SII-SWORD/CoKE huggingface dataset:
Polysaccharide deacetylase, ArnD subfamily (Polysacc_deacetylase_ArnD)
Type: Family

The polysaccharide deacetylase family, specifically the ArnD deformylase subfamily, consists of enzymes that play a crucial role in bacterial resistance to antimicrobial peptides. Members of this family catalyze the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol, producing 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. This reaction is part of a biosynthetic pathway that modifies lipid A, a component of the bacterial outer membrane. The addition of the modified arabinose to lipid A is essential for the bacteria's resistance to polymyxin and other cationic antimicrobial peptides. This modification helps protect pathogenic bacteria from the host's immune defenses, contributing to virulence and the ability to cause infection. Other members of the broader polysaccharide deacetylase family are involved in various biological processes, including chitin and peptidoglycan modification, which are important for cell wall integrity and evasion of host immune responses.
Pseudomonas-type Homoserine Kinase (Pseudomonas-type_ThrB)
Type: Family

The pseudomonas-type ThrB family is characterized by proteins that predominantly function as homoserine kinases. These enzymes play a crucial role in the biosynthesis of threonine, isoleucine, and methionine by catalyzing the ATP-dependent phosphorylation of L-homoserine to L-homoserine phosphate. This reaction is a key step in the aspartate pathway, which is essential for the production of essential amino acids in bacteria. Some members of the family may have evolved to acquire specialized functions, such as phosphorylating different substrates like 5-hydroxy-L-lysine or the antibiotic amicoumacin A, indicating a potential for functional diversity within the family.
Macrolide Exporter MacB (Macrolide_Exporter_MacB)
Type: Family

The Macrolide Exporter MacB family consists of non-canonical ABC transporters that play a crucial role in conferring resistance against macrolides. These transporters are characterized by transmembrane domains (TMD) that form a pore in the inner membrane and an ATP-binding domain (NBD) responsible for energy generation. Many family members are part of the tripartite efflux system MacAB-TolC, which actively exports macrolide compounds out of the cell. Some variants within the family, such as PvdT, are involved in the secretion of siderophores like pyoverdine for iron acquisition and may also contribute to resistance against other substances like ampicillin. The family also includes proteins potentially involved in the export of other compounds, such as syringafactins. The diverse functions of the Macrolide Exporter MacB family highlight its significance in bacterial survival and adaptation, particularly in the presence of antimicrobial agents.
HpcH/HpaI aldolase (HpcH-HpaI_aldolase)
Type: Family

The HpcH/HpaI aldolase family encompasses enzymes that catalyze the reversible retro-aldol cleavage of various substrates to produce pyruvate and a corresponding aldehyde. Members of this family are involved in diverse metabolic pathways, including the degradation of sugars and the biosynthesis of natural products. Some enzymes within this family exhibit broad substrate specificity and are capable of processing multiple aldol substrates, while others are more specialized. The family includes enzymes such as 5-keto-4-deoxy-D-glucarate aldolase and 2-keto-3-deoxy-L-rhamnonate aldolase, which participate in carbohydrate metabolism, as well as enzymes like 4-hydroxy-4-methyl-2-oxoglutarate aldolase, which are involved in the biosynthesis of complex molecules like anti-HIV fungal natural products. The family is characterized by a common mechanism of retro-aldol cleavage, although some members also possess additional activities such as oxaloacetate decarboxylase activity or the ability to catalyze aldol addition reactions.
Beta/Gamma-Crystallin (Beta/Gamma-Crystallin)
Type: Family

The beta/gamma-crystallin family comprises proteins that are primarily known as the dominant structural components of the vertebrate eye lens. These proteins are characterized by a two-domain beta-structure, which is folded into four highly similar Greek key motifs. The crystallins in this family contribute to the transparency and refractive properties of the lens, essential for proper vision. Some members of the family may also have roles beyond the eye lens, as suggested by their presence in other tissues and involvement in processes such as the integrity and function of auditory nuclei.
Seed Storage and Functional Proteins (Seed_Storage-Functional)
Type: Family

This family of proteins primarily serves as seed storage reserves, which are mobilized to provide a source of carbon and nitrogen for the seedling after germination. They accumulate during seed development and are hydrolyzed post-germination. Some members also exhibit additional functionalities, such as lectin-like activity, which may play a role in plant defense by recognizing and binding specific carbohydrate structures, and antimicrobial activity, which provides protection against a range of bacterial and fungal species. A few members are involved in sulfur amino acid provision from seed meals and may have roles in metalloprotease activity or inhibition of enzymes like alpha-amylase.
DNA-directed RNA polymerase, subunit beta'', eukaryote (RNA_pol_beta''_euk)
Type: Family

RNA polymerase beta'' is involved in the transcription of DNA into RNA. Members of this family are DNA-dependent RNA polymerases that utilise the four ribonucleoside triphosphates as substrates to catalyse the synthesis of RNA from a DNA template. This process is fundamental to the expression of genes and the regulation of cellular functions.
POU domain transcription factor (POU_domain_TF)
Type: Family

The POU transcription factor family is characterized by its involvement in the regulation of gene expression in various developmental and differentiation processes. Members of this family are known to bind specific DNA sequences, often referred to as octamer motifs, to modulate the transcription of target genes. They play pivotal roles in neurodevelopment, sensory neuron specification, and the maintenance of stem cell pluripotency. Additionally, they are implicated in the differentiation of specific cell types in the anterior pituitary and the regulation of immune and neural functions in mucosal epithelial tissues. The POU factors are also associated with the regulation of apoptosis, cell fate decisions during embryogenesis, and the development of the auditory system.
Glycosyltransferase 2 (Glycosyltransferase_2)
Type: Family

The glycosyltransferase 2 family is involved in various biosynthetic processes, including the modification of O antigen, the biosynthesis of 6-O-methylglucose lipopolysaccharides (MGLPs), and the assembly of N-linked glycans. Members of this family catalyze the transfer of sugar moieties from activated sugar donors like UDP-glucose to specific acceptor molecules, which can be lipids or other carbohydrates. This action is crucial for the formation of glycosidic bonds. A significant function of some members is the transfer of 4-deoxy-4-formamido-L-arabinose to undecaprenyl phosphate, modifying lipid A and conferring resistance to polymyxin and cationic antimicrobial peptides, which is essential for bacterial virulence and survival.
Large ribosomal subunit protein eL8/uL1-like (eL8/uL1-like)
Type: Family

This family represents a group of proteins involved in various RNA-related processes within the cell, including Large ribosomal subunit protein eL8 and Large ribosomal subunit protein uL1 . Members of this family are commonly found as components of the large ribosomal subunit, playing a role in protein synthesis by facilitating the translation of mRNA into polypeptide chains. Some proteins in this family are also involved in ribosome biogenesis, including the catalysis of pseudouridylation of rRNA, which contributes to the stabilization of rRNA structure. Additionally, certain members are associated with the spliceosome and rRNA processing machinery, participating in pre-mRNA splicing and the processing of pre-ribosomal RNA. They may bind to specific RNA motifs and contribute to the assembly of ribonucleoprotein complexes, such as the H/ACA snoRNP complex and the SSU processome.
Leguminous Lectin (Leguminous_Lectin)
Type: Family

The leguminous lectin family comprises proteins with a variety of functions, primarily related to carbohydrate recognition and binding. Members of this family are involved in diverse biological processes, including symbiotic interactions, defense mechanisms against pests and pathogens, cell recognition, and inflammatory responses. Lectins in this family typically bind specific sugar moieties such as mannose, glucose, galactose, and N-acetyl-D-galactosamine, and are known to agglutinate cells and precipitate glycoconjugates. Some lectins exhibit hemagglutinating activity and can be toxic to certain insects and other pests, suggesting a role in plant defense. Others are involved in symbiotic relationships, such as arbuscular mycorrhizal symbiosis, and may contribute to the development of symbiosomes. Additionally, certain lectins have been shown to have anti-inflammatory, antinociceptive, and antiviral activities, indicating potential therapeutic applications.
Short-chain dehydrogenases/reductases (SDR)
Type: Family

The Short-chain dehydrogenases/reductases (SDR) family encompasses enzymes that catalyze NAD(P)(H)-dependent redox reactions on a variety of substrates, including fatty acids, steroids, and aromatic compounds. Members of the SDR family are involved in key biosynthetic pathways, such as fatty acid elongation, where they reduce beta-ketoacyl-ACP substrates to beta-hydroxyacyl-ACP products, playing a crucial role in fatty acid biosynthesis. Other functions include the metabolism of bile acids, reduction of acetoacetyl-CoA in polyhydroxybutyrate biosynthesis, and modification of Nod factor fatty acyl chains. Some SDR enzymes are involved in antibiotic biosynthesis, such as novobiocin, or in the degradation of environmental pollutants. The family is characterized by a conserved catalytic motif and typically exhibits a Rossmann fold for binding the NAD(P) cofactor.
FAD-dependent oxidoreductase (FAD-bd_OxRdtase)
Type: Family

The FAD-dependent oxidoreductase family is characterized by its involvement in various redox reactions, where members typically utilize FAD as a cofactor to catalyze the transfer of electrons in diverse biological processes. Functions include the reduction of nitric oxide, rubredoxin, coenzyme A disulfides, and molecular oxygen, as well as the oxidation of NADH. These enzymes play crucial roles in anaerobic respiration, oxidative stress response, and maintenance of redox balance. They are also implicated in electron transfer systems that protect against oxygen exposure in anaerobes. Some family members are involved in hydrocarbon hydroxylation systems, transferring electrons to monooxygenases, and others participate in the reduction of elemental sulfur, contributing to sulfur metabolism.
FrsA esterase (FrsA_esterase)
Type: Family

The FrsA family proteins are esterases that catalyze the hydrolysis of esters. Members of this family are involved in various biological processes, including the degradation of cutin, a plant cuticle polyester, and the hydrolysis of synthetic polyesters like poly(ethylene terephthalate), commonly known as PET. Some family members participate in complex biosynthetic pathways for natural products with biological activities, such as mycotoxin production, antibiotic properties, and cell cycle inhibition. The family includes proteins that can act as quorum-quenching agents, disrupting bacterial communication. Additionally, certain FrsA family proteins are implicated in fungal virulence and plant pathogenicity, with roles in melanin biosynthesis and the production of fungal signals recognized by resistant plants.
Ribose 5-phosphate isomerase (Ribose-5P_isomerase)
Type: Family

The ribose 5-phosphate isomerase family consists of enzymes that play a crucial role in carbohydrate metabolism. Members of this family are responsible for the interconversion of ribose-5-phosphate and ribulose 5-phosphate, a reversible reaction that forms part of the non-oxidative phase of the pentose phosphate pathway. This pathway is essential for the production of ribose sugars for nucleotide synthesis and for the generation of reducing equivalents in the form of NADPH, which is used in various anabolic reactions, including fatty acid synthesis and the maintenance of redox balance within the cell.
Bacterial Fimbrial Adherence (Bact_Fimbrial_Adh_Pro)
Type: Family

The fimbrial protein family is involved in the formation of fimbriae, also known as pili, which are polar filaments extending from the bacterial cell surface. These structures, typically 0.5-1.5 micrometers in length and numbering 100-300 per cell, play a crucial role in bacterial adherence to host epithelial cells and colonization of specific host organs. Fimbriae facilitate the initial attachment of bacteria to host tissues, which is a critical step in the establishment of infections. They can bind to various receptors on host cells, including N-acetylglucosamine-containing receptors and laminin. Some family members are also implicated in microcolony formation and may contribute to adhesion to abiotic surfaces in specific environmental niches. The family includes major structural subunits, adhesins, and minor components that may influence pilus length and biogenesis.
Bacterial CCA-adding enzyme type 3 subfamily (Bact_CCA-adding_enz_type3_sf)
Type: Family

The CCA-adding enzyme family is responsible for the catalysis of the addition and repair of the essential 3'-terminal CCA sequence in tRNAs, a process that does not require a nucleic acid template. Members of this family sequentially add C, C, and A nucleotides to the tRNA nucleotide-73 using CTP and ATP as substrates, releasing inorganic pyrophosphate. The 3'-terminal CCA sequence is crucial for tRNA processing and repair, serving as the site for amino acid attachment during protein synthesis. Additionally, these enzymes participate in tRNA surveillance, marking unstable tRNAs with a CCACCA sequence for rapid degradation, thus distinguishing them from stable tRNAs that receive only the CCA end. The family's role is vital in maintaining the accuracy and efficiency of protein translation by ensuring the proper functioning of tRNAs.
Iron/Manganese Superoxide Dismutase (Fe/Mn_Superoxide_Dismutase)
Type: Family

The iron/manganese superoxide dismutase family comprises enzymes that play a crucial role in cellular defense against oxidative stress. Members of this family catalyze the dismutation of the superoxide anion radical (O2-) into oxygen (O2) and hydrogen peroxide (H2O2), effectively mitigating the potential damage caused by these reactive oxygen species. These radicals are byproducts of normal cellular metabolism and can be harmful to biological systems if not regulated. The enzymes in this family are characterized by their metal cofactor, which can be either iron or manganese, and are found in various cellular compartments, including mitochondria. Some members are known to be resistant to inhibition by cyanide and azide, and their activity can be modulated by various factors, including the presence of hydrogen peroxide or metallothioneins.
AB hydrolase superfamily (AB_hydrolase_sf)
Type: Family

The AB hydrolase superfamily protein family encompasses a diverse range of enzymes with hydrolytic activity on a variety of biological substrates. Members of this family are involved in numerous metabolic and regulatory processes, including lipid metabolism, pyrimidine catabolism, biotin biosynthesis, and peptide degradation. Enzymes in this family exhibit specificities for substrates such as monoacylglycerols, carbamates, esters, and peptides with N-terminal proline. Some members are involved in the degradation of environmental pollutants, playing a role in the bacterial meta-cleavage pathway. The family includes serine hydrolases, lipases, esterases, and peptidases, characterized by their ability to catalyze the cleavage of C-C, C-O, and C-N bonds. The functional diversity within this family reflects the broad range of chemical reactions they mediate, contributing to cellular homeostasis, signaling, and environmental adaptation.
Bacterial Anti-sigma-factor Serine-Protein Kinases (Anti-sigma-factor_SerPK)
Type: Family

The Anti-sigma-factor family consists of serine-protein kinases that function as negative regulators of sigma factor activity, which is crucial for bacterial RNA polymerase holoenzyme formation. Members of the family phosphorylate and inactivate specific antagonist proteins, such as RsbV or SpoIIAA, leading to the release of the kinase and subsequent binding to the sigma factor. This interaction prevents the sigma factor from forming a holoenzyme with RNA polymerase, thus modulating the transcriptional response to environmental stress or developmental changes. Some family members also have the ability to bind and potentially hydrolyze ATP and GTP, suggesting additional regulatory roles.
NADH-dependent flavin reductase (NADH-dep_flavin_reductase)
Type: Family

This family of proteins is involved in the reduction of flavin mononucleotide (FMN) to its reduced form (FMNH2), a critical step in various metabolic pathways. The reduced FMN acts as an electron donor for different enzymatic reactions, including the reduction of pyrimidine by RutA in the Rut pathway, the hydroxylation of aromatic compounds, and the desulfurization of dibenzothiophene. These proteins are capable of using NADH as an electron donor for the reduction of FMN, and some members can also reduce FAD. They play a role in the metabolism of various compounds, contributing to processes such as antibiotic biosynthesis, degradation of environmental pollutants, and iron acquisition.
Complex I Subunit 6 (ComplexI_Subunit6)
Type: Family

The Complex I Subunit 6 family comprises core subunits of the mitochondrial membrane respiratory chain NADH dehydrogenase, also known as Complex I. These proteins are essential for the catalytic activity and assembly of Complex I, which is responsible for the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme in this process is ubiquinone. Members of this family are believed to be part of the minimal assembly required for catalysis within the mitochondrial respiratory chain, playing a crucial role in cellular energy production.
DegV domain-containing (DegV_domain_contain)
Type: Family

The DegV family proteins are characterized by their ability to bind long-chain fatty acids, such as palmitate. Members of the DegV family are implicated in various biological processes, including lipid transport and fatty acid metabolism. The presence of a DegV domain suggests a role in the sequestration or transport of fatty acid molecules, which may be crucial for maintaining lipid homeostasis within the cell. The binding of fatty acids by DegV family proteins could potentially regulate their availability for enzymatic reactions or for the construction of cellular membranes. The consistent annotation across multiple proteins within this family highlights the conserved nature of this function in diverse bacterial species.
UDP-glycosyltransferase (UDP-glycosyltransferase)
Type: Family

The UDP-glycosyltransferase family is involved in phase II biotransformation reactions, where they conjugate lipophilic substrates with glucuronic acid to enhance water solubility and facilitate excretion. They play a crucial role in detoxifying xenobiotics and metabolizing endogenous compounds, including steroid hormones and bile acids. Some family members also contribute to the biosynthesis of complex lipids and glycosides, influencing processes like olfaction and insect development. The family includes enzymes that act on a variety of substrates, from small phenolic compounds to large steroid molecules, and are implicated in the metabolism of drugs, such as angiotensin receptor antagonists and anticancer agents.
Isochorismatase-like hydrolase (Isochorismatase-like_hydrls)
Type: Family

This family of proteins is involved in various metabolic processes, including the hydrolysis of specific substrates to release ammonia and other products. Members of this family catalyze the breakdown of ureidoacrylate to aminoacrylate and carbamate, which further decomposes to release ammonia and CO2. Some proteins in this family are implicated in the biosynthesis of antibiotics like phenazine, siderophores such as enterobactin and vibriobactin, and in the degradation of herbicides. They may also be involved in the regulation of seed germination and in the suppression of plant immunity. The family includes isochorismatase-like hydrolases with high specificity for their respective substrates, playing roles in nitrogen metabolism and bacterial virulence.
GppA/Ppx guanosine pentaphosphate hydrolase (GppA/Ppx_hydrolase)
Type: Family

The GppA/Ppx family is characterized by its members' enzymatic activities, which include the hydrolysis of guanosine pentaphosphate (pppGpp) to guanosine tetraphosphate (ppGpp) and the degradation of inorganic polyphosphates (polyP). The conversion of pppGpp to ppGpp is a crucial reaction in the bacterial stringent response, a cellular adaptation to amino acid starvation that coordinates various cellular activities. This response is mediated by pppGpp and ppGpp, which are signaling molecules in the cytoplasm. Some family members also exhibit exopolyphosphatase activity, releasing orthophosphate from the ends of polyP chains. This activity can be processive and may prefer long-chain polyphosphates, although some members have a preference for shorter chains. The family includes proteins with regulatory roles in interorganelle communication and metabolic interactions between cellular pathways in eukaryotes, such as the retrograde regulation protein in yeast.
Nuclear hormone receptor family NR2 subfamily (Nuclear_hormone_rcpt_NR2)
Type: Family

The nuclear hormone receptor family NR2 subfamily consists of transcription factors that play diverse roles in regulating gene expression in various biological processes, including development, metabolism, and immune response. Members of this family are characterized by their ability to bind DNA as monomers or heterodimers to hormone response elements (HREs) and modulate transcription in response to ligands such as retinoic acid. They are involved in critical functions such as retinal development, circadian rhythm maintenance, lipid metabolism, and embryogenesis. Some act as orphan receptors with no known ligands, while others are activated by retinoids. They can function as repressors or activators of transcription, influencing pathways like spermatogenesis, stem cell proliferation, and photoreceptor cell development. The family includes receptors that are essential for vision, regulators of hormonal responses, and mediators of developmental processes in both vertebrates and invertebrates.
Phosphoglycerate Mutase/Phosphatase (PGM_Phosphatase)
Type: Family

The phosphoglycerate mutase family is involved in various metabolic processes, including glycolysis and gluconeogenesis, by catalyzing the interconversion of 2-phosphoglycerate and 3-phosphoglycerate. Some members exhibit phosphatase activity, participating in the biosynthesis of compounds like mycobacterial methylglucose lipopolysaccharides or in the dephosphorylation of specific phosphosugars. Others have evolved to acquire specialized functions, such as the regulation of carbohydrate metabolism, involvement in serine biosynthesis, or the hydrolysis of phospho groups from vitamin B12 intermediates. The family also includes proteins with broader substrate specificity, acting on various phosphorylated compounds but lacking phosphoglycerate mutase activity. Collectively, the family plays a crucial role in carbohydrate metabolism and other biosynthetic pathways, with some members also implicated in stress response and immune modulation.