Experiment set3IT015 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 4 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	3
Aromatic amino acid interconversions with aryl acids	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine and Serine Utilization	1
Leucine Biosynthesis	1
Threonine anaerobic catabolism gene cluster	1
Threonine 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 biosynthesis
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Pyruvate metabolism
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-methionine degradation II	3	2	2
L-threonine degradation I	6	5	3
L-threonine degradation V	2	1	1
2-oxobutanoate degradation II	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
L-isoleucine biosynthesis V	3	3	1
L-valine degradation III (oxidative Stickland reaction)	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	2	1
L-leucine degradation V (oxidative Stickland reaction)	3	2	1
superpathway of branched chain amino acid biosynthesis	17	17	4
superpathway of L-isoleucine biosynthesis I	13	13	3
hypoglycin biosynthesis	14	4	3
L-leucine biosynthesis	6	6	1
superpathway of L-threonine metabolism	18	15	3
L-isoleucine biosynthesis IV	6	5	1
3-methylbutanol biosynthesis (engineered)	7	6	1
cyclosporin A biosynthesis	15	2	1