Experiment set2IT071 for Burkholderia phytofirmans PsJN
L-Fucose carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + L-Fucose (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 5.5 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 B3
Specific Phenotypes
For 6 genes in this experiment
For carbon source L-Fucose in Burkholderia phytofirmans PsJN
For carbon source L-Fucose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| L-fucose utilization temp | 2 |
| Bacterial Chemotaxis | 1 |
| L-rhamnose utilization | 1 |
| Lactate utilization | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Ascorbate and aldarate metabolism
- Pentose and glucuronate interconversions
- Fructose and mannose metabolism
- 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
- Phenylalanine metabolism
- Benzoate degradation via hydroxylation
- Inositol phosphate metabolism
- Biphenyl degradation
- Benzoate degradation via CoA ligation
- Ethylbenzene degradation
- Nicotinate and nicotinamide metabolism
- Limonene and pinene degradation
- Caprolactam degradation
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| D-xylose degradation VI | 5 | 3 | 2 |
| L-fucose degradation III | 8 | 5 | 3 |
| D-arabinose degradation IV | 6 | 4 | 2 |
| methylglyoxal degradation V | 3 | 2 | 1 |
| L-rhamnose degradation III | 7 | 6 | 2 |
| D-galacturonate degradation I | 5 | 4 | 1 |
| L-fucose degradation II | 5 | 2 | 1 |
| L-arabinose degradation V | 6 | 5 | 1 |
| L-rhamnose degradation II | 8 | 5 | 1 |
| lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) | 8 | 4 | 1 |
| superpathway of hexuronide and hexuronate degradation | 10 | 7 | 1 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 20 | 1 |