Re: [ccp4bb] Searching Sequence Motif

Hi, You can also use PatternSearch in the MPI toolkit (https://toolkit.tuebingen.mpg.de/tools/patsearch ). You can build the motif using the Prosite grammar or as a regular expression, and select the E coli proteome or the PDB as the search dat

Re: [ccp4bb] Searching Sequence Motif

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

Re: [ccp4bb] Searching Sequence Motif

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 hig

Re: [ccp4bb] Searching Sequence Motif

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

Re: [ccp4bb] Searching Sequence Motif

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 On