DBTBS (http://dbtbs.hgc.jp) was originally released in 1999 as a reference database of published transcriptional regulation events in Bacillus subtilis, one of the best studied bacteria. It is essentially a compilation of transcription factors with their regulated genes as well as their recognition sequences, which were experimentally characterized and reported in the literature. Here we report its major update, which contains information on 114 transcription factors, including sigma factors, and 633 promoters of 525 genes. The number of references cited in the database has increased from 291 to 378. It also supports a function to find putative transcription factor binding sites within input sequences by using our collection of weight matrices and consensus patterns. Furthermore, though preliminarily, DBTBS now aims to contribute to comparative genomics by showing the presence or absence of potentially orthologous transcription factors and their corresponding cis-elements on the promoters of their potentially orthologously regulated genes in 50 eubacterial genomes.