Experiment set1IT015 for Escherichia coli BW25113
D-Ribose carbon source
Group: carbon sourceMedia: M9 minimal media_noCarbon + D-Ribose (20 mM)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
Growth: about 5.6 generations
By: Kelly on 6/19/2014
Media components: 2 mM Magnesium sulfate, 0.1 mM Calcium chloride, 12.8 g/L Sodium phosphate dibasic heptahydrate, 3 g/L Potassium phosphate monobasic, 0.5 g/L Sodium Chloride, 1 g/L Ammonium chloride
Specific Phenotypes
For 15 genes in this experiment
For carbon source D-Ribose in Escherichia coli BW25113
For carbon source D-Ribose across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pentose phosphate pathway
- Pentose and glucuronate interconversions
- Biosynthesis of steroids
- Glycine, serine and threonine metabolism
- Selenoamino acid metabolism
- Lipopolysaccharide biosynthesis
- Glycerolipid metabolism
- Glyoxylate and dicarboxylate metabolism
- Propanoate metabolism
- Carbon fixation in photosynthetic organisms
- Carotenoid biosynthesis - General
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| ribose phosphorylation | 2 | 2 | 2 |
| 2-O-α-mannosyl-D-glycerate degradation | 2 | 2 | 1 |
| 2-deoxy-D-ribose degradation I | 3 | 3 | 1 |
| glycolate and glyoxylate degradation I | 4 | 4 | 1 |
| D-glucarate degradation I | 4 | 4 | 1 |
| D-galactarate degradation I | 4 | 4 | 1 |
| 2-methylcitrate cycle I | 5 | 5 | 1 |
| superpathway of D-glucarate and D-galactarate degradation | 5 | 5 | 1 |
| superpathway of glycol metabolism and degradation | 7 | 7 | 1 |
| 2-deoxy-D-ribose degradation II | 8 | 3 | 1 |
| Entner-Doudoroff pathway II (non-phosphorylative) | 9 | 6 | 1 |
| photorespiration III | 9 | 5 | 1 |
| photorespiration I | 9 | 5 | 1 |
| tunicamycin biosynthesis | 9 | 2 | 1 |
| Rubisco shunt | 10 | 9 | 1 |
| photorespiration II | 10 | 6 | 1 |
| Calvin-Benson-Bassham cycle | 13 | 10 | 1 |
| formaldehyde assimilation I (serine pathway) | 13 | 8 | 1 |
| oxygenic photosynthesis | 17 | 11 | 1 |
| ethene biosynthesis V (engineered) | 25 | 18 | 1 |
| photosynthetic 3-hydroxybutanoate biosynthesis (engineered) | 26 | 19 | 1 |
| 1-butanol autotrophic biosynthesis (engineered) | 27 | 19 | 1 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 19 | 1 |