Experiment set15S220 for Phocaeicola vulgatus CL09T03C04
Galactose 1-phosphate dipotassium salt pentahydrate 1 mM phosphorus source
Group: phosphorus sourceMedia: Varel_Bryant_medium_Glucose_minusP + Galactose 1-phosphate dipotassium salt pentahydrate (1 mM)
Culturing: Bvulgatus_CL09T03C04_ML5, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 7/3/25
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, 20 mM D-Glucose, Mineral 3B solution minus phosphorus (6.6 mM Potassium Chloride, 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 phosphorus source Galactose 1-phosphate dipotassium salt pentahydrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| High affinity phosphate transporter and control of PHO regulon | 1 |
| Phosphate metabolism | 1 |
| Potassium homeostasis | 1 |
| Serine-glyoxylate cycle | 1 |
| TCA Cycle | 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)
- Glyoxylate and dicarboxylate metabolism
- Biosynthesis of phenylpropanoids
- Biosynthesis of terpenoids and steroids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of alkaloids derived from terpenoid and polyketide
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| glyoxylate cycle | 6 | 4 | 1 |
| nitrogen remobilization from senescing leaves | 8 | 5 | 1 |
| partial TCA cycle (obligate autotrophs) | 8 | 5 | 1 |
| TCA cycle V (2-oxoglutarate synthase) | 9 | 7 | 1 |
| TCA cycle VII (acetate-producers) | 9 | 6 | 1 |
| TCA cycle II (plants and fungi) | 9 | 6 | 1 |
| TCA cycle IV (2-oxoglutarate decarboxylase) | 9 | 6 | 1 |
| TCA cycle VI (Helicobacter) | 9 | 6 | 1 |
| TCA cycle III (animals) | 10 | 7 | 1 |
| TCA cycle I (prokaryotic) | 10 | 7 | 1 |
| superpathway of glyoxylate bypass and TCA | 12 | 7 | 1 |
| superpathway of glyoxylate cycle and fatty acid degradation | 14 | 6 | 1 |
| mixed acid fermentation | 16 | 12 | 1 |
| methylaspartate cycle | 19 | 10 | 1 |
| superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle | 22 | 16 | 1 |
| ethene biosynthesis V (engineered) | 25 | 15 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 19 | 1 |