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 MG1655 Cannot be 100% sure if you select PDBSTR, if it will really use the PDB database, but it is worth trying. you can look up the list for all organisms here: https://www.genome.jp/kegg/catalog/org_list.html Best wishes, Nikolay Nikolay Dobrev Postdoctoral Fellow @ Wilmanns group EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22607 Hamburg, Germany T +49 40 89902 165 | M +49 173 684 0532 twitter.com/emblevents https://twitter.com/emblevents |http://facebook.com/embl.org | http://youtube.com/user/emblmedia Visit http://www.embl.org/events for a complete list of all EMBL events. > On 09/05/2021 5:54 PM Jon Cooper > <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > > > 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 5 Sep 2021, 16:23, Cryo EM < cryoemfa...@gmail.com> wrote: > > > > 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! > > > > > > > > > > --------------------------------------------- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > --------------------------------------------- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
