Experiment set12IT043 for Escherichia coli BW25113

LB with Trimethoprim 0.0025 mM

Group: stress
Media: LB + Trimethoprim (0.0025 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 C3

Specific Phenotypes

For 40 genes in this experiment

For stress Trimethoprim in Escherichia coli BW25113

For stress Trimethoprim across organisms

SEED Subsystems

Subsystem	#Specific
Rhamnose containing glycans	4
dTDP-rhamnose synthesis	4
linker unit-arabinogalactan synthesis	4
Deoxyribose and Deoxynucleoside Catabolism	2
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	2
Capsular heptose biosynthesis	1
CytR regulation	1
Folate Biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycine and Serine Utilization	1
KDO2-Lipid A biosynthesis	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Pyruvate Alanine Serine Interconversions	1
Threonine anaerobic catabolism gene cluster	1
Transcription initiation, bacterial sigma factors	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyrimidine metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Folate biosynthesis
• Drug metabolism - other enzymes
• Pentose and glucuronate interconversions
• Galactose metabolism
• Purine metabolism
• Lysine degradation
• Tryptophan metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Peptidoglycan biosynthesis
• One carbon pool by folate
• Methane metabolism
• Nicotinate and nicotinamide metabolism
• Biotin metabolism
• Biosynthesis of vancomycin group antibiotics
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
S-methyl-5'-thioadenosine degradation II	1	1	1
dTDP-β-L-rhamnose biosynthesis	5	5	4
adenine and adenosine salvage III	4	4	3
pyrimidine deoxyribonucleosides degradation	3	3	2
adenine and adenosine salvage V	3	3	2
pyrimidine ribonucleosides salvage I	3	3	2
adenosine nucleotides degradation II	5	5	3
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	3
purine ribonucleosides degradation	6	6	3
dTDP-N-acetylthomosamine biosynthesis	4	4	2
adenine and adenosine salvage I	2	2	1
UDP-α-D-glucose biosynthesis	2	2	1
pseudouridine degradation	2	2	1
pyrimidine ribonucleosides degradation	2	2	1
dTDP-L-daunosamine biosynthesis	6	3	3
dTDP-sibirosamine biosynthesis	6	3	3
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	2
dTDP-N-acetylviosamine biosynthesis	4	2	2
dTDP-β-D-fucofuranose biosynthesis	4	2	2
purine nucleotides degradation II (aerobic)	11	11	5
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	2
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	2
dTDP-α-D-mycaminose biosynthesis	5	2	2
O-antigen building blocks biosynthesis (E. coli)	11	11	4
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	2
tetrahydrofolate biosynthesis I	3	3	1
L-aspartate degradation III (anaerobic)	3	3	1
NAD salvage pathway III (to nicotinamide riboside)	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-aspartate degradation II (aerobic)	3	3	1
dTDP-D-desosamine biosynthesis	6	2	2
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	2
nucleoside and nucleotide degradation (archaea)	10	4	3
UTP and CTP dephosphorylation I	7	5	2
dTDP-β-L-olivose biosynthesis	7	3	2
dTDP-β-L-digitoxose biosynthesis	7	3	2
dTDP-β-L-mycarose biosynthesis	7	2	2
inosine 5'-phosphate degradation	4	4	1
guanosine nucleotides degradation III	4	4	1
guanosine nucleotides degradation II	4	4	1
adenosine nucleotides degradation I	8	7	2
purine nucleotides degradation I (plants)	12	10	3
preQ0 biosynthesis	4	3	1
tetrahydromonapterin biosynthesis	4	3	1
guanosine nucleotides degradation I	4	3	1
erythro-tetrahydrobiopterin biosynthesis I	4	2	1
threo-tetrahydrobiopterin biosynthesis	4	2	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	2
dTDP-β-L-megosamine biosynthesis	8	3	2
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis	9	3	2
dTDP-α-D-forosamine biosynthesis	9	3	2
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	7	4
superpathway of pyrimidine ribonucleosides salvage	10	10	2
superpathway of enterobacterial common antigen biosynthesis	10	9	2
sucrose degradation II (sucrose synthase)	5	4	1
superpathway of pyrimidine ribonucleosides degradation	5	4	1
superpathway of guanosine nucleotides degradation (plants)	6	5	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	5	1
superpathway of purines degradation in plants	18	13	3
superpathway of novobiocin biosynthesis	19	4	3
stachyose degradation	7	7	1
lipoprotein posttranslational modification (Gram-negative bacteria)	7	6	1
ureide biosynthesis	7	5	1
drosopterin and aurodrosopterin biosynthesis	7	5	1
sucrose biosynthesis II	8	6	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	14	4
folate transformations III (E. coli)	9	9	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
tunicamycin biosynthesis	9	2	1
superpathway of erythromycin biosynthesis	19	2	2
superpathway of tetrahydrofolate biosynthesis	10	9	1
colanic acid building blocks biosynthesis	11	11	1
folate transformations II (plants)	11	10	1
NAD salvage (plants)	11	5	1
L-methionine salvage cycle III	11	5	1
superpathway of megalomicin A biosynthesis	22	3	2
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	3	2
superpathway of tetrahydrofolate biosynthesis and salvage	12	11	1
superpathway of purine nucleotide salvage	14	13	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of chorismate metabolism	59	54	1