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.