Experiment set3S379 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 19 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
Menaquinone and Phylloquinone Biosynthesis	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	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
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Nicotinate and nicotinamide metabolism

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-glutamine biosynthesis I	1	1	1
L-glutamine degradation II	1	1	1
L-asparagine 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
NAD salvage pathway IV (from nicotinamide riboside)	2	1	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
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	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 III	6	6	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
UMP biosynthesis II	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
2-carboxy-1,4-naphthoquinol 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
superpathway of demethylmenaquinol-8 biosynthesis I	9	7	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	6	1
superpathway of demethylmenaquinol-9 biosynthesis	9	6	1
chitin biosynthesis	9	5	1
L-arginine biosynthesis IV (archaea)	9	4	1
allantoin degradation IV (anaerobic)	9	2	1
superpathway of menaquinol-8 biosynthesis I	10	8	1
superpathway of menaquinol-7 biosynthesis	10	7	1
superpathway of menaquinol-6 biosynthesis	10	7	1
superpathway of menaquinol-12 biosynthesis	10	7	1
superpathway of menaquinol-9 biosynthesis	10	7	1
superpathway of menaquinol-11 biosynthesis	10	7	1
superpathway of menaquinol-10 biosynthesis	10	7	1
superpathway of menaquinol-13 biosynthesis	10	7	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 NAD biosynthesis in eukaryotes	14	5	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	1
superpathway of phylloquinol biosynthesis	15	6	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
superpathway of chorismate metabolism	59	38	1