[modeller_usage] Regarding align2d & CS-BLAST alignments PLEASE ANSWER ME QUICKER ..I AM STUCK UP IN A FEW CASES

[Ashish Runthala <>]

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