The MSA Viewer and MSA Comparator. The reference alignment of the lipocalin superfamily proteins is displayed using the MSA Viewer (A). The secondary structures predicted by PSIPRED  are shown below the alignment. The information content  of each column of the alignment is displayed at the bottom, which illustrates the level of conservation. The completely conserved positions in the motif (positions 29 and 31; the motif region is indicated with the black bar) show the maximum information content (full-height bars). In the MSA Comparator (B), the ClustalW2 alignment (shown as "Other alignment") is compared against the "Reference" alignment. The blue selection bar, which is set to cover 35 sites, is shown above the reference alignment. The green range bar above the ClustalW2 alignment shows the column range that covers the characters selected in the reference alignment. The colored characters under the selection and range bars in the alignments show the sequence positions either in agreement (consistent) in blue, or else in red. The consistent (blue) columns largely correspond to the conserved motif (PROSITE motif PS00213). The column-wise Sum-of-Pairs Score (SPS) is shown between the two alignments. The SPS, column scores including and excluding gap columns ("with gaps" and "no gaps", respectively), and percent consistency for the alignment are shown in the statistics bar at the top of the window.
Anderson et al. BMC Bioinformatics 2011 12:184 doi:10.1186/1471-2105-12-184