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 Lipocalin example.

If you send the following data to the Match-Box server:

>>>>>>>>>>>> cut here - begin of file - cut here <<<<<<<<<<<<<<<
>1cbr_A
PNFAGTWKMRSSENFDELLKALGVNAMLRKVAVAAASKPHVEIRQDGDQF
YIKTSTTVRTTEINFKVGEGFEEETVDGRKCRSLPTWENENKIHCTQTLL
EGDGPKTYWTRELANDELILTFGADDVVCTRIYVRE
>1opa_A
MTKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDN
FKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQK
GEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK
>2hmb
VDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILT
LKTHSTFKNTEISFKLGVEFDETTADDRKVKSIVTLDGGKLVHLQKWDGQ
ETTLVRELIDGKLILTLTHGTAVCTRTYEKEA
>1ifb
AFDGTWKVDRNENYEKFMEKMGINVVKRKLGAHDNLKLTITQEGNKFTVK
ESSNFRNIDVVFELGVDFAYSLADGTELTGTWTMEGNKLVGKFKRVDNGK
ELIAVREISGNELIQTYTYEGVEAKRIFKKEENDFFRWARDEDMAILFRM
RIFFPASCALRIFFEI
end_sequences
>>>>>>>>>>>> cut here - begin of file - cut here <<<<<<<<<<<<<<<

The Match-Box server will give you the following alignment:

Sequences number, length and name
_________________________________


1   136 1cbr_A      2   134 1opa_A      3   132 2hmb         4   167 1ifb
       
           10        20        30        40        50        60        70
            +         +         +         +         +         +         +
1  --PnfagtwkmrssenfdellkalgvnamlrkvavaaasKPHVEirqdgdqfyiktsttvrtteinfkvg
2  MTKdqngtwemesnenfegymkaldidfatrkiavrltqTKI--ivqdgdnfktktnstfrnydldftvg
3  -VDaflgtwklvdsknfddymkslgvgfatrqvasmtkpTTI--iekngdiltlkthstfknteisfklg
4  ---afdgtwkvdrnenyekfmekmginvvkrklgahdnlKLT--itqegnkftvkessnfrnidvvfelg

      554333333333333333345555555555666666     55555555555555555555555555

           80        90       100       110       120       130       140
            +         +         +         +         +         +         +
1  egfeeet--vdgrkcrslptwenenkihCTQTLLEGDGPKTYWtrelandeliltfgadDvvctriyvre
2  vefdehtkgldgrnvktlvtwegntlvcVQKGEKENRGW----kqwvegdklyleltcgDqvcrqvfkkk
3  vefdett--addrkvksivtldggklvhLQKWDGQETTL----vrelidgkliltlthgTavctrtyeke
4  vdfaysl--adgteltgtwtmegnklvgKFKRVDNGKELIA--vreisgneliqtytyeGveakrifkke

   5555556  6666666666666666666               6666666666666666 5555555555      5555556  6666666666666666666               6666666666666666 5555555555

          150       160       170       180       190       200       210
            +         +         +         +         +         +         +
1  -----------------------------------
2  -----------------------------------
3  A----------------------------------
4  ENDFFRWARDEDMAILFRMRIFFPASCALRIFFEI

Discussion:

The amino-acids in lower case are aligned, and the amino-acids in upper case are not aligned. The Match-Box program tries to find "boxes" (like the blocks of the BLOCKMAKER (1) server), or segments that are similar in all the sequences submitted by the user. When lowercase amino-acids are aligned to gaps, it means that the position of the gaps is not completely defined. If two successive selected boxes are overlapping by a maximum of k amino acids in one of the sequences, the final alignment will show a gap aligned with lowercase amino acids. Part of this gap, or the whole gap, can be moved partially or totally to the right by r positions (r being lower or equal to k). It means that Match-Box is not able to fix exactly the position of this gap, but that the gap can be placed somewhere to the right within a range of k amino acids.

References:

Henikoff, S., Henikoff, J.G., Alford, W.J., Pietrokovski, S. (1995). Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene-COMBIS, Gene 13, GC 17-26.

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