Experiment set2IT034 for Pseudomonas fluorescens FW300-N2E2

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Sodium octanoate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium octanoate (20 mM), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/9/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 17 genes in this experiment

For carbon source Sodium octanoate in Pseudomonas fluorescens FW300-N2E2

For carbon source Sodium octanoate across organisms

SEED Subsystems

Subsystem #Specific
Pyruvate metabolism I: anaplerotic reactions, PEP 2
ABC transporter alkylphosphonate (TC 3.A.1.9.1) 1
Chorismate Synthesis 1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 1
Fermentations: Mixed acid 1
Formate hydrogenase 1
Glutamate dehydrogenases 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Methionine Salvage 1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 1
Queuosine-Archaeosine Biosynthesis 1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-glutamate degradation I 1 1 1
formate oxidation to CO2 1 1 1
3-methylthiopropanoate biosynthesis 1 1 1
CO2 fixation into oxaloacetate (anaplerotic) 2 2 1
3-dehydroquinate biosynthesis I 2 2 1
L-alanine degradation II (to D-lactate) 3 3 1
ethene biosynthesis IV (engineered) 3 1 1
oxalate degradation VI 4 1 1
adipate degradation 5 5 1
oxalate degradation III 5 1 1
fatty acid salvage 6 6 1
chorismate biosynthesis I 7 7 1
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 1
L-glutamate degradation XI (reductive Stickland reaction) 7 3 1
4-aminobutanoate degradation V 7 2 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I 7 2 1
partial TCA cycle (obligate autotrophs) 8 8 1
nitrogen remobilization from senescing leaves 8 6 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
L-glutamate degradation V (via hydroxyglutarate) 10 6 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 6 1
L-methionine salvage cycle III 11 5 1
L-methionine salvage cycle II (plants) 11 3 1
oleate β-oxidation 35 30 3
superpathway of C1 compounds oxidation to CO2 12 5 1
L-methionine salvage cycle I (bacteria and plants) 12 4 1
superpathway of L-tryptophan biosynthesis 13 13 1
formaldehyde assimilation I (serine pathway) 13 6 1
2-methyl-branched fatty acid β-oxidation 14 11 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 9 1
purine nucleobases degradation I (anaerobic) 15 6 1
mixed acid fermentation 16 12 1
superpathway of aromatic amino acid biosynthesis 18 18 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 9 1
methylaspartate cycle 19 9 1
purine nucleobases degradation II (anaerobic) 24 16 1
ethene biosynthesis V (engineered) 25 19 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 1
superpathway of chorismate metabolism 59 43 1