Experiment set3H8 for Dinoroseobacter shibae DFL-12
L-Rhamnose monohydrate carbon source
Group: carbon sourceMedia: DinoMM_noCarbon_HighNutrient + L-Rhamnose monohydrate (20 mM)
Culturing: Dino_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.8 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 10 genes in this experiment
For carbon source L-Rhamnose monohydrate in Dinoroseobacter shibae DFL-12
For carbon source L-Rhamnose monohydrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| L-rhamnose utilization | 9 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Fructose and mannose metabolism
- Pentose and glucuronate interconversions
- Nucleotide sugars metabolism
- Polyketide sugar unit biosynthesis
- Pyruvate metabolism
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-rhamnose degradation I | 5 | 5 | 4 |
| L-lactaldehyde degradation (aerobic) | 2 | 1 | 1 |
| superpathway of fucose and rhamnose degradation | 12 | 8 | 5 |
| methylglyoxal degradation V | 3 | 2 | 1 |
| methylglyoxal degradation IV | 3 | 1 | 1 |
| L-lyxose degradation | 4 | 1 | 1 |
| lactate biosynthesis (archaea) | 5 | 3 | 1 |
| superpathway of methylglyoxal degradation | 8 | 3 | 1 |
| L-rhamnose degradation II | 8 | 2 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 15 | 1 |