Gxxxg Motif And Proline-Induced-Kinks

Question

[User 0063]

Hi all

Do you know a tool to identify GXXXG motif and proline-induced-kinks in protein sequences?

Thanks

[Neilfws]

When you say "in protein sequences", do you mean: (1) you have some sequences that you would like to search or (2) you want to find sequences (from a database) that contain the motif?

Answer 1

[Niallhaslam]

You can try SLiMSearch or SIRW. Maybe MAST (from the MEME suite) too.

SLiMSearch is available here: http://bioware.ucd.ie/~compass/Server_pages/slimsearch.html Click on the all proteins link from the right and then enter the motif like this 'G...G'.

Here is one I ran earlier - for such a degenerative motif it takes a while: http://bioware.ucd.ie/~compass/cgi-bin/PHP_helper_files/slimsearchInfo.php?jobId=GC-OIO

There is a new version http://bioware.ucd.ie/slimsearch2.html but this is currently limited to human sequences. It does have some other proteomes in there and if you're particularly interested shoot me a mail and I can add more. Human results here: http://bioware.ucd.ie/~compass/cgi-bin/PHP_helper_files/slimsearch2Info.php?jobId=jpytnb

The advantage of the SLiMSearch method is that it will find instances of the G...G motif and rank them assigning significance to each instance based on the relative local conservation.

SIRW appears to be down at the moment but its http://sirw.embl.de.

Not sure about the second part of the question- identifying proline induced kinks.

Answer 2

[Julien]

EMBOSS (http://pro.genomics.purdue.edu/emboss/) has the very useful fuzzpro tool if you don't need to correct for conservation

[benaneely]

This is such an old thread to even be looking at, but fuzzpro did an excellent job for me with a similar question. Thanks for the suggestion almost half a decade ago. B-)

http://emboss.bioinformatics.nl/cgi-bin/emboss/fuzzpro

Answer 3

[Pierre Lindenbaum]

I tried "Scan prosite" with the pattern G-X-X-X-G but it said:

ERROR: user motif is too degenerated (generates >1000 matches on a sample of 5000 Swiss-Prot r34 shuffled sequences); CANCELLED

Answer 4

[Pawel Szczesny]

You could BLAST query sequence against subset of sequences from ArchDB (see example entry http://sbi.imim.es/cgi-bin/archdb/loops.pl?class=HH-35.1&set=ArchDB95), or equivalent database of loops.