Experiment set10IT009 for Agrobacterium fabrum C58
trans-aconitic acid carbon source
Group: carbon sourceMedia: MOPS minimal media_noCarbon + trans-aconitic acid (10 mM), pH=7
Culturing: Agro_ML11, 24-well plate, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 1/6/22
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 5 genes in this experiment
For carbon source trans-aconitic acid in Agrobacterium fabrum C58
For carbon source trans-aconitic acid across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Thiamin biosynthesis | 2 |
| Alkanesulfonate assimilation | 1 |
| DNA-binding regulatory proteins, strays | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| gallate degradation I | 4 | 2 | 1 |
| gallate degradation II | 5 | 3 | 1 |
| methylgallate degradation | 6 | 3 | 1 |
| protocatechuate degradation I (meta-cleavage pathway) | 8 | 4 | 1 |
| superpathway of vanillin and vanillate degradation | 10 | 5 | 1 |
| syringate degradation | 12 | 4 | 1 |