Experiment set2IT026 for Shewanella sp. ANA-3
L-Alanine nitrogen source
Group: nitrogen sourceMedia: ShewMM_noNitrogen + L-Alanine (20 mM), pH=7
Culturing: ANA3_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.1 generations
By: Jake on 2/20/2014
Media components: 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, 20 mM Sodium D,L-Lactate, 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 5 genes in this experiment
For nitrogen source L-Alanine in Shewanella sp. ANA-3
For nitrogen source L-Alanine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Arginine and Ornithine Degradation | 1 |
| Polyamine Metabolism | 1 |
| ZZ gjo need homes | 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
- Glutathione 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 | 1 | 1 |
| superpathway of putrescine biosynthesis | 4 | 2 | 1 |
| superpathway of polyamine biosynthesis II | 8 | 6 | 1 |
| superpathway of ornithine degradation | 8 | 6 | 1 |
| superpathway of polyamine biosynthesis I | 8 | 4 | 1 |
| superpathway of L-arginine and L-ornithine degradation | 13 | 8 | 1 |
| superpathway of hyoscyamine (atropine) and scopolamine biosynthesis | 16 | 3 | 1 |
| superpathway of arginine and polyamine biosynthesis | 17 | 12 | 1 |