Experiment set3S382 for Phocaeicola dorei CL03T12C01

L-Serine nitrogen source; Varel_Bryant_medium_Glucose_lowCys_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_lowCys_noNitrogen + L-Serine (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 27 genes in this experiment

For nitrogen source L-Serine in Phocaeicola dorei CL03T12C01

For nitrogen source L-Serine across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	4
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	3
De Novo Pyrimidine Synthesis	2
Macromolecular synthesis operon	2
Cobalt-zinc-cadmium resistance	1
Coenzyme B12 biosynthesis	1
DNA repair, UvrABC system	1
De Novo Purine Biosynthesis	1
F0F1-type ATP synthase	1
Glutamine synthetases	1
Lysine Biosynthesis DAP Pathway	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Na(+) H(+) antiporter	1
Peptidoglycan Biosynthesis	1
Queuosine-Archaeosine Biosynthesis	1
Sialic Acid Metabolism	1
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	1
Universal GTPases	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
• Cysteine metabolism
• Nucleotide sugars metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Photosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Aminosugars metabolism
• Glycosaminoglycan degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ammonia assimilation cycle III	3	3	3
L-serine degradation	3	3	3
ammonia assimilation cycle I	2	2	2
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
L-glutamate biosynthesis IV	1	1	1
L-glutamine biosynthesis I	1	1	1
D-serine degradation	3	2	2
L-tryptophan degradation II (via pyruvate)	3	2	2
superpathway of ammonia assimilation (plants)	3	2	2
L-cysteine degradation II	3	2	2
L-glutamate and L-glutamine biosynthesis	7	5	4
ammonia assimilation cycle II	2	1	1
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	4	3
glycine degradation	3	3	1
L-citrulline degradation	3	3	1
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
L-methionine biosynthesis II	6	3	2
L-arginine degradation V (arginine deiminase pathway)	4	3	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	2	2
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
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	3
UDP-N-acetyl-D-glucosamine biosynthesis I	5	3	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
UMP biosynthesis III	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
L-citrulline biosynthesis	8	7	1
purine nucleobases degradation II (anaerobic)	24	13	3
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