Experiment set1S644 for Mucilaginibacter yixingensis YX-36 DSM 26809
D-Xylose carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Xylose (20 mM)
Culturing: Mucilaginibacter_YX36_ML5a, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Marta Torres on 4/20/23
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Specific Phenotypes
For 2 genes in this experiment
For carbon source D-Xylose in Mucilaginibacter yixingensis YX-36 DSM 26809
For carbon source D-Xylose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Calvin-Benson cycle | 1 |
| Pentose phosphate pathway | 1 |
| Xylose utilization | 1 |
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
- Fructose and mannose metabolism
- Carbon fixation in photosynthetic organisms
- Biosynthesis of ansamycins
- Biosynthesis of phenylpropanoids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| pentose phosphate pathway (partial) | 3 | 3 | 2 |
| D-xylose degradation I | 2 | 2 | 1 |
| pentose phosphate pathway (non-oxidative branch) I | 5 | 5 | 2 |
| pentose phosphate pathway (non-oxidative branch) II | 6 | 5 | 2 |
| D-apiose degradation I | 3 | 1 | 1 |
| pentose phosphate pathway | 8 | 8 | 2 |
| formaldehyde assimilation II (assimilatory RuMP Cycle) | 9 | 7 | 2 |
| Rubisco shunt | 10 | 9 | 2 |
| superpathway of glucose and xylose degradation | 17 | 16 | 3 |
| formaldehyde assimilation III (dihydroxyacetone cycle) | 12 | 10 | 2 |
| Calvin-Benson-Bassham cycle | 13 | 10 | 2 |
| oxygenic photosynthesis | 17 | 10 | 2 |
| ethene biosynthesis V (engineered) | 25 | 17 | 2 |
| photosynthetic 3-hydroxybutanoate biosynthesis (engineered) | 26 | 16 | 2 |
| 1-butanol autotrophic biosynthesis (engineered) | 27 | 18 | 2 |
| Bifidobacterium shunt | 15 | 11 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 8 | 1 |