Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function.
Currently, about 20 crystal structures per day are released and deposited in the Protein Data Bank. A significant fraction of these structures is produced by research groups associated with the structural genomics consortium. The biological function of many of these proteins is generally unknown or...
| Publicado en: | Journal of Biomedicine & Biotechnology Vol. 2012; pp. 1 - 15 |
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| Autores principales: | , , , , , |
| Formato: | pictorial research tables/charts Journal Article |
| Publicado: |
Wiley-Blackwell
2012
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=104298133&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 104298133 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 11107243 137K jtl: Journal of Biomedicine & Biotechnology issn: 11107243 maglogo: N pubinfo: dt: 2012 vid: 2012 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 104298133 104298133 2011907056 NLM22505803 PMC3312330 104298133 ppf: 1 ppct: 14 formats: fmt: @attributes: type: P tig: atl: Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function. aug: au: Schüller, Andreas Slater, Alex W. Norambuena, Tomás Cifuentes, Juan J. Almonacid, Leonardo I. Melo, Francisco affil: Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, 8331150 Santiago, Chile sug: subj: Bioinformatics Methods Proteins Classification Resource Databases Proteins Physiology Bacteria Analysis Genomics Amino Acids Binding Sites Cluster Analysis Models, Theoretical Models, Statistical Models, Structural Data Analysis Software Sequence Analysis Human Funding Source ab: Currently, about 20 crystal structures per day are released and deposited in the Protein Data Bank. A significant fraction of these structures is produced by research groups associated with the structural genomics consortium. The biological function of many of these proteins is generally unknown or not validated by experiment. Therefore, a growing need for functional prediction of protein structures has emerged. Here we present an integrated bioinformatics method that combines sequence-based relationships and three-dimensional (3D) structural similarity of transcriptional regulators with computer prediction of their cognate DNA binding sequences. We applied this method to the AraC/XylS family of transcription factors, which is a large family of transcriptional regulators found in many bacteria controlling the expression of genes involved in diverse biological functions. Three putative new members of this family with known 3D structure but unknown function were identified for which a probable functional classification is provided. Our bioinformatics analyses suggest that they could be involved in plant cell wall degradation (Lin2118 protein from Listeria innocua, PDB code 3oou), symbiotic nitrogen fixation (protein from Chromobacterium violaceum, PDB code 3oio), and either metabolism of plant-derived biomass or nitrogen fixation (protein from Rhodopseudomonas palustris, PDB code 3mn2). pubtype: Academic Journal doctype: pictorial research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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