Experiment set16IT017 for Pseudomonas putida KT2440

L-Valine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Valine (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 18 genes in this experiment

For carbon source L-Valine in Pseudomonas putida KT2440

For carbon source L-Valine across organisms

SEED Subsystems

Subsystem	#Specific
Valine degradation	8
Isoleucine degradation	5
Leucine Degradation and HMG-CoA Metabolism	5
Isobutyryl-CoA to Propionyl-CoA Module	3
Branched-Chain Amino Acid Biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
HMG CoA Synthesis	1
Serine-glyoxylate cycle	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
• Propanoate metabolism
• Biosynthesis of plant hormones
• Fatty acid metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• beta-Alanine metabolism
• Benzoate degradation via CoA ligation
• Caprolactam degradation
• Biosynthesis of terpenoids and steroids
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fatty acid elongation in mitochondria
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Tryptophan metabolism
• Inositol phosphate metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Biosynthesis of unsaturated fatty acids
• 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
L-methionine degradation II	3	3	2
β-alanine degradation II	2	2	1
L-valine degradation I	8	6	4
L-threonine degradation I	6	4	3
β-alanine degradation I	2	1	1
L-threonine degradation V	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
propanoyl-CoA degradation II	5	3	2
benzoyl-CoA biosynthesis	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
glycine cleavage	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
glycine biosynthesis II	3	3	1
L-leucine degradation I	6	5	2
2-methyl-branched fatty acid β-oxidation	14	10	4
superpathway of L-isoleucine biosynthesis I	13	13	3
valproate β-oxidation	9	7	2
hypoglycin biosynthesis	14	4	3
adipate degradation	5	5	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
adipate biosynthesis	5	4	1
acrylate degradation I	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
superpathway of branched chain amino acid biosynthesis	17	17	3
L-isoleucine degradation I	6	5	1
β-alanine biosynthesis II	6	5	1
superpathway of L-threonine metabolism	18	12	3
propanoate fermentation to 2-methylbutanoate	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
benzoyl-CoA degradation I (aerobic)	7	3	1
myo-inositol degradation I	7	1	1
2,4-dinitrotoluene degradation	7	1	1
phenylacetate degradation I (aerobic)	9	9	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
3-phenylpropanoate degradation	10	4	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
superpathway of phenylethylamine degradation	11	11	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	30	3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
cyclosporin A biosynthesis	15	2	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
platensimycin biosynthesis	26	6	1