Experiment set1IT024 for Rhizobium sp. OAE497
D-Glucuronic Acid carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Glucuronic Acid (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 6 genes in this experiment
For carbon source D-Glucuronic Acid in Rhizobium sp. OAE497
For carbon source D-Glucuronic Acid across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| ABC transporter branched-chain amino acid (TC 3.A.1.4.1) | 1 |
| Pyruvate metabolism I: anaplerotic reactions, PEP | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pyruvate metabolism
- Carbon fixation in photosynthetic organisms
- Biosynthesis of terpenoids and steroids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of alkaloids derived from terpenoid and polyketide
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| C4 photosynthetic carbon assimilation cycle, NADP-ME type | 7 | 4 | 2 |
| methylgallate degradation | 6 | 2 | 1 |
| C4 photosynthetic carbon assimilation cycle, PEPCK type | 14 | 8 | 2 |
| protocatechuate degradation I (meta-cleavage pathway) | 8 | 3 | 1 |
| superpathway of vanillin and vanillate degradation | 10 | 3 | 1 |
| syringate degradation | 12 | 3 | 1 |
| gluconeogenesis I | 13 | 11 | 1 |