CHAIN analysis of P loop GTPase-specific constraints acting on the Giαsubunit. The displayed sequences are representatives of the Giαfamily of G
proteins from distinct phyla. The foreground sequence set, which also includes P loop GTPases outside of the Giαfamily, are represented by the conserved residue patterns below the alignments. The number specified after the word 'pattern' gives the actual number of aligned sequences. (A) Motif-based contrast hierarchical alignment. Phyla are indicated in the leftmost column. Note that a purged foreground set  was used for the motif-based alignment in (A) and is thus smaller than the full set used by PSI-BLAST in (B). PSI-BLAST compensates for sequence redundancy by down weighting sequences  rather than by purging. The corresponding residue frequencies are given in integer tenths below the conserved patterns. For example, a '7' in integer tenths indicates that the corresponding residue directly above it occurs in 70–80% of the sequences. Deletion frequencies are similarly given in integer tenths (black; range 10–100%) or hundredths (gray; range 1–9%) as indicated. Histograms above the alignments display the strengths of the selective constraints acting at each position; aligned residues subject to the strongest constraints are highlighted for emphasis. For a complete description of CHAIN analysis alignments see . (B) PSI-BLAST generated contrast hierarchical alignment. Sequence identifiers are indicated in the leftmost column. Note that, unlike the motif-based alignment in (A), PSI-BLAST misaligns the foreground set's Walker A region (represented by the patterns below the displayed alignment). In order to accentuate this alignment error, the background alignment in (B) consists of the foreground alignment in (A).