Experiment set10S238 for Phocaeicola vulgatus CL09T03C04

L-Glutamic acid nitrogen source; Varel_Bryant_medium_Glucose_lowCys_noNitrogen

Group: nitrogen source
Media: 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 6 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	3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	3
Cyanophycin Metabolism	1
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:

• Nitrogen metabolism
• Glutamate metabolism
• Alanine and aspartate 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
superpathway of L-asparagine biosynthesis	2	2	2
L-glutamate biosynthesis I	2	2	2
L-asparagine biosynthesis II	1	1	1
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
L-glutamine biosynthesis I	1	1	1
L-asparagine 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 II (aerobic)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	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