Experiment set4IT034 for Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868

LB_plus_SM_buffer with FelixO1_phage (wt new) 0.75 MOI

Group: phage
Media: LB_plus_SM_buffer + FelixO1_phage (wt new) (0.75 MOI) + Kanamycin sulfate (0.05 mg/mL), pH=7.2
Culturing: MS1868_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=750rpm
By: Ben Adler on 7/28/18
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 11 genes in this experiment

For phage FelixO1_phage (wt new) in Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868

For phage FelixO1_phage (wt new) across organisms

SEED Subsystems

Subsystem	#Specific
De Novo Pyrimidine Synthesis	3
Entner-Doudoroff Pathway	2
Glycolysis and Gluconeogenesis	2
Glycolysis and Gluconeogenesis, including Archaeal enzymes	2
Molybdenum cofactor biosynthesis	2
Histidine Biosynthesis	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyrimidine metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Glycolysis / Gluconeogenesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Geraniol degradation
• Lysine biosynthesis
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Carbon fixation in photosynthetic organisms
• Vitamin B6 metabolism
• Limonene and pinene degradation
• Alkaloid biosynthesis II
• Drug metabolism - other enzymes

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
molybdenum cofactor biosynthesis	3	3	2
UMP biosynthesis II	6	6	3
UMP biosynthesis I	6	6	3
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
superpathway of pyrimidine ribonucleotides de novo biosynthesis	9	9	3
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
UMP biosynthesis III	6	5	2
L-phenylalanine degradation II (anaerobic)	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
glycolysis III (from glucose)	11	11	3
glycolysis II (from fructose 6-phosphate)	11	11	3
glycolysis VI (from fructose)	11	8	3
homolactic fermentation	12	11	3
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
bis(tungstenpterin) cofactor biosynthesis	4	1	1
glycolysis I (from glucose 6-phosphate)	13	13	3
Entner-Doudoroff pathway I	9	9	2
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	2
Rubisco shunt	10	9	2
glycolysis IV	10	8	2
glycolysis V (Pyrococcus)	10	7	2
L-tyrosine degradation I	5	3	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
superpathway of plastoquinol biosynthesis	5	1	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	3
superpathway of hexitol degradation (bacteria)	18	18	3
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	18	3
molybdopterin biosynthesis	6	5	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	18	3
superpathway of anaerobic sucrose degradation	19	17	3
pyridoxal 5'-phosphate biosynthesis I	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
superpathway of N-acetylneuraminate degradation	22	22	3
Bifidobacterium shunt	15	12	2
glycerol degradation to butanol	16	11	2
superpathway of glucose and xylose degradation	17	16	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	24	3
superpathway of aromatic amino acid biosynthesis	18	18	2
heterolactic fermentation	18	15	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	2	1
superpathway of L-tyrosine biosynthesis	10	10	1
L-histidine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
photorespiration II	10	6	1
rosmarinic acid biosynthesis I	10	1	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
(S)-reticuline biosynthesis I	11	1	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	46	4
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	11	1
gluconeogenesis III	12	9	1
gluconeogenesis I	13	13	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
formaldehyde assimilation I (serine pathway)	13	8	1
1-butanol autotrophic biosynthesis (engineered)	27	19	2
superpathway of rosmarinic acid biosynthesis	14	1	1
mixed acid fermentation	16	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
ethene biosynthesis V (engineered)	25	18	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	2	1
superpathway of chorismate metabolism	59	54	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1