Experiment set1IT052 for Paraburkholderia graminis OAS925
L-Arabinose carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + L-Arabinose (20 mM)
Culturing: Burkholderia_OAS925_ML2, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Marta on 10-Apr-21
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 8 genes in this experiment
For carbon source L-Arabinose in Paraburkholderia graminis OAS925
For carbon source L-Arabinose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| L-Arabinose utilization | 6 |
| D-galactonate catabolism | 1 |
| Xylose utilization | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Ascorbate and aldarate metabolism
- Valine, leucine and isoleucine biosynthesis
- Lysine biosynthesis
- Pantothenate and CoA biosynthesis
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Biosynthesis of alkaloids derived from histidine and purine
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-arabinose degradation III | 6 | 5 | 4 |
| L-lyxonate degradation | 3 | 2 | 2 |
| D-glucarate degradation II | 3 | 3 | 1 |
| D-galactarate degradation II | 3 | 3 | 1 |
| L-arabinose degradation V | 6 | 5 | 2 |
| L-valine biosynthesis | 4 | 4 | 1 |
| L-arabinose degradation IV | 8 | 6 | 2 |
| trans-4-hydroxy-L-proline degradation II | 4 | 3 | 1 |
| D-glucuronate degradation II | 5 | 4 | 1 |
| pyruvate fermentation to isobutanol (engineered) | 5 | 4 | 1 |
| D-galacturonate degradation II | 5 | 3 | 1 |
| D-xylose degradation V | 5 | 2 | 1 |
| D-xylose degradation III | 5 | 2 | 1 |
| L-isoleucine biosynthesis IV | 6 | 4 | 1 |
| D-arabinose degradation III | 6 | 3 | 1 |
| L-isoleucine biosynthesis I (from threonine) | 7 | 7 | 1 |
| L-isoleucine biosynthesis III | 7 | 4 | 1 |
| L-isoleucine biosynthesis II | 8 | 5 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 21 | 5 |
| superpathway of branched chain amino acid biosynthesis | 17 | 17 | 2 |
| superpathway of L-isoleucine biosynthesis I | 13 | 13 | 1 |
| superpathway of L-threonine metabolism | 18 | 14 | 1 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 19 | 1 |