Experiment set5IT081 for Dinoroseobacter shibae DFL-12
marine broth with Sodium nitrite 0.6 mM
Group: stressMedia: marine_broth_2216 + Sodium nitrite (0.6 mM)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Adam on 5/14/2014
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: 917 B5,B6
Specific Phenotypes
For 15 genes in this experiment
For stress Sodium nitrite in Dinoroseobacter shibae DFL-12
For stress Sodium nitrite across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Biosynthesis of plant hormones
- Glycine, serine and threonine metabolism
- Methionine metabolism
- Cysteine metabolism
- Valine, leucine and isoleucine degradation
- 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
- Benzoate degradation via hydroxylation
- Selenoamino acid metabolism
- Naphthalene and anthracene degradation
- Propanoate metabolism
- Nicotinate and nicotinamide metabolism
- Carotenoid biosynthesis - General
- Nitrogen metabolism
- Sulfur metabolism
- Biosynthesis of phenylpropanoids
- Biosynthesis of terpenoids and steroids
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| sulfide oxidation II (flavocytochrome c) | 1 | 1 | 1 |
| choline degradation I | 2 | 1 | 1 |
| glycine betaine biosynthesis I (Gram-negative bacteria) | 2 | 1 | 1 |
| glycine betaine biosynthesis II (Gram-positive bacteria) | 2 | 1 | 1 |
| urate conversion to allantoin III | 3 | 3 | 1 |
| propanoyl CoA degradation I | 3 | 3 | 1 |
| choline-O-sulfate degradation | 3 | 1 | 1 |
| 2-oxobutanoate degradation I | 4 | 3 | 1 |
| anaerobic energy metabolism (invertebrates, mitochondrial) | 10 | 6 | 1 |
| 3-hydroxypropanoate cycle | 13 | 9 | 1 |
| superpathway of L-methionine salvage and degradation | 16 | 10 | 1 |
| superpathway of anaerobic energy metabolism (invertebrates) | 17 | 10 | 1 |
| superpathway of the 3-hydroxypropanoate cycle | 18 | 12 | 1 |
| 3-hydroxypropanoate/4-hydroxybutanate cycle | 18 | 11 | 1 |
| methylaspartate cycle | 19 | 14 | 1 |
| mycolate biosynthesis | 205 | 21 | 1 |
| superpathway of mycolate biosynthesis | 239 | 22 | 1 |