Experiment set22IT070 for Escherichia coli BW25113

T7_phage 0.00015625 MOI TC4

Group: phage
Media: LB_plus_SM_buffer + T7_phage (0.00015625 MOI)
Culturing: Keio_ML9a, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Crystal on 21-Aug-17
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride, 100 mM Sodium Chloride, 4 mM Magnesium sulfate, 0.005 vol% Gelatin, 25 mM Tris hydrochloride

Specific Phenotypes

For 22 genes in this experiment

For phage T7_phage in Escherichia coli BW25113

For phage T7_phage across organisms

SEED Subsystems

Subsystem	#Specific
Autoinducer 2 (AI-2) transport and processing (lsrACDBFGE operon)	1
Biotin biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
KDO2-Lipid A biosynthesis	1
LOS core oligosaccharide biosynthesis	1
Lipid A-Ara4N pathway ( Polymyxin resistance )	1
Lipid A modifications	1
Propionyl-CoA to Succinyl-CoA Module	1
Proteolysis in bacteria, ATP-dependent	1
Rhamnose containing glycans	1
Ribosomal protein S12p Asp methylthiotransferase	1
Serine-glyoxylate cycle	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	1
n-Phenylalkanoic acid degradation	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lipopolysaccharide biosynthesis
• Pentose phosphate pathway
• Tyrosine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Fructose and mannose metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Puromycin biosynthesis
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Benzoate degradation via hydroxylation
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• Nicotinate and nicotinamide metabolism
• Pantothenate and CoA biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
cinnamoyl-CoA biosynthesis	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
conversion of succinate to propanoate	3	3	1
autoinducer AI-2 degradation	3	3	1
propanoyl CoA degradation I	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
L-valine biosynthesis	4	4	1
D-xylose degradation to ethylene glycol (engineered)	4	3	1
phytol degradation	4	3	1
2-oxobutanoate degradation I	4	2	1
phosphatidylcholine acyl editing	4	2	1
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
pinosylvin metabolism	4	1	1
sporopollenin precursors biosynthesis	18	5	4
dTDP-β-L-rhamnose biosynthesis	5	5	1
5,6-dehydrokavain biosynthesis (engineered)	10	8	2
pyruvate fermentation to isobutanol (engineered)	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
octane oxidation	5	2	1
D-xylose degradation VI	5	1	1
D-xylose degradation V	5	1	1
D-xylose degradation III	5	1	1
fatty acid salvage	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
L-isoleucine biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	2	1
stearate biosynthesis I (animals)	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
pyruvate fermentation to propanoate I	7	5	1
L-isoleucine biosynthesis III	7	4	1
D-xylose degradation IV	7	3	1
ceramide degradation by α-oxidation	7	2	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
L-isoleucine biosynthesis II	8	4	1
2-deoxy-D-ribose degradation II	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of branched chain amino acid biosynthesis	17	17	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	1
lipid A-core biosynthesis (E. coli K-12)	10	9	1
lipid A-core biosynthesis (Salmonella)	10	8	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
3-phenylpropanoate degradation	10	4	1
suberin monomers biosynthesis	20	3	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
O-antigen building blocks biosynthesis (E. coli)	11	11	1
L-glutamate degradation VIII (to propanoate)	11	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
3-hydroxypropanoate cycle	13	7	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
superpathway of L-methionine salvage and degradation	16	6	1
cutin biosynthesis	16	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
superpathway of L-threonine metabolism	18	16	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
superpathway of the 3-hydroxypropanoate cycle	18	7	1
methylaspartate cycle	19	9	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	7	1
superpathway of Kdo2-lipid A biosynthesis	25	24	1
superpathway of fatty acids biosynthesis (E. coli)	53	51	2
palmitate biosynthesis III	29	21	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	14	1
oleate β-oxidation	35	32	1
superpathway of pentose and pentitol degradation	42	18	1