SII-SWORD/CoKE huggingface dataset:
SAM-dependent methyltransferase (SAM-dep_methyltransferase)
Type: Family

This family of proteins includes enzymes that function as methyltransferases, utilizing S-adenosyl-L-methionine (SAM) as the methyl donor to transfer methyl groups to various substrates. Members of this family are involved in the methylation of small molecules such as nicotinamide, phenylethanolamine, and indolethylamine, which are important in metabolic pathways, neurotransmitter synthesis, and detoxification processes. These enzymes play key roles in regulating cellular methylation potential, epigenetic and transcriptional changes, energy expenditure, gluconeogenesis, cholesterol biosynthesis, and the salvage pathway of NAD(+) synthesis. They also contribute to the detoxification of xenobiotics and selenium compounds. Some family members are involved in the synthesis of hormones such as adrenaline from noradrenaline and are implicated in the stability of specific deacetylases through their methylation products.
ABC_transport_system_permease (ABC_transport_permease)
Type: Family

This family of proteins is involved in the transport of specific substrates across cellular membranes. They are components of ABC transporter complexes, which typically consist of multiple subunits that work together to translocate substances into or out of the cell. Members of this family are likely to be responsible for the movement of their respective substrates through the membrane, contributing to the overall transport process. Some proteins in this family are specifically associated with the import of nickel ions, which are essential for various cellular functions, including the activity of certain enzymes. Other members are implicated in the transport of dipeptides. The function of these proteins is critical for nutrient uptake and can influence the virulence of pathogenic organisms in host infections.
Methyl-branched fatty acid synthase (MBFA_synthase)
Type: Family

This family of proteins includes enzymes primarily involved in the biosynthesis of complex lipids with methyl-branched fatty acids, such us Phthioceranic/hydroxyphthioceranic acid synthase and Mycocerosic acid synthase-like polyketide synthase from Mycobacterium sp. These lipids are significant components of the cell envelope in certain bacteria and play a role in host-pathogen interactions . Members of this family function as polyketide synthases that catalyse the elongation of long-chain fatty acyl-CoA with methylmalonyl-CoA to form various methyl-branched fatty acids. These fatty acids are key constituents of sulfolipids and other polyacylated molecules, which are crucial for the virulence and survival of the bacteria within the host. The enzymes exhibit a domain organization that includes a condensing ketosynthase-acyltransferase region and a modifying dehydratase-keto reductase-enoyl reductase-keto reductase region, often followed by an acyl carrier protein domain.
Bacterial ring-hydroxylating dioxygenase ferredoxin (Ring-hydroxylating_fd)
Type: Family

This family of proteins is involved in the bacterial degradation of aromatic compounds. Members of this family function as components of multicomponent dioxygenase systems, specifically as ferredoxins containing a 2Fe-2S cluster. These proteins participate in the oxidative conversion of 3-phenylpropionic acid and cinnamic acid into their respective dihydrodiol forms. The ferredoxin subunits are essential for electron transfer processes that facilitate the hydroxylation reactions carried out by the dioxygenase components.
Glu/Leu/Phe/Val dehydrogenases (GLPV_dehydrogenases)
Type: Family

This family of proteins includes enzymes that catalyze the oxidative deamination of glutamate to alpha-ketoglutarate and ammonia, a reaction that plays a central role in the metabolism of nitrogen. These enzymes are also involved in the catabolism of amino acids and the production of neurotransmitters. They are characterized by their ability to utilize various amino acids such as glutamate, leucine, phenylalanine, and valine as substrates, reflecting their name. The activity of these dehydrogenases is important for cellular processes including the regulation of amino acid levels, energy metabolism, and the biosynthesis of amino acid-derived neurotransmitters.
Pyruvate Synthase Subunit PorD (Pyruvate_synthase_PorD)
Type: Family

This family of proteins includes subunits of pyruvate synthase, an enzyme complex that catalyzes the conversion of pyruvate to acetyl-CoA, a key metabolic reaction in the process of energy production and biosynthesis. These proteins are typically found in anaerobic bacteria and archaea, where they play a crucial role in the Wood-Ljungdahl pathway, also known as the reductive acetyl-CoA pathway, which is one of the several pathways of carbon fixation. The activity of these proteins is essential for organisms that rely on this pathway for energy conservation and carbon fixation under anaerobic conditions.
Pyruvate Synthase Subunit PorA (Pyruvate_synthase_PorA)
Type: Family

This family of proteins includes subunits of pyruvate synthase, an enzyme that catalyzes the conversion of pyruvate to acetyl-CoA, a key metabolic reaction in the central metabolic pathway. The enzyme is essential for energy production in cells, as acetyl-CoA enters the citric acid cycle to be oxidized for energy. Pyruvate synthase is particularly important in anaerobic conditions where it helps in maintaining the redox balance by regenerating NAD+ from NADH. The subunit PorA is one part of the multimeric complex and may play a role in the enzyme's catalytic activity or structural integrity.
Teichoic Acid Biosynthesis Glycosyltransferase (TAB_Glycosyltransferase)
Type: Family

This family of proteins is involved in the biosynthesis of teichoic acid, a major component of the cell wall in certain bacteria. Members of this family are enzymes that catalyze the formation of a specific lipid-linked oligosaccharide. They convert N-acetylglucosamine linked to a lipid carrier (undecaprenol) into a disaccharide by adding an N-acetylmannosamine residue. This reaction represents a key step in the production of teichoic acid, which plays a crucial role in cell wall structure and function, including maintaining cell shape, protecting against environmental stress, and serving as a receptor for certain bacteriophages.
Transposase IS30-like (Transposase_IS30-like)
Type: Family

This family of proteins includes transposases which are enzymes that catalyze the movement of DNA segments within the genome. These proteins are responsible for the transposition of insertion elements, which are sequences of DNA that can change their position within the genome, sometimes creating or reversing mutations and altering the cell's genetic identity. Transposition typically involves the cutting and pasting of these elements, and is an important mechanism in the evolution of genomes, contributing to genetic diversity. Members of this family are characterized by their role in facilitating the mobility of specific insertion sequence elements, such as IS30, IS1161, IS1086, and IS4351, across different bacterial species.
Meromycolate extension acyl carrier (Meromycolate-ACP)
Type: Family

This family of proteins includes acyl carrier proteins (ACPs) that play a crucial role in the biosynthesis of fatty acids. Specifically, members of this family are involved in the extension of meromycolate, a significant component of the mycobacterial cell wall. These proteins serve as scaffolds that transiently carry the growing fatty acid chain during the biosynthetic process, facilitating the elongation and modification of the lipid molecule. The activity of these ACPs is essential for the production of complex lipids that are critical for the survival and pathogenicity of mycobacteria.
Signal Recognition Particle 19 kDa (SRP19)
Type: Family

This family of proteins is involved in the co-translational targeting of nascent membrane proteins, facilitating their insertion into the cytoplasmic membrane. Members of this family bind to 7S RNA and are responsible for the interaction with the 54 kDa subunit of the signal recognition particle (SRP), which is a critical step in the SRP pathway for protein translocation across membranes.
CRISPR-associated endoribonuclease Cas13a (Cas13a_endoribonuclease)
Type: Family

This family of proteins is involved in the CRISPR adaptive immune system, which provides defense against mobile genetic elements such as viruses, transposable elements, and conjugative plasmids. Members of this family are CRISPR-associated endoribonucleases known as Cas13a, which target and cleave RNA. They process pre-CRISPR RNA (crRNA) and are responsible for the cleavage of target single-stranded RNA (ssRNA) in a crRNA-dependent manner. Activation of these proteins for non-specific RNA degradation, also known as collateral RNA degradation, is triggered by the binding of a viable target RNA. The proteins contain two HEPN-like folds that interact to form the active site for RNA cleavage, and they undergo conformational changes upon RNA binding that are critical for their function.
Endonuclease V-like (Endonuclease_V-like)
Type: Family

This family of proteins includes DNA repair enzymes that are involved in the recognition and repair of deaminated bases within DNA. Members of this family exhibit a specific activity that cleaves double-stranded DNA at the second phosphodiester bond located 3' to a deoxyinosine. This cleavage action leaves the deaminated base lesion intact on the DNA strand that has been nicked. Some members have also shown the ability to cleave single-stranded DNA substrates containing inosine, as well as double-stranded DNA with apurinic sites, uracil, or mismatched bases. The enzymes can function in vitro to cleave both strands of DNA when present in molar excess and when two protein molecules bind to the same DNA substrate.
Archaeal Riboflavin Kinase (Archaeal_Riboflavin_Kinase)
Type: Family

This family of proteins catalyzes the phosphorylation of riboflavin (vitamin B2) to form flavin mononucleotide (FMN), primarily using CTP as the phosphate donor. Some members may also utilize UTP, but with less efficiency, and the potential for ATP and GTP to act as substrates has not been clearly established.
Hydroxypyruvate and 2-oxo-tetronate isomerases (HPT_OtnI_isomerases)
Type: Family

This family of proteins includes enzymes that catalyze isomerization reactions. Members of this family are involved in the reversible isomerization between hydroxypyruvate and 2-hydroxy-3-oxopropanoate, also known as tartronate semialdehyde. Additionally, some family members specifically catalyze the isomerization of 2-oxo-tetronate to 3-oxo-tetronate. These isomerization reactions are important steps in various metabolic pathways. The family is characterized by the absence of stimulation by cofactors such as pyridoxal 5'-phosphate, FAD, NAD(+), NADP(+), or ATP, and its activity is not affected by EDTA or metal ions like Ca(2+), Co(2+), Mg(2+), Ni(2+), or Zn(2+).
2-oxoacid:ferredoxin oxidoreductase beta subunit (2-oxoacid:Fd_oxidored_beta)
Type: Family

This family of proteins includes enzymes that catalyze the coenzyme A-dependent oxidative decarboxylation of various 2-oxoacids, such as 2-oxoglutarate, pyruvate, and 2-oxobutyrate, to generate their corresponding CoA derivatives. These reactions are crucial for metabolic pathways like the citric acid cycle and amino acid degradation. The enzymes are characterized by their interaction with ferredoxin, a small iron-sulfur protein, which acts as an electron carrier in the redox process. One member of this family is known to be inhibited by 4-fluoro-7-nitrobenzofurazan at low concentrations, suggesting a regulatory mechanism for the enzyme's activity.
2-oxoacid:ferredoxin oxidoreductase alpha (2-oxoacid_Fdx_oxidoreductase)
Type: Family

This family of proteins catalyzes the coenzyme A-dependent oxidative decarboxylation of various 2-oxoacids, including 2-oxoglutarate, pyruvate, 2-oxobutyrate, and glyoxylate, to generate their corresponding CoA derivatives. These reactions are crucial for several metabolic pathways, including the citric acid cycle and amino acid metabolism. The proteins share a conserved Tyr-Pro-Ile-Thr-Pro (YPITP) motif that is believed to be critical for the catalytic process, likely due to its ability to confer structural flexibility and mobility necessary for the enzymatic function. Additionally, the activity of these enzymes can be modulated by specific inhibitors, indicating a level of regulatory control over their metabolic functions.
Transcriptional regulator GfcR, halobacteria (GcfR_halob)
Type: Family

This entry represents transcriptional regulator GfcR found primarily in halobacteria.

GfcR is a DNA-binding transcriptional regulator that functions as a regulator of central sugar catabolic pathways. It acts by binding directly to the promoter region of the regulated genes. In the presence of D-glucose, activates expression of the gene encoding the gluconate dehydratase (gad), which is involved in D-glucose catabolism while In the presence of D-fructose, activates expression of the genes encoding the PTS system EIIC component (ptfC) and the fructose-1,6-bisphosphate aldolase (fba), which are involved in D-fructose uptake and degradation
Quorum sensing regulatory protein LuxO (QS_regulatory_LuxO)
Type: Family

This family of proteins is involved in the regulation of gene expression in response to cell density, a process known as quorum sensing. Members act as negative regulators, particularly affecting the expression of the luminescence operon luxCDABEGH in certain conditions. At low cell density, these proteins are phosphorylated and, in conjunction with sigma-54, they repress the operon, potentially by activating a negative regulator of luminescence. Conversely, at high cell density, they become dephosphorylated and inactive, leading to de-repression of the operon and resulting in light production. Additionally, these proteins are implicated in the activation of siderophore production and may influence colony morphology.
Quorum sensing phosphorelay intermediate (QS_phosphorelay_intermediate)
Type: Family

This family of proteins functions as phosphorelay intermediates in bacterial quorum sensing signal transduction pathways. They are involved in receiving sensory signals from sensor kinases such as LuxN and LuxP and transmitting these signals to the response regulator LuxO. The transmission process involves the transfer of a phosphoryl group to a conserved histidine residue on the phosphorelay protein at low cell density, which is then relayed to LuxO. At high cell density, these proteins may help to establish an equilibrium between phosphorylated forms of sensor kinases and LuxO, facilitating the dephosphorylation and attenuation of the quorum sensing signal.
Lactaldehyde dehydrogenase (Lactaldehyde_DH)
Type: Family

This family of proteins is involved in the biosynthesis of the coenzyme F420, a redox-active cofactor used by some archaea and bacteria. Members of this family catalyze the oxidation of lactaldehyde to lactate, a key step in the production of this coenzyme. The enzymes exhibit a preference for NAD over NADP as a cofactor and have varying substrate specificities, with some members showing activity towards a range of aldehydes. The family is part of the larger aldehyde dehydrogenase superfamily, which is characterized by the oxidation of aldehyde substrates to their corresponding carboxylic acids.
Molybdate/Tungstate ABC Transporter Permease (Mo/W_ABC_Transporter_Permease)
Type: Family

This family of proteins is involved in the transport of molybdate and tungstate across cellular membranes. They are part of an ABC transporter complex, likely playing a critical role in the translocation of these substrates. The proteins are suggested to be permeases, which are essential components in the binding-protein-dependent transport system, facilitating the import of specific molecules into the cell.
L-fuculose phosphate aldolase (Fuculose-P_aldolase)
Type: Family

This family of proteins is involved in the biosynthesis of coenzyme F420, a cofactor that plays a crucial role in various redox reactions. Members of this family function as enzymes that catalyze the reversible cleavage of L-fuculose 1-phosphate into dihydroxyacetone phosphate and S-lactaldehyde. This reaction is a key step in the metabolic pathway that leads to the production of phospholactate, which is subsequently used in the synthesis of coenzyme F420. The enzymes exhibit specificity for dihydroxyacetone phosphate but can accept a range of aldehyde substrates. They are characterized by their membership in the aldolase class II family, specifically within the AraD/FucA subfamily.
Diaminopimelate Epimerase (DAP_Epimerase)
Type: Family

This family of proteins is involved in the biosynthesis of lysine, an essential amino acid, through the stereoinversion of a specific diaminopimelate isomer. Members of this family catalyze the conversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), which is not only a precursor to lysine but also a critical component of bacterial cell wall peptidoglycan. This reaction is a key step in the anabolic pathway of lysine in bacteria and is essential for their growth and maintenance.
MlaE Permease (MlaE_Permease)
Type: Family

This family of proteins is involved in the maintenance of lipid asymmetry in bacterial outer membranes. Members function as part of the ABC transporter complex MlaFEDB and are implicated in a phospholipid transport pathway. They are likely responsible for the retrograde trafficking of phospholipids from the outer membrane to the inner membrane, facilitating the translocation of substrates across the membrane.
Mannuronan C5-epimerase (Mannuronan_C5-epimerase)
Type: Family

This family of proteins catalyzes the epimerization of beta-D-mannuronate to alpha-L-guluronate, a key step in the biosynthesis of alginate, a linear polysaccharide. Members of this family are also involved in the formation of a periplasmic protein complex that prevents alginate degradation by the lyase AlgL. This complex facilitates the transfer of the alginate polymer through the periplasmic space to the outer membrane secretin AlgE. Some family members contain a C-terminal right-handed beta-helix fold, which is typical for proteins interacting with long-chain linear polysaccharides. The activity of these epimerases can be regulated by substrate acetylation or the presence of zinc ions.
Mycobacterial enoyl-ACP reductase (Mycobact_enoyl-ACP_red)
Type: Family

This family of proteins includes enoyl-ACP reductases that are part of the type II fatty acid synthase (FAS-II) system, which plays a crucial role in the biosynthesis of mycolic acids, essential components of mycobacterial cell walls. These enzymes catalyze the NADH-dependent reduction of the double bond in 2-trans-enoyl-[acyl-carrier protein], a key step in the fatty acid elongation cycle within the FAS-II pathway. They exhibit a preference for long-chain fatty acyl thioester substrates and can also utilize 2-trans-enoyl-CoAs. The FAS-II system extends fatty acyl chain lengths using products from the FAS-I system as primers, leading to the formation of the meromycolate chain, a precursor for mycolic acids. Additionally, these proteins are known targets for antitubercular drugs such as isoniazid and ethionamide, which inhibit their activity by forming covalent adducts with NAD.
Malate Dehydrogenase (MDH)
Type: Family

This family of proteins includes enzymes that are responsible for the reversible conversion of malate into oxaloacetate, a critical step in the citric acid cycle. These enzymes play a pivotal role in the metabolic pathway that generates energy through the oxidation of various molecules. Members of this family are characterized by their participation in the LDH/MDH superfamily, which indicates a shared evolutionary history and similar structural features that are essential for their catalytic function.
Pyruvate Synthase Subunit PorC (Pyruvate_synthase_PorC)
Type: Family

This family of proteins includes subunits of pyruvate synthase, an enzyme complex that catalyzes the conversion of pyruvate to acetyl-CoA, a key metabolic intermediate. The reaction is part of the anaerobic respiratory chain in some microorganisms, allowing them to generate energy under oxygen-limited conditions. These proteins are involved in the reductive carboxylation of acetyl-CoA to pyruvate, with the concomitant oxidation of ferredoxin. The activity of pyruvate synthase is essential for the metabolism of sugars via the glycolytic pathway and for the synthesis of fatty acids and amino acids derived from acetyl-CoA.
Autoinducer 2 sensor kinase/phosphatase (AI-2_sensor_kinase/phosphatase)
Type: Family

This family of proteins functions as dual-role signal transducers in bacterial quorum sensing systems. They possess kinase activity at low cell densities, autophosphorylating on a histidine residue and subsequently transferring the phosphoryl group to an aspartate residue within their own response regulator domain. This phosphoryl group is then relayed to LuxU and ultimately to LuxO. Conversely, at high cell densities in the presence of autoinducer molecules, their kinase activity is suppressed, and the proteins exhibit phosphatase activity, reversing the phosphorylation state of the response regulator domain. This switch in activity modulates the downstream quorum sensing pathway, coordinating bacterial community behaviors in response to population density.
Fructose-bisphosphate aldolase class 1 (FBA_class_1)
Type: Family

This family of proteins includes enzymes known as fructose-bisphosphate aldolases, which are key components in the glycolytic pathway. They catalyze the reversible cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. This reaction is crucial for the metabolism of glucose and the production of energy. Members of this family are also regulated by citrate, which acts as an allosteric activator, enhancing the enzyme's activity. The presence of citrate thus influences the glycolytic flow, potentially linking the regulation of energy production with the availability of substrates and cellular energy status.
Entner-Doudoroff pathway aldolase (ED_pathway_aldolase)
Type: Family

This family of proteins is involved in the Entner-Doudoroff pathway, which is a metabolic route alternative to glycolysis for the degradation of glucose and galactose. Members of this family catalyze the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxygluconate (KDG), resulting in the formation of pyruvate and glyceraldehyde 3-phosphate or glyceraldehyde. While most members can also process 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) and 2-keto-3-deoxygalactonate (KDGal), some are specific to the glucose derivatives. The enzymatic activity is crucial for the utilization of these sugars in certain bacteria and reflects the versatility of bacterial metabolic pathways.
ATP-dependent DNA Hel308 helicase (Hel308_helicase)
Type: Family

This family of proteins includes ATP-dependent DNA helicases belonging to the Hel308 subfamily. They play a role in DNA repair processes, particularly in the resolution of stalled replication forks. Members of this family exhibit 3'-5' helicase activity, unwinding double-stranded DNA with overhangs and are involved in the displacement of proteins from DNA. Some members also show weak 5'-3' helicase activity. The helicase function is regulated by interactions with other proteins and DNA structures, and some members have been implicated in the repair of DNA interstrand cross-links. The helicase activity is typically modulated by the protein's own domains, with certain regions necessary for activity and others acting as inhibitors.