Experiment set10IT052 for Pseudomonas putida KT2440

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1-Pentanol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 1-Pentanol (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.9 generations
By: Mitchell Thompson on 10/18/18
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 26 genes in this experiment

For carbon source 1-Pentanol in Pseudomonas putida KT2440

For carbon source 1-Pentanol across organisms

SEED Subsystems

Subsystem #Specific
Arginine and Ornithine Degradation 2
Multidrug Resistance Efflux Pumps 2
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 2
Polyamine Metabolism 2
Acid resistance mechanisms 1
Biotin biosynthesis 1
Fermentations: Mixed acid 1
Glutathione: Redox cycle 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
HMG CoA Synthesis 1
Leucine Degradation and HMG-CoA Metabolism 1
Orphan regulatory proteins 1
Phosphate metabolism 1
Polyhydroxybutyrate metabolism 1
Proteasome bacterial 1
Proteolysis in bacteria, ATP-dependent 1
Triacylglycerol metabolism 1
n-Phenylalkanoic acid 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
acetaldehyde biosynthesis I 1 1 1
arginine dependent acid resistance 1 1 1
long-chain fatty acid activation 1 1 1
phenylethylamine degradation II 2 2 1
putrescine biosynthesis I 2 2 1
indole-3-acetate biosynthesis III (bacteria) 2 2 1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway) 2 2 1
phytol degradation 4 3 2
acrylonitrile degradation I 2 1 1
ethanol degradation I 2 1 1
pyruvate fermentation to ethanol II 2 1 1
γ-linolenate biosynthesis II (animals) 2 1 1
linoleate biosynthesis II (animals) 2 1 1
indole-3-acetate biosynthesis IV (bacteria) 2 1 1
superpathway of polyamine biosynthesis II 8 5 3
fatty acid salvage 6 6 2
ethanol degradation II 3 3 1
L-arginine degradation X (arginine monooxygenase pathway) 3 2 1
L-isoleucine degradation II 3 2 1
glutathione-peroxide redox reactions 3 2 1
L-valine degradation II 3 2 1
L-leucine degradation III 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
oleate biosynthesis I (plants) 3 1 1
superpathway of acrylonitrile degradation 3 1 1
pyruvate fermentation to ethanol I 3 1 1
pyruvate fermentation to ethanol III 3 1 1
L-methionine degradation III 3 1 1
alkane biosynthesis II 3 1 1
superpathway of putrescine biosynthesis 4 3 1
salidroside biosynthesis 4 3 1
phospholipid remodeling (phosphatidylethanolamine, yeast) 4 2 1
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
wax esters biosynthesis II 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
phosphatidylcholine acyl editing 4 1 1
cytidine-5'-diphosphate-glycerol biosynthesis 4 1 1
spermidine biosynthesis III 4 1 1
sporopollenin precursors biosynthesis 18 4 4
adipate degradation 5 5 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
ethanolamine utilization 5 4 1
octane oxidation 5 4 1
phenylethanol biosynthesis 5 3 1
acetylene degradation (anaerobic) 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
(S)-propane-1,2-diol degradation 5 2 1
stearate biosynthesis II (bacteria and plants) 6 5 1
stearate biosynthesis IV 6 4 1
6-gingerol analog biosynthesis (engineered) 6 3 1
stearate biosynthesis I (animals) 6 1 1
noradrenaline and adrenaline degradation 13 8 2
3-methylbutanol biosynthesis (engineered) 7 6 1
serotonin degradation 7 4 1
capsaicin biosynthesis 7 3 1
ceramide degradation by α-oxidation 7 2 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
superpathway of polyamine biosynthesis I 8 5 1
2-deoxy-D-ribose degradation II 8 4 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
oleate β-oxidation 35 30 4
superpathway of fermentation (Chlamydomonas reinhardtii) 9 4 1
suberin monomers biosynthesis 20 4 2
superpathway of fatty acid biosynthesis II (plant) 43 38 4
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 9 1
indole-3-acetate biosynthesis II 12 5 1
superpathway of L-arginine and L-ornithine degradation 13 11 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 4 1
L-tryptophan degradation V (side chain pathway) 13 1 1
2-methyl-branched fatty acid β-oxidation 14 10 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
mixed acid fermentation 16 12 1
cutin biosynthesis 16 1 1
superpathway of arginine and polyamine biosynthesis 17 14 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
superpathway of fatty acids biosynthesis (E. coli) 53 51 2
palmitate biosynthesis III 29 28 1