Experiment set1IT051 for Rhizobium sp. OAE497
D-Trehalose dihydrate carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Trehalose dihydrate (20 mM)
Culturing: Rhizobium_OAE497_ML5, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Dennis/Robin on 4/4/22
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)
Specific Phenotypes
For 8 genes in this experiment
For carbon source D-Trehalose dihydrate in Rhizobium sp. OAE497
For carbon source D-Trehalose dihydrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Chitin and N-acetylglucosamine utilization | 6 |
| Ketoisovalerate oxidoreductase | 1 |
| Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycolysis / Gluconeogenesis
- Nucleotide sugars metabolism
- Aminosugars metabolism
- Pyruvate metabolism
- Propanoate metabolism
- Reductive carboxylate cycle (CO2 fixation)
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| acetate conversion to acetyl-CoA | 1 | 1 | 1 |
| acetate and ATP formation from acetyl-CoA III | 1 | 1 | 1 |
| ethanol degradation IV | 3 | 3 | 1 |
| ethanol degradation II | 3 | 3 | 1 |
| N-acetylglucosamine degradation II | 3 | 3 | 1 |
| L-isoleucine biosynthesis V | 3 | 2 | 1 |
| ethanol degradation III | 3 | 2 | 1 |
| superpathway of acetate utilization and formation | 3 | 1 | 1 |
| chitin deacetylation | 4 | 3 | 1 |
| 2-methylcitrate cycle I | 5 | 1 | 1 |
| L-isoleucine biosynthesis IV | 6 | 4 | 1 |
| β-alanine biosynthesis II | 6 | 4 | 1 |
| superpathway of bitter acids biosynthesis | 18 | 3 | 3 |
| colupulone and cohumulone biosynthesis | 6 | 1 | 1 |
| lupulone and humulone biosynthesis | 6 | 1 | 1 |
| 2-methylcitrate cycle II | 6 | 1 | 1 |
| adlupulone and adhumulone biosynthesis | 6 | 1 | 1 |
| chitin derivatives degradation | 8 | 3 | 1 |
| reductive glycine pathway of autotrophic CO2 fixation | 9 | 5 | 1 |
| cis-geranyl-CoA degradation | 9 | 2 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 8 | 1 |