SII-SWORD/CoKE huggingface dataset:
Intimin/Invasin domain-containing protein (Intimin-Invasin_domain)
Type: Family

This family of proteins includes members that are involved in bacterial adhesion and invasion processes. They are known to mediate the attachment of enteric bacteria to mammalian cells, which is a critical step in the pathogenesis of certain infections. These proteins interact with host cell receptors, such as beta-1 chain integrins, to facilitate entry into the cells. Additionally, they are implicated in the formation of attaching and effacing lesions on tissue culture cells, which is a hallmark of enteropathogenic and enterohemorrhagic bacterial infections. The family is characterized by a conserved domain structure that allows for the adherence to and invasion of host tissues, playing a key role in bacterial virulence and host-pathogen interactions.
Plant receptor-like serine/threonine kinase (Plant_RL_S/T_kinase)
Type: Family

This family of proteins includes receptor-like kinases with serine/threonine specificity, which are involved in various signaling pathways in plants. Members of this family play key roles in plant immunity, development, and stress responses. They act as receptors for different peptides and pathogens, transducing extracellular signals into cellular responses that regulate processes such as immune response, cell differentiation, root growth, and maintenance of water transport. Some proteins in this family are involved in the perception of peptide hormones and contribute to the formation of physical barriers in plant tissues or mediate resistance to pathogens and herbivores by activating defense responses.
Major facilitator superfamily MFSD6 (MFS_MFSD6)
Type: Family

This family of proteins is part of the major facilitator superfamily (MFS), which is one of the largest groups of secondary transporters. Members of this family are involved in a diverse range of functions, typically concerning the transport of small solutes across cellular membranes in response to chemiosmotic gradients. The MFSD6 subgroup within this family appears to be evolutionarily conserved across various species. Although specific functions for all members of this subgroup are not detailed, at least one member is known to interact with MHC class I molecules, suggesting a potential role in immune response or antigen presentation. The diversity of the major facilitator superfamily indicates that other members of the MFSD6 subgroup may have distinct physiological roles related to membrane transport.
ADP Ribosylation Factor GTPase-Activating (ARF_GTPase-activating)
Type: Family

The protein family is characterized by its members' involvement in GTPase-activating processes, particularly for the ADP ribosylation factor family. Members of this family are implicated in various cellular transport mechanisms, including clathrin-dependent retrograde transport from early endosomes to the trans-Golgi network and clathrin-dependent endocytosis. Some family members are also associated with roles in erythropoiesis and the modulation of cell size and timing of budding, independent of the DNA replication cycle. Additionally, one member is noted to be a transcription factor involved in heat resistance and flocculation. The diverse functions of the family members suggest a broad involvement in cellular regulatory mechanisms and transport processes.
Cytosolic arginine sensor for mTORC1 (CASTOR_mTORC1)
Type: Family

This family of proteins functions as sensors and regulators within the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway, which is crucial for cellular growth and metabolism in response to nutrient availability. Members of this family can form homodimers or heterodimers and are involved in sensing intracellular levels of arginine. The binding of arginine to certain members allosterically inhibits their interaction with the GATOR2 subcomplex, thereby activating mTORC1. Other members, which do not bind arginine directly, still contribute to the negative regulation of the TORC1 pathway through their interaction with the GATOR complex.
rRNA N6-Adenosine-Methyltransferase/Polyamine Synthase (rRNA_MeTrfase/Polyamine_Synth)
Type: Family

The protein family includes enzymes involved in the modification of rRNA and the biosynthesis of branched-chain polyamines. Members of the family that act as rRNA N6-adenosine-methyltransferases function as catalytic subunits in heterodimers with TRMT112 or similar proteins, specifically methylating adenine in 18S rRNA, which is crucial for translation and cellular processes such as pluripotency and differentiation in embryonic stem cells. Other members are involved in the biosynthesis of branched-chain polyamines, supporting thermophilic growth at high temperatures by catalyzing the condensation of spermidine with aminopropyl groups from decarboxylated S-adenosylmethionines to produce N(4)-bis(aminopropyl)spermidine and related compounds.
Biopterin synthesis and organic compound reduction (Biopterin_syn/organic_redct)
Type: Family

The protein family includes enzymes that are involved in the biosynthesis and reduction of various biopterin derivatives and other organic compounds. Members of the family catalyze the final steps in the synthesis of 5,6,7,8-tetrahydrobiopterin, an essential cofactor for aromatic amino acid hydroxylases. Some members also reduce benzil to (S)-benzoin, showing a broader substrate specificity. The family's activity can be regulated by various inhibitors, such as Cibacron blue 3 GA and N-acetylserotonin. The enzymes play a crucial role in maintaining cellular redox state and protecting against oxidative stress. They are characterized by their ability to preferentially produce certain stereoisomers of their products, which is important for the proper function of downstream metabolic pathways.
Endocytosis and PI4K-regulating protein (Endocytosis_PI4K-reg_protein)
Type: Family

This family of proteins includes members that are involved in cellular transport processes. Specifically, they are implicated in endocytosis, a mechanism by which cells internalize molecules and particles from their surroundings. Some members of this family are also components of a complex that is essential for the localization of phosphatidylinositol 4-kinase to the plasma membrane. This complex regulates the synthesis of phosphatidylinositol 4-phosphate, a critical lipid signaling molecule. Within the complex, these proteins play a pivotal role in connecting the kinase to other components, facilitating the proper synthesis and distribution of the lipid.
Bacterial Outer Membrane Invasion-Related Protein (Bact_OM_Invasion-Related)
Type: Family

This family of proteins is involved in host-pathogen interactions, particularly during bacterial infection processes. Members are incorporated into the bacterial outer membrane and play roles in adhesion to and invasion of eukaryotic cells. Some proteins facilitate the invasion of epithelial mammalian cells by interacting with host cell receptors such as heparinated proteoglycan. Others are essential for bacterial virulence and survival within host cells, although the exact mechanisms of action remain to be fully elucidated. The family is part of the outer membrane OOP (TC 1.B.6) superfamily and includes proteins with functions during lysogeny in E.coli, promoting bacterial invasion, and contributing to full virulence.
Actin-based Motor Myosin (Actin_motor_Myosin)
Type: Family

The myosin family encompasses a group of actin-based motor molecules with ATPase activity, involved in various intracellular movements. Members of this family bind to actin filaments or bundles and function as plus end-directed motors, facilitating cargo transport along actin filaments. They play critical roles in cell shape regulation, cell spreading, adhesion, and the formation and elongation of filopodia. In specialized cells, they contribute to processes such as photoreceptor disk renewal, vesicle trafficking, and mechanotransduction in cochlear hair cells. Some family members also participate in the formation of dendritic filopodia in neurons, spine formation, and the organization of osteoclast podosome belts. The family's unconventional myosins, characterized by their divergent tail domains, interact with specific membranous compartments and are essential for the dynamic rearrangement of the cytoskeleton and the transport of cellular components.
SAM and SH3 domain-containing protein (SAM-SH3_domain_protein)
Type: Family

This family of proteins includes signaling adapter molecules that may function in lymphocyte signaling, negative regulation of B-cell activation, and modulation of cell proliferation. Members are involved in cytoskeletal reorganization, cell spreading, and polarization, and can influence histone deacetylase and kinase activity. Some proteins in this family act as scaffolds in NF-kappa-B signaling pathways, regulating ubiquitination of signaling components, cell mobility, and skin pigmentation by controlling melanocyte migration.
Chitin Synthase Regulator (Chitin_Synth_Reg)
Type: Family

This family of proteins includes regulators of chitin synthase, an enzyme responsible for the biosynthesis of chitin. Chitin is a key structural polymer in fungal cell walls. Members of this family are involved in the activation and regulation of chitin synthase activity, which is crucial for cell wall integrity, septum formation, and sporulation in fungi. Some proteins in this family are specifically required for the activation of chitin synthase III (CHS3), which polymerizes chitin into its polymeric form. Additionally, the chitin produced by CHS3 can be modified to chitosan, contributing to cell wall robustness, anchoring melanin, and evading host immune detection during infection.
DnaJ Homolog Subfamily C Member 3 Co-Chaperones (DnaJ_C3_Co-chaperones)
Type: Family

The DnaJ homolog subfamily C member 3 protein family is involved in various stress response mechanisms, particularly the unfolded protein response (UPR) during endoplasmic reticulum (ER) stress. Family members act as co-chaperones, interacting with molecular chaperones such as HSPA8/HSC70 to stimulate ATPase activity and assist in protein folding. They play roles in inhibiting the phosphorylation of eIF-2-alpha, thus regulating protein synthesis under stress conditions. Some members are implicated in cold adaptation, virulence factor production, and ER homeostasis. They may also participate in nuclear membrane fusion during mating and contribute to cell wall architecture maintenance. The family is characterized by the presence of TPR repeats, which mediate interaction with unfolded polypeptides, and a J domain essential for chaperone activity enhancement.
RING-FYVE domain-containing E3 ubiquitin-protein ligase (RING-FYVE_E3_ubiquitin-ligase)
Type: Family

This family of proteins functions as E3 ubiquitin-protein ligases, which play a crucial role in the ubiquitin-proteasome system. They are responsible for the transfer of ubiquitin from E2 enzymes to specific substrate proteins, marking them for proteasomal degradation. This process is essential for regulating a variety of biological processes including cell death, cell migration, and various signaling pathways. Members of this family are characterized by the presence of RING-type and FYVE-type zinc finger domains, which are essential for their ubiquitination activity and localization within the cell, respectively. The RING-type zinc finger domain is crucial for the recognition and ubiquitination of target proteins, while the FYVE-type domain is involved in membrane localization, often to endosomal compartments. Through the ubiquitination of various targets, including caspases and the tumor suppressor p53, these ligases are involved in the negative regulation of apoptosis, cell signaling, and immune responses.
Opine/Lysopine Dehydrogenase (Opine/Lysopine_DH)
Type: Family

This family of proteins is involved in the reductive condensation of pyruvate with various amino acids to form corresponding opines. These reactions typically utilize NADPH as the preferred cofactor, although NADH can also be used. The family includes enzymes that act on arginine, lysine, histidine, or octopine, producing octopine, lysopine, histopine, or octopinic acid, respectively. Some members also exhibit broader substrate specificity, acting on secondary amine dicarboxylates or neutral amino acids. Additionally, certain enzymes in this family can catalyze reverse reactions of dehydrogenation. The activity of some members is regulated by substrate inhibition or competitive inhibition by similar compounds.
Nuclear autoantigenic sperm protein-like (NASP-like)
Type: Family

This family of eukaryotic proteins includes human Nuclear autoantigenic sperm protein (NASP), a component of the histone chaperone network . Members of this family are involved in various cellular processes related to DNA replication, cell cycle progression, and cell proliferation. They form complexes with HSP90 and H1 linker histones, which facilitate the translocation of these histones to the nucleus for DNA binding. Some proteins in this family are implicated in nucleosome assembly, acting as chaperones for specific histones, such as H3 and CENP-A, and may also play roles in chromosome segregation and silencing. Additionally, certain members are associated with innate immune responses and may be involved in the uptake or spreading of dsRNA. The functions of these proteins are crucial for maintaining genomic stability and proper cell function.
DENND11/AVL9 guanine nucleotide exchange factors (DENND11/AVL9_GEFs)
Type: Family

The DENND11/AVL9 family includes proteins that function as guanine nucleotide exchange factors (GEFs), which are likely involved in the activation of small GTPases by promoting the exchange of GDP for GTP. This activity is crucial for various cellular processes, including neuritogenesis and neuronal recovery after cerebral ischemia. Members of the DENND11 subfamily are implicated in these neuronal functions. The AVL9 subfamily members are involved in the late secretory pathway, playing roles in cell migration, the generation of secretory vesicles, actin polarization, and polarized growth.
Upstream Stimulatory Factor (USF)
Type: Family

The Upstream Stimulatory Factor family comprises transcription factors that recognize and bind to E-boxes with the consensus DNA sequence 5'-CACGTG-3'. These binding sites are commonly found in the promoters of various viral and cellular genes, indicating a role for the family in the regulation of gene expression. Members of this family are involved in diverse biological processes, including the regulation of metabolic gene expression and the maintenance of metabolic interactions between cellular organelles. Some family members specifically regulate genes such as the surfactant protein-A (SP-A) and transcription factor IIIA (TFIIIA), while others may influence the expression of genes with the CACGTG motif on their promoters.
WD repeat-containing DCAF13/WDSOF1 (WD_repeat_DCAF13/WDSOF1)
Type: Family

This family of proteins is involved in various cellular processes, including the assembly of the small subunit processome, a precursor to the small eukaryotic ribosomal subunit. They are implicated in ribosomal RNA processing, which involves RNA folding, modifications, rearrangements, and cleavage, as well as targeted RNA degradation by the RNA exosome. Additionally, these proteins function as substrate-recognition components of the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex, playing a crucial role in embryo preimplantation, meiotic cycle progression in oocytes, and zygotic gene expression. They are also involved in the regulation of oocyte and zygotic chromatin structure during maternal to zygotic transition, as well as in the transformation of the endometrium for blastocyst implantation. They target specific proteins for polyubiquitination and proteasomal degradation, which is essential for various developmental and cellular processes.
Type II toxin-antitoxin VapB antitoxins (VapB_TA_antitoxins)
Type: Family

The VapB family consists of antitoxin components within type II toxin-antitoxin (TA) systems. Members of the VapB family are responsible for neutralizing the effects of cognate toxins, named VapC, thereby preventing harmful activity within the host organism. These antitoxins can inhibit the RNase activity of their cognate toxins, which is a common mechanism of action for VapC toxins. The VapB antitoxins are typically specific, neutralizing their corresponding VapC toxins but not non-cognate VapC variants. Some family members have been shown to regulate transcription of their own promoter when forming a complex with their cognate VapC. The VapB proteins play a crucial role in maintaining cellular stability and preventing the lethal action of the toxins, which may be part of a stress response or a cell growth regulation mechanism.
CFEM domain-containing protein (CFEM_domain)
Type: Family

This family of proteins includes GPI-anchored cell wall proteins and effectors with a CFEM domain, which is characterized by a unique helical-basket fold stabilized by disulfide bonds. The family members are involved in various functions related to fungal pathogenicity, including cell wall stabilization, heme-binding, and interactions with host proteins during infection. Some proteins in this family are known to suppress the host immune response or programmed cell death, aiding in the pathogen's evasion of host defenses. The CFEM domain's role in mediating these interactions highlights its significance in the virulence and survival of pathogenic fungi.
DnaJ homolog subfamily B member 11-like (DnaJ-B11-like)
Type: Family

This family of proteins functions as co-chaperones, primarily assisting the molecular chaperone HSPA5 in the endoplasmic reticulum. They are involved in the folding, trafficking, and degradation of proteins, particularly those that are misfolded or are substrates for ER-associated degradation (ERAD). These proteins bind to unfolded polypeptide chains and may facilitate the recruitment of HSPA5 and other chaperones to their substrates. Additionally, they are known to stimulate the ATPase activity of HSPA5, which is crucial for its chaperone function. The family members play a significant role in the maturation and trafficking of certain proteins, such as PKD1, which is essential for maintaining cellular homeostasis and proper protein function.
L-xylulose reductase/Carbonyl reductase (L-xylulose/Carbonyl_redctase)
Type: Family

The L-xylulose reductase family comprises enzymes that catalyze the NADPH-dependent reduction of various sugars and alpha-dicarbonyl compounds. Members of this family participate in the uronate cycle of glucose metabolism and may contribute to cellular osmoregulation in renal tubules by producing xylitol, an osmolyte. Some family members also metabolize endogenous carbonyl compounds, such as those derived from lipid peroxidation, and may play a role in xenobiotic metabolism. The family belongs to the broader short-chain dehydrogenases/reductases (SDR) superfamily, known for their involvement in the metabolism of steroids, prostaglandins, and xenobiotics.
Scaffold Attachment Factor and Modulators (SAF_Modulators)
Type: Family

This family of proteins is involved in the regulation of gene expression and cellular proliferation. Members bind to scaffold/matrix attachment region (S/MAR) DNA, which is crucial for the formation of a complex that couples transcription and RNA processing. Some act as corepressors for estrogen receptors and can negatively regulate cell proliferation by binding to certain promoters and modulating their transcription. Additionally, these proteins may play a role in apoptosis when overexpressed. One member is implicated in muscle development and lifespan determination in a nematode model.
Rhomboid-related Intramembrane Serine Proteases (Rhomboid_IM_Serine_Proteases)
Type: Family

The Rhomboid-related protein family is characterized by its involvement in regulated intramembrane proteolysis, which facilitates the release of functional polypeptides from their membrane anchors. Members of this family are known to cleave specific substrates, such as EFNB3, and participate in critical signaling pathways, including EGF receptor signaling. Some proteins within this family act as serine proteases with specific roles, such as activating growth factors or transmitting developmental signals. Others may be inactive but still retain similarity to active members. The family plays a role in various biological processes, from embryonic development and dorsoventral axis establishment to neuronal precursor cell fate specification and vulva development.
Double-stranded RNA-binding domain-containing protein (DRBM-containing_protein)
Type: Family

This family of proteins includes RNA-binding proteins that are involved in the transport and localization of RNAs within cells. They play a critical role in the microtubule-dependent transport of RNAs, particularly in polarized and neuronal cell types, facilitating the localization of specific mRNAs to dendrites and other cellular regions. This is essential for processes such as neurite outgrowth and synaptic plasticity. Members of this family contain domains that bind double-stranded RNA and interact with tubulin, contributing to their role in cross-linking cytoskeletal and RNA components. Some members are also implicated in viral processes, interacting with viral proteins during particle budding. The family is characterized by the presence of double-stranded RNA-binding motifs (DRBMs), with the DRBM 3 domain being a significant determinant for RNA-binding activity.
Partitioning defective 6 homolog protein (PAR6_homolog)
Type: Family

This family of proteins is involved in the regulation of asymmetrical cell division and cell polarization processes. Members of this family function as adapter proteins that are likely to be involved in the formation of epithelial tight junctions. They are known to interact with Rho small GTPases and atypical protein kinase C proteins through a complex with PARD3, which is important for tight junction assembly. Additionally, these proteins are implicated in the organization and function of centrosomes, including the recruitment of key proteins that control microtubule organization within centrosomes. Some family members also play roles in maintaining cell polarity in specific tissues during embryogenesis.
Ribosomal Assembly Factor uL10 (Ribosome_Assembly_uL10)
Type: Family

This family of proteins is involved in ribosome assembly. Members act as nuclear paralogs of the ribosomal protein P0 and bind to pre-60S subunits during the early stages of assembly within the nucleolus. These proteins are subsequently replaced by P0 in the cytoplasmic pre-60S subunits and in the mature 80S ribosomes, indicating a role in the maturation process of ribosomes from the nucleolus to the cytoplasm.
TAFA chemokine-like (TAFA_chemokine-like)
Type: Family

This family of proteins includes chemokine-like factors that are involved in various biological processes related to the immune system and neuronal functions. Members of this family have been shown to play roles in modulating pain hypersensitivity, chemoattracting macrophages, promoting phagocytosis, and increasing reactive oxygen species release. They are also implicated in the regulation of microglia polarization and act as neurotrophic factors contributing to neuronal survival and neurobiological functions. Additionally, some proteins in this family serve as ligands for specific receptors, influencing neural stem-cell proliferation and differentiation.