Experiment set4IT073 for Pseudomonas fluorescens FW300-N1B4

L-Valine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Valine (20 mM), pH=7
Culturing: pseudo1_N1B4_ML1, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/16/2014
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)
Growth plate: Cplate1 D1

Specific Phenotypes

For 9 genes in this experiment

For carbon source L-Valine in Pseudomonas fluorescens FW300-N1B4

For carbon source L-Valine across organisms

SEED Subsystems

Subsystem	#Specific
Isobutyryl-CoA to Propionyl-CoA Module	2
Propionate-CoA to Succinate Module	2
Serine-glyoxylate cycle	2
Valine degradation	2
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
HMG CoA Synthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Lipoic acid metabolism	1
Methylcitrate cycle	1
TCA 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
• beta-Alanine metabolism
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Glutamate metabolism
• Geraniol degradation
• Lysine degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• Inositol phosphate metabolism
• alpha-Linolenic acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Nitrogen metabolism
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• 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
L-glutamate degradation I	1	1	1
β-alanine degradation II	2	2	1
lipoate salvage I	2	1	1
β-alanine degradation I	2	1	1
propanoyl-CoA degradation II	5	3	2
L-alanine degradation II (to D-lactate)	3	3	1
benzoyl-CoA biosynthesis	3	3	1
glyoxylate cycle	6	5	2
ethene biosynthesis IV (engineered)	3	2	1
partial TCA cycle (obligate autotrophs)	8	8	2
L-valine degradation I	8	6	2
nitrogen remobilization from senescing leaves	8	5	2
lipoate salvage II	4	1	1
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle II (plants and fungi)	9	6	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	3
2-methyl-branched fatty acid β-oxidation	14	11	3
2-methylcitrate cycle I	5	5	1
adipate degradation	5	5	1
TCA cycle I (prokaryotic)	10	8	2
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
adipate biosynthesis	5	4	1
TCA cycle III (animals)	10	6	2
fatty acid β-oxidation II (plant peroxisome)	5	3	1
acrylate degradation I	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
reductive TCA cycle I	11	6	2
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
superpathway of glyoxylate bypass and TCA	12	10	2
L-leucine degradation I	6	5	1
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	5	1
methyl ketone biosynthesis (engineered)	6	3	1
reductive TCA cycle II	12	5	2
methylaspartate cycle	19	9	3
myo-inositol degradation I	7	6	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
4-aminobutanoate degradation V	7	2	1
2,4-dinitrotoluene degradation	7	2	1
mixed acid fermentation	16	12	2
valproate β-oxidation	9	7	1
phenylacetate degradation I (aerobic)	9	4	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
myo-, chiro- and scyllo-inositol degradation	10	6	1
3-phenylpropanoate degradation	10	3	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	2
superpathway of phenylethylamine degradation	11	6	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	30	3
ethene biosynthesis V (engineered)	25	19	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
platensimycin biosynthesis	26	6	1