SII-SWORD/CoKE huggingface dataset:
Notoamide biosynthesis regulator (Notoamide_regulator)
Type: Family

This family of proteins includes transcription factors that are likely involved in the regulation of gene clusters responsible for the biosynthesis of notoamides. Notoamides are fungal indole alkaloids known for their unique bicyclo[2.2.2]diazaoctane core structure. Members of this family play a key role in the production of these secondary metabolites, which have potential pharmacological applications due to their complex molecular architecture and biological activities.
FkbM Methyltransferase (FkbM_Methyltransferase)
Type: Family

This family of proteins is involved in the modification of Nod factors, which are signaling molecules central to the establishment of symbiotic relationships between certain plants and nitrogen-fixing bacteria. Specifically, these proteins carry out the 2-O-methylation of the fucosyl group on Nod factors, a modification that is crucial for the proper function of these signaling molecules. Members of this family share structural similarities that define their role in the methylation process.
Chloroplast Clp protease adapter protein ClpF (Clp_protease_adapter_ClpF)
Type: Family

ClpF is involved in the regulation of the plastid Clp protease system, which is essential for the maintenance of chloroplast function and protein quality control. ClpF acts as an adapter protein that facilitates the recruitment of the ClpS1 co-chaperone to ClpC chaperones . This interaction is crucial for the formation of a binary adapter complex that enables selective substrate recognition and delivery to the Clp protease complex (CLPC) within chloroplasts. The activity of ClpF is thus integral to the proper functioning of the Clp protease system, which plays a key role in the degradation of misfolded or damaged proteins and the regulation of various chloroplast processes.
Nicotinate phosphoribosyltransferase-like (NAPRTase-like)
Type: Family

This family of proteins is involved in the biosynthesis of NAD, a crucial coenzyme in redox reactions. Members of this family catalyze the conversion of nicotinate and 5-phospho-D-ribose 1-phosphate into beta-nicotinate D-ribonucleotide, utilizing ATP in the process. The proteins are characterized by a multi-domain structure, including an N-terminal domain, a central catalytic domain, and a distinctive C-terminal domain with a zinc knuckle-like motif. The central domain is responsible for the enzyme's primary function, while the C-terminal domain may play a role in regulation or additional, yet unidentified, functions. The family is a part of the NAPRTase superfamily, which is known for its role in NAD biosynthesis, but this particular group is noted for its significant divergence from other members.
D-cycloserine Biosynthesis Enzyme (DcsG_Biosynth_Enzyme)
Type: Family

This family of proteins is involved in the production of the antibiotic D-cycloserine, which is a structural analog of D-alanine and is used to treat tuberculosis. Members of this family are responsible for catalyzing the conversion of O-ureido-D-serine to D-cycloserine. They also interact with other substrates such as D-homocysteine and beta-aminooxy-D-alanine during the biosynthesis process.
Vacuole Formation Regulator (Vacuole_Formation_Reg)
Type: Family

This family of proteins is crucial for plant reproductive development. Members are involved in the formation of large vacuoles, which are essential during the early stages of gametophyte development. They may play a role in the regulation of vesicular fusion, facilitating vacuole formation in both female and male gametophytes. The proper function of these proteins ensures successful megagametogenesis and microgametogenesis, which are critical processes for sexual reproduction in plants.
Metallophosphoesterase YfcE-like (MetalloPDE_YfcE-like)
Type: Family

This family of proteins exhibits phosphodiesterase activity, specifically hydrolyzing artificial chromogenic substrates such as bis-p-nitrophenyl phosphate and, to a lesser extent, thymidine 5'-monophosphate p-nitrophenyl ester and p-nitrophenylphosphorylcholine. They do not show catalytic activity towards cyclic nucleotides like cAMP or cGMP, nor do they act on nucleotides or typical phospholipase substrates like phosphatidylcholine. The natural substrate for these enzymes remains unidentified. They are characterized by their membership in the metallophosphoesterase superfamily and are competitively inhibited by phosphate ions, suggesting a regulatory mechanism sensitive to phosphate levels.
tRNA methyltransferase O (tRNA_methyltr_O)
Type: Family

The tRNA methyltransferase O family is characterized by its members' involvement in the methylation of tRNA molecules. Proteins in this family are likely to bind S-adenosyl-L-methionine (SAM) and transfer a methyl group from SAM to specific nucleotides within tRNA, a process critical for the proper folding, stability, and function of tRNA. Methylation can affect tRNA's secondary and tertiary structures, impacting the accuracy and efficiency of protein synthesis. The exact substrates and specific roles of the AF_0433 protein within this family may vary, but its function is generally associated with tRNA modification and the fine-tuning of translational fidelity.
Bax-like (Bax-like)
Type: Family

This family of proteins is involved in a variety of cellular processes. The specific functions may include roles in metabolism, cell signaling, structural integrity, or other essential biological activities. The proteins may act as enzymes, receptors, transporters, or have other functions depending on their structure and cellular context. They can be involved in the regulation of pathways essential for cell survival, growth, and differentiation. The precise function of this family of proteins can vary widely among different organisms and cell types.
Uncharacterized lipoprotein YbaY-like (Lipoprotein_YbaY-like)
Type: Family

This family of proteins includes uncharacterized lipoproteins, such as YbaY from E. coli. Lipoproteins are typically associated with the bacterial cell membrane and can play diverse roles, including structural functions, acting as enzymes, or serving as factors in signal transduction. Given the uncharacterized nature of this protein, its specific function within the cell is not clearly defined. However, it may be involved in processes typical of membrane-associated lipoproteins, such as cell wall maintenance, response to environmental changes, or interaction with other cellular components.
F-box/SCF ubiquitin ligase complex component (F-box_SCFL_complex_component)
Type: Family

This family of proteins includes members that are likely part of the SCF (SKP1-CULLIN-F-box) E3 ubiquitin-protein ligase complex, suggesting a role in the ubiquitin-mediated protein degradation or signaling pathways. They are implicated in male meiotic prophase I progression, including telomere bouquet formation, homologous chromosome pairing, and synaptonemal complex formation, which is crucial for stabilizing chromosomal associations and promoting crossover events. Additionally, these proteins are involved in meiotic DNA double-strand break repair, playing a role in the recruitment of repair proteins to the sites of DNA damage.
Gynoecium Development Regulator (Gynoecium_Dev_Regulator)
Type: Family

This family of proteins is involved in the regulation of cell growth anisotropy during the development of the gynoecium, which is the female reproductive part of a flower. Members of this family work in conjunction with other proteins to coordinate cell-cell communication with cellular growth processes. Through this collaborative function, they play a crucial role in the proper formation and differentiation of the gynoecium, ensuring reproductive success in plants.
Cyclic 2,3-diphosphoglycerate synthetase-like (cDPG_synthetase-like)
Type: Family

This family of proteins includes enzymes that are responsible for the synthesis of cyclic 2,3-diphosphoglycerate (cDPG), a molecule with a role in adaptation to extreme environments. Members of this family catalyze the formation of cDPG through an ATP-dependent mechanism, creating an intramolecular phosphoanhydride bond. The activity of these enzymes is crucial for organisms that encounter conditions such as high salinity or temperature, as cDPG can act as a protective compound stabilizing proteins and other cellular structures.

This entry also includes Arginine synthetase ArcE which catalyses the conversion of L-arginine to citrulline while conserving the energy of arginine deimination to generate ATP from ADP and free phosphate .
Copper Efflux Major Facilitator (Copper_Efflux_MFS)
Type: Family

This family of proteins is involved in the efflux of copper or copper complexes, suggesting a role in copper resistance. Members are part of the major facilitator superfamily, which is characterized by facilitating the transport of a wide variety of substrates across cellular membranes.
Flavunoidine biosynthesis N-methyltransferase (Flavunoidine_N-MTase)
Type: Family

This family of proteins includes N-methyltransferases involved in the biosynthesis of complex alkaloidal terpenoids. They catalyze the methylation of L-lysine to produce N,N-dimethyl-L-lysine, a precursor for the synthesis of dimethylcadaverine. This reaction is a key step in the formation of flavunoidine, a compound with a tetracyclic terpenoid core. Members of this family are typically part of gene clusters that coordinate the synthesis of such specialized metabolites, which often have significant biological activity. The enzymes from this family share a common structural fold and utilize S-adenosylmethionine (SAM) as the methyl donor, characteristic of the class V-like SAM-binding methyltransferase superfamily.
EGF Receptor Signaling Regulator (EGF_Rcpt_Signaling_Reg)
Type: Family

This family of proteins is involved in early developmental processes, specifically in the formation and differentiation of photoreceptors. Members of this family play a crucial role in the epidermal growth factor (EGF) receptor signaling pathway. They are known to interact with specific receptors, such as the torpedo receptor, which is significant in the visual system.
Cisplatin resistance-associated protein (Cisplatin_resist-associated)
Type: Family

This family of proteins is associated with cellular mechanisms that confer resistance to the chemotherapeutic agent cisplatin. Members of this family are implicated in processes that likely involve the recognition and repair of cisplatin-induced DNA damage or the modulation of cellular pathways to mitigate the toxic effects of this compound. The exact molecular function and the pathway(s) in which these proteins operate may vary among different organisms and could involve a complex interplay with other cellular components.
Oxopyrrolidines Biosynthesis-associated Protein (Oxopyrrolidines_Biosynth-assoc)
Type: Family

This family of proteins is involved in the biosynthesis of oxopyrrolidines, which are polyketide-amino acid hybrid compounds characterized by tetramic acid structures. Although members of this family are associated with a gene cluster responsible for oxopyrrolidines production, they do not appear to contribute to the biosynthesis of oxopyrrolidines A and B specifically.
GHMP kinase superfamily L-arabinokinase (GHMP_kinase_L-arabinokinase)
Type: Family

This family of proteins includes enzymes that are involved in the metabolic conversion of L-arabinose, a type of sugar, into its activated form, UDP-L-arabinose. This process is part of the salvage pathway, which recycles free sugars for further biochemical utilization. Members of this family are also suggested to have a role in the transport of arabinose across cellular membranes. The family is a member of the GHMP kinase superfamily, which is characterized by a conserved kinase domain involved in the phosphorylation of small molecules.
Dimeric xanthone biosynthesis cluster protein (Dimeric_xanthone_biosynth)
Type: Family

This family of proteins is involved in the biosynthesis of dimeric xanthones, specifically the cryptosporioptides. Members of this family participate in various steps of the metabolic pathway, including the synthesis of atrochrysone thioester, release of atrochrysone carboxylic acid, decarboxylation, oxidation, reduction, dehydration, and Baeyer-Villiger oxidation. They also contribute to the formation of key intermediates such as emodin, chrysophanol, and dihydroxanthone, and are involved in the introduction of epoxides, carboxylation of butyrate, esterification, and the final dimerization process that leads to the production of cryptosporioptides A, B, and C.
Non-NMDA Glutamate Receptor Accessory Protein (Non-NMDA_GluR_Accessory)
Type: Family

This family of proteins includes accessory components that are essential for modulating glutamate-gated ion currents. Members of this family are believed to influence the gating mechanisms of ionotropic glutamate receptors, specifically those that are not classified as NMDA receptors. These proteins may play a role in the regulation of synaptic transmission and neuronal communication by affecting the function of glutamate receptors, which are critical for excitatory signaling in the nervous system.
GMC Oxidoreductase Cellobiose Dehydrogenase (GMC_Oxidoreductase_CD)
Type: Family

This family of proteins is involved in the degradation of plant cell wall components, specifically lignin and cellulose. Members of this family have the ability to oxidize cellobiose, a disaccharide derived from the hydrolysis of cellulose, converting it into cellobionolactone. The enzymatic activity of these proteins plays a crucial role in the biological process of lignocellulose breakdown, which is fundamental for carbon cycling in the environment. The family is part of the GMC oxidoreductase superfamily, which is characterized by a wide range of oxidoreductase activities.
Gramillin-biosynthesis-related methyltransferase (Gramillin-biosynth_MTr)
Type: Family

This family of proteins includes methyltransferases involved in the biosynthesis of specialized lipopeptides, such as gramillins. These enzymes participate in various steps of the biosynthetic pathway, including initiation of fatty acid synthesis, hydroxylation, oxidation, transamination, and disulfide bond formation. They may also play a role in the regulation of this pathway and possess broader enzymatic functions. The proteins are characterized by a SAM-binding motif and are related to the class V-like SAM-binding methyltransferase superfamily. They are implicated in the production of compounds that can induce cell death in specific plant species.
Ankyrin repeat domain-containing protein 12 (ANKRD12)
Type: Family

This family of proteins includes members that are involved in the regulation of gene expression by modulating the chromatin structure. They are known to interact with histone deacetylases (HDACs) and p160 coactivators, which are part of the nuclear receptor complexes. Through these interactions, they can inhibit the transactivation of genes that are regulated by ligand-dependent nuclear receptors. This regulatory mechanism is important for controlling gene expression in various cellular processes.
DNA damage-repair/toleration-associated protein (DNA_repair-toleration)
Type: Family

This family of proteins is involved in DNA damage repair and toleration. Members of this family have been shown to have the ability to complement bacterial recA mutations, indicating a role in DNA repair mechanisms. However, the specific function of these proteins within their native plant organisms remains to be fully elucidated.
2,6-Dihydroxypyridine 3-monooxygenase (DHP_3-monooxygenase)
Type: Family

This family of proteins includes enzymes that are involved in the metabolic breakdown of nicotine, such as 2,6-dihydroxypyridine 3-monooxygenase from Paenarthrobacter nicotinovorans. Specifically, they are responsible for the enzymatic reaction that transforms 2,6-dihydroxypyridine to 2,3,6-trihydroxypyridine. This reaction is a step in the nicotine degradation pathway, which is a process that allows organisms to utilize nicotine as a carbon and nitrogen source. The activity of these enzymes is crucial for the detoxification and catabolism of nicotine compounds .
Receptor-like protein 29 (RLP29)
Type: Family

This family of proteins includes receptors that are structurally similar to known receptor-like proteins (RLPs). RLPs typically function in signal transduction pathways and are involved in various biological processes, including development, immunity, and stress responses in plants. They are characterized by an extracellular domain that can bind specific ligands, a transmembrane region, and a short cytoplasmic tail. However, they lack the intrinsic kinase activity found in receptor-like kinases (RLKs). Instead, they may interact with other proteins to transduce signals within the cell.
Secreted chitinase LysM12-like (LysM12-like)
Type: Family

This family of proteins includes enzymes that exhibit exochitinase activity, which is involved in the degradation of chitin . Some members of this family are part of a multi-subunit toxin complex where one subunit acts as an exochitinase, contributing to the interaction with sensitive cells. This interaction facilitates the entry of another subunit, which is the active toxin component, into the target cell. The family is related to the glycosyl hydrolase 18 family, indicating a shared catalytic mechanism in chitin hydrolysis. This entry also includes Secreted chitinase LysM(11/12/19) and Secreted LysM effector LysM(3/6/9/14/17) with a role in sequestration of chitin oligosaccharides to dampen host defense .
TKL Ser/Thr protein kinase (TKL_Ser/Thr_kinase)
Type: Family

This family of proteins includes serine/threonine-protein kinases that are part of the protein kinase superfamily. Members of this family are characterized by their ability to phosphorylate various substrates on serine or threonine residues, which is a fundamental mechanism for regulating protein function and signaling pathways in cells. These kinases are involved in a wide range of cellular processes including cell growth, differentiation, metabolism, and apoptosis. The specific functions of these kinases can vary widely among different organisms and cell types, but they generally play critical roles in the transmission of cellular signals and the regulation of complex biological processes.
Appressorial penetration-associated (Appressorial_penetr-assoc)
Type: Family

This family of proteins includes secreted factors that are essential for the initial stages of host invasion by certain pathogens. Members are involved in the penetration of host epidermal cells, a critical step for establishing infection. These proteins are not required for the later stages of infection, such as biotrophic and necrotrophic colonization of the host tissue. Their role is specifically linked to the early interaction between the pathogen and its host, facilitating the pathogen's entry and subsequent establishment within the host organism.
Acetyl-CoA Carboxylase Biotin Carboxyl Carrier (ACC_Biotin_Carrier)
Type: Family

This family of proteins includes components of the acetyl coenzyme A carboxylase complex. Members of this family are involved in the initial carboxylation of biotin by biotin carboxylase and the subsequent transfer of the carboxyl group to acetyl-CoA to form malonyl-CoA, a critical step in fatty acid biosynthesis.
Pathogen-related defense protein (Pathogen-related_defense)
Type: Family

This family of proteins includes members that are typically associated with plant defense responses. They are often induced by pathogen attack and are part of the plant's innate immune system. These proteins can be involved in various mechanisms, such as the strengthening of cell walls, inhibition of pathogen enzymes, or direct antimicrobial activity. Their expression is usually regulated by pathogen recognition and signaling pathways that activate defense genes. The specific functions of individual members of this family may vary, but they generally contribute to the protection of the plant against a wide range of pathogens.
G-protein coupled receptor Dmsr-1 (GPCR_Dmsr-1)
Type: Family

This entry represents the Dmsr-1 (DroMyoSuppressin Receptor related-1) protein, a G-protein coupled receptor that functions as a receptor for FLP-13 neuropeptides in Caenorhabditis elegans. DMSR-1 is activated by neuropeptides with an amidated Arginine-Phenylalanine (RFamide) C terminus motif, particularly FLP-13 peptides. DMSR-1 is expressed in approximately one-tenth of all C. elegans neurons and localises diffusely to neuronal cell membranes. DMSR-1 plays a crucial role in stress-induced sleep (SIS), mediating behavioural quiescence (reduced feeding and body movements) in response to cellular stressors such as heat shock and ultraviolet light exposure. The protein belongs to the RFamide receptor family and is orthologous to Drosophila receptors for the neuropeptides dromyosuppressin and FMRFamide .
Nematode receptor-like serpentine class H (Nematode_rcpt-like_serp_H)
Type: Family

This family of proteins is characterized by its role in the nematode sensory system. Members of this family are typically G protein-coupled receptors (GPCRs) that are involved in the detection of environmental cues and the regulation of behaviors such as chemotaxis, thermotaxis, and mating. These receptors are distinguished by their serpentine topology, with seven transmembrane domains that facilitate signal transduction across the cell membrane. The specific functions of individual members may vary, but they generally contribute to the sophisticated network of signal perception and response in nematodes.
Burnettramic acid biosynthesis protein (Burnettramic_acid_biosynth)
Type: Family

This family of proteins is involved in the biosynthesis of burnettramic acids, which are bolaamphiphilic pyrrolizidinediones with antibacterial, antifungal, and cytotoxic properties. Members of this family participate in various steps of the biosynthetic pathway, including the hydroxylation of proline, construction of a highly reduced polyketide chain, amide bond formation, and Dieckmann condensation to form a bicyclic pyrrolidinedione moiety. Additionally, they may be involved in multiple hydroxylations on the polyketide chain and glycosylation of the aglycone to form the final burnettramic acid compounds. The exact role of some proteins within this family in the biosynthetic pathway remains to be elucidated.
Zygotic Embryogenesis-Associated Protein (Zygotic_Embryogenesis-Asso)
Type: Family

This family of proteins may be involved in the developmental processes that occur during embryogenesis. The exact role in embryonic development is not clearly defined, but members of this family are thought to contribute to the proper progression of embryonic stages.
Probable Methyltransferase (Prob_Methyltransferase)
Type: Family

This family of proteins includes enzymes that are characterized by their ability to transfer methyl groups to various substrates. Methyltransferases are involved in a wide range of biological processes, including the modification of DNA, RNA, proteins, and small molecules, which can affect gene expression, protein function, and metabolic reactions. The specific function of the protein within this family, identified as a probable methyltransferase At1g29790, suggests a role in catalyzing the transfer of methyl groups to specific targets, although the exact substrates and biological outcomes of this activity may vary among family members.
Sensory map formation adhesion molecule (Sensory_adhesion_molecule)
Type: Family

This family of proteins includes adhesion molecules that play a crucial role in the development of sensory processes within the nervous system. They are specifically involved in the formation of sensory maps, which are essential for processing sensory information and establishing the necessary neural connections.