Computational protocol: The Burkholderia bcpAIOB Genes Define Unique Classes of Two-Partner Secretion and Contact Dependent Growth Inhibition Systems

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Protocol publication

[…] Burkholderia-type CDI-encoding loci were identified by using the predicted BcpB protein sequence from B. pseudomallei K96243 as a pBLAST query against the entire NCBI genome database. DNA sequences encoding predicted TPS system-like proteins were analyzed in Vector NTI Advance 11. A locus was considered to encode a Burkholderia-type CDI system if it was composed of a large ORF (∼3000 codons) followed immediately 3′ by a small ORF (∼100 codons), both of which were 5′ to the tpsB homolog. Alignments were performed in Vector NTI and then analyzed in Jalview 2.7 with Taylor residue coloring. […]

Pipeline specifications

Software tools Vector NTI Advance, Jalview
Application Protein sequence analysis
Organisms Escherichia coli, Burkholderia thailandensis