Experiment set2IT016 for Agrobacterium fabrum C58
Sodium gluconate carbon source
Group: carbon sourceMedia: MOPS minimal media_noCarbon + Sodium gluconate (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 10/20/20
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 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 7 genes in this experiment
For carbon source Sodium gluconate in Agrobacterium fabrum C58
For carbon source Sodium gluconate across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pentose phosphate pathway
- Pentose and glucuronate interconversions
- Ascorbate and aldarate metabolism
- Lipopolysaccharide biosynthesis
- Glycerophospholipid metabolism
- 2,4-Dichlorobenzoate degradation
- Butanoate metabolism
- Nicotinate and nicotinamide metabolism
- Retinol metabolism
- Alkaloid biosynthesis II
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| D-gluconate degradation | 1 | 1 | 1 |
| L-idonate degradation | 3 | 3 | 1 |
| sorbitol biosynthesis II | 3 | 3 | 1 |
| D-fructuronate degradation | 4 | 4 | 1 |
| 4-deoxy-L-threo-hex-4-enopyranuronate degradation | 5 | 5 | 1 |
| D-galacturonate degradation I | 5 | 3 | 1 |
| superpathway of β-D-glucuronosides degradation | 7 | 5 | 1 |
| alginate degradation | 7 | 4 | 1 |
| 3,6-anhydro-α-L-galactopyranose degradation | 7 | 4 | 1 |
| ketogluconate metabolism | 8 | 4 | 1 |
| Entner-Doudoroff pathway III (semi-phosphorylative) | 9 | 7 | 1 |
| superpathway of hexuronide and hexuronate degradation | 10 | 6 | 1 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 22 | 1 |