Experiment set5IT060 for Dinoroseobacter shibae DFL-12
Urea nitrogen source
Group: nitrogen sourceMedia: DinoMM_noNitrogen_HighNutrient + Urea (5 mM), pH=7.2
Culturing: Dino_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.5 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 1 genes in this experiment
For nitrogen source Urea in Dinoroseobacter shibae DFL-12
For nitrogen source Urea across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 1 |
| TCA Cycle | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycolysis / Gluconeogenesis
- Citrate cycle (TCA cycle)
- Glycine, serine and threonine metabolism
- Valine, leucine and isoleucine degradation
- Pyruvate metabolism
- Biosynthesis of phenylpropanoids
- Biosynthesis of terpenoids and steroids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of alkaloids derived from terpenoid and polyketide
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| glycine cleavage | 3 | 3 | 1 |
| pyruvate decarboxylation to acetyl CoA I | 3 | 3 | 1 |
| glycine biosynthesis II | 3 | 3 | 1 |
| 2-oxoisovalerate decarboxylation to isobutanoyl-CoA | 3 | 3 | 1 |
| 2-oxoglutarate decarboxylation to succinyl-CoA | 3 | 3 | 1 |
| 3,3'-disulfanediyldipropannoate degradation | 4 | 2 | 1 |
| superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle | 22 | 19 | 1 |