Experiment set3H44 for Phaeobacter inhibens DSM 17395
Glycerol carbon source
Group: carbon sourceMedia: DinoMM_noCarbon + Glycerol (20 mM), pH=7
Culturing: Phaeo_ML1, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Jordan on 8/5/2013
Media components: 20 g/L Sea salts, 0.3 g/L Ammonium Sulfate, 0.1 g/L Potassium phosphate monobasic, Wolfe's mineral mix (0.003 g/L Magnesium Sulfate Heptahydrate, 0.0015 g/L Nitrilotriacetic acid, 0.001 g/L Sodium Chloride, 0.0005 g/L Manganese (II) sulfate monohydrate, 0.0001 g/L Cobalt chloride hexahydrate, 0.0001 g/L Zinc sulfate heptahydrate, 0.0001 g/L Calcium chloride dihydrate, 0.0001 g/L Iron (II) sulfate heptahydrate, 2.5e-05 g/L Nickel (II) chloride hexahydrate, 2e-05 g/L Aluminum potassium sulfate dodecahydrate, 1e-05 g/L Copper (II) sulfate pentahydrate, 1e-05 g/L Boric Acid, 1e-05 g/L Sodium Molybdate Dihydrate, 0.0003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.05 mg/L Pyridoxine HCl, 0.025 mg/L 4-Aminobenzoic acid, 0.025 mg/L Lipoic acid, 0.025 mg/L Nicotinic Acid, 0.025 mg/L Riboflavin, 0.025 mg/L Thiamine HCl, 0.025 mg/L calcium pantothenate, 0.01 mg/L biotin, 0.01 mg/L Folic Acid, 0.0005 mg/L Cyanocobalamin)
Growth plate: 621 D3,D4
Specific Phenotypes
For 7 genes in this experiment
For carbon source Glycerol in Phaeobacter inhibens DSM 17395
For carbon source Glycerol across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Aromatic amino acid interconversions with aryl acids | 1 |
| Glycerol and Glycerol-3-phosphate Uptake and Utilization | 1 |
| Pyrimidine utilization | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycolysis / Gluconeogenesis
- Ascorbate and aldarate metabolism
- Fatty acid metabolism
- Urea cycle and metabolism of amino groups
- Valine, leucine and isoleucine degradation
- Lysine degradation
- Arginine and proline metabolism
- Histidine metabolism
- Tryptophan metabolism
- beta-Alanine metabolism
- Taurine and hypotaurine metabolism
- Glycerolipid metabolism
- Pyruvate metabolism
- 1,2-Dichloroethane degradation
- Propanoate metabolism
- 3-Chloroacrylic acid degradation
- Butanoate metabolism
- Limonene and pinene degradation
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| taurine degradation I | 1 | 1 | 1 |
| hypotaurine degradation | 3 | 3 | 2 |
| ethanol degradation IV | 3 | 3 | 1 |
| ethanol degradation II | 3 | 3 | 1 |
| ethanol degradation III | 3 | 2 | 1 |
| histamine degradation | 3 | 1 | 1 |
| phytol degradation | 4 | 3 | 1 |
| fatty acid α-oxidation I (plants) | 4 | 2 | 1 |
| L-tryptophan degradation X (mammalian, via tryptamine) | 4 | 2 | 1 |
| putrescine degradation III | 4 | 1 | 1 |
| octane oxidation | 5 | 3 | 1 |
| sphingosine and sphingosine-1-phosphate metabolism | 10 | 4 | 2 |
| mitochondrial NADPH production (yeast) | 5 | 2 | 1 |
| dopamine degradation | 5 | 1 | 1 |
| superpathway of taurine degradation | 6 | 4 | 1 |
| 3-methyl-branched fatty acid α-oxidation | 6 | 3 | 1 |
| alkane oxidation | 6 | 1 | 1 |
| noradrenaline and adrenaline degradation | 13 | 4 | 2 |
| serotonin degradation | 7 | 3 | 1 |
| ceramide degradation by α-oxidation | 7 | 2 | 1 |
| limonene degradation IV (anaerobic) | 7 | 1 | 1 |
| superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) | 8 | 4 | 1 |
| ceramide and sphingolipid recycling and degradation (yeast) | 16 | 4 | 2 |
| aromatic biogenic amine degradation (bacteria) | 8 | 1 | 1 |