SII-SWORD/CoKE huggingface dataset:
Bacterial Luciferase Oxidoreductase (Bact_Lucif_Oxidored)
Type: Family

The bacterial luciferase oxidoreductase family encompasses a group of flavin-dependent enzymes involved in various bioluminescent and oxidative processes. Members of this family are responsible for light-emitting reactions in luminous bacteria, where the alpha and beta chains of alkanal monooxygenase work together to produce bioluminescence. Additionally, some family members participate in the degradation and assimilation of compounds such as camphor, contributing to bacterial growth on specific enantiomers as the sole carbon source. Other enzymes within the family are involved in the biosynthesis of antibiotics, the catabolism of alkylated cysteine, and the degradation of the pyridine ring of trigonelline. The family also includes enzymes that act on various substrates, including limonene, through epoxidation, and others that perform Baeyer-Villiger oxidations. The diverse functions of the family members highlight their role in bacterial metabolism and environmental adaptation.
Sel1/AlgK (Sel1_AlgK)
Type: Family

The Sel1/AlgK protein family is involved in various biological processes across different organisms. Members of the Sel1 subfamily, such as Protein sel-1 homologs and ERAD-associated E3 ubiquitin-protein ligase component HRD3, play crucial roles in the endoplasmic reticulum quality control system, particularly in the ER-associated degradation pathway for misfolded proteins. They are implicated in maintaining cellular homeostasis by enhancing the stability of specific proteins and may also participate in Notch signaling and the differentiation of pancreatic epithelium. The AlgK subfamily members are associated with the biosynthesis of alginate, a biopolymer involved in the formation of biofilms, by potentially catalyzing the polymerization of mannuronate. Other family members, such as Exopolysaccharide production negative regulators, are involved in modulating the biosynthesis of exopolysaccharides. The family also includes proteins like PodJL, which provides positional information for the localization of cell pole organelles, and secretory immunoglobulin A-binding proteins that interfere with host immune responses during infection.
UPF0353/GerABKA protein families (UPF0353/GerABKA_families)
Type: Family

The UPF0353 and GerABKA protein families consist of proteins with distinct functions. The UPF0353 family proteins are uncharacterized and their functions remain unknown. In contrast, the GerABKA family proteins are involved in the germination process of bacterial spores. They respond to various germinative agents such as L-asparagine, glucose, fructose, potassium ions, and inosine. Some members of the GerABKA family form complexes at the inner spore membrane, acting as receptors for specific nutrients like L-alanine, and are implicated in the germination response. The GerABKA family also includes proteins that contribute to virulence by enabling germination within phagocytic cells.
N-acetyltransferase, camello-type (NAT_camello-type)
Type: Family

This entry includes proteins from animals, fungi and bacteria with probable acetyltransferase activity, with many members belonging to the Camello family, including human N-acetylaspartate synthetase (NAT8L), which catalyses the synthesis of N-acetylaspartate (NAA) from L-aspartate and acetyl-CoA , and N-acetyltransferase 8 (NAT8), responsible for the acetylation of the free alpha-amino group of cysteine S-conjugates to form mercapturic acids, a detoxification pathway . The family also includes uncharacterised N-acetyltransferases and putative DNA-binding acetyltransferases. In addition, some members may act as transcription factors.
Intradiol Ring-Cleavage Dioxygenase (Intradiol_RC_Dioxygenase)
Type: Family

The Intradiol Ring-Cleavage Dioxygenase family comprises enzymes involved in the degradation of aromatic compounds through the beta-ketoadipate pathway. Members of this family are responsible for the ortho-cleavage of catechols and other dihydroxylated aromatic substrates, a critical step in the breakdown of complex aromatic molecules into simpler compounds that can be assimilated into central metabolic pathways such as the tricarboxylic acid cycle. These enzymes exhibit substrate specificity, with some preferring chlorinated catechols, while others act on non-chlorinated substrates or hydroxyquinol. Their activity is essential for the microbial utilization of a wide range of aromatic and hydroaromatic compounds, contributing to the biodegradation of pollutants and the recycling of organic matter in the environment.
Alpha-ketoacid dehydrogenase complex E1 component (Alpha-ketoacid_DH_E1_comp)
Type: Family

The protein family includes enzymes that are part of multi-component complexes responsible for the oxidative decarboxylation of alpha-keto acids. These enzymes play a crucial role in energy production by converting alpha-keto acids derived from branched-chain amino acids like valine, leucine, and isoleucine into acyl-CoA and CO2. The family encompasses the E1 subunit of the mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD) complex, as well as the pyruvate dehydrogenase complex, which converts pyruvate to acetyl-CoA and CO2. The E1 subunit specifically catalyzes the decarboxylation of the alpha-ketoacid and forms an enzyme-product intermediate, which is then processed by the E2 subunit. Some members also exhibit branched-chain 2-oxoacid dehydrogenase activity.
Hydratase/Decarboxylase Family, MhpD Subfamily (Hydratase-Decarb/MhpD_sf)
Type: Family

The hydratase/decarboxylase family, specifically the MhpD subfamily, consists of enzymes that play a crucial role in various bacterial catabolic pathways. Members of this family are responsible for the hydration of unsaturated keto acids, converting them into their corresponding hydroxy-keto acids. For instance, they catalyze the transformation of 2-hydroxypentadienoic acid to 4-hydroxy-2-ketopentanoic acid, a reaction involved in the breakdown of aromatic compounds. Some family members are also implicated in the degradation of testosterone and 2-aminophenol, indicating a broader metabolic significance. The enzymes exhibit a commonality in their reaction mechanism, which involves the addition of water across a double bond of an unsaturated substrate, demonstrating their functional coherence within the family.
CbxX/CfxQ RuBisCO activation and ESX secretion (CbxX/CfxQ_RuBisCO_ESX)
Type: Family

The CbxX/CfxQ family includes proteins with diverse functions, primarily associated with the activation and expression of RuBisCO, an enzyme critical for carbon fixation in photosynthetic organisms. Members of this family exhibit ATPase activity, which is necessary for the release of RuBP from inhibited RuBisCO, facilitating the carboxylation process. Additionally, some proteins within this family are part of the ESX specialized secretion systems (T7SS) in bacteria, playing roles in virulence, iron acquisition, and DNA conjugation. These proteins likely use their ATPase activity to provide energy for the export of various substrates through these secretion systems.
KCMF1 and Dystrophin (KCMF1/Dystrophin)
Type: Family

The KCMF1 and Dystrophin protein family is involved in a variety of cellular functions related to the maintenance of cellular structure, signaling, and protein degradation. Members of the family such as E3 ubiquitin-protein ligases KCMF1 have intrinsic E3 ubiquitin ligase activity, promoting ubiquitination and regulating signaling pathways. Dystrophin and related proteins anchor the extracellular matrix to the cytoskeleton, play roles in stabilizing the sarcolemma, and are involved in synaptic transmission. Dystrobrevins function as scaffolding proteins, assembling molecules to membranes and regulating gene expression. Utrophins may also anchor the cytoskeleton to the plasma membrane. Overall, the family is crucial for muscle integrity, synaptic function, and the regulation of protein turnover.
FAD-binding Monooxygenases in Secondary Metabolism (FAD-binding_Monooxygenases)
Type: Family

The FAD-binding monooxygenase family is involved in various biosynthetic pathways, catalyzing a range of oxidation reactions. Members of this family play key roles in the synthesis of diverse secondary metabolites, including fungal meroterpenoids, loline alkaloids, antibiotics, and mycotoxins. These enzymes typically perform Baeyer-Villiger oxidations, converting ketones to esters or lactones, and are also involved in epoxidation, hydroxylation, and other oxidative modifications. Their activities contribute to the structural complexity and biological activities of natural products, such as antimicrobial, insecticidal, and kinase inhibitory properties. The family includes dual-functional enzymes with additional methyltransferase domains, highlighting the versatility and multifunctional nature of these monooxygenases in natural product biosynthesis.
Ankyrin Repeat and Cyclin-Dependent Kinase Inhibitor (Ank_Repeat/CDKN_Inhibitor)
Type: Family

The protein family includes ankyrin repeat domain-containing proteins and cyclin-dependent kinase inhibitors. Ankyrin repeat proteins may play roles in cell division and other regulatory functions, while cyclin-dependent kinase inhibitors are involved in cell cycle regulation by interacting with CDK4 and CDK6, inhibiting cell growth and proliferation. Some family members are involved in endosomal mRNA transport, chitinase secretion, and phosphoprotein substrate recognition. Others may act as substrate-recognition components of E3 ubiquitin-protein ligase complexes, mediating ubiquitination and proteasomal degradation of target proteins.
SET2 Histone-Lysine N-Methyltransferase (SET2_Histone-Lys_MeTrsfase)
Type: Family

The SET2 histone-lysine N-methyltransferase family is involved in the methylation of histone H3 at lysine 36 (H3K36), which is a key post-translational modification associated with transcriptional activation or repression. Members of this family play critical roles in various biological processes, including transcription elongation, transcription repression, and the regulation of gene expression during development, cell differentiation, and immune responses. Some family members also methylate histone H3 at lysine 4 or 27, marking epigenetic transcriptional activation or repression. The family is characterized by the presence of AWS and SET domains, which are necessary for their methyltransferase activity and transcriptional regulatory functions.
Cueball/EGF/LRP/Nidogen (Cueball_EGF_LRP_Nidogen)
Type: Family

Cueball proteins are involved in reproductive processes, specifically in spermatogenesis and oogenesis across various species of Drosophila. They may also play a role in lipid metabolism and neuronal function. The epidermal growth factor (EGF) proteins within the family stimulate the growth of epidermal and epithelial tissues and have a magnesiotropic hormone function that regulates magnesium reabsorption in the renal distal convoluted tubule. The low-density lipoprotein receptor-related proteins (LRPs) act as coreceptors in the Wnt signalling pathway, crucial for bone formation, cell fate determination, and embryonic development. Nidogens are cell adhesion glycoproteins that contribute to the structure and function of basement membranes, mediating interactions between cells and the extracellular matrix, and are involved in processes such as osteoblast differentiation and neural plasticity.
Protein-glutamine gamma-glutamyltransferases (Transglutaminase)
Type: Family

The Transglutaminase family comprises enzymes that catalyze the formation of isopeptide bonds between glutamine and lysine residues, cross-linking proteins and stabilizing structures such as the cornified envelope in keratinocytes and fibrin clots. They also conjugate polyamines to proteins, contributing to various biological processes including cell proliferation, skin and hair formation, and wound healing. Some family members are involved in apoptosis by cross-linking cytoskeletal and extracellular matrix proteins, while others participate in post-translational modifications like protein serotonylation and dopaminylation, impacting chromatin organization and neurotransmission. Their activity is regulated by GTP and Ca(2+), with GTP inhibiting and Ca(2+) promoting the active conformation. They also play roles in cellular signaling independent of their enzymatic activity.
Mucin/von Willebrand/Thrombospondin superfamily (Mucin_vWF_Thrombospondin_sf)
Type: Family

The protein family is involved in various biological processes, including the protection of mucosal surfaces, hemostasis, and developmental events in the central nervous system. Members of the family function as gel-forming mucins that coat epithelia, providing a protective barrier against pathogens and facilitating nutrient absorption. They also play roles in platelet adhesion during vascular injury, neuronal aggregation, and gamete recognition during fertilization. Some family members act as chaperones for other proteins, contribute to the structural integrity of specific tissues, and participate in innate immunity by storing antimicrobial molecules.
Pre-mRNA-splicing factor CWC22 (CWC22_splicing_factor)
Type: Family

The CWC22 family is involved in pre-mRNA splicing and exon-junction complex (EJC) assembly. Members of this family are essential components of the spliceosome, participating in the splicing of both major and U12-type introns. They play a critical role in the regulation of mRNA splicing, influencing the expression of specific splice forms related to sexual differentiation in some species. Additionally, CWC22 proteins prevent EIF4A3 from non-specifically binding RNA, guiding it to the splicing machinery to facilitate EJC assembly on mature mRNAs. This function is crucial for nonsense-mediated mRNA decay, a surveillance pathway that degrades mRNAs with premature stop codons. In some organisms, CWC22 family members are also implicated in early embryogenesis, tissue differentiation, and other cellular processes such as nucleolar targeting of specific proteins and osmoregulatory glycerol response.
Protein phosphatase 1 regulatory subunit 3 (PP1_regulatory_subunit_3)
Type: Family

This family of proteins acts as regulatory subunits for protein phosphatase 1 (PP1), a serine/threonine-specific phosphatase involved in a variety of cellular processes. Members of this family target PP1 to glycogen particles and regulate its activity in glycogen metabolism. They play a crucial role in the activation of glycogen synthase, which facilitates glycogen synthesis, and in the inhibition of glycogen phosphorylase, thereby limiting glycogen breakdown. These proteins contain distinct regions responsible for binding to PP1, glycogen, and various enzymes involved in glycogen metabolism, such as glycogen phosphorylase and glycogen synthase. Some members are known to possess a carbohydrate-binding module (CBM21) that is involved in localizing to glycogen. The activity of these proteins is essential for the regulation of glycogen storage, particularly in response to insulin stimulation, and they may have roles in cell division, muscle contractility, and protein synthesis.
Oxylipin biosynthesis and metabolism (Oxylipin_biosynth_metab)
Type: Family

The protein family is involved in the biosynthesis and metabolism of oxylipins, which are signaling molecules derived from polyunsaturated fatty acids. Members of the family exhibit dual cyclooxygenase and peroxidase activities, catalyzing the conversion of arachidonic acid to prostaglandin G2 and subsequently to prostaglandin H2, precursors to various prostanoids involved in inflammatory responses. Some members also produce hydroxyoctadecadienoates from linoleic acid and contribute to the generation of specialized pro-resolving mediators during inflammation. Additionally, the family includes enzymes that catalyze the primary oxygenation of fatty acids into hydroperoxides, playing roles in cell signaling, wound healing, and protection from infection. The family's activity is regulated by nonsteroidal anti-inflammatory drugs and other inhibitors, indicating its significance in both physiological and pathological processes.
Inhibitor of Apoptosis (IAP)
Type: Family

The IAP family of proteins are multifunctional regulators of apoptosis, inflammation, immunity, cell proliferation, and cell cycle control . They exhibit E3 ubiquitin-protein ligase activity, modulating NF-kappa-B signalling and various cell signalling pathways. IAP proteins inhibit caspases and apoptosis, either directly by binding to caspases or indirectly through ubiquitination of pro-apoptotic proteins, promoting cell survival. They also play roles in innate immune signalling by regulating pattern recognition receptors and can suppress the formation of ripoptosomes, complexes capable of inducing cell death. Additionally, some IAP members are involved in Wnt signalling, copper homeostasis, and the regulation of cell motility. Their BIR domains are crucial for inhibiting caspases and interacting with other proteins, while RING domains are essential for their E3 ligase activity.
PAN2-PAN3 complex catalytic subunit (PAN2-PAN3_catalytic_subunit)
Type: Family

This family of proteins functions as catalytic subunits in the PAN2-PAN3 deadenylation complex, which is involved in the cytoplasmic degradation of mRNA. These proteins shorten poly(A) tails of RNA, a process that is stimulated by poly(A)-binding proteins. Following deadenylation, the mRNA is rapidly degraded by the CCR4-NOT complex. The deadenylated mRNAs are further degraded by either exosome-mediated 3'-5' exonucleolytic degradation or deadenylation-dependent decapping and 5'-3' exonucleolytic degradation. Additionally, these proteins may play a role in the post-transcriptional maturation of mRNA poly(A) tails and can be involved in regulating the stability of specific mRNAs under certain conditions, such as the HIF1A-mediated hypoxic response.
EFG1 rRNA-processing (EFG1_rRNA-proc)
Type: Family

The EFG1 family consists of rRNA-processing proteins that play a crucial role in the maturation and processing of ribosomal RNA, an essential step in the formation of functional ribosomes. Members of the EFG1 family are involved in various cellular processes, including growth at elevated temperatures, resistance to hydroxyurea, and cell cycle progression. The conservation of these proteins across different species highlights their fundamental role in the maintenance of cellular function and genome integrity.
Natriuretic Peptide Hormone (Natriuretic_peptide)
Type: Family

The natriuretic peptide family consists of hormones that play crucial roles in cardiovascular and renal homeostasis. Members of this family are involved in the regulation of extracellular fluid volume and electrolyte balance through processes such as natriuresis, diuresis, vasorelaxation, and the inhibition of renin and aldosterone secretion. They act by binding to specific receptors, such as NPR1, to stimulate the production of cGMP, which then activates downstream effector proteins. Some peptides in this family also have antifibrotic effects in the heart, serve as paracrine factors, and are implicated in vascular remodeling, energy metabolism regulation, and blood pressure control. They may also play roles in pregnancy by promoting trophoblast invasion and spiral artery remodeling, as well as in lipid metabolism and energy homeostasis in adipose tissue.
Yeast SRP1/TIP1 Cell Wall (Yeast_SRP1/TIP1_CWP)
Type: Family

The SRP1/TIP1 family is characterized by proteins that are predominantly involved in cell wall composition and organization. Members of this family are found as components of the cell wall, with some required for anaerobic growth and others contributing to cell surface hydrophobicity. A subset of proteins within this family, known as the Seripauperin subfamily, shares these characteristics. Additionally, one member of the SRP1/TIP1 family exhibits esterase activity, preferring esters of fatty acids with chain lengths ranging from 4 to 16 carbon atoms. The presence of intragenic tandem repeats is noted in some proteins, indicating potential variability in function or structure among different strains of S. cerevisiae.
Diverse Enzymatic Activities (Diverse_Enzym_Activities)
Type: Family

The protein family includes enzymes involved in various biological processes such as cell wall biosynthesis, antibiotic resistance, and secondary metabolite biosynthesis. Members of the family exhibit activities like D-alanyl-D-alanine carboxypeptidase, involved in peptidoglycan remodeling, and beta-lactamase activity, providing resistance to beta-lactam antibiotics. Some proteins are key in the biosynthesis of hypolipidemic agents like lovastatin and compactin, acting as acyltransferases and methylbutanoyltransferases. Others participate in the degradation of synthetic polymers like nylon or in the metabolism of esters such as methyl acetate. The family showcases diverse enzymatic functions, including amidase and esterase activities, highlighting a broad substrate specificity and a role in various metabolic pathways.
ExbB/TolQ Biopolymer Transport (ExbB/TolQ_transport)
Type: Family

The ExbB/TolQ family is involved in energy-dependent transport processes across the bacterial outer membrane. Members of this family, such as ExbB and TolQ, are integral components of systems like the TonB-dependent transporter and the Tol-Pal system. In the TonB-dependent transport system, ExbB works in conjunction with ExbD and TonB to facilitate the uptake of various receptor-bound substrates, protecting ExbD from proteolysis and stabilizing TonB. The Tol-Pal system, which includes TolQ, is essential for cell division, contributing to outer membrane invagination and maintaining membrane integrity. It is also involved in the activation of TolA, interaction with Pal, and the uptake of colicins and phage DNA. The ExbB/TolQ family plays a critical role in bacterial survival and adaptation by mediating the transport of nutrients and maintaining cellular structures.
Aldo/Keto Reductase (Aldo-Keto_reductase)
Type: Family

The Aldo/Keto Reductase family encompasses enzymes with oxidoreductase activity, catalyzing the reduction and oxidation of various aldehydes and ketones. Members of this family are involved in diverse biological processes, including the salvage pathway of pyridoxal phosphate, the biosynthesis of monoterpenoid indole alkaloids, and the degradation of plant-produced benzoxazolinones. They exhibit broad substrate specificity, with some acting on pyridoxal, alkaloids, and benzoxazolinones. These enzymes typically utilize NADPH or NADP(+) as cofactors. Their functions are crucial for maintaining cellular homeostasis of key metabolites and for plant-microbe interactions, such as nodulation inhibition and detoxification of phytoanticipins.
ADP-ribosylglycohydrolase (ADP-ribosylglycohydrolase)
Type: Family

The ADP-ribosylglycohydrolase family is involved in the regulation of various cellular processes through the hydrolysis of ADP-ribose attached to proteins. Members of the family act as hydrolases, preferentially targeting the alpha-O-linkage of ADP-ribose, particularly when attached to serine or threonine residues, playing a crucial role in the DNA damage response. The family includes both active enzymes that contribute to the reversal of ADP-ribosylation, a post-translational modification, and inactive members that may have alternative functions, such as involvement in myofibril assembly during cardiac development. Some members are implicated in the degradation of free poly(ADP-ribose), preventing cell death signaling pathways like parthanatos. Others may participate in interbacterial competition systems or the regulation of nitrogen fixation in prokaryotes. The family is characterized by a conformational change upon substrate binding, which facilitates substrate recognition and catalysis.