Experiment set9IT034 for Cupriavidus basilensis FW507-4G11
Defined media with exometabolites; 10% oxygen; 5 mM nitrate
Group: oxygen_nitrateMedia: SGW_Northen_Exometabolite_mix_1 + Sodium nitrate (5 mM), pH=7
Culturing: cupriavidus_4G11_ML11_FieldsLab, tube, Aerobic, at 15 (C), shaken=10 rpm
By: Katie Davis on 08/18/2019
Media components: 0.6 g/L Potassium phosphate monobasic, 0.15 g/L Ammonium chloride, Northen_Exometabolite_mix_1 (880.5 uM D-Mannitol, 824.8 uM D-Glucose, 806.5 uM D-Fructose, 561.8 uM D-Trehalose dihydrate, 207.6 uM D-Arabinose, 165.4 uM D-Maltose monohydrate, 105.2 uM Arabitol, 60 uM L-Leucine, 60 uM L-Isoleucine, 40 uM Glycine, 40 uM L-Arginine, 40 uM L-Proline, 40 uM L-Threonine, 40 uM L-Lysine, 40 uM L-Phenylalanine, 39.4 uM D-Mannose, 22.5 uM Uridine, 20 uM Carnitine Hydrochloride, 20 uM L-Asparagine, 20 uM L-Serine, 20 uM L-Valine, 20 uM L-tyrosine, 20 uM L-Tryptophan, 20 uM L-Methionine, 20 uM L-Glutamic acid monopotassium salt monohydrate, 20 uM L-Citrulline, 20 uM L-Aspartic Acid, 20 uM L-Alanine, 20 uM L-Histidine, 20 uM L-Glutamine, 5.9 uM 4-Guanidinobutyric acid, 4.2 uM Hypoxanthine, 3.2 uM Uracil, 3.2 uM Thiamine HCl, 3.2 uM Guanine, 3.2 uM Cytosine, 3.2 uM Adenine hydrochloride hydrate, 2.6 uM Thymidine, 2.6 uM spermidine, 2.6 uM Orotic acid, 2.6 uM Inosine, 2.6 uM 2'-Deoxyinosine, 2.6 uM Cytidine, 2.6 uM Choline chloride, 2.6 uM Adenosine, 2.6 uM 2'-Deoxyuridine), 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)
Specific Phenotypes
For 1 genes in this experiment
For oxygen_nitrate Sodium nitrate in Cupriavidus basilensis FW507-4G11
For oxygen_nitrate Sodium nitrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Entner-Doudoroff Pathway | 1 |
| Pentose phosphate pathway | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pentose phosphate pathway
- Glutathione metabolism
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| pentose phosphate pathway (oxidative branch) I | 3 | 3 | 1 |
| cytosolic NADPH production (yeast) | 5 | 4 | 1 |
| formaldehyde oxidation I | 6 | 3 | 1 |
| L-lysine biosynthesis VI | 7 | 6 | 1 |
| pentose phosphate pathway | 8 | 8 | 1 |
| superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) | 8 | 7 | 1 |
| L-lysine biosynthesis I | 9 | 9 | 1 |
| Entner-Doudoroff pathway I | 9 | 9 | 1 |
| L-lysine biosynthesis II | 9 | 7 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 13 | 1 |
| superpathway of glycolysis and the Entner-Doudoroff pathway | 17 | 15 | 1 |
| superpathway of glucose and xylose degradation | 17 | 14 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis I | 18 | 16 | 1 |
| heterolactic fermentation | 18 | 15 | 1 |
| aspartate superpathway | 25 | 23 | 1 |