Experiment set28IT005 for Pseudomonas putida KT2440

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Choline chloride nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + Choline chloride (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 16 genes in this experiment

For nitrogen source Choline chloride in Pseudomonas putida KT2440

For nitrogen source Choline chloride across organisms

SEED Subsystems

Subsystem #Specific
Choline and Betaine Uptake and Betaine Biosynthesis 9
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
glycine biosynthesis I 1 1 1
glycine betaine degradation III 7 7 4
glycine betaine biosynthesis I (Gram-negative bacteria) 2 2 1
choline degradation I 2 2 1
glycine betaine biosynthesis II (Gram-positive bacteria) 2 2 1
glycine betaine degradation I 8 6 3
choline-O-sulfate degradation 3 3 1
glycine degradation 3 3 1
dTMP de novo biosynthesis (mitochondrial) 3 3 1
superpathway of L-serine and glycine biosynthesis I 4 4 1
creatinine degradation I 4 2 1
glycine betaine degradation II (mammalian) 4 1 1
folate polyglutamylation 5 4 1
creatinine degradation II 5 3 1
folate transformations II (plants) 11 10 2
peptido-conjugates in tissue regeneration biosynthesis 17 6 3
leukotriene biosynthesis 6 2 1
folate transformations III (E. coli) 9 9 1
photorespiration I 9 6 1
photorespiration III 9 6 1
gliotoxin biosynthesis 9 2 1
photorespiration II 10 7 1
folate transformations I 13 9 1
formaldehyde assimilation I (serine pathway) 13 7 1
purine nucleobases degradation II (anaerobic) 24 16 1
arachidonate metabolites biosynthesis 74 3 1