Experiment set27IT061 for Pseudomonas putida KT2440

L-Valine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + L-Valine (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Mitchell Thompson on 11/8/20
Media components: 10 mM D-Glucose, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 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 nitrogen source L-Valine in Pseudomonas putida KT2440

For nitrogen source L-Valine across organisms

SEED Subsystems

Subsystem	#Specific
Valine degradation	3
Isoleucine degradation	2
Leucine Degradation and HMG-CoA Metabolism	2
Branched-Chain Amino Acid 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
• Fatty acid metabolism
• Geraniol degradation
• beta-Alanine metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Caprolactam degradation
• Biosynthesis of plant hormones
• Fatty acid elongation in mitochondria
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Tryptophan metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-methionine degradation II	3	3	2
L-threonine degradation I	6	4	3
L-threonine degradation V	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
benzoyl-CoA biosynthesis	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
2-methyl-branched fatty acid β-oxidation	14	10	4
L-valine degradation I	8	6	2
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
fatty acid β-oxidation II (plant peroxisome)	5	3	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	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
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
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
platensimycin biosynthesis	26	6	1