Experiment set1H7 for Dinoroseobacter shibae DFL-12
marine broth with copper (II) chloride dihydrate 0.64 mM
Group: stressMedia: marine_broth_2216 + copper (II) chloride dihydrate (0.64 mM)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 26 (C), shaken=orbital
By: Jordan on 8/16/2013
Media components: 5 g/L Bacto Peptone, 1 g/L Yeast Extract, 0.1 g/L Ferric citrate, 19.45 g/L Sodium Chloride, 5.9 g/L Magnesium chloride hexahydrate, 3.24 g/L Magnesium sulfate, 1.8 g/L Calcium chloride, 0.55 g/L Potassium Chloride, 0.16 g/L Sodium bicarbonate, 0.08 g/L Potassium bromide, 34 mg/L Strontium chloride, 22 mg/L Boric Acid, 4 mg/L Sodium metasilicate, 2.4 mg/L sodium fluoride, 8 mg/L Disodium phosphate
Growth plate: 641 C1,C2
Specific Phenotypes
For 4 genes in this experiment
For stress copper (II) chloride dihydrate in Dinoroseobacter shibae DFL-12
For stress copper (II) chloride dihydrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Bacterial Cell Division | 1 |
| Bacterial Cytoskeleton | 1 |
| Dissimilatory nitrite reductase | 1 |
| Heme biosynthesis orphans | 1 |
| L-rhamnose utilization | 1 |
| Methylglyoxal Metabolism | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Ubiquinone and menaquinone biosynthesis
- Histidine metabolism
- Tyrosine metabolism
- Tryptophan metabolism
- Benzoxazinone biosynthesis
- Pyruvate metabolism
- Naphthalene and anthracene degradation
- Porphyrin and chlorophyll metabolism
- Carotenoid biosynthesis - General
- Phenylpropanoid biosynthesis
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Alkaloid biosynthesis I
- Insect hormone biosynthesis
- Biosynthesis of alkaloids derived from shikimate pathway
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-lactaldehyde degradation (aerobic) | 2 | 1 | 1 |
| heme d1 biosynthesis | 3 | 2 | 1 |
| methylglyoxal degradation V | 3 | 2 | 1 |
| methylglyoxal degradation IV | 3 | 1 | 1 |
| heme b biosynthesis III (from siroheme) | 3 | 1 | 1 |
| lactate biosynthesis (archaea) | 5 | 3 | 1 |
| superpathway of methylglyoxal degradation | 8 | 3 | 1 |
| L-rhamnose degradation II | 8 | 2 | 1 |
| superpathway of fucose and rhamnose degradation | 12 | 8 | 1 |