Experiment set2IT070 for Burkholderia phytofirmans PsJN
D-Xylose carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Xylose (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 4.1 generations
By: Mark on 6/2/2015
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: BFirm_carbon_plate1 A5
Specific Phenotypes
For 7 genes in this experiment
For carbon source D-Xylose in Burkholderia phytofirmans PsJN
For carbon source D-Xylose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ammonia assimilation | 1 |
| Xylose utilization | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Fructose and mannose metabolism
- Nucleotide sugars metabolism
- Pentose and glucuronate interconversions
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| D-xylose degradation I | 2 | 2 | 1 |
| D-mannose degradation II | 2 | 1 | 1 |
| D-mannose degradation I | 2 | 1 | 1 |
| β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation | 3 | 2 | 1 |
| mannitol biosynthesis | 3 | 1 | 1 |
| GDP-mannose biosynthesis | 4 | 4 | 1 |
| mannitol degradation II | 4 | 2 | 1 |
| 1,5-anhydrofructose degradation | 5 | 2 | 1 |
| β-(1,4)-mannan degradation | 7 | 2 | 1 |
| colanic acid building blocks biosynthesis | 11 | 11 | 1 |
| superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis | 14 | 9 | 1 |
| superpathway of glucose and xylose degradation | 17 | 16 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 22 | 1 |