Experiment set1S426 for Escherichia coli ECOR38

TP7

Group: phage
Media: LB_plus_SM_buffer + MOI 10
Culturing: Ecoli_ECOR38_ML2, 48 well microplate, Aerobic, at 37 (C), shaken=double orbital, continuous, 205cpm
By: Lucas on 11/24/2024
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 29 genes in this experiment

For phage MOI 10 in Escherichia coli ECOR38

For phage MOI 10 across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	2
Transport of Molybdenum	2
Alkylphosphonate utilization	1
CBSS-562.2.peg.5158 SK3 including	1
D-Galacturonate and D-Glucuronate Utilization	1
DNA repair, bacterial	1
Deoxyribose and Deoxynucleoside Catabolism	1
Folate Biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine cleavage system	1
Maltose and Maltodextrin Utilization	1
Orphan regulatory proteins	1
Pentose phosphate pathway	1
Phosphate metabolism	1
Polyadenylation bacterial	1
Polyamine Metabolism	1
Proteolysis in bacteria, ATP-dependent	1
Respiratory dehydrogenases 1	1
Rhamnose containing glycans	1
Stringent Response, (p)ppGpp metabolism	1
Transcription factors bacterial	1
Transcription initiation, bacterial sigma factors	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Pentose phosphate pathway
• Pentose and glucuronate interconversions
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Tryptophan metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of vancomycin group antibiotics
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones
• mTOR signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
D-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	3	2
L-cysteine degradation II	3	2	2
polyphosphate metabolism	2	2	1
glycerol-3-phosphate to hydrogen peroxide electron transport	2	2	1
glycerophosphodiester degradation	2	2	1
glycerol-3-phosphate to fumarate electron transfer	2	2	1
glycerol-3-phosphate shuttle	2	2	1
nitrate reduction IX (dissimilatory)	2	2	1
glycerol 3-phosphate to cytochrome aa3 oxidase electron transfer	2	1	1
glycerol-3-phosphate to cytochrome bo oxidase electron transfer	2	1	1
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	4	3
sn-glycerol 3-phosphate anaerobic respiration	3	3	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	1
glycerol degradation I	3	3	1
molybdenum cofactor biosynthesis	3	3	1
glycine degradation	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
L-methionine biosynthesis II	6	5	2
pectin degradation I	3	1	1
peptidoglycan recycling II	10	7	3
dTDP-N-acetylthomosamine biosynthesis	4	4	1
glycerol and glycerophosphodiester degradation	4	4	1
dTDP-N-acetylviosamine biosynthesis	4	3	1
L-mimosine degradation	8	4	2
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
glutathione-mediated detoxification I	8	3	2
peptidoglycan recycling I	14	14	3
dTDP-β-L-rhamnose biosynthesis	5	5	1
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	1
pectin degradation II	5	3	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	1
dTDP-α-D-mycaminose biosynthesis	5	2	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	1
purine ribonucleosides degradation	6	6	1
ppGpp metabolism	6	6	1
polymyxin resistance	6	5	1
dTDP-L-daunosamine biosynthesis	6	3	1
dTDP-sibirosamine biosynthesis	6	3	1
dTDP-D-desosamine biosynthesis	6	2	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
superpathway of purine deoxyribonucleosides degradation	7	7	1
dTDP-β-L-olivose biosynthesis	7	3	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
pentose phosphate pathway	8	8	1
purine nucleobases degradation II (anaerobic)	24	17	3
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
dTDP-β-L-megosamine biosynthesis	8	3	1
dTDP-α-D-forosamine biosynthesis	9	3	1
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis	9	3	1
superpathway of enterobacterial common antigen biosynthesis	10	9	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	8	1
superpathway of novobiocin biosynthesis	19	4	1
superpathway of erythromycin biosynthesis	19	2	1
superpathway of megalomicin A biosynthesis	22	3	1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	3	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	13	1