ArticleBMC microbiology2006
ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms.
Article in BMC microbiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
26 citing papers in PubMed, 57 citations in OpenAlex.
- Article
- Fundamentals and Exceptions of the LysR-type Transcriptional Regulators.ACS synthetic biology · 2024Review
- The Structure of the LysR-type Transcriptional Regulator, CysB, Bound to the Inducer, N-acetylserine.European biophysics journal : EBJ · 2024Article
- YeiE Regulates Motility and Gut Colonization in Salmonella enterica Serotype Typhimurium.mBio · 2021Article
- Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites.Nucleic acids research · 2020Article
- Multi-Factor Regulation of the Master Modulator LeuO for the Cyclic-(Phe-Pro) Signaling Pathway in Vibrio vulnificus.Scientific reports · 2019Article
- DbdR, a New Member of the LysR Family of Transcriptional Regulators, Coordinately Controls Four Promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate Anaerobic Degradation Pathway.Applied and environmental microbiology · 2019Article
- Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors.PloS one · 2018Article
- The Global Regulators Lrp, LeuO, and HexA Control Secondary Metabolism in Entomopathogenic Bacteria.Frontiers in microbiology · 2017Article
- Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291.BMC microbiology · 2016Article
- The solution configurations of inactive and activated DntR have implications for the sliding dimer mechanism of LysR transcription factors.Scientific reports · 2016Article
- Transcription factor-based biosensors enlightened by the analyte.Frontiers in microbiology · 2015Review
- The Subtleties and Contrasts of the LeuO Regulator in Salmonella Typhi: Implications in the Immune Response.Frontiers in immunology · 2014Review
- Article
- Expression of the resistance-nodulation-cell division pump AdeIJK in Acinetobacter baumannii is regulated by AdeN, a TetR-type regulator.Antimicrobial agents and chemotherapy · 2012Article
- Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators.PloS one · 2012Article
- Regulation of transcription by SMU.1349, a TetR family regulator, in Streptococcus mutans.Journal of bacteriology · 2011Article
- PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes.BMC research notes · 2011Article
- The methanogen-specific transcription factor MsvR regulates the fpaA-rlp-rub oxidative stress operon adjacent to msvR in Methanothermobacter thermautotrophicus.Journal of bacteriology · 2010Article
- Characterization of tetracycline modifying enzymes using a sensitive in vivo reporter system.BMC biochemistry · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. In these processes, the regulatory proteins and the regulatory DNA signals located in extragenic regions are the key elements involved. As all extragenic spaces are putative regulatory regions, ExtraTrain covers all extragenic regions of available genomes and regulatory proteins from bacteria and archaea included in the UniProt database. DESCRIPTION: ExtraTrain provides integrated and easily manageable information for 679816 extragenic regions and for the genes delimiting each of them. In addition ExtraTrain supplies a tool to explore extragenic regions, named Palinsight, oriented to detect and search palindromic patterns. This interactive visual tool is totally integrated in the database, allowing the search for regulatory signals in user defined sets of extragenic regions. The 26046 regulatory proteins included in ExtraTrain belong to the families AraC/XylS, ArsR, AsnC, Cold shock domain, CRP-FNR, DeoR, GntR, IclR, LacI, LuxR, LysR, MarR, MerR, NtrC/Fis, OmpR and TetR. The database follows the InterPro criteria to define these families. The information about regulators includes manually curated sets of references specifically associated to regulator entries. In order to achieve a sustainable and maintainable knowledge database ExtraTrain is a platform open to the contribution of knowledge by the scientific community providing a system for the incorporation of textual knowledge.
conclusionExtraTrain is a new database for exploring Extragenic regions and Transcriptional information in bacteria and archaea. ExtraTrain database is available at http://www.era7.com/ExtraTrain/.
Indexed as
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.