SII-SWORD/CoKE huggingface dataset:
UPF0237/Glycine cleavage system regulator (UPF0237/GcvR_regulator)
Type: Family

This family of proteins includes transcriptional regulators and proteins of unknown function. One member is identified as a negative transcriptional regulator of the glycine cleavage system operon, which does not autoregulate its own expression and does not appear to bind DNA directly. The mechanism of repression is unclear, but it may involve interaction with another activator protein to suppress its activity. The majority of the family members are annotated as belonging to the UPF0237 family, which suggests a conserved but unspecified role across various species. The specific functions of these UPF0237 proteins have not been characterized, indicating a need for further research to elucidate their biological roles.
Extracellular Matrix Regulatory Proteins (ECM_Regulatory_Proteins)
Type: Family

This family of proteins is involved in the composition and function of the extracellular matrix (ECM). They play a crucial role in cell-matrix interactions, influencing cellular behaviors such as adhesion, motility, differentiation, and neurite outgrowth. These proteins interact with various cells and matrix components, modulating processes like synaptic plasticity, neuronal regeneration, and angiogenesis. They are implicated in the regulation of integrin-mediated cell adhesion, affecting phosphorylation and cell detachment. Additionally, they participate in the development and maintenance of the nervous system, including the clustering and regulation of sodium channels at nodes of Ranvier. Some family members are associated with tumor growth and metastasis, acting as ligands for multiple integrins and influencing cell migration and angiogenesis.
Bacterial chemotaxis CheZ family phosphatases (CheZ_family_phosphatases)
Type: Family

The CheZ family proteins are involved in bacterial chemotaxis signal transduction pathways. They function by accelerating the dephosphorylation of phosphorylated CheY (CheY-P), which is a response regulator involved in the flagellar motor control. This dephosphorylation process is crucial for the bacteria to adapt to changes in chemical gradients in their environment, allowing them to move toward attractants or away from repellents. The CheZ family members play a key role in resetting the signaling state of CheY-P to its unphosphorylated form, thereby modulating the chemotactic response and ensuring proper bacterial navigation and survival.
Isochorismatase domain-containing protein (Isochorismatase_domain)
Type: Family

This family of proteins is characterized by the presence of an isochorismatase domain, which suggests a role in the hydrolysis of isochorismate, a precursor in the biosynthesis of various metabolites. One member of this family has been described as a secreted effector that can suppress plant innate immunity by targeting salicylate metabolism, indicating a potential involvement in pathogen-host interactions and virulence. The family is implicated in diverse biological processes, likely related to their enzymatic activity in isochorismate hydrolysis and its impact on metabolic pathways.
Arabidopsis Inactive Receptor-like Kinases (At_inactive_RLKs)
Type: Family

The protein family is characterized by members that are receptor-like kinases, predominantly predicted to be catalytically inactive. They are involved in various plant processes, including early zygote development, effector-triggered immunity, recognition of growth-promoting fungi, and secondary cell wall formation in vascular tissues. Some members are essential for resistance against pathogens like Pseudomonas syringae. The family includes proteins with domains for calmodulin binding, G protein signaling, and leucine-rich repeats, indicating a role in signal transduction and cellular communication.
WD repeat and F-box domain-containing protein (WD-F-box_domain-protein)
Type: Family

This family of proteins includes components involved in various cellular processes such as ubiquitination, cell cycle regulation, mitochondrial fission, and ciliogenesis. Members act as substrate recognition components of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, mediating ubiquitination and proteasomal degradation of target proteins, often requiring substrate phosphorylation. They play roles in signaling pathways like Wnt and NF-kappa-B, influencing development and immune responses. Some members are involved in mitochondrial dynamics, particularly in the fission process. Others contribute to microtubule function, nuclear distribution, and ciliary movement. The family also includes proteins that regulate deubiquitinating complexes and transcriptional repression.
Docking Protein Family (DOK) (Docking_Protein_DOK)
Type: Family

The DOK family proteins are enzymatically inert adaptor or scaffolding proteins that provide a docking platform for the assembly of multimolecular signaling complexes. Members of the DOK family are involved in various cellular processes, including negative regulation of insulin and JNK signaling pathways, modulation of integrin activation, and promotion of neurite outgrowth. They play roles in cellular proliferation, MAP kinase activation, and may influence immune responses. The PTB domain is a common feature that mediates receptor interactions, suggesting a role in signal transduction. The family can be divided into Type A and Type B subfamilies, with each member contributing to specific signaling pathways and cellular functions.
Membrane-associated proteins in eicosanoid and glutathione metabolism (MAPEG)
Type: Family

This family of proteins is involved in the metabolism of lipid signaling molecules through enzymatic activities that include the conjugation of reduced glutathione to various electrophilic compounds. Members of this family are key players in the biosynthesis of leukotrienes, which are inflammatory mediators, by catalyzing the conjugation of leukotriene A4 with glutathione to form leukotriene C4. Some members also display glutathione peroxidase activity, reducing lipid hydroperoxides to their corresponding alcohols, and are involved in the detoxification of xenobiotic electrophiles. Additionally, they may participate in the formation of bioactive lipid mediators with anti-inflammatory and proresolving actions, such as maresin conjugates.
Forkhead box protein P (FOXP)
Type: Family

The FOXP family of transcription factors is characterized by a conserved fork-head DNA-binding domain and often contains a leucine-zipper motif for dimerization and transcriptional repression. Members of the family play critical roles in various biological processes, including immune system homeostasis, lung epithelium differentiation, neural development, and cardiovascular tissue formation. FOXP proteins can act as transcriptional repressors or activators, depending on their interaction partners. FOXP2 is notable for its involvement in speech and language development, while FOXP3 is essential for regulatory T-cell function and immune regulation. FOXP1 is involved in B-cell development, lung epithelium specification, and cardiac muscle cell proliferation. These proteins can interact with CTBP1 to repress transcription, influence synapse formation, and regulate the expression of genes involved in immune responses and cell fate determination.
Arg-specific ADP-ribosyltransferase (ADP-ribosyltransferase_ARG)
Type: Family

This family of proteins includes enzymes with ADP-ribosyltransferase activity, which typically modify arginine residues on target proteins using NAD(+) as a substrate [[cite21901419],

]. These modifications can regulate protein function and are involved in various cellular processes, including cell signaling and bacterial pathogenesis. Some members possess additional NAD(+) glycohydrolase activity. The family also includes toxins from pathogenic bacteria that interfere with host cell functions, often by ADP-ribosylating host proteins, which can lead to cell death or contribute to bacterial virulence .
Homeobox DNA-binding (Homeobox_DNA-bind_prot)
Type: Family

The Homeobox protein family is characterized by the presence of a homeobox domain, which enables these proteins to bind DNA and regulate gene expression. Members of this family function as transcription factors involved in a variety of developmental and cellular processes. They recognize specific DNA sequences to either activate or repress transcription, playing crucial roles in cell differentiation, organ development, and the establishment of body axes. Some members are involved in cell cycle regulation, acting as transcriptional repressors during specific phases. Others have roles in mating type determination in yeast, pharyngeal development, and the biosynthesis of compounds in pathogenicity. The family includes proteins that regulate hematopoietic differentiation, vascular endothelial cell proliferation, and anterior identity in embryogenesis. They may also interact with signaling pathways such as WNT and NODAL, and some have additional functions like mRNA nuclear export inhibition.
Calbindin Calcium-Binding (Calbindin_Ca-bind)
Type: Family

The Calbindin family comprises calcium-binding proteins involved in buffering cytosolic calcium levels and may influence various calcium-dependent processes. Members of this family, such as calbindin and calretinin, contain multiple functional calcium-binding sites, although some potential sites may have lost their affinity for calcium. These proteins are implicated in stimulating membrane Ca(2+)-ATPases and 3',5'-cyclic nucleotide phosphodiesterases, contributing to calcium homeostasis. Calretinin, in particular, is abundant in auditory neurons, suggesting a specialized role in the auditory system. Additionally, some family members are expected to play a crucial role in calcium-dependent regulation of ciliary movement, indicating a broad functional spectrum within the family.
Ubiquitin-binding and autophagy-associated domain-containing protein (UBA_autophagy_assoc_protein)
Type: Family

This family of proteins is involved in various cellular processes including anti-apoptotic activity, ubiquitin-mediated signaling, autophagy, and transcriptional coactivation. Members of this family act as ubiquitin-binding adapters that regulate inflammatory, antiviral, and innate immune responses. They play key roles in the negative regulation of NF-kappa-B and IRF3 signaling pathways by interacting with ubiquitin-editing enzymes. Some proteins in this family function as xenophagy-specific receptors that target bacteria for autophagy, while others may enhance inorganic pyrophosphatase activity and function as coactivators for aryl hydrocarbon and nuclear receptors. They are also involved in the organization of the actin cytoskeleton and may regulate constitutive secretion.
Anterior-posterior axis regulatory homeobox (AP_axis_regulatory_Homeobox)
Type: Family

This family of proteins includes sequence-specific transcription factors that are integral to a developmental regulatory system, providing cells with distinct positional identities along the anterior-posterior axis. Members of this family are characterized by their ability to bind to gene promoters and activate transcription. They play roles in various developmental processes, including hair follicle differentiation and early embryonic development. Some members show a preference for binding to methylated DNA.
Dendritic cell-specific ICAM-grabbing non-integrin domain-containing protein (DC-SIGN_domain-containing)
Type: Family

This family of proteins includes pathogen-recognition receptors predominantly expressed on the surface of immature dendritic cells, playing a crucial role in the initiation of the primary immune response. They are involved in the endocytosis of pathogens, which are then degraded in lysosomal compartments. Following endocytosis, these receptors return to the cell membrane surface, presenting pathogen-derived antigens to resting T-cells via MHC class II proteins. They are known to recognize high mannose N-linked oligosaccharides on a variety of pathogen antigens in a calcium-dependent manner. Additionally, these proteins act as attachment receptors for various viruses and may interact with ICAM2 and ICAM3, facilitating immune cell interactions and transendothelial migration of dendritic cell precursors. The family is characterized by a tandem repeat domain, also known as the neck domain, which mediates oligomerization.
Pentraxin domain-containing protein (Pentraxin_domain)
Type: Family

This family of proteins is involved in host defense mechanisms. Members of this family are known to participate in various immune responses, including promoting agglutination, bacterial capsular swelling, phagocytosis, and complement fixation. They achieve these functions through calcium-dependent binding to phosphorylcholine. Some members can also interact with DNA and histones, potentially scavenging nuclear material from damaged circulating cells. Additionally, certain proteins within this family may function as calcium-dependent lectins with specificity for beta-galactose.
T cell receptor variable domain (TCR_variable_domain)
Type: Family

The T cell receptor (TCR) variable domain family is involved in antigen recognition and the immune response. TCRs are present on T lymphocytes' surfaces and recognize peptide-major histocompatibility complexes displayed by antigen-presenting cells, initiating an immune response. The variable domain of the alpha or delta chain participates in antigen binding, leading to the activation of signaling pathways essential for T cell growth, differentiation, and the adaptive immune response. The TCR repertoire is generated through V-(D)-J rearrangement and shaped by selection events to create a pool of self-restricted, non-autoaggressive T cells.
creA/MIG C2H2-type Zinc-Finger (creA/MIG_C2H2-ZnF)
Type: Family

The creA/MIG C2H2-type zinc-finger protein family comprises transcriptional regulators involved in carbon catabolite repression and glucose repression mechanisms across various fungal species. Members of the family function by binding to GC-rich regions in the promoters of target genes, thereby repressing their transcription. This regulatory activity is crucial for the utilization of preferred carbon sources and for the response to carbon starvation. The family also plays a role in the control of extracellular proteases activity and influences the expression of genes related to cell viability, cell wall integrity, and virulence. Some members are involved in the regulatory network through ubiquitination and deubiquitination processes, affecting carbon source utilization.
Telomere Capping Maintenance Protein (Telomere_Capping_Maintenance)
Type: Family

This family of proteins is implicated in the protection of chromosome ends by playing a role in telomere capping. Telomere capping is a crucial process that prevents the degradation and fusion of chromosome termini, thereby maintaining genomic stability. Members of this family are characterized by their involvement in telomere maintenance, which is essential for cell viability and prevention of premature cellular aging or cancer.
Pheromone-regulated membrane protein (PRM)
Type: Family

This family of proteins is involved in cellular processes related to membrane function and regulation. Members of this family are typically associated with vacuolar membranes and may play roles in the regulation of pheromone responses. The proteins are characterized by similarities in their sequence that suggest a shared structural framework and possibly similar functional roles within the cell. The exact molecular functions and biological processes these proteins participate in could vary among family members and may include interactions with other proteins or complexes, involvement in signaling pathways, or contributing to the structural integrity of the vacuolar membrane.
Branched-chain amino acid transport protein (BCAA_transport)
Type: Family

This family of proteins is involved in the transport of amino acids across cellular membranes, specifically the branched-chain amino acids leucine, isoleucine, and valine. Members of this family are typically part of larger amino-acid transport systems and may also play a role in chemotaxis by binding attractant amino acids and transducing signals to other components of the chemotactic system. Although primarily associated with transport, some members may function as receptors in chemotactic pathways without an additional role in transport.
Metal-responsive transcriptional regulator (Metal_resp_trans_reg)
Type: Family

The protein family includes transcriptional regulators that respond to various metal ions and heavy metals, such as cadmium, bismuth, zinc, lead, nickel, and cobalt. Members of the family function as metal-binding repressors for operons involved in metal resistance or homeostasis. Binding of specific metal ions to these proteins typically results in dissociation from DNA, derepressing the operon and activating the expression of genes that help the cell to cope with metal stress. Some family members are also involved in the repression of genes associated with biofilm growth, nodulation, and arsenical resistance. The regulatory mechanisms of these proteins are crucial for bacterial adaptation to environmental changes and stress conditions.
Cellulose Synthase/LPS Assembly/PSI Assembly (CellSynth/LPSAsmb/PSIAsmb)
Type: Family

The protein family is involved in various biological processes, including bacterial cellulose synthesis, lipopolysaccharide (LPS) assembly, and photosystem I (PSI) assembly. Members of the AcsC/BcsC subfamily are essential for bacterial cellulose synthesis, possibly participating in membrane complex formation for cellulose extrusion. The LapB subfamily proteins modulate cellular LPS levels, influencing lipid A biosynthesis by regulating LpxC and potentially coordinating LPS synthesis proteins at the plasma membrane. The Ycf3 subfamily members are crucial for PSI complex assembly, acting as chaperone-like factors for PSI subunit assembly. The diverse functions of these proteins highlight their roles in cellular structure, energy capture, and membrane synthesis.
Metallo-beta-lactamase superfamily lactonases (MBL_superfamily_lactonases)
Type: Family

This family of proteins includes enzymes that exhibit hydrolytic activity on various lactone substrates. Members are characterized by their ability to catalyze the hydrolysis of N-acyl homoserine lactones, which are signaling molecules involved in bacterial quorum sensing. Some family members are involved in the degradation of plant-produced benzoxazolinones, acting as gamma-lactamases that convert these compounds into less toxic forms. The proteins typically show a preference for certain substrates based on acyl chain length and the presence of specific substitutions. They are part of the metallo-beta-lactamase superfamily and share a common structural fold that coordinates metal ions, which are essential for their catalytic function. The family also includes enzymes that degrade vitamin B6 derivatives and may have roles in defense against competing bacteria by disrupting their communication systems.
Cation Transport ATPase Type IB (Cation_Transport_ATPase_IB)
Type: Family

The cation transport ATPase (P-type) family, specifically the Type IB subfamily, is involved in the transport of heavy metals such as cadmium, zinc, and cobalt across cellular membranes. Members of this family couple the hydrolysis of ATP to the efflux of these metal ions, which is crucial for metal detoxification and homeostasis within the cell. Some family members are also involved in the transport of lead. The activity of these ATPases is essential for conferring resistance to toxic metal ions by exporting them out of the cell or sequestering them into vacuoles, thereby reducing their bioavailability and toxicity. The family includes proteins that are regulated by various inhibitors and may contain high-affinity metal-binding sites that are essential for their activity.
RcsB family transcriptional regulators (RcsB_transcriptional_reg)
Type: Family

The RcsB family proteins are involved in the Rcs signaling system, which is a complex regulatory network controlling the transcription of a diverse set of genes. RcsB, as the response regulator, plays a pivotal role in this system by binding to DNA regulatory regions. It can operate with or without the co-regulator RcsA, affecting processes such as colanic acid capsule synthesis, biofilm formation, cell division, outer membrane proteins synthesis, and acid resistance. Some family members also interact with other transcriptional regulators like GadE and BglJ, influencing glutamate-dependent acid resistance and the bgl operon, respectively. The activity of RcsB is modulated by phosphorylation and interaction with connector proteins, which integrate additional signals into the system.
Diverse Substrate Acetyltransferase (Diverse_Substrate_AcTransf)
Type: Family

The Acetyltransferase family is characterized by a diverse set of enzymes that catalyze the transfer of an acetyl group from acetyl-CoA to various substrates, including amino acids, polyamines, and histones. Members of the family are involved in the regulation of intracellular polyamine levels, which is crucial for cell growth and differentiation. Some enzymes specifically acetylate polyamines such as norspermidine, spermidine, and spermine, while others target amino acid derivatives like thialysine or D-amino acids. Certain family members also play roles in plant defense by modifying ornithine or participate in stress response by synthesizing hydroxycinnamic acid amides. Additionally, some acetyltransferases are involved in histone modification, influencing chromatin structure and gene expression. The family includes enzymes with varying substrate specificities and biological functions, reflecting their adaptation to different cellular contexts and organisms.
Aldolase class II Adducin subfamily (Aldolase-II_Adducin_sf)
Type: Family

The Aldolase class II, Adducin subfamily, consists of membrane-cytoskeleton-associated proteins that promote the assembly of the spectrin-actin network, which is crucial for maintaining cell shape and integrity. Members of this family are involved in various cellular processes including actin filament capping, cell migration, cell adhesion, and regulation of ion channels. They play significant roles in the structural and functional organization of the podocyte in the kidney, affecting glomerular filtration and blood flow autoregulation. Adducins bind to calmodulin and can interact with erythrocyte membrane receptors, linking the cytoskeleton to the plasma membrane. Some members are implicated in the biosynthesis of antibiotics by mediating oxidative decarboxylation steps. The family also includes proteins with roles in meiosis and memory retention.
Bacteriophage Glycosyl Hydrolase 24 (Bacteriophage_GH24)
Type: Family

The glycosyl hydrolase 24 family proteins are endolysins with lysozyme activity that degrade bacterial cell walls by hydrolyzing peptidoglycans. They play a crucial role in bacteriophage-mediated lysis of host cells. These proteins, along with holin, spanin, and sometimes pinholin proteins, participate in a sequential process leading to programmed host cell lysis, which facilitates the release of mature viral particles. Some members of this family are SAR-endolysins, which are tethered to the membrane by a signal-anchor sequence and released into the periplasm by the action of holin or pinholin, where they execute their lytic function.