FIG. 5.

Identification of a DNA-binding helix-turn-helix motif in Rtp52 and T1-gp23. (A) Alignment of the helix-turn-helix regions of Rtp52 and T1-gp23 with distantly related DNA-binding domains. The numbering of homologs refers to the PSI-BLAST results in panel B. Numbering of amino acids is shown at the right side of the alignment. A helix-turn-helix motif search by the Dodd-Egan method (32) identified the sequence GTKANIAKQLKVTPQAVEEWFK, starting at position 53 in Rtp52, with a score of 5.19, representing approximately 100% probability for a DNA-binding helix-turn-helix fold. The position of the predicted helix-turn-helix motif is shown by an arrow below the alignment. All of the other proteins in the alignment also contained a predicted helix-turn-helix motif in an equivalent position. (B) Result of PSI-BLAST iteration 5 with Rtp52 as the query sequence. The 10 best-scoring hits were tested for helix-turn-helix motifs. The probabilities for a helix-turn-helix motif based on the Dodd-Egan method are shown next to the PSI-BLAST expectation values. The annotation of each remote homolog was reexamined by BlastP database searches. In the PSI BLAST analysis of Rtp52, we excluded hits to the multidomain proteins of the nonribosomal peptide synthetase family from subsequent iterations of the search. Manual filtering was necessary since low-scoring PSI-BLAST search results tend to be drawn to large protein families.