Experiment set2IT089 for Cupriavidus basilensis FW507-4G11

L-Valine nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + L-Valine (20 mM), pH=7
Culturing: cupriavidus_4G11_ML11, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Jayashree on 3/3/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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 3 genes in this experiment

For nitrogen source L-Valine in Cupriavidus basilensis FW507-4G11

For nitrogen source L-Valine across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Leucine Biosynthesis	1
Valine degradation	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
• beta-Alanine metabolism
• Propanoate metabolism
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Geraniol degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Tryptophan metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
benzoyl-CoA biosynthesis	3	3	1
2-methyl-branched fatty acid β-oxidation	14	10	3
adipate degradation	5	5	1
adipate biosynthesis	5	5	1
propanoyl-CoA degradation II	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
fatty acid β-oxidation IV (unsaturated, even number)	5	3	1
acrylate degradation I	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
L-leucine biosynthesis	6	6	1
β-alanine biosynthesis II	6	5	1
methyl ketone biosynthesis (engineered)	6	3	1
benzoyl-CoA degradation I (aerobic)	7	6	1
3-methylbutanol biosynthesis (engineered)	7	6	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
L-valine degradation I	8	6	1
phenylacetate degradation I (aerobic)	9	7	1
valproate β-oxidation	9	6	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
3-phenylpropanoate degradation	10	6	1
superpathway of phenylethylamine degradation	11	9	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	29	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
superpathway of branched chain amino acid biosynthesis	17	17	1
platensimycin biosynthesis	26	7	1