Experiment set1IT089 for Escherichia coli BW25113

Gly-DL-Asp nitrogen source

Group: nitrogen source
Media: M9 minimal media_noNitrogen + Gly-DL-Asp (20 mM)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
Growth: about 7.0 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 10 genes in this experiment

For nitrogen source Gly-DL-Asp in Escherichia coli BW25113

For nitrogen source Gly-DL-Asp across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter dipeptide (TC 3.A.1.5.2)	5
Bacterial Chemotaxis	1
Cyanophycin Metabolism	1
DNA-binding regulatory proteins, strays	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Phenylalanine and Tyrosine Branches from Chorismate	1
p-Aminobenzoyl-Glutamate Utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Alanine and aspartate metabolism
• Methionine metabolism
• Lysine biosynthesis
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
superpathway of L-asparagine biosynthesis	2	2	2
L-glutamine degradation I	1	1	1
L-asparagine biosynthesis II	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-asparagine biosynthesis I	1	1	1
L-glutamate biosynthesis I	2	2	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
ammonia assimilation cycle III	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-leucine degradation III	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	1
L-tyrosine biosynthesis III	4	3	1
L-tyrosine degradation III	4	2	1
L-tyrosine biosynthesis II	4	2	1
L-phenylalanine degradation III	4	2	1
L-phenylalanine biosynthesis II	4	2	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	2	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
L-tyrosine degradation I	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
L-leucine biosynthesis	6	6	1
L-leucine degradation I	6	2	1
L-glutamate and L-glutamine biosynthesis	7	5	1
L-citrulline biosynthesis	8	6	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	1	1
tropane alkaloids biosynthesis	11	1	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of branched chain amino acid biosynthesis	17	17	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	54	2
odd iso-branched-chain fatty acid biosynthesis	34	24	1