Experiment set6S37 for Pseudomonas sp. RS175

L-Carnitine hydrochloride carbon source

Group: carbon source
Media: MME_noCarbon + L-Carnitine hydrochloride (10 mM)
Culturing: Pseudomonas_RS175_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C)
By: Andrew Frank on 1/31/23
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 5 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
Leucine Degradation and HMG-CoA Metabolism	2
Catechol branch of beta-ketoadipate pathway	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
HMG CoA Synthesis	1
Polyhydroxybutyrate metabolism	1
Protocatechuate branch of beta-ketoadipate pathway	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Butanoate metabolism
• Benzoate degradation via CoA ligation
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Biosynthesis of plant hormones
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Synthesis and degradation of ketone bodies
• Bile acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Lysine degradation
• Tryptophan metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-carnitine degradation III	3	3	2
D-carnitine degradation II	2	1	1
ketolysis	3	3	1
benzoyl-CoA biosynthesis	3	3	1
D-carnitine degradation I	3	2	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
TCA cycle VI (Helicobacter)	9	7	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