Experiment set3S380 for Phocaeicola dorei CL03T12C01

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: 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 17 genes in this experiment

For nitrogen source L-Glutamic acid in Phocaeicola dorei CL03T12C01

For nitrogen source L-Glutamic acid across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	3
De Novo Pyrimidine Synthesis	2
Macromolecular synthesis operon	2
Cobalt-zinc-cadmium resistance	1
Cyanophycin Metabolism	1
De Novo Purine Biosynthesis	1
Glutamine synthetases	1
Lysine Biosynthesis DAP Pathway	1
Peptidoglycan Biosynthesis	1
Sialic Acid Metabolism	1
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	1
cAMP signaling in bacteria	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
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Purine metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism

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
superpathway of L-asparagine biosynthesis	2	2	2
L-asparagine biosynthesis I	1	1	1
L-glutamine degradation II	1	1	1
L-glutamine biosynthesis I	1	1	1
L-glutamine degradation I	1	1	1
L-asparagine biosynthesis II	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-citrulline degradation	3	3	1
L-aspartate degradation III (anaerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	1
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 II	5	5	1
5-aminoimidazole ribonucleotide biosynthesis I	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
UMP biosynthesis III	6	6	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	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-lysine biosynthesis VI	7	7	1
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 L-lysine, L-threonine and L-methionine biosynthesis II	15	12	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