Experiment set1IT060 for Escherichia coli BW25113

casamino acids carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + casamino acids (2 mg/ml)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
Growth: about 5.3 generations
By: Kelly on 6/19/2014
Media components: 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 6 genes in this experiment

For carbon source casamino acids in Escherichia coli BW25113

For carbon source casamino acids across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Polyamine Metabolism	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine-glyoxylate cycle	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Urea cycle and metabolism of amino groups
• Methionine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-dehydroquinate biosynthesis I	2	2	1
spermidine biosynthesis I	2	2	1
spermine biosynthesis	2	1	1
aminopropylcadaverine biosynthesis	3	3	1
spermidine biosynthesis III	4	2	1
L-arginine degradation II (AST pathway)	5	5	1
TCA cycle VIII (Chlamydia)	6	5	1
chorismate biosynthesis I	7	7	1
incomplete reductive TCA cycle	7	5	1
pyruvate fermentation to propanoate I	7	5	1
partial TCA cycle (obligate autotrophs)	8	7	1
superpathway of polyamine biosynthesis I	8	7	1
superpathway of polyamine biosynthesis II	8	4	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle II (plants and fungi)	9	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle VII (acetate-producers)	9	6	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
TCA cycle I (prokaryotic)	10	9	1
TCA cycle III (animals)	10	8	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
reductive TCA cycle I	11	8	1
L-methionine salvage cycle III	11	5	1
L-glutamate degradation VIII (to propanoate)	11	5	1
superpathway of glyoxylate bypass and TCA	12	11	1
reductive TCA cycle II	12	8	1
L-methionine salvage cycle I (bacteria and plants)	12	5	1
superpathway of L-tryptophan biosynthesis	13	13	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
mixed acid fermentation	16	16	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
superpathway of aromatic amino acid biosynthesis	18	18	1
methylaspartate cycle	19	9	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1
superpathway of chorismate metabolism	59	54	1