Experiment set4IT016 for Escherichia coli BW25113

LB with 3-methyl-2-butenol 1.25 vol%

Group: stress
Media: LB + 3-methyl-2-butenol (1.25 vol%)
Culturing: Keio_ML9, 48 well microplate; Tecan Infinite F200, Aerobic, at 28 (C), shaken=orbital
By: Mitch on 3/15/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 14 genes in this experiment

For stress 3-methyl-2-butenol in Escherichia coli BW25113

For stress 3-methyl-2-butenol across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, UvrABC system	2
Glutathione-dependent pathway of formaldehyde detoxification	2
Experimental tye	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Heme and Siroheme Biosynthesis	1
Oxidative stress	1
Staphylococcal phi-Mu50B-like prophages	1
Transport of Manganese	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Methane metabolism
• Porphyrin and chlorophyll metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Aminophosphonate metabolism
• High-mannose type N-glycan biosynthesis
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
formaldehyde oxidation II (glutathione-dependent)	3	3	2
ethanol degradation I	2	2	1
pyruvate fermentation to ethanol II	2	1	1
pyruvate fermentation to ethanol I	3	3	1
cardiolipin biosynthesis II	3	3	1
pyruvate fermentation to ethanol III	3	3	1
ethanol degradation II	3	3	1
cardiolipin biosynthesis I	3	3	1
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-methionine degradation III	3	1	1
heme b biosynthesis V (aerobic)	4	4	1
heme b biosynthesis I (aerobic)	4	4	1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
phytol degradation	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
salidroside biosynthesis	4	2	1
ethanolamine utilization	5	5	1
acetylene degradation (anaerobic)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
protein S-nitrosylation and denitrosylation	5	3	1
(S)-propane-1,2-diol degradation	5	3	1
phenylethanol biosynthesis	5	2	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	6	1
superpathway of C1 compounds oxidation to CO2	12	4	2
superpathway of cardiolipin biosynthesis (bacteria)	13	11	2
noradrenaline and adrenaline degradation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	3	1
superpathway of heme b biosynthesis from glycine	8	7	1
butanol and isobutanol biosynthesis (engineered)	8	2	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	8	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
superpathway of phospholipid biosynthesis III (E. coli)	12	12	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	7	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	16	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	9	1
heterolactic fermentation	18	16	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