Experiment set6S91 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 18 genes in this experiment

For carbon source methyl ferulate in Pseudomonas sp. RS175

For carbon source methyl ferulate across organisms

SEED Subsystems

Subsystem	#Specific
Multidrug Resistance Efflux Pumps	2
Arginine and Ornithine Degradation	1
Copper homeostasis	1
Entner-Doudoroff Pathway	1
Glutathione-dependent pathway of formaldehyde detoxification	1
Glycolysis and Gluconeogenesis	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
Phenylpropanoid compound degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of terpenoids and steroids
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Lysine degradation
• Tyrosine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• 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
• Ethylbenzene degradation
• Styrene degradation
• Butanoate metabolism
• Methane metabolism
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• 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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine biosynthesis I	1	1	1
vanillin and vanillate degradation II	2	2	1
trehalose degradation II (cytosolic)	2	2	1
ammonia assimilation cycle I	2	2	1
trehalose degradation I (low osmolarity)	2	1	1
ammonia assimilation cycle II	2	1	1
ammonia assimilation cycle III	3	3	1
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
trehalose degradation IV	3	1	1
nylon-6 oligomer degradation	7	3	2
queuosine biosynthesis I (de novo)	4	4	1
sucrose degradation III (sucrose invertase)	4	3	1
L-arginine degradation II (AST pathway)	5	5	1
glucose and glucose-1-phosphate degradation	5	4	1
glycogen degradation II	6	5	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
L-glutamate and L-glutamine biosynthesis	7	5	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	1	1
glycogen degradation I	8	7	1
sucrose biosynthesis II	8	6	1
chitin biosynthesis	9	6	1
1,3-propanediol biosynthesis (engineered)	9	4	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	2	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	1	1
superpathway of demethylmenaquinol-9 biosynthesis	9	1	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of menaquinol-8 biosynthesis I	10	3	1
superpathway of menaquinol-12 biosynthesis	10	2	1
superpathway of menaquinol-11 biosynthesis	10	2	1
superpathway of menaquinol-13 biosynthesis	10	2	1
superpathway of menaquinol-7 biosynthesis	10	2	1
superpathway of menaquinol-9 biosynthesis	10	2	1
superpathway of menaquinol-10 biosynthesis	10	2	1
superpathway of menaquinol-6 biosynthesis	10	2	1
glycolysis III (from glucose)	11	9	1
homolactic fermentation	12	10	1
Bifidobacterium shunt	15	15	1
superpathway of phylloquinol biosynthesis	15	2	1
heterolactic fermentation	18	16	1
superpathway of chorismate metabolism	59	43	1