Experiment set6IT063 for Pseudomonas putida KT2440

Vanillic Acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Vanillic Acid (5 mM)
Culturing: Putida_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.8 generations
By: Mitch on 12/8/17
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 6 genes in this experiment

For carbon source Vanillic Acid in Pseudomonas putida KT2440

For carbon source Vanillic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Protocatechuate branch of beta-ketoadipate pathway	4
Chloroaromatic degradation pathway	2
Catechol branch of beta-ketoadipate pathway	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via hydroxylation
• 1- and 2-Methylnaphthalene degradation
• Geraniol degradation
• Histidine metabolism
• Phenylalanine metabolism
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Tyrosine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Toluene and xylene degradation
• 2,4-Dichlorobenzoate degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Styrene degradation
• Butanoate metabolism
• Methane metabolism
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-oxoadipate degradation	2	2	2
vanillin and vanillate degradation II	2	2	1
acetoacetate degradation (to acetyl CoA)	2	1	1
5,6-dehydrokavain biosynthesis (engineered)	10	6	4
catechol degradation III (ortho-cleavage pathway)	6	6	2
ketolysis	3	3	1
benzoyl-CoA biosynthesis	3	3	1
polyhydroxybutanoate biosynthesis	3	2	1
superpathway of salicylate degradation	7	7	2
4-methylcatechol degradation (ortho cleavage)	7	5	2
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
oleate β-oxidation	35	30	8
aromatic compounds degradation via β-ketoadipate	9	9	2
valproate β-oxidation	9	7	2
2-methyl-branched fatty acid β-oxidation	14	10	3
4-hydroxybenzoate biosynthesis III (plants)	5	5	1
adipate degradation	5	5	1
adipate biosynthesis	5	4	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
ketogenesis	5	3	1
glutaryl-CoA degradation	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
fatty acid β-oxidation VII (yeast peroxisome)	5	2	1
isopropanol biosynthesis (engineered)	5	1	1
ethylbenzene degradation (anaerobic)	5	1	1
pyruvate fermentation to acetone	5	1	1
pyruvate fermentation to hexanol (engineered)	11	8	2
toluene degradation III (aerobic) (via p-cresol)	11	7	2
fatty acid salvage	6	6	1
L-isoleucine degradation I	6	5	1
propanoate fermentation to 2-methylbutanoate	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
4-ethylphenol degradation (anaerobic)	6	2	1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
jasmonic acid biosynthesis	19	4	3
fatty acid β-oxidation I (generic)	7	5	1
acetyl-CoA fermentation to butanoate	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
pyruvate fermentation to butanoate	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
mevalonate pathway II (haloarchaea)	7	1	1
mevalonate pathway I (eukaryotes and bacteria)	7	1	1
2-deoxy-D-ribose degradation II	8	4	1
pyruvate fermentation to butanol I	8	3	1
2-methylpropene degradation	8	2	1
mevalonate pathway III (Thermoplasma)	8	1	1
mevalonate pathway IV (archaea)	8	1	1
isoprene biosynthesis II (engineered)	8	1	1
androstenedione degradation I (aerobic)	25	7	3
phenylacetate degradation I (aerobic)	9	9	1
mandelate degradation to acetyl-CoA	18	11	2
4-oxopentanoate degradation	9	5	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
superpathway of testosterone and androsterone degradation	28	7	3
L-glutamate degradation V (via hydroxyglutarate)	10	5	1
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
methyl tert-butyl ether degradation	10	2	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	9	4
superpathway of phenylethylamine degradation	11	11	1
(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
L-glutamate degradation VII (to butanoate)	12	3	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
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
superpathway of aerobic toluene degradation	30	13	2
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
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	2
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
toluene degradation VI (anaerobic)	18	4	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
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
platensimycin biosynthesis	26	6	1
superpathway of ergosterol biosynthesis I	26	3	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of cholesterol biosynthesis	38	3	1
superpathway of L-lysine degradation	43	23	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1