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Protocols

MiST specifications

Information


Unique identifier OMICS_02931
Name MiST
Alternative names Microbial Signal Transduction database, MiST2
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 2.0
Maintained No

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Publications for Microbial Signal Transduction database

MiST citations

 (15)
library_books

Phyletic Distribution and Lineage Specific Domain Architectures of Archaeal Two Component Signal Transduction Systems

2018
J Bacteriol
PMCID: 5847659
PMID: 29263101
DOI: 10.1128/JB.00681-17

[…] the REC domain assignments from the NCBI's CDD (). These lists of RRs were combined and sorted according to their domain architectures. The HK and RR counts obtained were checked against those in the MiST and P2CS databases (, ), and most discrepancies (caused largely by different counting strategies) have been reconciled. No attempt was made to identify potentially missed and/or untranslated HKs […]

call_split

In silico comparative analysis of GGDEF and EAL domain signaling proteins from the Azospirillum genomes

2018
BMC Microbiol
PMCID: 5845226
PMID: 29523074
DOI: 10.1186/s12866-018-1157-0
call_split See protocol

[…] database of the National Center for Biotechnology Information, with the Rapid annotation using subsystems technology (RAST) server [], PFAM [], SMART [], PROSITE [], conserved domain database [], and MiST2.2 [], websites to search for protein sequences from the Sp245, Sp7, Az39, 4B, B510, BV-ST, DMS3675, A2P and SgZ-5T genome sequences. The amino acids of the motifs present in the various domains […]

library_books

Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI 2C

2017
Sci Rep
PMCID: 5429845
PMID: 28408760
DOI: 10.1038/s41598-017-00893-3

[…] unication are signal transduction systems that enable bacteria to detect and respond to changes in the environment (Stock et al.). We investigated the genome for signal transduction systems using the MIST2 database. The genome of S. plymuthica PRI-2C encodes 428 one-component systems (1CSs) and 69 two-component systems (TCSs). Two extracytoplasmic function (ECF) sigma factors were found, which com […]

call_split

Global Gene Expression Analysis of Cross Protected Phenotype of Pectobacterium atrosepticum

2017
PLoS One
PMCID: 5230779
PMID: 28081189
DOI: 10.1371/journal.pone.0169536
call_split See protocol

[…] KEGG or GO category differ by group as described in David database [] (p-value≤0.05). Additional information about some genes was manually found using Uniprot http://www.genome.jp/kegg/pathway.html, MiST http://mistdb.com/, Pfam http://pfam.xfam.org/, PROSITE http://prosite.expasy.org/, ICEberg http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=467, Ecogene http://ecogene.org/, String http […]

library_books

Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes

2016
PLoS Comput Biol
PMCID: 4822843
PMID: 27049771
DOI: 10.1371/journal.pcbi.1004862

[…] A flow chart showing the model building approach is shown in . More than 1 million sequences containing at least one signal transduction output domain as defined in MiST2 database [] were retrieved from a local copy of the Pfam database (). Eukaryotic sequences were discarded, because domain boundaries for Cache domains in eukaryotes are unclear. Predicted extrac […]

library_books

Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex

2016
PLoS Comput Biol
PMCID: 4742279
PMID: 26844549
DOI: 10.1371/journal.pcbi.1004723

[…] The primary source of data in this study is the MiST2.2 database [] including pre-computed domain counts, classification of chemotaxis genes, protein and ribosomal 16S sequences. CheA and CheV proteins were assigned to chemotaxis classes [] using p […]

Citations

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MiST institution(s)
Agile Genomics LLC, Mount Pleasant, SC, USA; Department of Microbiology, University of Tennessee, Knoxville, TN, USA; BioEnergy Science Center and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
MiST funding source(s)
Supported by National Institutes of Health (GM083177 and GM72285); South Carolina Research Association (2008-009); BioEnergy Science Center which is supported by the Office of Biological and Environmental Research in the DOE Office of Science.

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