Dear Modellers and Sir Ben Webb, I am finding a critical difference in the pairwise alignment computed by MODELLER and the corresponding alignment cognitive to the CS-BLAST undertaken alignment.

These are the differences. Will someone help me understanding why there is the case of shifted alignments in the the alignment case mentioned below for the following alignments of templates 2Q7BA and 3PP9A for the CASP8 target T0400? I have written TARGE in the MODELLER Alignment file for target sequence for better one-to-one alignment residue correlation. On top of it the CS-BLAST residue order is not available in the template PDB files. So i am confused..Where CS-BLAST has got the altered sequences from, when i precisely called the PDB for it.

2Q7BA ALIGNMENT MODELLER ALIGNMENT 2Q7BA>FQGMEIKEYENNPYHLAQLVDLINYCQNIEAKLDIKMAEQDDIFQIENYYQNRKGQFWIALEN-EKVVGSIALLRIDDKTAVLKKFFTYPKYRGNPVRLGRKLFERFMLFARASKFTRIVLDTPEKEKRSHFFYENQGFKQITRDELDVDYIFPDRDSRIYVKLL--* TARGE>M-AINIIEY-NRSY-KEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYR-N-LKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLKD*

CS-BLAST ALIGNMENT Query: 1 MAINIIEYNRSYKEELIEFILSIQKNEFNIKIDRDDQPDLENIEHNYLNSGGQFWLAINN 60 M I E N + +L++ I Q E + I +Q D+ IE+ Y N GQFW Sbjct: 20 MEIKEYENNPYHLAQLVDLINYCQNIEAKLDIKMAEQDDIFQIENYYQNRKGQFW-IALE 78

Query: 61 HQNIVGTIGLIRLDNNMSALKKMFVDKGYRN--LKIGKKLLDKVIMTCKEQNIDGIYLGT 118 ++ +VG+I L+R+D+ + LKK F YR +++G+KL ++ ++ + I L T Sbjct: 79 NEKVVGSIALLRIDDKTAVLKKFFTYPKYRGNPVRLGRKLFERFMLFARASKFTRIVLDT 138

Query: 119 IDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLK 161 +K + +FY N GF++I R +L + D D+R Y + L Sbjct: 139 PEKEKRSHFFYENQGFKQITRDELDVDYIFPDRDSRIYVKLLD 181

3PP9A ALIGNMENT MODELLER ALIGNMENT 3PP9A>SLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIAQAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVIGGFDFLVYKGLNMTSDEVAIYWYLHF* TARGE>------M---AI-NIIEYNRSY-KEELIEFILS-I-QKNEFNIK-IDRDDQPDLENIEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLDKVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFREIKRGDLPSSFPKLDVDNRFYYRNLKD*

CS-BLAST ALIGNMENT Query: 1 MAINIIEYNRSYKEELIE----------FILSIQKNEFNIKIDRDDQPDLEN-------- 42 M++ I E + + E +LS+ K I+ +D P E Sbjct: 4 MSLLIRELETNDLDNFPEIDDSFIVNARLMLSLSKVNRRIEYTVEDVPSYEKSYLQNDNE 63

Query: 43 --IEHNYLNSGGQFWLAINNHQNIVGTIGLIRLDNNMSALKKMFVDKGYRNLKIGKKLLD 100 + + Y+N Q H I+G I L + NN + ++ + VDK YR L +GK+L+ Sbjct: 64 ELVYNEYINKPNQIIYIALLHNQIIGFIVLKKNWNNYAYIEDITVDKKYRTLGVGKRLIA 123

Query: 101 KVIMTCKEQNIDGIYLGTIDKFISAQYFYSNNGFRE 136 + KE N+ GI L T + ++A FY GF Sbjct: 124 QAKQWAKEGNMPGIMLETQNNNVAACKFYEKCGFVI 159

Thanks Ashish

Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA