Experiment set12IT037 for Pseudomonas putida KT2440

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2-methyl-1-butanol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 2-methyl-1-butanol (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Putida_ML5_JBEI, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: Matthew Incha on 12-Feb-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 16 genes in this experiment

For carbon source 2-methyl-1-butanol in Pseudomonas putida KT2440

For carbon source 2-methyl-1-butanol across organisms

SEED Subsystems

Subsystem #Specific
Isobutyryl-CoA to Propionyl-CoA Module 2
Valine degradation 2
Acetyl-CoA fermentation to Butyrate 1
Anaerobic respiratory reductases 1
Butanol Biosynthesis 1
Glycine and Serine Utilization 1
Glycine cleavage system 1
Isoleucine degradation 1
Phosphate metabolism 1
Photorespiration (oxidative C2 cycle) 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
acetate conversion to acetyl-CoA 1 1 1
acetate and ATP formation from acetyl-CoA III 1 1 1
superpathway of acetate utilization and formation 3 3 1
benzoyl-CoA biosynthesis 3 3 1
glycine cleavage 3 3 1
ethanol degradation IV 3 3 1
glycine biosynthesis II 3 3 1
ethanol degradation II 3 3 1
ethanol degradation III 3 2 1
L-isoleucine biosynthesis V 3 2 1
chitin deacetylation 4 2 1
2-methyl-branched fatty acid β-oxidation 14 10 3
adipate degradation 5 5 1
adipate biosynthesis 5 4 1
fatty acid β-oxidation IV (unsaturated, even number) 5 4 1
acrylate degradation I 5 3 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
propanoyl-CoA degradation II 5 3 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 2 1
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 2
β-alanine biosynthesis II 6 5 1
pyruvate fermentation to butanol II (engineered) 6 4 1
methyl ketone biosynthesis (engineered) 6 3 1
superpathway of bitter acids biosynthesis 18 3 3
colupulone and cohumulone biosynthesis 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
lupulone and humulone biosynthesis 6 1 1
fatty acid β-oxidation I (generic) 7 5 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 4 1
benzoyl-CoA degradation I (aerobic) 7 3 1
L-valine degradation I 8 6 1
phenylacetate degradation I (aerobic) 9 9 1
valproate β-oxidation 9 7 1
reductive glycine pathway of autotrophic CO2 fixation 9 5 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 1
cis-geranyl-CoA degradation 9 2 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 1
3-phenylpropanoate degradation 10 4 1
superpathway of phenylethylamine degradation 11 11 1
pyruvate fermentation to hexanol (engineered) 11 8 1
Spodoptera littoralis pheromone biosynthesis 22 4 2
oleate β-oxidation 35 30 3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
platensimycin biosynthesis 26 6 1
1-butanol autotrophic biosynthesis (engineered) 27 19 1