Experiment set2IT070 for Pseudomonas fluorescens GW456-L13

L-Valine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Valine (20 mM), pH=7
Culturing: pseudo13_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/10/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 15 genes in this experiment

For carbon source L-Valine in Pseudomonas fluorescens GW456-L13

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	4
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Branched-Chain Amino Acid Biosynthesis	1
Butanol Biosynthesis	1
HMG CoA Synthesis	1
Methylcitrate cycle	1
Propionate-CoA to Succinate Module	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
• Fatty acid metabolism
• Biosynthesis of plant hormones
• Glycine, serine and threonine metabolism
• Geraniol degradation
• beta-Alanine metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• 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
• 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	2	2
β-alanine degradation II	2	2	1
L-valine degradation I	8	6	4
L-threonine degradation I	6	4	3
L-threonine degradation V	2	1	1
β-alanine degradation I	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
propanoyl-CoA degradation II	5	3	2
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
benzoyl-CoA biosynthesis	3	3	1
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
L-leucine degradation I	6	5	2
2-methyl-branched fatty acid β-oxidation	14	11	4
superpathway of L-isoleucine biosynthesis I	13	13	3
valproate β-oxidation	9	7	2
hypoglycin biosynthesis	14	4	3
2-methylcitrate cycle I	5	5	1
adipate degradation	5	5	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation IV (unsaturated, even number)	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	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
superpathway of branched chain amino acid biosynthesis	17	17	3
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	5	1
L-isoleucine degradation I	6	5	1
superpathway of L-threonine metabolism	18	13	3
pyruvate fermentation to butanol II (engineered)	6	4	1
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
2,4-dinitrotoluene degradation	7	1	1
myo-inositol degradation I	7	1	1
phenylacetate degradation I (aerobic)	9	7	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	3	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
superpathway of phenylethylamine degradation	11	9	1
pyruvate fermentation to hexanol (engineered)	11	7	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	17	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1