SII-SWORD/CoKE huggingface dataset:
Transcription Termination Factor 1-like (TTF1-like)
Type: Family

This family of proteins includes multifunctional nucleolar components involved in the regulation of ribosomal gene transcription. They play a key role in both the activation and silencing of rDNA transcription. These proteins are responsible for terminating ribosomal gene transcription and mediating replication fork arrest. Additionally, they regulate RNA polymerase I transcription on chromatin. A notable feature is their dual role in rDNA regulation, which involves interactions with other proteins to modulate their DNA-binding activity and ensure proper transcriptional control within the nucleolus.
SPS2 domain-containing protein (SPS2_domain)
Type: Family

This family of proteins is involved in the structural development of cell walls in fungi, playing a crucial role in the formation of conidial and mycelial structures. Members of this family are implicated in the biogenesis of the cell wall, which is essential for cell shape, integrity, and response to environmental stresses. The family is characterized by its similarity to the SPS2 family, indicating a shared evolutionary background and potentially conserved functional mechanisms.
Protein phosphatase 1 regulatory subunit 27 (PP1_regulatory_subunit_27)
Type: Family

The Protein phosphatase 1 regulatory subunit 27 family consists of proteins that play a crucial role in the regulation of cellular processes by inhibiting the activity of protein phosphatase 1 (PP1) complexes. PP1 is a major serine/threonine phosphatase that is involved in the dephosphorylation of a variety of proteins, thereby controlling a wide range of cellular functions. Members of the Protein phosphatase 1 regulatory subunit 27 family bind to PP1 and modulate its activity, which is essential for maintaining the balance of phosphorylation within the cell. This regulatory mechanism is important for processes such as cell division, muscle contractility, protein synthesis, and neuronal signaling.
Small Integral Membrane Modulators (SIM_Modulators)
Type: Family

This family of proteins includes small integral membrane components that are implicated in the modulation of lipid droplet formation. They may exert their function through interactions with enzymes involved in lipid metabolism, such as squalene epoxidase.
Nuclear GTPase SLIP-GC (Nuclear_GTPase_SLIP-GC)
Type: Family

This family of proteins includes nuclear GTPases that are predominantly expressed in germinal center B-cells. Members of this family are implicated in the regulation of somatic hypermutation, a process critical for the diversification of the B-cell receptor repertoire. They exert their function by potentially inhibiting the activity of activation-induced cytidine deaminase (AICDA), an enzyme that introduces mutations into the immunoglobulin genes during somatic hypermutation and class switch recombination. Through this inhibition, these proteins may contribute to maintaining genome stability in B-cells by reducing the frequency of somatic mutations.
Transcription factor and kinase domain-containing protein (TF_kinase-domain_protein)
Type: Family

This family of proteins includes transcription factors involved in gene clusters that mediate biosynthesis of specific meroterpenoids with inhibitory effects on human receptors, as well as members that contain protein kinase domains. Some of these kinase domains may be catalytically inactive, yet they still belong to the protein kinase superfamily and are related to serine/threonine-specific protein kinases.
A-kinase anchor protein (AKAP)
Type: Family

This family of proteins is involved in the cellular anchoring of protein kinase A (PKA) regulatory subunits. Members of this family interact with the type II regulatory subunits of PKA, a pivotal enzyme in the cAMP signaling pathway, and play a crucial role in localizing the kinase to specific subcellular compartments. Through this targeting mechanism, they help orchestrate the spatial and temporal dynamics of PKA signaling, which is essential for a multitude of cellular processes.
Jasmonate-induced protein (Jasmonate-induced_protein)
Type: Family

This family of proteins is involved in the response to the plant hormone jasmonate. Jasmonates are lipid-based compounds that regulate various aspects of plant growth, development, and defense. Proteins in this family are typically induced by jasmonate signaling and may participate in diverse biological processes, including stress responses, secondary metabolism, and developmental pathways. Their specific functions can include roles in the regulation of gene expression, signaling pathways, and possibly direct defense mechanisms against biotic stressors. The exact molecular functions and mechanisms of action for these proteins may vary among family members and plant species.
RhoGEF domain-containing protein (RhoGEF_domain)
Type: Family

This family of proteins includes members with a RhoGEF domain, which suggests a role in regulating GTPase activity. The proteins are involved in the activation of GTPases, a critical process for various cellular functions including signal transduction and cytoskeletal organization. Some members of this family may contain a PH-like region, which is reminiscent of pleckstrin homology (PH) domains, although the exact nature and function of this region may vary and is not fully characterized.
Transmembrane protein 154-like (TMEM154-like)
Type: Family

This family of proteins includes transmembrane proteins that are characterized by their spanning of the cellular membrane. The specific functions of these proteins may involve various biological processes, including signal transduction, cellular adhesion, and the transport of molecules across the membrane. Due to the transmembrane nature, these proteins are likely to be involved in interactions with other proteins, lipids, or extracellular components, contributing to the dynamic regulation of cellular responses to environmental stimuli. The detailed molecular function and the pathways they are involved in may vary between different organisms and specific protein members of this family.
Cell surface beta-glucosidase/SUN-like (Beta-glucosidase/SUN-like)
Type: Family

This family of proteins includes members that are involved in cell wall biogenesis. One of the characterized functions within this family is that of a cell surface beta-glucosidase, which plays a role in the remodeling or degradation of cell wall components. The family is also noted for its similarity to the SUN family, suggesting a potential common structural or functional theme. However, the full range of activities and biological roles of this family may be diverse and is not fully characterized based on the available information.
Rho guanine nucleotide exchange factor 18 (Rho_GEF18)
Type: Family

The Rho guanine nucleotide exchange factor 18 family includes proteins that function as guanine nucleotide exchange factors (GEFs) for RhoA and RAC1 GTPases. Members of this family are involved in the regulation of the actin cytoskeleton, as their activation leads to the formation of actin stress fibers and induces changes in cell shape. Additionally, they are responsible for the production of reactive oxygen species (ROS) when acting as GEFs for RAC1. These proteins do not serve as GEFs for CDC42. The G protein beta-gamma subunits of heterotrimeric G proteins are known to activate these proteins, which contributes to the integrated cellular responses to LPA and other G-protein coupled receptor agonists. Moreover, they play a crucial role in the EPB41L4B-mediated regulation of the circumferential actomyosin belt within epithelial cells, highlighting their significance in maintaining cellular structure and signaling.
Centromere-associated KNL-2 homolog (Centromere_KNL-2_homolog)
Type: Family

This family of proteins is essential for various stages of cell division and development. Members are involved in the recognition and localization of centromeres during mitosis and meiosis, which is crucial for accurate chromosome segregation. They also contribute to the establishment of the epigenetic status of centromeres and are capable of binding to DNA and RNA. Additionally, these proteins are necessary for normal embryo development, indicating a role in early developmental processes.
Photosystem II Assembly and Photoprotection-Related Protein (PSII_Assembly/Photoprotect-Rel)
Type: Family

This family of proteins includes members that are involved in the photoprotection and assembly of photosystem II (PSII) as well as in the biogenesis and repair processes of PSII. They can form trimeric complexes with other proteins that are essential for the early assembly of PSII and its repair, and are also involved in the recruitment of ribosomes to specific mRNAs during these processes. Additionally, some members are thought to function in the delivery of pigments to PSII subunits and may bind chlorophylls and carotenoids. Others are putative zeaxanthin binding proteins that may form photoprotective complexes within the light-harvesting antennae.
Mitochondrial uncharacterized protein (Mitochondrial_unc_protein)
Type: Family

This family of proteins is currently uncharacterized and lacks detailed functional annotation. The proteins within this family are mitochondrial in location, as indicated by the names of the Swiss-Prot entries. They show similarity to each other, suggesting a conserved function or structural feature that is yet to be identified. Further research is necessary to elucidate the specific roles these proteins play within the mitochondria and to understand their biological significance in the organisms where they are found.
GPCR-like receptor (GPCR-like)
Type: Family

This family of proteins includes members that are putative G-protein coupled receptors (GPCRs). GPCRs constitute a large and diverse group of membrane proteins that play a critical role in signal transduction by responding to a variety of extracellular stimuli and activating intracellular signaling pathways. Although the specific functions of the proteins in this family are not known, they are believed to act as receptors based on sequence similarity to other GPCRs. As receptors, they may be involved in various physiological processes by interacting with ligands such as hormones, neurotransmitters, or sensory stimuli.
Zinc metalloprotease ZmpB (Zinc_metalloprotease_ZmpB)
Type: Family

This family of proteins includes zinc metalloproteases that are known to play a role in virulence, particularly in the context of bacterial pathogenicity. Members of this family are capable of inducing inflammation in the lower respiratory tract, which is evidenced by the increase of tumor necrosis factor alpha (TNF-alpha) in the lungs. The proteolytic activity of these enzymes is implicated in various processes important for the pathogenesis of diseases such as pneumonia and septicemia. The metalloprotease function suggests a broad spectrum of substrate specificity, which may include components of the host immune system or other proteins critical for maintaining host defenses.
Actin-binding & GATA zinc finger domain-containing protein (Actin-binding/GATA_Znf)
Type: Family

This family of proteins includes members that are involved in the regulation of actin cytoskeleton dynamics and transcriptional regulation. One protein in this family is known to bind actin, suggesting a role in the modulation of actin filament assembly and disassembly, which is crucial for various cellular processes such as cell shape maintenance, motility, and division. Another member of this family contains a GATA zinc finger domain, indicating a function in DNA binding and transcriptional regulation. GATA zinc finger domain-containing proteins typically interact with GATA consensus sequences in the promoters of target genes, thereby controlling the expression of genes involved in developmental processes and cellular differentiation pathways.
Cytotoxic and regulatory T-cell molecule (CRTAM)
Type: Family

This family of proteins mediates heterophilic cell-cell adhesion and plays a crucial role in the regulation of T-cell activation, differentiation, and tissue retention. Members of this family interact with CADM1 to enhance NK cell cytotoxicity and IFNG secretion by CD8+ T-cells, as well as to facilitate NK cell-mediated tumor rejection. These proteins are involved in CD8+ T-cell proliferation following TCR activation and are important for the retention of activated CD8+ T-cells within lymph nodes. They also contribute to the intestinal retention of various T-cell subsets and promote adhesion to gut-associated dendritic cells. This interaction may support the expression of gut-homing molecules and the conversion of CD4+ T-cells into CD4+ CD8+ T-cells. Additionally, the extracellular domain of these proteins is implicated in the regulation of cytokine production, although it is not essential for late T-cell polarization.
Prespore vesicle-associated protein (Prespore_vesicle_assoc)
Type: Family

This family of proteins includes members involved in the formation of prespore vesicles, which are essential for spore coat formation during the developmental process of cellular organisms such as Dictyostelium discoideum. The proteins in this family may play a role in the trafficking and sorting of cargo proteins to the prespore vesicles, a critical step in the sporulation process. Additionally, the family encompasses proteins that are currently uncharacterized but may have functions related to prespore vesicle dynamics or other developmental processes in cellular slime molds.
Petuviruses Genome Polyprotein (Petuviruses_polyprotein)
Type: Family

The Petuviruses genome polyprotein is involved in the life cycle of Petuviruses, a group of plant viruses. The polyproteins encoded by these viruses are processed to produce at least four distinct polypeptides, each with a specific role in the viral infection and replication process: Movement protein (MP), capsid protein (CP), Protease (PR), and reverse transcriptase (RT) . The MP is likely involved in the cell-to-cell movement of the virus within the host plant. The CP is responsible for encapsulating the viral RNA genome, protecting it from degradation and recognition by the host's defense mechanisms. The PR is involved in the cleavage of the polyprotein into its functional components. Lastly, the RT is critical for the replication of the viral RNA genome. Together, these proteins enable the virus to infect host cells, replicate, and spread to new cells, thereby facilitating the viral life cycle.
WAS/WASL-interacting domain-containing protein (WAS/WASL-interacting_domain)
Type: Family

This family of proteins is involved in the dynamic reorganization of the actin cytoskeleton. They are key players in the recruitment and activation of the WASL protein, working in conjunction with NCK1 and GRB2. These proteins are also implicated in the modulation of WASL's subcellular localization, which is crucial for the transition from stress fiber formation to the generation of filopodia and cell ruffles. Additionally, they have a role in intracellular viral motility, specifically by aiding the recruitment of WASL to certain viruses within infected cells.
Cytochrome b5-related (Cytochrome_b5-related)
Type: Family

This family of proteins includes members that are related to cytochrome b5. Cytochrome b5 proteins are involved in electron transport and play a crucial role in various metabolic processes, including fatty acid desaturation and elongation, and drug metabolism. Members of this family may have a specific function in muscle cell metabolism, suggesting a role in the cellular processes that support muscle physiology and energy production.
Transmembrane protein 221 (TM221)
Type: Family

This family of proteins includes transmembrane proteins that are characterized by their spanning of the cellular membrane. The specific functions of these proteins may vary, but they typically play roles in cellular processes such as signaling, transport, and maintaining structural integrity of the cell. As transmembrane proteins, they may act as gatekeepers, controlling the flow of substances into and out of the cell, or as receptors, receiving signals from the extracellular environment and initiating cellular responses. The detailed molecular functions and biological processes associated with this family may be diverse and are not fully elucidated based on the information provided.
Vacuolar Protein Sorting-Associated (VPS_Associated)
Type: Family

This family of proteins is involved in the process of vacuolar protein sorting, which is essential for directing proteins to the vacuole, an organelle that functions similarly to the lysosome in animal cells. Members of this family play a role in the trafficking pathway that ensures proteins are delivered to the vacuole for degradation, storage, or other cellular functions. The proper sorting and delivery of vacuolar proteins are crucial for maintaining cellular homeostasis and for the execution of various cellular processes.
IDLSRF-like signaling peptide (IDLSRF-like_peptide)
Type: Family

This family of proteins includes peptides that are likely involved in signaling pathways as prohormones. Prohormones are precursors of hormones, which are processed and cleaved to produce active hormones that participate in various regulatory functions. These proteins may undergo post-translational modifications and cleavage to generate smaller, biologically active peptides that can bind to receptors and elicit cellular responses. The specific functions of the peptides within this family may vary, but they generally play roles in intercellular communication and physiological regulation.
Tumor Necrosis Factor Ligand Superfamily Member 8 (TNF_ligand_SF_member_8)
Type: Family

This family of proteins includes cytokines that are members of the tumor necrosis factor (TNF) superfamily. These proteins are known to interact with the TNFRSF8/CD30 receptor, which is expressed on the surface of certain T-cells. The primary function of these proteins is to induce the proliferation of T-cells, which plays a critical role in the immune response. The interaction with their receptor is important for the regulation of apoptosis and immune response modulation.
Class V-like SAM-binding domain-containing protein (Class_V-like_SAM-MTase)
Type: Family

This family of proteins includes histone-lysine N-methyltransferases that are known to modify histones by di- and trimethylation, particularly 'Lys-9' of histone H3. These modifications are crucial for regulating gene expression and are involved in various cellular processes, including modulation of aging and stress resistance. Some family members are implicated in repressing mitochondrial function-related genes and modulating the mitochondrial unfolded protein response. Additionally, they may influence the levels of neurotransmitters such as serotonin and dopamine, thereby affecting longevity and behavioral responses. Members of this family belong to the class V-like SAM-binding methyltransferase superfamily, indicating a shared mechanism of action involving S-adenosylmethionine as a methyl donor.
Plant Male Germline-Regulatory Transcription Factors (Plant_Male-Germline_Reg_TFs)
Type: Family

This family of proteins includes transcription factors that play a crucial role in plant development and reproduction. Members of this family are involved in the regulation of gene expression by binding to specific DNA sequences. They function as activators of transcription, promoting the expression of genes that are essential for processes such as male germline development, cell cycle progression, and pollen maturation. These proteins are characterized by their ability to bind to MYB sites within gene promoters, thereby initiating transcriptional programs necessary for the proper functioning of gametic cells and fertilization.
TNF receptor superfamily member 18 (TNFRSF18)
Type: Family

This family of proteins includes receptors that bind to TNFSF18, a ligand involved in the regulation of immune responses. Members are implicated in the interaction between activated T-lymphocytes and endothelial cells, playing a role in the modulation of T-cell receptor-mediated apoptosis. They are also known to activate the NF-kappa-B signaling pathway through the TRAF2/NIK axis, which is crucial for immune and inflammatory responses.
Chlamydial Translocated Actin-Recruiting Phosphoprotein (Chlamydial_TARP)
Type: Family

The chlamydial CPn_0572/CT_456/TC_0741 family includes proteins that are involved in signaling events related to actin recruitment. Members of the family appear to play a role in initiating or participating in the cellular processes that lead to the internalization of the pathogen into host cells. The actin recruitment is a critical step in the infection mechanism of Chlamydia, facilitating the entry and survival of the bacteria within the host.
Serine/Threonine-Protein Kinase-Related (Ser/Thr-Kinase-Related)
Type: Family

This family of proteins includes serine/threonine kinases, which are typically involved in phosphorylating serine or threonine residues in substrate proteins, playing critical roles in various cellular processes such as signal transduction, cell division, and metabolism. Although one member of this family is predicted to be catalytically inactive, it may still participate in protein-protein interactions or act as a scaffold in signaling pathways. The presence of a protein kinase domain suggests that these proteins are structurally related to the protein kinase superfamily, despite potential differences in their enzymatic activity.
Ribosomal L1 domain-containing protein and Transcription factor (Ribosomal_L1-TF)
Type: Family

This family of proteins includes members that are involved in distinct cellular processes. One protein is implicated in the structure and function of ribosomes, specifically within the ribosomal L1 domain, suggesting a role in the translation machinery. Another member functions as a transcription factor, acting as a negative regulator of transcription elongation. Despite the divergent functions, these proteins share structural or sequence similarities that group them into a single family.
Chloroplastic FKBP-type Peptidyl-prolyl cis-trans Isomerase (Chloro_FKBP-type_PPIase)
Type: Family

The FKBP-type PPIase family comprises proteins that function as peptidyl-prolyl cis-trans isomerases (PPIases), which are enzymes that accelerate the folding of proteins by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. These proteins are typically involved in protein folding processes and may play a role in various cellular functions due to their impact on the conformational states of target proteins. Members of the FKBP-type PPIase family are characterized by their enzymatic activity and are found in various cellular compartments, including the chloroplast in plants.
Fungal Dehydratase/Hydratase (Fungal_Dehydratase/Hydratase)
Type: Family

This family of proteins includes enzymes involved in diverse biosynthetic and protective pathways in fungi. Members of this family function as dehydratases and hydratases, catalyzing the addition or removal of water from specific substrates. One member is involved in the biosynthesis of aspoquinolone mycotoxins, participating in a multi-step pathway that includes dehydration of an epoxide intermediate. Another member acts defensively by converting a fungitoxic compound into a less toxic form, aiding in the survival of the pathogenic fungus against plant defenses. These activities highlight the family's role in both fungal secondary metabolism and pathogen-host interactions.