Experiment set2IT077 for Burkholderia phytofirmans PsJN
Gly-Glu carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + Gly-Glu (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.1 generations
By: Mark on 6/2/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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: BFirm_carbon_plate2 C2
Specific Phenotypes
For 7 genes in this experiment
For carbon source Gly-Glu in Burkholderia phytofirmans PsJN
For carbon source Gly-Glu across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Flagellum | 1 |
| Glycine and Serine Utilization | 1 |
| Glycine cleavage system | 1 |
| Glycogen metabolism | 1 |
| Photorespiration (oxidative C2 cycle) | 1 |
| Type IV pilus | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Ubiquinone and menaquinone biosynthesis
- Glycine, serine and threonine metabolism
- Histidine metabolism
- Tyrosine metabolism
- Tryptophan metabolism
- Benzoxazinone biosynthesis
- Starch and sucrose metabolism
- Naphthalene and anthracene degradation
- Porphyrin and chlorophyll metabolism
- Carotenoid biosynthesis - General
- Phenylpropanoid biosynthesis
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Alkaloid biosynthesis I
- Insect hormone biosynthesis
- Biosynthesis of alkaloids derived from shikimate pathway
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| glycine biosynthesis II | 3 | 3 | 1 |
| glycine cleavage | 3 | 3 | 1 |
| glycogen biosynthesis I (from ADP-D-Glucose) | 4 | 4 | 1 |
| starch biosynthesis | 10 | 6 | 1 |