One of the formats for the alignment file is related to the PIR database format; this is the preferred format for comparative modeling:
C; A sample alignment in the PIR format; used in tutorial >P1;5fd1 structureX:5fd1:1 : :106 : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA EVWPNITEKKDPLPDAEDWDGVKGKLQHLER* >P1;1fdx sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED----------------- -------------------------------*
See Section 2.4.1 for a detailed description of the alignment file format and Section 1.7.3 for the meaning of the alignment in MODELLER. Influence of the alignment on the quality of the model cannot be overemphasized. Command CHECK_ALIGNMENT can be used to find some trivial alignment mistakes.