Experiment set3IT096 for Dyella japonica UNC79MFTsu3.2
Sodium nitrate nitrogen source
Group: nitrogen sourceMedia: RCH2_defined_Glucose_noNitrogen + Sodium nitrate (20 mM), pH=7
Culturing: Dyella79_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 3.9 generations
By: Adam on 17-May-17
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: 1768 D2
Specific Phenotypes
For 12 genes in this experiment
For nitrogen source Sodium nitrate in Dyella japonica UNC79MFTsu3.2
For nitrogen source Sodium nitrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Nitrate and nitrite ammonification | 4 |
| Molybdenum cofactor biosynthesis | 3 |
| Ammonia assimilation | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Nitrogen metabolism
- Puromycin biosynthesis
- Lipopolysaccharide biosynthesis
- Porphyrin and chlorophyll metabolism
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| alkylnitronates degradation | 2 | 2 | 1 |
| nitrate reduction V (assimilatory) | 2 | 1 | 1 |
| tetrapyrrole biosynthesis II (from glycine) | 4 | 3 | 1 |
| tetrapyrrole biosynthesis I (from glutamate) | 6 | 6 | 1 |
| superpathway of heme b biosynthesis from glycine | 8 | 6 | 1 |
| superpathway of heme b biosynthesis from glutamate | 10 | 9 | 1 |
| superpathway of bacteriochlorophyll a biosynthesis | 26 | 5 | 1 |
| adenosylcobalamin biosynthesis II (aerobic) | 33 | 20 | 1 |
| adenosylcobalamin biosynthesis I (anaerobic) | 36 | 20 | 1 |