Experiment set5S262 for Pseudomonas sp. RS175

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L-Carnitine hydrochloride 10 mM carbon source

Group: carbon source
Media: MME_noCarbon + L-Carnitine hydrochloride (10 mM)
Culturing: Pseudomonas_RS175_ML2, 96 deep well, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 11/17/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 6 genes in this experiment

For carbon source L-Carnitine hydrochloride in Pseudomonas sp. RS175

For carbon source L-Carnitine hydrochloride across organisms

SEED Subsystems

Subsystem #Specific
Choline and Betaine Uptake and Betaine Biosynthesis 1
HMG CoA Synthesis 1
Leucine Degradation and HMG-CoA Metabolism 1
Polyhydroxybutyrate metabolism 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
L-carnitine degradation III 3 3 3
D-carnitine degradation I 3 2 2
D-carnitine degradation II 2 1 1
benzoyl-CoA biosynthesis 3 3 1
oleate β-oxidation 35 30 8
valproate β-oxidation 9 6 2
adipate degradation 5 5 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 4 1
adipate biosynthesis 5 4 1
glutaryl-CoA degradation 5 3 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
pyruvate fermentation to hexanol (engineered) 11 7 2
fatty acid salvage 6 6 1
pyruvate fermentation to butanol II (engineered) 6 4 1
methyl ketone biosynthesis (engineered) 6 3 1
2-methyl-branched fatty acid β-oxidation 14 10 2
fatty acid β-oxidation I (generic) 7 5 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 4 1
pyruvate fermentation to butanoate 7 3 1
benzoyl-CoA degradation I (aerobic) 7 3 1
2-deoxy-D-ribose degradation II 8 4 1
pyruvate fermentation to butanol I 8 3 1
2-methylpropene degradation 8 2 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 1
phenylacetate degradation I (aerobic) 9 4 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 1
L-glutamate degradation V (via hydroxyglutarate) 10 6 1
3-phenylpropanoate degradation 10 3 1
methyl tert-butyl ether degradation 10 2 1
superpathway of phenylethylamine degradation 11 6 1
L-glutamate degradation VII (to butanoate) 12 3 1
androstenedione degradation I (aerobic) 25 6 2
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 5 1
androstenedione degradation II (anaerobic) 27 4 2
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
superpathway of cholesterol degradation I (cholesterol oxidase) 42 9 3
superpathway of testosterone and androsterone degradation 28 6 2
L-tryptophan degradation III (eukaryotic) 15 3 1
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 9 3
glycerol degradation to butanol 16 9 1
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 4 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 7 1
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 4 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 3 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 8 1
toluene degradation VI (anaerobic) 18 4 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 3 1
superpathway of cholesterol degradation III (oxidase) 49 5 2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 20 1
platensimycin biosynthesis 26 6 1
1-butanol autotrophic biosynthesis (engineered) 27 20 1