SII-SWORD/CoKE huggingface dataset:
Gal/GlcNAc/GalNAc Sulfotransferase (Gal/GlcNAc/GalNAc_ST)
Type: Family

The Gal/GlcNAc/GalNAc sulfotransferase family is involved in the post-translational modification of glycosaminoglycans and glycoproteins. Members of this family utilize 3'-phospho-5'-adenylyl sulfate (PAPS) as a sulfonate donor to catalyze the transfer of sulfate groups to various carbohydrate residues. This sulfation process is critical for the biosynthesis of chondroitin sulfate, a major component of cartilage, and keratan sulfate, which is essential for corneal transparency. Additionally, the family participates in the creation of SELL ligands, which are crucial for lymphocyte homing and immune surveillance. The enzymes exhibit substrate specificity, sulfating non-reducing ends of oligosaccharides and contributing to the generation of sialylated and sulfated motifs involved in cell signaling and adhesion.
Intracellular Lectin and Glycoprotein Transporter (Intracellular_Lectin-GPT)
Type: Family

This family of proteins includes intracellular lectins that play roles in the early secretory pathway. They are involved in the recognition and transport of glycoproteins, particularly those with specific glycan structures such as high mannose-type glycans, N-acetyl-D-galactosamine, and potentially O-linked glycans. These proteins are implicated in the sorting or recycling of glycoproteins and lipids, and some form complexes that act as cargo receptors for ER-to-Golgi transport. Additionally, members of this family may regulate the export of a subset of glycoproteins from the endoplasmic reticulum and have motifs that are important for their localization and function within the cell.
Serine/threonine-protein phosphatase 4 regulatory subunit 3-like (PP4R3-like)
Type: Family

This family includes Serine/threonine-protein phosphatase 4 regulatory subunit 3 (PP4R3) from Saccharomyces cerevisiae, a core regulatory subunit of the histone H2A phosphatase complex, which dephosphorylates H2AS128ph (gamma-H2A) that has been displaced from sites of DNA lesions in the double-stranded DNA break repair process . Members of this family are involved in various cellular processes, including DNA damage repair, cell cycle checkpoint recovery, and cytoskeletal organization, cell polarity, chemotaxis, gene expression, cytokinesis, and myosin II assembly. Some proteins in this group are also implicated in the localisation of cell fate determinants during cell division and in the exclusion of certain proteins from the nucleus.
PIM Serine/Threonine Kinase (PIM_Ser/Thr_kinase)
Type: Family

The PIM kinase family comprises serine/threonine kinases involved in cell survival, proliferation, and tumorigenesis. Members regulate various cellular processes, including MYC transcriptional activity, cell cycle progression, cap-dependent protein translation, and apoptosis inhibition. They phosphorylate and stabilize MYC, enhancing its activity, and phosphorylate pro-apoptotic proteins such as BAD, reducing apoptosis. PIM kinases also influence cell cycle regulators like CDKN1A/B and CDC25A/C, promoting cell cycle transitions. Their role in tumorigenesis is underscored by their proto-oncogenic activity and ability to mediate survival signaling. Some family members are implicated in energy metabolism, insulin secretion regulation, and drug resistance through ABC transporter activation. Additionally, they may participate in chromatin structure modulation and bone marrow cell homing and migration.
Mediator complex subunit 13 (Mediator_complx_sub13)
Type: Family

The Mediator complex subunit 13 family consists of proteins that are integral components of the Mediator complex, a key coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Members of the family function as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. They are recruited to promoters by direct interactions with regulatory proteins and serve as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Some family members are part of the SRB8-11 complex, a regulatory module of the Mediator complex that may be involved in transcriptional repression of certain genes and may inhibit the association of the Mediator complex with RNA polymerase II. Others may regulate transcription of targets of specific signaling pathways such as Wnt and SHH.
Plant GATA Transcription Factor (GATA_TF)
Type: Family

The GATA transcription factor family is characterized by the presence of type IV zinc-finger domains and is classified within the Class A subfamily. Members of this family function as transcriptional activators, with a specific affinity for binding to 5'-GATA-3' or 5'-GAT-3' motifs found within gene promoters. They play a crucial role in the regulation of gene expression, particularly for genes that are responsive to light. Additionally, some members are involved in developmental processes such as xylem formation in plants. The binding of these transcription factors to DNA is essential for the initiation of transcription and subsequent gene expression, influencing various biological pathways and responses.
UPF0339 domain-containing protein (UPF0339_domain)
Type: Family

This family of proteins is characterized by the UPF0339 domain. The precise biological functions of these proteins are not well-defined. However, proteins with the UPF0339 domain are often found in various bacterial species and may play a role in cellular processes. The domain's presence across different organisms suggests a conserved function, which could be related to cellular metabolism, stress response, or molecular interactions within the cell. Further research is required to elucidate the specific roles and mechanisms of action of UPF0339 domain-containing proteins.
Glycosyltransferase 29 (Glycosyltransferase_29)
Type: Family

The glycosyltransferase 29 family is responsible for the sialylation of glycoproteins and glycolipids, a process critical for various biological functions. Members of this family transfer sialic acid to terminal carbohydrate groups, forming specific sequences that are essential in cell-cell recognition, signaling, and immune responses. They play roles in hemostasis by sialylating plasma proteins like von Willebrand factor, regulating platelet clearance, and contributing to leukocyte extravasation through the biosynthesis of sialyl Lewis X epitopes. Additionally, they are involved in ganglioside biosynthesis, affecting neuronal development and function. The family's enzymes exhibit substrate specificity, mainly acting on structures such as Gal-beta-1,4-GlcNAc, and are implicated in the formation of gangliosides like GM3, influencing cellular processes like proliferation, differentiation, and oncogenesis.
TrkH Potassium Transport (TrkH_K-transport)
Type: Family

The TrkH potassium transport family is involved in the regulation of potassium-sodium homeostasis and the maintenance of the proper sodium/potassium ratio in cells. Members of this family function primarily as potassium transporters, with some also mediating sodium transport. They are characterized by having pore-forming regions that resemble potassium channel selectivity filter motifs. These transporters play critical roles in various physiological processes, including high-affinity potassium uptake, low-affinity potassium transport, sodium exclusion under salt stress, and candidacidal activities. Some members are also implicated in the efflux of chloride ions and other anions, contributing to cellular ion balance and adaptation to environmental stresses.
Formin homology domain-containing protein (Formin_homology_domain)
Type: Family

This family of proteins is involved in the regulation of actin cytoskeleton dynamics. Members of this family are known to nucleate the formation of linear actin filaments, which are essential for various cellular processes including cell shape determination, cell division, and cell signaling. The proteins typically contain domains that regulate their activity through autoinhibitory interactions, which can be released upon binding of activated GTPases, leading to actin filament nucleation and elongation.
Growth Arrest-Specific/Sex Hormone-Binding/Vitamin K-Dependent (GAS-SHBG-PROS)
Type: Family

The protein family includes proteins involved in various biological processes such as cell growth and survival, cell adhesion, cell migration, anticoagulation, steroid hormone regulation, and TGF-beta activation control. Members act as ligands for receptor tyrosine kinases, transport androgens, serve as cofactors in coagulation factor degradation, and regulate TGF-beta in a latent state. They are implicated in endothelial cell survival, cytokine signaling, hepatic regeneration, neuron survival and migration, platelet activation, thrombotic responses, and metabolic clearance rate of steroid hormones.
Cilia- and flagella-associated domain-containing protein (CFAP_domain-containing)
Type: Family

This family of proteins is involved in the structure and function of cilia and flagella, which are cellular appendages that play a critical role in cell motility, fluid movement, and sensory functions. Members of this family are associated with the axoneme, the core skeletal structure of cilia and flagella, and are implicated in the regulation of the assembly and activity of the axonemal inner dynein arm. This suggests a role in the control of ciliary and flagellar beating patterns. Some proteins within this family are also essential for sperm development, indicating a specific function in the reproductive system.
Zona Pellucida Domain Glycoprotein (Zona_Pellucida_Domain_gp)
Type: Family

The Zona Pellucida Domain (ZPD) family includes glycoproteins that are essential components of the zona pellucida, an extracellular matrix that surrounds oocytes. The ZPD family mediates critical reproductive processes such as sperm binding, induction of the acrosome reaction, and prevention of post-fertilization polyspermy. The zona pellucida is typically composed of three to four proteins, including ZP1, ZP2, ZP3, and sometimes ZP4. Members of the ZPD family contribute to the structural integrity of the zona pellucida and may serve as primary or secondary sperm receptors. The ZP domain within these proteins is crucial for the polymerization of ZP proteins, facilitating the formation of the zona pellucida matrix.
Spindly/BICDR Dynein Motor Adapter (Spindly/BICDR_Dynein_Adapter)
Type: Family

The Spindly/BICDR protein family is involved in the regulation of dynein motor activity and cargo transport. Members of this family are essential for the localization of dynein and dynactin to the mitotic kinetochore, controlling the interaction between the kinetochore and spindle microtubules and facilitating the formation of end-on kinetochore-microtubule attachments via the NDC80 complex. They act as adapter proteins, linking dynein to various cargos and enhancing dynein processivity, which is crucial for long-distance movement along microtubules. Additionally, they play roles in correct spindle orientation, cell migration, and neurite outgrowth by regulating secretory vesicle transport in developing neurons.
SWT21/TCAB1 mRNA Splicing and Telomere Maintenance (SWT21/TCAB1_mRNA_Telomere)
Type: Family

The SWT21 family proteins are primarily involved in mRNA splicing, where they help stabilize the U1 snRNP-5' splice site interaction. The TCAB1 family proteins function as RNA chaperones, playing a crucial role in telomere maintenance and RNA localization to Cajal bodies. They recognize and bind the Cajal body box (CAB box) in small Cajal body RNAs (scaRNAs) and telomerase RNA template component (TERC), essential for telomerase holoenzyme complex activity and localization. TCAB1 proteins also contribute to DNA repair by relocalizing to DNA double-strand breaks and recruiting the ubiquitin ligase RNF8 to promote homologous recombination and non-homologous end joining.
Group II Amino Acid Decarboxylase (Group_II_Decarboxylase)
Type: Family

This family of proteins includes enzymes that catalyze the decarboxylation of amino acids. Specifically, members of this family are involved in the biosynthesis of biogenic amines by removing a carboxyl group from their respective amino acid substrates. Some members are known to catalyze the formation of ethanolamine from serine, which is a critical step in the production of important phospholipids like phosphatidylethanolamine (PE) and phosphatidylcholine (PC). These phospholipids are essential for plant growth and membrane formation. Other members of the family are involved in the decarboxylation of histidine, although specific functions for these enzymes are not detailed in the provided annotations. The family belongs to the group II decarboxylase family, indicating a shared evolutionary origin and similar structural features among its members.
Caenorhabditis elegans Orphan Nuclear Receptors (C.elegans_Orphan_NR)
Type: Family

The nuclear hormone receptor family in Caenorhabditis elegans consists of proteins that are classified as orphan nuclear receptors. These proteins share a common structural similarity indicative of their membership in the nuclear hormone receptor superfamily. However, their specific biological functions remain largely unknown as they do not have identified endogenous ligands, hence the term 'orphan'. One member, nhr-127, is suggested to play a probable role in lifespan modulation and immunity. The family's characteristic feature is the ability to act as transcription factors, regulating gene expression in response to hormonal signals, although the exact pathways and target genes for these C. elegans receptors are yet to be elucidated.
Yeast Cell Wall Mannoprotein PIR (Yeast_CWMannoprotein_PIR)
Type: Family

The PIR protein family includes cell wall mannoproteins that are essential components of the outer cell wall layer in yeast. Members of the family play a crucial role in maintaining cell wall stability and integrity, which is vital for optimal yeast growth. They are necessary for the yeast's resistance to various antifungal agents and cell wall-perturbing substances, as well as for tolerance to heat shock. Some family members may also be involved in meiosis and sporulation processes. The defining feature of these proteins is the presence of PIR repeats, which are necessary for the covalent linkage of the proteins to the cell wall, although the number of repeats can vary among different yeast strains.
Prespore-cell-inducing factor (Prespore-cell_inducing_factor)
Type: Family

The prespore-cell-inducing factor family comprises proteins that play a role in the development and differentiation of the social amoeba Dictyostelium discoideum. Members of the family are involved in quorum sensing and the regulation of gene expression in response to cell density. Specifically, they can induce the expression of discoidin genes as cells reach high density, which is crucial for the transition from unicellular to multicellular development when food becomes scarce. Certain family members act as growth factors, triggering the differentiation of isolated amoebae into prespore cells, thus participating in the organism's developmental cycle and adaptation to environmental changes.
Nematode Major Sperm (Nematode_MSP)
Type: Family

The Major Sperm Protein (MSP) family is essential for the motility of sperm cells in nematodes. Members of the MSP family are key components in the molecular mechanisms that facilitate sperm crawling. They achieve this by forming an extensive filament system, which is crucial for the dynamic structure of the sperm cell's pseudopod. This filament system originates from the sperm villipoda and projects along the leading edge of the pseudopod, playing a central role in the cell's ability to navigate and move effectively.
Mitochondrial and Outer Membrane Metalloprotease (Mito/Outer_Membr_Metalloprot)
Type: Family

The protein family includes mitochondrial and outer membrane metalloproteases involved in quality control and stress response. Mitochondrial members act as part of the inner membrane quality control system, cleaving mistranslated or misfolded proteins and regulating mitochondrial dynamics and apoptosis in response to stress. They play roles in the integrated stress response, lipid metabolism, and energy expenditure. Outer membrane members function as chaperones and proteases, maintaining membrane integrity by assembling or eliminating proteins based on their folding state, and are involved in LPS-assembly protein degradation. The family is characterized by a stress-sensor region that regulates proteolytic activity, often activated by autocatalytic cleavage upon mitochondrial depolarization.
Pyruvate Dehydrogenase/Transketolase (PDH/Transketolase)
Type: Family

The protein family includes components of the pyruvate dehydrogenase (PDH) complex, which are responsible for the conversion of pyruvate to acetyl-CoA and CO2, a critical step in cellular respiration. Some family members also exhibit reductase activity with pyruvate. Additionally, the family encompasses transketolase-related proteins involved in various metabolic pathways, including the sulfo-TK pathway and the catabolism of D-apiose. These enzymes facilitate the transfer of glycolaldehyde groups between different sugar phosphates, playing a vital role in carbohydrate metabolism.
Metallophosphoesterase superfamily (Metallophosphoesterase_sf)
Type: Family

The metallophosphoesterase family encompasses enzymes that hydrolyze phosphoester bonds. Members of this family are involved in various biological processes, including the biosynthesis of lipid A, a component of the lipooligosaccharide that is essential for the structural integrity of the outer membrane in certain bacteria. Some family members, such as LpxG, specifically catalyze the hydrolysis of the pyrophosphate bond of UDP-2,3-diacylglucosamine, yielding 2,3-diacylglucosamine 1-phosphate and UMP. This reaction is a key step in the lipid A biosynthetic pathway. Other members of the family have been characterized as phosphodiesterases, indicating a broader role in phosphodiester bond cleavage. The family includes both characterized and uncharacterized proteins, with some members containing transmembrane domains, suggesting diverse functions and localizations within the cell.
Hexapeptide-repeat containing acetyltransferases (Hexapeptide_acetyltransf)
Type: Family

The protein family is characterized by a group of acetyltransferases that share a common feature of belonging to the transferase hexapeptide repeat family. Members of this family are involved in various biochemical processes, including the O-acetylation of Nod factors, capsular polymeric sialic acid, and sophorolipids, as well as the acetylation of maltose, glucose, and other sugars. Some proteins within this family have been implicated in the biosynthesis of lipopolysaccharides and colanic acid. The family exhibits a range of substrate specificities and biological functions, with some members having a role in the regulation of host cell processes, such as peroxisome homeostasis during mycobacterial infection. The commonality among these proteins is their enzymatic activity, which involves the transfer of an acetyl group from acetyl-CoA to various substrates, a key step in the modification of molecules that can affect their stability, recognition, and biological activity.
Membrane Fusion Protein (MFP) Efflux (MFP_Efflux)
Type: Family

The Membrane Fusion Protein (MFP) family consists of periplasmic linker proteins that are components of various efflux pumps. These proteins are involved in the transport of a wide range of substrates, including organic solvents, antibiotics, dyes, detergents, and other toxic compounds. The efflux activity is often driven by a proton gradient and is crucial for conferring resistance to these substances. Some family members are specific to certain substrates like toluene and styrene, while others have broad specificity. The MFPs may also play roles in quorum-sensing and secretion of siderophores. They are typically part of tripartite efflux systems that span the entire cell envelope, linking inner membrane transporters with outer membrane channels.
Mannose-6-phosphate isomerase type 2 (Mannose-6P_isomerase_type2)
Type: Family

The mannose-6-phosphate isomerase type 2 family includes enzymes primarily involved in the biosynthesis of GDP-mannose, which serves as a precursor for mannose residues in cell surface polysaccharides. Members of this family are implicated in the production of components critical for bacterial virulence, such as capsular polysaccharides, lipopolysaccharide O antigens, and alginate layers. These components contribute to the formation of protective barriers against host immune defenses and antibiotics, and are also involved in the biosynthesis of exopolysaccharides like xanthan, which have applications in various industries. The broad substrate specificity of some family members highlights a potential for diverse functional roles in bacterial carbohydrate metabolism.
Type IV secretion system component (T4SS_component)
Type: Family

This family of proteins includes components of type IV secretion systems (T4SS), which are multiprotein complexes that translocate a wide range of substrates across cell membranes in bacteria. Members of this family are involved in various processes such as the secretion of toxins, the transfer of DNA, and the translocation of effector proteins into host cells. They play a role in bacterial conjugation, virulence, and adaptation to different environments by facilitating horizontal gene transfer. Some family members are ATPases, providing the energy required for the transport of substrates through the T4SS. They are also involved in the assembly and stabilization of the secretion system's structural components.
Sodium:Solute Symporter (SSF) (Sodium:Solute_Symporter_SSF)
Type: Family

The Sodium:Solute Symporter (SSF) family is involved in the electrogenic transport of various substrates across cell membranes, utilizing a sodium gradient as the driving force. Members of this family transport a diverse range of molecules, including multivitamins (biotin, pantothenate), monocarboxylates (lactate, pyruvate, short-chain fatty acids), and inorganic ions (iodide, chloride, bromide, nitrate). The transport process is typically coupled to the co-transport of sodium ions, often with specific stoichiometries, which can be either 2:1 or 4:1 Na+:substrate. This family plays essential roles in nutrient uptake in the intestine, maintaining intestinal mucosa integrity, thyroid function through iodide transport, and energy status in neurons by transporting ketone bodies and lactate. Some members also have a regulatory role in cancer cell proliferation.
NmrA-like oxidoreductase (NmrA-like_oxidored)
Type: Family

The NmrA-like family is composed of redox sensor proteins that undergo structural and subcellular changes in response to intracellular NADPH/NADP(+) levels. These proteins can exist as monomers or dimers, with their oligomeric state influenced by NADPH concentrations. As monomers, they interact with argininosuccinate synthase, inhibiting nitric oxide synthesis and preventing apoptosis. As dimers, they bind NADPH, which is necessary for dimer stability. The family also includes proteins involved in the regulation of nitrogen metabolite repression and the biosynthesis of various secondary metabolites, such as mycotoxins, indole diterpenes, fungal indole alkaloids, and piperazines. These biosynthetic processes involve complex enzymatic reactions including prenylation, cyclization, hydroxylation, methylation, and redox reactions, contributing to the production of bioactive compounds with potential pharmaceutical relevance.