Experiment set1IT030 for Pseudomonas simiae WCS417
D-Glucose-6-Phosphate sodium salt carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Glucose-6-Phosphate sodium salt (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 9 genes in this experiment
For carbon source D-Glucose-6-Phosphate sodium salt in Pseudomonas simiae WCS417
For carbon source D-Glucose-6-Phosphate sodium salt across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Entner-Doudoroff Pathway | 1 |
| Glycolysis and Gluconeogenesis | 1 |
| Proteasome bacterial | 1 |
| Proteolysis in bacteria, ATP-dependent | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycolysis / Gluconeogenesis
- Galactose metabolism
- Starch and sucrose metabolism
- Nucleotide sugars metabolism
- Streptomycin biosynthesis
- Biosynthesis of phenylpropanoids
- Biosynthesis of terpenoids and steroids
- 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
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| trehalose degradation I (low osmolarity) | 2 | 2 | 1 |
| trehalose degradation II (cytosolic) | 2 | 1 | 1 |
| GDP-α-D-glucose biosynthesis | 3 | 2 | 1 |
| trehalose degradation V | 3 | 2 | 1 |
| trehalose degradation IV | 3 | 1 | 1 |
| sucrose degradation III (sucrose invertase) | 4 | 3 | 1 |
| glucose and glucose-1-phosphate degradation | 5 | 4 | 1 |
| glycogen degradation II | 6 | 5 | 1 |
| UDP-N-acetyl-D-glucosamine biosynthesis II | 6 | 4 | 1 |
| UDP-N-acetyl-D-galactosamine biosynthesis II | 7 | 5 | 1 |
| glycogen degradation I | 8 | 6 | 1 |
| sucrose biosynthesis II | 8 | 6 | 1 |
| chitin biosynthesis | 9 | 5 | 1 |
| 1,3-propanediol biosynthesis (engineered) | 9 | 4 | 1 |
| glycolysis III (from glucose) | 11 | 9 | 1 |
| homolactic fermentation | 12 | 9 | 1 |
| Bifidobacterium shunt | 15 | 12 | 1 |
| heterolactic fermentation | 18 | 14 | 1 |