SII-SWORD/CoKE huggingface dataset:
Dihydroxyphenylacetyl-CoA Dioxygenase (DPA-CoA_Dioxygenase)
Type: Family

This family of proteins is involved in the biosynthesis of nonproteinogenic amino acids that are precursors for the production of antibiotics such as vancomycin and teicoplanin. Members of this family catalyze the conversion of 3,5-dihydroxyphenylacetyl-CoA to 3,5-dihydroxyphenylglyoxylate, performing a four-electron oxidation and hydrolysis of the thioester bond to release free CoA. These enzymes can process a range of substituted phenylacetyl-CoA substrates, indicating a degree of substrate versatility. They are characterized by their enzymatic activity within the enoyl-CoA hydratase/isomerase superfamily, which is known for its role in various metabolic pathways, including fatty acid beta-oxidation.
HTH-type Lysine Biosynthesis Regulator (HTH-Lysine_Regulator)
Type: Family

This family of proteins includes transcriptional regulators that are involved in the activation of lysine biosynthesis when the amino acid is in low concentration or absent. They function through the alpha-aminoadipate pathway, which is a route for lysine biosynthesis in certain bacteria and fungi. These proteins are characterized by a helix-turn-helix (HTH) motif, which is a common structural motif capable of binding DNA and is often seen in proteins that regulate gene expression.
Malate Synthase-like Aldolase (Malate_Synthase-like_Aldolase)
Type: Family

This family of proteins is involved in key metabolic cycles that convert small carbon molecules into intermediates for carbohydrate synthesis. Members of this family catalyze the formation of malate through a two-step process. Initially, they facilitate the reversible condensation of acetyl-coenzyme A (acetyl-CoA) with glyoxylate to produce an intermediate, which is then hydrolyzed to yield malate and coenzyme A (CoA). While the enzymes can also condense other CoA derivatives with glyoxylate or acetyl-CoA with pyruvate, the hydrolysis reaction is highly specific for the intermediate formed from acetyl-CoA and glyoxylate. These proteins are part of the HpcH/HpaI aldolase family, indicating a similarity in their structural fold and catalytic mechanism.
tRNA guanine-N2-methyltransferase (tRNA_guanine-N2-MTase)
Type: Family

This family of proteins includes S-adenosyl-L-methionine-dependent methyltransferases that are responsible for the methylation of guanosine nucleotides at position 6 in tRNA. Specifically, they catalyze the formation of methylated guanosine (m2G6) which plays a crucial role in the stability and function of tRNA molecules. These enzymes are part of the larger methyltransferase superfamily and share a common mechanism involving the transfer of a methyl group from S-adenosyl-L-methionine to the guanine base.
Outer membrane lipoprotein MapA (MapA_lipoprotein)
Type: Family

This family of proteins includes outer membrane lipoproteins, commonly referred to as MapA. These proteins are typically found in the outer membrane of Gram-negative bacteria and are involved in various functions related to the integrity and maintenance of the cell envelope. They may play roles in cell adhesion, invasion, or interaction with the host immune system. The characteristic feature of these lipoproteins is the presence of a lipid moiety that anchors them to the outer membrane, which is essential for their function and localization.
Alpha-glycosidase (Alpha-glycosidase)
Type: Family

This family of proteins includes enzymes that hydrolyze a variety of alpha-glycoside bonds in di- and trisaccharides, including alpha-1,4; alpha-1,1; alpha-1,2; alpha-1,3; and alpha-1,6 linkages. They exhibit broad specificity, acting on substrates such as maltose, maltotriose, trehalose, sucrose, turanose, melizitose, isomaltose, and melibiose. These enzymes are characterized by their ability to act on the non-reducing end of the saccharide chain and their activity decreases with increasing chain length. They do not hydrolyze polysaccharides like starch, pullulan, amylose, amylopectin, or glycogen, nor do they cleave beta-glycosidic bonds. They are inhibited by Hg(2+) ions and EDTA, indicating a requirement for divalent cations for activity.
Dihydroorotate dehydrogenase Type 1 (DHODH_Type1)
Type: Family

This family of proteins includes enzymes that are involved in the de novo pyrimidine biosynthesis pathway. Specifically, they catalyze the fourth enzymatic step, which is the conversion of dihydroorotate to orotate. This reaction requires NAD(+) as an electron acceptor. Members of this family play a crucial role in the synthesis of pyrimidine nucleotides, which are essential for DNA and RNA synthesis. As such, they are key to the cellular processes that require nucleotides, including cell division and growth. The activity of these enzymes is important for the proper functioning of all living cells, particularly in rapidly dividing cells where the demand for nucleotides is high.
NAD(P)-dependent GAP dehydrogenase (NAD(P)-GAP_dehydrogenase)
Type: Family

This family of proteins includes enzymes that catalyze the irreversible oxidation of glyceraldehyde-3-phosphate (GAP) to 3-phosphoglycerate (3PG) in a non-phosphorylating, NAD(P)-dependent manner. These enzymes exhibit high specificity for D-GAP as a substrate. Regulation of their activity is allosteric, with activation by various compounds including AMP, ADP, glucose 1-phosphate (G1P), and fructose 6-phosphate (F6P). They are part of the aldehyde dehydrogenase superfamily, which is involved in various metabolic processes.
Nodulation factor fucose acetyltransferase (Nod_factor_Fuc_AcT)
Type: Family

This family of proteins is thought to function as acetyltransferases, with a specific role in modifying the fucose component of nodulation factors. These modifications are likely critical for the proper functioning of nodulation factors, which are signaling molecules essential for the symbiotic relationship between certain plants and nitrogen-fixing bacteria. Members of this family share a commonality in structure, hinting at a conserved mechanism of action within the acetyltransferase 3 group.
Short-chain Isoprenyl Diphosphate Synthase (Isoprenyl_diphosphate_synthase)
Type: Family

This family of proteins includes enzymes that are responsible for the synthesis of short-chain isoprenyl diphosphates. These molecules serve as key precursors in the biosynthesis of isoprenoids, a diverse class of compounds that play essential roles in various biological processes such as electron transport, cell wall biosynthesis, and the prenylation of proteins. Members of this family catalyze the condensation of isopentenyl diphosphate (IPP) with allylic diphosphates to produce distinct isoprenyl diphosphates of varying chain lengths, which are then utilized in the production of terpenes and terpenoids, crucial components of cellular membranes and hormones.
Cell Division Machinery Component (Cell_Div_Machinery_Comp)
Type: Family

This family of proteins is involved in cellular division processes. Members of this family are components of the cell division machinery, suggesting a role in the coordination or execution of cell division events. The exact molecular functions and mechanisms by which these proteins contribute to cell division may vary among family members and could include activities such as regulation of cell cycle phases, formation of the division septum, or interaction with other proteins involved in the division process.
Thermostable Carboxypeptidase (Thermostable_CP)
Type: Family

This family of proteins includes enzymes with carboxypeptidase activity, capable of hydrolyzing the terminal peptide bonds at the C-terminus of proteins and peptides. Members of this family exhibit a preference for removing basic, acidic, and aromatic amino acids, and to a lesser extent, aliphatic amino acids from the C-terminus of substrates. These enzymes play a role in protein processing and metabolism, contributing to the regulation of peptide hormone activity, maturation of enzyme precursors, and the recycling of amino acids. The family is characterized by the presence of peptidase M20 domain which is responsible for the catalytic function of these enzymes.
Glycosyl Hydrolase 15 Enzymes (GH15_Enzymes)
Type: Family

This family of proteins includes enzymes that are involved in the hydrolysis of alpha,alpha-trehalose, a disaccharide consisting of two glucose molecules linked by an alpha,alpha-1,1-glycosidic bond. Members of this family function as trehalases, catalyzing the conversion of trehalose into two glucose units. This reaction is important for the metabolism of trehalose, which is a source of glucose for many organisms and can serve as an energy reserve or protectant against stress conditions such as desiccation, freezing, and osmotic stress. The activity of these enzymes is crucial for the regulation of trehalose levels within cells and can have implications for various physiological processes.
Avirulence B/C-like (AvrB/C-like)
Type: Family

This family of proteins includes avirulence factors that are involved in the pathogenicity of certain bacterial strains. These factors are recognized by specific resistance proteins in host plants, leading to the activation of plant defense mechanisms. The interaction between avirulence proteins and plant resistance proteins is a key component of the gene-for-gene model of plant-pathogen interactions, where the presence of corresponding avirulence and resistance genes results in an incompatible interaction, often leading to localized cell death and the halting of pathogen spread.
Acryloyl-CoA Reductase Zinc-Containing Alcohol Dehydrogenase (Acryloyl-CoA_Reductase_Zn-ADH)
Type: Family

This family of proteins is involved in autotrophic carbon fixation processes, specifically through the 3-hydroxypropionate/4-hydroxybutyrate cycle. Members of this family are responsible for the enzymatic reduction of acryloyl-CoA to propionyl-CoA, a reaction that is coupled with the oxidation of NADPH. They exhibit no activity towards 3-hydroxypropionyl-CoA, NADH, or crotonyl-CoA. Structurally, these enzymes are part of the zinc-containing alcohol dehydrogenase superfamily, which is characterized by the presence of zinc ions that are essential for their catalytic activity.
Glycosyl Hydrolase 31 Enzymes (GH31_Enzymes)
Type: Family

This family of proteins includes enzymes with alpha-glucosidase activity, which catalyze the hydrolysis of alpha-glucosidic linkages in polysaccharides and oligosaccharides. These enzymes play a crucial role in the carbohydrate digestion process by converting complex dietary sugars into glucose. Alpha-glucosidases are also involved in the biosynthesis and degradation of glycogen in cells, thus participating in energy metabolism and storage. Members of this family are characterized by their major soluble form and are found across various organisms, indicating a conserved function in glucose regulation and utilization.
Retron-associated ATPase (Retron_ATPase)
Type: Family

This family of proteins includes probable ATPases that are components of antiviral defense systems known as retrons. Each retron is composed of a non-coding RNA, a reverse transcriptase, an ATPase, and a putative HNH endonuclease. These proteins are involved in conferring protection against specific bacteriophages by slowing down the growth of the host bacteria upon infection at low multiplicity of infection, and inducing growth stasis at higher levels of infection. The defense mechanism provided by these proteins is crucial for the survival of bacteria under phage predation.
HTH-type TrmB transcriptional regulator (HTH-type_TrmB_regulator)
Type: Family

This family of proteins includes transcriptional regulators that are involved in the control of gene expression. Members of this family are known to bind to DNA, influencing the architecture of the genome and the transcriptional activity of certain genes. They are characterized by a helix-turn-helix (HTH) motif, which facilitates DNA binding. However, they lack a C-terminal sugar-binding domain typically found in related proteins. These regulators have been observed to bind promoters of gene clusters, such as the maltodextrin transport gene cluster, and other specific DNA sequences. Binding within gene promoters is associated with repression of transcription, while binding within coding regions does not appear to have the same effect. The proteins in this family do not significantly compact DNA but can form fibrous structures upon interaction with DNA in vitro.
Prolidase archaeal-type (Prolidase_arc)
Type: Family

This family of proteins includes enzymes that function as dipeptidases, specifically cleaving dipeptides where the C-terminal amino acid is proline and the N-terminal amino acid is nonpolar. These enzymes are part of the M24B peptidase family and are categorized within the archaeal-type prolidase subfamily. Their enzymatic activity is essential for the metabolism of dipeptides, which are the building blocks of proteins and play a crucial role in various biological processes including protein turnover and peptide absorption.
Lysogenic regulator DNA-binding (Lysogenic_reg_DNA-binding)
Type: Family

This family of proteins includes sequence-specific DNA-binding proteins that play a crucial role in the regulation of lysogeny. Members of this family are responsible for recognizing specific DNA sequences to exert their regulatory functions, which are essential for the establishment and maintenance of a lysogenic state. The binding activity of these proteins to operator DNA is characterized by sensitivity to certain chemical modifications, indicating a level of regulatory complexity in their interaction with DNA.
Magnetosome CDF Transporter-Related (Magnetosome_CDF-Related)
Type: Family

This family of proteins is involved in the biogenesis of magnetosomes, which are intracellular organelles that allow magnetotactic bacteria to orient themselves along geomagnetic fields. Members of this family are essential for the stable accumulation of MamB, a key component of the magnetosome membrane. They likely play a role in biomineralization by nucleating iron crystal formation and are suggested to bind and transport iron, a critical step in magnetite biosynthesis. The proteins are characterized by a C-terminal domain that facilitates both hetero- and homodimerization and binds divalent metal cations, with a preference for iron in vivo. This domain adopts a V-shaped, metallo-chaperone-like fold that can undergo a conformational shift upon metal binding, leading to a tighter dimer formation. This conformational change is thought to confer functionality on the transmembrane domain, potentially activated by ligand binding.
Clavaminate Synthase (Clavaminate_Synthase)
Type: Family

This family of proteins includes enzymes that are involved in the biosynthesis of clavulanic acid, a secondary metabolite with clinically important antibiotic properties. Members of this family catalyze the oxidative cyclization of proclavaminic acid to clavaminic acid, which is a key step in the biosynthetic pathway. These enzymes are non-heme iron(II)-dependent dioxygenases and require 2-oxoglutarate as a co-substrate for their catalytic activity. They play a crucial role in the formation of the clavaminate skeleton by facilitating the incorporation of atmospheric oxygen into the substrate. The activity of these enzymes is essential for the production of clavulanic acid, which is used in combination with certain penicillins to overcome antibiotic resistance in bacteria that produce beta-lactamase enzymes.
Geranylgeranyl diphosphate synthase (GGPP_synthase)
Type: Family

This family of proteins includes enzymes that catalyze the biosynthesis of geranylgeranyl diphosphate (GGPP), a key precursor for the production of ether-linked lipids. These enzymes perform the condensation of isopentenyl pyrophosphate with various allylic pyrophosphates, including dimethylallyl diphosphate (DMAPP), geranyl diphosphate (GPP), and (all-E)-geranyl diphosphate (E-FPP). The resulting GGPP molecule is essential for the biosynthesis of a variety of isoprenoid compounds, which play critical roles in numerous biological processes including membrane formation, protein prenylation, and hormone biosynthesis.
Pectinesterase (Pectinesterase)
Type: Family

This family of proteins is involved in the modification of plant cell walls by catalyzing the demethylesterification of pectin, a major component of the plant cell wall. The enzymatic action results in the release of methanol and protons, leading to a decrease in the degree of methylation of pectin. This process is crucial for plant development and defense, as it affects cell adhesion, cell wall porosity, and firmness. In pathogenic contexts, these proteins are responsible for the maceration and soft-rotting of plant tissues, facilitating the spread of plant pathogens.
Cyclomaltodextrinase (Cyclomaltodextrinase)
Type: Family

This family of proteins includes enzymes with cyclomaltodextrinase activity, capable of hydrolyzing alpha-, beta-, and gamma-cyclomaltodextrins as well as linear maltooligosaccharides into smaller sugars such as glucose and maltose. These proteins act by decycling cyclodextrins and releasing glucose from the reducing end of the substrate molecules. They exhibit very weak activity on starch and do not hydrolyze maltose or disaccharides with various types of alpha-links. Notably, they are also capable of degrading acarbose, an alpha-amylase and alpha-glucosidase inhibitor, into glucose and other products. The activity of these enzymes is influenced by various metal ions and can be modulated by heating or the addition of specific chemical agents.
NADP-dependent Glyceraldehyde Dehydrogenase (NADP-Glyceraldehyde_DH)
Type: Family

This family of proteins includes NADP-dependent dehydrogenases that participate in the non-phosphorylated Entner-Doudoroff (nED) pathway. They exhibit the highest catalytic activity towards various forms of glyceraldehyde, including D,L-glyceraldehyde and D-glyceraldehyde. These enzymes also show activity towards D,L-glyceraldehyde-3-phosphate and glycolaldehyde, albeit to a lesser extent. However, they do not process aliphatic or aromatic aldehydes. The activity of these dehydrogenases can be modulated by different factors. Thiol-modifying reagents lead to complete inhibition, while the presence of reducing agents such as glutathione, DTT, or 2-mercaptoethanol can enhance their activity. The proteins are also sensitive to temperature and metal ions, with activity being inhibited by calcium, cadmium, copper, and mercury ions.
Plant pathogen avirulence protein (Pathogen_avirulence)
Type: Family

This family of proteins includes members that are involved in the interaction between plant pathogens and their host plants. The proteins in this family are typically secreted by bacterial pathogens and can function as avirulence factors. These factors are recognized by the plant immune system, leading to the activation of plant defense responses. The recognition of avirulence proteins by specific resistance proteins in the plant triggers a hypersensitive response, which is a form of programmed cell death in plants that restricts the spread of the pathogen. The detailed mechanisms of action and the specific targets of these avirulence proteins within the host plants may vary among family members.
Glucose-6-phosphate isomerase (GPI)
Type: Family

This family of proteins includes enzymes that catalyze the reversible isomerization of glucose-6-phosphate into fructose-6-phosphate, a reaction that is a critical step in the glycolysis and gluconeogenesis metabolic pathways. Members of this family are also known to be competitively inhibited by metabolites such as 6-phosphogluconate and erythrose 4-phosphate, indicating a regulatory role in carbohydrate metabolism.
Tyramine-Glutamate Amide Bond Synthase (Tyramine-Glutamate_Synthase)
Type: Family

This family of proteins includes enzymes that are responsible for the biosynthesis of amide bonds between aromatic amines and carboxylic acids. Specifically, they catalyze the formation of an amide linkage between tyramine and the gamma carboxy group of L-glutamate, a reaction that results in the production of a tyramyl-glutamate compound. These enzymes exhibit substrate flexibility, as they can also utilize phenylethylamine to form a similar amide bond with L-glutamate in vitro. The ability to form these amide bonds is significant in various biological processes, including the synthesis of bioactive compounds and the metabolism of neurotransmitters.
NiFe/NiFeSe hydrogenase large subunit (NiFe/NiFeSe_hydrogenase_LSU)
Type: Family

This family of proteins includes large subunits of [NiFe] and [NiFeSe] hydrogenases, which are enzymes that catalyze the reversible oxidation of hydrogen gas (H2). These hydrogenases play a crucial role in microbial energy metabolism, allowing organisms to use H2 as an electron donor or acceptor in various biochemical pathways. The large subunit of these hydrogenases contains the active site, typically comprising a nickel-iron cofactor, and is responsible for the binding and catalytic conversion of molecular hydrogen. The presence of selenium in some of these enzymes ([NiFeSe] hydrogenases) suggests a variation in the active site composition and possibly reflects adaptations to specific environmental conditions or metabolic requirements.
Magnetosome-associated regulatory protein (Magnetosome_regulatory)
Type: Family

This family of proteins is involved in the biomineralization process, specifically in the formation and regulation of magnetite crystals within magnetosomes. Members of this family are implicated in controlling the size and morphology of magnetite crystals, likely by binding iron ions and possibly influencing oxido-reduction reactions during crystal formation. They may also contribute to the nucleation process of magnetite crystals. The proteins contain a magnetite-interacting component that binds iron and potentially other metal ions, although the physiological relevance of non-iron metal binding is uncertain. Mutations within this region can affect crystal size, indicating a role in the regulation of crystal growth.
Class-III Pyridoxal-Phosphate Aminotransferase (Class-III_PLP_Aminotransferase)
Type: Family

This family of proteins is involved in the biosynthesis of the amino acid lysine through the aminoadipate pathway. Members of this family function as aminotransferases that catalyze the transfer of an amino group from L-glutamate to [LysW]-aminoadipate 6-semialdehyde, resulting in the production of [LysW]-gamma-L-lysine. These enzymes are dependent on pyridoxal phosphate as a cofactor and are part of the class-III aminotransferase family. Some members have also been shown to act on N(2)-acetyl-L-ornithine and N(2)-acetyl-L-lysine in vitro, suggesting a potential broader substrate specificity.
Decorin-Binding (Decorin-Binding)
Type: Family

This family of proteins is involved in the adherence of bacteria to host tissues. Members of this family have a specific function in binding to the extracellular matrix protein decorin. This interaction is thought to facilitate bacterial adherence to collagen fibers, which is a critical step in the colonization of host tissues. The binding to decorin may play a role in the pathogenesis of bacterial infections by promoting bacterial survival and proliferation within the host.
HTH-type Archaellar Gene Regulator (HTH-type_ArnR)
Type: Family

This family of proteins includes transcriptional activators that are characterized by a helix-turn-helix (HTH) motif. Members of this family are involved in the regulation of gene expression related to the structure known as the archaellum, which is analogous to the bacterial flagellum and is important for motility in archaea. These proteins are known to play a role in activating the transcription of flaB, a gene encoding a component of the archaellum, in response to nutrient starvation conditions. The activation occurs through interaction with the flaB promoter, suggesting a direct regulatory role in the expression of archaellar components under specific environmental stimuli.