Experiment set2IT072 for Escherichia coli BW25113

LB with 2-Furfuraldehyde 0.25 vol%

Group: stress
Media: LB + 2-Furfuraldehyde (0.25 vol%)
Culturing: Keio_ML9, 48 well microplate; Tecan Infinite F200, Aerobic, at 28 (C), shaken=orbital
By: Kelly on 6/30/2014
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 962 C1,C2

Specific Phenotypes

For 26 genes in this experiment

For stress 2-Furfuraldehyde in Escherichia coli BW25113

For stress 2-Furfuraldehyde across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, UvrABC system	2
Folate Biosynthesis	2
Formate hydrogenase	2
Glycine and Serine Utilization	2
Pentose phosphate pathway	2
Pyruvate Alanine Serine Interconversions	2
Capsular heptose biosynthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Experimental tye	1
Formate dehydrogenase	1
Fructose utilization	1
Glutathione: Non-redox reactions	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Heat shock dnaK gene cluster extended	1
Heme and Siroheme Biosynthesis	1
NAD and NADP cofactor biosynthesis global	1
Nitric oxide synthase	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Oxidative stress	1
Purine conversions	1
Rhamnose containing glycans	1
Threonine anaerobic catabolism gene cluster	1
cAMP signaling in bacteria	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Pentose phosphate pathway
• Porphyrin and chlorophyll metabolism
• Biosynthesis of plant hormones
• Puromycin biosynthesis
• Pyrimidine metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Trinitrotoluene degradation
• Methane metabolism
• Folate biosynthesis
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
thiosulfate disproportionation IV (rhodanese)	1	1	1
formate oxidation to CO2	1	1	1
superoxide radicals degradation	2	2	1
formate to trimethylamine N-oxide electron transfer	2	2	1
guanine and guanosine salvage II	2	2	1
formate to dimethyl sulfoxide electron transfer	2	2	1
nitrate reduction III (dissimilatory)	2	2	1
adenine and adenosine salvage I	2	2	1
guanine and guanosine salvage I	2	2	1
adenine and adenosine salvage II	2	2	1
pyrimidine deoxyribonucleosides salvage	5	4	2
prenylated FMNH2 biosynthesis	3	3	1
superpathway of guanine and guanosine salvage	3	3	1
adenine salvage	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
formate to nitrite electron transfer	3	2	1
pentose phosphate pathway	8	8	2
heme b biosynthesis V (aerobic)	4	4	1
reactive oxygen species degradation	4	4	1
heme b biosynthesis I (aerobic)	4	4	1
oxalate degradation VI	4	2	1
superpathway of pyrimidine deoxyribonucleoside salvage	9	8	2
pentose phosphate pathway (non-oxidative branch) I	5	5	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	1
sulfide oxidation IV (mitochondria)	5	2	1
oxalate degradation III	5	2	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	6	1
dTDP-L-daunosamine biosynthesis	6	3	1
dTDP-sibirosamine biosynthesis	6	3	1
superpathway of purine nucleotide salvage	14	13	2
ethene biosynthesis III (microbes)	7	6	1
glyphosate degradation III	7	4	1
(aminomethyl)phosphonate degradation	8	8	1
superpathway of heme b biosynthesis from glycine	8	7	1
superpathway of glucose and xylose degradation	17	17	2
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent)	9	3	1
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	9	3	1
superpathway of heme b biosynthesis from glutamate	10	10	1
Rubisco shunt	10	9	1
O-antigen building blocks biosynthesis (E. coli)	11	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
superpathway of C1 compounds oxidation to CO2	12	4	1
Bifidobacterium shunt	15	13	1
purine nucleobases degradation I (anaerobic)	15	6	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	7	1
superpathway of novobiocin biosynthesis	19	4	1
purine nucleobases degradation II (anaerobic)	24	17	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	14	1