Experiment set10IT039 for Pseudomonas putida KT2440

3-hydroxypentanoate

Group: carbon source
Media: MOPS minimal media_noCarbon + rac-3-Hydroxypentanoic Acid (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.2 generations
By: Mitchell Thompson on 10/1/18
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 10 genes in this experiment

For carbon source rac-3-Hydroxypentanoic Acid in Pseudomonas putida KT2440

For carbon source rac-3-Hydroxypentanoic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Glutathione-dependent pathway of formaldehyde detoxification	3
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
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Methane metabolism
• Glycolysis / Gluconeogenesis
• 1- and 2-Methylnaphthalene degradation
• Butanoate metabolism
• Fatty acid metabolism
• Synthesis and degradation of ketone bodies
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Tyrosine metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

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
ketolysis	3	3	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-valine degradation II	3	2	1
methylglyoxal degradation VIII	3	2	1
methylglyoxal degradation I	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
salidroside biosynthesis	4	3	1
phytol degradation	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
ethanolamine utilization	5	4	1
pyruvate fermentation to isobutanol (engineered)	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
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
TCA cycle VI (Helicobacter)	9	7	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	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