Experiment set1IT019 for Escherichia coli BW25113

a-Ketoglutaric acid disodium salt hydrate carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + a-Ketoglutaric acid disodium salt hydrate (20 mM)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
Growth: about 5.8 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 27 genes in this experiment

For carbon source a-Ketoglutaric acid disodium salt hydrate in Escherichia coli BW25113

For carbon source a-Ketoglutaric acid disodium salt hydrate across organisms

SEED Subsystems

Subsystem	#Specific
2-phosphoglycolate salvage	1
CBSS-562.2.peg.5158 SK3 including	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
D-ribose utilization	1
DNA-binding regulatory proteins, strays	1
Deoxyribose and Deoxynucleoside Catabolism	1
Entner-Doudoroff Pathway	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycolate, glyoxylate interconversions	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
MLST	1
Mannitol Utilization	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Nitric oxide synthase	1
Oxidative stress	1
Photorespiration (oxidative C2 cycle)	1
PnuC-like transporters	1
Polyamine Metabolism	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Ribosomal protein S5p acylation	1
Ribosome biogenesis bacterial	1
Universal stress protein family	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nicotinate and nicotinamide metabolism
• Biosynthesis of terpenoids and steroids
• 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 alkaloids derived from terpenoid and polyketide
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NAD salvage pathway IV (from nicotinamide riboside)	2	2	2
L-malate degradation I	1	1	1
superoxide radicals degradation	2	2	1
ribose phosphorylation	2	2	1
NAD biosynthesis from nicotinamide	2	1	1
spermine and spermidine degradation I	5	2	2
2-deoxy-D-ribose degradation I	3	3	1
glycerol degradation I	3	3	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
reactive oxygen species degradation	4	4	1
glycerol and glycerophosphodiester degradation	4	4	1
putrescine degradation III	4	2	1
NAD salvage pathway II (PNC IV cycle)	5	4	1
photorespiration II	10	6	2
methylgallate degradation	6	2	1
gluconeogenesis I	13	13	2
ethene biosynthesis III (microbes)	7	6	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
superpathway of NAD biosynthesis in eukaryotes	14	7	2
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
photorespiration III	9	5	1
photorespiration I	9	5	1
Rubisco shunt	10	9	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
superpathway of vanillin and vanillate degradation	10	3	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis III (from glucose)	11	11	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	12	1
syringate degradation	12	3	1
glycolysis I (from glucose 6-phosphate)	13	13	1
Bifidobacterium shunt	15	13	1
glycerol degradation to butanol	16	11	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of glucose and xylose degradation	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 cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
ethene biosynthesis V (engineered)	25	18	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1