Experiment set84S219 for Escherichia coli BW25113

Mnm2

Group: phage
Media: LB_plus_SM_buffer + Phage (10 MOI)
Culturing: Keio_ML9a, 48 well microplate, Aerobic, at 37 (C), shaken=double orbital, continuous, 205cpm
By: Lucas on 10/30/2025
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 35 genes in this experiment

For phage Phage in Escherichia coli BW25113

For phage Phage across organisms

SEED Subsystems

Subsystem	#Specific
Selenocysteine metabolism	3
Formate hydrogenase	2
Siderophore Enterobactin	2
Biogenesis of cytochrome c oxidases	1
DNA repair, bacterial	1
Formate dehydrogenase	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Iron acquisition in Vibrio	1
Listeria phi-A118-like prophages	1
Oxidative stress	1
Polyamine Metabolism	1
Ton and Tol transport systems	1
YeiH	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of siderophore group nonribosomal peptides
• Selenoamino acid metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Biosynthesis of phenylpropanoids
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Nucleotide sugars metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Methane metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Aminoacyl-tRNA biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
formate oxidation to CO2	1	1	1
thiosulfate disproportionation IV (rhodanese)	1	1	1
L-selenocysteine biosynthesis I (bacteria)	3	3	2
2,3-dihydroxybenzoate biosynthesis	3	3	2
nitrate reduction III (dissimilatory)	2	2	1
formate to trimethylamine N-oxide electron transfer	2	2	1
formate to dimethyl sulfoxide electron transfer	2	2	1
salicylate biosynthesis I	2	1	1
cardiolipin biosynthesis I	3	3	1
cardiolipin biosynthesis II	3	3	1
cardiolipin biosynthesis III	3	3	1
formate to nitrite electron transfer	3	2	1
salicylate biosynthesis II	3	2	1
vibriobactin biosynthesis	9	4	3
enterobactin biosynthesis	11	7	3
bacillibactin biosynthesis	12	6	3
L-selenocysteine biosynthesis II (archaea and eukaryotes)	4	2	1
oxalate degradation VI	4	2	1
oxalate degradation III	5	2	1
sulfide oxidation IV (mitochondria)	5	2	1
phosphatidylglycerol biosynthesis II	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	7	1
vanchrobactin biosynthesis	8	3	1
anguibactin biosynthesis	8	2	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	9	1
superpathway of demethylmenaquinol-9 biosynthesis	9	8	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	8	1
acinetobactin biosynthesis	9	3	1
myxochelin A and B biosynthesis	9	2	1
superpathway of menaquinol-8 biosynthesis I	10	10	1
superpathway of menaquinol-7 biosynthesis	10	9	1
superpathway of menaquinol-6 biosynthesis	10	9	1
superpathway of menaquinol-9 biosynthesis	10	9	1
superpathway of menaquinol-13 biosynthesis	10	9	1
superpathway of menaquinol-11 biosynthesis	10	9	1
superpathway of menaquinol-12 biosynthesis	10	9	1
superpathway of menaquinol-10 biosynthesis	10	9	1
superpathway of phospholipid biosynthesis III (E. coli)	12	12	1
superpathway of C1 compounds oxidation to CO2	12	4	1
superpathway of cardiolipin biosynthesis (bacteria)	13	11	1
superpathway of phylloquinol biosynthesis	15	7	1
purine nucleobases degradation I (anaerobic)	15	6	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
superpathway of chorismate metabolism	59	54	3
purine nucleobases degradation II (anaerobic)	24	17	1
superpathway of phospholipid biosynthesis II (plants)	28	10	1