Experiment set1IT058 for Phocaeicola vulgatus CL09T03C04
D-Mannose 20 mM carbon source
Group: carbon sourceMedia: Varel_Bryant_medium + D-Mannose (20 mM)
Culturing: Bvulgatus_CL09T03C04_ML5, 96 deep-well microplate; 0.5 mL volume, Anaerobic, at 34 (C), shaken=0 rpm
By: Surya Tripathi on 12/22/21
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 3 genes in this experiment
For carbon source D-Mannose in Phocaeicola vulgatus CL09T03C04
For carbon source D-Mannose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Butanol Biosynthesis | 1 |
| Entner-Doudoroff Pathway | 1 |
| Fermentations: Mixed acid | 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
- Pyruvate metabolism
- Propanoate metabolism
- Butanoate 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 |
|---|---|---|---|
| reductive monocarboxylic acid cycle | 2 | 2 | 1 |
| pyruvate fermentation to acetate IV | 3 | 3 | 1 |
| pentose phosphate pathway (oxidative branch) I | 3 | 3 | 1 |
| pyruvate fermentation to ethanol I | 3 | 2 | 1 |
| L-threonine degradation I | 6 | 6 | 1 |
| formaldehyde oxidation I | 6 | 3 | 1 |
| pentose phosphate pathway | 8 | 8 | 1 |
| Entner-Doudoroff pathway I | 9 | 8 | 1 |
| superpathway of fermentation (Chlamydomonas reinhardtii) | 9 | 7 | 1 |
| (S)-lactate fermentation to propanoate, acetate and hydrogen | 13 | 10 | 1 |
| mixed acid fermentation | 16 | 12 | 1 |
| superpathway of glucose and xylose degradation | 17 | 16 | 1 |
| superpathway of glycolysis and the Entner-Doudoroff pathway | 17 | 14 | 1 |
| superpathway of L-threonine metabolism | 18 | 15 | 1 |
| heterolactic fermentation | 18 | 14 | 1 |
| hexitol fermentation to lactate, formate, ethanol and acetate | 19 | 14 | 1 |
| superpathway of N-acetylneuraminate degradation | 22 | 17 | 1 |