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

1ako_A1   MKFVSFNINglr------------aRPHQLEAIVEKHQ----pDVIGLQeTKVHDDmf--------------------------pLEEVAKLGYNVFyhgqk---------------------ghyGVALLTKE----TPIAVRRGfpgdd--eeaqrRIIMAEIPSllgn
1ako_A2   VTVINGYFPqgesrdhpikfpakaqFYQNLQNYLETELkrdnpVLIMGD-MNISPTdldigigeenrkrwlrtgkcsflpeerewMDRLMSWGLVDTfrhanpqtadrfswfdyrskgfddnrglrIDLLLASQplaeCCVETGIDyeirsmekpsdhAPVWATFRR----

DALI alignment      superposition in PDB format     colored superposition in PyMol

1ako_A1   MKFVSFNING------------lRARPHQLEAIVEKHQ----pDVIGLQeTKVHDD--------------------------mfPLEEVAKLGYNVF---------------------yhgqkghyGVALLTKE----TPIAVRRgFPGDD-----EEAQrrIIMAEIPSllgn
1ako_A2   VTVINGYFPQgesrdhpikfpakAQFYQNLQNYLETELkrdnpVLIMGD-MNISPTdldigigeenrkrwlrtgkcsflpeereWMDRLMSWGLVDTfrhanpqtadrfswfdyrskgfddnrglrIDLLLASQplaeCCVETGI-DYEIRsmekpSDHA--PVWATFRR----

TM alignment      superposition in PDB format     colored superposition in PyMol

1ako_A1   MKFVSFNINGL--------R--AR--PHQLEAIVEKHQ----PDVIGLQETKVH----DD-----------------M---FP--LEEVAKLGYNV-FY----------HGQK-----------GHYGVALLTK--ET--PIAVRRGFPGDDE-----EAQRRIIMAEIPSLLGN
1ako_A2   VTVINGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGD-MNISPTDLDIGIGEENRKRWLRTGKCSFLPEEREWMDRLMSWGLVDTFRHANPQTADRFSWFDYRSKGFDDNRG-LRIDLLLASQPLAECCVETGID-YEIRSMEKPSDHA--PVWATFRR----

FAST alignment      superposition in PDB format     colored superposition in PyMol

1ako_A1   MKFVSFNING-------------LRARPHQLEAIVEKHQPD-------VIGLQETKVHDDMFP------------------------------LEEVAKLGYNVFYHGQKGHYG------------------------------VALLTK----ETPIAVRRGFPGDDEEAQR-------------RIIMAEIPSLLGN
1ako_A2   VTVINGYFP-QGESRDHPIKFPAKAQFYQNLQNYLETE---LKRDNPVLIMG-DMNISP----TDLDIGIGEENRKRWLRTGKCSFLPEEREWMDRLMSWGLVDT---------FRHANPQTADRFSWFDYRSKGFDDNRGLRIDLLLASQPLAECCVETGI-----------DYEIRSMEKPSDHAPVWATFRR----