SII-SWORD/CoKE huggingface dataset:
Glycosaminoglycan & Ulvan Degrading Sulfatases (GAG_Ulvan_Degrading_Sulfatases)
Type: Family

The sulfatase family is involved in the degradation of various sulfated polysaccharides. Members of this family include enzymes that play a crucial role in the breakdown of glycosaminoglycans such as chondroitin sulfate and dermatan sulfate, by hydrolyzing the 6-sulfate groups of the N-acetyl-D-galactosamine 6-sulfate units. This activity is essential for the persistence of gut symbionts like B.thetaiotaomicron in the gastrointestinal tract. Other family members are involved in the degradation of ulvan, a major polysaccharide in the cell walls of green seaweed, by desulfating specific disaccharide building blocks, aiding in the utilization of ulvan as a nutrient source. The family's collective activities are important for the recycling of complex carbohydrates in various biological systems, including marine ecosystems and the human gut microbiome.
Mechanosensitive channel MscS-like (MscS-like_channel)
Type: Family

This family of proteins includes mechanosensitive channels that respond to changes in membrane tension and specific ionic conditions. Members of this family are involved in the regulation of osmotic pressure within cells, although not all have a major role in this process. They can form ion channels with varying conductance and gating durations, and some are activated by high concentrations of certain ions such as K(+), NH(4)(+), Rb(+), or Cs(+). These channels are essential for protecting cells from hypoosmotic stress, and their activity is crucial for cellular responses to mechanical stimuli.
Aromatic CoA oxygenase/epoxidase components (Aromatic_CoA_ox/epox)
Type: Family

This family of proteins includes components of multicomponent enzyme systems that catalyze the oxygenation and epoxidation of CoA-thioester substrates. Members of this family are involved in the aerobic biodegradation of aromatic compounds, playing a role in the ring-cleavage step of the degradation pathway. They function by incorporating one atom of molecular oxygen into the substrate, resulting in the formation of an epoxide intermediate. These proteins are typically part of larger enzyme complexes and may serve as either the catalytic subunit directly involved in the oxygenation reaction or as structural subunits essential for the integrity and function of the catalytic components.
ECF Sigma-70 Factor Domain-Containing Protein (ECF_Sigma-70_Domain)
Type: Family

This family of proteins includes extracytoplasmic function (ECF) sigma factors that are involved in the initiation of RNA transcription. They promote the attachment of RNA polymerase to specific promoter DNA sites, facilitating the opening of the DNA double helix and the formation of the transcription bubble. These proteins contain a sigma-70 factor domain-2 for interaction with the -10 element and a sigma-70 factor domain-4 with a helix-turn-helix motif for binding the -35 element in promoter DNA. They interact with RNA polymerase subunits RpoA, RpoB, and RpoC. Although typically regulated by anti-sigma factors, no such regulators are known for these proteins, suggesting a unique regulatory mechanism within this subfamily.
Gliding Motility-Regulating GTPase (Gliding_Motility_GTPase)
Type: Family

This family of proteins includes members that are involved in gliding motility mechanisms in certain bacterial species. Specifically, one member is known to be essential for multicellular development and for coordinating different types of gliding motility, which are critical for bacterial movement on surfaces. The protein acts as an intracellular switch, regulating the direction and speed of gliding. Additionally, this protein belongs to the small GTPase superfamily, indicating a role in signal transduction processes involving GTP binding and hydrolysis. The family appears to be involved in cellular movement and signaling.
Membrane-associated Transporter-like (Membrane-Transporter-like)
Type: Family

This family of proteins includes members that are involved in transport across cellular membranes, particularly for sulfate ions. One characterized member is suggested to belong to the SLC26A/SulP transporter family, which is known for mediating the exchange of anions across the membrane. The functions of the other members are not well-defined, but they may be involved in similar transport processes or other vacuolar and membrane-associated roles in various organisms.
OsmC/Ohr Peroxiredoxin (OsmC_Ohr_Peroxiredoxin)
Type: Family

The OsmC/Ohr family proteins are involved in the detoxification of organic hydroperoxides, which are harmful by-products of oxidative stress. Members of this family exhibit a preference for metabolizing organic hydroperoxides rather than inorganic hydrogen peroxide. This activity is crucial for maintaining cellular redox balance and protecting cells from oxidative damage. The family includes proteins known as Peroxiredoxin OsmC, which are characterized by their ability to reduce peroxides, and also comprises uncharacterized proteins like YmaD, which share sequence similarity with characterized members, suggesting a related function.
5-oxoprolinase subunit C (PxpC)
Type: Family

The PxpC family proteins are enzymes that play a crucial role in the metabolic pathway of glutathione degradation. They catalyze the cleavage of 5-oxoproline (pyroglutamic acid) to form L-glutamate. This reaction is coupled with the hydrolysis of ATP to ADP and inorganic phosphate, which provides the necessary energy for the reaction to occur. In Bacillus subtilis, the PxpC family protein also interacts with PxpB (KipI), a sporulation inhibitor, by binding to it and preventing its inhibitory action on kinase A, thus having a regulatory role in the process of sporulation.
Transposase-Methyltransferase Hybrid (Transposase-MT_Hybrid)
Type: Family

This family of proteins includes DNA-binding transposases and methyltransferases. Members of this family are involved in various DNA-related processes such as DNA double-strand break repair, stalled replication fork restart, and DNA integration. They exhibit a sequence-specific DNA-binding activity, recognizing specific DNA sequences to mediate DNA nicking and end joining. Additionally, they possess histone methyltransferase activity, targeting specific lysine residues on histone H3, which plays a role in the regulation of DNA repair and replication. Some members have evolved from transposases and have retained nuclease activity, although they have lost the ability to catalyze transposition due to active site mutations.
CAAX motif-specific protease (CAAX_protease)
Type: Family

This family of proteins is involved in post-translational modification processes, specifically in the proteolytic cleavage of farnesylated peptides containing the CAAX motif, where C is cysteine, A is an aliphatic amino acid, and X is any amino acid. Members of this family are implicated in the regulation of cellular processes such as quorum sensing, which is crucial for virulence in some bacteria. The protease activity of these proteins does not involve processing of pheromone precursors but rather exerts control over signaling pathways through protease-dependent mechanisms.
Zinc-type Alcohol Dehydrogenase-like (Zinc_ADH-like)
Type: Family

This family of proteins includes zinc-type alcohol dehydrogenase-like enzymes that are part of the zinc-containing alcohol dehydrogenase family, specifically within the quinone oxidoreductase subfamily. Members of this family are involved in various metabolic processes, including the biosynthesis of complex organic molecules. For example, one member is implicated in the biosynthesis of phomenoic acid, a compound with antifungal properties, suggesting a role in microbial competition within environmental niches. Although the precise functions of some members remain to be fully characterized, the family generally participates in redox reactions where they may act on alcohols and other substrates, utilizing zinc as a cofactor for catalytic activity.
Acid resistance chaperone HdeD (Acid_resist_chaperone_HdeD)
Type: Family

This family of proteins includes HdeD, which is involved in the acid resistance system of bacteria. It functions by helping to maintain periplasmic pH under extremely acidic conditions, which is crucial for the survival of acid-sensitive proteins during acid stress. HdeD acts as a chaperone that binds to unfolded proteins, preventing their aggregation and facilitating their proper refolding when normal pH conditions are restored.
Fe(2+) transport protein A (FeoA)
Type: Family

This family of proteins is involved in the cellular uptake of ferrous ions (Fe(2+)). Members of this family facilitate the transport of Fe(2+) across the cell membrane, which is a critical process for cellular function and metabolism. Iron is an essential element for many biological processes, including oxygen transport, DNA synthesis, and electron transport in respiration. These proteins, however, are not known to influence the GTPase activity of associated proteins such as FeoB.
Major Facilitator Superfamily Exporter (MFS_Exporter)
Type: Family

This family of proteins is part of the major facilitator superfamily (MFS), which is one of the largest groups of secondary transporters. Members of this family are involved in various transport functions across the cellular membrane, utilizing the electrochemical gradient. The proteins in this family are characterized by their ability to facilitate the movement of small solutes in response to ion gradients. One characterized member is known to participate in the export of staphylopine, a metallophore, suggesting a role in metal ion homeostasis and transport. However, the specific functions of other members within this family may vary and are not fully characterized.
REP-associated tyrosine transposase (RAYT_transposase)
Type: Family

This family of proteins includes transposases that are associated with repeated extragenic palindromes (REPs) and are involved in the transposition of insertion sequence (IS) elements. Members of this family are responsible for the excision of the IS element from the donor DNA and its reinsertion into the target DNA, which can result in an increase in the copy number of the IS. These proteins are typically flanked by REPs and can bind and cleave at these sites, potentially playing a role in the generation of variability and amplification of bacterial interspersed mosaic elements (BIMEs). The activity of these transposases is regulated by metal ions such as magnesium and manganese.
MOSC domain-containing protein (MOSC_domain)
Type: Family

This family of proteins is involved in the biosynthesis and coordination of metal-sulfur clusters and the reduction of N-oxygenated molecules. Members of this family are characterized by the presence of a MOSC domain, which is responsible for the tight coordination of the molybdenum cofactor within the core of the enzyme. The proteins in this family play a role in various metabolic processes, including the reduction of N-hydroxylated prodrugs to increase drug bioavailability and the regulation of endogenous nitric oxide levels through the reduction of mitochondrial N(omega)-hydroxy-L-arginine. The enzymatic activity involves electron transfer from NADH to cytochrome b5 reductase and cytochrome b5, which primes the active site for substrate reduction.
Vacuolar processing and transposase activity regulators (Vacuolar_transposase_reg)
Type: Family

This family of proteins is involved in diverse cellular processes including vacuolar processing, morphology, transposase activity, and sumoylation. Members of this family are known to play roles in the regulation of transcription, cell proliferation, and may interact with viral elements during infection. Some proteins within this family have E3 SUMO-protein ligase activity, influencing chromatin remodeling and gene expression by modifying transcriptional repressors. Additionally, they may bind to specific DNA sequences in gene promoters, particularly those of ribosomal proteins, to modulate transcription.
NmrA-type domain-containing oxidoreductase (NmrA-type_oxidoreductase)
Type: Family

This family of proteins includes NmrA-type oxidoreductases involved in various redox reactions. Members of this family are implicated in the reduction of quinones and may have roles in redox sensing and regulation of growth. Additionally, some proteins in this family participate in complex biosynthetic pathways, such as the production of alkaloidal terpenoids. These processes involve multiple enzymatic steps, including cyclization of farnesyl pyrophosphate, oxidative conversions, decarboxylations, and acylations to produce bioactive compounds. The family members exhibit a conserved domain that is characteristic of the NmrA-type oxidoreductase family, indicating a shared evolutionary origin and similar catalytic functions.
Colicin_V_prod-like (CvpA-like)
Type: Family

This family includes proteins similar to the E. coli colicin V production protein (cvpA).
Glycosyl Hydrolase Family 97 (Glycosyl_hydrolase_97)
Type: Family

The glycosyl hydrolase 97 family encompasses enzymes with diverse substrate specificities, including alpha-galactosidases and glucan 1,4-alpha-glucosidases. Alpha-galactosidases in this family are capable of hydrolyzing alpha-1,6 disaccharides like melibiose and synthetic substrates such as p-nitrophenyl alpha-galactoside, retaining the anomeric configuration. They do not act on substrates like DNP-Glc or pNP-Glc. Another member, glucan 1,4-alpha-glucosidase, targets alpha-1,4-glucosidic linkages and can also cleave alpha-1,6-, alpha-1,3-, and alpha-1,2-glucosidic linkages in starch degradation. The activity of these enzymes is known to be inhibited by EDTA. Collectively, the glycosyl hydrolase 97 family plays a crucial role in carbohydrate metabolism by breaking down complex sugars into simpler forms, facilitating their utilization or further processing within various biological systems.
Electron Transfer Amicyanin (ET_Amicyanin)
Type: Family

This family of proteins serves as electron transfer intermediates in bacterial respiratory chains. Members of this family accept electrons from methylamine dehydrogenase and subsequently transfer them to other electron carriers such as soluble cytochrome c or pseudoazurin. These proteins play a crucial role in the energy metabolism of certain bacteria by facilitating the transfer of electrons in the process of oxidative phosphorylation.
Cyclic-di-AMP phosphodiesterase PgpH (PgpH_phosphodiesterase)
Type: Family

The PgpH phosphodiesterase family is characterized by its enzymatic activity as a phosphodiesterase, primarily hydrolyzing cyclic di-3',5'-adenylate (c-di-AMP), a second messenger involved in various cellular processes such as growth, DNA repair, and cell wall homeostasis. Members of the PgpH family are considered to be major c-di-AMP phosphodiesterases within their respective bacterial cells. Excess c-di-AMP is toxic, and its regulation is crucial for cellular function. Some family members are also implicated in host-pathogen interactions, where c-di-AMP is secreted into the host cytoplasm, triggering an immune response. Additionally, the family's activity can be regulated by other nucleotides such as ppGpp, which inhibits c-di-AMP hydrolysis without affecting binding. The family is defined by a conserved cytoplasmic HD domain responsible for its phosphodiesterase activity.
Acyl-coenzyme A thioesterase PaaI (Acyl-CoA_thioesterase_PaaI)
Type: Family

This family of proteins includes thioesterases that exhibit a preference for hydroxylated phenylacetyl-CoA esters. Members are known to hydrolyze substrates such as 3,4-dihydroxyphenylacetyl-CoA, 3-hydroxyphenylacetyl-CoA, and 4-hydroxyphenylacetyl-CoA. They are characterized by their inability to act on 4-hydroxybenzoyl-CoA and 4-hydroxyphenacyl-CoA. The enzymatic activity of these proteins plays a role in the breakdown and utilization of aromatic compounds, contributing to various metabolic processes.
Glycosyltransferase 117 domain-containing protein (GT117_domain-containing)
Type: Family

This family of proteins functions as O-mannosyl-transferases, enzymes that catalyze the transfer of mannosyl residues to the hydroxyl groups of serine or threonine residues within target proteins. They are known to specifically modify the IPT/TIG domain of certain proteins, such as MET and MST1R/RON. The mannosylation process carried out by these enzymes results in the addition of single mannose glycans, which are not further elongated or modified. This post-translational modification plays a crucial role in the function and regulation of the modified proteins.
Glutamine Synthetase Type-3 (GS_Type-3)
Type: Family

This family of proteins includes enzymes that catalyze the ATP-dependent biosynthesis of glutamine from glutamate and ammonia. These enzymes are not regulated by adenylation. Some members of this family may be inhibited by certain amino acids, such as L-histidine, L-arginine, and L-methionine-DL-sulphoximine, although this is not a universal characteristic of all family members.
Bacteriophage Baseplate Hub (Phage_Baseplate_Hub)
Type: Family

This family of proteins is involved in the assembly and structural integrity of bacteriophage baseplates. The baseplate is a critical component of the phage that mediates host cell recognition and attachment, initiating the infection process. Members of this family are thought to function as hub proteins that may form part of the central structure of the baseplate, providing a scaffold for other proteins to attach and interact. These proteins are essential for the proper assembly of the baseplate wedges, which are necessary for the phage to infect bacterial cells effectively.
Rab4/Rab5 effector domain-containing protein (Rab4/Rab5_effector)
Type: Family

This family of proteins includes effectors of Rab GTPases, specifically Rab4 and Rab5, involved in early endocytic membrane fusion and trafficking. Members of this family are essential for the fusion of endosomes and for the transport of recycling endosomes. They facilitate lysosomal trafficking of enzymes such as cathepsin D and are implicated in the recycling of membrane receptors like the transferrin receptor from endosomes back to the plasma membrane. These proteins have the ability to bind to phospholipid vesicles containing phosphatidylinositol 3-phosphate, indicating a role in phosphoinositide-mediated signaling pathways. Additionally, they may be involved in vacuole segregation and protein sorting in yeast, suggesting a broader function in interorganelle traffic across different species.
Oxygen and lipid transport regulator (O2_lipid_transport_reg)
Type: Family

This family of proteins is involved in various biological processes including the response to environmental oxygen levels, lipid and xenobiotic compound transport, and embryonic development. Members of this family may inhibit gene transcription related to hypoxia-inducible factors and are implicated in processes such as locomotion, egg-laying, and body morphogenesis. They also play a role in the transport of lipids from the intestine to other tissues, which is crucial for yolk transport into oocytes and embryonic development.
Acyl/Acetyltransferase Enzymes (Acyl/Acetyltrans_Enzymes)
Type: Family

This family of proteins includes enzymes with acyltransferase and acetyltransferase activities. Members of this family are involved in the biosynthesis of various compounds, such as antibiotics, by catalyzing the transfer of acyl or acetyl groups from CoA-linked donors to acceptor molecules. Some proteins in this family have a broad substrate specificity, accepting linear CoA substrates of different lengths and converting them into acylated products. These enzymes play a role in the formation of bioactive molecules, including thiomarinol analogs, by transferring acyl groups to specific substrates like holothin.
Sugar-specific ABC transporter permease (Sugar_ABC_transporter)
Type: Family

This family of proteins is involved in the transport of specific sugars across the cell membrane. They are components of ABC transporter complexes, which are highly specific for their sugar substrates. These proteins play a crucial role in the uptake of sugars like trehalose and glucose, which are essential for various cellular processes including virulence in certain bacteria. They are likely responsible for the translocation of these sugars across the membrane, facilitating their internalization into the cell.
Bacillus subtilis Transition State Regulators (B_subtilis_Trans_State_Reg)
Type: Family

The Bacillus subtilis transition state regulator family includes proteins that play a critical role in the transition from vegetative growth to stationary phase and sporulation. Members of the family function as transcriptional regulators, acting as repressors or activators of genes involved in these developmental stages. The family is characterized by its ability to bind DNA, with some members having specific binding sites, while others bind non-specifically. The activity and specificity of DNA-binding are influenced by different domains within the proteins, which may also interact with other factors to modulate gene expression. These regulators are essential for the proper timing of gene expression during the transition to stationary phase and for the development of the forespore, impacting spore germination and resistance.
Cell-binding uncharacterized protein (Cell-binding_unc_protein)
Type: Family

This family of proteins includes uncharacterized members that have been associated with cell-binding properties. Specifically, isolated peptides from one member have demonstrated the ability to interact with human monocytoblastic and epithelial cell lines. The exact biological functions and mechanisms of these proteins remain to be elucidated, but the observed cell-binding activity suggests a potential role in cell-cell or cell-matrix interactions, which could be important in processes such as cell adhesion, signaling, or immune response modulation.
Chloroplast-localized Quinone Oxidoreductase (Chloroplast_QOR)
Type: Family

This family of proteins includes NADPH-dependent quinone oxidoreductases that are involved in various redox reactions. Members of this family are capable of reducing quinones and other related compounds through single-electron transfers. These enzymes play roles in processes such as haustorium initiation in parasitic plants and the reduction of reactive electrophile species derived from poly-unsaturated fatty acid peroxides. They exhibit substrate specificity, with some members unable to reduce certain types of quinones or short-chain alkenals and alkenones. The proteins are characterized by the presence of a zinc-containing alcohol dehydrogenase domain and are localized to chloroplasts, indicating a role in plant-specific metabolic pathways.
Nodulation factor acetyltransferase (Nod_factor_acetyltransferase)
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 important in the nodulation process, which is a key aspect of the symbiotic relationship between certain plants and nitrogen-fixing bacteria. The proteins in this family share a commonality in structure, suggesting a conserved mechanism of action in their enzymatic activity.
Bacterial NAD biosynthesis/regulator protein (NAD_biosynth-regulator)
Type: Family

This family of proteins includes enzymes with multiple activities involved in NAD biosynthesis and regulation. They possess nicotinamide mononucleotide (NMN) adenylyltransferase activity, catalyzing the formation of NAD(+) from nicotinamide ribonucleotide and ATP. Additionally, they exhibit ribosylnicotinamide (RN) kinase activity, phosphorylating RN to produce nicotinamide ribonucleotide. Some members also have a DNA-binding domain that regulates the transcription of NAD biosynthetic genes in response to NAD and ATP levels. The enzymatic activities are subject to feedback regulation by NAD, with high levels inhibiting the RN kinase activity and repressing NAD synthetic genes, while low levels activate the enzymes and derepress biosynthetic genes.