Question: Searching NCBI database for proteins with specific C terminus
0
gravatar for gm434
9 weeks ago by
gm4340
gm4340 wrote:

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?

blast protein • 143 views
ADD COMMENTlink modified 8 weeks ago by Elisabeth Gasteiger1.7k • written 9 weeks ago by gm4340
2
gravatar for Elisabeth Gasteiger
8 weeks ago by
Geneva
Elisabeth Gasteiger1.7k wrote:

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

ADD COMMENTlink written 8 weeks ago by Elisabeth Gasteiger1.7k
1

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

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by genomax75k
1

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

ADD REPLYlink written 8 weeks ago by Elisabeth Gasteiger1.7k
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