Searching NCBI database for proteins with specific C terminus

Question

[gm434]

Hi all,

I am looking for a way to search the NCBI bacterial database for proteins with a specific C terminus sequence.

I have found the ProTeus tool, however this does not give a bacterial output.Is anyone able to point me in the right direction? I think there must be a way to do this with blast?

Answer 1

[Elisabeth Gasteiger]

You can use ScanProsite to submit MOTIFS to scan them against a PROTEIN sequence database: https://prosite.expasy.org/scanprosite/ Select option 2 and submit the N-terminal sequence, preceeded by "<" to anchor the sequence to the N-terminus:

<MPVNIKXF

Open "Filters" and specify "bacteria", or the corresponding tax_id, 2

[GenoMax]

Does MPVNIKXF> anchor to C-terminus? Original question is about C terminus.

[Elisabeth Gasteiger]

Yes, you are right, sequence> anchors sequence to the C-terminus. Thanks for spotting my mistake!