Computational protocol: Ancestral Genes Can Control the Ability of Horizontally Acquired Loci to Confer New Traits

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Protocol publication

[…] To identify homologs of the pmrD gene, the deduced PmrD protein sequences from E. coli K12 MG1655 and S. enterica serovar Typhimurium 14028s were used as query to search the NCBI microbial genomes database as well as the NCBI non-redundant nucleotide database using TBLASTN. In parallel, the UniProt database was searched for homologs using BLASTP . Similar results were obtained in these searches and the protein sequences of the homologs were used for phylogenetic analyses. The sequences of the pmrD gene were aligned using ClustalX2 and phylogenetic trees were constructed using the neighbor-joining algorithm with default parameters and 1000 bootstrap replicates using MEGA 4 . For comparison, the sequences of 4 housekeeping genes (gapA, groEL, gyrA and pgi) were concatenated, aligned using ClustalX2 and used for construction of a species tree. […]

Pipeline specifications

Software tools TBLASTN, BLASTP, Clustal W, MEGA
Databases PMRD
Applications Phylogenetics, Amino acid sequence alignment
Organisms Escherichia coli, Salmonella enterica