Experiment set1IT086 for Escherichia coli BW25113

D-Serine nitrogen source

Group: nitrogen source
Media: M9 minimal media_noNitrogen + D-Serine (20 mM)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
Growth: about 5.4 generations
By: Kelly on 6/19/2014
Media components: 4 g/L D-Glucose, 2 mM Magnesium sulfate, 0.1 mM Calcium chloride, 12.8 g/L Sodium phosphate dibasic heptahydrate, 3 g/L Potassium phosphate monobasic, 0.5 g/L Sodium Chloride

Specific Phenotypes

For 14 genes in this experiment

For nitrogen source D-Serine in Escherichia coli BW25113

For nitrogen source D-Serine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	5
Coenzyme A Biosynthesis	3
Glycine and Serine Utilization	2
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Phosphate metabolism	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Pantothenate and CoA biosynthesis
• beta-Alanine metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Pyruvate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-serine degradation	3	3	3
β-alanine biosynthesis III	1	1	1
L-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	3	2
L-cysteine degradation II	3	2	2
phosphopantothenate biosynthesis I	4	4	2
NAD phosphorylation and transhydrogenation	2	2	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
superpathway of coenzyme A biosynthesis I (bacteria)	9	9	3
NAD phosphorylation and dephosphorylation	3	3	1
L-methionine biosynthesis II	6	5	2
glycine betaine degradation III	7	4	2
glycine betaine degradation I	8	4	2
L-mimosine degradation	8	4	2
phosphopantothenate biosynthesis III (archaea)	4	2	1
glutathione-mediated detoxification I	8	3	2
superpathway of coenzyme A biosynthesis II (plants)	10	5	2
NAD(P)/NADPH interconversion	6	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
glycolysis V (Pyrococcus)	10	7	1
glycolysis II (from fructose 6-phosphate)	11	11	1
purine nucleobases degradation II (anaerobic)	24	17	2
gluconeogenesis I	13	13	1
glycolysis I (from glucose 6-phosphate)	13	13	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of hexitol degradation (bacteria)	18	18	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of N-acetylneuraminate degradation	22	22	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1