Hi,
Residue count in 1JNK goes from 45-400 instead 1-346. It should be:
structureX:1jnk: 45 : :400 : :C-JUN N-TERMINAL KINASE::-1.00: 2.30
Also, you are trying to model a large number of residues for which you don't
have a template. I suggest cutting the ends of your alignment to look like
this:
...
MLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPP-----QLDEREHTIEEWKELIYKEVMN*
...
MLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEVMD*
The same applies to the first 6 residues in your protein.
Hope this helps,
Mensur
On Fri, 7 May 2004, Chaitanya Reddy.A wrote:
|>Dear all,
|> We are modelling a molecule but we are facing a problem to
|>which i am unable to find it. We hope you can help me in
|>this regard. We want to model a map kinase 8 using the map
|>kinase 10 molecule which shows 93% homology. We aligned
|>using clustalx and we submitted to modeller as .ali file.
|>
|>Below is the alignment file we obtained from clustalx
|>
|>>P1;1jnk
|>structureX:1jnk:1 : :346 : :C-JUN N-TERMINAL KINASE::-1.00: 2.30
|>------DNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELV
|>LMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR
|>DLKPSNIVVKSDCTLKILDFGLA-----SFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILF
|>PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSK
|>MLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPP-----QLDEREHTIEEWKELIYKEVMN-------------
|>----------------------------------------------------*
|>>P1;output
|>sequence:output:1 : :427 : :JNK mitogen-activated protein
|>kinase:2.40:-1.00:-1.00
|>MSRSKRDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELV
|>LMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR
|>DLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDLWSVGCIMGEMVCHKILF
|>PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSK
|>MLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEVMDLEERTKNGVIRGQ
|>PSPLGAAVINGSQHPSSSSSVNDVSSMSTDPTLASDTDSSLEAAAGPLGCCR*
|>
|>After submitting to modeller, the following is the error..
|>
|>The error message
|>
|>rdabrk__288W> Protein not accepted: 1
|>rdabrk__290E> Number of residues in the alignment and pdb files are
|>different:
|> 346 0
|> For alignment entry: 1
|>recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
|>
|>Please help me in solving this problem.
|>
|>But we manually examined the number of residues in both pdb files and
|>alignment files and we found no difference.
|>
|>Regards
|>Chaitu
==========================================================================
| Mensur Dlakic, Ph.D. | Tel: (406) 994-6576 |
| Department of Microbiology | Fax: (406) 994-4926 |
| Montana State University | http://www.umich.edu/~mensur/ |
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