Experiment set10IT059 for Pseudomonas putida KT2440

Decanoic acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Decanoic acid (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.3 generations
By: Mitchell Thompson on 10/18/18
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 24 genes in this experiment

For carbon source Decanoic acid in Pseudomonas putida KT2440

For carbon source Decanoic acid across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Arginine and Ornithine Degradation	2
Biotin biosynthesis	2
Polyamine Metabolism	2
n-Phenylalkanoic acid degradation	2
Acid resistance mechanisms	1
Bacterial Cell Division	1
Lipid A modifications	1
Methionine Biosynthesis	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
Peptidoglycan Biosynthesis	1
Polyhydroxybutyrate metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Phenylalanine metabolism
• Lipopolysaccharide biosynthesis
• Benzoate degradation via CoA ligation
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Methionine metabolism
• Cysteine metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Ethylbenzene degradation
• Styrene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine biosynthesis II	3	3	3
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	3
long-chain fatty acid activation	1	1	1
arginine dependent acid resistance	1	1	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
L-homocysteine biosynthesis	2	2	1
putrescine biosynthesis I	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
acrylonitrile degradation I	2	1	1
indole-3-acetate biosynthesis IV (bacteria)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
superpathway of polyamine biosynthesis II	8	5	3
fatty acid salvage	6	6	2
polyhydroxydecanoate biosynthesis	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
superpathway of acrylonitrile degradation	3	1	1
oleate biosynthesis I (plants)	3	1	1
L-methionine biosynthesis III	4	4	1
superpathway of putrescine biosynthesis	4	3	1
phytol degradation	4	3	1
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
spermidine biosynthesis III	4	1	1
sporopollenin precursors biosynthesis	18	4	4
adipate degradation	5	5	1
octane oxidation	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	2	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
superpathway of L-cysteine biosynthesis (fungi)	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
superpathway of polyamine biosynthesis I	8	5	1
2-deoxy-D-ribose degradation II	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
oleate β-oxidation	35	30	4
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	8	1
suberin monomers biosynthesis	20	4	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
2-methyl-branched fatty acid β-oxidation	14	10	1
salinosporamide A biosynthesis	15	4	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of arginine and polyamine biosynthesis	17	14	1
superpathway of fatty acids biosynthesis (E. coli)	53	51	2
palmitate biosynthesis III	29	28	1