How to deal with a part of protein sequence that have no alignment with the template
alignment: _aln.pos 10 20 30 40 50 60 1kv9A -------------------------------------------------------------------- 1yiqA -------------------------------------------------------------------- 1kb0A -------------------------------------------------------------------- sldha MRRPYLLATAAGLALACSPLIAHAQFAPAGAGGEPSSSVPGPGNASEPTENSPKSQSYFAGPSPYAPQ _consrvd _aln.p 70 80 90 100 110 120 130 1kv9A ------------AGVDEAAIRATEQ------AGGEWLSHGRTYAEQRFSPLKQIDASNVRSLGLAWYM 1yiqA --------ADIPANVDGARIIAADK------EPGNWMSTGRTYDEQRYSPLKQISDQNVGQLGLAWSY 1kb0A -TGPAAQAAAAVQRVDGDFIRANAA------RTPDWPTIGVDYAETRYSRLDQINAANVKDLGLAWSY sldha APGVNAANLPDIESIDPSQVPAMAPQQSANPARGDWVAYGRDDHQTRYSPLSEITPENASKLKVAFVY _consrvd * * * * * * * * * * *
As we can see from above, the templates have no sequence from amino 1 to 70 to align with the target protein "sldha", and the modelling result is that the structure of sequence 1-70 is a just a long chain with no fold. So how can I get the structure of sequence 1-70? Best wishs. James
xiazhendong1986 wrote: ... > As we can see from above, the templates have no sequence from amino 1 to > 70 to align with the target protein "sldha", and the modelling result is > that the structure of sequence 1-70 is a just a long chain with no fold. > So how can I get the structure of sequence 1-70?
Modeller is a package for comparative modeling, so if you don't have a template, it won't be able to generate a reasonable-looking model. You may be able to find another template that aligns reasonably well with that range, for example by using a more sensitive search for templates such as profile-profile.
If you can't find a template for residues 1-70, you have no option with Modeller except to exclude those residues from your model sequence.
Ben Webb, Modeller Caretaker
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xiazhendong1986