ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organismsEduardo Pareja
Bioinformatics Unit, Era7 Information Technologies SL, BIC Granada CEEI, Parque Tecnológico de Ciencias de la Salud, Armilla Granada 18100, Spain
BMC Microbiol 6:29. 2006
..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...
- Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements
Raquel Tobes
Bioinformatics Unit, Era7 Information Technologies SL, BIC Granada CEEI, Parque Tecnológico de Ciencias de la Salud Armilla Granada 18100, Spain
BMC Genomics 7:62. 2006
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- Repetitive extragenic palindromic sequences in the Pseudomonas syringae pv. tomato DC3000 genome: extragenic signals for genome reannotation
Raquel Tobes
Bioinformatics Unit, Era7 Information Technologies, C Río Tajo 49, Las Gabias, Granada 18110, Spain
Res Microbiol 156:424-33. 2005
..In addition, as the P. syringae REP sequence is species-specific with respect to the sequenced genomes, it is an exceptional candidate for use as a fingerprint in precise genotyping and epidemiological studies...
- AraC-XylS database: a family of positive transcriptional regulators in bacteria
Raquel Tobes
Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, 18008 Granada, Spain
Nucleic Acids Res 30:318-21. 2002
..The AraC-XylS database is accessible on the World Wide Web at http://www.AraC-XylS.org...
- The TetR family of transcriptional repressors
Juan L Ramos
Department of Plant Biochemistry and Molecular and Cellular Biology, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain
Microbiol Mol Biol Rev 69:326-56. 2005
..Information related to the TetR family of regulators has been updated in a database that can be accessed at www.bactregulators.org...
- REP code: defining bacterial identity in extragenic space
Raquel Tobes
, , E-18008 Granada, Spain
Environ Microbiol 7:225-8. 2005
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- Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida
Isabel Aranda-Olmedo
, , , Apdo. de Correos 419, E-18080 Granada, Spain
Nucleic Acids Res 30:1826-33. 2002
..putida. For this reason we suggest that the P.putida 35 bp element is a distinctive REP sequence in P.putida. This is the first time that REP sequences have been described and characterised in a group of non-enterobacteriaceae...
- Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray
Luis Yuste
, , CSIC, , Cantoblanco, 28049 - Madrid, Spain
Environ Microbiol 8:165-77. 2006
..Expression of IHF was indicative of post-transcriptional control. These results provide the first global study of the expression of the transcriptional machinery through the exponential stationary-phase shift in P. putida...
- Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9
Mattias Magnusson
Department of Rheumatology and Inflammation Research, Goteborg University, Goteborg, Sweden
J Immunol 179:31-5. 2007
..Considering the involvement of TLRs in Gram-negative septic shock, it is conceivable that REPs play a role in its pathogenesis. This study highlights REPs as a potential novel target in septic shock treatment...
- Characterization of a Listeria monocytogenes protein interfering with Rab5a
Carmen Alvarez-Dominguez
Servicio de Inmunología and Instituto de Formación e Investigación Marqués de Valdecilla IFIMAV, Hospital Universitario Marques de Valdecilla, 39008 Santander, Spain
Traffic 9:325-37. 2008
..Listeria GAPDH might be the first intracellular gram-positive enzyme targeted to Rab proteins with ADP-ribosylating ability and a putative novel virulence factor...
