SII-SWORD/CoKE huggingface dataset:
Cytosolic carboxypeptidase (Cytosolic_carboxypeptidase)
Type: Family

This family of proteins includes metallocarboxypeptidases that are involved in the post-translational modification process known as deglutamylation. They are responsible for the removal of polyglutamate side chains from the gamma-carboxyl group of glutamate residues within the C-terminal tails of target proteins, including tubulin and non-tubulin proteins. This activity regulates the structural integrity and function of microtubules, as well as the localization and velocity of kinesin motors. Additionally, these proteins are implicated in the modulation of cellular processes such as antiviral defense response activation and cell pluripotency maintenance.
Cerebellin Synaptic Organizer (Cerebellin_Synaptic_Org)
Type: Family

The cerebellin family proteins are involved in the organization and modulation of synapses in the central nervous system (CNS). They play crucial roles in synapse integrity, synaptic plasticity, and the maintenance of excitatory synapses, but are not essential for their establishment. Cerebellins act as synaptic organizers, influencing both pre- and post-synaptic components. They are involved in the formation and maintenance of specific types of synapses, such as parallel fiber-Purkinje cell synapses in the cerebellum and inhibitory GABAergic synapses. Some family members also exhibit neuromodulatory functions, such as stimulating norepinephrine release and enhancing adrenocortical secretion. Additionally, certain cerebellins may regulate the number of excitatory synapses on hippocampus neurons and play roles in glucose homeostasis and energy balance regulation.
Plant Serine/Threonine-Protein Kinase (Plant_Ser_Thr_Prot_Kinase)
Type: Family

The Ser/Thr protein kinase family is involved in plant defense signaling and immune responses. Members of this family contribute to pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), regulating various processes such as reactive oxygen species production, calcium signaling, and hormone expression. Some kinases within this family act as positive regulators, phosphorylating key components of the immune response, while others function as negative regulators or decoys. The family includes kinases that are activated by specific PAMPs or endogenous elicitors, and some members are involved in growth and development regulation.
Bacterial Thiol:disulfide Interchange Protein DsbA (Thiol_disulfide_DsbA)
Type: Family

The DsbA family proteins are involved in the formation of disulfide bonds in periplasmic proteins, which is essential for the correct folding and function of many bacterial proteins. Members of the family act by transferring their own disulfide bonds to substrate proteins, becoming reduced in the process. They are subsequently reoxidized by the membrane protein DsbB or other partners, allowing them to engage in further rounds of disulfide bond formation. This catalytic cycle is crucial for the biogenesis of pili and the functional maturation of various virulence factors, as well as for the assembly of proteins like PhoA and OmpA. The DsbA family is part of the larger thioredoxin family and plays a key role in bacterial oxidative protein folding.
RNA-binding protein 42/Polyadenylate-binding protein RBP45/47-like (RBM42_RBP45_47-like)
Type: Family

This entry represents a group of eukaryotic proteins involved in various aspects of RNA metabolism, including pre-mRNA processing, mRNA stabilization, and transport, including sequences belonging to the RNA binding protein 44 (RBM42) family and polyadenylate-binding RBP45/RBP47 families. Members of the RBM42 family, characterised by the RNA recognition motif (RRM), are known to bind to the 3'-UTR of specific mRNAs, such as CDKN1A, influencing their stability and regulation. The polyadenylate-binding RBP45 and RBP47 families are heterogeneous nuclear ribonucleoproteins (hnRNPs) that bind to the poly(A) tail of mRNA, suggesting a role in mRNA maturation and possibly in the regulation of mRNA stability and translation. These proteins are essential for proper gene expression regulation and are involved in cellular processes such as cell cycle control and response to stress.
Krueppel C2H2-type Zinc Finger (Krueppel_C2H2_ZnFinger)
Type: Family

The Krueppel C2H2-type zinc-finger protein family is characterized by its involvement in transcriptional regulation. Members of this family typically contain C2H2-type zinc-finger domains, which are known for their role in DNA binding and gene expression modulation. Some proteins within the family may function as transcriptional repressors, potentially suppressing transcriptional activities mediated by specific signaling pathways, such as the MAPK pathway. Others may act as transcriptional activators, directly influencing the expression of genes like NPPA. Certain members are implicated in cellular processes like apoptosis, and may interact with proteins such as p53/TP53, BAX, and TRAF2 to mediate cell death pathways in response to DNA damage. Domains like the KRAB and SCAN domains contribute to the transcriptional repressor activity and enable dimerization, respectively, which further diversifies the regulatory roles of the family in gene expression.
CRP1/MDG1 DNA-binding & kinase subunit (CRP1_MDG1_kinase)
Type: Family

The CRP1/MDG1 family includes proteins involved in various cellular processes. Members like Cruciform DNA-recognizing protein 1 bind to cruciform DNA and enhance its cleavage by specific endonucleases, playing a role in DNA repair and maintenance. Other members, such as the SNF1 protein kinase subunits, are integral to the SNF1 kinase complex, which adapts to glucose limitation by regulating transcription, metabolism, and development. This complex also influences cellular aging and polarity. Additionally, the family encompasses proteins like MDG1, which are involved in G-protein mediated signal transduction and the regulation of polarized cell growth in response to pheromones. The AMP-activated protein kinase subunits within the family act as energy sensors, regulating cellular energy metabolism by activating energy-producing pathways and inhibiting energy-consuming processes in response to ATP level changes.
C-type lectin and matrix domain-containing protein (C-type_lectin/matrix_domain)
Type: Family

This family of proteins includes various C-type lectin domain-containing proteins, which are primarily involved in immune system processes. Members of this family function as cell surface receptors that can bind to specific carbohydrate structures. They are involved in a range of biological processes including lymphocyte proliferation, signal transduction, modulation of T-cell expansion, immune recognition, and inhibition of osteoclast formation. Some members have a role in antigen capture and presentation, potentially influencing dendritic cell function and interferon expression. Additionally, this family includes matrix proteins from sea urchin embryos that direct and inhibit crystal growth during spicule formation. There are also viral proteins that down-regulate MHC-I expression, participate in viral hemadsorption, and inhibit apoptosis. Collectively, these proteins contribute to immune defense, bone homeostasis, and developmental processes.
CorA Metal Ion Transporter (CorA_MIT)
Type: Family

The CorA metal ion transporter family is responsible for the regulation of magnesium ion concentrations within the cell. Members of this family mediate the influx of magnesium ions through a central ion permeation pathway formed by the first transmembrane domain of each of the five subunits. The binding of Mg(2+) ions leads to the formation of a symmetrical homopentamer, which surrounds a closed ion permeation pathway. When intracellular Mg(2+) levels are low, the CorA transporters are activated, triggering a conformational change within each subunit and loosening the interactions between subunits, resulting in an open ion conduction pathway. Conversely, high cytoplasmic Mg(2+) levels render the transporters inactive. Some members can also mediate the uptake of cobalt and nickel ions, and are inhibited by cation hexaammines.
Fungal fatty acid synthase (Fungal_FAS)
Type: Family

The fungal fatty acid synthase (FAS) family is responsible for the biosynthesis of long-chain fatty acids, which are essential components of cell membranes and precursors for various bioactive compounds. These enzymes catalyze the formation of fatty acids from acetyl-CoA, malonyl-CoA, and NADPH. The FAS complex is typically composed of two subunits, alpha and beta, each containing multiple catalytic domains that work in concert to extend the fatty acid chain. In fungi, these enzymes are also involved in the production of secondary metabolites, such as mycotoxins and bioactive lipopeptides, by providing starter units or precursors for non-ribosomal peptide synthetases and polyketide synthases. The FAS family plays a crucial role in fungal metabolism and pathogenicity, as some of the secondary metabolites synthesized are virulence factors or have pharmacological significance.
Carcinoembryonic antigen-related cell adhesion (CEA_cell_adhesion)
Type: Family

The CEA family proteins are predominantly involved in cell adhesion processes, with members functioning in homophilic and heterophilic interactions that are calcium-independent. They belong to the immunoglobulin superfamily and play roles in various biological processes including immune response regulation, insulin action, angiogenesis, and tumor progression. Some members are implicated in maintaining the integrity of the tectorial membrane for proper hearing, while others are involved in phagocytosis, metabolic regulation, and the transport of bile acids. Additionally, certain proteins within the family are associated with pregnancy, such as the pregnancy-specific beta-1-glycoproteins, which may have roles in immune modulation during gestation.
Bacterial Acetyltransferase (Bact_Acetyltransf)
Type: Family

The acetyltransferase family encompasses enzymes that catalyze the transfer of acetyl groups from acetyl-CoA to various substrates, conferring specific functions such as antibiotic resistance or metabolic regulation. Members of this family are involved in resistance mechanisms against aminoglycoside antibiotics by acetylating the 6'-amino group of the molecules, thus inactivating the drugs. Other family members acetylate mycothiol, a compound that acts as an antioxidant in certain bacteria, or are involved in the biosynthesis of bacterial cell components such as the enterobacterial common antigen. Some enzymes within this family also participate in phytohormone production or detoxification processes. The diversity of substrates and reactions highlights the family's role in bacterial survival and adaptation.
Polysaccharide Biosynthesis and Transport (Poly_Biosynth_Transport)
Type: Family

The AglR/Agl15 and polysaccharide synthase family is involved in various cellular processes related to the biosynthesis and transport of polysaccharides across the membrane. Members of this family function as flippases or transport proteins that facilitate the movement of lipid-linked saccharide precursors from the inner to the outer leaflet of the cytoplasmic membrane. These proteins are key components in the assembly of cell surface structures such as N-glycans, peptidoglycan, teichuronic acid, lipopolysaccharides, and capsular polysaccharides. They play crucial roles in the formation of protective layers, virulence factors, and biofilm matrices, contributing to the structural integrity and pathogenicity of various bacteria. The family includes proteins involved in the biosynthesis of specific glycan structures under low-salt conditions, the production of exopolysaccharides during biofilm formation, and the export of O-antigen components.
Glycosyltransferase 2 family enzymes (Glycosyltransf_2)
Type: Family

The glycosyltransferase 2 family is involved in various glycosylation processes, which are critical for the synthesis of diverse polysaccharides and glycoconjugates. Members of this family catalyze the transfer of sugar moieties from activated donor molecules, such as UDP-sugars, to specific acceptor molecules, forming glycosidic bonds. Functions include the biosynthesis of antifungal agents, N-glycosylation of proteins, production of exopolysaccharides for biofilm formation and maintenance, maturation of bacterial spore coats, and elongation of chondroitin chains. Some members exhibit specificity for different sugar donors and acceptors, contributing to the structural diversity of carbohydrates in biological systems. The family is characterized by variations in conserved motifs, such as the DTG sequence, which may influence metal ion binding and enzyme activity.
ATP-binding cassette sub-family D (ABC_transporter_sub-D)
Type: Family

The ABCD family of ATP-binding cassette (ABC) transporters is involved in the translocation of various substrates across cellular membranes using ATP hydrolysis for energy. Members of this family are predominantly associated with the transport of long-chain and very long-chain fatty acid-CoA esters from the cytosol to the peroxisome lumen for beta-oxidation. Some members also exhibit fatty acyl-CoA thioesterase activity, hydrolyzing fatty acyl-CoAs into free fatty acids before transport. This family plays a crucial role in lipid metabolism, energy homeostasis, and the regulation of mitochondrial and peroxisomal functions. Additionally, certain members are implicated in the transport of cobalamin (Vitamin B12) across the lysosomal membrane and the uptake of antimicrobial peptides across bacterial inner membranes.
SDS22/Internalin LRR-containing (SDS22/Internalin_LRR)
Type: Family

The SDS22 and internalin families encompass proteins with diverse roles in cellular regulation and pathogenicity. The SDS22 family members are regulatory subunits of protein phosphatase 1 (PP1), which modulate the phosphatase activity of PP1 complexes, playing a crucial role in various cellular processes including cell cycle regulation and muscle contractility. The internalin family proteins are characterized by their involvement in bacterial virulence, particularly in the genus Listeria. They mediate the entry of Listeria monocytogenes into host cells by interacting with specific host cell receptors such as E-cadherin and MET receptor tyrosine kinase. Internalins are also implicated in modulating host immune responses and facilitating bacterial spread within host tissues. These families share a common feature of leucine-rich repeat (LRR) domains, which are typically involved in protein-protein interactions, although they serve distinct biological functions.
Complex I 51 kDa subunit (ComplexI_51kDa_subunit)
Type: Family

The Complex I 51 kDa subunit family comprises core subunits of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), which are essential for catalyzing electron transfer from NADH to the respiratory chain, with ubiquinone or menaquinone as the electron acceptors. These proteins are part of the peripheral arm of Complex I, where electrons from NADH are initially accepted by flavin mononucleotide (FMN) and subsequently transferred through a series of iron-sulfur (Fe-S) clusters to the final acceptor by electron tunneling. This process is coupled with proton translocation across the membrane, contributing to the creation of a proton gradient that is used for ATP synthesis. The family plays a crucial role in cellular energy metabolism and is conserved across a wide range of species.
Ketopantoate reductase (Ketopantoate_reductase)
Type: Family

The ketopantoate reductase family includes enzymes that play a crucial role in the biosynthesis of key biological molecules. Members of this family are primarily involved in the reduction of keto acids to their corresponding hydroxy acids using NAD(P)H as a cofactor. Specifically, they catalyze the conversion of ketopantoate to pantoic acid, an essential step in the biosynthesis of pantothenate (vitamin B5), which is a precursor for the synthesis of coenzyme A. Additionally, some members are involved in the biosynthesis of non-ribosomal cyclic hexadepsipeptides, such as beauvericin, by reducing ketoisovaleric acid to hydroxyisovalerate. These peptides have various biological activities, including antibiotic, antifungal, and insecticidal properties. The activity of these enzymes can be regulated by environmental stimuli and metal ions, indicating a complex interaction with cellular processes.
Rho-associated Serine/Threonine Kinase (Rho-assoc_Ser/Thr_Kinase)
Type: Family

This family of proteins includes serine/threonine kinases that are key regulators of the actin cytoskeleton and cell polarity. They are involved in various cellular processes such as smooth muscle contraction, cytoskeleton organization, stress fiber and focal adhesion formation, cell adhesion and motility, cytokinesis, and cell migration. Members of this family play roles in the phosphorylation of a range of substrates leading to the regulation of actomyosin contractility, cell protrusion, and migration. They are also implicated in the regulation of centrosome duplication, angiogenesis, and various differentiation processes including keratinocyte terminal differentiation and erythroid differentiation. Activation of these kinases is typically regulated by RHOA binding and can be inhibited by specific compounds. Some members are involved in the regulation of synaptic properties and circadian rhythms in vascular contractility.
Adaptor Complexes Large Subunit (Adaptor_Complx_Large_Subunit)
Type: Family

The adaptor complexes large subunit family is involved in the selection and concentration of membrane proteins for transport via vesicles in various membrane traffic pathways. These proteins are components of adaptor protein complexes that link clathrin to receptors in coated vesicles, playing a crucial role in clathrin-dependent endocytosis and protein sorting at the trans-Golgi network and early endosomes. They mediate the recruitment of clathrin to membranes and recognize sorting signals within the cytosolic tails of transmembrane cargo molecules. Some family members are also involved in maintaining post-endocytic trafficking through non-clathrin pathways and may participate in the maturation of certain viruses. They bind to polyphosphoinositide-containing lipids, which positions the complexes on the membrane, and they may recognize various endocytosis signal motifs and sorting signals for proper cargo selection.
Glycosyl Hydrolase Family 38 (Glycosyl_Hydrlase_38)
Type: Family

The glycosyl hydrolase 38 family is involved in the catabolism and processing of N-linked carbohydrates. Members of this family are responsible for the hydrolysis of alpha-mannosidic linkages in various glycoconjugates, including glycoproteins and oligosaccharides. Some family members play a critical role in the biosynthesis of complex N-glycans by controlling the conversion of high mannose to complex N-glycans, which is a key step in the N-glycan maturation pathway. Others are necessary for the degradation of N-linked carbohydrates during glycoprotein turnover. Certain enzymes within the family have specific functions, such as involvement in spermatogenesis or resistance to salt stress. The family includes lysosomal alpha-mannosidases, which are essential for the breakdown of glycoproteins, and epididymis-specific alpha-mannosidases, which may play a role in sperm maturation and sperm-egg interaction. Activity of these enzymes can be regulated by various inhibitors, including swainsonine and metal ions.
Coatomer complex subunit (Coatomer_complex_subunit)
Type: Family

This family of proteins is involved in intracellular trafficking, specifically in the transport of proteins from the endoplasmic reticulum (ER) to the Golgi apparatus and from the Golgi back to the ER. Members of this family form part of the coatomer complex, which is a cytosolic protein complex that binds to specific motifs on cargo proteins and vesicles. This complex is essential for the formation of non-clathrin-coated vesicles and is required for vesicle budding from the Golgi. The coatomer complex is also implicated in maintaining Golgi structural integrity and in the processing and recycling of certain receptors, such as the low-density lipoprotein (LDL) receptor. The recruitment of the coatomer to membranes is dependent on ADP-ribosylation factors (ARFs), which are small GTP-binding proteins.
Copper-binding electron transfer protein (Cu-binding_ET)
Type: Family

This family of proteins is involved in electron transfer processes, acting as electron acceptors and donors in various biological redox reactions. Members of this family are known to transfer electrons to cytochrome oxidase, playing a role in the electron transport chain. Some proteins within this family are associated with copper tolerance, binding copper ions and protecting other proteins from copper-induced damage. The family includes soluble electron acceptors for membrane protein complexes and may participate in the oxidation of specific substrates such as methylamine. The proteins exhibit a cupredoxin domain, indicating their ability to bind copper and participate in redox reactions.
TLC domain-containing (TLCD)
Type: Family

The TLCD family proteins are involved in the regulation of plasma membrane composition and fluidity. They inhibit the incorporation of membrane-fluidizing phospholipids containing omega-3 long-chain polyunsaturated fatty acids (LCPUFA), promoting membrane rigidity. Some family members, known as ceramide synthases, are involved in ceramide synthesis, which may affect processes like adipogenesis and cell proliferation during neuronal differentiation. The family also includes proteins that could play a role in protection against cell death.
Small acid-soluble spore DNA-binding (SASP_DNA-binding)
Type: Family

This family of proteins is involved in the protection of spore DNA in dormant spores. They are characterized by their ability to bind to double-stranded DNA, inducing a conformational change to an a-like structure. This binding activity safeguards the DNA from both chemical and enzymatic damage. Members of this family play a crucial role in enhancing the resistance of dormant spores to ultraviolet light, contributing to their overall resilience in harsh environmental conditions.
Homeobox domain-containing transcription factors (Homeobox_TF)
Type: Family

The homeobox protein family is characterized by the presence of a homeobox domain, enabling these proteins to function as transcription factors. They are involved in a wide range of developmental processes, including craniofacial development, odontogenesis, stomach organogenesis, embryonic patterning, and neuron differentiation. Members of the family bind to specific DNA sequences to regulate gene expression, influencing cell fate specification, morphogenetic movements, and asymmetric cell division. Some proteins within the family also play roles in suppressing Wnt signaling, acting as transcriptional repressors or activators, and are essential for postnatal growth, nursing, and energy balance control. The family includes proteins that are part of negative regulatory loops, such as with microRNAs, and are involved in cell-type specific survival during sex determination. They are also implicated in the development of the brain, eyes, sensory organs, and limbs, as well as in the regulation of non-apoptotic cell death.
HAD-like hydrolase superfamily phosphatase (HAD-like_hydrolase_phosphatase)
Type: Family

This family of proteins includes enzymes with phosphatase activity, specifically involved in the dephosphorylation of various substrates. Members of this family play roles in metabolic processes such as the regulation of phosphate uptake and the prevention of toxic accumulation of polyol phosphates, which can interfere with glycolysis. Some proteins within this family are also implicated in the acetylation of histone proteins, which is critical for DNA damage checkpoint activation. The enzymes generally belong to the HAD-like hydrolase superfamily, indicating a shared structural fold and mechanistic features in their catalytic activity.