SII-SWORD/CoKE huggingface dataset:
Flagella-assembly related protein (Flagella_assembly_related)
Type: Family

This family of proteins is involved in the structure and function of flagella, which are whip-like appendages that enable motility in various microorganisms. Members of this family are implicated in the assembly or stability of the flagellar apparatus. They may interact with each other, suggesting a coordinated role in flagellar formation or function. The exact molecular functions and mechanisms of action for these proteins remain to be fully elucidated, but they are likely to be important for the proper operation of flagella in motility and possibly sensory roles.
Alpha-glucan-binding chloroplastic protein (Alpha-glucan_binding_chloro)
Type: Family

This family of proteins is involved in the binding and organization of alpha-glucans, particularly starch and crystalline maltodextrins, within the chloroplasts. Members of this family play a crucial role in starch metabolism by affecting the turnover of starch granules. They modulate the accessibility of starch polymers to various enzymes that are responsible for starch modification, degradation, and synthesis. These proteins are also essential for the regulation of starch degradation in leaves and the distribution of starch in nonphotosynthetic tissues. Additionally, they contribute to plant gravitropic responses by facilitating the formation and accumulation of starch granules, which serve as statoliths in plant cells, aiding in the plant's ability to sense gravity. This function is particularly significant in the development of gravitropic responses in both shoots and roots, as well as in the tight packing of starch granules in grains.
Orphan Nuclear Receptor (Orphan_Nuclear_Rcpt)
Type: Family

This family of proteins includes members that are classified as orphan nuclear receptors. Orphan receptors are a type of nuclear hormone receptor for which endogenous ligands have not yet been identified. They are capable of DNA binding and may be involved in the regulation of gene expression, development, metabolism, and homeostasis by acting as transcription factors. Despite the lack of identified ligands, these receptors share structural similarities with other nuclear hormone receptors, suggesting potential roles in ligand-dependent transcriptional activation or repression. The specific functions of these proteins may vary, but they are generally involved in the intricate network of nuclear signaling pathways.
H2.0 Homeobox Transcription Factors (H2.0_Homeobox_TF)
Type: Family

The H2.0 homeobox family comprises transcription factors that are pivotal in the maturation and maintenance of Th1 cells through TBX21/T-bet dependency. Members of this family are also involved in key developmental processes including embryogenesis and hematopoiesis. In Drosophila, they may contribute to pattern formation during embryonic and imaginal development, although they are not essential for visceral muscle morphogenesis.
E3 ubiquitin-protein ligase RNF138 (E3_ubiq-protein_ligase_RNF138)
Type: Family

The RNF138 ubiquitin-protein ligase family is involved in the cellular response to DNA damage, particularly in promoting DNA resection and homologous recombination for the repair of double-strand breaks. Members of this family are recruited to damaged DNA sites and facilitate repair through homologous recombination, potentially by mediating the ubiquitination of key repair proteins such as XRCC5/Ku80 and RBBP8/CtIP. This ubiquitination process may remove inhibitory complexes or promote the assembly of repair machinery. Additionally, the family is implicated in the ubiquitination and degradation of TCF/LEF transcription factors, influencing the Wnt/beta-catenin signaling pathway. The family's auto-ubiquitination activity, particularly in conjunction with UBE2K, suggests a role in self-regulation. The zinc finger domains of these proteins exhibit a strong binding preference for DNA with single-stranded overhangs, which is crucial for their recruitment to double-strand break sites and subsequent repair facilitation.
Caenorhabditis elegans Nuclear Hormone Receptors (C.elegans_NHRs)
Type: Family

The nuclear hormone receptor family in Caenorhabditis elegans includes orphan nuclear receptors that are implicated in various metabolic and physiological processes. While the specific functions of some members are not well characterized, at least one member, nhr-62, is known to play a role in the metabolic and physiological adaptations to dietary restriction, which contributes to longevity. This receptor is involved in modulating triglyceride and lipid metabolism as well as autophagy through the regulation of gene transcription. Other members of the family are similarly expected to function as transcriptional regulators, although their target genes and the pathways they influence remain to be fully elucidated.
Chloroplastic/Mitochondrial RNA Processing (Chloro/Mito_RNA_Process)
Type: Family

This family of proteins includes both chloroplastic pentatricopeptide repeat-containing proteins and mitochondrial intron-encoded endonucleases. The chloroplastic members are involved in the splicing of group II introns, which is essential for the assembly of photosystems I and II, and the proper functioning of the chloroplast. They are required for the splicing of various chloroplast transcripts, including those of ycf3, atpF, ndhA, petB, and rps16. The mitochondrial members are endonucleases that participate in intron homing, a process that facilitates the insertion of introns into intronless genes within the mitochondrial DNA. They recognize and cleave specific DNA sequences to mediate this process.
Alpha-1-2 Fucosyltransferase (Alpha-1-2_FucT)
Type: Family

This family of proteins includes enzymes that function as glycosyltransferases, specifically involved in the transfer of fucose to various acceptor substrates. Members of this family are characterized by their ability to catalyze the addition of fucose in alpha 1-2 linkage to different galactose-containing oligosaccharides. These enzymes play a role in the modification of cell surface glycoproteins and glycolipids, which is important for processes such as cell recognition and signaling. Some family members are implicated in physiological functions like axon regeneration after injury. The specificity of substrate recognition varies among family members, with some unable to fucosylate certain types of glycan acceptors, highlighting the diversity of enzyme activity within this family.
FAM241 domain-containing protein (FAM241_domain)
Type: Family

This family of proteins may be involved in maintaining lysosome homeostasis, which is crucial for cellular waste processing and recycling of biomolecules. The exact molecular functions and biological processes associated with this family remain to be fully characterized.
S100-fused Epidermal Structural Protein (S100-fused_Epidermal_Struct)
Type: Family

This family of proteins is involved in the structural integrity and mechanical strength of the epidermis, particularly in the formation of the stratum corneum. Members play a crucial role in cell-cell adhesion within the cornified cell layers and contribute to the assembly of the epidermal cornified cell envelopes. They are also implicated in the aggregation of keratin intermediate filaments and the promotion of disulfide-bond formation among these filaments during the terminal differentiation of mammalian epidermis.
Mucin-related_signaling_and_protection_protein (Mucin_signaling_protection)
Type: Family

This family of proteins includes mucins and transcription-associated components. Mucins are high molecular weight glycoproteins that form a protective, lubricating barrier on mucosal surfaces, playing a role in defense against pathogens and particles. They are involved in various cellular processes such as ligand binding, intracellular signaling, epithelial cell protection, adhesion modulation, and potentially in the regulation of epithelial cell growth. The family also appears to include proteins related to the PI3/PI4-kinase family, suggesting a role in signaling pathways. However, the function of some members remains uncharacterized.
Fungal Pathogen Heme-Binding RBT5 (Fungal_Heme-Binding_RBT5)
Type: Family

The RBT5 family comprises heme-binding proteins with a role in heme-iron utilization, a critical process for the virulence of pathogenic fungi. Members of the RBT5 family are characterized by the presence of a CFEM domain, which is distinguished by its novel helical-basket fold, composed of six alpha-helices and eight cysteines forming four disulfide bonds. This domain is essential for heme-binding and is found in various fungal pathogens. The proteins within this family are involved in biofilm formation and may participate in a heme-acquisition system through a cross-cell wall heme-transfer cascade, which includes cooperation among different CFEM proteins. This system is crucial for extracting iron from host tissues, a significant virulence factor for pathogenic microorganisms.
Bacterial Fibronectin-Binding (Bact_Fn-Binding)
Type: Family

This family of proteins is involved in bacterial adhesion and invasion processes. They facilitate the attachment of bacteria to various host substrates, including fibronectin, fibrinogen, elastin peptides, and tropoelastin. These interactions enable the bacteria to invade endothelial cells and adhere to activated platelets, contributing to bacterial colonization and persistence within the host. The proteins possess multiple binding regions that interact with both soluble and immobilized forms of fibronectin and fibrinogen. They can mediate invasion through actin rearrangement in host cells, a process that is also mediated by integrin alpha-5/beta-1. Additionally, they play a role in the induction of experimental endocarditis by promoting colonization and persistence of bacteria in host tissues.
BPI fold-containing antibacterial protein (BPI_fold-antibacterial)
Type: Family

This family of proteins exhibits antibacterial activity, particularly against Pseudomonas aeruginosa. Members of this family are part of the BPI/LBP/Plunc superfamily and are characterized by the presence of a BPI fold. The BPI fold is known to play a role in binding to and neutralizing lipopolysaccharides, which are components of the outer membrane of Gram-negative bacteria. The proteins in this family are likely involved in innate immune responses by providing a first line of defense against bacterial infections.
Maize Seed Storage Zein (Maize_Zein_Storage)
Type: Family

The Zein family comprises proteins that serve as major seed storage proteins. These proteins are predominantly found in maize and related cereal grains. They are synthesized during seed development and are deposited in protein bodies within the endosperm of the seed. The primary role of zein proteins is to serve as a nutrient reserve for the seedling during germination and early growth. Due to their high proline and glutamine content, zeins are classified as prolamin proteins. They are important for the nutritional quality of the grain, as they influence the amino acid profile and digestibility. The zein family proteins are also involved in the formation of the protein matrix that encapsulates starch granules in the endosperm, which affects the texture and processing properties of the grain.
Metal-responsive DNA-binding regulator (Metal_resp_DNA-bind_regulator)
Type: Family

This family of proteins includes DNA-binding proteins that are potentially involved in transcription regulation and may play a role in metal detoxification. Members of this family are known to bind to promoter regions, suggesting a regulatory function in gene expression. Some proteins within this family have been shown to bind various metal ions, including cadmium, zinc, manganese, and nickel, which may contribute to intracellular survival and metal tolerance in certain bacteria. The family features a winged-helix-turn-helix (wHTH) DNA-binding domain, typically located at the N-terminus, and a C-terminal alpha helix that is implicated in protein dimerization. Metal binding is associated with conformational changes that affect both metal-binding and DNA-binding residues.
ATP-dependent Helicase (ATP-dep_Helicase)
Type: Family

This family of proteins includes ATP-dependent helicases which are enzymes that utilize the energy derived from ATP hydrolysis to unwind double-stranded nucleic acids. Helicases are essential for many cellular processes, including DNA replication, repair, recombination, and transcription, as well as RNA processing and degradation. They play a critical role in maintaining genome stability and integrity. Members of this family are characterized by their ability to bind and hydrolyze ATP, and to exert force on nucleic acid substrates, thereby separating the strands to facilitate the processing of the nucleic acids by other enzymes.
4-carboxymuconolactone decarboxylase/NDH-1 regulator (4CMD/NDH-1_regulator)
Type: Family

This family of proteins includes enzymes known as 4-carboxymuconolactone decarboxylases, which are involved in the beta-ketoadipate pathway, a route for the degradation of aromatic compounds. These enzymes catalyze the decarboxylation step, converting 4-carboxymuconolactone to 3-oxoadipate, a key intermediate in the pathway. Additionally, some members of this family are uncharacterized proteins that are hypothesized to play a role in the regulation of NDH-1 biosynthesis, a complex involved in the respiratory chain and energy production in bacteria.
Thioester Dehydratase-Related Protein (Thioester_dehydratase-like)
Type: Family

This family of proteins includes members that are likely involved in metabolic processes, particularly in the degradation of specific molecules such as bile acids. Some members are predicted to have enzymatic activity, possibly functioning as hydratases within metabolic pathways. The family is related to thioester dehydratases, suggesting a role in the hydration of double bonds in thioester-linked substrates, which is a key step in various catabolic processes.
S-adenosyl-L-methionine-dependent methyltransferase (SAM-dependent_MTase)
Type: Family

This family of proteins includes S-adenosyl-L-methionine-dependent methyltransferases involved in diverse biosynthetic pathways. Members are responsible for the methylation of various substrates, contributing to the biosynthesis of complex molecules with antibiotic, immunosuppressant, or other bioactive properties. These enzymes play roles in the modification of secondary metabolites, such as glycoside antibiotics, iron-chelating compounds, and macrolide antibiotics. They catalyze the transfer of methyl groups to specific positions on their substrates, which can be part of larger biosynthetic gene clusters responsible for the production of medicinally relevant compounds.
Gfo/Idh/MocA Oxidoreductase (Gfo/Idh/MocA_Oxidoreductase)
Type: Family

This family of proteins includes enzymes that are involved in various oxidation-reduction processes. Members of this family are characterized by their ability to catalyze reactions involving the transfer of electrons, typically with NAD or NADH as cofactors. The reactions they catalyze are important in the metabolism of sugars and related compounds. Some family members are involved in the biosynthesis of bacterial O antigens by oxidizing specific UDP-sugars, while others may participate in the transformation of different glucosides. The exact physiological substrates and metabolic pathways can vary among the family members, and some enzymes exhibit substrate specificity, not acting on certain UDP-sugars or glucosamines.
Nicotinate and N-heterocyclic Hydroxylase (N-heterocyclic_Hydroxylase)
Type: Family

This family of proteins includes enzymes involved in the hydroxylation of nicotinate and other N-heterocyclic substrates. Members of this family function in the degradation pathways of nicotinate and isoquinoline, catalyzing the conversion of nicotinate to 6-hydroxynicotinate, as well as hydroxylating various N-containing heterocyclic compounds. Some family members are part of multi-component enzyme systems and may interact with the electron transfer chain, potentially delivering electrons to a cytochrome oxidase. The family includes proteins that are related to the xanthine dehydrogenase family and exhibit activity regulation by selenide and sulfide.
GlcG-related carbohydrate metabolism protein (GlcG_carb_metab_protein)
Type: Family

This family of proteins is involved in carbohydrate metabolism and transport. Members of the GlcG family are typically associated with the utilization of glucose and may play roles in the regulation of glucose levels within the cell. They may be involved in various biochemical pathways that process glucose or glucose-derived molecules, contributing to the overall energy metabolism and homeostasis. The specific functions of individual members can vary, and detailed characterization is necessary to elucidate the precise role of each protein within the family.
Chromate Ion Transporter (CHR_Transporter)
Type: Family

This family of proteins is involved in the transport of chromate ions across cellular membranes. Members of this family are characterized by their similarity to the chromate ion transporter (CHR) family, which is classified under the Transporter Classification (TC) system as 2.A.51. These transporters play a role in reducing chromate accumulation within cells, contributing to chromate resistance. The functional mechanism of these proteins likely involves the active or facilitated transport of chromate ions, potentially impacting the cell's ability to manage the toxic effects associated with chromate exposure.
Eukaryotic-type N-acetylglucosamine Kinase (Euk-type_GlcNAc_Kinase)
Type: Family

This family of proteins includes enzymes that phosphorylate various substrates, including amino sugars and sugar derivatives, using ATP. Members of this family are involved in metabolic pathways that process carbohydrates and are characterized by their kinase activity. They can phosphorylate N-acetylglucosamine (GlcNAc), glucosamine, N-acetylmuramic acid (MurNAc), and 2-keto-3-deoxygluconate (KDG), each at the 6-hydroxyl group. These phosphorylation reactions are crucial for the metabolism of complex carbohydrates and cell wall components in various organisms. The enzymes in this family show specificity for their respective substrates and are involved in different biological processes, such as cell wall turnover and carbohydrate utilization pathways.
Alkyltransferase-like DNA repair (ATL_DNA_repair)
Type: Family

The ATL subfamily of the MGMT family is involved in the recognition and repair of DNA damage. Members of this family bind to DNA containing O(6)-alkylguanine adducts, with a preference for larger alkyl groups. They facilitate the repair process by flipping the damaged base out of the DNA helix into an extrahelical position, which is then accessible to nucleotide excision repair (NER) proteins. The ATL proteins play a role in directing the repair pathway choice, with smaller adducts being processed by the global genome repair pathway and bulkier lesions stalling transcription and being directed to transcription-coupled repair. Some members also bind to AP sites and prevent methyl-directed mismatch repair of O(6)-alkylguanine:T mispairs for larger alkyl groups.
Bacterial cell division SPOR domain-containing protein (Cell_div_SPOR-domain)
Type: Family

This family of proteins is involved in bacterial cell division. Members of this family are associated with the septal ring structure and are implicated in septal peptidoglycan synthesis and cell constriction. They may interact with other cell division proteins to facilitate the division process. Some proteins in this family contain a SPOR domain that binds peptidoglycan, which is crucial for targeting the protein to the septal ring and may activate septal peptidoglycan synthesis. The family includes both essential and non-essential proteins for cell division, with some members required for efficient cell constriction and others potentially playing a regulatory role.
ABC-2 integral membrane transport permease (ABC-2_transport_permease)
Type: Family

This family of proteins is involved in the transport of various molecules across the inner membranes of bacterial cells. They are part of the ATP-binding cassette (ABC) transporter superfamily, specifically the ABC-2 integral membrane group. These proteins typically function as permeases, which are components of larger transporter complexes. They work in conjunction with other proteins, including those with ATPase activity, to facilitate the import or export of substances in an ATP-dependent manner. The substrates can range from ions and small molecules to larger organic compounds. The activity of these transporters is critical for cellular nutrient uptake, waste removal, and response to environmental changes.
Trichothecene Biosynthesis Acetyltransferases (Trichothecene_AcTrans)
Type: Family

The acetyltransferase family is involved in various biological processes, including the biosynthesis of secondary metabolites such as satratoxins, which are trichothecene mycotoxins linked to human food poisonings. Members of the family function as acetyltransferases, which are enzymes that transfer acetyl groups to substrates. Some family members are implicated in the detoxification of harmful compounds, such as puromycin, thereby contributing to cellular defense mechanisms. The family includes proteins that are part of gene clusters encoding multiple enzymes, which work together to synthesize and modify complex organic molecules. These proteins may also play roles in endogenous protection from toxicity and in the regulation of expression of gene clusters responsible for metabolite production.
Major Facilitator Superfamily Cyanate Porter (MFS_Cyanate_Porter)
Type: Family

This family of proteins is part of the major facilitator superfamily and is involved in the active transport of specific substrates across cellular membranes. Members of this family function as transporters for various compounds, including cyanate and anionic 4-hydroxy-benzoate, and are also implicated in the efflux of 2-nitroimidazole. These transport activities suggest roles in cellular detoxification, nutrient uptake, and metabolic processes.
HTH-type transcriptional regulators in bedaquiline tolerance (HTH-type_Bedaq_tolerance)
Type: Family

The HTH-type transcriptional regulator family is involved in a regulatory network that coordinates bacterial tolerance to the antitubercular drug bedaquiline. Members of the family are characterized by the presence of a winged helix-turn-helix (HTH) domain, which is typically involved in DNA binding and regulation of gene expression. The family's role in drug tolerance suggests a potential impact on the effectiveness of bedaquiline during tuberculosis treatment, making them a target of interest for understanding and overcoming drug resistance mechanisms.
Heavy metal cation-efflux system component (Metal_cation-efflux_comp)
Type: Family

This family of proteins includes components of cation-efflux systems that confer resistance to various heavy metals such as cobalt, zinc, cadmium, and nickel. Members of this family appear to be involved in the specificity and transport of these metals, contributing to the detoxification and resistance mechanisms in bacteria.
Putative sugar transporter and related proteins (Sugar_transport-like)
Type: Family

This family of proteins includes uncharacterized members and a characterized ribitol transporter. The ribitol transporter is part of the major facilitator superfamily, which is known for transporting sugars across membranes. The similarity to E. coli YihN suggests a potential function related to nucleotide sugar metabolism or transport, as YihN is implicated in such processes. The family appears to be involved in transport functions, possibly with specificity for sugar-like substrates, although the exact substrates and physiological roles for the uncharacterized proteins remain to be elucidated.