Experiment setAIT089 for Pseudomonas fluorescens FW300-N2E2
Cytidine nitrogen source
Group: nitrogen sourceMedia: RCH2_defined_Glucose_noNitrogen + Cytidine (20 mM)
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
Growth: about 4.5 generations
By: Mark on 1/21/2016
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 26 genes in this experiment
For nitrogen source Cytidine in Pseudomonas fluorescens FW300-N2E2
For nitrogen source Cytidine across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Lipopolysaccharide biosynthesis
- Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
- Sphingolipid metabolism
- Fructose and mannose metabolism
- Puromycin biosynthesis
- Pyrimidine metabolism
- Alanine and aspartate metabolism
- Glycine, serine and threonine metabolism
- Valine, leucine and isoleucine degradation
- Lysine biosynthesis
- Arginine and proline metabolism
- beta-Alanine metabolism
- Cyanoamino acid metabolism
- Glutathione metabolism
- N-Glycan biosynthesis
- O-Glycan biosynthesis
- High-mannose type N-glycan biosynthesis
- O-Mannosyl glycan biosynthesis
- Nucleotide sugars metabolism
- Keratan sulfate biosynthesis
- Peptidoglycan biosynthesis
- Glycerolipid metabolism
- Glycosphingolipid biosynthesis - lacto and neolacto series
- Glycosphingolipid biosynthesis - globo series
- Glycosphingolipid biosynthesis - ganglio series
- 1,4-Dichlorobenzene degradation
- Propanoate metabolism
- One carbon pool by folate
- Methane metabolism
- Nicotinate and nicotinamide metabolism
- Carotenoid biosynthesis - General
- Zeatin biosynthesis
- Caprolactam degradation
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Flavone and flavonol biosynthesis
- Drug metabolism - other enzymes
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| glycine biosynthesis I | 1 | 1 | 1 |
| poly-β-1,6-N-acetyl-D-glucosamine biosynthesis | 4 | 3 | 3 |
| β-alanine degradation II | 2 | 2 | 1 |
| pyrimidine nucleobases salvage II | 2 | 2 | 1 |
| pyrimidine ribonucleosides salvage III | 2 | 1 | 1 |
| glycine degradation | 3 | 3 | 1 |
| dTMP de novo biosynthesis (mitochondrial) | 3 | 3 | 1 |
| superpathway of L-serine and glycine biosynthesis I | 4 | 4 | 1 |
| glycine betaine degradation II (mammalian) | 4 | 1 | 1 |
| folate polyglutamylation | 5 | 4 | 1 |
| β-alanine biosynthesis II | 6 | 5 | 1 |
| glycine betaine degradation III | 7 | 7 | 1 |
| glycine betaine degradation I | 8 | 6 | 1 |
| folate transformations III (E. coli) | 9 | 9 | 1 |
| photorespiration III | 9 | 5 | 1 |
| photorespiration I | 9 | 5 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 9 | 1 |
| photorespiration II | 10 | 6 | 1 |
| folate transformations II (plants) | 11 | 10 | 1 |
| folate transformations I | 13 | 9 | 1 |
| formaldehyde assimilation I (serine pathway) | 13 | 6 | 1 |
| purine nucleobases degradation II (anaerobic) | 24 | 16 | 1 |