[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[modeller_usage] How to deal with a part of protein sequence that have no alignment with the template
- To: modeller_usage <modeller_usage@listsrv.ucsf.edu>
- Subject: [modeller_usage] How to deal with a part of protein sequence that have no alignment with the template
- From: xiazhendong1986 <xiazhendong1986 AT 163.com>
- Date: Mon, 28 Sep 2009 16:03:03 +0800 (CST)
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
网易邮箱用户购物独享现金返还