Experiment set8IT003 for Pseudomonas fluorescens FW300-N2E2

L-Lysine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Lysine (20 mM)
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
Growth: about 4.9 generations
By: Mark on 1/21/2016
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)

Specific Phenotypes

For 11 genes in this experiment

For nitrogen source L-Lysine in Pseudomonas fluorescens FW300-N2E2

For nitrogen source L-Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Lysine degradation	4
Arginine and Ornithine Degradation	3
D-gluconate and ketogluconates metabolism	1
Entner-Doudoroff Pathway	1
Polyamine Metabolism	1
Respiratory dehydrogenases 1	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine degradation
• Pentose phosphate pathway
• Glutamate metabolism
• Alanine and aspartate metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Retinol metabolism
• Limonene and pinene degradation
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-lysine degradation IV	5	5	3
indole-3-acetate biosynthesis III (bacteria)	2	2	1
4-aminobutanoate degradation II	2	2	1
4-aminobutanoate degradation III	2	2	1
4-aminobutanoate degradation I	2	1	1
superpathway of 4-aminobutanoate degradation	3	2	1
GABA shunt II	4	2	1
GABA shunt I	4	1	1
glucose and glucose-1-phosphate degradation	5	4	1
glucose degradation (oxidative)	5	4	1
L-lysine degradation X	6	5	1
L-lysine degradation III	6	2	1
L-lysine degradation I	7	4	1
L-ascorbate biosynthesis VIII (engineered pathway)	7	3	1
4-aminobutanoate degradation V	7	2	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
superpathway of L-lysine degradation	43	19	3
nicotine degradation I (pyridine pathway)	17	5	1