TAfinder: a web-based tool to identify Type II toxin-antitoxin loci in bacterial genome sequences

Type II TA loci in prokaryote
Bacterial type II toxin-antitoxin (TA) loci typically consist of two tandem protein-coding genes. They have been either demonstrated or hypothesized to play key roles in the stabilization of plasmid and other mobile genetic elements (Van et al. PLoS Genet., 2009), stress responses (Gerdes, et al. Nat Rev Microbiol., 2005), contribution to virulence (Lobato-Márquez, FEMS Microbiology Reviews, 2016), and persister cell formation (Harms, et al. Science, 2016). In addition, type II TA systems have also been researching hotspot in synthetic biology for its wide application in genetic manipulation. In recent years, bioinformatics analyses show that the type II TA modules are widely spread not only upon plasmids but also on chromosomes of bacteria and archaea (Pandey et al., NAR, 2005; Makarova, et al., Biol Direct, 2009; Leplae R et al., NAR, 2011).

TAfinder predict type II TA system
The TAfinder web server was designed to quickly predict and compare type II TA loci in newly sequenced bacterial genomes. It combines a homologous search module and an operon detection module to enhance the prediction performance. Briefly, TAfinder starts at searching the toxin or antitoxin protein homologues by using both NCBI BLASTp and HMMer3. The BLASTp subject data set contains all the TADB-archived type II TA systems. The 108 HMM-profiles for the conserved toxin domains and 201 for the antitoxin domains are also detected by HMMer3 with the default settings. Then, the short homologs of toxin proteins or antitoxin proteins with the length of 30-200 amino acid residues were kept as candidates. Finally, two flanking toxin and antitoxin candidate genes on the same DNA strand and with the intergenic distances of -20 to 150 bp were paired as an operon structure, and thus predicted as a putative Type II TA locus. Putative TA pairs are displayed in tabular form on the web, and hyperlink-paths to other public databases, such as NCBI and TADB, are be provided.