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. 2013 Apr 26;4:63. doi: 10.3389/fgene.2013.00063

Figure 2.

Figure 2

Top HHsearch PDB hits from a query with the endonuclease domain of the Drosophila melanogaster R2 non-LTR retrotransposon. (A) Hitlist graphical representation; (B) HHpred alignments (PDB accessions numbers in parentheses): 1—Holliday-junction resolvase of Pyrococcus furiosus (1gef); 2—Holliday-junction resolvase of Sulfolobus solfataricus (1ob8); 3—Holliday-junction resolvase of Archaeoglobus fulgidus (2wcw); 4—Holliday-junction resolving enzyme of S. solfataricus (1hh1); 13—FOKI restriction endonuclease of Planomicrobium okeanokoites (2fok). ss_pred, secondary-structure prediction by PSIPRED (H, α-helix; E, β-sheet; C, coil, absence of regular secondary structure); ss_conf, PSIPRED confidence values (0–9); consensus, query alignment consensus sequence, with uppercase >60% and lower case >40% probability. Column scores: =, below −1.5; −, −1.5 to −0.5;., −0.5 to +0.5; +, +0.5 to +1.5; |, above +1.5. The first and last amino acids of the compared sequences are indicated.