Experiment set1IT010 for Pseudomonas sp. RS175

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Shikimic Acid carbon 10 mM

Group: carbon source
Media: MME_noCarbon + Shikimic Acid (10 mM), pH=7
Culturing: Pseudomonas_RS175_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 1-Jul-22
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 11 genes in this experiment

For carbon source Shikimic Acid in Pseudomonas sp. RS175

For carbon source Shikimic Acid across organisms

SEED Subsystems

Subsystem #Specific
Aromatic amino acid degradation 2
Chorismate Synthesis 2
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 2
Homogentisate pathway of aromatic compound degradation 2
Plastoquinone Biosynthesis 2
Tocopherol Biosynthesis 2
Alginate metabolism 1
Cinnamic Acid Degradation 1
D-Galacturonate and D-Glucuronate Utilization 1
Gentisare degradation 1
Orphan regulatory proteins 1
Phenylpropanoid compound degradation 1
Quinate degradation 1
Salicylate and gentisate catabolism 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
shikimate degradation II 2 1 1
chorismate biosynthesis from 3-dehydroquinate 5 5 2
gallate biosynthesis 3 2 1
quinate degradation II 3 1 1
quinate degradation I 3 1 1
plastoquinol-9 biosynthesis I 3 1 1
chorismate biosynthesis I 7 7 2
superpathway of L-tyrosine biosynthesis 10 10 2
superpathway of L-phenylalanine 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 chorismate metabolism 59 43 2
superpathway of aromatic compound degradation via 3-oxoadipate 35 13 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 10 1