Two questions
(1) What is the rotation+translation operation that relates
solution #1 an solution #2?
(2) Have you double-checked and then checked yet again that both
solutions are in P43212? Could it be that one of them ended
up in, say, P414241?
it's happened to me :-(
Hi,
You can use Scan Prosite https://prosite.expasy.org/scanprosite/
Build your motif according to the pattern syntax described in the help
button (or here
https://prosite.expasy.org/scanprosite/scanprosite_doc.html#mo_motifs
?Try using the psi-blast package and search against the PDB.
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
From: CCP4 bulletin board on behalf of Cryo EM
Sent: Sunday, September 5,
Hello,
An easy way to do this would be to download the *E. coli* proteome as a
fasta file and search it using any text editor (if the motif has some
variance then you can use regular expressions) - or a spreadsheet. Or BLAST
the motif in the PDB limited to *E. coli* and set a high e-value (the
Hi there,
do you want only to search for motifs in the PDB database for E. coli proteins
or are you interested in the search for all E. coli proteins?
This tool might work for you:
https://www.genome.jp/tools/motif/MOTIF2.html
you need to pick for favourite organism eco for Escherichia coli K-12
How long and specific is the motif? If its something like GxxG, then I can't
help, sorry, but if it's something like a domain then will the search by
sequence tool at RCSB help at all or have I missed the point? Good luck, Jon.C.
Sent from ProtonMail mobile
Original Message
Hi all,
I want to search NCBI/PDB for all E.coli proteins with a specific sequence
motif.
Is there any server/software in which I can search and display all the
proteins in E.coli with this specific sequence motif?
Suggestions are highly appreciated.
Thanks!
