Experiment set9IT010 for Paraburkholderia graminis OAS925
Acetylated xylan 10 g/L carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + Acetylated xylan (10 g/L)
Culturing: Burkholderia_OAS925_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Marta Torres on 4-Jul-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 29 genes in this experiment
For carbon source Acetylated xylan in Paraburkholderia graminis OAS925
For carbon source Acetylated xylan across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Tryptophan metabolism
- Urea cycle and metabolism of amino groups
- Purine metabolism
- Arginine and proline metabolism
- Naphthalene and anthracene degradation
- Biosynthesis of alkaloids derived from shikimate pathway
- Ubiquinone and menaquinone biosynthesis
- Pyrimidine metabolism
- Geraniol degradation
- Lysine biosynthesis
- Histidine metabolism
- Tyrosine metabolism
- Phenylalanine, tyrosine and tryptophan biosynthesis
- Benzoxazinone biosynthesis
- Glutathione metabolism
- Pyruvate metabolism
- 1- and 2-Methylnaphthalene degradation
- Propanoate metabolism
- Methane metabolism
- Porphyrin and chlorophyll metabolism
- Limonene and pinene degradation
- Carotenoid biosynthesis - General
- Phenylpropanoid biosynthesis
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Alkaloid biosynthesis I
- Insect hormone biosynthesis
- Biosynthesis of phenylpropanoids
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| adenosine nucleotides degradation III | 1 | 1 | 1 |
| superoxide radicals degradation | 2 | 2 | 1 |
| methanol oxidation to formaldehyde IV | 2 | 1 | 1 |
| pseudouridine degradation | 2 | 1 | 1 |
| ethanol degradation IV | 3 | 3 | 1 |
| methylglyoxal degradation VIII | 3 | 3 | 1 |
| ppGpp metabolism | 6 | 5 | 2 |
| methylglyoxal degradation I | 3 | 2 | 1 |
| reactive oxygen species degradation | 4 | 4 | 1 |
| 2-methylcitrate cycle I | 5 | 5 | 1 |
| L-ornithine biosynthesis I | 5 | 5 | 1 |
| L-tryptophan biosynthesis | 6 | 6 | 1 |
| superpathway of methylglyoxal degradation | 8 | 4 | 1 |
| L-arginine biosynthesis I (via L-ornithine) | 9 | 9 | 1 |
| L-arginine biosynthesis III (via N-acetyl-L-citrulline) | 9 | 8 | 1 |
| L-arginine biosynthesis II (acetyl cycle) | 10 | 10 | 1 |
| superpathway of L-tryptophan biosynthesis | 13 | 13 | 1 |
| superpathway of arginine and polyamine biosynthesis | 17 | 14 | 1 |
| superpathway of aromatic amino acid biosynthesis | 18 | 18 | 1 |
| superpathway of chorismate metabolism | 59 | 42 | 1 |