Experiment set12IT018 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 39 genes in this experiment

For carbon source Delta-Undecalactone in Pseudomonas putida KT2440

For carbon source Delta-Undecalactone across organisms

SEED Subsystems

Subsystem	#Specific
Glycine and Serine Utilization	2
Glycine cleavage system	2
Multidrug Resistance Efflux Pumps	2
Orphan regulatory proteins	2
Photorespiration (oxidative C2 cycle)	2
Polyamine Metabolism	2
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Butanol Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Phosphate metabolism	1
Purine conversions	1
Ribosome biogenesis bacterial	1
Valine 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
• Fatty acid metabolism
• Purine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Tyrosine metabolism
• Tryptophan metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• One carbon pool by folate
• Limonene and pinene degradation
• Nitrogen 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
glycine cleavage	3	3	2
glycine biosynthesis II	3	3	2
adipate degradation	5	5	1
fatty acid salvage	6	6	1
β-alanine biosynthesis II	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
oleate β-oxidation	35	30	4
valproate β-oxidation	9	7	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
pyruvate fermentation to hexanol (engineered)	11	8	1
2-methyl-branched fatty acid β-oxidation	14	10	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1