Experiment set3H17 for Dinoroseobacter shibae DFL-12
Sodium propionate carbon source
Group: carbon sourceMedia: DinoMM_noCarbon_HighNutrient + Sodium propionate (20 mM)
Culturing: Dino_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.5 generations
By: Adam on 2/27/2014
Media components: 20 g/L Sea salts, 0.3 g/L Ammonium Sulfate, 0.1 g/L Potassium phosphate monobasic, 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 4 genes in this experiment
For carbon source Sodium propionate in Dinoroseobacter shibae DFL-12
For carbon source Sodium propionate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Propionyl-CoA to Succinyl-CoA Module | 3 |
| Serine-glyoxylate cycle | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| propanoyl CoA degradation I | 3 | 3 | 2 |
| 2-oxobutanoate degradation I | 4 | 3 | 2 |
| anaerobic energy metabolism (invertebrates, mitochondrial) | 10 | 6 | 2 |
| 3-hydroxypropanoate cycle | 13 | 9 | 2 |
| pyruvate fermentation to propanoate I | 7 | 4 | 1 |
| superpathway of L-methionine salvage and degradation | 16 | 10 | 2 |
| superpathway of anaerobic energy metabolism (invertebrates) | 17 | 10 | 2 |
| superpathway of the 3-hydroxypropanoate cycle | 18 | 12 | 2 |
| 3-hydroxypropanoate/4-hydroxybutanate cycle | 18 | 11 | 2 |
| methylaspartate cycle | 19 | 14 | 2 |
| ethylmalonyl-CoA pathway | 11 | 8 | 1 |
| L-glutamate degradation VIII (to propanoate) | 11 | 4 | 1 |
| (S)-lactate fermentation to propanoate, acetate and hydrogen | 13 | 7 | 1 |
| crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered) | 14 | 7 | 1 |
| mycolate biosynthesis | 205 | 21 | 1 |
| superpathway of mycolate biosynthesis | 239 | 22 | 1 |