Experiment set16IT023 for Pseudomonas putida KT2440

3-methyl-2-oxopentanoic acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 3-methyl-2-oxopentanoic acid (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.6 generations
By: Mitchell Thompson on 9/5/19
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 10 genes in this experiment

For carbon source 3-methyl-2-oxopentanoic acid in Pseudomonas putida KT2440

For carbon source 3-methyl-2-oxopentanoic acid across organisms

SEED Subsystems

Subsystem	#Specific
Isoleucine degradation	6
Valine degradation	6
Leucine Degradation and HMG-CoA Metabolism	4
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Butanol Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	3
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
sterculate biosynthesis	2	1	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
superpathway of acetate utilization and formation	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
L-isoleucine biosynthesis V	3	2	1
ethanol degradation III	3	2	1
chitin deacetylation	4	2	1
pyruvate fermentation to butanol II (engineered)	6	4	1
superpathway of bitter acids biosynthesis	18	3	3
colupulone and cohumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	2	1
pyruvate fermentation to hexanol (engineered)	11	8	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
mycolate biosynthesis	205	20	3
superpathway of mycolate biosynthesis	239	21	3