Experiment set7IT047 for Pseudomonas putida KT2440

3-methyl-3-buten-1-ol 0.25 vol% carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 3-methyl-3-butenol (0.25 vol%)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.9 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 18 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	4
Serine-glyoxylate cycle	3
Catechol branch of beta-ketoadipate pathway	2
HMG CoA Synthesis	2
Protocatechuate branch of beta-ketoadipate pathway	2
Biotin biosynthesis	1
Entner-Doudoroff Pathway	1
Glutathione-dependent pathway of formaldehyde detoxification	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1
Polyhydroxybutyrate metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
RNA processing and degradation, bacterial	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:

• Valine, leucine and isoleucine degradation
• Butanoate metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Propanoate metabolism
• Ascorbate and aldarate metabolism
• Geraniol degradation
• Tyrosine metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Methane metabolism
• Limonene and pinene degradation
• Fructose and mannose metabolism
• Synthesis and degradation of ketone bodies
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Ether lipid metabolism
• Sphingolipid metabolism
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• Ethylbenzene degradation
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• 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
phenylethylamine degradation II	2	2	2
acetaldehyde biosynthesis I	1	1	1
long-chain fatty acid activation	1	1	1
phytol degradation	4	3	3
ethanol degradation II	3	3	2
phenylethylamine degradation I	2	2	1
putrescine degradation V	2	2	1
3-methyl-branched fatty acid α-oxidation	6	3	3
ethanol degradation I	2	1	1
putrescine degradation I	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
phenylethanol degradation	2	1	1
linoleate biosynthesis II (animals)	2	1	1
ethylene glycol degradation	2	1	1
pyruvate fermentation to ethanol II	2	1	1
octane oxidation	5	4	2
sphingosine and sphingosine-1-phosphate metabolism	10	4	4
formaldehyde oxidation II (glutathione-dependent)	3	3	1
ethanol degradation IV	3	3	1
ketolysis	3	3	1
L-leucine degradation I	6	5	2
L-leucine degradation III	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
putrescine degradation IV	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
styrene degradation	3	1	1
pyruvate fermentation to ethanol I	3	1	1
pyruvate fermentation to ethanol III	3	1	1
histamine degradation	3	1	1
alkane biosynthesis II	3	1	1
L-methionine degradation III	3	1	1
oleate biosynthesis I (plants)	3	1	1
noradrenaline and adrenaline degradation	13	8	4
serotonin degradation	7	4	2
ceramide degradation by α-oxidation	7	2	2
salidroside biosynthesis	4	3	1
putrescine degradation III	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
L-phenylalanine degradation III	4	2	1
D-arabinose degradation II	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tyrosine degradation III	4	2	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	4
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
sporopollenin precursors biosynthesis	18	4	4
pyruvate fermentation to isobutanol (engineered)	5	4	1
ethanolamine utilization	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
acetylene degradation (anaerobic)	5	3	1
phenylethanol biosynthesis	5	3	1
protein S-nitrosylation and denitrosylation	5	3	1
(S)-propane-1,2-diol degradation	5	2	1
dopamine degradation	5	2	1
fatty acid salvage	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
alkane oxidation	6	1	1
stearate biosynthesis I (animals)	6	1	1
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glycol metabolism and degradation	7	6	1
capsaicin biosynthesis	7	3	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
limonene degradation IV (anaerobic)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
superpathway of ornithine degradation	8	6	1
2-deoxy-D-ribose degradation II	8	4	1
aromatic biogenic amine degradation (bacteria)	8	3	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
TCA cycle VI (Helicobacter)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	1
suberin monomers biosynthesis	20	4	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of phenylethylamine degradation	11	11	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of C1 compounds oxidation to CO2	12	5	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
L-tryptophan degradation V (side chain pathway)	13	1	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
mixed acid fermentation	16	12	1
cutin biosynthesis	16	1	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
superpathway of fatty acids biosynthesis (E. coli)	53	51	2
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
palmitate biosynthesis III	29	28	1
oleate β-oxidation	35	30	1
superpathway of pentose and pentitol degradation	42	10	1