Homology modeling with low sequence identity and missing loops in template
Hello,
I have two sequences with low sequence identity and I get an alignment in modeller different than clustalW, which also differs from when I use emboss matcher.
I also have a missing segment in my template, I want the final model to have the corresponding segments and the gaps unmodeled, same as the template.
I tried to modify the alignment manually, however I ran into the "SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :" error, which I think has to do with the number of residues in the header of the alignment.
I attached the modeller and matcher alignments, in pir and fasta respectively. I would appreciate if you tell me how to prevent the missing loops in the template from being built and how to modify the alignment manually bypassing the above error.
Also, do give your input regarding the difference in alignments, and how to choose the most accurate one. I'm also fine with sharing the files privately.
Best regards.
I would appreciate some input.
Best regards.
On Mon, Sep 2, 2019 at 7:00 PM Ahmad Khalifa underoath006@gmail.com wrote:
> Hello, > > I have two sequences with low sequence identity and I get an alignment in > modeller different than clustalW, which also differs from when I use emboss > matcher. > > I also have a missing segment in my template, I want the final model to > have the corresponding segments and the gaps unmodeled, same as the > template. > > I tried to modify the alignment manually, however I ran into the > "SequenceMismatchError: read_te_291E> Sequence difference between alignment > and pdb :" error, which I think has to do with the number of residues in > the header of the alignment. > > I attached the modeller and matcher alignments, in pir and fasta > respectively. I would appreciate if you tell me how to prevent the missing > loops in the template from being built and how to modify the alignment > manually bypassing the above error. > > Also, do give your input regarding the difference in alignments, and how > to choose the most accurate one. I'm also fine with sharing the files > privately. > > Best regards. > > >
On 9/2/19 4:00 PM, Ahmad Khalifa wrote: > I have two sequences with low sequence identity and I get an alignment > in modeller different than clustalW, which also differs from when I use > emboss matcher.
This is unsurprising, since different algorithms are likely being used here to make these alignments.
> I also have a missing segment in my template, I want the final model to > have the corresponding segments and the gaps unmodeled, same as the > template.
If you don't want part of the sequence in the model, exclude it from your alignment. Modeller only models the sequence you give it. You may need to add a chain break (/ character) to the alignment to prevent Modeller from trying to connect the residues on either side of the gap with a peptide bond.
Ben Webb, Modeller Caretaker
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Ahmad Khalifa -
Modeller Caretaker