Experiment set2H29 for Shewanella amazonensis SB2B

Minimal media with L-Glutamine as carbon source

Group: carbon source
Media: ShewMM_noCarbon + L-Glutamine (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/15/2013
Media components: 1.5 g/L Ammonium chloride, 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, 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: 505 E1,E2

Specific Phenotypes

For 10 genes in this experiment

For carbon source L-Glutamine in Shewanella amazonensis SB2B

For carbon source L-Glutamine across organisms

SEED Subsystems

Subsystem	#Specific
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Biosynthesis and gamma-glutamyl cycle	1
Mannose-sensitive hemagglutinin type 4 pilus	1
Utilization of glutathione as a sulphur source	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Lysine degradation
• Arginine and proline metabolism
• Taurine and hypotaurine metabolism
• Selenoamino acid metabolism
• Cyanoamino acid metabolism
• D-Glutamine and D-glutamate metabolism
• Glutathione metabolism
• Peptidoglycan biosynthesis
• Arachidonic acid metabolism
• Biotin metabolism
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine degradation I	1	1	1
glutathione degradation (DUG pathway)	2	2	1
L-glutamate biosynthesis I	2	2	1
ammonia assimilation cycle III	3	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
peptido-conjugates in tissue regeneration biosynthesis	17	6	3
γ-glutamyl cycle	6	5	1
leukotriene biosynthesis	6	2	1
L-glutamate and L-glutamine biosynthesis	7	6	1
L-citrulline biosynthesis	8	7	1
superpathway of L-citrulline metabolism	12	9	1
hypoglycin biosynthesis	14	4	1