Experiment set3H34 for Shewanella amazonensis SB2B

L-Leucine nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + L-Leucine (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/24/2013
Media components: 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 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)
Growth plate: 511 C7, C8

Specific Phenotypes

For 8 genes in this experiment

For nitrogen source L-Leucine in Shewanella amazonensis SB2B

For nitrogen source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
Leucine Degradation and HMG-CoA Metabolism	3
Serine-glyoxylate cycle	3
Catechol branch of beta-ketoadipate pathway	2
Protocatechuate branch of beta-ketoadipate pathway	2
HMG CoA Synthesis	1
PnuC-like transporters	1
Potassium homeostasis	1
Thiamin biosynthesis	1
ZZ gjo need homes	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
• Synthesis and degradation of ketone bodies
• Geraniol degradation
• 1- and 2-Methylnaphthalene degradation
• Butanoate metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ketolysis	3	3	1
L-leucine degradation I	6	5	2
TCA cycle VI (Helicobacter)	9	7	1