Figure 9

Secondary structure predictions for the first 120 amino acids of the IS 2 OrfAB TPase. (A) Comparison of secondary structure predictions based on the Protein Structure Prediction server protocol [51] and the PROF Secondary Structure Protocol [53]. The PCOILS analysis for coiled coils [57, 58] is also shown. Disordered regions (D) determined by the VSL2 predictor package from the DisProt database [111, 112] correspond well with these secondary structure predictions. (B) Secondary structure analysis of the first 60 amino acids of the IS2 TPase generated by the Pole Bioinformatique Lyonnais [54] PHD Secondary Structure Analysis algorithm [55]. H/h = alpha helix; C/c = random coil and e = extended strand. (C) Identification of a putative HTH motif in the first 60 amino acids of the IS2 TPase generated by the Pole Bioinformatique Lyonnais HTH Determination Algorithm of Dodd and Egan [56]. TPase: transposase.