TonB-dependent regulatory systems consist of six components, a specialized outer membrane-localized TonB-dependent receptor (TonB-dependent transducer) that interacts with its energizing TonB-ExbBD protein complex, a cytoplasmic membrane-localized anti-sigma factor and an extracytoplasmic function (ECF)-subfamily sigma factor. This sophisticated complex senses signals from outside the bacterial cell and transmits them via two membranes into the cytoplasm, leading to transcriptional activation of target genes. TonB-dependent transducers might be important for pathogenicity; therefore, a survey of their presence in bacteria was aimed. Genome-wide analyses indicate that these systems are commonly found in several environmental bacteria but are only seldom present in human and animal pathogens. Most systems have the same tandem organization of the corresponding genes: sigma factor-anti-sigma factor-TonB-dependent transducer. In the course of these analyses, a novel protein domain of unknown function was identified and four different modular structures of TonB-dependent receptors were detected.