Experiment set29IT013 for Pseudomonas putida KT2440

Caprolactam nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + Caprolactam (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: 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 13 genes in this experiment

For nitrogen source Caprolactam in Pseudomonas putida KT2440

For nitrogen source Caprolactam across organisms

SEED Subsystems

Subsystem	#Specific
Cobalt-zinc-cadmium resistance	3
Hydantoin metabolism	2
2-Ketogluconate Utilization	1
Polyamine Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
oleate β-oxidation (thioesterase-dependent, yeast)	2	2	1
4-aminobutanoate degradation II	2	2	1
4-aminobutanoate degradation III	2	2	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	2
superpathway of 4-aminobutanoate degradation	3	3	1
L-lysine degradation IV	5	5	1
creatinine degradation II	5	3	1
L-lysine degradation X	6	5	1
L-lysine degradation III	6	2	1
L-lysine degradation I	7	5	1
4-hydroxyphenylacetate degradation	8	2	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
nicotine degradation II (pyrrolidine pathway)	11	6	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
nicotine degradation I (pyridine pathway)	17	5	1
oleate β-oxidation	35	30	1
superpathway of L-lysine degradation	43	23	1