Experiment set1IT015 for Herbaspirillum seropedicae SmR1
Sodium pyruvate carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + Sodium pyruvate (20 mM), pH=7
Culturing: HerbieS_ML4, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.1 generations
By: Mark on 3/10/2016
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)
Growth plate: CARBON1 D3
Specific Phenotypes
For 1 genes in this experiment
For carbon source Sodium pyruvate in Herbaspirillum seropedicae SmR1
For carbon source Sodium pyruvate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| TCA Cycle | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Citrate cycle (TCA cycle)
- Glutathione metabolism
- Reductive carboxylate cycle (CO2 fixation)
- 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 |
|---|---|---|---|
| cytosolic NADPH production (yeast) | 5 | 4 | 1 |
| partial TCA cycle (obligate autotrophs) | 8 | 7 | 1 |
| superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) | 8 | 6 | 1 |
| nitrogen remobilization from senescing leaves | 8 | 6 | 1 |
| TCA cycle V (2-oxoglutarate synthase) | 9 | 7 | 1 |
| TCA cycle VI (Helicobacter) | 9 | 7 | 1 |
| TCA cycle VII (acetate-producers) | 9 | 7 | 1 |
| TCA cycle IV (2-oxoglutarate decarboxylase) | 9 | 6 | 1 |
| TCA cycle I (prokaryotic) | 10 | 8 | 1 |
| reductive TCA cycle I | 11 | 6 | 1 |
| superpathway of glyoxylate bypass and TCA | 12 | 10 | 1 |
| mixed acid fermentation | 16 | 12 | 1 |
| methylaspartate cycle | 19 | 9 | 1 |
| ethene biosynthesis V (engineered) | 25 | 17 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 22 | 1 |