Experiment set7IT049 for Pseudomonas putida KT2440

3-methyl-1-butanol 0.25 vol% carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 3-methyl-1-butanol (0.25 vol%)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.1 generations
By: Mitchell Thompson on 4/25/18
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 14 genes in this experiment

For carbon source 3-methyl-1-butanol in Pseudomonas putida KT2440

For carbon source 3-methyl-1-butanol across organisms

SEED Subsystems

Subsystem	#Specific
Leucine Degradation and HMG-CoA Metabolism	2
Serine-glyoxylate cycle	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Catechol branch of beta-ketoadipate pathway	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
HMG CoA Synthesis	1
Lysine degradation	1
Protocatechuate branch of beta-ketoadipate pathway	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Propanoate metabolism
• Butanoate metabolism
• Glycolysis / Gluconeogenesis
• Synthesis and degradation of ketone bodies
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Methane metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ketolysis	3	3	1
L-leucine degradation I	6	5	2
creatinine degradation I	4	2	1
creatinine degradation II	5	3	1
glycine betaine degradation I	8	6	1
TCA cycle VI (Helicobacter)	9	7	1