Experiment set2S519 for Bacteroides stercoris CC31F
beta-Cyclodextrin 2.5 mg/mL carbon source
Group: carbon sourceMedia: Varel_Bryant_medium + beta-Cyclodextrin (2.5 mg/mL)
Culturing: Bstercoris_CC31F_ML5, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 10/31/24
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 8.25 mM L-Cysteine, 23.8 mM Sodium bicarbonate, Mineral 3B solution (6.6 mM Potassium phosphate monobasic, 15.4 mM Sodium Chloride, 98 uM Magnesium chloride hexahydrate, 176.5 uM Calcium chloride dihydrate, 4.2 uM Cobalt chloride hexahydrate, 50.5 uM Manganese (II) chloride tetrahydrate, 9.3 mM Ammonium chloride, 1.75 mM Sodium sulfate)
Specific Phenotypes
For 12 genes in this experiment
For carbon source beta-Cyclodextrin in Bacteroides stercoris CC31F
For carbon source beta-Cyclodextrin across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Alkylphosphonate utilization | 1 |
| Terminal cytochrome d ubiquinol oxidases | 1 |
| Terminal cytochrome oxidases | 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 |
|---|---|---|---|
| L-tryptophan degradation II (via pyruvate) | 3 | 3 | 1 |
| L-serine degradation | 3 | 3 | 1 |
| D-serine degradation | 3 | 2 | 1 |
| L-cysteine degradation II | 3 | 2 | 1 |
| L-methionine degradation II | 3 | 2 | 1 |
| felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis | 5 | 2 | 1 |
| L-threonine degradation I | 6 | 5 | 1 |
| L-methionine biosynthesis II | 6 | 3 | 1 |
| L-isoleucine biosynthesis I (from threonine) | 7 | 6 | 1 |
| glycine betaine degradation III | 7 | 4 | 1 |
| L-mimosine degradation | 8 | 4 | 1 |
| glycine betaine degradation I | 8 | 4 | 1 |
| glutathione-mediated detoxification I | 8 | 2 | 1 |
| superpathway of L-isoleucine biosynthesis I | 13 | 11 | 1 |
| hypoglycin biosynthesis | 14 | 2 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 12 | 1 |
| superpathway of branched chain amino acid biosynthesis | 17 | 16 | 1 |
| superpathway of L-threonine metabolism | 18 | 14 | 1 |
| purine nucleobases degradation II (anaerobic) | 24 | 12 | 1 |