Experiment set16S238 for Agrobacterium fabrum C58
AgroPhage_D10
Group: phageMedia: LB_plus_SM_buffer + Kan (50 ug/ml)
Culturing: Agro_ML11a, 48 well microplate; Epoch2, Aerobic, at 30 (C), shaken=double orbital, continuous, 205cpm
By: James on 2/20/23
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride, 100 mM Sodium Chloride, 4 mM Magnesium sulfate, 0.005 vol% Gelatin, 25 mM Tris hydrochloride
Specific Phenotypes
For 45 genes in this experiment
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Flagellum | 27 |
| Flagellar motility | 11 |
| Bacterial Chemotaxis | 3 |
| Flagellum in Campylobacter | 3 |
| Peptidoglycan Biosynthesis | 1 |
| Type IV pilus | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Peptidoglycan biosynthesis
- Fructose and mannose metabolism
- Ascorbate and aldarate metabolism
- Ubiquinone and menaquinone biosynthesis
- Oxidative phosphorylation
- Photosynthesis
- Lysine degradation
- N-Glycan biosynthesis
- O-Glycan biosynthesis
- High-mannose type N-glycan biosynthesis
- O-Mannosyl glycan biosynthesis
- Nucleotide sugars metabolism
- Glycosaminoglycan degradation
- Keratan sulfate biosynthesis
- Lipopolysaccharide biosynthesis
- Glycerolipid metabolism
- Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
- Sphingolipid metabolism
- Glycosphingolipid biosynthesis - lacto and neolacto series
- Glycosphingolipid biosynthesis - globo series
- Glycosphingolipid biosynthesis - ganglio series
- Biotin metabolism
- Carotenoid biosynthesis - General
- Zeatin biosynthesis
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Flavone and flavonol biosynthesis
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| peptidoglycan biosynthesis II (staphylococci) | 17 | 12 | 2 |
| peptidoglycan biosynthesis IV (Enterococcus faecium) | 17 | 12 | 2 |
| peptidoglycan biosynthesis V (β-lactam resistance) | 17 | 11 | 2 |
| peptidoglycan biosynthesis I (meso-diaminopimelate containing) | 12 | 11 | 1 |
| peptidoglycan maturation (meso-diaminopimelate containing) | 12 | 3 | 1 |
| peptidoglycan biosynthesis III (mycobacteria) | 15 | 11 | 1 |