Experiment set1IT028 for Pseudomonas sp. S08-1
Sodium octanoate carbon source
Group: carbon sourceMedia: MME_noNitrogen_noCarbon + Sodium octanoate (7.5 mM) + Ammonium chloride (10 mM)
Culturing: Pseudomonas_S08_1_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 8-June-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)
Specific Phenotypes
For 3 genes in this experiment
For carbon source Sodium octanoate in Pseudomonas sp. S08-1
For carbon source Sodium octanoate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Arginine and Ornithine Degradation | 2 |
| Polyamine Metabolism | 2 |
| Arginine Deiminase Pathway | 1 |
| Glutathione: Non-redox reactions | 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
- Metabolism of xenobiotics by cytochrome P450
- Drug metabolism - cytochrome P450
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| putrescine biosynthesis II | 3 | 3 | 1 |
| L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) | 3 | 3 | 1 |
| 4-hydroxy-2-nonenal detoxification | 4 | 1 | 1 |
| pentachlorophenol degradation | 10 | 3 | 2 |
| superpathway of polyamine biosynthesis II | 8 | 6 | 1 |
| glutathione-mediated detoxification I | 8 | 3 | 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 |