Experiment set29IT030 for Pseudomonas putida KT2440

5-Hydroxydodecanoate carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 5-Hydroxydodecanoate (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Matthias Schmidt on 4/13/21
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 14 genes in this experiment

For carbon source 5-Hydroxydodecanoate in Pseudomonas putida KT2440

For carbon source 5-Hydroxydodecanoate across organisms

SEED Subsystems

Subsystem	#Specific
Polyhydroxybutyrate metabolism	2
Biotin biosynthesis	1
Coenzyme A Biosynthesis	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:

• Fatty acid 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
• C21-Steroid hormone metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Bisphenol A degradation
• beta-Alanine 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
• Propanoate metabolism
• 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 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
long-chain fatty acid activation	1	1	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	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
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	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
L-leucine degradation I	6	5	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
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (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