Experiment set3IT033 for Dyella japonica UNC79MFTsu3.2
LB with Spectinomycin dihydrochloride pentahydrate 0.04 mg/ml
Group: stressMedia: LB + Spectinomycin dihydrochloride pentahydrate (0.04 mg/ml)
Culturing: Dyella79_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.3 generations
By: Adam on 17-May-17
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1769 B6
Specific Phenotypes
For 11 genes in this experiment
For stress Spectinomycin dihydrochloride pentahydrate in Dyella japonica UNC79MFTsu3.2
For stress Spectinomycin dihydrochloride pentahydrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Multidrug Resistance Efflux Pumps | 4 |
| Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) | 3 |
| Propionate-CoA to Succinate Module | 1 |
| TCA Cycle | 1 |
| tRNA processing | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Citrate cycle (TCA cycle)
- Pyrimidine metabolism
- Lysine degradation
- Peptidoglycan biosynthesis
- Glyoxylate and dicarboxylate metabolism
- Reductive carboxylate cycle (CO2 fixation)
- Biotin metabolism
- Biosynthesis of phenylpropanoids
- Biosynthesis of terpenoids and steroids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of alkaloids derived from terpenoid and polyketide
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| pseudouridine degradation | 2 | 1 | 1 |
| glyoxylate cycle | 6 | 6 | 2 |
| nitrogen remobilization from senescing leaves | 8 | 7 | 2 |
| partial TCA cycle (obligate autotrophs) | 8 | 7 | 2 |
| TCA cycle II (plants and fungi) | 9 | 8 | 2 |
| TCA cycle IV (2-oxoglutarate decarboxylase) | 9 | 8 | 2 |
| TCA cycle V (2-oxoglutarate synthase) | 9 | 8 | 2 |
| TCA cycle VII (acetate-producers) | 9 | 6 | 2 |
| TCA cycle VI (Helicobacter) | 9 | 6 | 2 |
| 2-methylcitrate cycle I | 5 | 5 | 1 |
| TCA cycle III (animals) | 10 | 9 | 2 |
| TCA cycle I (prokaryotic) | 10 | 8 | 2 |
| reductive TCA cycle I | 11 | 6 | 2 |
| superpathway of glyoxylate bypass and TCA | 12 | 10 | 2 |
| 2-methylcitrate cycle II | 6 | 5 | 1 |
| reductive TCA cycle II | 12 | 6 | 2 |
| superpathway of glyoxylate cycle and fatty acid degradation | 14 | 11 | 2 |
| mixed acid fermentation | 16 | 11 | 2 |
| methylaspartate cycle | 19 | 11 | 2 |
| superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle | 22 | 19 | 2 |
| ethene biosynthesis V (engineered) | 25 | 17 | 2 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 23 | 2 |