Experiment set16IT006 for Pseudomonas putida KT2440

1,3-Butandiol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 1,3-Butandiol (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.6 generations
By: Mitchell Thompson on 9/5/19
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 8 genes in this experiment

For carbon source 1,3-Butandiol in Pseudomonas putida KT2440

For carbon source 1,3-Butandiol across organisms

SEED Subsystems

Subsystem	#Specific
Catechol branch of beta-ketoadipate pathway	2
Leucine Degradation and HMG-CoA Metabolism	2
Protocatechuate branch of beta-ketoadipate pathway	2
Serine-glyoxylate cycle	2
DNA-binding regulatory proteins, strays	1
Polyhydroxybutyrate metabolism	1
Ribosome biogenesis bacterial	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Synthesis and degradation of ketone bodies
• Butanoate metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Tryptophan metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of siderophore group nonribosomal peptides

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ketolysis	3	3	2
ketogenesis	5	3	1
TCA cycle VI (Helicobacter)	9	7	1