MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems
Abstract
Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated MiST database provides a comprehensive classification of microbial signal transduction systems. This update is a result of a substantial scaling to accommodate constantly growing microbial genomic data. More than 125 000 genomes, 516 million genes and almost 100 million unique protein sequences are currently stored in the database. For each bacterial and archaeal genome, MiST 3.0 provides a complete signal transduction profile, thus facilitating theoretical and experimental studies on signal transduction and gene regulation. New software infrastructure and distributed pipeline implemented in MiST 3.0 enable regular genome updates based on the NCBI RefSeq database. A novel MiST feature is the integration of unique profile HMMs to link complex chemosensory systems with corresponding chemoreceptors in bacterial and archaeal genomes. The data can be explored online or via RESTful API (freely available at https://mistdb.com).
Additional Information
© 2019 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received September 10, 2019; Revised October 11, 2019; Editorial Decision October 14, 2019; Accepted October 14, 2019; Published: 22 November 2019. Funding: National Institutes of Health (NIH) [R01DE024463 and R35GM131760 to I.B.Z., in part]. Funding for open access charge: NIH. Conflict of interest statement: None declared. The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.Attached Files
Published - gkz988.pdf
Supplemental Material - gkz988_supplemental_files.zip
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Additional details
- PMCID
- PMC6943060
- Eprint ID
- 100032
- Resolver ID
- CaltechAUTHORS:20191125-124058503
- R01DE024463
- NIH
- R35GM131760
- NIH
- Created
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2019-11-26Created from EPrint's datestamp field
- Updated
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2022-02-16Created from EPrint's last_modified field