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/ | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic@montana.edu | ==========================================================================