SII-SWORD/CoKE huggingface dataset:
Polyferredoxin-like electron transfer protein (Polyferredoxin-like_ET)
Type: Family

This family of proteins includes polyferredoxins, which are iron-sulfur proteins involved in electron transfer processes. Polyferredoxins typically contain multiple iron-sulfur clusters that facilitate the transfer of electrons within cellular redox reactions. These proteins play a crucial role in various metabolic pathways, including but not limited to photosynthesis, respiration, and nitrogen fixation. The presence of a polyferredoxin-like protein suggests a potential function in electron transfer, although the specific biochemical pathways and reactions may vary among family members.
Glyceraldehyde-3-phosphate dehydrogenase (GAP_dehydrogenase)
Type: Family

This family of proteins includes enzymes that are essential for the glycolytic pathway. They are responsible for the conversion of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate, a reaction that involves the use of NAD as a cofactor. Initially, a hemiacetal intermediate is formed between the substrate and a cysteine residue within the enzyme. This intermediate is then oxidized to a thioester, resulting in the reduction of NAD to NADH. Subsequently, the thioester is targeted by inorganic phosphate, leading to the production of 1,3-bisphosphoglycerate. The process is critical for cellular energy production, as it contributes to the generation of ATP and NADH, which are vital for various metabolic processes.
Adenylate-forming domain-containing protein (Adenylate-forming_domain)
Type: Family

This family of proteins includes enzymes that are involved in natural product biosynthesis, functioning similarly to non-ribosomal peptide synthetases. They are characterized by their ability to modify a single substrate rather than condensing multiple building blocks. Members of this family contain three distinct domains: an adenylation domain that activates substrate amino acids, a peptidyl carrier protein domain that carries the activated amino acid, and a reductase domain of the ferredoxin-NADP reductase type. The adenylation domain specifically recognizes and activates amino acids like L-serine, L-alanine, and L-valine, forming a thioester bond with the peptidyl carrier protein domain. The exact natural products synthesized by these enzymes are not yet known.
Crinkler effector (Crinkler_effector)
Type: Family

This family of proteins includes secreted effectors known to induce necrosis in host plants, which is a typical response of plant innate immunity. Members of this family possess a modular structure characterized by a signal peptide, a conserved N-terminal region, and variable C-terminal domains. The N-terminal region contains specific motifs essential for the translocation of these effectors into plant cells, facilitating their role in plant-pathogen interactions. The distinct motifs and domains within the N-terminus are crucial for their function and localization.
Ingression C2 domain-containing protein (Ingression_C2_domain)
Type: Family

This family of proteins is involved in cytokinesis, the process where the cytoplasm of a eukaryotic cell divides to form two daughter cells. Members of this family play a role in the ingression of the plasma membrane during this process, which is crucial for the separation of the daughter cells. They may also influence the synthesis of the primary septum, a structure essential for cell division in yeast. The presence of a C2 domain in some members suggests a role in membrane interaction during cytokinesis, although this domain is not necessary for the protein's recruitment to the actomyosin ring.
SRP1/TIP1-like Cell Wall Component (SRP1/TIP1-like)
Type: Family

This family of proteins includes members that are likely involved in the structure and integrity of the cell wall. They are characterized by similarity to the SRP1/TIP1 family, which suggests a role in cellular processes related to the cell wall. The exact functions of these proteins may vary, but one of the proteins is suggested to be a probable component of the cell wall, indicating a structural or functional role in maintaining the cell envelope.
Major Facilitator Superfamily Riboflavin Transporter (MFS_Riboflavin_Transporter)
Type: Family

This family of proteins is involved in the cellular uptake of riboflavin, also known as vitamin B2, which is an essential nutrient for many organisms. Members of this family are capable of transporting not only riboflavin but also its derivatives, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), across cellular membranes. These proteins are part of the major facilitator superfamily and facilitate the passage of these molecules through the cell membrane, impacting various biological processes by ensuring the availability of these critical cofactors for metabolic reactions.
UPF0421 (UPF0421)
Type: Family

This family of proteins is classified under the UPF0421 family, which is a group of uncharacterized proteins. Due to the lack of specific functional information, the precise biological roles of these proteins remain unknown. Typically, proteins grouped in such families are identified based on sequence similarities and conserved motifs that suggest a potential common function or structural framework. However, without experimental evidence or detailed bioinformatics analysis, it is not possible to ascribe a definitive function to the UPF0421 protein family. Further research, including experimental characterization, is necessary to elucidate the functions of proteins within this family.
CoA-transferase III family involved in biosynthesis and detoxification (CoA-trans_III_biosynth/detox)
Type: Family

The CoA-transferase III family is involved in diverse biosynthetic and degradation pathways. One member, Acetyl-coenzyme A transferase nodX, is crucial in the biosynthesis of indole diterpenes nodulisporic acids, which have potent insecticidal properties without adverse effects on mammals. It participates in multiple steps, including oxidation and prenylation, leading to the formation of various nodulisporic acids. Another member, Acyl-CoA transferase FVEG_12629, plays a role in the detoxification of benzoxazolinones in fungi, converting toxic compounds produced by host plants into non-toxic substances. This involves hydrolysis, N-malonylation, and possibly lactone hydrolysis, aiding in the degradation of plant-derived antimicrobial compounds.
Interferon-induced very large GTPase (VLIG_GTPase)
Type: Family

This family of proteins is characterized by GTPase activity and is implicated in cellular processes that are induced by interferon. Members of this family are part of the TRAFAC class dynamin-like GTPase superfamily and are known for their large size. These GTPases are involved in the immune response and may play a role in antiviral mechanisms within the cell. The exact functions of these proteins can vary, but they typically contribute to the remodeling of cellular membranes and the regulation of signaling pathways in response to external stimuli such as viral infections.
Chloroplastic ATP-dependent AMP-binding Enzymes (Chloroplast_AMP-bd_Enzymes)
Type: Family

The ATP-dependent AMP-binding enzyme family is involved in the activation of fatty acids to acyl-carrier-protein (ACP), a crucial step in fatty acid metabolism. Members of this family, such as the probable acyl-activating enzyme 16 and the long-chain-fatty-acid--[acyl-carrier-protein] ligase AEE15, both chloroplastic enzymes from Arabidopsis thaliana, are implicated in the preparation of fatty acids for subsequent elongation processes within plastids. They act on medium to long-chain fatty acids, suggesting a role in the diversification of fatty acid chain lengths, which is essential for the proper functioning of biological membranes and the production of lipid-derived molecules.
Oryzine biosynthesis lactonohydrolase (Oryzine_lactonohydrolase)
Type: Family

This family of proteins includes lactonohydrolases involved in the biosynthesis of oryzines, which are natural products with a unique maleidride backbone. These enzymes participate in a multi-step pathway that begins with the formation of octenoic acid by a fungal fatty acid synthase. The acid is then activated and condensed with oxaloacetate, followed by a series of reactions including decarboxylation, dehydration, tautomerization, and reduction to produce intermediates such as piliformic acid. Key steps in the pathway to oryzine A and B involve hydroxylation of a diene intermediate and subsequent lactonisation by these lactonohydrolases, with further reduction transforming oryzine B into oryzine A. The enzymes are characterized by their similarity to the SMP-30/CGR1 family.
Mg-chelatase D/I-like (Mg-chelatase_DI-like)
Type: Family

This family of proteins is involved in the process of magnesium chelation, which is a critical step in the biosynthesis of chlorophyll. Members of this family are part of the Mg-chelatase enzyme complex, which catalyzes the insertion of a magnesium ion into protoporphyrin IX, a precursor of chlorophyll and heme. The activity of these proteins is essential for the proper function of the photosynthetic apparatus in plants and algae, as well as for the production of heme in other organisms. The proteins in this family share structural similarities that are indicative of their role in the Mg-chelatase complex.
Sulfoquinovosidase Glycosyl Hydrolase (Sulfoquinovosidase_GH31)
Type: Family

The glycosyl hydrolase 31 family is involved in the degradation of sulfoquinovosyl diacylglycerides (SQDG) and sulfoquinovosyl glycerol (SQGro), releasing sulfoquinovose (SQ) which is utilized as a source of carbon and sulfur. In E. coli, SQ is further degraded through the SQ-EMP sulfoglycolysis pathway. The family includes enzymes that exhibit retaining glycoside hydrolase activity, forming the alpha anomer of SQ. They can hydrolyze substrate analogs like para-nitrophenyl alpha-sulfoquinovoside (PNPSQ), with no activity toward 4-nitrophenyl alpha-D-glucopyranoside (PNPGlc). Some members also show alpha-glucosidase activity in vitro. The family's enzymes are regulated by inactivators like 5-fluoro-beta-L-idopyranosyl fluoride (5FIdoF) and are characterized by molecular coevolution of amino acid pairs essential for substrate recognition and structural integrity.
Non-functional Type II TA System Antitoxin (Non-func_TypeII_TA_Antitoxin)
Type: Family

The protein family includes antitoxin components associated with non-functional type II toxin-antitoxin systems. Specifically, the family member Orphan antitoxin ParD2 is known to be an antitoxin component that does not counteract the effects of any known RelE or ParE toxins. The function of the other family member, an uncharacterized protein y4kO, has not been described. Given the lack of comprehensive functional information for the entire family, the precise biological role of the family remains unclear.
Short-chain dehydrogenases/reductases member 12 (SDR_member_12)
Type: Family

This family of proteins includes members that are putative oxidoreductases, suggesting a role in catalyzing redox reactions. These proteins are characterized by their membership in the short-chain dehydrogenases/reductases (SDR) family, which is known for its involvement in the metabolism of a wide variety of compounds, including steroids, prostaglandins, and xenobiotics. The SDR enzymes typically utilize NAD(P)(H) as cofactors and are involved in the reduction or oxidation of alcohols, ketones, and aldehydes. Given the broad substrate specificity and wide distribution of SDR family members, proteins in this family may be implicated in diverse biological processes and pathways.
Cilia- and flagella-associated protein 57 (CFA-57)
Type: Family

This family of proteins is associated with the structure and function of cilia and flagella, which are hair-like organelles protruding from the cell surface. These organelles are critical for movement and sensory functions in many eukaryotic cells. Proteins in this family are believed to play a role in the assembly, maintenance, and proper functioning of cilia and flagella, contributing to the complex processes of cell motility and signal transduction.
Tiny macrocysts signaling regulators (Tiny_macrocysts_regulators)
Type: Family

This family of proteins includes regulators of the cAMP signaling pathway that are specific to sexual development in certain eukaryotic organisms. Members of this family are involved in controlling the levels of extracellular cAMP, which is a key second messenger in many biological processes. They achieve this by influencing the expression of enzymes responsible for cAMP degradation and their respective inhibitors, thereby modulating the signal transduction pathways that rely on cAMP as a signaling molecule.
Low molecular weight protein-tyrosine-phosphatase (LMW-PTP)
Type: Family

This family of proteins includes enzymes that function as phosphatases, specifically targeting phosphotyrosine residues. Members of this family are characterized by their ability to dephosphorylate tyrosine-phosphorylated proteins, which is a critical step in reversing the phosphorylation events that occur in signal transduction pathways. By removing phosphate groups from tyrosine residues, these phosphatases play a role in regulating cellular processes such as cell growth, differentiation, and metabolism. Their activity is essential for maintaining the balance of phosphorylation-dephosphorylation and for the proper function of many cellular signaling networks.
Carbohydrate Metabolism Mutarotase (Carb_Metab_Mutarotase)
Type: Family

This family of proteins includes enzymes involved in carbohydrate metabolism. Members of this family are known to participate in the catabolism of sugars such as L-fucose, and are capable of catalyzing the anomeric conversion of specific sugar isomers. The enzymes may exhibit activity towards various pyranosides, including L-galactopyranoside and D-arabinopyranoside, although activity towards D-fucopyranoside has not been detected. The family encompasses proteins with mutarotase activity, which is crucial for the proper utilization and breakdown of sugars, thereby playing a significant role in cellular energy processes.
RRT15-like (RRT15-like)
Type: Family

This entry includes Regulator of rDNA transcription protein 15 (RRT15) from yeast, which is involved in the modulation of rDNA transcription . Members of this family are characterised by their role in the regulation of ribosomal DNA transcription, which is a critical process for ribosome biogenesis and cell growth. Another yeast protein, the putative uncharacterised protein ART2 in included here, which has been reported as a product of a dubious gene prediction unlikely to encode a functional protein and it is not part of the S. cerevisiae S288c complete/reference proteome set . The entry also includes uncharacterised sequences from plants.
Hetero-Diels-Alderase-like (Hetero-Diels-Alderase-like)
Type: Family

This family of proteins includes enzymes that are putative hetero-Diels-Alderase, which are involved in the biosynthesis of complex meroterpenoids. These enzymes are thought to catalyze the key step of linking a polyketide moiety with a terpene component, such as humulene or its derivatives, to form a distinctive tropolone-humulene skeleton. This reaction is a crucial part of the biosynthetic pathways leading to compounds with significant biological activities, including xenovulene A, which inhibits the human gamma-aminobutyrate A (GABAA) benzodiazepine receptor, and eupenifeldin, which has antitumor properties. The family members are characterized by their similarity to the eupF Diels-Alderase and are likely to share a common catalytic mechanism in the formation of these bioactive meroterpenoids.
Peroxisomal Targeting Signal 1 Protein (PTS1_Protein)
Type: Family

This family of proteins is likely involved in the biogenesis and maintenance of peroxisomes, cellular organelles that play a crucial role in the metabolism of specific fatty acids and the detoxification of reactive oxygen species. Members of this family may also participate in amino acid metabolism. They are characterized by the presence of a peroxisomal targeting signal 1 (PTS1) at the C-terminus, which is essential for the transport of matrix proteins into the peroxisome. The PTS1 motif typically consists of a tripeptide sequence, although variations exist, suggesting a broader consensus sequence for this targeting signal.
DNA-dependent metalloprotease WSS1-like (WSS1-like_metalloprotease)
Type: Family

This family of proteins includes metalloendopeptidases that selectively target DNA-binding proteins in the presence of DNA, which facilitates the interaction between the protease and its substrates. These enzymes play a critical role in the repair of toxic DNA-protein cross-links (DPCs), such as those formed by trapped topoisomerase 1 on DNA lesions or induced by reactive compounds like formaldehyde. They are involved in the DNA damage response and the processing of stalled or collapsed replication forks by excising covalently trapped topoisomerase 1 from chromatin. The proteolysis of DPCs allows for subsequent repair through downstream DNA repair pathways. Recruitment to DPCs may occur via the SUMOylation of substrate proteins at sites of DNA damage.
MNNG export permease-like (MNNG_permease-like)
Type: Family

This family of proteins includes members that may function in the cellular response to alkylating agents. One characterized member is suggested to act as an export permease for N-methyl-N'nitro-N-nitrosoguanidine (MNNG), a mutagenic and carcinogenic chemical. The proteins in this family are also noted for their similarity to each other, suggesting a conserved role or function within the yeast species from which they are derived.
Zinc-dependent metalloproteinase M10B (Metalloproteinase_M10B)
Type: Family

This family of proteins includes zinc-dependent metalloproteinases, which are part of the peptidase M10B subfamily. These enzymes are characterized by their ability to cleave peptide bonds in various protein substrates, a process essential for numerous biological functions. They typically contain a zinc-binding motif that is crucial for their catalytic activity. Members of this family are involved in the degradation of extracellular matrix components, which plays a significant role in tissue remodeling, cell migration, and other physiological processes. They may also be implicated in pathological conditions when their activity is dysregulated. The precise functions of individual family members can vary and are often determined by their specific substrate preferences and regulatory mechanisms.
TRIM/RBCC E3 ubiquitin-protein ligases (TRIM_RBCC_E3_ubiq-ligases)
Type: Family

The TRIM/RBCC family includes E3 ubiquitin-protein ligases involved in various cellular processes. Members of this family play a crucial role in maintaining centrosome integrity by preventing centriole reduplication, likely through ubiquitination of proteins that promote this process. They also participate in epigenetic regulation by monoubiquitinating histone H2A at Lys-119, which is associated with transcriptional repression within Polycomb group (PcG) PRC2-like complexes. Additionally, they positively regulate peroxisome import by monoubiquitinating the peroxisomal import receptor PEX5, thereby stabilizing it and preventing its degradation. Some members also exhibit anti-HIV activity, contributing to the cellular defense against viral infection.
MAGUK Family Regulators of Signaling Pathways (MAGUK_Signaling_Regulators)
Type: Family

The MAGUK family proteins are multifunctional regulators of various signaling pathways. They are pivotal in the Hippo signaling pathway, where they can both negatively and positively modulate the pathway's activity. They facilitate interactions between different kinases and other proteins to control kinase activity and pathway activation, impacting cell proliferation, epithelial polarity, and epithelial-mesenchymal transition. Additionally, they play roles in cell migration, invasion, dendritic spine formation, and synaptogenesis, particularly by modulating the cell surface localization of N-cadherin. MAGUK family members are also positive regulators of the hedgehog signaling pathway, influencing early stages of the smoothened activity cycle and promoting the activation of downstream effectors at the ciliary tip.
Nuclear Positioning and Cytoskeleton Interaction Protein (Nuclear_Pos-Cytoskel_Interact)
Type: Family

This family of proteins is involved in the regulation of nuclear positioning and cytoskeletal interactions during cell division. Members of this family play a crucial role in the completion of asexual development by ensuring proper nuclear placement within the cell. They are also responsible for the formation of cortical microtubule capture sites, which are essential for dynein-dependent microtubule sliding and subsequent nuclear migration. These proteins function in anchoring the dynein motor complex to the cell cortex, particularly during late anaphase, facilitating the interaction between the cytoskeleton and the nucleus in budding yeast cells.
Meiosis-associated regulatory protein (Meiosis_regulatory)
Type: Family

This family of proteins is involved in the process of meiosis, which is a type of cell division that reduces the chromosome number by half and results in the production of gametes or spores. The known function within this family is associated with a regulatory role during the meiotic phase of the cell cycle. While one member of this family has been specifically implicated in meiosis, the function of other members remains to be characterized. The family includes proteins that may share structural features or sequence motifs that suggest a common biological role or evolutionary origin, despite the lack of detailed functional information for some members.
Cytochrome P450 monooxygenase involved in secondary metabolism (CYP450_monoxygenase_sec-met)
Type: Family

This family of proteins includes cytochrome P450 monooxygenases involved in the biosynthesis of various secondary metabolites. These enzymes catalyze oxidation reactions that modify substrates by introducing oxygen atoms, often as part of larger biosynthetic pathways for complex organic compounds. They play crucial roles in the formation of lipopeptides, indole diterpenes, and other bioactive molecules with applications ranging from agriculture to medicine. The family members are characterized by their ability to perform epoxidation, hydroxylation, and other oxidative modifications, which are essential for the structural diversification and bioactivity of the metabolites they help produce.
Phomopsin biosynthesis-associated protein (Phomopsin_biosynth_assoc)
Type: Family

This family of proteins is involved in the biosynthesis of phomopsins, which are hexapeptide mycotoxins known to cause lupinosis in livestock. These proteins operate within a gene cluster, orchestrating a series of post-translational modifications (PTMs) to produce and modify the core hexapeptide derived from a precursor. The modifications include cyclization, chlorination, hydroxylation, and the introduction of dehydroamino acids, contributing to the unique structure of phomopsin A. Additionally, some members are implicated in the construction of a macrocyclic structure and in the methylation steps that convert precursors to the mature mycotoxin forms. The precise roles of individual proteins within this family in the biosynthetic pathway are yet to be fully elucidated, as is the order of PTM events.