Experiment set3H18 for Dinoroseobacter shibae DFL-12
Xylitol carbon source
Group: carbon sourceMedia: DinoMM_noCarbon_HighNutrient + Xylitol (20 mM)
Culturing: Dino_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 7.2 generations
By: Adam on 2/27/2014
Media components: 20 g/L Sea salts, 0.3 g/L Ammonium Sulfate, 0.1 g/L Potassium phosphate monobasic, 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)
Specific Phenotypes
For 12 genes in this experiment
For carbon source Xylitol in Dinoroseobacter shibae DFL-12
For carbon source Xylitol across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 7 |
| Xylose utilization | 3 |
| Maltose and Maltodextrin Utilization | 1 |
| Mannitol Utilization | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pentose and glucuronate interconversions
- Fructose and mannose metabolism
- Ascorbate and aldarate metabolism
- C21-Steroid hormone metabolism
- Glycine, serine and threonine metabolism
- Bisphenol A degradation
- Nucleotide sugars metabolism
- Polyketide sugar unit biosynthesis
- Aminosugars metabolism
- Linoleic acid metabolism
- Tetrachloroethene degradation
- Benzoate degradation via CoA ligation
- Butanoate metabolism
- Retinol metabolism
- Alkaloid biosynthesis I
- Insect hormone biosynthesis
- Biosynthesis of unsaturated fatty acids
- Biosynthesis of type II polyketide products
- Biosynthesis of alkaloids derived from shikimate pathway
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| xylitol degradation I | 2 | 2 | 2 |
| D-xylose degradation I | 2 | 2 | 1 |
| D-arabinitol degradation I | 2 | 1 | 1 |
| D-sorbitol degradation I | 3 | 3 | 1 |
| D-fructuronate degradation | 4 | 2 | 1 |
| mannitol cycle | 5 | 3 | 1 |
| superpathway of β-D-glucuronosides degradation | 7 | 3 | 1 |
| superpathway of hexuronide and hexuronate degradation | 10 | 4 | 1 |
| superpathway of glucose and xylose degradation | 17 | 14 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 15 | 2 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 9 | 1 |