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MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems

Gumerov, Vadim M. and Ortega, Davi R. and Adebali, Ogun and Ulrich, Luke E. and Zhulin, Igor B. (2020) MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems. Nucleic Acids Research, 48 (D1). D459-D464. ISSN 0305-1048. PMCID PMC6943060. https://resolver.caltech.edu/CaltechAUTHORS:20191125-124058503

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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).


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/nar/gkz988DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943060PubMed CentralArticle
ORCID:
AuthorORCID
Ortega, Davi R.0000-0002-8344-2335
Zhulin, Igor B.0000-0002-6708-5323
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.
Funders:
Funding AgencyGrant Number
NIHR01DE024463
NIHR35GM131760
Issue or Number:D1
PubMed Central ID:PMC6943060
Record Number:CaltechAUTHORS:20191125-124058503
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20191125-124058503
Official Citation:Vadim M Gumerov, Davi R Ortega, Ogun Adebali, Luke E Ulrich, Igor B Zhulin, MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D459–D464, https://doi.org/10.1093/nar/gkz988
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:100032
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:26 Nov 2019 00:03
Last Modified:09 Mar 2020 13:19

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