Experiment set28IT007 for Pseudomonas putida KT2440
Carnitine Hydrochloride nitrogen source
Group: nitrogen sourceMedia: MOPS minimal media_Glucose_noNitrogen + Carnitine Hydrochloride (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Mitchell Thompson on 11/16/20
Media components: 10 mM D-Glucose, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 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 22 genes in this experiment
For nitrogen source Carnitine Hydrochloride in Pseudomonas putida KT2440
For nitrogen source Carnitine Hydrochloride across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycine, serine and threonine metabolism
- Benzoate degradation via CoA ligation
- Fatty acid biosynthesis
- Ubiquinone and menaquinone biosynthesis
- Cyanoamino acid metabolism
- alpha-Linolenic acid metabolism
- Butanoate metabolism
- One carbon pool by folate
- Methane metabolism
- Limonene and pinene degradation
- Biosynthesis of unsaturated fatty acids
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-carnitine degradation III | 3 | 3 | 3 |
| glycine biosynthesis I | 1 | 1 | 1 |
| D-carnitine degradation I | 3 | 2 | 2 |
| glycine betaine degradation III | 7 | 7 | 4 |
| D-carnitine degradation II | 2 | 1 | 1 |
| glycine betaine degradation I | 8 | 6 | 3 |
| glycine degradation | 3 | 3 | 1 |
| dTMP de novo biosynthesis (mitochondrial) | 3 | 3 | 1 |
| superpathway of L-serine and glycine biosynthesis I | 4 | 4 | 1 |
| creatinine degradation I | 4 | 2 | 1 |
| glycine betaine degradation II (mammalian) | 4 | 1 | 1 |
| folate polyglutamylation | 5 | 4 | 1 |
| creatinine degradation II | 5 | 3 | 1 |
| folate transformations II (plants) | 11 | 10 | 2 |
| peptido-conjugates in tissue regeneration biosynthesis | 17 | 6 | 3 |
| leukotriene biosynthesis | 6 | 2 | 1 |
| folate transformations III (E. coli) | 9 | 9 | 1 |
| photorespiration III | 9 | 6 | 1 |
| photorespiration I | 9 | 6 | 1 |
| gliotoxin biosynthesis | 9 | 2 | 1 |
| photorespiration II | 10 | 7 | 1 |
| folate transformations I | 13 | 9 | 1 |
| formaldehyde assimilation I (serine pathway) | 13 | 7 | 1 |
| purine nucleobases degradation II (anaerobic) | 24 | 16 | 1 |
| arachidonate metabolites biosynthesis | 74 | 3 | 1 |