Experiment set1IT058 for Paraburkholderia graminis OAS925
D-Ribose carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Ribose (20 mM)
Culturing: Burkholderia_OAS925_ML2, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Marta on 10-Apr-21
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 3 genes in this experiment
For carbon source D-Ribose in Paraburkholderia graminis OAS925
For carbon source D-Ribose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 2 |
| Homogentisate pathway of aromatic compound degradation | 1 |
| Xylose utilization | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| xylitol degradation I | 2 | 2 | 2 |
| D-xylose degradation I | 2 | 2 | 1 |
| D-arabinitol degradation I | 2 | 2 | 1 |
| ribitol degradation I | 2 | 1 | 1 |
| L-arabinose degradation II | 3 | 2 | 1 |
| erythritol degradation II | 3 | 1 | 1 |
| L-threitol degradation | 4 | 1 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 21 | 4 |
| superpathway of glucose and xylose degradation | 17 | 16 | 1 |