Figure 4

CHAIN analysis of P loop GTPase-specific constraints acting on the G_iαsubunit. The displayed sequences are representatives of the G_iαfamily of G _α proteins from distinct phyla. The foreground sequence set, which also includes P loop GTPases outside of the G_iαfamily, 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 [5] 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 [35] 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 [3]. (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).