Experiment set16IT021 for Pseudomonas putida KT2440

L-Isoleucine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Isoleucine (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.7 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 27 genes in this experiment

For carbon source L-Isoleucine in Pseudomonas putida KT2440

For carbon source L-Isoleucine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	10
Valine degradation	8
Isoleucine degradation	6
ABC transporter dipeptide (TC 3.A.1.5.2)	4
Leucine Degradation and HMG-CoA Metabolism	4
Isobutyryl-CoA to Propionyl-CoA Module	3
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Arginine and Ornithine Degradation	1
Butanol Biosynthesis	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	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
• Arginine and proline metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Inositol phosphate metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• 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
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
L-proline degradation I	3	3	2
β-alanine degradation II	2	2	1
β-alanine degradation I	2	1	1
glycine cleavage	3	3	1
superpathway of acetate utilization and formation	3	3	1
ethanol degradation II	3	3	1
glycine biosynthesis II	3	3	1
ethanol degradation IV	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
ethanol degradation III	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-valine degradation I	8	6	2
chitin deacetylation	4	2	1
ethene biosynthesis II (microbes)	4	1	1
propanoyl-CoA degradation II	5	3	1
pyruvate fermentation to butanol II (engineered)	6	4	1
superpathway of bitter acids biosynthesis	18	3	3
(5R)-carbapenem carboxylate biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
L-Nδ-acetylornithine biosynthesis	7	5	1
myo-inositol degradation I	7	1	1
2,4-dinitrotoluene degradation	7	1	1
L-citrulline biosynthesis	8	7	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	2	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
pyruvate fermentation to hexanol (engineered)	11	8	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1