Experiment set7IT086 for Escherichia coli BW25113

Sodium Acetate carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + Sodium acetate (10 mM)
Culturing: Keio_ML9a, tube, Aerobic, at 37 (C), shaken=200 rpm
By: Ankita Kothari on 7/20/2015
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 Sodium acetate in Escherichia coli BW25113

For carbon source Sodium acetate across organisms

SEED Subsystems

Subsystem	#Specific
CBSS-562.2.peg.5158 SK3 including	2
Pyruvate metabolism I: anaplerotic reactions, PEP	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
D-ribose utilization	1
DNA-binding regulatory proteins, strays	1
Deoxyribose and Deoxynucleoside Catabolism	1
Flavodoxin	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Heat shock dnaK gene cluster extended	1
N-Acetyl-Galactosamine and Galactosamine Utilization	1
Photorespiration (oxidative C2 cycle)	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Purine metabolism
• Glyoxylate and dicarboxylate metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• 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
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-malate degradation I	1	1	1
ribose phosphorylation	2	2	1
glycolate and glyoxylate degradation II	2	2	1
polyphosphate metabolism	2	2	1
glyoxylate cycle	6	6	2
2-deoxy-D-ribose degradation I	3	3	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
chitin deacetylation	4	3	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
ppGpp metabolism	6	6	1
superpathway of glyoxylate bypass and TCA	12	11	2
methylgallate degradation	6	2	1
gluconeogenesis I	13	13	2
superpathway of glycol metabolism and degradation	7	7	1
chorismate biosynthesis I	7	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
D-xylose degradation IV	7	3	1
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
L-arabinose degradation IV	8	2	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	3
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	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
chorismate biosynthesis II (archaea)	12	8	1
syringate degradation	12	3	1
superpathway of L-tryptophan biosynthesis	13	13	1
glycolysis I (from glucose 6-phosphate)	13	13	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of aromatic amino acid biosynthesis	18	18	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 pentose and pentitol degradation	42	18	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1
superpathway of chorismate metabolism	59	54	1