SII-SWORD/CoKE huggingface dataset:
Cytokinesis and Rho signaling-related protein (Cytokinesis/Rho-signaling)
Type: Family

This family of proteins is involved in various cellular processes, including cytokinesis, the final step of cell division where the cell splits into two. Members of this family are essential for the structural integrity of the cleavage furrow, which is the indentation that begins the process of division, and for the completion of this furrow's ingression. They are also involved in organizing cortical structures such as septins and myosin II, which are important for membrane dynamics and cell shape. Some family members are implicated in signaling pathways, such as the Rho signaling pathway, which can activate transcription factors like NF-kappa-B and may influence apoptosis resistance in certain cancers. Additionally, these proteins play roles in the organization of the cell's cytoskeleton, including microtubules and actin filaments, which are crucial for maintaining cell shape, stability, and movement. They are also involved in developmental processes, such as the formation of germline cells in embryos and the maintenance of gonadal structures.
TOX high mobility group box domain-containing protein (TOX_HMG-box_domain)
Type: Family

This family of proteins includes transcriptional regulators and coactivators that play crucial roles in various biological processes such as neural stem cell commitment, corticogenesis, lymphoid cell development, and organogenesis. Members of this family are known to bind to GC-rich DNA sequences, potentially altering chromatin structure and modulating the accessibility of transcription factors to DNA. They are involved in the control of the neural stem cell pool, neurite outgrowth, and the development of lymphoid tissue-inducer cells, which are essential for the formation of secondary lymphoid organs. These proteins act as developmental checkpoints and are pivotal in thymocyte positive selection and T cell lineage commitment. They also contribute to the differentiation of innate lymphoid cells and the specification of natural killer cell lineage. Additionally, they have a role in cell fate reprogramming, chromatin structure control, and cell cycle progression. Some family members are implicated in the regulation of hormone-responsive genes and the response to various stimuli such as dexamethasone, cAMP, and insulin.
Differentially Expressed in FDCP 8 Homolog (DEF8)
Type: Family

The DEF8 family is involved in various cellular processes related to the endolysosomal system, autophagy, and bone resorption. Members of the family act as multivalent adapter proteins that regulate fusion events between late endosomes and lysosomes, which are essential for the maturation of endolysosomal compartments. They play a role in the degradation of growth factor receptors and clearance of autophagosomes, often through interactions with small GTPases like RAB7A and ARL8B. In osteoclasts, DEF8 family proteins are crucial for the peripheral distribution of lysosomes and the formation of ruffled borders, which are key for bone resorption. Some members also participate in muscle differentiation and may act as scaffold proteins for AKT1 signaling. Additionally, they can be involved in the transduction of apoptotic signals and contribute to the pathogenesis of infections by maintaining the integrity of pathogen-containing vacuoles.
mRNA Translation Regulation/Replication-dependent Histone mRNA Translation (mRNA_TranslReg/HistoneTransl)
Type: Family

The protein family is involved in the regulation of mRNA translation. Members of the family function as coactivators in translation initiation, interacting with polyadenylate-binding proteins to enhance translation of poly(A)-containing mRNAs. Some members are implicated in the replication-dependent translation of histone mRNAs, which lack a poly-A tail and end with a stem-loop, potentially aiding in mRNA circularization to enhance translation. Additionally, certain proteins within the family are involved in the pioneer round of mRNA translation mediated by the cap-binding complex and play a role in nonsense-mediated mRNA decay. The family also includes proteins that may be involved in translationally coupled mRNA turnover and are implicated in the interplay of mRNA decay and translation.
Serine Protease Inhibitor-like TIL Domain (SerProtInhib-TIL_Domain)
Type: Family

The serine protease inhibitor-like (TIL domain-containing) family comprises a diverse group of proteins that primarily function to inhibit serine proteases, defending the organism against host proteinases. Members of this family have been identified with various specific inhibitory activities, including chymotrypsin, cathepsin G, elastase, and metalloproteinases. Some proteins within the family also exhibit additional functions such as inducing physiological and behavioral changes in mated female flies, contributing to seminal fluid toxicity, affecting neuromuscular events post-mating, and possessing antibacterial activity. Others may play roles in inhibiting the host's immune response during parasitic infections or stabilizing venom components. The family's broad range of inhibitory activities and additional functions reflect its importance in various biological processes including defense mechanisms, reproduction, and parasitism.
Glutathione S-transferase Theta (GST_Theta)
Type: Family

This family of proteins is involved in the detoxification process by conjugating reduced glutathione to a variety of exogenous and endogenous hydrophobic electrophiles. Members of this family exhibit a range of activities, including sulfatase activity and the ability to bind to various substances such as steroids, bilirubin, carcinogens, and organic anions. Some proteins within this family also display glutathione peroxidase activity with specific hydroperoxides and are capable of dehalogenating dichloromethane. The diverse substrate specificity across family members reflects their role in cellular defense mechanisms against toxic compounds.
Peptidyl-prolyl cis-trans isomerase Pin1 (PPIase_Pin1)
Type: Family

The Pin1 family of peptidyl-prolyl cis-trans isomerases (PPIases) is involved in the isomerization of specific phosphorylated Ser/Thr-Pro motifs, acting as molecular switches in various cellular processes [

,

. Members of this family display a preference for acidic residues N-terminal to the proline bond to be isomerized . They play roles in mitosis regulation, transcriptional control, protein folding, and cell transformation. Some family members are involved in the dephosphorylation and recycling of proteins post-mitogen activation, degradation of specific substrates in a phosphorylation-dependent manner, and regulation of DNA repair pathways. The WW domain present in many family members mediates protein-protein interactions. The activity of these enzymes can be regulated by inhibitors like juglone, buparvaquone, and others.
Ras-specific palmitoyltransferase complex (Ras_palmitoyltransferase)
Type: Family

This family of proteins includes palmitoyltransferases that are involved in the post-translational modification of Ras proteins, which is crucial for their proper localization to the plasma membrane and subsequent function in cell signaling. Members of this family form complexes, such as ERF2-ERF4 in yeast and ZDHHC9-GOLGA7 in mammals, which specifically palmitoylate Ras proteins like RAS2, HRAS, and NRAS. This modification is essential for the anchoring of these Ras proteins to the plasma membrane, where they participate in signal transduction pathways that regulate cell growth and differentiation. Some family members are also implicated in protein transport from the Golgi apparatus to the cell surface and may play roles in cell adhesion.
Pre-mRNA-splicing factor CWC21 (CWC21)
Type: Family

This family of proteins is involved in the process of pre-mRNA splicing. Members of this family are thought to act at or before the first catalytic step in the spliceosome, potentially by stabilizing the catalytic center or the RNA substrate's position. Some members may also interact with RNA polymerase II, influencing its chromatin distribution and phosphorylation state, and may play a role in regulating pathways such as germline sex determination.
Lin-28 homolog RNA-binding protein (Lin-28_RNA-binding)
Type: Family

This family of proteins is involved in the regulation of microRNA (miRNA) biogenesis and mRNA translation. Members of this family bind to primary miRNA transcripts, particularly those with a 5'-GGAG-3' motif, and can sequester them to prevent processing into mature miRNAs. They are also known to bind mRNAs and enhance their translation, particularly those related to developmental timing, pluripotency, and metabolism. The proteins can recognize structural features in RNA, such as G-quartets, and are associated with the translational machinery, affecting initiation events and mRNA stability. They have roles in muscle differentiation, tissue repair, and maintaining the pluripotent state of stem cells by suppressing differentiation-inducing miRNAs like let-7.
Ataxin-10 and Copper transport protein 86 families (Ataxin-10/CTR86_families)
Type: Family

The Ataxin-10 family proteins are essential for the survival and maintenance of cerebellar neurons. They are involved in neuritogenesis through the activation of the Ras-MAP kinase pathway. Additionally, they may contribute to the regulation of intracellular glycosylation levels and homeostasis. The Copper transport protein 86 family members are implicated in threonine biosynthesis and are considered essential proteins.
Tuftelin/GRINL1A/MYZAP/CCD68 (Tuftelin_GRINL1A/MYZAP/CCD68)
Type: Family

The protein family includes proteins involved in various cellular processes. The tuftelin subfamily members are implicated in the mineralization and structural organization of enamel, suggesting a role in dental development. The GRINL1 subfamily is associated with the Pol II(G) complex form of RNA polymerase II, contributing to mRNA and non-coding RNA synthesis, and may regulate transcription activation via the Mediator complex. The MYZAP subfamily is involved in cellular signaling, targeting proteins to cell junctions, and may interact with NMDA receptor subunits in neurons. The CCD68 subfamily proteins are centriolar, necessary for centriole subdistal appendage assembly and microtubule anchoring in interphase cells.
Pre-mRNA-splicing factor CWC25 (CWC25_splicing_factor)
Type: Family

The CWC25 family comprises proteins that are involved in the process of pre-mRNA splicing. Members of the CWC25 family are recognized as components of the spliceosome, a complex molecular machine responsible for the removal of introns from a pre-mRNA transcript and the ligation of the remaining exons to form a mature mRNA molecule. The precise role of CWC25 proteins within the spliceosome is not detailed in the provided information, but their ubiquitous presence in organisms ranging from yeast to humans suggests a conserved function in the splicing pathway. The involvement in such a critical step of gene expression regulation underscores the importance of CWC25 family proteins in cellular biology.
DNA Polymerase Epsilon Subunit (DNA_Pol-Epsilon_Subunit)
Type: Family

The DNA Polymerase Epsilon Subunit Family is involved in essential cellular processes including chromosomal DNA replication and DNA repair. Members of this family function as accessory components of the DNA polymerase epsilon complex. They are implicated in the binding of naked DNA and its incorporation into chromatin, a process that is facilitated by nucleosome-remodeling activities. Some members also participate in the formation of complexes with other proteins such as CHRAC1, contributing to chromatin accessibility and nucleosome sliding, although they do not enhance the sliding activity of certain remodeling complexes. In addition to replication and repair, some family members are involved in the inheritance of epigenetic marks and the coordination of transcriptional repression.
Cell-to-cell trafficking and antifungal protein (Cell2Cell_Antifungal)
Type: Family

This family of proteins is involved in modulating cell-to-cell trafficking and plays a role in plant innate immunity. Members of this family are implicated in systemic acquired resistance, a defense mechanism that utilizes signaling molecules such as azelaic acid, glycerol-3-phosphate, and salicylic acid. Some proteins within this family are also responsible for callose deposition during immune responses, which affects plasmodesmata permeability. Additionally, certain members exhibit antifungal activity by binding to specific carbohydrates on fungal cell walls, which can interfere with fungal growth and actin remodeling, leading to actin-dependent fungal cell death.
C-type Lectin Receptor Immune Modulators (C-type_Lectin_Receptor_IMM)
Type: Family

The protein family is composed of C-type lectin domain-containing receptors with diverse roles in the immune system. Members are involved in pathogen recognition, mediating immune cell interactions, and antigen presentation. They recognize various molecular patterns, including those from bacteria, fungi, and damaged cells, and are implicated in the activation and modulation of immune responses. Some family members function as costimulatory molecules, enhancing T-cell proliferation, or as endocytic receptors, facilitating antigen uptake and presentation. Others contain ITIM motifs, which modulate cellular responses by binding phosphatases upon phosphorylation. Collectively, the family contributes to innate and adaptive immunity by detecting pathogens, presenting antigens, and regulating immune cell signaling.
Fungal pH-response regulator palI/RIM9 (pH-response_reg_palI/RIM9)
Type: Family

The palI/RIM9 family is involved in the regulation of pH response in various fungi. Members of this family are essential for the proteolytic cleavage of transcription factors, such as RIM101 or its homologs, which is a crucial step in the adaptation to alkaline environments. This cleavage event activates the transcription factors, enabling the expression of genes necessary for processes like sporulation, invasive growth, and correct cell separation under specific conditions. Some members may also function as pH sensors, contributing to the detection of ambient pH changes and initiating appropriate cellular responses.
cAMP-responsive element-binding ATF subfamily (CREB_ATF_subfamily)
Type: Family

This family of proteins includes transcriptional activators that are involved in the unfolded protein response (UPR) and cellular stress responses. They bind to specific DNA elements such as the cAMP response element (CRE) and the unfolded protein response element (UPRE), thereby regulating gene expression. These proteins play roles in various cellular processes including cell survival, proliferation, migration, differentiation, and inflammatory responses. They are also implicated in the regulation of lipid metabolism, particularly in maintaining normal plasma triglyceride concentrations. Some family members are involved in the response to endoplasmic reticulum stress by activating target genes that help in adapting to and surviving stress conditions. Additionally, they may interact with other transcription factors and histone deacetylases to modulate transcriptional outcomes.
Cytochrome P450 Amino Acid/Fatty Acid Hydroxylases (CYP450_AA/FA_Hydroxylases)
Type: Family

The Cytochrome P450 family is involved in diverse biosynthetic processes, including the production of defensive cyanogenic glycosides, glucosinolates, and other specialized metabolites. Members of the family catalyze the N-hydroxylation of amino acids such as phenylalanine, isoleucine, valine, and tryptophan, converting them into their corresponding aldoximes, which serve as precursors for various bioactive compounds. Some members also hydroxylate fatty acids like lauric acid, contributing to the development of pollen walls. The family's enzymes exhibit substrate specificity, with certain members unable to process amino acids like leucine, tyrosine, or tryptophan. Regulatory mechanisms include inhibition by compounds such as tetcyclasis, highlighting the family's role in plant metabolism and defense.
Cytochrome c oxidase assembly protein COX19 (COX19)
Type: Family

This family of proteins is involved in the assembly of mitochondrial cytochrome c oxidase, a key component of the respiratory chain. Members of this family may also play a role in the transduction of an SCO1-dependent redox signal from the mitochondrion to ATP7A, which is important for regulating cellular copper homeostasis.
Methuselah G-protein coupled receptor (Mth_GPCR)
Type: Family

The Mth G-protein coupled receptor family is involved in key physiological processes such as biological aging and stress response. These receptors are essential for adult survival across various species. In Drosophila, the Mth receptors play a critical role in the nervous system by up-regulating neurotransmitter exocytosis at larval glutamatergic neuromuscular junctions, which is crucial for proper synaptic function and muscle control. They are implicated in vesicle docking and clustering at release sites, indicating a significant role in synaptic transmission. Agonists like SP/Acp70A and sun can activate Mth receptors in vitro, suggesting a ligand-specific response mechanism.
Ceramide-binding SVF1-like (Ceramide-binding_SVF1)
Type: Family

This family of proteins is involved in sphingolipid biosynthesis by potentially transferring ceramides from the endoplasmic reticulum membrane to the cis-Golgi network membrane. These proteins are essential for the production of complex sphingolipids, which are crucial components of cell membranes and play a role in signaling and cellular recognition. Additionally, some members of this family are implicated in the cellular response to oxidative stress and are involved in metabolic transitions such as the diauxic shift in yeast.
Guanyl-specific ribonuclease N1/T1 (Ribonuclease_N1/T1)
Type: Family

The ribonuclease N1/T1 family comprises enzymes that specialize in the hydrolysis of RNA, specifically cleaving the phosphodiester bond between nucleotides. These guanyl-specific ribonucleases exhibit a preference for guanine bases adjacent to the phosphodiester linkage being targeted. Members of the ribonuclease N1/T1 family are characterized by their ability to act extracellularly, suggesting a role in defense mechanisms or nutrient acquisition by processing extracellular RNA. Some family members are regulated by divalent cations, which can inhibit their enzymatic activity.
Barrier-to-autointegration factor (BAF)
Type: Family

The BAF family comprises non-specific DNA-binding proteins with key roles in nuclear dynamics and cellular defense mechanisms. Members of the BAF family are involved in mitotic nuclear reassembly, chromatin organization, and DNA damage response. They contain helix-hairpin-helix (HhH) structural motifs, allowing them to bind non-specifically to double-stranded DNA and promote DNA cross-bridging. This facilitates the formation of a dense chromatin network during mitosis, which is crucial for nuclear membrane reformation and chromosome segregation. BAF proteins also regulate gene expression and play a protective role in intrinsic immunity against foreign DNA by competing with CGAS for DNA binding, thus preventing autoinflammatory responses. Additionally, they interact with PARP1 to modulate its ADP-ribosyltransferase activity in response to DNA damage. Some BAF proteins are implicated in the recognition of exogenous dsDNA to prevent autophagy and have antiviral activities against poxvirus infection. They are also exploited by retroviruses to integrate viral DNA into the host genome.
Serine protease inhibitor and venom toxin (Serpin_venom_toxin)
Type: Family

This family of proteins includes serine protease inhibitors with diverse biological functions. Members are involved in male reproduction and fertility, modulating sperm motility, and providing antimicrobial protection for spermatozoa. Some family members are toxins from venomous species, inhibiting serine proteases and voltage-gated potassium channels, or interacting with vasopressin receptors to modulate diuresis. Others are involved in immune responses, such as preventing accidental activation of prophenoloxidase, which is crucial for the insect immune system. The family exhibits a range of inhibitory activities against enzymes like trypsin, kallikrein, chymotrypsin, and elastase, and some have been characterized by their interaction with specific receptors or channels, contributing to their selectivity and potency in various biological processes.
Cytochrome c oxidase subunit VIc (Cytochrome_c_oxidase_VIc)
Type: Family

Cytochrome c oxidase (CcO;

), a 13 subunit complex, is the terminal oxidase in the mitochondrial electron transport chain. Cytochrome c oxidase is the component of the respiratory chain that catalyses the reduction of oxygen to water .

This
entry contains of cytochrome c oxidase subunit VIc (also known as Cytochrome c oxidase subunit 6C), which is found only in eukaryotes and its specific function remains unclear. It has been reported that the relative concentrations of some nuclear encoded CcO subunits, including subunit VIc, compared to those of the mitochondrial encoded subunits, are altered significantly during the progression of prostate cancer .
Biogenesis of lysosome-related organelles complex 1 subunit KXD1 (BLOC-1_subunit_KXD1)
Type: Family

The KXD1 family comprises proteins that are integral components of the biogenesis of lysosome-related organelles complex-1 (BLOC-1). Members of the KXD1 family are involved in the crucial process of endosomal cargo sorting, which is essential for the proper functioning and distribution of materials to lysosome-related organelles. These proteins play a significant role in the cellular trafficking pathway, ensuring that enzymes, membrane proteins, and other vital substances reach their target organelles within the cell.
Protease inhibitor I20 (potato type II proteinase inhibitor) (Protease_inhibitor_I20)
Type: Family

The protease inhibitor I20 (potato type II proteinase inhibitor) family consists of proteins that function primarily as inhibitors of proteolytic enzymes such as trypsin and chymotrypsin. Members of this family are potent inhibitors of trypsin, with varying degrees of effectiveness against chymotrypsin. Some members do not inhibit elastase and subtilisin DY, while others also show inhibitory activity against pronase E. These inhibitors are typically induced in response to wounding and may play a role in plant defense by limiting protein degradation caused by endogenous or pathogen-derived proteases.
ABC transporter permease component (ABC_transporter_permease)
Type: Family

This family of proteins is involved in the transport of various substrates across cellular membranes. Members of this family are typically part of ATP-binding cassette (ABC) transporter complexes, which are binding-protein-dependent systems. These proteins are likely responsible for the translocation of substrates such as sugars, osmoprotective compounds, and other molecules, facilitating their uptake into the cell. The substrates mentioned include starch degradation products, sugars like melibiose, raffinose, lactose, and alpha-glucosides, as well as osmoprotective compounds like glucosylglycerol, sucrose, and trehalose. The transport process is probable and involves the movement of these molecules through the permease component of the ABC transporter, which is integral to the membrane.