Experiment set5IT086 for Pseudomonas putida KT2440

Vanillin carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Vanillin (5 mM) + Dimethyl Sulfoxide (0.5 vol%), pH=7
Culturing: Putida_ML5, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Jayashree on 27-Feb-17
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 28 genes in this experiment

For carbon source Vanillin in Pseudomonas putida KT2440

For carbon source Vanillin across organisms

SEED Subsystems

Subsystem	#Specific
Protocatechuate branch of beta-ketoadipate pathway	7
Molybdenum cofactor biosynthesis	6
Chloroaromatic degradation pathway	3
Catechol branch of beta-ketoadipate pathway	2
Glutathione-dependent pathway of formaldehyde detoxification	2
Multidrug Resistance Efflux Pumps	2
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	2
N-heterocyclic aromatic compound degradation	2
Transport of Molybdenum	2
Glycine cleavage system	1
Orphan regulatory proteins	1
Phenylpropanoid compound degradation	1
Purine Utilization	1
Soluble cytochromes and functionally related electron carriers	1
Triacylglycerol 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 hydroxylation
• 1- and 2-Methylnaphthalene degradation
• Fatty acid metabolism
• Geraniol degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• 2,4-Dichlorobenzoate degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Methane metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Toluene and xylene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• 3-Chloroacrylic acid degradation
• Styrene degradation
• Butanoate metabolism
• Retinol metabolism
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis II
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• 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
acetaldehyde biosynthesis I	1	1	1
protocatechuate degradation II (ortho-cleavage pathway)	4	4	3
aromatic compounds degradation via β-ketoadipate	9	9	5
catechol degradation III (ortho-cleavage pathway)	6	6	3
vanillin and vanillate degradation II	2	2	1
ethanol degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
acetoacetate degradation (to acetyl CoA)	2	1	1
toluene degradation III (aerobic) (via p-cresol)	11	7	5
superpathway of salicylate degradation	7	7	3
4-methylcatechol degradation (ortho cleavage)	7	5	3
5,6-dehydrokavain biosynthesis (engineered)	10	6	4
benzoyl-CoA biosynthesis	3	3	1
ethanol degradation II	3	3	1
ketolysis	3	3	1
formaldehyde oxidation II (glutathione-dependent)	3	3	1
molybdopterin biosynthesis	6	4	2
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
polyhydroxybutanoate biosynthesis	3	2	1
L-valine degradation II	3	2	1
pyruvate fermentation to ethanol I	3	1	1
pyruvate fermentation to ethanol III	3	1	1
L-methionine degradation III	3	1	1
catechol degradation to β-ketoadipate	4	4	1
salidroside biosynthesis	4	3	1
phytol degradation	4	3	1
2-deoxy-D-ribose degradation II	8	4	2
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
4-sulfocatechol degradation	4	2	1
oleate β-oxidation	35	30	8
valproate β-oxidation	9	7	2
2-methyl-branched fatty acid β-oxidation	14	10	3
adipate degradation	5	5	1
4-hydroxybenzoate biosynthesis III (plants)	5	5	1
adipate biosynthesis	5	4	1
ethanolamine utilization	5	4	1
gallate degradation II	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
glutaryl-CoA degradation	5	3	1
protein S-nitrosylation and denitrosylation	5	3	1
acetylene degradation (anaerobic)	5	3	1
ketogenesis	5	3	1
phenylethanol biosynthesis	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
(S)-propane-1,2-diol degradation	5	2	1
fatty acid β-oxidation VII (yeast peroxisome)	5	2	1
pyruvate fermentation to acetone	5	1	1
ethylbenzene degradation (anaerobic)	5	1	1
isopropanol biosynthesis (engineered)	5	1	1
pyruvate fermentation to hexanol (engineered)	11	8	2
fatty acid salvage	6	6	1
L-isoleucine degradation I	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
propanoate fermentation to 2-methylbutanoate	6	4	1
mandelate degradation to acetyl-CoA	18	11	3
superpathway of aerobic toluene degradation	30	13	5
4-ethylphenol degradation (anaerobic)	6	2	1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
jasmonic acid biosynthesis	19	4	3
noradrenaline and adrenaline degradation	13	8	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
fatty acid β-oxidation I (generic)	7	5	1
serotonin degradation	7	4	1
acetyl-CoA fermentation to butanoate	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	5
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
butanol and isobutanol biosynthesis (engineered)	8	3	1
pyruvate fermentation to butanol I	8	3	1
2-methylpropene degradation	8	2	1
mevalonate pathway IV (archaea)	8	1	1
isoprene biosynthesis II (engineered)	8	1	1
mevalonate pathway III (Thermoplasma)	8	1	1
androstenedione degradation I (aerobic)	25	7	3
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	2
phenylacetate degradation I (aerobic)	9	9	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
4-oxopentanoate degradation	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	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
3-phenylpropanoate degradation	10	4	1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)	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
superpathway of C1 compounds oxidation to CO2	12	5	1
L-glutamate degradation VII (to butanoate)	12	3	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
L-tryptophan degradation V (side chain pathway)	13	1	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
L-tryptophan degradation III (eukaryotic)	15	3	1
mixed acid fermentation	16	12	1
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
heterolactic fermentation	18	12	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
toluene degradation VI (anaerobic)	18	4	1
sitosterol degradation to androstenedione	18	1	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of anaerobic sucrose degradation	19	13	1
superpathway of N-acetylneuraminate degradation	22	12	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