TADB 2.0: An Updated Database of Bacterial Type II Toxin-Antitoxin Loci

Nucleic Acids Res. 2018 Jan 4;46(D1):D749-D753. doi: 10.1093/nar/gkx1033.

Abstract

TADB2.0 (http://bioinfo-mml.sjtu.edu.cn/TADB2/) is an updated database that provides comprehensive information about bacterial type II toxin-antitoxin (TA) loci. Compared with the previous version, the database refined and the new data schema is employed. With the aid of text mining and manual curation, it recorded 6193 type II TA loci in 870 replicons of bacteria and archaea, including 105 experimentally validated TA loci. In addition, the newly developed tool TAfinder combines the homolog searches and the operon structure detection, allowing the prediction for type II TA pairs in bacterial genome sequences. It also helps to investigate the genomic context of predicted TA loci for putative virulence factors, antimicrobial resistance determinants and mobile genetic elements via alignments to the specific public databases. Additionally, the module TAfinder-Compare allows comparing the presence of the given TA loci across the close relative genomes. With the recent updates, TADB2.0 might provide better support for understanding the important roles of type II TA systems in the prokaryotic life activities.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics
  • Bacterial Physiological Phenomena
  • Bacterial Toxins / antagonists & inhibitors
  • Bacterial Toxins / classification
  • Bacterial Toxins / genetics*
  • Chromosomes, Bacterial / genetics
  • Data Mining
  • Databases, Genetic*
  • Datasets as Topic
  • Genes, Bacterial*
  • Genome, Bacterial
  • Operon / genetics
  • Plasmids / genetics
  • Prophages / genetics
  • RNA, Bacterial / genetics*
  • RNA, Small Untranslated / genetics*
  • Species Specificity

Substances

  • Bacterial Toxins
  • RNA, Bacterial
  • RNA, Small Untranslated