Experiment set5IT027 for Pseudomonas fluorescens FW300-N2E3
Carnitine Hydrochloride nitrogen source
Group: nitrogen sourceMedia: RCH2_defined_Glucose_noNitrogen + Carnitine Hydrochloride (5 mM), pH=7
Culturing: pseudo3_N2E3_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Specific Phenotypes
For 17 genes in this experiment
For nitrogen source Carnitine Hydrochloride in Pseudomonas fluorescens FW300-N2E3
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
- alpha-Linolenic acid metabolism
- Benzoate degradation via CoA ligation
- Fatty acid biosynthesis
- Ubiquinone and menaquinone biosynthesis
- Puromycin biosynthesis
- Cyanoamino acid metabolism
- Nucleotide sugars metabolism
- Trinitrotoluene degradation
- Butanoate metabolism
- One carbon pool by folate
- Methane metabolism
- Porphyrin and chlorophyll metabolism
- Limonene and pinene degradation
- Carotenoid biosynthesis - General
- Alkaloid biosynthesis I
- Insect hormone biosynthesis
- Biosynthesis of unsaturated fatty acids
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| glycine biosynthesis I | 1 | 1 | 1 |
| L-carnitine degradation III | 3 | 3 | 2 |
| glycine betaine degradation III | 7 | 7 | 4 |
| D-carnitine degradation II | 2 | 1 | 1 |
| glycine betaine degradation I | 8 | 6 | 3 |
| dTMP de novo biosynthesis (mitochondrial) | 3 | 3 | 1 |
| glycine degradation | 3 | 3 | 1 |
| D-carnitine degradation I | 3 | 2 | 1 |
| superpathway of L-serine and glycine biosynthesis I | 4 | 4 | 1 |
| glycine betaine degradation II (mammalian) | 4 | 1 | 1 |
| creatinine degradation I | 4 | 1 | 1 |
| folate polyglutamylation | 5 | 4 | 1 |
| creatinine degradation II | 5 | 1 | 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 | 5 | 1 |
| photorespiration I | 9 | 5 | 1 |
| gliotoxin biosynthesis | 9 | 2 | 1 |
| photorespiration II | 10 | 6 | 1 |
| folate transformations I | 13 | 9 | 1 |
| formaldehyde assimilation I (serine pathway) | 13 | 6 | 1 |
| purine nucleobases degradation II (anaerobic) | 24 | 16 | 1 |
| arachidonate metabolites biosynthesis | 74 | 3 | 1 |