A comprehensive analysis of non-sequential alignments between all protein structures-3

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive analysis of non-sequential alignments between all protein structures"</p><p>http://www.biomedcentral.com/1472-6807/7/78</p><p>BMC Structural Biology 2007;7():78-78.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2213659.</p><p></p>PDB-code :A) have been aligned by TOPOFIT with of 115/1.7 Å. The longest sequential alignment is colored in blue. The fragment aligned in reverse order is colored in orange. The right side of the picture displays the corresponding alignment plot

A comprehensive analysis of non-sequential alignments between all protein structures-6

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive analysis of non-sequential alignments between all protein structures"</p><p>http://www.biomedcentral.com/1472-6807/7/78</p><p>BMC Structural Biology 2007;7():78-78.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2213659.</p><p></p>g protein (PDB-code , show on b) have been aligned by TOPOFIT with of 85/1.5 Å. Alignment segments are shown by different colors. In each segment the order of residues is different in the compared protein. c) displays the corresponding alignment plot. d) displays a schematic linear diagram of segment permutation in the alignment

A comprehensive analysis of non-sequential alignments between all protein structures-8

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive analysis of non-sequential alignments between all protein structures"</p><p>http://www.biomedcentral.com/1472-6807/7/78</p><p>BMC Structural Biology 2007;7():78-78.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2213659.</p><p></p>th the displayed topologies of -strands can be aligned in a sequential way. Picture is adopted from Figure 1 in [44]

A comprehensive analysis of non-sequential alignments between all protein structures-0

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive analysis of non-sequential alignments between all protein structures"</p><p>http://www.biomedcentral.com/1472-6807/7/78</p><p>BMC Structural Biology 2007;7():78-78.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2213659.</p><p></p>of resulting segments. The most dramatic changes occur when the value changes from 2 to 3 residues, clearly identifying the threshold for noise discrimination. The distributions are almost the same for values 3–6 of , while for higher values, the distributions start to deviate from each other (marked as regions of differences), thus identifying the threshold for clear signal separation. Therefore, the optimal value of for analysis should be between 3 and 6 because here is where the noise is eliminated without significant affect on the signal

A comprehensive analysis of non-sequential alignments between all protein structures-7

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive analysis of non-sequential alignments between all protein structures"</p><p>http://www.biomedcentral.com/1472-6807/7/78</p><p>BMC Structural Biology 2007;7():78-78.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2213659.</p><p></p>een aligned by TOPOFIT with Ne/RMSD of 142/1.8 Å. While the structures can be aligned in a sequential way, the best alignment found by TOPOFIT is a circular permutation. The alignment consists of two segments colored blue and green. The segment shown in green is located at C-terminal end in transaldolase, while in aldolase it is located at N-terminal end. The TOPOFIT alignment reflects the correct "biological" alignment as discussed in [43]

A comprehensive analysis of non-sequential alignments between all protein structures-5

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive analysis of non-sequential alignments between all protein structures"</p><p>http://www.biomedcentral.com/1472-6807/7/78</p><p>BMC Structural Biology 2007;7():78-78.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2213659.</p><p></p>olybdenum cofactor biosynthetic enzyme (PDB-code :A) have been aligned by TOPOFIT with of 95/1.6 Å. Both proteins have /structure but belong to different folds: the THDP-fold and to the fold of molybdenum cofactor biosynthetic enzymes respectively. The longest sequential alignment (composed of blue and red segments) has 25 residues. a) displays superposition of the aligned regions. b) and c) display the topologies of the secondary structure elements in the proteins. d) displays the corresponding alignment plot. e) displays a schematic linear diagram of segment permutation in the alignment

A comprehensive analysis of non-sequential alignments between all protein structures-2

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive analysis of non-sequential alignments between all protein structures"</p><p>http://www.biomedcentral.com/1472-6807/7/78</p><p>BMC Structural Biology 2007;7():78-78.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2213659.</p><p></p> :D) have been aligned by TOPOFIT with of 234/1.7 Å. Alignment segments are colored in blue, magenta and orange. The right side of the picture displays the corresponding alignment plot. It is easy to see that if the orange and magenta segments would be swapped in either sequence of the compared proteins the result would be a perfect sequential alignment

A comprehensive analysis of non-sequential alignments between all protein structures-9

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive analysis of non-sequential alignments between all protein structures"</p><p>http://www.biomedcentral.com/1472-6807/7/78</p><p>BMC Structural Biology 2007;7():78-78.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2213659.</p><p></p>r of fragments in the alignment. Bar charts on the top and on the right of the picture reflect the occurrence of alignments with a particular number of fragments and number of rearrangements. Only alignments with more that one fragment rearrangement have been considered to calculate the bar proportion. The numbers on the bars help visualize the scale. The area in the right-upper corner is not populated because of a lack of statistics (see text)

A comprehensive analysis of non-sequential alignments between all protein structures-1

<p><b>Copyright information:</b></p><p>Taken from "A comprehensive analysis of non-sequential alignments between all protein structures"</p><p>http://www.biomedcentral.com/1472-6807/7/78</p><p>BMC Structural Biology 2007;7():78-78.</p><p>Published online 16 Nov 2007</p><p>PMCID:PMC2213659.</p><p></p>) and C2-domain of synaptotagmin I (PDB-code , shown on b) have been aligned by TOPOFIT with the of 108/1.2 Å. The alignment consists of two segments colored in blue and green. The green segment represents a -strand and is located at N-terminal in synaptotagmin and at C-terminal in phospholipase. Thus the alignment is the circular permutation. c) displays the circular diagram of the alignment. d) displays the alignment plot corresponding to the alignment