Experiment set11IT004 for Burkholderia phytofirmans PsJN

Azelaic acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Azelaic acid (10 mM)
Culturing: BFirm_ML3_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.4 generations
By: Allie Pearson on 8/26/19
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 4 genes in this experiment

For carbon source Azelaic acid in Burkholderia phytofirmans PsJN

For carbon source Azelaic acid across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	1
Butanol Biosynthesis	1
Isoleucine degradation	1
Polyhydroxybutyrate metabolism	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
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• Butanoate metabolism
• Caprolactam degradation
• Biosynthesis of plant hormones
• Fatty acid elongation in mitochondria
• Valine, leucine and isoleucine degradation
• alpha-Linolenic acid metabolism
• Propanoate metabolism
• Limonene and pinene degradation
• Bile acid biosynthesis
• Tyrosine metabolism
• beta-Alanine metabolism
• Ethylbenzene degradation
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
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	3	3
fatty acid β-oxidation I (generic)	7	5	4
oleate β-oxidation (thioesterase-dependent, yeast)	2	1	1
oleate β-oxidation	35	29	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	2	2
pyruvate fermentation to hexanol (engineered)	11	7	4
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	4
2-methyl-branched fatty acid β-oxidation	14	9	5
fatty acid salvage	6	5	2
valproate β-oxidation	9	6	3
L-isoleucine degradation I	6	4	2
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
benzoyl-CoA degradation I (aerobic)	7	6	2
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	2
pyruvate fermentation to butanoate	7	3	2
L-valine degradation I	8	5	2
pyruvate fermentation to butanol I	8	4	2
oleate β-oxidation (isomerase-dependent, yeast)	4	1	1
phenylacetate degradation I (aerobic)	9	9	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	5	2
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	2
4-hydroxybenzoate biosynthesis III (plants)	5	3	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	3	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	2
3-phenylpropanoate degradation	10	5	2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
superpathway of phenylethylamine degradation	11	11	2
6-gingerol analog biosynthesis (engineered)	6	2	1
L-glutamate degradation VII (to butanoate)	12	3	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	8	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	10	2
glycerol degradation to butanol	16	11	2
2-methylpropene degradation	8	2	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	10	2
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	2
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	2
toluene degradation VI (anaerobic)	18	3	2
methyl tert-butyl ether degradation	10	3	1
gallate degradation III (anaerobic)	11	5	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
androstenedione degradation I (aerobic)	25	6	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	4	2
superpathway of cholesterol degradation I (cholesterol oxidase)	42	9	3
superpathway of testosterone and androsterone degradation	28	6	2
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	3	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	3	1
superpathway of cholesterol degradation III (oxidase)	49	5	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	18	1