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


_______________________________________________
modeller_usage mailing list
modeller_usage@salilab.org
http://salilab.org/mailman/listinfo/modeller_usage