Experiment set2H32 for Pseudomonas stutzeri RCH2
Adenine hydrochloride hydrate nitrogen source
Group: nitrogen sourceMedia: RCH2_defined_noNitrogen + Adenine hydrochloride hydrate (5 mM), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Kelly on 6/20/2013
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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: 552 D7,D8
Specific Phenotypes
For 11 genes in this experiment
For nitrogen source Adenine hydrochloride hydrate in Pseudomonas stutzeri RCH2
For nitrogen source Adenine hydrochloride hydrate across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Urea decomposition | 3 |
| Allantoin Utilization | 1 |
| Lysine degradation | 1 |
| Purine conversions | 1 |
| cAMP signaling in bacteria | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Purine metabolism
- Ascorbate and aldarate metabolism
- Ubiquinone and menaquinone biosynthesis
- Urea cycle and metabolism of amino groups
- Caffeine metabolism
- Arginine and proline metabolism
- Tyrosine metabolism
- 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
- Phenylalanine metabolism
- Benzoate degradation via hydroxylation
- Tryptophan metabolism
- Pyruvate metabolism
- Biphenyl degradation
- 1- and 2-Methylnaphthalene degradation
- Fluorene degradation
- 3-Chloroacrylic acid degradation
- Atrazine degradation
- Phenylpropanoid biosynthesis
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| urea degradation II | 1 | 1 | 1 |
| urate conversion to allantoin I | 3 | 2 | 2 |
| guanine and guanosine salvage II | 2 | 1 | 1 |
| guanine and guanosine salvage I | 2 | 1 | 1 |
| adenine and adenosine salvage II | 2 | 1 | 1 |
| adenine and adenosine salvage I | 2 | 1 | 1 |
| superpathway of allantoin degradation in plants | 8 | 4 | 3 |
| adenine salvage | 3 | 2 | 1 |
| allantoin degradation to glyoxylate I | 3 | 2 | 1 |
| urate conversion to allantoin III | 3 | 1 | 1 |
| urate conversion to allantoin II | 3 | 1 | 1 |
| superpathway of guanine and guanosine salvage | 3 | 1 | 1 |
| ureide biosynthesis | 7 | 5 | 2 |
| allantoin degradation to glyoxylate II | 5 | 1 | 1 |
| allantoin degradation to glyoxylate III | 5 | 1 | 1 |
| superpathway of allantoin degradation in yeast | 6 | 5 | 1 |
| superpathway of purines degradation in plants | 18 | 11 | 3 |
| superpathway of purine nucleotide salvage | 14 | 11 | 2 |
| glyphosate degradation III | 7 | 4 | 1 |
| (aminomethyl)phosphonate degradation | 8 | 6 | 1 |