Experiment set12IT048 for Pseudomonas putida KT2440

Delta-Undecalactone carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Delta-Undecalactone (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 45 genes in this experiment

For carbon source Delta-Undecalactone in Pseudomonas putida KT2440

For carbon source Delta-Undecalactone across organisms

SEED Subsystems

Subsystem	#Specific
Multidrug Resistance Efflux Pumps	4
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	2
Orphan regulatory proteins	2
Phosphate metabolism	2
Biotin biosynthesis	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Methylglyoxal Metabolism	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Purine conversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	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:

• Arginine and proline metabolism
• Tryptophan metabolism
• Propanoate metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Geraniol degradation
• 1,2-Dichloroethane degradation
• Butanoate metabolism
• Ascorbate and aldarate metabolism
• Purine metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Methane metabolism
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of plant hormones

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
putrescine degradation V	2	2	1
phytol degradation	4	3	2
3-methyl-branched fatty acid α-oxidation	6	3	3
linoleate biosynthesis II (animals)	2	1	1
putrescine degradation I	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
ethylene glycol degradation	2	1	1
octane oxidation	5	4	2
sphingosine and sphingosine-1-phosphate metabolism	10	4	4
fatty acid salvage	6	6	2
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
oleate biosynthesis I (plants)	3	1	1
histamine degradation	3	1	1
alkane biosynthesis II	3	1	1
ceramide degradation by α-oxidation	7	2	2
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	4	1
L-arginine degradation VIII (arginine oxidase pathway)	4	3	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
long chain fatty acid ester synthesis (engineered)	4	1	1
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
adipate degradation	5	5	1
mitochondrial NADPH production (yeast)	5	4	1
dopamine degradation	5	2	1
β-alanine biosynthesis II	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
alkane oxidation	6	1	1
stearate biosynthesis I (animals)	6	1	1
noradrenaline and adrenaline degradation	13	8	2
oleate β-oxidation	35	30	5
superpathway of glycol metabolism and degradation	7	6	1
serotonin degradation	7	4	1
capsaicin biosynthesis	7	3	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
limonene degradation IV (anaerobic)	7	1	1
arachidonate biosynthesis III (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
superpathway of ornithine degradation	8	6	1
2-deoxy-D-ribose degradation II	8	4	1
aromatic biogenic amine degradation (bacteria)	8	3	1
valproate β-oxidation	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	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
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	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 fatty acids biosynthesis (E. coli)	53	51	2
palmitate biosynthesis III	29	28	1
superpathway of pentose and pentitol degradation	42	10	1