Experiment set7IT046 for Pseudomonas putida KT2440

3-methyl-3-buten-1-ol 0.1 vol% carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 3-methyl-3-butenol (0.1 vol%)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.6 generations
By: Mitchell Thompson on 4/25/18
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 3-methyl-3-butenol in Pseudomonas putida KT2440

For carbon source 3-methyl-3-butenol across organisms

SEED Subsystems

Subsystem	#Specific
Leucine Degradation and HMG-CoA Metabolism	3
Serine-glyoxylate cycle	3
Catechol branch of beta-ketoadipate pathway	2
Protocatechuate branch of beta-ketoadipate pathway	2
DNA-binding regulatory proteins, strays	1
Glutathione-dependent pathway of formaldehyde detoxification	1
HMG CoA Synthesis	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
• Glycolysis / Gluconeogenesis
• Geraniol degradation
• Tyrosine metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Propanoate metabolism
• Butanoate metabolism
• Methane metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Synthesis and degradation of ketone bodies
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
phenylethylamine degradation II	2	2	1
ethanol degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation II	3	3	1
formaldehyde oxidation II (glutathione-dependent)	3	3	1
ketolysis	3	3	1
L-leucine degradation I	6	5	2
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine 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
phytol degradation	4	3	1
salidroside biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
ethanolamine utilization	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
acetylene degradation (anaerobic)	5	3	1
protein S-nitrosylation and denitrosylation	5	3	1
phenylethanol biosynthesis	5	3	1
(S)-propane-1,2-diol degradation	5	2	1
noradrenaline and adrenaline degradation	13	8	2
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
TCA cycle VI (Helicobacter)	9	7	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	1
superpathway of C1 compounds oxidation to CO2	12	5	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	1
heterolactic fermentation	18	12	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