Experiment set36IT052 for Escherichia coli BW25113

Phage_N4_cage_4_mouse_3_Cecum_40 hr

Group: phage
Media: mouse gut + Phage_N4 (1 MOI) + cage (4 )
Culturing: Keio_ML9a, mouse gut, Anaerobic, at 37 (C)
Growth: about 40.0 generations
By: Denish/Ben on 4-Jun-19

Specific Phenotypes

For 11 genes in this experiment

For phage Phage_N4 in Escherichia coli BW25113

For phage Phage_N4 across organisms

SEED Subsystems

Subsystem	#Specific
D-Tagatose and Galactitol Utilization	3
L-Arabinose utilization	3
Deoxyribose and Deoxynucleoside Catabolism	1
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Rhamnose containing glycans	1
YeiH	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:

• Galactose metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• 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
galactitol degradation	5	5	3
D-galactosamine and N-acetyl-D-galactosamine degradation	4	4	2
N-acetyl-D-galactosamine degradation	5	4	2
lactose degradation I	5	2	2
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	1
2-deoxy-D-ribose degradation I	3	3	1
D-tagatose degradation	3	1	1
superpathway of hexitol degradation (bacteria)	18	18	4
dTDP-β-L-rhamnose biosynthesis	5	5	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	1
superpathway of purine deoxyribonucleosides degradation	7	7	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
Rubisco shunt	10	9	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
photorespiration II	10	6	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	11	1
O-antigen building blocks biosynthesis (E. coli)	11	11	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	12	1
glycolysis I (from glucose 6-phosphate)	13	13	1
gluconeogenesis I	13	13	1
Bifidobacterium shunt	15	13	1
glycerol degradation to butanol	16	11	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	7	1
superpathway of N-acetylneuraminate degradation	22	22	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
ethene biosynthesis V (engineered)	25	18	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	14	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1