Experiment set2S774 for Pseudomonas aeruginosa MRSN321

carbon source 10 mM Carnitine Hydrochloride

Group: carbon source
Media: Hans_Basal_Media + Carnitine Hydrochloride (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 19 genes in this experiment

For carbon source Carnitine Hydrochloride in Pseudomonas aeruginosa MRSN321

For carbon source Carnitine Hydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	6
Acetyl-CoA fermentation to Butyrate	2
Alanine biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
Isoleucine degradation	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Methionine Biosynthesis	1
Polyhydroxybutyrate metabolism	1
Pyrroloquinoline Quinone biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Threonine and Homoserine Biosynthesis	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• alpha-Linolenic acid metabolism
• Pantothenate and CoA biosynthesis
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-carnitine degradation III	3	3	3
D-carnitine degradation I	3	2	2
L-threonine biosynthesis	2	2	1
L-alanine biosynthesis I	2	2	1
D-carnitine degradation II	2	1	1
glycine betaine degradation III	7	7	3
L-leucine degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
glycine betaine degradation I	8	6	2
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
creatinine degradation I	4	1	1
creatinine degradation II	5	1	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
superpathway of branched chain amino acid biosynthesis	17	17	3
peptido-conjugates in tissue regeneration biosynthesis	17	8	3
L-leucine biosynthesis	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
L-leucine degradation I	6	5	1
L-methionine biosynthesis II	6	5	1
L-isoleucine degradation I	6	4	1
L-isoleucine biosynthesis IV	6	4	1
leukotriene biosynthesis	6	2	1
superpathway of L-isoleucine biosynthesis I	13	13	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
acetyl-CoA fermentation to butanoate	7	4	1
L-isoleucine biosynthesis III	7	4	1
L-valine degradation I	8	5	1
L-isoleucine biosynthesis II	8	4	1
gliotoxin biosynthesis	9	2	1
ethylmalonyl-CoA pathway	11	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of L-threonine metabolism	18	14	1
aspartate superpathway	25	22	1
even iso-branched-chain fatty acid biosynthesis	34	24	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1
odd iso-branched-chain fatty acid biosynthesis	34	24	1
arachidonate metabolites biosynthesis	74	5	1