Experiment set29IT005 for Pseudomonas putida KT2440

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Propandiamine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + Propandiamine (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Matthias Schmidt on 4/13/21
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 43 genes in this experiment

For nitrogen source Propandiamine in Pseudomonas putida KT2440

For nitrogen source Propandiamine across organisms

SEED Subsystems

Subsystem #Specific
Arginine and Ornithine Degradation 4
Cobalt-zinc-cadmium resistance 4
Choline and Betaine Uptake and Betaine Biosynthesis 2
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 2
Conserved gene cluster associated with Met-tRNA formyltransferase 2
Folate Biosynthesis 2
Polyamine Metabolism 2
Tryptophan synthesis 2
Acid resistance mechanisms 1
Arginine Biosynthesis extended 1
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
D-gluconate and ketogluconates metabolism 1
DNA-binding regulatory proteins, strays 1
Fructose utilization 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Isobutyryl-CoA to Propionyl-CoA Module 1
Ketoisovalerate oxidoreductase 1
Methionine Biosynthesis 1
Phosphate metabolism 1
Proline, 4-hydroxyproline uptake and utilization 1
Pyruvate Alanine Serine Interconversions 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Respiratory dehydrogenases 1 1
Ribosome biogenesis bacterial 1
Valine degradation 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
putrescine biosynthesis II 3 3 3
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) 3 3 3
β-alanine degradation II 2 2 2
L-glutamine biosynthesis I 1 1 1
acetate conversion to acetyl-CoA 1 1 1
acetate and ATP formation from acetyl-CoA III 1 1 1
L-glutamine degradation I 1 1 1
arginine dependent acid resistance 1 1 1
ammonia assimilation cycle III 3 3 2
L-proline degradation I 3 3 2
ammonia assimilation cycle II 2 2 1
4-aminobenzoate biosynthesis I 2 2 1
indole-3-acetate biosynthesis III (bacteria) 2 2 1
L-glutamate biosynthesis I 2 2 1
putrescine biosynthesis I 2 2 1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway) 2 2 1
ammonia assimilation cycle I 2 2 1
L-homocysteine biosynthesis 2 2 1
putrescine degradation II 4 3 2
β-alanine degradation I 2 1 1
indole-3-acetate biosynthesis IV (bacteria) 2 1 1
acrylonitrile degradation I 2 1 1
superpathway of polyamine biosynthesis II 8 5 3
superpathway of acetate utilization and formation 3 3 1
ethanol degradation IV 3 3 1
ethanol degradation II 3 3 1
superpathway of ammonia assimilation (plants) 3 3 1
β-alanine biosynthesis II 6 5 2
L-arginine degradation I (arginase pathway) 3 2 1
L-aspartate degradation II (aerobic) 3 2 1
ethanol degradation III 3 2 1
L-isoleucine biosynthesis V 3 2 1
L-aspartate degradation III (anaerobic) 3 2 1
L-arginine degradation X (arginine monooxygenase pathway) 3 2 1
superpathway of acrylonitrile degradation 3 1 1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis 3 1 1
L-arginine biosynthesis II (acetyl cycle) 10 10 3
L-glutamate and L-glutamine biosynthesis 7 6 2
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 9 3
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
queuosine biosynthesis I (de novo) 4 4 1
L-methionine biosynthesis III 4 4 1
L-citrulline biosynthesis 8 7 2
superpathway of ornithine degradation 8 6 2
superpathway of putrescine biosynthesis 4 3 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
chitin deacetylation 4 2 1
spermidine biosynthesis III 4 1 1
ethene biosynthesis II (microbes) 4 1 1
superpathway of L-arginine and L-ornithine degradation 13 11 3
L-ornithine biosynthesis I 5 5 1
L-arginine degradation II (AST pathway) 5 5 1
2-methylcitrate cycle I 5 5 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 2
acrylate degradation I 5 3 1
queuosine biosynthesis III (queuosine salvage) 5 3 1
propanoyl-CoA degradation II 5 3 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II 5 2 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III 5 2 1
2-methylcitrate cycle II 6 5 1
superpathway of L-citrulline metabolism 12 9 2
superpathway of L-cysteine biosynthesis (fungi) 6 4 1
L-isoleucine biosynthesis IV 6 4 1
superpathway of bitter acids biosynthesis 18 3 3
adlupulone and adhumulone biosynthesis 6 1 1
(5R)-carbapenem carboxylate biosynthesis 6 1 1
lupulone and humulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
L-Nδ-acetylornithine biosynthesis 7 5 1
myo-inositol degradation I 7 1 1
2,4-dinitrotoluene degradation 7 1 1
L-valine degradation I 8 6 1
superpathway of polyamine biosynthesis I 8 5 1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis 8 1 1
superpathway of arginine and polyamine biosynthesis 17 14 2
L-arginine biosynthesis I (via L-ornithine) 9 9 1
L-arginine biosynthesis III (via N-acetyl-L-citrulline) 9 8 1
reductive glycine pathway of autotrophic CO2 fixation 9 5 1
cis-geranyl-CoA degradation 9 2 1
chloramphenicol biosynthesis 9 1 1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 8 1
superpathway of tetrahydrofolate biosynthesis 10 8 1
myo-, chiro- and scyllo-inositol degradation 10 1 1
superpathway of candicidin biosynthesis 11 4 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 1
superpathway of tetrahydrofolate biosynthesis and salvage 12 10 1
indole-3-acetate biosynthesis II 12 5 1
superpathway of chorismate metabolism 59 42 1