Experiment set2H47 for Shewanella amazonensis SB2B

Minimal media with Putrescine Dihydrochloride as carbon source

Group: carbon source
Media: ShewMM_noCarbon + Putrescine Dihydrochloride (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: 508 A3,A4

Specific Phenotypes

For 17 genes in this experiment

For carbon source Putrescine Dihydrochloride in Shewanella amazonensis SB2B

For carbon source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Bacterial Chemotaxis	2
Bacterial hemoglobins	1
Biogenesis of c-type cytochromes	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Flagellar motility	1
Folate Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Menaquinone and Phylloquinone Biosynthesis	1
Methylcitrate cycle	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Periplasmic disulfide interchange	1
Polyamine Metabolism	1
Propionate-CoA to Succinate Module	1
Tryptophan synthesis	1
Two-component regulatory systems in Campylobacter	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Propanoate metabolism
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Methionine metabolism
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• Aminophosphonate metabolism
• Nucleotide sugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Butanoate metabolism
• Folate biosynthesis
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of phenylpropanoids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine degradation I	1	1	1
putrescine degradation V	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
4-aminobutanoate degradation III	2	2	1
L-glutamate biosynthesis I	2	2	1
putrescine degradation II	4	3	2
4-aminobutanoate degradation II	2	1	1
4-aminobutanoate degradation I	2	1	1
ammonia assimilation cycle III	3	3	1
superpathway of 4-aminobutanoate degradation	3	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	3
superpathway of ornithine degradation	8	6	2
GABA shunt II	4	3	1
GABA shunt I	4	2	1
L-arginine degradation VIII (arginine oxidase pathway)	4	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	1	1
superpathway of L-arginine and L-ornithine degradation	13	8	3
2-methylcitrate cycle I	5	5	1
L-lysine degradation IV	5	2	1
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	4	1
L-lysine degradation X	6	2	1
L-lysine degradation III	6	1	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	7	1
L-glutamate and L-glutamine biosynthesis	7	6	1
4-aminobutanoate degradation V	7	3	1
L-lysine degradation I	7	1	1
L-citrulline biosynthesis	8	7	1
L-valine degradation I	8	6	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	9	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	8	1
superpathway of demethylmenaquinol-9 biosynthesis	9	8	1
valproate β-oxidation	9	6	1
chloramphenicol biosynthesis	9	1	1
superpathway of menaquinol-8 biosynthesis I	10	10	1
superpathway of menaquinol-7 biosynthesis	10	9	1
superpathway of menaquinol-13 biosynthesis	10	9	1
superpathway of menaquinol-10 biosynthesis	10	9	1
superpathway of menaquinol-6 biosynthesis	10	9	1
superpathway of menaquinol-9 biosynthesis	10	9	1
superpathway of menaquinol-11 biosynthesis	10	9	1
superpathway of menaquinol-12 biosynthesis	10	9	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
superpathway of candicidin biosynthesis	11	2	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of phylloquinol biosynthesis	15	8	1
nicotine degradation I (pyridine pathway)	17	4	1
superpathway of chorismate metabolism	59	50	2
oleate β-oxidation	35	33	1
superpathway of L-lysine degradation	43	8	1