Experiment set15IT079 for Pseudomonas putida KT2440

Sodium butyrate carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Sodium butyrate (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Mitchell Thompson on 10/22/19
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 8 genes in this experiment

For carbon source Sodium butyrate in Pseudomonas putida KT2440

For carbon source Sodium butyrate across organisms

SEED Subsystems

Subsystem	#Specific
2-Ketogluconate Utilization	1
Acetyl-CoA fermentation to Butyrate	1
Butanol Biosynthesis	1
Polyhydroxybutyrate metabolism	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via CoA ligation
• Geraniol degradation
• Tyrosine metabolism
• alpha-Linolenic acid metabolism
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-oxopentanoate degradation	9	5	2
adipate degradation	5	5	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
glutaryl-CoA degradation	5	3	1
fatty acid salvage	6	6	1
pyruvate fermentation to butanol II (engineered)	6	4	1
pyruvate fermentation to butanoate	7	3	1
pyruvate fermentation to butanol I	8	3	1
2-methylpropene degradation	8	2	1
oleate β-oxidation	35	30	4
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	1
methyl tert-butyl ether degradation	10	2	1
pyruvate fermentation to hexanol (engineered)	11	8	1
L-glutamate degradation VII (to butanoate)	12	3	1
cannabinoid biosynthesis	13	6	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
2-methyl-branched fatty acid β-oxidation	14	10	1
L-tryptophan degradation III (eukaryotic)	15	3	1
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
toluene degradation VI (anaerobic)	18	4	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1