Computational protocol: Multiple and Variable NHEJ-Like Genes Are Involved in Resistance to DNA Damage in Streptomyces ambofaciens

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Protocol publication

[…] A total of 38 sequenced Streptomyces genomes, including that of S. ambofaciens ATCC23877 was scanned to identify genes putatively encoding NHEJ Ku-like or LigD-like proteins based on BLAST similarity search against the non-redundant database. A preliminary BLASTP search (e-value cut-off 10-30; identity threshold 30%) using M. tuberculosis Rv0937c and Rv0938 (Ku and LigD respectively) protein sequences as a query allow to identify and numerate the candidates. Secondly, BLASTP were performed using S. ambofaciens ATCC23877 NHEJ-like genes and reciprocal best hits allowed to organize them into groups of orthologs.For the phylogeny of Ku-like proteins, the tree was built using a maximum-likelihood method based on a GTR + G + I model. Phylogenetic trees were built and edited with Mega6 (). Support of the tree branches was estimated with 100 bootstrap replicates and all positions with <80% site coverage were eliminated. A total of 295 and 309 positions were respectively used for the Ku-like and the LigC/LigD protein phylogenetic trees. […]

Pipeline specifications

Software tools BLASTP, MEGA
Application Phylogenetics