Experiment set16IT020 for Pseudomonas putida KT2440

Compare to:

L-Isoleucine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Isoleucine (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.3 generations
By: Mitchell Thompson on 9/5/19
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 25 genes in this experiment

For carbon source L-Isoleucine in Pseudomonas putida KT2440

For carbon source L-Isoleucine across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 10
Valine degradation 8
Isoleucine degradation 6
Leucine Degradation and HMG-CoA Metabolism 4
ABC transporter dipeptide (TC 3.A.1.5.2) 3
Isobutyryl-CoA to Propionyl-CoA Module 3
Acetyl-CoA fermentation to Butyrate 1
Anaerobic respiratory reductases 1
Arginine and Ornithine Degradation 1
Butanol Biosynthesis 1
Proline, 4-hydroxyproline uptake and utilization 1
Respiratory dehydrogenases 1 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
2-oxoisovalerate decarboxylation to isobutanoyl-CoA 3 3 3
acetate conversion to acetyl-CoA 1 1 1
acetate and ATP formation from acetyl-CoA III 1 1 1
L-proline degradation I 3 3 2
β-alanine degradation II 2 2 1
β-alanine degradation I 2 1 1
glycine biosynthesis II 3 3 1
ethanol degradation II 3 3 1
pyruvate decarboxylation to acetyl CoA I 3 3 1
2-oxoglutarate decarboxylation to succinyl-CoA 3 3 1
superpathway of acetate utilization and formation 3 3 1
ethanol degradation IV 3 3 1
glycine cleavage 3 3 1
L-arginine degradation I (arginase pathway) 3 2 1
ethanol degradation III 3 2 1
L-isoleucine biosynthesis V 3 2 1
L-valine degradation I 8 6 2
chitin deacetylation 4 2 1
ethene biosynthesis II (microbes) 4 1 1
propanoyl-CoA degradation II 5 3 1
pyruvate fermentation to butanol II (engineered) 6 4 1
superpathway of bitter acids biosynthesis 18 3 3
lupulone and humulone biosynthesis 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
(5R)-carbapenem carboxylate biosynthesis 6 1 1
L-Nδ-acetylornithine biosynthesis 7 5 1
myo-inositol degradation I 7 1 1
2,4-dinitrotoluene degradation 7 1 1
L-citrulline biosynthesis 8 7 1
reductive glycine pathway of autotrophic CO2 fixation 9 5 1
cis-geranyl-CoA degradation 9 2 1
myo-, chiro- and scyllo-inositol degradation 10 1 1
pyruvate fermentation to hexanol (engineered) 11 8 1
superpathway of L-citrulline metabolism 12 9 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 18 1
1-butanol autotrophic biosynthesis (engineered) 27 19 1