Experiment set1IT090 for Pseudomonas sp. RS175

5-Aminovaleric acid carbon 10 mM

Group: carbon source
Media: MME_noCarbon + 5-Aminovaleric acid (10 mM), pH=7
Culturing: Pseudomonas_RS175_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 1-Jul-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 9 genes in this experiment

For carbon source 5-Aminovaleric acid in Pseudomonas sp. RS175

For carbon source 5-Aminovaleric acid across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	2
Acetyl-CoA fermentation to Butyrate	1
Butanol Biosynthesis	1
Coenzyme A Biosynthesis	1
Orphan regulatory proteins	1
Polyhydroxybutyrate metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via CoA ligation
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Aminosugars metabolism
• Butanoate metabolism
• Fatty acid metabolism
• C21-Steroid hormone metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Linoleic acid metabolism
• Sphingolipid metabolism
• Tetrachloroethene degradation
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Pantothenate and CoA biosynthesis
• Retinol metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
phosphopantothenate biosynthesis I	4	4	1
phosphopantothenate biosynthesis III (archaea)	4	2	1
L-lysine degradation IV	5	4	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
glutaryl-CoA degradation	5	3	1
L-lysine degradation X	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
pyruvate fermentation to butanoate	7	3	1
pyruvate fermentation to butanol I	8	3	1
2-methylpropene degradation	8	2	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	9	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
methyl tert-butyl ether degradation	10	2	1
pyruvate fermentation to hexanol (engineered)	11	7	1
L-glutamate degradation VII (to butanoate)	12	3	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation III (eukaryotic)	15	3	1
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
toluene degradation VI (anaerobic)	18	4	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	20	1
1-butanol autotrophic biosynthesis (engineered)	27	20	1
oleate β-oxidation	35	30	1
superpathway of L-lysine degradation	43	18	1