Experiment set25S12 for Pseudomonas fluorescens SBW25-INTG
D-Xylose carbon source
Group: carbon sourceMedia: MME_noCarbon + D-Xylose (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 31-Jan-23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium 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 9 genes in this experiment
For carbon source D-Xylose in Pseudomonas fluorescens SBW25-INTG
For carbon source D-Xylose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 3 |
| Xylose utilization | 2 |
| D-galactonate catabolism | 1 |
| L-Arabinose utilization | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pentose and glucuronate interconversions
- Fructose and mannose metabolism
- Ascorbate and aldarate metabolism
- Valine, leucine and isoleucine biosynthesis
- Pantothenate and CoA biosynthesis
- Biosynthesis of alkaloids derived from histidine and purine
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| D-xylose degradation I | 2 | 2 | 2 |
| xylitol degradation I | 2 | 2 | 1 |
| D-arabinitol degradation I | 2 | 1 | 1 |
| L-valine biosynthesis | 4 | 4 | 1 |
| pyruvate fermentation to isobutanol (engineered) | 5 | 4 | 1 |
| L-arabinose degradation III | 6 | 5 | 1 |
| L-isoleucine biosynthesis IV | 6 | 4 | 1 |
| L-arabinose degradation V | 6 | 3 | 1 |
| L-isoleucine biosynthesis I (from threonine) | 7 | 7 | 1 |
| L-isoleucine biosynthesis III | 7 | 4 | 1 |
| L-isoleucine biosynthesis II | 8 | 5 | 1 |
| L-arabinose degradation IV | 8 | 5 | 1 |
| superpathway of branched chain amino acid biosynthesis | 17 | 17 | 2 |
| superpathway of glucose and xylose degradation | 17 | 16 | 2 |
| superpathway of L-isoleucine biosynthesis I | 13 | 13 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 16 | 3 |
| superpathway of L-threonine metabolism | 18 | 11 | 1 |