Experiment set2S874 for Pseudomonas aeruginosa MRSN321

carbon source 10 mM Beta-alanine

Group: carbon source
Media: Hans_Basal_Media + Beta-alanine (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 37 genes in this experiment

For carbon source Beta-alanine in Pseudomonas aeruginosa MRSN321

For carbon source Beta-alanine across organisms

SEED Subsystems

Subsystem	#Specific
Phosphate metabolism	3
Pyruvate Alanine Serine Interconversions	3
Arginine and Ornithine Degradation	2
Alanine biosynthesis	1
Aromatic amino acid degradation	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
DNA-binding regulatory proteins, strays	1
DNA repair, UvrABC system	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine and Serine Utilization	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Methionine Biosynthesis	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Queuosine-Archaeosine 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:

• Alanine and aspartate metabolism
• Nicotinate and nicotinamide metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Propanoate metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Cysteine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• beta-Alanine metabolism
• D-Alanine metabolism
• Starch and sucrose metabolism
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• Thiamine metabolism
• Riboflavin metabolism
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine degradation II	2	2	2
alanine racemization	1	1	1
L-glutamine biosynthesis I	1	1	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
choline degradation I	2	2	1
ammonia assimilation cycle I	2	2	1
ammonia assimilation cycle II	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
L-homocysteine biosynthesis	2	2	1
L-alanine degradation I	2	2	1
β-alanine degradation I	2	1	1
choline-O-sulfate degradation	3	3	1
superpathway of ammonia assimilation (plants)	3	3	1
ammonia assimilation cycle III	3	3	1
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
N-methylpyrrolidone degradation	3	1	1
L-methionine biosynthesis III	4	4	1
queuosine biosynthesis I (de novo)	4	4	1
L-arginine degradation II (AST pathway)	5	5	1
queuosine biosynthesis III (queuosine salvage)	5	3	1
propanoyl-CoA degradation II	5	2	1
acrylate degradation I	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	2	1
superpathway of L-cysteine biosynthesis (fungi)	6	5	1
NAD de novo biosynthesis I	6	5	1
NAD de novo biosynthesis IV (anaerobic)	6	5	1
β-alanine biosynthesis II	6	4	1
NAD(P)/NADPH interconversion	6	4	1
L-glutamate and L-glutamine biosynthesis	7	6	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
2,4-dinitrotoluene degradation	7	1	1
myo-inositol degradation I	7	1	1
L-valine degradation I	8	5	1
nicotine biosynthesis	9	3	1
ansatrienin biosynthesis	9	1	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	9	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of nicotine biosynthesis	12	4	1
cyclosporin A biosynthesis	15	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	11	1
nicotine degradation I (pyridine pathway)	17	5	1
aspartate superpathway	25	22	1