SII-SWORD/CoKE huggingface dataset:
E3 ubiquitin-protein ligase RING-type (E3_ubiquitin-ligase_RING)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases that are involved in the ubiquitination process. Members of this family catalyze the attachment of ubiquitin to substrate proteins, typically through 'Lys-48'-linked polyubiquitination, which targets the substrates for proteasomal degradation. This process is crucial for various cellular functions, including protein turnover, signal transduction, and the regulation of other cellular processes. Some members are known to interact with specific proteins to maintain cellular homeostasis, such as ensuring appropriate levels of proteins involved in apoptotic cell clearance. The family also includes proteins with RING finger domains, which are characteristic of many E3 ubiquitin ligases and are important for their ligase activity.
SL1/TIF-IB Complex Component (SL1/TIF-IB_Component)
Type: Family

This family of proteins includes components of the SL1/TIF-IB complex, which plays a crucial role in the initiation of RNA polymerase I-dependent transcription. These proteins are key in the formation of the pre-initiation complex (PIC) by associating with the rDNA promoter, a process that is essential for the transcription of ribosomal RNA genes. They also contribute to the stabilization of nucleolar transcription factor 1 (UBTF) on rDNA. Additionally, their presence in the SL1/TIF-IB complex prevents the binding of TATA box-binding protein (TBP) with TFIID subunits, thus influencing the overall transcription machinery.
UPF0654 domain-containing protein (UPF0654_domain)
Type: Family

This family of proteins may be involved in the protection of dormant spores from desiccation and could play a role in the formation or survival of specific fungal reproductive structures such as microconidia and ascospores. Members of this family are characterized by a shared domain, indicating a potential commonality in function or structure among the proteins.
Acrosomal SP-10-like (Acrosomal_SP-10-like)
Type: Family

This family of proteins is involved in the reproductive process, specifically within the acrosome reaction of sperm cells. Acrosomal proteins are known to play a role in the binding and penetration of the sperm into the egg during fertilization. They are typically associated with the acrosome, an organelle that caps the anterior part of the sperm head and contains enzymes that, when released, facilitate the sperm's passage through the protective layers surrounding the oocyte. The members of this family are characterized by their presence in the acrosome and are implicated in sperm-egg recognition and interaction, which are critical steps in the fertilization process.
Type I Cytokine Receptor Family, Type 2 Subfamily (Type1_Cytokine_Rcpt_Type2)
Type: Family

The Type I Cytokine Receptor family, Type 2 subfamily, includes receptors that play crucial roles in immune system regulation and defense mechanisms. Members of this family are receptors for interleukins, such as IL27 and IL23, and mediate signal transduction through the Jak-Stat signaling pathway. They are involved in the regulation of Th1-type immune responses and may participate in both innate and adaptive immunity. These receptors are essential for responding to infections in peripheral tissues and may be implicated in autoimmune inflammatory diseases and tumorigenesis. The family is characterized by the presence of specific motifs such as the box 1 motif, necessary for JAK interaction and activation, and the WSXWS motif, important for protein folding, intracellular transport, and cell-surface receptor binding.
Ni-sirohydrochlorin a,c-diamide reductive cyclase complex, CfbD (Ni-siroh_cyclase_CfbD)
Type: Family

The NifD/NifK/NifE/NifN family is involved in the biosynthesis of coenzyme F430, essential for methanogenesis and anaerobic methane oxidation. Members catalyze the reduction and gamma-lactamization of Ni-sirohydrochlorin a,c-diamide, producing seco-F430, a precursor to coenzyme F430.
Selenoprotein SelWTH-like (SelWTH-like)
Type: Family

This family of proteins may play a role in redox processes, which are chemical reactions involving the transfer of electrons. These reactions are fundamental to numerous metabolic pathways and cellular functions, including the detoxification of harmful compounds, the synthesis of certain biomolecules, and the regulation of oxidative stress. One member of the family is also implicated in developmental processes, such as salivary gland morphogenesis in a model organism. The proteins in this family are characterized by their similarity to the SelWTH family, suggesting a conserved structure or function across different species.
Zinc finger translocation-associated & Spindlin interactor (ZnF_transloc-Spindlin_int)
Type: Family

The Zinc finger translocation-associated and Spindlin interactor and repressor of chromatin-binding protein family is involved in the regulation of gene expression and response to DNA damage. Members of the family negatively regulate the transcriptional activator activity of SPIN proteins by inhibiting their ability to bind methylated histones, thereby repressing the expression of SPIN-regulated genes and the activation of the Wnt signaling pathway. They can inhibit the histone methyl-binding abilities of multiple SPIN proteins. Additionally, they positively regulate poly-ADP-ribosylation following DNA damage by enhancing PARP1 ADP-ribosyltransferase activity.
Zinc-sensing G-protein coupled receptor (Zinc-sensing_GPCR)
Type: Family

This family of proteins functions as zinc-sensing receptors that detect changes in extracellular zinc ion concentrations. They are involved in transmitting zinc signals and play a role in various physiological processes, including the regulation of glucose homeostasis, gastrointestinal mobility, hormone secretion, and cell survival. Upon zinc activation, these proteins can increase intracellular calcium levels and activate key signaling pathways such as ERK/MAPK and PI3K/AKT, which contribute to epithelial repair and normal wound healing. They also influence adipose tissue metabolism by regulating lipolysis and the activity of specific lipases. Additionally, these receptors help protect cells from different types of stress by promoting the secretion of cytoprotective factors. They are capable of forming heteroreceptor complexes with other receptors, which can either enhance or inhibit signaling pathways, depending on the cellular context.
Dinucleoside polyphosphate hydrolase (Dinucleoside_ppp_hydrolase)
Type: Family

This family of proteins exhibits a multifaceted enzymatic activity, including the hydrolysis of dinucleoside polyphosphates such as Ap3A and Ap4A into AMP and ADP or ADP and AMP, respectively. They also show adenylylsulfatase activity, converting adenosine 5'-phosphosulfate into AMP and sulfate, and adenosine 5'-monophosphoramidase activity, hydrolyzing purine nucleotide phosphoramidates to AMP and ammonia. Additionally, they can catalyze the ammonolysis of adenosine 5'-phosphosulfate and other substrates. Beyond their catalytic roles, these proteins modulate transcriptional activation by CTNNB1, influencing cell proliferation and survival gene expression. They are involved in apoptosis through SRC and AKT1 signaling pathways and inhibit MDM2-mediated degradation of p53/TP53, contributing to p53/TP53-mediated apoptosis. Their tumor suppressor function is linked to their ability to bind specific nucleotide compounds, independent of their catalytic activity.
Organic solute transporter beta subunit (OST-beta_subunit)
Type: Family

This family of proteins includes essential components of the Ost-alpha/Ost-beta complex, which functions as a heterodimeric intestinal basolateral transporter. These proteins are responsible for the export of bile acids from enterocytes into portal blood, with a higher efficiency for transporting taurine-conjugated bile acids compared to glycine-conjugated ones. They also facilitate the enterohepatic circulation of sterols by transporting various steroids, including estrone 3-sulfate and dehydroepiandrosterone 3-sulfate. Additionally, they can transport eicosanoids like prostaglandin E2. These proteins interact with SLC51A, influencing its glycosylation, membrane trafficking, and stability, which are critical for the formation and function of the Ost-alpha/Ost-beta complex at the cell membrane surface.
Cell Proliferation Regulator (Cell_Prolif_Regulator)
Type: Family

This family of proteins is implicated in cellular growth processes, with a potential role in the regulation of cell proliferation. The members of this family are conserved across various species, suggesting a fundamental biological function related to cell division and growth regulation.
Glycoprotein Hormones Alpha Subunit (Glyco_Hormone_Alpha)
Type: Family

This family of proteins functions as heterodimeric glycoprotein hormones that are involved in the regulation of thyroid cell metabolism. Members of this family can bind and activate the thyroid-stimulating hormone receptor (TSHR), which leads to an increase in cyclic AMP (cAMP) production. This signaling pathway is crucial for controlling the metabolic processes within thyroid cells.
CRISPR-associated Cas7/Cst2/DevR (CRISPR-Cas7/Cst2/DevR)
Type: Family

This family of proteins is involved in the CRISPR adaptive immune system, which provides defense mechanisms against mobile genetic elements such as viruses, transposable elements, and conjugative plasmids. Members of this family are associated with the processing of CRISPR clusters into CRISPR RNA (crRNA), which contains sequences that are complementary to those of invading nucleic acids, thereby targeting them for degradation or interference. These proteins play a crucial role in the immunity provided by the CRISPR system by participating in the recognition and cleavage of foreign genetic material.
Marginal zone B- and B1-cell-specific protein (MZB1)
Type: Family

This family of proteins is involved in the immune response by associating with immunoglobulin M (IgM) heavy and light chains to promote IgM assembly and secretion. They may function as molecular chaperones or oxidoreductases, given their low level of oxidoreductase activity. These proteins play a role in diversifying peripheral B-cell functions through the regulation of calcium stores, antibody secretion, and integrin activation. Additionally, they are implicated as hormone-regulated adipokines/pro-inflammatory cytokines, contributing to chronic inflammation, cellular expansion, and the modulation of insulin response in adipocytes, which may be linked to the development of insulin resistance.
Ciliary Microtubule Inner Protein 2A (CIMIP2A)
Type: Family

This family of proteins is involved in the structural integrity and function of cilia. Members are thought to be microtubule inner proteins that are part of the dynein-decorated doublet microtubules within the flagellum axoneme. These proteins likely play a role in the stability and movement of cilia by interacting with the microtubules, which are essential components of the ciliary structure.
Podoplanin domain-containing protein (Podoplanin_domain)
Type: Family

This family of proteins mediates various cellular processes including cell migration, adhesion, and morphological changes. They play a crucial role in the separation of blood and lymphatic vessels during development by interacting with CLEC1B, which leads to platelet activation. They also modulate platelet aggregation through interaction with CD9. These proteins are involved in epithelial-mesenchymal transition by interacting with cytoskeletal proteins such as MSN and EZR, which results in RHOA activation and increased cell invasiveness. They are responsible for fibroblastic reticular cells' adhesion and contraction within lymph nodes, as well as for the relaxation of these cells through engagement with CLEC1B. Additionally, they participate in the connection of lymphatic endothelium to the extracellular matrix and control the stability and maturation of invadopodia in tumor cells, affecting the degradation of the extracellular matrix. They are essential for normal lung cell proliferation and alveolus formation at birth. Notably, they do not function as water channels or affect the transport of folic acid or amino acids.
Apoptosis Repressor CARD Domain-Containing Protein (Apoptosis_Repressor_CARD)
Type: Family

This family of proteins functions as apoptosis repressors, playing a critical role in blocking multiple modes of cell death. They inhibit both extrinsic and intrinsic apoptotic pathways by interacting with key components such as FAS, FADD, CASP8, and BAX. These interactions prevent the assembly of death-inducing signaling complexes, limit the availability of soluble caspases, and inactivate pro-apoptotic factors to prevent mitochondrial dysfunction. Additionally, they serve as cytosolic calcium buffers, maintaining calcium homeostasis and protecting against calcium-mediated cell death. They also have a role in negatively regulating apoptosis in response to oxidative stress, hypoxia, and TNF-induced necrosis. Through their apoptosis-repressing activities, they contribute to vascular remodeling by promoting cell proliferation and inhibiting apoptosis under hypoxic conditions. Furthermore, they are implicated in inhibiting myoblast differentiation.
Cancer-associated gene 1 homolog (CAGE1_homolog)
Type: Family

This family of proteins is associated with cancer-related processes. Members of this family are homologous and share a common function in cellular mechanisms that may contribute to the development or progression of cancer. The exact molecular function and biological role of these proteins remain to be fully elucidated, but they are named for their association with cancer. As homologs across different species, they likely play a conserved role in cell biology that could be relevant to oncogenesis or tumor biology. Further research is necessary to determine the specific activities and interactions of these proteins within the cell.
Succinate Dehydrogenase Assembly Factor 1 (SDHAF1)
Type: Family

The SDHAF1 subfamily is involved in the assembly of succinate dehydrogenase (SDH), a key enzyme complex in both the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain. It facilitates the oxidation of succinate to fumarate and the reduction of ubiquinone to ubiquinol. The family plays a crucial role in the maturation of the iron-sulfur protein subunit SDHB, protecting it from oxidative damage and promoting iron-sulfur cluster incorporation. Members of the family bind to SDHB and recruit the iron-sulfur transfer complex, which includes HSC20, HSPA9, and ISCU, to assist in the assembly process. The SDHAF1 subfamily may also work in concert with SDHAF3 to ensure proper SDH function.
Gamma-glutamyltransferase (Gamma-glutamyltransfase)
Type: Family

The gamma-glutamyltransferase family is characterized by its enzymatic ability to hydrolyze and transfer gamma-glutamyl moieties from glutathione and other gamma-glutamyl compounds to various acceptors. The enzymatic activity of the family members is crucial for the metabolism of glutathione, which plays a significant role in cellular antioxidant defense, detoxification processes, and the regulation of various cellular functions. By facilitating the breakdown and resynthesis of glutathione, the gamma-glutamyltransferase family contributes to maintaining the homeostasis of intracellular glutathione levels, which is essential for protecting cells against oxidative stress and maintaining redox balance.
Fanconi anemia core complex-associated protein (FA_core_complex_assoc)
Type: Family

This family of proteins is involved in the cellular response to DNA damage, specifically in the repair of DNA interstrand cross-links (ICLs). Members of this family possess a UBZ2-type zinc finger domain that preferentially binds 'Lys-63'-linked polyubiquitin, a post-translational modification often associated with DNA repair pathways. These proteins are essential components of the Fanconi anemia (FA) complex, a multiprotein assembly that plays a pivotal role in the recognition and repair of ICLs. Upon DNA damage, they bind ubiquitin chains generated at the site of damage, facilitating the recruitment of the FA complex to enable repair. Additionally, they interact with translesion synthesis machinery, such as the REV1 protein, to promote DNA synthesis across damaged templates, thereby contributing to genomic stability.
Antho-RFamide neuropeptide (Antho-RFamide)
Type: Family

This family of proteins includes Antho-RFamide neuropeptides which are likely transcriptional transactivators and potential neuromuscular transmitters. They share similarity to the FARP (FMRFamide related peptide) family, suggesting a role in neuronal signaling or modulation. One member is known to bind DNA at the transcription initiation site and upstream sequences of a specific promoter, thereby activating transcription. Other members, while their exact functions are not fully elucidated, are hypothesized to act as transmitters at neuromuscular synapses.
Sperm Maturation Cystatin (Sperm_Mat_Cystatin)
Type: Family

The Cystatin family is characterized by its members' role in sperm development and maturation. Cystatins are known to be involved in the regulation of protease activity, which is crucial for various physiological processes including the modulation of sperm maturation. Members of this family, such as Cystatin-8 and Cystatin-13, are suggested to have specialized functions during this developmental stage, although the exact mechanisms of action remain to be fully elucidated. The family's involvement in reproductive biology highlights its importance in fertility and the potential for targeted therapeutic interventions in cases of male infertility.
DVL/RTFL small polypeptides (DVL_RTFL_polypeptides)
Type: Family

The DVL/RTFL small polypeptides family comprises regulatory molecules that play a crucial role in coordinating cellular responses essential for plant differentiation, growth, and development. Members of the family are involved in restricting polar cell proliferation within lateral organs and orchestrating the recruitment and differentiation of socket cells at trichome sites, thereby contributing to the precise formation and patterning of plant structures.
Yeast Multidrug Resistance Regulatory Proteins (Yeast_MDR_Regulatory)
Type: Family

This family of proteins includes zinc finger transcription factors and other regulatory proteins involved in the control of gene expression related to multidrug resistance. Members of this family are known to regulate the transcription of various genes, including those encoding ATP-binding cassette (ABC) transporters, major facilitator superfamily transporters, and other components that contribute to the cellular response to different drugs and toxic compounds. Some proteins within this family function in a coordinated manner to modulate the expression of genes that confer resistance to a broad range of substances, thereby playing a crucial role in cellular detoxification processes.
Mitochondrial uS3-like protein (Mt_uS3-like)
Type: Family

This family of proteins includes uncharacterized mitochondrial proteins from Arabidopsis thaliana. One member is similar to the universal ribosomal protein uS3, suggesting a role in mitochondrial ribosome function. Ribosomal protein uS3 is known to be involved in the initiation of protein synthesis and may have additional roles in RNA processing and repair. The exact functions of the other family members remain to be elucidated, but their mitochondrial localization implies a role in mitochondrial biogenesis, energy metabolism, or the regulation of mitochondrial gene expression.
Kinetoplast-associated DNA-binding (Kinetoplast-DNA-binding)
Type: Family

This family of proteins includes histone H1-like DNA-binding proteins that are involved in the organization and segregation of kinetoplast DNA (kDNA), a unique mitochondrial DNA structure found in kinetoplastid protozoa. These proteins bind to specific fragments of minicircle DNA and play a crucial role in maintaining the highly organized compact disk structure of the kDNA network. Through DNA charge neutralization and condensation, they are able to compact the kDNA networks, which consist of thousands of minicircles and dozens of maxicircles catenated together.
Coiled-coil domain-containing protein (Coiled-coil_domain)
Type: Family

This family of proteins contains a coiled-coil domain, which suggests that they may be involved in facilitating protein-protein interactions. The presence of a glutamate-rich region indicates a potential for interactions with other proteins or nucleic acids, possibly through electrostatic interactions. These features are often found in proteins that play roles in cellular structure, signaling, and regulation. The exact functions of this family of proteins may vary among different organisms and could be involved in diverse biological processes such as gene expression regulation, cell division, or intracellular trafficking. Further experimental evidence would be required to determine the specific roles of these proteins in cellular physiology.
FNIP repeat-containing protein (FNIP_repeat)
Type: Family

This family of proteins contains FNIP repeats, which are typically involved in protein-protein interactions. Members of this family may play roles in various cellular processes, including signal transduction, cell adhesion, and the regulation of transcription and translation. The FNIP repeat is a structural motif that may mediate complex formation with other proteins, contributing to the functional diversity of the proteins within this family. The specific functions of the individual members may vary, reflecting the diverse biological contexts in which these proteins operate.
Molybdenum Cofactor Utilization and Processing (MoCofactor_Util/Proc)
Type: Family

The protein family in question is involved in the utilization and processing of the molybdenum cofactor, a critical component for the activity of various enzymes. Members of the family have functions that include oxidizing purines such as hypoxanthine and xanthine to uric acid, and acting as chaperones for the insertion of the molybdenum cofactor into other subunits of enzyme complexes. The family appears to be involved in stabilizing certain enzyme subunits and may play a role in recruiting the molybdenum cofactor. Additionally, one member is known to bind the molybdopterin cytosine dinucleotide form of the molybdenum cofactor, indicating a direct interaction with this essential cofactor.
Carbohydrate kinase PfkB-like (Carb_kinase_PfkB-like)
Type: Family

This family of proteins includes enzymes that are involved in carbohydrate metabolism, specifically in the phosphorylation of various sugar derivatives. Members of this family are known to catalyze the phosphorylation of 2-keto-3-deoxy sugars, playing a role in different metabolic pathways. Some enzymes in this family are involved in galactose catabolism, converting 2-keto-3-deoxygalactonate to its phosphorylated form, while others participate in the semi-phosphorylative Entner-Doudoroff pathway, phosphorylating 2-keto-3-deoxygluconate. The catalytic efficiency and substrate specificity can vary among family members, with some showing a preference for specific substrates over others.