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.
abstract: 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 N2to 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.
  
  
  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.
authors.affiliation: Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil.|, Rua Dr. Alcides Vieira Arcoverde 1225, Curitiba, Paraná, Brazil.
authors.forename: Elisa Terumi
authors.initials: ET
authors.lastname: Rubel
authors.affiliation: Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil.|, Rua Dr. Alcides Vieira Arcoverde 1225, Curitiba, Paraná, Brazil.
authors.forename: Roberto Tadeu
authors.initials: RT
authors.lastname: Raittz
authors.affiliation: Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil.|, Rua Dr. Alcides Vieira Arcoverde 1225, Curitiba, Paraná, Brazil.
authors.forename: Nilson Antonio da Rocha
authors.initials: NA
authors.lastname: Coimbra
authors.affiliation: Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil.|, Rua Dr. Alcides Vieira Arcoverde 1225, Curitiba, Paraná, Brazil.
authors.forename: Michelly Alves Coutinho
authors.initials: MA
authors.lastname: Gehlen
authors.affiliation: Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, PR, Brazil. fpedrosa@ufpr.br.|, Av. Cel. Francisco H. dos Santos, s/n, Curitiba, Paraná, Brazil. fpedrosa@ufpr.br.
authors.forename: Fábio de Oliveira
authors.initials: FO
authors.lastname: Pedrosa
mesh_terms: D015806:Azospirillum brasilense / Q000737:chemistry* / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D005798:Genes, Bacterial; D009586:Nitrogen Fixation; D009591:Nitrogenase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D009876:Operon
chemical_list: D001426:Bacterial Proteins; D009591:Nitrogenase
keywords: Artificial neural networks; Azospirillum brasilense; Biological nitrogen fixation; Nitrogenase; Nitrogenase associated NifO protein; Operon draTGB; Protein classification