Experiment set2H17 for Shewanella amazonensis SB2B

Minimal media with a-Ketoglutaric acid disodium salt hydrate as carbon source

Group: carbon source
Media: ShewMM_noCarbon + a-Ketoglutaric acid disodium salt hydrate (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 A5,A6

Specific Phenotypes

For 15 genes in this experiment

For carbon source a-Ketoglutaric acid disodium salt hydrate in Shewanella amazonensis SB2B

For carbon source a-Ketoglutaric acid disodium salt hydrate across organisms

SEED Subsystems

Subsystem	#Specific
Isobutyryl-CoA to Propionyl-CoA Module	1
Methylcitrate cycle	1
Polyamine Metabolism	1
Propionate-CoA to Succinate Module	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine-glyoxylate cycle	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Propanoate metabolism
• Valine, leucine and isoleucine degradation
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Purine metabolism
• Alanine and aspartate metabolism
• beta-Alanine metabolism
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Folate biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine degradation II	2	2	2
β-alanine degradation I	2	1	1
2-methylcitrate cycle I	5	5	1
propanoyl-CoA degradation II	5	2	1
acrylate degradation I	5	2	1
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	4	1
myo-inositol degradation I	7	1	1
2,4-dinitrotoluene degradation	7	1	1
L-valine degradation I	8	6	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
gluconeogenesis I	13	13	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1