Experiment set3IT028 for Escherichia coli BW25113

protonated glucose in D2O

Group: protonated/deuterated
Media: M9-D2O
Culturing: Keio_ML9, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Garth on dec_2014
Media components: 100 vol% deuterated water, 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 11 genes in this experiment

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	5
Arginine Biosynthesis extended	1
Lysine Biosynthesis DAP Pathway	1
Pentose phosphate pathway	1
Phenylalanine and Tyrosine Branches from Chorismate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine biosynthesis
• Arginine and proline metabolism
• Pentose phosphate pathway
• Urea cycle and metabolism of amino groups
• Methionine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Glutathione metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine biosynthesis I	3	3	1
pentose phosphate pathway (oxidative branch) 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
L-tyrosine biosynthesis III	4	3	1
L-tyrosine biosynthesis II	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine biosynthesis II	4	2	1
L-arginine degradation II (AST pathway)	5	5	1
L-ornithine biosynthesis I	5	5	1
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tyrosine degradation I	5	1	1
L-leucine biosynthesis	6	6	1
thiazole component of thiamine diphosphate biosynthesis I	6	6	1
L-leucine degradation I	6	2	1
pentose phosphate pathway	8	8	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of thiamine diphosphate biosynthesis I	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
L-arginine biosynthesis II (acetyl cycle)	10	9	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	1	1
tropane alkaloids biosynthesis	11	1	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
aspartate superpathway	25	24	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