Experiment set18IT034 for Pseudomonas simiae WCS417

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Chemotaxis:Motility:: Method=Plug_approach; Chemical=L-Proline; Chemical_conc=5mM; Distance=2cm; Sample=outer; Collection=outgrowth_in_LBkan50

Group: motility_chemotaxis
Media: RCH2_defined_NO_salts_with_Glycerol + Method=Plug_approach; Chemical=L-Proline; Chemical_conc=5mM; Distance=2cm; Sample=outer; Collection=outgrowth_in_LBkan50
Culturing: fluoroDangl_ML3, soft agar plate, Aerobic, at 30 (C), shaken=0 rpm, (solid)
By: Peter Kim on 17-Aug-21
Media components: 2.2 mM Glycerol, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 20 genes in this experiment

For motility_chemotaxis Method=Plug_approach; Chemical=L-Proline; Chemical_conc=5mM; Distance=2cm; Sample=outer; Collection=outgrowth_in_LBkan50 in Pseudomonas simiae WCS417

For motility_chemotaxis Method=Plug_approach; Chemical=L-Proline; Chemical_conc=5mM; Distance=2cm; Sample=outer; Collection=outgrowth_in_LBkan50 across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 3
Lysine degradation 2
Arginine Deiminase Pathway 1
Arginine and Ornithine Degradation 1
Bacterial Chemotaxis 1
Chorismate Synthesis 1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 1
Flagellar motility 1
Glycerol and Glycerol-3-phosphate Uptake and Utilization 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Heat shock dnaK gene cluster extended 1
MLST 1
Nitrate and nitrite ammonification 1
Peptidoglycan Biosynthesis 1
Polyamine Metabolism 1
tRNA processing 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-dehydroquinate biosynthesis I 2 2 1
alkylnitronates degradation 2 2 1
nitrate reduction V (assimilatory) 2 1 1
glycerol degradation I 3 3 1
glycerol and glycerophosphodiester degradation 4 4 1
tRNA processing 10 8 2
chorismate biosynthesis I 7 7 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-tryptophan biosynthesis 13 13 1
superpathway of aromatic amino acid biosynthesis 18 18 1
superpathway of chorismate metabolism 59 44 1