Experiment set53IT040 for Escherichia coli BW25113

M9 with Methotrexate 0.06 mM 48 hr

Group: stress
Media: M9 + Methotrexate (0.06 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Keio_ML9a_ucsf, tube, Aerobic, at 37 (C), shaken=200 rpm
By: Ben Guthrie on 8/11/21
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, 1 g/L Ammonium chloride

Specific Phenotypes

For 5 genes in this experiment

For stress Methotrexate in Escherichia coli BW25113

For stress Methotrexate across organisms

SEED Subsystems

Subsystem	#Specific
Chorismate Synthesis	2
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	2
Ammonia assimilation	1
Biogenesis of cytochrome c oxidases	1
CBSS-562.2.peg.5158 SK3 including	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Photosynthesis
• Glutamate metabolism
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
ammonia assimilation cycle III	3	3	2
3-dehydroquinate biosynthesis I	2	2	1
chorismate biosynthesis I	7	7	2
L-glutamate and L-glutamine biosynthesis	7	5	2
photosynthesis light reactions	4	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
NADPH to cytochrome c oxidase via plastocyanin (thylakoid membrane)	4	1	1
superpathway of L-phenylalanine biosynthesis	10	10	2
superpathway of L-tyrosine biosynthesis	10	10	2
chorismate biosynthesis from 3-dehydroquinate	5	5	1
superpathway of photosynthetic hydrogen production	6	3	1
superpathway of L-tryptophan biosynthesis	13	13	2
L-citrulline biosynthesis	8	6	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-citrulline metabolism	12	8	1
chorismate biosynthesis II (archaea)	12	8	1
oxygenic photosynthesis	17	11	1
ethene biosynthesis V (engineered)	25	18	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of chorismate metabolism	59	54	2