Experiment set12IT050 for Pseudomonas putida KT2440

Delta-Decalactone carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Delta-Decalactone (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 46 genes in this experiment

For carbon source Delta-Decalactone in Pseudomonas putida KT2440

For carbon source Delta-Decalactone across organisms

SEED Subsystems

Subsystem	#Specific
Oxidative stress	3
Glycine and Serine Utilization	2
Photorespiration (oxidative C2 cycle)	2
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Alginate metabolism	1
Bacterial Cell Division	1
Biotin biosynthesis	1
Entner-Doudoroff Pathway	1
Folate Biosynthesis	1
Formate hydrogenase	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine Biosynthesis	1
Glycine cleavage system	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
LMPTP YwlE cluster	1
Methylglyoxal Metabolism	1
Peptidoglycan Biosynthesis	1
Polyamine Metabolism	1
Polyhydroxybutyrate metabolism	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Ribosome biogenesis bacterial	1
Serine-glyoxylate cycle	1
Serine 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:

• Limonene and pinene degradation
• Benzoate degradation via CoA ligation
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Methane metabolism
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Pyrimidine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Arginine and proline metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Cyanoamino acid metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• One carbon pool by folate
• Reductive carboxylate cycle (CO2 fixation)
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
glycine biosynthesis I	1	1	1
phenylethylamine degradation I	2	2	1
putrescine degradation V	2	2	1
phenylethylamine degradation II	2	2	1
oleate β-oxidation (thioesterase-dependent, yeast)	2	2	1
phytol degradation	4	3	2
3-methyl-branched fatty acid α-oxidation	6	3	3
ethylene glycol degradation	2	1	1
linoleate biosynthesis II (animals)	2	1	1
putrescine degradation I	2	1	1
phenylethanol degradation	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	2
octane oxidation	5	4	2
sphingosine and sphingosine-1-phosphate metabolism	10	4	4
fatty acid salvage	6	6	2
glycine degradation	3	3	1
ethanol degradation II	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
ethanol degradation IV	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
polyhydroxydecanoate biosynthesis	3	2	1
putrescine degradation IV	3	2	1
histamine degradation	3	1	1
oleate biosynthesis I (plants)	3	1	1
styrene degradation	3	1	1
alkane biosynthesis II	3	1	1
ceramide degradation by α-oxidation	7	2	2
superpathway of L-serine and glycine biosynthesis I	4	4	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
putrescine degradation III	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
D-arabinose degradation II	4	2	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	4
phosphatidylcholine acyl editing	4	1	1
glycine betaine degradation II (mammalian)	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
wax esters biosynthesis II	4	1	1
sporopollenin precursors biosynthesis	18	4	4
adipate degradation	5	5	1
mitochondrial NADPH production (yeast)	5	4	1
folate polyglutamylation	5	4	1
dopamine degradation	5	2	1
oleate β-oxidation	35	30	6
stearate biosynthesis II (bacteria and plants)	6	5	1
β-alanine biosynthesis II	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
stearate biosynthesis I (animals)	6	1	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
glycine betaine degradation III	7	7	1
superpathway of glycol metabolism and degradation	7	6	1
serotonin degradation	7	4	1
capsaicin biosynthesis	7	3	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
limonene degradation IV (anaerobic)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
glycine betaine degradation I	8	6	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
folate transformations III (E. coli)	9	9	1
valproate β-oxidation	9	7	1
photorespiration I	9	6	1
photorespiration III	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
photorespiration II	10	7	1
glycolysis V (Pyrococcus)	10	7	1
suberin monomers biosynthesis	20	4	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of phenylethylamine degradation	11	11	1
folate transformations II (plants)	11	10	1
glycolysis II (from fructose 6-phosphate)	11	9	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	1
superpathway of L-arginine and L-ornithine degradation	13	11	1
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	10	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
folate transformations I	13	9	1
formaldehyde assimilation I (serine pathway)	13	7	1
2-methyl-branched fatty acid β-oxidation	14	10	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of hexitol degradation (bacteria)	18	13	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	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
purine nucleobases degradation II (anaerobic)	24	16	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	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
superpathway of pentose and pentitol degradation	42	10	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1