Figure 1

Multiple alignment of Thg1 catalytic domain with other RRM-fold polymerase domains. A. Multiple sequence alignment of the Thg1 catalytic domain was constructed using Kalign after parsing high-scoring pairs from PSI-BLAST search results. The alignment with the other RRM-fold polymerase plam domains was constructed based on the PSI-BLAST search results, pairwise alignments produced by the profile-profile searches with the HHpred program against the Thg1 catalytic domain, and DALI searches with the X-ray structures shown in the alignment (PDB codes). The secondary structure from the crystal structures is shown above the alignment with E representing a strand and H a helix. The 90% consensus shown below the alignment was derived for the Thg1 catalytic domains alone using the following amino acid classes: hydrophobic (h: ALICVMYFW, yellow shading); small (s: ACDGNPSTV, green); polar (p: CDEHKNQRST, blue) and its charged subset (c: DEHKR, pink), and big (b: FILMQRWYEK; grey shading). The limits of the domains are indicated by the residue positions, on each end of the sequence. The numbers within the alignment are non-conserved inserts that have not been shown. The sequences are denoted by their gene name followed by the species abbreviation and GenBank Identifier (gi). The active site residues are marked with a blue box. The mutated residues that affected Thg1 activity are shown below the alignment with orange circles. B. Multiple Alignment of the C terminal extension of the Thg1 domain. The multiple alignments of the C terminal extension of the Thg1 domain was constructed as described above. The abbreviations and legends are also as above.