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era7 bioinformatics R&D group

Escherichia coli plasmid pEC_Bactec is a part of EHEC H112180280 strain

As it was suggested by Kat Holt (http://bacpathgenomics.wordpress.com/2011/06/05/ehec-genomes-snp-locations/) and others a plasmid very similar to pEC_Bactec is a part of the genome of the recently sequenced EHEC H112180280 strain.

The figure displays a simple alignment obtained using MAUVE  Move Contigs tool between pEC_Bactec plasmid (above) and the scaffolds 7 and 13 of H112180280 genome (below):

Scaffolds 7 and 13 cover practically all pEC-Bactec plasmid sequence. The two white pEC-Bactec regions that hasn’t associated similar regions in H112180280 correspond to the genes:

  • pndC and  TnpA OrfB IS66 (the left white region into the red similarity block)
  • TnpA IS26 transposase (The white patch into the blue block)

The H112180280 sequence regions without any similarity conexion with  pEC-Bactec flanking the two little green blocks correspond to N regions that remain undefined in the H112180280 sequence obtained with paired end 454 technology.