Ying_all64 rep B; time point 3
Group:
carbon source
Media:
SDM_noCarbon + 1X Ying_all64
Culturing: Bosea_OAE506_ML2, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on
1-Sep-23
Media components: 1.5 g/L
Ammonium chloride, 0.6 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)
Ying_all64 1x includes: 40 uM Sucrose, 40 uM D-Glucose, 40 uM D-Trehalose dihydrate, 40 uM m-Inositol, 40 uM D-Xylose, 40 uM D-Mannitol, 40 uM N-Acetyl-D-Glucosamine, 40 uM Sodium L-Lactate, 40 uM D,L-Malic Acid, 40 uM Citric Acid, 40 uM Succinic Acid, 40 uM Sodium pyruvate, 40 uM a-Ketoglutaric acid disodium salt hydrate, 40 uM L-Citrulline, 40 uM 5-methyluridine, 40 uM Adenine, 40 uM Adenosine, 40 uM Cytidine, 40 uM Cytosine, 40 uM Guanine, 40 uM Guanosine, 40 uM Hypoxanthine, 40 uM Inosine, 40 uM Thymine, 40 uM Uracil, 40 uM Uridine, 40 uM Xanthine, 40 uM Xanthosine, 40 uM L-Alanine, 40 uM L-Arginine, 40 uM L-Asparagine, 40 uM L-Aspartic Acid, 40 uM L-Cysteine, 40 uM L-Glutamic acid, 40 uM L-Glutamine, 40 uM Glycine, 40 uM L-Histidine, 40 uM L-Isoleucine, 40 uM L-Leucine, 40 uM L-Lysine, 40 uM L-Methionine, 40 uM L-Phenylalanine, 40 uM L-Proline, 40 uM L-Serine, 40 uM L-Threonine, 40 uM L-Tryptophan, 40 uM L-tyrosine, 40 uM L-Valine, 40 uM Gamma-Aminobutyric Acid Hydrochloride, 40 uM Ectoine, 40 uM Betaine, 40 uM N-Acetyl-L-glutamic acid, 40 uM Nicotinamide, 40 uM L-Ornithine, 40 uM Shikimic Acid, 40 uM spermidine, 40 uM Taurine, 40 uM Trigonelline HCl, 40 uM L-Carnitine hydrochloride, 40 uM Choline, 40 uM N-alpha-Acetyl-L-glutamate, 40 uM n-Acetyl-lysine, 40 uM n-Acetyl-muramic acid, 40 uM sn-glycero-3-phosphocholine
Specific Phenotypes
For 1 genes in this experiment
For carbon source Ying_all64 in Bosea sp. OAE506
For carbon source Ying_all64 across organisms
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 |
|---|
| acetoacetate degradation (to acetyl CoA) | 2 | 2 | 1 |
| 5,6-dehydrokavain biosynthesis (engineered) | 10 | 6 | 4 |
| ketolysis | 3 | 3 | 1 |
| benzoyl-CoA biosynthesis | 3 | 3 | 1 |
| polyhydroxybutanoate biosynthesis | 3 | 2 | 1 |
| (2S)-ethylmalonyl-CoA biosynthesis | 4 | 3 | 1 |
| oleate β-oxidation | 35 | 28 | 8 |
| valproate β-oxidation | 9 | 5 | 2 |
| 2-methyl-branched fatty acid β-oxidation | 14 | 9 | 3 |
| ketogenesis | 5 | 4 | 1 |
| pyruvate fermentation to acetone | 5 | 3 | 1 |
| (R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) | 5 | 3 | 1 |
| glutaryl-CoA degradation | 5 | 3 | 1 |
| fatty acid β-oxidation II (plant peroxisome) | 5 | 3 | 1 |
| 9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) | 10 | 4 | 2 |
| isopropanol biosynthesis (engineered) | 5 | 2 | 1 |
| 4-hydroxybenzoate biosynthesis III (plants) | 5 | 2 | 1 |
| fatty acid β-oxidation VII (yeast peroxisome) | 5 | 1 | 1 |
| ethylbenzene degradation (anaerobic) | 5 | 1 | 1 |
| pyruvate fermentation to hexanol (engineered) | 11 | 7 | 2 |
| fatty acid salvage | 6 | 5 | 1 |
| pyruvate fermentation to butanol II (engineered) | 6 | 4 | 1 |
| L-isoleucine degradation I | 6 | 4 | 1 |
| propanoate fermentation to 2-methylbutanoate | 6 | 4 | 1 |
| 4-ethylphenol degradation (anaerobic) | 6 | 2 | 1 |
| 10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast) | 6 | 1 | 1 |
| jasmonic acid biosynthesis | 19 | 4 | 3 |
| acetyl-CoA fermentation to butanoate | 7 | 5 | 1 |
| fatty acid β-oxidation I (generic) | 7 | 5 | 1 |
| pyruvate fermentation to butanoate | 7 | 3 | 1 |
| fatty acid β-oxidation VI (mammalian peroxisome) | 7 | 3 | 1 |
| mevalonate pathway I (eukaryotes and bacteria) | 7 | 1 | 1 |
| mevalonate pathway II (haloarchaea) | 7 | 1 | 1 |
| 2-deoxy-D-ribose degradation II | 8 | 5 | 1 |
| pyruvate fermentation to butanol I | 8 | 4 | 1 |
| 2-methylpropene degradation | 8 | 2 | 1 |
| mevalonate pathway IV (archaea) | 8 | 1 | 1 |
| isoprene biosynthesis II (engineered) | 8 | 1 | 1 |
| mevalonate pathway III (Thermoplasma) | 8 | 1 | 1 |
| androstenedione degradation I (aerobic) | 25 | 6 | 3 |
| superpathway of Clostridium acetobutylicum acidogenic fermentation | 9 | 5 | 1 |
| benzoate biosynthesis I (CoA-dependent, β-oxidative) | 9 | 3 | 1 |
| 4-oxopentanoate degradation | 9 | 2 | 1 |
| superpathway of testosterone and androsterone degradation | 28 | 6 | 3 |
| L-glutamate degradation V (via hydroxyglutarate) | 10 | 7 | 1 |
| superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) | 10 | 4 | 1 |
| 3-phenylpropanoate degradation | 10 | 4 | 1 |
| L-lysine fermentation to acetate and butanoate | 10 | 4 | 1 |
| methyl tert-butyl ether degradation | 10 | 2 | 1 |
| superpathway of cholesterol degradation I (cholesterol oxidase) | 42 | 8 | 4 |
| (8E,10E)-dodeca-8,10-dienol biosynthesis | 11 | 6 | 1 |
| ethylmalonyl-CoA pathway | 11 | 6 | 1 |
| superpathway of cholesterol degradation II (cholesterol dehydrogenase) | 47 | 9 | 4 |
| L-glutamate degradation VII (to butanoate) | 12 | 4 | 1 |
| 10-cis-heptadecenoyl-CoA degradation (yeast) | 12 | 2 | 1 |
| 10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) | 12 | 2 | 1 |
| superpathway of Clostridium acetobutylicum solventogenic fermentation | 13 | 7 | 1 |
| (4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) | 13 | 2 | 1 |
| androstenedione degradation II (anaerobic) | 27 | 4 | 2 |
| superpathway of glyoxylate cycle and fatty acid degradation | 14 | 12 | 1 |
| docosahexaenoate biosynthesis III (6-desaturase, mammals) | 14 | 2 | 1 |
| L-tryptophan degradation III (eukaryotic) | 15 | 5 | 1 |
| glycerol degradation to butanol | 16 | 9 | 1 |
| crotonate fermentation (to acetate and cyclohexane carboxylate) | 16 | 3 | 1 |
| superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation | 17 | 9 | 1 |
| benzoate fermentation (to acetate and cyclohexane carboxylate) | 17 | 3 | 1 |
| cholesterol degradation to androstenedione I (cholesterol oxidase) | 17 | 2 | 1 |
| 3-hydroxypropanoate/4-hydroxybutanate cycle | 18 | 13 | 1 |
| toluene degradation VI (anaerobic) | 18 | 3 | 1 |
| sitosterol degradation to androstenedione | 18 | 1 | 1 |
| cholesterol degradation to androstenedione II (cholesterol dehydrogenase) | 22 | 3 | 1 |
| superpathway of cholesterol degradation III (oxidase) | 49 | 5 | 2 |
| photosynthetic 3-hydroxybutanoate biosynthesis (engineered) | 26 | 18 | 1 |
| platensimycin biosynthesis | 26 | 6 | 1 |
| superpathway of ergosterol biosynthesis I | 26 | 3 | 1 |
| 1-butanol autotrophic biosynthesis (engineered) | 27 | 19 | 1 |
| superpathway of cholesterol biosynthesis | 38 | 3 | 1 |
| superpathway of L-lysine degradation | 43 | 13 | 1 |
| Methanobacterium thermoautotrophicum biosynthetic metabolism | 56 | 18 | 1 |