SII-SWORD/CoKE huggingface dataset:
AB hydrolase superfamily, subfamily 4 (AB_hydrolase_4_sf)
Type: Family

The AB hydrolase 4 family is characterized by a diverse set of enzymatic activities associated with lipid metabolism. Members of this family are involved in the synthesis and hydrolysis of medium-chain fatty acid ethyl esters, which may play a role in detoxification processes. Some proteins within this family function as phospholipases, participating in phospholipid remodeling by selectively cleaving myristate-containing phosphatidylcholines and other medium-chain-containing phospholipids. Additionally, certain family members exhibit monoacylglycerol lipase activity, which is activated by progesterone binding and is crucial for sperm capacitation and smooth muscle cell migration. This activity involves the hydrolysis of endocannabinoids, such as arachidonoylglycerol, from cell membranes. Other proteins in the family may regulate adipocyte lipolysis and liver lipid accumulation. Overall, the AB hydrolase 4 family plays significant roles in lipid modification and signaling, with implications for cellular functions such as reproduction and metabolism.
BolA/IbaG family stress response and morphology regulators (BolA/IbaG_stress_morph_reg)
Type: Family

The BolA/IbaG family includes transcriptional regulators and proteins involved in stress response and cell morphology. Members of this family play a crucial role in the general stress response, with some acting as transcriptional regulators that influence gene expression related to cell shape, growth, division, and biofilm development. Certain proteins within the family are implicated in resistance to acid stress. Additionally, some eukaryotic members function as mitochondrial iron-sulfur (Fe-S) cluster assembly factors, aiding in the insertion of Fe-S clusters into mitochondrial proteins and potentially protecting against oxidative stress. The family's involvement in such diverse processes reflects its significance in cellular adaptation to environmental challenges and maintenance of cellular integrity.
Phosphate-binding protein PstS (Phosphate-bind_PstS)
Type: Family

The PstS family comprises phosphate-binding proteins that are integral components of the ABC transporter complex PstSACB, which is involved in the import of phosphate. Members of the family are responsible for binding and transporting inorganic phosphate across the cell membrane, with some proteins identified as the primary carriers for phosphate uptake, especially under conditions of phosphate starvation. Additionally, certain PstS proteins have been implicated in host-pathogen interactions, acting as agonists for toll-like receptors TLR1 and TLR2, and playing roles in host immune responses, including cytokine production, macrophage apoptosis, and phagosome maturation arrest. The family also includes proteins with enzymatic activities, such as phosphomonoesterase and phosphodiesterase, contributing to broader metabolic functions.
Sirohydrochlorin Cobaltochelatase/CbiX (Sirohydro_Cobaltochel/CbiX)
Type: Family

The CbiX family proteins are involved in the anaerobic biosynthesis of cobalamin (vitamin B12) and the unique nickel-containing tetrapyrrole coenzyme F430. Members of the family catalyze the insertion of Co(2+) or Ni(2+) into sirohydrochlorin to yield cobalt-sirohydrochlorin or Ni-sirohydrochlorin, respectively. These steps are crucial for the production of cobalamin and coenzyme F430, the latter being the prosthetic group of methyl-coenzyme M reductase (MCR), essential for methanogenesis and anaerobic methane oxidation. Some subfamilies, such as the SirB subfamily, are involved in siroheme biosynthesis, catalyzing the chelation of iron into the siroheme precursor. The CbiX family displays a diversity of domain arrangements and may contain additional features such as an [Fe-S] cluster, which plays a regulatory role in iron, sulfur, and tetrapyrrole metabolism.
Striated Muscle Structural and Regulatory Protein (Striated_Muscle_Regulatory)
Type: Family

This family of proteins is involved in the structural organization and functional regulation of striated muscle cells. They are associated with the myofibrillar M band and A bands, where they interact with major components such as myosin, actin, and titin. These interactions are important for maintaining the integrity of the sarcomere structure and for modulating the activity of muscle contraction. Some family members are also implicated in cardiac function, potentially influencing muscle contraction and the conduction systems of the heart. Additionally, certain proteins within this family may play a role in myofibrillogenesis, the process of forming the contractile threads in muscle cells.
UPF0336/Enoyl-CoA hydratase-related (UPF0336/Enoyl-CoA_hydratase)
Type: Family

This family of proteins includes members that are involved in various metabolic processes, such as fatty acid synthesis and the hydration of enoyl-CoA substrates. Some proteins within this family function as 3-hydroxyacyl-[acyl-carrier-protein] dehydratases, which are essential for mitochondrial fatty acid synthesis and plant development. They may influence mitochondrial membrane lipid composition and contribute to energy supply and reactive oxygen species homeostasis. Other members are involved in the hydration of trans-2-enoyl-CoAs, playing a role in the production of polyhydroxyalkanoates, which are biopolyesters. The functions of some proteins in this family are not well characterized and are annotated based on sequence similarity.
Glutamyl Endopeptidase (Glutamyl_endopeptidase)
Type: Family

The Glutamyl endopeptidase family comprises enzymes that cleave peptide bonds preferentially at the carboxyl-terminal side of aspartate and glutamate. They play a role in bacterial colonization and infection of human tissues by processing proteins like thiol protease SspB and fibronectin-binding proteins, which are crucial for adherence to host cells. Some family members can degrade host immunoglobulins, potentially protecting bacteria from the immune system. They may also contribute to the stability of secreted lipases. Certain enzymes within this family show specificity for glutamic acid residues and can hydrolyze human fibronectin and type 1 collagen. Activity of some members is regulated by inhibitors like diisopropyl fluorophosphate.
Thiamine Salvage Pathway TenA (Thiamine_Salvage_TenA)
Type: Family

The TenA family is involved in the thiamine salvage pathway, which regenerates thiamine pyrimidine from degraded thiamine products. Members of the family catalyze the hydrolysis of amino-pyrimidine at the C5' of the pyrimidine moiety of thiamine compounds, converting 4-amino-5-aminomethyl-2-methylpyrimidine to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP). Some members also exhibit thiaminase activity, although this is not considered physiologically relevant. Additionally, certain bifunctional proteins within the family possess a HAD-like hydrolase domain, conferring phosphatase activity on thiamine monophosphate and other substrates. The family also includes proteins with formylamino-HMP amidohydrolase activity, which do not display thiaminase II activity. These enzymes are crucial for the utilization of thiamine breakdown products, preventing the accumulation of potentially harmful compounds.
Cytochrome c oxidase bacterial subunit 4 (Cytochrome_c_oxidase_bac_sub4)
Type: Family

The cytochrome c oxidase bacterial subunit 4 family includes proteins that play a crucial role in the aerobic respiratory chain, predominantly in conditions of high aeration. Members of this family are involved in the catalysis of quinol oxidation, coupled with the reduction of oxygen to water. Additionally, some proteins within this family exhibit proton pump activity, transferring protons across the membrane during electron transfer, which contributes to the generation of a proton gradient used for energy production. These proteins are essential for energy conversion processes during vegetative growth in bacteria.
Developmental Signaling Modulators (Dev_Signal_Modulators)
Type: Family

The protein family is involved in various signaling pathways critical for embryonic development and cellular functions. Members of the family serve as ligands, coreceptors, or inhibitors in processes such as mesoderm segmentation, Nodal signaling, and establishment of the left-right axis during gastrulation. Some proteins bind to WNT proteins, inhibiting their activities, while others are involved in Notch signaling, contributing to cell fate determination and organogenesis. Additionally, family members regulate vascular tubulogenesis and angiogenesis, influencing cell migration and adhesion to the extracellular matrix. The family also includes proteins that stabilize morphogen interactions, playing roles in patterning and growth control.
Voltage-gated chloride channel (Cl_channel_volt-gated)
Type: Family

The chloride channel family encompasses voltage-gated chloride channels that are crucial for various physiological processes, including membrane repolarization in skeletal muscle cells, regulation of cell volume, membrane potential stabilization, signal transduction, and transepithelial transport. Some members are involved in urinary concentrating mechanisms and aldosterone production regulation. The channels' activation is influenced by membrane potential changes, and they may also be regulated by extracellular calcium, protons, and other factors. Subfamilies within this family are distinguished by their tissue-specific roles and regulatory mechanisms, contributing to the diverse functionality of chloride channels in different cellular contexts.
Cadherin domain-containing protein (Cadherin-domain_protein)
Type: Family

This family of proteins includes components of intercellular desmosome junctions, which are critical for cell-cell adhesion. They interact with plaque proteins and intermediate filaments, playing a key role in maintaining tissue integrity. Some members are involved in the maintenance of planar cell polarity and inhibition of cell proliferation and differentiation. Others mediate calcium-dependent heterophilic interactions and are essential for normal sensory functions. These proteins typically contain cadherin domains that bind calcium ions to ensure structural rigidity and proper function.
Serine-aspartate repeat-containing protein-like (SDr-like)
Type: Family

This entry represents the serine-aspartate repeat-containing protein (SDr) family.

This family includes proteins involved in bacterial virulence mechanisms. These proteins are cell surface-associated and play a role in promoting bacterial attachment to human fibrinogen, facilitating the formation of bacterial clumps. These clumps can interfere with host defence mechanisms, such as preventing bacterial phospholipid hydrolysis by phospholipase A2 and reducing macrophage phagocytosis. Additionally, some members are responsible for inducing human platelet aggregation, which may contribute to the development of infective endocarditis. The proteins also interact with components of the extracellular matrix, which is crucial for bacterial adhesion and pathogenesis.

This entry also include eukaryotic members, such as Germ cell nuclear acidic protein from Mus musculus, which may play a role in DNA-protein cross-links (DPCs) clearance through a SUMO-dependent recruitment to sites of DPCs, ensuring the genomic stability by protecting germ cells and early embryos from various sources of damage .
Histone-lysine N-methyltransferase, H3 Lys-9 specific (H3K9_Histone-Lys_N-MTase)
Type: Family

The protein family includes histone-lysine N-methyltransferases that specifically methylate 'Lys-9' of histone H3, marking it for epigenetic transcriptional repression. The trimethylation of H3 'Lys-9' serves as a tag for recruiting HP1 proteins to methylated histones, predominantly functioning in heterochromatin regions. This modification plays a pivotal role in the establishment of constitutive heterochromatin at pericentric and telomere regions and is necessary for directing DNA methylation at these sites. Members of the family are involved in various cellular processes, including cell cycle regulation, transcriptional repression, and telomere length regulation. Some family members also participate in the regulation of higher-order chromatin organization and may have roles in the transgenerational transmission of environmental information. The family's SET domain, along with pre-SET and post-SET domains, is essential for methyltransferase activity and stable heterochromatin binding.
Plant Zinc finger CCCH domain-containing (Plant_ZF_CCCH)
Type: Family

The Zinc finger CCCH domain-containing protein family is characterized by the presence of the CCCH-type zinc finger motif, which is implicated in RNA binding. Members of this family are involved in various biological processes, including flower development and floral reproductive organ identity. They function by binding to specific pre-mRNAs, such as AGAMOUS (AG), and promoting their processing, often in association with other proteins. Some family members also exhibit RNA-binding and ribonuclease activities in vitro, suggesting a role in RNA metabolism.
Sleep homeostasis regulator (Sleep_regulator)
Type: Family

This family of proteins is involved in the homeostatic regulation of sleep. Members of this family are essential for maintaining normal sleep patterns and for the recovery of sleep after periods of sleep deprivation. They function as important regulators of potassium channels, specifically the Shaker (Sh) K(+) channel. By potentially enhancing the activity of these channels, they contribute to the reduction of neuronal excitability, thereby linking the physiological need for sleep to a decrease in neuronal activity.
Snake venom C-type lectin-like (Snaclec)
Type: Family

This family of proteins includes members that interact with components of the hemostatic system, particularly platelets, to modulate aggregation and coagulation processes. They typically act by binding to specific platelet receptors such as integrin alpha-2/beta-1, GPIbalpha, and potentially others, blocking interactions with collagen, von Willebrand factor, or other agonists that promote platelet aggregation. Some members exhibit anticoagulant properties by binding to coagulation factors. Additionally, certain proteins within this family may have roles in immune responses, such as inducing histamine release, or possess antiparasitic and antibiotic activities. The functions of these proteins are often associated with their ability to regulate cell adhesion, migration, proliferation, and angiogenesis, which may be mediated through interactions with integrin receptors.
Fungal Meroterpenoid Biosynthesis Isomerase (Fungal_Meroterpenoid_Isomerase)
Type: Family

The trt14 isomerase family is involved in the biosynthesis of various fungal meroterpenoids, which are compounds derived from terpenoid and polyketide precursors. Members of this family catalyze critical steps in the formation of complex molecular architectures, including ring expansion and rearrangement reactions. These enzymes play roles in the formation of compounds such as terretonin, acetoxydehydroaustin, and paraherquonin, which exhibit a range of biological activities including mycotoxin production and initiation of conidiation. The isomerases are part of gene clusters that orchestrate the conversion of simpler precursors into structurally diverse and bioactive meroterpenoids through a series of oxidation, prenylation, cyclization, and rearrangement steps.
Y' element ATP-dependent helicase (Y'_ATP-dependent_helicase)
Type: Family

This family of proteins includes ATP-dependent helicases that play a role in DNA unwinding. They are implicated in the maintenance of telomeres, specifically through a telomerase-independent mechanism. Members of this family are associated with the yeast subtelomeric Y' repeat, suggesting a specialized function in the genomic regions close to the telomeres of yeast chromosomes.
Bacterial L,D-transpeptidase (LD-transpeptidase)
Type: Family

The L,D-transpeptidase family is involved in cell wall biology, specifically in the formation of peptidoglycan cross-links which are crucial for bacterial cell wall integrity. Members of the family catalyze the formation of 3->3 cross-links between peptidoglycan layers by cleaving the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and forming a bond with the mDap(3) side chain of an acceptor stem. This activity is specific to tetrapeptide stems as they cannot utilize pentapeptide stems. Some family members are also involved in anchoring major outer membrane lipoproteins to the peptidoglycan. The family includes proteins that are inactivated by beta-lactam antibiotics such as carbapenems, which acylate the catalytic Cys residue, although some members show resistance to this inactivation. The family proteins may contain domains such as LysM, which are thought to be involved in peptidoglycan binding, and immunoglobulin-like domains that may play a role in enzyme structure and function.
Two-component sensor histidine kinase (2C_sensor_his_kinase)
Type: Family

This family of proteins includes sensor histidine kinases that are part of two-component regulatory systems, which are involved in various cellular responses to environmental stimuli. These proteins typically function as membrane-associated protein kinases that undergo autophosphorylation and subsequently transfer the phosphate to a response regulator, modulating its activity. They play key roles in processes such as osmoregulation, virulence, alginate biosynthesis, glucose metabolism, cell envelope stability, oxygen sensing, and nitrogen level control. The proteins contain several domains, including a cytoplasmic domain, transmembrane helices, a periplasmic domain, a HAMP domain, and a histidine kinase domain. The activity of these kinases is often regulated by environmental signals, interaction with other proteins, or small molecules, and they may also function as phosphatases to dephosphorylate their response regulators.
Auxin biosynthesis and cation transport (Auxin_biosynth/cation_transpt)
Type: Family

The protein family is involved in various biological processes, primarily including auxin biosynthesis and the transport of potassium and divalent cations. Members of the family function as monooxygenases, catalyzing the conversion of indole-3-pyruvic acid to indole-3-acetic acid, a key step in auxin production, which is crucial for plant growth and development. Some members are also involved in the degradation pathway of urate to allantoin and may participate in endoplasmic reticulum associated degradation (ERAD) by binding non-native proteins for ubiquitination. The family includes proteins that enhance the activity of cation/potassium transporters, indicating a role in ion homeostasis.
Glutathione S-transferase Omega/HSP26 (GST_Omega/HSP26)
Type: Family

The GST Omega/HSP26 family is characterized by a diverse set of functions, primarily associated with enzymatic activities that involve glutathione. Members of the Omega subfamily exhibit glutathione-dependent thiol transferase and dehydroascorbate reductase activities, contributing to the recycling of ascorbic acid and the biotransformation of inorganic arsenic, reducing compounds such as monomethylarsonic acid. They also display S-(phenacyl)glutathione reductase activity and general glutathione S-transferase activity. In contrast, the HSP26 subfamily members form complexes with the RNA polymerase holoenzyme, playing roles in gene expression regulation during stringent starvation conditions. The family includes proteins that protect against environmental and oxidative stress, and some are involved in the biosynthesis of pigments, such as the red eye pigment drosopterin in Drosophila.
Gfo/Idh/MocA domain-containing protein (Gfo/Idh/MocA_domain)
Type: Family

This family of proteins includes oxidoreductases that participate in various metabolic pathways. Members are involved in the biosynthesis of deoxy sugars, which are components of antibiotics and other bioactive natural products. They catalyze the reduction of keto moieties in sugar nucleotides to produce different deoxy sugar derivatives. Some family members function in the degradation of D-xylose, a component of hemicelluloses, by oxidizing it into D-xylonolactone. They exhibit a preference for NADP(H) as a cofactor, although some can also use NAD(H). Activity regulation by various compounds and salts is noted in certain members, indicating a complex regulation of their enzymatic activities. The family is characterized by a conserved domain structure that aligns them with the Gfo/Idh/MocA family, suggesting a shared evolutionary origin and similar catalytic mechanisms.
Alpha-glycosidase and related enzymes (Alpha-glycosidase_related)
Type: Family

This family of proteins includes enzymes with glycosidase activity, which are involved in the hydrolysis of glycosidic bonds in glycoconjugates, oligosaccharides, and polysaccharides. Members of this family are capable of processing a variety of substrates, including alpha-D-galactosides, xyloglucan oligosaccharides, and isoprimeverose, releasing monosaccharides like xylose and galactose. Some proteins within this family are implicated in specific biological processes such as myogenesis, while others contribute to the metabolism of dietary sugars or the modification of blood group antigens. The family encompasses enzymes that are inhibited by their reaction products or other sugars, and some members exhibit bifunctional activities, such as kinase activity in addition to glycosidase activity.
SIS family GutQ/KpsF subfamily isomerases (GutQ/KpsF_isomerases)
Type: Family

The GutQ/KpsF subfamily of the SIS family comprises enzymes that catalyze the reversible aldol-ketol isomerization between D-ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P). Members of this family are involved in the biosynthesis of 3-deoxy-D-manno-octulosonate (KDO), an essential 8-carbon sugar component of lipopolysaccharides (LPSs) in bacterial outer membranes. Some family members also participate in the biosynthesis of K-antigen capsules. The activity of these enzymes can be regulated by metal ions, and they may play a role in the regulation of the gut operon through the synthesis of the regulatory molecule A5P.
ABC-transporter-regulating transcription factor-like (AtrR-like)
Type: Family

This entry represents a family of fungal transcription factors, including ABC-transporter-regulating transcription factor from Aspergillus oryzae (AtrR), which regulates expression of the genes related to resistance to azole compounds . Members of this family are involved in the activation of gluconeogenic enzymes, regulation of drug-responsive genes, and control of biosynthetic gene clusters for secondary metabolites such as ergot pigments, fusaridione A, oryzines, AAL-toxins, and fumonisins. Some family members are uncharacterised.
Mannitol Dehydrogenase/Oxidoreductase (Mannitol_DH/Oxidoreductase)
Type: Family

This family of proteins includes enzymes that catalyze the NAD(H)-dependent interconversion of D-fructose and D-mannitol, which is a key reaction in the mannitol metabolic pathway. Some members are also involved in the reduction of D-fructuronate to D-mannonate. These enzymes typically show a preference for NADH over NADPH as a cofactor. The family also encompasses uncharacterized oxidoreductases that are presumed to have similar activities based on their sequence similarity.
Rap1/Ran GTPase-activating (Rap1_Ran_GAP)
Type: Family

The protein family is involved in the regulation of GTPase activity for nuclear Ras-related regulatory proteins such as Rap1, Rap2, and Ran, typically converting them to an inactive GDP-bound state. Members of the family play key roles in various cellular processes including cell cycle progression, epithelial cell morphogenesis, polarity, adhesion, cytoskeletal organization, and dendritic spine morphogenesis. They are also implicated in the regulation of cell adhesion and chemotaxis by controlling myosin II assembly and disassembly. The family contributes to the spatial and temporal regulation of these processes, which are crucial for proper cell function and development.