Experiment set13IT062 for Bifidobacterium breve UCC2003
CDM1Gut with 50% spent media from Bifidobacterium adolescentis L2-32
Group: supernatantMedia: CDM1Gut + Bifidobacterium adolescentis L2-32 supernatant in CDM1Gut (0.5 x), pH=7
Culturing: Bifido_ML2, tube, Anaerobic, at 37 (C), shaken=0 rpm
By: Rebecca Culver on 4/1/2021
Specific Phenotypes
For 2 genes in this experiment
For supernatant Bifidobacterium adolescentis L2-32 supernatant in CDM1Gut across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Serine-glyoxylate cycle | 1 |
| TCA Cycle | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Citrate cycle (TCA cycle)
- Glyoxylate and dicarboxylate 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 |
|---|---|---|---|
| glyoxylate cycle | 6 | 3 | 1 |
| nitrogen remobilization from senescing leaves | 8 | 5 | 1 |
| partial TCA cycle (obligate autotrophs) | 8 | 5 | 1 |
| TCA cycle V (2-oxoglutarate synthase) | 9 | 5 | 1 |
| TCA cycle VII (acetate-producers) | 9 | 4 | 1 |
| TCA cycle VI (Helicobacter) | 9 | 4 | 1 |
| TCA cycle II (plants and fungi) | 9 | 4 | 1 |
| TCA cycle IV (2-oxoglutarate decarboxylase) | 9 | 4 | 1 |
| TCA cycle I (prokaryotic) | 10 | 5 | 1 |
| TCA cycle III (animals) | 10 | 5 | 1 |
| superpathway of glyoxylate bypass and TCA | 12 | 5 | 1 |
| superpathway of glyoxylate cycle and fatty acid degradation | 14 | 3 | 1 |
| mixed acid fermentation | 16 | 11 | 1 |
| methylaspartate cycle | 19 | 6 | 1 |
| superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle | 22 | 12 | 1 |
| ethene biosynthesis V (engineered) | 25 | 16 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 15 | 1 |