Experiment set6IT056 for Pseudomonas putida KT2440

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Cholinium lysinate carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Cholinium lysinate (0.5 vol%)
Culturing: Putida_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.1 generations
By: Mitch on 12/8/17
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 16 genes in this experiment

For carbon source Cholinium lysinate in Pseudomonas putida KT2440

For carbon source Cholinium lysinate across organisms

SEED Subsystems

Subsystem #Specific
Choline and Betaine Uptake and Betaine Biosynthesis 7
Lysine degradation 2
Acetyl-CoA fermentation to Butyrate 1
Folate Biosynthesis 1
Glutathione-dependent pathway of formaldehyde detoxification 1
Glycine Biosynthesis 1
Glycine and Serine Utilization 1
LMPTP YwlE cluster 1
Photorespiration (oxidative C2 cycle) 1
Pyrroloquinoline Quinone biosynthesis 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 betaine biosynthesis II (Gram-positive bacteria) 2 2 2
choline degradation I 2 2 2
glycine betaine biosynthesis I (Gram-negative bacteria) 2 2 2
acetaldehyde biosynthesis I 1 1 1
glycine biosynthesis I 1 1 1
choline-O-sulfate degradation 3 3 2
ethanol degradation II 3 3 2
glycine betaine degradation III 7 7 4
phytol degradation 4 3 2
β-alanine biosynthesis I 2 1 1
pyruvate fermentation to ethanol II 2 1 1
β-alanine biosynthesis IV 2 1 1
ethanol degradation I 2 1 1
glycine betaine degradation I 8 6 3
ethanol degradation IV 3 3 1
glycine degradation 3 3 1
formaldehyde oxidation II (glutathione-dependent) 3 3 1
dTMP de novo biosynthesis (mitochondrial) 3 3 1
ethanol degradation III 3 2 1
hypotaurine degradation 3 2 1
L-leucine degradation III 3 2 1
L-valine degradation II 3 2 1
glycine betaine biosynthesis III (plants) 3 2 1
L-isoleucine degradation II 3 2 1
pyruvate fermentation to ethanol III 3 1 1
pyruvate fermentation to ethanol I 3 1 1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia) 3 1 1
L-methionine degradation III 3 1 1
histamine degradation 3 1 1
noradrenaline and adrenaline degradation 13 8 4
serotonin degradation 7 4 2
superpathway of L-serine and glycine biosynthesis I 4 4 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 3 1
putrescine degradation III 4 3 1
salidroside biosynthesis 4 3 1
L-tyrosine degradation III 4 2 1
choline degradation IV 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
creatinine degradation I 4 2 1
L-phenylalanine degradation III 4 2 1
glycine betaine degradation II (mammalian) 4 1 1
dimethylsulfoniopropanoate biosynthesis II (Spartina) 4 1 1
folate polyglutamylation 5 4 1
octane oxidation 5 4 1
ethanolamine utilization 5 4 1
mitochondrial NADPH production (yeast) 5 4 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
protein S-nitrosylation and denitrosylation 5 3 1
creatinine degradation II 5 3 1
phenylethanol biosynthesis 5 3 1
acetylene degradation (anaerobic) 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
dopamine degradation 5 2 1
(S)-propane-1,2-diol degradation 5 2 1
folate transformations II (plants) 11 10 2
peptido-conjugates in tissue regeneration biosynthesis 17 6 3
3-methyl-branched fatty acid α-oxidation 6 3 1
leukotriene biosynthesis 6 2 1
alkane oxidation 6 1 1
3-methylbutanol biosynthesis (engineered) 7 6 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 7 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
aromatic biogenic amine degradation (bacteria) 8 3 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
folate transformations III (E. coli) 9 9 1
L-lysine degradation V 9 9 1
photorespiration III 9 6 1
photorespiration I 9 6 1
L-lysine degradation II (L-pipecolate pathway) 9 5 1
superpathway of fermentation (Chlamydomonas reinhardtii) 9 4 1
gliotoxin biosynthesis 9 2 1
photorespiration II 10 7 1
superpathway of C1 compounds oxidation to CO2 12 5 1
folate transformations I 13 9 1
formaldehyde assimilation I (serine pathway) 13 7 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 4 1
L-tryptophan degradation V (side chain pathway) 13 1 1
mixed acid fermentation 16 12 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 6 1
heterolactic fermentation 18 12 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 14 1
superpathway of anaerobic sucrose degradation 19 13 1
superpathway of N-acetylneuraminate degradation 22 12 1
purine nucleobases degradation II (anaerobic) 24 16 1
superpathway of L-lysine degradation 43 23 1
arachidonate metabolites biosynthesis 74 3 1