Match-Box Web Server 1.3

Guy Baudoux, Christophe Lambert, Ernest Feytmans and Eric Depiereux.

Laboratory of Structural Molecular Biology, The University of Namur, Belgium.

Project supported by the Walloon Government, Federal State of Belgium.

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The lysozyme and alpha-lactalbumin example.

The lysozyme and alpha-lactalbumin is a well-known family of enzymes discussed in depth by H.A.McKenzie and F.H.White (1). If you send the following data to the Match-Box server:

>>>>>>>>>>>>> cut here - begin of file - cut here <<<<<<<<<<<<<<
>1ALC
KQFTKCELSQNLYDIDGYGRIALPELICTMFHTSGYDTQAIVENDE
STEYGLFQISNALWCKSSQSPQSRNICDITCDKFLDDDITDDIMCAKKIL
DIKGIDYWIAHKALCTEKLEQWLCEK
>1LZ1
KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDR
STDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVV
RDPQGIRAWVAWRNRCQNRDVRQYVQGCGV
>2LZ2
KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDG
STDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIA
SGGNGMNAWVAWRNRCKGTDVHAWIRGCRL
>2LZT
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDG
STDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIV
SDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
 >>>>>>>>>>>>> cut here - end of file - cut here <<<<<<<<<<<<<<

you will obtain the following alignment:

 

Sequences number, length and name
_________________________________

 1   122 1ALC        2   130 1LZ1        3   129 2LZ2        4   129 2LZT      

            10        20        30        40        50        60        70
             +         +         +         +         +         +         +
 1  kqftkcelsqnly--didgygrialpelictmfhtsgydtqai--vendesteyglfqisnalwckssqs
 2  kvfercelartlkRLgmdgyrgislanwmclakwesgyntratNYnagdrstdygifqinsrywcndgkt
 3  kvygrcelaaamkRLgldnyrgyslgnwvcaakfesnfnthatN-rntdgstdygilqinsrwwcndgrt
 4  kvfgrcelaaamkRHgldnyrgyslgnwvcaakfesnfntqatN-rntdgstdygilqinsrwwcndgrt

    4444444444444  5555555555555555555555555555  4422222222222224444444444

            80        90       100       110       120       130       140
             +         +         +         +         +         +         +
 1  pqsrnicditcdkflddditddimcakkild-ikgidywiahkalctekLEQWLCEK--
 2  pgavnachlscsallqdniadavacakrvvrDpqgirawvawrnrcqnrDVRQYVQGCG
 3  pgsknlcnipcsallssditasvncakkiasGgngmnawvawrnrckgtDVHAWIRGCR
 4  pgsrnlcnipcsallssditasvncakkivsDgngmnawvawrnrckgtDVQAWIRGCR

    4444444444444444444444444444444 44444444444444456

Discussion:

The amino-acids in lowercase are aligned, and the amino-acids in uppercase are not aligned. The Match-Box program tries to find "boxes" (like the blocks of the BLOCKMAKER (2) server) or segments that are similar in all the sequences submitted by the user.

Amino-acids in lowercase are aligned to gaps when two boxes overlap over several positions. This overlapping region may be precisely delineated from the list of the boxes in the table 3 of the alignment listing.

This occur when several possible alignments lead to a comparable level of similarity. Additional information, such as comparaison with known structure or site mutagenesis results may be considered in order to fix the gap position.

References:

  1. McKenzie, H.A. & White, F.H. (Jr) (1991). Lysozyme and alpha-lactalbumin, function and interrelationships. Adv. Prot. Chem. 41, 173-258.
  2. Henikoff, S., Henikoff, J.G., Alford, W.J., Pietrokovski, S. (1995). Automated construction and graphicl presentation of protein blocks from unligned sequences. Gene-COMBIS, Gene 163, GC 17-26.

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