Experiment set4IT023 for Pantoea sp. MT58
nitrogen source Sodium nitrate 20mM
Group: nitrogen sourceMedia: RCH2_defined_Glucose_noNitrogen + Sodium nitrate (20 mM), pH=7
Culturing: MT058_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 30-Jul-20
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 11 genes in this experiment
For nitrogen source Sodium nitrate in Pantoea sp. MT58
For nitrogen source Sodium nitrate across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Porphyrin and chlorophyll metabolism
- Nitrogen metabolism
- Phenylalanine, tyrosine and tryptophan biosynthesis
- Pyruvate metabolism
- Biosynthesis of phenylpropanoids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| siroheme biosynthesis | 4 | 4 | 4 |
| nitrate reduction V (assimilatory) | 2 | 1 | 1 |
| alkylnitronates degradation | 2 | 1 | 1 |
| β-alanine degradation III | 2 | 1 | 1 |
| factor 430 biosynthesis | 7 | 3 | 3 |
| methylglyoxal degradation VIII | 3 | 2 | 1 |
| methylglyoxal degradation I | 3 | 2 | 1 |
| uracil degradation III | 5 | 5 | 1 |
| cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion) | 15 | 3 | 3 |
| L-tryptophan biosynthesis | 6 | 6 | 1 |
| cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation) | 13 | 2 | 2 |
| superpathway of methylglyoxal degradation | 8 | 5 | 1 |
| adenosylcobalamin biosynthesis I (anaerobic) | 36 | 12 | 3 |
| superpathway of L-tryptophan biosynthesis | 13 | 13 | 1 |
| 3-hydroxypropanoate cycle | 13 | 6 | 1 |
| glyoxylate assimilation | 13 | 5 | 1 |
| adenosylcobalamin biosynthesis II (aerobic) | 33 | 13 | 2 |
| superpathway of aromatic amino acid biosynthesis | 18 | 18 | 1 |
| 3-hydroxypropanoate/4-hydroxybutanate cycle | 18 | 9 | 1 |
| superpathway of the 3-hydroxypropanoate cycle | 18 | 6 | 1 |
| superpathway of chorismate metabolism | 59 | 44 | 1 |