Experiment set1H10 for Shewanella amazonensis SB2B
Minimal media with Sodium D,L-Lactate as carbon source
Group: carbon sourceMedia: ShewMM_noCarbon + Sodium D,L-Lactate (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/15/2013
Media components: 1.5 g/L Ammonium chloride, 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, 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)
Growth plate: 509 B7,B8
Specific Phenotypes
For 8 genes in this experiment
For carbon source Sodium D,L-Lactate in Shewanella amazonensis SB2B
For carbon source Sodium D,L-Lactate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Glutathione: Non-redox reactions | 1 |
| Synechocystis experimental | 1 |
| Triacylglycerol metabolism | 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
- Glycerophospholipid metabolism
- Atrazine degradation
- Metabolism of xenobiotics by cytochrome P450
- Drug metabolism - cytochrome P450
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| urea degradation I | 3 | 3 | 3 |
| superpathway of allantoin degradation in yeast | 6 | 3 | 3 |
| cyanuric acid degradation II | 5 | 3 | 2 |
| cyanuric acid degradation I | 5 | 2 | 2 |
| L-citrulline degradation | 3 | 3 | 1 |
| cyanate degradation | 3 | 2 | 1 |
| L-arginine degradation V (arginine deiminase pathway) | 4 | 3 | 1 |
| phospholipid remodeling (phosphatidylethanolamine, yeast) | 4 | 2 | 1 |
| superpathway of atrazine degradation | 8 | 3 | 2 |
| 4-hydroxy-2-nonenal detoxification | 4 | 1 | 1 |
| uracil degradation III | 5 | 2 | 1 |
| pentachlorophenol degradation | 10 | 3 | 2 |
| γ-glutamyl cycle | 6 | 5 | 1 |
| 5-oxo-L-proline metabolism | 6 | 5 | 1 |
| glutathione-mediated detoxification I | 8 | 3 | 1 |
| allantoin degradation IV (anaerobic) | 9 | 2 | 1 |
| gliotoxin biosynthesis | 9 | 2 | 1 |
| glutathione-mediated detoxification II | 9 | 1 | 1 |
| indole glucosinolate activation (intact plant cell) | 12 | 3 | 1 |
| camalexin biosynthesis | 12 | 2 | 1 |