Experiment set8IT052 for Escherichia coli BW25113

LB Aerobic with Nitrofurantoin 0.00003125 mM

Group: stress
Media: LB + Nitrofurantoin (3.13E-02 mM)
Culturing: Keio_ML9a, 96 deep-well microplate; Multitron, Aerobic, at 37 (C), shaken=750 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 28 genes in this experiment

For stress Nitrofurantoin in Escherichia coli BW25113

For stress Nitrofurantoin across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, bacterial RecFOR pathway	5
DNA-replication	4
Formate hydrogenase	3
Formate dehydrogenase	2
Selenocysteine metabolism	2
D-allose utilization	1
DNA Repair Base Excision	1
DNA repair, UvrABC system	1
DNA repair, bacterial	1
DNA repair, bacterial DinG and relatives	1
Folate Biosynthesis	1
Fructose utilization	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Nitric oxide synthase	1
Oxidative stress	1
Pentose phosphate pathway	1
Pterin biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Redox-dependent regulation of nucleus processes	1
Trehalose Uptake and Utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Nicotinate and nicotinamide metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Selenoamino acid metabolism
• Starch and sucrose metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Glyoxylate and dicarboxylate metabolism
• Trinitrotoluene degradation
• Methane metabolism
• Thiamine metabolism
• Riboflavin metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Aminoacyl-tRNA biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
formate oxidation to CO2	1	1	1
superoxide radicals degradation	2	2	1
formate to trimethylamine N-oxide electron transfer	2	2	1
tetrahydropteridine recycling	2	2	1
L-threonine degradation II	2	2	1
formate to dimethyl sulfoxide electron transfer	2	2	1
nitrate reduction III (dissimilatory)	2	2	1
L-selenocysteine biosynthesis I (bacteria)	3	3	1
formate to nitrite electron transfer	3	2	1
L-phenylalanine degradation V	3	1	1
reactive oxygen species degradation	4	4	1
oxalate degradation VI	4	2	1
pentose phosphate pathway (non-oxidative branch) I	5	5	1
CMP-3-deoxy-D-manno-octulosonate biosynthesis	5	5	1
NAD salvage pathway V (PNC V cycle)	5	3	1
oxalate degradation III	5	2	1
ethene biosynthesis III (microbes)	7	6	1
NAD salvage pathway I (PNC VI cycle)	7	5	1
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	4	1
toxoflavin biosynthesis	7	4	1
pentose phosphate pathway	8	8	1
flavin biosynthesis I (bacteria and plants)	9	9	1
flavin biosynthesis III (fungi)	9	8	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
Rubisco shunt	10	9	1
flavin biosynthesis II (archaea)	10	6	1
NAD salvage (plants)	11	5	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
superpathway of C1 compounds oxidation to CO2	12	4	1
superpathway of NAD biosynthesis in eukaryotes	14	7	1
Bifidobacterium shunt	15	13	1
purine nucleobases degradation I (anaerobic)	15	6	1
superpathway of (Kdo)2-lipid A biosynthesis	17	17	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of L-threonine metabolism	18	16	1
purine nucleobases degradation II (anaerobic)	24	17	1
superpathway of Kdo2-lipid A biosynthesis	25	24	1