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Background    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 N 2  to NH 4   +  by nitrogenase occurs only under limiting conditions of NH 4   +  and O 2 . 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.    Results  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 .    Conclusions  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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12859-016-1338-5) contains supplementary material, which is available to authorized users.

bmc bioinformatics

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