Hi, I am trying to model a hetero dimer protein using modeller and I couldnt make it up..
the error which i was not able to rectify is "PROTEIN SPECIFIED IN ALIGN CODES WAS NOT FOUND IN THE ALIGNMENT FILE"
The alignment file is as follows:
>P1;queryAB sequence:queryAB:1: :1691: : : : : MGPRAKTISSLFFLLWVLAEPAENSDFY-----LPGDYLLGGLFSLHANMKGIVHLNFLQ VPMCKEYEVKV-IGYNLMQAMRFAVEEINNDSSLLPGVLLGYEIVDVCYISNNVQPVLYF LAHEDNLLPIQEDYSNYISRVVAVIGPDNSESVMTVANFLSLFLLPQITYSAISDELRDK VRFPALLRTTPSADHHIEAMVQLMLHFRWNWIIVLVSSDTYGRDNGQLLGERVARRDICI AFQETLPTLQPNQNMTSEERQRLVTIVDKLQQ--STARVVVVFSPDLTLYHFFNEVLRQN FTGAV-WIASESWA-IDPVLHNLTELRHLGTFLGITIQSVPIPGFSEF-----------R EWGPQAGPPPL-----SRTSQSYTCNQECDNCLNATLSFNTILRLSGERVVYSVYSAVYA VAHAL----HSLLGCDKSTC-TKRVVYPWQLLEEIWKVNFT-LLDHQIFFDPQGDVALHL EIVQWQWDRSQNPFQSVASYYPLQRQLKNIQDISWHTINNTIPMSMCSKRCQSGQKKKPV GIHVCCFECIDCLPGTFLNHTEDEYECQACPNNEWSYQSETSCFKRQLVFLEWHEAPTIA VALLAALGFLSTLAILVIFWRHFQTPIVRSAGGPMCFLMLTLLLVAYMVVPVYVGPPKVS TCLCRQALFPLCFTICISCIAVRSFQIVCAFKMASRFPRAYSYWVRYQGPYVSMAFITVL KMVIVVIGMLATGLSPTTRTDPDDPKITIVSCNPNYRNSLLFNTSLDLLLSVVGFSFAYM GKELPTNYNEAKFITLSMTFYFTSSVSLCTFMSAYSGVLVTIVDLLVTVLNLLAISLGYF GPKCYMILFYPERNTPAYFNSMIQGYTMRRD-------------------------- / MLGPAVLGLSLWALLHPGTGAPLCLSQQL-----RMKGDYVLGGLFPLGEAEEAGLRSRT RPSSPVCTRFSSNGLLWALAMKMAVEEINNKSDLLPGLRLGYDLFDTCSEPVVAMKPSLM FLAKAGSRDIAAYCNYTQYQPRVLAVIGPHSSELAMVTGKFFSFFLMPQVSYGASMELLS ARETFPSFFRTVPSDRVQLTAAAELLQEFGWNWVAALGSDDEYGRQGLSIFSALAAARGI CIAHEGLV---PLPRADDSRLGKVQDVLHQVNQSSVQVVLLFASVHAAHALFNYSISSRL ---SPKVWVASEAWLTSDLVMGLPGMAQMGTVLGFLQRGAQLHEFPQY-VKTHLALAT-D PAFCSALGEREQGLEEDVVGQRCPQCDCITLQNVSAGLNHHQTFS---VYAAVYSVAQAL HNTLQCNASG----CPAQDPVKPWQLLENMYNLTF-HVGGLPLRFDSSGNVDMEYDLKLW VWQGSVPRLHDVGRFNGSLRTERLKIRWHTSDNQKPVSRCSRQCQEGQVRRVKGFHSCCY DCVDCEAGSYRQNPDDIACTFCGQDEWSPERSTRCFRRRSRFLAWGEPAVLLLLLLLSLA LGLVLAALGLFVHHRDSPLVQASGGPLACFGLVCLGLVCLSVLLFPGQPSPARCLAQQPL SHLPLTGCLSTLFLQAAEIFVESELPLSWADRLSGCLRGPWAWLVVLLAMLVEVALCTWY LVAFPPEVVTDWHMLPTEALVHCRTRSWVSFGLAHATNATLAFLCFLGTFLVRSQPGCYN RARGLTFAMLAYFITWVSFVPLLANVQVVLRPAVQMGALLLCVLGILAAFHLPRCYLLMR QPGLNTPEFFLGGGPGDAQGQNDGNTGNQGKHE--------------------------- ---- * >P1;1ewkAB structureX:1ewkAB:36:A:512:B: : : : ----------------------------RSVARMDGDVIIGALFSVHHQPPAE------K VPERKCGEIREQYGIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSS-------- VALEQSIEFIRKP-------IAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDK TLYKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMDAFKELAAQEGLCI AHSD---KIYSNAGEKSFDR-----LLRKLRERLPKARVVVCFCEGMTVRGLLSAMRRLG VVGEFSLIGSDGWADRDEVIEGYEVEANGG--ITIKLQSPEVRSFDDYFLKLRLDTNTRN PWFPEFWQHRFQCRLPGHLLENPNFKKVCTG--NESLEENYV----QDSKMGFVINAIYA MAHGLQNMHHALCPGHVGLCDAMKPIDGRKLLDFLIKSSFVGVSGEEVWFDEKGDAPGRY DIMNLQY----------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------TEANRYDYVHVGTWHEGVLNIDDYKI / -----------------------------QRSVARMDGDVIIGALFSVHHQPPAE-KVPE RKCGEIREQY---GIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSSVALEQSIE FIRKP-----------------IAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLS DKTLYKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMDAFKELAAQEGL CIAHSDKIYSNAGEKSFDRLLRKLRERL-----PKARVVVCFCEGMTVRGLL--SAMRRL GVVGEFSLIGSDGWADRDEVIEGYEVEANGGITIKLQ-SPEVRSFDDYFLKLRLDTNTRN PWFPEFWQHRFQCRLPGHLLEN-PNFKKVCTGNESLEENYVQDSKMGFVINAIYAMAHGL QNMHHALCPGHVGLCDAMKPIDGRKLLDFLIKSSFVGVSGEEVWFDEKGDAPGRYDI--- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------MNLQYTEANRYDYVHVGTWHEGVLNID DYKI *
Please help me to overcome this and to get a best model.
thanks in advance.
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