Sodium Fumarate dibasic carbon source
Group:
carbon source
Media:
ShewMM_noCarbon +
Sodium Fumarate dibasic (10 mM), pH=7
Culturing: PV4_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.3
generations
By: Adam on
12/11/2013
Media components: 1.5 g/L
Ammonium chloride, 1.75 g/L
Sodium Chloride, 0.61 g/L
Magnesium chloride hexahydrate, 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 4 genes in this experiment
For carbon source Sodium Fumarate dibasic in Shewanella loihica PV-4
For carbon source Sodium Fumarate dibasic across organisms
SEED Subsystems
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 |
|---|
| fatty acid β-oxidation III (unsaturated, odd number) | 1 | 1 | 1 |
| benzoyl-CoA biosynthesis | 3 | 3 | 2 |
| fatty acid β-oxidation IV (unsaturated, even number) | 5 | 3 | 3 |
| fatty acid β-oxidation I (generic) | 7 | 6 | 4 |
| oleate β-oxidation (thioesterase-dependent, yeast) | 2 | 2 | 1 |
| oleate β-oxidation | 35 | 33 | 16 |
| adipate degradation | 5 | 4 | 2 |
| adipate biosynthesis | 5 | 3 | 2 |
| glutaryl-CoA degradation | 5 | 3 | 2 |
| fatty acid β-oxidation II (plant peroxisome) | 5 | 3 | 2 |
| fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent) | 5 | 2 | 2 |
| pyruvate fermentation to hexanol (engineered) | 11 | 7 | 4 |
| (8E,10E)-dodeca-8,10-dienol biosynthesis | 11 | 6 | 4 |
| 2-methyl-branched fatty acid β-oxidation | 14 | 9 | 5 |
| pyruvate fermentation to butanol II (engineered) | 6 | 5 | 2 |
| fatty acid salvage | 6 | 5 | 2 |
| valproate β-oxidation | 9 | 6 | 3 |
| L-isoleucine degradation I | 6 | 4 | 2 |
| propanoate fermentation to 2-methylbutanoate | 6 | 3 | 2 |
| methyl ketone biosynthesis (engineered) | 6 | 3 | 2 |
| oleate β-oxidation (reductase-dependent, yeast) | 3 | 1 | 1 |
| fatty acid β-oxidation VI (mammalian peroxisome) | 7 | 3 | 2 |
| pyruvate fermentation to butanoate | 7 | 3 | 2 |
| benzoyl-CoA degradation I (aerobic) | 7 | 2 | 2 |
| L-valine degradation I | 8 | 6 | 2 |
| pyruvate fermentation to butanol I | 8 | 4 | 2 |
| oleate β-oxidation (isomerase-dependent, yeast) | 4 | 1 | 1 |
| superpathway of Clostridium acetobutylicum acidogenic fermentation | 9 | 5 | 2 |
| phenylacetate degradation I (aerobic) | 9 | 3 | 2 |
| benzoate biosynthesis I (CoA-dependent, β-oxidative) | 9 | 3 | 2 |
| (R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) | 5 | 4 | 1 |
| L-glutamate degradation V (via hydroxyglutarate) | 10 | 5 | 2 |
| 3-phenylpropanoate degradation | 10 | 4 | 2 |
| 9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) | 10 | 4 | 2 |
| 4-hydroxybenzoate biosynthesis III (plants) | 5 | 2 | 1 |
| benzoate biosynthesis III (CoA-dependent, non-β-oxidative) | 5 | 1 | 1 |
| superpathway of phenylethylamine degradation | 11 | 4 | 2 |
| 6-gingerol analog biosynthesis (engineered) | 6 | 2 | 1 |
| L-glutamate degradation VII (to butanoate) | 12 | 3 | 2 |
| superpathway of Clostridium acetobutylicum solventogenic fermentation | 13 | 6 | 2 |
| superpathway of glyoxylate cycle and fatty acid degradation | 14 | 11 | 2 |
| Spodoptera littoralis pheromone biosynthesis | 22 | 4 | 3 |
| L-tryptophan degradation III (eukaryotic) | 15 | 4 | 2 |
| glycerol degradation to butanol | 16 | 10 | 2 |
| crotonate fermentation (to acetate and cyclohexane carboxylate) | 16 | 4 | 2 |
| 2-methylpropene degradation | 8 | 2 | 1 |
| superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation | 17 | 8 | 2 |
| benzoate fermentation (to acetate and cyclohexane carboxylate) | 17 | 4 | 2 |
| 3-hydroxypropanoate/4-hydroxybutanate cycle | 18 | 8 | 2 |
| toluene degradation VI (anaerobic) | 18 | 4 | 2 |
| methyl tert-butyl ether degradation | 10 | 2 | 1 |
| gallate degradation III (anaerobic) | 11 | 3 | 1 |
| 10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) | 12 | 2 | 1 |
| 10-cis-heptadecenoyl-CoA degradation (yeast) | 12 | 2 | 1 |
| androstenedione degradation I (aerobic) | 25 | 6 | 2 |
| platensimycin biosynthesis | 26 | 6 | 2 |
| (4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) | 13 | 2 | 1 |
| 1-butanol autotrophic biosynthesis (engineered) | 27 | 21 | 2 |
| androstenedione degradation II (anaerobic) | 27 | 4 | 2 |
| superpathway of testosterone and androsterone degradation | 28 | 6 | 2 |
| superpathway of cholesterol degradation I (cholesterol oxidase) | 42 | 8 | 3 |
| docosahexaenoate biosynthesis III (6-desaturase, mammals) | 14 | 2 | 1 |
| superpathway of cholesterol degradation II (cholesterol dehydrogenase) | 47 | 8 | 3 |
| cholesterol degradation to androstenedione I (cholesterol oxidase) | 17 | 2 | 1 |
| cholesterol degradation to androstenedione II (cholesterol dehydrogenase) | 22 | 2 | 1 |
| superpathway of cholesterol degradation III (oxidase) | 49 | 4 | 2 |
| photosynthetic 3-hydroxybutanoate biosynthesis (engineered) | 26 | 20 | 1 |