Experiment set2S878 for Pseudomonas aeruginosa MRSN321

carbon source 10 mM 5-Aminovaleric acid

Group: carbon source
Media: Hans_Basal_Media + 5-Aminovaleric 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 20 genes in this experiment

For carbon source 5-Aminovaleric acid in Pseudomonas aeruginosa MRSN321

For carbon source 5-Aminovaleric acid across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	4
Arginine Biosynthesis extended	1
Branched-Chain Amino Acid Biosynthesis	1
Fatty Acid Biosynthesis FASII	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Phosphate metabolism	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Threonine degradation	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine biosynthesis
• Arginine and proline metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Tryptophan metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• Benzoate degradation via CoA ligation
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Nitrogen metabolism
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation I	1	1	1
L-methionine degradation II	3	2	2
L-threonine degradation I	6	5	3
L-threonine degradation V	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
L-alanine degradation II (to D-lactate)	3	3	1
ethene biosynthesis IV (engineered)	3	1	1
gondoate biosynthesis (anaerobic)	4	4	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	9	3
palmitate biosynthesis III	29	21	7
tetradecanoate biosynthesis (mitochondria)	25	17	6
superpathway of L-isoleucine biosynthesis I	13	13	3
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	9	2
oleate biosynthesis IV (anaerobic)	14	13	3
hypoglycin biosynthesis	14	4	3
superpathway of fatty acids biosynthesis (E. coli)	53	51	11
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	20	4
cis-vaccenate biosynthesis	5	5	1
fatty acid elongation -- saturated	5	5	1
L-ornithine biosynthesis I	5	5	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
L-lysine degradation IV	5	4	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
superpathway of branched chain amino acid biosynthesis	17	17	3
anteiso-branched-chain fatty acid biosynthesis	34	24	6
even iso-branched-chain fatty acid biosynthesis	34	24	6
odd iso-branched-chain fatty acid biosynthesis	34	24	6
(5Z)-dodecenoate biosynthesis I	6	6	1
L-lysine degradation X	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis II	6	5	1
superpathway of L-threonine metabolism	18	14	3
stearate biosynthesis IV	6	4	1
petroselinate biosynthesis	6	2	1
streptorubin B biosynthesis	34	20	5
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	2	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	15	2
2-allylmalonyl-CoA biosynthesis	8	2	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
cyclosporin A biosynthesis	15	2	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
methylaspartate cycle	19	10	1
aspartate superpathway	25	22	1
mycolate biosynthesis	205	20	5
superpathway of L-lysine degradation	43	15	1
superpathway of mycolate biosynthesis	239	21	5