Experiment set9S487 for Escherichia coli BL21

EV116

Group: phage
Media: LB_plus_SM_buffer + MOI 10
Culturing: BL21_ML4, 48 well microplate, Aerobic, at 37 (C), shaken=double orbital, continuous, 205cpm
By: Lucas on 9/11/24
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 38 genes in this experiment

For phage MOI 10 in Escherichia coli BL21

For phage MOI 10 across organisms

SEED Subsystems

Subsystem	#Specific
Glycerol and Glycerol-3-phosphate Uptake and Utilization	2
Glycine and Serine Utilization	2
Iron acquisition in Vibrio	2
Pyruvate Alanine Serine Interconversions	2
Threonine anaerobic catabolism gene cluster	2
Transport of Iron	2
Ammonia assimilation	1
Campylobacter Iron Metabolism	1
D-gluconate and ketogluconates metabolism	1
DNA-binding regulatory proteins, strays	1
Flavodoxin	1
Glycerol fermenation to 1,3-propanediol	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
LOS core oligosaccharide biosynthesis	1
Lipid A modifications	1
MLST	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
NAD and NADP cofactor biosynthesis global	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Orphan regulatory proteins	1
Peptidoglycan Biosynthesis	1
Proline, 4-hydroxyproline uptake and utilization	1
Proteolysis in bacteria, ATP-dependent	1
Purine conversions	1
Ton and Tol transport systems	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Ubiquinone and menaquinone biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Naphthalene and anthracene degradation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
guanine and guanosine salvage III	1	1	1
glycerol degradation I	3	3	2
glycerol and glycerophosphodiester degradation	4	4	2
arsenate detoxification III	2	2	1
di-trans,poly-cis-undecaprenyl phosphate biosynthesis	2	2	1
ppGpp metabolism	6	6	2
adenine and adenosine salvage V	3	3	1
prenylated FMNH2 biosynthesis	3	3	1
superpathway of guanine and guanosine salvage	3	3	1
polyisoprenoid biosynthesis (E. coli)	5	5	1
arsenic detoxification (plants)	6	5	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	6	2
arsenic detoxification (yeast)	12	4	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
arsenic detoxification (mammals)	17	8	1