Experiment set3S381 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	3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	3
DNA repair, UvrABC system	2
De Novo Pyrimidine Synthesis	2
Macromolecular synthesis operon	2
Coenzyme B12 biosynthesis	1
Cyanophycin Metabolism	1
De Novo Purine Biosynthesis	1
F0F1-type ATP synthase	1
Glutamine synthetases	1
High affinity phosphate transporter and control of PHO regulon	1
Lysine Biosynthesis DAP Pathway	1
Peptidoglycan Biosynthesis	1
Phosphate metabolism	1
Potassium homeostasis	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
• Nucleotide sugars metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Photosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• 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
L-glutamate biosynthesis I	2	2	2
superpathway of L-asparagine biosynthesis	2	2	2
L-glutamine biosynthesis I	1	1	1
L-asparagine biosynthesis I	1	1	1
L-glutamine degradation II	1	1	1
L-asparagine biosynthesis II	1	1	1
L-glutamine degradation I	1	1	1
L-cysteine degradation II	3	2	2
L-tryptophan degradation II (via pyruvate)	3	2	2
D-serine degradation	3	2	2
ammonia assimilation cycle I	2	2	1
ammonia assimilation cycle II	2	1	1
L-glutamate and L-glutamine biosynthesis	7	5	3
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
superpathway of ammonia assimilation (plants)	3	2	1
L-methionine biosynthesis II	6	3	2
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	1
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 II	5	5	1
5-aminoimidazole ribonucleotide biosynthesis I	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
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
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