Experiment set16IT005 for Pseudomonas putida KT2440

Butanol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Butanol (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 2.4 generations
By: Mitchell Thompson on 9/5/19
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 Butanol in Pseudomonas putida KT2440

For carbon source Butanol across organisms

SEED Subsystems

Subsystem	#Specific
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
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• alpha-Linolenic acid metabolism
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Biosynthesis of plant hormones
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid elongation in mitochondria
• Synthesis and degradation of ketone bodies
• Lysine degradation
• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• Pyruvate metabolism
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Terpenoid biosynthesis
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetoacetate degradation (to acetyl CoA)	2	1	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	2
5,6-dehydrokavain biosynthesis (engineered)	10	6	4
glutaryl-CoA degradation	5	3	2
oleate β-oxidation	35	30	12
fatty acid salvage	6	6	2
ketolysis	3	3	1
benzoyl-CoA biosynthesis	3	3	1
pyruvate fermentation to butanol II (engineered)	6	4	2
polyhydroxybutanoate biosynthesis	3	2	1
4-oxopentanoate degradation	9	5	3
2-methyl-branched fatty acid β-oxidation	14	10	4
pyruvate fermentation to butanoate	7	3	2
pyruvate fermentation to hexanol (engineered)	11	8	3
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
pyruvate fermentation to butanol I	8	3	2
2-methylpropene degradation	8	2	2
valproate β-oxidation	9	7	2
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	2
4-hydroxybenzoate biosynthesis III (plants)	5	5	1
adipate degradation	5	5	1
ketogenesis	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
fatty acid β-oxidation VII (yeast peroxisome)	5	2	1
methyl tert-butyl ether degradation	10	2	2
pyruvate fermentation to acetone	5	1	1
isopropanol biosynthesis (engineered)	5	1	1
ethylbenzene degradation (anaerobic)	5	1	1
L-isoleucine degradation I	6	5	1
propanoate fermentation to 2-methylbutanoate	6	4	1
4-ethylphenol degradation (anaerobic)	6	2	1
L-glutamate degradation VII (to butanoate)	12	3	2
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
jasmonic acid biosynthesis	19	4	3
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	2
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
acetyl-CoA fermentation to butanoate	7	4	1
mevalonate pathway II (haloarchaea)	7	1	1
mevalonate pathway I (eukaryotes and bacteria)	7	1	1
L-tryptophan degradation III (eukaryotic)	15	3	2
glycerol degradation to butanol	16	9	2
2-deoxy-D-ribose degradation II	8	4	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	2
mevalonate pathway III (Thermoplasma)	8	1	1
isoprene biosynthesis II (engineered)	8	1	1
mevalonate pathway IV (archaea)	8	1	1
androstenedione degradation I (aerobic)	25	7	3
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	2
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	2
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
toluene degradation VI (anaerobic)	18	4	2
superpathway of testosterone and androsterone degradation	28	7	3
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)	10	4	1
3-phenylpropanoate degradation	10	4	1
L-lysine fermentation to acetate and butanoate	10	3	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	9	4
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	1
ethylmalonyl-CoA pathway	11	2	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	9	4
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
cannabinoid biosynthesis	13	6	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
1-butanol autotrophic biosynthesis (engineered)	27	19	2
androstenedione degradation II (anaerobic)	27	5	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
sitosterol degradation to androstenedione	18	1	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	2	1
superpathway of cholesterol degradation III (oxidase)	49	5	2
platensimycin biosynthesis	26	6	1
superpathway of ergosterol biosynthesis I	26	3	1
superpathway of cholesterol biosynthesis	38	3	1
superpathway of L-lysine degradation	43	23	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1