SII-SWORD/CoKE huggingface dataset:
RNA Processing and DNA Damage Response Regulator (RNA_Proc_DNA_Dmg_Regulator)
Type: Family

This family of proteins is involved in various aspects of RNA processing and DNA damage response. Members play a role in pre-mRNA splicing, particularly in the excision of introns with certain features, such as weak 3'-splice sites and high GC content. They are implicated in ribosome biogenesis through the cleavage of rRNA precursors, mediated by specific binding to non-coding RNAs like snoRNAs. Additionally, these proteins contribute to the maintenance of genomic integrity by inhibiting translesion DNA synthesis, a process that counteracts replication stress caused by DNA damage, such as that induced by ultraviolet light. This inhibition is achieved by preventing the monoubiquitination of proliferating cell nuclear antigen (PCNA), a key factor in DNA replication and repair. The family includes proteins with domains that suggest DNA-binding capabilities, ubiquitin-like folds, and motifs for interacting with PCNA.
AlkB Family tRNA Methyltransferase/Dioxygenase (AlkB_tRNA_MeTrf/Diox)
Type: Family

The AlkB family proteins are involved in the post-transcriptional modification of tRNA, specifically at the wobble position of the anticodon loop. They catalyze the methylation of 5-carboxymethyl uridine to 5-methylcarboxymethyl uridine, with a preference for tRNA(Arg) and tRNA(Glu), and are also capable of hydroxylating 5-methylcarboxymethyl uridine to form 5-(S)-methoxycarbonylhydroxymethyluridine, with a preference for tRNA(Gly). These modifications are crucial for the proper decoding of mRNA during protein synthesis. Additionally, some members of the family may play roles in stress response, DNA damage survival, apoptosis inhibition, cell survival, and angiogenesis. The family includes proteins with tumor suppressor activity, promoting the expression of genes involved in cell cycle regulation.
CD225/Dispanin domain-containing protein (CD225/Dispanin)
Type: Family

This family of proteins is involved in various cellular processes including the regulation of glucose uptake and transport, synaptic transmission, and neurotransmitter release. Members of this family modulate the recycling of glucose transporters in response to insulin, are implicated in maintaining pools of neurotransmitter receptors necessary for synapse development and function, and may play roles in regulating the function of voltage-gated sodium channels and synaptic facilitation. They are associated with the regulation of AMPA receptor function and expression, and may influence the final steps of neurotransmitter release by modulating calcium sensing and SNARE complex formation.
Transketolase-like (Transketolase-like)
Type: Family

This family of proteins is involved in the pentose phosphate pathway, a metabolic pathway parallel to glycolysis. They catalyze the transfer of two-carbon units by transferring a ketol group from a ketose donor to an aldose acceptor, forming a covalent intermediate with the cofactor thiamine pyrophosphate. This reaction is crucial for the synthesis of nucleotides and the generation of reducing power in the form of NADPH. Some members of this family are also implicated in cell proliferation and carcinogenesis, suggesting a role beyond their enzymatic activity in the metabolism of cancer cells. They are essential for maintaining the activity of the transketolase enzyme complex and have been linked to the regulation of neural progenitor cells during fetal neocortex development.
Formin Homology (Formin_Homology)
Type: Family

The Formin Homology protein family is involved in the regulation of the actin cytoskeleton, playing a crucial role in actin nucleation and the formation of linear actin filaments. Members of this family interact with Rho GTPases and are important for processes such as cell migration, filopodia formation, and the establishment of cell polarity. They participate in signaling pathways like the Wnt pathway, influencing developmental processes including dorsal patterning, left/right symmetry, and myocardial maturation. Some members act as scaffolding proteins, linking signaling molecules to the actin cytoskeleton, and are involved in the formation and maintenance of cilia and the organization of the subapical actin network in multiciliated cells. The family's domains, such as the FH2 and DAD domains, are key to their function, with the DAD domain regulating activation through autoinhibitory interactions that are relieved upon binding of activated GTPases, allowing actin filament elongation.
Peflin/Sorcin Calcium-Binding (Peflin/Sorcin_CaBP)
Type: Family

The Peflin/Sorcin family comprises calcium-binding proteins that function as adapters, bridging unrelated proteins or stabilizing weak protein-protein complexes in response to calcium. Members of the family are involved in various cellular processes, including ER-Golgi vesicular transport, endosomal biogenesis, membrane repair, and apoptosis. They play roles in cellular signaling pathways, such as inhibiting angiogenesis by affecting the Akt signaling pathway. The family proteins contain EF-hand domains, with some members having high-affinity calcium-binding sites and others binding magnesium. The proteins interact with a variety of partners through hydrophobic pockets, which are exposed upon calcium binding, facilitating translocation to membranes and involvement in processes like collagen export and vesicle formation.
Nectin and Nectin-like (Nectin/Nectin-like)
Type: Family

The Nectin family is involved in various cell-cell adhesion processes. Members of this family mediate adhesion through homophilic and heterophilic interactions, which can include specific interactions between different nectins. These interactions are crucial for the formation of cell-cell junctions, including adherens junctions and synapses. Some family members act as receptors for viruses, facilitating entry into cells, while others are involved in neurite outgrowth by interacting with growth factor receptors. Additionally, the family plays roles in synaptic inhibition in the brain, regulating presynaptic differentiation through interactions with other synaptic proteins. The family's involvement in cell adhesion and signaling underpins its importance in tissue morphogenesis, immune response, and neural network formation.
Sphingolipid Activators and Surfactant Proteins (Sphingo_Act-Surfact_Prot)
Type: Family

This family of proteins includes activators of lysosomal sphingolipid degradation and pulmonary surfactant-associated factors. Members are involved in the sequential hydrolysis of sphingolipids by specific hydrolases, forming complexes with enzymes and lipids to enhance substrate solubilization and degradation. Some proteins in this family act as sphingomyelin phosphodiesterase activators, while others are known to promote alveolar stability by reducing surface tension in the lungs. Additionally, certain members exhibit neurotrophic and myelinotrophic effects through G-protein-coupled receptor signaling pathways.
Encapsulin nanocompartment (Encapsulin_nc)
Type: Family

The encapsulin family is characterized by its ability to form proteinaceous nanocompartments, typically ranging from 21 to 33 nm in diameter, with walls about 2-2.5 nm thick. These nanocompartments serve as specialized storage vessels, often for iron, and may protect against oxidative damage. Encapsulins assemble into icosahedral shells with pores that can regulate the passage of molecules. Cargo proteins, such as ferritin-like proteins or enzymes like DyP, are targeted to the interior via C-terminal extensions. Some encapsulins are fused with cargo proteins, such as ferritin or diheme-cytochrome, and exhibit additional functions like ferroxidase activity. These nanocompartments are implicated in various cellular processes, including iron storage and protection from oxidative stress, and may be involved in the immune response. The encapsulin family displays a remarkable structural diversity, with variations in size, pore dynamics, and cargo protein incorporation, reflecting their specialized functions across different organisms.
Fungal Transcription Factors for Environmental Response (Fungal_TF_Env_Response)
Type: Family

The protein family comprises transcription factors that regulate gene expression in response to various stimuli, including heme availability, iron stress, and antifungal drug presence. Members of the family are involved in the biosynthesis of secondary metabolites like tenellin-type 2-pyridones, aspyridones, leporins, and xenovulene A, as well as in the control of oxidative damage, respiration, and multidrug resistance. They bind to specific DNA sequences to modulate the transcription of target genes, contributing to cellular adaptation and survival under different environmental conditions. Some members are also implicated in virulence and membrane permeability in pathogenic fungi.
Transcription initiation factor TFIID subunit 9 (TFIID_subunit_9)
Type: Family

The TAF9 family is involved in the initiation of RNA polymerase II-dependent transcription. Members of the family function as components of the TFIID complex, which is essential for promoter recognition and pre-initiation complex formation, regardless of the presence of a TATA box. The TAF9 family includes subunits that are also part of the TBP-free TAFII complex, PCAF histone acetylase complex, and STAGA transcription coactivator-HAT complex. These proteins play roles in transcriptional activation and repression, gene regulation associated with apoptosis, and are essential for cell viability. They interact with transcription activators, contribute to chromatin modification through histone acetylation, and facilitate DNA opening for transcription initiation. The family is also implicated in the regulation of a subset of genes through the SAGA and SLIK HAT complexes, influencing RNA polymerase II activity and promoter selectivity.
Voltage and calcium-activated potassium channel auxiliary protein (KCNMA1_auxiliary)
Type: Family

This family of proteins includes auxiliary components of large-conductance, voltage and calcium-activated potassium channels (BK alpha). They are involved in modulating the gating properties of these channels, including shifts in voltage dependence of activation and conversion of channel types in various cellular contexts. Some members interact with the KCNMA1 channel, influencing its activation at different voltages and calcium levels. Additionally, the family encompasses proteins that participate in platelet adhesion and aggregation through binding to von Willebrand factor, playing a crucial role in hemostasis. Other members are involved in hormonal cascades, such as the ecdysone-induced gene regulation in insects, and in stabilizing enzymes within the circulatory system.
Calcium and Integrin-Binding (CIBP)
Type: Family

The Calcium and integrin-binding protein family is involved in a wide range of cellular processes including cell differentiation, proliferation, migration, thrombosis, angiogenesis, cardiac hypertrophy, and apoptosis. Members of this family play key roles in bone marrow megakaryocyte differentiation, integrin signaling, focal adhesion formation, MAP kinase signaling pathways, and calcium homeostasis. They are also implicated in sensory mechanoelectrical transduction in hair cells, essential for hearing and photoreceptor cell function. Additionally, they participate in the regulation of cell cycle progression, microtubule dynamics, and stress response, and are involved in pathological and adaptive angiogenesis, as well as cancer cell survival and proliferation.
DnaJ homolog subfamily C member 5 (DnaJ_C_subfamily_member5)
Type: Family

The DnaJ homolog subfamily C member 5 family comprises chaperones involved in regulated exocytosis and presynaptic functions. They act as co-chaperones for the SNARE protein SNAP-25 and play a role in the calcium-mediated control of late-stage exocytosis. These proteins are implicated in calcium-dependent neurotransmitter release at nerve endings, indicating a significant role in synaptic transmission and neural communication.
RING finger E3 ubiquitin-protein ligases (RING_finger_E3_ubiq-ligases)
Type: Family

The RING finger protein family comprises E3 ubiquitin-protein ligases involved in various cellular processes, including apoptotic signaling pathways activated by endoplasmic reticulum stress, the unfolded protein response, autophagy, and nutrient sensing. Members of the family ubiquitinate specific substrates, regulating their localization, stability, and function. For instance, they ubiquitinate BNIP1 affecting its mitochondrial localization, ATF6 to promote UPR, and EPHB2 for autophagy induction. They also control mTORC1 activity by ubiquitinating Sestrin-2. The RING-type domain within these proteins is essential for their ubiquitination activity.
Autophagy-related EPG5 (Autophagy-related_EPG5)
Type: Family

This family of proteins is involved in the cellular process of autophagy, which is the degradation and recycling of cellular components. Members of this family play a role in various stages of autophagy, including the maturation of autophagosomes into autolysosomes, the clearance of autophagosomal cargo, and the degradation of protein aggregates within autophagosomes. Some proteins in this family are essential for starvation-induced autophagy and omegasome development. Additionally, certain members have a key role in the immune response, particularly in the recognition of unmethylated CpG dinucleotides from pathogens and the subsequent activation of the TLR9 signaling pathway. This involves the translocation of CpG dinucleotides to the lysosome, where TLR9 is located, triggering innate and adaptive immune responses.
Tubulin tyrosine ligase-like monoglycylase (TTLL_monoglycylase)
Type: Family

This family of proteins is involved in the post-translational modification of tubulin, specifically through the addition of glycine side chains to the gamma-carboxyl groups of glutamate residues within the C-terminal tail of tubulin. Members of this family act as monoglycylases, initiating the addition of single glycine residues, a process known as glycylation. This modification is crucial for the stability and maintenance of microtubules, particularly in the cilia and flagella, where it plays a role in motility and cell signaling. Some family members can also modify non-tubulin proteins, adding versatility to their functional repertoire. The glycylation activity competes with polyglutamylases, suggesting a regulatory mechanism between glycylation and glutamylation that impacts microtubule dynamics.
RNF E3 ubiquitin-protein ligase (RNF_E3_ubiq-protein_ligase)
Type: Family

The RNF E3 ubiquitin-protein ligase family mediates ubiquitination and proteasomal degradation of various target proteins, regulating multiple biological processes such as cell cycle, apoptosis, osteoclastogenesis, innate and adaptive immunity, and interferon production. Family members act as negative regulators of NF-kappa-B-dependent transcription, promoting ubiquitination and stabilization of NF-kappa-B inhibitors. They also ubiquitinate CDK inhibitors, stimulating cell cycle transition and suppressing senescence. Some members negatively regulate type I interferon production and T-cell activation, while others facilitate xenophagic targeting of bacteria and inhibit viral replication. The family's domain structure, including the C2HC RNF-type zinc finger and RING-type zinc finger, is crucial for binding to ubiquitin-conjugating enzymes.
Xylanolytic/Arabinanolytic transcriptional activators (XlnR/Xlr1)
Type: Family

The xlnR/xlr1 family consists of transcriptional activators involved in the regulation of genes associated with the pentose catabolic pathway (PCP). Members of this family are primarily responsible for the induction of extracellular cellulolytic and xylanolytic enzymes, as well as the intracellular activities of D-xylose catabolic genes, in response to the presence of D-xylose. Certain members also regulate arabinanolytic genes in response to L-arabinose. These proteins typically bind to specific DNA sequences to exert their regulatory functions, contributing to the efficient utilization of pentose sugars by the cell.
Goosecoid-like homeobox (Goosecoid-like_HB)
Type: Family

This family of proteins includes transcription factors characterized by a homeobox domain, which is a DNA-binding motif. They are involved in early embryonic development and organogenesis. Members of this family play crucial roles in regulating the expression of genes that are essential for the development of various structures, such as the middle ear components, and are implicated in the establishment of body axes during gastrulation. They may also participate in defining cell fate specification and lineage determination, particularly in neural crest cells and mesoderm-derived tissues. Some proteins in this family are capable of inducing secondary body axis formation, a process known as organizer activity, which is fundamental in vertebrate developmental biology.
Selenoprotein W and related (SelW_related)
Type: Family

This family of proteins includes members that are involved in cellular antioxidant activities, particularly as glutathione (GSH)-dependent antioxidants. They may participate in redox-related processes and could play roles in conditions related to selenium deficiency, such as myopathies. Some family members are implicated in cell migration, potentially by inducing filopodia formation, and may regulate apoptosis, possibly through interaction with caspase-3. The diverse functions suggest a broad involvement in cellular protective mechanisms and structural dynamics.
B3 domain-containing protein (B3_domain)
Type: Family

This family of proteins contains the B3 domain, which is a DNA-binding domain involved in various biological processes. Members of this family are known to function as transcription factors that regulate gene expression in response to developmental cues and environmental signals. They play pivotal roles in plant growth, development, and differentiation. The B3 domain facilitates the recognition and binding to specific DNA sequences, allowing these proteins to control the transcription of target genes that are essential for processes such as hormone signaling pathways, organ development, and stress responses.
X-linked Lymphocyte-regulated/Synaptonemal Complex Protein 3 (XLR/SYCP3)
Type: Family

The XLR/SYCP3 family proteins are key components of the synaptonemal complexes (SCS), which form between homologous chromosomes during meiotic prophase. They play a crucial role in centromere pairing during meiosis in male germ cells, which is essential for normal meiosis and male fertility. These proteins also contribute to female fertility, albeit to a lesser extent. They are involved in the efficient phosphorylation of HORMAD1 and HORMAD2, which are important for meiotic progression. The family members are characterized by a long central coiled coil domain, with N-terminal and C-terminal regions that interact with DNA, indicating a structural role in chromosome pairing and synapsis.
Parasitic Reproductive and Invasion Surface Protein (Parasite_Repro/Invasion_Surf)
Type: Family

This family of proteins includes surface proteins primarily involved in the reproductive processes and lifecycle progression of a parasitic organism. Members of this family are essential for male gamete fertility, playing a crucial role in gamete fusion and interaction with host cells. Some proteins are necessary for the formation of exflagellation centers, which are critical for the binding to erythrocytes. Other members are implicated in the initial stages of host infection, specifically the invasion of hepatocytes by sporozoites and subsequent replication within these cells. Collectively, these proteins contribute to the successful propagation and transmission of the parasite.
Lymphocyte Antigen 6 Family Modulators (LY6H/LY6L_nAChR_modulators)
Type: Family

The LY6H/LY6L protein family is characterized by its role in modulating the activity of nicotinic acetylcholine receptors (nAChRs). Members of this family, such as LY6H in humans and mice, are believed to inhibit the maximum response of alpha-3:beta-4-containing nAChRs. They may also be involved in the intracellular trafficking of alpha-7-containing nAChRs, potentially inhibiting their surface expression and affecting alpha-7/CHRNA7 signaling in hippocampal neurons. While the specific functions of some members are not detailed, the shared LY6 domain suggests a conserved role in immune cell signaling, as indicated by the involvement of LY6A in T-cell activation.
HTH-type transcriptional regulator with aminotransferase domain (HTH_trans_reg/aminotransferase)
Type: Family

This family of proteins includes transcriptional regulators with a helix-turn-helix (HTH) motif, which are involved in various cellular processes. Members of this family are known to regulate the expression of operons related to amino acid metabolism, such as taurine and gamma-aminobutyrate (GABA), as well as pathways for vitamin B6 salvage and pyridoxine biosynthesis. Some proteins in this family can act as both activators and repressors of transcription, binding to specific DNA sequences to modulate gene expression. Additionally, certain proteins within this family may possess aminotransferase activity, suggesting a dual regulatory and enzymatic role. The presence of a class-I pyridoxal-phosphate-dependent aminotransferase domain in the C-terminal section is a characteristic feature of this family, indicating a potential involvement in amino acid and cofactor metabolism.
Lipoprotein-releasing system transmembrane protein (Lipoprotein-release_system)
Type: Family

This family of proteins is involved in an ATP-dependent transport system that facilitates the release of lipoproteins from the inner membrane, targeting them to the outer membrane in bacteria. The release mechanism is contingent on a specific sorting signal, which is the absence of an aspartic acid residue at the second position of the mature lipoprotein. These proteins are integral components of the membrane and are part of a larger complex known as the LolCDE system, which is essential for the proper localization of lipoproteins, playing a critical role in bacterial membrane organization and function.
CdaR-like transcriptional regulators (CdaR-like_regulators)
Type: Family

This family of proteins includes transcriptional activators that regulate the expression of various operons. Members of this family are involved in the response to specific environmental stimuli or intracellular signals, such as the availability of certain amino acids or the presence of specific metabolites. They can activate or repress the transcription of genes involved in metabolic pathways, including those for proline and purine catabolism, as well as the utilization of specific carbohydrates. Some members are also implicated in important cellular processes like sporulation. The DNA-binding activity of these proteins is often regulated by the presence of coactivators or the recognition of specific DNA sequences.
ABC-2 integral membrane transporter component (ABC-2_transporter_component)
Type: Family

This family of proteins includes integral membrane components of ABC transporter complexes, which are involved in the translocation of substrates across cellular membranes. Members of this family are implicated in various functions, such as antibiotic resistance and efflux of specific compounds like cefoperazone. Some proteins within this family are essential for the secretion of other proteins and may also play a role in biofilm morphology through interactions with signaling proteins. Additionally, certain members are associated with the ESX secretion system and may act as regulators or components of this system, which is involved in the secretion of virulence factors and other proteins.