Experiment set1IT045 for Herbaspirillum seropedicae SmR1
Xylitol carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + Xylitol (20 mM), pH=7
Culturing: HerbieS_ML4, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.8 generations
By: Mark on 3/10/2016
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: CARBON4 A1
Specific Phenotypes
For 9 genes in this experiment
For carbon source Xylitol in Herbaspirillum seropedicae SmR1
For carbon source Xylitol across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization | 6 |
| Glycerol and Glycerol-3-phosphate Uptake and Utilization | 1 |
| L-rhamnose utilization | 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 and glucuronate interconversions
- Fructose and mannose metabolism
- Pentose phosphate pathway
- Lipopolysaccharide biosynthesis
- Pyruvate metabolism
- Nicotinate and nicotinamide metabolism
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| xylitol degradation I | 2 | 2 | 2 |
| D-arabinitol degradation I | 2 | 2 | 1 |
| ribitol degradation I | 2 | 2 | 1 |
| D-xylose degradation I | 2 | 1 | 1 |
| D-arabinose degradation I | 2 | 1 | 1 |
| L-lactaldehyde degradation (aerobic) | 2 | 1 | 1 |
| D-sorbitol degradation I | 3 | 3 | 1 |
| methylglyoxal degradation V | 3 | 2 | 1 |
| methylglyoxal degradation IV | 3 | 1 | 1 |
| D-arabinose degradation V | 3 | 1 | 1 |
| L-rhamnose degradation I | 5 | 4 | 1 |
| lactate biosynthesis (archaea) | 5 | 2 | 1 |
| superpathway of fucose and rhamnose degradation | 12 | 6 | 2 |
| superpathway of methylglyoxal degradation | 8 | 4 | 1 |
| L-rhamnose degradation II | 8 | 2 | 1 |
| superpathway of pentose and pentitol degradation | 42 | 19 | 3 |
| superpathway of glucose and xylose degradation | 17 | 14 | 1 |