SII-SWORD/CoKE huggingface dataset:
Membrane-associated protease and related proteins (Membrane_assoc_protease)
Type: Family

This family of proteins includes membrane-bound proteases and uncharacterized membrane proteins. The protease member is known to cleave substrates preferentially near hydrophobic or aromatic residues and can degrade casein and a stomatin homolog in vitro. Its activity is regulated by inhibition with divalent metal cations and detergents. Other members of the family are less characterized but are suggested to have a role associated with the inner membrane, potentially in transport or signaling processes. The diversity within this family indicates a range of functions tied to membrane association and proteolysis.
Diverse substrate specificity acyl-CoA dehydrogenase (Diverse_Acyl-CoA_DH)
Type: Family

This family of proteins includes acyl-CoA dehydrogenases with diverse substrate specificities, including broad-specificity enzymes that prefer long-chain substrates and those involved in specific metabolic pathways. Members are key in various biochemical processes, such as the oxidation of fatty acids and the assimilation of carbon from marine phytoplankton compounds. They catalyze the dehydrogenation of acyl-CoA derivatives to enoyl-CoA, playing a pivotal role in fatty acid beta-oxidation and other metabolic pathways. Some family members are implicated in syntrophic butyrate oxidation, converting butanoyl-CoA to crotonyl-CoA and transferring electrons to electron-transfer flavoproteins.
Cytochrome b561 superoxide oxidase (Cytochrome_b561_oxidase)
Type: Family

This family of proteins includes B-type di-heme cytochromes that are involved in the redox reactions of cellular respiration. They catalyze the oxidation of superoxide to molecular oxygen, playing a role in the detoxification of reactive oxygen species. Additionally, they transfer electrons to quinones such as ubiquinone and menaquinone, which are part of the electron transport chain. Some members of this family are also capable of reducing ubiquinol to superoxide under physiological conditions, indicating a dual role in both the formation and detoxification of superoxide.
Cell Wall Biosynthesis Accessory Protein (CW_Biosynth-Accessory)
Type: Family

This family of proteins appears to be primarily involved in the biosynthesis, transport, or localization of cell wall components, which may include poly-alpha-L-glutamine (PLG) or gamma-polyglutamic acid (PGA). These components are significant for the structural integrity of the cell wall and may contribute to stress tolerance and virulence in certain bacterial species. Some members of this family are suggested to be essential for the synthesis of a polyglutamate capsule, which is a key virulence factor during specific bacterial infections. The proteins may work in conjunction with other proteins to form complexes that facilitate the synthesis of these cell wall components.
Metal-dependent Exopeptidase M29 (M29_Exopeptidase)
Type: Family

This family of proteins includes metal-dependent exopeptidases that cleave amino acids from the N-terminus of peptides. Members of this family exhibit broad specificity towards various N-terminal amino acids, including arginine and aromatic residues. Some proteins within this family are involved in bacterial growth by supplying amino acids through their enzymatic activity. Additionally, one member is known to catalyze the dioxygenolytic ring cleavage of 2,5-dihydroxypyridine in the aerobic nicotinate degradation pathway, although this function appears to be an exception rather than a characteristic of the family as a whole.
Non-homologous end joining protein LigD (NHEJ_LigD)
Type: Family

The LigD protein family is involved in non-homologous end joining (NHEJ), a DNA repair mechanism that fixes double-strand breaks with varying fidelity. Members of the LigD family possess multiple functional domains, including a polymerase/primase domain that prefers ribonucleotides over deoxynucleotides, which may be beneficial in dormant cells with limited dNTP pools. The central 3'-phosphoesterase domain is implicated in processing DNA ends, while the C-terminal ATP-dependent ligase domain is responsible for sealing nicks in DNA. The LigD family proteins often work in conjunction with the Ku protein to form a repair complex capable of handling blunt-end and 5'-overhang DSBs, as well as incompatible DSBs requiring 3'-resection, gap filling, and ligation. These multifunctional enzymes exhibit DNA ligase, DNA-directed DNA/RNA polymerase, terminal transferase, and 3'-ribonuclease/phosphatase activities, contributing to their role in maintaining genome integrity under various conditions.
UxaA family altronate/galactarate dehydratases (UxaA_altronate/galactarate_dh)
Type: Family

The UxaA family encompasses enzymes that catalyze various dehydration reactions in bacterial metabolism. Members of the UxaA family are involved in the dehydration of D-altronate and galactarate, yielding their respective dehydrated products. Some UxaA family proteins function in concert with other subunits, such as the desulfonation of sulfolactate to produce pyruvate and sulfite. The family is characterized by a conserved domain structure, with some members having a domain that likely participates in substrate recognition and another domain implicated in dimerization and catalytic activity, potentially including metal binding. The activity of some UxaA enzymes can be inhibited by high concentrations of Fe(2+) or by chelating agents like EDTA.
Beta-lactam antibiotic response regulator (Beta-lactam_resp_regulator)
Type: Family

This family of proteins includes members that are involved in the response to antibiotic stress, particularly beta-lactam antibiotics. They function as penicillin-interactive proteins and have a potential role as antirepressors. These proteins are integral membrane proteins that can sense the presence of beta-lactam antibiotics and transduce this information to the cytoplasm. This process involves the acylation of a serine residue in the sensor domain upon antibiotic binding, leading to a conformational change that activates a zinc protease domain. This domain then initiates autoproteolysis and cleavage of a transcriptional repressor, resulting in the derepression of antibiotic resistance genes.
Flavoredoxin (Flavoredoxin)
Type: Family

The flavoredoxin family comprises proteins that are involved in the reduction of hydrogensulfite to hydrogen. Flavoredoxins contain a flavin mononucleotide (FMN) or flavin adenine dinucleotide (FAD) as a prosthetic group, which is essential for their redox activity. These proteins play a role in various cellular processes, including the detoxification of reactive sulfur species and the maintenance of cellular redox balance. Flavoredoxins are found across a range of microorganisms and may be involved in responses to oxidative stress and in metabolic pathways where redox reactions are critical.
Complex I-like Hydrogenase Component (ComplexI-like_HydComp)
Type: Family

This family of proteins includes components that are potentially involved in the formation of hydrogenase complexes, specifically hydrogenase 4 in bacteria such as E. coli. These proteins are homologous to subunits of complex I, which is a large enzyme complex involved in the electron transport chain and energy metabolism. The exact function within the hydrogenase complex may vary, but they are likely to play a role in the catalytic activity or structural integrity of the complex, contributing to the process of oxidative phosphorylation and possibly the metabolism of formate in some organisms.
Glycosyl Hydrolase Family 43 Enzymes (Glycosyl_Hydrlase_43_Enz)
Type: Family

The glycosyl hydrolase 43 family encompasses enzymes with diverse functions related to the degradation of plant cell wall components. Members of this family are involved in the hydrolysis of glycosidic bonds in beta-galactofuranoside-containing glycans, arabinoxylans, and xylooligosaccharides. They exhibit activities such as beta-D-galactofuranosidase, xylosidase/arabinosidase, and arabinoxylan arabinofuranohydrolase. These enzymes assist in the breakdown of complex carbohydrates into simpler sugars, which can be utilized by the organism. Some family members have lost carbohydrate-binding capacity, while others are regulated by ions such as calcium and magnesium, and inhibited by copper. The family plays a crucial role in the utilization of plant-derived polysaccharides by various organisms.
Divisome-localized Glycosyl Hydrolase (Divisome_Glycosyl_Hydrolase)
Type: Family

This family of proteins includes glycosyl hydrolases that localize to the divisome, a complex involved in bacterial cell division. Members of this family are involved in the cleavage of peptidoglycans, specifically targeting regions that lack peptide side chains, known as denuded peptidoglycans. The enzymatic activity exhibited by these proteins may include glucosaminidase or muramidase functions, which are essential for cell wall remodeling and turnover during bacterial growth and division. The family is characterized by a structural similarity to the glycosyl hydrolase-like 10 (GHL10) family, suggesting a conserved mechanism of action across its members.
Secondary Metabolite Biosynthesis SDR (Sec_Metab_Biosynth_SDR)
Type: Family

This family of proteins includes short-chain dehydrogenases/reductases (SDRs) involved in various biosynthetic pathways for secondary metabolites in fungi and bacteria. These enzymes typically function in the reduction or oxidation of substrates using NAD(P)H as a cofactor. Members of this family are implicated in the biosynthesis of mycotoxins such as phomopsins and satratoxins, antibacterial compounds like viriditoxin, and biosurfactants such as rhamnolipids. They are responsible for key steps in these pathways, including the reduction of keto groups to hydroxyl groups, the formation of dihydropyrones, and the generation of beta-hydroxy acid moieties. The exact roles of some members within their respective pathways are yet to be fully elucidated, and they may exhibit broad substrate specificity, contributing to the diversity of secondary metabolites produced.
Bacterial Peptidoglycan Processing Enzymes (Bact_PeptidoProc_Enz)
Type: Family

The protein family includes enzymes involved in peptidoglycan processing, such as D-alanyl-D-alanine carboxypeptidases and endopeptidases. These enzymes play a role in bacterial cell wall synthesis and remodeling by cleaving specific peptide bonds in peptidoglycan precursors. D-alanyl-D-alanine carboxypeptidases remove the terminal D-alanine residue from pentapeptide chains in peptidoglycan precursors, which is a key step in cell wall maturation and recycling. Some family members are involved in antibiotic resistance by hydrolyzing depsipeptides that mimic antibiotic targets. Endopeptidases in the family cleave the L-alanine-D-glutamate bond in the peptidoglycan, contributing to cell wall turnover and maintenance. The family's activity is generally not inhibited by beta-lactam antibiotics, indicating a distinct mechanism of action from beta-lactamase enzymes.
NhaC Na(+)/H(+) Antiporter (NhaC_Na-H+_Antiporter)
Type: Family

This family of proteins is involved in the transport of ions across cellular membranes, functioning primarily as antiporters. They play a crucial role in maintaining pH homeostasis by exchanging sodium ions (Na+) for protons (H+). Some members are also capable of exchanging other ions such as arginine and ornithine, or coupling proton uptake with sodium efflux to facilitate the antiport of substrates like malate and lactate. These proteins are essential for various physiological processes, including growth in specific conditions and regulation of intracellular sodium levels. Their activity can be influenced by environmental factors and may be regulated by certain inhibitors.
5-Hydroxymethylcytosine binding (5hmC_binding)
Type: Family

This family of proteins is characterized by their ability to specifically interact with 5-hydroxymethylcytosine (5hmC), a modified form of the DNA base cytosine. The binding to 5hmC suggests a role in recognizing this epigenetic mark, which is involved in DNA methylation processes that regulate gene expression. The members of this family are implicated in reading the epigenetic code, which may influence chromatin structure and function, impacting cellular differentiation and development.
Glycogen_Maltodextrin_Phosphorylase (Glycogen/Maltodextrin_Phosph)
Type: Family

This family of proteins includes allosteric enzymes involved in carbohydrate metabolism. Members of this family catalyze the phosphorolytic cleavage of glycogen, maltodextrins, and other polysaccharides to produce glucose-1-phosphate. They play a key role in energy mobilization and are regulated by various mechanisms depending on the organism and tissue type. Structural and catalytic properties are conserved across the family, although substrate preferences and regulatory details may vary. Some members have specificity for maltodextrins and are known to act on substrates with a minimal chain length, showing reduced or no activity with shorter oligosaccharides.
Bacterial Insertion Sequence Transposase (IS_Transposase)
Type: Family

This family of proteins includes transposases that are responsible for the movement of insertion sequences within the genomes of bacteria. These enzymes facilitate the cut-and-paste mechanism of transposition, which can result in the insertion of these sequences into new genomic locations. Such mobility can contribute to genetic diversity, adaptation, and evolution by causing mutations, altering gene expression, or contributing to the spread of antibiotic resistance genes and other mobile genetic elements. The members of this family are typically associated with specific insertion sequences, as indicated by their names, and play a crucial role in the dynamics of bacterial genomes.
Short-chain dehydrogenases/reductases (SDR) enzymes (SDR_enzymes)
Type: Family

The Short-chain dehydrogenases/reductases (SDR) family is involved in various biosynthetic pathways for natural products, including fungal metabolites, meroterpenoids, and isoprene degradation. Members of this family function as oxidoreductases, catalyzing NAD(+)-dependent reactions. They play roles in the formation of multicellular structures, the biosynthesis of bioactive compounds with anticancer properties, and the degradation of environmental pollutants. The SDR enzymes exhibit diverse substrate specificities and participate in complex chemical transformations, such as ketoreduction, epoxidation, and dehydration, contributing to the structural diversity of natural products and their bioactivities.
Inositol Phosphorylceramide Synthase-Related (IPC_Synthase-Related)
Type: Family

This family of proteins includes enzymes that are involved in the biosynthesis of sphingolipids, a class of lipids that play a crucial role in cell membrane structure and function. Members of this family are responsible for catalyzing the addition of a phosphorylinositol group to ceramide or dihydroceramide, forming inositol phosphorylceramide or phosphoinositol dihydroceramide, respectively. These reactions are essential steps in the production of complex sphingolipids. The activity of these enzymes is known to be inhibited by specific compounds, indicating a level of regulatory control over sphingolipid synthesis.
Hydantoin racemase-like (Hydantoin_racemase-like)
Type: Family

This family of proteins is involved in the racemization of 5-substituted hydantoins, facilitating the conversion of these compounds to L-amino acids. The racemization process occurs through the enolization of both D- and L-enantiomers of hydantoins, which may have various side chains, including arylalkyl and aliphatic groups. Members of this family show different substrate preferences and are subject to regulation by various metal ions, with some being inhibited by heavy metals such as mercury and copper, while others are stimulated by reducing agents or slightly by divalent cations like manganese or cobalt. The activity of these enzymes is crucial for the utilization of hydantoins as nitrogen sources and for the production of L-amino acids, which are important building blocks for protein synthesis.
Lysosomal dipeptide transporter MFSD1 (MFSD1)
Type: Family

This family of proteins includes lysosomal transporters that are crucial for maintaining liver homeostasis. Human MFSD1 is a lysosomal dipeptide uniporter that selectively exports lysine, arginine or histidine-containing dipeptides with a net positive charge from the lysosome lumen into the cytosol . Members of this family are responsible for the stability and lysosomal localization of the protein GLMP. They feature a characteristic dileucine internalization motif that is essential for their localization to the lysosome. These proteins are part of the major facilitator superfamily, which is known for facilitating the transport of various substrates across cellular membranes.
Nickel-pincer cofactor biosynthesis protein (Ni-pincer_cofactor_biosynth)
Type: Family

This family of proteins is involved in the biosynthesis of a nickel-pincer cofactor, which is a (SCS)Ni(II) pincer complex. Members of this family catalyze the ATP-dependent incorporation of sulfur atoms into pyridinium-3,5-biscarboxylic acid mononucleotide (P2CMN) to form pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN). The sulfur transfer is mediated by a cysteine residue within the enzyme, which is converted into dehydroalanine in the process, rendering the enzyme inactive after the reaction. This sacrificial mechanism indicates that two enzyme molecules are consumed for each P2TMN produced. Additionally, these proteins are known to bind nickel and are implicated in the activation of lactate racemase and potentially other enzymes dependent on the nickel-pincer cofactor.
L-aspartate N-monooxygenase (nitrosuccinate-forming) (L-asp_N-monooxygenase_NS-form)
Type: Family

The L-aspartate N-monooxygenase (nitrosuccinate-forming) family is involved in the biosynthesis of various compounds with biological activity. Members of the family catalyze the iterative oxidation of L-aspartic acid to nitrosuccinic acid via intermediate steps involving N-hydroxyaspartic acid and nitrososuccinic acid. These enzymes play a role in the production of cremeomycin, a compound with antibacterial and antiproliferative properties, and desferrioxamine derivatives, which are potential siderophores due to their iron-binding capabilities.
Eukaryotic/Archaeal PrmC-Related Methyltransferase (Euk-Arch_PrmC-MTase)
Type: Family

The PrmC-related methyltransferase family is composed of enzymes that primarily function as methyltransferases using S-adenosyl-L-methionine as the methyl donor. Members of the family are known to methylate proteins, including the methylation of 'Lys-12' of histone H4 and 'Gln' residues within specific motifs of target proteins. The methylation of histone H4 is linked to the regulation of cell cycle genes. Some family members form heterodimers with TRMT112 to carry out their function. Additionally, there is evidence suggesting a role in the detoxification of arsenic, although this is a secondary function compared to other arsenic-metabolizing enzymes. The family is characterized by its presence in both eukaryotic and archaeal organisms, indicating a conserved mechanism across diverse life forms.
tRNA nucleotidyltransferase/poly(A) polymerase I (tRNA_ntf/polyA_polymerase_I)
Type: Family

The Poly(A) polymerase I family is characterized by enzymes that add poly(A) tails to the 3' ends of various RNAs, a process that typically marks these RNAs for degradation. The addition of poly(A) tails is a crucial step in the regulation of gene expression, as it affects the rate of RNA transcript degradation and plays a vital role in maintaining RNA quality control. Members of the family are involved in the global control of gene expression. Additionally, some family members have been implicated in plasmid copy number control and may recognize Rho-independent transcription terminators as signals for polyadenylation.
Insect Ionotropic Receptors for Sensory Perception (Insect_Ionotropic_Sensory_Rcpt)
Type: Family

The Ionotropic Receptor family is characterized by its role in sensory perception within the antenna of insects, particularly in Drosophila. Members of the family are integral to the detection of environmental changes such as temperature (thermosensation) and humidity (hygrosensation), as well as the recognition of specific odorants like acetic, propionic, butyric, and 2-oxopentanoic acids. These receptors function as part of olfactory receptor complexes and are essential for behaviors such as cool avoidance, dry detection, humidity preference, and heat-stimulated blood feeding. They are also implicated in forming neural sensory systems that underpin the response to cooling and changes in relative humidity, contributing to the survival and adaptation of insects to their environments.
Peptidase C59 family enzymes (Peptidase_C59)
Type: Family

The peptidase C59 family includes enzymes with diverse functions such as bile salt hydrolases and penicillin acylases. Bile salt hydrolases deconjugate glycine- and taurine-linked bile salts in the intestines of humans and animals, releasing amino acid residues and bile acids. They can hydrolyze major human bile salts like GCA, TCA, and TDCA, with varying substrate preferences. Penicillin acylases convert penicillin to 6-aminopenicillanate and act as self-processing peptidases. The family's activity is regulated by products like cholate and deoxycholate, phenylacetate, and penicillin derivatives. Thiol enzyme inhibitors also inhibit these enzymes in vitro.
Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (MESH1)
Type: Family

This family of proteins includes guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolases, commonly known as MESH1 enzymes. These enzymes play a crucial role in the bacterial stringent response to starvation by hydrolyzing the signaling molecule ppGpp (guanosine pentaphosphate or tetraphosphate), which is involved in the regulation of cellular processes in response to nutritional availability. The hydrolysis of ppGpp by MESH1 enzymes helps to adapt the cellular metabolism to conditions of nutrient limitation, thus contributing to the survival of the organism during periods of environmental stress.
Bacterial Alkyl/Aryl-Sulfatase (Bact_Alkyl/Aryl-Sulfatase)
Type: Family

The alkylsulfatase family comprises enzymes that catalyze the hydrolysis of alkyl sulfate esters, a reaction that is crucial for the utilization of sulfate esters as carbon or sulfur sources. Members of this family are involved in the degradation of various substrates, including the detergent sodium dodecyl sulfate (SDS), allowing bacteria to exploit these compounds as nutrients. Some family members display specificity for primary alkyl sulfates, while others can act on secondary alkyl sulfates or even aryl sulfates. The enzymes typically possess a binuclear Zn(2+) cluster within their N-terminal catalytic domain, a central dimerization domain that may confer resistance to SDS, and a C-terminal domain that may be involved in substrate recruitment. The activity of these enzymes can be modulated by metal ions such as Ca(2+) and Zn(2+). The alkylsulfatase family is part of the metallo-beta-lactamase superfamily and the Type III sulfatase family, playing a significant role in bacterial virulence and environmental sulfate cycling.