Sequence To Structure Alignment

This tool helps in finding the correspondence between residues in a protein sequence and its structure.

The algorithm used is the Needleman-Wunsch global sequence alignment method as implemented in the program "needle" from the EMBOSS tools.

Example

first line: swissprot AC P00508

second line: structure 1TAR, chain A/#65

     1 mallqsrlll saprraaata raSSWWSHVE MGPPDPILGV TEAFKRDTNS KKMNLGVGAY
     3                         SSWWSHVE MGPPDPILGV TEAFKRDTNS KKMNLGVGAY

    61 RDDNGKsYVL NCVRKAEAMI AAKKMDKEYL PIAGLADFTR ASAELALGEN SEAFKSGRYV
    41 RDDNGKpYVL NCVRKAEAMI AAKKMDKEYL PIAGLADFTR ASAELALGEN SEAFKSGRYV

   121 TVQGISGTGS LRVGANFLQR FFKFSRDVYL PKPSWGNHTP IFRDAGLQLQ AYRYYDPKTC
   102 TVQGISGTGS LRVGANFLQR FFKFSRDVYL PKPSWGNHTP IFRDAGLQLQ AYRYYDPKTC

   181 SLDFTGAMED ISKIPEKSII LLHACAHNPT GVDPRQEQWK ELASVVKKRN LLAYFDMAYQ
   167 SLDFTGAMED ISKIPEKSII LLHACAHNPT GVDPRQEQWK ELASVVKKRN LLAYFDMAYQ

   241 GFASGDINRD AWALRHFIEQ GIDVVLSQSY AKNMGLYGER AGAFTVICRD AEEAKRVESQ
   227 GFASGDINRD AWALRHFIEQ GIDVVLSQSY AKNMGLYGER AGAFTVICRD AEEAKRVESQ

   301 LKILIRPMYS NPPMNGARIA SLILNTPELR KEWLVEVKGM ADRIISMRTQ LVSNLKKEGS
   287 LKILIRPMYS NPPMNGARIA SLILNTPELR KEWLVEVKGM ADRIISMRTQ LVSNLKKEGS

   361 SHNWQHITDQ IGMFCFTGLK PEQVERLTKE FSIYMTKDGR ISVAGVASSN VGYLAHAIHQ
   347 SHNWQHITDQ IGMFCFTGLK PEQVERLTKE FSIYMTKDGR ISVAGVASSN VGYLAHAIHQ

   421 VTK
   408 VTK

It clearly shows that the structure lacks the N-terminal signal sequence. S67 in the sequence of P00508 is P47 in the structure derived sequence.

SequenceToStructureAlignment

Example