Experiment set39IT044 for Pseudomonas putida KT2440

DL-3-Hydroxyisobutyric acid sodium salt carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + DL-3-Hydroxyisobutyric acid sodium salt (10 mM)
Culturing: Putida_ML5_JBEI, 24-well plate, Aerobic, at 30 (C), shaken=200 rpm
By: Allie Pearson on 28-Sep
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 DL-3-Hydroxyisobutyric acid sodium salt in Pseudomonas putida KT2440

For carbon source DL-3-Hydroxyisobutyric acid sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Isobutyryl-CoA to Propionyl-CoA Module	4
Valine degradation	4
Choline and Betaine Uptake and Betaine Biosynthesis	1
DNA-binding regulatory proteins, strays	1
Flavodoxin	1
Pyruvate Alanine Serine Interconversions	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
• Propanoate metabolism
• beta-Alanine metabolism
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• Inositol phosphate metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine degradation II	2	2	2
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
choline degradation I	2	2	1
β-alanine degradation I	2	1	1
propanoyl-CoA degradation II	5	3	2
acrylate degradation I	5	3	2
L-valine degradation I	8	6	3
choline-O-sulfate degradation	3	3	1
benzoyl-CoA biosynthesis	3	3	1
β-alanine biosynthesis II	6	5	2
2-methyl-branched fatty acid β-oxidation	14	10	3
adipate degradation	5	5	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	2
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
methyl ketone biosynthesis (engineered)	6	3	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
benzoyl-CoA degradation I (aerobic)	7	3	1
2,4-dinitrotoluene degradation	7	1	1
myo-inositol degradation I	7	1	1
phenylacetate degradation I (aerobic)	9	9	1
valproate β-oxidation	9	7	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
3-phenylpropanoate degradation	10	4	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
superpathway of phenylethylamine degradation	11	11	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	30	3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
platensimycin biosynthesis	26	6	1