Experiment set2IT029 for Pseudomonas fluorescens FW300-N2E2

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Carnitine Hydrochloride carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Carnitine Hydrochloride (20 mM), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/9/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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)

Specific Phenotypes

For 27 genes in this experiment

For carbon source Carnitine Hydrochloride in Pseudomonas fluorescens FW300-N2E2

For carbon source Carnitine Hydrochloride across organisms

SEED Subsystems

Subsystem #Specific
Choline and Betaine Uptake and Betaine Biosynthesis 8
Glutathione-dependent pathway of formaldehyde detoxification 2
Glycine and Serine Utilization 2
Leucine Degradation and HMG-CoA Metabolism 2
Polyhydroxybutyrate metabolism 2
Serine-glyoxylate cycle 2
Acetyl-CoA fermentation to Butyrate 1
Catechol branch of beta-ketoadipate pathway 1
Ethanolamine utilization 1
Fermentations: Lactate 1
Fermentations: Mixed acid 1
Folate Biosynthesis 1
Glycine Biosynthesis 1
HMG CoA Synthesis 1
L-rhamnose utilization 1
LMPTP YwlE cluster 1
Lactate utilization 1
MLST 1
Photorespiration (oxidative C2 cycle) 1
Propanediol utilization 1
Protocatechuate branch of beta-ketoadipate pathway 1
Pyrroloquinoline Quinone biosynthesis 1
Pyruvate Alanine Serine Interconversions 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Serine Biosynthesis 1
Threonine anaerobic catabolism gene cluster 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 betaine degradation III 7 7 7
L-carnitine degradation III 3 3 3
L-serine degradation 3 3 3
glycine biosynthesis I 1 1 1
γ-butyrobetaine degradation II 1 1 1
acetaldehyde biosynthesis I 1 1 1
glycine betaine degradation I 8 6 6
L-cysteine degradation II 3 3 2
D-serine degradation 3 3 2
glycine degradation 3 3 2
L-tryptophan degradation II (via pyruvate) 3 2 2
D-carnitine degradation I 3 2 2
ethanol degradation I 2 2 1
acetate and ATP formation from acetyl-CoA I 2 2 1
pyruvate fermentation to ethanol II 2 1 1
sulfoacetaldehyde degradation I 2 1 1
D-carnitine degradation II 2 1 1
ethanolamine utilization 5 5 2
acetylene degradation (anaerobic) 5 4 2
(S)-propane-1,2-diol degradation 5 2 2
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis 5 2 2
ketolysis 3 3 1
superpathway of acetate utilization and formation 3 3 1
dTMP de novo biosynthesis (mitochondrial) 3 3 1
ethanol degradation II 3 3 1
pyruvate fermentation to acetate II 3 3 1
benzoyl-CoA biosynthesis 3 3 1
formaldehyde oxidation II (glutathione-dependent) 3 3 1
L-methionine biosynthesis II 6 5 2
pyruvate fermentation to acetate IV 3 2 1
L-leucine degradation III 3 2 1
pyruvate fermentation to acetate VII 3 2 1
pyruvate fermentation to ethanol III 3 2 1
pyruvate fermentation to ethanol I 3 2 1
L-valine degradation II 3 2 1
L-isoleucine degradation II 3 2 1
pyruvate fermentation to acetate I 3 2 1
L-methionine degradation III 3 1 1
superpathway of L-serine and glycine biosynthesis I 4 4 1
pyruvate fermentation to acetate and (S)-lactate I 4 3 1
phytol degradation 4 3 1
L-mimosine degradation 8 4 2
pyruvate fermentation to acetate and lactate II 4 2 1
L-phenylalanine degradation III 4 2 1
salidroside biosynthesis 4 2 1
L-tyrosine degradation III 4 2 1
glutathione-mediated detoxification I 8 3 2
sulfolactate degradation II 4 1 1
creatinine degradation I 4 1 1
L-carnitine biosynthesis 4 1 1
glycine betaine degradation II (mammalian) 4 1 1
oleate β-oxidation 35 30 8
valproate β-oxidation 9 7 2
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 2
superpathway of fermentation (Chlamydomonas reinhardtii) 9 5 2
purine nucleobases degradation II (anaerobic) 24 16 5
adipate degradation 5 5 1
adipate biosynthesis 5 4 1
folate polyglutamylation 5 4 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 4 1
protein S-nitrosylation and denitrosylation 5 3 1
glutaryl-CoA degradation 5 3 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
phenylethanol biosynthesis 5 2 1
creatinine degradation II 5 1 1
folate transformations II (plants) 11 10 2
pyruvate fermentation to hexanol (engineered) 11 7 2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 7 3
peptido-conjugates in tissue regeneration biosynthesis 17 6 3
fatty acid salvage 6 6 1
pyruvate fermentation to butanol II (engineered) 6 4 1
L-threonine degradation I 6 4 1
methyl ketone biosynthesis (engineered) 6 3 1
methanogenesis from acetate 6 2 1
superpathway of taurine degradation 6 2 1
superpathway of sulfolactate degradation 6 2 1
leukotriene biosynthesis 6 2 1
noradrenaline and adrenaline degradation 13 8 2
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 5 2
3-methylbutanol biosynthesis (engineered) 7 6 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
serotonin degradation 7 4 1
benzoyl-CoA degradation I (aerobic) 7 3 1
pyruvate fermentation to butanoate 7 3 1
acetyl-CoA fermentation to butanoate 7 3 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 2
mixed acid fermentation 16 12 2
2-deoxy-D-ribose degradation II 8 4 1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) 8 3 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
pyruvate fermentation to butanol I 8 3 1
2-methylpropene degradation 8 2 1
folate transformations III (E. coli) 9 9 1
heterolactic fermentation 18 15 2
TCA cycle VI (Helicobacter) 9 7 1
photorespiration III 9 5 1
photorespiration I 9 5 1
phenylacetate degradation I (aerobic) 9 4 1
superpathway of L-alanine fermentation (Stickland reaction) 9 4 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 1
gliotoxin biosynthesis 9 2 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 14 2
L-glutamate degradation V (via hydroxyglutarate) 10 6 1
photorespiration II 10 6 1
3-phenylpropanoate degradation 10 5 1
L-lysine fermentation to acetate and butanoate 10 4 1
methyl tert-butyl ether degradation 10 3 1
superpathway of N-acetylneuraminate degradation 22 13 2
superpathway of phenylethylamine degradation 11 6 1
gallate degradation III (anaerobic) 11 3 1
superpathway of C1 compounds oxidation to CO2 12 5 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
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 4 1
L-tryptophan degradation V (side chain pathway) 13 1 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
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 4 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 3 1
superpathway of L-threonine metabolism 18 13 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 9 1
toluene degradation VI (anaerobic) 18 4 1
superpathway of anaerobic sucrose degradation 19 14 1
superpathway of methanogenesis 21 2 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
superpathway of L-lysine degradation 43 19 1
arachidonate metabolites biosynthesis 74 3 1