SII-SWORD/CoKE huggingface dataset:
Mitochondrial GTP/GDP Carrier (Mito_GTP/GDP_Carrier)
Type: Family

This family of proteins includes mitochondrial carriers that facilitate the transport of nucleotides across the inner mitochondrial membrane. Specifically, they are involved in the exchange of GTP and GDP, which is crucial for various mitochondrial functions including iron transport and the maintenance of mitochondrial DNA. These carriers are integral to the mitochondrial membrane and play a key role in cellular energy metabolism by regulating the availability of GTP, an essential molecule for numerous cellular processes.
Ras-cAMP pathway regulatory protein (Ras-cAMP_regulatory)
Type: Family

This family of proteins includes members that are involved in the negative regulation of the Ras-cAMP signaling pathway. They play a role in the transcriptional regulation of genes that are inducible by galactose. The family features proteins that may have a regulatory function in signal transduction processes and could be involved in modulating cellular responses to nutritional changes.
Metallo-dependent Hydrolase/TatD-type (Metallo-hydrolase/TatD-type)
Type: Family

This family of proteins includes members that are involved in interactions with other proteins, such as the Cut9 protein, suggesting a role in cellular processes that require protein-protein interactions. Additionally, the family is characterized by a similarity to metallo-dependent hydrolases, indicating that members may possess enzymatic activity, particularly hydrolysis involving metal ions. Some proteins within this family are putatively identified as deoxyribonucleases, which are enzymes that cleave DNA molecules. The presence of TatD-type hydrolase domain suggests a specialization in hydrolytic functions related to nucleic acid metabolism.
Zinc cluster transcription regulator (Zinc_cluster_trans_reg)
Type: Family

This family of proteins includes zinc cluster transcription factors that are involved in the regulation of various metabolic processes. Members of this family are known to govern gene expression related to iron acquisition, both through reductive and siderophore-mediated pathways, which are crucial for organismal virulence. Additionally, these proteins regulate carbon metabolism by influencing genes associated with gluconeogenesis, the tricarboxylic acid (TCA) cycle, and glucose metabolism. Some family members also play a role in cellular processes such as cell wall remodeling and the development of drug resistance.
ABC-5 integral membrane transporter (ABC-5_transporter)
Type: Family

This family of proteins is involved in the transport of specific substrates across cellular membranes. Members of this family are integral components of ABC transporter complexes, which are typically involved in the import or export of various molecules in response to cellular needs. Specifically, these proteins have been implicated in the utilization of acetoin, a process that is particularly important during the stationary phase of growth and sporulation in bacteria. The activity of these proteins is essential for the proper functioning of the ABC transporter complex, which relies on the coordinated action of multiple protein subunits to translocate substrates across the membrane using energy derived from ATP hydrolysis.
E3 ubiquitin ligase TRAF3IP2 (E3_ubiq_ligase_TRAF3IP2)
Type: Family

This family of proteins includes E3 ubiquitin ligases that are involved in 'Lys-63'-linked polyubiquitination, a post-translational modification that enhances protein-protein interactions and cell signaling. Members of this family function as adapter molecules in IL17A-mediated signaling pathways. They are capable of interacting with IL17 receptor chains and catalyzing the polyubiquitination of TRAF6, which is a key step in the activation of NF-kappa-B and MAPkinase pathways. These proteins transfer ubiquitin from E2 ubiquitin-conjugating enzyme complexes to specific substrate proteins, thereby modulating various signaling cascades.
TSC22 domain-containing protein 2 (TSC22_domain_protein_2)
Type: Family

This family of proteins is involved in the regulation of cell growth through the modulation of specific isoforms of nuclear enzymes and transcription factors. Members of this family can reduce the levels of the nuclear PKM isoform M2, leading to the repression of cyclin CCND1 transcription. This action is associated with a decrease in cell proliferation. Additionally, these proteins may play a role in cellular responses to hyperosmotic stress, particularly in kidney cells, by providing a protective function under such conditions. The family is characterized by a shared domain, indicating a common structural feature and evolutionary origin.
Acetolactate synthase regulatory subunit (ALS_regulatory_subunit)
Type: Family

This family of proteins includes regulatory subunits of acetolactate synthase, an enzyme that catalyzes the first step in the biosynthesis of branched-chain amino acids. Members of this family stimulate the activity of the catalytic subunit of acetolactate synthase, significantly enhancing its function. They also play a role in the enzyme's sensitivity to feedback inhibition by valine and are involved in the regulation by ATP. These proteins are found in the mitochondria and are essential for the production of the amino acids leucine, isoleucine, and valine, which are vital for various cellular functions.
Histone deacetylase complex subunit (HDAC_complex_subunit)
Type: Family

This family of proteins includes subunits of the RPD3C(L) histone deacetylase complex (HDAC), which are involved in the removal of acetyl groups from lysine residues on the N-terminal part of core histones such as H2A, H2B, H3, and H4. This deacetylation process is crucial for epigenetic repression, influencing transcriptional regulation, cell cycle progression, and developmental events. Members of this family are also implicated in linking transcriptional coactivators and corepressors, as well as in the regulation of transcription of specific genes through mechanisms involving recruitment of other proteins to promoters and modification of histones.
Imprinting Balance Regulator (Imprinting_Balance_Reg)
Type: Family

This family of proteins includes members involved in the regulation of gene expression through imprinting mechanisms. They play a crucial role in maintaining the balance of parental gene contributions, particularly in the endosperm, which is essential for proper seed development. These proteins are also implicated in postzygotic reproductive isolation by influencing triploid seed development, serving as a component of interploidy hybridization barriers. Their function is dosage-sensitive, indicating that the level of protein expression is key to their role in developmental processes.
WD repeat-containing protein (WD_repeat_protein)
Type: Family

This family of proteins contains WD repeat domains, which are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his (GH) and tryptophan-aspartic acid (WD) dipeptides. Proteins with WD repeats are involved in a variety of cellular processes, including signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly, and may also serve as platforms for protein-protein interactions. The specific functions of WD repeat-containing protein 25 in mice and humans are not detailed in the provided information, but by virtue of the WD repeat domain, these proteins are likely to participate in some of the aforementioned processes.
DNA repair-scaffolding protein (DNA_repair-scaffolding)
Type: Family

This family of proteins is involved in the cellular response to DNA damage, specifically in the repair of double-strand breaks (DSBs) through the homologous recombination (HR) pathway. Members of this family function as scaffolding proteins, facilitating the assembly of DNA repair complexes at sites of damage. They are crucial for the recruitment of key DNA-processing enzymes, including helicases and recombinases, which are essential for the HR process. By doing so, these proteins play a significant role in maintaining genomic stability and preventing the accumulation of DNA errors.
Vacuolar Protein Sorting-Associated 17 (VPS17)
Type: Family

This family of proteins is involved in the endosomal sorting and trafficking pathway. Members play a crucial role in the retrograde transport from endosomes to the Golgi apparatus. They are components of the retromer complex, which is essential for the retrieval of specific cargo proteins, including the vacuolar protein sorting receptor. These proteins are also implicated in the recycling of soluble vacuolar hydrolases, retention of late Golgi membrane proteins, vacuolar biogenesis, and vacuolar maintenance during cellular stress conditions.
Lipid Metabolism-Associated Protein (Lipid_Metab_Assoc_Protein)
Type: Family

This family of proteins may be associated with cellular lipid metabolic processes. The precise functions of these proteins remain to be fully characterized, but they are hypothesized to play a role in the metabolism of lipids, which are crucial components of cell membranes and serve as energy storage molecules. Further research is needed to elucidate the specific activities and mechanisms by which these proteins influence lipid metabolism.
Extra-large GTP-binding protein (XLG_GTP-binding)
Type: Family

This family of proteins includes guanine nucleotide-binding proteins that act as modulators or transducers in various transmembrane signaling systems. They specifically bind GTP and are implicated in the regulation of cell proliferation during root morphogenesis. Additionally, members of this family serve as positive regulators in pathogen resistance, particularly in pathways involving salicylic acid. They are also known to influence the DNA binding activity of certain proteins, thereby activating genes integral to floral initiation.
Mulikevirus tape measure (Mulikevirus_tape_measure)
Type: Family

The Mulikevirus tape measure protein family is involved in the assembly and length determination of bacteriophage tails. Members of this family serve as a scaffold for the polymerization of tail tube proteins, ensuring the correct tail length is achieved. These proteins may also be involved in the ejection process of the phage DNA, potentially being expelled from the tail prior to DNA release during the infection of a host cell.
Inactive Ser/Thr Kinase-like ABA Signaling (Inactive_SerThr-Kinase_ABA)
Type: Family

The protein family includes receptor-like serine/threonine-protein kinases that are involved in abscisic acid (ABA) signaling, particularly in the regulation of stomatal movement in response to various environmental stimuli such as darkness, high CO2, and light stress. Despite the predicted catalytic inactivity of their kinase domains, members of the family function as scaffolding components or may act through phosphorylation of other proteins like the anion channel SLAC1, contributing to stomatal closure. The family is also implicated in local and systemic responses to light stress, and its activity is subject to negative regulation by ABI2.
Cytokinesis Signaling Regulator (Cytokinesis_Signaling_Reg)
Type: Family

This family of proteins is involved in cytokinesis, the process of cell division that results in the separation of a cell into two daughter cells. Members of this family play roles in signaling pathways that regulate cell wall synthesis and actin assembly during this critical phase of the cell cycle. Some proteins in this family function as cofactors that ensure the proper localization of guanine nucleotide exchange factors (GEFs) for key regulatory GTPases, such as RHO1, to specific cellular sites. These GTPases, in turn, activate various effectors necessary for the maintenance of cell wall integrity and successful cytokinesis.
AN1-type zinc finger domain-containing protein (AN1-type_zinc_finger)
Type: Family

This family of proteins includes members that contain AN1-type zinc finger domains. These domains are typically involved in protein-protein interactions and may bind zinc ions to stabilize their structure. Proteins in this family are likely to be involved in various cellular processes, including signal transduction, DNA repair, transcriptional regulation, and ubiquitin-mediated proteolysis. The presence of zinc finger motifs suggests that these proteins may interact with other proteins or nucleic acids, potentially acting as transcription factors or playing a role in the ubiquitin-proteasome system.
Cytochrome P450 84A (CYP450_84A)
Type: Family

This family of proteins includes enzymes that are part of the cytochrome P450 superfamily, known for their role in the oxidative metabolism of a wide range of substrates. Members of this family are involved in various biosynthetic processes, including the conversion of p-coumaraldehyde to caffealdehyde, which is a step in the biosynthesis of arabidopyrones. These proteins are characterized by their ability to catalyze reactions that introduce oxygen into non-activated hydrocarbons, which is a fundamental component of secondary metabolite synthesis in plants.
PWWP domain-containing (PWWP_domain_containing_PDP)
Type: Family

The PDP family is involved in the regulation of flowering in Arabidopsis thaliana. Members of the PDP family, such as PDP2 and PDP5, interact with components of the Polycomb Repressive Complex 2 (PRC2) and influence gene expression by modulating the levels of the histone modification H3K27me3. Through this interaction, they suppress the expression of flowering locus C (FLC), MAF4, and MAF5, which are key repressors of flowering. The PDP family thus plays a crucial role in the transition from vegetative growth to flowering, an essential process for plant reproduction.
Ankyrin repeat and MYND domain-containing protein (Ankyrin-MYND_domain-protein)
Type: Family

This family of proteins includes members that contain both ankyrin repeats and MYND-type zinc fingers. Ankyrin repeats are known to mediate protein-protein interactions, and are typically involved in various cellular processes such as signaling, cell cycle control, and transcriptional regulation. MYND-type zinc fingers are typically involved in protein-protein interactions as well, and are often found in proteins that play roles in chromatin remodeling, transcriptional repression, and developmental processes. Proteins in this family are likely to be involved in the regulation of gene expression through their interaction with other proteins and may have roles in cellular differentiation and development.
Archenteron Induction-Related (Archenteron_Induction-Rel)
Type: Family

This family of proteins includes factors that may play a role in early developmental processes such as gastrulation. Specifically, members of this family have been implicated in influencing the movement of the archenteron, a structure involved in the development of the gut in embryos. The exact mechanisms and the breadth of functions within this family are not fully characterized, as it also includes proteins that are currently uncharacterized and may have diverse roles in cellular processes.
Adhesion G-protein coupled receptor G7 (ADGR_G7)
Type: Family

This family of proteins includes orphan receptors that are part of the G-protein coupled receptor 2 family, specifically within the Adhesion G-protein coupled receptor (ADGR) subfamily. These receptors are characterized by their seven transmembrane domains, typical of G-protein coupled receptors, and are involved in cell adhesion processes. The exact physiological roles of these orphan receptors are not well-defined due to the lack of identified endogenous ligands. However, they are believed to play roles in various biological processes through interactions with other cell surface proteins, extracellular matrix components, or by sensing mechanical changes in the environment.
Sushi domain-containing protein 3 (SUSD3)
Type: Family

This family of proteins may be involved in processes related to breast tumorigenesis, including estrogen-dependent cell proliferation, cellular interactions, and migration. The presence of a sushi domain suggests a potential role in protein-protein or protein-carbohydrate interactions, which could be critical in cell adhesion and signaling pathways.
TVP38/Transmembrane protein 64 (TVP38/TMEM64)
Type: Family

The TVP38/TMEM64 family is involved in the regulation of cell differentiation processes, particularly affecting osteoclast and adipocyte lineage commitment. Family members positively regulate osteoclast differentiation by enhancing TNFSF11-induced calcium signaling pathways, which involve interaction with SERCA2. This interaction is crucial for CREB1 activation and mitochondrial ROS production, essential for osteoclast generation. The calcium spikes in the cytosol and subsequent activation of NFATC1 lead to osteoclast differentiation and activation. Conversely, the TVP38/TMEM64 family negatively regulates osteoblast differentiation and promotes adipocyte differentiation by modulating the canonical Wnt signaling pathway. It influences mesenchymal stem cell fate by downregulating CTNNB1 expression, activity, and nuclear localization, favoring osteogenesis over adipogenesis.
RING-type zinc finger E3 ubiquitin-protein ligase (RING-type_E3_ubiquitin-ligase)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases that are capable of catalyzing the polyubiquitination process. They interact with various ubiquitin-conjugating enzymes (E2s) such as UBC8, UBC10, UBC11, and UBC34 in vitro. The presence of a RING-type zinc finger domain is characteristic of these proteins, which is essential for their interaction with E2 enzymes. Members of this family play a role in the ubiquitin-proteasome pathway, which is a critical mechanism for protein degradation and regulation in eukaryotic cells. The ubiquitination process mediated by these ligases typically tags proteins for degradation, thus controlling protein levels and influencing various cellular processes.
GPCR1-related receptor (GPCR1-related_rcpt)
Type: Family

This family of proteins includes G-protein coupled receptors that interact with diverse ligands to mediate various physiological responses. Members are involved in controlling reproductive behaviors and sleep homeostasis in Drosophila, as well as aversive gustatory associative learning and long-term memory formation in Caenorhabditis elegans. They function by modulating the synaptic output of neurons and activating transcription factors, which are crucial for behavioral adaptations and memory processes.
BEN domain-containing protein 7 (BEN_domain_protein_7)
Type: Family

This family of proteins includes members that contain a BEN domain, which is known to mediate protein-DNA and protein-protein interactions. These interactions are often involved in chromatin organization and gene expression regulation. Proteins with a BEN domain may play roles in various cellular processes, including cell cycle regulation, development, and differentiation. The specific functions of BEN domain-containing protein 7 in humans and mice are not detailed in the provided information, but generally, proteins in this family are likely to be involved in nuclear functions related to chromatin architecture and transcriptional control.
Interleukin-11/Interleukin-27 subunit beta (IL11/IL27_subunit_beta)
Type: Family

Interleukin-27 subunit beta is involved in the formation of IL-27, a heterodimeric cytokine playing a role in innate immunity. IL-27 has both pro- and anti-inflammatory properties, influencing T-helper cell development, suppressing T-cell proliferation, and stimulating cytotoxic T-cell activity. It is pivotal for the differentiation of CD4 T-helper cells into TH1, TH2, and TH17 cells, promoting the rapid expansion of naive CD4 T-cells. IL-27 works synergistically with IL-12 in naive CD4 T-cells to induce interferon-gamma production and binds to the WSX-1/TCCR cytokine receptor. Additionally, it exhibits antitumor and antiangiogenic activities by activating the production of antiangiogenic chemokines .

Interleukins (IL) are a group of cytokines that play an important role in the immune system. They modulate inflammation and immunity by regulating growth, mobility and differentiation of lymphoid and other cells.

Interleukin-11 (IL-11) is a pleiotropic cytokine that stimulates megakaryocytopoiesis, resulting in increased production of platelets, as well as activating osteoclasts, inhibiting epithelial cell proliferation and apoptosis, and inhibiting macrophage mediator production. These functions may be particularly important in mediating the hematopoietic, osseous and mucosal protective effects of IL-11 . The cytokine also possesses anti-inflammatory activity, and has been proposed as a therapeutic agent in the treatment of chronic inflammatory diseases, such as Crohn's disease and rheumatoid arthritis .

Although IL-11 was initially believed to be restricted to mammals, subsequent studies demonstrated it to be expressed in ray-finned fish . Two fish paralogues have now been identified, designated IL-11A and IL-11B .
Nuclear Pore Complex Nucleoporin (NPC_Nucleoporin)
Type: Family

This family of proteins includes components of the nuclear pore complex (NPC), which is essential for the transport of molecules between the nucleus and the cytoplasm. Members of this family, known as nucleoporins (NUPs), serve dual functions as structural elements of the NPC and as interaction partners for nuclear transport factors. They facilitate active directional transport across the NPC by establishing an affinity gradient through Phe-Gly (FG) repeats that interact with transport proteins. These FG repeats are flexible, lack a defined secondary structure, and vary in sequence, spacing, and length. The gradient is maintained by a differential distribution of transport cofactors, which are predominantly associated with GTP in the nucleus and GDP in the cytoplasm. Some family members may also be involved in mitotic spindle assembly and function.
Tumor necrosis factor receptor superfamily member 11A (TNFRSF11A)
Type: Family

This family of proteins includes receptors that are crucial for the process of osteoclastogenesis, which is the formation of osteoclasts. These receptors bind to the ligand TNFSF11/RANKL/TRANCE/OPGL and are essential for the signaling that leads to the differentiation and activation of osteoclasts. They are also involved in the immune system, playing a role in the regulation of T-cell and dendritic cell interactions. The signaling cascade initiated by these receptors includes the activation of transcription factors like NFATC1 and enzymes such as PLCG2, which are important for the transcriptional events and cellular responses necessary for osteoclast development.
WW domain-containing protein (WW_domain_protein)
Type: Family

This family of proteins includes members that contain WW domains, which are known to mediate protein-protein interactions. The WW domains in these proteins specifically recognize and bind to proline-rich motifs that are flanked by arginine and glycine residues in their target proteins. The presence of multiple WW domains suggests a role in signaling pathways where complex formation is mediated by these modular interaction domains. The N-terminal WW domain is particularly adept at binding to these proline-rich ligands, indicating a possible regulatory or scaffolding function where the spatial orientation and specific recognition of binding partners is crucial.
MARVEL domain-containing protein 3 (MARVEL_domain_protein_3)
Type: Family

This family of proteins includes members that are integral components of tight junctions, which are structures that seal the space between adjacent epithelial cells. They are implicated in the regulation of paracellular ion transport across epithelial cell layers. The proteins in this family contain a MARVEL domain, which is associated with processes involving membrane apposition and formation of vesicle-like structures, suggesting a role in membrane trafficking and tight junction assembly or maintenance.