Identification of HelixTurnHelix HTH DNABinding Motifs

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Identification of Helix-Turn-Helix (HTH)
DNA-Binding Motifs

• Changhui Yan
• Department of Computer Science
• Utah State University

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HTH Motifs

• Protein sequences sharing low similarities can
  fold into a similar HTH structure.
• Identifying HTH motifs from sequence is extremely
  challenging
• 7 families containing HTH motifs from the Pfam
  database. Positive data set 2,198 proteins.
• Negative data set 1,518 proteins.

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Combination of Amino Acid Sequence and Predicted
Secondary Structure
LQQITHIANQL-GLE----KDVVRVWF
LQQITHIANQL-GLE----KDVVRVWF
HHHEEHEEEHMHE----HHEEMMEH
HMM_AA
HMM_AA_SS
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Reduced Alphabets

• Schemes for reducing amino acid alphabet based on
  the BLOSUM50 matrix by Henikoff and Henikoff
  (1992) derived by grouping and averaging the
  similarity matrix elements as described in the
  text. (Murphy et al. 2000)

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Results
Table 1. Cross-Families Evaluations

• True positive HTH motifs that are correctly
  identified as such.
• False positive Non-HTH motifs that are
  identified as HTH motifs.
• The alphabet used to encode amino acid sequences.

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Results
Table 2. Comparisons with a method based on
profile-profile comparisons
Table 3. Putative HTH motifs in Ureaplasma parvum