Experiment set6S90 for Pseudomonas sp. RS175

methyl-trans-p-coumarate carbon source

Group: carbon source
Media: MME_noCarbon + methyl-trans-p-coumarate (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 55 genes in this experiment

For carbon source methyl-trans-p-coumarate in Pseudomonas sp. RS175

For carbon source methyl-trans-p-coumarate across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	3
Bacterial Chemotaxis	3
Multidrug Resistance Efflux Pumps	3
Glycogen metabolism	2
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
ATP-dependent RNA helicases, bacterial	1
Entner-Doudoroff Pathway	1
Flagellar motility	1
Flagellum	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Glycolysis and Gluconeogenesis	1
Heat shock dnaK gene cluster extended	1
Lipid A modifications	1
Lysine degradation	1
Maltose and Maltodextrin Utilization	1
Peptidoglycan Biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Potassium homeostasis	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Purine conversions	1
Rhamnose containing glycans	1
Transcription initiation, bacterial sigma factors	1
Trehalose Biosynthesis	1
Two-component regulatory systems in Campylobacter	1
cAMP signaling in bacteria	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	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:

• Arginine and proline metabolism
• Histidine metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Lysine degradation
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Butanoate metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Galactose metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• beta-Alanine metabolism
• Polyketide sugar unit biosynthesis
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 2,4-Dichlorobenzoate degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• One carbon pool by folate
• Porphyrin and chlorophyll metabolism
• Flavonoid biosynthesis
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• 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
adenosine nucleotides degradation III	1	1	1
L-glutamine biosynthesis I	1	1	1
trehalose degradation II (cytosolic)	2	2	1
ammonia assimilation cycle I	2	2	1
ammonia assimilation cycle II	2	1	1
trehalose degradation I (low osmolarity)	2	1	1
glycine cleavage	3	3	1
ethanol degradation IV	3	3	1
trehalose biosynthesis V	3	3	1
glycine biosynthesis II	3	3	1
ethanol degradation II	3	3	1
glycine degradation	3	3	1
ammonia assimilation cycle III	3	3	1
L-aspartate degradation III (anaerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
ethanol degradation III	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
hypotaurine degradation	3	2	1
trehalose degradation V	3	2	1
histamine degradation	3	1	1
trehalose degradation IV	3	1	1
glycogen degradation I	8	7	2
sucrose biosynthesis II	8	6	2
sucrose degradation III (sucrose invertase)	4	3	1
putrescine degradation III	4	3	1
starch degradation V	4	3	1
phytol degradation	4	3	1
4-chlorobenzoate degradation	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
ferulate and sinapate biosynthesis	4	1	1
4-methylphenol degradation to protocatechuate	4	1	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
octane oxidation	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
4-coumarate degradation (aerobic)	5	2	1
dopamine degradation	5	2	1
bisphenol A degradation	5	1	1
glycogen degradation II	6	5	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
4-hydroxymandelate degradation	6	2	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
L-glutamate and L-glutamine biosynthesis	7	5	1
serotonin degradation	7	4	1
ceramide degradation by α-oxidation	7	2	1
spongiadioxin C biosynthesis	7	2	1
limonene degradation IV (anaerobic)	7	1	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
polybrominated dihydroxylated diphenyl ethers biosynthesis	8	2	1
folate transformations III (E. coli)	9	9	1
chitin biosynthesis	9	6	1
photorespiration I	9	5	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
photorespiration III	9	5	1
1,3-propanediol biosynthesis (engineered)	9	4	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	2	1
superpathway of demethylmenaquinol-9 biosynthesis	9	1	1
starch degradation II	9	1	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	1	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
peptidoglycan recycling II	10	8	1
photorespiration II	10	6	1
superpathway of menaquinol-8 biosynthesis I	10	3	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 menaquinol-12 biosynthesis	10	2	1
superpathway of menaquinol-11 biosynthesis	10	2	1
superpathway of menaquinol-10 biosynthesis	10	2	1
folate transformations II (plants)	11	10	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
glycolysis III (from glucose)	11	9	1
toluene degradation III (aerobic) (via p-cresol)	11	7	1
homolactic fermentation	12	10	1
folate transformations I	13	9	1
peptidoglycan recycling I	14	11	1
Bifidobacterium shunt	15	15	1
superpathway of phylloquinol biosynthesis	15	2	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
heterolactic fermentation	18	16	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	6	1
superpathway of aerobic toluene degradation	30	11	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	13	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	10	1
superpathway of chorismate metabolism	59	43	1