SII-SWORD/CoKE huggingface dataset:
AN1/A20 Zinc Finger (AN1_A20_ZnFinger)
Type: Family

The AN1/A20 zinc finger protein family is characterized by the presence of AN1-type and A20-type zinc finger domains, which are implicated in a variety of cellular processes. Members of this family are involved in the regulation of NF-kappa-B activity, apoptosis, and the ubiquitin-proteasome system. They play roles in environmental stress response, protein import into peroxisomes, and the stability of PEX5. Some family members are also associated with TRAF2 and are involved in modulating 'Lys-48'-linked polyubiquitination status. Additionally, they may act in anchoring ubiquitinated proteins to the proteasome and in inhibiting osteoclast differentiation. The family's functions are crucial in cellular responses to stress, inflammation, and protein homeostasis.
Protease Inhibitors and Growth Factor Antagonists (Prot_Inhib_GrowthFact_Antg)
Type: Family

The protein family encompasses a group of secreted proteins that play diverse roles in physiological processes such as inhibition of proteases, antagonism of growth factors, and regulation of cell proliferation, differentiation, and immune responses. Members of the family are known to interact with and inhibit various proteases like subtilisin-like serine proteases and trypsin, as well as growth factors such as activin and TGF-beta family members. They are involved in defense mechanisms between plants and pathogens, neural induction, angiogenesis, and hematopoiesis. Some members also possess neurotoxic properties by inhibiting ion channels. The family includes proteins with kazal serine protease inhibitor signatures and those that bind directly to activin, functioning as activin antagonists, thereby regulating the biosynthesis and secretion of hormones like FSH.
Acetylcholinesterase-related enzymes (AChE-related_enzymes)
Type: Family

This family of proteins is involved in the hydrolysis of the neurotransmitter acetylcholine, a critical step in terminating signal transduction at neuromuscular junctions. Members of this family exhibit broad substrate specificity and contribute to the inactivation of acetylcholine, thereby playing a key role in regulating cholinergic neurotransmission. Some family members can also degrade neurotoxic organophosphate esters, which indicates a potential role in detoxification processes. The proteins may also participate in cell-cell interactions and have been implicated in neuronal apoptosis. In some species, these enzymes are found in venom, where their function may contribute to prey immobilization.
Plant B3 domain-containing (Plant_B3_domain)
Type: Family

The B3 domain-containing protein family is characterized by the presence of the B3 domain, which is involved in DNA binding and transcriptional regulation. Members of this family play roles in various plant developmental processes and stress responses. A notable example is the B3 domain-containing transcription factor VRN1, which is essential for the regulation of vernalization in Arabidopsis thaliana. VRN1 acts as a transcriptional repressor of FLC, a key gene in the vernalization pathway, and binds DNA in a non-sequence-specific manner. While the specific functions of many family members remain to be fully characterized, the shared B3 domain suggests a general role in gene expression modulation.
PIN2/TERF1-interacting telomerase inhibitor (PINX1)
Type: Family

The PINX1 family proteins are involved in ribosomal RNA (rRNA) processing, specifically at the A0, A1, and A2 sites, and play a role in the negative regulation of telomerase activity. They are implicated in the final trimming of U18 and U24 small nucleolar RNAs (snoRNAs). Some family members have been identified as microtubule-binding proteins essential for chromosome segregation, mediating the accumulation of TRF1 and TERT in the nucleolus, enhancing TRF1 binding to telomeres, and acting as telomerase inhibitors. These functions suggest a role in cell proliferation control and potential tumor suppressor activity. The family also includes proteins involved in ribosome biogenesis and cell proliferation in plants.
Ankyrin repeat domain-containing protein (Ankyrin_repeat_domain)
Type: Family

This family of proteins features ankyrin repeats, a common protein-protein interaction motif involved in various cellular functions. Members of this family are implicated in diverse biological processes, including the regulation of adipogenesis and feeding behavior. Some proteins within this family belong to the POTE family, which are characterized by ankyrin domains and may have roles in actin binding or cytoskeletal organization, as suggested by the presence of actin family annotations in certain members. The ankyrin repeats allow these proteins to mediate interactions with various other proteins, potentially influencing signaling pathways, structural integrity, and cellular localization.
Peptidase M24B family (Peptidase_M24B)
Type: Family

Members of the peptidase M24B family are involved in the hydrolysis of specific peptide bonds. Members of this family exhibit a range of functions, including the hydrolysis of N-terminal amino acid residues from polypeptides, with preferences for substrates containing alanine or for dipeptides with a prolyl in the C-terminal position. Some members are involved in the degradation of specific compounds such as ectoine, contributing to the utilisation of these compounds as carbon and nitrogen sources. Others are implicated in the cleavage of dimethylsulfonioproprionate (DMSP), releasing dimethyl sulfide (DMS), although the native substrate for some of these enzymes remains unclear. The family also includes enzymes like creatinase, which hydrolyse creatine, and aminopeptidases that preferentially remove methionine when followed by specific amino acids. Collectively, the peptidase M24B family plays diverse roles in nitrogen metabolism, peptide degradation, and in some cases, environmental sulfur cycling.
NEK Serine/Threonine Protein Kinase (NEK_Ser/Thr_kinase)
Type: Family

The NEK Ser/Thr protein kinase family, part of the larger protein kinase superfamily, plays a significant role in various cellular processes across different organisms. In plants, members of this family are implicated in development processes, potentially influencing epidermal-cell morphogenesis and microtubule function, and may contribute to the mechanism of cytoplasmic male sterility. In humans and other animals, these kinases are involved in cell cycle regulation, responding to UV irradiation by mediating G2/M arrest and activating the ERK1/2-signaling pathway. Some family members also participate in intracellular signaling and transport regulation, such as mucociliary transport in ciliated cells. The family includes kinases with atypical folds and potentially inactive forms, suggesting diverse regulatory mechanisms and evolutionary adaptations.
BglG family transcriptional antiterminators (BglG_antiterminators)
Type: Family

The BglG family proteins function as transcriptional antiterminators, regulating gene expression in response to specific inducers. They are RNA-binding proteins that prevent premature transcription termination by interacting with RNA-antiterminator sequences. This regulation typically involves operons associated with carbohydrate uptake and metabolism, such as the lac, mtl, and bgl operons. The activity of BglG family members is often modulated by phosphorylation, reflecting their integration into the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). Some family members also contain PTS EIIA type-2 domains, which may serve regulatory functions through phosphorylation.
Secondary metabolite biosynthesis-associated thioesterase (Sec-metab_biosynth-thioest)
Type: Family

This family of proteins includes enzymes with diverse functions, primarily involved in the biosynthesis of various secondary metabolites, such as polyketides, neuropeptide antagonists, and anthraquinones. Members of this family typically exhibit thioesterase activity, catalyzing the hydrolysis of thioester bonds in non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) systems to release products like atrochrysone carboxylic acid. They also participate in cyclization and decarboxylation reactions essential for the formation of complex natural products with potential pharmacological activities. Some proteins in this family also display endoribonuclease activity, playing a role in mitochondrial function and cell viability by cleaving single-stranded RNA.
Ankyrin Repeat and SOCS Box (Ankyrin-SOCS_Box)
Type: Family

The Ankyrin Repeat and SOCS Box (ASB) family proteins are involved in a variety of cellular processes, including transcription regulation, ubiquitination, and proteasomal degradation of target proteins. They often act as substrate-recognition components of E3 ubiquitin-protein ligase complexes, which are part of the ubiquitin-proteasome system responsible for protein turnover. Some family members function as transcription factors interacting with purine-rich repeats, while others may play roles in the immune response or cell cycle regulation. The ankyrin repeats typically mediate protein-protein interactions, and the SOCS box domain is crucial for binding to the Elongin BC complex, an adapter in E3 ligase complexes.
Octanoyltransferase LipM/LipL (Octanoyltrans_LipM/LipL)
Type: Family

The octanoyltransferase LipM/LipL family includes enzymes that play a crucial role in the post-translational modification of lipoate-dependent enzymes. Members of the family catalyze the transfer of octanoic acid from octanoyl-acyl-carrier-protein to the lipoyl domain of GcvH, which is an intermediate step in protein lipoylation. Additionally, some family members are involved in the transamidation of the octanoyl moiety from octanoyl-GcvH to the lipoyl domain of the E2 subunit of lipoate-dependent enzymes. This process is essential for the activation of lipoate-dependent enzymes, which are involved in critical metabolic pathways such as the citric acid cycle and glycine cleavage system. The family is characterized by the presence of octanoyltransferase activity and does not display lipoate protein ligase activity, despite some sequence similarities to LplA.
Plant Cytochrome P450 Monooxygenases (Cytochrome_P450_Monooxygen)
Type: Family

The Cytochrome P450 family is a diverse group of enzymes that play key roles in the metabolism of various biological molecules. Members of this family are involved in the biosynthesis and inactivation of plant hormones such as gibberellins and brassinosteroids, which are crucial for growth and development. They also participate in the biosynthesis of monoterpenoid indole alkaloids and triterpenoid saponins, compounds important for plant defense and with pharmaceutical applications. Additionally, some family members are implicated in stress responses, although their exact functions in these processes may be uncertain. The family's enzymatic activities include hydroxylation, oxidation, epoxidation, and carboxylation, highlighting their multifunctional and multisubstrate nature.
Epithelial Splicing Regulatory (ESRP)
Type: Family

The ESRP family is involved in the regulation of mRNA splicing, playing a crucial role in the formation of cell type-specific isoforms, particularly in epithelial cells. Family members are known to regulate the expression of FGFR2-IIIb, an epithelial-specific isoform of FGFR2, and are implicated in the splicing of various transcripts during the epithelial-to-mesenchymal transition (EMT). They act by directly binding to specific sequences in mRNAs, such as GU-rich motifs in regulatory regions. Some family members also participate in the regulation of alternative splicing in embryo development and are involved in processes like inner ear development and auditory hair cell differentiation. Additionally, hnRNP proteins within this family contribute to pre-mRNA processing events, forming complexes that are essential for the conversion of pre-mRNAs into functional, translatable mRNAs in the cytoplasm.
Pentatricopeptide repeat-containing protein (PPR-containing_protein)
Type: Family

This family of proteins is characterized by the presence of pentatricopeptide repeat (PPR) motifs, which are typically involved in post-transcriptional processes within organelles. Members of this family are known to bind RNA and play roles in RNA editing, stability, and processing, which are crucial for the expression and maintenance of mitochondrial and chloroplast genomes. They are implicated in the biogenesis of organelle ribosomes and in the specific splicing of group I introns. Some proteins within this family are also associated with the translation of organelle mRNAs, indicating a multifaceted role in organelle gene expression regulation.
Cytochrome b5 (Cytochrome_b5)
Type: Family

The cytochrome b5 family comprises membrane-bound hemoproteins that serve as electron carriers for various membrane-bound oxygenases. These proteins play a crucial role in multiple metabolic pathways, including fatty acid desaturation and sterol biosynthesis. Cytochrome b5 proteins are involved in the introduction of double bonds during desaturation steps and in the reduction of cytochrome P-450, which may be linked to flavonoid biosynthesis in certain species. The family's function is essential for the modification of fatty acids within the endoplasmic reticulum, which is critical for membrane synthesis and storage lipid production during seed development.
Hemerythrin (Hemerythrin)
Type: Family

The hemerythrin family comprises oxygen-binding proteins predominantly found in marine worms and some bacteria. Members of this family are involved in various respiratory functions, acting as oxygen carriers in the blood cells of certain marine invertebrates or serving as oxygen storage or delivery proteins for oxygen-requiring enzymes. Hemerythrins are characterized by a distinctive oxygen-binding site that contains two iron atoms, which is essential for their oxygen-binding capability. Some family members are also implicated in defense mechanisms, such as acting as iron scavengers or participating in the innate immune response. The diversity of functions within the hemerythrin family reflects the adaptation of these proteins to different biological roles and environmental conditions.
Signal Transducing Adapter Molecule (STAM)
Type: Family

The STAM family proteins are involved in intracellular signaling and trafficking processes. They are key components of the ESCRT-0 complex, which recognizes and sorts ubiquitinated cargo proteins at the multivesicular body (MVB) for lysosomal degradation. This sorting is crucial for the down-regulation of receptor tyrosine kinases and mediates signaling pathways in response to cytokines and growth factors. Some family members are implicated in T-cell development, DNA synthesis, and MYC induction. The family also includes proteins that function as osmosensors, activate MAPK signaling in response to osmotic stress, and play roles in meiosis, sporulation, and cytoskeletal organization. The STAM family proteins typically contain domains such as VHS, UIM, SH3, and PxVxL motifs, which mediate interactions with ubiquitinated proteins, chromoshadow domains, and other signaling molecules.
CD300 family immune receptors (CD300_family_receptors)
Type: Family

The CD300 family of receptors is involved in various immune system processes. Members typically possess immunoglobulin-like domains and are expressed on the surface of immune cells such as myeloid cells, mast cells, and natural killer (NK) cells. They play roles in immune homeostasis, phagocytosis of apoptotic cells, and regulation of immune cell activation. Some act as activating receptors, enhancing cytokine production and immune cell activation, while others function as inhibitory receptors, down-regulating cell activation and signaling pathways. The family also includes receptors that mediate transcytosis of immunoglobulins across mucosal surfaces, contributing to pathogen neutralization. Additionally, some members regulate osteoclast formation, B cell development, and primary immune responses to infection. The CD300 family receptors interact with various ligands, including phospholipids, ceramide, and immunoglobulins, and are implicated in both innate and adaptive immunity.
F-box/SPRY and SOCS box protein families (FBXO45-Fsn/SPSB_families)
Type: Family

The FBXO45/Fsn and SPSB protein families are involved in various cellular processes through their roles in the ubiquitin-proteasome system. Members of these families function as components of E3 ubiquitin ligase complexes, which are crucial for the ubiquitination and subsequent proteasomal degradation of target proteins. These proteins play key roles in synaptic development and function, including the regulation of synaptic terminal growth at the neuromuscular junction, neuron migration, neurotransmission, and the maintenance of axon integrity. They are also implicated in the negative regulation of nitric oxide production in macrophages, and in the modulation of immune responses to viral infections. The FBXO45/Fsn family members are characterized by the presence of an F-box and SPRY domain, while the SPSB family members contain a SPRY domain and a SOCS box domain, which mediates interaction with the Elongin BC complex.
Mitochondrial import inner membrane translocase subunit (Mito_inner_translocase_sub)
Type: Family

The small Tim family comprises mitochondrial intermembrane chaperones involved in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. They facilitate the transfer of beta-barrel precursors from the TOM complex to the SAM complex of the outer membrane. Acting as chaperone-like proteins, they prevent the aggregation of hydrophobic precursors and guide them through the mitochondrial intermembrane space. The family members contain a twin CX3C motif with conserved Cys residues that likely coordinate zinc during transit from the cytoplasm into the mitochondrion, preventing premature folding.
Msh Homeobox Transcriptional Regulators (Msh_Homeobox_Regulators)
Type: Family

The Msh homeobox family is involved in a variety of developmental processes, including transcriptional repression, bone and tooth development, limb-pattern formation, and embryonic morphogenesis. Members act as transcriptional regulators, with some repressing the transcription of genes involved in myoblast differentiation and odontoblast differentiation. They bind to specific DNA sequences to regulate gene expression and are involved in reciprocal signaling between dental epithelial and mesenchymal cells. They also play roles in the development of the inner ear, the formation of the middle ear, skull, and nasal bones, and the proper production of touch cell precursors. The family's functions are stage-specific and involve interactions with other proteins such as PIAS1 and histone methyltransferases to modulate gene expression and cellular differentiation.
Oleate Activated Transcription Factor 3 (OAF3)
Type: Family

The OAF3 family comprises transcription factors that are primarily involved in the regulation of gene expression in response to specific environmental or cellular signals. Members of the OAF3 family function as transcriptional activators or inhibitors, with some showing increased activity in the presence of oleate, thereby regulating genes involved in fatty acid metabolism and peroxisomal functions. Additionally, certain members are involved in the biosynthesis of mycotoxins, host-selective toxins, and other secondary metabolites, playing a role in pathogenicity and ecological interactions. The family also includes proteins that regulate drug resistance, thiamine biosynthesis, and chromatin remodeling, indicating a broad functional spectrum related to cellular adaptation and stress response.
Interleukin-12 (IL-12)
Type: Family

This entry represents Interleukin-12 alpha and beta.

Interleukins are a group of cytokines that have important roles in cell growth, differentiation, and motility, and in the functioning of the immune system.

Interleukin-12 (also known as natural killer cell stimulatory factor, and cytotoxic lymphocyte maturation factor) is a 75kDa heterodimer composed of two genetically unrelated subunits - an alpha chain (p35 subunit) and a beta chain (p40 subunit). Production of the cytokine plays an important role in the generation of cell-mediated immunity against many infectious pathogens . The interluekin-12 beta chain also associates with interleukin-23 alpha to form interleukin-23 , a proinflammatory cytokine that is overexpressed in and around tumour tissues, where it induces local inflammation and promotes tumour development .
Actinoporin Pore-Forming Toxin (Actinoporin_PFT)
Type: Family

The actinoporin family comprises pore-forming toxins that target cell membranes, forming cation-selective hydrophilic pores around 1 nm in diameter, leading to cytolysis. These proteins share a domain architecture with a long N-terminal alpha-helix and a beta-sheet rich core. The pore formation process is multi-step, beginning with membrane binding via recognition of sphingomyelin, followed by oligomerization of monomers. Actinoporins are known for their hemolytic activity, and in some cases, they can cause cardiac stimulation, platelet aggregation, and cytotoxic effects. They are found in various organisms, including sea anemones, Hydra, and some plants, and are involved in defense and predation.
DNA Partitioning ATPase (DNA_Partitioning_ATPase)
Type: Family

This family of proteins is involved in various cellular processes related to DNA dynamics, particularly in the partitioning of plasmids and chromosomes during cell division. Members of this family are known to bind DNA and exhibit ATPase activity, which is often regulated by interaction with other proteins or DNA sequences. They play essential roles in ensuring the proper distribution of genetic material to daughter cells, which is critical for maintaining genetic stability and cell viability. Some members are implicated in inhibiting sporulation, while others are associated with virulence and growth within host cells. The ATPase activity of these proteins is typically stimulated by specific protein-protein and protein-DNA interactions, underscoring their regulatory complexity.
Bacterial HTH-type transcriptional regulator (Bact_HTH_transcr_reg)
Type: Family

The protein family includes transcriptional regulators that typically function as repressors, binding to specific DNA regions to control gene expression. These proteins are involved in various cellular processes, including the utilization of different sugars, amino acids, and other compounds, as well as the response to environmental conditions such as nutrient availability. They often regulate operons responsible for the uptake and degradation of specific substrates, linking metabolic pathways to gene expression. Some family members are also implicated in bacterial virulence and stress adaptation. The family is characterized by the presence of a helix-turn-helix (HTH) motif, which facilitates DNA binding, and many are regulated by effector molecules that modulate their DNA-binding activity.
YpeA/RimI acetyltransferase (YpeA/RimI_acetyltransf)
Type: Family

The YpeA/RimI acetyltransferase family encompasses enzymes that catalyze the transfer of an acetyl group from acetyl-CoA to various substrates, including proteins and polyamines. Members of the YpeA subfamily are acetyltransferases with unspecified functions, while those in the RimI subfamily specifically acetylate the N-terminal alanine of ribosomal protein bS18. Other members display diverse specificities, such as acetylation of polyamines, mycothiol, or antibiotics like gentamicin and streptothricin, contributing to metabolic processes and antibiotic resistance.