Experiment set12IT040 for Pseudomonas putida KT2440

4-Methyl-2-oxopentanoic acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 4-Methyl-2-oxovaleric acid (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 4-Methyl-2-oxovaleric acid in Pseudomonas putida KT2440

For carbon source 4-Methyl-2-oxovaleric acid across organisms

SEED Subsystems

Subsystem	#Specific
Leucine Degradation and HMG-CoA Metabolism	7
Isoleucine degradation	5
Valine degradation	5
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	3
Serine-glyoxylate cycle	3
Catechol branch of beta-ketoadipate pathway	2
Protocatechuate branch of beta-ketoadipate pathway	2
HMG CoA Synthesis	1
Protein chaperones	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
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Synthesis and degradation of ketone bodies
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Butanoate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	3
ketolysis	3	3	1
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
L-leucine degradation I	6	5	2
TCA cycle VI (Helicobacter)	9	7	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1