Experiment set39IT048 for Pseudomonas putida KT2440

1,3-Hexanediol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 1,3-Hexanediol (10 mM)
Culturing: Putida_ML5_JBEI, 24-well plate, Aerobic, at 30 (C), shaken=200 rpm
By: Allie Pearson on 28-Sep
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 16 genes in this experiment

For carbon source 1,3-Hexanediol in Pseudomonas putida KT2440

For carbon source 1,3-Hexanediol across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	2
Butanol Biosynthesis	2
Polyhydroxybutyrate metabolism	2
Isoleucine degradation	1
Multidrug Resistance Efflux Pumps	1
Ribosome biogenesis bacterial	1
Ton and Tol transport systems	1
Trehalose Biosynthesis	1
Valine degradation	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:

• Fatty acid metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Geraniol degradation
• Tryptophan metabolism
• Caprolactam degradation
• Biosynthesis of plant hormones
• Fatty acid elongation in mitochondria
• Valine, leucine and isoleucine degradation
• Lysine degradation
• alpha-Linolenic acid metabolism
• Propanoate metabolism
• Limonene and pinene degradation
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Bile acid biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Tyrosine metabolism
• beta-Alanine metabolism
• Starch and sucrose metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• Ethylbenzene degradation
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of siderophore group nonribosomal peptides

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
trehalose biosynthesis IV	1	1	1
fatty acid β-oxidation III (unsaturated, odd number)	1	1	1
benzoyl-CoA biosynthesis	3	3	2
fatty acid β-oxidation IV (unsaturated, even number)	5	4	3
fatty acid β-oxidation I (generic)	7	5	4
oleate β-oxidation (thioesterase-dependent, yeast)	2	2	1
oleate β-oxidation	35	30	16
adipate degradation	5	5	2
adipate biosynthesis	5	4	2
glutaryl-CoA degradation	5	3	2
fatty acid β-oxidation II (plant peroxisome)	5	3	2
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent)	5	3	2
pyruvate fermentation to hexanol (engineered)	11	8	4
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	4
2-methyl-branched fatty acid β-oxidation	14	10	5
fatty acid salvage	6	6	2
L-isoleucine degradation I	6	5	2
valproate β-oxidation	9	7	3
propanoate fermentation to 2-methylbutanoate	6	4	2
pyruvate fermentation to butanol II (engineered)	6	4	2
methyl ketone biosynthesis (engineered)	6	3	2
oleate β-oxidation (reductase-dependent, yeast)	3	1	1
Arg/N-end rule pathway (eukaryotic)	14	8	4
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	2
benzoyl-CoA degradation I (aerobic)	7	3	2
pyruvate fermentation to butanoate	7	3	2
L-valine degradation I	8	6	2
pyruvate fermentation to butanol I	8	3	2
oleate β-oxidation (isomerase-dependent, yeast)	4	1	1
phenylacetate degradation I (aerobic)	9	9	2
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	2
4-hydroxybenzoate biosynthesis III (plants)	5	5	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	2
3-phenylpropanoate degradation	10	4	2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
superpathway of phenylethylamine degradation	11	11	2
6-gingerol analog biosynthesis (engineered)	6	3	1
L-glutamate degradation VII (to butanoate)	12	3	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
Spodoptera littoralis pheromone biosynthesis	22	4	3
L-tryptophan degradation III (eukaryotic)	15	3	2
glycerol degradation to butanol	16	9	2
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	2
2-methylpropene degradation	8	2	1
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
toluene degradation VI (anaerobic)	18	4	2
methyl tert-butyl ether degradation	10	2	1
gallate degradation III (anaerobic)	11	3	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
androstenedione degradation I (aerobic)	25	7	2
platensimycin biosynthesis	26	6	2
(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 testosterone and androsterone degradation	28	7	2
superpathway of cholesterol degradation I (cholesterol oxidase)	42	9	3
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	9	3
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	2	1
superpathway of cholesterol degradation III (oxidase)	49	5	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1