Experiment set10S247 for Phocaeicola vulgatus CL09T03C04
L-Serine nitrogen source; Varel_Bryant_medium_Glucose_DTT_NaS_noNitrogen
Group: nitrogen sourceMedia: Varel_Bryant_medium_Glucose_DTT_NaS_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 Dithiothreitol, 23.8 mM Sodium bicarbonate, 20 mM D-Glucose, 3 mM Sodium sulfide nonahydrate, 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 degradation II | 1 | 1 | 1 |
| L-glutamine biosynthesis I | 1 | 1 | 1 |
| L-glutamine degradation I | 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 |
| L-aspartate degradation III (anaerobic) | 3 | 2 | 1 |
| L-aspartate degradation II (aerobic) | 3 | 2 | 1 |
| superpathway of ammonia assimilation (plants) | 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 |