Experiment set5IT071 for Dinoroseobacter shibae DFL-12
Uridine nitrogen source
Group: nitrogen sourceMedia: DinoMM_noNitrogen_HighNutrient + Uridine (5 mM), pH=7.2
Culturing: Dino_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.0 generations
By: Adam on 5/14/2014
Media components: 20 g/L Sea salts, 0.1 g/L Potassium phosphate monobasic, 1.37 g/L Sodium acetate, 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 3 genes in this experiment
For nitrogen source Uridine in Dinoroseobacter shibae DFL-12
For nitrogen source Uridine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Pyrimidine utilization | 2 |
| Pyruvate Alanine Serine Interconversions | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glutamate metabolism
- beta-Alanine metabolism
- Nitrogen metabolism
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Pyrimidine metabolism
- Alanine and aspartate metabolism
- Valine, leucine and isoleucine degradation
- 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
- Propanoate metabolism
- Pantothenate and CoA biosynthesis
- Limonene and pinene degradation
- Drug metabolism - other enzymes
- Biosynthesis of alkaloids derived from shikimate pathway
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-glutamate biosynthesis I | 2 | 2 | 2 |
| L-glutamate biosynthesis IV | 1 | 1 | 1 |
| L-glutamine degradation I | 1 | 1 | 1 |
| L-glutamine degradation II | 1 | 1 | 1 |
| ammonia assimilation cycle III | 3 | 3 | 2 |
| β-alanine degradation II | 2 | 2 | 1 |
| ammonia assimilation cycle I | 2 | 2 | 1 |
| L-glutamate and L-glutamine biosynthesis | 7 | 6 | 3 |
| thymine degradation | 3 | 3 | 1 |
| uracil degradation I (reductive) | 3 | 3 | 1 |
| superpathway of ammonia assimilation (plants) | 3 | 3 | 1 |
| L-asparagine biosynthesis III (tRNA-dependent) | 4 | 4 | 1 |
| glutaminyl-tRNAgln biosynthesis via transamidation | 4 | 4 | 1 |
| superpathway of pyrimidine ribonucleosides degradation | 5 | 5 | 1 |
| β-alanine biosynthesis II | 6 | 4 | 1 |
| L-citrulline biosynthesis | 8 | 7 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 8 | 1 |
| superpathway of L-citrulline metabolism | 12 | 9 | 1 |