Experiment set12IT012 for Pseudomonas putida KT2440
Hydroxy-L-Proline carbon source
Group: carbon sourceMedia: MOPS minimal media_noCarbon + Hydroxy-L-Proline (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Putida_ML5_JBEI, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: Matthew Incha on 12-Feb-19
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate
Specific Phenotypes
For 6 genes in this experiment
For carbon source Hydroxy-L-Proline in Pseudomonas putida KT2440
For carbon source Hydroxy-L-Proline across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Proline, 4-hydroxyproline uptake and utilization | 4 |
| D-Galacturonate and D-Glucuronate Utilization | 1 |
| Respiratory dehydrogenases 1 | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Arginine and proline metabolism
- Ascorbate and aldarate metabolism
- Lysine biosynthesis
- Phenylalanine metabolism
- Nitrogen metabolism
- Caprolactam degradation
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| trans-4-hydroxy-L-proline degradation II | 4 | 4 | 4 |
| pyruvate fermentation to acetate VIII | 2 | 1 | 1 |
| D-glucarate degradation II | 3 | 3 | 1 |
| D-galactarate degradation II | 3 | 3 | 1 |
| L-carnitine degradation II | 3 | 1 | 1 |
| L-lyxonate degradation | 3 | 1 | 1 |
| superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) | 8 | 7 | 2 |
| 1,2-dichloroethane degradation | 4 | 2 | 1 |
| mitochondrial NADPH production (yeast) | 5 | 4 | 1 |
| cytosolic NADPH production (yeast) | 5 | 4 | 1 |
| D-glucuronate degradation II | 5 | 4 | 1 |
| D-galacturonate degradation II | 5 | 3 | 1 |
| D-xylose degradation III | 5 | 1 | 1 |
| D-xylose degradation V | 5 | 1 | 1 |
| D-arabinose degradation III | 6 | 3 | 1 |
| L-arabinose degradation III | 6 | 2 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 10 | 2 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 13 | 1 |