Experiment set3IT074 for Burkholderia phytofirmans PsJN
Putrescine Dihydrochloride nitrogen source
Group: nitrogen sourceMedia: RCH2_defined_Glucose_noNitrogen + Putrescine Dihydrochloride (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 4.6 generations
By: Mark on 1/27/2016
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)
Growth plate: Plate 2 A6
Specific Phenotypes
For 4 genes in this experiment
For nitrogen source Putrescine Dihydrochloride in Burkholderia phytofirmans PsJN
For nitrogen source Putrescine Dihydrochloride across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ribosome biogenesis bacterial | 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
- Urea cycle and metabolism of amino groups
- Pyrimidine metabolism
- Glutamate metabolism
- Nitrogen metabolism
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-glutamine biosynthesis I | 1 | 1 | 1 |
| ammonia assimilation cycle II | 2 | 2 | 1 |
| ammonia assimilation cycle I | 2 | 2 | 1 |
| pseudouridine degradation | 2 | 1 | 1 |
| superpathway of ammonia assimilation (plants) | 3 | 3 | 1 |
| ammonia assimilation cycle III | 3 | 3 | 1 |
| L-aspartate degradation III (anaerobic) | 3 | 1 | 1 |
| L-aspartate degradation II (aerobic) | 3 | 1 | 1 |
| putrescine degradation II | 4 | 3 | 1 |
| L-glutamate and L-glutamine biosynthesis | 7 | 7 | 1 |
| superpathway of ornithine degradation | 8 | 6 | 1 |
| L-arginine biosynthesis II (acetyl cycle) | 10 | 10 | 1 |
| superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation | 11 | 7 | 1 |
| superpathway of L-arginine and L-ornithine degradation | 13 | 9 | 1 |