Experiment set4IT077 for Acidovorax sp. GW101-3H11
L-Proline nitrogen source
Group: nitrogen sourceMedia: RCH2_defined_Glucose_noNitrogen + L-Proline (20 mM), pH=7
Culturing: acidovorax_3H11_ML3a, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 5.5 generations
By: Mark on 6/10/2015
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)
Growth plate: Nplate1 B6
Specific Phenotypes
For 4 genes in this experiment
For nitrogen source L-Proline in Acidovorax sp. GW101-3H11
For nitrogen source L-Proline across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Arginine and proline metabolism
- Biosynthesis of terpenoids and steroids
- Fatty acid biosynthesis
- Glutamate metabolism
- Lysine degradation
- Histidine metabolism
- Tyrosine metabolism
- Phenylalanine metabolism
- Lipopolysaccharide biosynthesis
- Glycerophospholipid metabolism
- Ether lipid metabolism
- Glycosphingolipid biosynthesis - ganglio series
- Pyruvate metabolism
- 1- and 2-Methylnaphthalene degradation
- Benzoate degradation via CoA ligation
- Ethylbenzene degradation
- Butanoate metabolism
- Carbon fixation in photosynthetic organisms
- Limonene and pinene degradation
- Diterpenoid biosynthesis
- Carotenoid biosynthesis - General
- Anthocyanin biosynthesis
- Alkaloid biosynthesis I
- Alkaloid biosynthesis II
- Biosynthesis of unsaturated fatty acids
- Biosynthesis of type II polyketide backbone
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of alkaloids derived from terpenoid and polyketide
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-malate degradation I | 1 | 1 | 1 |
| L-proline degradation I | 3 | 3 | 2 |
| proline to cytochrome bo oxidase electron transfer | 2 | 2 | 1 |
| polyhydroxybutanoate biosynthesis | 3 | 3 | 1 |
| L-arginine degradation I (arginase pathway) | 3 | 2 | 1 |
| C4 photosynthetic carbon assimilation cycle, NADP-ME type | 7 | 4 | 2 |
| ethene biosynthesis II (microbes) | 4 | 1 | 1 |
| methylgallate degradation | 6 | 6 | 1 |
| (5R)-carbapenem carboxylate biosynthesis | 6 | 1 | 1 |
| L-Nδ-acetylornithine biosynthesis | 7 | 5 | 1 |
| C4 photosynthetic carbon assimilation cycle, PEPCK type | 14 | 8 | 2 |
| protocatechuate degradation I (meta-cleavage pathway) | 8 | 8 | 1 |
| L-citrulline biosynthesis | 8 | 7 | 1 |
| superpathway of vanillin and vanillate degradation | 10 | 9 | 1 |
| superpathway of L-citrulline metabolism | 12 | 9 | 1 |
| syringate degradation | 12 | 8 | 1 |
| gluconeogenesis I | 13 | 11 | 1 |