Experiment set6S92 for Pseudomonas sp. RS175

methyl ferulate carbon source

Group: carbon source
Media: MME_noCarbon + methyl ferulate (2 mM)
Culturing: Pseudomonas_RS175_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C)
By: Andrew Frank on 1/31/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 22 genes in this experiment

For carbon source methyl ferulate in Pseudomonas sp. RS175

For carbon source methyl ferulate across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	2
Glutathione-dependent pathway of formaldehyde detoxification	2
Multidrug Resistance Efflux Pumps	2
Polyamine Metabolism	2
Copper homeostasis	1
Glycogen metabolism	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
Trehalose Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• 1- and 2-Methylnaphthalene degradation
• Ubiquinone and menaquinone biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Benzoate degradation via CoA ligation
• Methane metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Biosynthesis of terpenoids and steroids
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Arginine and proline metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Toluene and xylene degradation
• 2,4-Dichlorobenzoate degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Styrene degradation
• Butanoate metabolism
• Retinol metabolism
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis II
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
ethanol degradation I	2	2	1
vanillin and vanillate degradation II	2	2	1
pyruvate fermentation to ethanol II	2	1	1
trehalose biosynthesis V	3	3	1
formaldehyde oxidation II (glutathione-dependent)	3	3	1
ethanol degradation II	3	3	1
pyruvate fermentation to ethanol III	3	2	1
L-valine degradation II	3	2	1
pyruvate fermentation to ethanol I	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
L-methionine degradation III	3	1	1
nylon-6 oligomer degradation	7	3	2
phytol degradation	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
salidroside biosynthesis	4	2	1
ethanolamine utilization	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
acetylene degradation (anaerobic)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
protein S-nitrosylation and denitrosylation	5	3	1
(S)-propane-1,2-diol degradation	5	2	1
phenylethanol biosynthesis	5	2	1
noradrenaline and adrenaline degradation	13	8	2
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	4	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	1	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	2	1
superpathway of demethylmenaquinol-9 biosynthesis	9	1	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	1	1
superpathway of menaquinol-8 biosynthesis I	10	3	1
superpathway of menaquinol-11 biosynthesis	10	2	1
superpathway of menaquinol-10 biosynthesis	10	2	1
superpathway of menaquinol-12 biosynthesis	10	2	1
superpathway of menaquinol-7 biosynthesis	10	2	1
superpathway of menaquinol-6 biosynthesis	10	2	1
superpathway of menaquinol-9 biosynthesis	10	2	1
superpathway of menaquinol-13 biosynthesis	10	2	1
superpathway of C1 compounds oxidation to CO2	12	5	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of phylloquinol biosynthesis	15	2	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	16	1
superpathway of anaerobic sucrose degradation	19	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of N-acetylneuraminate degradation	22	15	1
superpathway of chorismate metabolism	59	43	1