Experiment set8IT070 for Cupriavidus basilensis FW507-4G11
Carbon source 2-Deoxy-D-Ribose 20 mM
Group: carbon sourceMedia: RCH2_defined_noCarbon + 2-Deoxy-D-Ribose (20 mM), pH=7
Culturing: cupriavidus_4G11_ML11, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
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: Cup4G11_plate A6
Specific Phenotypes
For 7 genes in this experiment
For carbon source 2-Deoxy-D-Ribose in Cupriavidus basilensis FW507-4G11
For carbon source 2-Deoxy-D-Ribose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Branched-Chain Amino Acid Biosynthesis | 1 |
| Glutathione: Non-redox reactions | 1 |
| Leucine Biosynthesis | 1 |
| Methylglyoxal Metabolism | 1 |
| Pyruvate Alanine Serine Interconversions | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pyruvate metabolism
- Fatty acid metabolism
- Valine, leucine and isoleucine degradation
- Valine, leucine and isoleucine biosynthesis
- Lysine degradation
- Arginine and proline metabolism
- Phenylalanine metabolism
- beta-Alanine metabolism
- D-Arginine and D-ornithine metabolism
- D-Alanine metabolism
- Propanoate metabolism
- Biosynthesis of alkaloids derived from histidine and purine
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| D-alanine degradation | 1 | 1 | 1 |
| methylglyoxal degradation VIII | 3 | 3 | 1 |
| methylglyoxal degradation I | 3 | 2 | 1 |
| L-leucine biosynthesis | 6 | 6 | 1 |
| L-leucine degradation I | 6 | 5 | 1 |
| 3-methylbutanol biosynthesis (engineered) | 7 | 6 | 1 |
| superpathway of methylglyoxal degradation | 8 | 4 | 1 |
| superpathway of branched chain amino acid biosynthesis | 17 | 17 | 1 |