SII-SWORD/CoKE huggingface dataset:
Small ribosomal subunit protein bS1-like (Ribos_protein_bS1-like)
Type: Family

The bacterial ribosomal protein bS1 family is involved in the initiation of protein synthesis by binding mRNA and facilitating its recognition by the 30S ribosomal subunit . Members of the family play a role in unwinding double-stranded RNA, preferentially binding to polypyrimidine tracts and transiently formed single-stranded RNA regions. Some family members are involved in trans-translation, a process that rescues stalled ribosomes by binding transfer-messenger RNA (tmRNA). Additionally, certain proteins within the family negatively autoregulate their own translation and may be involved in the translation of chloroplast-encoded proteins, heat stress response, and biosynthesis of thylakoid membrane proteins. The family includes proteins that are essential for the translation of most natural mRNAs, except for leaderless mRNA, and may act as RNA chaperones to unfold structured mRNA on the ribosome.
Low Molecular Weight Phosphotyrosine Protein Phosphatase (LMW_PTPase)
Type: Family

The Low Molecular Weight Phosphotyrosine Protein Phosphatase family comprises enzymes that dephosphorylate phosphotyrosine residues in proteins, playing a role in various cellular processes. Members of this family are involved in the regulation of cell signaling pathways by acting on tyrosine-phosphorylated proteins and low molecular weight aryl phosphates. Some members are implicated in bacterial virulence, aiding in survival within host macrophages by modulating host immune responses and phagosome maturation. Others are involved in the synthesis and export of polysaccharides, contributing to bacterial virulence factors and stress resistance. Additionally, certain members dephosphorylate phosphoarginine residues, counteracting protein arginine kinases and influencing gene expression and protein activity. The family's activity is regulated by various inhibitors, including sulfhydryl reagents, metal ions, and competitive inhibitors like vanadate.
ADAMTS and ADAMTS-like (ADAMTS_ADAMTS-like)
Type: Family

The ADAMTS and ADAMTS-like protein family is involved in various biological processes, including the regulation of extracellular matrix (ECM) composition, cell migration, development, and apoptosis. Members of this family are metalloproteinases that cleave components such as aggrecan and versican, contributing to ECM remodeling. Some proteins within this family have a role in inhibiting angiogenesis, while others facilitate microfibril biogenesis and influence tissue organization. The family includes proteins with thrombospondin type-1 motifs, which are important for ECM interaction, and some members possess a cysteine-switch motif that regulates their enzymatic activity. Additionally, certain ADAMTS-like proteins may have protease-independent functions in cellular processes such as ER to Golgi transport.
Laminin/Netrin Extracellular Matrix (Laminin/Netrin_ECM)
Type: Family

The laminin/netrin protein family is involved in the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. Laminins are crucial for the formation of stable basement membranes and organizing receptor complexes and cytoskeletal components. Netrins control guidance of central nervous system commissural axons and peripheral motor axons, serving as survival factors and regulating apoptosis. They are implicated in various developmental processes including neural, kidney, and vascular development, as well as in tumorigenesis. This family includes proteins that promote neurite outgrowth and are involved in the regulation of skeletogenesis and neuromuscular junction formation.
RNA-binding motif (RBM)
Type: Family

The RNA-binding motif (RBM) protein family is involved in various aspects of RNA metabolism, including pre-mRNA splicing, mRNA stabilization, and transcription regulation. Members of this family are characterized by their ability to bind RNA, often through RNA recognition motifs (RRMs) and arginine/glycine-rich (RGG) domains. They play roles in tissue-specific gene expression, alternative splicing, and are implicated in processes such as tumor suppression, stress response, and embryonic development. Some family members are also involved in the regulation of exon inclusion or suppression, and may form part of larger complexes like the supraspliceosome that govern splice site selection. The family includes proteins that function in spermatogenesis and sex determination, as well as those that respond to temperature changes by modulating mRNA stability and translation.
Peptidase S1 family, coagulation factors (Peptidase_S1_coag_factors)
Type: Family

The peptidase S1 family, including vitamin K-dependent and snake venom subfamilies, consists of serine proteases involved in blood coagulation. Members of this family initiate various pathways of the coagulation cascade, convert prothrombin to thrombin, and regulate coagulation by inactivating factors. They participate in both intrinsic and extrinsic pathways, with some acting as zymogens in blood. Vitamin K-dependent proteins are crucial for the activation of these proteases, and calcium binding is a common feature that affects their conformation and interactions. The snake venom subfamily members attack prey hemostatic systems by mimicking mammalian coagulation factors, inducing blood clotting. This family also includes proteins that may control axon guidance in the CNS and influence cell surface receptor expression.
RbsD/FucU L-fucose mutarotase (RbsD/FucU_mutarotase)
Type: Family

The RbsD/FucU family, specifically the FucU mutarotase subfamily, is involved in the anomeric conversion of L-fucose, a process critical for the interconversion between alpha- and beta-L-fucoses. L-Fucose, also known as 6-deoxy-L-galactose, predominantly exists in the beta form, which is metabolized through the salvage pathway. The GDP-L-fucose produced is then transported into the endoplasmic reticulum, where it is used as a substrate for N- and O-glycosylations by fucosyltransferases. These fucosylated structures are essential for cell-cell adhesion and recognition processes, as they are expressed on cell surfaces or secreted in biological fluids.
Polyketide synthase (Polyketide_Synthase)
Type: Family

The polyketide synthase family is involved in the biosynthesis of a diverse range of secondary metabolites with various biological activities, including antibiotics, mycotoxins, and other bioactive compounds . These modular enzymes catalyse the condensation of acyl-CoA units through decarboxylative Claisen condensation reactions, forming complex polyketide chains. The family includes non-reducing, reducing, and iterative polyketide synthases, each with distinct domain architectures that determine the structural diversity of the polyketides produced. The enzymes typically possess domains for ketosynthase, acyltransferase, acyl carrier protein, and additional domains for methylation, reduction, or cyclization, which contribute to the functional versatility of the family in generating polyketides with specific chemical modifications and biological functions.
Bacterial polysaccharide biosynthesis and export (Bact_polysacc_biosynth/exp)
Type: Family

The protein family is involved in the biosynthesis, regulation, and export of capsular and extracellular polysaccharides, which are critical for bacterial virulence and survival. Members of the family function as tyrosine-protein kinases that autophosphorylate, regulating their activity and the biosynthesis of polysaccharides. Some proteins act as chain-length determinants for lipopolysaccharides, modulating the length of polysaccharide chains. Others form ATP-driven export apparatuses, working in conjunction with additional proteins to translocate capsular polysaccharides across the inner membrane. The family also includes proteins required for the phosphorylation of tyrosine-protein kinases involved in capsular polysaccharide biosynthesis, suggesting a complex that coordinates polymerization and export to the cell surface.
FAD-dependent Oxidoreductases and Apoptosis Regulators (FAD-oxidoreductase/Apoptosis)
Type: Family

The FAD-dependent oxidoreductase family is characterized by its involvement in various oxidation-reduction processes. Members of this family function as electron transfer components in multicomponent enzyme systems, catalyzing reactions that involve the transfer of electrons from NAD(P)H to different substrates, often through intermediary proteins like ferredoxins. These proteins play roles in the metabolism of aromatic compounds, including the degradation of herbicides and pollutants, and in the regulation of apoptosis. Some family members are involved in the detoxification of reactive oxygen species, while others participate in normal mitochondrial function and biogenesis of the respiratory chain. The family includes proteins that act as NADH oxidoreductases, apoptosis-inducing factors, and components of dioxygenase systems for the hydroxylation of aromatic rings.
Erg6/SMT methyltransferase (Erg6_SMT_methyltransf)
Type: Family

The Erg6/SMT methyltransferase family is involved in various methylation processes essential for the biosynthesis of sterols, alkaloids, and other compounds. Members of this family catalyze the transfer of methyl groups from S-adenosyl-methionine to specific substrates, such as the C-24 position of sterols like zymosterol and lanosterol, leading to the production of ergosterol and other sterols. This modification is a key step in the ergosterol biosynthesis pathway, crucial for fungal cell membrane integrity. Additionally, family members participate in the biosynthesis of monoterpenoid indole alkaloids, including vindoline, and in the modification of lipid moieties of mycobacterial cell wall components. The family also includes enzymes involved in the biosynthesis of vitamin E, where they methylate tocopherols, and in the modification of antibiotics like erythromycin. The diverse functions of the Erg6/SMT family highlight its importance in the production of biologically active molecules with roles in cell structure, defense, and metabolism.
OpgB/LTA synthase bacterial cell wall biosynthesis (OpgB/LTA_synthase_biosynth)
Type: Family

The OpgB/LTA synthase family is characterized by proteins involved in the biosynthesis of important cell wall components in bacteria. Members of the OpgB subfamily function as phosphoglycerol transferases, transferring phosphoglycerol residues from phosphatidylglycerol to membrane-bound nascent glucan backbones, a crucial step in the production of certain polysaccharides. The LTA synthase subfamily members catalyze the polymerization of lipoteichoic acid (LTA) polyglycerol phosphate, using phosphatidylglycerol as a substrate. This process is essential for bacterial growth and cell division. The family plays a significant role in the structural integrity and functionality of bacterial cell walls, influencing processes such as cell shape maintenance, protection against environmental stress, and interaction with host immune systems.
Ephrin receptor tyrosine kinases (Ephrin_rcpt_TKs)
Type: Family

The Ephrin receptor family is a group of receptor tyrosine kinases that bind to membrane-bound ephrin ligands on adjacent cells, facilitating contact-dependent bidirectional signaling. These interactions are crucial for various developmental processes, including axon guidance, synaptic plasticity, cell migration, and differentiation. The family is characterized by forward signaling through the receptor and reverse signaling through the ephrin ligand. Members of this family play roles in the nervous system, such as in the guidance of neuronal axons and the formation of dendritic spines and excitatory synapses. They are also involved in angiogenesis, heart morphogenesis, and the maintenance of satellite cells. Some receptors are promiscuous, binding both A and B ephrin ligands, while others have more specific interactions. Certain family members are kinase-defective but still participate in cell adhesion and migration regulation.
COX15/CtaA Heme A Synthase (COX15/CtaA_HemeA_synthase)
Type: Family

The COX15/CtaA family is responsible for the biosynthesis of heme A, a critical component of cytochrome c oxidase, the terminal enzyme of the mitochondrial respiratory chain. Members of this family catalyze the conversion of heme O into heme A through two successive hydroxylations at the methyl group at carbon 8 of the heme molecule. The initial hydroxylation produces heme I, followed by a second hydroxylation that generates an unstable dihydroxymethyl group. This group spontaneously dehydrates to form the characteristic formyl group of heme A. The enzymatic activity of the COX15/CtaA family is essential for the proper functioning of aerobic energy metabolism.
Metacaspase (Metacaspase)
Type: Family

The Metacaspase family comprises cysteine proteases that are involved in programmed cell death, which is analogous to apoptosis in multicellular organisms. These enzymes typically cleave after arginine or lysine residues and are implicated in various cellular processes including stress responses, aging, and the maintenance of cellular homeostasis. Metacaspases are activated by calcium ions, which induce conformational changes necessary for their proteolytic activity. Some family members are involved in the regulation of cell death in response to oxidative stress or immune responses, while others may play roles in parasite growth and virulence. The family also includes inactive metacaspases that may have regulatory functions.
LIM/homeobox transcription factors (LIM_Homeobox_TF)
Type: Family

The LIM/homeobox protein family comprises transcription factors with diverse roles in embryonic development and cell differentiation. Members of the family are involved in specifying cell fates in various tissues, including the nervous system, limbs, gonads, and sensory organs. They regulate gene expression by binding to DNA, often acting synergistically with other transcription factors. LIM domains within these proteins typically contribute to transcriptional activation and can exert regulatory functions. The family plays critical roles in processes such as limb dorsalization, neuronal specification and migration, sensory neuron differentiation, and gonadal development. Some members are also implicated in mesoderm formation, neurogenesis, and the development of the pituitary gland and respiratory system.
RTT106/SSRP1 Histone Chaperone/FACT Complex (RTT106/SSRP1_HistChap/FACT)
Type: Family

The RTT106/SSRP1 family includes histone chaperones and components of the FACT complex, which are involved in nucleosome formation, heterochromatin silencing, and transcriptional regulation. Members of this family are essential for depositing acetylated H3-H4 complexes onto newly-replicated DNA and play a role in the transcriptional regulation of cell-cycle dependent histone genes. The FACT complex members act to reorganize nucleosomes and are involved in processes requiring DNA templates, such as mRNA elongation, DNA replication, and DNA repair. They facilitate RNA polymerase II transcription by modulating nucleosomal structure, promoting the dissociation and reestablishment of histone H2A-H2B dimers. Some members also bind specifically to double-stranded DNA and may have additional roles in cell cycle progression, development, and response to DNA damage.
Thiol Peroxidase Tpx Subfamily (Tpx_Peroxidase_subfamily)
Type: Family

The Tpx peroxidase family consists of thiol-specific peroxidases that play a crucial role in cellular defense against oxidative stress. Members of this family catalyze the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, thereby detoxifying peroxides and protecting cells. These enzymes are characterized by their preference for alkyl hydroperoxides and can act as lipid peroxidases to inhibit membrane oxidation. They are particularly important antioxidants during anaerobic growth and may provide defense against cytotoxic peroxides such as peroxynitrite, which are produced by activated macrophages during infection.
DeoC/FbaB aldolase (DeoC/FbaB_aldolase)
Type: Family

The DeoC/FbaB aldolase family is involved in various metabolic processes, including the degradation of signaling molecules and the biosynthesis of aromatic amino acids. Members of this family catalyze aldol condensation and transaldol reactions, playing key roles in pathways such as the degradation of phospho-AI-2, which terminates the induction of the lsr operon and closes the AI-2 signaling cycle. This results in the formation of glycerone phosphate and acetyl-CoA. Additionally, some members are involved in an alternative pathway for the biosynthesis of 3-dehydroquinate, a precursor in the canonical pathway for aromatic amino acid biosynthesis. The family also includes enzymes that catalyze the reversible aldol condensation/cleavage of fructose-bisphosphate, as well as other aldolase activities related to carbohydrate metabolism.
Zinc finger and BTB domain-containing (ZnFinger_BTB_dom_contain)
Type: Family

The Zinc finger and BTB domain-containing protein family is involved in transcriptional regulation, with members acting as transcriptional repressors or activators. They bind to specific DNA sequences, regulate chromatin organization, and recruit transcription factors to gene regulatory regions. Some family members are implicated in lineage commitment of T-cell precursors, tumor suppression, metabolic regulation, and response to oxidative stress. They interact with various proteins, including HDACs, NuRD complex, and androgen receptor, influencing cell proliferation, differentiation, and immune responses. The family also plays roles in myogenesis, adipogenesis, chondrogenesis, and DNA repair.
Outer-membrane lipoprotein LolB (LolB)
Type: Family

The LolB family is involved in the process of lipoprotein trafficking to the outer membrane of Gram-negative bacteria. Members of the LolB family are critical for the final step of lipoprotein transport, where they facilitate the incorporation of lipoproteins into the outer membrane. These lipoproteins are initially released by the LolA protein, and LolB proteins play an essential role in anchoring them to the outer membrane, which is crucial for maintaining cell envelope integrity and viability in bacteria such as E. coli.
WD repeat RBAP46/RBAP48/MSI1 (WD_repeat_RBAP46/RBAP48/MSI1)
Type: Family

The WD repeat RBAP46/RBAP48/MSI1 family is involved in chromatin metabolism and regulation. Members of this family function as core histone-binding subunits targeting chromatin assembly factors, chromatin remodeling factors, and histone deacetylases to histone substrates, regulated by nucleosomal DNA. They are components of several complexes, including the type B histone acetyltransferase (HAT-B) complex for chromatin assembly post-DNA replication, the core histone deacetylase (HDAC) complex for transcriptional repression, the NuRD complex for transcriptional repression through histone deacetylation and nucleosome remodeling, and the PRC2/EED-EZH2 complex for homeotic gene repression during development. Additionally, they play roles in telomeric silencing, meiotic regulation, and various developmental processes by maintaining transcriptionally repressive states of genes.
Distal-less homeobox transcription factors (Distal-less_Homeobox_TF)
Type: Family

The distal-less homeobox family is a group of transcription factors characterized by a conserved homeobox DNA-binding domain. Members of this family are involved in a variety of developmental processes across different species. They play key roles in the differentiation of interneurons, such as amacrine and bipolar cells in the retina, and contribute to craniofacial patterning and morphogenesis. Some family members act as transcriptional activators or repressors, influencing hematopoietic cell differentiation by modulating cytokine signaling pathways. They are also implicated in bone development, osteoblast differentiation, and chondrogenesis. In addition, certain proteins within this family are essential for zygotic genome activation during early embryonic development, and others, like the Nanog homeobox proteins, are crucial for maintaining pluripotency and self-renewal in embryonic stem cells.
Nitroreductase family, HadB/RutE subfamily (Nitroreductase_HadB/RutE)
Type: Family

The HadB/RutE subfamily is a group of proteins that belong to the broader nitroreductase family. Members of this subfamily are primarily involved in the reduction of toxic compounds. Specifically, they are known to reduce malonic semialdehyde to 3-hydroxypropionic acid, which is then excreted from the cell. This reaction is part of the metabolic process that deals with the degradation of pyrimidine nitrogen. The activity of these enzymes is crucial for cellular detoxification and the maintenance of metabolic balance. The HadB/RutE subfamily is characterized by the presence of proteins that share a common function and sequence similarity, suggesting a conserved mechanism of action across different species.
Retroviral Gag-Pol polyproteins (Retroviral_Gag-Pol_poly)
Type: Family

This family of proteins is involved in the life cycle of retroviruses, including the formation of virions, virus budding, and integration of viral DNA into the host genome. They play a role in the packaging and encapsidation of the viral genome, forming the core of the virion that houses the RNA-nucleocapsid complex. These proteins are also implicated in the reverse transcription process, where viral RNA is converted into DNA, and in the subsequent integration of this DNA into the host's genome, a critical step for viral replication. Additionally, they interact with host cell factors to facilitate the release of new viral particles. Some members of this family have enzymatic functions, such as protease, integrase, and reverse transcriptase activities, which are essential for viral maturation and replication. They are also targets for antiretroviral drugs that aim to inhibit these processes.
Gfo/Idh/MocA family oxidoreductases and glycosidases (Gfo/Idh/MocA_oxidrdct_glycsds)
Type: Family

The Gfo/Idh/MocA family proteins are involved in various oxidation-reduction processes and play a role in carbohydrate metabolism. Members of this family exhibit a range of enzymatic activities, including glycosidase activity specific to alpha-N-acetylgalactosaminidase, catalysis of sugar dehydrogenation, and promoting matrix assembly. Some proteins within this family are involved in the degradation pathways of sugars like L-arabinose, allowing for growth on these sugars as sole carbon sources. Others are implicated in the metabolism of 1,5-anhydro-D-fructose and may participate in ulvan degradation. The family includes proteins with specificity towards different substrates, such as D-galactose, L-arabinose, and myo-inositol, reflecting a broad functional diversity.
Zeta Carotene Desaturase and Related Oxidoreductases (Zeta_carotene_desat/Oxidored)
Type: Family

The zeta carotene desaturase family is involved in the biosynthesis of carotenoids, which are essential for plant growth, development, and photoprotection. Members of this family catalyze the conversion of zeta-carotene to lycopene through the introduction of double bonds at specific positions, often involving intermediates such as neurosporene. The enzymes exhibit stereoselectivity and may require isomerization of substrates for activity. The family also includes proteins involved in the biosynthesis of heme b, where they catalyze the oxidation of coproporphyrinogen III to coproporphyrin III, and in the biosynthesis of protoporphyrin IX from protoporphyrinogen IX. Additionally, some members are implicated in the synthesis of fungal neurotoxins and antibiotics, as well as the biosynthesis of hopanoid precursors and sesterterpenes with potential anti-cancer activities.