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

1ala_A1   kytrgtvtafspfDARADAEALRKAMKGMGTDEETILKILTSRNNAQRQEIASAFKTLFGRDLVDDLKSELTGKFETLMVSLMRP
1ala_A4   ------------sVPAYFAETLYYSMKGAGTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLLCGG

DALI alignment      superposition in PDB format     colored superposition in PyMol

1ala_A1   kytrgtvtafspFDARADAEALRKAMKGMGTDEETILKILTSRNNAQRQEIASAFKTLFGRDLVDDLKSELTGKFETLMVSLMRp
1ala_A4   ------------SVPAYFAETLYYSMKGAGTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLLCGg

TM alignment      superposition in PDB format     colored superposition in PyMol

1ala_A1   KYTRGTVTAFSPFDARADAEALRKAMKGMGTDEETILKILTSR-NNAQRQEIASAFKTLFGRDLVDDLKSELTGKFETLMVSLMRP
1ala_A4   ------------SVPAYFAETLYYSMKGAGTDDDTLIRVMVSRSE-IDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLLCGG

FAST alignment      superposition in PDB format     colored superposition in PyMol

1ala_A1   KYTRGTVTAFSPFD--ARADAEALRKAMKGMGTDEETILKILTSRNN--AQRQEIASAFKTLFGRDLVDDLKSELTGKFETLMVSLMRP
1ala_A4   --------------SVPAYFAETLYYSMKGAGTDDDTLIRVMVSR--SEIDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLLCGG