Experiment set25S76 for Pseudomonas fluorescens SBW25-INTG

Shikimic Acid carbon source

Group: carbon source
Media: MME_noCarbon + Shikimic Acid (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
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 6 genes in this experiment

For carbon source Shikimic Acid in Pseudomonas fluorescens SBW25-INTG

For carbon source Shikimic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Alginate metabolism	1
Aromatic amino acid degradation	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	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:

• Tyrosine metabolism
• Phenylalanine metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Alkaloid biosynthesis I
• Drug metabolism - cytochrome P450
• 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
phenylethylamine degradation I	2	2	1
plastoquinol-9 biosynthesis I	3	1	1
L-tryptophan degradation VI (via tryptamine)	3	1	1
noradrenaline and adrenaline degradation	13	8	4
putrescine degradation III	4	3	1
aromatic biogenic amine degradation (bacteria)	8	4	2
salidroside biosynthesis	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
melatonin degradation II	4	1	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	2
L-tyrosine degradation I	5	5	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
dopamine degradation	5	2	1
phenylethanol biosynthesis	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
chorismate biosynthesis I	7	7	1
serotonin degradation	7	4	1
vitamin E biosynthesis (tocopherols)	7	1	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of phenylethylamine degradation	11	6	1
superpathway of melatonin degradation	11	1	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of chorismate metabolism	59	42	1