Experiment set4S78 for Pseudomonas sp. RS175

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Shikimic Acid carbon source 10 mM

Group: carbon source
Media: MME_noCarbon + Shikimic Acid (10 mM)
Culturing: Pseudomonas_RS175_ML2, 96 deep well, 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 sp. RS175

For carbon source Shikimic Acid across organisms

SEED Subsystems

Subsystem #Specific
Chorismate Synthesis 2
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 2
Alginate metabolism 1
Cinnamic Acid Degradation 1
D-Galacturonate and D-Glucuronate Utilization 1
Gentisare degradation 1
Phenylalanine and Tyrosine Branches from Chorismate 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
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
L-phenylalanine biosynthesis III (cytosolic, plants) 2 2 1
shikimate degradation II 2 1 1
atromentin biosynthesis 2 1 1
L-tyrosine degradation II 2 1 1
chorismate biosynthesis from 3-dehydroquinate 5 5 2
L-tyrosine biosynthesis I 3 3 1
L-phenylalanine biosynthesis I 3 3 1
L-phenylalanine degradation II (anaerobic) 3 2 1
gallate biosynthesis 3 2 1
quinate degradation II 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
quinate degradation I 3 1 1
superpathway of L-phenylalanine biosynthesis 10 10 3
superpathway of L-tyrosine biosynthesis 10 10 3
chorismate biosynthesis I 7 7 2
L-tyrosine biosynthesis III 4 3 1
L-phenylalanine biosynthesis II 4 3 1
L-tyrosine biosynthesis II 4 2 1
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
superpathway of aromatic amino acid biosynthesis 18 18 4
L-tyrosine degradation I 5 5 1
superpathway of L-phenylalanine and L-tyrosine biosynthesis 5 3 1
superpathway of plastoquinol biosynthesis 5 2 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
chorismate biosynthesis II (archaea) 12 8 2
superpathway of L-tryptophan biosynthesis 13 13 2
L-phenylalanine degradation IV (mammalian, via side chain) 9 5 1
L-histidine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 2 1
tropane alkaloids biosynthesis 11 1 1
(S)-reticuline biosynthesis I 11 1 1
superpathway of rosmarinic acid biosynthesis 14 2 1
superpathway of chorismate metabolism 59 43 4
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis 16 3 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 4 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 histidine, purine, and pyrimidine biosynthesis 46 44 1