SII-SWORD/CoKE huggingface dataset:
Non-receptor Tyrosine-protein Phosphatases (NonRcpt_TyrProt_Phosphatase)
Type: Family

The protein family includes tyrosine-protein phosphatases that are non-receptor types and are involved in various cellular processes. Members of the family are targeted to sites of actin polymerization in response to extracellular stimuli and exhibit tyrosine phosphatase activity towards tyrosyl phosphorylated substrates. Some family members negatively regulate apoptosis induced by FAS and NGFR-mediated pro-apoptotic signaling, potentially through the dephosphorylation of PIK3R2 and regulation of PI3K signaling. Additionally, a member of the family may play a role in tight junction formation and binds to phosphatidylinositol 3,4-bisphosphate, which is necessary for localization to the basolateral cell membrane. The family's involvement in these processes highlights their role in cell signaling and structural organization.
Heme exporter protein D (Heme_exporter_D)
Type: Family

This family of proteins is involved in the transport of heme, an essential cofactor for various biological processes. Members of this family are responsible for exporting heme to the periplasmic space in bacterial cells, where it is utilized for the assembly of c-type cytochromes. These cytochromes play a crucial role in electron transport and energy conservation during cellular respiration. The proper functioning of this protein family is therefore integral to the biogenesis of these important components of the respiratory chain.
Transient receptor potential cation channel (TRP_cation_channel)
Type: Family

This family of proteins includes receptor-activated non-selective cation channels that play a central role in the detection of pain, temperature, and other sensations. They are involved in various physiological processes such as pain response to inflammatory mediators, cold perception, oxygen concentration perception, cough, itch, and inner ear function. These proteins show a preference for divalent cations over monovalent ones and can be activated by a wide range of chemical compounds, including electrophilic and non-electrophilic ligands. Some family members are also implicated in cannabinoid signaling and mechanosensitive transduction in hair cells, contributing to sound perception. They are regulated by various factors, including inositol polyphosphates and cytosolic factors, and can be inhibited by specific blockers.
Cell Cycle Regulator and Phase Variation Mediator (CcrZ_PhaseVar_Mediator)
Type: Family

The protein family is involved in cell cycle regulation and chromosome integrity. Members of the family activate DnaA-dependent chromosomal DNA replication initiation, ensuring timely replication during the cell cycle. They may regulate replication initiation through phosphorylation of potential second messengers or metabolites and by interacting with replication initiation proteins. Some family members exhibit ATPase activity with D-ribose and 2-deoxy-D-ribose. They are also involved in the DNA damage response. Additionally, certain members mediate phase variation of lipopolysaccharide (LPS) and lipooligosaccharide (LOS) epitopes in bacteria, which is determined by a translational switch. This phase variation contributes to the evasion of host immune responses.
Trehalose Metabolism Glycosyltransferase (Trehalose_Metab_GTase)
Type: Family

This family of proteins includes enzymes involved in the metabolism of trehalose, a disaccharide sugar. Members of this family are capable of synthesizing trehalose through a reversible reaction, predominantly from ADP-glucose and glucose, although some can also use UDP-glucose or GDP-glucose. The equilibrium of this reaction generally favors trehalose synthesis. Additionally, certain members can reversibly catalyze the synthesis and degradation of trehalose from glucose and alpha-D-glucose 1-phosphate. The activity of these enzymes can be modulated by various metal ions, with some enhancing or inhibiting the enzymatic function.
E3 ubiquitin-ligases/Copine domain-containing protein (E3_ligase/Copine_domain)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases and copine domain-containing proteins. The E3 ubiquitin-protein ligases are involved in various cellular processes, including the modulation of hormone signaling pathways such as jasmonate and abscisic acid, which are crucial for plant responses to stress and developmental cues. They function by mediating the ubiquitination and subsequent proteasomal degradation of specific target proteins, thus regulating protein levels within the cell. The copine domain-containing proteins are implicated in muscle development, particularly in the assembly of dense bodies and M lines, by recruiting various components to integrin-mediated attachment sites. Collectively, these proteins play significant roles in cellular signaling, protein turnover, and structural organization.
von Willebrand factor C/EGF & Fibrillin (vWF_C/EGF_Fibrillin)
Type: Family

The von Willebrand factor C and EGF domain-containing protein family includes regulatory elements in signaling pathways, structural components of the extracellular matrix, and regulators of growth factor bioavailability. Members of this family are involved in the beta-catenin signaling pathway and may play a role in the prevention of hepatocellular carcinoma. Fibrillin-1 and -2 are crucial for the structural integrity and regulatory functions of microfibrils in connective tissues, influencing tissue homeostasis, osteoblast maturation, and osteoclastogenesis. They also interact with growth factors and integrins, contributing to cell adhesion and microfibril assembly. Latent-transforming growth factor beta-binding proteins control TGF-beta activation, maintaining it in a latent state and regulating its activation. The family's diverse functions include structural support, regulation of cell differentiation, and interaction with hormones that influence glucose metabolism and appetite.
Dispatched hedgehog regulator (Dispatched_Hh_regulator)
Type: Family

This family of proteins is involved in the hedgehog (Hh) signaling pathway. Members of this family play a crucial role in regulating the release and extracellular accumulation of cholesterol-modified hedgehog proteins, which is essential for the effective production of the Hh signal. Some family members have been shown to synergize with SCUBE2 to enhance the secretion of SHH, a ligand in the Hh signaling pathway. The function of these proteins is critical for various developmental processes and cellular communication.
Peripheral myelin sheath structural protein (Myelin_sheath_structural)
Type: Family

This family of proteins includes scaffolding components that are essential for the structural integrity and function of myelinated nerves. They play a crucial role in the maintenance of the peripheral myelin sheath, which is crucial for efficient nerve impulse transmission and sensory perception. These proteins are involved in the transport of specific mRNAs and are necessary for remyelination after nerve injury. They also contribute to the elongation of Schwann cells and the proper spacing of nodes of Ranvier, affecting the speed of nerve impulse conduction. Additionally, they participate in the formation of specific cytoplasmic structures in myelinated nerves and are implicated in recruiting other proteins to the Schwann cell membrane. In the eye lens fiber cells, they are part of complexes that maintain proper cell morphology and plasma membrane composition.
Aminoacylase-1 peptidase M20A (Aminoacylase-1_M20A)
Type: Family

The Aminoacylase-1 family is characterized by its enzymatic function in catalyzing the hydrolysis of N-acetylated amino acids, resulting in the release of acetate and free amino acids. This reaction is a key step in the metabolism of acetylated amino acids, which are not only intermediates in the degradation of proteins but also play roles in various metabolic pathways. The family is part of the peptidase M20A family, indicating a shared structural fold and catalytic mechanism among its members. The enzymes in this family are involved in the breakdown of N-acylated or N-acetylated amino acids, with the exception of L-aspartate, which is not a substrate for these enzymes. The Aminoacylase-1 family is conserved across various species, including humans, mice, rats, pigs, and the organism Dictyostelium discoideum, highlighting its fundamental role in nitrogen metabolism.
Spliceosome-associated SF3B4 subunit (SF3B4_spliceosome_assoc)
Type: Family

This family of proteins is involved in the splicing of pre-mRNAs, a critical step in gene expression. Members of this family are components of the spliceosome, particularly the 17S U2 small nuclear ribonucleoprotein (snRNP) complex. They play a role in early spliceosome assembly and in recognizing the intron branch site during splicing. This recognition is crucial for selecting the branch-site adenosine, which acts as the nucleophile in the first step of splicing. The proteins are part of the SF3B subcomplex, which is necessary for the formation of the 'A' complex by stabilizing the binding of U2 snRNP to the pre-mRNA. Their binding upstream of the branch site is sequence-independent and may serve to anchor the U2 snRNP to the pre-mRNA. Additionally, they are implicated in the assembly of the 'E' complex and participate in the minor spliceosome responsible for splicing U12-type introns.
WD repeat, SAM and U-box domain-containing (WD-SAM-U-box)
Type: Family

The WD repeat, SAM and U-box domain-containing protein family is characterized by the presence of WD repeats, SAM, and U-box domains. Members of this family are involved in protein-protein interactions and cellular processes. The U-box domain suggests that these proteins may function as E3 ubiquitin ligases, which play a crucial role in ubiquitination, a process that tags proteins for degradation by the proteasome or alters their activity and localization. Ubiquitination is essential for various cellular functions, including cell cycle regulation, DNA repair, and signal transduction. The presence of WD repeats and SAM domains indicates that these proteins may also be involved in the assembly of protein complexes or in intracellular signaling pathways.
Mannan Polymerase Complex Subunit (Mannan_Polymerase_Subunit)
Type: Family

This family of proteins is involved in the biosynthesis of the mannan backbone of N-linked glycans, which are essential components of cell wall and periplasmic proteins. Members of this family exhibit alpha-1,6-mannosyltransferase activity, playing a crucial role in the elongation process of the mannan chains. Some proteins within this family may also contribute alpha-1,2-mannosyltransferase activity. Additionally, certain members are implicated in the organization of the secretory pathway and the maintenance of Golgi apparatus functionality. Regulatory functions have also been attributed to this family, including the regulation of protein phosphorylation that may be important for cell growth control and response to environmental stress such as vanadate exposure.
Ribosomal RNA-processing protein RRP12 (RRP12)
Type: Family

Ribosomal RNA-processing protein 12 (RRP12) proteins are members of pre-ribosome-associated HEAT repeats-containing proteins . They are involved in the maturation and nuclear export of both pre-40S and pre-60S ribosomal subunits. They are required for the processing of RNA components within pre-ribosomes, which is a critical step in the assembly of functional ribosomes. They are associated with the late maturation of the 18S and 5.8S rRNA of the pre-40S ribosomes and for maturation of the 25S and 5.8S rRNA of the pre-60S ribosomes .
E3 ubiquitin-protein ligase SINA (E3_ubiquitin-ligase_SINA)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases that are involved in the ubiquitination and subsequent proteasomal degradation of various target proteins. They contain a RING-type zinc finger domain crucial for their ligase activity and a substrate-binding domain (SBD) that mediates homodimerization and interaction with substrates, related to the TRAF family. These proteins play significant roles in plant physiological processes such as response to auxin signals, formation of lateral roots, autophagy, and stress responses including drought tolerance and abscisic acid-mediated stomatal closure.
Ankyrin repeat and BTB/POZ domain-containing protein (Ankyrin-BTB/POZ_domain)
Type: Family

This family of proteins includes members that contain ankyrin repeats and a BTB/POZ domain, suggesting a role in protein-protein interactions. Some members are implicated in cellular processes such as the initiation of hepatocyte growth, indicating a potential involvement in liver function and possibly regeneration. The presence of ankyrin repeats typically confers flexibility and adaptability in various molecular functions, including signal transduction, cell-cycle control, and transcriptional regulation. The BTB/POZ domain is known to mediate homomeric dimerization and heteromeric interactions with other proteins, which may be crucial for the assembly of multiprotein complexes. Together, these domains contribute to the diverse roles these proteins may play in cellular physiology.
Cytolytic pore-forming toxin (Cytolytic_pore-forming_toxin)
Type: Family

This family of proteins includes toxins that exhibit a range of biological activities, primarily associated with cytolytic functions. They are capable of forming pores in cell membranes, leading to hemolytic activity. These proteins are known to interact with erythrocytes, inducing potent hemolysis and displaying cardiovascular effects, such as vasorelaxation potentially via the L-arginine-nitric oxide synthase pathway. They also have edema-inducing properties, increase vascular permeability, show myotoxicity, and interfere with neuromuscular function. Some family members are known to induce platelet aggregation in certain mammals and increase neurotransmitter release at neuromuscular junctions. Their structure typically includes domains homologous to MACPF/CDC, FAT, thioredoxin, and B30.2/SPRY, which contribute to their interaction with cell membranes and structural integrity.
Beta-alanine Activation and Resistance (Beta-ala_Activ/Resist)
Type: Family

The Beta-alanine-activating enzyme family is involved in the ATP-dependent activation of beta-alanine, a process that forms a thioester bond with the enzyme's phosphopantetheine group. The activated beta-alanine is then transferred to an unknown acceptor, which may be part of a post-translational protein modification or post-transcriptional RNA modification pathway. Additionally, a member of the family catalyzes the condensation of beta-alanine with tryptamine, producing a pheromone essential for stimulating female sexual development during pairing. Another family member is implicated in providing resistance to desiccation and radiation, potentially by protecting genomic integrity under extreme conditions. Overall, the family encompasses enzymes with diverse functions, including activation of beta-alanine, synthesis of nonribosomal peptides, and stress response mechanisms.
Splicing Factor 3A Subunit 2 (SF3A2)
Type: Family

The SF3A2 family is involved in the critical process of pre-mRNA splicing, which is essential for the removal of introns from transcribed pre-mRNAs. Members of the SF3A2 family are components of the 17S U2 SnRNP complex within the spliceosome. They play a pivotal role in early spliceosome assembly and in recognizing the intron branch site during splicing. This recognition is crucial for selecting the branch-site adenosine, which serves as the nucleophile in the first step of splicing. The SF3A2 family is also part of the SF3A subcomplex, which is necessary for the formation of the pre-spliceosome 'E' complex and the pre-catalytic spliceosome 'A' complex. Additionally, they are involved in the constitution of pre-catalytic spliceosome 'B' complexes, including the Bact complex, further underscoring their importance in the splicing pathway.
Homologous Recombination Repair Mediator (HR_Repair_Mediator)
Type: Family

This family of proteins is involved in the homologous recombination (HR) pathway of DNA repair, specifically in the repair of double-stranded DNA breaks that may arise during DNA replication or as a result of DNA-damaging agents. Members of this family participate in the formation of RAD51 foci in response to DNA damage, indicating a role in the early stages of HR, likely during the invasion step. They are also implicated in the phosphorylation of checkpoint kinase CHEK2, contributing to cell cycle arrest and HR activation. These proteins are components of RAD51 paralog protein complexes, such as BCDX2 and CX3, which function at different stages of the BRCA1-BRCA2-dependent HR pathway. They are involved in branch migration and Holliday junction resolution, essential for processing HR intermediates. Additionally, they contribute to DNA cross-link resistance, sister chromatid cohesion, genomic stability, and the maintenance of centrosome number during mitosis.
Pre-mRNA-splicing and ERAD-associated protein (Pre-mRNA-splicing_ERAD)
Type: Family

This family of proteins includes members that are involved in pre-mRNA splicing, a fundamental process in gene expression where introns are removed and exons are joined to form a mature mRNA transcript. Some members of this family are also implicated in the endoplasmic reticulum-associated protein degradation pathway (ERAD), which is responsible for the disposal of misfolded proteins in the endoplasmic reticulum. Additionally, certain proteins within this family may play a role in the regulation of transcription, specifically by negatively affecting the transcription of thyroglobulin, which is mediated by the PAX8 transcription factor.
UNC-13 domain-containing protein (UNC-13_domain)
Type: Family

This family of proteins is involved in various intracellular trafficking processes, including endosome to Golgi retrograde transport, and the regulation of secretory lysosome exocytosis. Members of this family play a crucial role in cytotoxic granule exocytosis in lymphocytes, which is essential for immune response. They are required for granule maturation, docking, and priming at the immunologic synapse. These proteins also regulate the assembly of recycling and late endosomal structures, leading to the formation of an endosomal exocytic compartment that fuses with granules at the immunologic synapse. Additionally, they are involved in the maturation and exocytosis of secretory lysosome-related organelles, particularly in tracheal development and neuronal signaling. They may interact with SNARE fusion receptors and membrane phospholipids in response to calcium influx, influencing neurotransmitter and hormone secretion, which can affect behavior and food intake.
Endocannabinoid-regulating amidase (Endocannabinoid_amidase)
Type: Family

This family of proteins includes enzymes that hydrolyze endogenous amidated lipids, such as the endocannabinoid anandamide and other fatty amides, to their corresponding fatty acids. This hydrolytic activity regulates the signaling functions of these molecules, which are involved in various physiological processes including sleep induction, pain modulation, and inflammation. Some family members also hydrolyze monoacylglycerides like 2-arachidonoylglycerol, influencing the degradation of endocannabinoid-related monoacylglycerides. Additionally, these enzymes cooperate with PM20D1 in the hydrolysis of amino acid-conjugated fatty acids, acting as physiological regulators of specific subsets of intracellular N-fatty acyl amino acids. They play roles in longevity, resistance to oxidative stress, and axon regeneration after injury. The family is characterized by its membership in the amidase enzyme family and is subject to inhibition by various compounds.
SET and MYND domain-containing protein (SET-MYND_domain_protein)
Type: Family

This family of proteins includes SET and MYND domain-containing proteins that are implicated in epigenetic regulation. Members of this family are characterized by their dual activities as methyltransferases and as negative regulators of HDAC1. They play a crucial role in cardiac development by regulating gene expression through their epigenetic modification capabilities. The SET domain suggests a role in chromatin remodeling, while the MYND domain indicates potential protein-protein interactions. Collectively, these proteins are vital for proper heart formation and function.
Presynaptic Scaffold Protein Bassoon/Piccolo (Presynaptic_Scaffold_Bsn/Pclo)
Type: Family

The protein family functions as scaffold proteins at the presynaptic cytomatrix of the active zone (CAZ), a key site for neurotransmitter release. They are involved in the formation of Piccolo-Bassoon transport vesicles (PTVs), which are essential for synaptic contact development. At the CAZ, they organize synaptic vesicle clusters and regulate membrane fusion and endocytosis. Beyond assembly, they interact with proteins like SIAH1 and ATG5 to modulate presynaptic protein ubiquitination and autophagy. They also play a role in synapse to nucleus signaling, affecting gene expression by associating with transcriptional corepressor CTBP1, influencing its nuclear import.
Diverse Regulatory Transcription Factors (Regulatory_TF_Diverse)
Type: Family

The protein family encompasses transcription factors that regulate various biological processes, including carbohydrate metabolism, sterol synthesis, filamentous growth, and virulence in response to environmental cues such as oxygen levels and nutrient availability. Members of the family are involved in the activation of gene clusters for biosynthesis of compounds like gramillins and glycolytic enzymes, and in the regulation of processes like biofilm formation, hyphal growth, and cellular differentiation. They bind to specific DNA motifs to modulate gene expression, contributing to the organism's adaptability and pathogenicity.
Synaptic vesicle ATPase and mitochondrial regulator (SV-ATPase_mito-regulator)
Type: Family

This family of proteins includes members that exhibit ATPase activity and are involved in cellular processes such as calcium-regulated keratinocyte activation during epidermal repair mechanisms. They do not influence cell proliferation but are implicated in the negative regulation of mitochondrial fusion, often in cooperation with mitofusin proteins. Additionally, these proteins may play a central role in the functions mediated by specific classes of synaptic vesicles.
Plant Stress Response Kinase (Plant_StressResp_Kinase)
Type: Family

The protein family in question is characterized by its members' involvement in various signaling pathways related to plant stress responses and growth regulation. Members of the family function as kinases, with some acting as serine-threonine kinases and others as tyrosine kinases. They play roles in hypersensitive response signaling, abscisic acid signaling for drought tolerance, and oxidative burst-mediated signaling. The family includes kinases that are activated by different stimuli, such as phosphatidic acid, xylanase, hydrogen peroxide, and flagellin, indicating a broad spectrum of functions related to plant defense and adaptation.
Enkurin domain-containing protein (Enkurin_domain-protein)
Type: Family

This family of proteins includes microtubule-binding proteins that play a role in the organization and stability of microtubules. They are involved in the localization of calcium-sensitive signal transduction machinery in sperm and are essential for the beating of motile cilia by being part of the dynein-decorated doublet microtubules in the cilia axoneme. These proteins also contribute to the assembly of both primary and motile cilia by facilitating the removal of specific proteins from the mother centriole, which is a prerequisite for ciliogenesis. Additionally, they are implicated in the orientation of the mitotic spindle and the oriented division of keratinocytes, which is important for epidermal stratification.