Experiment set12IT049 for Pseudomonas putida KT2440

Delta-Dodecalactone carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Delta-Dodecalactone (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Putida_ML5_JBEI, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: Matthew Incha on 12-Feb-19
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 24 genes in this experiment

For carbon source Delta-Dodecalactone in Pseudomonas putida KT2440

For carbon source Delta-Dodecalactone across organisms

SEED Subsystems

Subsystem	#Specific
Polyhydroxybutyrate metabolism	2
Biotin biosynthesis	1
Coenzyme A Biosynthesis	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Purine conversions	1
Ribosome biogenesis 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:

• Glycine, serine and threonine metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Alkaloid biosynthesis I
• Biosynthesis of unsaturated fatty acids
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• C21-Steroid hormone metabolism
• Purine metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Bisphenol A degradation
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Linoleic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Ethylbenzene degradation
• Pantothenate and CoA biosynthesis
• Retinol metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of type II polyketide backbone
• Biosynthesis of type II polyketide products
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
long-chain fatty acid activation	1	1	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
polyhydroxydecanoate biosynthesis	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
phosphopantothenate biosynthesis I	4	4	1
phytol degradation	4	3	1
phosphopantothenate biosynthesis III (archaea)	4	2	1
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
sporopollenin precursors biosynthesis	18	4	4
octane oxidation	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
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
stearate biosynthesis I (animals)	6	1	1
capsaicin biosynthesis	7	3	1
ceramide degradation by α-oxidation	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
2-deoxy-D-ribose degradation II	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of coenzyme A biosynthesis I (bacteria)	9	8	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
suberin monomers biosynthesis	20	4	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
salinosporamide A biosynthesis	15	4	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of fatty acids biosynthesis (E. coli)	53	51	2
palmitate biosynthesis III	29	28	1
oleate β-oxidation	35	30	1