Experiment set2S820 for Pseudomonas aeruginosa MRSN321

carbon source 10 mM Sodium benzoate

Group: carbon source
Media: Hans_Basal_Media + Sodium Benzoate (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 27 genes in this experiment

For carbon source Sodium Benzoate in Pseudomonas aeruginosa MRSN321

For carbon source Sodium Benzoate across organisms

SEED Subsystems

Subsystem	#Specific
Protocatechuate branch of beta-ketoadipate pathway	2
Toluene degradation	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
Alkylphosphonate utilization	1
Benzoate degradation	1
Catechol branch of beta-ketoadipate pathway	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Folate Biosynthesis	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Selenocysteine metabolism	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via hydroxylation
• Fluorobenzoate degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Citrate cycle (TCA cycle)
• Alanine and aspartate metabolism
• gamma-Hexachlorocyclohexane degradation
• Selenoamino acid metabolism
• Glutathione metabolism
• Toluene and xylene degradation
• 1,4-Dichlorobenzene degradation
• Carbazole degradation
• Benzoate degradation via CoA ligation
• Styrene degradation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Folate biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine degradation I	1	1	1
3-oxoadipate degradation	2	2	1
L-glutamate biosynthesis I	2	2	1
benzoate degradation I (aerobic)	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
aromatic compounds degradation via β-ketoadipate	9	9	3
catechol degradation III (ortho-cleavage pathway)	6	6	2
L-selenocysteine biosynthesis I (bacteria)	3	3	1
ammonia assimilation cycle III	3	3	1
superpathway of salicylate degradation	7	7	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
catechol degradation to β-ketoadipate	4	4	1
protocatechuate degradation II (ortho-cleavage pathway)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
L-selenocysteine biosynthesis II (archaea and eukaryotes)	4	2	1
cytosolic NADPH production (yeast)	5	4	1
methylphosphonate degradation I	5	3	1
methylphosphonate degradation II	5	2	1
toluene degradation III (aerobic) (via p-cresol)	11	8	2
NAD de novo biosynthesis IV (anaerobic)	6	5	1
NAD de novo biosynthesis I	6	5	1
mandelate degradation to acetyl-CoA	18	11	3
L-glutamate and L-glutamine biosynthesis	7	6	1
4-methylcatechol degradation (ortho cleavage)	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
partial TCA cycle (obligate autotrophs)	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
nitrogen remobilization from senescing leaves	8	6	1
L-citrulline biosynthesis	8	6	1
(aminomethyl)phosphonate degradation	8	5	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	22	4
TCA cycle V (2-oxoglutarate synthase)	9	8	1
TCA cycle VII (acetate-producers)	9	7	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
nicotine biosynthesis	9	3	1
chloramphenicol biosynthesis	9	1	1
superpathway of tetrahydrofolate biosynthesis	10	9	1
TCA cycle I (prokaryotic)	10	9	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
superpathway of aerobic toluene degradation	30	12	3
meta cleavage pathway of aromatic compounds	10	3	1
reductive TCA cycle I	11	7	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	11	1
superpathway of glyoxylate bypass and TCA	12	11	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of nicotine biosynthesis	12	4	1
toluene degradation IV (aerobic) (via catechol)	13	4	1
mixed acid fermentation	16	13	1
methylaspartate cycle	19	10	1
aspartate superpathway	25	22	1
ethene biosynthesis V (engineered)	25	18	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	15	1
superpathway of chorismate metabolism	59	45	1