Exploring the Escherichia coli K-12 genome
Start in Ensembl Beta and select the Escherichia coli K-12 (ASM584v2) genome in the Species selector.
- Open the species information page.
- What substrain is this genome?
- What is the assembly (GCA_) ID? In what year was the the original K-12 isolate obtained?
- Find the era gene in E. coli K-12.
- Is the gene known under a different name?
- What are the coordinates for this gene?
- What is the biological function of the gene according to PDBe-KB?
- Go to Species selector and search for Escherichia coli by entering the species name in the search bar or by clicking on the species icon in the species list underneath. Select to add the species and click on the green Add button. You should now see the E. coli in your species list at the top of the page. Click on the blue Escherichia coli K-12 ASM584v2 to open the assembly information page. Open the track panel on the right.
The genome assembly is substrain MG1655.
Stay in the track panel. You can find the assembly ID under Assembly. Click on the assembly ID to open the corresponding entry in the European Nucleotide Archive (ENA), where the original sequence was submitted to.
The assembly ID is GCA_000005845.2. In the description in the ENA entry, we can see that MG1655 was derived from strain W1485, which was derived by Joshua Lederberg from the original K-12 isolate obtained from a patient in 1922.
- In the track panel, click on the Search icon, enter era into the text box and click on era b2566 in the results underneath.
The era_ gene in the E. coli K-12 genome is also known ‘b2566’ and the coordinates are 2,702,481-2,703,386.
In the pop-up menu, click on View in Entity Viewer. Switch to the Gene function tab and click on PDBe-KB P06616 to open the corresponding entry in PDBe-KB.
Accroding to PDBe-KB, the biological function is as follows: An essential GTPase that binds both GDP and GTP, with nucleotide exchange occurring on the order of seconds whereas hydrolysis occurs on the order of minutes. Plays a role in numerous processes, including cell cycle regulation, energy metabolism, as a chaperone for 16S rRNA processing and 30S ribosomal subunit biogenesis. This description is imported from UniProt.
