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.

3D VIEW
We prepared three kinds of way for viewing superimposed structures: image, Chime-plugin and rasmol external application. Details of them are described in How to see 3D structure?. The raw PDB file of superimposed structures can be download from [superimposed_pdb_file]. A following picture is an example of [3D(image)], which does not required any plug-ins.
View of Multiple 3D Alignment using Matras 1.1: 1mbd- 1ecd- 4hhbA 4hhbB [IMAGE OF SUPERIMPOSED STRUCTURES]
```
  1mbd- : "blue"
  1ecd- : "red"
  4hhbA : "green"
  4hhbB : "cyan"
```

ALIGNMENT
Users can download multiple alignment in three different formats. The first one [ClustalW] is the Clustal W format, which is the most popular program for sequence multiple alignment. The second format [Sequence] is the multiple alignment of amino acids with residue number and average secondary structure. The third format [SecStr] is the multiple alignment of secondary structures with residue number and average amino acids. A following alignment is an example of the [SecStr] format. In the [AVE_SEQUENCE] row, completely and halfly conserved sites are shown in upper and lower letters, respectively.

[AVE_SEQUENCE]        .vLsp.eks.V.a.wgKV.....v.e.g.eaL.rlfks.P.t..kF..F..l.t..s.kg
1ecd-               1:--ccHHHHHHHHHHHHTTTT------cHHHHHHHHHHHcHHHHTTcTTTTTS-cHHHHTT:51
1mbd-               1:-cccHHHHHHHHHHHHHHGG--GHHHHHHHHHHHHHHHcHHHHTTcTTTTTccSHHHHHH:57
4hhbA               1:-cccHHHHHHHHHHHHHH--TTTHHHHHHHHHHHHHHHcGGGGGGcTTSc-c----S-TT:51
4hhbB               1:ccccHHHHHHHHHHHTTc----cHHHHHHHHHHHHHHHSGGGGGGcGGGcccSSHHHHHH:56

[AVE_SEQUENCE]        sa.vk.Hgkkvlgals.ilahldn.ea.l.tls.lHa.kl.vdp.nl.lls..lv.vlaa
1ecd-              52:SHHHHHHHHHHHHHHHHHHHTTTccHHHHHHHHHHHGG-GTccHHHHHHHHHHHHHHHHH:110
1mbd-              58:cHHHHHHHHHHHHHHHHHHTTTTccHHHHHHHHHHHHHTScccHHHHHHHHHHHHHHHHH:117
4hhbA              52:cHHHHHHHHHHHHHHHHHHHTGGGHHHHTHHHHHHHHHTTcccTHHHHHHHHHHHHHHHH:111
4hhbB              57:cHHHHHHHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHTTcccTHHHHHHHHHHHHHHHH:116

[AVE_SEQUENCE]        h.p.eFtp.aqaa..k.la.f...iasKy.......
1ecd-             111:HSc--GG-GGHHHHHHHHHHHHHHHHHHc-------:136
1mbd-             118:HcGGGccHHHHHHHHHHHHHHHHHHHHHHHHHTccc:153
4hhbA             112:HcTTTccHHHHHHHHHHHHHHHHHHTTTcc------:141
4hhbB             117:HHGGGScHHHHHHHHHHHHHHHHHHHTTcc------:146

SIMILARITY
All the similarities between proteins are shown in the matrix style. [SimMatrix(pairwise)] shows various kinds of similarities which are obtained from pairwise 3D alignments as follows:

 #These similarities are obtained by the pairwise 3D alignments.
 [RDIS(%)]
 1ecd-              0.0  65.1  57.0  59.1 
 1mbd-             65.1   0.0  70.7  72.0 
 4hhbA             57.0  70.7   0.0  76.9 
 4hhbB             59.1  72.0  76.9   0.0 
 [RMS(A)] #for aligned Calpha atoms
 1ecd-            0.000 1.652 2.397 2.252 
 1mbd-            1.652 0.000 1.560 1.617 
 4hhbA            2.397 1.560 0.000 1.451 
 4hhbB            2.252 1.617 1.451 0.000 
 [DRMS(A)] #for aligned Cbeta atoms
 1ecd-            0.000 1.462 1.916 1.875 
 1mbd-            1.462 0.000 1.398 1.417 
 4hhbA            1.916 1.398 0.000 1.125 
 4hhbB            1.875 1.417 1.125 0.000 
 [SqID(%)]
 1ecd-            100.0  20.6  18.3  19.1 
 1mbd-             20.6 100.0  27.0  24.8 
 4hhbA             18.3  27.0 100.0  43.9 
 4hhbB             19.1  24.8  43.9 100.0

Note that we cannot guarantee all the pair of alignments considered the same number of sites. Therefore, these values may not have "metric" property, such as triangle inequality. To draw a dendrogram, we recommend to use [DRMS(all-align)] or [SeqID(all-align)], which are calculated by sites in whici all the proteins are aligned.

TREE
A dendrogram is effective way to show similarities graphically. We prepared two-kinds of dendrogram based on [DRMS(all-aligned)] and [SEQ(all-aligned)]. Both are calculated from the all aligned sites using the Neighbor Joining method. A following picture is an example of [SEQ(all-aligned)]. A raw tree file (in phylip format) can be downloaded.
```
PROCESS_ID       11213
TREE_ID          D
ConservedSites   T
type             DRMS
Algorithm        NJ


 [DistanceMatrix] [TreeFile(phylip format)]
```

Comments and Questions to :

Back to MATRAS HELP page

Back to MATRAS title page

Help Page "Multiple 3D Alignment"

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

Help Page
"Multiple 3D Alignment"