Experiment set3H41 for Shewanella amazonensis SB2B
Glycine nitrogen source
Group: nitrogen sourceMedia: ShewMM_noNitrogen + Glycine (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/24/2013
Media components: 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, 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: 511 E7, E8
Specific Phenotypes
For 6 genes in this experiment
For nitrogen source Glycine in Shewanella amazonensis SB2B
For nitrogen source Glycine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| ATP-dependent RNA helicases, bacterial | 1 |
| Glycine and Serine Utilization | 1 |
| Pyridoxin (Vitamin B6) Biosynthesis | 1 |
| Serine Biosynthesis | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glutamate metabolism
- Alanine and aspartate metabolism
- Glycine, serine and threonine metabolism
- Valine, leucine and isoleucine degradation
- beta-Alanine metabolism
- Nucleotide sugars metabolism
- Lipopolysaccharide biosynthesis
- Propanoate metabolism
- Butanoate metabolism
- Biosynthesis of siderophore group nonribosomal peptides
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| 4-aminobutanoate degradation III | 2 | 2 | 1 |
| 4-aminobutanoate degradation II | 2 | 1 | 1 |
| 4-aminobutanoate degradation I | 2 | 1 | 1 |
| L-serine biosynthesis I | 3 | 3 | 1 |
| L-cysteine biosynthesis IX (Trichomonas vaginalis) | 3 | 2 | 1 |
| superpathway of 4-aminobutanoate degradation | 3 | 1 | 1 |
| superpathway of L-serine and glycine biosynthesis I | 4 | 4 | 1 |
| GABA shunt II | 4 | 3 | 1 |
| GABA shunt I | 4 | 2 | 1 |
| L-lysine degradation IV | 5 | 2 | 1 |
| L-lysine degradation X | 6 | 2 | 1 |
| L-lysine degradation III | 6 | 1 | 1 |
| 4-aminobutanoate degradation V | 7 | 3 | 1 |
| L-lysine degradation I | 7 | 1 | 1 |
| L-valine degradation I | 8 | 6 | 1 |
| superpathway of sulfate assimilation and cysteine biosynthesis | 9 | 9 | 1 |
| superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation | 11 | 6 | 1 |
| superpathway of L-arginine and L-ornithine degradation | 13 | 8 | 1 |
| nicotine degradation I (pyridine pathway) | 17 | 4 | 1 |
| superpathway of L-lysine degradation | 43 | 8 | 1 |