Experiment set3H35 for Shewanella amazonensis SB2B

Compare to:

L-Lysine nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + L-Lysine (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 D1, D2

Specific Phenotypes

For 12 genes in this experiment

For nitrogen source L-Lysine in Shewanella amazonensis SB2B

For nitrogen source L-Lysine across organisms

SEED Subsystems

Subsystem #Specific
Arginine and Ornithine Degradation 4
Polyamine Metabolism 2
Ammonia assimilation 1
Arginine Biosynthesis extended 1
Glycogen metabolism 1
Lysine Biosynthesis DAP Pathway 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-arginine degradation II (AST pathway) 5 5 3
putrescine biosynthesis III 2 1 1
L-ornithine biosynthesis II 3 3 1
L-proline biosynthesis III (from L-ornithine) 3 3 1
L-arginine degradation I (arginase pathway) 3 2 1
glycogen biosynthesis I (from ADP-D-Glucose) 4 4 1
L-arginine degradation VI (arginase 2 pathway) 4 3 1
superpathway of putrescine biosynthesis 4 2 1
L-ornithine biosynthesis I 5 5 1
L-arginine degradation XIII (reductive Stickland reaction) 5 4 1
L-Nδ-acetylornithine biosynthesis 7 5 1
L-citrulline biosynthesis 8 7 1
superpathway of ornithine degradation 8 6 1
superpathway of polyamine biosynthesis II 8 6 1
superpathway of polyamine biosynthesis I 8 5 1
superpathway of arginine and polyamine biosynthesis 17 14 2
L-lysine biosynthesis I 9 9 1
L-arginine biosynthesis I (via L-ornithine) 9 9 1
L-arginine biosynthesis III (via N-acetyl-L-citrulline) 9 8 1
L-arginine biosynthesis II (acetyl cycle) 10 9 1
starch biosynthesis 10 6 1
superpathway of L-citrulline metabolism 12 9 1
superpathway of L-arginine and L-ornithine degradation 13 8 1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis 16 3 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 17 1
aspartate superpathway 25 23 1