Experiment set5H20 for Shewanella oneidensis MR-1

Putrescine Dihydrochloride nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + Putrescine Dihydrochloride (10 mM), pH=7
Culturing: MR1_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.0 generations
By: Adam on 8/21/2013
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)

Specific Phenotypes

For 8 genes in this experiment

For nitrogen source Putrescine Dihydrochloride in Shewanella oneidensis MR-1

For nitrogen source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycogen metabolism	1
Methylglyoxal Metabolism	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
• Glutamate metabolism
• Butanoate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Tyrosine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Starch and sucrose metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Propanoate metabolism
• Limonene and pinene degradation
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobutanoate degradation III	2	2	2
L-glutamine biosynthesis I	1	1	1
putrescine degradation II	4	3	3
ammonia assimilation cycle II	2	2	1
ammonia assimilation cycle I	2	2	1
superpathway of ornithine degradation	8	6	4
4-aminobutanoate degradation I	2	1	1
putrescine degradation V	2	1	1
L-lactaldehyde degradation (aerobic)	2	1	1
putrescine degradation I	2	1	1
4-aminobutanoate degradation II	2	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	5
L-lysine degradation IV	5	2	2
superpathway of L-arginine and L-ornithine degradation	13	8	5
ammonia assimilation cycle III	3	3	1
superpathway of ammonia assimilation (plants)	3	3	1
methylglyoxal degradation V	3	2	1
putrescine degradation IV	3	2	1
L-lysine degradation III	6	2	2
L-lysine degradation X	6	2	2
L-aspartate degradation II (aerobic)	3	1	1
superpathway of 4-aminobutanoate degradation	3	1	1
L-aspartate degradation III (anaerobic)	3	1	1
methylglyoxal degradation IV	3	1	1
L-lysine degradation I	7	2	2
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
GABA shunt II	4	3	1
GABA shunt I	4	2	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	1	1
L-arginine degradation VIII (arginine oxidase pathway)	4	1	1
L-ornithine biosynthesis I	5	5	1
L-arginine biosynthesis II (acetyl cycle)	10	9	2
lactate biosynthesis (archaea)	5	2	1
L-glutamate and L-glutamine biosynthesis	7	6	1
4-aminobutanoate degradation V	7	2	1
L-valine degradation I	8	7	1
superpathway of methylglyoxal degradation	8	4	1
L-rhamnose degradation II	8	2	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
starch biosynthesis	10	6	1
superpathway of fucose and rhamnose degradation	12	3	1
superpathway of arginine and polyamine biosynthesis	17	13	1
nicotine degradation I (pyridine pathway)	17	4	1
superpathway of L-lysine degradation	43	8	2