Experiment set29IT031 for Pseudomonas putida KT2440

Valerolactone carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Valerolactone (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Matthias Schmidt on 4/13/21
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 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 12 genes in this experiment

For carbon source Valerolactone in Pseudomonas putida KT2440

For carbon source Valerolactone across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Hfl operon	1
Methylglyoxal Metabolism	1
Polyamine Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Universal GTPases	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine degradation V	2	2	1
glutarate degradation	2	2	1
phenylethylamine degradation I	2	2	1
phenylethylamine degradation II	2	2	1
phenylethanol degradation	2	1	1
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
putrescine degradation IV	3	2	1
styrene degradation	3	1	1
histamine degradation	3	1	1
putrescine degradation III	4	3	1
phytol degradation	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
D-arabinose degradation II	4	2	1
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
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
superpathway of ornithine degradation	8	6	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
photorespiration I	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
superpathway of phenylethylamine degradation	11	11	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of pentose and pentitol degradation	42	10	1