Experiment set2H43 for Shewanella amazonensis SB2B
Minimal media with D-Glucose as carbon source
Group: carbon sourceMedia: ShewMM_noCarbon + D-Glucose (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/15/2013
Media components: 1.5 g/L Ammonium chloride, 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 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)
Growth plate: 505 A1,A2
Specific Phenotypes
For 11 genes in this experiment
For carbon source D-Glucose in Shewanella amazonensis SB2B
For carbon source D-Glucose across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Pentose and glucuronate interconversions
- Galactose metabolism
- Nucleotide sugars metabolism
- Aminosugars metabolism
- Glycolysis / Gluconeogenesis
- Biosynthesis of steroids
- Cyanoamino acid metabolism
- Starch and sucrose metabolism
- Other glycan degradation
- Lipopolysaccharide biosynthesis
- Inositol phosphate metabolism
- Carotenoid biosynthesis - General
- Phenylpropanoid biosynthesis
- Biosynthesis of ansamycins
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
Pathway | #Steps | #Present | #Specific |
---|---|---|---|
N-acetylglucosamine degradation II | 3 | 3 | 2 |
neolinustatin bioactivation | 3 | 2 | 2 |
N-acetylglucosamine degradation I | 2 | 2 | 1 |
linustatin bioactivation | 4 | 2 | 2 |
linamarin degradation | 2 | 1 | 1 |
trehalose degradation VI (periplasmic) | 2 | 1 | 1 |
lotaustralin degradation | 2 | 1 | 1 |
cellulose degradation II (fungi) | 3 | 1 | 1 |
D-galactosamine and N-acetyl-D-galactosamine degradation | 4 | 2 | 1 |
chitin derivatives degradation | 8 | 3 | 2 |
D-galactose degradation I (Leloir pathway) | 5 | 4 | 1 |
N-acetyl-D-galactosamine degradation | 5 | 2 | 1 |
coumarin biosynthesis (via 2-coumarate) | 5 | 2 | 1 |
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation | 6 | 2 | 1 |
α-tomatine degradation | 6 | 1 | 1 |
peptidoglycan recycling I | 14 | 11 | 1 |
firefly bioluminescence | 14 | 2 | 1 |
superpathway of N-acetylneuraminate degradation | 22 | 16 | 1 |