Experiment set1IT084 for Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868

LB_plus_SM_buffer with FelixO1_phage 0.05 MOI

Group: phage
Media: LB_plus_SM_buffer + FelixO1_phage (0.05 MOI)
Culturing: MS1868_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Ben Adler on 3-Aug-17
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 12 genes in this experiment

For phage FelixO1_phage in Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868

For phage FelixO1_phage across organisms

SEED Subsystems

Subsystem	#Specific
CBSS-214092.1.peg.3450	1
Capsular heptose biosynthesis	1
Deoxyribose and Deoxynucleoside Catabolism	1
Entner-Doudoroff Pathway	1
Flagellar motility	1
Flagellum	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
LOS core oligosaccharide biosynthesis	1
Orphan regulatory proteins	1
Potassium homeostasis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Ubiquinone Biosynthesis	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of terpenoids and steroids
• Glycolysis / Gluconeogenesis
• Pentose and glucuronate interconversions
• Galactose metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of ansamycins
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• 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
4-hydroxybenzoate biosynthesis II (bacteria)	1	1	1
GDP-D-glycero-α-D-manno-heptose biosynthesis	4	1	1
polybrominated phenols biosynthesis	4	1	1
ADP-L-glycero-β-D-manno-heptose biosynthesis	5	5	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
spongiadioxin C biosynthesis	7	1	1
polybrominated dihydroxylated diphenyl ethers biosynthesis	8	1	1
Entner-Doudoroff pathway I	9	9	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	7	1
ubiquinol-8 biosynthesis (late decarboxylation)	9	6	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
p-HBAD biosynthesis	9	1	1
Rubisco shunt	10	9	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis III (from glucose)	11	11	1
glycolysis VI (from fructose)	11	8	1
superpathway of ubiquinol-8 biosynthesis (early decarboxylation)	12	12	1
homolactic fermentation	12	11	1
glycolysis I (from glucose 6-phosphate)	13	13	1
tetrahydromethanopterin biosynthesis	14	3	1
Bifidobacterium shunt	15	12	1
mixed acid fermentation	16	16	1
glycerol degradation to butanol	16	11	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of hexitol degradation (bacteria)	18	18	1
heterolactic fermentation	18	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	18	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of polybrominated aromatic compound biosynthesis	20	2	1
superpathway of N-acetylneuraminate degradation	22	22	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
phenolphthiocerol biosynthesis	23	1	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	24	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of chorismate metabolism	59	54	1