Experiment set1H28 for Shewanella sp. ANA-3
L-Arabinose carbon source
Group: carbon sourceMedia: ShewMM_noCarbon + L-Arabinose (20 mM), pH=7
Culturing: ANA3_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Jake on 2/12/2014
Media components: 1.5 g/L Ammonium chloride, 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 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 7 genes in this experiment
For carbon source L-Arabinose in Shewanella sp. ANA-3
For carbon source L-Arabinose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| L-Arabinose utilization | 7 |
| L-ascorbate utilization (and related gene clusters) | 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
- Pentose and glucuronate interconversions
- Glycolysis / Gluconeogenesis
- Valine, leucine and isoleucine biosynthesis
- Pantothenate and CoA biosynthesis
- Biosynthesis of alkaloids derived from histidine and purine
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-arabinose degradation I | 4 | 4 | 2 |
| trehalose degradation VI (periplasmic) | 2 | 1 | 1 |
| L-valine biosynthesis | 4 | 4 | 1 |
| L-lyxose degradation | 4 | 1 | 1 |
| pyruvate fermentation to isobutanol (engineered) | 5 | 4 | 1 |
| D-galactose degradation I (Leloir pathway) | 5 | 4 | 1 |
| L-ascorbate degradation I (bacterial, anaerobic) | 5 | 1 | 1 |
| L-isoleucine biosynthesis IV | 6 | 4 | 1 |
| L-arabinose degradation III | 6 | 3 | 1 |
| L-arabinose degradation V | 6 | 3 | 1 |
| L-isoleucine biosynthesis I (from threonine) | 7 | 7 | 1 |
| L-isoleucine biosynthesis III | 7 | 4 | 1 |
| L-ascorbate degradation II (bacterial, aerobic) | 7 | 3 | 1 |
| L-isoleucine biosynthesis II | 8 | 5 | 1 |
| L-arabinose degradation IV | 8 | 4 | 1 |
| superpathway of branched chain amino acid biosynthesis | 17 | 17 | 2 |
| superpathway of L-isoleucine biosynthesis I | 13 | 13 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 10 | 3 |
| superpathway of L-threonine metabolism | 18 | 15 | 1 |