run a query using partial sequences/partial alignments

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sre5
Posts: 2
Joined: Fri May 07, 2021 9:08 pm

run a query using partial sequences/partial alignments

Post by sre5 »

Hello - I am trying to run a query where the sequence and the template are partial sequences. I have adjusted the PDB file coordinates for the template structure by selecting only the residues I am interested in, and then renumbering.

Is this possible? I am getting an error as follows: "Either the format of the FASTA alignment is wrong or the PDB file for the template protein is missing in the uploaded file."

ex.
>sequence 1
[sequence entered below]

>template sequence
[sequence entered below]

ATOM 1 N LEU 1 10.85 30.821 2.186
ATOM 2 CA LEU 1 12.095 31.185 1.51
ATOM 3 C LEU 1 11.806 31.986 0.263
ATOM 4 O LEU 1 12.42 33.015 0.02
ATOM 5 CB LEU 1 12.888 29.939 1.111
ATOM 6 CG LEU 1 13.602 29.141 2.202
ATOM 7 CD1 LEU 1 14.323 27.944 1.581
ATOM 8 CD2 LEU 1 14.581 30.024 2.984
ATOM 9 N ALA 2 10.867 31.492 -0.53
ATOM 10 CA ALA 2 10.433 32.171 -1.741
ATOM 11 C ALA 2 9.89 33.578 -1.473
ATOM 12 O ALA 2 10.035 34.461 -2.314
ATOM 13 CB ALA 2 9.391 31.33 -2.45
robpearc
Posts: 40
Joined: Sun May 02, 2021 5:49 pm

Re: run a query using partial sequences/partial alignments

Post by robpearc »

Hello,

Yes, this is possible. If you know the alignment between your protein sequence and the template structure, you may specify this under Option 1: Assign additional restraints and templates to guide I-TASSER modeling. When you click on this option, there will be an explanation link that you can follow to explain how to upload your template information.
sre5
Posts: 2
Joined: Fri May 07, 2021 9:08 pm

Re: run a query using partial sequences/partial alignments

Post by sre5 »

Hello robpearc,

Thank you for your reply - Can you be more specific about the template information?

I have copied over a template of the file that I am submitting in my original comment for reference. I have used the template explanation link (I think) you refer to (https://zhanglab.dcmb.med.umich.edu/I-T ... raint.html) and followed the instructions for the FASTA input. Even following these instructions, I am getting an error, so I am looking to see what I might be missing.

For example: I am submitting only a part of the alignment for both proteins. In the example, there are many gaps in the input sequence: Does this imply that I need to include the entire template sequence?
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