title: Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites.
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.
authors.affiliation: Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA.
authors.forename: Joshua K
authors.initials: JK
authors.lastname: Sailsbery
authors.forename: Ralph A
authors.initials: RA
authors.lastname: Dean
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000145:classification / Q000235:genetics; D005658:Fungi / Q000235:genetics*; D018257:Helix-Loop-Helix Motifs / Q000235:genetics*; D008390:Markov Chains; D015233:Models, Statistical; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D010944:Plants / Q000235:genetics*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D005656:Fungal Proteins; D010940:Plant Proteins