Experiment set10IT013 for Pseudomonas fluorescens SBW25-INTG
Sodium malate (C) and Ammonium chloride (N); with MOPS
Group: stressMedia: MME_noNitrogen_noCarbon + Sodium malate (30 mM) + Ammonium chloride (10 mM) + 3-(N-morpholino)propanesulfonic acid (20 mM) + Sodium Chloride (400 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1300 rpm
By: Rob Egbert on 11-May-21
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 12 genes in this experiment
For stress Sodium malate in Pseudomonas fluorescens SBW25-INTG
For stress Sodium malate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Glycogen metabolism | 1 |
| HMG CoA Synthesis | 1 |
| Leucine Degradation and HMG-CoA Metabolism | 1 |
| Maltose and Maltodextrin Utilization | 1 |
| TCA Cycle | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Synthesis and degradation of ketone bodies
- Valine, leucine and isoleucine degradation
- Starch and sucrose metabolism
- Pyruvate metabolism
- Butanoate metabolism
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| mevalonate degradation | 2 | 1 | 1 |
| oxalate degradation II | 3 | 1 | 1 |
| starch degradation V | 4 | 3 | 1 |
| ketogenesis | 5 | 3 | 1 |
| L-leucine degradation I | 6 | 5 | 1 |
| partial TCA cycle (obligate autotrophs) | 8 | 8 | 1 |
| sucrose biosynthesis II | 8 | 6 | 1 |
| glycogen degradation I | 8 | 6 | 1 |
| TCA cycle VII (acetate-producers) | 9 | 7 | 1 |
| TCA cycle VI (Helicobacter) | 9 | 7 | 1 |
| cis-geranyl-CoA degradation | 9 | 4 | 1 |
| starch degradation II | 9 | 1 | 1 |
| TCA cycle I (prokaryotic) | 10 | 9 | 1 |
| superpathway of glyoxylate bypass and TCA | 12 | 11 | 1 |
| 3-hydroxypropanoate cycle | 13 | 6 | 1 |
| superpathway of the 3-hydroxypropanoate cycle | 18 | 6 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 22 | 1 |