Key to alignment
Key to alignmentThe sequences of the query and target proteins are aligned by using the matched residues from the template search, together with any equivalenced residues within 10Å of the template centre, to drive the alignment. An example alignment is shown in Figure 1.
The various features of the alignment are described in detail below, using the numbering in Figure 1.
Sequence of the query protein: shows the amino acid sequence, residue numbers and secondary structure "wiring diagram" of the query protein. The wiring diagram schematically illustrates the protein's helices as the red jagged elements, its beta strands as the yellow arrows, and its coil regions as purple lines. The sequence itself is coloured according to the residue similarity to the aligned residues in the target protein.
Sequence of the target protein: as for , but for the target protein.
Template residues: the three residues highlighted in red correspond to the three template residues and the equivalent residues in the other structure that they matched.
Equivalenced residues: the dots identify which residues in each sequence lie within 10Å of the template centre and hence show which were used to drive the alignment. Not all equivalenced residues in the 3D structures end up being equivalenced in the alignment (ie the cases where only one of the sequences has a dot are those where the equivalenced residues in 3D have become separated during the alignment).
Boxed regions: the boxed regions of the alignment represent segments where the sequence identity of the two sequences exceeds 35%; that is, regions of reasonably significant sequence similarity.
Fittable regions: the blue and red line segments identify the structurally "fittable" regions in the alignment. These correspond to segments from both proteins whose C-alpha coordinates can be structurally superposed with an r.m.s.d. of less than 3.0Å. The red region is the longest such segment (and is only shown if it is at least 20 residues in length).
In the example in Figure 1, the segment corresponding to the longest fittable region shows a high level of sequence identity (identified by the boxed regions in ), contains the three matched template sidechains (the highlighted residues in ), and also includes several equivalenced residues from the 10Å environment surrounding the matched template residues in both structures (the double-dot equivalences in ). It could thus be a conserved functional region, common to these two proteins which might themselves be so distantly related that the remainder of their structures and sequences have diverged so far apart that their evolutionary relationship is now difficult to detect.