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SpeciesSubsystemsGene TreesAnnotation and Model Generation 

Gramene/Ensembl Plants Species

Poaceae

Brachypodium distachyon Brachypodium distachyon (1.0)
Brachypodium distachyon (L.) Beauv
Genome links
PubSEED
Gramene | Ensembl
BIR
Model links
HTML
SBML
Oryza glaberrima Oryza glaberrima (AGI 1.1)
Oryza glaberrima
Genome links
PubSEED
Gramene | Ensembl
AGI
Model links
HTML
SBML
Oryza sativa Oryza sativa (MSU 6)
Oryza sativa Nipponbare (Japonica rice)
Genome links
PubSEED
Gramene | Ensembl
MSU
Model links
HTML
SBML
Sorghum bicolor Sorghum bicolor (Sorbi1)
Sorghum bicolor BTX623
Genome links
PubSEED
Gramene | Ensembl
JGI
Model links
HTML
SBML
Zea mays Zea mays (AGP 2)
Zea mays
Genome links
PubSEED
Gramene | Ensembl
MaizeSequence
Model links
HTML
SBML

Eudicotyledons

Arabidopsis lyrata Arabidopsis lyrata (1.0)
Arabidopsis lyrata
Genome links
PubSEED
Ensembl
JGI
Model links
HTML
SBML
Arabidopsis thaliana Arabidopsis thaliana (TAIR 10)
Arabidopsis thaliana
Genome links
PubSEED
Ensembl
TAIR
Model links
HTML
SBML
Glycine max Glycine max (1.0)
Glycine max
Genome links
PubSEED
Ensembl
JGI
Model links
HTML
SBML
Populus trichocarpa Populus trichocarpa (JGI 2.0)
Populus trichocarpa
Genome links
PubSEED
Ensembl
JGI
Model links
HTML
SBML
Vitis vinifera Vitis vinifera (IGGP 12x)
Vitis vinifera
Genome links
PubSEED
Ensembl
Genoscope
Model links
HTML
SBML

PlantSEED Metabolic Subsystems

Central Carbon Metabolism

Glycolysis and Gluconeogenesis Pentose Phosphate Cycle Calvin-Benson-Bassham Cycle
TCA Cycle Acetyl-CoA biosynthesis Rubisco Shunt
Photorespiration

Mitochondrial Respiratory Electron Transport

Respiratory Complex I Respiratory Complex II Respiratory Complex III
Respiratory Complex IV Quinol Oxidases Mitochondrial ATP Synthase

Plastidial Respiratory and Photosynthetic Electron Transport

Photosystem I Photosystem II Cytochrome b6f
Respiratory Complex I (Plastidial) Plastidial Quinol Oxidases Soluble Electron Carriers
Plastidial ATP Synthase

Vacuolar Electron Transport

Vacuolar ATP Synthase

Amino Acid Metabolism

Glycine, Alanine, and Serine Metabolism Threonine and Lysine Metabolism Branched-chain Amino-acid Metabolism
Asparagine, Aspartate, Glutamine, and Glutamate Metabolism Cysteine and Methionine Metabolism Proline Metabolism
Tyrosine and Phenylalanine Metabolism Tryptophan Metabolism Histidine Metabolism
Arginine Biosynthesis Homomethionine Biosynthesis Chorismate Biosynthesis

Cofactors, Vitamins, Prosthetic Groups, Pigments

Riboflavin, FMN and FAD biosynthesis Biotin biosynthesis Thiamin biosynthesis
Pyridoxine (vitamin B6) biosynthesis Niacin, NAD and NADP biosynthesis Folate biosynthesis
Pantothenate and CoA biosynthesis Tetrapyrrole Biosynthesis Phylloquinone Biosynthesis
Plastoquinone Biosynthesis Chlorophyll Biosynthesis Tocopherol Biosynthesis
Ubiquinone Biosynthesis One-carbon Metabolism Heme Biosynthesis

Nucleotide Metabolism

Purine Biosynthesis Pyrimidine Biosynthesis

Cell Wall Metabolism

Phenylpropanoid Biosynthesis Lignin Biosynthesis Pectin Metabolism
Callose Biosynthesis Cellulose Biosynthesis Xylan Degradation
Xyloglucan Biosynthesis

Fatty Acid (FA) Metabolism

FA Biosynthesis (Plastidial) FA Biosynthesis (Mitochondrial) Unsaturated FA Biosynthesis
Very Long FA Biosynthesis Polyunsaturated FA Biosynthesis Poly-hydroxy FA Metabolism
Cyclopropane FA Biosynthesis Acetyl-CoA Carboxylases

Lipid Metabolism

CDP-diacylglycerol Biosynthesis Triacylglycerol Biosynthesis Lipid A Biosynthesis
Isoprenoid Biosynthesis
(Mevalonate)
Isoprenoid Biosynthesis
(Non-Mevalonate)
Choline Biosynthesis
Phosphatidylcholine Biosynthesis Phosphatidylethanolamine Biosynthesis Phosphatidylglycerol Biosynthesis
Phospholipid Desaturation Cardiolipin Biosynthesis PUFA Enrichment
Sphingolipid Biosynthesis Glycosylglycerides Biosynthesis Cuticular Wax Biosynthesis
Cutin Biosynthesis Suberin Biosynthesis Phosphoinositdes Biosynthesis

Carbohydrate Metabolism

Galactose Degradation Mannose Degradation Xylose Utilization
Trehalose Metabolism Sucrose Metabolism Melibiose Degradation
Starch Biosynthesis Starch Degradation Fructan Degradation
UDP Glucose Biosynthesis UDP Glucuronate Biosynthesis UDP-Galacturonate Biosynthesis
UDP-Arabinose Biosynthesis UDP-Rhamnose Biosynthesis GDP Sugars Biosynthesis

Other Subsystems

Sinapate Ester Biosynthesis Alt. NAD(P)H Dehydrogenases Flavonoid Biosynthesis
(p)ppGpp-Mediated Response Sporopollenin Biosynthesis Biosynthesis of Aliphatic Glucosinolates
Biosynthesis of Benzenic and Indolic Glucosinolates
Trees were only computed for families that contained more than two species

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