Experiment set10S238 for Phocaeicola vulgatus CL09T03C04
L-Glutamic acid nitrogen source; Varel_Bryant_medium_Glucose_lowCys_noNitrogen
Group: nitrogen sourceMedia: Varel_Bryant_medium_Glucose_lowCys_noNitrogen + L-Glutamic acid (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 5 genes in this experiment
For nitrogen source L-Glutamic acid in Phocaeicola vulgatus CL09T03C04
For nitrogen source L-Glutamic acid 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 degradation I | 1 | 1 | 1 |
| L-glutamine biosynthesis 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 |
| superpathway of ammonia assimilation (plants) | 3 | 2 | 1 |
| L-aspartate degradation II (aerobic) | 3 | 2 | 1 |
| glutaminyl-tRNAgln biosynthesis via transamidation | 4 | 1 | 1 |
| L-asparagine biosynthesis III (tRNA-dependent) | 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 |