Experiment set12IT004 for Pseudomonas putida KT2440

Sodium propionate carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Sodium propionate (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Putida_ML5_JBEI, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: Matthew Incha on 12-Feb-19
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 3 genes in this experiment

For carbon source Sodium propionate in Pseudomonas putida KT2440

For carbon source Sodium propionate across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Butanol Biosynthesis	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Brassinosteroid biosynthesis
• Caprolactam degradation
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyruvate fermentation to butanol II (engineered)	6	4	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis II (from fructose 6-phosphate)	11	9	1
pyruvate fermentation to hexanol (engineered)	11	8	1
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	10	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of hexitol degradation (bacteria)	18	13	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of anaerobic sucrose degradation	19	13	1
superpathway of N-acetylneuraminate degradation	22	12	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1