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Updated: Jun 14, 2026

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Identification and classification of a two-component system based on domain structures in bacteria and differences in
Sangwan Kim1, Hideki Hirakawa, Shigeru Muta
1Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan.
Abstract:
Genome sequencing has revealed many pairs of proteins termed two-component systems (TCSs) in bacteria. Each pair consists of a sensor or histidine kinase (HK) and an effector or response regulator (RR). The HK is usually a membrane-spanning protein that senses specific environmental parameters and communicates this information to the cytoplasmic RR protein through phosphotransfer reactions to cope with a variety of environmental stresses, including osmotic pressure, nitrogen lack, phosphoric acid lack, and the presence of oxygen. Furthermore, some proteins have been identified as hybrid kinases composed of HK and RR. We identified the domain structures of 360 bacteria and 43 archaea by domain search against the PFAM database using HMMER. We then classified 8,573 HK, 10,807 RR, and 2,477 hybrid kinases. In addition, we identified specific domains among phylogenic clusters based on differences in domain structure of TCS genes applying the Signal-to-Noise ratio.
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