Experiment set6IT022 for Phaeobacter inhibens DSM 17395
L-Serine carbon source
Group: carbon sourceMedia: DinoMM_noCarbon_HighNutrient + L-Serine (20 mM), pH=7
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
Growth: about 5.4 generations
By: Adam on marchapr14
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 L-Serine in Phaeobacter inhibens DSM 17395
For carbon source L-Serine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Allantoin Utilization | 1 |
| D-galactarate, D-glucarate and D-glycerate catabolism | 1 |
| Glutathione: Non-redox reactions | 1 |
| Photorespiration (oxidative C2 cycle) | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Valine, leucine and isoleucine degradation
- Glutathione metabolism
- Glyoxylate and dicarboxylate metabolism
- Metabolism of xenobiotics by cytochrome P450
- Drug metabolism - cytochrome P450
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| glycolate and glyoxylate degradation I | 4 | 2 | 1 |
| D-glucarate degradation I | 4 | 1 | 1 |
| D-galactarate degradation I | 4 | 1 | 1 |
| 4-hydroxy-2-nonenal detoxification | 4 | 1 | 1 |
| pentachlorophenol degradation | 10 | 3 | 2 |
| superpathway of D-glucarate and D-galactarate degradation | 5 | 1 | 1 |
| superpathway of glycol metabolism and degradation | 7 | 4 | 1 |
| L-valine degradation I | 8 | 5 | 1 |
| glutathione-mediated detoxification I | 8 | 3 | 1 |
| gliotoxin biosynthesis | 9 | 2 | 1 |
| nicotinate degradation III | 9 | 1 | 1 |
| glutathione-mediated detoxification II | 9 | 1 | 1 |
| indole glucosinolate activation (intact plant cell) | 12 | 3 | 1 |
| camalexin biosynthesis | 12 | 2 | 1 |
| superpathway of nicotinate degradation | 18 | 2 | 1 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 6 | 1 |