Hello,
I am currently modelling a heteromeric protein using a homomeric protein as a template, as follows: - heteromer subunits (target): 2 x aaaaaaaa + bbbbbbbbb - homomer subunits (template): 3 x cccccccccc
When aligning the monomer sequences to be used in the .ali file, should I align aaaaaaaa and cccccccccc separately, then bbbbbbbbb and cccccccccc and use the sequences generated in the FASTA file of each alignment in the .ali file -- or should I align all three sequences at once and use the sequences in the FASTA file in the .ali file? (In the first case, there would be two FASTA files and "cccccccccc" would be aligned differently, and both alignments of cccccccccc would be used in the .ali file. In the second case, there would be one FASTA file.)
I look forward to your response.
Kind regards, Amanda
On 3/18/24 8:13 AM, hmad3--- via modeller_usage wrote: > I am currently modelling a heteromeric protein using a homomeric > protein as a template, as follows: > - heteromer subunits (target): 2 x aaaaaaaa + bbbbbbbbb > - homomer subunits (template): 3 x cccccccccc > > When aligning the monomer sequences to be used in the .ali file, > should I align aaaaaaaa and cccccccccc separately, then bbbbbbbbb and > cccccccccc and use the sequences generated in the FASTA file of each > alignment in the .ali file -- or should I align all three sequences at > once and use the sequences in the FASTA file in the .ali file? (In the > first case, there would be two FASTA files and "cccccccccc" would be > aligned differently, and both alignments of cccccccccc would be used in > the .ali file. In the second case, there would be one FASTA file.)
Usually for modeling you would want a single alignment containing all the sequences. See the FAQ for an example: https://salilab.org/modeller/FAQ.html#1
Your alignment would end up looking something like
temp1: aaaaaaaa/aaaaaaaa/---------* temp2: --------/--------/bbbbbbbbb* target: cccccccc/cccccccc/ccccccccc*
How you produce the alignment (e.g. manually combining two or more initial alignments in a text editor) is up to you.
Ben Webb, Modeller Caretaker