Experiment set12IT003 for Pseudomonas putida KT2440

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Crotonic acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Crotonic acid (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Putida_ML5_JBEI, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: Matthew Incha on 12-Feb-19
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 6 genes in this experiment

For carbon source Crotonic acid in Pseudomonas putida KT2440

For carbon source Crotonic acid across organisms

SEED Subsystems

Subsystem #Specific
Protocatechuate branch of beta-ketoadipate pathway 4
Catechol branch of beta-ketoadipate pathway 2
Chloroaromatic degradation pathway 2
Thiamin biosynthesis 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
glyphosate degradation II 1 1 1
protocatechuate degradation II (ortho-cleavage pathway) 4 4 2
3-oxoadipate degradation 2 2 1
aromatic compounds degradation via β-ketoadipate 9 9 3
catechol degradation III (ortho-cleavage pathway) 6 6 2
superpathway of salicylate degradation 7 7 2
4-methylcatechol degradation (ortho cleavage) 7 5 2
toluene degradation III (aerobic) (via p-cresol) 11 7 3
catechol degradation to β-ketoadipate 4 4 1
4-sulfocatechol degradation 4 2 1
gallate degradation II 5 4 1
thiazole component of thiamine diphosphate biosynthesis II 7 4 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
mandelate degradation to acetyl-CoA 18 11 2
superpathway of aerobic toluene degradation 30 13 3
superpathway of thiamine diphosphate biosynthesis II 11 8 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 19 3