Experiment set12IT044 for Escherichia coli BW25113

LB with Trimethoprim 0.005 mM

Group: stress
Media: LB + Trimethoprim (0.005 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Keio_ML9a, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.8 generations
By: Adam on 30-Jun-16
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: TnSeq_Plate1 C4

Specific Phenotypes

For 11 genes in this experiment

For stress Trimethoprim in Escherichia coli BW25113

For stress Trimethoprim across organisms

SEED Subsystems

Subsystem	#Specific
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	1
Orphan regulatory proteins	1
Redox-dependent regulation of nucleus processes	1
Rhamnose containing glycans	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
• Puromycin biosynthesis
• Lysine degradation
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Peptidoglycan biosynthesis
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Nicotinate and nicotinamide metabolism
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
polyphosphate metabolism	2	2	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
NAD salvage pathway V (PNC V cycle)	5	3	1
ppGpp metabolism	6	6	1
lipoprotein posttranslational modification (Gram-negative bacteria)	7	6	1
NAD salvage pathway I (PNC VI cycle)	7	5	1
O-antigen building blocks biosynthesis (E. coli)	11	11	1
NAD salvage (plants)	11	5	1
superpathway of NAD biosynthesis in eukaryotes	14	7	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	7	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	14	1