Experiment set5IT084 for Pseudomonas putida KT2440

Levulinic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Levulinic Acid (20 mM), 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 14 genes in this experiment

For carbon source Levulinic Acid in Pseudomonas putida KT2440

For carbon source Levulinic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Serine-glyoxylate cycle	3
Catechol branch of beta-ketoadipate pathway	2
Leucine Degradation and HMG-CoA Metabolism	2
Methylcitrate cycle	2
Protocatechuate branch of beta-ketoadipate pathway	2
Acetyl-CoA fermentation to Butyrate	1
Butanol Biosynthesis	1
DNA-binding regulatory proteins, strays	1
Flavodoxin	1
Polyhydroxybutyrate metabolism	1
Propionate-CoA to Succinate Module	1
Purine conversions	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Butanoate metabolism
• Fatty acid metabolism
• Synthesis and degradation of ketone bodies
• Geraniol degradation
• Benzoate degradation via CoA ligation
• Fatty acid elongation in mitochondria
• Purine metabolism
• Lysine degradation
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Propanoate metabolism
• Ethylbenzene degradation
• Terpenoid biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
ketolysis	3	3	2
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
benzoyl-CoA biosynthesis	3	3	1
pyruvate fermentation to butanol II (engineered)	6	4	2
polyhydroxybutanoate biosynthesis	3	2	1
pyruvate fermentation to butanoate	7	3	2
pyruvate fermentation to hexanol (engineered)	11	8	3
oleate β-oxidation	35	30	9
(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-oxopentanoate degradation	9	5	2
2-methyl-branched fatty acid β-oxidation	14	10	3
4-hydroxybenzoate biosynthesis III (plants)	5	5	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
ketogenesis	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
isopropanol biosynthesis (engineered)	5	1	1
pyruvate fermentation to acetone	5	1	1
ethylbenzene degradation (anaerobic)	5	1	1
fatty acid salvage	6	6	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 I (eukaryotes and bacteria)	7	1	1
mevalonate pathway II (haloarchaea)	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
isoprene biosynthesis II (engineered)	8	1	1
mevalonate pathway IV (archaea)	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
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	2
TCA cycle VI (Helicobacter)	9	7	1
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-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	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 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