SII-SWORD/CoKE huggingface dataset:
Multifunctional Ankyrin Repeat Domain-Containing Protein (Multifunctional_ANK_Repeat)
Type: Family

This family of proteins includes members involved in various cellular processes such as translational fidelity, neurotransmitter release, symbiosis, ubiquitination, mycotoxin biosynthesis, membrane stabilization, ion transport, endocytosis, protein transport, and phosphoprotein substrate recognition. Some proteins in this family function by preventing the misactivation of amino acids during protein synthesis, while others are involved in the formation of membrane pores for neurotransmitter release. Certain members play a role in the maintenance of cell structure and signaling, and others are implicated in the regulation of protein degradation through the ubiquitin-proteasome system. Additionally, some proteins are associated with the biosynthesis of secondary metabolites like mycotoxins, and others act as regulatory subunits for protein phosphatases.
Threonine Synthase (Threonine_Synthase)
Type: Family

The Threonine Synthase family is characterized by enzymes that catalyze the final step in the biosynthesis of L-threonine from L-phosphohomoserine through a gamma-elimination of phosphate and beta-addition of water. Additionally, some family members possess catabolic phospho-lyase activity, degrading O-phospho-threonine to alpha-ketobutyrate, ammonia, and phosphate. Certain variants within the family may also degrade other substrates like L-serine, 3-chloroalanine, and vinylglycine, or have roles in inducing osteoblastic production of IL6, potentially influencing inflammation and bone turnover.
Prolyl oligopeptidase and macrocyclase (Prolyl_oligopep/macrocyclase)
Type: Family

The Prolyl oligopeptidase family, part of the peptidase S9A and S9B subfamilies, encompasses enzymes with diverse functions including conventional prolyl endopeptidases that cleave peptide bonds on the C-terminal side of prolyl residues within short peptides, and specialized macrocyclase-peptidases involved in the biosynthesis of cyclic peptides with biological activities such as nematodicidal and toxicity properties. These enzymes typically act on peptides up to approximately 30 amino acids long and often have a strict requirement for an X-Pro bond in the trans configuration immediately before the scissible bond. Some members perform a two-step cleavage and macrocyclization of core peptides, playing a crucial role in the production of bioactive cyclic compounds.
Alpha-aminoadipic semialdehyde synthase (AASS)
Type: Family

The Alpha-aminoadipic semialdehyde synthase family comprises bifunctional enzymes involved in lysine degradation. Members of the family catalyze the first two steps of this process, which involve the conversion of lysine to alpha-aminoadipic semialdehyde via the lysine ketoglutarate reductase activity and subsequently to saccharopine through saccharopine dehydrogenase activity. Additionally, some family members are involved in the alpha-aminoadipate pathway for lysine biosynthesis, where they catalyze the cleavage of saccharopine to L-lysine and 2-oxoglutarate. This dual functionality is reflected in the presence of two distinct domains within these proteins: the N-terminal domain, which belongs to the AlaDH/PNT family and contains lysine ketoglutarate reductase activity, and the C-terminal domain, which belongs to the saccharopine dehydrogenase family and exhibits saccharopine dehydrogenase activity. The enzymes are found in a variety of organisms, including mammals, fungi, and plants, indicating a conserved role in amino acid metabolism.
NADH:quinone oxidoreductase/NAD(P)H-quinone oxidoreductase (NADH-Q_oxidoreductase)
Type: Family

This family of proteins includes enzymes that participate in the electron transport chain by catalyzing the oxidation of NADH and the reduction of quinones. These activities are crucial for the regeneration of NAD+, which is essential for various metabolic processes. Some members of this family are involved in alternative nonproton pumping pathways, which contribute to the respiratory chain without the translocation of protons across the membrane. Additionally, certain proteins within this family have a bifunctional oxidoreductase activity, playing a role in the biosynthesis of vitamin K1 and in the redox metabolism of plastoquinone-9. They are also involved in the tocopherol recycling pathway. The family includes proteins that can be inhibited by specific compounds such as dicumarol and quinone derivatives, indicating a regulatory aspect to their function.
Neural and epithelial cell adhesion domain-containing protein (Neural/epithelial_adhesion)
Type: Family

This family of proteins includes cell adhesion molecules that are primarily involved in neural development and function. They play crucial roles in neuron-neuron adhesion, neurite outgrowth, fasciculation, and the development of nerve fascicles. Some members are implicated in maintaining the integrity of the trans-epithelial diffusion barrier and may also participate in early neuronal differentiation. Additionally, certain proteins within this family have been identified as receptors for various microbial infections, indicating a role in immune response or pathogen interaction. The family also includes proteins that contribute to cell migration, proliferation, morphology, and survival, particularly in the context of renal epithelial cells. Overall, these proteins are essential for proper neural network formation and maintenance, as well as other cellular processes.
Calcium/Cation Antiporter (CaCA)
Type: Family

The Ca(2+):cation antiporter (CaCA) family is involved in the regulation of cytoplasmic Ca(2+) levels and Ca(2+)-dependent cellular processes. Members of this family mediate the exchange of Ca(2+) ions against various cations, such as Na(+) or protons, across the cell membrane. This exchange contributes to processes such as excitation-contraction coupling in muscle, synaptic plasticity, learning, memory, and the maintenance of cellular Ca(2+) homeostasis in excitable cells. Some subfamily members are involved in vacuolar transport of divalent cations like Mg(2+), Zn(2+), and Fe(2+) in plants, which may affect the partitioning of these ions between organs. The activity of these exchangers is regulated by cytoplasmic Ca(2+) levels and can be modulated by Na(+) ions. The family includes subfamilies such as SLC8 and MHX, with members having additional roles in embryonic heart development, myelination, mitochondrial Ca(2+) ion homeostasis, and protection against light-dependent retinal degeneration.
Chlamydia Large Cysteine-rich Periplasmic OmcB (Chlamydia_OmcB)
Type: Family

The OmcB protein family consists of large cysteine-rich periplasmic proteins found in Chlamydia species. These proteins play a crucial role in the structural integrity of the outer envelope of elementary bodies (EBs), which are the infectious form of the bacteria. OmcB proteins achieve this by forming disulfide cross-links with small cysteine-rich proteins and major outer membrane porins or proteins. This cross-linking creates a Sarkosyl-insoluble complex known as the Chlamydia outer membrane complex (COMC), which acts as a functional equivalent to peptidoglycan, a component typically found in bacterial cell walls. In reticulate bodies (RBs), the non-infectious, replicative stage of Chlamydia, the disulfide bonds in OmcB proteins are reduced, indicating a different structural state.
Voltage-dependent calcium channel subunit alpha-2/delta (Ca_channel_alpha-2/delta)
Type: Family

The calcium channel subunit alpha-2/delta family comprises proteins that act as regulatory subunits for voltage-dependent calcium channels, influencing calcium current density and activation/inactivation kinetics. These subunits are involved in various calcium-dependent processes, including excitation-contraction coupling and neural depolarization-induced calcium influx. They contain a MIDAS-like motif within the VWFA domain that binds divalent metal cations, essential for trafficking the alpha-1 subunit to the plasma membrane. Some family members may also regulate calcium-activated signaling pathways affecting motor activity and neurotransmitter responses.
Cytochrome c-type Electron Transfer (Cytochrome_c-type_ET)
Type: Family

This family of proteins is involved in electron transfer processes within the cell, particularly in anaerobic respiration. Members of this family are typically cytochrome c-type proteins that mediate electron flow from quinones to various complexes, such as the NapAB complex in nitrate reduction and the TorA or TorZ enzymes in trimethylamine-N-oxide (TMAO) reduction. These proteins are essential components of the bacterial respiratory chain, transferring electrons to terminal reductases that catalyze the reduction of substrates like nitrite or TMAO. Some members are also implicated in extracellular electron transfer, playing roles in processes such as detoxification of nitrite and direct interspecies electron transfer (DIET). The family includes proteins with multiple heme-binding sites, which are likely involved in the sequential transfer of electrons through their heme groups.
Dual specificity CLK kinases (CLK_kinases)
Type: Family

This family of proteins includes dual specificity kinases that act on serine/threonine and tyrosine residues. They phosphorylate serine- and arginine-rich proteins of the spliceosomal complex, influencing RNA splicing. Members of this family are involved in the regulation of alternative splicing of pre-mRNAs, such as tissue factor (F3) in endothelial cells. Some members also play roles in cellular processes like gluconeogenesis suppression, cell wall and septum formation, and cell separation. They may also regulate transcriptional activity by phosphorylating transcriptional activators or repressors. Inhibitors like Leucettine L41 and TG003 can affect their kinase activity and subsequent regulatory functions.
Centrosomal and Immune Signaling Modulators (Cent_Immune-Sig_Mod)
Type: Family

This family of proteins includes various members with roles in cellular structure and signaling. Some proteins in this family are involved in the organization of microtubules and are essential for the assembly of centriole subdistal appendages, indicating a role in cell division and cytoskeletal organization. Other members function as adapter proteins that are crucial for both innate and adaptive immune responses. They mediate T-cell receptor-stimulated activation, regulate thymocyte development, and contribute to regulatory T-cell stability and function. These proteins also modulate signaling pathways by facilitating the recruitment of specific kinases to the Golgi apparatus and lysosomes, and by regulating the translocation of receptors to lipid rafts in response to external stimuli such as viral infection or inflammation. Additionally, some proteins may play a role in myoblast fusion during muscle development and in acrosome formation in spermatogenesis.
Catalytically Inactive Kinase-Related Protein (CIK-Related_Protein)
Type: Family

This family of proteins includes members that are structurally related to the protein kinase superfamily but are predicted to be catalytically inactive. Despite the lack of detectable kinase activity, these proteins are implicated in various cellular processes. Some family members are involved in the regulation of COPI-mediated retrograde protein traffic between the Golgi apparatus and the endoplasmic reticulum, contributing to the maintenance of Golgi morphology. Others are components of the AP2-containing clathrin coat, playing a role in clathrin-dependent trafficking at the plasma membrane, trans-Golgi network, and endosomal system. These proteins are essential for cell growth, development, and specialized functions such as polarized root hair development in plants and neuronal function and signaling in animals. Additionally, certain isoforms may act as transcriptional activators, influencing gene expression.
TfdA dioxygenase (TfdA_dioxygenase)
Type: Family

The TfdA dioxygenase family is involved in various oxidative decarboxylation and hydroxylation reactions that are crucial for the metabolism of diverse substrates, including herbicides, fatty acids, and purines. Members of this family play roles in the biosynthesis of isonitrile lipopeptides, which are implicated in virulence and metal acquisition in mycobacteria, and in the degradation of phenoxypropionate herbicides. They also participate in the biosynthesis of antibiotics like pentalenolactone and diterpene glucosides such as brassicicene C and fusicoccins. These enzymes typically require Fe(2+) and alpha-ketoglutarate to catalyze the oxidation of their respective substrates, producing compounds like uric acid from xanthine. Activity regulation is observed with ascorbate activation and inhibition by various divalent cations and specific inhibitors.
Multifunctional WD repeat-containing protein (WD_repeat_multifunction)
Type: Family

This family of proteins is involved in various cellular processes, including angiogenesis, cell migration, mitochondrial fission, and the regulation of proteasome assembly and activity. Some members act as adapter proteins that facilitate the formation of mitochondrial fission complexes, which are essential for the division of mitochondria. Other members play roles in inhibiting the assembly and proteolytic function of the 26S proteasome, impacting protein degradation pathways. Additionally, certain proteins within this family contribute to ribosome assembly, histone modification, and the establishment of heterochromatin, indicating a broad functional spectrum related to cell structure, division, and gene expression regulation.
Inhibitor of nuclear factor kappa-B kinase (IKK)
Type: Family

The I-kappa-B kinase (IKK) family comprises serine/threonine kinases essential for the NF-kappa-B signaling pathway, which is activated by various stimuli including inflammatory cytokines, bacterial or viral products, DNA damage, and other cellular stresses. Family members phosphorylate inhibitors of NF-kappa-B, leading to their ubiquitination and degradation, and subsequent nuclear translocation of NF-kappa-B to activate gene transcription involved in immune response, growth control, and apoptosis protection. Additionally, the family plays roles in antiviral responses by phosphorylating interferon regulatory factors and in energy balance regulation. Some members also phosphorylate histones, modulating chromatin accessibility, and have roles in autophagy, cell survival, and lymphoid organogenesis. The family's activity is regulated by phosphorylation and is crucial for both canonical and non-canonical NF-kappa-B signaling pathways, as well as for maintaining a balance between type I and type II interferon responses.
CAF1 family poly(A)-specific ribonucleases (CAF1_poly(A)_ribonucleases)
Type: Family

The CAF1 family proteins are specialized 3'-exoribonucleases with a preference for degrading poly(A) tails of mRNAs, a key step in eukaryotic mRNA decay. They play roles in various biological processes including translational silencing of maternal mRNAs during oocyte maturation and early embryonic development, nonsense-mediated mRNA decay, and the degradation of unstable mRNAs with AU-rich elements. Some family members are also involved in the maturation and processing of snRNAs, piRNAs, and the regulation of microRNAs and small nucleolar RNAs. Their functions are critical for cell growth regulation, fertility, gene silencing, and stress response.
Eukaryotic NMN adenylyltransferase (Euk_NMN_adenylyltrnsfrase)
Type: Family

The eukaryotic NMN adenylyltransferase family is responsible for the biosynthesis of NAD(+) from nicotinamide mononucleotide (NMN) and ATP, a key step in both de novo and salvage pathways for NAD(+) production. Members of the family can also utilize the deamidated form, nicotinic acid mononucleotide (NaMN), with varying efficiencies. These enzymes are involved in the maintenance of healthy axons by delaying Wallerian axon degeneration. They also participate in the synthesis of nuclear ATP, necessary for chromatin remodeling, and support ADP-ribosylation reactions. The family's pyrophosphorolytic activity allows for the cleavage of NAD(+), with some members also able to degrade other dinucleotides. Regulatory mechanisms include inhibition by specific phosphorylated dinucleotides and galotannin.
U1 snRNP 70 kDa and U11/U12 snRNP 35 kDa (U1_U11-U12_snRNP_70-35kDa)
Type: Family

The protein family is involved in the splicing of pre-mRNA, a critical step in gene expression where introns are removed and exons are joined to form a mature mRNA molecule. Members of the family are components of the spliceosomal U1 small nuclear ribonucleoprotein (snRNP) complex, which recognizes the pre-mRNA 5' splice-site and facilitates the assembly of the spliceosome. The family includes proteins that bind to the U1-snRNA, particularly to the loop I region, through an RNA recognition motif (RRM) domain. Some members may also interact with the minor spliceosome and contribute to the recognition of 5' splice sites in U12-type introns. Additionally, certain proteins in the family are implicated in essential cellular processes such as oogenesis and meiotic chromosomal segregation. The family's involvement extends to nutritional signaling pathways and the regulation of sporulation-specific genes.
Tyrosine-phosphorylated adapter molecule (Tyrosine-phos_adapter)
Type: Family

This family of proteins includes adapter molecules that play a crucial role in signal transduction pathways. They are involved in various cellular processes such as cell adhesion, migration, branching, and apoptosis. These proteins typically associate with tyrosine-phosphorylated receptors or substrates, mediating downstream signaling events. They contribute to the regulation of gene transcription in response to extracellular signals and are implicated in the DNA damage response. Additionally, they participate in the regulation of cytoskeletal dynamics, influencing cell motility and morphology. Some family members are also involved in the engulfment of apoptotic cells and may have roles in the immune response.
Abnormal Spindle-like Microcephaly-associated (ASPM)
Type: Family

The Abnormal Spindle-like Microcephaly-associated (ASPM) protein family is involved in the regulation and coordination of mitotic spindle dynamics during cell division. Members of this family play a crucial role in maintaining the structure of the centrosomal microtubule organizing center (MTOC) and are essential for proper neurogenesis, germ cell mitosis, and oocyte differentiation. They interact with the katanin complex, enhancing microtubule severing activity and influencing microtubule dynamics at spindle poles, including spindle orientation, astral microtubule density, and poleward microtubule flux. The family's ability to block microtubule minus-end growth is also modulated by its association with the katanin complex.
RRM HNRPC family, RALY subfamily (RRM_HNRPC/RALY_subfam)
Type: Family

The RRM HNRPC family, RALY subfamily, comprises RNA-binding proteins involved in various aspects of RNA metabolism. Members of this family bind to pre-mRNA and are implicated in the assembly of hnRNP particles, playing a role in mRNA stability, translation, and splicing. They interact with poly-U tracts in mRNA UTRs and respond to m6A modifications, which can influence mRNA splicing. Some family members are involved in transcriptional regulation of cholesterol biosynthesis by binding non-coding RNAs like LeXis. Others may contribute to nucleosome assembly and maintenance of mRNA levels. The family is characterized by the RNA recognition motif (RRM) and is associated with heterogeneous nuclear ribonucleoproteins (hnRNPs), which are key components in the post-transcriptional regulation of gene expression.
Pre-mRNA 3'-end-processing regulator (Pre-mRNA_3'-end_processing_reg)
Type: Family

This family of proteins is involved in the regulation of pre-mRNA 3'-end processing, a crucial step in mRNA maturation. Members of this family are key components of the cleavage and polyadenylation specificity factor (CPSF) complex, which recognizes specific signal sequences in pre-mRNA and interacts with poly(A) polymerase and other factors to facilitate cleavage and the addition of a poly(A) tail. These proteins contribute to the recognition of polyadenylation sites and may enhance the polyadenylation process. They are known to bind to U-rich RNA sequence elements near the poly(A) site and may serve to anchor poly(A) polymerase to the CPSF complex, thereby influencing the efficiency and specificity of mRNA 3'-end formation.
PHD-type Zinc Finger Domain-Containing Protein (PHD-type_Zinc_Finger)
Type: Family

This family of proteins includes regulators of transcription and ubiquitination processes. Members are involved in the regulation of Th1-type cytokine gene expression, which suggests a role in immune response modulation. Some proteins within this family function as E3 ubiquitin-protein ligases, accepting ubiquitin from E2 enzymes and transferring it to substrates, which is essential for preventing apoptotic cell death during early embryogenesis. Other members act as transcriptional regulators, with specific proteins suppressing ribosomal RNA transcription, potentially influencing ribosome biogenesis. Additionally, certain proteins may be involved in spermatogenesis, indicating a role in reproductive biology. The presence of PHD-type zinc fingers in these proteins suggests a role in chromatin-mediated transcriptional regulation, DNA binding, or protein-protein interactions.
Splicing-associated domain-containing protein (Splicing_assoc_domain)
Type: Family

This family of proteins appears to be primarily involved in the process of splicing, with several members having annotations suggesting a role in this fundamental aspect of gene expression. Splicing is a critical step in the post-transcriptional modification of RNA, where introns are removed and exons are joined to form a mature messenger RNA molecule. Some family members are noted to potentially influence the splicing mechanism, with overexpression affecting the suppression of splicing defects in certain mutants. Additionally, one member is described to enhance the ATPase activity of another protein in vitro, indicating a possible regulatory function in ATP-dependent molecular processes. Another protein within the family is implicated in meiosis and sporulation, suggesting a broader range of biological activities.
Baculoviral IAP repeat-containing (Baculoviral_IAP)
Type: Family

The Baculoviral IAP repeat-containing protein family is involved in various cellular processes, primarily acting as a key component of the chromosomal passenger complex (CPC), which is crucial for chromosome alignment, segregation during mitosis, and cytokinesis. Family members are multitasking proteins that promote cell proliferation and prevent apoptosis, associating with polymerized microtubules to organize the center spindle. They participate in spindle assembly, recruitment of CPC to centromeres, and serve as scaffolds for mitotic spindle formation. Some members are involved in vascular development, while others play a role in transcriptional regulation and maintaining mitochondrial integrity. They may also inhibit apoptosis by interacting with caspases and have potential roles in neoplasia.
DDB1-CUL4-associated factor 12 (DCAF12)
Type: Family

This family of proteins functions as substrate-recognition components of DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes, which are involved in the DesCEND (destruction via C-end degrons) pathway. They recognize and bind to specific C-degron motifs, typically less than ten residues in length, located at the extreme C terminus of target proteins. This interaction leads to the ubiquitination and subsequent proteasomal degradation of these targets. The family is characterized by its ability to recognize diglutamate (Glu-Glu) C-terminal sequences, as well as an alternative glutamate-leucine (Glu-Leu) degron. These proteins play a crucial role in various cellular processes, including starvation-induced autophagy, spermatogenesis, and T cell activation.