Experiment set39IT049 for Pseudomonas putida KT2440

2-Methylbutanoic acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 2-Methylbutanoic acid (10 mM)
Culturing: Putida_ML5_JBEI, 24-well plate, Aerobic, at 30 (C), shaken=200 rpm
By: Allie Pearson on 28-Sep
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 9 genes in this experiment

For carbon source 2-Methylbutanoic acid in Pseudomonas putida KT2440

For carbon source 2-Methylbutanoic acid across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	2
Butanol Biosynthesis	2
Anaerobic respiratory reductases	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Polyhydroxybutyrate metabolism	1
RNA processing and degradation, bacterial	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via CoA ligation
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Butanoate metabolism
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Geraniol degradation
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Folate biosynthesis
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	3
oleate β-oxidation (thioesterase-dependent, yeast)	2	2	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
superpathway of acetate utilization and formation	3	3	1
pyruvate fermentation to butanol II (engineered)	6	4	2
ethanol degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
chitin deacetylation	4	2	1
glutaryl-CoA degradation	5	3	1
pyruvate fermentation to hexanol (engineered)	11	8	2
superpathway of bitter acids biosynthesis	18	3	3
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
pyruvate fermentation to butanoate	7	3	1
pyruvate fermentation to butanol I	8	3	1
2-methylpropene degradation	8	2	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	3
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	2	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	1
methyl tert-butyl ether degradation	10	2	1
L-glutamate degradation VII (to butanoate)	12	3	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
1-butanol autotrophic biosynthesis (engineered)	27	19	2
L-tryptophan degradation III (eukaryotic)	15	3	1
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	1
oleate β-oxidation	35	30	2
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
toluene degradation VI (anaerobic)	18	4	1