Experiment set28IT009 for Pseudomonas putida KT2440

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Betaine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + Betaine (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Mitchell Thompson on 11/16/20
Media components: 10 mM D-Glucose, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 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 15 genes in this experiment

For nitrogen source Betaine in Pseudomonas putida KT2440

For nitrogen source Betaine across organisms

SEED Subsystems

Subsystem #Specific
Choline and Betaine Uptake and Betaine Biosynthesis 6
Glutathione-dependent pathway of formaldehyde detoxification 2
Acetyl-CoA fermentation to Butyrate 1
Folate Biosynthesis 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
acetaldehyde biosynthesis I 1 1 1
glycine biosynthesis I 1 1 1
glycine betaine degradation III 7 7 4
ethanol degradation I 2 1 1
pyruvate fermentation to ethanol II 2 1 1
glycine betaine degradation I 8 6 3
glycine degradation 3 3 1
dTMP de novo biosynthesis (mitochondrial) 3 3 1
ethanol degradation II 3 3 1
formaldehyde oxidation II (glutathione-dependent) 3 3 1
L-leucine degradation III 3 2 1
L-valine degradation II 3 2 1
L-isoleucine degradation II 3 2 1
pyruvate fermentation to ethanol I 3 1 1
L-methionine degradation III 3 1 1
pyruvate fermentation to ethanol III 3 1 1
superpathway of L-serine and glycine biosynthesis I 4 4 1
phytol degradation 4 3 1
salidroside biosynthesis 4 3 1
creatinine degradation I 4 2 1
L-tyrosine degradation III 4 2 1
L-phenylalanine degradation III 4 2 1
glycine betaine degradation II (mammalian) 4 1 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
ethanolamine utilization 5 4 1
folate polyglutamylation 5 4 1
protein S-nitrosylation and denitrosylation 5 3 1
creatinine degradation II 5 3 1
acetylene degradation (anaerobic) 5 3 1
phenylethanol biosynthesis 5 3 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
leukotriene biosynthesis 6 2 1
noradrenaline and adrenaline degradation 13 8 2
3-methylbutanol biosynthesis (engineered) 7 6 1
serotonin degradation 7 4 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
folate transformations III (E. coli) 9 9 1
photorespiration III 9 6 1
photorespiration I 9 6 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
arachidonate metabolites biosynthesis 74 3 1