Experiment set1S506 for Escherichia coli Nissle 1917

Bas45

Group: phage
Media: LB_plus_SM_buffer + MOI 10
Culturing: Ecoli_Nissle_ML2, 48 well microplate, Aerobic, at 37 (C), shaken=double orbital, continuous, 205cpm
By: Lucas on 12/4/2024
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 26 genes in this experiment

For phage MOI 10 in Escherichia coli Nissle 1917

For phage MOI 10 across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	1
DNA-replication	1
DNA Repair Base Excision	1
DNA repair, bacterial RecFOR pathway	1
DNA repair, bacterial UvrD and related helicases	1
De Novo Pyrimidine Synthesis	1
Flagellar motility	1
Flagellum	1
LMPTP YwlE cluster	1
Lipid A modifications	1
Proline Synthesis	1
Rrf2 family transcriptional regulators	1
Terminal cytochrome O ubiquinol oxidase	1
Terminal cytochrome oxidases	1
ZZ gjo need homes	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyrimidine metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Methionine metabolism
• Arginine and proline metabolism
• Tryptophan metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Riboflavin metabolism
• Porphyrin and chlorophyll metabolism
• Terpenoid biosynthesis
• Carotenoid biosynthesis - General
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyrimidine nucleobases salvage I	1	1	1
pyrimidine nucleobases salvage II	2	2	1
pseudouridine degradation	2	2	1
UDP-α-D-glucose biosynthesis	2	2	1
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
L-proline biosynthesis III (from L-ornithine)	3	2	1
superpathway of pyrimidine nucleobases salvage	4	4	1
L-proline biosynthesis I (from L-glutamate)	4	4	1
sucrose degradation IV (sucrose phosphorylase)	4	4	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
starch degradation V	4	3	1
L-arginine degradation VI (arginase 2 pathway)	4	2	1
heme a biosynthesis	4	2	1
starch degradation III	4	2	1
D-galactose degradation I (Leloir pathway)	5	5	1
glucose and glucose-1-phosphate degradation	5	5	1
sucrose degradation II (sucrose synthase)	5	4	1
L-arginine degradation XIII (reductive Stickland reaction)	5	4	1
dTDP-β-L-rhamnose biosynthesis	5	3	1
glucosylglycerol biosynthesis	5	3	1
CDP-6-deoxy-D-gulose biosynthesis	5	1	1
glycogen degradation II	6	4	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
glycogen degradation I	8	8	1
sucrose biosynthesis II	8	6	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
chitin biosynthesis	9	6	1
superpathway of pyrimidine ribonucleosides salvage	10	10	1
peptidoglycan recycling II	10	7	1
starch biosynthesis	10	6	1
colanic acid building blocks biosynthesis	11	11	1
O-antigen building blocks biosynthesis (E. coli)	11	8	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	6	1
peptidoglycan recycling I	14	14	1
streptomycin biosynthesis	18	1	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	11	1