Experiment set1IT017 for Burkholderia phytofirmans PsJN
Tween 20 carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + Tween 20 (0.5 vol%), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 5.5 generations
By: Mark on 6/2/2015
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 5 genes in this experiment
For carbon source Tween 20 in Burkholderia phytofirmans PsJN
For carbon source Tween 20 across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| 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:
- Fructose and mannose metabolism
- Ascorbate and aldarate metabolism
- Fatty acid metabolism
- Valine, leucine and isoleucine degradation
- Geraniol degradation
- Aminosugars metabolism
- Lipopolysaccharide biosynthesis
- Ether lipid metabolism
- Sphingolipid metabolism
- Pyruvate metabolism
- 1- and 2-Methylnaphthalene degradation
- Glyoxylate and dicarboxylate metabolism
- Benzoate degradation via CoA ligation
- Thiamine metabolism
- Riboflavin metabolism
- Nicotinate and nicotinamide metabolism
- Brassinosteroid biosynthesis
- Caprolactam degradation
- Biosynthesis of terpenoids and steroids
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| glycolate and glyoxylate degradation II | 2 | 2 | 1 |
| chitin deacetylation | 4 | 2 | 1 |
| adipate degradation | 5 | 5 | 1 |
| glyoxylate cycle | 6 | 6 | 1 |
| fatty acid salvage | 6 | 5 | 1 |
| superpathway of glycol metabolism and degradation | 7 | 5 | 1 |
| D-xylose degradation IV | 7 | 4 | 1 |
| L-arabinose degradation IV | 8 | 6 | 1 |
| butanol and isobutanol biosynthesis (engineered) | 8 | 4 | 1 |
| oleate β-oxidation | 35 | 29 | 3 |
| superpathway of glyoxylate bypass and TCA | 12 | 10 | 1 |
| superpathway of glyoxylate cycle and fatty acid degradation | 14 | 11 | 1 |
| 2-methyl-branched fatty acid β-oxidation | 14 | 9 | 1 |
| crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered) | 14 | 2 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 22 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 22 | 1 |