In the alignments below, two upper-case letters are aligned, and two lower-case letters are NOT aligned. The superposition files are re-constructed from the corresponding alignments by minimizing the overall RMSD. In a PDB-format superposition file, the first domain is represented by chain S and the second domain is represented by chain A. The coordinates of the first domain are transformed, while the coordinates of the second domain are the same as in the original PDB file.

MANUAL alignment      superposition in PDB format     colored superposition in PyMol

1bj5_A1   hkSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADesaeNCDksLHTLFGDKLCTVATlretYGEMADCCAKQEPERNECFLQHkddnpnl----prlvrpevDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQ
1bj5_A2   --RLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGdl-lECAd-DRADLAKYICENQD--siSSKLKECCEKPLLEKSHCIAEVendempadlpslaadfvesKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLI

DALI alignment      superposition in PDB format     colored superposition in PyMol

1bj5_A1   hkSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADeSAENCdkslHTLFGDKLCTVATLretYGEMADCCAKQEPERNECFLQHKDdNPNL-PRLVRP---EVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLpKLDELRDEGKASSAKQ-
1bj5_A2   --RLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHG-DLLEC-addRADLAKYICENQDS--iSSKLKECCEKPLLEKSHCIAEVENdEMPAdLPSLAAdfvESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYA-KVFDEFKPLVEEPQNLi

TM alignment      superposition in PDB format     colored superposition in PyMol

1bj5_A1   HKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDK-SLHTLFGDKLCTV-ATLRETYGEMADCCAK---QE-PERNECFLQHKDDNPNLPRLV-RP--EVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAK-Q
1bj5_A2   R--LKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECC-HGDLLECADD----R-ADLAKYICENQDSISSKLKECCEKPLLEKS-HCIAEVE--NDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAK-VFDEFKPLVEEPQNLI

FAST alignment      superposition in PDB format     colored superposition in PyMol

1bj5_A1   HKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKS--------LHTLFGDKLCTVATLRE----TYGEM-ADCCAKQEPERNECFLQ-HKDDNP-NLPRLVRPEV-------DVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQ-----
1bj5_A2   --RLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCH----------GDLLECADDRADLAKYICE------NQDSISSK-LKECCEKPLLEKSHCIAEVENDEMPADLPSL-----AADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAK----VFDEFKPLVEE-PQNLI