Could any one explain about the pairwise alignment matrix.
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5 months ago

d. You are given this FASTA Sequence:

>Q8TAX7_Protein
MKTLPLFVCICALSACFSFSEGRERDHELRHRRHHHQSPKSHFELPHYPGLLAHQKPFIRKSYKCLHKRCRPKLPPSPNNPPKFPNPHQPPKHPDKNSSVVNPTLVATTQIPSVTFPSASTKITTLPNVTFLPQNATTISSRENVNTSSSVATLAPVNSPAPQDTTAAPPTPSATTPAPPSSSAPPETTAAPPTPSATTQAPPSSSAPPETTAAPPTPPATTPAPPSSSAPPETTAAPPTPSATTPAPLSSSAPPETTAVPPTPSATTLDPSSASAPPETTAAPPTPSATTPAPPSSPAPQETTAAPITTPNSSPTTLAPDTSETSAAPTHQTTTSVTTQTTTTKQPTSAPGQNKISRFLLYMKNLLNRIIDDMVEQ

Given your expertise working with PDB, Blast, and Swissmodel, generate a 3D structure for this protein. Do you think Homology Modelling or Protein Threading would be the better technique towards deriving the 3D structure for this sequence? Explain which method you would choose. Justify your answer based on the findings you have observed from either running PDB, Blast, or Swissmodel, or any combination of these tools. Limit your response to 5 sentences maximum.

alignment sequence gene • 201 views
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Is this a homework/test? Otherwise please justify your questions

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Its a home work, i m trying to learn it

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how is your actual question related to "pairwise alignment matrix" as stated in the title?

Did you actually try to run PDB, Blast, or Swissmodel?

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its not a pairwise alignment i am sorry

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Please adjust the title accordingly

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I have done the swiss model and i got Template as 3wa5.1.B Seq Identity as 26.98% Coverage Description

Tse3-specific immunity protein Crystal Structure of type VI peptidoglycan muramidase effector Tse3 in complex with its cognate immunity protein Tsi3
![enter image description here][1]

https://swissmodel.expasy.org/interactive/YEcTU9/models/

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Congrats, you've done step 1 "generate a 3D structure for this protein".

Based on the remainder of the question, you should probably determine which tool uses Homology Modelling and which one uses Protein Threading and compare the results you obtain from either one.

Unless you can come up with a specific question (that is not just restating the question you were given), we will probably have to close this post.

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thanks for your feedback. I think Homology modeling predicts the 3D structure of a query protein through the sequence alignment of template protein whereas with protein threading, for full 3-D threading, the problem of identifying the best alignment is very difficult (it is an NP-hard problem for some models of threading).

Thanks, I got it. But here, I do have one question like is that possible to draw a 3D structure by PDB or Blast

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If that is your question, I recommend you either close this one and post a new question or you edit your question and title accordingly so that the right people will pick it up.

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