Experiment set2S414 for Phocaeicola vulgatus CL09T03C04
D-Galactose carbon source
Group: carbon sourceMedia: Varel_Bryant_medium + D-Galactose (20 mM)
Culturing: Bvulgatus_CL09T03C04_ML5, 24-well microplate; 1.2 mL volume, Anaerobic, at 34 (C), shaken=0 rpm
By: Surya Tripathi on 3-Jul-23
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 8.25 mM L-Cysteine, 23.8 mM Sodium bicarbonate, Mineral 3B solution (6.6 mM Potassium phosphate monobasic, 15.4 mM Sodium Chloride, 98 uM Magnesium chloride hexahydrate, 176.5 uM Calcium chloride dihydrate, 4.2 uM Cobalt chloride hexahydrate, 50.5 uM Manganese (II) chloride tetrahydrate, 9.3 mM Ammonium chloride, 1.75 mM Sodium sulfate)
Specific Phenotypes
For 11 genes in this experiment
For carbon source D-Galactose in Phocaeicola vulgatus CL09T03C04
For carbon source D-Galactose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Entner-Doudoroff Pathway | 1 |
| Oxidative stress | 1 |
| Pentose phosphate pathway | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pentose phosphate pathway
- Glutathione metabolism
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| pentose phosphate pathway (oxidative branch) I | 3 | 3 | 1 |
| cytosolic NADPH production (yeast) | 5 | 3 | 1 |
| formaldehyde oxidation I | 6 | 3 | 1 |
| L-lysine biosynthesis VI | 7 | 7 | 1 |
| pentose phosphate pathway | 8 | 8 | 1 |
| superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) | 8 | 3 | 1 |
| Entner-Doudoroff pathway I | 9 | 8 | 1 |
| L-lysine biosynthesis II | 9 | 6 | 1 |
| L-lysine biosynthesis I | 9 | 6 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 12 | 1 |
| superpathway of glucose and xylose degradation | 17 | 16 | 1 |
| superpathway of glycolysis and the Entner-Doudoroff pathway | 17 | 14 | 1 |
| heterolactic fermentation | 18 | 14 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis I | 18 | 12 | 1 |
| aspartate superpathway | 25 | 19 | 1 |