Experiment set19IT058 for Pseudomonas simiae WCS417
Chemotaxis:Motility:: Method=Plug_approach; Chemical=L-Proline; 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 9 genes in this experiment
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Purine metabolism
- Pyrimidine metabolism
- Glycerolipid metabolism
- Nicotinate and nicotinamide metabolism
- Biosynthesis of alkaloids derived from histidine and purine
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| glycerol degradation I | 3 | 3 | 1 |
| NAD salvage pathway III (to nicotinamide riboside) | 3 | 2 | 1 |
| UTP and CTP dephosphorylation I | 7 | 5 | 2 |
| purine nucleotides degradation II (aerobic) | 11 | 11 | 3 |
| glycerol and glycerophosphodiester degradation | 4 | 4 | 1 |
| guanosine nucleotides degradation III | 4 | 4 | 1 |
| guanosine nucleotides degradation II | 4 | 4 | 1 |
| inosine 5'-phosphate degradation | 4 | 4 | 1 |
| adenosine nucleotides degradation I | 8 | 7 | 2 |
| purine nucleotides degradation I (plants) | 12 | 10 | 3 |
| guanosine nucleotides degradation I | 4 | 3 | 1 |
| adenosine nucleotides degradation II | 5 | 5 | 1 |
| superpathway of guanosine nucleotides degradation (plants) | 6 | 5 | 1 |
| superpathway of purines degradation in plants | 18 | 14 | 3 |
| ureide biosynthesis | 7 | 6 | 1 |
| tunicamycin biosynthesis | 9 | 2 | 1 |
| NAD salvage (plants) | 11 | 5 | 1 |