Experiment set1IT030 for Pseudomonas fluorescens GW456-L13

Putrescine Dihydrochloride carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Putrescine Dihydrochloride (20 mM), pH=7
Culturing: pseudo13_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/10/2015
Media components: 0.25 g/L Ammonium chloride, 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)

Specific Phenotypes

For 9 genes in this experiment

For carbon source Putrescine Dihydrochloride in Pseudomonas fluorescens GW456-L13

For carbon source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Biogenesis of cbb3-type cytochrome c oxidases	1
DNA-replication	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1
Polyamine Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Terminal cytochrome C oxidases	1
Transcription factors bacterial	1
Universal stress protein family	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
• Purine metabolism
• Puromycin biosynthesis
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Trinitrotoluene degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

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