Experiment set2S918 for Pseudomonas aeruginosa MRSN321

carbon source 10 mM Sodium 4-hydroxybenzoate

Group: carbon source
Media: Hans_Basal_Media + Sodium 4-Hydroxybenzoate (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 28 genes in this experiment

For carbon source Sodium 4-Hydroxybenzoate in Pseudomonas aeruginosa MRSN321

For carbon source Sodium 4-Hydroxybenzoate across organisms

SEED Subsystems

Subsystem	#Specific
Phosphate metabolism	3
Protocatechuate branch of beta-ketoadipate pathway	3
Benzoate degradation	2
Phenylpropanoid compound degradation	2
Alginate metabolism	1
Bacterial Chemotaxis	1
Calvin-Benson cycle	1
Central meta-cleavage pathway of aromatic compound degradation	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Cinnamic Acid Degradation	1
Cysteine Biosynthesis	1
D-Galacturonate and D-Glucuronate Utilization	1
DNA-binding regulatory proteins, strays	1
Entner-Doudoroff Pathway	1
Flagellar motility	1
Folate Biosynthesis	1
Gentisare degradation	1
Glycolysis and Gluconeogenesis	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Redox-dependent regulation of nucleus processes	1
Salicylate and gentisate catabolism	1
p-Hydroxybenzoate degradation	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
• Biosynthesis of phenylpropanoids
• Glycolysis / Gluconeogenesis
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• Toluene and xylene degradation
• 2,4-Dichlorobenzoate degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Styrene degradation
• Nicotinate and nicotinamide metabolism
• Folate biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• 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
protocatechuate degradation II (ortho-cleavage pathway)	4	4	2
L-glutamate biosynthesis I	2	2	1
3-oxoadipate degradation	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
toluene degradation III (aerobic) (via p-cresol)	11	8	4
aromatic compounds degradation via β-ketoadipate	9	9	3
ethanol degradation II	3	3	1
ammonia assimilation cycle III	3	3	1
ethanol degradation IV	3	3	1
hypotaurine degradation	3	2	1
D-phenylglycine degradation	3	2	1
ethanol degradation III	3	2	1
1,3-dimethylbenzene degradation to 3-methylbenzoate	3	1	1
histamine degradation	3	1	1
toluene degradation to benzoate	3	1	1
1,4-dimethylbenzene degradation to 4-methylbenzoate	3	1	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
3-chlorotoluene degradation II	3	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
putrescine degradation III	4	3	1
phytol degradation	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
4-methylphenol degradation to protocatechuate	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
benzoate biosynthesis II (CoA-independent, non-β-oxidative)	4	1	1
4-sulfocatechol degradation	4	1	1
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	5	4	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	5	2
gallate degradation II	5	2	1
dopamine degradation	5	2	1
mandelate degradation I	5	2	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
NAD(P)/NADPH interconversion	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
4-hydroxymandelate degradation	6	3	1
superpathway of aerobic toluene degradation	30	12	5
salicin biosynthesis	6	1	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
pyridoxal 5'-phosphate biosynthesis I	7	7	1
superpathway of salicylate degradation	7	7	1
L-glutamate and L-glutamine biosynthesis	7	6	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	22	5
serotonin degradation	7	4	1
4-methylcatechol degradation (ortho cleavage)	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
ceramide degradation by α-oxidation	7	2	1
2,4-xylenol degradation to protocatechuate	7	1	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
L-citrulline biosynthesis	8	6	1
aromatic biogenic amine degradation (bacteria)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
Entner-Doudoroff pathway I	9	8	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
mandelate degradation to acetyl-CoA	18	11	2
chloramphenicol biosynthesis	9	1	1
superpathway of tetrahydrofolate biosynthesis	10	9	1
glycolysis IV	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
glycolysis II (from fructose 6-phosphate)	11	9	1
glycolysis III (from glucose)	11	9	1
glycolysis VI (from fructose)	11	7	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	11	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
homolactic fermentation	12	9	1
gluconeogenesis III	12	9	1
superpathway of L-citrulline metabolism	12	8	1
gluconeogenesis I	13	13	1
glycolysis I (from glucose 6-phosphate)	13	10	1
toluene degradation IV (aerobic) (via catechol)	13	4	1
Bifidobacterium shunt	15	12	1
glycerol degradation to butanol	16	9	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of glucose and xylose degradation	17	14	1
heterolactic fermentation	18	14	1
superpathway of hexitol degradation (bacteria)	18	11	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	13	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	15	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of N-acetylneuraminate degradation	22	15	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of chorismate metabolism	59	45	1