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Open Access Research article

Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites

Joshua K Sailsbery12 and Ralph A Dean13*

Author Affiliations

1 Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27606, USA

2 Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27606, USA

3 Centennial Campus, Center for Integrated Fungal Research, North Carolina State University, 851 Main Campus Drive, Suite 233, Raleigh, NC, 27606, USA

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BMC Evolutionary Biology 2012, 12:154  doi:10.1186/1471-2148-12-154

Published: 24 August 2012

Abstract

Background

The highly conserved bHLH (basic Helix-Loop-Helix) domain, found in many transcription factors, has been well characterized separately in Plants, Animals, and Fungi. While conserved, even functionally constrained sites have varied since the Eukarya split. Our research identifies those slightly variable sites that were highly characteristic of Plants, Animals, or Fungi.

Results

Through discriminant analysis, we identified five highly discerning DNA-binding amino acid sites. Additionally, by incorporating Kingdom specific HMMs, we were able to construct a tool to quickly and accurately identify and classify bHLH sequences using these sites.

Conclusions

We conclude that highly discerning sites identified through our analysis were likely under functional constraints specific to each Kingdom. We also demonstrated the utility of our tool by identifying and classifying previously unknown bHLH domains in both characterized genomes and from sequences in a large environmental sample.

Keywords:
bHLH; Discriminant analysis; Classification; Plants; Animals; Fungi; Environmental sequencing; HMM; Discerning sites; Conserved sites; Variable sites