Experiment set1IT074 for Phocaeicola vulgatus CL09T03C04
D-Galacturonic Acid monohydrate 20 mM carbon source
Group: carbon sourceMedia: Varel_Bryant_medium + D-Galacturonic Acid monohydrate (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 8 genes in this experiment
For carbon source D-Galacturonic Acid monohydrate in Phocaeicola vulgatus CL09T03C04
For carbon source D-Galacturonic Acid monohydrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Phosphate metabolism | 1 |
| Signal peptidase | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Citrate cycle (TCA cycle)
- Fructose and mannose metabolism
- Oxidative phosphorylation
- Alanine and aspartate metabolism
- N-Glycan biosynthesis
- O-Glycan biosynthesis
- High-mannose type N-glycan biosynthesis
- O-Mannosyl glycan biosynthesis
- Keratan sulfate biosynthesis
- Lipopolysaccharide biosynthesis
- Peptidoglycan biosynthesis
- Glycerolipid metabolism
- Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
- Sphingolipid metabolism
- Glycosphingolipid biosynthesis - lacto and neolacto series
- Glycosphingolipid biosynthesis - globo series
- Glycosphingolipid biosynthesis - ganglio series
- Pyruvate metabolism
- Carotenoid biosynthesis - General
- Zeatin biosynthesis
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Flavone and flavonol biosynthesis
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| incomplete reductive TCA cycle | 7 | 5 | 1 |
| glyphosate degradation III | 7 | 2 | 1 |
| (aminomethyl)phosphonate degradation | 8 | 2 | 1 |
| reductive TCA cycle I | 11 | 8 | 1 |
| gluconeogenesis III | 12 | 10 | 1 |
| (S)-lactate fermentation to propanoate, acetate and hydrogen | 13 | 10 | 1 |
| gluconeogenesis II (Methanobacterium thermoautotrophicum) | 18 | 8 | 1 |
| Methanobacterium thermoautotrophicum biosynthetic metabolism | 56 | 18 | 1 |