Matras1.1 : Help Page for Multiple 3D Alignment


Help Page
"Multiple 3D Alignment"


A multiple 3D alignment compares several structures belonging to the same superfamily, which provides important biological insight such as conserved sites or conserved structural features. However, it is well known that the problem of multiple sequence alignment is difficult to solve strictly, and that for 3D structures must be much more difficult because of the multi-body properties of 3D structures. To solve the problem within a reasonable computational time, we used the progressive alignment algorithm, which is the most popular heuristics for multiple sequence alignment. The progressive alignment consists of the following three steps. (i) Calculate pairwise 3D alignments and similarities for all of the protein pairs. (ii)Construct a guide tree using the R-score by the UPGMA method. (iii)Starting from the leaf nodes of the guide tree, progressively align all of the nodes, in order of decreasing similarity. For aligning a group to another group, all of the protein pairs between the two groups are tried, and the best pairwise alignment determines the alignment of the two groups. In other words, our multiple 3D alignment is performed by assembling the results of the pairwise 3D alignments in the proper order. Using our web server, a user can compare up to five structures. It also shows the superimposed structures and a dendrogram of structural similarities. The following is an example of Multiple 3D Alignment.

Multiple 3D Alignment using Matras 1.1: 1mbd- 1ecd- 4hhbA 4hhbB

[pid]  11213
[Npro] 4
[pro0] 1mbd-  ["" - ""]
[pro1] 1ecd-  ["" - ""]
[pro2] 4hhbA  ["" - ""]
[pro3] 4hhbB  ["" - ""]
Now calculating. Wait a while.
[MULTIPLE ALIGNMENT]
[AVE_SECSTR]    ccCCHHHHHHHHHHHhhhggttghhhhHHHHHHHHHHHcggggggCtttctcsshhhhhh
1ecd-           --LSADQISTVQASFDKVKG------DPVGILYAVFKADPSIMAKFTQFAGK-DLESIKG:51
1mbd-           -VLSEGEWQLVLHVWAKVEA--DVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKA:57
4hhbA           -VLSPADKTNVKAAWGKV--GAHAGEYGAEALERMFLSFPTTKTYFPHFD-L----S-HG:51
4hhbB           VHLTPEEKSAVTALWGKV----NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMG:56
                 .*:. ... * : :.**     . . : ..* :.:.. * :  .*  *  : .  . .:

[AVE_SECSTR]    cHHHHHHHHHHHHHHHHHHhTggghHHHhHHHHHHHhhttcCChHHHHHHHHHHHHHHHH
1ecd-           TAPFETHANRIVGFFSKIIGELPNIEADVNTFVASHKP-RGVTHDQLNNFRAGFVSYMKA:110
1mbd-           SEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHS:117
4hhbA           SAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAA:111
4hhbB           NPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAH:116
                .. .: *:..:..:.. ....... .. . .:. .*. :. :.. .. ...  .. .:..

[AVE_SECSTR]    HcgggcchhhHHHHHHHHHHHHHHHhhhcchhtccc
1ecd-           HTD--FA-GAEAAWGATLDTFFGMIFSKM-------:136
1mbd-           RHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG:153
4hhbA           HLPAEFTPAVHASLDKFLASVSTVLTSKYR------:141
4hhbB           HFGKEFTPPVQAAYQKVVAGVANALAHKYH------:146
                : . .*.. ..::  : :. .   ...*:
3D VIEW: [3D(image)] [3D(Chime-plugin)] [3D(rasmol)] [superimposed_pdb_file]

ALIGNMENT: [ClustalW] [Sequence] [SecStr]

SIMILARITY: [SimMatrix(pairwise)] [DRMS(all-align)] [SeqID(all-align)]

TREE: [DRMS(all-aligned)] [SEQ(all-aligned)]


The row [AVE_SECSTR] is the average secondary structure of each site. Secondary structures were assigned by DSSP program (Kabsh & Sander), and completely conserved sites are shown in upper letters.

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