Experiment set4H3 for Phaeobacter inhibens DSM 17395
L-Citrulline carbon source
Group: carbon sourceMedia: DinoMM_noCarbon + L-Citrulline (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 F1,F2
Specific Phenotypes
For 2 genes in this experiment
For carbon source L-Citrulline in Phaeobacter inhibens DSM 17395
For carbon source L-Citrulline across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Arginine and Ornithine Degradation | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Urea cycle and metabolism of amino groups
- Arginine and proline metabolism
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| putrescine biosynthesis III | 2 | 2 | 1 |
| L-arginine degradation VII (arginase 3 pathway) | 2 | 2 | 1 |
| L-canavanine degradation I | 2 | 1 | 1 |
| L-arginine degradation I (arginase pathway) | 3 | 3 | 1 |
| L-arginine degradation VI (arginase 2 pathway) | 4 | 4 | 1 |
| superpathway of putrescine biosynthesis | 4 | 4 | 1 |
| urea cycle | 5 | 4 | 1 |
| L-Nδ-acetylornithine biosynthesis | 7 | 6 | 1 |
| L-citrulline biosynthesis | 8 | 8 | 1 |
| superpathway of polyamine biosynthesis I | 8 | 8 | 1 |
| superpathway of polyamine biosynthesis II | 8 | 6 | 1 |
| superpathway of L-citrulline metabolism | 12 | 10 | 1 |
| superpathway of hyoscyamine (atropine) and scopolamine biosynthesis | 16 | 4 | 1 |
| superpathway of arginine and polyamine biosynthesis | 17 | 17 | 1 |