Experiment set29IT017 for Pseudomonas putida KT2440
2,6-diaminopimelic acid nitrogen source
Group: nitrogen sourceMedia: MOPS minimal media_Glucose_noNitrogen + 2,6-diaminopimelic acid (4 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Matthias Schmidt on 4/13/21
Media components: 10 mM D-Glucose, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate
Specific Phenotypes
For 9 genes in this experiment
For nitrogen source 2,6-diaminopimelic acid in Pseudomonas putida KT2440
For nitrogen source 2,6-diaminopimelic acid across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ammonia assimilation | 1 |
| Glycogen metabolism | 1 |
| Lysine degradation | 1 |
| Maltose and Maltodextrin Utilization | 1 |
| Polyamine Metabolism | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Lysine degradation
- Tryptophan metabolism
- Starch and sucrose metabolism
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| indole-3-acetate biosynthesis III (bacteria) | 2 | 2 | 1 |
| glycogen degradation I | 8 | 6 | 3 |
| glycogen degradation II | 6 | 5 | 2 |
| starch degradation V | 4 | 3 | 1 |
| starch degradation III | 4 | 2 | 1 |
| L-lysine degradation IV | 5 | 5 | 1 |
| sucrose biosynthesis II | 8 | 6 | 1 |
| superpathway of L-lysine degradation | 43 | 23 | 1 |