Experiment set19IT066 for Pseudomonas simiae WCS417
Chemotaxis:Motility:: Method=Plug_approach; Chemical=L-Threonine; Chemical_conc=5mM; Distance=2cm; Sample=outer; Collection=outgrowth_in_LBkan50
Group: motility_chemotaxisMedia: RCH2_defined_NO_ammonium_with_Glycerol
Culturing: fluoroDangl_ML3, soft agar plate, Aerobic, at 30 (C), shaken=0 rpm, (solid)
By: Peter Kim on 4-Oct-21
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, 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 3 genes in this experiment
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ammonia assimilation | 1 |
| Glycine and Serine Utilization | 1 |
| Glycine cleavage system | 1 |
| Photorespiration (oxidative C2 cycle) | 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 |
|---|---|---|---|
| glycine biosynthesis IV | 1 | 1 | 1 |
| L-threonine degradation IV | 2 | 2 | 1 |
| glycine degradation | 3 | 3 | 1 |
| glycine biosynthesis II | 3 | 3 | 1 |
| glycine cleavage | 3 | 3 | 1 |
| folate transformations III (E. coli) | 9 | 9 | 1 |
| photorespiration III | 9 | 5 | 1 |
| reductive glycine pathway of autotrophic CO2 fixation | 9 | 5 | 1 |
| photorespiration I | 9 | 5 | 1 |
| photorespiration II | 10 | 6 | 1 |
| folate transformations II (plants) | 11 | 10 | 1 |
| folate transformations I | 13 | 9 | 1 |
| superpathway of L-threonine metabolism | 18 | 12 | 1 |