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Open Access Research article

Protein evolution of ANTP and PRD homeobox genes

Nuno A Fonseca1, Cristina P Vieira1, Peter WH Holland2 and Jorge Vieira1*

Author Affiliations

1 Instituto de Biologia Molecular e Celular (IBMC); University of Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal

2 Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK

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BMC Evolutionary Biology 2008, 8:200  doi:10.1186/1471-2148-8-200

Published: 11 July 2008

Abstract

Background

Although homeobox genes have been the subject of many studies, little is known about the main amino acid changes that occurred early in the evolution of genes belonging to different classes.

Results

In this study, we report a method for the fast and efficient retrieval of sequences belonging to the ANTP (HOXL and NKL) and PRD classes. Furthermore, we look for diagnostic amino acid residues that can be used to distinguish HOXL, NKL and PRD genes.

Conclusion

The reported protein features will facilitate the robust classification of homeobox genes from newly sequenced bilaterian genomes. Nevertheless, in non-bilaterian genomes our findings must be cautiously applied. In principle, as long as a good manually curated data set is available the approach here described can be applied to non-bilaterian organisms as well. Our results help focus experimental studies onto investigating the biochemical functions of key homeodomain residues in different gene classes.