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

1hg7_A1   mnqaSVVANQLIPINTALTLVMMRSEVVtpvgipaedi
1hg7_A2   prlvSMQVNRAVPLGTTLMPDMVKGYAA----------

TM alignment      superposition in PDB format     colored superposition in PyMol

1hg7_A1   ----MNQASVVANQLIPINTALTLVMMRSEVVTPVGIPA-EDI
1hg7_A2   PRLV----SMQVNRAVPLGTTLMPDMVKG---------YA--A

FAST alignment      superposition in PDB format     colored superposition in PyMol

1hg7_A1   MNQAS-----VVANQLIPINTALTLVMMRSEVVTPVGIPAEDI----
1hg7_A2   -----PRLVSMQVNRAVPLGTTLMPDMVK--------------GYAA