Experiment set3IT068 for Burkholderia phytofirmans PsJN
D-Alanine nitrogen source
Group: nitrogen sourceMedia: RCH2_defined_Glucose_noNitrogen + D-Alanine (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 5.5 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 1 D4
Specific Phenotypes
For 6 genes in this experiment
For nitrogen source D-Alanine in Burkholderia phytofirmans PsJN
For nitrogen source D-Alanine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ammonia assimilation | 1 |
| Folate Biosynthesis | 1 |
| Pyruvate Alanine Serine Interconversions | 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:
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-alanine degradation I | 2 | 2 | 1 |
| dTMP de novo biosynthesis (mitochondrial) | 3 | 3 | 1 |
| tetrahydrofolate biosynthesis I | 3 | 3 | 1 |
| folate transformations III (E. coli) | 9 | 8 | 1 |
| superpathway of tetrahydrofolate biosynthesis | 10 | 9 | 1 |
| folate transformations II (plants) | 11 | 9 | 1 |
| superpathway of tetrahydrofolate biosynthesis and salvage | 12 | 11 | 1 |
| superpathway of chorismate metabolism | 59 | 42 | 1 |