We classified nucleotide positions in the genome into four categories ranging from highly conserved positions to less conserved positions within group M (Q1 Q4) using the same alignment as above.
In this way, it can differentiate subtly conserved positions from the non-conserved ones [ 28].
This revealed that Boule differs from Dazl in 20 invariant and/or conserved positions, besides 27 invariant and/or conserved positions common to both Boule and Dazl (Figure 2A).
A multiple sequence alignment of the RRM reveals that Boule differ from Dazl proteins in 20 invariant and/or conserved positions, besides 27 invariant and/or conserved positions common to both Boule and Dazl (Fig. 2A).
Later, when more sequences are added, less conserved positions emerge and sequences carrying appropriate residues on conserved positions, but possibly different residues on other positions, are allowed to join the cluster.
They compute the matrix score by multiplying the base frequency with the information content value at each position, in order to emphasize the fact that mismatches at less conserved positions are more easily tolerated than mismatches at highly conserved positions.
The resulting datasets consisted in 147 sequences with 96 conserved positions for the HK alignment and 149 sequences and 158 conserved positions for the RR alignment (additional file 2).
Universally conserved positions (U) were subsequently subtracted from the bacterial and archaeal/eukaryal datasets of conserved positions, in order to generate "bacterial-specific" and "archaeal/eukaryal-specific" datasets.
Using the less conservative Poisson model of substitution, 97% of sequences do not have any conserved positions and the remaining 3% had either only 1 or 2 conserved positions.
The results provide information above and beyond that revealed by consensus design alone, especially at poorly conserved positions.
Sequence alignments previously identified certain conserved positions, which have been shown to stabilize AR domains and promote their folding.
