Experiment set3IT056 for Burkholderia phytofirmans PsJN

L-Lysine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Lysine (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 5.8 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 1 A3

Specific Phenotypes

For 7 genes in this experiment

For nitrogen source L-Lysine in Burkholderia phytofirmans PsJN

For nitrogen source L-Lysine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	3
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-lactaldehyde degradation (aerobic)	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
ethanol degradation III	3	2	1
methylglyoxal degradation V	3	2	1
hypotaurine degradation	3	2	1
methylglyoxal degradation IV	3	1	1
histamine degradation	3	1	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
putrescine degradation III	4	2	1
NAD salvage pathway II (PNC IV cycle)	5	5	1
mitochondrial NADPH production (yeast)	5	3	1
octane oxidation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
lactate biosynthesis (archaea)	5	2	1
dopamine degradation	5	2	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
L-rhamnose degradation II	8	5	1
superpathway of methylglyoxal degradation	8	4	1
aromatic biogenic amine degradation (bacteria)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of fucose and rhamnose degradation	12	4	1