Experiment set64S268 for Escherichia coli BW25113

Lambda_ci1857

Group: phage
Media: LB_plus_SM_buffer + MOI 10
Culturing: KEIO_ML9a, 48 well microplate, Aerobic, at 37 (C), shaken=double orbital, continuous, 205cpm
By: Lucas on 1/29/24
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 21 genes in this experiment

For phage MOI 10 in Escherichia coli BW25113

For phage MOI 10 across organisms

SEED Subsystems

Subsystem	#Specific
Maltose and Maltodextrin Utilization	7
Choline and Betaine Uptake and Betaine Biosynthesis	2
Glycogen metabolism	2
ATP-dependent RNA helicases, bacterial	1
CBSS-562.2.peg.5158 SK3 including	1
Capsular heptose biosynthesis	1
DNA repair, bacterial	1
Entner-Doudoroff Pathway	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycine and Serine Utilization	1
Glycolysis and Gluconeogenesis	1
Hfl operon	1
LOS core oligosaccharide biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Threonine anaerobic catabolism gene cluster	1
Trehalose Uptake and Utilization	1
Universal GTPases	1
YeiH	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Starch and sucrose metabolism
• Galactose metabolism
• Glycolysis / Gluconeogenesis
• Pentose and glucuronate interconversions
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Inositol phosphate metabolism
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
thiosulfate disproportionation IV (rhodanese)	1	1	1
L-tryptophan degradation II (via pyruvate)	3	3	2
D-serine degradation	3	3	2
L-cysteine degradation II	3	2	2
glycogen degradation I	8	8	5
trehalose degradation II (cytosolic)	2	2	1
trehalose degradation I (low osmolarity)	2	2	1
starch degradation V	4	3	2
glycogen degradation II	6	4	3
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
sucrose biosynthesis II	8	6	3
glycine betaine degradation I	8	4	3
trehalose degradation IV	3	3	1
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
sucrose degradation III (sucrose invertase)	4	3	1
L-mimosine degradation	8	4	2
starch degradation III	4	2	1
glutathione-mediated detoxification I	8	3	2
GDP-D-glycero-α-D-manno-heptose biosynthesis	4	1	1
glucose and glucose-1-phosphate degradation	5	5	1
ADP-L-glycero-β-D-manno-heptose biosynthesis	5	5	1
sulfide oxidation IV (mitochondria)	5	2	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	17	3
chitin derivatives degradation	8	4	1
1,3-propanediol biosynthesis (engineered)	9	7	1
chitin biosynthesis	9	6	1
starch degradation II	9	1	1
glycolysis III (from glucose)	11	11	1
homolactic fermentation	12	12	1
Bifidobacterium shunt	15	13	1
heterolactic fermentation	18	16	1