Experiment set28IT028 for Pseudomonas putida KT2440

spermidine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + spermidine (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Mitchell Thompson on 11/16/20
Media components: 10 mM D-Glucose, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 15 genes in this experiment

For nitrogen source spermidine in Pseudomonas putida KT2440

For nitrogen source spermidine across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	5
DNA-binding regulatory proteins, strays	1
Entner-Doudoroff Pathway	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Methylglyoxal Metabolism	1
Phosphate metabolism	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	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
• Valine, leucine and isoleucine degradation
• Propanoate metabolism
• Urea cycle and metabolism of amino groups
• Tryptophan metabolism
• beta-Alanine metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Glycerolipid metabolism
• Inositol phosphate metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

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