Experiment set21IT080 for Pseudomonas fluorescens SBW25-INTG

Quinic Acid 10 mM carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + Quinic Acid (10 mM) + Ammonium chloride (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 8-Mar-22
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 5 genes in this experiment

For carbon source Quinic Acid in Pseudomonas fluorescens SBW25-INTG

For carbon source Quinic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Chorismate Synthesis	3
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	2
Quinate degradation	2
Alginate metabolism	1
Aromatic amino acid degradation	1
D-Galacturonate and D-Glucuronate Utilization	1
Homogentisate pathway of aromatic compound degradation	1
Plastoquinone Biosynthesis	1
Tocopherol Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Ubiquinone and menaquinone biosynthesis
• Tyrosine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Retinol metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
quinate degradation I	3	2	2
shikimate degradation I	2	1	1
chorismate biosynthesis from 3-dehydroquinate	5	5	2
gallate biosynthesis	3	2	1
plastoquinol-9 biosynthesis I	3	1	1
quinate degradation II	3	1	1
chorismate biosynthesis I	7	7	2
superpathway of L-phenylalanine biosynthesis	10	10	2
superpathway of L-tyrosine biosynthesis	10	10	2
L-tyrosine degradation I	5	5	1
superpathway of plastoquinol biosynthesis	5	2	1
chorismate biosynthesis II (archaea)	12	8	2
superpathway of L-tryptophan biosynthesis	13	13	2
vitamin E biosynthesis (tocopherols)	7	1	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	3
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	13	3
superpathway of chorismate metabolism	59	42	2