Research article

BMC Evolutionary Biology

, 12:154

First online:

Open Access This content is freely available online to anyone, anywhere at any time.

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

  • Joshua K SailsberyAffiliated withFungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State UniversityBioinformatics Research Center, North Carolina State University
  • , Ralph A DeanAffiliated withFungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State UniversityCentennial Campus, Center for Integrated Fungal Research, North Carolina State University Email author 

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