Experiment set3IT071 for Burkholderia phytofirmans PsJN

Carnitine Hydrochloride nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Carnitine Hydrochloride (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 4.5 generations
By: Mark on 1/27/2016
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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: Plate 2 A3

Specific Phenotypes

For 8 genes in this experiment

For nitrogen source Carnitine Hydrochloride in Burkholderia phytofirmans PsJN

For nitrogen source Carnitine Hydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	3
Choline and Betaine Uptake and Betaine Biosynthesis	3
Polyhydroxybutyrate metabolism	2
Butanol Biosynthesis	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• alpha-Linolenic acid metabolism
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-carnitine degradation III	3	3	3
D-carnitine degradation I	3	2	2
D-carnitine degradation II	2	1	1
glycine betaine degradation I	8	6	2
(2S)-ethylmalonyl-CoA biosynthesis	4	3	1
creatinine degradation I	4	1	1
creatinine degradation II	5	2	1
acetyl-CoA fermentation to butanoate	7	6	1
ethylmalonyl-CoA pathway	11	3	1