Experiment set6IT020 for Klebsiella michiganensis M5al
D-Serine nitrogen source
Group: nitrogen sourceMedia: RCH2_defined_Glucose_noNitrogen + D-Serine (20 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 27-Apr-17
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 30 mM PIPES sesquisodium salt, 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)
Growth plate: 1808 D3
Specific Phenotypes
For 6 genes in this experiment
For nitrogen source D-Serine in Klebsiella michiganensis M5al
For nitrogen source D-Serine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Pyruvate Alanine Serine Interconversions | 2 |
| Alanine biosynthesis | 1 |
| Glycine and Serine Utilization | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Alanine and aspartate metabolism
- Glycine, serine and threonine metabolism
- Tryptophan metabolism
- D-Alanine metabolism
- Biosynthesis of siderophore group nonribosomal peptides
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| D-serine degradation | 3 | 3 | 3 |
| alanine racemization | 1 | 1 | 1 |
| L-serine degradation | 3 | 3 | 2 |
| L-cysteine degradation II | 3 | 3 | 2 |
| L-tryptophan degradation II (via pyruvate) | 3 | 3 | 2 |
| L-alanine degradation I | 2 | 2 | 1 |
| felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis | 5 | 2 | 2 |
| L-methionine biosynthesis II | 6 | 5 | 2 |
| glycine betaine degradation III | 7 | 4 | 2 |
| L-mimosine degradation | 8 | 4 | 2 |
| glycine betaine degradation I | 8 | 4 | 2 |
| glutathione-mediated detoxification I | 8 | 3 | 2 |
| peptidoglycan recycling II | 10 | 7 | 2 |
| peptidoglycan recycling I | 14 | 14 | 2 |
| anaerobic energy metabolism (invertebrates, cytosol) | 7 | 5 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 13 | 2 |
| ansatrienin biosynthesis | 9 | 1 | 1 |
| purine nucleobases degradation II (anaerobic) | 24 | 17 | 2 |
| cyclosporin A biosynthesis | 15 | 2 | 1 |
| superpathway of anaerobic energy metabolism (invertebrates) | 17 | 12 | 1 |