SII-SWORD/CoKE huggingface dataset:
Alanyl-tRNA Editing Enzymes (Alanyl-tRNA_Editing_Enzymes)
Type: Family

This family of proteins functions in the editing of tRNA molecules to ensure the correct amino acid is attached. Members of this family act in trans to remove incorrect amino acid moieties from tRNA(Ala), which is charged with alanine. They are responsible for the hydrolytic editing of mischarged Ser-tRNA(Ala) and, in some cases, Gly-tRNA(Ala), preventing errors in protein synthesis. The specificity of this editing function is crucial for maintaining the fidelity of the genetic code during translation. These proteins belong to the class-II aminoacyl-tRNA synthetase family and are characterized by their ability to recognize and correct specific tRNA charging errors.
Rho GTPase-activating Guanine Nucleotide Exchange Factors (RhoGEF_Guanine_NuclExch_SF)
Type: Family

The protein family is characterized by its role as guanine nucleotide exchange factors (GEFs) that activate Rho GTPase family members, influencing signaling pathways that regulate neuronal shape, growth, and plasticity. These proteins are involved in actin cytoskeleton reorganization, contributing to cell migration, growth, and various developmental processes such as neuronal development, axonal outgrowth, dendrite formation, and synaptic function. Some family members also play a role in adipogenesis and myogenesis. They typically possess one or more DH domains that catalyze nucleotide exchange for RAC1 and/or RHOA, and may be regulated by interactions with SH3 domains or inositol phospholipids.
Organophosphate:Pi Antiporter (OPA_Antiporter)
Type: Family

This family of proteins includes transporters that facilitate the exchange of organic phosphate compounds and inorganic phosphate across cellular membranes. Members of this family are predominantly involved in the uptake of hexose-6-phosphate, glycerol-3-phosphate, and other related phosphate esters, which are essential for various metabolic processes. Some proteins in this family also function as sensors in signaling cascades, regulating the expression of other transporters in response to extracellular signals such as glucose-6-phosphate. The transport activity of these proteins is critical for maintaining cellular phosphate homeostasis and is integral to metabolic pathways such as glycogenolysis and gluconeogenesis.
NodU/CmcH Carbamoyltransferase (NodU/CmcH_Carbamoyltrnsfr)
Type: Family

The NodU/CmcH family consists of carbamoyltransferases involved in various biosynthetic pathways. Members of this family play key roles in the modification of natural compounds, such as antibiotics and nodulation factors. For instance, they are responsible for the 3'-carbamoylation of the noviosyl ring in novobiocin biosynthesis, a crucial step in producing this aminocoumarin antibiotic that inhibits bacterial DNA gyrases. Additionally, they participate in the 6-O-carbamoylation of Nod-factors, which are signaling molecules essential for symbiotic nitrogen fixation in legumes. Some members also catalyze the carbamoylation reaction in cephamycin biosynthesis, an important process for the production of this class of β-lactam antibiotics. Furthermore, the family includes enzymes involved in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, such as nebramycin and kanamycin, by transferring carbamoyl groups to these compounds. The family's activities are critical for the modification and effectiveness of these bioactive molecules.
DnaJ homolog subfamily B (DnaJ_subfamily_B)
Type: Family

This family of proteins includes molecular chaperones that are involved in the folding of unfolded proteins. They interact with HSP70 heat shock proteins, stimulating ATP hydrolysis and assisting in the proper folding of non-native proteins. Some members are implicated in the regulation of heat shock-induced transcriptional activity, while others are essential for cellular processes such as nuclear migration during mitosis and the initiation of translation. Additionally, certain members function within axonemal radial spoke complexes, contributing to the motility of sperm and cilia.
Haloalkane Dehalogenase Enzyme (Haloalkane_dehalogenase)
Type: Family

The haloalkane dehalogenase family encompasses enzymes that catalyze the hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds. This reaction results in the formation of primary alcohols, halide ions, and protons. Members of this family exhibit a broad substrate specificity, which includes various mono- and di-halogenated linear alkanes, and they are capable of processing environmental pollutants such as 1,2-dichloroethane. The family is divided into subfamilies based on sequence similarity, with Type 1 being the most common among the characterized enzymes. These enzymes play a crucial role in the detoxification of halogenated compounds and have potential applications in bioremediation.
Zyg-11-related ubiquitin ligase adapter protein (Zyg-11_UBL_adapter)
Type: Family

This family of proteins functions as substrate adapter subunits in E3 ubiquitin ligase complexes, which are involved in targeting proteins for proteasomal degradation. Members of this family recognize substrates bearing N-terminal glycine degrons, which are often exposed following caspase cleavage during apoptosis or after a failure of N-myristoylation. This recognition is crucial for the clearance of proteolytic fragments and the quality control of protein N-myristoylation. Some family members also play roles in cell cycle regulation, polarity establishment, and enhancing innate immune responses by modulating cGAS activity in antiviral defense.
PDZ domain-containing scaffold protein (PDZ_scaffold)
Type: Family

This family of proteins includes scaffolding proteins that play key roles in cellular signaling, localization, and structural integrity. They are involved in the formation and maintenance of tight junctions and epithelial cell polarity. Some family members act as E3 ubiquitin-protein ligases, mediating ubiquitination and degradation of specific substrates. Others are implicated in synaptic plasticity, participating in NMDAR signaling complexes that may control AMPAR potentiation. These proteins often contain PDZ domains that mediate interactions with various partners, influencing processes such as vesicle transport, cell migration, and the organization of multiprotein complexes. The family also includes proteins that regulate the feedback of phototransduction in photoreceptors and proteins that may affect the surface expression and function of ion channels in sensory neurons.
G-type lectin S-receptor-like kinases and EP1-like glycoproteins (G-type_lectin_kinases/EP1-like)
Type: Family

This family of proteins includes G-type lectin S-receptor-like serine/threonine-protein kinases and EP1-like glycoproteins. The kinases are part of the protein kinase superfamily and are involved in various defense mechanisms in plants. They play a role in innate immunity, resistance to pathogens such as fungi and bacteria, and defense against herbivorous insects like the brown planthopper. Some members are also implicated in seed germination by regulating the expression of alpha-amylase genes. The EP1-like glycoproteins may be involved in cell-to-cell signaling and could have a role in programmed cell death or in limiting water flow through the epidermal cell wall.
Virginiamycin B lyase (Vgb)
Type: Family

The Vgb family consists of enzymes known as Virginiamycin B lyases. These enzymes are responsible for inactivating type B streptogramin antibiotics. They achieve this by cleaving the lactone ring at the ester linkage, which results in the formation of a free phenylglycine carboxylate. Additionally, the threonyl moiety is converted into 2-amino-butenoic acid during this process. The action of the Vgb family members is crucial for conferring resistance to certain antibiotics, making them significant in the study of antibiotic resistance mechanisms.
Importin beta-like nuclear transport receptors (Importin_beta-like_NTR)
Type: Family

The importin beta family is involved in the nuclear-cytoplasmic transport of proteins. Members of this family function as nuclear transport receptors, mediating the import of proteins into the nucleus by recognizing nuclear localization signals (NLS) in cargo substrates. They are also involved in the nuclear export of certain proteins. The transport process is typically energy-dependent, requiring the GTPase Ran, which helps dissociate the cargo-importin complex within the nucleus. The family plays a crucial role in various cellular processes, including mRNA transport, protein import for transcription, splicing, and ribonucleotide reductase function. Some members are also implicated in plant immunity and viral infection processes, such as HIV-1 integration.
OTU Domain-Containing Deubiquitinase (OTU_Deubiquitinase)
Type: Family

The protein family includes deubiquitinating enzymes that are involved in various cellular processes such as the regulation of the Wnt signaling pathway, autophagy, cell morphology, cytoskeletal organization, immune and inflammatory responses, and T cell homeostasis. Members of the family possess an OTU domain that mediates deubiquitinating activity, with some showing specificity for 'Lys-29'-, 'Lys-33'-, 'Lys-48'-, 'Lys-63'-, and 'Lys-11'-linked polyubiquitin chains. They are capable of hydrolyzing both linear and branched forms of polyubiquitin. Some members contain RanBP2-type zinc fingers or A20-type zinc fingers that contribute to ubiquitin chain linkage specificity. The family plays a role in terminating NF-kappa-B activity by editing ubiquitin chains on key signaling proteins, thus ensuring transient nature of inflammatory signaling pathways. They are also involved in the regulation of programmed cell death and are essential for the production of pro-inflammatory cytokines in response to pathogens.
Circadian clock KaiC-related (Circadian_clock_KaiC-rel)
Type: Family

This family of proteins constitutes the main circadian regulators in cyanobacteria, forming the KaiABC oscillator complex. The proteins undergo autophosphorylation and autodephosphorylation, which are central to the circadian rhythm generation. They exhibit weak, temperature-independent ATPase activity that is crucial for defining the circadian period. The phosphorylation state of these proteins modulates their ATPase activity and affects binding to other clock proteins, such as KaiA and KaiB. KaiA enhances phosphorylation, while KaiB interaction leads to dephosphorylation. These proteins are involved in metabolic partitioning and control various output pathways that affect transcriptional regulators, contributing to the regulation of cellular processes in accordance with the circadian cycle.
U-box domain-containing ubiquitin ligases (U-box_ubiquitin_ligases)
Type: Family

The U-box domain-containing protein family is characterized by its members' role as E3 ubiquitin ligases. These proteins are involved in the ubiquitination process, which tags substrates for degradation by the proteasome, thus regulating protein turnover. Some family members are known to participate in signaling pathways related to stress responses, such as the abscisic acid signaling pathway, which is important for drought stress tolerance in plants. Although many members are predicted to belong to the protein kinase superfamily and the Ser/Thr protein kinase family, several have a protein kinase domain that is predicted to be catalytically inactive, suggesting a divergent evolution where the ubiquitin ligase function has been conserved while kinase activity has been lost. This indicates a specialized function in ubiquitin-mediated proteolysis rather than phosphorylation.
Hydrogenase complex-associated protein (Hydrogenase_assoc-protein)
Type: Family

This family of proteins is involved in the biological process of hydrogen metabolism. Members of this family are typically part of enzyme complexes that play a role in the reduction of various electron acceptors. Some proteins in this family are known to reduce coenzyme F420, a low-potential two-electron acceptor, as well as artificial one-electron acceptors such as methylviologen. Others are part of bifunctional enzyme complexes with hydrogen-evolving hydrogenase activity, which can reduce protons to evolve hydrogen and may also have sulfur-reducing activity. These proteins are important for hydrogen cycling during fermentative growth and may interact with different cofactors such as NADPH or NAD.
WD repeat-containing signal transduction regulator (WD_repeat-ST_regulator)
Type: Family

This family of proteins is involved in various cellular processes including signal transduction, proteasomal degradation, cell growth and migration, and response to stress. Members act as scaffolding proteins, coordinating the activity of multiple signaling pathways such as MAPK, Wnt, and PI3K/AKT. They are implicated in the regulation of ubiquitination, playing roles in both the promotion and inhibition of this process. Some family members are involved in the cellular response to glucose availability, oxidative stress, and hypoxia, with functions ranging from the degradation of gluconeogenic enzymes to the protection against apoptosis and the promotion of autophagy and mitophagy.
Ascorbate-specific PTS system EIIA component (Ascorbate-PTS_EIIA_comp)
Type: Family

The ascorbate-specific PTS system EIIA component family is involved in the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS), which is a key carbohydrate active transport system. Members of this family catalyze the phosphorylation of incoming sugar substrates while simultaneously translocating them across the cell membrane. Specifically, the ascorbate-specific PTS system EIIA components are part of the UlaABC PTS system, which is responsible for the transport of ascorbate. These proteins contain a PTS EIIA type-2 domain that is phosphorylated by phospho-HPr on a histidine residue, and subsequently, they transfer the phosphoryl group to the PTS EIIB type-2 domain, facilitating the transport process.
Tobamovirus Resistance UPF0261 (Tobamovirus_resist_UPF0261)
Type: Family

The UPF0261 family includes proteins that function as inhibitors of viral RNA replication, conferring resistance to various tobamoviruses. Members of the family interfere with the replication process by disrupting the association of tobamovirus replication proteins with host membrane-associated proteins, thereby preventing the formation of the replication complex necessary for viral negative-strand RNA synthesis. Specific proteins within the family have been shown to inhibit tobamoviruses such as tobacco mild green mosaic virus, pepper mild mottle virus, and certain strains of tomato mosaic virus and tobacco mosaic virus.
Transposase 27 family, IS1 element (Transposase_27_IS1)
Type: Family

The transposase 27 family is comprised of proteins that are essential for the transposition of the IS1 insertion element. Members of this family share a common function in facilitating the movement of the IS1 element within the genome, a process that can impact genetic variation and adaptation. These proteins are characterized by their ability to recognize specific DNA sequences and catalyze the cutting and rejoining of DNA strands, thereby enabling the insertion element to relocate within the genome. The transposition activity is crucial for the propagation of the IS1 element and can have significant implications for genomic stability and the evolution of bacterial species.
Notch and Slit guidance protein (Notch/Slit_guidance)
Type: Family

This family of proteins includes members that are involved in various cellular and developmental processes, such as neural progenitor proliferation, brain neocortex expansion, and axonal guidance. They function by modulating the Notch signaling pathway, which influences cell fate determination, differentiation, proliferation, and apoptosis. Some family members interact with membrane-bound ligands and receptors to activate transcriptional activator complexes, while others act as molecular guidance cues for cellular migration by interacting with roundabout homolog receptors. They are implicated in neural development, bone remodeling, and leukocyte migration, and may also play roles in axon navigation, midline guidance in the forebrain, and neuronal cell migration.
SOX/SOX-like transcription factors (SOX/SOX-like_TF)
Type: Family

This family of proteins includes transcription factors that play crucial roles in developmental processes such as chondrocyte differentiation, cartilage formation, and neurogenesis. They are characterized by their ability to bind to a specific DNA motif, which is essential for the regulation of gene expression related to chondrogenesis. Members of this family are involved in various stages of chondrocyte maturation, from prechondrocyte differentiation to the maintenance of proliferating chondroblasts and the regulation of chondrocyte hypertrophy. They also have roles in oligodendroglia differentiation in the developing spinal tube and may act as transcriptional repressors for certain genes. Additionally, some members are implicated in the modulation of WNT signaling and the differentiation of specific T-cell subsets, as well as in promoting brown adipocyte differentiation.
Histone-lysine N-methyltransferase SUVAR3-9 (H3K9_HMTase_SUVAR3-9)
Type: Family

This family of proteins includes histone-lysine N-methyltransferases, which are primarily involved in the methylation of 'Lys-9' of histone H3, a post-translational modification that is recognized as a marker for epigenetic transcriptional repression. These proteins contain SET domains that are responsible for their enzymatic activity, and they typically require both pre-SET and post-SET domains for full methyltransferase function. The pre-SET domain often binds zinc ions, which are crucial for the structural integrity of the protein. Some members of this family may lack methyltransferase activity or have altered enzymatic function due to the absence of certain domains or conserved residues. The family plays a significant role in the regulation of gene expression through epigenetic mechanisms, and is involved in the silencing of transposable elements and the maintenance of chromatin structure.
Transcription factor AMS/ICE1/BHLH6-like (TF_AMS/ICE1/BHLH6-like)
Type: Family

This entry includes bHLH transcription factors from plants that play diverse roles in plant development and responses. ICE1 is involved in regulating cold-induced transcription of CBF/DREB1 genes, and stomatal differentiation . Transcription factor FIT is involved in iron acquisition while AMS (ABORTED MICROSPORES) plays a crucial role in tapetum development and it is required for male fertility and pollen differentiation, especially during the post-meiotic transcriptional regulation of microspore development within the developing anther . Transcription factor BHLB6 is involved in phosphate starvation response and acts as a positive regulator of phosphate homeostasis and phosphate signalling by antagonising SPX4. It also playa a role as transcriptional activator in the regulation of jasmonate-mediated stress-inducible gene expression. The family is characterised by the ability to bind specific DNA sequences, often containing E-box motifs, and to function as dimers, which is crucial for their regulatory roles.
Calcium:cation antiporter (CaCA_antiporter)
Type: Family

This family of proteins includes membrane-localized transporters involved in the exchange of cations, particularly calcium, across cellular membranes. They function by mediating the efflux of calcium in exchange for sodium or lithium ions, which is crucial for maintaining calcium homeostasis within various organelles, including mitochondria. These transporters play a vital role in a range of physiological processes, such as insulin secretion, cell survival, and B-lymphocyte chemotaxis. Some family members are also implicated in the regulation of neural circuit patterning. The activity of these proteins can be modulated by specific inhibitors, highlighting their potential as therapeutic targets.
Neuronal Pentraxin and Related (Neuronal_Pentraxin_Related)
Type: Family

This family of proteins includes members that are implicated in synaptic processes such as the uptake of synaptic material during synapse remodeling and the clustering of AMPA glutamate receptors at excitatory synapses. Some family members are thought to play a role in long-term plasticity and may bind to specific matrices in a calcium-dependent manner. Additionally, certain proteins within this family are suggested to have immunological functions that could be analogous to those of immunoglobulins.
ThrE/Ser Exporter (ThrE/Ser_Exporter)
Type: Family

This family of proteins includes members that are involved in the transport of amino acids across cellular membranes. Specifically, they are associated with the export of threonine and serine from the cell to the extracellular environment. The transport mechanism is believed to be dependent on the proton motive force. These proteins are essential for certain cellular processes, including growth and survival in specific environments, such as within macrophages for some bacteria. The family is part of a larger group of transporters that facilitate the movement of a variety of substrates across biological membranes, playing a crucial role in cellular homeostasis and intercellular communication.
WD repeat creC family regulators (WD_repeat_creC_regulators)
Type: Family

The WD repeat creC family is involved in the regulation of carbon source utilization and protein stability through ubiquitination and deubiquitination processes. Members of the family function as components of a regulatory network that includes creA, creB, creC, creD, and acrB. They are essential for preventing the proteolysis of deubiquitinating enzymes such as CreB in the absence of carbon catabolite repression. By stabilizing CreB in a complex with CreC, they facilitate the expression of genes in specific metabolic pathways, including those for proline and quinate. Additionally, some family members act as regulators of deubiquitinating complexes, promoting the enzymatic activity of USP12 and other similar enzymes, and are involved in the localization and activity of deubiquitinating enzymes at specific cellular sites.
RIG-I-like Receptor (RLR) Helicase (RLR_Helicase)
Type: Family

The RLR helicase family plays a crucial role in the innate immune response to viral infections. Members of this family act as cytoplasmic sensors that detect viral nucleic acids, leading to the activation of antiviral signaling pathways. These pathways result in the production of type I interferons and pro-inflammatory cytokines. The family includes proteins with helicase domains responsible for recognizing double-stranded RNA, and in some cases, proteins also contain CARD domains for signaling through the MAVS/IPS1 pathway. The family's regulatory functions can be both positive and negative, influencing the signaling mediated by RIG-I and IFIH1/MDA5. Some members lack the CARD domain, thus cannot initiate signaling but can regulate it by various mechanisms, including competition for viral RNA binding and inhibition of RIG-I dimerization. The family is involved in the immune response to a wide range of RNA and DNA viruses, as well as bacterial pathogens, and plays roles in cell processes such as granulocyte production, bacterial phagocytosis, and cell migration.