Experiment set13H17 for Pseudomonas stutzeri RCH2

Putrescine Dihydrochloride nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + Putrescine Dihydrochloride (5 mM), pH=7.2
Culturing: psRCH2_ML7c, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 2.7 generations
By: Kelly on 2/27/2014
Media components: 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 5 genes in this experiment

For nitrogen source Putrescine Dihydrochloride in Pseudomonas stutzeri RCH2

For nitrogen source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	3
Entner-Doudoroff Pathway	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	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
• Tryptophan metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine biosynthesis I	1	1	1
ammonia assimilation cycle I	2	2	1
putrescine degradation V	2	2	1
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
ammonia assimilation cycle II	2	1	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
ammonia assimilation cycle III	3	3	1
putrescine degradation IV	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
histamine degradation	3	1	1
superpathway of ornithine degradation	8	6	2
phytol degradation	4	3	1
putrescine degradation II	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
L-arginine degradation VIII (arginine oxidase pathway)	4	1	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	1	1
putrescine degradation III	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
D-arabinose degradation II	4	1	1
octane oxidation	5	3	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	2
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
superpathway of L-arginine and L-ornithine degradation	13	8	2
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	5	1
L-glutamate and L-glutamine biosynthesis	7	5	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	5	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of pentose and pentitol degradation	42	7	1