Experiment set4S871 for Pseudomonas aeruginosa PA14

carbon source 10 mM Putrescine Dihydrochloride

Group: carbon source
Media: Hans_Basal_Media + Putrescine Dihydrochloride (10 mM), pH=7
Culturing: Paeruginosa_PA14_ML18, 96 deep-well block, Aerobic, at 30 (C), shaken=700 rpm
By: Hans and Ryan on 6/3/25
Media components: 0.03 M PIPES sesquisodium salt, 0.1 g/L Potassium Chloride, 0.01 g/L Sodium Chloride, 0.01 g/L Calcium chloride dihydrate, 0.1 g/L Magnesium chloride hexahydrate, 0.1 g/L Sodium sulfate, 0.25 g/L Ammonium chloride, 0.1 g/L Disodium phosphate, DL vitamins (0.0002 mg/L biotin, 0.0002 mg/L Folic Acid, 0.001 mg/L Pyridoxine HCl, 0.0005 mg/L Riboflavin, 0.0005 mg/L Thiamine HCl, 0.0005 mg/L Nicotinic Acid, 0.0005 mg/L calcium pantothenate, 1e-05 mg/L Cyanocobalamin, 0.0005 mg/L 4-Aminobenzoic acid, 0.0005 mg/L Lipoic acid), Sulfur-free DL minerals (0.0003 g/L Magnesium chloride hexahydrate, 0.00015 g/L Nitrilotriacetic acid disodium salt, 0.0001 g/L Sodium Chloride, 5e-05 g/L Manganese (II) chloride tetrahydrate, 1e-05 g/L Cobalt chloride hexahydrate, 1.3e-05 g/L Zinc chloride, 1e-05 g/L Calcium chloride dihydrate, 1e-05 g/L Iron (II) chloride tetrahydrate, 2.5e-06 g/L Nickel (II) chloride hexahydrate, 2e-06 g/L Aluminum chloride hydrate, 1e-06 g/L copper (II) chloride dihydrate, 1e-06 g/L Boric Acid, 1e-06 g/L Sodium Molybdate Dihydrate, 3e-05 g/L Sodium selenite pentahydrate, 2.5e-05 g/L Sodium tungstate dihydrate)

Specific Phenotypes

For 14 genes in this experiment

For carbon source Putrescine Dihydrochloride in Pseudomonas aeruginosa PA14

For carbon source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	4
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1
Pyruvate Alanine Serine Interconversions	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
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Lysine degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• Propanoate metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Alanine and aspartate metabolism
• Methionine metabolism
• Geraniol degradation
• Histidine metabolism
• Aminophosphonate metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine degradation V	2	2	2
β-alanine degradation II	2	2	1
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
putrescine degradation IV	3	2	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
histamine degradation	3	1	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	4	1
putrescine degradation III	4	3	1
L-arginine degradation VIII (arginine oxidase pathway)	4	3	1
phytol degradation	4	3	1
superpathway of ornithine degradation	8	5	2
D-arabinose degradation II	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
putrescine degradation II	4	2	1
octane oxidation	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	5	2
dopamine degradation	5	2	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	2
β-alanine biosynthesis II	6	4	1
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	8	2
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	5	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
superpathway of pentose and pentitol degradation	42	11	1