Aligning TvLDF with the template

A good way of aligning the sequence of TvLDH with the structure of 4mdhA is the ALIGN2D  command in MODELLER. Although ALIGN2D is based on a dynamic programming algorithm [75], it is different from standard sequence-sequence alignment methods because it takes into account structural information from the template when constructing an alignment. This task is achieved through a variable gap penalty function that tends to place gaps in solvent exposed and curved regions, outside secondary structure segments, and between two $\mbox{C}_\alpha$ positions that are close in space. As a result, the alignment errors are reduced by approximately one third relative to those that occur with standard sequence alignment techniques. This improvement becomes more important as the similarity between the sequences decreases and the number of gaps increases. In the current example, the template-target similarity is so high that almost any alignment method with reasonable parameters will result in the same alignment. The following MODELLER script aligns the TvLDH sequence in file `TvLDH.seq' with the 4mdhA structure in the PDB file `4mdh.pdb' (file `align2d.top').

1.81.0

READ_MODEL FILE = '4mdh.pdb'
SEQUENCE_TO_ALI ALIGN_CODES = '4mdhA'
READ_ALIGNMENT FILE = 'TvLDH.ali', ALIGN_CODES = 'TvLDH', ADD_SEQUENCE = ON
ALIGN2D
WRITE_ALIGNMENT FILE='TvLDH-4mdh.ali', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE='TvLDH-4mdh.pap', ALIGNMENT_FORMAT = 'PAP'

In the first line, MODELLER reads the 4mdhA structure file. The SEQUENCE_TO_ALI  command transfers the sequence to the alignment array and assigns it the name of `4mdhA' (ALIGN_CODES ). The third line reads the TvLDH sequence from file `TvLDH.seq', assigns it the name `TvLDH' (ALIGN_CODES ) and adds it to the alignment array (`ADD_SEQUENCE  = ON'). The fourth line executes the ALIGN2D  command to perform the alignment. Finally, the alignment is written out in two formats, PIR (`TvLDH-4mdh.ali') and PAP (`TvLDH-4mdh.pap'). The PIR format is used by MODELLER in the subsequent model building stage. The PAP alignment format is easier to inspect visually. Due to the high target-template similarity, there are only a few gaps in the alignment. In the PAP format, all identical positions are marked with a `*' (file `TvLDH-4mdh.pap').

1.81.0

 _aln.pos         10        20        30        40        50        60
4mdhA     GSEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDV 
TvLDH     MSEAAHVLITGAAGQIGYILSHWIASGELYG-DRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGF 
 _consrvd  **   ** ******* * *   *  *   * *    * **** * *  *    *** *** * *


 _aln.p   70        80        90       100       110       120       130
4mdhA     IATDKEEIAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTN 
TvLDH     VATTDPKAAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTN 
 _consrvd  **     **** * * ** ***   *  * **   *  ***  *  * * ** **** * *** ***


 _aln.pos  140       150       160       170       180       190       200
4mdhA     CLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQA 
TvLDH     CEIAMLHAKNLKPENFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEG 
 _consrvd *  *   *     **** *  ** ***    * ****   **   * ****      *   *


 _aln.pos    210       220       230       240       250       260       270
4mdhA     KEVGVYEAVKDDSWLKGEFITTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGII 
TvLDH     KTQKVVDVLDHDYVFDTFFKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPV 
 _consrvd *   *      *      *                 * *     **           *


 _aln.pos      280       290       300       310       320       330
4mdhA     SDGNSYGVPDDLLYSFPVTIK-DKTWKIVEGLPINDFSREKMDLTAKELAEEKETAFEFLSSA- 
TvLDH     PEGNPYGIKPGVVFSFPCNVDKEGKIHVVEGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG 
 _consrvd   ** **       ***           ***   **  *** * * * *  *** *   *