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

1ock_A1   PLRGIAVGIKDiidtanmptemgseiyrgwqprsdAPVVMMLKRAGATIIgKTTTTafasrdptatlnphnt-------------------------------------ghspggsssgsaaavgAGMIPLALGTQ-------------TGGSVIRPAAYCGTAAIKPSfrmLPTVGVkcyswALDTVGLFGA--RAEDLARGLLAMTG
1ock_A2   PAKAPRIGVVRqefagav---------epaaeqglQAAIKAAERAGASVQ-AIDLPeavheawrihpiiqdfeahralawefsehhdeiapmlrasldatvgltpkeydearrigrrgrrelgevFEGVDVLLTYSapgtapakalastGDPRYNRLWTLMGNPCVNVP---VLKVGG-----LPIGVQVIARfgNDAHALATAWFLED

DALI alignment      superposition in PDB format     colored superposition in PyMol

1ock_A1   plRGIAVGIKDiidtanmptemgseiyrgwqprsdAPVVMMLKRAGATIiGKTTttafasrdpTATLNphntgHSPG------------------------------------------------gsssgsaaavGAGM--IPLALGTQT--------------GGSViRPAAYCGTAAIKPsfrmLPTVgvkcyswALDTVGLFGA--RAEDLARGLLAMTG
1ock_A2   paKAPRIGVVR---------qefagavepaaeqglQAAIKAAERAGASV-QAID--------lPEAVH-----EAWRihpiiqdfeahralawefsehhdeiapmlrasldatvgltpkeydearrigrrgrrelGEVFegVDVLLTYSApgtapakalastgdPRYN-RLWTLMGNPCVNV----PVLK----vggLPIGVQVIARfgNDAHALATAWFLED

TM alignment      superposition in PDB format     colored superposition in PyMol

1ock_A1   -PLRGIAVGIKDIIDTANMPTEMGS-EI--------YRGWQPRSDAPVVMMLKRAGATIIGKTTTTAFASRDPTATLNPHNTGHSPGG-----------------------------------------------------SSSGSAA-AVGA-GM-IPLALGTQT-------------GG-SVIRPAAYCGTAAIKPSFRMLPTV-GVKCYSWALDTVGLFGA--RAEDLARGLLAMTG
1ock_A2   PAKA-PRIGVVRQ---------EFAG-AVEPAAEQG--------LQAAIKAAERAGASVQAIDL----------PEAV-----HEAWRIHPIIQDFEAHRALAWEFSEHHDEIAPMLRASLDATVGLTPKEYDEARRIGRR-----GRRELGEVFEGVDVLLTYSAPGTAPAKALASTGDPRYN-RLWTLMGNPCVNV---PVLKVG------GLPIGVQVIARFGNDAHALATAWFLED

FAST alignment      superposition in PDB format     colored superposition in PyMol

1ock_A1   PLRGIAVGIKDIIDTANMPTEMGSEIYRGWQPRSDA-----------------PVVMMLKRAGATIIGKTTTTAFASRDPTATLNPHNTGHSPGGSSSGSAAAVGAG------------------------------------------------------------------------MIPLALGTQT-------------GGSVIRPAAYCGTAAIKPSFRMLPTVGVKCYSWA-------LDTVGLFGAR--AEDLARGLLAMTG
1ock_A2   PAKAPRIGVV--------------------------RQEFAGAVEPAAEQGLQAAIKAAERAGASVQ-AIDL-----------------------------------PEAVHEAWRIHPIIQDFEAHRALAWEFSEHHDEIAPMLRASLDATVGLTPKEYDEARRIGRRGRRELGEVFEGVDVLLTYSAPGTAPAKALASTGDPRYNRLWTLMGNPCVNVP---------------VLKVGGLPIGVQVIARFGNDAHALATAWFLED