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ProClaT, a new bioinformatics tool for in silico protein reclassification: case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense

Overview of attention for article published in BMC Bioinformatics, December 2016
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Title
ProClaT, a new bioinformatics tool for in silico protein reclassification: case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense
Published in
BMC Bioinformatics, December 2016
DOI 10.1186/s12859-016-1338-5
Pubmed ID
Authors

Elisa Terumi Rubel, Roberto Tadeu Raittz, Nilson Antonio da Rocha Coimbra, Michelly Alves Coutinho Gehlen, Fábio de Oliveira Pedrosa

Abstract

Azopirillum brasilense is a plant-growth promoting nitrogen-fixing bacteria that is used as bio-fertilizer in agriculture. Since nitrogen fixation has a high-energy demand, the reduction of N2 to NH4(+) by nitrogenase occurs only under limiting conditions of NH4(+) and O2. Moreover, the synthesis and activity of nitrogenase is highly regulated to prevent energy waste. In A. brasilense nitrogenase activity is regulated by the products of draG and draT. The product of the draB gene, located downstream in the draTGB operon, may be involved in the regulation of nitrogenase activity by an, as yet, unknown mechanism. A deep in silico analysis of the product of draB was undertaken aiming at suggesting its possible function and involvement with DraT and DraG in the regulation of nitrogenase activity in A. brasilense. In this work, we present a new artificial intelligence strategy for protein classification, named ProClaT. The features used by the pattern recognition model were derived from the primary structure of the DraB homologous proteins, calculated by a ProClaT internal algorithm. ProClaT was applied to this case study and the results revealed that the A. brasilense draB gene codes for a protein highly similar to the nitrogenase associated NifO protein of Azotobacter vinelandii. This tool allowed the reclassification of DraB/NifO homologous proteins, hypothetical, conserved hypothetical and those annotated as putative arsenate reductase, ArsC, as NifO-like. An analysis of co-occurrence of draB, draT, draG and of other nif genes was performed, suggesting the involvement of draB (nifO) in nitrogen fixation, however, without the definition of a specific function.

Twitter Demographics

The data shown below were collected from the profile of 1 tweeter who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 28 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Switzerland 1 4%
Unknown 27 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 8 29%
Researcher 4 14%
Other 3 11%
Student > Master 3 11%
Student > Doctoral Student 1 4%
Other 3 11%
Unknown 6 21%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 5 18%
Computer Science 4 14%
Agricultural and Biological Sciences 3 11%
Business, Management and Accounting 2 7%
Social Sciences 2 7%
Other 5 18%
Unknown 7 25%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 July 2017.
All research outputs
#10,229,102
of 11,530,102 outputs
Outputs from BMC Bioinformatics
#3,923
of 4,261 outputs
Outputs of similar age
#221,827
of 262,978 outputs
Outputs of similar age from BMC Bioinformatics
#80
of 89 outputs
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