Experiment set4S69 for Rhodopseudomonas palustris CGA009
PM with benzoic acid carbon source
Group: carbon sourceMedia: PM + benzoic acid (3 mM) + Sodium bicarbonate (10 mM)
Culturing: RPal_CGA009_ML8, Anaerobic, at 30 (C), shaken=0 rpm
By: Yasu on 23-Mar-23
Media components: 12.5 mM Disodium phosphate, 12.5 mM Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 0.1 mM Sodium thiosulfate pentahydrate, 0.002 g/L 4-Aminobenzoic acid, UW concentrated base (0.02 g/L Nitrilotriacetic acid, 0.0289 g/L Magnesium sulfate, 0.00667 g/L Calcium chloride dihydrate, 1.85e-05 g/L ammonium molybdate tetrahydrate, 0.000698 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L EDTA, 0.001095 g/L Zinc sulfate heptahydrate, 0.000154 g/L Manganese (II) sulfate monohydrate, 3.92e-05 g/L Copper (II) sulfate pentahydrate, 2.5e-05 g/L Cobalt(II) nitrate hexahydrate, 1.77e-05 g/L sodium tetraborate decahydrate)
Specific Phenotypes
For 2 genes in this experiment
For carbon source benzoic acid in Rhodopseudomonas palustris CGA009
For carbon source benzoic acid across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Isoleucine degradation | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Benzoate degradation via CoA ligation
- Fatty acid metabolism
- Valine, leucine and isoleucine degradation
- Geraniol degradation
- Butanoate metabolism
- Caprolactam degradation
- Biosynthesis of plant hormones
- Fructose and mannose metabolism
- Ascorbate and aldarate metabolism
- C21-Steroid hormone metabolism
- Glycine, serine and threonine metabolism
- Tyrosine metabolism
- Bisphenol A degradation
- Nucleotide sugars metabolism
- Polyketide sugar unit biosynthesis
- Aminosugars metabolism
- Linoleic acid metabolism
- alpha-Linolenic acid metabolism
- 1- and 2-Methylnaphthalene degradation
- Tetrachloroethene degradation
- Propanoate metabolism
- Ethylbenzene degradation
- Retinol metabolism
- Limonene and pinene degradation
- Brassinosteroid biosynthesis
- Alkaloid biosynthesis I
- Alkaloid biosynthesis II
- Insect hormone biosynthesis
- Biosynthesis of unsaturated fatty acids
- Biosynthesis of type II polyketide products
- Biosynthesis of terpenoids and steroids
- Biosynthesis of alkaloids derived from shikimate pathway
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| cyclohexane-1-carboxylate degradation (anaerobic) | 2 | 2 | 2 |
| pyruvate fermentation to butanol II (engineered) | 6 | 4 | 1 |
| pyruvate fermentation to hexanol (engineered) | 11 | 7 | 1 |
| crotonate fermentation (to acetate and cyclohexane carboxylate) | 16 | 5 | 1 |
| benzoate fermentation (to acetate and cyclohexane carboxylate) | 17 | 7 | 1 |
| 1-butanol autotrophic biosynthesis (engineered) | 27 | 21 | 1 |