DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

Abstract

DBTBS, first released in 1999, is a reference database on transcriptional regulation in Bacillus subtilis, summarizing the experimentally characterized transcription factors, their recognition sequences and the genes they regulate. Since the previous release, the original content was extended by the addition of the data contained in 569 new publications, the total of which now reaches 947. The number of B. subtilis promoters annotated in the database was more than doubled to 1475. In addition, 463 experimentally validated B. subtilis operons and their terminators have been included. Given the increase in the number of fully sequenced bacterial genomes, we decided to extend the usability of DBTBS in comparative regulatory genomics. We therefore created a new section on the conservation of the upstream regulatory sequences between homologous genes in 40 Gram-positive bacterial species, as well as on the presence of overrepresented hexameric motifs that may have regulatory functions. DBTBS can be accessed at: http://dbtbs.hgc.jp.

Figure 1.

Hexameric motif conservation in an upstream intergenic region. The upper part shows the search entry box, with the criteria selected for filtering of the displayed hexameric motifs. The lower part is the resulting figure, showing the conservation profile as a black line and the alignment used to obtain it. The blue line represents the calculated conserved region and the red boxes the found hexameric motifs. A 2×/4× magnifier is available in order to conveniently scan the sequence alignment.