Experiment set3H16 for Shewanella amazonensis SB2B

L-Aspartic Acid nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + L-Aspartic Acid (6 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: 510 D3, D4

Specific Phenotypes

For 11 genes in this experiment

For nitrogen source L-Aspartic Acid in Shewanella amazonensis SB2B

For nitrogen source L-Aspartic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Lactose and Galactose Uptake and Utilization	1
Mannose-sensitive hemagglutinin type 4 pilus	1
PnuC-like transporters	1
Potassium homeostasis	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Thiamin biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Geraniol degradation
• Lysine biosynthesis
• Arginine and proline metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-galactose detoxification	3	2	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	1	1
L-arginine degradation VIII (arginine oxidase pathway)	4	1	1
D-galactose degradation I (Leloir pathway)	5	4	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	7	1
stachyose degradation	7	3	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	9	1
superpathway of demethylmenaquinol-9 biosynthesis	9	8	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	8	1
superpathway of menaquinol-8 biosynthesis I	10	10	1
superpathway of menaquinol-11 biosynthesis	10	9	1
superpathway of menaquinol-12 biosynthesis	10	9	1
superpathway of menaquinol-7 biosynthesis	10	9	1
superpathway of menaquinol-13 biosynthesis	10	9	1
superpathway of menaquinol-6 biosynthesis	10	9	1
superpathway of menaquinol-9 biosynthesis	10	9	1
superpathway of menaquinol-10 biosynthesis	10	9	1
superpathway of phylloquinol biosynthesis	15	8	1
superpathway of chorismate metabolism	59	50	1