Experiment set16IT022 for Pseudomonas putida KT2440
3-methyl-2-oxopentanoic acid carbon source
Group: carbon sourceMedia: MOPS minimal media_noCarbon + 3-methyl-2-oxopentanoic acid (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.0 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 9 genes in this experiment
For carbon source 3-methyl-2-oxopentanoic acid in Pseudomonas putida KT2440
For carbon source 3-methyl-2-oxopentanoic acid across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Valine, leucine and isoleucine degradation
- Fatty acid metabolism
- Biosynthesis of terpenoids and steroids
- Biosynthesis of plant hormones
- Glycolysis / Gluconeogenesis
- Citrate cycle (TCA cycle)
- Glycine, serine and threonine metabolism
- Geraniol degradation
- Pyruvate metabolism
- 1- and 2-Methylnaphthalene degradation
- Benzoate degradation via CoA ligation
- Butanoate metabolism
- Brassinosteroid biosynthesis
- Caprolactam degradation
- Biosynthesis of phenylpropanoids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of alkaloids derived from terpenoid and polyketide
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| 2-oxoisovalerate decarboxylation to isobutanoyl-CoA | 3 | 3 | 3 |
| cis-cyclopropane fatty acid (CFA) biosynthesis | 1 | 1 | 1 |
| sterculate biosynthesis | 2 | 1 | 1 |
| 2-oxoglutarate decarboxylation to succinyl-CoA | 3 | 3 | 1 |
| glycine cleavage | 3 | 3 | 1 |
| glycine biosynthesis II | 3 | 3 | 1 |
| pyruvate decarboxylation to acetyl CoA I | 3 | 3 | 1 |
| pyruvate fermentation to butanol II (engineered) | 6 | 4 | 1 |
| pyruvate fermentation to hexanol (engineered) | 11 | 8 | 1 |
| superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle | 22 | 18 | 1 |
| 1-butanol autotrophic biosynthesis (engineered) | 27 | 19 | 1 |
| mycolate biosynthesis | 205 | 20 | 3 |
| superpathway of mycolate biosynthesis | 239 | 21 | 3 |