Experiment set3S378 for Phocaeicola dorei CL03T12C01

L-Glutamine nitrogen source; Varel_Bryant_medium_Glucose_lowCys_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_lowCys_noNitrogen + L-Glutamine (10 mM)
Culturing: Bdorei_CL03T12C01_ML9, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya Tripathi on 20-Mar-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 4 genes in this experiment

For nitrogen source L-Glutamine in Phocaeicola dorei CL03T12C01

For nitrogen source L-Glutamine across organisms

SEED Subsystems

Subsystem	#Specific
De Novo Pyrimidine Synthesis	2
Macromolecular synthesis operon	2
De Novo Purine Biosynthesis	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Purine metabolism
• Pyrimidine metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine degradation I	1	1	1
L-glutamate biosynthesis I	2	2	1
ammonia assimilation cycle III	3	3	1
L-citrulline degradation	3	3	1
L-arginine degradation V (arginine deiminase pathway)	4	3	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
5-aminoimidazole ribonucleotide biosynthesis II	5	5	1
5-aminoimidazole ribonucleotide biosynthesis I	5	5	1
UMP biosynthesis III	6	6	1
UMP biosynthesis II	6	6	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
UMP biosynthesis I	6	5	1
guadinomine B biosynthesis	13	2	2
L-glutamate and L-glutamine biosynthesis	7	5	1
L-citrulline biosynthesis	8	7	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
superpathway of pyrimidine ribonucleotides de novo biosynthesis	9	8	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
L-arginine biosynthesis IV (archaea)	9	4	1
allantoin degradation IV (anaerobic)	9	2	1
L-arginine biosynthesis II (acetyl cycle)	10	9	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of arginine and polyamine biosynthesis	17	11	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	16	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	2
superpathway of purine nucleotides de novo biosynthesis II	26	23	1