Question: Could any one explain about the pairwise alignment matrix.
0
gravatar for saikishoremudhiraj2311
4 weeks ago by

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.

sequence alignment gene • 133 views
ADD COMMENTlink modified 4 weeks ago by h.mon31k • written 4 weeks ago by saikishoremudhiraj23110

Is this a homework/test? Otherwise please justify your questions

ADD REPLYlink written 4 weeks ago by JC12k

Its a home work, i m trying to learn it

ADD REPLYlink written 4 weeks ago by saikishoremudhiraj23110

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?

ADD REPLYlink written 4 weeks ago by Friederike6.5k

its not a pairwise alignment i am sorry

ADD REPLYlink written 4 weeks ago by saikishoremudhiraj23110

Please adjust the title accordingly

ADD REPLYlink written 4 weeks ago by Friederike6.5k

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/

ADD REPLYlink written 4 weeks ago by saikishoremudhiraj23110
1

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.

ADD REPLYlink written 4 weeks ago by Friederike6.5k

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

ADD REPLYlink written 4 weeks ago by saikishoremudhiraj23110

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.

ADD REPLYlink written 4 weeks ago by Friederike6.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1214 users visited in the last hour