SII-SWORD/CoKE huggingface dataset:
Polyketide Synthase Associated Protein (PKS_Associated_Protein)
Type: Family

This family of proteins includes members involved in the biosynthesis of polyketides, a class of secondary metabolites with diverse structures and functions. The proteins in this family are associated with type II polyketide synthases (PKS), which are multi-enzyme complexes that catalyze the formation of polyketide chains through the condensation of acyl-CoA precursors. Some members of this family may act as cyclases, aiding in the formation of aromatic rings during the biosynthesis of specific polyketides, such as tetracenomycin C. The presence of these proteins is indicative of their role in the production of complex polyketide structures, which can have antibiotic, antifungal, or anticancer properties.
Sulfur Carrier/Protein Modifier (Sulfur_Carrier/Prot_Modifier)
Type: Family

This family of proteins includes sulfur carrier components that are involved in cysteine biosynthesis and protein modification processes. In certain members, the thiocarboxylated form acts as a sulfur donor in a pathway dependent on CysM for cysteine production, which is crucial for survival in specific bacterial phases. Other members function as protein modifiers, attaching covalently to lysine residues of substrate proteins through a process known as sampylation, which may involve the formation of isopeptide bonds. Some are also implicated in the regulation of molybdenum cofactor biosynthesis and may influence proteolytic signaling for protein degradation.
Glycosyl Hydrolase 57 Enzymes (GH57_Enzymes)
Type: Family

This family of proteins is involved in the modification and degradation of carbohydrates. Members of this family exhibit a range of substrate specificities, including the ability to act on maltooligosaccharides and simpler carbohydrates such as maltotriose. They are capable of catalyzing transglycosylation reactions, which result in the production of maltooligosaccharides of varying lengths and glucose. Some family members also display hydrolytic activity, breaking down carbohydrates into smaller sugars. The enzymatic activity of these proteins can be regulated by various inhibitors, including specific chemical reagents and metal ions.
Glycosyl Hydrolase 94 Enzymes (GH94_Enzymes)
Type: Family

This family of proteins includes enzymes that catalyze the reversible phosphorolysis of various glycosidic bonds. Members of this family are involved in the metabolism of carbohydrates such as beta-(1->2)-D-glucans, N,N'-diacetylchitobiose, cellobionic acid, and cellobiose. These enzymes function by breaking down these carbohydrates into smaller sugar molecules and phosphate derivatives, which can then be utilized in various metabolic pathways including glycolysis and the pentose phosphate pathway. Some members are also implicated in the biosynthesis of cyclic beta-(1,2)-glucan, which is important for processes such as nodule invasion and bacteroid development in certain bacteria. The enzymes typically show specificity for their substrates, which range from di- to oligosaccharides, and are characterized by their ability to invert the anomeric configuration during the reaction.
Signal Transduction Response Regulator (ST_Response_Regulator)
Type: Family

This family of proteins includes response regulators that are integral to His-to-Asp phosphorelay signal transduction systems. They are phosphorylated on an Asp residue within a receiver domain, which activates their ability to regulate the transcription of target genes. Some members act as negative regulators of cytokinin signaling, while others may activate type-A response regulators in response to cytokinins. Additionally, this family encompasses proteins involved in sensory signal transmission to flagellar motors, influencing their rotation and thus affecting chemotaxis. Another member functions as part of a two-component system that regulates gene expression in response to specific environmental stimuli, such as glutamine levels.
Membrane-bound electron transfer protein (Electron_transfer_protein)
Type: Family

This family of proteins is involved in electron transfer processes within cellular respiration. Members are typically integral membrane components that interact with the quinone pool, facilitating the transfer of electrons to various terminal electron acceptors such as cytochrome c, menaquinol, tetrathionate, dimethyl sulfoxide (DMSO), and polysulfides. These proteins play a role in anaerobic respiration and are implicated in various reduction reactions, contributing to the energy metabolism of the cell. They may also function in anchoring other subunits of multi-protein complexes to the membrane, thereby assisting in the formation of functional electron transport systems.
Secreted Effector and Ankyrin Repeat (SecEffector_AnkRepeat)
Type: Family

This family of proteins includes secreted effectors with a role in host-pathogen interactions. One member is known to contain an RxLR-dEER motif, which is involved in the translocation of the effector into the host cell by binding to specific phospholipids on the cell surface. The same member is also implicated in the suppression of host cell death triggered by other proteins, indicating a possible function in manipulating host cell pathways to benefit the pathogen. Other members are annotated as putative ankyrin repeat proteins, suggesting a potential role in protein-protein interactions, although their specific functions remain uncharacterized.
T cell receptor complex component (TCR_complex_component)
Type: Family

This family of proteins includes components of the T cell receptor (TR) complex, which are crucial for the adaptive immune response. Members of this family are involved in recognizing peptide-major histocompatibility (MH) complexes displayed by antigen-presenting cells, a key step for T cell-mediated immunity against pathogens. Upon binding to these complexes, the TR proteins initiate a cascade of intracellular signaling events that lead to T cell activation and differentiation. This signaling involves the phosphorylation of immune receptor tyrosine-based activation motifs (ITAMs) and the formation of the LAT signalosome, which further propagates the signal to activate pathways such as calcium, MAPK kinase, and NF-kappa-B. These pathways are essential for gene expression, T cell growth, and differentiation. The T cell repertoire is generated through V-(D)-J rearrangement in the thymus and is shaped by selection events to produce a pool of self-MH restricted, non-autoaggressive T cells. The interaction of TR with peptide-MH complexes post-thymus also influences the structural and functional avidity of the T cell receptor.
Polysaccharide Lyase 9 (Polysaccharide_Lyase_9)
Type: Family

The Polysaccharide Lyase 9 family includes enzymes with pectate lyase activity, which are involved in the degradation of pectin, a component of the plant cell wall. Members of this family exhibit endo-cleaving activity on homogalacturonan, a region in pectin, and can also act on partially methylated pectin. They release monogalacturonate or oligogalacturonates of various sizes as products. These enzymes play a role in plant tissue maceration and are implicated in soft-rot disease in plants. Their activity is regulated by various factors, including metal ions and surfactants, and can be inhibited by metal chelators like EDTA. The family's enzymes are important for the catabolism of pectate and have applications in the processing of plant-based materials.
Inner Membrane YidH-like (IM_YidH-like)
Type: Family

This family of proteins is involved in cellular processes associated with the inner membrane, as suggested by the name 'Inner membrane protein YidH'. The exact functions of these proteins are not clearly defined in the provided annotations. However, the similarity to proteins from different species, such as M.tuberculosis Rv2272 and E.coli YidH, indicates a conserved role across these organisms. The proteins may be involved in transport, signaling, or other membrane-associated functions, but further experimental evidence is required to specify their roles.
Oxidative DNA damage repair enzyme (Oxidative_DNA_repair_enzyme)
Type: Family

This family of proteins is involved in the cellular response to oxidative DNA damage. Members of this family function as DNA repair enzymes that recognize and excise oxidized DNA bases, specifically 7,8-dihydro-8-oxoguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine (FAPY). They exhibit a beta-lyase activity that cleaves the DNA backbone 3' to the damaged site, facilitating the removal of the lesion and subsequent DNA repair processes. The ability to repair oxidative DNA damage is crucial for maintaining genomic stability and preventing mutagenesis.
Hepadnavirus polymerase/reverse transcriptase (Hepadnavirus_pol/RT)
Type: Family

This family of proteins includes multifunctional enzymes that play a crucial role in the replication of hepadnaviruses by converting the viral RNA genome into double-stranded DNA within cytoplasmic capsids. These enzymes exhibit both DNA polymerase activity, which can utilize DNA or RNA templates, and ribonuclease H activity, responsible for cleaving RNA strands of RNA-DNA heteroduplexes. The initiation of reverse transcription is a unique process involving protein priming, where the enzyme binds to an epsilon loop on the pregenomic RNA and the newly synthesized DNA becomes covalently attached to the enzyme itself. This leads to the formation of a relaxed circular DNA genome that, upon infection of a new cell, is transported to the nucleus and transformed into covalently closed circular DNA, a key intermediate for establishing infection.
Mono-ADP-ribosyltransferase ARTD/PARP (Mono-ARTD/PARP)
Type: Family

This family of proteins includes mono-ADP-ribosyltransferases that are involved in various cellular processes, including DNA damage repair, immune responses, and regulation of transcription. Members of this family are capable of mediating mono-ADP-ribosylation of target proteins, which is a post-translational modification affecting protein function and signaling. Some members interact with E3 ligases to modulate ubiquitination, influencing DNA repair mechanisms and the recruitment of repair proteins to DNA damage sites. They also play roles in immune responses by regulating cytokine production and STAT protein phosphorylation. These proteins are distinct from other PARP family members in that they do not support poly-ADP-ribosylation.
IS150/IS1296 orfA-like (IS150/IS1296_orfA-like)
Type: Family

This family of proteins is associated with mobile genetic elements known as insertion sequences (IS). Members of this family are typically involved in the transposition process, which allows the IS elements to move within the genome. The proteins may possess functions such as DNA binding, endonuclease activity, and/or binding to transposase enzymes, facilitating the integration and excision of the IS elements. These activities are crucial for the mobility of the IS elements, which can have significant impacts on the genetic variability and evolution of bacterial genomes by causing mutations, gene disruptions, or the creation of new gene combinations when they insert into new genomic locations.
Alcohol O-acetyltransferase-related protein (Alcohol_O-acetyltransferase)
Type: Family

This family of proteins includes enzymes that are involved in the acetylation of alcohols using acetyl-CoA, producing various acetate esters. These esters can have roles in detoxification processes, interaction with insect vectors for dispersal, and resistance to inhibitors of sphingolipid biosynthesis. Some members are also capable of thioesterase activity with specificity towards medium-chain-length acyl-CoAs. The family appears to be functionally diverse, with some members implicated in the biosynthesis of cytokinins and other growth-promoting metabolites in plants. The proteins are characterized by the presence of amphipathic helices essential for membrane association and share sequence similarity indicative of a common evolutionary origin.
Cysteine-rich Ser/Thr receptor-like kinase (CR_Ser/Thr_kinase)
Type: Family

This family of proteins includes serine/threonine kinases that are characterized by cysteine-rich sequences. Members are involved in various signaling pathways and cellular processes. One member is known to be activated by cold and acts as a negative regulator of freezing tolerance by phosphorylating specific target proteins, which leads to their translocation into the nucleus in response to cold stress. The family is part of the larger protein kinase superfamily and shares common structural features that are typical of serine/threonine kinases.
Bromodomain and WD repeat-containing (Bromo_WD_repeat)
Type: Family

The Bromodomain and WD repeat-containing protein family is involved in various cellular processes including the regulation of cell morphology, cytoskeletal organization, and control of cell shape. Members of this family may function as transcriptional activators and could be implicated in chromatin remodeling. Some proteins within this family are likely to play a role in signaling pathways related to insulin and insulin-like growth factor, stimulating cell proliferation through cyclin transcription and possessing anti-apoptotic activity via AKT1 phosphorylation and activation.
Post-transcriptional expression and antimicrobial biosynthesis protein (PTE-AB_protein)
Type: Family

This family of proteins includes components involved in various cellular processes, including post-transcriptional gene expression and biosynthesis of bioactive compounds. Some members are part of large complexes that coordinate ribosomal functions with gene expression steps. Others are implicated in the production of secondary metabolites with antimicrobial properties, such as the biosynthesis of cyclic lipopeptides that can inhibit the growth of pathogenic fungi. The specific roles of some members within these processes remain to be elucidated, while others are characterized by their similarity to known protein families.
Murein DD-endopeptidase/LD-carboxypeptidase (Murein_DD/LD_carboxypeptidase)
Type: Family

This family of proteins includes enzymes with murein DD-endopeptidase activity, which specifically target D-Ala-meso-diaminopimelic acid (mDAP) cross-links within bacterial cell walls. Their primary function is to facilitate cell wall expansion by cleaving these cross-links, allowing for the insertion of new glycan strands. Members of this family are functionally redundant, meaning that multiple enzymes can perform the same role within the cell. Additionally, some members exhibit weak LD-carboxypeptidase activity, which involves cleaving peptide bonds between L-mDAP and D-Ala. These activities are crucial for maintaining cell wall integrity and remodeling during growth and division.
Polysaccharide Lyase 1 (Polysaccharide_Lyase_1)
Type: Family

The Polysaccharide Lyase 1 family includes pectinolytic enzymes that play a crucial role in the degradation of pectin, a plant cell wall polysaccharide. Members of the family are characterized by their ability to cleave internal glycosidic bonds in highly methylated pectins, a process that is essential for the breakdown of this complex carbohydrate. The enzymes preferentially act on pectate, the anionic form of pectin, rather than on the methyl ester form. The family encompasses four classes of enzymes: pectin lyase, polygalacturonase, pectin methylesterase, and rhamnogalacturonase. Pectin lyase, in particular, is significant for its role in the depolymerization of pectin, facilitating the disassembly of the plant cell wall structure during various biological processes.
Mitochondrial Inner Membrane Protease Subunit 1 (Mito_IMP1_subunit)
Type: Family

The Mitochondrial Inner Membrane Protease (IMP) Subunit 1 family comprises enzymes that play a crucial role in the maturation of mitochondrial proteins. Members of this family are responsible for catalyzing the removal of transit peptides from precursor proteins that are targeted from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. This proteolytic process is essential for the proper functioning of the mitochondrial protein import machinery. Specific substrates for these proteases include nuclear-encoded proteins such as DIABLO, CYB2, and GUT2, as well as mitochondrially encoded proteins like COX2. The IMP1 subfamily belongs to the broader peptidase S26 family and includes both catalytic and non-catalytic components that may have distinct substrate specificities, ensuring a wide range of mitochondrial proteins are correctly processed and matured.
Complement and asymmetry regulator (Compl_asym_regulator)
Type: Family

This family of proteins includes regulators of the alternate pathway of complement. Members are characterized by their ability to bind and stabilize C3- and C5-convertase enzyme complexes, thereby playing a crucial role in the innate immune response. They are also involved in inhibiting the degradation of the Complement C3 beta chain (C3b) by CFI-CFH. Additionally, some family members are implicated in the determination of left/right asymmetry in the nervous system, particularly in the polarization and migration of neuroblasts. The family is characterized by the presence of TSP type-1 domains, which are known to mediate protein multimerization through specific domain-domain interactions.
Glycosphingolipid Hydrolyzing Enzymes (Glycosphingolipid_Hydrolases)
Type: Family

This family of proteins is involved in the hydrolysis of glycosidic linkages in various glycosphingolipids. Members exhibit a range of substrate specificities, with some acting on glycosphingolipids with gangliotetraose structures and others on glucosylceramide. They play roles in the catabolism of complex lipids, preventing the accumulation of immature ceramide-containing compounds, and are involved in processes such as vacuole formation. The activity of these enzymes is regulated by various factors, including metal ions and detergents, with some members requiring the presence of detergents for activity and others being inhibited by specific metal ions or detergents.
Metal-responsive HTH-type transcriptional regulators (Metal_resp_HTH_trans_reg)
Type: Family

The protein family includes transcriptional regulators that respond to environmental stimuli such as metal ions, specifically zinc, to regulate gene expression. Members of the family act as repressors or activators by binding to specific DNA motifs in the promoter regions of target genes. They are involved in various biological processes including multidrug resistance, metal ion homeostasis, and biosynthesis pathways. The family's regulatory mechanisms are often dependent on the presence of coregulators like zinc, which influences their DNA-binding activity. Some members also autoregulate their own expression.
GW182 domain-containing protein (GW182_domain)
Type: Family

This family of proteins is involved in RNA-mediated gene silencing mechanisms, including those mediated by micro-RNAs (miRNAs) and short interfering RNAs (siRNAs). Members of this family are essential for the miRNA-dependent translational repression and siRNA-dependent cleavage of target mRNAs. They function as scaffolding proteins, associating with argonaute proteins that are bound to mRNAs with partial complementarity. These proteins are capable of recruiting various complexes such as CCR4-NOT and PAN deadenylase, which are involved in mRNA degradation processes. Some members contain a silencing domain known as the C-terminal effector domain (CED), which is implicated in the repression of translation and mRNA decay.
Calcium-regulated mRNA-binding domain-containing protein (Ca-reg_mRNA-binding_domain)
Type: Family

This family of proteins includes RNA-binding factors that are involved in the regulation of mRNA stability and the synthesis of histone variants. Members of this family have been shown to bind specifically to mRNA, including the 3'-UTR ends of histone H1 and H3.3 mRNAs, which encompasses the polyadenylation signal. This binding activity suggests a role in the post-transcriptional regulation of gene expression. Some members are also known to bind single-stranded DNA in vitro. The functions of these proteins are crucial in processes such as the negative regulation of histone variant synthesis, particularly in the context of brain development. The calcium-regulated members of this family are responsive to changes in intracellular calcium levels, which may influence their interaction with target mRNAs.
ESCRT-I complex UEV domain-containing protein (ESCRT-I_UEV_domain)
Type: Family

This family of proteins is involved in the endosomal sorting complex required for transport (ESCRT) pathway, specifically as components of the ESCRT-I complex. They play a crucial role in the sorting of ubiquitinated cargo into multivesicular bodies (MVBs), which is essential for vesicular trafficking processes. Members of this family are also implicated in the regulation of cell growth and differentiation, acting as negative growth regulators. They have a role in cytokinesis and are involved in the budding of various viruses. Additionally, these proteins are associated with the exosomal release of certain molecules and may participate in the release of microvesicles distinct from exosomes.
Signal peptide, CUB and EGF-like domain-containing protein (SCUB_EGF-like_domain)
Type: Family

This family of proteins includes coreceptors and regulators of signaling pathways essential for developmental processes such as chondrogenesis, osteogenesis, and angiogenesis. Members of this family facilitate the interaction of ligands with their respective receptors, enhancing signaling cascades. They are involved in the bone morphogenetic protein (BMP) signaling pathway, acting as coreceptors for BMP2 and BMP4, and are necessary for the recruitment of BMP receptors to lipid rafts. Some members bind to TGFBR2, activating transforming growth factor-beta (TGFB) signaling, which plays a role in epithelial-mesenchymal transition and cancer progression. Additionally, these proteins participate in the sonic hedgehog (SHH) signaling pathway by binding to lipid-modified SHH, promoting its mobilization and release from the cell membrane, and facilitating its long-range signaling. They also synergize with other proteins to enhance SHH secretion. Furthermore, they may function as adhesive molecules in vascular biology and as coreceptors for vascular endothelial growth factor receptor 2 (VEGFR2), contributing to angiogenesis.
Vascular development regulator domain-containing protein (Vascular_dev_regulator)
Type: Family

This family of proteins includes members that are involved in the regulation of GTPase signaling pathways, particularly in the context of vascular development and endothelial cell function. They play a crucial role in the formation of vascular structures through vasculogenesis and angiogenesis. These proteins modulate the activity of Rho GTPases, which are key regulators of cell architecture and adhesion, thereby influencing endothelial cell morphogenesis and tubulogenesis of blood vessels. Some family members act as downstream effectors of Ras and Rap proteins, impacting processes such as cell adhesion, migration, and possibly transformation. Additionally, certain proteins in this family have been implicated as negative regulators of autophagy under conditions of amino acid starvation.
Amide and Lactam Catabolism Regulators (Amide_Lactam_Regulators)
Type: Family

This family of proteins includes transcription factors that regulate the expression of genes involved in the catabolism of amides, omega amino acids, and lactams. Some members are also implicated in the biosynthesis and detoxification of fusaric acid and its derivatives, which are mycotoxins with phytotoxic properties. The proteins play a role in the positive regulation of gene expression in response to specific inducers and contribute to the self-protection of the fungus by preventing the accumulation of toxic compounds.