Experiment set3S377 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 6 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
Ammonia assimilation	1
De Novo Purine Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutamine synthetases	1
Peptidoglycan Biosynthesis	1
Sialic Acid Metabolism	1
UDP-N-acetylmuramate from Fructose-6-phosphate 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
• Arginine and proline metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine biosynthesis I	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
L-glutamate biosynthesis I	2	2	1
ammonia assimilation cycle I	2	2	1
ammonia assimilation cycle II	2	1	1
L-citrulline degradation	3	3	1
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-glutamate and L-glutamine biosynthesis	7	5	2
L-arginine degradation V (arginine deiminase pathway)	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
5-aminoimidazole ribonucleotide biosynthesis I	5	5	1
5-aminoimidazole ribonucleotide biosynthesis II	5	5	1
L-arginine biosynthesis II (acetyl cycle)	10	9	2
UDP-N-acetyl-D-glucosamine biosynthesis I	5	3	1
UMP biosynthesis II	6	6	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
UMP biosynthesis III	6	6	1
UMP biosynthesis I	6	5	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	3	1
UDP-N-acetyl-D-galactosamine biosynthesis III	6	2	1
guadinomine B biosynthesis	13	2	2
L-citrulline biosynthesis	8	7	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
superpathway of pyrimidine ribonucleotides de novo biosynthesis	9	8	1
chitin biosynthesis	9	5	1
L-arginine biosynthesis IV (archaea)	9	4	1
allantoin degradation IV (anaerobic)	9	2	1
CMP-legionaminate biosynthesis I	10	2	1
O-antigen building blocks biosynthesis (E. coli)	11	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 UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	4	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	11	1