Using SCAN mode as the starting point for multiple alignment

In certain instances initial fits based on multiple sequence alignment will be far from accurate, such that even an initial conformation based fit will not be able to correct the poor initial superposition, and even genuine structural homology will be missed. In these instances it is possible to make use of the SCAN mode to provide a more accurate initial superimposition.

To do this one need only select one representative of the domains to be superimposed and use this domain in a sensiitve scan of the other domains. By applying the same techinques as used for the scan with the Ig light variable domain (see the previous section) one can create a set of transformations of the searched domains onto the query domain. This set of transformations constitutes a rough multiple structure alignment which can be used by STAMP as the starting point for an accurate alignment.

Aspartic Proteinase Domains

The output files for this example are in the directory examples/ac_prot.

In this example the aspartyl proteinase N- and C-terminal lobes are aligned.
The N-terminal domain of 1CMS (in the file 1cmsN.domain) is used as the query domain to scan a list of aspartyl proteinase N- and C- terminal domains (ac_prot.domains). Running:

stamp -l 1cmsN.domain -n 2 -s -slide 5 -d ac_prot.domains -prefix ac_prot

should produce:

STAMP Structural Alignment of Multiple Proteins

Version 4.4 (May 2010)

 by Robert B. Russell & Geoffrey J. Barton 
 Please cite PROTEINS, v14, 309-323, 1992

Results of scan will be written to file ac_prot.scan
Fits  = no. of fits performed, Sc = STAMP score, RMS = RMS deviation
Align = alignment length, Nfit = residues fitted, Eq. = equivalent residues
Secs  = no. equiv. secondary structures, %I = seq. identity, %S = sec. str. identity
P(m)  = P value (p=1/10) calculated after Murzin (1993), JMB, 230, 689-694
        (NC = P value not calculated - potential FP overflow)

     Domain1         Domain2          Fits  Sc      RMS   Len1 Len2 Align Fit   Eq. Secs    %I    %S     P(m)
Scan 1cmsN           1cmsN              1   9.800   0.000  175  175  175  175  175   18 100.00  94.86 0.00e+00
Scan 1cmsN           1cmsC              1   3.214   2.065  175  148  204   68   62   11  19.35  83.87 1.11e-02
Scan 1cmsN           4apeN              1   8.209   1.300  175  178  182  162  159   15  30.82  87.42 2.82e-13
Scan 1cmsN           4apeC              1   3.420   1.948  175  152  205   70   67   13  14.93  79.10 6.11e-02
Scan 1cmsN           3appN              1   7.976   1.280  175  174  183  157  157   19  29.30  90.45 1.01e-11
Scan 1cmsN           3appC              1   3.269   2.068  175  149  205   68   59   12  13.56  81.36 1.00e+00
Scan 1cmsN           2aprN              1   8.435   1.075  175  178  178  164  162   15  33.33  85.80 4.60e-16
Scan 1cmsN           2aprC              1   3.304   1.973  175  147  200   67   64   13  18.75  76.56 1.37e-02
Scan 1cmsN           4pepN              1   8.836   0.930  175  173  174  169  169   15  57.99  83.43 3.00e-53
Scan 1cmsN           4pepC              1   3.223   2.105  175  152  206   68   57   10  21.05  85.96 6.17e-03
See the file ac_prot.scan

The file ac_prot.scan will contain all 10 domains superimposed onto 1cmsN. Note that we haven't run the program with the `-cut' option, since the file ac_prot.domains contains an assignment of domains. Running SORTTRANS removes any redundancies:

sorttrans -f ac_prot.scan -s Sc 2.5 > ac_prot.sorted

and running STAMP will generate the multiple alignment as described for the examples above.

stamp -l ac_prot.sorted -prefix ac_prot