Experiment set29IT073 for Pseudomonas putida KT2440

3-Hydroxyhexanoic acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 3-Hydroxyhexanoic acid (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Matthias Schmidt on 4/13/21
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 11 genes in this experiment

For carbon source 3-Hydroxyhexanoic acid in Pseudomonas putida KT2440

For carbon source 3-Hydroxyhexanoic acid across organisms

SEED Subsystems

Subsystem	#Specific
Glutathione-dependent pathway of formaldehyde detoxification	3
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Propanoate metabolism
• Methane metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Tyrosine metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• beta-Alanine metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Butanoate metabolism
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Retinol metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis II
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
formaldehyde oxidation II (glutathione-dependent)	3	3	2
ethanol degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation II	3	3	1
methylglyoxal degradation VIII	3	2	1
L-isoleucine degradation II	3	2	1
methylglyoxal degradation I	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
pyruvate fermentation to ethanol III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
L-methionine degradation III	3	1	1
2,3-dihydroxybenzoate biosynthesis	3	1	1
salidroside biosynthesis	4	3	1
phytol degradation	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
ethanolamine utilization	5	4	1
protein S-nitrosylation and denitrosylation	5	3	1
acetylene degradation (anaerobic)	5	3	1
phenylethanol biosynthesis	5	3	1
(S)-propane-1,2-diol degradation	5	2	1
L-leucine degradation I	6	5	1
superpathway of C1 compounds oxidation to CO2	12	5	2
noradrenaline and adrenaline degradation	13	8	2
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	4	1
superpathway of methylglyoxal degradation	8	5	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	1
vibriobactin biosynthesis	9	1	1
enterobactin biosynthesis	11	4	1
bacillibactin biosynthesis	12	3	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	1
heterolactic fermentation	18	12	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of anaerobic sucrose degradation	19	13	1
superpathway of N-acetylneuraminate degradation	22	12	1
superpathway of chorismate metabolism	59	42	1