Experiment set2IT059 for Pedobacter sp. GW460-11-11-14-LB5
L-Arabinose carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + L-Arabinose (20 mM), pH=7
Culturing: Pedo557_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.8 generations
By: Adam on 16-May-17
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)
Growth plate: 1742 A3
Specific Phenotypes
For 11 genes in this experiment
For carbon source L-Arabinose in Pedobacter sp. GW460-11-11-14-LB5
For carbon source L-Arabinose across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pentose and glucuronate interconversions
- Ascorbate and aldarate metabolism
- Purine metabolism
- Starch and sucrose metabolism
- Streptomycin biosynthesis
- Lipopolysaccharide biosynthesis
- Inositol phosphate metabolism
- Folate biosynthesis
- Phosphatidylinositol signaling system
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-arabinose degradation I | 4 | 4 | 3 |
| myo-inositol biosynthesis | 2 | 2 | 1 |
| maltose degradation | 2 | 2 | 1 |
| D-arabinose degradation I | 2 | 1 | 1 |
| trehalose degradation III | 2 | 1 | 1 |
| kojibiose degradation | 2 | 1 | 1 |
| ribitol degradation I | 2 | 1 | 1 |
| trehalose degradation IV | 3 | 3 | 1 |
| D-arabinose degradation V | 3 | 1 | 1 |
| D-myo-inositol (1,4,5)-trisphosphate degradation | 3 | 1 | 1 |
| L-lyxose degradation | 4 | 1 | 1 |
| L-ascorbate degradation I (bacterial, anaerobic) | 5 | 1 | 1 |
| superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism | 6 | 1 | 1 |
| L-ascorbate degradation II (bacterial, aerobic) | 7 | 3 | 1 |
| phytate degradation I | 14 | 3 | 2 |
| superpathway of pentose and pentitol degradation | 42 | 12 | 4 |