summary: generated: '2026-10-21' n_pathways: 107 coverage: NO_MODULE: 35 MODULE_WITHOUT_ARABIDOPSIS: 21 MODULE_WITHOUT_ARATH_GENES: 17 MODULE_WITH_ARATH_GENES: 34 n_kegg_ath_maps: 162 n_kegg_maps_mapped: 69 n_kegg_maps_out_of_scope: 32 n_kegg_maps_not_assessed: 61 kegg_maps_not_assessed: - ath00051 Fructose and mannose metabolism - ath00232 Caffeine metabolism - ath00240 Pyrimidine metabolism - ath00280 Valine, leucine and isoleucine degradation - ath00310 Lysine degradation - ath00350 Tyrosine metabolism - ath00360 Phenylalanine metabolism - ath00410 beta-Alanine metabolism - ath00430 Taurine and hypotaurine metabolism - ath00440 Phosphonate and phosphinate metabolism - ath00450 Selenocompound metabolism - ath00460 Cyanoamino acid metabolism - ath00470 D-Amino acid metabolism - ath00510 N-Glycan biosynthesis - ath00511 Other glycan degradation - ath00513 Various types of N-glycan biosynthesis - ath00514 Other types of O-glycan biosynthesis - ath00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - ath00565 Ether lipid metabolism - ath00566 Sulfoquinovose metabolism - ath00590 Arachidonic acid metabolism - ath00591 Linoleic acid metabolism - ath00620 Pyruvate metabolism - ath00640 Propanoate metabolism - ath00650 Butanoate metabolism - ath00660 C5-Branched dibasic acid metabolism - ath00785 Lipoic acid metabolism - ath00901 Indole alkaloid biosynthesis - ath00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis - ath00950 Isoquinoline alkaloid biosynthesis - ath00960 Tropane, piperidine and pyridine alkaloid biosynthesis - ath00965 Betalain biosynthesis - ath00970 Aminoacyl-tRNA biosynthesis - ath00999 Biosynthesis of various plant secondary metabolites - ath02010 ABC transporters - ath03008 Ribosome biogenesis in eukaryotes - ath03010 Ribosome - ath03013 Nucleocytoplasmic transport - ath03015 mRNA surveillance pathway - ath03018 RNA degradation - ath03020 RNA polymerase - ath03022 Basal transcription factors - ath03030 DNA replication - ath03040 Spliceosome - ath03050 Proteasome - ath03060 Protein export - ath03082 ATP-dependent chromatin remodeling - ath03410 Base excision repair - ath03420 Nucleotide excision repair - ath03430 Mismatch repair - ath03440 Homologous recombination - ath03450 Non-homologous end-joining - ath03460 Fanconi anemia pathway - ath04070 Phosphatidylinositol signaling system - ath04120 Ubiquitin mediated proteolysis - ath04122 Sulfur relay system - ath04130 SNARE interactions in vesicular transport - ath04144 Endocytosis - ath04156 Integrated stress response (ISR) signaling pathway - ath04814 Motor proteins - ath04981 Folate transport and metabolism pathways: - name: Cold acclimation (ICE1-CBF) group: abiotic_stress coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: - CBF1 - ICE1 arath_genes_outside_any_module: - CBF1 notes: ICE1 sits in the stomatal lineage module as SCRM. - name: Drought and osmotic signaling (DREB2) group: abiotic_stress coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: - DREB2A arath_genes_outside_any_module: [] notes: DREB2A sits in the heat stress module as an HSFA1 target. - name: Hypoxia sensing (N-degron pathway of ERF-VII factors) group: abiotic_stress coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Iron deficiency response and uptake group: abiotic_stress coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Phosphate starvation response group: abiotic_stress coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Pectin, xyloglucan and callose biosynthesis group: cell_wall coverage: NO_MODULE kegg: - ath00040 Pentose and glucuronate interconversions modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Nucleotide sugar interconversion group: central_metabolism coverage: NO_MODULE kegg: - ath00520 Amino sugar and nucleotide sugar metabolism - ath00541 Biosynthesis of various nucleotide sugars modules: [] related_modules: - udp_glucose_and_udp_galactose_biosynthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: The UDP-glucose/UDP-galactose module is bacterial. - name: Ascorbate biosynthesis (Smirnoff-Wheeler, L-galactose route) group: cofactors_and_vitamins coverage: NO_MODULE kegg: - ath00053 Ascorbate and aldarate metabolism modules: [] related_modules: - erythroascorbate_biosynthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: The erythroascorbate module is the fungal analogue, not the plant pathway. - name: Molybdenum cofactor biosynthesis group: cofactors_and_vitamins coverage: NO_MODULE kegg: [] modules: [] related_modules: - molybdenum_cofactor_biosynthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: The existing module is prokaryotic. - name: Tocopherol, plastoquinone and phylloquinone biosynthesis group: cofactors_and_vitamins coverage: NO_MODULE kegg: - ath00130 Ubiquinone and other terpenoid-quinone biosynthesis modules: [] related_modules: - ubiquinone_biosynthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Abscisic acid biosynthesis group: hormone_biosynthesis coverage: NO_MODULE kegg: - ath00906 Carotenoid biosynthesis modules: [] related_modules: [] arath_genes_named: - NCED3 arath_genes_outside_any_module: - NCED3 notes: The ABA signaling module excludes biosynthesis from its boundary. - name: Auxin biosynthesis (TAA/YUCCA indole-3-pyruvate route) group: hormone_biosynthesis coverage: NO_MODULE kegg: - ath00380 Tryptophan metabolism modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Brassinosteroid biosynthesis group: hormone_biosynthesis coverage: NO_MODULE kegg: - ath00905 Brassinosteroid biosynthesis modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Cytokinin biosynthesis group: hormone_biosynthesis coverage: NO_MODULE kegg: - ath00908 Zeatin biosynthesis modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Ethylene biosynthesis group: hormone_biosynthesis coverage: NO_MODULE kegg: - ath00270 Cysteine and methionine metabolism modules: [] related_modules: - methionine_salvage_mta_cycle arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Jasmonate biosynthesis (oxylipin pathway) group: hormone_biosynthesis coverage: NO_MODULE kegg: - ath00592 alpha-Linolenic acid metabolism modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Strigolactone biosynthesis group: hormone_biosynthesis coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Cutin, suberin and cuticular wax biosynthesis group: lipids coverage: NO_MODULE kegg: - ath00073 Cutin, suberine and wax biosynthesis modules: [] related_modules: [] arath_genes_named: - CER1 arath_genes_outside_any_module: - CER1 notes: null - name: Fatty acid desaturation group: lipids coverage: NO_MODULE kegg: - ath01040 Biosynthesis of unsaturated fatty acids modules: [] related_modules: [] arath_genes_named: - FAD2 arath_genes_outside_any_module: - FAD2 notes: null - name: Galactolipid (thylakoid membrane lipid) biosynthesis group: lipids coverage: NO_MODULE kegg: - ath00561 Glycerolipid metabolism modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Phytosterol biosynthesis (cycloartenol route) group: lipids coverage: NO_MODULE kegg: - ath00100 Steroid biosynthesis modules: [] related_modules: - sterol_commitment_squalene_to_lanosterol - ergosterol_biosynthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: Related modules use the lanosterol route of animals and fungi. - name: Plastid de novo fatty acid synthesis (type II FAS) group: lipids coverage: NO_MODULE kegg: - ath00061 Fatty acid biosynthesis modules: [] related_modules: - fatty_acid_de_novo_synthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: The existing module is the cytosolic type I FAS. - name: Ammonium assimilation (GS/GOGAT) group: nitrogen_and_sulfur coverage: NO_MODULE kegg: - ath00910 Nitrogen metabolism - ath00250 Alanine, aspartate and glutamate metabolism modules: [] related_modules: - nitrogen_assimilation_glutamate_glutamine - glutamate_glutamine_ammonia_hub arath_genes_named: [] arath_genes_outside_any_module: [] notes: Related modules are fungal and human. - name: Nitrate assimilation (nitrate reductase, nitrite reductase) group: nitrogen_and_sulfur coverage: NO_MODULE kegg: - ath00910 Nitrogen metabolism modules: [] related_modules: - bacterial_assimilatory_nitrate_reduction - molybdenum_cofactor_biosynthesis arath_genes_named: - CHL1 arath_genes_outside_any_module: - CHL1 notes: CHL1 (NRT1.1) is the nitrate transporter/sensor, not an assimilation enzyme. - name: Autophagy group: organelles coverage: NO_MODULE kegg: - ath04136 Autophagy - other modules: [] related_modules: - metazoan_autophagosome_biogenesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Chloroplast protein import (TOC/TIC) group: organelles coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Starch synthesis and degradation group: photosynthesis_and_carbon coverage: NO_MODULE kegg: - ath00500 Starch and sucrose metabolism modules: [] related_modules: - tres_mak_glge_branched_alpha_glucan_biosynthesis - glycogen_biosynthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: Related modules are bacterial or animal alpha-glucan pathways. - name: Sucrose synthesis and degradation group: photosynthesis_and_carbon coverage: NO_MODULE kegg: - ath00500 Starch and sucrose metabolism modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Blue-light signaling (cryptochromes and phototropins) group: signaling coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: - CRY1 - CRY2 arath_genes_outside_any_module: [] notes: CRY1 and CRY2 sit in the photomorphogenesis and photoperiod modules as inputs; there is no module for blue-light signaling or phototropism itself. - name: Karrikin (KAI2) signaling group: signaling coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: UV-B signaling (UVR8) group: signaling coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: - UVR8 arath_genes_outside_any_module: - UVR8 notes: null - name: siRNA, tasiRNA and RNA-directed DNA methylation group: small_rna_and_chromatin coverage: NO_MODULE kegg: [] modules: [] related_modules: [] arath_genes_named: - RDR6 arath_genes_outside_any_module: [] notes: RDR6 sits in the miRNA biogenesis module. - name: Flavonoid, flavonol and anthocyanin biosynthesis group: specialised_metabolism coverage: NO_MODULE kegg: - ath00941 Flavonoid biosynthesis - ath00944 Flavone and flavonol biosynthesis - ath00942 Anthocyanin biosynthesis modules: [] related_modules: [] arath_genes_named: - TT8 - TTG1 arath_genes_outside_any_module: - TT8 notes: TT8 and TTG1 are the bHLH and WD40 parts of the MBW complex that activates late flavonoid genes; TTG1 sits in the trichome module. - name: Indolic glucosinolate biosynthesis and its MYB regulation group: specialised_metabolism coverage: NO_MODULE kegg: - ath00966 Glucosinolate biosynthesis modules: [] related_modules: [] arath_genes_named: - MYB34 - MYB51 - MYB122 arath_genes_outside_any_module: - MYB122 - MYB34 - MYB51 notes: CYP79B2/B3 sit in the camalexin module; the indole glucosinolate branch beyond indole-3-acetaldoxime has no module. - name: Mono-, sesqui- and triterpenoid biosynthesis group: specialised_metabolism coverage: NO_MODULE kegg: - ath00902 Monoterpenoid biosynthesis - ath00909 Sesquiterpenoid and triterpenoid biosynthesis modules: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Branched-chain amino acid biosynthesis group: amino_acids coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00290 Valine, leucine and isoleucine biosynthesis modules: - module: branched_chain_amino_acid_biosynthesis title: L-valine, L-leucine, and L-isoleucine biosynthesis status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Glutathione biosynthesis group: amino_acids coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00480 Glutathione metabolism modules: - module: glutathione_biosynthesis title: Glutathione biosynthesis status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Histidine biosynthesis group: amino_acids coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00340 Histidine metabolism modules: - module: histidine_biosynthesis title: L-histidine biosynthesis status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Polyamine metabolism group: amino_acids coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00330 Arginine and proline metabolism modules: - module: polyamine_metabolism title: Eukaryotic polyamine metabolism (biosynthesis, back-conversion and antizyme feedback) status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Glycolysis and gluconeogenesis group: central_metabolism coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00010 Glycolysis / Gluconeogenesis modules: - module: emp_glycolysis title: Generic Embden-Meyerhof-Parnas (EMP) glycolysis module status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] - module: gluconeogenesis title: Generic gluconeogenesis module status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Inositol phosphate metabolism group: central_metabolism coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00562 Inositol phosphate metabolism modules: - module: myo_inositol_and_inositol_phosphate_biosynthesis title: myo-Inositol and inositol (pyro)phosphate biosynthesis (MIPS/IMPase and the PLC-IPMK-IPK1-IP6K-PPIP5K route) status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Oxidative phosphorylation group: central_metabolism coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00190 Oxidative phosphorylation modules: - module: oxphos title: Oxidative phosphorylation (OXPHOS) module status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Pentose phosphate pathway group: central_metabolism coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00030 Pentose phosphate pathway modules: - module: pentose_phosphate_pathway title: Pentose phosphate pathway status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Tricarboxylic acid cycle group: central_metabolism coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00020 Citrate cycle (TCA cycle) modules: - module: tca_cycle title: Tricarboxylic acid cycle status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Biotin biosynthesis group: cofactors_and_vitamins coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00780 Biotin metabolism modules: - module: biotin_biosynthesis title: De novo biotin biosynthesis (pimelate-thioester supply and BioF-BioA-BioD-BioB ring assembly) status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Coenzyme A biosynthesis group: cofactors_and_vitamins coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00770 Pantothenate and CoA biosynthesis modules: - module: coenzyme_a_biosynthesis title: Pantoate-derived coenzyme A biosynthesis status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: MEP and mevalonate isoprenoid precursor supply group: cofactors_and_vitamins coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00900 Terpenoid backbone biosynthesis modules: - module: mep_isoprenoid_precursor_biosynthesis title: MEP isoprenoid precursor biosynthesis status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] - module: mevalonate_pathway title: Mevalonate pathway (acetyl-CoA -> isopentenyl diphosphate) status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] - module: isoprenoid_diphosphate_biosynthesis title: Isoprenoid (prenyl) diphosphate biosynthesis (IPP/DMAPP -> GPP -> FPP -> GGPP) status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: NAD biosynthesis group: cofactors_and_vitamins coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00760 Nicotinate and nicotinamide metabolism modules: - module: nad_biosynthesis_salvage title: L-aspartate de novo and selected salvage routes to NAD+ status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Riboflavin biosynthesis group: cofactors_and_vitamins coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00740 Riboflavin metabolism modules: - module: riboflavin_biosynthesis title: De novo riboflavin biosynthesis and flavin cofactor activation status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Vitamin B6 metabolism group: cofactors_and_vitamins coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00750 Vitamin B6 metabolism modules: - module: vitamin_b6_plp_metabolism title: Vitamin B6 (pyridoxal 5'-phosphate) supply by PdxS/PdxT synthesis or vitamer salvage, and PLP homeostasis status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Peroxisomal fatty acid beta-oxidation group: lipids coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00071 Fatty acid degradation modules: - module: peroxisomal_beta_oxidation title: Peroxisomal fatty-acid beta-oxidation status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Phospholipid biosynthesis group: lipids coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00564 Glycerophospholipid metabolism modules: - module: cdp_dag_phospholipid_synthesis title: CDP-diacylglycerol pathway of phospholipid synthesis (PS, PE, PC by methylation, PI, PG and cardiolipin) status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Sphingolipid biosynthesis group: lipids coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00600 Sphingolipid metabolism modules: - module: sphingolipid_de_novo_synthesis title: De novo sphingolipid biosynthesis (ceramide core, with fungal inositol-phosphorylceramide head groups) status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Sulfate assimilation group: nitrogen_and_sulfur coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00920 Sulfur metabolism modules: - module: aps_dependent_assimilatory_sulfate_reduction title: Assimilatory sulfate reduction to sulfide (APS and PAPS routes) status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] - module: paps_sulfate_activation title: PAPS biosynthesis and Golgi import (sulfate activation) (PAPSS1/2 -> SLC35B2/3) status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Peroxisome biogenesis and matrix protein import group: organelles coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath04146 Peroxisome modules: - module: peroxisome-lifecycle title: Peroxisome lifecycle and matrix protein import module status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Trehalose 6-phosphate metabolism group: photosynthesis_and_carbon coverage: MODULE_WITHOUT_ARABIDOPSIS kegg: - ath00500 Starch and sucrose metabolism modules: - module: trehalose_metabolism title: Trehalose synthesis via trehalose 6-phosphate and trehalase hydrolysis status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Aspartate-family amino acid biosynthesis (Lys, Thr, Met) group: amino_acids coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00300 Lysine biosynthesis - ath00260 Glycine, serine and threonine metabolism - ath00270 Cysteine and methionine metabolism modules: - module: aspartate_family_threonine_biosynthesis title: L-threonine biosynthesis from L-aspartate status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] - module: methionine_biosynthesis title: L-methionine biosynthesis (from homoserine) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: - lysine_biosynthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: The lysine module is the succinylated DAP route; plants use the LL-diaminopimelate aminotransferase variant. - name: GABA shunt group: amino_acids coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00250 Alanine, aspartate and glutamate metabolism modules: - module: gaba_shunt title: GABA shunt (glutamate to GABA to succinate) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Proline and arginine metabolism group: amino_acids coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00330 Arginine and proline metabolism - ath00220 Arginine biosynthesis modules: - module: proline_metabolism title: Proline-P5C biosynthesis and catabolism status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] - module: arginine_catabolism_arginase_pathway title: Arginine catabolism via arginase and ornithine aminotransferase status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: - arginine_biosynthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: The arginine biosynthesis module is scoped to microbes and fungi. - name: Shikimate and aromatic amino acid biosynthesis group: amino_acids coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00400 Phenylalanine, tyrosine and tryptophan biosynthesis modules: - module: bacterial_shikimate_chorismate_biosynthesis title: Shikimate pathway to chorismate status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] - module: phenylalanine_tyrosine_biosynthesis title: L-phenylalanine and L-tyrosine biosynthesis from chorismate status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] - module: tryptophan_biosynthesis title: L-tryptophan biosynthesis status: DRAFT mentions_arabidopsis: false arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Cellulose biosynthesis group: cell_wall coverage: MODULE_WITHOUT_ARATH_GENES kegg: [] modules: - module: cellulose_biosynthesis title: Plant cellulose biosynthesis module status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Xylan biosynthesis group: cell_wall coverage: MODULE_WITHOUT_ARATH_GENES kegg: [] modules: - module: xylan_biosynthesis title: Plant xylan (glucuronoxylan) biosynthesis module status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Alcoholic fermentation group: central_metabolism coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00010 Glycolysis / Gluconeogenesis modules: - module: alcoholic_fermentation title: Alcoholic fermentation of pyruvate to ethanol status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Galactose metabolism (Leloir) group: central_metabolism coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00052 Galactose metabolism modules: - module: galactose_leloir_pathway title: Galactose catabolism (Leloir pathway) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Glyoxylate cycle group: central_metabolism coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00630 Glyoxylate and dicarboxylate metabolism modules: - module: glyoxylate_cycle title: Glyoxylate cycle status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Folate biosynthesis and one-carbon metabolism group: cofactors_and_vitamins coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00790 Folate biosynthesis - ath00670 One carbon pool by folate modules: - module: tetrahydrofolate_biosynthesis title: De novo tetrahydrofolate and folylpolyglutamate biosynthesis status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] - module: folate_one_carbon_interconversion title: Folate one-carbon carrier-state interconversion status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Siroheme biosynthesis group: cofactors_and_vitamins coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00860 Porphyrin metabolism modules: - module: siroheme_biosynthesis title: Siroheme biosynthesis from uroporphyrinogen III status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Thiamine biosynthesis group: cofactors_and_vitamins coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00730 Thiamine metabolism modules: - module: eukaryotic_thiamine_biosynthesis title: Eukaryotic (THI4/THI5-type) de novo thiamine diphosphate biosynthesis status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Ureide catabolism group: nitrogen_and_sulfur coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00230 Purine metabolism modules: - module: ureide_urea_catabolism title: Ureide pathway - nitrogen recovery from allantoin via urea to ammonia status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: ER unfolded protein response group: organelles coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath04141 Protein processing in endoplasmic reticulum modules: - module: er_unfolded_protein_response title: Endoplasmic reticulum unfolded protein response status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Calvin-Benson-Bassham cycle (carbon fixation) group: photosynthesis_and_carbon coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00710 Carbon fixation by Calvin cycle modules: - module: photosynthesis title: Oxygenic photosynthesis module status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: A part of the taxon-neutral photosynthesis module. - name: Chlorophyll biosynthesis group: photosynthesis_and_carbon coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00860 Porphyrin metabolism modules: - module: photosynthesis title: Oxygenic photosynthesis module status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: - heme_biosynthesis - siroheme_biosynthesis arath_genes_named: [] arath_genes_outside_any_module: [] notes: Included in the photosynthesis module only as a supporting part (magnesium chelatase onward). Chlorophyll degradation is not covered. - name: Photosynthetic light reactions and antenna complexes group: photosynthesis_and_carbon coverage: MODULE_WITHOUT_ARATH_GENES kegg: - ath00195 Photosynthesis - ath00196 Photosynthesis - antenna proteins modules: - module: photosynthesis title: Oxygenic photosynthesis module status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Heat stress response group: abiotic_stress coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: plant_hsfa1_heat_stress_response title: HSFA1-driven heat stress response in Arabidopsis status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - AT1G32330 - AT1G74310 - AT2G26150 - AT3G02990 - AT4G17750 - AT5G02500 - AT5G03720 - AT5G16820 - AT5G52640 - DREB2A - HSP17.6A - HSP17.7 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Salt tolerance (SOS pathway) group: abiotic_stress coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: sos_salt_tolerance title: Salt Overly Sensitive (SOS) pathway (SOS3/CBL4 - SOS2/CIPK24 - SOS1 Na+/H+ antiporter) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CBL10 - CBL4 - CIPK24 - SOS1 related_modules: [] arath_genes_named: - SOS1 - CIPK24 - HKT1 arath_genes_outside_any_module: - HKT1 notes: null - name: Floral meristem and floral organ identity group: development coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: floral_meristem_identity title: Specification of floral meristem identity at the Arabidopsis shoot apex status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - AP1 - AP2 - CAL - FD - FT - FUL - LFY - SOC1 - TFL1 - UFO - module: floral_organ_identity_abce title: ABCE model of floral organ identity (MADS floral quartets) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - AG - AP1 - AP2 - AP3 - PI - SEP1 - SEP2 - SEP3 - SEP4 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Flowering time (photoperiod, vernalization, autonomous pathways) group: development coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: photoperiodic_flowering_co_ft title: Photoperiodic (long-day) flowering via the CONSTANS-FLOWERING LOCUS T pathway (Arabidopsis) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CDF1 - CO - COP1 - CRY2 - FD - FKF1 - FT - GI - PHYA - SOC1 - SPA1 - ZTL - module: vernalization_flc_silencing title: FRIGIDA-dependent FLC activation and vernalization-induced Polycomb silencing of FLC status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CLF - FIE - FLC - FRI - FT - LHP1 - MSI1 - SOC1 - SVP - SWN - VAL1 - VIN3 - VRN1 - VRN2 - VRN5 - module: autonomous_flowering_pathway title: Autonomous flowering pathway repressing FLOWERING LOCUS C (Arabidopsis) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - FCA - FLC - FLD - FPA - FT - FVE - FY - LD - SOC1 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Root radial patterning (SHR-SCR) group: development coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: root_radial_patterning_shr_scr title: Root ground-tissue radial patterning by the SHORT-ROOT-SCARECROW-BIRD module status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CYCD6-1 - JKD - MGP - SCR - SHR - WOX5 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Shoot apical meristem maintenance (CLV-WUS) group: development coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: shoot_meristem_clv_wus_feedback title: CLAVATA-WUSCHEL negative feedback loop in shoot apical meristem stem-cell homeostasis status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - BAM1 - CLV1 - CLV2 - CLV3 - CRN - STM - WUS related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Stomatal development group: development coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: stomatal_lineage_development title: Stomatal lineage progression and spacing (EPF-ERECTA-YODA-MAPK and SPCH/MUTE/FAMA-SCRM) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - EPF2 - ERECTA - FAMA - ICE1 - MKK4 - MKK5 - MPK3 - MPK6 - MUTE - SPCH - TMM - YDA related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Trichome initiation and patterning group: development coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: trichome_initiation_mbw title: Leaf trichome initiation and patterning by the MYB-bHLH-WD40 activator complex and R3 MYB lateral inhibitors status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CPC - EGL3 - GL1 - GL2 - GL3 - TRY - TTG1 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Gibberellin biosynthesis group: hormone_biosynthesis coverage: MODULE_WITH_ARATH_GENES kegg: - ath00904 Diterpenoid biosynthesis modules: - module: gibberellin_biosynthesis title: Bioactive gibberellin (GA4/GA1) biosynthesis from geranylgeranyl diphosphate status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - GA1 - GA2 - GA20OX1 - GA3 - GA3OX1 - KAO1 - KAO2 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Salicylic acid biosynthesis and NPR1 signaling group: hormone_biosynthesis coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: salicylic_acid_biosynthesis_npr1_signaling title: Salicylic acid biosynthesis (isochorismate route) and NPR1-dependent defence signalling status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - ICS1 - NPR1 - WRKY70 related_modules: [] arath_genes_named: - ICS1 - NPR1 - WRKY70 arath_genes_outside_any_module: [] notes: null - name: Bacterial PAMP perception (FLS2/EFR) group: immunity coverage: MODULE_WITH_ARATH_GENES kegg: - ath04626 Plant-pathogen interaction - ath04016 MAPK signaling pathway - plant modules: - module: bacterial_pamp_lrr_receptor_signaling title: Bacterial PAMP perception by LRR receptor kinases (FLS2/EFR with BAK1) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - BAK1 - BIK1 - EFR - FLS2 - MAPKKK5 - MKK4 - MKK5 - MPK3 - MPK6 - RBOHD related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Chitin perception group: immunity coverage: MODULE_WITH_ARATH_GENES kegg: - ath04016 MAPK signaling pathway - plant modules: - module: chitin_perception title: Plant chitin perception by LysM receptor complexes status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - BIK1 - CERK1 - LYK4 - LYK5 - MAPKKK5 - MKK4 - MKK5 - MPK3 - MPK6 - PBL1 - PBL27 - RBOHD related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: NLR (effector-triggered) immunity group: immunity coverage: MODULE_WITH_ARATH_GENES kegg: - ath04626 Plant-pathogen interaction modules: - module: plant_nlr_resistosome_signaling title: Plant NLR resistosome activation and signalling status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - EDS1 - PAD4 related_modules: [] arath_genes_named: - RPM1 - RPS2 arath_genes_outside_any_module: - RPM1 - RPS2 notes: null - name: Microsomal fatty acid elongation group: lipids coverage: MODULE_WITH_ARATH_GENES kegg: - ath00062 Fatty acid elongation modules: - module: fatty_acid_elongation_cycle title: Microsomal fatty-acid elongation cycle (ELOVL or KCS -> KAR -> HACD -> ECR) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CUT1 - ECR - FAE1 - KCR1 - PAS2 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Triacylglycerol (seed oil) biosynthesis group: lipids coverage: MODULE_WITH_ARATH_GENES kegg: - ath00561 Glycerolipid metabolism modules: - module: seed_triacylglycerol_biosynthesis title: Plant seed triacylglycerol (oil) biosynthesis module status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - DGAT1 - module: triacylglycerol_biosynthesis title: Glycerolipid / triacylglycerol biosynthesis (glycerol-3-phosphate and DHAP routes) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: [] related_modules: [] arath_genes_named: - DGAT1 - WRI1 arath_genes_outside_any_module: - WRI1 notes: null - name: Nuclear envelope LINC complex group: organelles coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: linc_complex title: LINC complex (SUN-KASH nuclear envelope bridge) module status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - SUN1 - SUN2 - WIP1 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Photorespiration (C2 cycle) group: photosynthesis_and_carbon coverage: MODULE_WITH_ARATH_GENES kegg: - ath00630 Glyoxylate and dicarboxylate metabolism modules: - module: photorespiration_c2_cycle title: Photorespiratory C2 cycle (2-phosphoglycolate to 3-phosphoglycerate) in land plants status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - AGT1 - CAT2 - GDCH - GDCST - GGAT1 - GGAT2 - GLDP1 - GLDP2 - GLN2 - GLO1 - GLO2 - GLU1 - GLYK - HPR - HPR2 - PGLP1 - PLGG1 - SHM1 - mtLPD1 - mtLPD2 related_modules: - glycolate_glyoxylate_assimilation arath_genes_named: [] arath_genes_outside_any_module: [] notes: The photorespiration module includes glycine_cleavage_system by reference; the glycolate/glyoxylate module is bacterial. - name: Abscisic acid signaling group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: - ath04075 Plant hormone signal transduction modules: - module: abscisic_acid_signaling title: Abscisic acid core signaling (PYR/PYL receptor - clade A PP2C - SnRK2 - ABF/ABI5 and SLAC1 outputs) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - ABI1 - ABI5 - OST1 - PYR1 - SLAC1 - SnRK2.2 - SnRK2.3 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Auxin nuclear signaling group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: - ath04075 Plant hormone signal transduction modules: - module: auxin_nuclear_signaling title: Nuclear auxin signaling (TIR1/AFB-Aux/IAA-TOPLESS-ARF module) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - AFB2 - ARF19 - ARF5 - ARF7 - IAA12 - IAA17 - TIR1 - TPL related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Brassinosteroid signaling group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: - ath04075 Plant hormone signal transduction modules: - module: brassinosteroid_signaling title: Brassinosteroid signal perception and relay to BZR1/BES1 transcription factors status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - BAK1 - BES1 - BIN2 - BKI1 - BRI1 - BSK1 - BSU1 - BZR1 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Circadian clock group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: - ath04712 Circadian rhythm - plant modules: - module: plant_circadian_clock_oscillator title: Arabidopsis core circadian oscillator (CCA1/LHY - PRR - evening complex - ZTL) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CCA1 - ELF3 - ELF4 - GI - LHY - LUX - PRR5 - PRR7 - PRR9 - TOC1 - ZTL related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Cytokinin signaling group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: - ath04075 Plant hormone signal transduction modules: - module: cytokinin_two_component_signaling title: Cytokinin two-component (His-Asp phosphorelay) signaling in Arabidopsis status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - AHK2 - AHK3 - AHK4 - AHP1 - ARR1 - ARR12 - ARR5 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Ethylene signaling group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: - ath04075 Plant hormone signal transduction modules: - module: ethylene_signaling title: Ethylene signaling (ETR/ERS receptor-CTR1-EIN2-EBF-EIN3/EIL1 module) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CTR1 - EBF1 - EBF2 - EIL1 - EIN2 - EIN3 - ERS1 - ETR1 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Gibberellin signaling group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: - ath04075 Plant hormone signal transduction modules: - module: gibberellin_della_signaling title: Gibberellin perception and DELLA derepression (GID1-DELLA-SCF(SLY1) module) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - GAI - GID1A - GID1B - GID1C - PIF3 - PIF4 - RGA - SLY1 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Jasmonate signaling group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: - ath04075 Plant hormone signal transduction modules: - module: jasmonate_coi1_jaz_signaling title: Jasmonate perception and JAZ derepression (JAR1-COI1-JAZ-NINJA/TPL-MYC module) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - COI1 - JAR1 - JAZ1 - MYC2 - MYC3 - NINJA - TPL related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Phytochrome signaling and photomorphogenesis group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: phytochrome_photomorphogenesis title: Phytochrome control of photomorphogenesis (phyA/phyB - PIF - COP1/SPA - HY5) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - COP1 - CRY1 - HY5 - PHYA - PHYB - PIF1 - PIF3 - PIF4 - SPA1 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Polar auxin transport group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: auxin_polar_transport title: Polar (cell-to-cell) auxin transport status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - ABCB19 - AUX1 - D6PK - PID - PIN1 - PIN2 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Strigolactone signaling group: signaling coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: strigolactone_signaling_shoot_branching title: Strigolactone perception and D14-MAX2-SMXL signalling in shoot-branching control status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - BRC1 - D14 - MAX2 - SMXL6 - SMXL7 - SMXL8 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Polycomb (PRC2) silencing group: small_rna_and_chromatin coverage: MODULE_WITH_ARATH_GENES kegg: - ath03083 Polycomb repressive complex modules: - module: vernalization_flc_silencing title: FRIGIDA-dependent FLC activation and vernalization-induced Polycomb silencing of FLC status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CLF - FIE - FLC - FRI - FT - LHP1 - MSI1 - SOC1 - SVP - SWN - VAL1 - VIN3 - VRN1 - VRN2 - VRN5 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: Covered only as it acts at FLC. - name: miRNA biogenesis and AGO1 loading group: small_rna_and_chromatin coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: plant_mirna_biogenesis title: Plant miRNA biogenesis and AGO1 RISC loading status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - AGO1 - DCL1 - DRB1 - HEN1 - RDR6 - SERRATE related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Aliphatic glucosinolate biosynthesis and myrosinase defence group: specialised_metabolism coverage: MODULE_WITH_ARATH_GENES kegg: - ath00966 Glucosinolate biosynthesis modules: - module: aliphatic_glucosinolate_myrosinase_defense title: Aliphatic glucosinolate biosynthesis and myrosinase activation (glucosinolate-myrosinase defense system) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - AOP2 - BCAT3 - BCAT4 - CYP79F1 - CYP79F2 - CYP83A1 - ESP - FMOGS-OX1 - GGP1 - GSTF11 - GSTU20 - IIL1 - IMDH1 - MAM1 - MAM3 - NSP1 - SOT17 - SOT18 - SSU3 - SUR1 - TGG1 - TGG2 - UGT74C1 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Camalexin biosynthesis group: specialised_metabolism coverage: MODULE_WITH_ARATH_GENES kegg: [] modules: - module: camalexin_biosynthesis title: Camalexin biosynthesis (tryptophan-derived indole phytoalexin) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CYP71A12 - CYP71A13 - CYP71B15 - CYP79B2 - CYP79B3 - GGP1 - GSTF6 - MPK3 - MPK6 - WRKY33 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null - name: Carotenoid biosynthesis group: specialised_metabolism coverage: MODULE_WITH_ARATH_GENES kegg: - ath00906 Carotenoid biosynthesis modules: - module: carotene_backbone_biosynthesis title: Carotenoid biosynthesis I — carotene backbone (GGPP -> phytoene -> lycopene -> cyclic carotenes) status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - CRTISO - LCYB - LCYE - PDS - PSY - Z-ISO - ZDS related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: Covers carotenes only; xanthophylls are not modelled. - name: Monolignol (lignin) biosynthesis group: specialised_metabolism coverage: MODULE_WITH_ARATH_GENES kegg: - ath00940 Phenylpropanoid biosynthesis modules: - module: lignin_monolignol_biosynthesis title: Plant lignin (monolignol) biosynthesis module status: DRAFT mentions_arabidopsis: true arath_reviewed_members: - PAL1 related_modules: [] arath_genes_named: [] arath_genes_outside_any_module: [] notes: null