Experiment set2IT066 for Pseudomonas simiae WCS417
m-Inositol carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + m-Inositol (20 mM), pH=7
Culturing: fluoroDangl_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 2/18/2015
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 11 genes in this experiment
For carbon source m-Inositol in Pseudomonas simiae WCS417
For carbon source m-Inositol across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Inositol catabolism | 9 |
| Isobutyryl-CoA to Propionyl-CoA Module | 1 |
| Pyruvate Alanine Serine Interconversions | 1 |
| Valine degradation | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Inositol phosphate metabolism
- Propanoate metabolism
- Alanine and aspartate metabolism
- Valine, leucine and isoleucine degradation
- beta-Alanine metabolism
- Pentose and glucuronate interconversions
- Galactose metabolism
- Ascorbate and aldarate metabolism
- 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
- Phenylalanine metabolism
- Benzoate degradation via hydroxylation
- Streptomycin biosynthesis
- Biphenyl degradation
- Benzoate degradation via CoA ligation
- Ethylbenzene degradation
- Nicotinate and nicotinamide metabolism
- Limonene and pinene degradation
- Caprolactam degradation
- Biosynthesis of ansamycins
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| myo-inositol degradation I | 7 | 7 | 7 |
| β-alanine degradation II | 2 | 2 | 2 |
| myo-, chiro- and scyllo-inositol degradation | 10 | 7 | 7 |
| β-alanine degradation I | 2 | 1 | 1 |
| acrylate degradation I | 5 | 3 | 1 |
| propanoyl-CoA degradation II | 5 | 3 | 1 |
| myo-inositol degradation II | 5 | 1 | 1 |
| β-alanine biosynthesis II | 6 | 5 | 1 |
| 2,4-dinitrotoluene degradation | 7 | 3 | 1 |
| L-valine degradation I | 8 | 6 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 9 | 1 |
| streptomycin biosynthesis | 18 | 3 | 1 |