that regulates various aspects of growth, development, and stress responses. Members of this family catalyze the conversion of S-adenosyl-L-methionine (SAM) into 1-aminocyclopropane-1-carboxylate (ACC), which is a direct precursor of ethylene. Some proteins within this family also have aminotransferase activity, participating in the biosynthesis of other compounds such as auxins, which are essential for plant growth and development. Additionally, certain members are involved in the production of sulfur-containing compounds that contribute to the characteristic aroma and potential health benefits of plants like garlic. The family also includes proteins with a domain that may serve as a binding site for other proteins or act as a docking site for receptors, although the exact function of this domain is not fully understood.
Cytochrome P450, families 11 and 27 (CYP11_CYP27_families)
Type: Family

The Cytochrome P450, family 11 (CYP11) and family 27 (CYP27), are mitochondrial monooxygenases involved in steroid hormone biosynthesis and vitamin D metabolism. Members of this family catalyze hydroxylation reactions essential for the production of mineralocorticoids, glucocorticoids, and sex steroids from cholesterol or its derivatives. They also play roles in the activation and inactivation of vitamin D, regulating calcium and phosphorus homeostasis. Some family members are involved in the metabolism of retinoids, affecting vision adaptation. The enzymes use molecular oxygen, inserting one oxygen atom into substrates and reducing the second into water, with electrons provided by NADPH via a mitochondrial electron transfer system. They are also implicated in the regulation of blood pressure, inflammatory responses, and cholesterol homeostasis through the production of active metabolites that act as ligands for nuclear receptors.
Proton-dependent sulfate transporter CysZ (CysZ_sulfate_transptr)
Type: Family

The CysZ family comprises high affinity, high specificity proton-dependent sulfate transporters. Members of this family are responsible for mediating sulfate uptake into the cell, which is a critical step in providing the sulfur source necessary for the cysteine synthesis pathway. Sulfate transport by these proteins is essential for the biosynthesis of sulfur-containing amino acids and plays a vital role in cellular sulfur homeostasis. Some members of the family are known to be inhibited by sulfite, indicating a regulatory mechanism for sulfate transport activity. The CysZ family proteins do not transport thiosulfate, highlighting their specificity for sulfate ions.
UDP-glycosyltransferase, plant-type (UDP-glycosyltransf_plant)
Type: Family

The UDP-glycosyltransferase family is involved in the biosynthesis of a wide range of glycosylated compounds, which play crucial roles in plant metabolism and defence . Members of this family catalyse the transfer of sugar moieties from activated sugar donors like UDP-glucose to acceptor molecules, including flavonoids, hydroxycoumarins, and triterpenes. These glycosylation reactions enhance the solubility, stability, and biological activity of the compounds, contributing to processes such as pigment formation, fruit ripening, and the production of saponins with medicinal properties. The family exhibits substrate specificity, with some members showing multifunctional activity towards various substrates, while others are more specialised. The glycosylated products are involved in plant colouration, antioxidant activity, and the detoxification of xenobiotics.
Sensor Histidine Kinase Two-Component System (Sensor_HK_TwoCompSys)
Type: Family

The Sensor Histidine Kinase family comprises proteins that function as part of two-component regulatory systems, typically involved in environmental signal detection and response. These kinases autophosphorylate a conserved histidine residue in response to specific stimuli such as oxygen levels, nitrate/nitrite presence, or cell wall stress. The phosphoryl group is then transferred to a conserved aspartate residue on a response regulator, which modulates gene expression to adapt to changing conditions. Functions include regulation of genetic competence, sporulation, nitrate/nitrite reduction, biofilm formation, antibiotic response, and methanol utilization. Some members also exhibit phosphatase activity, reversing the phosphorylation state of the response regulator to modulate the signaling pathway.
CoA-transferase III domain-containing protein (CoA-transferase_III_domain)
Type: Family

This family of proteins is involved in various metabolic processes, primarily acting as CoA-transferases. They catalyze the transfer of coenzyme A (CoA) from one molecule to another, typically involving carboxylic acids as substrates. Members of this family participate in pathways such as the catabolism of oxalate, the methylaspartate cycle, and the degradation of aromatic compounds. Some proteins within this family are implicated in the adaptation to low pH environments through the oxalate-dependent acid tolerance response. Others are involved in the metabolism of fatty acids and may play roles in host-pathogen interactions. The enzymes exhibit a range of substrate specificities, with some showing activity towards succinate, mesaconate, glutarate, and various aromatic substrates. The family includes proteins that are part of the degradation pathways for plant-derived compounds, contributing to the detoxification processes in certain organisms.
Transferase Hexapeptide/Carbonic Anhydrase (Transf_Hexapept/Carb_Anhydrase)
Type: Family

The protein family is involved in various biological processes, including the stimulation of the activity of other proteins and the assembly of complex I in mitochondria, which is essential for respiration. Members of the family are characterized by a transferase hexapeptide repeat motif, suggesting a role in transferase activity. Some proteins within the family are associated with the carnitine operon and are implicated in stimulating the activity of CaiB and CaiD when overproduced. Other members are part of the gamma-class carbonic anhydrase family, which are enzymes that do not mediate the reversible hydration of carbon dioxide but are involved in the catabolism of bicarbonate and contribute to mitochondrial complex I assembly and respiration. The family also includes proteins that are uncharacterized but share similarity with known functional domains, indicating a potential for diverse enzymatic or regulatory roles within cellular metabolism.
Proline metabolism enzyme (Proline_metab_enzyme)
Type: Family

This family of proteins includes enzymes that are involved in the metabolism of the amino acid proline. Members of this family are responsible for the oxidation of proline to glutamate, which is a key step in the interconversion between proline and glutamate and is important for cellular processes such as energy production and redox balance. Some members are bifunctional and also have a role in the transcriptional regulation of genes involved in proline metabolism. These enzymes are typically found in the mitochondria and are part of the aldehyde dehydrogenase superfamily, which is characterized by the oxidation of aldehydes to their corresponding carboxylic acids.
Mannose-1-phosphate guanyltransferase (Mannose-1P_guanyltransferase)
Type: Family

The Mannose-1-phosphate guanyltransferase family is involved in several critical cellular processes across various organisms . Members of this family primarily catalyze the formation of GDP-mannose from mannose-1-phosphate and GTP, which is an essential precursor for the glycosylation of glycoproteins and glycolipids. This reaction is pivotal in cell wall synthesis, particularly in fungi where it is necessary for cell cycle progression and maintaining the cell-size checkpoint. In plants, some family members participate in the Smirnoff-Wheeler pathway, which is the major route to ascorbate biosynthesis, a process crucial for plant growth, development, and antioxidant production. Additionally, in certain species, the alpha subunit may serve as a regulatory component, allowing for allosteric feedback inhibition by GDP-mannose to finely tune the enzymatic activity of the beta subunit.
Bacterial Cell Division FtsQ/DivIB (FtsQ_DivIB)
Type: Family

The FtsQ/DivIB family comprises essential cell division proteins that play a crucial role in bacterial cytokinesis. Members of this family are involved in stabilizing or promoting the assembly of the cell division complex, a critical step in the bacterial cell cycle. Proteins in the DivIB subfamily may protect other division proteins from degradation, facilitate the formation of protein complexes essential for cell division, and modulate enzymatic activities related to cell wall synthesis. They may also be directly involved in processes such as engulfment during sporulation. The extracellular region of these proteins typically contains distinct subdomains that contribute to their function, including interactions with other divisomal proteins.
Immunoglobulin Fc region receptor (Ig_Fc_receptor)
Type: Family

The protein family includes receptors that bind to the Fc region of immunoglobulins, particularly IgG and IgE, and are involved in various immune response functions. Members of the family mediate processes such as antibody-dependent cellular cytotoxicity (ADCC), phagocytosis, antigen presentation, and modulation of B-cell and T-cell activation. These receptors are expressed on a variety of immune cells, including natural killer (NK) cells, monocytes, and mast cells, and play roles in both innate and adaptive immunity. They can influence the outcome of infections, inflammatory responses, and allergic reactions. Some family members are also implicated in B-cell differentiation and may have regulatory roles in normal and neoplastic B-cell development. The family's involvement in immune complex clearance from circulation and the modulation of antibody production further highlights its significance in maintaining immune homeostasis and responding to pathogenic challenges.
Tyrosine--tRNA ligase (Tyr-tRNA_synthase)
Type: Family

The Tyrosine--tRNA ligase family is responsible for the aminoacylation of tRNA(Tyr) with the amino acid tyrosine, a fundamental process in protein synthesis. Members of the family perform a two-step reaction where tyrosine is first activated by ATP to form Tyr-AMP, and subsequently transferred to the acceptor end of tRNA(Tyr). This reaction ensures the correct addition of tyrosine to the growing polypeptide chain during mRNA translation. The family includes enzymes that may also be involved in nuclear tRNA export and can exhibit specificity for certain tRNA determinants. Some members are capable of attaching D-tyrosine to tRNA(Tyr), albeit less efficiently than L-tyrosine.
Bacterial solute-binding protein 1 (Bact_solute-bd_prot1)
Type: Family

The bacterial solute-binding protein 1 family consists of periplasmic proteins that are typically part of ABC transporter complexes. These proteins are involved in the import of a variety of substrates, including sugars, glycerol-3-phosphate (G3P), osmoprotective compounds, and possibly amino acids. Members of the family bind specific ligands with high affinity, which is essential for the transport process. Some proteins within the family have additional functions, such as molecular chaperone activity, which is regulated by pH and the presence of substrate. The specificity of these proteins towards their ligands is critical for the survival and virulence of the bacteria, as it allows them to utilize diverse nutrients from their environment.