[modeller_usage] How to deal with a part of protein sequence that have no alignment with the template

[xiazhendong1986 <>]

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

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