MSA Viewer - TUM-CBR/pymol-plugins GitHub Wiki

The "MSA Viewer" tool allows you to visualize the regions with conserved amino-acids in a MSA file.

Demonstration by Example

  1. Load the structure on which you would like to observe the conserved regions. The sequence of this structure will be aligned to one of the sequences in the MSA file that will be provided. For this example you can try 8AXI by using fetch 8AXI in the PyMol prompt.
  2. Click the "Refresh" button to refresh the list of structures and select "8AXI/A" from the options.

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  1. Click the "Browse" button and select the MSA file you wish to use. It must be in "clustal" format. As an example you can try saving the sample "GH181" (of the appendix below) as a file.

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  1. Once the file is loaded, you must select the sequence you wish to align with the structure's sequence. For this example simply select "8AXI".

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  1. Finally, click the "Color Conserved Regions" button. If you followed the example here, you should see that one of the chains is colored as below. The closer to green the color, the higher the conservation at that part of the structure in the MSA file.

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Appendix

GH181

CLUSTAL O(1.2.4) multiple sequence alignment


8AXI            -----------------------------MAPVPEPEVVATPPADAGRGLIRVDSREIRH
QAA41707.1      ----mknllfalltgsfcccyaqq----kdapvpepevvatppadagrglirvdsreirh
QWP55491.1      mkr--lstlcllaagffipgqaqqarptvldsvyaplkvatppsdayiglslldngeirh
QIA36466        ----mknllfalftgsfcccyaqq----kaapvpepevvatppadagrglirvdsreirh
QNN21869.1      mrwtipallillavaspilaepdaqtlaalrrihapqvvgvppanacrglmvmpdgeirh
                                                :  *  *..**::*  **  : . ****

8AXI            YSGT--------RKEPDYLVSRDNGKTWEMKAAPAGYPPNYGGIPKESPAIVRNPLTREF
QAA41707.1      ysgt--------rkepdylvsrdngktwemkaapagyppnyggipkespaivrnpltref
QWP55491.1      ynyge-----qavagtvylsstdhgltwkrvnrpkemp----------fadcqspvskey
QIA36466        ysgt--------rkepdylvsrdngktwemkaapagyppnyggipkespaivrnpltref
QNN21869.1      ygfriadggdrhdtvpiyisshdyglswrqlpvegdsa----------aamvrspwsgdy
                *.               *: * * * :*.                    *  :.* : ::

8AXI            IRVQ--------------------PIGGFVFLSRGGLDGKWLAVTNDGKLEEDWKDPEKR
QAA41707.1      irvq--------------------piggfvflsrggldgkwlavtndgkleedwkdpekr
QWP55491.1      irlv-----------------dmgamgvycirtsggltggrtl----------------t
QIA36466        irvq--------------------piggfvflsrggldgkwlavtndgkleedwkdpekr
QNN21869.1      ltvlcqtkrpnhsmaaatylknidtvglhavrssqgpggpfeh----------------v
                : :                      :* . . :  *  *                     

8AXI            KNLKKLGGIMRTPVFVNKGRRVIVPFHNMGGG-----TKFHISDDGGLTWHVSRNGVTSP
QAA41707.1      knlkklggimrtpvfvnkgrrvivpfhnmgsg-----tkfhisddggltwhvsengitsp
QWP55491.1      kvadrnsimikppvfirngkrivva---ahggvtpkgcytyfsdddgltwkcs-ntvtsp
QIA36466        kslkklggimrtpvfvnkgrrvivpfhnmggg-----tkfhisddggltwhvsrngvtsp
QNN21869.1      lagrrigflprlplplrhrqrwvqpiqcsvgg--pqqpgvllsdddgktwrqv-llpspp
                    : . : : *: :.: :* :       .*         :***.* **:      : *

8AXI            RHEARPPHQGVRWFNNAVEATVLEMKDGTLWALARTSQDQAWQAFSKDYGETWSKPEPSR
QAA41707.1      rhearpphqgvrwfnnaveatvlemkdgtlwalvrtsldqawqafsrdygetwskpepsr
QWP55491.1      dhqgggfhkgirwnhgaveptvvelkdgtlwmlmrtsqdfhyqafskdggqtwgesepsp
QIA36466        rhearpphqgvrwfnnaveatvlemkdgtlwalartsqdqawqafskdygetwskpepsr
QNN21869.1      ahqvewphqgvrwqnygcepsvvelsdgrlwmlirtsqdhhyeafsndggdtwtdpapsr
                 *:    *:*:** : . * :*:*:.** ** * *** *  ::***.* *:** .  ** 

8AXI            FFGTLTMNTLGRLDDGTIVSLWTNTMALPENAT---------AGNGTWEDVFTNRDSHHI
QAA41707.1      ffgtltmntlgrlddgtivslwtntmalpenat---------agngtwedvftnrdshhi
QWP55491.1      fygtitmptlgrladgrlllfwcnttplpekeg----------tdgvwddvftnrdvthv
QIA36466        ffgtltmntlgrlddgtivslwtntmalpenat---------agngtwedvftnrdshhi
QNN21869.1      fyasitmpllfrlsdgrilvvwnnttplpeldhetqpglnhseregrsedfftnrdaiha
                *:.::**  * ** ** :: .* **  ***              :*  :*.*****  * 

8AXI            AMSGDEGKTWYGFREIILDEHRNHPGYATLDG---PEDRGKHQSEMVQLDKNRILISLGQ
QAA41707.1      amsgdegktwygfreiildehrnhpgyatldg---pedrgkhqsemvqldknrilislgq
QWP55491.1      avsdddgktwkgfrelymdpmrndtdyavhgg---gidrgvhqaqfvevapgkvlasigq
QIA36466        amsgdegktwygfreiildehrnhpgyatldg---pedrgkhqsemvqldknrilislgq
QNN21869.1      aisdddgktwrgfrelhlndhrnaadfrtvdgsaasldksihqcqavelpegkvllafgq
                *:*.*:**** ****: ::  **  .: . .*     *:. **.: *::  .::* ::**

8AXI            HKNHRRLVIVDRRWVGAKTRATQTGKDLDSQWTIHTYIP-------QKKGHCSYNRKPSA
QAA41707.1      hknhrrlvivdrrwvgaktratqtgkdsdsqwtihtyip-------qkkghcsynrkpsa
QWP55491.1      hplhrammmfdvnwlyeksrfndft-dslsqwstfnymn-------gikghcaynriqgc
QIA36466        hknhrrlvivdrrwvgaktratqtgkdldsqwtihtyip-------hkkghcsynrkpsa
QNN21869.1      hpacrrliifdpdwllethraddfs-qglggwsvqqyvksvpgnfrgtsghcaynrrpga
                *   * :::.*  *:  . *  :   :  . *:   *:          .***:***  ..

8AXI            ELVQDPSGGTKKVLQIKRLDDPELVNEKSNVDYRNGGATWNFPNGTTGLVKFRFRVVDGE
QAA41707.1      elvpdpsgstkkvlqikrlndpelvneksnvdyrnagaawnfpngttglvkfrfraadgd
QWP55491.1      mlephprkegrqvlhltyrpdaslvadt-------rgavwnfpamkkgtftvslripegs
QIA36466        eliqdpsggtkkvlqikrlddpelvneksnvdyrnggatwnfpngttglvkfrfrvadge
QNN21869.1      alvphpdgqprevlqvahypdprlvhek-------qgavwnfpnaprgrltlrlrmptgs
                 *  .*    ::**::    *  ** :.        **.****    * ... :*   *.

8AXI            QADDSGLQVSLTDRLFNACDSTTKDYALFTFPIRLKPAPHLLLGMKKVPFTPGAWHEISL
QAA41707.1      qaddsglqvsltdrlfnacdsttkdyalftfpirlrpaphlllgmkkapftpgawheisl
QWP55491.1      ----hsvslllndhwmnpsdtvaryqsmyelp-----lt-----rkqlgvkddrwhevsl
QIA36466        qaddsglqvsltdrlfnacdsttkdyalftfpirlrpaphlllgmkkvpfspgawheisl
QNN21869.1      ----qglqiclvdrwfnpvdpvvdrfaqhvlrldpagri-----ndapglkpdtwadlei
                     .:.: * *: :*  * ..   : . :              .   .. . * ::.:

8AXI            LWQGGQA----VVSLDGKKA--GTLKMANKSPNGASYIHFISTGSQPDA-GILLDTVNAR
QAA41707.1      lwqggqa----vvsldgkka--gtlkmankspngasyihfistgsqpda-gilldtvnar
QWP55491.1      ewdllqkhpqarvrvd-grlrplrlplknksqngisyvhfiappaeanp-gvylewvrae
QIA36466        lwqggqa----vvsldgkka--gtlkmankspngvsyihfistgsqpda-gilldtvnar
QNN21869.1      qwdeqaa----rfridqgdwhp--lprlfptrngisylhlqspatspdplgvliesvsat
                 *:         . :*        *     : ** **:*: :  :. :  *: :: * * 

8AXI            VKLE-
QAA41707.1      vk---
QWP55491.1      adgai
QIA36466        vk---
QNN21869.1      rtd--