SII-SWORD/CoKE huggingface dataset:
MshD Mycothiol Acetyltransferase (MshD_Acetyltransferase)
Type: Family

The MshD acetyltransferase family is characterized by its ability to catalyze the transfer of an acetyl group from acetyl-CoA to desacetylmycothiol, forming mycothiol. Mycothiol is a thiol compound that acts as an antioxidant in certain bacteria, playing a crucial role in protecting against oxidative stress and maintaining the redox balance within the cell. Members of the MshD subfamily are involved in the final step of mycothiol biosynthesis. This family also includes other N-acetyltransferases with diverse functions, such as acetylation of ribosomal proteins, detoxification of aminoacyl adenylates, and resistance to antibiotics through acetylation. The family is part of the broader acetyltransferase superfamily, which encompasses enzymes that transfer acetyl groups to various substrates, impacting a wide range of biological processes.
Sodium:Solute Symporter (Sodium:Solute_Symporter)
Type: Family

The Sodium:Solute Symporter (SSF) family encompasses a range of transporters that facilitate the movement of solutes across cellular membranes in conjunction with sodium ions. Members of this family are integral membrane proteins that typically operate via a secondary active transport mechanism, using the electrochemical gradient of sodium ions to drive the transport of solutes such as acetate, proline, pantothenate, monocarboxylates, and spermidine. These transporters play crucial roles in nutrient uptake, osmoregulation, and metabolic processes across various organisms. Some members are also involved in the uptake of compounds that are part of host defense mechanisms, such as histatin 5 in Candida albicans. The activity of these transporters can be regulated by various factors, including membrane lipid composition, osmotic conditions, and the presence of specific inhibitors.
Serine protease S9B/DPPIV (Serine_Prot_S9B/DPPIV)
Type: Family

The peptidase S9B family, also known as the DPPIV subfamily, includes serine proteases with dipeptidyl peptidase activity, which cleave off N-terminal dipeptides from proteins with a preference for a proline residue at the penultimate position. Members of this family are involved in various physiological processes, including immune response regulation, tissue remodeling, and cell signaling. Some proteins within this family act as venom toxins, contributing to the processing of venom proteins and modulation of immune cell chemotaxis. Others are involved in cell surface expression and modulation of potassium channels, although they lack dipeptidyl aminopeptidase activity. The family also includes prolyl tripeptidyl peptidases that release tripeptides from protein N-termini, and proteins that participate in extracellular matrix degradation and play roles in tissue remodeling, fibrosis, wound healing, inflammation, and tumor growth.
Plant defense and hormone signaling protein (Plant_def-hormone_signal)
Type: Family

This family of proteins is involved in various plant-specific physiological processes, including pathogen defense, hormone binding and signaling, and allergenic responses. Members of the family are known to participate in the recognition and response to pathogens, as well as in the regulation of plant growth and development through interaction with hormones such as abscisic acid, cytokinins, gibberellins, and melatonin. Some proteins within this family have enzymatic activity, such as ribonuclease activity, and are implicated in the biosynthesis of alkaloids. Additionally, several members are associated with allergenic reactions in humans, particularly in response to pollen and certain fruits.
Outer Membrane Protein Chaperone SurA (OMP_Chaperone_SurA)
Type: Family

The SurA chaperone family is involved in the correct folding and assembly of outer membrane proteins. Members of this family recognize specific patterns of aromatic residues and the orientation of their side chains, which are typically found in integral outer membrane proteins. The SurA chaperones may function at both early periplasmic and late outer membrane-associated steps of protein maturation. They contain a peptidyl-prolyl cis-trans isomerase (PPIase) activity within the second parvulin domain, although this isomerase activity is not essential for their chaperone function. The N-terminal region and the C-terminal tail of SurA proteins are necessary and sufficient for their chaperone activity and are also required for porin recognition. These chaperones are essential for the survival of bacteria in various stages of growth and are involved in processes such as pilus biogenesis.
Flavin monoamine oxidase and related enzymes (Flavin_monoamine_oxidase)
Type: Family

This family of proteins includes enzymes that catalyze the oxidative deamination of various L-amino acids, producing hydrogen peroxide and other byproducts. Members of this family exhibit a range of biological activities, such as antibacterial, antiparasitic, and cytotoxic effects against cancer cell lines. Some are involved in the regulation of polyamine intracellular concentration and may play roles in immune regulation by affecting T-cell activation and differentiation. They are also implicated in epigenetic regulation through histone demethylation, influencing transcriptional activation or repression. The family includes L-amino acid oxidases with diverse substrate specificities, polyamine oxidases, and lysine-specific histone demethylases, among others.
Cycloisomerase 2 (Cycloisomerase_2)
Type: Family

The Cycloisomerase 2 family proteins are primarily involved in the hydrolysis of 6-phosphogluconolactone to 6-phosphogluconate, a key step in the pentose phosphate pathway which is crucial for cellular processes such as nucleotide synthesis and the generation of NADPH. Additionally, some members of the family have been implicated in a syn cycloisomerization process, and one member is suggested to have a role in ulvan degradation, indicating a potential for diverse substrate specificity and enzymatic functions within the family.
E-box Binding Transcriptional Regulators (E-box_TF_Regulators)
Type: Family

The protein family functions as transcriptional regulators with diverse roles in development, differentiation, and metabolism. Members of the family are characterized by their ability to bind E-box consensus sequences (5'-CANNTG-3') and modulate gene expression. They are involved in processes such as myogenesis inhibition, neurogenesis, cardiac morphogenesis, pancreas development, limb development, and epithelial-mesenchymal interactions. Some act as transcriptional repressors, while others form heterodimers with E proteins to activate or repress transcription. They play roles in cell fate determination, maintenance of stem cell pluripotency, and regulation of metabolic pathways. The family includes factors that are essential for the development of specific tissues and organs, and for the maintenance of homeostasis in adult tissues.
STE20 Serine/Threonine-Protein Kinase (STE20_Ser/Thr_kinase)
Type: Family

The STE20 protein kinase family is involved in various signaling pathways that regulate key cellular processes. Members of this family function as MAP4K components in the MAPK pathway, playing crucial roles in responses to mating pheromones, cell polarity, and cell cycle regulation. They are also integral to the Hippo signaling pathway, which is pivotal for organ size control and tumor suppression by modulating cell proliferation and apoptosis. STE20 kinases phosphorylate a range of substrates, including histone H2B and various regulatory proteins, influencing apoptosis, cytoskeleton dynamics, cell adhesion, migration, and transcriptional regulation. Their kinase activity is regulated by caspase cleavage, homodimerization, autophosphorylation, and interactions with small G proteins and regulatory proteins.
Gram-negative Bacterial Carbohydrate Uptake Porin (G_neg_Bact_CarbUptk_Porin)
Type: Family

The LamB porin family is characterized by proteins involved in the transport of various carbohydrates across the outer membrane of Gram-negative bacteria. Members of this family facilitate the uptake of maltose, maltodextrins, and potentially other sugars such as sucrose, with some showing broad carbohydrate specificity. These porins typically form trimeric beta-barrel structures that allow the passive diffusion of substrates. Certain members also serve as receptors for bacteriophages. The family includes well-characterized maltoporins, which are essential for the translocation of larger maltodextrins and may contain a hydrophobic path to guide sugars through the channel. Some variants are known to not act as phage receptors, while others are indispensable for this function. Additionally, cryptic porins with low affinity for aromatic beta-D-glucosides suggest an evolutionary diversity within the family.
5-Methylthioadenosine/S-adenosylhomocysteine deaminase (MTA/SAH_deaminase)
Type: Family

The MTA/SAH deaminase family consists of enzymes that catalyze the deamination of 5-methylthioadenosine (MTA), S-adenosyl-L-homocysteine (SAH), and adenosine, producing their respective inosine analogs. These reactions are crucial for the recycling of S-adenosyl-L-methionine (SAM), a vital methyl group donor in numerous methylation reactions. The deamination process facilitates the conversion of SAH, a byproduct of SAM-dependent methylation, back into methionine, which can then be used to regenerate SAM, thereby maintaining the cellular methyl cycle. Some members of the family also deaminate 5'-deoxyadenosine, playing a role in the recycling of 5'-deoxyadenosine for the biosynthesis of aromatic amino acids in certain organisms. The family belongs to the metallo-dependent hydrolases superfamily, indicating a dependence on metal ions for catalytic activity.
Cellulose-degrading glycosyl hydrolase 3 (Cellulose_deg_GH3)
Type: Family

The glycosyl hydrolase 3 family encompasses enzymes primarily involved in the hydrolysis of glycosidic bonds, facilitating the degradation of cellulosic biomass. Members of this family catalyze the cleavage of beta-glucosidic linkages in cellobiose, cellotriose, and various glucan polymers, releasing glucose. This process is crucial in the cellulolytic system, as it represents the final step in the conversion of cellulose to glucose, which can then be utilized by the organism. Some family members exhibit broad substrate specificity, extending their activity to different oligosaccharides and glycosides. The activity of these enzymes is essential for the complete breakdown of cellulose, a major component of plant cell walls, and thus plays a significant role in carbon cycling and biomass conversion. Additionally, certain enzymes within the family are subject to regulation by metal ions, indicating a level of control over their catalytic activity in response to environmental factors.
TorD/DmsD family chaperones (TorD/DmsD_chaperones)
Type: Family

The TorD/DmsD family includes chaperone proteins that are involved in the biogenesis and assembly of various molybdoenzymes, such as DMSO reductase and TorA. These chaperones may act by facilitating the correct folding and maturation of substrate proteins, ensuring that they are in a conformation competent for acquiring necessary cofactors like molybdenum. Some family members are also involved in the assembly of enzyme complexes prior to their periplasmic translocation via the Tat pathway. Additionally, certain chaperones within this family may increase the activity of other proteins, such as YcdX, by assisting in the proper insertion of metal ions into catalytic sites.
NAD(P)H-quinone oxidoreductase subunit 6, plant (NAD(P)H-Q_Oxidoreduct_6)
Type: Family

NAD(P)H-quinone oxidoreductase subunit 6 is involved in the photosynthetic electron transport chain within chloroplasts. It is responsible for shuttling electrons from NAD(P)H to plastoquinone via FMN and iron-sulfur (Fe-S) centers. The process is coupled with proton translocation across the membrane, which contributes to the creation of a proton gradient. This gradient is then utilised for ATP synthesis, thereby conserving the energy from the redox reaction. NAD(P)H-quinone oxidoreductase subunit 6's role is not limited to photosynthesis, as it may also participate in a chloroplast respiratory chain, indicating a broader involvement in plant energy metabolism.
Cation Diffusion Facilitator Transporter (CDF_Transporter)
Type: Family

The Cation Diffusion Facilitator (CDF) family is involved in the transport of divalent metal cations across cellular membranes to maintain metal homeostasis. Members of this family function as efflux pumps, exporting excess metal ions such as Zn(2+), Cd(2+), and Fe(2+) from the cytoplasm, thereby playing a crucial role in metal detoxification. Some members are also involved in the sequestration of metals into vacuoles or are part of systems like magnetosome formation, which requires the transport and biomineralization of iron. The activity of these transporters can be regulated by metal binding, which may induce conformational changes affecting the transport mechanism.
Glutamine Synthetase (Glutamine_Synthetase)
Type: Family

The glutamine synthetase family comprises enzymes that catalyze the ATP-dependent conversion of glutamate and ammonia to glutamine, playing a crucial role in nitrogen metabolism. In the brain, they regulate ammonia levels and convert neurotoxic glutamate to glutamine, while in the liver, they are involved in ammonia removal. These enzymes are essential for cell proliferation and vascular development. Some isozymes are involved in the reassimilation of ammonia generated by photorespiration in plants, contributing to metabolic homeostasis and plant growth. Certain members may also have palmitoyltransferase activity, influencing GTPase activation and ribosomal biogenesis.
Light-independent protochlorophyllide reductase (LIPOR_BchN/ChlN)
Type: Family

The BchN/ChlN family includes proteins that are components of the dark-operative protochlorophyllide reductase (DPOR) complex. DPOR is responsible for the light-independent reduction of protochlorophyllide (Pchlide) ring D, resulting in the formation of chlorophyllide a (Chlide). This reaction is a key step in the biosynthesis of chlorophyll, which is essential for photosynthesis. The family members utilize Mg-ATP and reduced ferredoxin as substrates for the reduction process. The NB-protein complex, consisting of subunits BchN-BchB or ChlN-ChlB, serves as the catalytic component of DPOR. Some members of the family are also involved in the conversion of chlorophylls into bacteriochlorophylls by reducing ring B of the tetrapyrrole.
Ion-translocating oxidoreductase complex subunit B (RnfB_subfamily)
Type: Family

The RnfB subfamily is a group of iron-sulfur proteins that are part of a membrane-bound complex known as the ion-translocating oxidoreductase complex. The primary function of the RnfB subfamily is to couple electron transfer with the translocation of ions across the membrane. These proteins are involved in a variety of metabolic reactions, facilitating the transfer of electrons. The RnfB subfamily is characterized by the presence of a 4Fe4S bacterial-type ferredoxin domain, which plays a crucial role in their electron transfer capabilities. Members of this subfamily are essential for the proper functioning of the ion-translocating oxidoreductase complex, contributing to the energy metabolism and homeostasis of the cell.
Plant 2-oxoglutarate-dependent oxidoreductases (Plant_2OG-oxidoreductases)
Type: Family

The iron/ascorbate-dependent oxidoreductase family encompasses enzymes involved in plant secondary metabolite biosynthesis, including flavonoids, anthocyanidins, and plant hormones like ethylene. Members catalyze various reactions such as hydroxylation, demethylation, and oxidation, often using 2-oxoglutarate as a co-substrate. They play roles in plant development, defense against pathogens, and response to environmental stress. Some family members regulate salicylic acid homeostasis and shoot development, while others participate in the biosynthesis of phytosiderophores and the degradation of melatonin. The family also includes enzymes involved in the metabolism of benzylisoquinoline alkaloids, contributing to the production of compounds like morphine.
Antennapedia-type homeobox (Antp_homeobox)
Type: Family

The Antp homeobox family comprises sequence-specific transcription factors that play a crucial role in the developmental regulatory system. These proteins are responsible for providing cells with specific positional identities along the anterior-posterior axis during development. They are involved in the regulation of segmental identity and pattern formation, controlling cell differentiation in various tissues including epidermal, neuronal, and mesodermal cells. Some family members also have the ability to bind to their own promoters and regulate their expression. The DNA-binding specificity of these transcription factors is often characterized by a conserved motif that they recognize on the DNA. The family is essential for proper development and body segmentation, influencing the fate of cells and tissues in a wide range of organisms from invertebrates to vertebrates.
Lipid A-modifying glycosyltransferase 83 (LipidA_mod_glycosyltrf_83)
Type: Family

The glycosyltransferase 83 family is involved in the modification of lipid A, a component of the lipopolysaccharide (LPS) in bacterial outer membranes. Members of the family catalyze the transfer of specific sugar moieties to lipid A, which is crucial for bacterial resistance to polymyxin and cationic antimicrobial peptides. For example, they transfer the L-Ara4N moiety of the glycolipid undecaprenyl phosphate-alpha-L-Ara4N to lipid A. This modification helps bacteria evade the host's immune defenses, contributing to their survival and virulence. Some members are also involved in the modification of the LPS inner core by transferring galacturonic acid residues to specific positions, which is essential for the proper assembly and function of the LPS molecule.
Gram-negative bacterial outer membrane porin (Gram-neg_bact_OMP)
Type: Family

The Gram-negative porin family is characterized by its role in forming pores within the outer membrane of Gram-negative bacteria. These pores are essential for the passive diffusion of small molecules, including nutrients like monosaccharides, disaccharides, trisaccharides, and inorganic phosphate, as well as various negatively charged solutes. Some family members are selective for specific ions, such as cations. The porins also play a role in antibiotic resistance by altering the transverse electric field within the constriction zone of the pore, which affects the passage of antibiotics. Additionally, certain porins serve as receptors for bacteriophages and bacterial toxins, indicating a role in microbial infection processes. The family includes major antigens on bacterial surfaces, which may contribute to pathogenic properties. Overall, the Gram-negative porin family is integral to bacterial survival, pathogenicity, and interaction with the environment.
YjjX NTPase (YjjX_NTPase)
Type: Family

The YjjX NTPase family consists of enzymes that play a crucial role in maintaining the fidelity of nucleotide pools by hydrolyzing non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives. By doing so, the family members prevent the incorporation of these non-canonical purines into DNA and RNA, thereby avoiding potential chromosomal lesions that could arise from their presence. Some members of the family also exhibit bifunctional activity, including the reversible adenylyl transfer from ATP to 4'-phosphopantetheine, contributing to CoA biosynthesis. The family's enzymatic action is essential for genomic stability and proper cellular metabolism.
GDXG lipolytic enzyme (GDXG_lipolytic_enzyme)
Type: Family

The 'GDXG' lipolytic enzyme family is characterised by a conserved GDXG motif and includes proteins with esterase and lipase activities. Members of this family are involved in the hydrolysis of short-chain fatty esters, with specificity generally towards acyl chain lengths of up to 8 carbons. They can hydrolyse substrates such as triacetylglycerol and tributyrylglycerol, but typically not trioleylglycerol or cholesterol oleate. Some family members also exhibit regulatory functions, such as antagonising maltotriose binding to negatively regulate MalT activity or inhibiting MelA galactosidase activity. Additionally, certain enzymes within this family contribute to the degradation of plant cell wall polysaccharides, tryptophan metabolism via the kynurenine pathway, and the regulation of sterol deacetylation. The family also includes proteins involved in the biosynthesis of natural products with cholesterol-lowering activity, the maintenance of mycobacterial cell envelope permeability, and the detoxification of organophosphorus compounds.
Neuropathy target esterase (NTE)
Type: Family

The NTE family proteins are characterized by their phospholipase B activity, catalyzing the double deacylation of phosphatidylcholine to glycerophosphocholine, which is essential for membrane lipid homeostasis. They play a crucial role in the turnover of phosphatidylcholine in response to various stimuli such as inositol, elevated temperatures, or the presence of choline in the growth medium. Members of the NTE family are also involved in the signaling mechanisms between neurons and glia, regulating glia wrapping during brain development and are essential for cell survival. The family's activity is notably inhibited by organophosphorus esters, which can lead to distal axonopathy upon specific chemical modification of the proteins.
Rab GTPase-activating TBC domain-containing protein (Rab_GAP_TBC_domain)
Type: Family

This family of proteins includes GTPase-activating proteins (GAPs) that regulate the activity of Rab GTPases, which are key regulators of intracellular membrane trafficking. Members of this family are involved in various cellular processes such as autophagosome formation, cell cycle progression, cytokinesis, endocytosis, and vesicular transport. They function by accelerating the hydrolysis of GTP bound to Rab proteins, converting them from an active GTP-bound state to an inactive GDP-bound state. This action is critical for the control of vesicle budding, transport, and fusion events within the cell. The proteins typically contain TBC domains and may interact with specific Rab GTPases, influencing processes like microtubule nucleation, glucose uptake, and cell migration.
GatZ/KbaZ carbohydrate metabolism (GatZ_KbaZ_carbometab)
Type: Family

The GatZ/KbaZ family is involved in carbohydrate metabolism, specifically in the catabolism of galactitol and N-acetylgalactosamine. Members of the GatZ subfamily function as components of the tagatose-1,6-bisphosphate aldolase GatYZ complex, which is essential for full activity and stability of the Y subunit. GatZ alone lacks aldolase activity but may act as a chaperone for proper folding of GatY. Similarly, the KbaZ subfamily members are part of the tagatose-1,6-bisphosphate aldolase KbaYZ complex, also required for the Y subunit's activity and stability, with KbaZ potentially serving a chaperone-like role. The family also includes proteins involved in the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which transports and phosphorylates sugars like mannose, fructose, and N-acetylgalactosamine. Additionally, some family members are implicated in the isomerization-deamination of galactosamine 6-phosphate, contributing to the degradation pathways of specific amino sugars.