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

1fyz_E1   --klgihsNDTRDAWVNKIAQLNTLEKAAEMLKQFRMDHTtpfrnsyelDNDYLWIEAKLEEKVAVLKARAFNevdfrh---------------
1fyz_E2   ktafgedaKSVLDGTVAKMNAAKDKWEAEKIHIGFRQAYKpp----impVNYFLDGERQLGTRLMELRNLNYYdtpleelrkqrgvrvvhlqsp

DALI alignment      superposition in PDB format     colored superposition in PyMol

1fyz_E1   --klgihsNDTRDAWVNKIAQLNTLEKAAEMLKQFRMDHTtpfrnSYELD-NDYLWIEAKLEEKVAVLKARAFNEV---------------dfrh
1fyz_E2   ktafgedaKSVLDGTVAKMNAAKDKWEAEKIHIGFRQAYK-----PPIMPvNYFLDGERQLGTRLMELRNLNYYDTpleelrkqrgvrvvhlqsp

TM alignment      superposition in PDB format     colored superposition in PyMol

1fyz_E1   -------KLGIHSNDT-RDAWVNKIAQLNTLEKAAEMLKQFRMDHTTPFRNSYELD-NDYLWIEAKLEEKVAVLKARAFNE--VD-----------------FRH
1fyz_E2   KTAFGED------AKSVLDGTVAKMNAAKDKWEAEKIHIGFRQAYKPP----I-MPVNYFLDGERQLGTRLMELRNLNYYDTP-LEELRKQRGVRVVHLQSP---

FAST alignment      superposition in PDB format     colored superposition in PyMol

1fyz_E1   KLGIHS--------NDTRDAWVNKIAQLNTLEKAAEMLKQFRMDHTTPFRNSYEL--DNDYLWIEAKLEEKVAVLKARAF------NEVDFRH-------------
1fyz_E2   ------KTAFGEDAKSVLDGTVAKMNAAKDKWEAEKIHIGFRQAYKPPI------MPVNYFLDGERQLGTRLMELRN---LNYYDTPLEELR-KQRGVRVVHLQSP