Experiment set13IT050 for Pseudomonas fluorescens SBW25-INTG

D,L-Malic Acid (C) and Ammonium chloride (N); with MOPS; with Sodium chloride

Group: stress
Media: MME_noNitrogen_noCarbon + D,L-Malic Acid (20 mM) + Ammonium chloride (10 mM) + Sodium Chloride (400 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on September 1, 2021
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 11 genes in this experiment

For stress D,L-Malic Acid in Pseudomonas fluorescens SBW25-INTG

For stress D,L-Malic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	2
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Butanol Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Oxidative stress	1
TCA Cycle	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
• 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
fatty acid salvage	6	6	1
pyruvate fermentation to butanol II (engineered)	6	4	1
partial TCA cycle (obligate autotrophs)	8	8	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle VII (acetate-producers)	9	7	1
TCA cycle I (prokaryotic)	10	9	1
pyruvate fermentation to hexanol (engineered)	11	7	1
superpathway of glyoxylate bypass and TCA	12	11	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
oleate β-oxidation	35	33	1