Experiment set1H19 for Shewanella amazonensis SB2B
Minimal media with Gelatin as carbon source
Group: carbon sourceMedia: ShewMM_noCarbon + Gelatin (1 mg/ml), 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 F5,F6
Specific Phenotypes
For 1 genes in this experiment
For carbon source Gelatin in Shewanella amazonensis SB2B
For carbon source Gelatin across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| D-Galacturonate and D-Glucuronate Utilization | 1 |
| Proline, 4-hydroxyproline uptake and utilization | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| pyruvate fermentation to acetate VIII | 2 | 2 | 1 |
| L-carnitine degradation II | 3 | 2 | 1 |
| D-galactarate degradation II | 3 | 1 | 1 |
| D-glucarate degradation II | 3 | 1 | 1 |
| L-lyxonate degradation | 3 | 1 | 1 |
| superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) | 8 | 6 | 2 |
| trans-4-hydroxy-L-proline degradation II | 4 | 3 | 1 |
| 1,2-dichloroethane degradation | 4 | 2 | 1 |
| cytosolic NADPH production (yeast) | 5 | 4 | 1 |
| mitochondrial NADPH production (yeast) | 5 | 3 | 1 |
| D-glucuronate degradation II | 5 | 2 | 1 |
| D-xylose degradation III | 5 | 1 | 1 |
| D-xylose degradation V | 5 | 1 | 1 |
| D-galacturonate degradation II | 5 | 1 | 1 |
| L-arabinose degradation III | 6 | 2 | 1 |
| D-arabinose degradation III | 6 | 2 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 6 | 2 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 7 | 1 |