Experiment set12IT042 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 8 genes in this experiment
For carbon source Hydroxy-L-Proline in Pseudomonas putida KT2440
For carbon source Hydroxy-L-Proline across organisms
SEED Subsystems
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
- Glycine, serine and threonine 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 |
| glycine biosynthesis II | 3 | 3 | 1 |
| D-galactarate degradation II | 3 | 3 | 1 |
| glycine cleavage | 3 | 3 | 1 |
| L-lyxonate degradation | 3 | 1 | 1 |
| L-carnitine degradation II | 3 | 1 | 1 |
| superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) | 8 | 7 | 2 |
| 1,2-dichloroethane degradation | 4 | 2 | 1 |
| D-glucuronate degradation II | 5 | 4 | 1 |
| mitochondrial NADPH production (yeast) | 5 | 4 | 1 |
| cytosolic NADPH production (yeast) | 5 | 4 | 1 |
| D-galacturonate degradation II | 5 | 3 | 1 |
| D-xylose degradation V | 5 | 1 | 1 |
| D-xylose degradation III | 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 |