Experiment set5IT020 for Agrobacterium fabrum C58
R2A with Calcium Chloride Dihydrate 87.5 mM
Group: stressMedia: R2A + Calcium chloride dihydrate (87.5 mM)
Culturing: Agro_ML11, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 28 (C), shaken=700 rpm
By: Hans Carlson and Mitchell Thompson on 22-Jun-21
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate
Growth plate: 2B D3
Specific Phenotypes
For 9 genes in this experiment
For stress Calcium chloride dihydrate in Agrobacterium fabrum C58
For stress Calcium chloride dihydrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Transport of Manganese | 3 |
| Arginine Biosynthesis extended | 1 |
| Copper homeostasis: copper tolerance | 1 |
| Phosphate metabolism | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Urea cycle and metabolism of amino groups
- Arginine and proline metabolism
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Fatty acid biosynthesis
- Lysine degradation
- Histidine metabolism
- Tyrosine metabolism
- Phenylalanine metabolism
- Lipopolysaccharide biosynthesis
- Glycerophospholipid metabolism
- Ether lipid metabolism
- Glycosphingolipid biosynthesis - ganglio series
- 1- and 2-Methylnaphthalene degradation
- Benzoate degradation via CoA ligation
- Ethylbenzene degradation
- Butanoate metabolism
- Limonene and pinene degradation
- Diterpenoid biosynthesis
- Carotenoid biosynthesis - General
- Anthocyanin biosynthesis
- Alkaloid biosynthesis I
- Alkaloid biosynthesis II
- Biosynthesis of unsaturated fatty acids
- Biosynthesis of type II polyketide backbone
- Biosynthesis of terpenoids and steroids
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-arginine biosynthesis II (acetyl cycle) | 10 | 10 | 2 |
| tRNA processing | 10 | 10 | 2 |
| L-ornithine biosynthesis I | 5 | 5 | 1 |
| L-arginine biosynthesis I (via L-ornithine) | 9 | 9 | 1 |
| L-arginine biosynthesis III (via N-acetyl-L-citrulline) | 9 | 8 | 1 |
| superpathway of arginine and polyamine biosynthesis | 17 | 14 | 1 |