Experiment set2S930 for Pseudomonas aeruginosa MRSN321

carbon source 10 mM Adipic acid

Group: carbon source
Media: Hans_Basal_Media + Adipic acid (10 mM), pH=7
Culturing: Paeruginosa_MRSN321_ML2, 96 deep-well block, Aerobic, at 30 (C), shaken=700 rpm
By: Hans and Ryan on 7/7/2025
Media components: 0.03 M PIPES sesquisodium salt, 0.1 g/L Potassium Chloride, 0.01 g/L Sodium Chloride, 0.01 g/L Calcium chloride dihydrate, 0.1 g/L Magnesium chloride hexahydrate, 0.1 g/L Sodium sulfate, 0.25 g/L Ammonium chloride, 0.1 g/L Disodium phosphate, DL vitamins (0.0002 mg/L biotin, 0.0002 mg/L Folic Acid, 0.001 mg/L Pyridoxine HCl, 0.0005 mg/L Riboflavin, 0.0005 mg/L Thiamine HCl, 0.0005 mg/L Nicotinic Acid, 0.0005 mg/L calcium pantothenate, 1e-05 mg/L Cyanocobalamin, 0.0005 mg/L 4-Aminobenzoic acid, 0.0005 mg/L Lipoic acid), Sulfur-free DL minerals (0.0003 g/L Magnesium chloride hexahydrate, 0.00015 g/L Nitrilotriacetic acid disodium salt, 0.0001 g/L Sodium Chloride, 5e-05 g/L Manganese (II) chloride tetrahydrate, 1e-05 g/L Cobalt chloride hexahydrate, 1.3e-05 g/L Zinc chloride, 1e-05 g/L Calcium chloride dihydrate, 1e-05 g/L Iron (II) chloride tetrahydrate, 2.5e-06 g/L Nickel (II) chloride hexahydrate, 2e-06 g/L Aluminum chloride hydrate, 1e-06 g/L copper (II) chloride dihydrate, 1e-06 g/L Boric Acid, 1e-06 g/L Sodium Molybdate Dihydrate, 3e-05 g/L Sodium selenite pentahydrate, 2.5e-05 g/L Sodium tungstate dihydrate)

Specific Phenotypes

For 23 genes in this experiment

For carbon source Adipic acid in Pseudomonas aeruginosa MRSN321

For carbon source Adipic acid across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter oligopeptide (TC 3.A.1.5.1)	3
Acetyl-CoA fermentation to Butyrate	2
Anaerobic respiratory reductases	2
Butanol Biosynthesis	2
Isobutyryl-CoA to Propionyl-CoA Module	2
Isoleucine degradation	2
Protocatechuate branch of beta-ketoadipate pathway	2
Valine degradation	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Butanoate metabolism
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Benzoate degradation via CoA ligation
• Geraniol degradation
• Caprolactam degradation
• Biosynthesis of plant hormones
• Fatty acid elongation in mitochondria
• Bile acid biosynthesis
• Lysine degradation
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Glutathione metabolism
• 1- and 2-Methylnaphthalene degradation
• Styrene degradation
• Brassinosteroid biosynthesis
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
8-amino-7-oxononanoate biosynthesis III	2	2	1
3-oxoadipate degradation	2	2	1
adipate degradation	5	5	2
benzoyl-CoA biosynthesis	3	3	1
pyruvate fermentation to butanol II (engineered)	6	4	2
pyruvate fermentation to hexanol (engineered)	11	7	3
oleate β-oxidation	35	30	8
valproate β-oxidation	9	6	2
4-hydroxybenzoate biosynthesis III (plants)	5	4	1
adipate biosynthesis	5	4	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	2
glutaryl-CoA degradation	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
fatty acid salvage	6	6	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
biotin biosynthesis II	6	5	1
methyl ketone biosynthesis (engineered)	6	3	1
superpathway of salicylate degradation	7	7	1
2-methyl-branched fatty acid β-oxidation	14	10	2
fatty acid β-oxidation I (generic)	7	5	1
4-methylcatechol degradation (ortho cleavage)	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
pyruvate fermentation to butanoate	7	3	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
pyruvate fermentation to butanol I	8	3	1
2-methylpropene degradation	8	2	1
aromatic compounds degradation via β-ketoadipate	9	9	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	1
phenylacetate degradation I (aerobic)	9	4	1
3-phenylpropanoate degradation	10	5	1
methyl tert-butyl ether degradation	10	3	1
toluene degradation III (aerobic) (via p-cresol)	11	8	1
superpathway of phenylethylamine degradation	11	6	1
L-glutamate degradation VII (to butanoate)	12	3	1
androstenedione degradation I (aerobic)	25	6	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
1-butanol autotrophic biosynthesis (engineered)	27	19	2
androstenedione degradation II (anaerobic)	27	4	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
superpathway of testosterone and androsterone degradation	28	6	2
superpathway of cholesterol degradation I (cholesterol oxidase)	42	8	3
L-tryptophan degradation III (eukaryotic)	15	6	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	9	3
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
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
mandelate degradation to acetyl-CoA	18	11	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
toluene degradation VI (anaerobic)	18	4	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	3	1
superpathway of cholesterol degradation III (oxidase)	49	5	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
platensimycin biosynthesis	26	7	1
superpathway of aerobic toluene degradation	30	12	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	22	1