Experiment set4IT095 for Pseudomonas fluorescens FW300-N1B4

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Carnitine Hydrochloride nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + Carnitine Hydrochloride (5 mM), pH=7
Culturing: pseudo1_N1B4_ML1, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/16/2014
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Growth plate: Nplate1 B4

Specific Phenotypes

For 10 genes in this experiment

For nitrogen source Carnitine Hydrochloride in Pseudomonas fluorescens FW300-N1B4

For nitrogen source Carnitine Hydrochloride across organisms

SEED Subsystems

Subsystem #Specific
Choline and Betaine Uptake and Betaine Biosynthesis 4
Folate Biosynthesis 1
Glycine Biosynthesis 1
Glycine and Serine Utilization 1
L-rhamnose utilization 1
LMPTP YwlE cluster 1
Lactate utilization 1
Photorespiration (oxidative C2 cycle) 1
Serine-glyoxylate cycle 1
Serine 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
glycine biosynthesis I 1 1 1
L-carnitine degradation III 3 3 2
glycine betaine degradation III 7 7 4
D-carnitine degradation II 2 1 1
glycine betaine degradation I 8 6 3
benzoyl-CoA biosynthesis 3 3 1
dTMP de novo biosynthesis (mitochondrial) 3 3 1
glycine degradation 3 3 1
D-carnitine degradation I 3 2 1
superpathway of L-serine and glycine biosynthesis I 4 4 1
creatinine degradation I 4 1 1
glycine betaine degradation II (mammalian) 4 1 1
oleate β-oxidation 35 30 8
valproate β-oxidation 9 7 2
adipate degradation 5 5 1
adipate biosynthesis 5 4 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 4 1
folate polyglutamylation 5 4 1
glutaryl-CoA degradation 5 3 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
creatinine degradation II 5 1 1
folate transformations II (plants) 11 10 2
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 11 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
pyruvate fermentation to butanol I 8 4 1
2-methylpropene degradation 8 2 1
folate transformations III (E. coli) 9 9 1
photorespiration I 9 6 1
photorespiration III 9 6 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
photorespiration II 10 7 1
L-glutamate degradation V (via hydroxyglutarate) 10 6 1
methyl tert-butyl ether degradation 10 3 1
3-phenylpropanoate degradation 10 3 1
superpathway of phenylethylamine degradation 11 6 1
L-glutamate degradation VII (to butanoate) 12 3 1
androstenedione degradation I (aerobic) 25 6 2
folate transformations I 13 9 1
formaldehyde assimilation I (serine pathway) 13 6 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 6 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 10 1
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 4 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 8 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 9 1
toluene degradation VI (anaerobic) 18 4 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 3 1
purine nucleobases degradation II (anaerobic) 24 16 1
superpathway of cholesterol degradation III (oxidase) 49 5 2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 19 1
platensimycin biosynthesis 26 6 1
1-butanol autotrophic biosynthesis (engineered) 27 19 1