Experiment set17IT002 for Pseudomonas fluorescens SBW25-INTG

p-Coumaric acid (C) 5 mM

Group: carbon source
Media: MME_noNitrogen_noCarbon + p-Coumaric acid (5 mM) + Ammonium chloride (10 mM)
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on October 1, 2021
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium 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 49 genes in this experiment

For carbon source p-Coumaric acid in Pseudomonas fluorescens SBW25-INTG

For carbon source p-Coumaric acid across organisms

SEED Subsystems

Subsystem	#Specific
Transport of Zinc	5
Lipid A modifications	4
Flagellum	2
Orphan regulatory proteins	2
Trehalose Uptake and Utilization	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Alkanesulfonate assimilation	1
Bacterial Cytoskeleton	1
CBSS-562.2.peg.5158 SK3 including	1
Cinnamic Acid Degradation	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA repair, bacterial	1
DNA repair, bacterial MutL-MutS system	1
Experimental tye	1
Folate Biosynthesis	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
Gentisare degradation	1
Heat shock dnaK gene cluster extended	1
Mannitol Utilization	1
Peptidoglycan Biosynthesis	1
Phenylpropanoid compound degradation	1
Polyamine Metabolism	1
Queuosine-Archaeosine Biosynthesis	1
Salicylate and gentisate catabolism	1
Taurine Utilization	1
Thiamin biosynthesis	1
p-Hydroxybenzoate degradation	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Ascorbate and aldarate metabolism
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Galactose metabolism
• Fatty acid biosynthesis
• Glycine, serine and threonine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Taurine and hypotaurine metabolism
• Starch and sucrose metabolism
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Thiamine metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• T cell receptor signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
taurine degradation IV	1	1	1
glyphosate degradation II	1	1	1
oleate β-oxidation (thioesterase-dependent, yeast)	2	2	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	2
6-hydroxymethyl-dihydropterin diphosphate biosynthesis IV (Plasmodium)	3	2	1
sucrose degradation I (sucrose phosphotransferase)	3	2	1
threo-tetrahydrobiopterin biosynthesis	4	2	1
preQ0 biosynthesis	4	2	1
tetrahydromonapterin biosynthesis	4	2	1
erythro-tetrahydrobiopterin biosynthesis I	4	2	1
tRNA processing	10	10	2
6-hydroxymethyl-dihydropterin diphosphate biosynthesis I	5	3	1
superpathway of taurine degradation	6	2	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
drosopterin and aurodrosopterin biosynthesis	7	5	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
superpathway of thiamine diphosphate biosynthesis II	11	9	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
oleate β-oxidation	35	33	1
superpathway of chorismate metabolism	59	42	1