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

1li1_A1   GFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGN-ERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFasrNDYSYWLSTPepm----pmsMAPITGENIRPFISRCAVCEAP
1li1_A2   AMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAgAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNY-yaNAYSFWLATIersemfkkptPSTLKAGELRTHVSRCQVCMRR

DALI alignment      superposition in PDB format     colored superposition in PyMol

1li1_A1   GFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGN-ERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFaSRNDYSYWLSTP-------ePMPMsmaPITGENIRPFISRCAVCEAP
1li1_A2   AMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAgAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNY-YANAYSFWLATIersemfkkPTPS---TLKAGELRTHVSRCQVCMRR

TM alignment      superposition in PDB format     colored superposition in PyMol

1li1_A1   GFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGN-ERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPE--------PMPMSMAPITGENIRPFISRCAVCEAP
1li1_A2   AMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNY-YANAYSFWLATIERSEMFKKPTPS----TLKAGELRTHVSRCQVCMRR

FAST alignment      superposition in PDB format     colored superposition in PyMol

1li1_A1   GFLVTRHSQTIDDPQCPSGTKILYHGYSLLYVQGNE-RAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPM----------SMAPITGENIRPFISRCAVCEAP
1li1_A2   AMVMAVHSQTIQIPPCPSGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNY-YANAYSFWLAT------IERSEMFKKPTPSTLKAGELRTHVSRCQVCMRR