MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems
Open Access
- 8 January 2020
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 48 (D1), D459-D464
- https://doi.org/10.1093/nar/gkz988
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. Newsoftware 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.Funding Information
- National Institutes of Health (R01DE024463, R35GM131760)
This publication has 24 references indexed in Scilit:
- What bacteria wantEnvironmental Microbiology, 2018
- The European Bioinformatics Institute in 2016: Data growth and integrationNucleic Acids Research, 2015
- Phosphate Flow between Hybrid Histidine Kinases CheA3 and CheS3 Controls Rhodospirillum centenum Cyst FormationPLoS Genetics, 2013
- Origins and Diversification of a Complex Signal Transduction System in ProkaryotesScience Signaling, 2010
- Faculty Opinions recommendation of A new generation of homology search tools based on probabilistic inference.Published by H1 Connect ,2010
- The MiST2 database: a comprehensive genomics resource on microbial signal transductionNucleic Acids Research, 2009
- The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein familyMolecular Microbiology, 2009
- Role of CheB and CheR in the Complex Chemotactic and Aerotactic Pathway of Azospirillum brasilenseJournal of Bacteriology, 2006
- One-component systems dominate signal transduction in prokaryotesTrends in Microbiology, 2005
- Non-globular domains in protein sequences: Automated segmentation using complexity measuresComputers & Chemistry, 1994