Experiment set12IT007 for Pseudomonas putida KT2440

2-methyl-1-butanol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 2-methyl-1-butanol (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 15 genes in this experiment

For carbon source 2-methyl-1-butanol in Pseudomonas putida KT2440

For carbon source 2-methyl-1-butanol across organisms

SEED Subsystems

Subsystem	#Specific
Glycine and Serine Utilization	1
Glycine cleavage system	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Propanoate metabolism
• Glycolysis / Gluconeogenesis
• Valine, leucine and isoleucine degradation
• beta-Alanine metabolism
• Butanoate metabolism
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
benzoyl-CoA biosynthesis	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
glycine biosynthesis II	3	3	1
superpathway of acetate utilization and formation	3	3	1
glycine cleavage	3	3	1
ethanol degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
chitin deacetylation	4	2	1
2-methyl-branched fatty acid β-oxidation	14	10	3
adipate degradation	5	5	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
propanoyl-CoA degradation II	5	3	1
acrylate degradation I	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
β-alanine biosynthesis II	6	5	1
methyl ketone biosynthesis (engineered)	6	3	1
superpathway of bitter acids biosynthesis	18	3	3
lupulone and humulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
benzoyl-CoA degradation I (aerobic)	7	3	1
L-valine degradation I	8	6	1
phenylacetate degradation I (aerobic)	9	9	1
valproate β-oxidation	9	7	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
cis-geranyl-CoA degradation	9	2	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
3-phenylpropanoate degradation	10	4	1
superpathway of phenylethylamine degradation	11	11	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	30	3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
platensimycin biosynthesis	26	6	1