Experiment set2IT046 for Variovorax sp. OAS795
L-Fucose carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + L-Fucose (20 mM)
Culturing: Variovorax_OAS795_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 2 genes in this experiment
For carbon source L-Fucose in Variovorax sp. OAS795
For carbon source L-Fucose across organisms
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pentose and glucuronate interconversions
- Lysine biosynthesis
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| dipicolinate biosynthesis | 4 | 3 | 1 |
| D-galacturonate degradation I | 5 | 3 | 1 |
| D-arabinose degradation IV | 6 | 4 | 1 |
| D-arabinose degradation III | 6 | 3 | 1 |
| L-lysine biosynthesis VI | 7 | 6 | 1 |
| L-lysine biosynthesis III | 7 | 6 | 1 |
| L-lysine biosynthesis I | 9 | 9 | 1 |
| L-lysine biosynthesis II | 9 | 6 | 1 |
| superpathway of hexuronide and hexuronate degradation | 10 | 4 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 13 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis I | 18 | 17 | 1 |
| aspartate superpathway | 25 | 24 | 1 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 13 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 15 | 1 |