Experiment set10S240 for Phocaeicola vulgatus CL09T03C04
L-Serine nitrogen source; Varel_Bryant_medium_Glucose_lowCys_noNitrogen
Group: nitrogen sourceMedia: Varel_Bryant_medium_Glucose_lowCys_noNitrogen + L-Serine (10 mM)
Culturing: Bvulgatus_CL09T03C04_ML5, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya Tripathi on 3/20/24
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 3 mM L-Cysteine, 23.8 mM Sodium bicarbonate, 20 mM D-Glucose, Mineral 3B solution minus Nitrogen (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, 1.75 mM Sodium sulfate)
Specific Phenotypes
For 3 genes in this experiment
For nitrogen source L-Serine in Phocaeicola vulgatus CL09T03C04
For nitrogen source L-Serine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ammonia assimilation | 2 |
| Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 2 |
| Glutamine synthetases | 1 |
| Peptidoglycan Biosynthesis | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glutamate metabolism
- Nitrogen metabolism
- Arginine and proline metabolism
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| ammonia assimilation cycle III | 3 | 3 | 3 |
| L-glutamate biosynthesis I | 2 | 2 | 2 |
| L-glutamine biosynthesis I | 1 | 1 | 1 |
| L-glutamine degradation I | 1 | 1 | 1 |
| L-glutamine degradation II | 1 | 1 | 1 |
| ammonia assimilation cycle I | 2 | 2 | 1 |
| ammonia assimilation cycle II | 2 | 1 | 1 |
| L-glutamate and L-glutamine biosynthesis | 7 | 5 | 3 |
| superpathway of ammonia assimilation (plants) | 3 | 2 | 1 |
| L-aspartate degradation II (aerobic) | 3 | 2 | 1 |
| L-aspartate degradation III (anaerobic) | 3 | 2 | 1 |
| L-asparagine biosynthesis III (tRNA-dependent) | 4 | 1 | 1 |
| glutaminyl-tRNAgln biosynthesis via transamidation | 4 | 1 | 1 |
| L-citrulline biosynthesis | 8 | 7 | 1 |
| L-arginine biosynthesis II (acetyl cycle) | 10 | 9 | 1 |
| superpathway of L-citrulline metabolism | 12 | 9 | 1 |