SII-SWORD/CoKE huggingface dataset:
Pyruvate/Ketoisovalerate Oxidoreductase Gamma Subunit (Oxidoreductase_gamma_subunit)
Type: Family

This family of proteins includes subunits of pyruvate and ketoisovalerate oxidoreductases, which are key enzymes in the central metabolism of various microorganisms. These enzymes catalyze the oxidative decarboxylation of pyruvate and ketoisovalerate to acetyl-CoA and isobutyryl-CoA, respectively, which are important intermediates in the energy metabolism and biosynthesis of cellular components. The common subunit gamma is likely involved in the electron transfer process within the enzyme complex. One member of this family is also known to function in the anaerobic metabolism of phenylalanine and phenylacetate, catalyzing the oxidative decarboxylation of phenylglyoxylate to benzoyl-CoA, and can utilize various electron acceptors, indicating a potential for diverse metabolic roles.
SLIT-ROBO Rho GTPase-activating (SLIT-ROBO_RhoGAP)
Type: Family

The SLIT-ROBO Rho GTPase-activating protein family is involved in neuronal morphogenesis, migration, and synapse maturation, particularly in the cerebral cortex. Members of the family act as GTPase-activating proteins (GAPs) for RAC1, CDC42, and potentially other small GTPases, influencing actin dynamics and cell migration. They play roles in regulating synapse density and maturation in cortical neurons, with some members also affecting cell migration in non-neuronal cells. The family includes a human-specific member that modifies cortical connectivity by inhibiting ancestral paralog functions, leading to increased synaptic density and maturation. Members share an F-BAR domain that mediates oligomerization, membrane binding, and induction of plasma membrane protrusions. Some members also interact with postsynaptic scaffolding proteins, contributing to synapse development. The family's activity is modulated by heterodimerization and proteasome-dependent degradation, influencing synaptic and cortical circuit connectivity.
Linear Ubiquitination-Associated E3 Ligases (LUBAC_E3_Ligases)
Type: Family

The protein family is involved in the regulation of various cellular processes through ubiquitination. Members function as E3 ubiquitin-protein ligases, accepting ubiquitin from E2 enzymes and transferring it to substrates. They play a crucial role in the NF-kappa-B signaling pathway, inflammation regulation, and innate immunity. The family is part of the LUBAC complex, which conjugates linear polyubiquitin chains to substrates, mediating NF-kappa-B activation and protecting against TNF-induced cell death. They also participate in xenophagy by forming a ubiquitin coat on bacteria, signaling for degradation. Additionally, they regulate the Wnt signaling pathway during angiogenesis and are involved in synaptic plasticity, spermatogenesis, and antiviral responses.
Sulfite Efflux Tellurite-Resistance Transporter (Sulfite_efflux_TDT)
Type: Family

This family of proteins includes transporters that are involved in the efflux of sulfite, a reducing agent. The efflux activity is crucial for various organisms, including yeasts and dermatophytes, as it contributes to resistance against environmental stresses such as the presence of sulfite and the immune response during infection. In dermatophytes, the efflux of sulfite is also linked to the degradation of keratin-rich tissues, facilitating infection of the epidermal stratum corneum, hair, and nails. The proteins are implicated in the detoxification pathway and are associated with the tellurite-resistance/dicarboxylate transporter family, indicating a broader role in resistance to toxic compounds.
Transcriptional Corepressor and Histone Demethylase (Corepressor-Demethylase)
Type: Family

This family of proteins includes transcriptional corepressors and histone demethylases. The corepressors are involved in gene repression through the formation of complexes that recruit histone deacetylases, leading to a repressive chromatin structure and direct interference with the transcriptional machinery. They play roles in various physiological processes and are essential for normal growth and development. The histone demethylases are involved in the dynamic regulation of histone methylation, specifically demethylating 'Lys-27' of histone H3, which is a key modification in the histone code. These enzymes are implicated in developmental processes by regulating HOX gene expression, and they also participate in inflammatory responses and macrophage differentiation. Some members of this family have additional roles in chromatin remodeling independent of their demethylase activity.
Ankyrin repeat and KH/SAM domain-containing protein (Ankyrin-KH/SAM_domain)
Type: Family

This family of proteins includes members that are involved in various cellular processes such as receptor tyrosine kinase signaling, cell cycle and DNA regulation, innate immune defense against viruses and bacteria, and vascular and renal function maintenance. Some proteins in this family act as scaffolding proteins, potentially influencing the phenotype of leukemia cells and regulating apoptosis. The ankyrin repeats within these proteins are crucial for binding to specific partners, indicating a role in protein-protein interactions. The presence of SAM domains suggests additional interaction capabilities, which may be important for cellular signaling pathways.
Rho guanine nucleotide exchange factor (Rho_GEF)
Type: Family

This family of proteins includes Rho guanine nucleotide exchange factors (GEFs) that activate Rho-GTPases by facilitating the exchange of GDP for GTP. They play a pivotal role in various cellular processes such as cell motility, polarization, cytoskeletal dynamics, and signal transduction pathways. These proteins are involved in focal adhesion formation, axonal branching, synapse formation, dendritic morphogenesis, and B-lymphocyte activation. Some members are implicated in innate immune responses, acting as signaling intermediaries and participating in cytokine secretion. They also contribute to cell cycle regulation, apoptosis, and cancer progression. Additionally, they are involved in the development and differentiation of neuronal progenitor cells and the migration of precerebellar neurons. Certain members function as scaffold proteins, assembling signaling complexes downstream of G protein-coupled receptors, and are involved in cardiac hypertrophy and osteogenesis.
Acetate Uptake Transporter (AceTr)
Type: Family

The acetate uptake transporter family is involved in the transport of acetate and ammonia across the cell membrane. Members of the family play various roles in cellular metabolism and regulation, including the uptake of acetate for biosynthesis processes, such as the production of mycotoxins like patulin, and the export of ammonia. Some proteins in the family are implicated in the adaptation of cell metabolism to utilize acetic acid, potentially affecting membrane ATPases and the repression of glyoxylate cycle enzymes. Others are involved in meiotic processes or are upregulated in response to specific cellular conditions, such as the absence of mitochondrial DNA. The family's functions are essential for the regulation of metabolic pathways and cellular responses to environmental changes.
Extended Synaptotagmin (Extended_Synaptotagmin)
Type: Family

The Extended Synaptotagmin family is involved in tethering the endoplasmic reticulum to the cell membrane and promoting the formation of appositions between these two cellular structures. Members of the family bind glycerophospholipids within a barrel-like domain, which may play a significant role in cellular lipid transport. The family's C2 domains are responsible for mediating lipid and calcium binding, with the N-terminal C2 domain being crucial for calcium-dependent lipid binding and membrane interaction. These proteins are capable of binding multiple calcium ions with varying affinities and are essential for translocating to the cell membrane in response to increased cytosolic calcium levels. Additionally, some members are implicated in FGF signaling, particularly in the rapid internalization of FGFR1 upon FGF1 binding, which is likely facilitated by the AP-2 complex. This function is crucial for normal embryonic development and downstream signaling cascades.
Serotonin N-acetyltransferase-like (SNAT-like)
Type: Family

This family of proteins is involved in the regulation of circadian rhythms through the synthesis of melatonin, a hormone that signals night and day cycles to the body. Members of this family catalyze the N-acetylation of serotonin to produce N-acetylserotonin, which is then converted to melatonin in the pineal gland. Some members may also acetylate other substrates such as polyamines and arylalkylamines, suggesting a broader role in cellular regulation through the modification of biogenic amines.
Plant lipid transfer/defense-related protein (Plant_LTP/defense-related)
Type: Family

This family of proteins includes lipid transfer proteins (LTPs) that are likely involved in the transport of lipid molecules. They may play roles in improving plant freezing survival, controlling flowering and lignin synthesis, and conferring resistance to certain pathogens like Botrytis cinerea and Pseudomonas syringae. Some members are implicated in systemic acquired resistance (SAR) and induced systemic resistance (ISR), suggesting a function in plant immunity. These proteins may also be involved in early seedling development under stress conditions and exhibit anti-fungal activity, potentially by affecting membrane permeability.
Ankyrin repeat domain-containing protein 49 (Ank_repeat_dom-contain_49)
Type: Family

The Ankyrin repeat domain-containing protein 49 family is involved in various cellular processes. Members of this family play roles in spermatogenesis, promoting autophagy in response to serum starvation through the NF-kappaB pathway. They are also implicated in the regulation of planar cell polarity, particularly in the wing, by forming complexes that stabilize partners and promote the activity of key signaling molecules during polarity establishment. Additionally, some family members are involved in the regulation of gene expression, such as inducing HBG1 expression. The family includes proteins that function independently of their canonical roles, such as acting as chaperones in the assembly of the 26S proteasome and participating in signal transduction pathways like the EGF-induced AKT activation. They also have roles in tumorigenesis, apoptosis, and the regulation of tumor suppressors and transcription factors.
C-terminal-binding dehydrogenase (CTBP_dehydrogenase)
Type: Family

This family of proteins functions as corepressors that interact with various transcription regulators, influencing gene expression. Members exhibit dehydrogenase activity and are involved in the regulation of the Golgi complex's structure. They play a significant role in the differentiation of brown adipose tissue (BAT). Some isoforms act as scaffolds at specialized synapses. Additionally, certain family members are implicated in lifespan regulation and lipid metabolism through gene repression.
Box C/D snoRNA (BCD1)
Type: Family

The BCD1 family proteins are essential for the accumulation of box C/D small nucleolar RNAs (snoRNAs). They play a crucial role in snoRNA processing, which is a fundamental step in the maturation of ribosomal RNAs (rRNAs). Additionally, these proteins are involved in the transport of snoRNAs to the nucleolus, a subnuclear structure where rRNA synthesis and ribosome assembly occur. The proper function of BCD1 family members is necessary for efficient ribosome biogenesis, a process critical for protein synthesis in all cells.
GRB10-interacting GYF (GRB10-interact_GYF)
Type: Family

The GIGYF family proteins are involved in the regulation of translation initiation and mRNA decay. They are key components of the 4EHP-GYF2 complex, which represses translation initiation by sequestering the mRNA cap, thus blocking ribosome initiation and reducing the translational load on problematic messages. This complex also links translation repression with mRNA decay by recruiting decapping effector proteins and the deadenylation CCR4-NOT complex. GIGYF proteins may cooperate with GRB10 to modulate tyrosine kinase receptor signaling, including IGF1 and insulin receptors. They are implicated in ribosome-associated quality control (RQC) by sequestering faulty mRNA, working downstream of ZNF598. Additionally, GIGYF proteins are involved in cellular responses to stress, such as starvation-induced autophagy, and play a role in maintaining tissue homeostasis. In the context of viral infection, GIGYF proteins can affect the translation of genes involved in the antiviral immune response.
RGK GTP-binding regulators (RGK_GTP-binding_reg)
Type: Family

This family of proteins includes GTP-binding members that are implicated in various cellular processes, including signal transduction, regulation of voltage-dependent L-type Ca(2+) currents, and cardiac function. Some proteins in this family have been shown to interact with the plasma membrane and may participate in receptor-mediated signaling pathways. They exhibit guanine nucleotide-binding activity and are characterized by a low intrinsic GTPase activity or undetectable GTPase activity. Additionally, these proteins may play roles in the regulation of heart rate, contractile force, and cardiac hypertrophy, as well as in the trafficking of calcium channel subunits to the cell membrane. They may also be involved in actin cytoskeletal reorganization and angiogenesis, suggesting a broad functional spectrum within cellular and physiological contexts.
Regulatory protein SWI6-like (SWI6-like)
Type: Family

This entry represents Regulatory protein SWI6 from Saccharomyces cerevisiae and similar fungal proteins involved in the regulation of the cell cycle, particularly in the transition between different phases. Members of this family function as components of complexes that are essential for cell-cycle-dependent transcription. They are known to bind specific DNA sequences, such as the cell cycle box (CCB) and Mlu I cell cycle box (MCB), to regulate the expression of genes critical for cell cycle progression. These proteins play roles in the initiation of DNA synthesis, acting as transcriptional activators at certain cell cycle stages and as repressors at others. Some members are implicated in the regulation of mitotic and meiotic divisions, sexual differentiation, rRNA production, and stress response regulation.
Transcriptional Regulators with Zinc Finger Domains (Transcr_Reg_ZincFinger)
Type: Family

The protein family is involved in transcriptional regulation, linking histone methyltransferases to corepressor machinery and regulating gene expression in response to extracellular amino acid levels. Members are synthesized as latent cytoplasmic precursors, activated by specific sensor systems, and then translocate to the nucleus to induce expression of regulated genes. Some members contain C2H2-type zinc fingers mediating interactions with other proteins, while others have inhibitory domains for cytoplasmic retention and negative regulation of transcription.
TRAMP complex component and AT-rich DNA-binding protein (TRAMP_AT-DNA-binding)
Type: Family

This family of proteins includes components of the TRAMP and TRAMP5 complexes, which exhibit poly(A) RNA polymerase activity. They are implicated in a post-transcriptional quality control mechanism that restricts the expression of genetic information that is deemed inappropriate. These proteins are involved in the polyadenylation and subsequent degradation of various nuclear RNA substrates, including cryptic transcripts and hypomethylated pre-tRNAi-Met, by the exosome. Some family members also play a role in inhibiting the methylation of specific proteins, such as NPL3, by interacting with methyltransferases. Additionally, there are members with potential DNA-binding properties, particularly to AT-rich regions, suggesting a possible function in transcription regulation.
PER33/POM33 transmembrane regulator (PER33/POM33_regulator)
Type: Family

This family of proteins is involved in various cellular processes, including the regulation of the tubular endoplasmic reticulum network and intracellular calcium homeostasis. They play roles in the unfolded protein response signaling, angiogenesis, innate immune signaling, and lipid metabolism. Some family members are essential for the proper distribution and assembly of nuclear pores, while others contribute to cytokinesis by influencing the actomyosin ring assembly. They interact with various proteins such as RNF26 and RNF5, modulating processes like polyubiquitination and degradation of target proteins.
N-terminal NatB acetyltransferase catalytic subunit (NatB_acetyltransferase_subunit)
Type: Family

This family of proteins functions as the catalytic subunit of the NatB N-terminal acetyltransferase complex. Members are responsible for the acetylation of N-terminal methionine residues in nascent polypeptides that start with certain amino acids, including aspartate, glutamate, asparagine, and glutamine. This modification can influence the stability, localization, and function of the proteins. In some species, these proteins are involved in the regulation of actomyosin fibers, cellular migration, and cell cycle. Additionally, in plants, they play a role in immunity through the regulation of specific protein stability.
Mediator complex subunit 12 (Mediator_comp_sub12)
Type: Family

The Mediator complex subunit 12 family comprises proteins that are integral components of the Mediator complex, serving as coactivators in the regulated transcription of RNA polymerase II-dependent genes. These proteins act as bridges, relaying information from gene-specific regulatory proteins to the basal transcription machinery. They are involved in the recruitment of the Mediator complex to gene promoters, facilitating the assembly of a functional preinitiation complex with RNA polymerase II and general transcription factors. Members of this family may specifically regulate transcription in pathways such as Wnt signaling and SHH signaling. They play roles in various developmental processes, including body axis formation, brain, ear, kidney, limb development, neural crest formation, pigmentation, and vulval induction. Additionally, they are implicated in asymmetric cell division and hypodermal development.
Cell Wall Integrity and Assembly Regulator (CWI-Assembly_Regulator)
Type: Family

This family of proteins is involved in the structural integrity and assembly of cell walls, particularly in the formation of the mannoprotein outer layer. Members of this family play a role in maintaining cell wall integrity, which is crucial for cell survival and growth. Some proteins within this family are important for apical bud growth in yeast, while others are implicated in the repair mechanisms in response to cell wall damage. Additionally, certain family members are required for the organization of the beta-glucan layer of the spore wall during meiosis, indicating a role in reproductive processes.
CUT Homeobox Domain-Containing Protein (CUT_Homeobox)
Type: Family

This family of proteins includes transcriptional activators that bind to specific DNA consensus sequences to regulate gene expression. Members of this family are involved in various biological processes, including liver gene transcription, sex determination, X chromosome dosage compensation, and cell-fate specification. They recognize and bind to distinct DNA motifs, which can vary slightly among different family members, to modulate the transcription of target genes such as HNF3B and TTR. Some proteins within this family are also implicated in the development of the endoderm and may have differential DNA-binding affinities based on target sequences and protein isoforms.
Strigolactone signaling regulator (SL_signaling_regulator)
Type: Family

This family of proteins is involved in the regulation of plant growth and development processes, particularly in response to environmental signals such as strigolactones and karrikins. Members act as components of transcriptional corepressor complexes, repressing the signaling pathways that control various aspects of plant physiology including tiller development, seedling growth, and branching control. They also play roles in modulating reactive oxygen species levels, abscisic acid-dependent stomatal closure, photosynthesis, and ion homeostasis. The proteins contain EAR motifs, which are associated with active repression of target genes, and some have ATPase activity.
DMTF1 DNA-binding transcriptional regulators (DMTF1_DNA-bind_reg)
Type: Family

The DMTF1 family comprises DNA-binding proteins involved in transcriptional regulation and replication termination. Members of this family function as transcriptional activators, recognizing specific DNA sequences to regulate gene expression. For instance, they activate the CDKN2A/ARF locus in response to signaling pathways, promoting growth arrest through p53/TP53. Some family members bind to rDNA terminator elements, mediating RNA polymerase I transcription termination and contributing to rDNA stability. Others may have roles in cell integrity and transcription of RNA binding proteins. The family includes proteins that may stimulate or inhibit transcription, recognizing enhancer and promoter sites of rRNA transcription and other genes transcribed by RNA polymerase II. They are also involved in genome partitioning and may act as chromatin insulators.
MDM2/MDM4 and MUL1 (MDM2_MDM4_MUL1)
Type: Family

The MDM2/MDM4 and MUL1 family includes proteins that regulate cell cycle arrest and apoptosis, as well as mitochondrial morphology and localization. Members of the family, such as MDM4, inhibit TP53 and TP73, preventing cell cycle arrest and apoptosis by binding their transcriptional activation domains. They also inhibit the degradation of MDM2 and can reverse MDM2-targeted degradation of TP53, while suppressing TP53 transactivation and apoptotic functions. MUL1 proteins, on the other hand, exhibit E3 ubiquitin-protein ligase activity, accepting ubiquitin from E2 enzymes and transferring it to substrates. They play roles in mitochondrial dynamics, promoting fragmentation and influencing localization. MUL1 proteins also ubiquitinate and regulate proteins like AKT1 and TP53, and are involved in immune defense by modulating antiviral responses. The family is characterized by the presence of zinc finger domains and, in some members, RING finger domains that mediate specific protein interactions.
E3 ubiquitin-protein ligase and sorting receptor (E3_ligase_sorting_rcpt)
Type: Family

This family of proteins is involved in various cellular processes including protein ubiquitination, signaling pathway regulation, protein trafficking, and cellular growth control. Members of this family function as E3 ubiquitin-protein ligases, catalyzing the attachment of ubiquitin to substrate proteins, thereby targeting them for degradation or altering their cellular location and function. They play roles in the regulation of the TORC1 signaling pathway through polyubiquitination of specific proteins, influencing nutrient response and growth regulation. Some members are also implicated in the sorting and trafficking of proteins to vacuoles, acting as sorting receptors. Additionally, they are involved in synaptic transmission regulation and endosomal trafficking by mediating ubiquitination of receptors and vesicular proteins. The family includes proteins that regulate lysosome positioning and are involved in the G1/S transition of the cell cycle.