Experiment set9IT052 for Escherichia coli BW25113

LB Anaerobic with Nitrofurantoin 0.000015625 mM

Group: stress
Media: LB + Nitrofurantoin (1.56E-02 mM)
Culturing: Keio_ML9a, 96 deep-well microplate; Multitron, Anaerobic, at 37 (C), shaken=0 rpm
By: Hans_Hualan on 7/20/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 22 genes in this experiment

For stress Nitrofurantoin in Escherichia coli BW25113

For stress Nitrofurantoin across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, UvrABC system	3
DNA repair, bacterial RecFOR pathway	3
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Iron acquisition in Vibrio	2
Respiratory dehydrogenases 1	2
Transport of Iron	2
Campylobacter Iron Metabolism	1
Cobalt-zinc-cadmium resistance	1
DNA-replication	1
Fermentations: Mixed acid	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
Menaquinone and Phylloquinone Biosynthesis	1
Molybdenum cofactor biosynthesis	1
Peptidyl-prolyl cis-trans isomerase	1
Potassium homeostasis	1
Serine-glyoxylate cycle	1
Succinate dehydrogenase	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fatty acid metabolism
• Oxidative phosphorylation
• Tyrosine metabolism
• Glutathione metabolism
• Glycerophospholipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of phenylpropanoids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycerol-3-phosphate to fumarate electron transfer	2	2	2
acetaldehyde biosynthesis I	1	1	1
NADH to fumarate electron transfer	2	2	1
glycerol-3-phosphate to hydrogen peroxide electron transport	2	2	1
glutathione degradation (DUG pathway)	2	2	1
glycerophosphodiester degradation	2	2	1
ethanol degradation I	2	2	1
glycerol-3-phosphate shuttle	2	2	1
L-threonine degradation II	2	2	1
nitrate reduction IX (dissimilatory)	2	2	1
glycerol-3-phosphate to cytochrome bo oxidase electron transfer	2	1	1
pyruvate fermentation to ethanol II	2	1	1
succinate to cytochrome aa3 oxidase electron transfer	2	1	1
glycerol 3-phosphate to cytochrome aa3 oxidase electron transfer	2	1	1
hydrogen to fumarate electron transfer	2	1	1
glycerol degradation I	3	3	1
L-aspartate degradation II (aerobic)	3	3	1
pyruvate fermentation to ethanol I	3	3	1
L-aspartate degradation III (anaerobic)	3	3	1
pyruvate fermentation to ethanol III	3	3	1
ethanol degradation II	3	3	1
sn-glycerol 3-phosphate anaerobic respiration	3	3	1
L-leucine degradation III	3	2	1
acrylate degradation II	3	2	1
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
L-methionine degradation III	3	1	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	7	2
glycerol and glycerophosphodiester degradation	4	4	1
phytol degradation	4	3	1
L-phenylalanine degradation III	4	2	1
salidroside biosynthesis	4	2	1
L-tyrosine degradation III	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	9	2
superpathway of demethylmenaquinol-9 biosynthesis	9	8	2
superpathway of demethylmenaquinol-6 biosynthesis I	9	8	2
superpathway of menaquinol-8 biosynthesis I	10	10	2
ethanolamine utilization	5	5	1
CMP-3-deoxy-D-manno-octulosonate biosynthesis	5	5	1
superpathway of menaquinol-10 biosynthesis	10	9	2
superpathway of menaquinol-7 biosynthesis	10	9	2
superpathway of menaquinol-6 biosynthesis	10	9	2
superpathway of menaquinol-13 biosynthesis	10	9	2
superpathway of menaquinol-11 biosynthesis	10	9	2
superpathway of menaquinol-12 biosynthesis	10	9	2
superpathway of menaquinol-9 biosynthesis	10	9	2
pyruvate fermentation to isobutanol (engineered)	5	4	1
acetylene degradation (anaerobic)	5	4	1
(S)-propane-1,2-diol degradation	5	3	1
phenylethanol biosynthesis	5	2	1
molybdopterin biosynthesis	6	6	1
γ-glutamyl cycle	6	5	1
noradrenaline and adrenaline degradation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
incomplete reductive TCA cycle	7	5	1
pyruvate fermentation to propanoate I	7	5	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	4	1
serotonin degradation	7	3	1
superpathway of phylloquinol biosynthesis	15	7	2
mixed acid fermentation	16	16	2
butanol and isobutanol biosynthesis (engineered)	8	2	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	8	1
TCA cycle VI (Helicobacter)	9	7	1
NiFe(CO)(CN)2 cofactor biosynthesis	10	9	1
reductive TCA cycle I	11	8	1
L-glutamate degradation VIII (to propanoate)	11	5	1
reductive TCA cycle II	12	8	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	7	1
3-hydroxypropanoate cycle	13	7	1
glyoxylate assimilation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of (Kdo)2-lipid A biosynthesis	17	17	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	9	1
superpathway of L-threonine metabolism	18	16	1
heterolactic fermentation	18	16	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
superpathway of the 3-hydroxypropanoate cycle	18	7	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 Kdo2-lipid A biosynthesis	25	24	1
superpathway of chorismate metabolism	59	54	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1