Experiment set3IT093 for Agrobacterium fabrum C58
Orotic acid nitrogen source
Group: nitrogen sourceMedia: MOPS minimal media_Succinate_noNitrogen + Orotic acid (5 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 11/20/20
Media components: 10 mM Sodium succinate dibasic hexahydrate, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate
Specific Phenotypes
For 15 genes in this experiment
For nitrogen source Orotic acid in Agrobacterium fabrum C58
For nitrogen source Orotic acid across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Pyrimidine utilization | 4 |
| Ammonia assimilation | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Carotenoid biosynthesis - General
- Ascorbate and aldarate metabolism
- Biosynthesis of steroids
- Ubiquinone and menaquinone biosynthesis
- Purine metabolism
- Puromycin biosynthesis
- Caffeine metabolism
- gamma-Hexachlorocyclohexane degradation
- Tryptophan metabolism
- Benzoxazinone biosynthesis
- Nucleotide sugars metabolism
- alpha-Linolenic acid metabolism
- Sphingolipid metabolism
- Naphthalene and anthracene degradation
- 1,4-Dichlorobenzene degradation
- Trinitrotoluene degradation
- Porphyrin and chlorophyll metabolism
- Limonene and pinene degradation
- Diterpenoid biosynthesis
- Brassinosteroid biosynthesis
- Phenylpropanoid biosynthesis
- Alkaloid biosynthesis I
- Insect hormone biosynthesis
- Biosynthesis of phenylpropanoids
- Biosynthesis of terpenoids and steroids
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| uracil degradation III | 5 | 5 | 4 |
| β-alanine degradation III | 2 | 1 | 1 |
| urate conversion to allantoin I | 3 | 2 | 1 |
| ureide biosynthesis | 7 | 6 | 1 |
| 3-hydroxypropanoate cycle | 13 | 8 | 1 |
| glyoxylate assimilation | 13 | 5 | 1 |
| superpathway of purines degradation in plants | 18 | 12 | 1 |
| 3-hydroxypropanoate/4-hydroxybutanate cycle | 18 | 11 | 1 |
| superpathway of the 3-hydroxypropanoate cycle | 18 | 8 | 1 |