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      Bioinformatics based structural characterization of glucose dehydrogenase ( gdh) gene and growth promoting activity of Leclercia sp. QAU-66

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          Abstract

          Glucose dehydrogenase (GDH; EC 1.1. 5.2) is the member of quinoproteins group that use the redox cofactor pyrroloquinoline quinoine, calcium ions and glucose as substrate for its activity. In present study, Leclercia sp. QAU-66, isolated from rhizosphere of Vigna mungo, was characterized for phosphate solubilization and the role of GDH in plant growth promotion of Phaseolus vulgaris. The strain QAU-66 had ability to solubilize phosphorus and significantly (p ≤ 0.05) promoted the shoot and root lengths of Phaseolus vulgaris. The structural determination of GDH protein was carried out using bioinformatics tools like Pfam, InterProScan, I-TASSER and COFACTOR. These tools predicted the structural based functional homology of pyrroloquinoline quinone domains in GDH. GDH of Leclercia sp. QAU-66 is one of the main factor that involved in plant growth promotion and provides a solid background for further research in plant growth promoting activities.

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          Most cited references51

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          Protein Identification and Analysis Tools on the ExPASy Server

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            The Pfam protein families database.

            Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/).
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              Is Open Access

              COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

              We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computational modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structure through three representative template libraries that have known protein–ligand binding interactions, Enzyme Commission number or Gene Ontology terms. The biological function insights in these three aspects are then deduced from the functional templates, the confidence of which is evaluated by a scoring function that combines both global and local structural similarities. The algorithm has been extensively benchmarked by large-scale benchmarking tests and demonstrated significant advantages compared to traditional sequence-based methods. In the recent community-wide CASP9 experiment, COFACTOR was ranked as the best method for protein–ligand binding site predictions. The COFACTOR sever and the template libraries are freely available at http://zhanglab.ccmb.med.umich.edu/COFACTOR.
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                Author and article information

                Journal
                Braz J Microbiol
                Braz. J. Microbiol
                Brazilian Journal of Microbiology
                Sociedade Brasileira de Microbiologia
                1517-8382
                1678-4405
                2014
                29 August 2014
                : 45
                : 2
                : 603-611
                Affiliations
                [1 ]orgdiv0Plant Genomics Lab orgdiv0Department of Plant Sciences orgnameQuaid-i-Azam University IslamabadPakistanoriginalPlant Genomics Lab, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
                [2 ]orgdiv0National Institute for Genomics & Advanced Biotechnology orgnameNational Agricultural Research Centre IslamabadPakistanoriginalNational Institute for Genomics & Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan.
                [3 ]orgdiv0Graduate School of Agricultural and Life Sciences orgnameThe University of Tokyo TokyoJapanoriginalGraduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
                Author notes
                Send correspondence to M. Naveed. Plant Genomics Lab, Department of Plant Sciences, Quaid-i-Azam University, 44000 Islamabad, Pakistan. E-mail: naveed.quaidian@ 123456gmail.com .
                Article
                bjm-45-603
                10.1590/S1517-83822014000200031
                4166288
                25242947
                e1eb46b0-7632-4629-814b-184ecf345760
                Copyright © 2014, Sociedade Brasileira de Microbiologia

                All the content of the journal, except where otherwise noted, is licensed under a Creative Commons License CC BY-NC.

                History
                : 09 June 2013
                : 09 September 2013
                Page count
                Figures: 4, Tables: 1, References: 43, Pages: 9
                Categories
                Research Paper

                glucose dehydrogenase,pyrroloquinoline quinone,leclercia sp.,pgpr,bioinformatics

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